diff --git a/UDef-ARP.py b/UDef-ARP.py
index 1e1f0bd..a582172 100644
--- a/UDef-ARP.py
+++ b/UDef-ARP.py
@@ -1,3227 +1,3227 @@
-import sys
-import os
-from PyQt5 import QtWidgets
-from PyQt5.QtCore import Qt,QUrl
-from PyQt5.QtWidgets import QDialog, QFileDialog, QMessageBox, QProgressDialog, QApplication, QWidget, QPushButton,QTextEdit,QSizePolicy
-from PyQt5.QtGui import QFontDatabase, QIcon, QFont, QDesktopServices
-from PyQt5.uic import loadUi
-from allocation_tool import AllocationTool
-from vulnerability_map import VulnerabilityMap
-from model_evaluation import ModelEvaluation
-from osgeo import gdal
-from pathlib import Path, PureWindowsPath
-import numpy as np
-import traceback
-
-# GDAL exceptions
-gdal.UseExceptions()
-
-class IntroScreen(QDialog):
-    def __init__(self):
-        super(IntroScreen, self).__init__()
-        loadUi(Path(PureWindowsPath("data\\intro_screen.ui")), self)
-        # Set window properties
-        self.setWindowTitle('JNR Allocated Risk Mapping Procedure (UDef-ARP)')
-        # Set window icon
-        self.setWindowIcon(QIcon(str(Path(PureWindowsPath("data\\icon.ico")))))
-        self.Fit_Cal_button.clicked.connect(self.gotofitcal)
-        self.Pre_Cnf_button.clicked.connect(self.gotoprecnf)
-        self.Fit_Hrp_button.clicked.connect(self.gotofithrp)
-        self.Pre_VP_button.clicked.connect(self.gotoprevp)
-        self.doc_button.clicked.connect(self.openDocument)
-
-    def gotofitcal(self):
-        rmt_fit_cal = RMT_FIT_CAL_SCREEN()
-        widget.addWidget(rmt_fit_cal)
-        widget.setCurrentIndex(widget.currentIndex() + 1)
-
-    def gotoprecnf(self):
-        rmt_pre_cnf = RMT_PRE_CNF_SCREEN()
-        widget.addWidget(rmt_pre_cnf)
-        widget.setCurrentIndex(widget.currentIndex() + 1)
-
-    def gotofithrp(self):
-        rmt_fit_hrp = RMT_FIT_HRP_SCREEN()
-        widget.addWidget(rmt_fit_hrp)
-        widget.setCurrentIndex(widget.currentIndex() + 1)
-
-    def gotoprevp(self):
-        rmt_pre_vp = RMT_PRE_VP_SCREEN()
-        widget.addWidget(rmt_pre_vp)
-        widget.setCurrentIndex(widget.currentIndex() + 1)
-
-    def openDocument(self):
-        pdf_path = Path(PureWindowsPath("doc\\UDef-ARP_Introduction.pdf"))
-        QDesktopServices.openUrl(QUrl.fromLocalFile(str(pdf_path)))
-
-class RMT_FIT_CAL_SCREEN(QDialog):
-    def __init__(self):
-        super(RMT_FIT_CAL_SCREEN, self).__init__()
-        # Store the initial directory path
-        self.initial_directory = os.getcwd()
-        loadUi(Path(PureWindowsPath("data\\rmt_fit_cal_screen.ui")), self)
-        if central_data_store.directory is not None and self.folder_entry is not None:
-            self.directory = central_data_store.directory
-            self.folder_entry.setText(str(central_data_store.directory))
-        if central_data_store.directory is not None and self.folder_entry_2 is not None:
-            self.directory_2 = central_data_store.directory
-            self.folder_entry_2.setText(str(central_data_store.directory))
-        self.AT_button2.clicked.connect(self.gotoat2)
-        self.Intro_button2.clicked.connect(self.gotointro2)
-        self.MCT_button2.clicked.connect(self.gotomct2)
-        self.doc_button = self.tab1.findChild(QWidget, "doc_button")
-        self.select_folder_button = self.tab1.findChild(QWidget, "select_folder_button")
-        self.deforestation_hrp_button = self.tab1.findChild(QWidget, "deforestation_hrp_button")
-        self.mask_button = self.tab1.findChild(QWidget, "mask_button")
-        self.fd_button = self.tab1.findChild(QWidget, "fd_button")
-        self.calculate_button2 = self.tab1.findChild(QWidget, "calculate_button2")
-        self.ok_button2 = self.tab1.findChild(QWidget, "ok_button2")
-
-        self.doc_button_2 = self.tab2.findChild(QWidget, "doc_button_2")
-        self.select_folder_button_2 = self.tab2.findChild(QWidget, "select_folder_button_2")
-        self.mask_button_2 = self.tab2.findChild(QWidget, "mask_button_2")
-        self.fmask_button_2 = self.tab2.findChild(QWidget, "fmask_button_2")
-        self.fd_button_2 = self.tab2.findChild(QWidget, "fd_button_2")
-        self.ok_button2_2 = self.tab2.findChild(QWidget, "ok_button2_2")
-
-        self.doc_button.clicked.connect(self.openDocument)
-        self.select_folder_button.clicked.connect(self.select_working_directory)
-        self.deforestation_hrp_button.clicked.connect(self.select_deforestation_hrp)
-        self.mask_button.clicked.connect(self.select_mask)
-        self.fd_button.clicked.connect(self.select_fd)
-        self.calculate_button2.clicked.connect(self.process_data2_nrt)
-        self.ok_button2.clicked.connect(self.process_data2)
-
-        self.doc_button_2.clicked.connect(self.openDocument_2)
-        self.select_folder_button_2.clicked.connect(self.select_working_directory_2)
-        self.mask_button_2.clicked.connect(self.select_mask_2)
-        self.fmask_button_2.clicked.connect(self.select_fmask_2)
-        self.fd_button_2.clicked.connect(self.select_fd_2)
-        self.ok_button2_2.clicked.connect(self.process_data2_2)
-
-        self.vulnerability_map = VulnerabilityMap()
-        self.vulnerability_map.progress_updated.connect(self.update_progress)
-        self.directory = None
-        self.in_fn = None
-        self.deforestation_hrp = None
-        self.mask = None
-        self.NRT = None
-        if central_data_store.NRT is not None:
-            self.nrt_entry.setText(str(central_data_store.NRT))
-        self.n_classes = None
-        self.out_fn = None
-        self.out_fn_entry.setPlaceholderText('e.g., Acre_Vulnerability_CAL.tif')
-        self.directory_2 = None
-        self.mask_2 = None
-        self.fmask_2 = None
-        self.in_fn_2 = None
-        self.out_fn_2 = None
-        self.n_classes_2 = None
-        self.file_path_directory = None
-        self.file_path2_directory = None
-        self.file_path3_directory = None
-        self.file_path4_directory = None
-        self.file_path5_directory = None
-        self.file_path6_directory = None
-        self.out_fn_entry_2.setPlaceholderText('e.g., Acre_Vulnerability_CAL.tif')
-        self.setWindowTitle("JNR Integrated Risk/Allocation Tool")
-
-    def gotoat2(self):
-        os.chdir(self.initial_directory)
-        at2 = AT_FIT_CAL_Screen()
-        widget.addWidget(at2)
-        widget.setCurrentIndex(widget.currentIndex() + 1)
-
-    def gotomct2(self):
-        os.chdir(self.initial_directory)
-        mct2 = MCT_FIT_CAL_Screen()
-        widget.addWidget(mct2)
-        widget.setCurrentIndex(widget.currentIndex() + 1)
-
-    def gotointro2(self):
-        os.chdir(self.initial_directory)
-        intro2 = IntroScreen()
-        widget.addWidget(intro2)
-        widget.setCurrentIndex(widget.currentIndex() + 1)
-
-    def openDocument(self):
-        pdf_path = Path(PureWindowsPath("doc\\TestFitVM.pdf"))
-        QDesktopServices.openUrl(QUrl.fromLocalFile(str(pdf_path)))
-
-    def openDocument_2(self):
-        pdf_path = Path(PureWindowsPath("doc\\TestFitVM.pdf"))
-        QDesktopServices.openUrl(QUrl.fromLocalFile(str(pdf_path)))
-
-    def select_working_directory(self):
-        data_folder = QFileDialog.getExistingDirectory(self, "Working Directory")
-        data_folder_path = Path(data_folder)
-        self.directory = str(data_folder_path)
-        self.folder_entry.setText(self.directory)
-        self.folder_entry_2.setText(self.directory)
-        central_data_store.directory = self.directory
-
-    def select_fd(self):
-        file_path, _ = QFileDialog.getOpenFileName(self, 'Map of Distance from the Forest Edge in CAL')
-        if file_path:
-            self.in_fn = Path(PureWindowsPath(file_path))
-            self.in_fn_entry.setText(file_path.split('/')[-1])
-            self.file_path_directory = '\\'.join(file_path.split('/')[:-1])
-
-    def select_deforestation_hrp(self):
-        file_path3, _ = QFileDialog.getOpenFileName(self, "Map of Deforestation in the CAL")
-        if file_path3:
-            self.deforestation_hrp = Path(PureWindowsPath(file_path3))
-            self.deforestation_hrp_entry.setText(file_path3.split('/')[-1])
-            self.file_path3_directory = '\\'.join(file_path3.split('/')[:-1])
-    def select_mask(self):
-        file_path2, _ = QFileDialog.getOpenFileName(self, 'Mask of Study Area')
-        if file_path2:
-            self.mask = Path(PureWindowsPath(file_path2))
-            self.mask_entry.setText(file_path2.split('/')[-1])
-            self.file_path2_directory = '\\'.join(file_path2.split('/')[:-1])
-    def select_working_directory_2(self):
-        data_folder_2 = QFileDialog.getExistingDirectory(self, "Working Directory")
-        data_folder_path_2 = Path(data_folder_2)
-        self.directory_2 = str(data_folder_path_2)
-        self.folder_entry_2.setText(self.directory_2)
-        self.folder_entry.setText(self.directory_2)
-        central_data_store.directory = self.directory_2
-
-    def select_fd_2(self):
-        file_path4, _ = QFileDialog.getOpenFileName(self, 'Map of Distance from the Forest Edge in CAL')
-        if file_path4:
-            self.in_fn_2 = Path(PureWindowsPath(file_path4))
-            self.in_fn_entry_2.setText(file_path4.split('/')[-1])
-            self.file_path4_directory = '\\'.join(file_path4.split('/')[:-1])
-
-    def select_mask_2(self):
-        file_path5, _ = QFileDialog.getOpenFileName(self, 'Mask of Study Area')
-        if file_path5:
-            self.mask_2 = Path(PureWindowsPath(file_path5))
-            self.mask_entry_2.setText(file_path5.split('/')[-1])
-            self.file_path5_directory = '\\'.join(file_path5.split('/')[:-1])
-
-    def select_fmask_2(self):
-        file_path6, _ = QFileDialog.getOpenFileName(self, 'Mask of Forest Area')
-        if file_path6:
-            self.fmask_2 = file_path6
-            self.fmask_entry_2.setText(file_path6.split('/')[-1])
-            self.file_path6_directory = '\\'.join(file_path6.split('/')[:-1])
-
-    def get_full_path(self,base_dir, user_input):
-        if os.path.isabs(user_input):
-            return user_input
-        else:
-            return f"{base_dir}\\{user_input}"
-    def process_data2_nrt(self):
-        directory = self.folder_entry.text()
-        central_data_store.directory = directory
-        self.folder_entry_2.setText(directory)
-        if not directory:
-            QMessageBox.critical(self, "Error", "Please select or enter the working directory!")
-            return
-
-        if not self.file_path_directory:
-            self.file_path_directory=directory
-        if not self.file_path2_directory:
-            self.file_path2_directory=directory
-        if not self.file_path3_directory:
-            self.file_path3_directory=directory
-
-        self.in_fn = self.get_full_path(self.file_path_directory, self.in_fn_entry.text())
-        self.mask = self.get_full_path(self.file_path2_directory,self.mask_entry.text())
-        self.deforestation_hrp = self.get_full_path(self.file_path3_directory,self.deforestation_hrp_entry.text())
-
-        if not self.in_fn or not self.deforestation_hrp or not self.mask:
-            QMessageBox.critical(self, "Error", "Please select or enter all input files!")
-            return
-
-        images = [self.in_fn, self.deforestation_hrp, self.mask]
-
-        # Check if all images have the same resolution
-        resolutions = [map_checker.get_image_resolution(img) for img in images]
-        if len(set(resolutions)) != 1:
-            QMessageBox.critical(None, "Error", "All the input raster images must have the same spatial resolution!")
-            return
-
-        # Check if all images have the same number of rows and columns
-        dimensions = [map_checker.get_image_dimensions(img) for img in images]
-        if len(set(dimensions)) != 1:
-            QMessageBox.critical(None, "Error",
-                                 "All the input raster images must have the same number of rows and columns!")
-            return
-
-        if not map_checker.check_binary_map(self.deforestation_hrp):
-            QMessageBox.critical(None, "Error",
-                                 "'MAP OF DEFORESTATION IN THE HRP' must be a binary map (0 and 1) where the 1’s indicate deforestation.")
-            return
-
-        if not map_checker.check_binary_map(self.mask):
-            QMessageBox.critical(None, "Error",
-                                 "'MASK OF THE JURISDICTION' must be a binary map (0 and 1) where the 1’s indicate jurisdiction.")
-            return
-
-        # Show "Processing" message
-        processing_message = "Calculating NRT..."
-        self.progressDialog = QProgressDialog(processing_message, None, 0, 100, self)
-
-        # Change the font size
-        font = QFont()
-        font.setPointSize(9)
-        self.progressDialog.setFont(font)
-
-        self.progressDialog.setWindowTitle("Calculating")
-        self.progressDialog.setWindowModality(Qt.WindowModal)
-        self.progressDialog.setMinimumDuration(0)
-        self.progressDialog.resize(400, 300)
-        self.progressDialog.show()
-        QApplication.processEvents()
-
-        try:
-            self.vulnerability_map.set_working_directory(directory)
-            NRT = self.vulnerability_map.nrt_calculation(self.in_fn, self.deforestation_hrp, self.mask)
-            # Update the central data store
-            central_data_store.NRT = NRT
-            QMessageBox.information(self, "Processing Completed", f"Processing completed!\nNRT is: {NRT}")
-            self.nrt_entry.setText(str(NRT))
-            self.progressDialog.close()
-
-        except Exception:
-            self.progressDialog.close()
-            tb = traceback.format_exc()
-
-            error_box = QMessageBox(self)
-            error_box.setIcon(QMessageBox.Critical)
-            error_box.setWindowTitle("Error")
-            error_box.setText(f"<b>An Error Occurred During Processing</b>")
-            error_box.setTextInteractionFlags(Qt.TextSelectableByMouse | Qt.TextSelectableByKeyboard)
-            error_box.setDetailedText(tb)
-
-            details_frame = error_box.findChild(QTextEdit)
-            if details_frame:
-                details_frame.setSizePolicy(QSizePolicy.Expanding, QSizePolicy.Expanding)
-                details_frame.setMaximumHeight(800)
-                details_frame.setMaximumWidth(1000)
-                details_frame.setMinimumHeight(400)
-                details_frame.setMinimumWidth(600)
-
-            error_box_layout = error_box.layout()
-            error_box_layout.setContentsMargins(10, 10, 10, 10)
-
-            copy_button = QPushButton("Copy Error Message")
-            error_box.addButton(copy_button, QMessageBox.ActionRole)
-            def copy_error_txt():
-                QApplication.clipboard().setText(tb)
-            copy_button.clicked.connect(copy_error_txt)
-            error_box.exec_()
-
-    def process_data2(self):
-        directory = self.folder_entry.text()
-        central_data_store.directory = directory
-        self.folder_entry_2.setText(directory)
-        if not directory:
-            QMessageBox.critical(self, "Error", "Please select or enter the working directory!")
-            return
-        if not self.file_path_directory:
-            self.file_path_directory = directory
-        if not self.file_path2_directory:
-            self.file_path2_directory = directory
-        self.in_fn = self.get_full_path(self.file_path_directory, self.in_fn_entry.text())
-        self.mask = self.get_full_path(self.file_path2_directory, self.mask_entry.text())
-
-        if not self.in_fn or not self.mask:
-            QMessageBox.critical(self, "Error", "Please select or enter all input files!")
-            return
-
-        NRT = self.nrt_entry.text()
-        if not NRT:
-            QMessageBox.critical(self, "Error", "Please enter the NRT value!")
-            return
-        try:
-            self.NRT = int(NRT)
-            if (self.NRT <= 0):
-                QMessageBox.critical(self, "Error", "NRT value should be larger than 0!")
-                return
-        except ValueError:
-            QMessageBox.critical(self, "Error", "NRT value should be a valid number!")
-            return
-
-        n_classes = int(29)
-        if not n_classes:
-            QMessageBox.critical(self, "Error", "Please enter the number of classes!")
-            return
-        try:
-            self.n_classes = int(n_classes)
-            if (self.n_classes <= 0):
-                QMessageBox.critical(self, "Error", "Number of classes should be larger than 0!")
-                return
-        except ValueError:
-            QMessageBox.critical(self, "Error", "Number of classes value should be a valid number!")
-            return
-
-        out_fn = self.out_fn_entry.text()
-        if not out_fn:
-            QMessageBox.critical(self, "Error", "Please enter the name of Vulnerability Map in CAL!")
-            return
-
-        # Check if the out_fn has the correct file extension
-        if not (out_fn.endswith('.tif') or out_fn.endswith('.rst')):
-            QMessageBox.critical(self, "Error",
-                                 "Please enter .rst or .tif extension in the name of Vulnerability Map in CAL!")
-            return
-
-        # Show "Processing" message
-        processing_message = "Processing data..."
-        self.progressDialog = QProgressDialog(processing_message, None, 0, 100, self)
-
-        # Change the font size
-        font = QFont()
-        font.setPointSize(9)
-        self.progressDialog.setFont(font)
-
-        self.progressDialog.setWindowTitle("Processing")
-        self.progressDialog.setWindowModality(Qt.WindowModal)
-        self.progressDialog.setMinimumDuration(0)
-        self.progressDialog.resize(400, 300)
-        self.progressDialog.show()
-        QApplication.processEvents()
-
-        try:
-            self.vulnerability_map.set_working_directory(directory)
-            mask_arr = self.vulnerability_map.geometric_classification(self.in_fn, NRT, n_classes, self.mask)
-            self.vulnerability_map.array_to_image(self.in_fn, out_fn, mask_arr, gdal.GDT_Int16, -1)
-            self.vulnerability_map.replace_ref_system(self.in_fn, out_fn)
-
-            QMessageBox.information(self, "Processing Completed", "Processing completed!")
-
-            self.progressDialog.close()
-
-        except Exception:
-            self.progressDialog.close()
-            tb = traceback.format_exc()
-
-            error_box = QMessageBox(self)
-            error_box.setIcon(QMessageBox.Critical)
-            error_box.setWindowTitle("Error")
-            error_box.setText(f"<b>An Error Occurred During Processing</b>")
-            error_box.setTextInteractionFlags(Qt.TextSelectableByMouse | Qt.TextSelectableByKeyboard)
-            error_box.setDetailedText(tb)
-
-            details_frame = error_box.findChild(QTextEdit)
-            if details_frame:
-                details_frame.setSizePolicy(QSizePolicy.Expanding, QSizePolicy.Expanding)
-                details_frame.setMaximumHeight(800)
-                details_frame.setMaximumWidth(1000)
-                details_frame.setMinimumHeight(400)
-                details_frame.setMinimumWidth(600)
-
-            error_box_layout = error_box.layout()
-            error_box_layout.setContentsMargins(10, 10, 10, 10)
-
-            copy_button = QPushButton("Copy Error Message")
-            error_box.addButton(copy_button, QMessageBox.ActionRole)
-            def copy_error_txt():
-                QApplication.clipboard().setText(tb)
-            copy_button.clicked.connect(copy_error_txt)
-            error_box.exec_()
-
-
-    def process_data2_2(self):
-        directory_2 = self.folder_entry_2.text()
-        central_data_store.directory = directory_2
-        self.folder_entry.setText(directory_2)
-        if not directory_2 :
-            QMessageBox.critical(self, "Error", "Please select or enter the working directory!")
-            return
-        if not self.file_path4_directory:
-            self.file_path4_directory = directory_2
-        if not self.file_path5_directory:
-            self.file_path5_directory = directory_2
-        if not self.file_path6_directory:
-            self.file_path6_directory = directory_2
-
-        self.in_fn_2 = self.get_full_path(self.file_path4_directory, self.in_fn_entry_2.text())
-        self.mask_2 = self.get_full_path(self.file_path5_directory, self.mask_entry_2.text())
-        self.fmask_2 = self.get_full_path(self.file_path6_directory, self.fmask_entry_2.text())
-
-        if not self.in_fn_2 or not self.mask_2 or not self.fmask_2:
-            QMessageBox.critical(self, "Error", "Please select or enter all input files!")
-            return
-
-        images = [self.in_fn_2, self.mask_2, self.fmask_2]
-
-        # Check if all images have the same resolution
-        resolutions = [map_checker.get_image_resolution(img) for img in images]
-        if len(set(resolutions)) != 1:
-            QMessageBox.critical(None, "Error", "All the input raster images must have the same spatial resolution!")
-            return
-
-        # Check if all images have the same number of rows and columns
-        dimensions = [map_checker.get_image_dimensions(img) for img in images]
-        if len(set(dimensions)) != 1:
-            QMessageBox.critical(None, "Error",
-                                 "All the input raster images must have the same number of rows and columns!")
-            return
-
-        n_classes_2 = int(30)
-        out_fn_2 = self.out_fn_entry_2.text()
-        if not out_fn_2:
-            QMessageBox.critical(self, "Error", "Please enter the name of Vulnerability Map in CAL!")
-            return
-
-        # Check if the out_fn has the correct file extension
-        if not (out_fn_2.endswith('.tif') or out_fn_2.endswith('.rst')):
-            QMessageBox.critical(self, "Error",
-                                 "Please enter .rst or .tif extension in the name of Vulnerability Map in CAL!")
-            return
-
-        if not map_checker.check_binary_map(self.fmask_2):
-            QMessageBox.critical(None, "Error",
-                                 "'MASK OF FOREST AREAS IN THE CAL' must be a binary map (0 and 1) where the 1’s indicate forest areas.")
-            return
-
-        if not map_checker.check_binary_map(self.mask_2):
-            QMessageBox.critical(None, "Error",
-                                 "'MASK OF THE NON-EXCLUDED JURISDICTION' must be a binary map (0 and 1) where the 1’s indicate areas inside the jurisdiction.")
-            return
-
-        # Show "Processing" message
-        processing_message = "Processing data..."
-        self.progressDialog = QProgressDialog(processing_message, None, 0, 100, self)
-
-        # Change the font size
-        font = QFont()
-        font.setPointSize(9)
-        self.progressDialog.setFont(font)
-
-        self.progressDialog.setWindowTitle("Processing")
-        self.progressDialog.setWindowModality(Qt.WindowModal)
-        self.progressDialog.setMinimumDuration(0)
-        self.progressDialog.resize(400, 300)
-        self.progressDialog.show()
-        QApplication.processEvents()
-
-        try:
-            self.vulnerability_map.set_working_directory(directory_2)
-            mask_arr = self.vulnerability_map.geometric_classification_alternative(self.in_fn_2, n_classes_2, self.mask_2, self.fmask_2)
-            self.vulnerability_map.array_to_image(self.in_fn_2, out_fn_2, mask_arr, gdal.GDT_Int16, -1)
-            self.vulnerability_map.replace_ref_system(self.in_fn_2, out_fn_2)
-
-            QMessageBox.information(self, "Processing Completed", "Processing completed!")
-
-            self.progressDialog.close()
-
-        except Exception:
-            self.progressDialog.close()
-            tb = traceback.format_exc()
-
-            error_box = QMessageBox(self)
-            error_box.setIcon(QMessageBox.Critical)
-            error_box.setWindowTitle("Error")
-            error_box.setText(f"<b>An Error Occurred During Processing</b>")
-            error_box.setTextInteractionFlags(Qt.TextSelectableByMouse | Qt.TextSelectableByKeyboard)
-            error_box.setDetailedText(tb)
-
-            details_frame = error_box.findChild(QTextEdit)
-            if details_frame:
-                details_frame.setSizePolicy(QSizePolicy.Expanding, QSizePolicy.Expanding)
-                details_frame.setMaximumHeight(800)
-                details_frame.setMaximumWidth(1000)
-                details_frame.setMinimumHeight(400)
-                details_frame.setMinimumWidth(600)
-
-            error_box_layout = error_box.layout()
-            error_box_layout.setContentsMargins(10, 10, 10, 10)
-
-            copy_button = QPushButton("Copy Error Message")
-            error_box.addButton(copy_button, QMessageBox.ActionRole)
-            def copy_error_txt():
-                QApplication.clipboard().setText(tb)
-            copy_button.clicked.connect(copy_error_txt)
-            error_box.exec_()
-
-    def update_progress(self, value):
-        # Update QProgressDialog with the new value
-        if self.progressDialog is not None:
-            self.progressDialog.setValue(value)
-
-class AT_FIT_CAL_Screen(QDialog):
-    def __init__(self):
-        super(AT_FIT_CAL_Screen, self).__init__()
-        self.initial_directory = os.getcwd()
-        loadUi(Path(PureWindowsPath("data\\at_fit_cal_screen.ui")), self)
-        if central_data_store.directory is not None and self.folder_entry is not None:
-            self.directory = central_data_store.directory
-            self.folder_entry.setText(str(central_data_store.directory))
-        self.Intro_button3.clicked.connect(self.gotointro3)
-        self.RMT_button3.clicked.connect(self.gotormt3)
-        self.MCT_button3.clicked.connect(self.gotomct3)
-        self.doc_button.clicked.connect(self.openDocument)
-        self.select_folder_button.clicked.connect(self.select_working_directory)
-        self.municipality_button.clicked.connect(self.select_municipality)
-        self.risk30_hrp_button.clicked.connect(self.select_risk30_hrp)
-        self.deforestation_hrp_button.clicked.connect(self.select_deforestation_hrp)
-        self.ok_button3.clicked.connect(self.process_data3)
-        self.allocation_tool = AllocationTool()
-        # Connect the progress_updated signal to the update_progress method
-        self.allocation_tool.progress_updated.connect(self.update_progress)
-        self.directory = None
-        self.risk30_hrp = None
-        self.municipality = None
-        self.deforestation_hrp = None
-        self.out_fn1 = None
-        self.out_fn2 = None
-        self.csv_name = None
-        self.file_path_directory = None
-        self.file_path1_directory = None
-        self.file_path3_directory = None
-        self.image1_entry.setPlaceholderText('e.g., Acre_Modeling_Region_CAL.tif')
-        self.csv_entry.setPlaceholderText('e.g., Relative_Frequency_Table_CAL.csv')
-        self.image2_entry.setPlaceholderText('e.g., Acre_Fitted_Density_Map_CAL.tif')
-        self.setWindowTitle("JNR Integrated Risk/Allocation Tool")
-
-    def gotormt3(self):
-        os.chdir(self.initial_directory)
-        rmt3 = RMT_FIT_CAL_SCREEN()
-        widget.addWidget(rmt3)
-        widget.setCurrentIndex(widget.currentIndex() + 1)
-
-    def gotointro3(self):
-        os.chdir(self.initial_directory)
-        intro3 = IntroScreen()
-        widget.addWidget(intro3)
-        widget.setCurrentIndex(widget.currentIndex() + 1)
-
-    def gotomct3(self):
-        os.chdir(self.initial_directory)
-        mct3 = MCT_FIT_CAL_Screen()
-        widget.addWidget(mct3)
-        widget.setCurrentIndex(widget.currentIndex() + 1)
-
-    def openDocument(self):
-        pdf_path = Path(PureWindowsPath("doc\\TestFitAM.pdf"))
-        QDesktopServices.openUrl(QUrl.fromLocalFile(str(pdf_path)))
-
-    def select_working_directory(self):
-        data_folder = QFileDialog.getExistingDirectory(self, "Working Directory")
-        data_folder_path = Path(data_folder)
-        self.directory = str(data_folder_path)
-        self.folder_entry.setText(self.directory)
-        central_data_store.directory = self.directory
-
-    def select_municipality(self):
-        file_path, _ = QFileDialog.getOpenFileName(self, 'Map of Administrative Divisions')
-        if file_path:
-            self.municipality = Path(PureWindowsPath(file_path))
-            self.municipality_entry.setText(file_path.split('/')[-1])
-            self.file_path_directory = '\\'.join(file_path.split('/')[:-1])
-
-    def select_risk30_hrp(self):
-        file_path1, _ = QFileDialog.getOpenFileName(self, "Vulnerability Map in CAL")
-        if file_path1:
-            self.risk30_hrp = Path(file_path1)
-            self.risk30_hrp_entry.setText(file_path1.split('/')[-1])
-            self.file_path1_directory = '\\'.join(file_path1.split('/')[:-1])
-
-    def select_deforestation_hrp(self):
-        file_path3, _ = QFileDialog.getOpenFileName(self, "Map of Deforestation in the CAL")
-        if file_path3:
-            self.deforestation_hrp = Path(file_path3)
-            self.deforestation_hrp_entry.setText(file_path3.split('/')[-1])
-            self.file_path3_directory = '\\'.join(file_path3.split('/')[:-1])
-    def get_full_path(self, base_dir, user_input):
-        if os.path.isabs(user_input):
-            return user_input
-        else:
-            return f"{base_dir}\\{user_input}"
-    def process_data3(self):
-        directory = self.folder_entry.text()
-        central_data_store.directory = directory
-        if not directory:
-            QMessageBox.critical(self, "Error", "Please select or enter the working directory!")
-            return
-        if not self.file_path_directory:
-            self.file_path_directory = directory
-        if not self.file_path1_directory:
-            self.file_path1_directory = directory
-        if not self.file_path3_directory:
-            self.file_path3_directory = directory
-
-        self.municipality = self.get_full_path(self.file_path_directory, self.municipality_entry.text())
-        self.risk30_hrp = self.get_full_path(self.file_path1_directory, self.risk30_hrp_entry.text())
-        self.deforestation_hrp = self.get_full_path(self.file_path3_directory, self.deforestation_hrp_entry.text())
-
-        if not self.risk30_hrp or not self.municipality or not self.deforestation_hrp:
-            QMessageBox.critical(self, "Error", "Please select or enter all input files!")
-            return
-
-        images = [self.risk30_hrp, self.municipality, self.deforestation_hrp]
-
-        # Check if all images have the same resolution
-        resolutions = [map_checker.get_image_resolution(img) for img in images]
-        if len(set(resolutions)) != 1:
-            QMessageBox.critical(None, "Error", "All the input raster images must have the same spatial resolution!")
-            return
-
-        # Check if all images have the same number of rows and columns
-        dimensions = [map_checker.get_image_dimensions(img) for img in images]
-        if len(set(dimensions)) != 1:
-            QMessageBox.critical(None, "Error",
-                                 "All the input raster images must have the same number of rows and columns!")
-            return
-
-        out_fn1 = self.image1_entry.text()
-        if not out_fn1:
-            QMessageBox.critical(self, "Error", "Please enter the name for Modeling Region Map in CAL!")
-            return
-
-        if not (out_fn1.endswith('.tif') or out_fn1.endswith('.rst')):
-            QMessageBox.critical(self, "Error",
-                                 "Please enter .rst or .tif extension in the name for Modeling Region Map in CAL!")
-            return
-
-        csv_name = self.csv_entry.text()
-        if not csv_name:
-            QMessageBox.critical(self, "Error", "Please enter the name for the Relative Frequency Table!")
-            return
-
-        if not (csv_name.endswith('.csv')):
-            QMessageBox.critical(self, "Error",
-                                 "Please enter .csv extension in the name of Relative Frequency Table!")
-            return
-
-        out_fn2 = self.image2_entry.text()
-        if not out_fn2:
-            QMessageBox.critical(self, "Error", "Please enter the name for Fitted Density Map in the CAL!")
-            return
-
-        if not (out_fn2.endswith('.tif') or out_fn2.endswith('.rst')):
-            QMessageBox.critical(self, "Error",
-                                 "Please enter .rst or .tif extension in the name for Fitted Density Map in the CAL!")
-            return
-
-        if not map_checker.check_binary_map(self.deforestation_hrp):
-            QMessageBox.critical(None, "Error",
-                                 "'MAP OF DEFORESTATION IN THE CAL' must be a binary map (0 and 1) where the 1’s indicate deforestation.")
-            return
-
-        # Show "Processing" message
-        processing_message = "Processing data..."
-        self.progressDialog = QProgressDialog(processing_message, None, 0, 100, self)
-
-        # Change the font size
-        font = QFont()
-        font.setPointSize(9)
-        self.progressDialog.setFont(font)
-
-        self.progressDialog.setWindowTitle("Processing")
-        self.progressDialog.setWindowModality(Qt.WindowModal)
-        self.progressDialog.setMinimumDuration(0)
-        self.progressDialog.resize(400, 300)
-        self.progressDialog.show()
-        QApplication.processEvents()
-
-        try:
-            self.allocation_tool.execute_workflow_fit(directory, self.risk30_hrp,
-                                                        self.municipality,self.deforestation_hrp, csv_name,
-                                                        out_fn1,out_fn2)
-            QMessageBox.information(self, "Processing Completed", "Processing completed!")
-            self.progressDialog.close()
-
-        except Exception:
-            self.progressDialog.close()
-            tb = traceback.format_exc()
-
-            error_box = QMessageBox(self)
-            error_box.setIcon(QMessageBox.Critical)
-            error_box.setWindowTitle("Error")
-            error_box.setText(f"<b>An Error Occurred During Processing</b>")
-            error_box.setTextInteractionFlags(Qt.TextSelectableByMouse | Qt.TextSelectableByKeyboard)
-            error_box.setDetailedText(tb)
-
-            details_frame = error_box.findChild(QTextEdit)
-            if details_frame:
-                details_frame.setSizePolicy(QSizePolicy.Expanding, QSizePolicy.Expanding)
-                details_frame.setMaximumHeight(800)
-                details_frame.setMaximumWidth(1000)
-                details_frame.setMinimumHeight(400)
-                details_frame.setMinimumWidth(600)
-
-            error_box_layout = error_box.layout()
-            error_box_layout.setContentsMargins(10, 10, 10, 10)
-
-            copy_button = QPushButton("Copy Error Message")
-            error_box.addButton(copy_button, QMessageBox.ActionRole)
-            def copy_error_txt():
-                QApplication.clipboard().setText(tb)
-            copy_button.clicked.connect(copy_error_txt)
-            error_box.exec_()
-
-    def update_progress(self, value):
-        # Update QProgressDialog with the new value
-        if self.progressDialog is not None:
-            self.progressDialog.setValue(value)
-
-
-class MCT_FIT_CAL_Screen(QDialog):
-    def __init__(self):
-        super(MCT_FIT_CAL_Screen, self).__init__()
-        # Store the initial directory path
-        self.initial_directory = os.getcwd()
-        loadUi(Path(PureWindowsPath("data\\mct_fit_cal_screen.ui")), self)
-        if central_data_store.directory is not None and self.folder_entry is not None:
-            self.directory = central_data_store.directory
-            self.folder_entry.setText(str(central_data_store.directory))
-        self.AT_button4.clicked.connect(self.gotoat4)
-        self.Intro_button4.clicked.connect(self.gotointro4)
-        self.RMT_button4.clicked.connect(self.gotormt4)
-        self.doc_button.clicked.connect(self.openDocument)
-        self.select_folder_button.clicked.connect(self.select_working_directory)
-        self.mask_button.clicked.connect(self.select_mask)
-        self.deforestation_hrp_button.clicked.connect(self.select_deforestation_hrp)
-        self.density_button.clicked.connect(self.select_density)
-        self.ok_button.clicked.connect(self.process_data4)
-        self.model_evaluation = ModelEvaluation()
-        self.model_evaluation.progress_updated.connect(self.update_progress)
-        self.directory = None
-        self.mask = None
-        self.deforestation_hrp = None
-        self.density = None
-        self.grid_area = None
-        self.grid_area_entry.setPlaceholderText('Type default 100000 or other number')
-        self.title = None
-        self.out_fn = None
-        self.out_fn_entry.setPlaceholderText('e.g., Plot_CAL.png')
-        self.raster_fn = None
-        self.raster_fn_entry.setPlaceholderText('e.g., Acre_Residuals_CAL.tif')
-        self.xmax = None
-        self.xmax = None
-        self.file_path_directory = None
-        self.file_path2_directory = None
-        self.file_path3_directory = None
-        self.setWindowTitle("JNR Integrated Risk/Allocation Tool")
-
-    def gotoat4(self):
-        os.chdir(self.initial_directory)
-        at4 = AT_FIT_CAL_Screen()
-        widget.addWidget(at4)
-        widget.setCurrentIndex(widget.currentIndex() + 1)
-
-    def gotointro4(self):
-        os.chdir(self.initial_directory)
-        intro4 = IntroScreen()
-        widget.addWidget(intro4)
-        widget.setCurrentIndex(widget.currentIndex() + 1)
-
-    def gotormt4(self):
-        os.chdir(self.initial_directory)
-        rmt4 = RMT_FIT_CAL_SCREEN()
-        widget.addWidget(rmt4)
-        widget.setCurrentIndex(widget.currentIndex() + 1)
-
-    def openDocument(self):
-        pdf_path = Path(PureWindowsPath("doc\\TestFitMA.pdf"))
-        QDesktopServices.openUrl(QUrl.fromLocalFile(str(pdf_path)))
-
-    def select_working_directory(self):
-        data_folder = QFileDialog.getExistingDirectory(self, "Working Directory")
-        data_folder_path = Path(data_folder)
-        self.directory = str(data_folder_path)
-        self.folder_entry.setText(self.directory)
-        central_data_store.directory = self.directory
-
-    def select_mask(self):
-        file_path, _ = QFileDialog.getOpenFileName(self, 'Mask of Study Area')
-        if file_path:
-            self.mask = Path(PureWindowsPath(file_path))
-            self.mask_entry.setText(file_path.split('/')[-1])
-            self.file_path_directory = '\\'.join(file_path.split('/')[:-1])
-
-    def select_deforestation_hrp(self):
-        file_path3, _ = QFileDialog.getOpenFileName(self, "Map of Deforestation in the HRP")
-        if file_path3:
-            self.deforestation_hrp = Path(PureWindowsPath(file_path3))
-            self.deforestation_hrp_entry.setText(file_path3.split('/')[-1])
-            self.file_path3_directory = '\\'.join(file_path3.split('/')[:-1])
-
-    def select_density(self):
-        file_path2, _ = QFileDialog.getOpenFileName(self, 'Deforestation Density Map')
-        if file_path2:
-            self.density = Path(PureWindowsPath(file_path2))
-            self.density_entry.setText(file_path2.split('/')[-1])
-            self.file_path2_directory = '\\'.join(file_path2.split('/')[:-1])
-    def get_full_path(self, base_dir, user_input):
-        if os.path.isabs(user_input):
-            return user_input
-        else:
-            return f"{base_dir}\\{user_input}"
-    def process_data4(self):
-        directory = self.folder_entry.text()
-        central_data_store.directory = directory
-        if not directory:
-            QMessageBox.critical(self, "Error", "Please select or enter the working directory!")
-            return
-        if not self.file_path_directory:
-            self.file_path_directory = directory
-        if not self.file_path2_directory:
-            self.file_path2_directory = directory
-        if not self.file_path3_directory:
-            self.file_path3_directory = directory
-
-        self.mask = self.get_full_path(self.file_path_directory, self.mask_entry.text())
-        self.density = self.get_full_path(self.file_path2_directory, self.density_entry.text())
-        self.deforestation_hrp = self.get_full_path(self.file_path3_directory, self.deforestation_hrp_entry.text())
-
-        if not self.mask or not self.deforestation_hrp or not self.density :
-            QMessageBox.critical(self, "Error", "Please select or enter all input files!")
-            return
-
-        images = [self.mask, self.deforestation_hrp, self.density]
-
-        # Check if all images have the same resolution
-        resolutions = [map_checker.get_image_resolution(img) for img in images]
-        if len(set(resolutions)) != 1:
-            QMessageBox.critical(None, "Error", "All the input raster images must have the same spatial resolution!")
-            return
-
-        # Check if all images have the same number of rows and columns
-        dimensions = [map_checker.get_image_dimensions(img) for img in images]
-        if len(set(dimensions)) != 1:
-            QMessageBox.critical(None, "Error",
-                                 "All the input raster images must have the same number of rows and columns!")
-            return
-
-        grid_area = self.grid_area_entry.text()
-        if not grid_area:
-            QMessageBox.critical(self, "Error", "Please enter the thiessen polygon grid area value!")
-            return
-        try:
-            self.grid_area = float(grid_area)
-            if not (0 < self.grid_area):
-                QMessageBox.critical(self, "Error", "Thiessen polygon grid area value should larger than 0!")
-                return
-        except ValueError:
-            QMessageBox.critical(self, "Error", "Thiessen polygon grid area value should be a valid number!")
-            return
-
-
-        xmax = self.xmax_entry.text()
-        if xmax.lower() != "default":
-            try:
-                xmax = float(xmax)
-                if xmax <= 0:
-                    raise ValueError("The plot x-axis limit should be larger than 0!")
-            except ValueError:
-                QMessageBox.critical(self, "Error", "The plot x-axis limit should be a valid number or 'Default'!")
-                return
-
-        ymax = self.ymax_entry.text()
-        if ymax.lower() != "default":
-            try:
-                ymax = float(ymax)
-                if ymax <= 0:
-                    raise ValueError("The plot y-axis limit should be larger than 0!")
-            except ValueError:
-                QMessageBox.critical(self, "Error", "The plot y-axis limit should be a valid number or 'Default'!")
-                return
-
-        title = self.title_entry.text()
-        if not title:
-            QMessageBox.critical(self, "Error", "Please enter the title of plot!")
-            return
-
-        out_fn = self.out_fn_entry.text()
-        if not out_fn:
-            QMessageBox.critical(self, "Error", "Please enter the name of plot!")
-            return
-
-        # Check if the out_fn has the correct file extension
-        if not (out_fn.endswith('.png') or out_fn.endswith('.jpg') or out_fn.endswith('.pdf') or out_fn.endswith(
-                '.svg') or out_fn.endswith('.eps') or out_fn.endswith('.ps') or out_fn.endswith('.tif')):
-            QMessageBox.critical(self, "Error",
-                                 "Please enter extension(.png/.jpg/.pdf/.svg/.eps/.ps/.tif) in the name of plot!")
-            return
-
-        raster_fn = self.raster_fn_entry.text()
-        if not raster_fn:
-            QMessageBox.critical(self, "Error", "Please enter the name for Residual Map!")
-            return
-
-        if not (raster_fn.endswith('.tif') or raster_fn.endswith('.rst')):
-            QMessageBox.critical(self, "Error",
-                                 "Please enter .rst or .tif extension in the name of Residual Map!")
-            return
-
-        if not map_checker.check_binary_map(self.mask):
-            QMessageBox.critical(None, "Error",
-                                 "'MASK OF THE NON-EXCLUDED JURISDICTION' must be a binary map (0 and 1) where the 1’s indicate areas inside the jurisdiction.")
-            return
-
-        if not map_checker.check_binary_map(self.deforestation_hrp):
-            QMessageBox.critical(None, "Error",
-                                 "'MAP OF DEFORESTATION IN THE CAL' must be a binary map (0 and 1) where the 1’s indicate deforestation.")
-            return
-
-        # Show "Processing" message
-        processing_message = "Processing data..."
-        self.progressDialog = QProgressDialog(processing_message, None, 0, 100, self)
-
-        # Change the font size
-        font = QFont()
-        font.setPointSize(9)
-        self.progressDialog.setFont(font)
-
-        self.progressDialog.setWindowTitle("Processing")
-        self.progressDialog.setWindowModality(Qt.WindowModal)
-        self.progressDialog.setMinimumDuration(0)
-        self.progressDialog.resize(400, 300)
-        self.progressDialog.show()
-        QApplication.processEvents()
-
-        try:
-            self.model_evaluation.set_working_directory(directory)
-            self.model_evaluation.create_mask_polygon(self.mask)
-            clipped_gdf = self.model_evaluation.create_thiessen_polygon(self.grid_area, self.mask,self.density, self.deforestation_hrp, out_fn,raster_fn)
-            self.model_evaluation.replace_ref_system(self.mask, raster_fn)
-            self.model_evaluation.create_plot(grid_area,clipped_gdf, title, out_fn, xmax, ymax)
-            self.model_evaluation.remove_temp_files()
-
-            QMessageBox.information(self, "Processing Completed", "Processing completed!")
