From 4a3e4585c4e41982b8adb859960ae998d11d10d5 Mon Sep 17 00:00:00 2001
From: polarbean <harry.carey95@gmail.com>
Date: Fri, 14 Mar 2025 16:43:40 +0100
Subject: [PATCH] measure damaged and undamaged region areas
---
PyNutil/processing/coordinate_extraction.py | 2 +-
PyNutil/processing/counting_and_load.py | 12 +++++++++++-
.../segmentations/test_s003.png | Bin 120 -> 6768 bytes
.../segmentations/test_s003_.png | Bin 6768 -> 0 bytes
4 files changed, 12 insertions(+), 2 deletions(-)
delete mode 100644 tests/test_data/nonlinear_allen_mouse/segmentations/test_s003_.png
diff --git a/PyNutil/processing/coordinate_extraction.py b/PyNutil/processing/coordinate_extraction.py
index 38c291f..37e5358 100644
--- a/PyNutil/processing/coordinate_extraction.py
+++ b/PyNutil/processing/coordinate_extraction.py
@@ -389,7 +389,7 @@ def get_region_areas(
atlas_map = load_image(flat_file_atlas,slice_dict["anchoring"], atlas_volume, triangulation, (seg_width, seg_height), atlas_labels)
region_areas = flat_to_dataframe(
- atlas_map, (seg_width, seg_height)
+ atlas_map, damage_mask, (seg_width, seg_height)
)
return region_areas, atlas_map
diff --git a/PyNutil/processing/counting_and_load.py b/PyNutil/processing/counting_and_load.py
index f15ff36..c09dc67 100644
--- a/PyNutil/processing/counting_and_load.py
+++ b/PyNutil/processing/counting_and_load.py
@@ -270,6 +270,7 @@ def warp_image(image, triangulation, rescaleXY):
def flat_to_dataframe(
image,
+ damage_mask,
rescaleXY=None):
"""
Converts a flat file to a DataFrame.
@@ -287,7 +288,16 @@ def flat_to_dataframe(
np.array: array in shape of alignment XY scaled by rescaleXY with allen ID for each point
"""
scale_factor = calculate_scale_factor(image, rescaleXY)
- df_area_per_label = count_pixels_per_label(image, scale_factor)
+ if damage_mask is not None:
+ damage_mask = cv2.resize(damage_mask.astype(np.uint8), (image.shape[::-1]), interpolation=cv2.INTER_NEAREST).astype(bool)
+ undamaged_df_area_per_label = count_pixels_per_label(image[damage_mask], scale_factor)
+ damaged_df_area_per_label = count_pixels_per_label(image[~damage_mask], scale_factor)
+ undamaged_df_area_per_label = undamaged_df_area_per_label.rename(columns={"region_area": "undamaged_region_area"})
+ damaged_df_area_per_label = damaged_df_area_per_label.rename(columns={"region_area": "damaged_region_area"})
+ df_area_per_label = pd.merge(undamaged_df_area_per_label, damaged_df_area_per_label, on='idx', how='outer').fillna(0)
+ df_area_per_label["region_area"] = df_area_per_label["undamaged_region_area"] + df_area_per_label["damaged_region_area"]
+ else:
+ df_area_per_label = count_pixels_per_label(image, scale_factor)
return df_area_per_label
diff --git a/tests/test_data/nonlinear_allen_mouse/segmentations/test_s003.png b/tests/test_data/nonlinear_allen_mouse/segmentations/test_s003.png
index 7ff61a5947eca46caa8b304805a5210b93dbd5d7..260f98b911f9071cb51e7d5a47bd263866afae6b 100644
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diff --git a/tests/test_data/nonlinear_allen_mouse/segmentations/test_s003_.png b/tests/test_data/nonlinear_allen_mouse/segmentations/test_s003_.png
deleted file mode 100644
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--
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