Merge

.vs/vision-macula/v17/DocumentLayout.json

@@ -0,0 +1,12 @@
+{
+  "Version": 1,
+  "WorkspaceRootPath": "C:\\Users\\Elena_Himbitskaya\\Desktop\\macula 12.08\\database\\vision-macula\\",
+  "Documents": [],
+  "DocumentGroupContainers": [
+    {
+      "Orientation": 0,
+      "VerticalTabListWidth": 256,
+      "DocumentGroups": []
+    }
+  ]
+}

requirements.txt

@@ -1,4 +1,4 @@
-git+https://github.com/BSMU-ITLab/vision.git@v0.31.2
+#git+https://github.com/BSMU-ITLab/vision.git@v0.31.2
 coloredlogs==15.0.1
 cx_Freeze==7.2.5
 cx_Logging==3.2.1
@@ -9,7 +9,7 @@ lazy_loader==0.4
 lief==0.15.1
 mpmath==1.3.0
 networkx==3.4.2
-numpy==2.1.3
+numpy~=1.26.4
 onnxruntime-gpu==1.20.0
 opencv-python==4.10.0.84
 packaging==24.2
@@ -27,3 +27,5 @@ shiboken6==6.8.0.2
 sortedcontainers==2.4.0
 sympy==1.13.3
 tifffile==2024.9.20
+
+pandas~=2.2.3

src/bsmu/macula/configs/default/bsmu.macula/app.MaculaApp.conf.yaml

@@ -12,7 +12,7 @@ plugins:
   - bsmu.vision.plugins.visualizers.image.layered.LayeredImageVisualizerPlugin
 
   - bsmu.vision.plugins.overlayers.image.ImageViewerOverlayerPlugin
-#  - bsmu.vision.plugins.overlayers.path.ImageViewerPathOverlayerPlugin
+  - bsmu.vision.plugins.overlayers.path.ImageViewerPathOverlayerPlugin
 #  - bsmu.vision.plugins.overlayers.intersection.ImageViewerIntersectionOverlayerPlugin
 
   - bsmu.vision.plugins.writers.image.common.CommonImageFileWriterPlugin
@@ -21,11 +21,15 @@ plugins:
   - bsmu.vision.plugins.tools.viewer.image.hand_tool.HandImageViewerToolPlugin
   - bsmu.vision.plugins.tools.viewer.image.wsi_smart_brush.WsiSmartBrushImageViewerToolPlugin
 
-#  - bsmu.vision.plugins.walkers.file.MdiImageLayerFileWalkerPlugin
+  - bsmu.vision.plugins.walkers.file.MdiImageLayerFileWalkerPlugin
 
   - bsmu.vision.plugins.layer_controller.MdiImageViewerLayerControllerPlugin
   - bsmu.vision.plugins.layers_view.LayersTableViewPlugin
 
   - bsmu.vision.plugins.task_storage_view.TaskStorageViewPlugin
 
+  - bsmu.macula.plugins.db.BD.BD
   - bsmu.macula.plugins.gui.ensemble_segmenter_gui.EnsembleSegmenterGuiPlugin
+  - bsmu.macula.plugins.db.database_manager.DatabaseManager
+
+  - bsmu.macula.plugins.analyser.mask_analyser.MaskAnalyserPlugin

src/bsmu/macula/configs/default/bsmu.macula/plugins.BD.conf.yaml

@@ -0,0 +1 @@
+edit_picture: ':/dbicons/edit.png'

src/bsmu/macula/configs/default/bsmu.macula/plugins.BinaryEnsemblePlugin.conf.yaml