-            self.progressDialog.close()
-
-        except Exception:
-            self.progressDialog.close()
-            tb = traceback.format_exc()
-
-            error_box = QMessageBox(self)
-            error_box.setIcon(QMessageBox.Critical)
-            error_box.setWindowTitle("Error")
-            error_box.setText(f"<b>An Error Occurred During Processing</b>")
-            error_box.setTextInteractionFlags(Qt.TextSelectableByMouse | Qt.TextSelectableByKeyboard)
-            error_box.setDetailedText(tb)
-
-            details_frame = error_box.findChild(QTextEdit)
-            if details_frame:
-                details_frame.setSizePolicy(QSizePolicy.Expanding, QSizePolicy.Expanding)
-                details_frame.setMaximumHeight(800)
-                details_frame.setMaximumWidth(1000)
-                details_frame.setMinimumHeight(400)
-                details_frame.setMinimumWidth(600)
-
-            error_box_layout = error_box.layout()
-            error_box_layout.setContentsMargins(10, 10, 10, 10)
-
-            copy_button = QPushButton("Copy Error Message")
-            error_box.addButton(copy_button, QMessageBox.ActionRole)
-            def copy_error_txt():
-                QApplication.clipboard().setText(tb)
-            copy_button.clicked.connect(copy_error_txt)
-            error_box.exec_()
-
-    def update_progress(self, value):
-        # Update QProgressDialog with the new value
-        if self.progressDialog is not None:
-            self.progressDialog.setValue(value)
-
-class RMT_PRE_CNF_SCREEN(QDialog):
-    def __init__(self):
-        super(RMT_PRE_CNF_SCREEN, self).__init__()
-        # Store the initial directory path
-        self.initial_directory = os.getcwd()
-        loadUi(Path(PureWindowsPath("data\\rmt_pre_cnf_screen.ui")), self)
-        if central_data_store.directory is not None and self.folder_entry is not None:
-            self.directory = central_data_store.directory
-            self.folder_entry.setText(str(central_data_store.directory))
-        if central_data_store.directory is not None and self.folder_entry_2 is not None:
-            self.directory_2 = central_data_store.directory
-            self.folder_entry_2.setText(str(central_data_store.directory))
-        self.AT_button2.clicked.connect(self.gotoat2)
-        self.Intro_button2.clicked.connect(self.gotointro2)
-        self.MCT_button2.clicked.connect(self.gotomct2)
-        self.doc_button = self.tab1.findChild(QWidget, "doc_button")
-        self.select_folder_button = self.tab1.findChild(QWidget, "select_folder_button")
-        self.fd_button = self.tab1.findChild(QWidget, "fd_button")
-        self.mask_button = self.tab1.findChild(QWidget, "mask_button")
-        self.ok_button2 = self.tab1.findChild(QWidget, "ok_button2")
-
-        self.doc_button_2 = self.tab2.findChild(QWidget, "doc_button_2")
-        self.select_folder_button_2 = self.tab2.findChild(QWidget, "select_folder_button_2")
-        self.mask_button_2 = self.tab2.findChild(QWidget, "mask_button_2")
-        self.fmask_button_2 = self.tab2.findChild(QWidget, "fmask_button_2")
-        self.fd_button_2 = self.tab2.findChild(QWidget, "fd_button_2")
-        self.ok_button2_2 = self.tab2.findChild(QWidget, "ok_button2_2")
-
-        self.doc_button.clicked.connect(self.openDocument)
-        self.select_folder_button.clicked.connect(self.select_working_directory)
-        self.fd_button.clicked.connect(self.select_fd)
-        self.mask_button.clicked.connect(self.select_mask)
-        self.ok_button2.clicked.connect(self.process_data2)
-
-        self.doc_button_2.clicked.connect(self.openDocument_2)
-        self.select_folder_button_2.clicked.connect(self.select_working_directory_2)
-        self.mask_button_2.clicked.connect(self.select_mask_2)
-        self.fmask_button_2.clicked.connect(self.select_fmask_2)
-        self.fd_button_2.clicked.connect(self.select_fd_2)
-        self.ok_button2_2.clicked.connect(self.process_data2_2)
-
-        self.vulnerability_map = VulnerabilityMap()
-        self.vulnerability_map.progress_updated.connect(self.update_progress)
-        self.directory = None
-        self.in_fn = None
-        self.NRT = None
-        self.mask = None
-        # Use NRT from the data store
-        if central_data_store.NRT is not None:
-            self.nrt_entry.setText(str(central_data_store.NRT))
-        self.n_classes = None
-        self.out_fn = None
-        self.out_fn_entry.setPlaceholderText('e.g., Acre_Vulnerability_CNF.tif')
-
-        self.directory_2 = None
-        self.mask_2 = None
-        self.fmask_2 = None
-        self.in_fn_2 = None
-        self.out_fn_2 = None
-        self.n_classes_2 = None
-        self.out_fn_entry_2.setPlaceholderText('e.g., Acre_Vulnerability_CNF.tif')
-        self.file_path_directory = None
-        self.file_path2_directory = None
-        self.file_path4_directory = None
-        self.file_path5_directory = None
-        self.file_path6_directory = None
-        self.setWindowTitle("JNR Integrated Risk/Allocation Tool")
-
-    def gotoat2(self):
-        os.chdir(self.initial_directory)
-        at2 = AT_PRE_CNF_Screen()
-        widget.addWidget(at2)
-        widget.setCurrentIndex(widget.currentIndex() + 1)
-
-    def gotomct2(self):
-        os.chdir(self.initial_directory)
-        mct2 = MCT_PRE_CNF_Screen()
-        widget.addWidget(mct2)
-        widget.setCurrentIndex(widget.currentIndex() + 1)
-
-    def gotointro2(self):
-        os.chdir(self.initial_directory)
-        intro2 = IntroScreen()
-        widget.addWidget(intro2)
-        widget.setCurrentIndex(widget.currentIndex() + 1)
-
-    def openDocument(self):
-        pdf_path = Path(PureWindowsPath("doc\\TestPreVM.pdf"))
-        QDesktopServices.openUrl(QUrl.fromLocalFile(str(pdf_path)))
-
-    def openDocument_2(self):
-        pdf_path = Path(PureWindowsPath("doc\\TestPreVM.pdf"))
-        QDesktopServices.openUrl(QUrl.fromLocalFile(str(pdf_path)))
-
-    def select_working_directory(self):
-        data_folder = QFileDialog.getExistingDirectory(self, "Working Directory")
-        data_folder_path = Path(data_folder)
-        self.directory = str(data_folder_path)
-        self.folder_entry.setText(self.directory)
-        self.folder_entry_2.setText(self.directory)
-        central_data_store.directory = self.directory
-
-    def select_fd(self):
-        file_path, _ = QFileDialog.getOpenFileName(self, 'Map of Distance from the Forest Edge in CNF')
-        if file_path:
-            self.in_fn = Path(PureWindowsPath(file_path))
-            self.in_fn_entry.setText(file_path.split('/')[-1])
-            self.file_path_directory = '\\'.join(file_path.split('/')[:-1])
-
-    def select_mask(self):
-        file_path2, _ = QFileDialog.getOpenFileName(self, 'Mask of Study Area')
-        if file_path2:
-            self.mask = Path(PureWindowsPath(file_path2))
-            self.mask_entry.setText(file_path2.split('/')[-1])
-            self.file_path2_directory = '\\'.join(file_path2.split('/')[:-1])
-
-    def select_working_directory_2(self):
-        data_folder_2 = QFileDialog.getExistingDirectory(self, "Working Directory")
-        data_folder_path_2 = Path(data_folder_2)
-        self.directory_2 = str(data_folder_path_2)
-        self.folder_entry_2.setText(self.directory_2)
-        self.folder_entry.setText(self.directory_2)
-        central_data_store.directory = self.directory_2
-    def select_fd_2(self):
-        file_path4, _ = QFileDialog.getOpenFileName(self, 'Map of Distance from the Forest Edge in CNF')
-        if file_path4:
-            self.in_fn_2 = Path(PureWindowsPath(file_path4))
-            self.in_fn_entry_2.setText(file_path4.split('/')[-1])
-            self.file_path4_directory = '\\'.join(file_path4.split('/')[:-1])
-
-    def select_mask_2(self):
-        file_path5, _ = QFileDialog.getOpenFileName(self, 'Mask of Study Area')
-        if file_path5:
-            self.mask_2 = Path(PureWindowsPath(file_path5))
-            self.mask_entry_2.setText(file_path5.split('/')[-1])
-            self.file_path5_directory = '\\'.join(file_path5.split('/')[:-1])
-
-    def select_fmask_2(self):
-        file_path6, _ = QFileDialog.getOpenFileName(self, 'Mask of Forest Area')
-        if file_path6:
-            self.fmask_2 = file_path6
-            self.fmask_entry_2.setText(file_path6.split('/')[-1])
-            self.file_path6_directory = '\\'.join(file_path6.split('/')[:-1])
-    def get_full_path(self, base_dir, user_input):
-        if os.path.isabs(user_input):
-            return user_input
-        else:
-            return f"{base_dir}\\{user_input}"
-    def process_data2(self):
-        directory = self.folder_entry.text()
-        central_data_store.directory = directory
-        self.folder_entry_2.setText(directory)
-        if not directory:
-            QMessageBox.critical(self, "Error", "Please select or enter the working directory!")
-            return
-        if not self.file_path_directory:
-            self.file_path_directory = directory
-        if not self.file_path2_directory:
-            self.file_path2_directory = directory
-        self.in_fn = self.get_full_path(self.file_path_directory, self.in_fn_entry.text())
-        self.mask = self.get_full_path(self.file_path2_directory, self.mask_entry.text())
-
-        if not self.in_fn or not self.mask:
-            QMessageBox.critical(self, "Error", "Please select or enter all input files!")
-            return
-
-        NRT = self.nrt_entry.text()
-        if not NRT:
-            QMessageBox.critical(self, "Error", "Please enter the NRT value!")
-            return
-        try:
-            self.NRT = int(NRT)
-            if (self.NRT <= 0):
-                QMessageBox.critical(self, "Error", "NRT value should be larger than 0!")
-                return
-        except ValueError:
-            QMessageBox.critical(self, "Error", "NRT value should be a valid number!")
-            return
-
-        n_classes = int(29)
-        if not n_classes:
-            QMessageBox.critical(self, "Error", "Please enter the number of classes!")
-            return
-        try:
-            self.n_classes = int(n_classes)
-            if (self.n_classes <= 0):
-                QMessageBox.critical(self, "Error", "Number of classes should be larger than 0!")
-                return
-        except ValueError:
-            QMessageBox.critical(self, "Error", "Number of classes value should be a valid number!")
-            return
-
-        out_fn = self.out_fn_entry.text()
-        if not out_fn:
-            QMessageBox.critical(self, "Error", "Please enter the name of Vulnerability Map in CNF!")
-            return
-
-        if not (out_fn.endswith('.tif') or out_fn.endswith('.rst')):
-            QMessageBox.critical(self, "Error",
-                                 "Please enter .rst or .tif extension in the name of Vulnerability Map in CNF!")
-            return
-
-        # Show "Processing" message
-        processing_message = "Processing data..."
-        self.progressDialog = QProgressDialog(processing_message, None, 0, 100, self)
-
-        # Change the font size
-        font = QFont()
-        font.setPointSize(9)
-        self.progressDialog.setFont(font)
-
-        self.progressDialog.setWindowTitle("Processing")
-        self.progressDialog.setWindowModality(Qt.WindowModal)
-        self.progressDialog.setMinimumDuration(0)
-        self.progressDialog.resize(400, 300)
-        self.progressDialog.show()
-        QApplication.processEvents()
-
-        try:
-            self.vulnerability_map.set_working_directory(directory)
-            mask_arr = self.vulnerability_map.geometric_classification(self.in_fn, NRT, n_classes, self.mask)
-            self.vulnerability_map.array_to_image(self.in_fn, out_fn, mask_arr, gdal.GDT_Int16, -1)
-            self.vulnerability_map.replace_ref_system(self.in_fn, out_fn)
-
-            QMessageBox.information(self, "Processing Completed", "Processing completed!")
-            self.progressDialog.close()
-
-        except Exception:
-            self.progressDialog.close()
-            tb = traceback.format_exc()
-
-            error_box = QMessageBox(self)
-            error_box.setIcon(QMessageBox.Critical)
-            error_box.setWindowTitle("Error")
-            error_box.setText(f"<b>An Error Occurred During Processing</b>")
-            error_box.setTextInteractionFlags(Qt.TextSelectableByMouse | Qt.TextSelectableByKeyboard)
-            error_box.setDetailedText(tb)
-
-            details_frame = error_box.findChild(QTextEdit)
-            if details_frame:
-                details_frame.setSizePolicy(QSizePolicy.Expanding, QSizePolicy.Expanding)
-                details_frame.setMaximumHeight(800)
-                details_frame.setMaximumWidth(1000)
-                details_frame.setMinimumHeight(400)
-                details_frame.setMinimumWidth(600)
-
-            error_box_layout = error_box.layout()
-            error_box_layout.setContentsMargins(10, 10, 10, 10)
-
-            copy_button = QPushButton("Copy Error Message")
-            error_box.addButton(copy_button, QMessageBox.ActionRole)
-            def copy_error_txt():
-                QApplication.clipboard().setText(tb)
-            copy_button.clicked.connect(copy_error_txt)
-            error_box.exec_()
-
-    def process_data2_2(self):
-        directory_2 = self.folder_entry_2.text()
-        central_data_store.directory = directory_2
-        self.folder_entry.setText(directory_2)
-        if not directory_2 :
-            QMessageBox.critical(self, "Error", "Please select or enter the working directory!")
-            return
-        if not self.file_path4_directory:
-            self.file_path4_directory = directory_2
-        if not self.file_path5_directory:
-            self.file_path5_directory = directory_2
-        if not self.file_path6_directory:
-            self.file_path6_directory = directory_2
-
-        self.in_fn_2 = self.get_full_path(self.file_path4_directory, self.in_fn_entry_2.text())
-        self.mask_2 = self.get_full_path(self.file_path5_directory, self.mask_entry_2.text())
-        self.fmask_2 = self.get_full_path(self.file_path6_directory, self.fmask_entry_2.text())
-
-        if not self.in_fn_2 or not self.mask_2 or not self.fmask_2:
-            QMessageBox.critical(self, "Error", "Please select or enter all input files!")
-            return
-
-        images = [self.in_fn_2, self.mask_2, self.fmask_2]
-
-        # Check if all images have the same resolution
-        resolutions = [map_checker.get_image_resolution(img) for img in images]
-        if len(set(resolutions)) != 1:
-            QMessageBox.critical(None, "Error", "All the input raster images must have the same spatial resolution!")
-            return
-
-        # Check if all images have the same number of rows and columns
-        dimensions = [map_checker.get_image_dimensions(img) for img in images]
-        if len(set(dimensions)) != 1:
-            QMessageBox.critical(None, "Error",
-                                 "All the input raster images must have the same number of rows and columns!")
-            return
-
-        n_classes_2 = int(30)
-        out_fn_2 = self.out_fn_entry_2.text()
-        if not out_fn_2:
-            QMessageBox.critical(self, "Error", "Please enter the name of Vulnerability Map in CNF!")
-            return
-
-        # Check if the out_fn has the correct file extension
-        if not (out_fn_2.endswith('.tif') or out_fn_2.endswith('.rst')):
-            QMessageBox.critical(self, "Error",
-                                 "Please enter .rst or .tif extension in the name of Vulnerability Map in CNF!")
-            return
-
-        if not map_checker.check_binary_map(self.fmask_2):
-            QMessageBox.critical(None, "Error",
-                                 "'MASK OF FOREST AREAS IN THE CNF' must be a binary map (0 and 1) where the 1’s indicate forest areas.")
-            return
-
-        if not map_checker.check_binary_map(self.mask_2):
-            QMessageBox.critical(None, "Error",
-                                 "'MASK OF THE NON-EXCLUDED JURISDICTION' must be a binary map (0 and 1) where the 1’s indicate areas inside the jurisdiction.")
-            return
-
-        # Show "Processing" message
-        processing_message = "Processing data..."
-        self.progressDialog = QProgressDialog(processing_message, None, 0, 100, self)
-
-        # Change the font size
-        font = QFont()
-        font.setPointSize(9)
-        self.progressDialog.setFont(font)
-
-        self.progressDialog.setWindowTitle("Processing")
-        self.progressDialog.setWindowModality(Qt.WindowModal)
-        self.progressDialog.setMinimumDuration(0)
-        self.progressDialog.resize(400, 300)
-        self.progressDialog.show()
-        QApplication.processEvents()
-
-        try:
-            self.vulnerability_map.set_working_directory(directory_2)
-            mask_arr = self.vulnerability_map.geometric_classification_alternative(self.in_fn_2, n_classes_2,
-                                                                                   self.mask_2, self.fmask_2)
-            self.vulnerability_map.array_to_image(self.in_fn_2, out_fn_2, mask_arr, gdal.GDT_Int16, -1)
-            self.vulnerability_map.replace_ref_system(self.in_fn_2, out_fn_2)
-
-            QMessageBox.information(self, "Processing Completed", "Processing completed!")
-
-            self.progressDialog.close()
-
-        except Exception:
-            self.progressDialog.close()
-            tb = traceback.format_exc()
-
-            error_box = QMessageBox(self)
-            error_box.setIcon(QMessageBox.Critical)
-            error_box.setWindowTitle("Error")
-            error_box.setText(f"<b>An Error Occurred During Processing</b>")
-            error_box.setTextInteractionFlags(Qt.TextSelectableByMouse | Qt.TextSelectableByKeyboard)
-            error_box.setDetailedText(tb)
-
-            details_frame = error_box.findChild(QTextEdit)
-            if details_frame:
-                details_frame.setSizePolicy(QSizePolicy.Expanding, QSizePolicy.Expanding)
-                details_frame.setMaximumHeight(800)
-                details_frame.setMaximumWidth(1000)
-                details_frame.setMinimumHeight(400)
-                details_frame.setMinimumWidth(600)
-
-            error_box_layout = error_box.layout()
-            error_box_layout.setContentsMargins(10, 10, 10, 10)
-
-            copy_button = QPushButton("Copy Error Message")
-            error_box.addButton(copy_button, QMessageBox.ActionRole)
-            def copy_error_txt():
-                QApplication.clipboard().setText(tb)
-            copy_button.clicked.connect(copy_error_txt)
-            error_box.exec_()
-
-    def update_progress(self, value):
-        # Update QProgressDialog with the new value
-        if self.progressDialog is not None:
-            self.progressDialog.setValue(value)
-
-class AT_PRE_CNF_Screen(QDialog):
-    def __init__(self):
-        super(AT_PRE_CNF_Screen, self).__init__()
-        self.initial_directory = os.getcwd()
-        loadUi(Path(PureWindowsPath("data\\at_pre_cnf_screen.ui")), self)
-        if central_data_store.directory is not None and self.folder_entry is not None:
-            self.directory = central_data_store.directory
-            self.folder_entry.setText(str(central_data_store.directory))
-        self.Intro_button3.clicked.connect(self.gotointro3)
-        self.RMT_button3.clicked.connect(self.gotormt3)
-        self.MCT_button3.clicked.connect(self.gotomct3)
-        self.doc_button.clicked.connect(self.openDocument)
-        self.select_folder_button.clicked.connect(self.select_working_directory)
-        self.municipality_button.clicked.connect(self.select_municipality)
-        self.csv_button.clicked.connect(self.select_csv)
-        self.risk30_vp_button.clicked.connect(self.select_risk30_vp)
-        self.deforestation_cnf_button.clicked.connect(self.select_deforestation_cnf)
-        self.ok_button3.clicked.connect(self.process_data3)
-        self.allocation_tool = AllocationTool()
-        self.allocation_tool.progress_updated.connect(self.update_progress)
-        self.directory = None
-        self.csv = None
-        self.municipality = None
-        self.risk30_vp = None
-        self.deforestation_cnf = None
-        self.max_iterations = None
-        self.image1 = None
-        self.image2 = None
-        self.file_path_directory = None
-        self.file_path1_directory = None
-        self.file_path2_directory = None
-        self.file_path3_directory = None
-        self.iteration_entry.setPlaceholderText('The suggestion max iteration number is 5')
-        self.image1_entry.setPlaceholderText('e.g., Acre_Prediction_Modeling_Region_CNF.tif')
-        self.image2_entry.setPlaceholderText('e.g., Acre_Adjucted_Density_Map_CNF.tif')
-        self.setWindowTitle("JNR Integrated Risk/Allocation Tool")
-
-    def gotormt3(self):
-        os.chdir(self.initial_directory)
-        rmt3 = RMT_PRE_CNF_SCREEN()
-        widget.addWidget(rmt3)
-        widget.setCurrentIndex(widget.currentIndex() + 1)
-
-    def gotointro3(self):
-        os.chdir(self.initial_directory)
-        intro3 = IntroScreen()
-        widget.addWidget(intro3)
-        widget.setCurrentIndex(widget.currentIndex() + 1)
-
-    def gotomct3(self):
-        os.chdir(self.initial_directory)
-        mct3 = MCT_PRE_CNF_Screen()
-        widget.addWidget(mct3)
-        widget.setCurrentIndex(widget.currentIndex() + 1)
-
-    def openDocument(self):
-        pdf_path = Path(PureWindowsPath("doc\\TestPreAM.pdf"))
-        QDesktopServices.openUrl(QUrl.fromLocalFile(str(pdf_path)))
-
-    def select_working_directory(self):
-        data_folder = QFileDialog.getExistingDirectory(self, "Working Directory")
-        data_folder_path = Path(data_folder)
-        self.directory = str(data_folder_path)
-        self.folder_entry.setText(self.directory)
-        central_data_store.directory = self.directory
-
-    def select_municipality(self):
-        file_path, _ = QFileDialog.getOpenFileName(self, 'Map of Administrative Divisions')
-        if file_path:
-            self.municipality = Path(PureWindowsPath(file_path))
-            self.municipality_entry.setText(file_path.split('/')[-1])
-            self.file_path_directory = '\\'.join(file_path.split('/')[:-1])
-    def select_csv(self):
-        file_path1, _ = QFileDialog.getOpenFileName(self, "CAL Relative Frequency Table (.csv)")
-        if file_path1:
-            self.csv = Path(PureWindowsPath(file_path1))
-            self.csv_entry.setText(file_path1.split('/')[-1])
-            self.file_path1_directory = '\\'.join(file_path1.split('/')[:-1])
-
-    def select_risk30_vp(self):
-        file_path2, _ = QFileDialog.getOpenFileName(self, "Vulnerability Map in CNF")
-        if file_path2:
-            self.risk30_vp = Path(PureWindowsPath(file_path2))
-            self.risk30_vp_entry.setText(file_path2.split('/')[-1])
-            self.file_path2_directory = '\\'.join(file_path2.split('/')[:-1])
-
-    def select_deforestation_cnf(self):
-        file_path3, _ = QFileDialog.getOpenFileName(self, "Map of Deforestation in CNF")
-        if file_path3:
-            self.deforestation_cnf = Path(PureWindowsPath(file_path3))
-            self.deforestation_cnf_entry.setText(file_path3.split('/')[-1])
-            self.file_path3_directory = '\\'.join(file_path3.split('/')[:-1])
-    def get_full_path(self, base_dir, user_input):
-        if os.path.isabs(user_input):
-            return user_input
-        else:
-            return f"{base_dir}\\{user_input}"
-
-    def process_data3(self):
-        directory = self.folder_entry.text()
-        central_data_store.directory = directory
-        if not directory:
-            QMessageBox.critical(self, "Error", "Please select or enter the working directory!")
-            return
-
-        if not self.file_path_directory:
-            self.file_path_directory = directory
-        if not self.file_path1_directory:
-            self.file_path1_directory = directory
-        if not self.file_path2_directory:
-            self.file_path2_directory = directory
-        if not self.file_path3_directory:
-            self.file_path3_directory = directory
-
-        self.municipality = self.get_full_path(self.file_path_directory, self.municipality_entry.text())
-        self.csv = self.get_full_path(self.file_path1_directory, self.csv_entry.text())
-        self.risk30_vp = self.get_full_path(self.file_path2_directory, self.risk30_vp_entry.text())
-        self.deforestation_cnf = self.get_full_path(self.file_path3_directory, self.deforestation_cnf_entry.text())
-
-        if not self.municipality or not self.csv or not self.deforestation_cnf or not self.risk30_vp:
-            QMessageBox.critical(self, "Error", "Please select or enter all input files!")
-            return
-
-        images = [self.municipality, self.deforestation_cnf, self.risk30_vp]
-
-        # Check if all images have the same resolution
-        resolutions = [map_checker.get_image_resolution(img) for img in images]
-        if len(set(resolutions)) != 1:
-            QMessageBox.critical(None, "Error", "All the input raster images must have the same spatial resolution!")
-            return
-
-        # Check if all images have the same number of rows and columns
-        dimensions = [map_checker.get_image_dimensions(img) for img in images]
-        if len(set(dimensions)) != 1:
-            QMessageBox.critical(None, "Error",
-                                 "All the input raster images must have the same number of rows and columns!")
-            return
-
-        out_fn1 = self.image1_entry.text()
-        if not out_fn1:
-            QMessageBox.critical(self, "Error", "Please enter the name of Prediction Modeling Region Map in CNF!")
-            return
-
-        if not (out_fn1.endswith('.tif') or out_fn1.endswith('.rst')):
-            QMessageBox.critical(self, "Error",
-                                 "Please enter .rst or .tif extension in the name of Prediction Modeling Region Map in CNF!")
-            return
-
-        out_fn2 = self.image2_entry.text()
-        if not out_fn2:
-            QMessageBox.critical(self, "Error", "Please enter the name of Adjusted Prediction Density Map in CNF!")
-            return
-
-        if not (out_fn2.endswith('.tif') or out_fn2.endswith('.rst')):
-            QMessageBox.critical(self, "Error",
-                                 "Please enter .rst or .tif extension in the name of Adjusted Prediction Density Map in CNF!")
-            return
-
-        max_iterations = self.iteration_entry.text()
-        if not max_iterations:
-            QMessageBox.critical(self, "Error", "Please enter the max iterations! The suggestion number is 5.")
-            return
-        try:
-            self.max_iterations = int(max_iterations)
-        except ValueError:
-            QMessageBox.critical(self, "Error", "Max iteration value should be a valid number!")
-            return
-
-        if not map_checker.check_binary_map(self.deforestation_cnf):
-            QMessageBox.critical(None, "Error",
-                                 "'MAP OF DEFORESTATION IN THE CNF' must be a binary map (0 and 1) where the 1’s indicate deforestation.")
-            return
-
-        # Show "Processing" message
-        processing_message = "Processing data..."
-        self.progressDialog = QProgressDialog(processing_message, None, 0, 100, self)
-
-        # Change the font size
-        font = QFont()
-        font.setPointSize(9)
-        self.progressDialog.setFont(font)
-
-        self.progressDialog.setWindowTitle("Processing")
-        self.progressDialog.setWindowModality(Qt.WindowModal)
-        self.progressDialog.setMinimumDuration(0)
-        self.progressDialog.resize(400, 300)
-        self.progressDialog.show()
-        QApplication.processEvents()
-
-        try:
-            id_difference,iteration_count = self.allocation_tool.execute_workflow_cnf(directory,
-                                                            self.max_iterations, self.csv,
-                                                            self.municipality,
-                                                            self.deforestation_cnf,
-                                                            self.risk30_vp, out_fn1,
-                                                            out_fn2)
-            if id_difference.size > 0:
-                QMessageBox.warning(self, " Warning ", f"Modeling Region ID {','.join(map(str, id_difference))} do not exist in the Calculation Period. A new CSV has been created for the CAL where relative frequencies for missing bins have been estimated from corresponding vulnerability zones over the entire jurisdiction.")
-            if iteration_count > int(max_iterations):
-                QMessageBox.warning(self, " Warning ", f"Maximum iterations limit reached. Please increase the Maximum Iterations and try running the tool again.")
-            else:
-                QMessageBox.information(self, "Processing Completed", "Processing completed!")
-            self.progressDialog.close()
-
-        except Exception:
-            self.progressDialog.close()
-            tb = traceback.format_exc()
-
-            error_box = QMessageBox(self)
-            error_box.setIcon(QMessageBox.Critical)
-            error_box.setWindowTitle("Error")
-            error_box.setText(f"<b>An Error Occurred During Processing</b>")
-            error_box.setTextInteractionFlags(Qt.TextSelectableByMouse | Qt.TextSelectableByKeyboard)
-            error_box.setDetailedText(tb)
-
-            details_frame = error_box.findChild(QTextEdit)
-            if details_frame:
-                details_frame.setSizePolicy(QSizePolicy.Expanding, QSizePolicy.Expanding)
-                details_frame.setMaximumHeight(800)
-                details_frame.setMaximumWidth(1000)
-                details_frame.setMinimumHeight(400)
-                details_frame.setMinimumWidth(600)
-
-            error_box_layout = error_box.layout()
-            error_box_layout.setContentsMargins(10, 10, 10, 10)
-
-            copy_button = QPushButton("Copy Error Message")
-            error_box.addButton(copy_button, QMessageBox.ActionRole)
-            def copy_error_txt():
-                QApplication.clipboard().setText(tb)
-            copy_button.clicked.connect(copy_error_txt)
-            error_box.exec_()
-
-    def update_progress(self, value):
-        # Update QProgressDialog with the new value
-        if self.progressDialog is not None:
-            self.progressDialog.setValue(value)
-
-class MCT_PRE_CNF_Screen(QDialog):
-    def __init__(self):
-        super(MCT_PRE_CNF_Screen, self).__init__()
-        # Store the initial directory path
-        self.initial_directory = os.getcwd()
-        loadUi(Path(PureWindowsPath("data\\mct_pre_cnf_screen.ui")), self)
-        if central_data_store.directory is not None and self.folder_entry is not None:
-            self.directory = central_data_store.directory
-            self.folder_entry.setText(str(central_data_store.directory))
-        self.AT_button4.clicked.connect(self.gotoat4)
-        self.Intro_button4.clicked.connect(self.gotointro4)
-        self.RMT_button4.clicked.connect(self.gotormt4)
-        self.doc_button.clicked.connect(self.openDocument)
-        self.select_folder_button.clicked.connect(self.select_working_directory)
-        self.mask_button.clicked.connect(self.select_mask)
-        self.fmask_button.clicked.connect(self.select_fmask)
-        self.deforestation_cal_button.clicked.connect(self.select_deforestation_cal)
-        self.deforestation_hrp_button.clicked.connect(self.select_deforestation_hrp)
-        self.density_button.clicked.connect(self.select_density)
-        self.ok_button.clicked.connect(self.process_data4)
-        self.model_evaluation = ModelEvaluation()
-        self.model_evaluation.progress_updated.connect(self.update_progress)
-        self.directory = None
-        self.mask = None
-        self.fmask = None
-        self.deforestation_cal = None
-        self.deforestation_hrp = None
-        self.density = None
-        self.grid_area = None
-        self.grid_area_entry.setPlaceholderText('Type default 100000 or other number')
-        self.title = None
-        self.out_fn = None
-        self.out_fn_def = None
-        self.raster_fn = None
-        self.file_path_directory = None
-        self.file_path1_directory = None
-        self.file_path2_directory = None
-        self.file_path3_directory = None
-        self.file_path4_directory = None
-        self.out_fn_entry.setPlaceholderText('e.g., Plot_CNF.png')
-        self.out_fn_def_entry.setPlaceholderText('e.g., Acre_Def_Review.tif')
-        self.raster_fn_entry.setPlaceholderText('e.g., Acre_Residuals_CNF.tif')
-        self.setWindowTitle("JNR Integrated Risk/Allocation Tool")
-
-    def gotoat4(self):
-        os.chdir(self.initial_directory)
-        at4 = AT_PRE_CNF_Screen()
-        widget.addWidget(at4)
-        widget.setCurrentIndex(widget.currentIndex() + 1)
-
-    def gotointro4(self):
-        os.chdir(self.initial_directory)
-        intro4 = IntroScreen()
-        widget.addWidget(intro4)
-        widget.setCurrentIndex(widget.currentIndex() + 1)
-
-    def gotormt4(self):
-        os.chdir(self.initial_directory)
-        rmt4 = RMT_PRE_CNF_SCREEN()
-        widget.addWidget(rmt4)
-        widget.setCurrentIndex(widget.currentIndex() + 1)
-
-    def openDocument(self):
-        pdf_path = Path(PureWindowsPath("doc\\TestPreMA.pdf"))
-        QDesktopServices.openUrl(QUrl.fromLocalFile(str(pdf_path)))
-
-    def select_working_directory(self):
-        data_folder = QFileDialog.getExistingDirectory(self, "Working Directory")
-        data_folder_path = Path(data_folder)
-        self.directory = str(data_folder_path)
-        self.folder_entry.setText(self.directory)
-        central_data_store.directory = self.directory
-
-    def select_mask(self):
-        file_path, _ = QFileDialog.getOpenFileName(self, 'Mask of Study Area')
-        if file_path:
-            self.mask = Path(PureWindowsPath(file_path))
-            self.mask_entry.setText(file_path.split('/')[-1])
-            self.file_path_directory = '\\'.join(file_path.split('/')[:-1])
-    def select_fmask(self):
-        file_path1, _ = QFileDialog.getOpenFileName(self, 'Mask of Forest Area')
-        if file_path1:
-            self.fmask = Path(PureWindowsPath(file_path1))
-            self.fmask_entry.setText(file_path1.split('/')[-1])
-            self.file_path1_directory = '\\'.join(file_path1.split('/')[:-1])
-
-    def select_deforestation_cal(self):
-        file_path2, _ = QFileDialog.getOpenFileName(self, "Actual Deforestation Map in CAL")
-        if file_path2:
-            self.deforestation_cal = Path(PureWindowsPath(file_path2))
-            self.deforestation_cal_entry.setText(file_path2.split('/')[-1])
-            self.file_path2_directory = '\\'.join(file_path2.split('/')[:-1])
-
-    def select_deforestation_hrp(self):
-        file_path3, _ = QFileDialog.getOpenFileName(self, "Actual Deforestation Map in CNF")
-        if file_path3:
-            self.deforestation_hrp = Path(PureWindowsPath(file_path3))
-            self.deforestation_hrp_entry.setText(file_path3.split('/')[-1])
-            self.file_path3_directory = '\\'.join(file_path3.split('/')[:-1])
-    def select_density(self):
-        file_path4, _ = QFileDialog.getOpenFileName(self, 'Adjusted Prediction Density Map in CNF')
-        if file_path4:
-            self.density = Path(PureWindowsPath(file_path4))
-            self.density_entry.setText(file_path4.split('/')[-1])
-            self.file_path4_directory = '\\'.join(file_path4.split('/')[:-1])
-
-    def get_full_path(self, base_dir, user_input):
-        if os.path.isabs(user_input):
-            return user_input
-        else:
-            return f"{base_dir}\\{user_input}"
-
-    def process_data4(self):
-        directory = self.folder_entry.text()
-        central_data_store.directory = directory
-        if not directory:
-            QMessageBox.critical(self, "Error", "Please select or enter the working directory!")
-            return
-
-        if not self.file_path_directory:
-            self.file_path_directory = directory
-        if not self.file_path1_directory:
-            self.file_path1_directory = directory
-        if not self.file_path2_directory:
-            self.file_path2_directory = directory
-        if not self.file_path3_directory:
-            self.file_path3_directory = directory
-        if not self.file_path4_directory:
-            self.file_path4_directory = directory
-
-        self.mask = self.get_full_path(self.file_path_directory, self.mask_entry.text())
-        self.fmask = self.get_full_path(self.file_path1_directory, self.fmask_entry.text())
-        self.deforestation_cal = self.get_full_path(self.file_path2_directory, self.deforestation_cal_entry.text())
-        self.deforestation_hrp = self.get_full_path(self.file_path3_directory, self.deforestation_hrp_entry.text())
-        self.density = self.get_full_path(self.file_path4_directory, self.density_entry.text())
-
-        if not self.mask or not self.fmask or not self.deforestation_cal or not self.deforestation_hrp or not self.density :
-            QMessageBox.critical(self, "Error", "Please select or enter all input files!")
-            return
-
-        images = [self.mask, self.fmask, self.deforestation_cal, self.deforestation_hrp, self.density]
-
-        # Check if all images have the same resolution
-        resolutions = [map_checker.get_image_resolution(img) for img in images]
-        if len(set(resolutions)) != 1:
-            QMessageBox.critical(None, "Error", "All the input raster images must have the same spatial resolution!")
-            return
-
-        # Check if all images have the same number of rows and columns
-        dimensions = [map_checker.get_image_dimensions(img) for img in images]
-        if len(set(dimensions)) != 1:
-            QMessageBox.critical(None, "Error",
-                                 "All the input raster images must have the same number of rows and columns!")
-            return
-
-        grid_area = self.grid_area_entry.text()
-        if not grid_area:
-            QMessageBox.critical(self, "Error", "Please enter the thiessen polygon grid area value!")
-            return
-        try:
-            self.grid_area = float(grid_area)
-            if not (0 < self.grid_area):
-                QMessageBox.critical(self, "Error", "Thiessen polygon grid area value should larger than 0!")
-                return
-        except ValueError:
-            QMessageBox.critical(self, "Error", "Thiessen polygon grid area value should be a valid number!")
-            return
-
-        xmax = self.xmax_entry.text()
-        if xmax.lower() != "default":
-            try:
-                xmax = float(xmax)
-                if xmax <= 0:
-                    raise ValueError("The plot x-axis limit should be larger than 0!")
-            except ValueError:
-                QMessageBox.critical(self, "Error", "The plot x-axis limit should be a valid number or 'Default'!")
-                return
-
-        ymax = self.ymax_entry.text()
-        if ymax.lower() != "default":
-            try:
-                ymax = float(ymax)
-                if ymax <= 0:
-                    raise ValueError("The plot y-axis limit should be larger than 0!")
-            except ValueError:
-                QMessageBox.critical(self, "Error", "The plot y-axis limit should be a valid number or 'Default'!")
-                return
-
-        title = self.title_entry.text()
-        if not title:
-            QMessageBox.critical(self, "Error", "Please enter the title of plot!")
-            return
-
-        out_fn = self.out_fn_entry.text()
-        if not out_fn:
-            QMessageBox.critical(self, "Error", "Please enter the name used for the plot, performace chart and assessment polygons!")
-            return
-
-        # Check if the out_fn has the correct file extension
-        if not (out_fn.endswith('.png') or out_fn.endswith('.jpg') or out_fn.endswith('.pdf') or out_fn.endswith(
-                '.svg') or out_fn.endswith('.eps') or out_fn.endswith('.ps') or out_fn.endswith('.tif')):
-            QMessageBox.critical(self, "Error",
-                                 "Please enter extension(.png/.jpg/.pdf/.svg/.eps/.ps/.tif) in the name of plot!")
-            return
-
-        raster_fn = self.raster_fn_entry.text()
-        if not raster_fn:
-            QMessageBox.critical(self, "Error", "Please enter the name for Residual Map!")
-            return
-
-        if not (raster_fn.endswith('.tif') or raster_fn.endswith('.rst')):
-            QMessageBox.critical(self, "Error",
-                                 "Please enter .rst or .tif extension in the name of Residual Map!")
-            return
-
-        out_fn_def = self.out_fn_def_entry.text()
-        if not out_fn_def:
-            QMessageBox.critical(self, "Error", "Please enter the name for Combined Deforestation Reference Map!")
-            return
-
-        if not (out_fn_def.endswith('.tif') or out_fn_def.endswith('.rst')):
-            QMessageBox.critical(self, "Error",
-                                 "Please enter .rst or .tif extension in the name of Combined Deforestation Reference Map!")
-            return
-
-        if not map_checker.check_binary_map(self.mask):
-            QMessageBox.critical(None, "Error",
-                                 "'MASK OF THE NON-EXCLUDED JURISDICTION' must be a binary map (0 and 1) where the 1’s indicate areas inside the jurisdiction.")
-            return
-
-        if not map_checker.check_binary_map(self.deforestation_hrp):
-            QMessageBox.critical(None, "Error",
-                                 "'MAP OF DEFORESTATION IN THE CNF' must be a binary map (0 and 1) where the 1’s indicate deforestation.")
-            return
-
-        if not map_checker.check_binary_map(self.deforestation_cal):
-            QMessageBox.critical(None, "Error",
-                                 "'MAP OF DEFORESTATION IN THE CAL' must be a binary map (0 and 1) where the 1’s indicate deforestation.")
-            return
-
-        if not map_checker.check_binary_map(self.fmask):
-            QMessageBox.critical(None, "Error",
-                                 "'MASK OF FOREST AREAS IN THE CAL' must be a binary map (0 and 1) where the 1’s indicate forest areas.")
-            return
-
-        # Show "Processing" message
-        processing_message = "Processing data..."
-        self.progressDialog = QProgressDialog(processing_message, None, 0, 100, self)
-
-        # Change the font size
-        font = QFont()
-        font.setPointSize(9)
-        self.progressDialog.setFont(font)
-
-        self.progressDialog.setWindowTitle("Processing")
-        self.progressDialog.setWindowModality(Qt.WindowModal)
-        self.progressDialog.setMinimumDuration(0)
-        self.progressDialog.resize(400, 300)
-        self.progressDialog.show()
-        QApplication.processEvents()
-
-        try:
-            self.model_evaluation.set_working_directory(directory)
-            self.model_evaluation.create_mask_polygon(self.mask)
-            clipped_gdf = self.model_evaluation.create_thiessen_polygon(self.grid_area, self.mask, self.density,
-                                                                             self.deforestation_hrp, out_fn, raster_fn)
-            self.model_evaluation.replace_ref_system(self.mask, raster_fn)
-            self.model_evaluation.create_deforestation_map(self.fmask, self.deforestation_cal, self.deforestation_hrp,
-                                                           out_fn_def)
-            self.model_evaluation.replace_ref_system(self.fmask, out_fn_def)
-            self.model_evaluation.replace_legend(out_fn_def)
-            self.model_evaluation.create_plot(grid_area,clipped_gdf, title, out_fn, xmax, ymax)
-            self.model_evaluation.remove_temp_files()
-
-            QMessageBox.information(self, "Processing Completed", "Processing completed!")
