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adding clipping warning flag to d/f corrector to improve performance #264

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Merged
dkazanc merged 1 commit into from
Aug 24, 2026
Merged

adding clipping warning flag to d/f corrector to improve performance #264

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44 changes: 23 additions & 21 deletions httomolibgpu/prep/normalize.py
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Original file line number Diff line number Diff line change
Expand Up @@ -40,7 +40,7 @@
mean = Mock()

from typing import Union, Optional
from numpy import float32, int64
from numpy import float32
from httomolibgpu.misc.utils import (
__check_variable_type,
__check_if_data_3D_array,
Expand All @@ -58,6 +58,7 @@ def dark_flat_field_correction(
darks_multiplier: Union[float, int] = 1.0,
upper_bound: Optional[Union[float, int]] = None,
lower_bound: Optional[Union[float, int]] = None,
clipping_warning: bool = False,
) -> cp.ndarray:
"""
Perform dark/flat field correction of raw projection data.
Expand All @@ -78,6 +79,8 @@ def dark_flat_field_correction(
All values above the upper bound are set to the provided value. Default None.
lower_bound : Optional[float, int]
All values bellow the lower bound are set to the provided value. Default None.
clipping_warning: bool,
Set to True if you want to check if the data is not clipped too much (more than 50%) with the provided upper_bound or/and lower_bound value.

Returns
-------
Expand Down Expand Up @@ -171,30 +174,29 @@ def dark_flat_field_correction(

normalisation_kernel(data, flat0, dark0, upper_bound, lower_bound, out)

# Count the amount of clipping and raise warnings if required
clipped_percentage_warning = (
50.0 # warning if more clipped values than given percentage
)

clipped_total_up = int(count_greater_kernel(out, float32(upper_bound)))
clipped_up_percent = clipped_total_up / data_elements_num * 100

if clipped_up_percent >= clipped_percentage_warning:
print(
"Warning! The output data of 'dark_flat_field_correction' method contains \033[31m{}\033[0m percent of 'upper_bound' clipped data.".format(
int(clipped_up_percent)
)
if clipping_warning:
# Count the amount of clipping and print warnings if required
clipped_percentage_warning = (
50.0 # warning if more clipped values than given percentage
)

clipped_total_lower = int(count_smaller_kernel(out, float32(lower_bound)))
clipped_down_percent = clipped_total_lower / data_elements_num * 100
clipped_total_up = int(count_greater_kernel(out, float32(upper_bound)))
clipped_up_percent = clipped_total_up / data_elements_num * 100
clipped_total_lower = int(count_smaller_kernel(out, float32(lower_bound)))
clipped_down_percent = clipped_total_lower / data_elements_num * 100

if clipped_down_percent >= clipped_percentage_warning:
print(
"Warning! The output data of 'dark_flat_field_correction' method contains \033[31m{}\033[0m percent of 'lower_bound' clipped data.".format(
int(clipped_down_percent)
if clipped_up_percent >= clipped_percentage_warning:
print(
"Warning! The output data of 'dark_flat_field_correction' method contains \033[31m{}\033[0m percent of 'upper_bound' clipped data.".format(
int(clipped_up_percent)
)
)
if clipped_down_percent >= clipped_percentage_warning:
print(
"Warning! The output data of 'dark_flat_field_correction' method contains \033[31m{}\033[0m percent of 'lower_bound' clipped data.".format(
int(clipped_down_percent)
)
)
)

return out

Expand Down
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