@@ -1,11 +1,19 @@
 binary_ensemble_models:
-  name: {"class_1.onnx":1, "class_6.onnx":6, "class_9.onnx":9, "class_12.onnx":12, "class_14.onnx":14, "class_2.onnx":2, "class_11.onnx":2}
+  class_models: { 1: "Class_1.onnx", 3: "Class_3.onnx", 4: "Class_4.onnx",
+                  5: "Class_5.onnx", 6: "Class_6.onnx", 9: "Class_9.onnx",
+                  12: "Class_12.onnx", 13: "Class_13.onnx", 14: "Class_14.onnx",
+                  15: "Class_15.onnx" }
+  boundary_model: "Class_bnd.onnx"
+  ped_model: "Class_4PED.onnx"
+  three_and_six_model: "Class_3and6.onnx"
+  tr_model: "Class_tr.onnx"
+  catboost_model: "catboost_model.onnx"
   output_object_name: 'Tissue'
   output_object_short_name: 'T'
   preload: false
   batch_size: 4
-  input_size: [1, 512, 512]
+  input_size: [1, 256, 512]
   channels_axis: 0
   channels_order: 'rgb'
-  normalize: true
+  normalize: false
   mask_binarization_threshold: 0.5

src/bsmu/macula/configs/default/bsmu.macula/plugins.MaskAnalyserPlugin.conf.yaml

@@ -0,0 +1,70 @@
+classes:
+  - id: 1
+    name: "Drusen"
+    attributes:
+      - name: "Width"
+        description: "The width of the drusen object"
+      - name: "Height"
+        description: "The height of the drusen object"
+      - name: "Area"
+        description: "The area of the drusen object"
+
+  - id: 2
+    name: "Serous PED"
+    attributes:
+      - name: "Width"
+        description: "The width of the serous PED object"
+      - name: "Height"
+        description: "The height of the serous PED object"
+      - name: "Area"
+        description: "The area of the serous PED object"
+
+  - id: 4
+    name: "Hyperreflective Subretinal Fluid"
+    attributes:
+      - name: "Width"
+        description: "The width of the subretinal fluid object"
+      - name: "Height"
+        description: "The height of the subretinal fluid object"
+      - name: "Area"
+        description: "The area of the subretinal fluid object"
+
+  - id: 5
+    name: "Hyperreflective Intraretinal Fluid"
+    attributes:
+      - name: "Width"
+        description: "The width of the intraretinal fluid object"
+      - name: "Height"
+        description: "The height of the intraretinal fluid object"
+      - name: "Area"
+        description: "The area of the intraretinal fluid object"
+
+  - id: 10
+    name: "Fibrovascular PED"
+    attributes:
+      - name: "Width"
+        description: "The width of the fibrovascular PED object"
+      - name: "Height"
+        description: "The height of the fibrovascular PED object"
+      - name: "Area"
+        description: "The area of the fibrovascular PED object"
+
+  - id: 11
+    name: "Drusenoid PED"
+    attributes:
+      - name: "Width"
+        description: "The width of the drusenoid PED object"
+      - name: "Height"
+        description: "The height of the drusenoid PED object"
+      - name: "Area"
+        description: "The area of the drusenoid PED object"
+
+  - id: 16
+    name: "Hemorrhagic PED"
+    attributes:
+      - name: "Width"
+        description: "The width of the hemorrhagic PED object"
+      - name: "Height"
+        description: "The height of the hemorrhagic PED object"
+      - name: "Area"
+        description: "The area of the hemorrhagic PED object"

src/bsmu/macula/configs/default/bsmu.macula/plugins.MultiSegmPlugin.conf.yaml

@@ -0,0 +1,10 @@
+multi_segmenter_model:
+  name: "model_segmentation.onnx"
+  numclasses: 10
+  output_object_name: 'Tissue'
+  output_object_short_name: 'T'
+  preload: false
+  channels_axis: 0
+  channels_order: 'rgb'
+  normalize: true
+  mask_binarization_threshold: 0.5

src/bsmu/macula/configs/default/bsmu.macula/plugins.analyser.MaskAnalyserPlugin.conf.yaml