-            self.progressDialog.close()
-
-        except Exception:
-            self.progressDialog.close()
-            tb = traceback.format_exc()
-
-            error_box = QMessageBox(self)
-            error_box.setIcon(QMessageBox.Critical)
-            error_box.setWindowTitle("Error")
-            error_box.setText(f"<b>An Error Occurred During Processing</b>")
-            error_box.setTextInteractionFlags(Qt.TextSelectableByMouse | Qt.TextSelectableByKeyboard)
-            error_box.setDetailedText(tb)
-
-            details_frame = error_box.findChild(QTextEdit)
-            if details_frame:
-                details_frame.setSizePolicy(QSizePolicy.Expanding, QSizePolicy.Expanding)
-                details_frame.setMaximumHeight(800)
-                details_frame.setMaximumWidth(1000)
-                details_frame.setMinimumHeight(400)
-                details_frame.setMinimumWidth(600)
-
-            error_box_layout = error_box.layout()
-            error_box_layout.setContentsMargins(10, 10, 10, 10)
-
-            copy_button = QPushButton("Copy Error Message")
-            error_box.addButton(copy_button, QMessageBox.ActionRole)
-            def copy_error_txt():
-                QApplication.clipboard().setText(tb)
-            copy_button.clicked.connect(copy_error_txt)
-            error_box.exec_()
-
-    def update_progress(self, value):
-        # Update QProgressDialog with the new value
-        if self.progressDialog is not None:
-            self.progressDialog.setValue(value)
-
-class RMT_FIT_HRP_SCREEN(QDialog):
-    def __init__(self):
-        super(RMT_FIT_HRP_SCREEN, self).__init__()
-        # Store the initial directory path
-        self.initial_directory = os.getcwd()
-        loadUi(Path(PureWindowsPath("data\\rmt_fit_hrp_screen.ui")), self)
-        if central_data_store.directory is not None and self.folder_entry is not None:
-            self.directory = central_data_store.directory
-            self.folder_entry.setText(str(central_data_store.directory))
-        if central_data_store.directory is not None and self.folder_entry_2 is not None:
-            self.directory_2 = central_data_store.directory
-            self.folder_entry_2.setText(str(central_data_store.directory))
-        self.AT_button2.clicked.connect(self.gotoat2)
-        self.Intro_button2.clicked.connect(self.gotointro2)
-
-        self.doc_button = self.tab1.findChild(QWidget, "doc_button")
-        self.select_folder_button = self.tab1.findChild(QWidget, "select_folder_button")
-        self.fd_button = self.tab1.findChild(QWidget, "fd_button")
-        self.mask_button = self.tab1.findChild(QWidget, "mask_button")
-        self.ok_button2 = self.tab1.findChild(QWidget, "ok_button2")
-
-        self.doc_button_2 = self.tab2.findChild(QWidget, "doc_button_2")
-        self.select_folder_button_2 = self.tab2.findChild(QWidget, "select_folder_button_2")
-        self.mask_button_2 = self.tab2.findChild(QWidget, "mask_button_2")
-        self.fmask_button_2 = self.tab2.findChild(QWidget, "fmask_button_2")
-        self.fd_button_2 = self.tab2.findChild(QWidget, "fd_button_2")
-        self.ok_button2_2 = self.tab2.findChild(QWidget, "ok_button2_2")
-
-        self.doc_button.clicked.connect(self.openDocument)
-        self.select_folder_button.clicked.connect(self.select_working_directory)
-        self.fd_button.clicked.connect(self.select_fd)
-        self.mask_button.clicked.connect(self.select_mask)
-        self.ok_button2.clicked.connect(self.process_data2)
-
-        self.doc_button_2.clicked.connect(self.openDocument_2)
-        self.select_folder_button_2.clicked.connect(self.select_working_directory_2)
-        self.mask_button_2.clicked.connect(self.select_mask_2)
-        self.fmask_button_2.clicked.connect(self.select_fmask_2)
-        self.fd_button_2.clicked.connect(self.select_fd_2)
-        self.ok_button2_2.clicked.connect(self.process_data2_2)
-
-        self.vulnerability_map = VulnerabilityMap()
-        self.vulnerability_map.progress_updated.connect(self.update_progress)
-        self.directory = None
-        self.in_fn = None
-        self.NRT = None
-        if central_data_store.NRT is not None:
-            self.nrt_entry.setText(str(central_data_store.NRT))
-        self.n_classes = None
-        self.mask = None
-        self.out_fn = None
-        self.out_fn_entry.setPlaceholderText('e.g., Acre_Vulnerability_HRP.tif')
-
-        self.directory_2 = None
-        self.mask_2 = None
-        self.fmask_2 = None
-        self.in_fn_2 = None
-        self.out_fn_2 = None
-        self.n_classes_2 = None
-        self.out_fn_entry_2.setPlaceholderText('e.g., Acre_Vulnerability_HRP.tif')
-        self.file_path_directory = None
-        self.file_path2_directory = None
-        self.file_path4_directory = None
-        self.file_path5_directory = None
-        self.file_path6_directory = None
-        self.setWindowTitle("JNR Integrated Risk/Allocation Tool")
-
-    def gotoat2(self):
-        os.chdir(self.initial_directory)
-        at2 = AT_FIT_HRP_Screen()
-        widget.addWidget(at2)
-        widget.setCurrentIndex(widget.currentIndex() + 1)
-
-    def gotointro2(self):
-        os.chdir(self.initial_directory)
-        intro2 = IntroScreen()
-        widget.addWidget(intro2)
-        widget.setCurrentIndex(widget.currentIndex() + 1)
-
-    def openDocument(self):
-        pdf_path = Path(PureWindowsPath("doc\\AppFitVM.pdf"))
-        QDesktopServices.openUrl(QUrl.fromLocalFile(str(pdf_path)))
-
-    def openDocument_2(self):
-        pdf_path = Path(PureWindowsPath("doc\\AppFitVM.pdf"))
-        QDesktopServices.openUrl(QUrl.fromLocalFile(str(pdf_path)))
-
-    def select_working_directory(self):
-        data_folder = QFileDialog.getExistingDirectory(self, "Working Directory")
-        data_folder_path = Path(data_folder)
-        self.directory = str(data_folder_path)
-        self.folder_entry.setText(self.directory)
-        self.folder_entry_2.setText(self.directory)
-        central_data_store.directory = self.directory
-
-    def select_fd(self):
-        file_path, _ = QFileDialog.getOpenFileName(self, 'Map of Distance from the Forest Edge in HRP')
-        if file_path:
-            self.in_fn = Path(PureWindowsPath(file_path))
-            self.in_fn_entry.setText(file_path.split('/')[-1])
-            self.file_path_directory = '\\'.join(file_path.split('/')[:-1])
-
-    def select_mask(self):
-        file_path2, _ = QFileDialog.getOpenFileName(self, 'Mask of Study Area')
-        if file_path2:
-            self.mask = Path(PureWindowsPath(file_path2))
-            self.mask_entry.setText(file_path2.split('/')[-1])
-            self.file_path2_directory = '\\'.join(file_path2.split('/')[:-1])
-
-    def select_working_directory_2(self):
-        data_folder_2 = QFileDialog.getExistingDirectory(self, "Working Directory")
-        data_folder_path_2 = Path(data_folder_2)
-        self.directory_2 = str(data_folder_path_2)
-        self.folder_entry_2.setText(self.directory_2)
-        self.folder_entry.setText(self.directory_2)
-        central_data_store.directory = self.directory_2
-
-    def select_fd_2(self):
-        file_path4, _ = QFileDialog.getOpenFileName(self, 'Map of Distance from the Forest Edge in HRP')
-        if file_path4:
-            self.in_fn_2 = Path(PureWindowsPath(file_path4))
-            self.in_fn_entry_2.setText(file_path4.split('/')[-1])
-            self.file_path4_directory = '\\'.join(file_path4.split('/')[:-1])
-
-    def select_mask_2(self):
-        file_path5, _ = QFileDialog.getOpenFileName(self, 'Mask of Study Area')
-        if file_path5:
-            self.mask_2 = Path(PureWindowsPath(file_path5))
-            self.mask_entry_2.setText(file_path5.split('/')[-1])
-            self.file_path5_directory = '\\'.join(file_path5.split('/')[:-1])
-
-    def select_fmask_2(self):
-        file_path6, _ = QFileDialog.getOpenFileName(self, 'Mask of Forest Area')
-        if file_path6:
-            self.fmask_2 = file_path6
-            self.fmask_entry_2.setText(file_path6.split('/')[-1])
-            self.file_path6_directory = '\\'.join(file_path6.split('/')[:-1])
-    def get_full_path(self, base_dir, user_input):
-        if os.path.isabs(user_input):
-            return user_input
-        else:
-            return f"{base_dir}\\{user_input}"
-    def process_data2(self):
-        directory = self.folder_entry.text()
-        central_data_store.directory = directory
-        self.folder_entry_2.setText(directory)
-        if not directory:
-            QMessageBox.critical(self, "Error", "Please select or enter the working directory!")
-            return
-        if not self.file_path_directory:
-            self.file_path_directory = directory
-        if not self.file_path2_directory:
-            self.file_path2_directory = directory
-        self.in_fn = self.get_full_path(self.file_path_directory, self.in_fn_entry.text())
-        self.mask = self.get_full_path(self.file_path2_directory, self.mask_entry.text())
-
-        if not self.in_fn or not self.mask:
-            QMessageBox.critical(self, "Error", "Please select or enter all input files!")
-            return
-
-        NRT = self.nrt_entry.text()
-        if not NRT:
-            QMessageBox.critical(self, "Error", "Please enter the NRT value!")
-            return
-        try:
-            self.NRT = int(NRT)
-            if (self.NRT <= 0):
-                QMessageBox.critical(self, "Error", "NRT value should be larger than 0!")
-                return
-        except ValueError:
-            QMessageBox.critical(self, "Error", "NRT value should be a valid number!")
-            return
-
-        n_classes = int(29)
-        if not n_classes:
-            QMessageBox.critical(self, "Error", "Please enter the number of classes!")
-            return
-        try:
-            self.n_classes = int(n_classes)
-            if (self.n_classes <= 0):
-                QMessageBox.critical(self, "Error", "Number of classes should be larger than 0!")
-                return
-        except ValueError:
-            QMessageBox.critical(self, "Error", "Number of classes value should be a valid number!")
-            return
-
-        out_fn = self.out_fn_entry.text()
-        if not out_fn:
-            QMessageBox.critical(self, "Error", "Please enter the name of Vulnerability Map in HRP!")
-            return
-
-        if not (out_fn.endswith('.tif') or out_fn.endswith('.rst')):
-            QMessageBox.critical(self, "Error",
-                                 "Please enter .rst or .tif extension in the name of Vulnerability Map in HRP!")
-            return
-
-        # Show "Processing" message
-        processing_message = "Processing data..."
-        self.progressDialog = QProgressDialog(processing_message, None, 0, 100, self)
-
-        # Change the font size
-        font = QFont()
-        font.setPointSize(9)
-        self.progressDialog.setFont(font)
-
-        self.progressDialog.setWindowTitle("Processing")
-        self.progressDialog.setWindowModality(Qt.WindowModal)
-        self.progressDialog.setMinimumDuration(0)
-        self.progressDialog.resize(400, 300)
-        self.progressDialog.show()
-        QApplication.processEvents()
-
-        try:
-            self.vulnerability_map.set_working_directory(directory)
-            mask_arr = self.vulnerability_map.geometric_classification(self.in_fn, NRT, n_classes, self.mask)
-            self.vulnerability_map.array_to_image(self.in_fn, out_fn, mask_arr, gdal.GDT_Int16, -1)
-            self.vulnerability_map.replace_ref_system(self.in_fn, out_fn)
-
-            QMessageBox.information(self, "Processing Completed", "Processing completed!")
-            self.progressDialog.close()
-
-        except Exception:
-            self.progressDialog.close()
-            tb = traceback.format_exc()
-
-            error_box = QMessageBox(self)
-            error_box.setIcon(QMessageBox.Critical)
-            error_box.setWindowTitle("Error")
-            error_box.setText(f"<b>An Error Occurred During Processing</b>")
-            error_box.setTextInteractionFlags(Qt.TextSelectableByMouse | Qt.TextSelectableByKeyboard)
-            error_box.setDetailedText(tb)
-
-            details_frame = error_box.findChild(QTextEdit)
-            if details_frame:
-                details_frame.setSizePolicy(QSizePolicy.Expanding, QSizePolicy.Expanding)
-                details_frame.setMaximumHeight(800)
-                details_frame.setMaximumWidth(1000)
-                details_frame.setMinimumHeight(400)
-                details_frame.setMinimumWidth(600)
-
-            error_box_layout = error_box.layout()
-            error_box_layout.setContentsMargins(10, 10, 10, 10)
-
-            copy_button = QPushButton("Copy Error Message")
-            error_box.addButton(copy_button, QMessageBox.ActionRole)
-            def copy_error_txt():
-                QApplication.clipboard().setText(tb)
-            copy_button.clicked.connect(copy_error_txt)
-            error_box.exec_()
-
-    def process_data2_2(self):
-        directory_2 = self.folder_entry_2.text()
-        central_data_store.directory = directory_2
-        self.folder_entry.setText(directory_2)
-        if not directory_2 :
-            QMessageBox.critical(self, "Error", "Please select or enter the working directory!")
-            return
-
-        if not self.file_path4_directory:
-            self.file_path4_directory = directory_2
-        if not self.file_path5_directory:
-            self.file_path5_directory = directory_2
-        if not self.file_path6_directory:
-            self.file_path6_directory = directory_2
-
-        self.in_fn_2 = self.get_full_path(self.file_path4_directory, self.in_fn_entry_2.text())
-        self.mask_2 = self.get_full_path(self.file_path5_directory, self.mask_entry_2.text())
-        self.fmask_2 = self.get_full_path(self.file_path6_directory, self.fmask_entry_2.text())
-
-        if not self.in_fn_2 or not self.mask_2 or not self.fmask_2:
-            QMessageBox.critical(self, "Error", "Please select or enter all input files!")
-            return
-
-        images = [self.in_fn_2, self.mask_2, self.fmask_2]
-
-        # Check if all images have the same resolution
-        resolutions = [map_checker.get_image_resolution(img) for img in images]
-        if len(set(resolutions)) != 1:
-            QMessageBox.critical(None, "Error", "All the input raster images must have the same spatial resolution!")
-            return
-
-        # Check if all images have the same number of rows and columns
-        dimensions = [map_checker.get_image_dimensions(img) for img in images]
-        if len(set(dimensions)) != 1:
-            QMessageBox.critical(None, "Error",
-                                 "All the input raster images must have the same number of rows and columns!")
-            return
-
-        n_classes_2 = int(30)
-        out_fn_2 = self.out_fn_entry_2.text()
-        if not out_fn_2:
-            QMessageBox.critical(self, "Error", "Please enter the name of Vulnerability Map in HRP!")
-            return
-
-        # Check if the out_fn has the correct file extension
-        if not (out_fn_2.endswith('.tif') or out_fn_2.endswith('.rst')):
-            QMessageBox.critical(self, "Error",
-                                 "Please enter .rst or .tif extension in the name of Vulnerability Map in HRP!")
-            return
-
-        if not map_checker.check_binary_map(self.mask_2):
-            QMessageBox.critical(None, "Error",
-                                 "'MASK OF THE NON-EXCLUDED JURISDICTION' must be a binary map (0 and 1) where the 1’s indicate areas inside the jurisdiction.")
-            return
-
-        if not map_checker.check_binary_map(self.fmask_2):
-            QMessageBox.critical(None, "Error",
-                                 "'MASK OF FOREST AREAS IN THE HRP' must be a binary map (0 and 1) where the 1’s indicate forest areas.")
-            return
-
-        # Show "Processing" message
-        processing_message = "Processing data..."
-        self.progressDialog = QProgressDialog(processing_message, None, 0, 100, self)
-
-        # Change the font size
-        font = QFont()
-        font.setPointSize(9)
-        self.progressDialog.setFont(font)
-
-        self.progressDialog.setWindowTitle("Processing")
-        self.progressDialog.setWindowModality(Qt.WindowModal)
-        self.progressDialog.setMinimumDuration(0)
-        self.progressDialog.resize(400, 300)
-        self.progressDialog.show()
-        QApplication.processEvents()
-
-        try:
-            self.vulnerability_map.set_working_directory(directory_2)
-            mask_arr = self.vulnerability_map.geometric_classification_alternative(self.in_fn_2, n_classes_2,
-                                                                                   self.mask_2, self.fmask_2)
-            self.vulnerability_map.array_to_image(self.in_fn_2, out_fn_2, mask_arr, gdal.GDT_Int16, -1)
-            self.vulnerability_map.replace_ref_system(self.in_fn_2, out_fn_2)
-
-            QMessageBox.information(self, "Processing Completed", "Processing completed!")
-
-            self.progressDialog.close()
-
-        except Exception:
-            self.progressDialog.close()
-            tb = traceback.format_exc()
-
-            error_box = QMessageBox(self)
-            error_box.setIcon(QMessageBox.Critical)
-            error_box.setWindowTitle("Error")
-            error_box.setText(f"<b>An Error Occurred During Processing</b>")
-            error_box.setTextInteractionFlags(Qt.TextSelectableByMouse | Qt.TextSelectableByKeyboard)
-            error_box.setDetailedText(tb)
-
-            details_frame = error_box.findChild(QTextEdit)
-            if details_frame:
-                details_frame.setSizePolicy(QSizePolicy.Expanding, QSizePolicy.Expanding)
-                details_frame.setMaximumHeight(800)
-                details_frame.setMaximumWidth(1000)
-                details_frame.setMinimumHeight(400)
-                details_frame.setMinimumWidth(600)
-
-            error_box_layout = error_box.layout()
-            error_box_layout.setContentsMargins(10, 10, 10, 10)
-
-            copy_button = QPushButton("Copy Error Message")
-            error_box.addButton(copy_button, QMessageBox.ActionRole)
-            def copy_error_txt():
-                QApplication.clipboard().setText(tb)
-            copy_button.clicked.connect(copy_error_txt)
-            error_box.exec_()
-
-    def update_progress(self, value):
-        # Update QProgressDialog with the new value
-        if self.progressDialog is not None:
-            self.progressDialog.setValue(value)
-
-class AT_FIT_HRP_Screen(QDialog):
-    def __init__(self):
-        super(AT_FIT_HRP_Screen, self).__init__()
-        self.initial_directory = os.getcwd()
-        loadUi(Path(PureWindowsPath("data\\at_fit_hrp_screen.ui")), self)
-        if central_data_store.directory is not None and self.folder_entry is not None:
-            self.directory = central_data_store.directory
-            self.folder_entry.setText(str(central_data_store.directory))
-        self.Intro_button3.clicked.connect(self.gotointro3)
-        self.RMT_button3.clicked.connect(self.gotormt3)
-        self.doc_button.clicked.connect(self.openDocument)
-        self.select_folder_button.clicked.connect(self.select_working_directory)
-        self.municipality_button.clicked.connect(self.select_municipality)
-        self.risk30_hrp_button.clicked.connect(self.select_risk30_hrp)
-        self.deforestation_hrp_button.clicked.connect(self.select_deforestation_hrp)
-        self.ok_button3.clicked.connect(self.process_data3)
-        self.allocation_tool = AllocationTool()
-        self.allocation_tool.progress_updated.connect(self.update_progress)
-        self.directory = None
-        self.risk30_hrp = None
-        self.municipality = None
-        self.deforestation_hrp = None
-        self.out_fn1 = None
-        self.out_fn2 = None
-        self.csv_name = None
-        self.file_path_directory = None
-        self.file_path1_directory = None
-        self.file_path3_directory = None
-        self.image1_entry.setPlaceholderText('e.g., Acre_Modeling_Region_HRP.tif')
-        self.csv_entry.setPlaceholderText('e.g., Relative_Frequency_Table_HRP.csv')
-        self.image2_entry.setPlaceholderText('e.g., Acre_Fitted_Density_Map_HRP.tif')
-
-        self.setWindowTitle("JNR Integrated Risk/Allocation Tool")
-
-    def gotormt3(self):
-        os.chdir(self.initial_directory)
-        rmt3 = RMT_FIT_HRP_SCREEN()
-        widget.addWidget(rmt3)
-        widget.setCurrentIndex(widget.currentIndex() + 1)
-
-    def gotointro3(self):
-        os.chdir(self.initial_directory)
-        intro3 = IntroScreen()
-        widget.addWidget(intro3)
-        widget.setCurrentIndex(widget.currentIndex() + 1)
-
-    def openDocument(self):
-        pdf_path = Path(PureWindowsPath("doc\\AppFitAM.pdf"))
-        QDesktopServices.openUrl(QUrl.fromLocalFile(str(pdf_path)))
-
-    def select_working_directory(self):
-        data_folder = QFileDialog.getExistingDirectory(self, "Working Directory")
-        data_folder_path = Path(data_folder)
-        self.directory = str(data_folder_path)
-        self.folder_entry.setText(self.directory)
-        central_data_store.directory = self.directory
-
-    def select_municipality(self):
-        file_path, _ = QFileDialog.getOpenFileName(self, 'Map of Administrative Divisions')
-        if file_path:
-            self.municipality = Path(PureWindowsPath(file_path))
-            self.municipality_entry.setText(file_path.split('/')[-1])
-            self.file_path_directory = '\\'.join(file_path.split('/')[:-1])
-
-    def select_risk30_hrp(self):
-        file_path1, _ = QFileDialog.getOpenFileName(self, "Vulnerability Map in HRP")
-        if file_path1:
-            self.risk30_hrp = Path(file_path1)
-            self.risk30_hrp_entry.setText(file_path1.split('/')[-1])
-            self.file_path1_directory = '\\'.join(file_path1.split('/')[:-1])
-    def select_deforestation_hrp(self):
-        file_path3, _ = QFileDialog.getOpenFileName(self, "Map of Deforestation in the HRP")
-        if file_path3:
-            self.deforestation_hrp = Path(file_path3)
-            self.deforestation_hrp_entry.setText(file_path3.split('/')[-1])
-            self.file_path3_directory = '\\'.join(file_path3.split('/')[:-1])
-    def get_full_path(self, base_dir, user_input):
-        if os.path.isabs(user_input):
-            return user_input
-        else:
-            return f"{base_dir}\\{user_input}"
-    def process_data3(self):
-        directory = self.folder_entry.text()
-        central_data_store.directory = directory
-        if not directory:
-            QMessageBox.critical(self, "Error", "Please select or enter the working directory!")
-            return
-        if not self.file_path_directory:
-            self.file_path_directory = directory
-        if not self.file_path1_directory:
-            self.file_path1_directory = directory
-        if not self.file_path3_directory:
-            self.file_path3_directory = directory
-
-        self.municipality = self.get_full_path(self.file_path_directory, self.municipality_entry.text())
-        self.risk30_hrp = self.get_full_path(self.file_path1_directory, self.risk30_hrp_entry.text())
-        self.deforestation_hrp = self.get_full_path(self.file_path3_directory, self.deforestation_hrp_entry.text())
-
-        if not self.risk30_hrp or not self.municipality or not self.deforestation_hrp:
-            QMessageBox.critical(self, "Error", "Please select or enter all input files!")
-            return
-
-        images = [self.risk30_hrp, self.municipality, self.deforestation_hrp]
-
-        # Check if all images have the same resolution
-        resolutions = [map_checker.get_image_resolution(img) for img in images]
-        if len(set(resolutions)) != 1:
-            QMessageBox.critical(None, "Error", "All the input raster images must have the same spatial resolution!")
-            return
-
-        # Check if all images have the same number of rows and columns
-        dimensions = [map_checker.get_image_dimensions(img) for img in images]
-        if len(set(dimensions)) != 1:
-            QMessageBox.critical(None, "Error",
-                                 "All the input raster images must have the same number of rows and columns!")
-            return
-
-        out_fn1 = self.image1_entry.text()
-        if not out_fn1:
-            QMessageBox.critical(self, "Error", "Please enter the name for Modeling Region Map in HRP!")
-            return
-
-        if not (out_fn1.endswith('.tif') or out_fn1.endswith('.rst')):
-            QMessageBox.critical(self, "Error",
-                                 "Please enter .rst or .tif extension in the name for Modeling Region Map in HRP!")
-            return
-
-        csv_name = self.csv_entry.text()
-        if not csv_name:
-            QMessageBox.critical(self, "Error", "Please enter the name for the Relative Frequency Table!")
-            return
-
-        if not (csv_name.endswith('.csv')):
-            QMessageBox.critical(self, "Error",
-                                 "Please enter .csv extension in the name of Relative Frequency Table!")
-            return
-
-        out_fn2 = self.image2_entry.text()
-        if not out_fn2:
-            QMessageBox.critical(self, "Error", "Please enter the name for Fitted Density Map in the HRP!")
-            return
-
-        if not (out_fn2.endswith('.tif') or out_fn2.endswith('.rst')):
-            QMessageBox.critical(self, "Error",
-                                 "Please enter .rst or .tif extension in the name of Fitted Density Map in the HRP!")
-            return
-
-        if not map_checker.check_binary_map(self.deforestation_hrp):
-            QMessageBox.critical(None, "Error",
-                                 "'MAP OF DEFORESTATION IN THE HRP' must be a binary map (0 and 1) where the 1’s indicate deforestation.")
-            return
-
-        # Show "Processing" message
-        processing_message = "Processing data..."
-        self.progressDialog = QProgressDialog(processing_message, None, 0, 100, self)
-
-        # Change the font size
-        font = QFont()
-        font.setPointSize(9)
-        self.progressDialog.setFont(font)
-
-        self.progressDialog.setWindowTitle("Processing")
-        self.progressDialog.setWindowModality(Qt.WindowModal)
-        self.progressDialog.setMinimumDuration(0)
-        self.progressDialog.resize(400, 300)
-        self.progressDialog.show()
-        QApplication.processEvents()
-
-        try:
-            self.allocation_tool.execute_workflow_fit(directory, self.risk30_hrp,
-                                                        self.municipality,self.deforestation_hrp, csv_name,
-                                                        out_fn1,out_fn2)
-            QMessageBox.information(self, "Processing Completed", "Processing completed!")
-            self.progressDialog.close()
-
-        except Exception:
-            self.progressDialog.close()
-            tb = traceback.format_exc()
-
-            error_box = QMessageBox(self)
-            error_box.setIcon(QMessageBox.Critical)
-            error_box.setWindowTitle("Error")
-            error_box.setText(f"<b>An Error Occurred During Processing</b>")
-            error_box.setTextInteractionFlags(Qt.TextSelectableByMouse | Qt.TextSelectableByKeyboard)
-            error_box.setDetailedText(tb)
-
-            details_frame = error_box.findChild(QTextEdit)
-            if details_frame:
-                details_frame.setSizePolicy(QSizePolicy.Expanding, QSizePolicy.Expanding)
-                details_frame.setMaximumHeight(800)
-                details_frame.setMaximumWidth(1000)
-                details_frame.setMinimumHeight(400)
-                details_frame.setMinimumWidth(600)
-
-            error_box_layout = error_box.layout()
-            error_box_layout.setContentsMargins(10, 10, 10, 10)
-
-            copy_button = QPushButton("Copy Error Message")
-            error_box.addButton(copy_button, QMessageBox.ActionRole)
-            def copy_error_txt():
-                QApplication.clipboard().setText(tb)
-            copy_button.clicked.connect(copy_error_txt)
-            error_box.exec_()
-
-    def update_progress(self, value):
-        # Update QProgressDialog with the new value
-        if self.progressDialog is not None:
-            self.progressDialog.setValue(value)
-
-
-class RMT_PRE_VP_SCREEN(QDialog):
-    def __init__(self):
-        super(RMT_PRE_VP_SCREEN, self).__init__()
-        # Store the initial directory path
-        self.initial_directory = os.getcwd()
-        loadUi(Path(PureWindowsPath("data\\rmt_pre_vp_screen.ui")), self)
-        if central_data_store.directory is not None and self.folder_entry is not None:
-            self.directory = central_data_store.directory
-            self.folder_entry.setText(str(central_data_store.directory))
-        if central_data_store.directory is not None and self.folder_entry_2 is not None:
-            self.directory_2 = central_data_store.directory
-            self.folder_entry_2.setText(str(central_data_store.directory))
-        self.AT_button2.clicked.connect(self.gotoat2)
-        self.Intro_button2.clicked.connect(self.gotointro2)
-
-        self.doc_button = self.tab1.findChild(QWidget, "doc_button")
-        self.select_folder_button = self.tab1.findChild(QWidget, "select_folder_button")
-        self.fd_button = self.tab1.findChild(QWidget, "fd_button")
-        self.mask_button = self.tab1.findChild(QWidget, "mask_button")
-        self.ok_button2 = self.tab1.findChild(QWidget, "ok_button2")
-
-        self.doc_button_2 = self.tab2.findChild(QWidget, "doc_button_2")
-        self.select_folder_button_2 = self.tab2.findChild(QWidget, "select_folder_button_2")
-        self.mask_button_2 = self.tab2.findChild(QWidget, "mask_button_2")
-        self.fmask_button_2 = self.tab2.findChild(QWidget, "fmask_button_2")
-        self.fd_button_2 = self.tab2.findChild(QWidget, "fd_button_2")
-        self.ok_button2_2 = self.tab2.findChild(QWidget, "ok_button2_2")
-
-        self.doc_button.clicked.connect(self.openDocument)
-        self.select_folder_button.clicked.connect(self.select_working_directory)
-        self.fd_button.clicked.connect(self.select_fd)
-        self.mask_button.clicked.connect(self.select_mask)
-        self.ok_button2.clicked.connect(self.process_data2)
-
-        self.doc_button_2.clicked.connect(self.openDocument_2)
-        self.select_folder_button_2.clicked.connect(self.select_working_directory_2)
-        self.mask_button_2.clicked.connect(self.select_mask_2)
-        self.fmask_button_2.clicked.connect(self.select_fmask_2)
-        self.fd_button_2.clicked.connect(self.select_fd_2)
-        self.ok_button2_2.clicked.connect(self.process_data2_2)
-
-        self.vulnerability_map = VulnerabilityMap()
-        self.vulnerability_map.progress_updated.connect(self.update_progress)
-        self.directory = None
-        self.in_fn = None
-        self.NRT = None
-        if central_data_store.NRT is not None:
-            self.nrt_entry.setText(str(central_data_store.NRT))
-        self.n_classes = None
-        self.mask = None
-        self.out_fn = None
-        self.out_fn_entry.setPlaceholderText('e.g., Acre_Vulnerability_VP.tif')
-
-        self.directory_2 = None
-        self.mask_2 = None
-        self.fmask_2 = None
-        self.in_fn_2 = None
-        self.out_fn_2 = None
-        self.n_classes_2 = None
-        self.file_path_directory = None
-        self.file_path2_directory = None
-        self.file_path4_directory = None
-        self.file_path5_directory = None
-        self.file_path6_directory = None
-        self.out_fn_entry_2.setPlaceholderText('e.g., Acre_Vulnerability_VP.tif')
-
-        self.setWindowTitle("JNR Integrated Risk/Allocation Tool")
-
-    def gotoat2(self):
-        os.chdir(self.initial_directory)
-        at2 = AT_PRE_VP_Screen()
-        widget.addWidget(at2)
-        widget.setCurrentIndex(widget.currentIndex() + 1)
-
-    def gotointro2(self):
-        os.chdir(self.initial_directory)
-        intro2 = IntroScreen()
-        widget.addWidget(intro2)
-        widget.setCurrentIndex(widget.currentIndex() + 1)
-
-    def openDocument(self):
-        pdf_path = Path(PureWindowsPath("doc\\AppPreVM.pdf"))
-        QDesktopServices.openUrl(QUrl.fromLocalFile(str(pdf_path)))
-
-    def openDocument_2(self):
-        pdf_path = Path(PureWindowsPath("doc\\AppPreVM.pdf"))
-        QDesktopServices.openUrl(QUrl.fromLocalFile(str(pdf_path)))
-
-    def select_working_directory(self):
-        data_folder = QFileDialog.getExistingDirectory(self, "Working Directory")
-        data_folder_path = Path(data_folder)
-        self.directory = str(data_folder_path)
-        self.folder_entry.setText(self.directory)
-        self.folder_entry_2.setText(self.directory)
-        central_data_store.directory = self.directory
-
-    def select_fd(self):
-        file_path, _ = QFileDialog.getOpenFileName(self, 'Map of Distance from the Forest Edge in VP')
-        if file_path:
-            self.in_fn = Path(PureWindowsPath(file_path))
-            self.in_fn_entry.setText(file_path.split('/')[-1])
-            self.file_path_directory = '\\'.join(file_path.split('/')[:-1])
-
-    def select_mask(self):
-        file_path2, _ = QFileDialog.getOpenFileName(self, 'Mask of Study Area')
-        if file_path2:
-            self.mask = Path(PureWindowsPath(file_path2))
-            self.mask_entry.setText(file_path2.split('/')[-1])
-            self.file_path2_directory = '\\'.join(file_path2.split('/')[:-1])
-    def select_working_directory_2(self):
-        data_folder_2 = QFileDialog.getExistingDirectory(self, "Working Directory")
-        data_folder_path_2 = Path(data_folder_2)
-        self.directory_2 = str(data_folder_path_2)
-        self.folder_entry_2.setText(self.directory_2)
-        self.folder_entry.setText(self.directory_2)
-        central_data_store.directory = self.directory_2
-
-    def select_fd_2(self):
-        file_path4, _ = QFileDialog.getOpenFileName(self, 'Map of Distance from the Forest Edge in VP')
-        if file_path4:
-            self.in_fn_2 = Path(PureWindowsPath(file_path4))
-            self.in_fn_entry_2.setText(file_path4.split('/')[-1])
-            self.file_path4_directory = '\\'.join(file_path4.split('/')[:-1])
-
-    def select_mask_2(self):
-        file_path5, _ = QFileDialog.getOpenFileName(self, 'Mask of Study Area')
-        if file_path5:
-            self.mask_2 = Path(PureWindowsPath(file_path5))
-            self.mask_entry_2.setText(file_path5.split('/')[-1])
-            self.file_path5_directory = '\\'.join(file_path5.split('/')[:-1])
-
-    def select_fmask_2(self):
-        file_path6, _ = QFileDialog.getOpenFileName(self, 'Mask of Forest Area')
-        if file_path6:
-            self.fmask_2 = file_path6
-            self.fmask_entry_2.setText(file_path6.split('/')[-1])
-            self.file_path6_directory = '\\'.join(file_path6.split('/')[:-1])
-    def get_full_path(self, base_dir, user_input):
-        if os.path.isabs(user_input):
-            return user_input
-        else:
-            return f"{base_dir}\\{user_input}"
-    def process_data2(self):
-        directory = self.folder_entry.text()
-        central_data_store.directory = directory
-        self.folder_entry_2.setText(directory)
-        if not directory:
-            QMessageBox.critical(self, "Error", "Please select or enter the working directory!")
-            return
-
-        if not self.file_path_directory:
-            self.file_path_directory = directory
-        if not self.file_path2_directory:
-            self.file_path2_directory = directory
-
-        self.in_fn = self.get_full_path(self.file_path_directory, self.in_fn_entry.text())
-        self.mask = self.get_full_path(self.file_path2_directory, self.mask_entry.text())
-
-        if not self.in_fn or not self.mask:
-            QMessageBox.critical(self, "Error", "Please select or enter all input files!")
-            return
-
-        NRT = self.nrt_entry.text()
-        if not NRT:
-            QMessageBox.critical(self, "Error", "Please enter the NRT value!")
-            return
-        try:
-            self.NRT = int(NRT)
-            if (self.NRT <= 0):
-                QMessageBox.critical(self, "Error", "NRT value should be larger than 0!")
-                return
-        except ValueError:
-            QMessageBox.critical(self, "Error", "NRT value should be a valid number!")
-            return
-
-        n_classes = int(29)
-        if not n_classes:
-            QMessageBox.critical(self, "Error", "Please enter the number of classes!")
-            return
-        try:
-            self.n_classes = int(n_classes)
-            if (self.n_classes <= 0):
-                QMessageBox.critical(self, "Error", "Number of classes should be larger than 0!")
-                return
-        except ValueError:
-            QMessageBox.critical(self, "Error", "Number of classes value should be a valid number!")
-            return
-
-        out_fn = self.out_fn_entry.text()
-        if not out_fn:
-            QMessageBox.critical(self, "Error", "Please enter the name of Vulnerability Map in VP!")
-            return
-
-        if not (out_fn.endswith('.tif') or out_fn.endswith('.rst')):
-            QMessageBox.critical(self, "Error",
-                                 "Please enter .rst or .tif extension in the name of Vulnerability Map in VP!")
-            return
-
-        # Show "Processing" message
-        processing_message = "Processing data..."
-        self.progressDialog = QProgressDialog(processing_message, None, 0, 100, self)
-
-        # Change the font size
-        font = QFont()
-        font.setPointSize(9)
-        self.progressDialog.setFont(font)
-
-        self.progressDialog.setWindowTitle("Processing")
-        self.progressDialog.setWindowModality(Qt.WindowModal)
-        self.progressDialog.setMinimumDuration(0)
-        self.progressDialog.resize(400, 300)
-        self.progressDialog.show()
-        QApplication.processEvents()
-
-        try:
-            self.vulnerability_map.set_working_directory(directory)
-            mask_arr = self.vulnerability_map.geometric_classification(self.in_fn, NRT, n_classes, self.mask)
-            self.vulnerability_map.array_to_image(self.in_fn, out_fn, mask_arr, gdal.GDT_Int16, -1)
-            self.vulnerability_map.replace_ref_system(self.in_fn, out_fn)
-
-            QMessageBox.information(self, "Processing Completed", "Processing completed!")
-            self.progressDialog.close()
-
-        except Exception:
-            self.progressDialog.close()
-            tb = traceback.format_exc()
-
-            error_box = QMessageBox(self)
-            error_box.setIcon(QMessageBox.Critical)
-            error_box.setWindowTitle("Error")
-            error_box.setText(f"<b>An Error Occurred During Processing</b>")
-            error_box.setTextInteractionFlags(Qt.TextSelectableByMouse | Qt.TextSelectableByKeyboard)
-            error_box.setDetailedText(tb)
-
-            details_frame = error_box.findChild(QTextEdit)
-            if details_frame:
-                details_frame.setSizePolicy(QSizePolicy.Expanding, QSizePolicy.Expanding)
-                details_frame.setMaximumHeight(800)
-                details_frame.setMaximumWidth(1000)
-                details_frame.setMinimumHeight(400)
-                details_frame.setMinimumWidth(600)
-
-            error_box_layout = error_box.layout()
-            error_box_layout.setContentsMargins(10, 10, 10, 10)
-
-            copy_button = QPushButton("Copy Error Message")
-            error_box.addButton(copy_button, QMessageBox.ActionRole)
-            def copy_error_txt():
-                QApplication.clipboard().setText(tb)
-            copy_button.clicked.connect(copy_error_txt)
-            error_box.exec_()
-
-    def process_data2_2(self):
-        directory_2 = self.folder_entry_2.text()
-        central_data_store.directory = directory_2
-        self.folder_entry.setText(directory_2)
-        if not directory_2 :
-            QMessageBox.critical(self, "Error", "Please select or enter the working directory!")
-            return
-
-        if not self.file_path4_directory:
-            self.file_path4_directory = directory_2
-        if not self.file_path5_directory:
-            self.file_path5_directory = directory_2
-        if not self.file_path6_directory:
-            self.file_path6_directory = directory_2
-
-        self.in_fn_2 = self.get_full_path(self.file_path4_directory, self.in_fn_entry_2.text())
-        self.mask_2 = self.get_full_path(self.file_path5_directory, self.mask_entry_2.text())
-        self.fmask_2 = self.get_full_path(self.file_path6_directory, self.fmask_entry_2.text())
-
-        if not self.in_fn_2 or not self.mask_2 or not self.fmask_2:
-            QMessageBox.critical(self, "Error", "Please select or enter all input files!")
-            return
-
-        images = [self.in_fn_2, self.mask_2, self.fmask_2]
-
-        # Check if all images have the same resolution
-        resolutions = [map_checker.get_image_resolution(img) for img in images]
-        if len(set(resolutions)) != 1:
-            QMessageBox.critical(None, "Error", "All the input raster images must have the same spatial resolution!")
-            return
-
-        # Check if all images have the same number of rows and columns
-        dimensions = [map_checker.get_image_dimensions(img) for img in images]
-        if len(set(dimensions)) != 1:
-            QMessageBox.critical(None, "Error",
-                                 "All the input raster images must have the same number of rows and columns!")
-            return
-
-        n_classes_2 = int(30)
-        out_fn_2 = self.out_fn_entry_2.text()
-        if not out_fn_2:
-            QMessageBox.critical(self, "Error", "Please enter the name of Vulnerability Map in VP!")
-            return
-
-        # Check if the out_fn has the correct file extension
-        if not (out_fn_2.endswith('.tif') or out_fn_2.endswith('.rst')):
-            QMessageBox.critical(self, "Error",
-                                 "Please enter .rst or .tif extension in the name of Vulnerability Map in VP!")
-            return
-
-        if not map_checker.check_binary_map(self.mask_2):
-            QMessageBox.critical(None, "Error",
-                                 "'MASK OF THE NON-EXCLUDED JURISDICTION' must be a binary map (0 and 1) where the 1’s indicate areas inside the jurisdiction.")
-            return
-
-        if not map_checker.check_binary_map(self.fmask_2):
-            QMessageBox.critical(None, "Error",
-                                 "'MASK OF FOREST AREAS IN THE VP' must be a binary map (0 and 1) where the 1’s indicate forest areas.")
-            return
-
-        # Show "Processing" message
-        processing_message = "Processing data..."
-        self.progressDialog = QProgressDialog(processing_message, None, 0, 100, self)
-
-        # Change the font size
-        font = QFont()
-        font.setPointSize(9)
-        self.progressDialog.setFont(font)
-
-        self.progressDialog.setWindowTitle("Processing")
-        self.progressDialog.setWindowModality(Qt.WindowModal)
-        self.progressDialog.setMinimumDuration(0)
-        self.progressDialog.resize(400, 300)
-        self.progressDialog.show()
-        QApplication.processEvents()
-
-        try:
-            self.vulnerability_map.set_working_directory(directory_2)
-            mask_arr = self.vulnerability_map.geometric_classification_alternative(self.in_fn_2, n_classes_2,
-                                                                                   self.mask_2, self.fmask_2)
-            self.vulnerability_map.array_to_image(self.in_fn_2, out_fn_2, mask_arr, gdal.GDT_Int16, -1)
-            self.vulnerability_map.replace_ref_system(self.in_fn_2, out_fn_2)
-
-            QMessageBox.information(self, "Processing Completed", "Processing completed!")
