Fix for "per_pixel"

PyNutil only worked for method = "all". Fix so that it works for "per_pixel" and "per_object".

PyNutil/coordinate_extraction.py

@@ -309,6 +309,7 @@ def segmentation_to_atlas_space(
     region_areas = get_region_areas(use_flat, atlas_labels, flat_file_atlas, seg_width, seg_height, slice_dict, atlas_volume, triangulation)
     y_scale, x_scale = transform_to_registration(seg_height, seg_width, reg_height, reg_width)
     centroids, points = None, None
+    scaled_centroidsX, scaled_centroidsY, scaled_x, scaled_y = None, None, None, None 
     if method in ["per_object", "all"]:
         centroids, scaled_centroidsX, scaled_centroidsY = get_centroids(segmentation, pixel_id, y_scale, x_scale, object_cutoff)
     if method in ["per_pixel", "all"]:

testOOP.py

@@ -2,11 +2,13 @@
 import os
 
 os.chdir("..")
+
+
 pnt = PyNutil(settings_file=r"PyNutil/test/test10_PyNutil_web.json")
 
 ##Use flat can be set to True if you want to use the flat file
 # instead of the visualign json (this is only useful for testing and will be removed)
-pnt.get_coordinates(object_cutoff=0, use_flat=False)
+pnt.get_coordinates(object_cutoff=0, method="per_pixel")
 
 pnt.quantify_coordinates()