@@ -0,0 +1,70 @@
+classes:
+  - id: 1
+    name: "Drusen"
+    attributes:
+      - name: "Width"
+        description: "The width of the drusen object"
+      - name: "Height"
+        description: "The height of the drusen object"
+      - name: "Area"
+        description: "The area of the drusen object"
+
+  - id: 2
+    name: "Serous PED"
+    attributes:
+      - name: "Width"
+        description: "The width of the serous PED object"
+      - name: "Height"
+        description: "The height of the serous PED object"
+      - name: "Area"
+        description: "The area of the serous PED object"
+
+  - id: 4
+    name: "Hyperreflective Subretinal Fluid"
+    attributes:
+      - name: "Width"
+        description: "The width of the subretinal fluid object"
+      - name: "Height"
+        description: "The height of the subretinal fluid object"
+      - name: "Area"
+        description: "The area of the subretinal fluid object"
+
+  - id: 5
+    name: "Hyperreflective Intraretinal Fluid"
+    attributes:
+      - name: "Width"
+        description: "The width of the intraretinal fluid object"
+      - name: "Height"
+        description: "The height of the intraretinal fluid object"
+      - name: "Area"
+        description: "The area of the intraretinal fluid object"
+
+  - id: 10
+    name: "Fibrovascular PED"
+    attributes:
+      - name: "Width"
+        description: "The width of the fibrovascular PED object"
+      - name: "Height"
+        description: "The height of the fibrovascular PED object"
+      - name: "Area"
+        description: "The area of the fibrovascular PED object"
+
+  - id: 11
+    name: "Drusenoid PED"
+    attributes:
+      - name: "Width"
+        description: "The width of the drusenoid PED object"
+      - name: "Height"
+        description: "The height of the drusenoid PED object"
+      - name: "Area"
+        description: "The area of the drusenoid PED object"
+
+  - id: 16
+    name: "Hemorrhagic PED"
+    attributes:
+      - name: "Width"
+        description: "The width of the hemorrhagic PED object"
+      - name: "Height"
+        description: "The height of the hemorrhagic PED object"
+      - name: "Area"
+        description: "The area of the hemorrhagic PED object"

src/bsmu/macula/configs/default/bsmu.vision/plugins.palette.PalettePackSettingsPlugin.conf.yaml

@@ -1,66 +1,61 @@
 main_palette:
   default_color: [ 190, 255, 0, 255 ]
   row_by_name:
-    background:    [   0,   0,   0,   0,   0 ]
+    background: [   0,   0,   0,   0,   0 ]
 
     # Drusen
-    foreground:    [   1, 154, 205,  50, 255 ]  # YellowGreen
+    foreground: [   1, 154, 205,  50, 255 ]  # YellowGreen
 
-    # Serous Pigment Epithelial Detachment (SPED)
-    sped:          [   2, 148,   0, 211, 255 ]  # DarkViolet
+    # Sub-Retinal Pigment Epithelium Fluid (SRPEF)
+    sped:      [   2, 148,   0, 211, 255 ]  # DarkViolet
 
     # Intraretinal Fluid (IRF)
-    irf:           [   3,   0,   0, 255, 255 ]  # Blue
+    irf:        [   3,   0,   0, 255, 255 ]  # Blue
 
     # Subretinal Hyperreflective Material (SHRM)
-    shrm:          [   4, 255, 255,   0, 255 ]  # Yellow
+    shrm:       [   4, 255, 255,   0, 255 ]  # Yellow
 
     # Intraretinal Hyperreflective Foci (IHRF)
-    ihrf:          [   5, 184, 134,  11, 255 ]  # DarkGoldenrod
+    ihrf:       [   5, 184, 134,  11, 255 ]  # DarkGoldenrod
 
     # Subretinal Fluid (SRF) / Neuroepithelial Detachment (NED)
-    srf:           [   6, 255,   0, 255, 255 ]  # Fuchsia
+    srf:        [   6, 255,   0, 255, 255 ]  # Fuchsia
 
-    # Sub-Bruch’s Fluid (SBF)
-    sbf:           [   7, 238, 130, 238, 255 ]  # Violet
+    # Sub-Bruch’s Fluid
+    sbf:      [   7, 238, 130, 238, 255 ]  # Violet
 
     # Retinal Angiomatous Proliferation (RAP)
-    rap:           [   8, 255,   0,   0, 255 ]  # Red
+    rap:        [   8, 255,   0,   0, 255 ]  # Red
 