-
-            self.progressDialog.close()
-
-        except Exception:
-            self.progressDialog.close()
-            tb = traceback.format_exc()
-
-            error_box = QMessageBox(self)
-            error_box.setIcon(QMessageBox.Critical)
-            error_box.setWindowTitle("Error")
-            error_box.setText(f"<b>An Error Occurred During Processing</b>")
-            error_box.setTextInteractionFlags(Qt.TextSelectableByMouse | Qt.TextSelectableByKeyboard)
-            error_box.setDetailedText(tb)
-
-            details_frame = error_box.findChild(QTextEdit)
-            if details_frame:
-                details_frame.setSizePolicy(QSizePolicy.Expanding, QSizePolicy.Expanding)
-                details_frame.setMaximumHeight(800)
-                details_frame.setMaximumWidth(1000)
-                details_frame.setMinimumHeight(400)
-                details_frame.setMinimumWidth(600)
-
-            error_box_layout = error_box.layout()
-            error_box_layout.setContentsMargins(10, 10, 10, 10)
-
-            copy_button = QPushButton("Copy Error Message")
-            error_box.addButton(copy_button, QMessageBox.ActionRole)
-            def copy_error_txt():
-                QApplication.clipboard().setText(tb)
-            copy_button.clicked.connect(copy_error_txt)
-            error_box.exec_()
-
-    def update_progress(self, value):
-        # Update QProgressDialog with the new value
-        if self.progressDialog is not None:
-            self.progressDialog.setValue(value)
-
-class AT_PRE_VP_Screen(QDialog):
-    def __init__(self):
-        super(AT_PRE_VP_Screen, self).__init__()
-        self.initial_directory = os.getcwd()
-        loadUi(Path(PureWindowsPath("data\\at_pre_vp_screen.ui")), self)
-        if central_data_store.directory is not None and self.folder_entry is not None:
-            self.directory = central_data_store.directory
-            self.folder_entry.setText(str(central_data_store.directory))
-        self.Intro_button3.clicked.connect(self.gotointro3)
-        self.RMT_button3.clicked.connect(self.gotormt3)
-        self.doc_button.clicked.connect(self.openDocument)
-        self.select_folder_button.clicked.connect(self.select_working_directory)
-        self.municipality_button.clicked.connect(self.select_municipality)
-        self.csv_button.clicked.connect(self.select_csv)
-        self.risk30_vp_button.clicked.connect(self.select_risk30_vp)
-        self.ok_button3.clicked.connect(self.process_data3)
-        self.allocation_tool = AllocationTool()
-        # Connect the progress_updated signal to the update_progress method
-        self.allocation_tool.progress_updated.connect(self.update_progress)
-        self.directory = None
-        self.csv = None
-        self.municipality = None
-        self.risk30_vp = None
-        self.expected_deforestation = None
-        self.max_iterations = None
-        self.image1 = None
-        self.image2 = None
-        self.file_path_directory = None
-        self.file_path1_directory = None
-        self.file_path2_directory = None
-        self.iteration_entry.setPlaceholderText('The suggestion max iteration number is 5')
-        self.image1_entry.setPlaceholderText('e.g., Acre_Prediction_Modeling_Region_VP.tif')
-        self.image2_entry.setPlaceholderText('e.g., Acre_Adjucted_Density_Map_VP.tif')
-        self.setWindowTitle("JNR Integrated Risk/Allocation Tool")
-
-    def gotormt3(self):
-        os.chdir(self.initial_directory)
-        rmt3 = RMT_PRE_VP_SCREEN()
-        widget.addWidget(rmt3)
-        widget.setCurrentIndex(widget.currentIndex() + 1)
-
-    def gotointro3(self):
-        os.chdir(self.initial_directory)
-        intro3 = IntroScreen()
-        widget.addWidget(intro3)
-        widget.setCurrentIndex(widget.currentIndex() + 1)
-
-    def openDocument(self):
-        pdf_path = Path(PureWindowsPath("doc\\AppPreAM.pdf"))
-        QDesktopServices.openUrl(QUrl.fromLocalFile(str(pdf_path)))
-
-    def select_working_directory(self):
-        data_folder = QFileDialog.getExistingDirectory(self, "Working Directory")
-        data_folder_path = Path(data_folder)
-        self.directory = str(data_folder_path)
-        self.folder_entry.setText(self.directory)
-        central_data_store.directory = self.directory
-
-    def select_municipality(self):
-        file_path, _ = QFileDialog.getOpenFileName(self, 'Map of Administrative Divisions')
-        if file_path:
-            self.municipality = Path(PureWindowsPath(file_path))
-            self.municipality_entry.setText(file_path.split('/')[-1])
-            self.file_path_directory = '\\'.join(file_path.split('/')[:-1])
-
-    def select_csv(self):
-        file_path1, _ = QFileDialog.getOpenFileName(self, "VP Relative Frequency Table (.csv)")
-        if file_path1:
-            self.csv = Path(PureWindowsPath(file_path1))
-            self.csv_entry.setText(file_path1.split('/')[-1])
-            self.file_path1_directory = '\\'.join(file_path1.split('/')[:-1])
-
-    def select_risk30_vp(self):
-        file_path2, _ = QFileDialog.getOpenFileName(self, "Vulnerability Map in VP")
-        if file_path2:
-            self.risk30_vp = Path(PureWindowsPath(file_path2))
-            self.risk30_vp_entry.setText(file_path2.split('/')[-1])
-            self.file_path2_directory = '\\'.join(file_path2.split('/')[:-1])
-    def get_full_path(self, base_dir, user_input):
-        if os.path.isabs(user_input):
-            return user_input
-        else:
-            return f"{base_dir}\\{user_input}"
-    def process_data3(self):
-        directory = self.folder_entry.text()
-        central_data_store.directory = directory
-        if not directory:
-            QMessageBox.critical(self, "Error", "Please select or enter the working directory!")
-            return
-        if not self.file_path_directory:
-            self.file_path_directory = directory
-        if not self.file_path1_directory:
-            self.file_path1_directory = directory
-        if not self.file_path2_directory:
-            self.file_path2_directory = directory
-
-        self.municipality = self.get_full_path(self.file_path_directory, self.municipality_entry.text())
-        self.csv = self.get_full_path(self.file_path1_directory, self.csv_entry.text())
-        self.risk30_vp = self.get_full_path(self.file_path2_directory, self.risk30_vp_entry.text())
-
-        if not self.csv or not self.municipality or not self.risk30_vp:
-            QMessageBox.critical(self, "Error", "Please select or enter all input files!")
-            return
-
-        images = [self.municipality, self.risk30_vp]
-
-        # Check if all images have the same resolution
-        resolutions = [map_checker.get_image_resolution(img) for img in images]
-        if len(set(resolutions)) != 1:
-            QMessageBox.critical(None, "Error", "All the input raster images must have the same spatial resolution!")
-            return
-
-        # Check if all images have the same number of rows and columns
-        dimensions = [map_checker.get_image_dimensions(img) for img in images]
-        if len(set(dimensions)) != 1:
-            QMessageBox.critical(None, "Error",
-                                 "All the input raster images must have the same number of rows and columns!")
-            return
-
-        expected_deforestation = self.expected_entry.text()
-        if not expected_deforestation:
-            QMessageBox.critical(self, "Error", "Please enter the expected annual jurisdictional deforestation rate (ha/year)!")
-            return
-        try:
-            self.expected_deforestation = float(expected_deforestation)
-        except ValueError:
-            QMessageBox.critical(self, "Error", "Expected annual jurisdictional deforestation rate should be a valid number!")
-            return
-
-        out_fn1 = self.image1_entry.text()
-        if not out_fn1:
-            QMessageBox.critical(self, "Error", "Please enter the name of Prediction Modeling Region Map in VP!")
-            return
-
-        if not (out_fn1.endswith('.tif') or out_fn1.endswith('.rst')):
-            QMessageBox.critical(self, "Error",
-                                 "Please enter .rst or .tif extension in the name of Prediction Modeling Region Map in VP!")
-            return
-
-        out_fn2 = self.image2_entry.text()
-        if not out_fn2:
-            QMessageBox.critical(self, "Error", "Please enter the name of Adjusted Prediction Density Map in VP!")
-            return
-
-        if not (out_fn2.endswith('.tif') or out_fn2.endswith('.rst')):
-            QMessageBox.critical(self, "Error",
-                                 "Please enter .rst or .tif extension in the name of Adjusted Prediction Density Map in VP!")
-            return
-
-        max_iterations = self.iteration_entry.text()
-        if not max_iterations:
-            QMessageBox.critical(self, "Error", "Please enter the max iterations! The suggestion number is 5.")
-            return
-        try:
-            self.max_iterations = int(max_iterations)
-        except ValueError:
-            QMessageBox.critical(self, "Error", "Max iteration value should be a valid number!")
-            return
-
-        # Show "Processing" message
-        processing_message = "Processing data..."
-        self.progressDialog = QProgressDialog(processing_message, None, 0, 100, self)
-
-        # Change the font size
-        font = QFont()
-        font.setPointSize(9)
-        self.progressDialog.setFont(font)
-
-        self.progressDialog.setWindowTitle("Processing")
-        self.progressDialog.setWindowModality(Qt.WindowModal)
-        self.progressDialog.setMinimumDuration(0)
-        self.progressDialog.resize(400, 300)
-        self.progressDialog.show()
-        QApplication.processEvents()
-
-        try:
-            id_difference,iteration_count = self.allocation_tool.execute_workflow_vp(directory, self.max_iterations,
-                                                                           self.csv,
-                                                                           self.municipality,
-                                                                           self.expected_deforestation,
-                                                                           self.risk30_vp, out_fn1,out_fn2)
-
-            if id_difference.size > 0:
-                QMessageBox.warning(self, " Warning ", f"Modeling Region ID {','.join(map(str, id_difference))} do not exist in the Historical Reference Period. A new CSV has been created for the HRP where relative frequencies for missing bins have been estimated from corresponding vulnerability zones over the entire jurisdiction.")
-            if iteration_count > int(max_iterations):
-                QMessageBox.warning(self, " Warning ",
-                                    f"Maximum iterations limit reached. Please increase the Maximum Iterations and try running the tool again.")
-            else:
-                QMessageBox.information(self, "Processing Completed", "Processing completed!")
-            self.progressDialog.close()
-
-        except Exception:
-            self.progressDialog.close()
-            tb = traceback.format_exc()
-
-            error_box = QMessageBox(self)
-            error_box.setIcon(QMessageBox.Critical)
-            error_box.setWindowTitle("Error")
-            error_box.setText(f"<b>An Error Occurred During Processing</b>")
-            error_box.setTextInteractionFlags(Qt.TextSelectableByMouse | Qt.TextSelectableByKeyboard)
-            error_box.setDetailedText(tb)
-
-            details_frame = error_box.findChild(QTextEdit)
-            if details_frame:
-                details_frame.setSizePolicy(QSizePolicy.Expanding, QSizePolicy.Expanding)
-                details_frame.setMaximumHeight(800)
-                details_frame.setMaximumWidth(1000)
-                details_frame.setMinimumHeight(400)
-                details_frame.setMinimumWidth(600)
-
-            error_box_layout = error_box.layout()
-            error_box_layout.setContentsMargins(10, 10, 10, 10)
-
-            copy_button = QPushButton("Copy Error Message")
-            error_box.addButton(copy_button, QMessageBox.ActionRole)
-            def copy_error_txt():
-                QApplication.clipboard().setText(tb)
-            copy_button.clicked.connect(copy_error_txt)
-            error_box.exec_()
-
-    def update_progress(self, value):
-        # Update QProgressDialog with the new value
-        if self.progressDialog is not None:
-            self.progressDialog.setValue(value)
-
-class CentralDataStore:
-    def __init__(self):
-        self.NRT = None
-        self.directory = None
-
-class MapChecker:
-    def __init__(self):
-        self.image=None
-        self.arr=None
-        self.in_fn=None
-
-    def get_image_resolution(self,image):
-        in_ds = gdal.Open(image)
-        P = in_ds.GetGeoTransform()[1]
-        return P
-
-    def get_image_dimensions(self, image):
-        dataset = gdal.Open(image)
-        cols = dataset.RasterXSize
-        rows = dataset.RasterYSize
-        return rows, cols
-
-    def get_image_datatype(self, image):
-        in_ds = gdal.Open(image)
-        in_band = in_ds.GetRasterBand(1)
-        datatype = gdal.GetDataTypeName(in_band.DataType)
-        return datatype
-
-    def get_image_max_min(self, image):
-        in_ds = gdal.Open(image)
-        in_band = in_ds.GetRasterBand(1)
-        min, max= in_band.ComputeRasterMinMax()
-        return min, max
-
-    def find_unique_values(self, arr, limit=2):
-        unique_values = set()
-        for value in np.nditer(arr):
-            unique_values.add(value.item())
-            if len(unique_values) > limit:
-                return False
-        return True
-
-    def check_binary_map(self, in_fn):
-        '''
-        Check if input image is binary map
-        :param in_fn: input image
-        :return: True if the file is a binary map, False otherwise
-        '''
-        file_extension = in_fn.split('.')[-1].lower()
-        file_name, _ = os.path.splitext(in_fn)
-        if file_extension == 'rst':
-            with open(file_name + '.rdc', 'r') as read_file:
-                rdc_content = read_file.read().lower()
-                byte_or_integer_binary = "data type   : byte" in rdc_content or (
-                        "data type   : integer" in rdc_content and "min. value  : 0" in rdc_content and "max. value  : 1" in rdc_content)
-                float_binary = "data type   : real" in rdc_content and "min. value  : 0.0000000" in rdc_content and "max. value  : 1.0000000" in rdc_content
-        elif file_extension == 'tif':
-            datatype = self.get_image_datatype(in_fn)
-            min_val, max_val = self.get_image_max_min(in_fn)
-            byte_or_integer_binary = datatype in ['Byte', 'CInt16', 'CInt32', 'Int16', 'Int32', 'UInt16',
-                                                      'UInt32'] and max_val == 1 and min_val == 0
-            float_binary = datatype in ['Float32', 'Float64', 'CFloat32', 'CFloat64'] and max_val == 1.0000000 and min_val == 0.0000000
-
-        if byte_or_integer_binary or (float_binary):
-            # For float_binary, use find_unique_values function to check if data only have two unique values [0.0000000, 1.0000000].
-            if float_binary:
-                in_ds = gdal.Open(in_fn)
-                in_band = in_ds.GetRasterBand(1)
-                arr = in_band.ReadAsArray()
-                # If more than two unique values are found, it's not a binary map, return False.
-                if not self.find_unique_values(arr, 2):
-                    return False
-            # Binary map: byte_or_integer_binary or float_binary with two unique values [0.0000000, 1.0000000], it returns True.
-            return True
-        # For any other scenario, it returns False.
-        return False
-
-if __name__ == "__main__":
-    # main
-    app = QApplication(sys.argv)
-    # Load custom fonts
-    font_id = QFontDatabase.addApplicationFont(str(Path(PureWindowsPath("font\\AvenirNextLTPro-DemiCn.otf"))))
-
-    intro = IntroScreen()
-    # Create a global instance of this store
-    central_data_store = CentralDataStore()
-    map_checker = MapChecker()
-
-    widget = QtWidgets.QStackedWidget()
-    widget.addWidget(intro)
-    widget.setFixedHeight(1000)
-    widget.setFixedWidth(1800)
-    widget.show()
-
-    try:
-        sys.exit(app.exec_())
-    except:
+import sys
+import os
+from PyQt5 import QtWidgets
+from PyQt5.QtCore import Qt,QUrl
+from PyQt5.QtWidgets import QDialog, QFileDialog, QMessageBox, QProgressDialog, QApplication, QWidget, QPushButton,QTextEdit,QSizePolicy
+from PyQt5.QtGui import QFontDatabase, QIcon, QFont, QDesktopServices
+from PyQt5.uic import loadUi
+from allocation_tool import AllocationTool
+from vulnerability_map import VulnerabilityMap
+from model_evaluation import ModelEvaluation
+from osgeo import gdal
+from pathlib import Path, PureWindowsPath
+import numpy as np
+import traceback
+
+# GDAL exceptions
+gdal.UseExceptions()
+
+class IntroScreen(QDialog):
+    def __init__(self):
+        super(IntroScreen, self).__init__()
+        loadUi(Path(PureWindowsPath("data\\intro_screen.ui")), self)
+        # Set window properties
+        self.setWindowTitle('JNR Allocated Risk Mapping Procedure (UDef-ARP)')
+        # Set window icon
+        self.setWindowIcon(QIcon(str(Path(PureWindowsPath("data\\icon.ico")))))
+        self.Fit_Cal_button.clicked.connect(self.gotofitcal)
+        self.Pre_Cnf_button.clicked.connect(self.gotoprecnf)
+        self.Fit_Hrp_button.clicked.connect(self.gotofithrp)
+        self.Pre_VP_button.clicked.connect(self.gotoprevp)
+        self.doc_button.clicked.connect(self.openDocument)
+
+    def gotofitcal(self):
+        rmt_fit_cal = RMT_FIT_CAL_SCREEN()
+        widget.addWidget(rmt_fit_cal)
+        widget.setCurrentIndex(widget.currentIndex() + 1)
+
+    def gotoprecnf(self):
+        rmt_pre_cnf = RMT_PRE_CNF_SCREEN()
+        widget.addWidget(rmt_pre_cnf)
+        widget.setCurrentIndex(widget.currentIndex() + 1)
+
+    def gotofithrp(self):
+        rmt_fit_hrp = RMT_FIT_HRP_SCREEN()
+        widget.addWidget(rmt_fit_hrp)
+        widget.setCurrentIndex(widget.currentIndex() + 1)
+
+    def gotoprevp(self):
+        rmt_pre_vp = RMT_PRE_VP_SCREEN()
+        widget.addWidget(rmt_pre_vp)
+        widget.setCurrentIndex(widget.currentIndex() + 1)
+
+    def openDocument(self):
+        pdf_path = Path(PureWindowsPath("doc\\UDef-ARP_Introduction.pdf"))
+        QDesktopServices.openUrl(QUrl.fromLocalFile(str(pdf_path)))
+
+class RMT_FIT_CAL_SCREEN(QDialog):
+    def __init__(self):
+        super(RMT_FIT_CAL_SCREEN, self).__init__()
+        # Store the initial directory path
+        self.initial_directory = os.getcwd()
+        loadUi(Path(PureWindowsPath("data\\rmt_fit_cal_screen.ui")), self)
+        if central_data_store.directory is not None and self.folder_entry is not None:
+            self.directory = central_data_store.directory
+            self.folder_entry.setText(str(central_data_store.directory))
+        if central_data_store.directory is not None and self.folder_entry_2 is not None:
+            self.directory_2 = central_data_store.directory
+            self.folder_entry_2.setText(str(central_data_store.directory))
+        self.AT_button2.clicked.connect(self.gotoat2)
+        self.Intro_button2.clicked.connect(self.gotointro2)
+        self.MCT_button2.clicked.connect(self.gotomct2)
+        self.doc_button = self.tab1.findChild(QWidget, "doc_button")
+        self.select_folder_button = self.tab1.findChild(QWidget, "select_folder_button")
+        self.deforestation_hrp_button = self.tab1.findChild(QWidget, "deforestation_hrp_button")
+        self.mask_button = self.tab1.findChild(QWidget, "mask_button")
+        self.fd_button = self.tab1.findChild(QWidget, "fd_button")
+        self.calculate_button2 = self.tab1.findChild(QWidget, "calculate_button2")
+        self.ok_button2 = self.tab1.findChild(QWidget, "ok_button2")
+
+        self.doc_button_2 = self.tab2.findChild(QWidget, "doc_button_2")
+        self.select_folder_button_2 = self.tab2.findChild(QWidget, "select_folder_button_2")
+        self.mask_button_2 = self.tab2.findChild(QWidget, "mask_button_2")
+        self.fmask_button_2 = self.tab2.findChild(QWidget, "fmask_button_2")
+        self.fd_button_2 = self.tab2.findChild(QWidget, "fd_button_2")
+        self.ok_button2_2 = self.tab2.findChild(QWidget, "ok_button2_2")
+
+        self.doc_button.clicked.connect(self.openDocument)
+        self.select_folder_button.clicked.connect(self.select_working_directory)
+        self.deforestation_hrp_button.clicked.connect(self.select_deforestation_hrp)
+        self.mask_button.clicked.connect(self.select_mask)
+        self.fd_button.clicked.connect(self.select_fd)
+        self.calculate_button2.clicked.connect(self.process_data2_nrt)
+        self.ok_button2.clicked.connect(self.process_data2)
+
+        self.doc_button_2.clicked.connect(self.openDocument_2)
+        self.select_folder_button_2.clicked.connect(self.select_working_directory_2)
+        self.mask_button_2.clicked.connect(self.select_mask_2)
+        self.fmask_button_2.clicked.connect(self.select_fmask_2)
+        self.fd_button_2.clicked.connect(self.select_fd_2)
+        self.ok_button2_2.clicked.connect(self.process_data2_2)
+
+        self.vulnerability_map = VulnerabilityMap()
+        self.vulnerability_map.progress_updated.connect(self.update_progress)
+        self.directory = None
+        self.in_fn = None
+        self.deforestation_hrp = None
+        self.mask = None
+        self.NRT = None
+        if central_data_store.NRT is not None:
+            self.nrt_entry.setText(str(central_data_store.NRT))
+        self.n_classes = None
+        self.out_fn = None
+        self.out_fn_entry.setPlaceholderText('e.g., Acre_Vulnerability_CAL.tif')
+        self.directory_2 = None
+        self.mask_2 = None
+        self.fmask_2 = None
+        self.in_fn_2 = None
+        self.out_fn_2 = None
+        self.n_classes_2 = None
+        self.file_path_directory = None
+        self.file_path2_directory = None
+        self.file_path3_directory = None
+        self.file_path4_directory = None
+        self.file_path5_directory = None
+        self.file_path6_directory = None
+        self.out_fn_entry_2.setPlaceholderText('e.g., Acre_Vulnerability_CAL.tif')
+        self.setWindowTitle("JNR Integrated Risk/Allocation Tool")
+
+    def gotoat2(self):
+        os.chdir(self.initial_directory)
+        at2 = AT_FIT_CAL_Screen()
+        widget.addWidget(at2)
+        widget.setCurrentIndex(widget.currentIndex() + 1)
+
+    def gotomct2(self):
+        os.chdir(self.initial_directory)
+        mct2 = MCT_FIT_CAL_Screen()
+        widget.addWidget(mct2)
+        widget.setCurrentIndex(widget.currentIndex() + 1)
+
+    def gotointro2(self):
+        os.chdir(self.initial_directory)
+        intro2 = IntroScreen()
+        widget.addWidget(intro2)
+        widget.setCurrentIndex(widget.currentIndex() + 1)
+
+    def openDocument(self):
+        pdf_path = Path(PureWindowsPath("doc\\TestFitVM.pdf"))
+        QDesktopServices.openUrl(QUrl.fromLocalFile(str(pdf_path)))
+
+    def openDocument_2(self):
+        pdf_path = Path(PureWindowsPath("doc\\TestFitVM.pdf"))
+        QDesktopServices.openUrl(QUrl.fromLocalFile(str(pdf_path)))
+
+    def select_working_directory(self):
+        data_folder = QFileDialog.getExistingDirectory(self, "Working Directory")
+        data_folder_path = Path(data_folder)
+        self.directory = str(data_folder_path)
+        self.folder_entry.setText(self.directory)
+        self.folder_entry_2.setText(self.directory)
+        central_data_store.directory = self.directory
+
+    def select_fd(self):
+        file_path, _ = QFileDialog.getOpenFileName(self, 'Map of Distance from the Forest Edge in CAL')
+        if file_path:
+            self.in_fn = Path(PureWindowsPath(file_path))
+            self.in_fn_entry.setText(file_path.split('/')[-1])
+            self.file_path_directory = '\\'.join(file_path.split('/')[:-1])
+
+    def select_deforestation_hrp(self):
+        file_path3, _ = QFileDialog.getOpenFileName(self, "Map of Deforestation in the CAL")
+        if file_path3:
+            self.deforestation_hrp = Path(PureWindowsPath(file_path3))
+            self.deforestation_hrp_entry.setText(file_path3.split('/')[-1])
+            self.file_path3_directory = '\\'.join(file_path3.split('/')[:-1])
+    def select_mask(self):
+        file_path2, _ = QFileDialog.getOpenFileName(self, 'Mask of Study Area')
+        if file_path2:
+            self.mask = Path(PureWindowsPath(file_path2))
+            self.mask_entry.setText(file_path2.split('/')[-1])
+            self.file_path2_directory = '\\'.join(file_path2.split('/')[:-1])
+    def select_working_directory_2(self):
+        data_folder_2 = QFileDialog.getExistingDirectory(self, "Working Directory")
+        data_folder_path_2 = Path(data_folder_2)
+        self.directory_2 = str(data_folder_path_2)
+        self.folder_entry_2.setText(self.directory_2)
+        self.folder_entry.setText(self.directory_2)
+        central_data_store.directory = self.directory_2
+
+    def select_fd_2(self):
+        file_path4, _ = QFileDialog.getOpenFileName(self, 'Map of Distance from the Forest Edge in CAL')
+        if file_path4:
+            self.in_fn_2 = Path(PureWindowsPath(file_path4))
+            self.in_fn_entry_2.setText(file_path4.split('/')[-1])
+            self.file_path4_directory = '\\'.join(file_path4.split('/')[:-1])
+
+    def select_mask_2(self):
+        file_path5, _ = QFileDialog.getOpenFileName(self, 'Mask of Study Area')
+        if file_path5:
+            self.mask_2 = Path(PureWindowsPath(file_path5))
+            self.mask_entry_2.setText(file_path5.split('/')[-1])
+            self.file_path5_directory = '\\'.join(file_path5.split('/')[:-1])
+
+    def select_fmask_2(self):
+        file_path6, _ = QFileDialog.getOpenFileName(self, 'Mask of Forest Area')
+        if file_path6:
+            self.fmask_2 = file_path6
+            self.fmask_entry_2.setText(file_path6.split('/')[-1])
+            self.file_path6_directory = '\\'.join(file_path6.split('/')[:-1])
+
+    def get_full_path(self,base_dir, user_input):
+        if os.path.isabs(user_input):
+            return user_input
+        else:
+            return f"{base_dir}\\{user_input}"
+    def process_data2_nrt(self):
+        directory = self.folder_entry.text()
+        central_data_store.directory = directory
+        self.folder_entry_2.setText(directory)
+        if not directory:
+            QMessageBox.critical(self, "Error", "Please select or enter the working directory!")
+            return
+
+        if not self.file_path_directory:
+            self.file_path_directory=directory
+        if not self.file_path2_directory:
+            self.file_path2_directory=directory
+        if not self.file_path3_directory:
+            self.file_path3_directory=directory
+
+        self.in_fn = self.get_full_path(self.file_path_directory, self.in_fn_entry.text())
+        self.mask = self.get_full_path(self.file_path2_directory,self.mask_entry.text())
+        self.deforestation_hrp = self.get_full_path(self.file_path3_directory,self.deforestation_hrp_entry.text())
+
+        if not self.in_fn or not self.deforestation_hrp or not self.mask:
+            QMessageBox.critical(self, "Error", "Please select or enter all input files!")
+            return
+
+        images = [self.in_fn, self.deforestation_hrp, self.mask]
+
+        # Check if all images have the same resolution
+        resolutions = [map_checker.get_image_resolution(img) for img in images]
+        if len(set(resolutions)) != 1:
+            QMessageBox.critical(None, "Error", "All the input raster images must have the same spatial resolution!")
+            return
+
+        # Check if all images have the same number of rows and columns
+        dimensions = [map_checker.get_image_dimensions(img) for img in images]
+        if len(set(dimensions)) != 1:
+            QMessageBox.critical(None, "Error",
+                                 "All the input raster images must have the same number of rows and columns!")
+            return
+
+        if not map_checker.check_binary_map(self.deforestation_hrp):
+            QMessageBox.critical(None, "Error",
+                                 "'MAP OF DEFORESTATION IN THE HRP' must be a binary map (0 and 1) where the 1’s indicate deforestation.")
+            return
+
+        if not map_checker.check_binary_map(self.mask):
+            QMessageBox.critical(None, "Error",
+                                 "'MASK OF THE JURISDICTION' must be a binary map (0 and 1) where the 1’s indicate jurisdiction.")
+            return
+
+        # Show "Processing" message
+        processing_message = "Calculating NRT..."
+        self.progressDialog = QProgressDialog(processing_message, None, 0, 100, self)
+
+        # Change the font size
+        font = QFont()
+        font.setPointSize(9)
+        self.progressDialog.setFont(font)
+
+        self.progressDialog.setWindowTitle("Calculating")
+        self.progressDialog.setWindowModality(Qt.WindowModal)
+        self.progressDialog.setMinimumDuration(0)
+        self.progressDialog.resize(400, 300)
+        self.progressDialog.show()
+        QApplication.processEvents()
+
+        try:
+            self.vulnerability_map.set_working_directory(directory)
+            NRT = self.vulnerability_map.nrt_calculation(self.in_fn, self.deforestation_hrp, self.mask)
+            # Update the central data store
+            central_data_store.NRT = NRT
+            QMessageBox.information(self, "Processing Completed", f"Processing completed!\nNRT is: {NRT}")
+            self.nrt_entry.setText(str(NRT))
+            self.progressDialog.close()
+
+        except Exception:
+            self.progressDialog.close()
+            tb = traceback.format_exc()
+
+            error_box = QMessageBox(self)
+            error_box.setIcon(QMessageBox.Critical)
+            error_box.setWindowTitle("Error")
+            error_box.setText(f"<b>An Error Occurred During Processing</b>")
+            error_box.setTextInteractionFlags(Qt.TextSelectableByMouse | Qt.TextSelectableByKeyboard)
+            error_box.setDetailedText(tb)
+
+            details_frame = error_box.findChild(QTextEdit)
+            if details_frame:
+                details_frame.setSizePolicy(QSizePolicy.Expanding, QSizePolicy.Expanding)
+                details_frame.setMaximumHeight(800)
+                details_frame.setMaximumWidth(1000)
+                details_frame.setMinimumHeight(400)
+                details_frame.setMinimumWidth(600)
+
+            error_box_layout = error_box.layout()
+            error_box_layout.setContentsMargins(10, 10, 10, 10)
+
+            copy_button = QPushButton("Copy Error Message")
+            error_box.addButton(copy_button, QMessageBox.ActionRole)
+            def copy_error_txt():
+                QApplication.clipboard().setText(tb)
+            copy_button.clicked.connect(copy_error_txt)
+            error_box.exec_()
+
+    def process_data2(self):
+        directory = self.folder_entry.text()
+        central_data_store.directory = directory
+        self.folder_entry_2.setText(directory)
+        if not directory:
+            QMessageBox.critical(self, "Error", "Please select or enter the working directory!")
+            return
+        if not self.file_path_directory:
+            self.file_path_directory = directory
+        if not self.file_path2_directory:
+            self.file_path2_directory = directory
+        self.in_fn = self.get_full_path(self.file_path_directory, self.in_fn_entry.text())
+        self.mask = self.get_full_path(self.file_path2_directory, self.mask_entry.text())
+
+        if not self.in_fn or not self.mask:
+            QMessageBox.critical(self, "Error", "Please select or enter all input files!")
+            return
+
+        NRT = self.nrt_entry.text()
+        if not NRT:
+            QMessageBox.critical(self, "Error", "Please enter the NRT value!")
+            return
+        try:
+            self.NRT = int(NRT)
+            if (self.NRT <= 0):
+                QMessageBox.critical(self, "Error", "NRT value should be larger than 0!")
+                return
+        except ValueError:
+            QMessageBox.critical(self, "Error", "NRT value should be a valid number!")
+            return
+
+        n_classes = int(29)
+        if not n_classes:
+            QMessageBox.critical(self, "Error", "Please enter the number of classes!")
+            return
+        try:
+            self.n_classes = int(n_classes)
+            if (self.n_classes <= 0):
+                QMessageBox.critical(self, "Error", "Number of classes should be larger than 0!")
+                return
+        except ValueError:
+            QMessageBox.critical(self, "Error", "Number of classes value should be a valid number!")
+            return
+
+        out_fn = self.out_fn_entry.text()
+        if not out_fn:
+            QMessageBox.critical(self, "Error", "Please enter the name of Vulnerability Map in CAL!")
+            return
+
+        # Check if the out_fn has the correct file extension
+        if not (out_fn.endswith('.tif') or out_fn.endswith('.rst')):
+            QMessageBox.critical(self, "Error",
+                                 "Please enter .rst or .tif extension in the name of Vulnerability Map in CAL!")
+            return
+
+        # Show "Processing" message
+        processing_message = "Processing data..."
+        self.progressDialog = QProgressDialog(processing_message, None, 0, 100, self)
+
+        # Change the font size
+        font = QFont()
+        font.setPointSize(9)
+        self.progressDialog.setFont(font)
+
+        self.progressDialog.setWindowTitle("Processing")
+        self.progressDialog.setWindowModality(Qt.WindowModal)
+        self.progressDialog.setMinimumDuration(0)
+        self.progressDialog.resize(400, 300)
+        self.progressDialog.show()
+        QApplication.processEvents()
+
+        try:
+            self.vulnerability_map.set_working_directory(directory)
+            mask_arr = self.vulnerability_map.geometric_classification(self.in_fn, NRT, n_classes, self.mask)
+            self.vulnerability_map.array_to_image(self.in_fn, out_fn, mask_arr, gdal.GDT_Int16, -1)
+            self.vulnerability_map.replace_ref_system(self.in_fn, out_fn)
+
+            QMessageBox.information(self, "Processing Completed", "Processing completed!")
+
+            self.progressDialog.close()
+
+        except Exception:
+            self.progressDialog.close()
+            tb = traceback.format_exc()
+
+            error_box = QMessageBox(self)
+            error_box.setIcon(QMessageBox.Critical)
+            error_box.setWindowTitle("Error")
+            error_box.setText(f"<b>An Error Occurred During Processing</b>")
+            error_box.setTextInteractionFlags(Qt.TextSelectableByMouse | Qt.TextSelectableByKeyboard)
+            error_box.setDetailedText(tb)
+
+            details_frame = error_box.findChild(QTextEdit)
+            if details_frame:
+                details_frame.setSizePolicy(QSizePolicy.Expanding, QSizePolicy.Expanding)
+                details_frame.setMaximumHeight(800)
+                details_frame.setMaximumWidth(1000)
+                details_frame.setMinimumHeight(400)
+                details_frame.setMinimumWidth(600)
+
+            error_box_layout = error_box.layout()
+            error_box_layout.setContentsMargins(10, 10, 10, 10)
+
+            copy_button = QPushButton("Copy Error Message")
+            error_box.addButton(copy_button, QMessageBox.ActionRole)
+            def copy_error_txt():
+                QApplication.clipboard().setText(tb)
+            copy_button.clicked.connect(copy_error_txt)
+            error_box.exec_()
+
+
+    def process_data2_2(self):
+        directory_2 = self.folder_entry_2.text()
+        central_data_store.directory = directory_2
+        self.folder_entry.setText(directory_2)
+        if not directory_2 :
+            QMessageBox.critical(self, "Error", "Please select or enter the working directory!")
+            return
+        if not self.file_path4_directory:
+            self.file_path4_directory = directory_2
+        if not self.file_path5_directory:
+            self.file_path5_directory = directory_2
+        if not self.file_path6_directory:
+            self.file_path6_directory = directory_2
+
+        self.in_fn_2 = self.get_full_path(self.file_path4_directory, self.in_fn_entry_2.text())
+        self.mask_2 = self.get_full_path(self.file_path5_directory, self.mask_entry_2.text())
+        self.fmask_2 = self.get_full_path(self.file_path6_directory, self.fmask_entry_2.text())
+
+        if not self.in_fn_2 or not self.mask_2 or not self.fmask_2:
+            QMessageBox.critical(self, "Error", "Please select or enter all input files!")
+            return
+
+        images = [self.in_fn_2, self.mask_2, self.fmask_2]
+
+        # Check if all images have the same resolution
+        resolutions = [map_checker.get_image_resolution(img) for img in images]
+        if len(set(resolutions)) != 1:
+            QMessageBox.critical(None, "Error", "All the input raster images must have the same spatial resolution!")
+            return
+
+        # Check if all images have the same number of rows and columns
+        dimensions = [map_checker.get_image_dimensions(img) for img in images]
+        if len(set(dimensions)) != 1:
+            QMessageBox.critical(None, "Error",
+                                 "All the input raster images must have the same number of rows and columns!")
+            return
+
+        n_classes_2 = int(30)
+        out_fn_2 = self.out_fn_entry_2.text()
+        if not out_fn_2:
+            QMessageBox.critical(self, "Error", "Please enter the name of Vulnerability Map in CAL!")
+            return
+
+        # Check if the out_fn has the correct file extension
+        if not (out_fn_2.endswith('.tif') or out_fn_2.endswith('.rst')):
+            QMessageBox.critical(self, "Error",
+                                 "Please enter .rst or .tif extension in the name of Vulnerability Map in CAL!")
+            return
+
+        if not map_checker.check_binary_map(self.fmask_2):
+            QMessageBox.critical(None, "Error",
+                                 "'MASK OF FOREST AREAS IN THE CAL' must be a binary map (0 and 1) where the 1’s indicate forest areas.")
+            return
+
+        if not map_checker.check_binary_map(self.mask_2):
+            QMessageBox.critical(None, "Error",
+                                 "'MASK OF THE NON-EXCLUDED JURISDICTION' must be a binary map (0 and 1) where the 1’s indicate areas inside the jurisdiction.")
+            return
+
+        # Show "Processing" message
+        processing_message = "Processing data..."
+        self.progressDialog = QProgressDialog(processing_message, None, 0, 100, self)
+
+        # Change the font size
+        font = QFont()
+        font.setPointSize(9)
+        self.progressDialog.setFont(font)
+
+        self.progressDialog.setWindowTitle("Processing")
+        self.progressDialog.setWindowModality(Qt.WindowModal)
+        self.progressDialog.setMinimumDuration(0)
+        self.progressDialog.resize(400, 300)
+        self.progressDialog.show()
+        QApplication.processEvents()
+
+        try:
+            self.vulnerability_map.set_working_directory(directory_2)
+            mask_arr = self.vulnerability_map.geometric_classification_alternative(self.in_fn_2, n_classes_2, self.mask_2, self.fmask_2)
+            self.vulnerability_map.array_to_image(self.in_fn_2, out_fn_2, mask_arr, gdal.GDT_Int16, -1)
+            self.vulnerability_map.replace_ref_system(self.in_fn_2, out_fn_2)
+
+            QMessageBox.information(self, "Processing Completed", "Processing completed!")
+
+            self.progressDialog.close()
+
+        except Exception:
+            self.progressDialog.close()
+            tb = traceback.format_exc()
+
+            error_box = QMessageBox(self)
+            error_box.setIcon(QMessageBox.Critical)
+            error_box.setWindowTitle("Error")
+            error_box.setText(f"<b>An Error Occurred During Processing</b>")
+            error_box.setTextInteractionFlags(Qt.TextSelectableByMouse | Qt.TextSelectableByKeyboard)
+            error_box.setDetailedText(tb)
+
+            details_frame = error_box.findChild(QTextEdit)
+            if details_frame:
+                details_frame.setSizePolicy(QSizePolicy.Expanding, QSizePolicy.Expanding)
+                details_frame.setMaximumHeight(800)
+                details_frame.setMaximumWidth(1000)
+                details_frame.setMinimumHeight(400)
+                details_frame.setMinimumWidth(600)
+
+            error_box_layout = error_box.layout()
+            error_box_layout.setContentsMargins(10, 10, 10, 10)
+
+            copy_button = QPushButton("Copy Error Message")
+            error_box.addButton(copy_button, QMessageBox.ActionRole)
+            def copy_error_txt():
+                QApplication.clipboard().setText(tb)
+            copy_button.clicked.connect(copy_error_txt)
+            error_box.exec_()
+
+    def update_progress(self, value):
+        # Update QProgressDialog with the new value
+        if self.progressDialog is not None:
+            self.progressDialog.setValue(value)
+
+class AT_FIT_CAL_Screen(QDialog):
+    def __init__(self):
+        super(AT_FIT_CAL_Screen, self).__init__()
+        self.initial_directory = os.getcwd()
+        loadUi(Path(PureWindowsPath("data\\at_fit_cal_screen.ui")), self)
+        if central_data_store.directory is not None and self.folder_entry is not None:
+            self.directory = central_data_store.directory
+            self.folder_entry.setText(str(central_data_store.directory))
+        self.Intro_button3.clicked.connect(self.gotointro3)
+        self.RMT_button3.clicked.connect(self.gotormt3)
+        self.MCT_button3.clicked.connect(self.gotomct3)
+        self.doc_button.clicked.connect(self.openDocument)
+        self.select_folder_button.clicked.connect(self.select_working_directory)
+        self.municipality_button.clicked.connect(self.select_municipality)
+        self.risk30_hrp_button.clicked.connect(self.select_risk30_hrp)
+        self.deforestation_hrp_button.clicked.connect(self.select_deforestation_hrp)
+        self.ok_button3.clicked.connect(self.process_data3)
+        self.allocation_tool = AllocationTool()
+        # Connect the progress_updated signal to the update_progress method
+        self.allocation_tool.progress_updated.connect(self.update_progress)
+        self.directory = None
+        self.risk30_hrp = None
+        self.municipality = None
+        self.deforestation_hrp = None
+        self.out_fn1 = None
+        self.out_fn2 = None
+        self.csv_name = None
+        self.file_path_directory = None
+        self.file_path1_directory = None
+        self.file_path3_directory = None
+        self.image1_entry.setPlaceholderText('e.g., Acre_Modeling_Region_CAL.tif')
+        self.csv_entry.setPlaceholderText('e.g., Relative_Frequency_Table_CAL.csv')
+        self.image2_entry.setPlaceholderText('e.g., Acre_Fitted_Density_Map_CAL.tif')
+        self.setWindowTitle("JNR Integrated Risk/Allocation Tool")
+
+    def gotormt3(self):
+        os.chdir(self.initial_directory)
+        rmt3 = RMT_FIT_CAL_SCREEN()
+        widget.addWidget(rmt3)
+        widget.setCurrentIndex(widget.currentIndex() + 1)
+
+    def gotointro3(self):
+        os.chdir(self.initial_directory)
+        intro3 = IntroScreen()
+        widget.addWidget(intro3)
+        widget.setCurrentIndex(widget.currentIndex() + 1)
+
+    def gotomct3(self):
+        os.chdir(self.initial_directory)
+        mct3 = MCT_FIT_CAL_Screen()
+        widget.addWidget(mct3)
+        widget.setCurrentIndex(widget.currentIndex() + 1)
+
+    def openDocument(self):
+        pdf_path = Path(PureWindowsPath("doc\\TestFitAM.pdf"))
+        QDesktopServices.openUrl(QUrl.fromLocalFile(str(pdf_path)))
+
+    def select_working_directory(self):
+        data_folder = QFileDialog.getExistingDirectory(self, "Working Directory")
+        data_folder_path = Path(data_folder)
+        self.directory = str(data_folder_path)
+        self.folder_entry.setText(self.directory)
+        central_data_store.directory = self.directory
+
+    def select_municipality(self):
+        file_path, _ = QFileDialog.getOpenFileName(self, 'Map of Administrative Divisions')
+        if file_path:
+            self.municipality = Path(PureWindowsPath(file_path))
+            self.municipality_entry.setText(file_path.split('/')[-1])
+            self.file_path_directory = '\\'.join(file_path.split('/')[:-1])
+
+    def select_risk30_hrp(self):
+        file_path1, _ = QFileDialog.getOpenFileName(self, "Vulnerability Map in CAL")
+        if file_path1:
+            self.risk30_hrp = Path(file_path1)
+            self.risk30_hrp_entry.setText(file_path1.split('/')[-1])
+            self.file_path1_directory = '\\'.join(file_path1.split('/')[:-1])
+
+    def select_deforestation_hrp(self):
+        file_path3, _ = QFileDialog.getOpenFileName(self, "Map of Deforestation in the CAL")
+        if file_path3:
+            self.deforestation_hrp = Path(file_path3)
+            self.deforestation_hrp_entry.setText(file_path3.split('/')[-1])
+            self.file_path3_directory = '\\'.join(file_path3.split('/')[:-1])
+    def get_full_path(self, base_dir, user_input):
+        if os.path.isabs(user_input):
+            return user_input
+        else:
+            return f"{base_dir}\\{user_input}"
+    def process_data3(self):
+        directory = self.folder_entry.text()
+        central_data_store.directory = directory
+        if not directory:
+            QMessageBox.critical(self, "Error", "Please select or enter the working directory!")
+            return
+        if not self.file_path_directory:
+            self.file_path_directory = directory
+        if not self.file_path1_directory:
+            self.file_path1_directory = directory
+        if not self.file_path3_directory:
+            self.file_path3_directory = directory
+
+        self.municipality = self.get_full_path(self.file_path_directory, self.municipality_entry.text())
+        self.risk30_hrp = self.get_full_path(self.file_path1_directory, self.risk30_hrp_entry.text())
+        self.deforestation_hrp = self.get_full_path(self.file_path3_directory, self.deforestation_hrp_entry.text())
+
+        if not self.risk30_hrp or not self.municipality or not self.deforestation_hrp:
+            QMessageBox.critical(self, "Error", "Please select or enter all input files!")
+            return
+
+        images = [self.risk30_hrp, self.municipality, self.deforestation_hrp]
+
+        # Check if all images have the same resolution
+        resolutions = [map_checker.get_image_resolution(img) for img in images]
+        if len(set(resolutions)) != 1:
+            QMessageBox.critical(None, "Error", "All the input raster images must have the same spatial resolution!")
+            return
+
+        # Check if all images have the same number of rows and columns
+        dimensions = [map_checker.get_image_dimensions(img) for img in images]
+        if len(set(dimensions)) != 1:
+            QMessageBox.critical(None, "Error",
+                                 "All the input raster images must have the same number of rows and columns!")
+            return
+
+        out_fn1 = self.image1_entry.text()
+        if not out_fn1:
+            QMessageBox.critical(self, "Error", "Please enter the name for Modeling Region Map in CAL!")
+            return
+
+        if not (out_fn1.endswith('.tif') or out_fn1.endswith('.rst')):
+            QMessageBox.critical(self, "Error",
+                                 "Please enter .rst or .tif extension in the name for Modeling Region Map in CAL!")
+            return
+
+        csv_name = self.csv_entry.text()
+        if not csv_name:
+            QMessageBox.critical(self, "Error", "Please enter the name for the Relative Frequency Table!")
+            return
+
+        if not (csv_name.endswith('.csv')):
+            QMessageBox.critical(self, "Error",
+                                 "Please enter .csv extension in the name of Relative Frequency Table!")
+            return
+
+        out_fn2 = self.image2_entry.text()
+        if not out_fn2:
+            QMessageBox.critical(self, "Error", "Please enter the name for Fitted Density Map in the CAL!")
