Problem solving nonlinear issues

- Revert padding change as it did not fix the bug
- Create black atlas maps from nonlinear alignment.json to investigate error
- found that regions that differ between black atlas maps and VisuAlign atlas maps give different numerical output in reports (e.g. s005).

PyNutil/processing/counting_and_load.py

@@ -224,8 +224,14 @@ def flat_to_dataframe(
     if (image_vector is not None) and (volume is not None):
         image = generate_target_slice(image_vector, volume)
         image = np.float64(image)
+        random_number = np.random.randint(0,1000)
+        outim = ((image==0) * 255).astype(np.uint8)
+        cv2.imwrite(f"{random_number}_linear.jpg",  outim)
         if triangulation is not None:
             image = warp_image(image, triangulation, rescaleXY)
+            outim = ((image==0) * 255).astype(np.uint8)
+
+            cv2.imwrite(f"{random_number}_warped.jpg", outim)
     elif file.endswith(".flat"):
         image = read_flat_file(file)
     elif file.endswith(".seg"):

workflows/basic_example_custom_atlas.py

@@ -13,14 +13,15 @@ from PyNutil import PyNutil
 ###The label_path is the path to the corresponding atlas .csv
 ###The object_cutoff is a cut-off for min object size
 ### get_coordinates, if use_flat=True, place flat files in folder titled "flat_files" at same level as "segmentations" folder 
+#This does not use BrainGlobe API.
 
 pnt = PyNutil(
-    segmentation_folder="../tests/test_data/linear_allen_mouse/",
-    alignment_json="../tests/test_data/linear_allen_mouse/alignment_linear.json",
+    segmentation_folder="../tests/test_data/nonlinear_allen_mouse/",
+    alignment_json="../tests/test_data/nonlinear_allen_mouse/alignment.json",
     colour=[0, 0, 0],
     atlas_path="../tests/test_data/allen_mouse_2017_atlas/annotation_25_reoriented_2017.nrrd",
     label_path="../tests/test_data/allen_mouse_2017_atlas//allen2017_colours.csv",
 )
 pnt.get_coordinates(object_cutoff=0, use_flat=False)
 pnt.quantify_coordinates()
-pnt.save_analysis("../test_result/test_linear_allen_mouse")
+pnt.save_analysis("../test_result/test_nonlinear_allen_mouse_noflat_24_02_25")