     # Retinal Pigment Epithelium (RPE)
-    rpe:           [   9,   0, 255,   0, 255 ]  # Lime
+    rpe:        [   9,   0, 255,   0, 255 ]  # Lime
 
-    # Fibrovascular Pigment Epithelial Detachment (FVPED)
-    fvped:         [  10,   0, 255, 255, 255 ]  # Aqua
+    class_10:   [  10,   0, 255, 255, 255 ]  # Aqua
 
     # Drusenoid Pigment Epithelial Detachment (Drusenoid PED)
-    drusenoid_ped: [  11, 255, 160, 122, 255 ]  # LightSalmon
+    drusenoid_ped:   [  11, 255, 160, 122, 255 ]  # LightSalmon
 
     # Ellipsoid Zone (EZ)
-    ez:            [  12,  85, 107,  47, 255 ]  # DarkOliveGreen
+    ez:   [  12,  85, 107,  47, 255 ]  # DarkOliveGreen
 
     # Myoid Zone (MZ)
-    mz:            [  13,  60, 179, 113, 255 ]  # MediumSeaGreen
+    mz:   [  13,  60, 179, 113, 255 ]  # MediumSeaGreen
 
     # Choroid
-    choroid:       [  14,   0, 139, 139, 255 ]  # DarkCyan
-
-    # Photoreceptor Outer Segments (POS)
-    pos:           [  15,  72,  61, 139, 255 ]  # DarkSlateBlue
-
-    # Hemorrhagic Pigment Epithelial Detachment (HPED)
-    hped:          [  16, 127, 255,   0, 255 ]  # Chartreuse
-
-    # Sub-Retinal Pigment Epithelium Fluid (SRPEF)
-    srpef:         [  17, 143, 188, 139, 255 ]  # DarkSeaGreen
-
-    class_18:      [  18, 139,  69,  19, 255 ]  # SaddleBrown
-    class_19:      [  19,   0, 191, 255, 255 ]  # DeepSkyBlue
-    class_20:      [  20,  65, 105, 225, 255 ]  # RoyalBlue
-    class_21:      [  21, 255,  69,   0, 255 ]  # OrangeRed
-    class_22:      [  22, 240, 230, 140, 255 ]  # Khaki
-    class_23:      [  23, 219, 112, 147, 255 ]  # PaleVioletRed
-    class_24:      [  24, 186,  85, 211, 255 ]  # MediumOrchid
-    class_25:      [  25, 178,  34,  34, 255 ]  # FireBrick
-    class_26:      [  26,   0,   0,   0, 255 ]  # Black
-    class_255:     [ 255,  50,   0,  50, 255 ]  # Dark Purple
+    choroid:    [  14,   0, 139, 139, 255 ]  # DarkCyan
+
+    # Photoreceptor Outer Segments
+    pos:   [  15,  72,  61, 139, 255 ]  # DarkSlateBlue
+
+    class_16:   [  16, 127, 255,   0, 255 ]  # Chartreuse
+    class_17:   [  17, 143, 188, 139, 255 ]  # DarkSeaGreen
+    class_18:   [  18, 139,  69,  19, 255 ]  # SaddleBrown
+    class_19:   [  19,   0, 191, 255, 255 ]  # DeepSkyBlue
+    class_20:   [  20,  65, 105, 225, 255 ]  # RoyalBlue
+    class_21:   [  21, 255,  69,   0, 255 ]  # OrangeRed
+    class_22:   [  22, 240, 230, 140, 255 ]  # Khaki
+    class_23:   [  23, 219, 112, 147, 255 ]  # PaleVioletRed
+    class_24:   [  24, 186,  85, 211, 255 ]  # MediumOrchid
+    class_25:   [  25, 178,  34,  34, 255 ]  # FireBrick
+    class_26:   [  26,   0,   0,   0, 255 ]  # Black
+    class_255:  [ 255,  50,   0,  50, 255 ]  # Dark Purple