+            return
+
+        if not (out_fn2.endswith('.tif') or out_fn2.endswith('.rst')):
+            QMessageBox.critical(self, "Error",
+                                 "Please enter .rst or .tif extension in the name for Fitted Density Map in the CAL!")
+            return
+
+        if not map_checker.check_binary_map(self.deforestation_hrp):
+            QMessageBox.critical(None, "Error",
+                                 "'MAP OF DEFORESTATION IN THE CAL' must be a binary map (0 and 1) where the 1’s indicate deforestation.")
+            return
+
+        # Show "Processing" message
+        processing_message = "Processing data..."
+        self.progressDialog = QProgressDialog(processing_message, None, 0, 100, self)
+
+        # Change the font size
+        font = QFont()
+        font.setPointSize(9)
+        self.progressDialog.setFont(font)
+
+        self.progressDialog.setWindowTitle("Processing")
+        self.progressDialog.setWindowModality(Qt.WindowModal)
+        self.progressDialog.setMinimumDuration(0)
+        self.progressDialog.resize(400, 300)
+        self.progressDialog.show()
+        QApplication.processEvents()
+
+        try:
+            self.allocation_tool.execute_workflow_fit(directory, self.risk30_hrp,
+                                                        self.municipality,self.deforestation_hrp, csv_name,
+                                                        out_fn1,out_fn2)
+            QMessageBox.information(self, "Processing Completed", "Processing completed!")
+            self.progressDialog.close()
+
+        except Exception:
+            self.progressDialog.close()
+            tb = traceback.format_exc()
+
+            error_box = QMessageBox(self)
+            error_box.setIcon(QMessageBox.Critical)
+            error_box.setWindowTitle("Error")
+            error_box.setText(f"<b>An Error Occurred During Processing</b>")
+            error_box.setTextInteractionFlags(Qt.TextSelectableByMouse | Qt.TextSelectableByKeyboard)
+            error_box.setDetailedText(tb)
+
+            details_frame = error_box.findChild(QTextEdit)
+            if details_frame:
+                details_frame.setSizePolicy(QSizePolicy.Expanding, QSizePolicy.Expanding)
+                details_frame.setMaximumHeight(800)
+                details_frame.setMaximumWidth(1000)
+                details_frame.setMinimumHeight(400)
+                details_frame.setMinimumWidth(600)
+
+            error_box_layout = error_box.layout()
+            error_box_layout.setContentsMargins(10, 10, 10, 10)
+
+            copy_button = QPushButton("Copy Error Message")
+            error_box.addButton(copy_button, QMessageBox.ActionRole)
+            def copy_error_txt():
+                QApplication.clipboard().setText(tb)
+            copy_button.clicked.connect(copy_error_txt)
+            error_box.exec_()
+
+    def update_progress(self, value):
+        # Update QProgressDialog with the new value
+        if self.progressDialog is not None:
+            self.progressDialog.setValue(value)
+
+
+class MCT_FIT_CAL_Screen(QDialog):
+    def __init__(self):
+        super(MCT_FIT_CAL_Screen, self).__init__()
+        # Store the initial directory path
+        self.initial_directory = os.getcwd()
+        loadUi(Path(PureWindowsPath("data\\mct_fit_cal_screen.ui")), self)
+        if central_data_store.directory is not None and self.folder_entry is not None:
+            self.directory = central_data_store.directory
+            self.folder_entry.setText(str(central_data_store.directory))
+        self.AT_button4.clicked.connect(self.gotoat4)
+        self.Intro_button4.clicked.connect(self.gotointro4)
+        self.RMT_button4.clicked.connect(self.gotormt4)
+        self.doc_button.clicked.connect(self.openDocument)
+        self.select_folder_button.clicked.connect(self.select_working_directory)
+        self.mask_button.clicked.connect(self.select_mask)
+        self.deforestation_hrp_button.clicked.connect(self.select_deforestation_hrp)
+        self.density_button.clicked.connect(self.select_density)
+        self.ok_button.clicked.connect(self.process_data4)
+        self.model_evaluation = ModelEvaluation()
+        self.model_evaluation.progress_updated.connect(self.update_progress)
+        self.directory = None
+        self.mask = None
+        self.deforestation_hrp = None
+        self.density = None
+        self.grid_area = None
+        self.grid_area_entry.setPlaceholderText('Type default 100000 or other number')
+        self.title = None
+        self.out_fn = None
+        self.out_fn_entry.setPlaceholderText('e.g., Plot_CAL.png')
+        self.raster_fn = None
+        self.raster_fn_entry.setPlaceholderText('e.g., Acre_Residuals_CAL.tif')
+        self.xmax = None
+        self.xmax = None
+        self.file_path_directory = None
+        self.file_path2_directory = None
+        self.file_path3_directory = None
+        self.setWindowTitle("JNR Integrated Risk/Allocation Tool")
+
+    def gotoat4(self):
+        os.chdir(self.initial_directory)
+        at4 = AT_FIT_CAL_Screen()
+        widget.addWidget(at4)
+        widget.setCurrentIndex(widget.currentIndex() + 1)
+
+    def gotointro4(self):
+        os.chdir(self.initial_directory)
+        intro4 = IntroScreen()
+        widget.addWidget(intro4)
+        widget.setCurrentIndex(widget.currentIndex() + 1)
+
+    def gotormt4(self):
+        os.chdir(self.initial_directory)
+        rmt4 = RMT_FIT_CAL_SCREEN()
+        widget.addWidget(rmt4)
+        widget.setCurrentIndex(widget.currentIndex() + 1)
+
+    def openDocument(self):
+        pdf_path = Path(PureWindowsPath("doc\\TestFitMA.pdf"))
+        QDesktopServices.openUrl(QUrl.fromLocalFile(str(pdf_path)))
+
+    def select_working_directory(self):
+        data_folder = QFileDialog.getExistingDirectory(self, "Working Directory")
+        data_folder_path = Path(data_folder)
+        self.directory = str(data_folder_path)
+        self.folder_entry.setText(self.directory)
+        central_data_store.directory = self.directory
+
+    def select_mask(self):
+        file_path, _ = QFileDialog.getOpenFileName(self, 'Mask of Study Area')
+        if file_path:
+            self.mask = Path(PureWindowsPath(file_path))
+            self.mask_entry.setText(file_path.split('/')[-1])
+            self.file_path_directory = '\\'.join(file_path.split('/')[:-1])
+
+    def select_deforestation_hrp(self):
+        file_path3, _ = QFileDialog.getOpenFileName(self, "Map of Deforestation in the HRP")
+        if file_path3:
+            self.deforestation_hrp = Path(PureWindowsPath(file_path3))
+            self.deforestation_hrp_entry.setText(file_path3.split('/')[-1])
+            self.file_path3_directory = '\\'.join(file_path3.split('/')[:-1])
+
+    def select_density(self):
+        file_path2, _ = QFileDialog.getOpenFileName(self, 'Deforestation Density Map')
+        if file_path2:
+            self.density = Path(PureWindowsPath(file_path2))
+            self.density_entry.setText(file_path2.split('/')[-1])
+            self.file_path2_directory = '\\'.join(file_path2.split('/')[:-1])
+    def get_full_path(self, base_dir, user_input):
+        if os.path.isabs(user_input):
+            return user_input
+        else:
+            return f"{base_dir}\\{user_input}"
+    def process_data4(self):
+        directory = self.folder_entry.text()
+        central_data_store.directory = directory
+        if not directory:
+            QMessageBox.critical(self, "Error", "Please select or enter the working directory!")
+            return
+        if not self.file_path_directory:
+            self.file_path_directory = directory
+        if not self.file_path2_directory:
+            self.file_path2_directory = directory
+        if not self.file_path3_directory:
+            self.file_path3_directory = directory
+
+        self.mask = self.get_full_path(self.file_path_directory, self.mask_entry.text())
+        self.density = self.get_full_path(self.file_path2_directory, self.density_entry.text())
+        self.deforestation_hrp = self.get_full_path(self.file_path3_directory, self.deforestation_hrp_entry.text())
+
+        if not self.mask or not self.deforestation_hrp or not self.density :
+            QMessageBox.critical(self, "Error", "Please select or enter all input files!")
+            return
+
+        images = [self.mask, self.deforestation_hrp, self.density]
+
+        # Check if all images have the same resolution
+        resolutions = [map_checker.get_image_resolution(img) for img in images]
+        if len(set(resolutions)) != 1:
+            QMessageBox.critical(None, "Error", "All the input raster images must have the same spatial resolution!")
+            return
+
+        # Check if all images have the same number of rows and columns
+        dimensions = [map_checker.get_image_dimensions(img) for img in images]
+        if len(set(dimensions)) != 1:
+            QMessageBox.critical(None, "Error",
+                                 "All the input raster images must have the same number of rows and columns!")
+            return
+
+        grid_area = self.grid_area_entry.text()
+        if not grid_area:
+            QMessageBox.critical(self, "Error", "Please enter the thiessen polygon grid area value!")
+            return
+        try:
+            self.grid_area = float(grid_area)
+            if not (0 < self.grid_area):
+                QMessageBox.critical(self, "Error", "Thiessen polygon grid area value should larger than 0!")
+                return
+        except ValueError:
+            QMessageBox.critical(self, "Error", "Thiessen polygon grid area value should be a valid number!")
+            return
+
+
+        xmax = self.xmax_entry.text()
+        if xmax.lower() != "default":
+            try:
+                xmax = float(xmax)
+                if xmax <= 0:
+                    raise ValueError("The plot x-axis limit should be larger than 0!")
+            except ValueError:
+                QMessageBox.critical(self, "Error", "The plot x-axis limit should be a valid number or 'Default'!")
+                return
+
+        ymax = self.ymax_entry.text()
+        if ymax.lower() != "default":
+            try:
+                ymax = float(ymax)
+                if ymax <= 0:
+                    raise ValueError("The plot y-axis limit should be larger than 0!")
+            except ValueError:
+                QMessageBox.critical(self, "Error", "The plot y-axis limit should be a valid number or 'Default'!")
+                return
+
+        title = self.title_entry.text()
+        if not title:
+            QMessageBox.critical(self, "Error", "Please enter the title of plot!")
+            return
+
+        out_fn = self.out_fn_entry.text()
+        if not out_fn:
+            QMessageBox.critical(self, "Error", "Please enter the name of plot!")
+            return
+
+        # Check if the out_fn has the correct file extension
+        if not (out_fn.endswith('.png') or out_fn.endswith('.jpg') or out_fn.endswith('.pdf') or out_fn.endswith(
+                '.svg') or out_fn.endswith('.eps') or out_fn.endswith('.ps') or out_fn.endswith('.tif')):
+            QMessageBox.critical(self, "Error",
+                                 "Please enter extension(.png/.jpg/.pdf/.svg/.eps/.ps/.tif) in the name of plot!")
+            return
+
+        raster_fn = self.raster_fn_entry.text()
+        if not raster_fn:
+            QMessageBox.critical(self, "Error", "Please enter the name for Residual Map!")
+            return
+
+        if not (raster_fn.endswith('.tif') or raster_fn.endswith('.rst')):
+            QMessageBox.critical(self, "Error",
+                                 "Please enter .rst or .tif extension in the name of Residual Map!")
+            return
+
+        if not map_checker.check_binary_map(self.mask):
+            QMessageBox.critical(None, "Error",
+                                 "'MASK OF THE NON-EXCLUDED JURISDICTION' must be a binary map (0 and 1) where the 1’s indicate areas inside the jurisdiction.")
+            return
+
+        if not map_checker.check_binary_map(self.deforestation_hrp):
+            QMessageBox.critical(None, "Error",
+                                 "'MAP OF DEFORESTATION IN THE CAL' must be a binary map (0 and 1) where the 1’s indicate deforestation.")
+            return
+
+        # Show "Processing" message
+        processing_message = "Processing data..."
+        self.progressDialog = QProgressDialog(processing_message, None, 0, 100, self)
+
+        # Change the font size
+        font = QFont()
+        font.setPointSize(9)
+        self.progressDialog.setFont(font)
+
+        self.progressDialog.setWindowTitle("Processing")
+        self.progressDialog.setWindowModality(Qt.WindowModal)
+        self.progressDialog.setMinimumDuration(0)
+        self.progressDialog.resize(400, 300)
+        self.progressDialog.show()
+        QApplication.processEvents()
+
+        try:
+            self.model_evaluation.set_working_directory(directory)
+            self.model_evaluation.create_mask_polygon(self.mask)
+            clipped_gdf = self.model_evaluation.create_thiessen_polygon(self.grid_area, self.mask,self.density, self.deforestation_hrp, out_fn,raster_fn)
+            self.model_evaluation.replace_ref_system(self.mask, raster_fn)
+            self.model_evaluation.create_plot(grid_area,clipped_gdf, title, out_fn, xmax, ymax)
+            self.model_evaluation.remove_temp_files()
+
+            QMessageBox.information(self, "Processing Completed", "Processing completed!")
+            self.progressDialog.close()
+
+        except Exception:
+            self.progressDialog.close()
+            tb = traceback.format_exc()
+
+            error_box = QMessageBox(self)
+            error_box.setIcon(QMessageBox.Critical)
+            error_box.setWindowTitle("Error")
+            error_box.setText(f"<b>An Error Occurred During Processing</b>")
+            error_box.setTextInteractionFlags(Qt.TextSelectableByMouse | Qt.TextSelectableByKeyboard)
+            error_box.setDetailedText(tb)
+
+            details_frame = error_box.findChild(QTextEdit)
+            if details_frame:
+                details_frame.setSizePolicy(QSizePolicy.Expanding, QSizePolicy.Expanding)
+                details_frame.setMaximumHeight(800)
+                details_frame.setMaximumWidth(1000)
+                details_frame.setMinimumHeight(400)
+                details_frame.setMinimumWidth(600)
+
+            error_box_layout = error_box.layout()
+            error_box_layout.setContentsMargins(10, 10, 10, 10)
+
+            copy_button = QPushButton("Copy Error Message")
+            error_box.addButton(copy_button, QMessageBox.ActionRole)
+            def copy_error_txt():
+                QApplication.clipboard().setText(tb)
+            copy_button.clicked.connect(copy_error_txt)
+            error_box.exec_()
+
+    def update_progress(self, value):
+        # Update QProgressDialog with the new value
+        if self.progressDialog is not None:
+            self.progressDialog.setValue(value)
+
+class RMT_PRE_CNF_SCREEN(QDialog):
+    def __init__(self):
+        super(RMT_PRE_CNF_SCREEN, self).__init__()
+        # Store the initial directory path
+        self.initial_directory = os.getcwd()
+        loadUi(Path(PureWindowsPath("data\\rmt_pre_cnf_screen.ui")), self)
+        if central_data_store.directory is not None and self.folder_entry is not None:
+            self.directory = central_data_store.directory
+            self.folder_entry.setText(str(central_data_store.directory))
+        if central_data_store.directory is not None and self.folder_entry_2 is not None:
+            self.directory_2 = central_data_store.directory
+            self.folder_entry_2.setText(str(central_data_store.directory))
+        self.AT_button2.clicked.connect(self.gotoat2)
+        self.Intro_button2.clicked.connect(self.gotointro2)
+        self.MCT_button2.clicked.connect(self.gotomct2)
+        self.doc_button = self.tab1.findChild(QWidget, "doc_button")
+        self.select_folder_button = self.tab1.findChild(QWidget, "select_folder_button")
+        self.fd_button = self.tab1.findChild(QWidget, "fd_button")
+        self.mask_button = self.tab1.findChild(QWidget, "mask_button")
+        self.ok_button2 = self.tab1.findChild(QWidget, "ok_button2")
+
+        self.doc_button_2 = self.tab2.findChild(QWidget, "doc_button_2")
+        self.select_folder_button_2 = self.tab2.findChild(QWidget, "select_folder_button_2")
+        self.mask_button_2 = self.tab2.findChild(QWidget, "mask_button_2")
+        self.fmask_button_2 = self.tab2.findChild(QWidget, "fmask_button_2")
+        self.fd_button_2 = self.tab2.findChild(QWidget, "fd_button_2")
+        self.ok_button2_2 = self.tab2.findChild(QWidget, "ok_button2_2")
+
+        self.doc_button.clicked.connect(self.openDocument)
+        self.select_folder_button.clicked.connect(self.select_working_directory)
+        self.fd_button.clicked.connect(self.select_fd)
+        self.mask_button.clicked.connect(self.select_mask)
+        self.ok_button2.clicked.connect(self.process_data2)
+
+        self.doc_button_2.clicked.connect(self.openDocument_2)
+        self.select_folder_button_2.clicked.connect(self.select_working_directory_2)
+        self.mask_button_2.clicked.connect(self.select_mask_2)
+        self.fmask_button_2.clicked.connect(self.select_fmask_2)
+        self.fd_button_2.clicked.connect(self.select_fd_2)
+        self.ok_button2_2.clicked.connect(self.process_data2_2)
+
+        self.vulnerability_map = VulnerabilityMap()
+        self.vulnerability_map.progress_updated.connect(self.update_progress)
+        self.directory = None
+        self.in_fn = None
+        self.NRT = None
+        self.mask = None
+        # Use NRT from the data store
+        if central_data_store.NRT is not None:
+            self.nrt_entry.setText(str(central_data_store.NRT))
+        self.n_classes = None
+        self.out_fn = None
+        self.out_fn_entry.setPlaceholderText('e.g., Acre_Vulnerability_CNF.tif')
+
+        self.directory_2 = None
+        self.mask_2 = None
+        self.fmask_2 = None
+        self.in_fn_2 = None
+        self.out_fn_2 = None
+        self.n_classes_2 = None
+        self.out_fn_entry_2.setPlaceholderText('e.g., Acre_Vulnerability_CNF.tif')
+        self.file_path_directory = None
+        self.file_path2_directory = None
+        self.file_path4_directory = None
+        self.file_path5_directory = None
+        self.file_path6_directory = None
+        self.setWindowTitle("JNR Integrated Risk/Allocation Tool")
+
+    def gotoat2(self):
+        os.chdir(self.initial_directory)
+        at2 = AT_PRE_CNF_Screen()
+        widget.addWidget(at2)
+        widget.setCurrentIndex(widget.currentIndex() + 1)
+
+    def gotomct2(self):
+        os.chdir(self.initial_directory)
+        mct2 = MCT_PRE_CNF_Screen()
+        widget.addWidget(mct2)
+        widget.setCurrentIndex(widget.currentIndex() + 1)
+
+    def gotointro2(self):
+        os.chdir(self.initial_directory)
+        intro2 = IntroScreen()
+        widget.addWidget(intro2)
+        widget.setCurrentIndex(widget.currentIndex() + 1)
+
+    def openDocument(self):
+        pdf_path = Path(PureWindowsPath("doc\\TestPreVM.pdf"))
+        QDesktopServices.openUrl(QUrl.fromLocalFile(str(pdf_path)))
+
+    def openDocument_2(self):
+        pdf_path = Path(PureWindowsPath("doc\\TestPreVM.pdf"))
+        QDesktopServices.openUrl(QUrl.fromLocalFile(str(pdf_path)))
+
+    def select_working_directory(self):
+        data_folder = QFileDialog.getExistingDirectory(self, "Working Directory")
+        data_folder_path = Path(data_folder)
+        self.directory = str(data_folder_path)
+        self.folder_entry.setText(self.directory)
+        self.folder_entry_2.setText(self.directory)
+        central_data_store.directory = self.directory
+
+    def select_fd(self):
+        file_path, _ = QFileDialog.getOpenFileName(self, 'Map of Distance from the Forest Edge in CNF')
+        if file_path:
+            self.in_fn = Path(PureWindowsPath(file_path))
+            self.in_fn_entry.setText(file_path.split('/')[-1])
+            self.file_path_directory = '\\'.join(file_path.split('/')[:-1])
+
+    def select_mask(self):
+        file_path2, _ = QFileDialog.getOpenFileName(self, 'Mask of Study Area')
+        if file_path2:
+            self.mask = Path(PureWindowsPath(file_path2))
+            self.mask_entry.setText(file_path2.split('/')[-1])
+            self.file_path2_directory = '\\'.join(file_path2.split('/')[:-1])
+
+    def select_working_directory_2(self):
+        data_folder_2 = QFileDialog.getExistingDirectory(self, "Working Directory")
+        data_folder_path_2 = Path(data_folder_2)
+        self.directory_2 = str(data_folder_path_2)
+        self.folder_entry_2.setText(self.directory_2)
+        self.folder_entry.setText(self.directory_2)
+        central_data_store.directory = self.directory_2
+    def select_fd_2(self):
+        file_path4, _ = QFileDialog.getOpenFileName(self, 'Map of Distance from the Forest Edge in CNF')
+        if file_path4:
+            self.in_fn_2 = Path(PureWindowsPath(file_path4))
+            self.in_fn_entry_2.setText(file_path4.split('/')[-1])
+            self.file_path4_directory = '\\'.join(file_path4.split('/')[:-1])
+
+    def select_mask_2(self):
+        file_path5, _ = QFileDialog.getOpenFileName(self, 'Mask of Study Area')
+        if file_path5:
+            self.mask_2 = Path(PureWindowsPath(file_path5))
+            self.mask_entry_2.setText(file_path5.split('/')[-1])
+            self.file_path5_directory = '\\'.join(file_path5.split('/')[:-1])
+
+    def select_fmask_2(self):
+        file_path6, _ = QFileDialog.getOpenFileName(self, 'Mask of Forest Area')
+        if file_path6:
+            self.fmask_2 = file_path6
+            self.fmask_entry_2.setText(file_path6.split('/')[-1])
+            self.file_path6_directory = '\\'.join(file_path6.split('/')[:-1])
+    def get_full_path(self, base_dir, user_input):
+        if os.path.isabs(user_input):
+            return user_input
+        else:
+            return f"{base_dir}\\{user_input}"
+    def process_data2(self):
+        directory = self.folder_entry.text()
+        central_data_store.directory = directory
+        self.folder_entry_2.setText(directory)
+        if not directory:
+            QMessageBox.critical(self, "Error", "Please select or enter the working directory!")
+            return
+        if not self.file_path_directory:
+            self.file_path_directory = directory
+        if not self.file_path2_directory:
+            self.file_path2_directory = directory
+        self.in_fn = self.get_full_path(self.file_path_directory, self.in_fn_entry.text())
+        self.mask = self.get_full_path(self.file_path2_directory, self.mask_entry.text())
+
+        if not self.in_fn or not self.mask:
+            QMessageBox.critical(self, "Error", "Please select or enter all input files!")
+            return
+
+        NRT = self.nrt_entry.text()
+        if not NRT:
+            QMessageBox.critical(self, "Error", "Please enter the NRT value!")
+            return
+        try:
+            self.NRT = int(NRT)
+            if (self.NRT <= 0):
+                QMessageBox.critical(self, "Error", "NRT value should be larger than 0!")
+                return
+        except ValueError:
+            QMessageBox.critical(self, "Error", "NRT value should be a valid number!")
+            return
+
+        n_classes = int(29)
+        if not n_classes:
+            QMessageBox.critical(self, "Error", "Please enter the number of classes!")
+            return
+        try:
+            self.n_classes = int(n_classes)
+            if (self.n_classes <= 0):
+                QMessageBox.critical(self, "Error", "Number of classes should be larger than 0!")
+                return
+        except ValueError:
+            QMessageBox.critical(self, "Error", "Number of classes value should be a valid number!")
+            return
+
+        out_fn = self.out_fn_entry.text()
+        if not out_fn:
+            QMessageBox.critical(self, "Error", "Please enter the name of Vulnerability Map in CNF!")
+            return
+
+        if not (out_fn.endswith('.tif') or out_fn.endswith('.rst')):
+            QMessageBox.critical(self, "Error",
+                                 "Please enter .rst or .tif extension in the name of Vulnerability Map in CNF!")
+            return
+
+        # Show "Processing" message
+        processing_message = "Processing data..."
+        self.progressDialog = QProgressDialog(processing_message, None, 0, 100, self)
+
+        # Change the font size
+        font = QFont()
+        font.setPointSize(9)
+        self.progressDialog.setFont(font)
+
+        self.progressDialog.setWindowTitle("Processing")
+        self.progressDialog.setWindowModality(Qt.WindowModal)
+        self.progressDialog.setMinimumDuration(0)
+        self.progressDialog.resize(400, 300)
+        self.progressDialog.show()
+        QApplication.processEvents()
+
+        try:
+            self.vulnerability_map.set_working_directory(directory)
+            mask_arr = self.vulnerability_map.geometric_classification(self.in_fn, NRT, n_classes, self.mask)
+            self.vulnerability_map.array_to_image(self.in_fn, out_fn, mask_arr, gdal.GDT_Int16, -1)
+            self.vulnerability_map.replace_ref_system(self.in_fn, out_fn)
+
+            QMessageBox.information(self, "Processing Completed", "Processing completed!")
+            self.progressDialog.close()
+
+        except Exception:
+            self.progressDialog.close()
+            tb = traceback.format_exc()
+
+            error_box = QMessageBox(self)
+            error_box.setIcon(QMessageBox.Critical)
+            error_box.setWindowTitle("Error")
+            error_box.setText(f"<b>An Error Occurred During Processing</b>")
+            error_box.setTextInteractionFlags(Qt.TextSelectableByMouse | Qt.TextSelectableByKeyboard)
+            error_box.setDetailedText(tb)
+
+            details_frame = error_box.findChild(QTextEdit)
+            if details_frame:
+                details_frame.setSizePolicy(QSizePolicy.Expanding, QSizePolicy.Expanding)
+                details_frame.setMaximumHeight(800)
+                details_frame.setMaximumWidth(1000)
+                details_frame.setMinimumHeight(400)
+                details_frame.setMinimumWidth(600)
+
+            error_box_layout = error_box.layout()
+            error_box_layout.setContentsMargins(10, 10, 10, 10)
+
+            copy_button = QPushButton("Copy Error Message")
+            error_box.addButton(copy_button, QMessageBox.ActionRole)
+            def copy_error_txt():
+                QApplication.clipboard().setText(tb)
+            copy_button.clicked.connect(copy_error_txt)
+            error_box.exec_()
+
+    def process_data2_2(self):
+        directory_2 = self.folder_entry_2.text()
+        central_data_store.directory = directory_2
+        self.folder_entry.setText(directory_2)
+        if not directory_2 :
+            QMessageBox.critical(self, "Error", "Please select or enter the working directory!")
+            return
+        if not self.file_path4_directory:
+            self.file_path4_directory = directory_2
+        if not self.file_path5_directory:
+            self.file_path5_directory = directory_2
+        if not self.file_path6_directory:
+            self.file_path6_directory = directory_2
+
+        self.in_fn_2 = self.get_full_path(self.file_path4_directory, self.in_fn_entry_2.text())
+        self.mask_2 = self.get_full_path(self.file_path5_directory, self.mask_entry_2.text())
+        self.fmask_2 = self.get_full_path(self.file_path6_directory, self.fmask_entry_2.text())
+
+        if not self.in_fn_2 or not self.mask_2 or not self.fmask_2:
+            QMessageBox.critical(self, "Error", "Please select or enter all input files!")
+            return
+
+        images = [self.in_fn_2, self.mask_2, self.fmask_2]
+
+        # Check if all images have the same resolution
+        resolutions = [map_checker.get_image_resolution(img) for img in images]
+        if len(set(resolutions)) != 1:
+            QMessageBox.critical(None, "Error", "All the input raster images must have the same spatial resolution!")
+            return
+
+        # Check if all images have the same number of rows and columns
+        dimensions = [map_checker.get_image_dimensions(img) for img in images]
+        if len(set(dimensions)) != 1:
+            QMessageBox.critical(None, "Error",
+                                 "All the input raster images must have the same number of rows and columns!")
+            return
+
+        n_classes_2 = int(30)
+        out_fn_2 = self.out_fn_entry_2.text()
+        if not out_fn_2:
+            QMessageBox.critical(self, "Error", "Please enter the name of Vulnerability Map in CNF!")
+            return
+
+        # Check if the out_fn has the correct file extension
+        if not (out_fn_2.endswith('.tif') or out_fn_2.endswith('.rst')):
+            QMessageBox.critical(self, "Error",
+                                 "Please enter .rst or .tif extension in the name of Vulnerability Map in CNF!")
+            return
+
+        if not map_checker.check_binary_map(self.fmask_2):
+            QMessageBox.critical(None, "Error",
+                                 "'MASK OF FOREST AREAS IN THE CNF' must be a binary map (0 and 1) where the 1’s indicate forest areas.")
+            return
+
+        if not map_checker.check_binary_map(self.mask_2):
+            QMessageBox.critical(None, "Error",
+                                 "'MASK OF THE NON-EXCLUDED JURISDICTION' must be a binary map (0 and 1) where the 1’s indicate areas inside the jurisdiction.")
+            return
+
+        # Show "Processing" message
+        processing_message = "Processing data..."
+        self.progressDialog = QProgressDialog(processing_message, None, 0, 100, self)
+
+        # Change the font size
+        font = QFont()
+        font.setPointSize(9)
+        self.progressDialog.setFont(font)
+
+        self.progressDialog.setWindowTitle("Processing")
+        self.progressDialog.setWindowModality(Qt.WindowModal)
+        self.progressDialog.setMinimumDuration(0)
+        self.progressDialog.resize(400, 300)
+        self.progressDialog.show()
+        QApplication.processEvents()
+
+        try:
+            self.vulnerability_map.set_working_directory(directory_2)
+            mask_arr = self.vulnerability_map.geometric_classification_alternative(self.in_fn_2, n_classes_2,
+                                                                                   self.mask_2, self.fmask_2)
+            self.vulnerability_map.array_to_image(self.in_fn_2, out_fn_2, mask_arr, gdal.GDT_Int16, -1)
+            self.vulnerability_map.replace_ref_system(self.in_fn_2, out_fn_2)
+
+            QMessageBox.information(self, "Processing Completed", "Processing completed!")
+
+            self.progressDialog.close()
+
+        except Exception:
+            self.progressDialog.close()
+            tb = traceback.format_exc()
+
+            error_box = QMessageBox(self)
+            error_box.setIcon(QMessageBox.Critical)
+            error_box.setWindowTitle("Error")
+            error_box.setText(f"<b>An Error Occurred During Processing</b>")
+            error_box.setTextInteractionFlags(Qt.TextSelectableByMouse | Qt.TextSelectableByKeyboard)
+            error_box.setDetailedText(tb)
+
+            details_frame = error_box.findChild(QTextEdit)
+            if details_frame:
+                details_frame.setSizePolicy(QSizePolicy.Expanding, QSizePolicy.Expanding)
+                details_frame.setMaximumHeight(800)
+                details_frame.setMaximumWidth(1000)
+                details_frame.setMinimumHeight(400)
+                details_frame.setMinimumWidth(600)
+
+            error_box_layout = error_box.layout()
+            error_box_layout.setContentsMargins(10, 10, 10, 10)
+
+            copy_button = QPushButton("Copy Error Message")
+            error_box.addButton(copy_button, QMessageBox.ActionRole)
+            def copy_error_txt():
+                QApplication.clipboard().setText(tb)
+            copy_button.clicked.connect(copy_error_txt)
+            error_box.exec_()
+
+    def update_progress(self, value):
+        # Update QProgressDialog with the new value
+        if self.progressDialog is not None:
+            self.progressDialog.setValue(value)
+
+class AT_PRE_CNF_Screen(QDialog):
+    def __init__(self):
+        super(AT_PRE_CNF_Screen, self).__init__()
+        self.initial_directory = os.getcwd()
+        loadUi(Path(PureWindowsPath("data\\at_pre_cnf_screen.ui")), self)
+        if central_data_store.directory is not None and self.folder_entry is not None:
+            self.directory = central_data_store.directory
+            self.folder_entry.setText(str(central_data_store.directory))
+        self.Intro_button3.clicked.connect(self.gotointro3)
+        self.RMT_button3.clicked.connect(self.gotormt3)
+        self.MCT_button3.clicked.connect(self.gotomct3)
+        self.doc_button.clicked.connect(self.openDocument)
+        self.select_folder_button.clicked.connect(self.select_working_directory)
+        self.municipality_button.clicked.connect(self.select_municipality)
+        self.csv_button.clicked.connect(self.select_csv)
+        self.risk30_vp_button.clicked.connect(self.select_risk30_vp)
+        self.deforestation_cnf_button.clicked.connect(self.select_deforestation_cnf)
+        self.ok_button3.clicked.connect(self.process_data3)
+        self.allocation_tool = AllocationTool()
+        self.allocation_tool.progress_updated.connect(self.update_progress)
+        self.directory = None
+        self.csv = None
+        self.municipality = None
+        self.risk30_vp = None
+        self.deforestation_cnf = None
+        self.max_iterations = None
+        self.image1 = None
+        self.image2 = None
+        self.file_path_directory = None
+        self.file_path1_directory = None
+        self.file_path2_directory = None
+        self.file_path3_directory = None
+        self.iteration_entry.setPlaceholderText('The suggestion max iteration number is 5')
+        self.image1_entry.setPlaceholderText('e.g., Acre_Prediction_Modeling_Region_CNF.tif')
+        self.image2_entry.setPlaceholderText('e.g., Acre_Adjucted_Density_Map_CNF.tif')
+        self.setWindowTitle("JNR Integrated Risk/Allocation Tool")
+
+    def gotormt3(self):
+        os.chdir(self.initial_directory)
+        rmt3 = RMT_PRE_CNF_SCREEN()
+        widget.addWidget(rmt3)
+        widget.setCurrentIndex(widget.currentIndex() + 1)
+
+    def gotointro3(self):
+        os.chdir(self.initial_directory)
+        intro3 = IntroScreen()
+        widget.addWidget(intro3)
+        widget.setCurrentIndex(widget.currentIndex() + 1)
+
+    def gotomct3(self):
+        os.chdir(self.initial_directory)
+        mct3 = MCT_PRE_CNF_Screen()
+        widget.addWidget(mct3)
+        widget.setCurrentIndex(widget.currentIndex() + 1)
+
+    def openDocument(self):
+        pdf_path = Path(PureWindowsPath("doc\\TestPreAM.pdf"))
+        QDesktopServices.openUrl(QUrl.fromLocalFile(str(pdf_path)))
+
+    def select_working_directory(self):
+        data_folder = QFileDialog.getExistingDirectory(self, "Working Directory")
+        data_folder_path = Path(data_folder)
+        self.directory = str(data_folder_path)
+        self.folder_entry.setText(self.directory)
+        central_data_store.directory = self.directory
+
+    def select_municipality(self):
+        file_path, _ = QFileDialog.getOpenFileName(self, 'Map of Administrative Divisions')
+        if file_path:
+            self.municipality = Path(PureWindowsPath(file_path))
+            self.municipality_entry.setText(file_path.split('/')[-1])
+            self.file_path_directory = '\\'.join(file_path.split('/')[:-1])
+    def select_csv(self):
+        file_path1, _ = QFileDialog.getOpenFileName(self, "CAL Relative Frequency Table (.csv)")
+        if file_path1:
+            self.csv = Path(PureWindowsPath(file_path1))
+            self.csv_entry.setText(file_path1.split('/')[-1])
+            self.file_path1_directory = '\\'.join(file_path1.split('/')[:-1])
+
+    def select_risk30_vp(self):
+        file_path2, _ = QFileDialog.getOpenFileName(self, "Vulnerability Map in CNF")
+        if file_path2:
+            self.risk30_vp = Path(PureWindowsPath(file_path2))
+            self.risk30_vp_entry.setText(file_path2.split('/')[-1])
+            self.file_path2_directory = '\\'.join(file_path2.split('/')[:-1])
+
+    def select_deforestation_cnf(self):
+        file_path3, _ = QFileDialog.getOpenFileName(self, "Map of Deforestation in CNF")
+        if file_path3:
+            self.deforestation_cnf = Path(PureWindowsPath(file_path3))
+            self.deforestation_cnf_entry.setText(file_path3.split('/')[-1])
+            self.file_path3_directory = '\\'.join(file_path3.split('/')[:-1])
+    def get_full_path(self, base_dir, user_input):
+        if os.path.isabs(user_input):
+            return user_input
+        else:
+            return f"{base_dir}\\{user_input}"
+
+    def process_data3(self):
+        directory = self.folder_entry.text()
+        central_data_store.directory = directory
+        if not directory:
+            QMessageBox.critical(self, "Error", "Please select or enter the working directory!")
+            return
+
+        if not self.file_path_directory:
+            self.file_path_directory = directory
+        if not self.file_path1_directory:
+            self.file_path1_directory = directory
+        if not self.file_path2_directory:
+            self.file_path2_directory = directory
+        if not self.file_path3_directory:
+            self.file_path3_directory = directory
+
+        self.municipality = self.get_full_path(self.file_path_directory, self.municipality_entry.text())
+        self.csv = self.get_full_path(self.file_path1_directory, self.csv_entry.text())
+        self.risk30_vp = self.get_full_path(self.file_path2_directory, self.risk30_vp_entry.text())
+        self.deforestation_cnf = self.get_full_path(self.file_path3_directory, self.deforestation_cnf_entry.text())
+
+        if not self.municipality or not self.csv or not self.deforestation_cnf or not self.risk30_vp:
+            QMessageBox.critical(self, "Error", "Please select or enter all input files!")
+            return
+
+        images = [self.municipality, self.deforestation_cnf, self.risk30_vp]
+
+        # Check if all images have the same resolution
+        resolutions = [map_checker.get_image_resolution(img) for img in images]
+        if len(set(resolutions)) != 1:
+            QMessageBox.critical(None, "Error", "All the input raster images must have the same spatial resolution!")
+            return
+
+        # Check if all images have the same number of rows and columns
+        dimensions = [map_checker.get_image_dimensions(img) for img in images]
+        if len(set(dimensions)) != 1:
+            QMessageBox.critical(None, "Error",
+                                 "All the input raster images must have the same number of rows and columns!")
+            return
+
+        out_fn1 = self.image1_entry.text()
+        if not out_fn1:
+            QMessageBox.critical(self, "Error", "Please enter the name of Prediction Modeling Region Map in CNF!")
+            return
+
+        if not (out_fn1.endswith('.tif') or out_fn1.endswith('.rst')):
+            QMessageBox.critical(self, "Error",
+                                 "Please enter .rst or .tif extension in the name of Prediction Modeling Region Map in CNF!")
+            return
+
+        out_fn2 = self.image2_entry.text()
+        if not out_fn2:
+            QMessageBox.critical(self, "Error", "Please enter the name of Adjusted Prediction Density Map in CNF!")
+            return
+
+        if not (out_fn2.endswith('.tif') or out_fn2.endswith('.rst')):
+            QMessageBox.critical(self, "Error",
+                                 "Please enter .rst or .tif extension in the name of Adjusted Prediction Density Map in CNF!")
+            return
+
+        max_iterations = self.iteration_entry.text()
+        if not max_iterations:
+            QMessageBox.critical(self, "Error", "Please enter the max iterations! The suggestion number is 5.")
+            return
+        try:
+            self.max_iterations = int(max_iterations)
+        except ValueError:
+            QMessageBox.critical(self, "Error", "Max iteration value should be a valid number!")
+            return
+
+        if not map_checker.check_binary_map(self.deforestation_cnf):
+            QMessageBox.critical(None, "Error",
+                                 "'MAP OF DEFORESTATION IN THE CNF' must be a binary map (0 and 1) where the 1’s indicate deforestation.")
+            return
+
+        # Show "Processing" message
+        processing_message = "Processing data..."
+        self.progressDialog = QProgressDialog(processing_message, None, 0, 100, self)
+
+        # Change the font size
+        font = QFont()
+        font.setPointSize(9)
+        self.progressDialog.setFont(font)
+
+        self.progressDialog.setWindowTitle("Processing")
+        self.progressDialog.setWindowModality(Qt.WindowModal)
+        self.progressDialog.setMinimumDuration(0)
+        self.progressDialog.resize(400, 300)
+        self.progressDialog.show()
+        QApplication.processEvents()
+
+        try:
+            id_difference,iteration_count = self.allocation_tool.execute_workflow_cnf(directory,
+                                                            self.max_iterations, self.csv,
+                                                            self.municipality,
+                                                            self.deforestation_cnf,
+                                                            self.risk30_vp, out_fn1,
+                                                            out_fn2)
+            if id_difference.size > 0:
+                QMessageBox.warning(self, " Warning ", f"Modeling Region ID {','.join(map(str, id_difference))} do not exist in the Calculation Period. A new CSV has been created for the CAL where relative frequencies for missing bins have been estimated from corresponding vulnerability zones over the entire jurisdiction.")
+            if iteration_count > int(max_iterations):
+                QMessageBox.warning(self, " Warning ", f"Maximum iterations limit reached. Please increase the Maximum Iterations and try running the tool again.")
+            else:
+                QMessageBox.information(self, "Processing Completed", "Processing completed!")
