renamed main file to pynutil and introduced a workflow example

ProjectSegmentation3D_vec.py → PyNutil.py

@@ -26,7 +26,7 @@ def assignPointsToRegions(points, regionVolume):
     return regionDict
 
 
-def transformToRegistration( SegHeight, SegWidth, RegHeight, RegWidth):
+def transformToRegistration(SegHeight, SegWidth, RegHeight, RegWidth):
     Yscale = RegHeight/SegHeight
     Xscale = RegWidth/SegWidth
     return  Yscale,Xscale
@@ -97,22 +97,6 @@ def SegmentationToAtlasSpace(slice, SegmentationPath, pixelID='auto', nonLinear=
     # points = points.reshape(-1)
     return points
 
-# def applyTransformationToPoints(ID_pixels, slice,SegHeight, SegWidth, nonLinear=True):
-#     RegHeight = slice["height"]
-#     RegWidth  = slice["width"]
-#     #this calculates reg/seg
-#     Yscale , Xscale = transformToRegistration(SegHeight,SegWidth,  RegHeight,RegWidth)
-#     #this creates a triangulation using the reg width
-#     triangulation   = triangulate(RegWidth, RegHeight, slice["markers"])
-#     #scale the seg coordinates to reg/seg
-#     scaledY,scaledX = scalePositions(ID_pixels[0], ID_pixels[1], Yscale, Xscale)
-#     if nonLinear:
-#         newX, newY = transform_vec(triangulation, scaledX, scaledY)
-#     else:
-#         newX, newY = scaledX, scaledY
-#     #scale U by Uxyz/RegWidth and V by Vxyz/RegHeight
-#     points = transformToAtlasSpace(slice['anchoring'], newY, newX, RegHeight, RegWidth)
-#     return points
 
 def FolderToAtlasSpace(folder, QUINT_alignment, pixelID=[0, 0, 0], nonLinear=True):
     slices = loadVisuAlignJson(QUINT_alignment)

basic_workflow.py

+#pandas is used for working with csv files
+import pandas as pd
+#nrrd just lets us open nrrd files
+import nrrd
+#import our function for converting a folder of segmentations to points
+from PyNutil import FolderToAtlasSpace
+
+
+
+#now we can use our function to convert the folder of segmentations to points
+points = FolderToAtlasSpace("test_data/oneSection15/", "test_data/C68_nonlinear.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"
+#then the path to the volume
+volume_path = "annotation_volumes//annotation_10.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
+data, header = nrrd.read(volume_path)
\ No newline at end of file

reformat_allen_label.py

+import pandas as pd
+#open colour txt file
+path = "itksnap_label_description.txt"
+
+
+# use " " as separator
+#set column names
+df = pd.read_csv(path, sep=" ", header=None,  names=["id", "r", "g", "b", "1a", "1b", "1c", "name"])
+df[["name", "allenID"]] = df["name"].str.split(' - ', expand=True)
+df.to_csv("allen2022_colours.csv", index=False)
+