restructuring and adding comments

workflows/basic_workflow.py → workflows/folder_of_segmentations_to_meshview.py

@@ -10,14 +10,14 @@ sys.path.append('..')
 from PyNutil.PyNutil import FolderToAtlasSpace, labelPoints, WritePointsToMeshview
 
 
-segmentation_folder = "test_data/oneSection15/"
-alignment_json = "test_data/C68_nonlinear.json"
+segmentation_folder = "../test_data/oneSection15/"
+alignment_json = "../test_data/C68_nonlinear.json"
 #now we can use our function to convert the folder of segmentations to points
 points = FolderToAtlasSpace(segmentation_folder,alignment_json, pixelID=[255, 0, 255], nonLinear=True)
 #first we need to find the label file for the volume
-label_path = "annotation_volumes//allen2022_colours.csv"
+label_path = "../annotation_volumes//allen2022_colours.csv"
 #then the path to the volume
-volume_path = "annotation_volumes//annotation_10_reoriented.nrrd"
+volume_path = "../annotation_volumes//annotation_10_reoriented.nrrd"
 #read the label file
 label_df = pd.read_csv(label_path)
 #read the annotation volume, it also has a header but we don't need it
@@ -25,4 +25,7 @@ data, header = nrrd.read(volume_path)
 #now we can get the labels for each point
 labels = labelPoints(points, data, scale_factor=2.5)
 #save points to a meshview json
-WritePointsToMeshview(points, labels,"outputs/points.json", label_df)
+WritePointsToMeshview(points, labels,"../outputs/points.json", label_df)
+
+#while we havent added it here it would be good to next quantify the number of cells for each label.
+