+            self.progressDialog.close()
+
+        except Exception:
+            self.progressDialog.close()
+            tb = traceback.format_exc()
+
+            error_box = QMessageBox(self)
+            error_box.setIcon(QMessageBox.Critical)
+            error_box.setWindowTitle("Error")
+            error_box.setText(f"<b>An Error Occurred During Processing</b>")
+            error_box.setTextInteractionFlags(Qt.TextSelectableByMouse | Qt.TextSelectableByKeyboard)
+            error_box.setDetailedText(tb)
+
+            details_frame = error_box.findChild(QTextEdit)
+            if details_frame:
+                details_frame.setSizePolicy(QSizePolicy.Expanding, QSizePolicy.Expanding)
+                details_frame.setMaximumHeight(800)
+                details_frame.setMaximumWidth(1000)
+                details_frame.setMinimumHeight(400)
+                details_frame.setMinimumWidth(600)
+
+            error_box_layout = error_box.layout()
+            error_box_layout.setContentsMargins(10, 10, 10, 10)
+
+            copy_button = QPushButton("Copy Error Message")
+            error_box.addButton(copy_button, QMessageBox.ActionRole)
+            def copy_error_txt():
+                QApplication.clipboard().setText(tb)
+            copy_button.clicked.connect(copy_error_txt)
+            error_box.exec_()
+
+    def update_progress(self, value):
+        # Update QProgressDialog with the new value
+        if self.progressDialog is not None:
+            self.progressDialog.setValue(value)
+
+class MCT_PRE_CNF_Screen(QDialog):
+    def __init__(self):
+        super(MCT_PRE_CNF_Screen, self).__init__()
+        # Store the initial directory path
+        self.initial_directory = os.getcwd()
+        loadUi(Path(PureWindowsPath("data\\mct_pre_cnf_screen.ui")), self)
+        if central_data_store.directory is not None and self.folder_entry is not None:
+            self.directory = central_data_store.directory
+            self.folder_entry.setText(str(central_data_store.directory))
+        self.AT_button4.clicked.connect(self.gotoat4)
+        self.Intro_button4.clicked.connect(self.gotointro4)
+        self.RMT_button4.clicked.connect(self.gotormt4)
+        self.doc_button.clicked.connect(self.openDocument)
+        self.select_folder_button.clicked.connect(self.select_working_directory)
+        self.mask_button.clicked.connect(self.select_mask)
+        self.fmask_button.clicked.connect(self.select_fmask)
+        self.deforestation_cal_button.clicked.connect(self.select_deforestation_cal)
+        self.deforestation_hrp_button.clicked.connect(self.select_deforestation_hrp)
+        self.density_button.clicked.connect(self.select_density)
+        self.ok_button.clicked.connect(self.process_data4)
+        self.model_evaluation = ModelEvaluation()
+        self.model_evaluation.progress_updated.connect(self.update_progress)
+        self.directory = None
+        self.mask = None
+        self.fmask = None
+        self.deforestation_cal = None
+        self.deforestation_hrp = None
+        self.density = None
+        self.grid_area = None
+        self.grid_area_entry.setPlaceholderText('Type default 100000 or other number')
+        self.title = None
+        self.out_fn = None
+        self.out_fn_def = None
+        self.raster_fn = None
+        self.file_path_directory = None
+        self.file_path1_directory = None
+        self.file_path2_directory = None
+        self.file_path3_directory = None
+        self.file_path4_directory = None
+        self.out_fn_entry.setPlaceholderText('e.g., Plot_CNF.png')
+        self.out_fn_def_entry.setPlaceholderText('e.g., Acre_Def_Review.tif')
+        self.raster_fn_entry.setPlaceholderText('e.g., Acre_Residuals_CNF.tif')
+        self.setWindowTitle("JNR Integrated Risk/Allocation Tool")
+
+    def gotoat4(self):
+        os.chdir(self.initial_directory)
+        at4 = AT_PRE_CNF_Screen()
+        widget.addWidget(at4)
+        widget.setCurrentIndex(widget.currentIndex() + 1)
+
+    def gotointro4(self):
+        os.chdir(self.initial_directory)
+        intro4 = IntroScreen()
+        widget.addWidget(intro4)
+        widget.setCurrentIndex(widget.currentIndex() + 1)
+
+    def gotormt4(self):
+        os.chdir(self.initial_directory)
+        rmt4 = RMT_PRE_CNF_SCREEN()
+        widget.addWidget(rmt4)
+        widget.setCurrentIndex(widget.currentIndex() + 1)
+
+    def openDocument(self):
+        pdf_path = Path(PureWindowsPath("doc\\TestPreMA.pdf"))
+        QDesktopServices.openUrl(QUrl.fromLocalFile(str(pdf_path)))
+
+    def select_working_directory(self):
+        data_folder = QFileDialog.getExistingDirectory(self, "Working Directory")
+        data_folder_path = Path(data_folder)
+        self.directory = str(data_folder_path)
+        self.folder_entry.setText(self.directory)
+        central_data_store.directory = self.directory
+
+    def select_mask(self):
+        file_path, _ = QFileDialog.getOpenFileName(self, 'Mask of Study Area')
+        if file_path:
+            self.mask = Path(PureWindowsPath(file_path))
+            self.mask_entry.setText(file_path.split('/')[-1])
+            self.file_path_directory = '\\'.join(file_path.split('/')[:-1])
+    def select_fmask(self):
+        file_path1, _ = QFileDialog.getOpenFileName(self, 'Mask of Forest Area')
+        if file_path1:
+            self.fmask = Path(PureWindowsPath(file_path1))
+            self.fmask_entry.setText(file_path1.split('/')[-1])
+            self.file_path1_directory = '\\'.join(file_path1.split('/')[:-1])
+
+    def select_deforestation_cal(self):
+        file_path2, _ = QFileDialog.getOpenFileName(self, "Actual Deforestation Map in CAL")
+        if file_path2:
+            self.deforestation_cal = Path(PureWindowsPath(file_path2))
+            self.deforestation_cal_entry.setText(file_path2.split('/')[-1])
+            self.file_path2_directory = '\\'.join(file_path2.split('/')[:-1])
+
+    def select_deforestation_hrp(self):
+        file_path3, _ = QFileDialog.getOpenFileName(self, "Actual Deforestation Map in CNF")
+        if file_path3:
+            self.deforestation_hrp = Path(PureWindowsPath(file_path3))
+            self.deforestation_hrp_entry.setText(file_path3.split('/')[-1])
+            self.file_path3_directory = '\\'.join(file_path3.split('/')[:-1])
+    def select_density(self):
+        file_path4, _ = QFileDialog.getOpenFileName(self, 'Adjusted Prediction Density Map in CNF')
+        if file_path4:
+            self.density = Path(PureWindowsPath(file_path4))
+            self.density_entry.setText(file_path4.split('/')[-1])
+            self.file_path4_directory = '\\'.join(file_path4.split('/')[:-1])
+
+    def get_full_path(self, base_dir, user_input):
+        if os.path.isabs(user_input):
+            return user_input
+        else:
+            return f"{base_dir}\\{user_input}"
+
+    def process_data4(self):
+        directory = self.folder_entry.text()
+        central_data_store.directory = directory
+        if not directory:
+            QMessageBox.critical(self, "Error", "Please select or enter the working directory!")
+            return
+
+        if not self.file_path_directory:
+            self.file_path_directory = directory
+        if not self.file_path1_directory:
+            self.file_path1_directory = directory
+        if not self.file_path2_directory:
+            self.file_path2_directory = directory
+        if not self.file_path3_directory:
+            self.file_path3_directory = directory
+        if not self.file_path4_directory:
+            self.file_path4_directory = directory
+
+        self.mask = self.get_full_path(self.file_path_directory, self.mask_entry.text())
+        self.fmask = self.get_full_path(self.file_path1_directory, self.fmask_entry.text())
+        self.deforestation_cal = self.get_full_path(self.file_path2_directory, self.deforestation_cal_entry.text())
+        self.deforestation_hrp = self.get_full_path(self.file_path3_directory, self.deforestation_hrp_entry.text())
+        self.density = self.get_full_path(self.file_path4_directory, self.density_entry.text())
+
+        if not self.mask or not self.fmask or not self.deforestation_cal or not self.deforestation_hrp or not self.density :
+            QMessageBox.critical(self, "Error", "Please select or enter all input files!")
+            return
+
+        images = [self.mask, self.fmask, self.deforestation_cal, self.deforestation_hrp, self.density]
+
+        # Check if all images have the same resolution
+        resolutions = [map_checker.get_image_resolution(img) for img in images]
+        if len(set(resolutions)) != 1:
+            QMessageBox.critical(None, "Error", "All the input raster images must have the same spatial resolution!")
+            return
+
+        # Check if all images have the same number of rows and columns
+        dimensions = [map_checker.get_image_dimensions(img) for img in images]
+        if len(set(dimensions)) != 1:
+            QMessageBox.critical(None, "Error",
+                                 "All the input raster images must have the same number of rows and columns!")
+            return
+
+        grid_area = self.grid_area_entry.text()
+        if not grid_area:
+            QMessageBox.critical(self, "Error", "Please enter the thiessen polygon grid area value!")
+            return
+        try:
+            self.grid_area = float(grid_area)
+            if not (0 < self.grid_area):
+                QMessageBox.critical(self, "Error", "Thiessen polygon grid area value should larger than 0!")
+                return
+        except ValueError:
+            QMessageBox.critical(self, "Error", "Thiessen polygon grid area value should be a valid number!")
+            return
+
+        xmax = self.xmax_entry.text()
+        if xmax.lower() != "default":
+            try:
+                xmax = float(xmax)
+                if xmax <= 0:
+                    raise ValueError("The plot x-axis limit should be larger than 0!")
+            except ValueError:
+                QMessageBox.critical(self, "Error", "The plot x-axis limit should be a valid number or 'Default'!")
+                return
+
+        ymax = self.ymax_entry.text()
+        if ymax.lower() != "default":
+            try:
+                ymax = float(ymax)
+                if ymax <= 0:
+                    raise ValueError("The plot y-axis limit should be larger than 0!")
+            except ValueError:
+                QMessageBox.critical(self, "Error", "The plot y-axis limit should be a valid number or 'Default'!")
+                return
+
+        title = self.title_entry.text()
+        if not title:
+            QMessageBox.critical(self, "Error", "Please enter the title of plot!")
+            return
+
+        out_fn = self.out_fn_entry.text()
+        if not out_fn:
+            QMessageBox.critical(self, "Error", "Please enter the name used for the plot, performace chart and assessment polygons!")
+            return
+
+        # Check if the out_fn has the correct file extension
+        if not (out_fn.endswith('.png') or out_fn.endswith('.jpg') or out_fn.endswith('.pdf') or out_fn.endswith(
+                '.svg') or out_fn.endswith('.eps') or out_fn.endswith('.ps') or out_fn.endswith('.tif')):
+            QMessageBox.critical(self, "Error",
+                                 "Please enter extension(.png/.jpg/.pdf/.svg/.eps/.ps/.tif) in the name of plot!")
+            return
+
+        raster_fn = self.raster_fn_entry.text()
+        if not raster_fn:
+            QMessageBox.critical(self, "Error", "Please enter the name for Residual Map!")
+            return
+
+        if not (raster_fn.endswith('.tif') or raster_fn.endswith('.rst')):
+            QMessageBox.critical(self, "Error",
+                                 "Please enter .rst or .tif extension in the name of Residual Map!")
+            return
+
+        out_fn_def = self.out_fn_def_entry.text()
+        if not out_fn_def:
+            QMessageBox.critical(self, "Error", "Please enter the name for Combined Deforestation Reference Map!")
+            return
+
+        if not (out_fn_def.endswith('.tif') or out_fn_def.endswith('.rst')):
+            QMessageBox.critical(self, "Error",
+                                 "Please enter .rst or .tif extension in the name of Combined Deforestation Reference Map!")
+            return
+
+        if not map_checker.check_binary_map(self.mask):
+            QMessageBox.critical(None, "Error",
+                                 "'MASK OF THE NON-EXCLUDED JURISDICTION' must be a binary map (0 and 1) where the 1’s indicate areas inside the jurisdiction.")
+            return
+
+        if not map_checker.check_binary_map(self.deforestation_hrp):
+            QMessageBox.critical(None, "Error",
+                                 "'MAP OF DEFORESTATION IN THE CNF' must be a binary map (0 and 1) where the 1’s indicate deforestation.")
+            return
+
+        if not map_checker.check_binary_map(self.deforestation_cal):
+            QMessageBox.critical(None, "Error",
+                                 "'MAP OF DEFORESTATION IN THE CAL' must be a binary map (0 and 1) where the 1’s indicate deforestation.")
+            return
+
+        if not map_checker.check_binary_map(self.fmask):
+            QMessageBox.critical(None, "Error",
+                                 "'MASK OF FOREST AREAS IN THE CAL' must be a binary map (0 and 1) where the 1’s indicate forest areas.")
+            return
+
+        # Show "Processing" message
+        processing_message = "Processing data..."
+        self.progressDialog = QProgressDialog(processing_message, None, 0, 100, self)
+
+        # Change the font size
+        font = QFont()
+        font.setPointSize(9)
+        self.progressDialog.setFont(font)
+
+        self.progressDialog.setWindowTitle("Processing")
+        self.progressDialog.setWindowModality(Qt.WindowModal)
+        self.progressDialog.setMinimumDuration(0)
+        self.progressDialog.resize(400, 300)
+        self.progressDialog.show()
+        QApplication.processEvents()
+
+        try:
+            self.model_evaluation.set_working_directory(directory)
+            self.model_evaluation.create_mask_polygon(self.mask)
+            clipped_gdf = self.model_evaluation.create_thiessen_polygon(self.grid_area, self.mask, self.density,
+                                                                             self.deforestation_hrp, out_fn, raster_fn)
+            self.model_evaluation.replace_ref_system(self.mask, raster_fn)
+            self.model_evaluation.create_deforestation_map(self.mask, self.fmask, self.deforestation_cal, self.deforestation_hrp,
+                                                           out_fn_def)
+            self.model_evaluation.replace_ref_system(self.fmask, out_fn_def)
+            self.model_evaluation.replace_legend(out_fn_def)
+            self.model_evaluation.create_plot(grid_area,clipped_gdf, title, out_fn, xmax, ymax)
+            self.model_evaluation.remove_temp_files()
+
+            QMessageBox.information(self, "Processing Completed", "Processing completed!")
+            self.progressDialog.close()
+
+        except Exception:
+            self.progressDialog.close()
+            tb = traceback.format_exc()
+
+            error_box = QMessageBox(self)
+            error_box.setIcon(QMessageBox.Critical)
+            error_box.setWindowTitle("Error")
+            error_box.setText(f"<b>An Error Occurred During Processing</b>")
+            error_box.setTextInteractionFlags(Qt.TextSelectableByMouse | Qt.TextSelectableByKeyboard)
+            error_box.setDetailedText(tb)
+
+            details_frame = error_box.findChild(QTextEdit)
+            if details_frame:
+                details_frame.setSizePolicy(QSizePolicy.Expanding, QSizePolicy.Expanding)
+                details_frame.setMaximumHeight(800)
+                details_frame.setMaximumWidth(1000)
+                details_frame.setMinimumHeight(400)
+                details_frame.setMinimumWidth(600)
+
+            error_box_layout = error_box.layout()
+            error_box_layout.setContentsMargins(10, 10, 10, 10)
+
+            copy_button = QPushButton("Copy Error Message")
+            error_box.addButton(copy_button, QMessageBox.ActionRole)
+            def copy_error_txt():
+                QApplication.clipboard().setText(tb)
+            copy_button.clicked.connect(copy_error_txt)
+            error_box.exec_()
+
+    def update_progress(self, value):
+        # Update QProgressDialog with the new value
+        if self.progressDialog is not None:
+            self.progressDialog.setValue(value)
+
+class RMT_FIT_HRP_SCREEN(QDialog):
+    def __init__(self):
+        super(RMT_FIT_HRP_SCREEN, self).__init__()
+        # Store the initial directory path
+        self.initial_directory = os.getcwd()
+        loadUi(Path(PureWindowsPath("data\\rmt_fit_hrp_screen.ui")), self)
+        if central_data_store.directory is not None and self.folder_entry is not None:
+            self.directory = central_data_store.directory
+            self.folder_entry.setText(str(central_data_store.directory))
+        if central_data_store.directory is not None and self.folder_entry_2 is not None:
+            self.directory_2 = central_data_store.directory
+            self.folder_entry_2.setText(str(central_data_store.directory))
+        self.AT_button2.clicked.connect(self.gotoat2)
+        self.Intro_button2.clicked.connect(self.gotointro2)
+
+        self.doc_button = self.tab1.findChild(QWidget, "doc_button")
+        self.select_folder_button = self.tab1.findChild(QWidget, "select_folder_button")
+        self.fd_button = self.tab1.findChild(QWidget, "fd_button")
+        self.mask_button = self.tab1.findChild(QWidget, "mask_button")
+        self.ok_button2 = self.tab1.findChild(QWidget, "ok_button2")
+
+        self.doc_button_2 = self.tab2.findChild(QWidget, "doc_button_2")
+        self.select_folder_button_2 = self.tab2.findChild(QWidget, "select_folder_button_2")
+        self.mask_button_2 = self.tab2.findChild(QWidget, "mask_button_2")
+        self.fmask_button_2 = self.tab2.findChild(QWidget, "fmask_button_2")
+        self.fd_button_2 = self.tab2.findChild(QWidget, "fd_button_2")
+        self.ok_button2_2 = self.tab2.findChild(QWidget, "ok_button2_2")
+
+        self.doc_button.clicked.connect(self.openDocument)
+        self.select_folder_button.clicked.connect(self.select_working_directory)
+        self.fd_button.clicked.connect(self.select_fd)
+        self.mask_button.clicked.connect(self.select_mask)
+        self.ok_button2.clicked.connect(self.process_data2)
+
+        self.doc_button_2.clicked.connect(self.openDocument_2)
+        self.select_folder_button_2.clicked.connect(self.select_working_directory_2)
+        self.mask_button_2.clicked.connect(self.select_mask_2)
+        self.fmask_button_2.clicked.connect(self.select_fmask_2)
+        self.fd_button_2.clicked.connect(self.select_fd_2)
+        self.ok_button2_2.clicked.connect(self.process_data2_2)
+
+        self.vulnerability_map = VulnerabilityMap()
+        self.vulnerability_map.progress_updated.connect(self.update_progress)
+        self.directory = None
+        self.in_fn = None
+        self.NRT = None
+        if central_data_store.NRT is not None:
+            self.nrt_entry.setText(str(central_data_store.NRT))
+        self.n_classes = None
+        self.mask = None
+        self.out_fn = None
+        self.out_fn_entry.setPlaceholderText('e.g., Acre_Vulnerability_HRP.tif')
+
+        self.directory_2 = None
+        self.mask_2 = None
+        self.fmask_2 = None
+        self.in_fn_2 = None
+        self.out_fn_2 = None
+        self.n_classes_2 = None
+        self.out_fn_entry_2.setPlaceholderText('e.g., Acre_Vulnerability_HRP.tif')
+        self.file_path_directory = None
+        self.file_path2_directory = None
+        self.file_path4_directory = None
+        self.file_path5_directory = None
+        self.file_path6_directory = None
+        self.setWindowTitle("JNR Integrated Risk/Allocation Tool")
+
+    def gotoat2(self):
+        os.chdir(self.initial_directory)
+        at2 = AT_FIT_HRP_Screen()
+        widget.addWidget(at2)
+        widget.setCurrentIndex(widget.currentIndex() + 1)
+
+    def gotointro2(self):
+        os.chdir(self.initial_directory)
+        intro2 = IntroScreen()
+        widget.addWidget(intro2)
+        widget.setCurrentIndex(widget.currentIndex() + 1)
+
+    def openDocument(self):
+        pdf_path = Path(PureWindowsPath("doc\\AppFitVM.pdf"))
+        QDesktopServices.openUrl(QUrl.fromLocalFile(str(pdf_path)))
+
+    def openDocument_2(self):
+        pdf_path = Path(PureWindowsPath("doc\\AppFitVM.pdf"))
+        QDesktopServices.openUrl(QUrl.fromLocalFile(str(pdf_path)))
+
+    def select_working_directory(self):
+        data_folder = QFileDialog.getExistingDirectory(self, "Working Directory")
+        data_folder_path = Path(data_folder)
+        self.directory = str(data_folder_path)
+        self.folder_entry.setText(self.directory)
+        self.folder_entry_2.setText(self.directory)
+        central_data_store.directory = self.directory
+
+    def select_fd(self):
+        file_path, _ = QFileDialog.getOpenFileName(self, 'Map of Distance from the Forest Edge in HRP')
+        if file_path:
+            self.in_fn = Path(PureWindowsPath(file_path))
+            self.in_fn_entry.setText(file_path.split('/')[-1])
+            self.file_path_directory = '\\'.join(file_path.split('/')[:-1])
+
+    def select_mask(self):
+        file_path2, _ = QFileDialog.getOpenFileName(self, 'Mask of Study Area')
+        if file_path2:
+            self.mask = Path(PureWindowsPath(file_path2))
+            self.mask_entry.setText(file_path2.split('/')[-1])
+            self.file_path2_directory = '\\'.join(file_path2.split('/')[:-1])
+
+    def select_working_directory_2(self):
+        data_folder_2 = QFileDialog.getExistingDirectory(self, "Working Directory")
+        data_folder_path_2 = Path(data_folder_2)
+        self.directory_2 = str(data_folder_path_2)
+        self.folder_entry_2.setText(self.directory_2)
+        self.folder_entry.setText(self.directory_2)
+        central_data_store.directory = self.directory_2
+
+    def select_fd_2(self):
+        file_path4, _ = QFileDialog.getOpenFileName(self, 'Map of Distance from the Forest Edge in HRP')
+        if file_path4:
+            self.in_fn_2 = Path(PureWindowsPath(file_path4))
+            self.in_fn_entry_2.setText(file_path4.split('/')[-1])
+            self.file_path4_directory = '\\'.join(file_path4.split('/')[:-1])
+
+    def select_mask_2(self):
+        file_path5, _ = QFileDialog.getOpenFileName(self, 'Mask of Study Area')
+        if file_path5:
+            self.mask_2 = Path(PureWindowsPath(file_path5))
+            self.mask_entry_2.setText(file_path5.split('/')[-1])
+            self.file_path5_directory = '\\'.join(file_path5.split('/')[:-1])
+
+    def select_fmask_2(self):
+        file_path6, _ = QFileDialog.getOpenFileName(self, 'Mask of Forest Area')
+        if file_path6:
+            self.fmask_2 = file_path6
+            self.fmask_entry_2.setText(file_path6.split('/')[-1])
+            self.file_path6_directory = '\\'.join(file_path6.split('/')[:-1])
+    def get_full_path(self, base_dir, user_input):
+        if os.path.isabs(user_input):
+            return user_input
+        else:
+            return f"{base_dir}\\{user_input}"
+    def process_data2(self):
+        directory = self.folder_entry.text()
+        central_data_store.directory = directory
+        self.folder_entry_2.setText(directory)
+        if not directory:
+            QMessageBox.critical(self, "Error", "Please select or enter the working directory!")
+            return
+        if not self.file_path_directory:
+            self.file_path_directory = directory
+        if not self.file_path2_directory:
+            self.file_path2_directory = directory
+        self.in_fn = self.get_full_path(self.file_path_directory, self.in_fn_entry.text())
+        self.mask = self.get_full_path(self.file_path2_directory, self.mask_entry.text())
+
+        if not self.in_fn or not self.mask:
+            QMessageBox.critical(self, "Error", "Please select or enter all input files!")
+            return
+
+        NRT = self.nrt_entry.text()
+        if not NRT:
+            QMessageBox.critical(self, "Error", "Please enter the NRT value!")
+            return
+        try:
+            self.NRT = int(NRT)
+            if (self.NRT <= 0):
+                QMessageBox.critical(self, "Error", "NRT value should be larger than 0!")
+                return
+        except ValueError:
+            QMessageBox.critical(self, "Error", "NRT value should be a valid number!")
+            return
+
+        n_classes = int(29)
+        if not n_classes:
+            QMessageBox.critical(self, "Error", "Please enter the number of classes!")
+            return
+        try:
+            self.n_classes = int(n_classes)
+            if (self.n_classes <= 0):
+                QMessageBox.critical(self, "Error", "Number of classes should be larger than 0!")
+                return
+        except ValueError:
+            QMessageBox.critical(self, "Error", "Number of classes value should be a valid number!")
+            return
+
+        out_fn = self.out_fn_entry.text()
+        if not out_fn:
+            QMessageBox.critical(self, "Error", "Please enter the name of Vulnerability Map in HRP!")
+            return
+
+        if not (out_fn.endswith('.tif') or out_fn.endswith('.rst')):
+            QMessageBox.critical(self, "Error",
+                                 "Please enter .rst or .tif extension in the name of Vulnerability Map in HRP!")
+            return
+
+        # Show "Processing" message
+        processing_message = "Processing data..."
+        self.progressDialog = QProgressDialog(processing_message, None, 0, 100, self)
+
+        # Change the font size
+        font = QFont()
+        font.setPointSize(9)
+        self.progressDialog.setFont(font)
+
+        self.progressDialog.setWindowTitle("Processing")
+        self.progressDialog.setWindowModality(Qt.WindowModal)
+        self.progressDialog.setMinimumDuration(0)
+        self.progressDialog.resize(400, 300)
+        self.progressDialog.show()
+        QApplication.processEvents()
+
+        try:
+            self.vulnerability_map.set_working_directory(directory)
+            mask_arr = self.vulnerability_map.geometric_classification(self.in_fn, NRT, n_classes, self.mask)
+            self.vulnerability_map.array_to_image(self.in_fn, out_fn, mask_arr, gdal.GDT_Int16, -1)
+            self.vulnerability_map.replace_ref_system(self.in_fn, out_fn)
+
+            QMessageBox.information(self, "Processing Completed", "Processing completed!")
+            self.progressDialog.close()
+
+        except Exception:
+            self.progressDialog.close()
+            tb = traceback.format_exc()
+
+            error_box = QMessageBox(self)
+            error_box.setIcon(QMessageBox.Critical)
+            error_box.setWindowTitle("Error")
+            error_box.setText(f"<b>An Error Occurred During Processing</b>")
+            error_box.setTextInteractionFlags(Qt.TextSelectableByMouse | Qt.TextSelectableByKeyboard)
+            error_box.setDetailedText(tb)
+
+            details_frame = error_box.findChild(QTextEdit)
+            if details_frame:
+                details_frame.setSizePolicy(QSizePolicy.Expanding, QSizePolicy.Expanding)
+                details_frame.setMaximumHeight(800)
+                details_frame.setMaximumWidth(1000)
+                details_frame.setMinimumHeight(400)
+                details_frame.setMinimumWidth(600)
+
+            error_box_layout = error_box.layout()
+            error_box_layout.setContentsMargins(10, 10, 10, 10)
+
+            copy_button = QPushButton("Copy Error Message")
+            error_box.addButton(copy_button, QMessageBox.ActionRole)
+            def copy_error_txt():
+                QApplication.clipboard().setText(tb)
+            copy_button.clicked.connect(copy_error_txt)
+            error_box.exec_()
+
+    def process_data2_2(self):
+        directory_2 = self.folder_entry_2.text()
+        central_data_store.directory = directory_2
+        self.folder_entry.setText(directory_2)
+        if not directory_2 :
+            QMessageBox.critical(self, "Error", "Please select or enter the working directory!")
+            return
+
+        if not self.file_path4_directory:
+            self.file_path4_directory = directory_2
+        if not self.file_path5_directory:
+            self.file_path5_directory = directory_2
+        if not self.file_path6_directory:
+            self.file_path6_directory = directory_2
+
+        self.in_fn_2 = self.get_full_path(self.file_path4_directory, self.in_fn_entry_2.text())
+        self.mask_2 = self.get_full_path(self.file_path5_directory, self.mask_entry_2.text())
+        self.fmask_2 = self.get_full_path(self.file_path6_directory, self.fmask_entry_2.text())
+
+        if not self.in_fn_2 or not self.mask_2 or not self.fmask_2:
+            QMessageBox.critical(self, "Error", "Please select or enter all input files!")
+            return
+
+        images = [self.in_fn_2, self.mask_2, self.fmask_2]
+
+        # Check if all images have the same resolution
+        resolutions = [map_checker.get_image_resolution(img) for img in images]
+        if len(set(resolutions)) != 1:
+            QMessageBox.critical(None, "Error", "All the input raster images must have the same spatial resolution!")
+            return
+
+        # Check if all images have the same number of rows and columns
+        dimensions = [map_checker.get_image_dimensions(img) for img in images]
+        if len(set(dimensions)) != 1:
+            QMessageBox.critical(None, "Error",
+                                 "All the input raster images must have the same number of rows and columns!")
+            return
+
+        n_classes_2 = int(30)
+        out_fn_2 = self.out_fn_entry_2.text()
+        if not out_fn_2:
+            QMessageBox.critical(self, "Error", "Please enter the name of Vulnerability Map in HRP!")
+            return
+
+        # Check if the out_fn has the correct file extension
+        if not (out_fn_2.endswith('.tif') or out_fn_2.endswith('.rst')):
+            QMessageBox.critical(self, "Error",
+                                 "Please enter .rst or .tif extension in the name of Vulnerability Map in HRP!")
+            return
+
+        if not map_checker.check_binary_map(self.mask_2):
+            QMessageBox.critical(None, "Error",
+                                 "'MASK OF THE NON-EXCLUDED JURISDICTION' must be a binary map (0 and 1) where the 1’s indicate areas inside the jurisdiction.")
+            return
+
+        if not map_checker.check_binary_map(self.fmask_2):
+            QMessageBox.critical(None, "Error",
+                                 "'MASK OF FOREST AREAS IN THE HRP' must be a binary map (0 and 1) where the 1’s indicate forest areas.")
+            return
+
+        # Show "Processing" message
+        processing_message = "Processing data..."
+        self.progressDialog = QProgressDialog(processing_message, None, 0, 100, self)
+
+        # Change the font size
+        font = QFont()
+        font.setPointSize(9)
+        self.progressDialog.setFont(font)
+
+        self.progressDialog.setWindowTitle("Processing")
+        self.progressDialog.setWindowModality(Qt.WindowModal)
+        self.progressDialog.setMinimumDuration(0)
+        self.progressDialog.resize(400, 300)
+        self.progressDialog.show()
+        QApplication.processEvents()
+
+        try:
+            self.vulnerability_map.set_working_directory(directory_2)
+            mask_arr = self.vulnerability_map.geometric_classification_alternative(self.in_fn_2, n_classes_2,
+                                                                                   self.mask_2, self.fmask_2)
+            self.vulnerability_map.array_to_image(self.in_fn_2, out_fn_2, mask_arr, gdal.GDT_Int16, -1)
+            self.vulnerability_map.replace_ref_system(self.in_fn_2, out_fn_2)
+
+            QMessageBox.information(self, "Processing Completed", "Processing completed!")
+
+            self.progressDialog.close()
+
+        except Exception:
+            self.progressDialog.close()
+            tb = traceback.format_exc()
+
+            error_box = QMessageBox(self)
+            error_box.setIcon(QMessageBox.Critical)
+            error_box.setWindowTitle("Error")
+            error_box.setText(f"<b>An Error Occurred During Processing</b>")
+            error_box.setTextInteractionFlags(Qt.TextSelectableByMouse | Qt.TextSelectableByKeyboard)
+            error_box.setDetailedText(tb)
+
+            details_frame = error_box.findChild(QTextEdit)
+            if details_frame:
+                details_frame.setSizePolicy(QSizePolicy.Expanding, QSizePolicy.Expanding)
+                details_frame.setMaximumHeight(800)
+                details_frame.setMaximumWidth(1000)
+                details_frame.setMinimumHeight(400)
+                details_frame.setMinimumWidth(600)
+
+            error_box_layout = error_box.layout()
+            error_box_layout.setContentsMargins(10, 10, 10, 10)
+
+            copy_button = QPushButton("Copy Error Message")
+            error_box.addButton(copy_button, QMessageBox.ActionRole)
+            def copy_error_txt():
+                QApplication.clipboard().setText(tb)
+            copy_button.clicked.connect(copy_error_txt)
+            error_box.exec_()
+
+    def update_progress(self, value):
+        # Update QProgressDialog with the new value
+        if self.progressDialog is not None:
+            self.progressDialog.setValue(value)
+
+class AT_FIT_HRP_Screen(QDialog):
+    def __init__(self):
+        super(AT_FIT_HRP_Screen, self).__init__()
+        self.initial_directory = os.getcwd()
+        loadUi(Path(PureWindowsPath("data\\at_fit_hrp_screen.ui")), self)
+        if central_data_store.directory is not None and self.folder_entry is not None:
+            self.directory = central_data_store.directory
+            self.folder_entry.setText(str(central_data_store.directory))
+        self.Intro_button3.clicked.connect(self.gotointro3)
+        self.RMT_button3.clicked.connect(self.gotormt3)
+        self.doc_button.clicked.connect(self.openDocument)
+        self.select_folder_button.clicked.connect(self.select_working_directory)
+        self.municipality_button.clicked.connect(self.select_municipality)
+        self.risk30_hrp_button.clicked.connect(self.select_risk30_hrp)
+        self.deforestation_hrp_button.clicked.connect(self.select_deforestation_hrp)
+        self.ok_button3.clicked.connect(self.process_data3)
+        self.allocation_tool = AllocationTool()
+        self.allocation_tool.progress_updated.connect(self.update_progress)
+        self.directory = None
+        self.risk30_hrp = None
+        self.municipality = None
+        self.deforestation_hrp = None
+        self.out_fn1 = None
+        self.out_fn2 = None
+        self.csv_name = None
+        self.file_path_directory = None
+        self.file_path1_directory = None
+        self.file_path3_directory = None
+        self.image1_entry.setPlaceholderText('e.g., Acre_Modeling_Region_HRP.tif')
+        self.csv_entry.setPlaceholderText('e.g., Relative_Frequency_Table_HRP.csv')
+        self.image2_entry.setPlaceholderText('e.g., Acre_Fitted_Density_Map_HRP.tif')
+
+        self.setWindowTitle("JNR Integrated Risk/Allocation Tool")
+
+    def gotormt3(self):
+        os.chdir(self.initial_directory)
+        rmt3 = RMT_FIT_HRP_SCREEN()
+        widget.addWidget(rmt3)
+        widget.setCurrentIndex(widget.currentIndex() + 1)
+
+    def gotointro3(self):
+        os.chdir(self.initial_directory)
+        intro3 = IntroScreen()
+        widget.addWidget(intro3)
+        widget.setCurrentIndex(widget.currentIndex() + 1)
+
+    def openDocument(self):
+        pdf_path = Path(PureWindowsPath("doc\\AppFitAM.pdf"))
+        QDesktopServices.openUrl(QUrl.fromLocalFile(str(pdf_path)))
+
+    def select_working_directory(self):
+        data_folder = QFileDialog.getExistingDirectory(self, "Working Directory")
+        data_folder_path = Path(data_folder)
+        self.directory = str(data_folder_path)
+        self.folder_entry.setText(self.directory)
+        central_data_store.directory = self.directory
+
+    def select_municipality(self):
+        file_path, _ = QFileDialog.getOpenFileName(self, 'Map of Administrative Divisions')
+        if file_path:
+            self.municipality = Path(PureWindowsPath(file_path))
+            self.municipality_entry.setText(file_path.split('/')[-1])
+            self.file_path_directory = '\\'.join(file_path.split('/')[:-1])
+
+    def select_risk30_hrp(self):
+        file_path1, _ = QFileDialog.getOpenFileName(self, "Vulnerability Map in HRP")
+        if file_path1:
+            self.risk30_hrp = Path(file_path1)
+            self.risk30_hrp_entry.setText(file_path1.split('/')[-1])
+            self.file_path1_directory = '\\'.join(file_path1.split('/')[:-1])
+    def select_deforestation_hrp(self):
+        file_path3, _ = QFileDialog.getOpenFileName(self, "Map of Deforestation in the HRP")
+        if file_path3:
+            self.deforestation_hrp = Path(file_path3)
+            self.deforestation_hrp_entry.setText(file_path3.split('/')[-1])
+            self.file_path3_directory = '\\'.join(file_path3.split('/')[:-1])
+    def get_full_path(self, base_dir, user_input):
+        if os.path.isabs(user_input):
+            return user_input
+        else:
+            return f"{base_dir}\\{user_input}"
+    def process_data3(self):
+        directory = self.folder_entry.text()
+        central_data_store.directory = directory
+        if not directory:
+            QMessageBox.critical(self, "Error", "Please select or enter the working directory!")
+            return
+        if not self.file_path_directory:
+            self.file_path_directory = directory
+        if not self.file_path1_directory:
+            self.file_path1_directory = directory
+        if not self.file_path3_directory:
+            self.file_path3_directory = directory
+
+        self.municipality = self.get_full_path(self.file_path_directory, self.municipality_entry.text())
+        self.risk30_hrp = self.get_full_path(self.file_path1_directory, self.risk30_hrp_entry.text())
+        self.deforestation_hrp = self.get_full_path(self.file_path3_directory, self.deforestation_hrp_entry.text())
+
+        if not self.risk30_hrp or not self.municipality or not self.deforestation_hrp:
+            QMessageBox.critical(self, "Error", "Please select or enter all input files!")
+            return
+
+        images = [self.risk30_hrp, self.municipality, self.deforestation_hrp]
+
+        # Check if all images have the same resolution
+        resolutions = [map_checker.get_image_resolution(img) for img in images]
+        if len(set(resolutions)) != 1:
+            QMessageBox.critical(None, "Error", "All the input raster images must have the same spatial resolution!")
+            return
+
+        # Check if all images have the same number of rows and columns
+        dimensions = [map_checker.get_image_dimensions(img) for img in images]
+        if len(set(dimensions)) != 1:
+            QMessageBox.critical(None, "Error",
+                                 "All the input raster images must have the same number of rows and columns!")
+            return
+
+        out_fn1 = self.image1_entry.text()
+        if not out_fn1:
+            QMessageBox.critical(self, "Error", "Please enter the name for Modeling Region Map in HRP!")
+            return
+
+        if not (out_fn1.endswith('.tif') or out_fn1.endswith('.rst')):
+            QMessageBox.critical(self, "Error",
+                                 "Please enter .rst or .tif extension in the name for Modeling Region Map in HRP!")
+            return
+
+        csv_name = self.csv_entry.text()
+        if not csv_name:
+            QMessageBox.critical(self, "Error", "Please enter the name for the Relative Frequency Table!")
+            return
+
+        if not (csv_name.endswith('.csv')):
+            QMessageBox.critical(self, "Error",
+                                 "Please enter .csv extension in the name of Relative Frequency Table!")
+            return
+
+        out_fn2 = self.image2_entry.text()
+        if not out_fn2:
+            QMessageBox.critical(self, "Error", "Please enter the name for Fitted Density Map in the HRP!")
+            return
+
+        if not (out_fn2.endswith('.tif') or out_fn2.endswith('.rst')):
+            QMessageBox.critical(self, "Error",
+                                 "Please enter .rst or .tif extension in the name of Fitted Density Map in the HRP!")
+            return
+
+        if not map_checker.check_binary_map(self.deforestation_hrp):
+            QMessageBox.critical(None, "Error",
+                                 "'MAP OF DEFORESTATION IN THE HRP' must be a binary map (0 and 1) where the 1’s indicate deforestation.")
+            return
+
+        # Show "Processing" message
+        processing_message = "Processing data..."
+        self.progressDialog = QProgressDialog(processing_message, None, 0, 100, self)
+
+        # Change the font size
+        font = QFont()
+        font.setPointSize(9)
+        self.progressDialog.setFont(font)
+
+        self.progressDialog.setWindowTitle("Processing")
+        self.progressDialog.setWindowModality(Qt.WindowModal)
+        self.progressDialog.setMinimumDuration(0)
+        self.progressDialog.resize(400, 300)
+        self.progressDialog.show()
+        QApplication.processEvents()
+
+        try:
+            self.allocation_tool.execute_workflow_fit(directory, self.risk30_hrp,
+                                                        self.municipality,self.deforestation_hrp, csv_name,
+                                                        out_fn1,out_fn2)
+            QMessageBox.information(self, "Processing Completed", "Processing completed!")
+            self.progressDialog.close()
+
+        except Exception:
+            self.progressDialog.close()
+            tb = traceback.format_exc()
+
+            error_box = QMessageBox(self)
+            error_box.setIcon(QMessageBox.Critical)
+            error_box.setWindowTitle("Error")
+            error_box.setText(f"<b>An Error Occurred During Processing</b>")
+            error_box.setTextInteractionFlags(Qt.TextSelectableByMouse | Qt.TextSelectableByKeyboard)
+            error_box.setDetailedText(tb)
+
+            details_frame = error_box.findChild(QTextEdit)
+            if details_frame:
+                details_frame.setSizePolicy(QSizePolicy.Expanding, QSizePolicy.Expanding)
+                details_frame.setMaximumHeight(800)
+                details_frame.setMaximumWidth(1000)
+                details_frame.setMinimumHeight(400)
+                details_frame.setMinimumWidth(600)
+
+            error_box_layout = error_box.layout()
+            error_box_layout.setContentsMargins(10, 10, 10, 10)
+
+            copy_button = QPushButton("Copy Error Message")
+            error_box.addButton(copy_button, QMessageBox.ActionRole)
+            def copy_error_txt():
+                QApplication.clipboard().setText(tb)
+            copy_button.clicked.connect(copy_error_txt)
+            error_box.exec_()
+
+    def update_progress(self, value):
+        # Update QProgressDialog with the new value
+        if self.progressDialog is not None:
+            self.progressDialog.setValue(value)
+
+
+class RMT_PRE_VP_SCREEN(QDialog):
+    def __init__(self):
+        super(RMT_PRE_VP_SCREEN, self).__init__()
+        # Store the initial directory path
+        self.initial_directory = os.getcwd()
+        loadUi(Path(PureWindowsPath("data\\rmt_pre_vp_screen.ui")), self)
+        if central_data_store.directory is not None and self.folder_entry is not None:
+            self.directory = central_data_store.directory
+            self.folder_entry.setText(str(central_data_store.directory))
+        if central_data_store.directory is not None and self.folder_entry_2 is not None:
+            self.directory_2 = central_data_store.directory
+            self.folder_entry_2.setText(str(central_data_store.directory))
+        self.AT_button2.clicked.connect(self.gotoat2)
+        self.Intro_button2.clicked.connect(self.gotointro2)
+
+        self.doc_button = self.tab1.findChild(QWidget, "doc_button")
+        self.select_folder_button = self.tab1.findChild(QWidget, "select_folder_button")
+        self.fd_button = self.tab1.findChild(QWidget, "fd_button")
+        self.mask_button = self.tab1.findChild(QWidget, "mask_button")
+        self.ok_button2 = self.tab1.findChild(QWidget, "ok_button2")
+
+        self.doc_button_2 = self.tab2.findChild(QWidget, "doc_button_2")
+        self.select_folder_button_2 = self.tab2.findChild(QWidget, "select_folder_button_2")
+        self.mask_button_2 = self.tab2.findChild(QWidget, "mask_button_2")
+        self.fmask_button_2 = self.tab2.findChild(QWidget, "fmask_button_2")
+        self.fd_button_2 = self.tab2.findChild(QWidget, "fd_button_2")
+        self.ok_button2_2 = self.tab2.findChild(QWidget, "ok_button2_2")
+
+        self.doc_button.clicked.connect(self.openDocument)
+        self.select_folder_button.clicked.connect(self.select_working_directory)
+        self.fd_button.clicked.connect(self.select_fd)
+        self.mask_button.clicked.connect(self.select_mask)
+        self.ok_button2.clicked.connect(self.process_data2)
+
+        self.doc_button_2.clicked.connect(self.openDocument_2)
+        self.select_folder_button_2.clicked.connect(self.select_working_directory_2)
+        self.mask_button_2.clicked.connect(self.select_mask_2)
+        self.fmask_button_2.clicked.connect(self.select_fmask_2)
+        self.fd_button_2.clicked.connect(self.select_fd_2)
+        self.ok_button2_2.clicked.connect(self.process_data2_2)
+
+        self.vulnerability_map = VulnerabilityMap()
+        self.vulnerability_map.progress_updated.connect(self.update_progress)
+        self.directory = None
+        self.in_fn = None
+        self.NRT = None
+        if central_data_store.NRT is not None:
+            self.nrt_entry.setText(str(central_data_store.NRT))
+        self.n_classes = None
+        self.mask = None
+        self.out_fn = None
+        self.out_fn_entry.setPlaceholderText('e.g., Acre_Vulnerability_VP.tif')
+
+        self.directory_2 = None
+        self.mask_2 = None
+        self.fmask_2 = None
+        self.in_fn_2 = None
+        self.out_fn_2 = None
+        self.n_classes_2 = None
+        self.file_path_directory = None
+        self.file_path2_directory = None
+        self.file_path4_directory = None
+        self.file_path5_directory = None
+        self.file_path6_directory = None
+        self.out_fn_entry_2.setPlaceholderText('e.g., Acre_Vulnerability_VP.tif')
+
+        self.setWindowTitle("JNR Integrated Risk/Allocation Tool")
+
+    def gotoat2(self):
+        os.chdir(self.initial_directory)
+        at2 = AT_PRE_VP_Screen()
+        widget.addWidget(at2)
+        widget.setCurrentIndex(widget.currentIndex() + 1)
+
+    def gotointro2(self):
+        os.chdir(self.initial_directory)
+        intro2 = IntroScreen()
+        widget.addWidget(intro2)
+        widget.setCurrentIndex(widget.currentIndex() + 1)
+
+    def openDocument(self):
+        pdf_path = Path(PureWindowsPath("doc\\AppPreVM.pdf"))
+        QDesktopServices.openUrl(QUrl.fromLocalFile(str(pdf_path)))
+
+    def openDocument_2(self):
+        pdf_path = Path(PureWindowsPath("doc\\AppPreVM.pdf"))
+        QDesktopServices.openUrl(QUrl.fromLocalFile(str(pdf_path)))
+
+    def select_working_directory(self):
+        data_folder = QFileDialog.getExistingDirectory(self, "Working Directory")
+        data_folder_path = Path(data_folder)
+        self.directory = str(data_folder_path)
+        self.folder_entry.setText(self.directory)
+        self.folder_entry_2.setText(self.directory)
+        central_data_store.directory = self.directory
+
+    def select_fd(self):
+        file_path, _ = QFileDialog.getOpenFileName(self, 'Map of Distance from the Forest Edge in VP')
+        if file_path:
+            self.in_fn = Path(PureWindowsPath(file_path))
+            self.in_fn_entry.setText(file_path.split('/')[-1])
+            self.file_path_directory = '\\'.join(file_path.split('/')[:-1])
+
+    def select_mask(self):
+        file_path2, _ = QFileDialog.getOpenFileName(self, 'Mask of Study Area')
+        if file_path2:
+            self.mask = Path(PureWindowsPath(file_path2))
+            self.mask_entry.setText(file_path2.split('/')[-1])
+            self.file_path2_directory = '\\'.join(file_path2.split('/')[:-1])
+    def select_working_directory_2(self):
+        data_folder_2 = QFileDialog.getExistingDirectory(self, "Working Directory")
+        data_folder_path_2 = Path(data_folder_2)
+        self.directory_2 = str(data_folder_path_2)
+        self.folder_entry_2.setText(self.directory_2)
+        self.folder_entry.setText(self.directory_2)
+        central_data_store.directory = self.directory_2
+
+    def select_fd_2(self):
+        file_path4, _ = QFileDialog.getOpenFileName(self, 'Map of Distance from the Forest Edge in VP')
+        if file_path4:
+            self.in_fn_2 = Path(PureWindowsPath(file_path4))
+            self.in_fn_entry_2.setText(file_path4.split('/')[-1])
+            self.file_path4_directory = '\\'.join(file_path4.split('/')[:-1])
+
+    def select_mask_2(self):
+        file_path5, _ = QFileDialog.getOpenFileName(self, 'Mask of Study Area')
+        if file_path5:
+            self.mask_2 = Path(PureWindowsPath(file_path5))
+            self.mask_entry_2.setText(file_path5.split('/')[-1])
+            self.file_path5_directory = '\\'.join(file_path5.split('/')[:-1])
+
+    def select_fmask_2(self):
+        file_path6, _ = QFileDialog.getOpenFileName(self, 'Mask of Forest Area')
+        if file_path6:
+            self.fmask_2 = file_path6
+            self.fmask_entry_2.setText(file_path6.split('/')[-1])
+            self.file_path6_directory = '\\'.join(file_path6.split('/')[:-1])
+    def get_full_path(self, base_dir, user_input):
+        if os.path.isabs(user_input):
+            return user_input
+        else:
+            return f"{base_dir}\\{user_input}"
+    def process_data2(self):
+        directory = self.folder_entry.text()
+        central_data_store.directory = directory
+        self.folder_entry_2.setText(directory)
+        if not directory:
+            QMessageBox.critical(self, "Error", "Please select or enter the working directory!")
+            return
+
+        if not self.file_path_directory:
+            self.file_path_directory = directory
+        if not self.file_path2_directory:
+            self.file_path2_directory = directory
+
+        self.in_fn = self.get_full_path(self.file_path_directory, self.in_fn_entry.text())
+        self.mask = self.get_full_path(self.file_path2_directory, self.mask_entry.text())
+
+        if not self.in_fn or not self.mask:
+            QMessageBox.critical(self, "Error", "Please select or enter all input files!")
+            return
+
+        NRT = self.nrt_entry.text()
+        if not NRT:
+            QMessageBox.critical(self, "Error", "Please enter the NRT value!")
+            return
+        try:
+            self.NRT = int(NRT)
+            if (self.NRT <= 0):
+                QMessageBox.critical(self, "Error", "NRT value should be larger than 0!")
+                return
+        except ValueError:
+            QMessageBox.critical(self, "Error", "NRT value should be a valid number!")
+            return
+
+        n_classes = int(29)
+        if not n_classes:
+            QMessageBox.critical(self, "Error", "Please enter the number of classes!")
+            return
+        try:
+            self.n_classes = int(n_classes)
+            if (self.n_classes <= 0):
+                QMessageBox.critical(self, "Error", "Number of classes should be larger than 0!")
+                return
+        except ValueError:
+            QMessageBox.critical(self, "Error", "Number of classes value should be a valid number!")
+            return
+
+        out_fn = self.out_fn_entry.text()
+        if not out_fn:
+            QMessageBox.critical(self, "Error", "Please enter the name of Vulnerability Map in VP!")
+            return
+
+        if not (out_fn.endswith('.tif') or out_fn.endswith('.rst')):
+            QMessageBox.critical(self, "Error",
+                                 "Please enter .rst or .tif extension in the name of Vulnerability Map in VP!")
+            return
+
+        # Show "Processing" message
+        processing_message = "Processing data..."
+        self.progressDialog = QProgressDialog(processing_message, None, 0, 100, self)
+
+        # Change the font size
+        font = QFont()
+        font.setPointSize(9)
+        self.progressDialog.setFont(font)
+
+        self.progressDialog.setWindowTitle("Processing")
+        self.progressDialog.setWindowModality(Qt.WindowModal)
+        self.progressDialog.setMinimumDuration(0)
+        self.progressDialog.resize(400, 300)
+        self.progressDialog.show()
+        QApplication.processEvents()
+
+        try:
+            self.vulnerability_map.set_working_directory(directory)
+            mask_arr = self.vulnerability_map.geometric_classification(self.in_fn, NRT, n_classes, self.mask)
+            self.vulnerability_map.array_to_image(self.in_fn, out_fn, mask_arr, gdal.GDT_Int16, -1)
+            self.vulnerability_map.replace_ref_system(self.in_fn, out_fn)
+
+            QMessageBox.information(self, "Processing Completed", "Processing completed!")
+            self.progressDialog.close()
+
+        except Exception:
+            self.progressDialog.close()
+            tb = traceback.format_exc()
+
+            error_box = QMessageBox(self)
+            error_box.setIcon(QMessageBox.Critical)
+            error_box.setWindowTitle("Error")
+            error_box.setText(f"<b>An Error Occurred During Processing</b>")
+            error_box.setTextInteractionFlags(Qt.TextSelectableByMouse | Qt.TextSelectableByKeyboard)
+            error_box.setDetailedText(tb)
+
+            details_frame = error_box.findChild(QTextEdit)
+            if details_frame:
+                details_frame.setSizePolicy(QSizePolicy.Expanding, QSizePolicy.Expanding)
+                details_frame.setMaximumHeight(800)
+                details_frame.setMaximumWidth(1000)
+                details_frame.setMinimumHeight(400)
+                details_frame.setMinimumWidth(600)
+
+            error_box_layout = error_box.layout()
+            error_box_layout.setContentsMargins(10, 10, 10, 10)
+
+            copy_button = QPushButton("Copy Error Message")
+            error_box.addButton(copy_button, QMessageBox.ActionRole)
+            def copy_error_txt():
+                QApplication.clipboard().setText(tb)
+            copy_button.clicked.connect(copy_error_txt)
+            error_box.exec_()
+
+    def process_data2_2(self):
+        directory_2 = self.folder_entry_2.text()
+        central_data_store.directory = directory_2
+        self.folder_entry.setText(directory_2)
+        if not directory_2 :
+            QMessageBox.critical(self, "Error", "Please select or enter the working directory!")
+            return
+
+        if not self.file_path4_directory:
+            self.file_path4_directory = directory_2
+        if not self.file_path5_directory:
+            self.file_path5_directory = directory_2
+        if not self.file_path6_directory:
+            self.file_path6_directory = directory_2
+
+        self.in_fn_2 = self.get_full_path(self.file_path4_directory, self.in_fn_entry_2.text())
+        self.mask_2 = self.get_full_path(self.file_path5_directory, self.mask_entry_2.text())
+        self.fmask_2 = self.get_full_path(self.file_path6_directory, self.fmask_entry_2.text())
+
+        if not self.in_fn_2 or not self.mask_2 or not self.fmask_2:
+            QMessageBox.critical(self, "Error", "Please select or enter all input files!")
+            return
+
+        images = [self.in_fn_2, self.mask_2, self.fmask_2]
+
+        # Check if all images have the same resolution
+        resolutions = [map_checker.get_image_resolution(img) for img in images]
+        if len(set(resolutions)) != 1:
+            QMessageBox.critical(None, "Error", "All the input raster images must have the same spatial resolution!")
+            return
+
+        # Check if all images have the same number of rows and columns
+        dimensions = [map_checker.get_image_dimensions(img) for img in images]
+        if len(set(dimensions)) != 1:
+            QMessageBox.critical(None, "Error",
+                                 "All the input raster images must have the same number of rows and columns!")
+            return
+
+        n_classes_2 = int(30)
+        out_fn_2 = self.out_fn_entry_2.text()
+        if not out_fn_2:
+            QMessageBox.critical(self, "Error", "Please enter the name of Vulnerability Map in VP!")
+            return
+
+        # Check if the out_fn has the correct file extension
+        if not (out_fn_2.endswith('.tif') or out_fn_2.endswith('.rst')):
+            QMessageBox.critical(self, "Error",
+                                 "Please enter .rst or .tif extension in the name of Vulnerability Map in VP!")
+            return
+
+        if not map_checker.check_binary_map(self.mask_2):
+            QMessageBox.critical(None, "Error",
+                                 "'MASK OF THE NON-EXCLUDED JURISDICTION' must be a binary map (0 and 1) where the 1’s indicate areas inside the jurisdiction.")
+            return
+
+        if not map_checker.check_binary_map(self.fmask_2):
+            QMessageBox.critical(None, "Error",
+                                 "'MASK OF FOREST AREAS IN THE VP' must be a binary map (0 and 1) where the 1’s indicate forest areas.")
+            return
+
+        # Show "Processing" message
+        processing_message = "Processing data..."
+        self.progressDialog = QProgressDialog(processing_message, None, 0, 100, self)
+
+        # Change the font size
+        font = QFont()
+        font.setPointSize(9)
+        self.progressDialog.setFont(font)
+
+        self.progressDialog.setWindowTitle("Processing")
+        self.progressDialog.setWindowModality(Qt.WindowModal)
+        self.progressDialog.setMinimumDuration(0)
+        self.progressDialog.resize(400, 300)
+        self.progressDialog.show()
+        QApplication.processEvents()
+
+        try:
+            self.vulnerability_map.set_working_directory(directory_2)
+            mask_arr = self.vulnerability_map.geometric_classification_alternative(self.in_fn_2, n_classes_2,
+                                                                                   self.mask_2, self.fmask_2)
+            self.vulnerability_map.array_to_image(self.in_fn_2, out_fn_2, mask_arr, gdal.GDT_Int16, -1)
+            self.vulnerability_map.replace_ref_system(self.in_fn_2, out_fn_2)
+
+            QMessageBox.information(self, "Processing Completed", "Processing completed!")
+
+            self.progressDialog.close()
+
+        except Exception:
+            self.progressDialog.close()
+            tb = traceback.format_exc()
+
+            error_box = QMessageBox(self)
+            error_box.setIcon(QMessageBox.Critical)
+            error_box.setWindowTitle("Error")
+            error_box.setText(f"<b>An Error Occurred During Processing</b>")
+            error_box.setTextInteractionFlags(Qt.TextSelectableByMouse | Qt.TextSelectableByKeyboard)
+            error_box.setDetailedText(tb)
+
+            details_frame = error_box.findChild(QTextEdit)
+            if details_frame:
+                details_frame.setSizePolicy(QSizePolicy.Expanding, QSizePolicy.Expanding)
+                details_frame.setMaximumHeight(800)
+                details_frame.setMaximumWidth(1000)
+                details_frame.setMinimumHeight(400)
+                details_frame.setMinimumWidth(600)
+
+            error_box_layout = error_box.layout()
+            error_box_layout.setContentsMargins(10, 10, 10, 10)
+
+            copy_button = QPushButton("Copy Error Message")
+            error_box.addButton(copy_button, QMessageBox.ActionRole)
+            def copy_error_txt():
+                QApplication.clipboard().setText(tb)
+            copy_button.clicked.connect(copy_error_txt)
+            error_box.exec_()
+
+    def update_progress(self, value):
+        # Update QProgressDialog with the new value
+        if self.progressDialog is not None:
+            self.progressDialog.setValue(value)
+
+class AT_PRE_VP_Screen(QDialog):
+    def __init__(self):
+        super(AT_PRE_VP_Screen, self).__init__()
+        self.initial_directory = os.getcwd()
+        loadUi(Path(PureWindowsPath("data\\at_pre_vp_screen.ui")), self)
+        if central_data_store.directory is not None and self.folder_entry is not None:
+            self.directory = central_data_store.directory
+            self.folder_entry.setText(str(central_data_store.directory))
+        self.Intro_button3.clicked.connect(self.gotointro3)
+        self.RMT_button3.clicked.connect(self.gotormt3)
+        self.doc_button.clicked.connect(self.openDocument)
+        self.select_folder_button.clicked.connect(self.select_working_directory)
+        self.municipality_button.clicked.connect(self.select_municipality)
+        self.csv_button.clicked.connect(self.select_csv)
+        self.risk30_vp_button.clicked.connect(self.select_risk30_vp)
+        self.ok_button3.clicked.connect(self.process_data3)
+        self.allocation_tool = AllocationTool()
+        # Connect the progress_updated signal to the update_progress method
+        self.allocation_tool.progress_updated.connect(self.update_progress)
+        self.directory = None
+        self.csv = None
+        self.municipality = None
+        self.risk30_vp = None
+        self.expected_deforestation = None
+        self.max_iterations = None
+        self.image1 = None
+        self.image2 = None
+        self.file_path_directory = None
+        self.file_path1_directory = None
+        self.file_path2_directory = None
+        self.iteration_entry.setPlaceholderText('The suggestion max iteration number is 5')
+        self.image1_entry.setPlaceholderText('e.g., Acre_Prediction_Modeling_Region_VP.tif')
+        self.image2_entry.setPlaceholderText('e.g., Acre_Adjucted_Density_Map_VP.tif')
+        self.setWindowTitle("JNR Integrated Risk/Allocation Tool")
+
+    def gotormt3(self):
+        os.chdir(self.initial_directory)
+        rmt3 = RMT_PRE_VP_SCREEN()
+        widget.addWidget(rmt3)
+        widget.setCurrentIndex(widget.currentIndex() + 1)
+
+    def gotointro3(self):
+        os.chdir(self.initial_directory)
+        intro3 = IntroScreen()
+        widget.addWidget(intro3)
+        widget.setCurrentIndex(widget.currentIndex() + 1)
+
+    def openDocument(self):
+        pdf_path = Path(PureWindowsPath("doc\\AppPreAM.pdf"))
+        QDesktopServices.openUrl(QUrl.fromLocalFile(str(pdf_path)))
+
+    def select_working_directory(self):
+        data_folder = QFileDialog.getExistingDirectory(self, "Working Directory")
+        data_folder_path = Path(data_folder)
+        self.directory = str(data_folder_path)
+        self.folder_entry.setText(self.directory)
+        central_data_store.directory = self.directory
+
+    def select_municipality(self):
+        file_path, _ = QFileDialog.getOpenFileName(self, 'Map of Administrative Divisions')
+        if file_path:
+            self.municipality = Path(PureWindowsPath(file_path))
+            self.municipality_entry.setText(file_path.split('/')[-1])
+            self.file_path_directory = '\\'.join(file_path.split('/')[:-1])
+
+    def select_csv(self):
+        file_path1, _ = QFileDialog.getOpenFileName(self, "VP Relative Frequency Table (.csv)")
+        if file_path1:
+            self.csv = Path(PureWindowsPath(file_path1))
+            self.csv_entry.setText(file_path1.split('/')[-1])
+            self.file_path1_directory = '\\'.join(file_path1.split('/')[:-1])
+
+    def select_risk30_vp(self):
+        file_path2, _ = QFileDialog.getOpenFileName(self, "Vulnerability Map in VP")
+        if file_path2:
+            self.risk30_vp = Path(PureWindowsPath(file_path2))
+            self.risk30_vp_entry.setText(file_path2.split('/')[-1])
+            self.file_path2_directory = '\\'.join(file_path2.split('/')[:-1])
+    def get_full_path(self, base_dir, user_input):
+        if os.path.isabs(user_input):
+            return user_input
+        else:
+            return f"{base_dir}\\{user_input}"
+    def process_data3(self):
+        directory = self.folder_entry.text()
+        central_data_store.directory = directory
+        if not directory:
+            QMessageBox.critical(self, "Error", "Please select or enter the working directory!")
+            return
+        if not self.file_path_directory:
+            self.file_path_directory = directory
+        if not self.file_path1_directory:
+            self.file_path1_directory = directory
+        if not self.file_path2_directory:
+            self.file_path2_directory = directory
+
+        self.municipality = self.get_full_path(self.file_path_directory, self.municipality_entry.text())
+        self.csv = self.get_full_path(self.file_path1_directory, self.csv_entry.text())
+        self.risk30_vp = self.get_full_path(self.file_path2_directory, self.risk30_vp_entry.text())
+
+        if not self.csv or not self.municipality or not self.risk30_vp:
+            QMessageBox.critical(self, "Error", "Please select or enter all input files!")
+            return
+
+        images = [self.municipality, self.risk30_vp]
+
+        # Check if all images have the same resolution
+        resolutions = [map_checker.get_image_resolution(img) for img in images]
+        if len(set(resolutions)) != 1:
+            QMessageBox.critical(None, "Error", "All the input raster images must have the same spatial resolution!")
+            return
+
+        # Check if all images have the same number of rows and columns
+        dimensions = [map_checker.get_image_dimensions(img) for img in images]
+        if len(set(dimensions)) != 1:
+            QMessageBox.critical(None, "Error",
+                                 "All the input raster images must have the same number of rows and columns!")
+            return
+
+        expected_deforestation = self.expected_entry.text()
+        if not expected_deforestation:
+            QMessageBox.critical(self, "Error", "Please enter the expected annual jurisdictional deforestation rate (ha/year)!")
+            return
+        try:
+            self.expected_deforestation = float(expected_deforestation)
+        except ValueError:
+            QMessageBox.critical(self, "Error", "Expected annual jurisdictional deforestation rate should be a valid number!")
+            return
+
+        out_fn1 = self.image1_entry.text()
+        if not out_fn1:
+            QMessageBox.critical(self, "Error", "Please enter the name of Prediction Modeling Region Map in VP!")
+            return
+
+        if not (out_fn1.endswith('.tif') or out_fn1.endswith('.rst')):
+            QMessageBox.critical(self, "Error",
+                                 "Please enter .rst or .tif extension in the name of Prediction Modeling Region Map in VP!")
+            return
+
+        out_fn2 = self.image2_entry.text()
+        if not out_fn2:
+            QMessageBox.critical(self, "Error", "Please enter the name of Adjusted Prediction Density Map in VP!")
+            return
+
+        if not (out_fn2.endswith('.tif') or out_fn2.endswith('.rst')):
+            QMessageBox.critical(self, "Error",
+                                 "Please enter .rst or .tif extension in the name of Adjusted Prediction Density Map in VP!")
+            return
+
+        max_iterations = self.iteration_entry.text()
+        if not max_iterations:
+            QMessageBox.critical(self, "Error", "Please enter the max iterations! The suggestion number is 5.")
+            return
+        try:
+            self.max_iterations = int(max_iterations)
+        except ValueError:
+            QMessageBox.critical(self, "Error", "Max iteration value should be a valid number!")
+            return
+
+        # Show "Processing" message
+        processing_message = "Processing data..."
+        self.progressDialog = QProgressDialog(processing_message, None, 0, 100, self)
+
+        # Change the font size
+        font = QFont()
+        font.setPointSize(9)
+        self.progressDialog.setFont(font)
+
+        self.progressDialog.setWindowTitle("Processing")
+        self.progressDialog.setWindowModality(Qt.WindowModal)
+        self.progressDialog.setMinimumDuration(0)
+        self.progressDialog.resize(400, 300)
+        self.progressDialog.show()
+        QApplication.processEvents()
+
+        try:
+            id_difference,iteration_count = self.allocation_tool.execute_workflow_vp(directory, self.max_iterations,
+                                                                           self.csv,
+                                                                           self.municipality,
+                                                                           self.expected_deforestation,
+                                                                           self.risk30_vp, out_fn1,out_fn2)
+
+            if id_difference.size > 0:
+                QMessageBox.warning(self, " Warning ", f"Modeling Region ID {','.join(map(str, id_difference))} do not exist in the Historical Reference Period. A new CSV has been created for the HRP where relative frequencies for missing bins have been estimated from corresponding vulnerability zones over the entire jurisdiction.")
+            if iteration_count > int(max_iterations):
+                QMessageBox.warning(self, " Warning ",
+                                    f"Maximum iterations limit reached. Please increase the Maximum Iterations and try running the tool again.")
+            else:
+                QMessageBox.information(self, "Processing Completed", "Processing completed!")
+            self.progressDialog.close()
+
+        except Exception:
+            self.progressDialog.close()
+            tb = traceback.format_exc()
+
+            error_box = QMessageBox(self)
+            error_box.setIcon(QMessageBox.Critical)
+            error_box.setWindowTitle("Error")
+            error_box.setText(f"<b>An Error Occurred During Processing</b>")
+            error_box.setTextInteractionFlags(Qt.TextSelectableByMouse | Qt.TextSelectableByKeyboard)
+            error_box.setDetailedText(tb)
+
+            details_frame = error_box.findChild(QTextEdit)
+            if details_frame:
+                details_frame.setSizePolicy(QSizePolicy.Expanding, QSizePolicy.Expanding)
+                details_frame.setMaximumHeight(800)
+                details_frame.setMaximumWidth(1000)
+                details_frame.setMinimumHeight(400)
+                details_frame.setMinimumWidth(600)
+
+            error_box_layout = error_box.layout()
+            error_box_layout.setContentsMargins(10, 10, 10, 10)
+
+            copy_button = QPushButton("Copy Error Message")
+            error_box.addButton(copy_button, QMessageBox.ActionRole)
+            def copy_error_txt():
+                QApplication.clipboard().setText(tb)
+            copy_button.clicked.connect(copy_error_txt)
+            error_box.exec_()
+
+    def update_progress(self, value):
+        # Update QProgressDialog with the new value
+        if self.progressDialog is not None:
+            self.progressDialog.setValue(value)
+
+class CentralDataStore:
+    def __init__(self):
+        self.NRT = None
+        self.directory = None
+
+class MapChecker:
+    def __init__(self):
+        self.image=None
+        self.arr=None
+        self.in_fn=None
+
+    def get_image_resolution(self,image):
+        in_ds = gdal.Open(image)
+        P = in_ds.GetGeoTransform()[1]
+        return P
+
+    def get_image_dimensions(self, image):
+        dataset = gdal.Open(image)
+        cols = dataset.RasterXSize
+        rows = dataset.RasterYSize
+        return rows, cols
+
+    def get_image_datatype(self, image):
+        in_ds = gdal.Open(image)
+        in_band = in_ds.GetRasterBand(1)
+        datatype = gdal.GetDataTypeName(in_band.DataType)
+        return datatype
+
+    def get_image_max_min(self, image):
+        in_ds = gdal.Open(image)
+        in_band = in_ds.GetRasterBand(1)
+        min, max= in_band.ComputeRasterMinMax()
+        return min, max
+
+    def find_unique_values(self, arr, limit=2):
+        unique_values = set()
+        for value in np.nditer(arr):
+            unique_values.add(value.item())
+            if len(unique_values) > limit:
+                return False
+        return True
+
+    def check_binary_map(self, in_fn):
+        '''
+        Check if input image is binary map
+        :param in_fn: input image
+        :return: True if the file is a binary map, False otherwise
+        '''
+        file_extension = in_fn.split('.')[-1].lower()
+        file_name, _ = os.path.splitext(in_fn)
+        if file_extension == 'rst':
+            with open(file_name + '.rdc', 'r') as read_file:
+                rdc_content = read_file.read().lower()
+                byte_or_integer_binary = "data type   : byte" in rdc_content or (
+                        "data type   : integer" in rdc_content and "min. value  : 0" in rdc_content and "max. value  : 1" in rdc_content)
+                float_binary = "data type   : real" in rdc_content and "min. value  : 0.0000000" in rdc_content and "max. value  : 1.0000000" in rdc_content
+        elif file_extension == 'tif':
+            datatype = self.get_image_datatype(in_fn)
+            min_val, max_val = self.get_image_max_min(in_fn)
+            byte_or_integer_binary = datatype in ['Byte', 'CInt16', 'CInt32', 'Int16', 'Int32', 'UInt16',
+                                                      'UInt32'] and max_val == 1 and min_val == 0
+            float_binary = datatype in ['Float32', 'Float64', 'CFloat32', 'CFloat64'] and max_val == 1.0000000 and min_val == 0.0000000
+
+        if byte_or_integer_binary or (float_binary):
+            # For float_binary, use find_unique_values function to check if data only have two unique values [0.0000000, 1.0000000].
+            if float_binary:
+                in_ds = gdal.Open(in_fn)
+                in_band = in_ds.GetRasterBand(1)
+                arr = in_band.ReadAsArray()
+                # If more than two unique values are found, it's not a binary map, return False.
+                if not self.find_unique_values(arr, 2):
+                    return False
+            # Binary map: byte_or_integer_binary or float_binary with two unique values [0.0000000, 1.0000000], it returns True.
+            return True
+        # For any other scenario, it returns False.
+        return False
+
+if __name__ == "__main__":
+    # main
+    app = QApplication(sys.argv)
+    # Load custom fonts
+    font_id = QFontDatabase.addApplicationFont(str(Path(PureWindowsPath("font\\AvenirNextLTPro-DemiCn.otf"))))
+
+    intro = IntroScreen()
+    # Create a global instance of this store
+    central_data_store = CentralDataStore()
+    map_checker = MapChecker()
+
+    widget = QtWidgets.QStackedWidget()
+    widget.addWidget(intro)
+    widget.setFixedHeight(1000)
+    widget.setFixedWidth(1800)
+    widget.show()
+
+    try:
+        sys.exit(app.exec_())
+    except:
         print("Exiting")
\ No newline at end of file
diff --git a/model_evaluation.py b/model_evaluation.py
index 559c802..5b7db9b 100644
--- a/model_evaluation.py
+++ b/model_evaluation.py
@@ -1,756 +1,769 @@
-import os
-import sys
-from osgeo import gdal, osr, ogr
-from osgeo.gdalconst import *
-import matplotlib.pyplot as plt
-import numpy as np
-from scipy.spatial import Voronoi
-import scipy.stats as stats
-import geopandas as gpd
-import shapely
-import seaborn as sns
-from shapely.geometry import Point
-import pandas as pd
-from PyQt5.QtCore import QObject, pyqtSignal
-import shutil
-from geopandas import GeoDataFrame
-import plotly.graph_objects as go
-import plotly.io as pio
-
-# GDAL exceptions
-gdal.UseExceptions()
-
-class ModelEvaluation(QObject):
-    progress_updated = pyqtSignal(int)
-    def __init__(self):
-        super(ModelEvaluation, self).__init__()
-        self.data_folder = None
-
-    def set_working_directory(self, directory: object) -> object:
-        '''
-        Set up the working directory
-        :param directory: your local directory with all dat files
-        '''
-        self.progress_updated.emit(0)
-        self.data_folder = directory
-        os.chdir(self.data_folder)
-
-    def image_to_array(self,image):
-        # Set up a GDAL dataset
-        in_ds = gdal.Open(image)
-        # Set up a GDAL band
-        in_band = in_ds.GetRasterBand(1)
-        # Create Numpy Array1
-        arr = in_band.ReadAsArray()
-        return arr
-
-    def array_to_image(self, in_fn, out_fn, data, data_type, nodata=None):
-        '''
-          Create image from array
-         :param in_fn: datasource to copy projection and geotransform from
-         :param out_fn:path to the file to create
-         :param data:the NumPy array
-         :param data_type:output data type
-         :param nodata:optional NoData value
-         :return:
-        '''
-        in_ds = gdal.Open(in_fn)
-        output_format = out_fn.split('.')[-1].upper()
-        if (output_format == 'TIF'):
-            output_format = 'GTIFF'
-        elif (output_format == 'RST'):
-            output_format = 'rst'
-        driver = gdal.GetDriverByName(output_format)
-        out_ds = driver.Create(out_fn, in_ds.RasterXSize, in_ds.RasterYSize, 1, data_type, options=["BigTIFF=YES"])
-        out_band = out_ds.GetRasterBand(1)
-        out_ds.SetGeoTransform(in_ds.GetGeoTransform())
-        out_ds.SetProjection(in_ds.GetProjection().encode('utf-8', 'backslashreplace').decode('utf-8'))
-        if nodata is not None:
-            out_band.SetNoDataValue(nodata)
-        out_band.WriteArray(data)
-        out_band.FlushCache()
-        out_ds.FlushCache()
-        return
-
-    def replace_ref_system(self, in_fn, out_fn):
-        '''
-         RST raster format: correct reference system name in rdc file
-         :param in_fn: datasource to copy correct projection name
-         :param out_fn: rst raster file
-        '''
-        if out_fn.split('.')[-1] == 'rst':
-            if in_fn.split('.')[-1] == 'rst':
-                read_file_name, _ = os.path.splitext(in_fn)
-                write_file_name, _ = os.path.splitext(out_fn)
-                temp_file_path = 'rdc_temp.rdc'
-
-                with open(read_file_name + '.rdc', 'r') as read_file:
-                    for line in read_file:
-                        if line.startswith("ref. system :"):
-                            correct_name = line
-                            break
-
-                if correct_name:
-                    with open(write_file_name + '.rdc', 'r') as read_file, open(temp_file_path, 'w') as write_file:
-                        for line in read_file:
-                            if line.startswith("ref. system :"):
-                                write_file.write(correct_name)
-                            else:
-                                write_file.write(line)
-
-                    # Move the temp file to replace the original
-                    shutil.move(temp_file_path, write_file_name + '.rdc')
-
-            elif in_fn.split('.')[-1] == 'tif':
-                # Read projection information from the .tif file using GDAL
-                dataset = gdal.Open(in_fn)
-                projection = dataset.GetProjection()
-                dataset = None
-
-                # Extract the reference system name from the wkt projection
-                ref_system_name = projection.split('PROJCS["')[1].split('"')[0]
-
-                write_file_name, _ = os.path.splitext(out_fn)
-                temp_file_path = 'rdc_temp.rdc'
-
-                with open(write_file_name + '.rdc', 'r') as read_file, open(temp_file_path, 'w') as write_file:
-                    for line in read_file:
-                        if line.startswith("ref. system :"):
-                            write_file.write(f"ref. system : {ref_system_name}\n")
-                        else:
-                            write_file.write(line)
-
-                shutil.move(temp_file_path, write_file_name + '.rdc')
-
-    def replace_legend(self, out_fn):
-        '''
-         RST raster format: correct legend in rdc file of Combined Deforestation Review Map
-         :param out_fn: rst raster file
-        '''
-        if out_fn.split('.')[-1] == 'rst':
-            base_name, _ = os.path.splitext(out_fn)
-            temp_file_path = 'rdc_temp.rdc'
-
-            with open(base_name + '.rdc', 'r') as read_file, open(temp_file_path, 'w') as write_file:
-                for line in read_file:
-                    if line.startswith("legend cats :"):
-                        write_file.write("legend cats : " + '3'+'\n')
-                        # Write the three new lines
-                        write_file.write("code 1      : "+"Forest at the start of HRP"+"\n")
-                        write_file.write("code 2      : "+"Deforestation within CAL"+"\n")
-                        write_file.write("code 3      : "+"Deforestation within CNF"+"\n")
-                    else:
-                        write_file.write(line)
-            shutil.move(temp_file_path, base_name + '.rdc')
-
-    def create_mask_polygon(self, mask):
-        '''
-        Create municipality mask polygon
-        :param mask: mask of the jurisdiction (binary map)
-        :return:
-        '''
-        in_ds = gdal.Open(mask)
-        in_band = in_ds.GetRasterBand(1)
-
-        # Set up osr spatial reference
-        projection = in_ds.GetProjection().encode('utf-8', 'backslashreplace').decode('utf-8')
-        self.progress_updated.emit(10)
-        spatial_ref = osr.SpatialReference()
-        spatial_ref.ImportFromWkt(projection)
-
-        # Create a temporary shapefile to store all polygons
-        temp_layername = "POLYGONIZED_MASK"
-        driver = ogr.GetDriverByName("ESRI Shapefile")
-        temp_ds = driver.CreateDataSource(temp_layername + ".shp")
-        temp_layer = temp_ds.CreateLayer(temp_layername, srs=spatial_ref)
-        gdal.Polygonize(in_band, in_band, temp_layer, -1, [], callback=None)
-        self.progress_updated.emit(20)
-        return
-
-    def bbox_to_pixel_offsets(self,gt, bbox):
-        '''
-        https://gist.github.com/perrygeo/5667173
-        '''
-        originX = gt[0]
-        originY = gt[3]
-        pixel_width = gt[1]
-        pixel_height = gt[5]
-        x1 = int((bbox[0] - originX) / pixel_width)
-        x2 = int((bbox[1] - originX) / pixel_width) + 1
-
-        y1 = int((bbox[3] - originY) / pixel_height)
-        y2 = int((bbox[2] - originY) / pixel_height) + 1
-
-        xsize = x2 - x1
-        ysize = y2 - y1
-        return (x1, y1, xsize, ysize)
-
-    def zonal_stats(self, vector_path, raster_path, nodata_value=None, global_src_extent=False):
-        '''
-        https://gist.github.com/perrygeo/5667173
-        '''
-        rds = gdal.Open(raster_path, GA_ReadOnly)
-        assert (rds)
-        rb = rds.GetRasterBand(1)
-        rgt = rds.GetGeoTransform()
-
-        if nodata_value:
-            nodata_value = float(nodata_value)
-            rb.SetNoDataValue(nodata_value)
-
-        vds = ogr.Open(vector_path, GA_ReadOnly)  # TODO maybe open update if we want to write stats
-        assert (vds)
-        vlyr = vds.GetLayer(0)
-
-        # create an in-memory numpy array of the source raster data
-        # covering the whole extent of the vector layer
-        if global_src_extent:
-            # use global source extent
-            # useful only when disk IO or raster scanning inefficiencies are your limiting factor
-            # advantage: reads raster data in one pass
-            # disadvantage: large vector extents may have big memory requirements
-            src_offset = self.bbox_to_pixel_offsets(rgt, vlyr.GetExtent())
-            src_array = rb.ReadAsArray(*src_offset)
-
-            # calculate new geotransform of the layer subset
-            new_gt = (
-                (rgt[0] + (src_offset[0] * rgt[1])),
-                rgt[1],
-                0.0,
-                (rgt[3] + (src_offset[1] * rgt[5])),
-                0.0,
-                rgt[5]
-            )
-
-        mem_drv = ogr.GetDriverByName('Memory')
-        driver = gdal.GetDriverByName('MEM')
-
-        # Loop through vectors
-        stats = []
-        feat = vlyr.GetNextFeature()
-        while feat is not None:
-
-            if not global_src_extent:
-                # use local source extent
-                # fastest option when you have fast disks and well indexed raster (ie tiled Geotiff)
-                # advantage: each feature uses the smallest raster chunk
-                # disadvantage: lots of reads on the source raster
-                src_offset = self.bbox_to_pixel_offsets(rgt, feat.geometry().GetEnvelope())
-                src_array = rb.ReadAsArray(*src_offset)
-
-                # calculate new geotransform of the feature subset
-                new_gt = (
-                    (rgt[0] + (src_offset[0] * rgt[1])),
-                    rgt[1],
-                    0.0,
-                    (rgt[3] + (src_offset[1] * rgt[5])),
-                    0.0,
-                    rgt[5]
-                )
-
-            # Create a temporary vector layer in memory
-            mem_ds = mem_drv.CreateDataSource('out')
-            mem_layer = mem_ds.CreateLayer('poly', None, ogr.wkbPolygon)
-            mem_layer.CreateFeature(feat.Clone())
-
-            # Rasterize it
-            rvds = driver.Create('', src_offset[2], src_offset[3], 1, gdal.GDT_Byte)
-            rvds.SetGeoTransform(new_gt)
-            gdal.RasterizeLayer(rvds, [1], mem_layer, burn_values=[1])
-            rv_array = rvds.ReadAsArray()
-
-            # Mask the source data array with our current feature
-            # we take the logical_not to flip 0<->1 to get the correct mask effect
-            # we also mask out nodata values explictly
-            masked = np.ma.MaskedArray(
-                src_array,
-                mask=np.logical_or(
-                    src_array == nodata_value,
-                    np.logical_not(rv_array)
-                )
-            )
-
-            feature_stats = {
-                'sum': float(masked.sum())}
-
-            stats.append(feature_stats)
-
-            rvds = None
-            mem_ds = None
-            feat = vlyr.GetNextFeature()
-
-        vds = None
-        rds = None
-        return stats
-
-    def vector_to_raster(self,vector_fn,in_fn,raster_fn,data_type, nodata=None):
-        '''
-          Create residual raster image from vector file
-         :param vector_fn: vector datasource
-         :param in_fn: datasource to copy projection and geotransform from
-         :param raster_fn:path to create raster file
-         :param data_type:output data type
-         :param nodata:optional NoData value
-         :return
-        '''
-        # Open the vector data source
-        source_ds = ogr.Open(vector_fn)
-        source_layer = source_ds.GetLayer()
-
-        in_ds = gdal.Open(in_fn)
-        output_format = raster_fn.split('.')[-1].upper()
-        if (output_format == 'TIF'):
-            output_format = 'GTIFF'
-        elif (output_format == 'RST'):
-            output_format = 'rst'
-        driver = gdal.GetDriverByName(output_format)
-        out_ds = driver.Create(raster_fn, in_ds.RasterXSize, in_ds.RasterYSize, 1, data_type, options=["BigTIFF=YES"])
-        out_band = out_ds.GetRasterBand(1)
-        out_ds.SetGeoTransform(in_ds.GetGeoTransform())
-
-        out_ds.SetProjection(in_ds.GetProjection().encode('utf-8', 'backslashreplace').decode('utf-8'))
-
-        if nodata is not None:
-            out_band.SetNoDataValue(nodata)
-        # Rasterize
-        gdal.RasterizeLayer(out_ds, [1], source_layer, options=["ATTRIBUTE=Residuals"])
-
-        # Cleanup
-        out_band.FlushCache()
-        out_ds.FlushCache()
-        return
-
-    def remove_edge_cells(self, full_voronoi_grid: GeoDataFrame, area_mask: GeoDataFrame,
-                          area_percentile_threshold: float) -> GeoDataFrame:
-        '''
-        Ensure thiessen polygon cells retain percentile threshold of maximum size after intersection with mask of the jurisdiction
-         :param full_voronoi_grid: thiessen polygon dataframe
-         :param area_mask: mask of the jurisdiction
-         :param area_percentile_threshold: area percentile threshold
-         :return  thiessen_gdf: result dataframe
-        '''
-        thiessen_gdf = gpd.overlay(full_voronoi_grid, area_mask, how="intersection", keep_geom_type=False)
-        # get area of each polygon
-        thiessen_gdf["area"] = thiessen_gdf.area
-
-        max_area = thiessen_gdf["area"].max()
-        # using the area, calculate size of cell compared to max
-        thiessen_gdf["percentcell"] = thiessen_gdf["area"] / max_area
-
-        # select cells with more than thresh% of their area within the mask
-        thiessen_gdf = thiessen_gdf[thiessen_gdf["percentcell"] > area_percentile_threshold]
-
-        return thiessen_gdf
-
-    def create_thiessen_polygon (self, grid_area, mask, density, deforestation, out_fn, raster_fn):
-        '''
-          Create thiessen polygon
-         :param grid_area: assessment grid cell area or 100,000 (ha)
-         :param mask: mask of the jurisdiction (binary map)
-         :param density: adjusted prediction density map
-         :param deforestation:Deforestation Map during the HRP
-         :param csv_name:Name of performance chart
-         :return  clipped_gdf: thiessen polygon dataframe
-        '''
-        ## Create sample points:
-        # Open the Polygonized_Mask shapefile
-        mask_df = gpd.GeoDataFrame.from_file('POLYGONIZED_MASK.shp')
-
-        # Calculate grid size
-        in_ds = gdal.Open(mask)
-        grid_size = int(np.sqrt(grid_area * 10000)) // int(in_ds.GetGeoTransform()[1])
-
-        # Systematic Sampling
-        sample_points = []
-        for y in range(-1 * grid_size, in_ds.RasterYSize + 1 * grid_size, grid_size):
-            for x in range(-1 * grid_size, in_ds.RasterXSize + 1 * grid_size, grid_size):
-                # Convert raster coordinates to geographic coordinates
-                geo_x = in_ds.GetGeoTransform()[0] + x * in_ds.GetGeoTransform()[1]
-                geo_y = in_ds.GetGeoTransform()[3] + y * in_ds.GetGeoTransform()[5]
-                sample_points.append((geo_x, geo_y))
-
-        # Convert sample_points list to DataFrame
-        df = pd.DataFrame(sample_points, columns=['geo_x', 'geo_y'])
-        df['coords'] = list(zip(df['geo_x'], df['geo_y']))
-        df['coords_P'] = df['coords'].apply(Point)
-        points_df = gpd.GeoDataFrame(df, geometry='coords_P', crs=mask_df.crs)
-
-        # Convert the 'coords' column to a numpy array
-        coords = np.array(points_df['coords'].tolist())
-
-        ## Create thiessen polygon
-        vor = Voronoi(points=coords)
-
-        # Polygonize the line ridge is not infinity
-        lines = [shapely.geometry.LineString(vor.vertices[line]) for line in
-                 vor.ridge_vertices if -1 not in line]
-
-        polys = shapely.ops.polygonize(lines)
-
-        # Convert Voronoi polygons (polys) into a GeoDataFrame.
-        voronois = gpd.GeoDataFrame(geometry=gpd.GeoSeries(polys), crs=mask_df.crs)
-        self.progress_updated.emit(30)
-
-        # Ensure Thiessen Polygon cells retain 99.9% of maximum size after intersection with study area
-        thiessen_gdf = self.remove_edge_cells(voronois, mask_df, 0.999)
-
-        self.progress_updated.emit(40)
-
-        # Extract polygons and multipolygons from the entire thiessen_gdf (including GeometryCollections)
-        extracted_gdf = thiessen_gdf['geometry'].apply(
-            lambda geom: [g for g in geom.geoms if
-                          g.geom_type in ['Polygon', 'MultiPolygon']] if geom.geom_type == 'GeometryCollection' else [
-                geom]
-        ).explode().reset_index(drop=True)
-
-        clipped_gdf = gpd.GeoDataFrame({'geometry': extracted_gdf}, crs=thiessen_gdf.crs)
-
-        # Calculate area in hectares
-        clipped_gdf['Area_ha'] = clipped_gdf['geometry'].area / 10000
-
-        ## Calculate zonal statistics
-
-        ## Convert clipped_gdf to shapefile
-        vector_temp_path = "temp_vector.shp"
-        clipped_gdf.to_file(vector_temp_path)
-
-        # Actual Deforestation(ha)
-        stats = self.zonal_stats(vector_temp_path, deforestation, nodata_value=0)
-
-        self.progress_updated.emit(50)
-
-        # Calculate areal_resolution_of_map_pixels
-        in_ds4 = gdal.Open(density)
-        P1 = in_ds4.GetGeoTransform()[1]
-        P2 = abs(in_ds4.GetGeoTransform()[5])
-        areal_resolution_of_map_pixels = P1 * P2 / 10000
-
-        # Add the results back to the GeoDataFrame
-        clipped_gdf['Actual Deforestation(ha)'] = [(item['sum'] if item['sum'] is not None else 0) * areal_resolution_of_map_pixels for item in stats]
-        self.progress_updated.emit(60)
-
-        # Predicted Deforestation(ha)
-        stats1 = self.zonal_stats(vector_temp_path, density, nodata_value=0)
-        self.progress_updated.emit(70)
-
-        clipped_gdf['Predicted Deforestation(ha)'] = [(item['sum'] if item['sum'] is not None else 0) for item in stats1]
-
-        # ID
-        clipped_gdf['ID'] = range(1, len(clipped_gdf) + 1)
-
-        # Replace NaN or blank values with '0'
-        columns_to_fill = ['Actual Deforestation(ha)', 'Predicted Deforestation(ha)']
-        for column in columns_to_fill:
-            clipped_gdf[column] = clipped_gdf[column].fillna(0)
-
-        # Calculate residuals
-        clipped_gdf['Residuals(ha)'] = clipped_gdf['Predicted Deforestation(ha)'] - clipped_gdf['Actual Deforestation(ha)']
-
-        # Export to csv
-        csv_file_path = out_fn.split('.')[0]+'.csv'
-        clipped_gdf.drop('geometry', axis=1).to_csv(csv_file_path, columns=['ID', 'Actual Deforestation(ha)', 'Predicted Deforestation(ha)','Residuals(ha)'],
-                                                    index=False)
-
-        # Rename columns title for shapefile
-        clipped_gdf = clipped_gdf.rename(columns={'Predicted Deforestation(ha)': 'PredDef',
-                                                  'Actual Deforestation(ha)': 'ActualDef',
-                                                  'Residuals(ha)':'Residuals'})
-
-        # Save the updated GeoDataFrame back to a shapefile
-
-        tp_file_path = out_fn.split('.')[0]+'.shp'
-        clipped_gdf.to_file(tp_file_path)
-
-        # Create residual map
-        self.vector_to_raster(tp_file_path, mask, raster_fn, gdal.GDT_Float32,-1)
-
-        return clipped_gdf
-
-    def create_deforestation_map (self, fmask, deforestation_cal, deforestation_cnf, out_fn_def):
-        self.progress_updated.emit(80)
-        arr_fmask = self.image_to_array(fmask)
-        arr_def_cal = self.image_to_array(deforestation_cal)
-        arr_def_cnf = self.image_to_array(deforestation_cnf)
-
-        deforestation_arr=np.copy(arr_fmask)
-
-        deforestation_arr[arr_def_cnf == 1] = 3
-        deforestation_arr[(arr_def_cnf == 0) & (arr_def_cal == 1)] = 2
-        deforestation_arr[(arr_def_cnf == 0) & (arr_def_cal == 0) & (arr_fmask == 1)] = 1
-
-        #write deforestation_map
-        self.array_to_image(fmask, out_fn_def, deforestation_arr, gdal.GDT_Int16, -1)
-
-        return
-
-    def create_plot(self, grid_area, clipped_gdf, title, out_fn,xmax=None, ymax=None):
-        '''
-        Create plot and save to local directory
-        :param grid_area: assessment grid cell area or 100,000 (ha)
-        :param clipped_gdf: thiessen_polygon geo-dataframe
-        :param title:plot title
-        :param out_fn: plot path
-        :param xmax: maximum x-axis value
-        :param ymax: maximum y-axis value
-        :return
-        '''
-        self.progress_updated.emit(90)
-        # Set Seaborn Style
-        sns.set()
-
-        # prepare the X/Y data
-        X = np.array(clipped_gdf['ActualDef'], dtype=np.float32)
-        Y = np.array(clipped_gdf['PredDef'], dtype=np.float32)
-        ids = np.asarray(clipped_gdf["ID"])
-
-        # Set a proportion to extend the limits
-        extension_f = 0.1
-
-        # Check if lim is string and "default"
-        if isinstance(xmax, str) and xmax.lower() == "default":
-            xmax = max(X) * (1 + extension_f)
-        else:
-            xmax = float(xmax)
-
-        if isinstance(ymax, str) and ymax.lower() == "default":
-            ymax = max(Y) * (1 + extension_f)
-        else:
-            ymax = float(ymax)
-
-        # Set a new X range from 0 to the xmax
-        X_extended = np.linspace(0, xmax, 500)
-
-        ## Perform linear regression
-        slope, intercept, _, _, _ = stats.linregress(X, Y)
-
-        # Create the equation string
-        equation = f'Y = {slope:.4f} * X + {intercept:.2f}'
-
-        # Calculate the trend line
-        trend_line = slope * X_extended + intercept
-
-        # 1-to-1 Line
-        one_to_one_line = X_extended
-
-        ## Calculate R square
-        # Get the correlation coefficient
-        r = np.corrcoef(X, Y)[0, 1]
-        # Square the correlation coefficient
-        r_squared = r ** 2
-
-        ##Calculate MedAE
-        distance_arr = [abs(X[i] - Y[i]) for i in range(len(X))]
-        MedAE = np.median(distance_arr)
-
-        ## Calculate MedAE percent
-        MedAE_percent = (MedAE / int(grid_area)) * 100
-
-        ## Calculate MAE
-        MAE=np.sum(distance_arr)/len(X)
-        MAE_percent = (MAE / int(grid_area)) * 100
-
-        ## Calculate the IoU
-        # agreement=intersection: Minimum of actual and predicted deforestation for each dot and add them all
-        agree_arr = [min(X[i],Y[i]) for i in range(len(X))]
-        agree = np.sum(agree_arr)   
-
-        # union
-        union_arr = [max(X[i],Y[i]) for i in range(len(X))]
-        union = np.sum(union_arr)
-
-        # IoU
-        iou = 0 if union == 0 else agree / union * 100
-
-        ## Calculate the Difference
-        # Absolute value of predicted deforestation minus actual deforestation of each point and add them all
-        difference=np.sum(distance_arr)
-
-        # Set the figure size
-        plt.figure(figsize=(8, 6))
-
-        # Create a scatter plot
-        plt.scatter(clipped_gdf['ActualDef'], clipped_gdf['PredDef'], color='steelblue', alpha=0.5, linewidth=1.0, s=50)
-
-        # Add labels and title
-        plt.xlabel('Actual Deforestation (ha)', color='black', fontweight='bold', labelpad=10)
-        plt.ylabel('Predicted Deforestation (ha)', color='black', fontweight='bold', labelpad=10)
-        plt.title(title, color='firebrick', fontweight='bold', fontsize=20, pad=20)
-
-        # Plot the trend line
-        plt.plot(X_extended, trend_line, color='mediumseagreen', linestyle='-', label='OLS Line')
-
-        # Plot a 1-to-1 line
-        plt.plot(X_extended, one_to_one_line, color='crimson', linestyle='--',label='1:1 Line')
-
-        ## Theil-Sen Regressor
-        # Fit Theil-Sen Regressor
-        # Compute Theil-Sen estimator
-        ts_slope, ts_intercept, _, _ = stats.theilslopes(Y, X)
-
-        # Generate predictions
-        y_pred = ts_slope * X_extended + ts_intercept
-
-        # Equation of the line
-        ts_equation = f'Y = {ts_slope:.4f} * X + {ts_intercept:.2f}'
-
-        # Plot Theil-Sen Line
-        plt.plot(X_extended, y_pred, color='orange', linestyle='-', label='Theil-Sen Line')
-
-        # Add a legend in the bottom right position
-        plt.legend(loc='lower right')
-
-        plt.xlim([0, xmax])
-        plt.ylim([0, ymax])
-
-        text_x_pos = ymax * 0.05
-        text_y_start_pos = ymax * 0.9
-        text_y_gap = ymax * 0.05
-
-        # Adjust plt texts with the new calculated positions
-        plt.text(text_x_pos, text_y_start_pos, f'Theil-Sen : {ts_equation}', fontsize=11,
-                 color='black')
-        plt.text(text_x_pos, text_y_start_pos - text_y_gap, f'OLS : {equation}', fontsize=11, color='black')
-        plt.text(text_x_pos, text_y_start_pos - 2 * text_y_gap, f'Samples = {len(X)}', fontsize=11, color='black')
-        plt.text(text_x_pos, text_y_start_pos - 3 * text_y_gap, f'R^2 = {r_squared:.4f}', fontsize=11, color='black')
-        plt.text(text_x_pos, text_y_start_pos - 4 * text_y_gap, f'MedAE = {MedAE:.2f} ({MedAE_percent:.2f}%)',
-                 fontsize=11, color='black')
-        plt.text(text_x_pos, text_y_start_pos - 5 * text_y_gap, f'IoU = {iou:.2f}%',fontsize=11, color='black')
-
-        ## Save metrics to txt file
-        base, ext = os.path.splitext(out_fn)
-        txt_out = base + ".txt"
-        lines_to_write = [
-        f"OLS: {equation}\n",
-        f"Theil Sen: {ts_equation}\n",
-        f"Samples = {len(X)}\n",
-        f"R^2 = {r_squared:.4f}\n",
-        f"MedAE = {MedAE:.2f} ({MedAE_percent:.2f}%)\n",
-        f"MAE = {MAE:.2f} ({MAE_percent:.2f}%)\n",
-        f"IoU : {iou:.2f}%\n",
-        f"Agreement : {agree:.2f}\n",
-        f"Difference : {difference:.2f}\n",
-        ]
-
-        with open(txt_out, "w") as file:
-            file.writelines(lines_to_write)
-      
-        # x, yticks
-        plt.yticks(fontsize=10, color='dimgrey')
-        plt.xticks(fontsize=10, color='dimgrey')
-
-        # Save the plot
-        plt.savefig(out_fn)
-
-        ## html
-        # Build Plotly figure
-        fig = go.Figure()
-
-        # Hover 
-        fig.add_trace(go.Scatter(
-            x=X, y=Y, mode="markers",
-            name="Cells",
-            customdata=np.stack([ids, X, Y, agree_arr,distance_arr], axis=-1),
-            hovertemplate="ID: %{customdata[0]}<br>Actual: %{x:.2f} ha<br>Predicted: %{y:.2f} ha<br>Agreement: %{customdata[3]}<br>Difference: %{customdata[4]}<br><extra></extra>",
-            marker=dict(size=8, line=dict(width=0.5), color="steelblue", opacity=0.5), showlegend=False
-        ))
-
-        # OLS line trace
-        fig.add_trace(go.Scatter(
-        x=X_extended, y=trend_line, mode="lines",
-        name="OLS Line",
-        line=dict(color="mediumseagreen", dash="solid")
-        , hoverinfo="skip", hovertemplate=None
-        ))
-
-        # Theil–Sen line trace
-        fig.add_trace(go.Scatter(
-        x=X_extended, y=y_pred, mode="lines",
-        name="Theil–Sen Line",
-        line=dict(color="orange", dash="solid")
-        , hoverinfo="skip", hovertemplate=None
-        ))
-
-        # 1:1 line trace
-        fig.add_trace(go.Scatter(
-        x=X_extended, y=one_to_one_line, mode="lines",
-        name="1:1 Line",
-        line=dict(color="crimson", dash="dash")
-        , hoverinfo="skip", hovertemplate=None
-        ))
-
-        # Layout setting
-        fig.update_layout(
-        title=dict(
-            text=f"<b>{title}</b>",
-            font=dict(color="firebrick", size=20),
-            x=0.5, xanchor="center"
-        ),
-        xaxis=dict(
-            title=dict(text="<b>Actual Deforestation (ha)</b>",
-                    font=dict(color="black"),
-                    standoff=10),                 
-            tickfont=dict(size=10, color="dimgrey"),
-            range=[0, xmax],
-            constrain="domain"
-        ),
-        yaxis=dict(
-            title=dict(text="<b>Predicted Deforestation (ha)</b>",
-                    font=dict(color="black"),
-                    standoff=10),
-            tickfont=dict(size=10, color="dimgrey"),
-            range=[0, ymax]
-        ),
-        hovermode="closest",
-        legend=dict(                    
-            x=0.99, y=0.01, xanchor="right", yanchor="bottom", orientation="v"
-        ),
-        margin=dict(l=60, r=30, t=80, b=60),
-        paper_bgcolor= 'rgb(255,255,255)',
-        plot_bgcolor=  'rgb(234,234,242)',
-        )
-
-        # Annotations 
-        stats_text = (
-            f"Theil–Sen: {ts_equation}<br>"
-            f"OLS: {equation}<br>"
-            f"Samples = {len(X)}<br>"
-            f"R² = {r_squared:.4f}<br>"
-            f"MedAE = {MedAE:.2f} ({MedAE_percent:.2f}%)<br>"
-            f"IoU = {iou:.2f}%<br>"
-        )
-        
-        fig.add_annotation(
-            x=0.02, y=0.98, xref="paper", yref="paper", xanchor="left", yanchor="top",
-            text=stats_text, showarrow=False, align="left"
-        )
-
-        # Save a HTML
-        html_out = base + ".html"
-        
-        pio.write_html(fig, file=html_out, include_plotlyjs=True, full_html=True)
-
-        return
-
-    def remove_temp_files(self):
-        # Files to check for and delete
-        mask_file = 'mask'
-        shapefiles_to_delete = ["TEMP_POLYGONIZED","POLYGONIZED_MASK","thiessen_polygon_temp","temp_vector"]
-
-        # Shapefile associated extensions
-        mask_file_extensions =[".tif",".rst",".rdc",".RST",".RST.aux.xml",".ref"]
-        shapefile_extensions = [".shp", ".shx", ".dbf", ".prj", ".sbn", ".sbx",".cpg", ".shp.xml"]
-
-        # Delete mask files
-        for mask_ext in mask_file_extensions:
-            mask_filename = f"{mask_file}{mask_ext}"
-            if os.path.exists(mask_filename):
-                os.remove(mask_filename)
-
-        # Delete shapefiles with associated extensions
-        for shp_base in shapefiles_to_delete:
-            for ext in shapefile_extensions:
-                full_filename = f"{shp_base}{ext}"
-                if os.path.exists(full_filename):
-                    os.remove(full_filename)
-        self.progress_updated.emit(100)
-        return
\ No newline at end of file
+import os
+import sys
+from osgeo import gdal, osr, ogr
+from osgeo.gdalconst import *
+import matplotlib.pyplot as plt
+import numpy as np
+from scipy.spatial import Voronoi
+import scipy.stats as stats
+import geopandas as gpd
+import shapely
+import seaborn as sns
+from shapely.geometry import Point
+import pandas as pd
+from PyQt5.QtCore import QObject, pyqtSignal
+import shutil
+from geopandas import GeoDataFrame
+import plotly.graph_objects as go
+import plotly.io as pio
+
+# GDAL exceptions
+gdal.UseExceptions()
+
+class ModelEvaluation(QObject):
+    progress_updated = pyqtSignal(int)
+    def __init__(self):
+        super(ModelEvaluation, self).__init__()
+        self.data_folder = None
+
+    def set_working_directory(self, directory: object) -> object:
+        '''
+        Set up the working directory
+        :param directory: your local directory with all dat files
+        '''
+        self.progress_updated.emit(0)
+        self.data_folder = directory
+        os.chdir(self.data_folder)
+
+    def image_to_array(self,image):
+        # Set up a GDAL dataset
+        in_ds = gdal.Open(image)
+        # Set up a GDAL band
+        in_band = in_ds.GetRasterBand(1)
+        # Create Numpy Array1
+        arr = in_band.ReadAsArray()
+        return arr
+
+    def array_to_image(self, in_fn, out_fn, data, data_type, nodata=None):
+        '''
+          Create image from array
+         :param in_fn: datasource to copy projection and geotransform from
+         :param out_fn:path to the file to create
+         :param data:the NumPy array
+         :param data_type:output data type
+         :param nodata:optional NoData value
+         :return:
+        '''
+        in_ds = gdal.Open(in_fn)
+        output_format = out_fn.split('.')[-1].upper()
+        if (output_format == 'TIF'):
+            output_format = 'GTIFF'
+        elif (output_format == 'RST'):
+            output_format = 'rst'
+        driver = gdal.GetDriverByName(output_format)
+        out_ds = driver.Create(out_fn, in_ds.RasterXSize, in_ds.RasterYSize, 1, data_type, options=["BigTIFF=YES"])
+        out_band = out_ds.GetRasterBand(1)
+        out_ds.SetGeoTransform(in_ds.GetGeoTransform())
+        out_ds.SetProjection(in_ds.GetProjection().encode('utf-8', 'backslashreplace').decode('utf-8'))
+        if nodata is not None:
+            out_band.SetNoDataValue(nodata)
+        out_band.WriteArray(data)
+        out_band.FlushCache()
+        out_ds.FlushCache()
+        return
+
+    def replace_ref_system(self, in_fn, out_fn):
+        '''
+         RST raster format: correct reference system name in rdc file
+         :param in_fn: datasource to copy correct projection name
+         :param out_fn: rst raster file
+        '''
+        if out_fn.split('.')[-1] == 'rst':
+            if in_fn.split('.')[-1] == 'rst':
+                read_file_name, _ = os.path.splitext(in_fn)
+                write_file_name, _ = os.path.splitext(out_fn)
+                temp_file_path = 'rdc_temp.rdc'
+
+                with open(read_file_name + '.rdc', 'r') as read_file:
+                    for line in read_file:
+                        if line.startswith("ref. system :"):
+                            correct_name = line
+                            break
+
+                if correct_name:
+                    with open(write_file_name + '.rdc', 'r') as read_file, open(temp_file_path, 'w') as write_file:
+                        for line in read_file:
+                            if line.startswith("ref. system :"):
+                                write_file.write(correct_name)
+                            else:
+                                write_file.write(line)
+
+                    # Move the temp file to replace the original
+                    shutil.move(temp_file_path, write_file_name + '.rdc')
+
+            elif in_fn.split('.')[-1] == 'tif':
+                # Read projection information from the .tif file using GDAL
+                dataset = gdal.Open(in_fn)
+                projection = dataset.GetProjection()
+                dataset = None
+
+                # Extract the reference system name from the wkt projection
+                ref_system_name = projection.split('PROJCS["')[1].split('"')[0]
+
+                write_file_name, _ = os.path.splitext(out_fn)
+                temp_file_path = 'rdc_temp.rdc'
+
+                with open(write_file_name + '.rdc', 'r') as read_file, open(temp_file_path, 'w') as write_file:
+                    for line in read_file:
+                        if line.startswith("ref. system :"):
+                            write_file.write(f"ref. system : {ref_system_name}\n")
+                        else:
+                            write_file.write(line)
+
+                shutil.move(temp_file_path, write_file_name + '.rdc')
+
+    def replace_legend(self, out_fn):
+        '''
+         RST raster format: correct legend in rdc file of Combined Deforestation Review Map
+         :param out_fn: rst raster file
+        '''
+        if out_fn.split('.')[-1] == 'rst':
+            base_name, _ = os.path.splitext(out_fn)
+            temp_file_path = 'rdc_temp.rdc'
+
+            with open(base_name + '.rdc', 'r') as read_file, open(temp_file_path, 'w') as write_file:
+                for line in read_file:
+                    if line.startswith("legend cats :"):
+                        """
+                        write_file.write("legend cats : " + '3'+'\n')
+                        # Write the three new lines
+                        write_file.write("code 1      : "+"Forest at the start of HRP"+"\n")
+                        write_file.write("code 2      : "+"Deforestation within CAL"+"\n")
+                        write_file.write("code 3      : "+"Deforestation within CNF"+"\n")
+                        """
+                        write_file.write("legend cats : " + '4'+'\n')
+                        # Write the four new lines of legend categories
+                        write_file.write("code 1      : "+"Stable Forest (HRP)"+"\n")
+                        write_file.write("code 2      : "+"Forest Loss within CAL"+"\n")
+                        write_file.write("code 3      : "+"Forest Loss within CNF"+"\n")
+                        write_file.write("code 4      : "+"Stable Nonforest (HRP)"+"\n") 
+                    else:
+                        write_file.write(line)
+            shutil.move(temp_file_path, base_name + '.rdc')
+
+    def create_mask_polygon(self, mask):
+        '''
+        Create municipality mask polygon
+        :param mask: mask of the jurisdiction (binary map)
+        :return:
+        '''
+        in_ds = gdal.Open(mask)
+        in_band = in_ds.GetRasterBand(1)
+
+        # Set up osr spatial reference
+        projection = in_ds.GetProjection().encode('utf-8', 'backslashreplace').decode('utf-8')
+        self.progress_updated.emit(10)
+        spatial_ref = osr.SpatialReference()
+        spatial_ref.ImportFromWkt(projection)
+
+        # Create a temporary shapefile to store all polygons
+        temp_layername = "POLYGONIZED_MASK"
+        driver = ogr.GetDriverByName("ESRI Shapefile")
+        temp_ds = driver.CreateDataSource(temp_layername + ".shp")
+        temp_layer = temp_ds.CreateLayer(temp_layername, srs=spatial_ref)
+        gdal.Polygonize(in_band, in_band, temp_layer, -1, [], callback=None)
+        self.progress_updated.emit(20)
+        return
+
+    def bbox_to_pixel_offsets(self,gt, bbox):
+        '''
+        https://gist.github.com/perrygeo/5667173
+        '''
+        originX = gt[0]
+        originY = gt[3]
+        pixel_width = gt[1]
+        pixel_height = gt[5]
+        x1 = int((bbox[0] - originX) / pixel_width)
+        x2 = int((bbox[1] - originX) / pixel_width) + 1
+
+        y1 = int((bbox[3] - originY) / pixel_height)
+        y2 = int((bbox[2] - originY) / pixel_height) + 1
+
+        xsize = x2 - x1
+        ysize = y2 - y1
+        return (x1, y1, xsize, ysize)
+
+    def zonal_stats(self, vector_path, raster_path, nodata_value=None, global_src_extent=False):
+        '''
+        https://gist.github.com/perrygeo/5667173
+        '''
+        rds = gdal.Open(raster_path, GA_ReadOnly)
+        assert (rds)
+        rb = rds.GetRasterBand(1)
+        rgt = rds.GetGeoTransform()
+
+        if nodata_value:
+            nodata_value = float(nodata_value)
+            rb.SetNoDataValue(nodata_value)
+
+        vds = ogr.Open(vector_path, GA_ReadOnly)  # TODO maybe open update if we want to write stats
+        assert (vds)
+        vlyr = vds.GetLayer(0)
+
+        # create an in-memory numpy array of the source raster data
+        # covering the whole extent of the vector layer
+        if global_src_extent:
+            # use global source extent
+            # useful only when disk IO or raster scanning inefficiencies are your limiting factor
+            # advantage: reads raster data in one pass
+            # disadvantage: large vector extents may have big memory requirements
+            src_offset = self.bbox_to_pixel_offsets(rgt, vlyr.GetExtent())
+            src_array = rb.ReadAsArray(*src_offset)
+
+            # calculate new geotransform of the layer subset
+            new_gt = (
+                (rgt[0] + (src_offset[0] * rgt[1])),
+                rgt[1],
+                0.0,
+                (rgt[3] + (src_offset[1] * rgt[5])),
+                0.0,
+                rgt[5]
+            )
+
+        mem_drv = ogr.GetDriverByName('Memory')
+        driver = gdal.GetDriverByName('MEM')
+
+        # Loop through vectors
+        stats = []
+        feat = vlyr.GetNextFeature()
+        while feat is not None:
+
+            if not global_src_extent:
+                # use local source extent
+                # fastest option when you have fast disks and well indexed raster (ie tiled Geotiff)
+                # advantage: each feature uses the smallest raster chunk
+                # disadvantage: lots of reads on the source raster
+                src_offset = self.bbox_to_pixel_offsets(rgt, feat.geometry().GetEnvelope())
+                src_array = rb.ReadAsArray(*src_offset)
+
+                # calculate new geotransform of the feature subset
+                new_gt = (
+                    (rgt[0] + (src_offset[0] * rgt[1])),
+                    rgt[1],
+                    0.0,
+                    (rgt[3] + (src_offset[1] * rgt[5])),
+                    0.0,
+                    rgt[5]
+                )
+
+            # Create a temporary vector layer in memory
+            mem_ds = mem_drv.CreateDataSource('out')
+            mem_layer = mem_ds.CreateLayer('poly', None, ogr.wkbPolygon)
+            mem_layer.CreateFeature(feat.Clone())
+
+            # Rasterize it
+            rvds = driver.Create('', src_offset[2], src_offset[3], 1, gdal.GDT_Byte)
+            rvds.SetGeoTransform(new_gt)
+            gdal.RasterizeLayer(rvds, [1], mem_layer, burn_values=[1])
+            rv_array = rvds.ReadAsArray()
+
+            # Mask the source data array with our current feature
+            # we take the logical_not to flip 0<->1 to get the correct mask effect
+            # we also mask out nodata values explictly
+            masked = np.ma.MaskedArray(
+                src_array,
+                mask=np.logical_or(
+                    src_array == nodata_value,
+                    np.logical_not(rv_array)
+                )
+            )
+
+            feature_stats = {
+                'sum': float(masked.sum())}
+
+            stats.append(feature_stats)
+
+            rvds = None
+            mem_ds = None
+            feat = vlyr.GetNextFeature()
+
+        vds = None
+        rds = None
+        return stats
+
+    def vector_to_raster(self,vector_fn,in_fn,raster_fn,data_type, nodata=None):
+        '''
+          Create residual raster image from vector file
+         :param vector_fn: vector datasource
+         :param in_fn: datasource to copy projection and geotransform from
+         :param raster_fn:path to create raster file
+         :param data_type:output data type
+         :param nodata:optional NoData value
+         :return
+        '''
+        # Open the vector data source
+        source_ds = ogr.Open(vector_fn)
+        source_layer = source_ds.GetLayer()
+
+        in_ds = gdal.Open(in_fn)
+        output_format = raster_fn.split('.')[-1].upper()
+        if (output_format == 'TIF'):
+            output_format = 'GTIFF'
+        elif (output_format == 'RST'):
+            output_format = 'rst'
+        driver = gdal.GetDriverByName(output_format)
+        out_ds = driver.Create(raster_fn, in_ds.RasterXSize, in_ds.RasterYSize, 1, data_type, options=["BigTIFF=YES"])
+        out_band = out_ds.GetRasterBand(1)
+        out_ds.SetGeoTransform(in_ds.GetGeoTransform())
+
+        out_ds.SetProjection(in_ds.GetProjection().encode('utf-8', 'backslashreplace').decode('utf-8'))
+
+        if nodata is not None:
+            out_band.SetNoDataValue(nodata)
+        # Rasterize
+        gdal.RasterizeLayer(out_ds, [1], source_layer, options=["ATTRIBUTE=Residuals"])
+
+        # Cleanup
+        out_band.FlushCache()
+        out_ds.FlushCache()
+        return
+
+    def remove_edge_cells(self, full_voronoi_grid: GeoDataFrame, area_mask: GeoDataFrame,
+                          area_percentile_threshold: float) -> GeoDataFrame:
+        '''
+        Ensure thiessen polygon cells retain percentile threshold of maximum size after intersection with mask of the jurisdiction
+         :param full_voronoi_grid: thiessen polygon dataframe
+         :param area_mask: mask of the jurisdiction
+         :param area_percentile_threshold: area percentile threshold
+         :return  thiessen_gdf: result dataframe
+        '''
+        thiessen_gdf = gpd.overlay(full_voronoi_grid, area_mask, how="intersection", keep_geom_type=False)
+        # get area of each polygon
+        thiessen_gdf["area"] = thiessen_gdf.area
+
+        max_area = thiessen_gdf["area"].max()
+        # using the area, calculate size of cell compared to max
+        thiessen_gdf["percentcell"] = thiessen_gdf["area"] / max_area
+
+        # select cells with more than thresh% of their area within the mask
+        thiessen_gdf = thiessen_gdf[thiessen_gdf["percentcell"] > area_percentile_threshold]
+
+        return thiessen_gdf
+
+    def create_thiessen_polygon (self, grid_area, mask, density, deforestation, out_fn, raster_fn):
+        '''
+          Create thiessen polygon
+         :param grid_area: assessment grid cell area or 100,000 (ha)
+         :param mask: mask of the jurisdiction (binary map)
+         :param density: adjusted prediction density map
+         :param deforestation:Deforestation Map during the HRP
+         :param csv_name:Name of performance chart
+         :return  clipped_gdf: thiessen polygon dataframe
+        '''
+        ## Create sample points:
+        # Open the Polygonized_Mask shapefile
+        mask_df = gpd.GeoDataFrame.from_file('POLYGONIZED_MASK.shp')
+
+        # Calculate grid size
+        in_ds = gdal.Open(mask)
+        grid_size = int(np.sqrt(grid_area * 10000)) // int(in_ds.GetGeoTransform()[1])
+
+        # Systematic Sampling
+        sample_points = []
+        for y in range(-1 * grid_size, in_ds.RasterYSize + 1 * grid_size, grid_size):
+            for x in range(-1 * grid_size, in_ds.RasterXSize + 1 * grid_size, grid_size):
+                # Convert raster coordinates to geographic coordinates
+                geo_x = in_ds.GetGeoTransform()[0] + x * in_ds.GetGeoTransform()[1]
+                geo_y = in_ds.GetGeoTransform()[3] + y * in_ds.GetGeoTransform()[5]
+                sample_points.append((geo_x, geo_y))
+
+        # Convert sample_points list to DataFrame
+        df = pd.DataFrame(sample_points, columns=['geo_x', 'geo_y'])
+        df['coords'] = list(zip(df['geo_x'], df['geo_y']))
+        df['coords_P'] = df['coords'].apply(Point)
+        points_df = gpd.GeoDataFrame(df, geometry='coords_P', crs=mask_df.crs)
+
+        # Convert the 'coords' column to a numpy array
+        coords = np.array(points_df['coords'].tolist())
+
+        ## Create thiessen polygon
+        vor = Voronoi(points=coords)
+
+        # Polygonize the line ridge is not infinity
+        lines = [shapely.geometry.LineString(vor.vertices[line]) for line in
+                 vor.ridge_vertices if -1 not in line]
+
+        polys = shapely.ops.polygonize(lines)
+
+        # Convert Voronoi polygons (polys) into a GeoDataFrame.
+        voronois = gpd.GeoDataFrame(geometry=gpd.GeoSeries(polys), crs=mask_df.crs)
+        self.progress_updated.emit(30)
+
+        # Ensure Thiessen Polygon cells retain 99.9% of maximum size after intersection with study area
+        thiessen_gdf = self.remove_edge_cells(voronois, mask_df, 0.999)
+
+        self.progress_updated.emit(40)
+
+        # Extract polygons and multipolygons from the entire thiessen_gdf (including GeometryCollections)
+        extracted_gdf = thiessen_gdf['geometry'].apply(
+            lambda geom: [g for g in geom.geoms if
+                          g.geom_type in ['Polygon', 'MultiPolygon']] if geom.geom_type == 'GeometryCollection' else [
+                geom]
+        ).explode().reset_index(drop=True)
+
+        clipped_gdf = gpd.GeoDataFrame({'geometry': extracted_gdf}, crs=thiessen_gdf.crs)
+
+        # Calculate area in hectares
+        clipped_gdf['Area_ha'] = clipped_gdf['geometry'].area / 10000
+
+        ## Calculate zonal statistics
+
+        ## Convert clipped_gdf to shapefile
+        vector_temp_path = "temp_vector.shp"
+        clipped_gdf.to_file(vector_temp_path)
+
+        # Actual Deforestation(ha)
+        stats = self.zonal_stats(vector_temp_path, deforestation, nodata_value=0)
+
+        self.progress_updated.emit(50)
+
+        # Calculate areal_resolution_of_map_pixels
+        in_ds4 = gdal.Open(density)
+        P1 = in_ds4.GetGeoTransform()[1]
+        P2 = abs(in_ds4.GetGeoTransform()[5])
+        areal_resolution_of_map_pixels = P1 * P2 / 10000
+
+        # Add the results back to the GeoDataFrame
+        clipped_gdf['Actual Deforestation(ha)'] = [(item['sum'] if item['sum'] is not None else 0) * areal_resolution_of_map_pixels for item in stats]
+        self.progress_updated.emit(60)
+
+        # Predicted Deforestation(ha)
+        stats1 = self.zonal_stats(vector_temp_path, density, nodata_value=0)
+        self.progress_updated.emit(70)
+
+        clipped_gdf['Predicted Deforestation(ha)'] = [(item['sum'] if item['sum'] is not None else 0) for item in stats1]
+
+        # ID
+        clipped_gdf['ID'] = range(1, len(clipped_gdf) + 1)
+
+        # Replace NaN or blank values with '0'
+        columns_to_fill = ['Actual Deforestation(ha)', 'Predicted Deforestation(ha)']
+        for column in columns_to_fill:
+            clipped_gdf[column] = clipped_gdf[column].fillna(0)
+
+        # Calculate residuals
+        clipped_gdf['Residuals(ha)'] = clipped_gdf['Predicted Deforestation(ha)'] - clipped_gdf['Actual Deforestation(ha)']
+
+        # Export to csv
+        csv_file_path = out_fn.split('.')[0]+'.csv'
+        clipped_gdf.drop('geometry', axis=1).to_csv(csv_file_path, columns=['ID', 'Actual Deforestation(ha)', 'Predicted Deforestation(ha)','Residuals(ha)'],
+                                                    index=False)
+
+        # Rename columns title for shapefile
+        clipped_gdf = clipped_gdf.rename(columns={'Predicted Deforestation(ha)': 'PredDef',
+                                                  'Actual Deforestation(ha)': 'ActualDef',
+                                                  'Residuals(ha)':'Residuals'})
+
+        # Save the updated GeoDataFrame back to a shapefile
+
+        tp_file_path = out_fn.split('.')[0]+'.shp'
+        clipped_gdf.to_file(tp_file_path)
+
+        # Create residual map
+        self.vector_to_raster(tp_file_path, mask, raster_fn, gdal.GDT_Float32,-1)
+
+        return clipped_gdf
+
+    def create_deforestation_map (self, juris_mask, fmask, deforestation_cal, deforestation_cnf, out_fn_def):
+        self.progress_updated.emit(80)
+        arr_fmask = self.image_to_array(fmask)
+        arr_def_cal = self.image_to_array(deforestation_cal)
+        arr_def_cnf = self.image_to_array(deforestation_cnf)
+        arr_juris_mask = self.image_to_array(juris_mask)
+
+        deforestation_arr=np.copy(arr_fmask)
+
+        deforestation_arr[arr_def_cnf == 1] = 3
+        deforestation_arr[(arr_def_cnf == 0) & (arr_def_cal == 1)] = 2
+        deforestation_arr[(arr_def_cnf == 0) & (arr_def_cal == 0) & (arr_fmask == 1)] = 1
+        deforestation_arr[(arr_fmask == 0)] = 4  #tw 6/25/26
+        #ToDo: mask out the background
+        deforestation_arr[(arr_juris_mask == 0)] = 0  #tw 6/25/26
+        #ToDo: fix the legend
+        #        
+        #write deforestation_map
+        self.array_to_image(fmask, out_fn_def, deforestation_arr, gdal.GDT_Int16, -1)
+
+        return
+
+    def create_plot(self, grid_area, clipped_gdf, title, out_fn,xmax=None, ymax=None):
+        '''
+        Create plot and save to local directory
+        :param grid_area: assessment grid cell area or 100,000 (ha)
+        :param clipped_gdf: thiessen_polygon geo-dataframe
+        :param title:plot title
+        :param out_fn: plot path
+        :param xmax: maximum x-axis value
+        :param ymax: maximum y-axis value
+        :return
+        '''
+        self.progress_updated.emit(90)
+        # Set Seaborn Style
+        sns.set()
+
+        # prepare the X/Y data
+        X = np.array(clipped_gdf['ActualDef'], dtype=np.float32)
+        Y = np.array(clipped_gdf['PredDef'], dtype=np.float32)
+        ids = np.asarray(clipped_gdf["ID"])
+
+        # Set a proportion to extend the limits
+        extension_f = 0.1
+
+        # Check if lim is string and "default"
+        if isinstance(xmax, str) and xmax.lower() == "default":
+            xmax = max(X) * (1 + extension_f)
+        else:
+            xmax = float(xmax)
+
+        if isinstance(ymax, str) and ymax.lower() == "default":
+            ymax = max(Y) * (1 + extension_f)
+        else:
+            ymax = float(ymax)
+
+        # Set a new X range from 0 to the xmax
+        X_extended = np.linspace(0, xmax, 500)
+
+        ## Perform linear regression
+        slope, intercept, _, _, _ = stats.linregress(X, Y)
+
+        # Create the equation string
+        equation = f'Y = {slope:.4f} * X + {intercept:.2f}'
+
+        # Calculate the trend line
+        trend_line = slope * X_extended + intercept
+
+        # 1-to-1 Line
+        one_to_one_line = X_extended
+
+        ## Calculate R square
+        # Get the correlation coefficient
+        r = np.corrcoef(X, Y)[0, 1]
+        # Square the correlation coefficient
+        r_squared = r ** 2
+
+        ##Calculate MedAE
+        distance_arr = [abs(X[i] - Y[i]) for i in range(len(X))]
+        MedAE = np.median(distance_arr)
+
+        ## Calculate MedAE percent
+        MedAE_percent = (MedAE / int(grid_area)) * 100
+
+        ## Calculate MAE
+        MAE=np.sum(distance_arr)/len(X)
+        MAE_percent = (MAE / int(grid_area)) * 100
+
+        ## Calculate the IoU
+        # agreement=intersection: Minimum of actual and predicted deforestation for each dot and add them all
+        agree_arr = [min(X[i],Y[i]) for i in range(len(X))]
+        agree = np.sum(agree_arr)   
+
+        # union
+        union_arr = [max(X[i],Y[i]) for i in range(len(X))]
+        union = np.sum(union_arr)
+
+        # IoU
+        iou = 0 if union == 0 else agree / union * 100
+
+        ## Calculate the Difference
+        # Absolute value of predicted deforestation minus actual deforestation of each point and add them all
+        difference=np.sum(distance_arr)
+
+        # Set the figure size
+        plt.figure(figsize=(8, 6))
+
+        # Create a scatter plot
+        plt.scatter(clipped_gdf['ActualDef'], clipped_gdf['PredDef'], color='steelblue', alpha=0.5, linewidth=1.0, s=50)
+
+        # Add labels and title
+        plt.xlabel('Actual Deforestation (ha)', color='black', fontweight='bold', labelpad=10)
+        plt.ylabel('Predicted Deforestation (ha)', color='black', fontweight='bold', labelpad=10)
+        plt.title(title, color='firebrick', fontweight='bold', fontsize=20, pad=20)
+
+        # Plot the trend line
+        plt.plot(X_extended, trend_line, color='mediumseagreen', linestyle='-', label='OLS Line')
+
+        # Plot a 1-to-1 line
+        plt.plot(X_extended, one_to_one_line, color='crimson', linestyle='--',label='1:1 Line')
+
+        ## Theil-Sen Regressor
+        # Fit Theil-Sen Regressor
+        # Compute Theil-Sen estimator
+        ts_slope, ts_intercept, _, _ = stats.theilslopes(Y, X)
+
+        # Generate predictions
+        y_pred = ts_slope * X_extended + ts_intercept
+
+        # Equation of the line
+        ts_equation = f'Y = {ts_slope:.4f} * X + {ts_intercept:.2f}'
+
+        # Plot Theil-Sen Line
+        plt.plot(X_extended, y_pred, color='orange', linestyle='-', label='Theil-Sen Line')
+
+        # Add a legend in the bottom right position
+        plt.legend(loc='lower right')
+
+        plt.xlim([0, xmax])
+        plt.ylim([0, ymax])
+
+        text_x_pos = ymax * 0.05
+        text_y_start_pos = ymax * 0.9
+        text_y_gap = ymax * 0.05
+
+        # Adjust plt texts with the new calculated positions
+        plt.text(text_x_pos, text_y_start_pos, f'Theil-Sen : {ts_equation}', fontsize=11,
+                 color='black')
+        plt.text(text_x_pos, text_y_start_pos - text_y_gap, f'OLS : {equation}', fontsize=11, color='black')
+        plt.text(text_x_pos, text_y_start_pos - 2 * text_y_gap, f'Samples = {len(X)}', fontsize=11, color='black')
+        plt.text(text_x_pos, text_y_start_pos - 3 * text_y_gap, f'R^2 = {r_squared:.4f}', fontsize=11, color='black')
+        plt.text(text_x_pos, text_y_start_pos - 4 * text_y_gap, f'MedAE = {MedAE:.2f} ({MedAE_percent:.2f}%)',
+                 fontsize=11, color='black')
+        plt.text(text_x_pos, text_y_start_pos - 5 * text_y_gap, f'IoU = {iou:.2f}%',fontsize=11, color='black')
+
+        ## Save metrics to txt file
+        base, ext = os.path.splitext(out_fn)
+        txt_out = base + ".txt"
+        lines_to_write = [
+        f"OLS: {equation}\n",
+        f"Theil Sen: {ts_equation}\n",
+        f"Samples = {len(X)}\n",
+        f"R^2 = {r_squared:.4f}\n",
+        f"MedAE = {MedAE:.2f} ({MedAE_percent:.2f}%)\n",
+        f"MAE = {MAE:.2f} ({MAE_percent:.2f}%)\n",
+        f"IoU : {iou:.2f}%\n",
+        f"Agreement : {agree:.2f}\n",
+        f"Difference : {difference:.2f}\n",
+        ]
+
+        with open(txt_out, "w") as file:
+            file.writelines(lines_to_write)
+      
+        # x, yticks
+        plt.yticks(fontsize=10, color='dimgrey')
+        plt.xticks(fontsize=10, color='dimgrey')
+
+        # Save the plot
+        plt.savefig(out_fn)
+
+        ## html
+        # Build Plotly figure
+        fig = go.Figure()
+
+        # Hover 
+        fig.add_trace(go.Scatter(
+            x=X, y=Y, mode="markers",
+            name="Cells",
+            customdata=np.stack([ids, X, Y, agree_arr,distance_arr], axis=-1),
+            hovertemplate="ID: %{customdata[0]}<br>Actual: %{x:.2f} ha<br>Predicted: %{y:.2f} ha<br>Agreement: %{customdata[3]}<br>Difference: %{customdata[4]}<br><extra></extra>",
+            marker=dict(size=8, line=dict(width=0.5), color="steelblue", opacity=0.5), showlegend=False
+        ))
+
+        # OLS line trace
+        fig.add_trace(go.Scatter(
+        x=X_extended, y=trend_line, mode="lines",
+        name="OLS Line",
+        line=dict(color="mediumseagreen", dash="solid")
+        , hoverinfo="skip", hovertemplate=None
+        ))
+
+        # Theil–Sen line trace
+        fig.add_trace(go.Scatter(
+        x=X_extended, y=y_pred, mode="lines",
+        name="Theil–Sen Line",
+        line=dict(color="orange", dash="solid")
+        , hoverinfo="skip", hovertemplate=None
+        ))
+
+        # 1:1 line trace
+        fig.add_trace(go.Scatter(
+        x=X_extended, y=one_to_one_line, mode="lines",
+        name="1:1 Line",
+        line=dict(color="crimson", dash="dash")
+        , hoverinfo="skip", hovertemplate=None
+        ))
+
+        # Layout setting
+        fig.update_layout(
+        title=dict(
+            text=f"<b>{title}</b>",
+            font=dict(color="firebrick", size=20),
+            x=0.5, xanchor="center"
+        ),
+        xaxis=dict(
+            title=dict(text="<b>Actual Deforestation (ha)</b>",
+                    font=dict(color="black"),
+                    standoff=10),                 
+            tickfont=dict(size=10, color="dimgrey"),
+            range=[0, xmax],
+            constrain="domain"
+        ),
+        yaxis=dict(
+            title=dict(text="<b>Predicted Deforestation (ha)</b>",
+                    font=dict(color="black"),
+                    standoff=10),
+            tickfont=dict(size=10, color="dimgrey"),
+            range=[0, ymax]
+        ),
+        hovermode="closest",
+        legend=dict(                    
+            x=0.99, y=0.01, xanchor="right", yanchor="bottom", orientation="v"
+        ),
+        margin=dict(l=60, r=30, t=80, b=60),
+        paper_bgcolor= 'rgb(255,255,255)',
+        plot_bgcolor=  'rgb(234,234,242)',
+        )
+
+        # Annotations 
+        stats_text = (
+            f"Theil–Sen: {ts_equation}<br>"
+            f"OLS: {equation}<br>"
+            f"Samples = {len(X)}<br>"
+            f"R² = {r_squared:.4f}<br>"
+            f"MedAE = {MedAE:.2f} ({MedAE_percent:.2f}%)<br>"
+            f"IoU = {iou:.2f}%<br>"
+        )
+        
+        fig.add_annotation(
+            x=0.02, y=0.98, xref="paper", yref="paper", xanchor="left", yanchor="top",
+            text=stats_text, showarrow=False, align="left"
+        )
+
+        # Save a HTML
+        html_out = base + ".html"
+        
+        pio.write_html(fig, file=html_out, include_plotlyjs=True, full_html=True)
+
+        return
+
+    def remove_temp_files(self):
+        # Files to check for and delete
+        mask_file = 'mask'
+        shapefiles_to_delete = ["TEMP_POLYGONIZED","POLYGONIZED_MASK","thiessen_polygon_temp","temp_vector"]
+
+        # Shapefile associated extensions
+        mask_file_extensions =[".tif",".rst",".rdc",".RST",".RST.aux.xml",".ref"]
+        shapefile_extensions = [".shp", ".shx", ".dbf", ".prj", ".sbn", ".sbx",".cpg", ".shp.xml"]
+
+        # Delete mask files
+        for mask_ext in mask_file_extensions:
+            mask_filename = f"{mask_file}{mask_ext}"
+            if os.path.exists(mask_filename):
+                os.remove(mask_filename)
+
+        # Delete shapefiles with associated extensions
+        for shp_base in shapefiles_to_delete:
+            for ext in shapefile_extensions:
+                full_filename = f"{shp_base}{ext}"
+                if os.path.exists(full_filename):
+                    os.remove(full_filename)
+        self.progress_updated.emit(100)
+        return