Move functions to read_and_write.py

PyNutil/coordinate_extraction.py

@@ -78,17 +78,6 @@ def transformToAtlasSpace(anchoring, Y, X, RegHeight, RegWidth):
     return (O+XYZU+XYZV).T
 
 
-#related to read and write: loadVisuAlignJson
-# this has been moved successfully to read_and_write
-"""
-def loadVisuAlignJson(filename):
-    with open(filename) as f:
-        vafile = json.load(f)
-    slices = vafile["slices"]
-    return slices
-"""
-
-
 # related to coordinate extraction
 def SegmentationToAtlasSpace(slice, SegmentationPath, pixelID='auto', nonLinear=True):
     """combines many functions to convert a segmentation to atlas space. It takes care
@@ -149,6 +138,7 @@ def FolderToAtlasSpace(folder, QUINT_alignment, pixelID=[0, 0, 0], nonLinear=Tru
 
 
 #related to coordinate extraction
+#this function returns an array of points
 def FolderToAtlasSpaceMultiThreaded(folder, QUINT_alignment, pixelID=[0, 0, 0], nonLinear=True):
     "apply Segmentation to atlas space to all segmentations in a folder"
     slices = loadVisuAlignJson(QUINT_alignment)
@@ -178,6 +168,7 @@ def FolderToAtlasSpaceMultiThreaded(folder, QUINT_alignment, pixelID=[0, 0, 0],
 
 
 # related to coordinate extraction
+# this function returns an array of points
 def SegmentationToAtlasSpaceMultiThreaded(slice, SegmentationPath, pixelID='auto', nonLinear=True, pointsList=None, index=None):
     """combines many functions to convert a segmentation to atlas space. It takes care
     of deformations"""
@@ -216,43 +207,3 @@ def SegmentationToAtlasSpaceMultiThreaded(slice, SegmentationPath, pixelID='auto
     pointsList[index] = np.array(points)
 
 
-#related to counting_and_load
-def createRegionDict(points, regions):
-    """points is a list of points and regions is an id for each point"""
-    regionDict = {region:points[regions==region].flatten().tolist() for region in np.unique(regions)}
-    return regionDict
-
-
-#related to read and write: WritePoints
-def WritePoints(pointsDict, filename, infoFile):
-
-    meshview = [
-    {
-        "idx": idx,
-        "count": len(pointsDict[name])//3,
-        "name"  :str(infoFile["name"].values[infoFile["allenID"]==name][0]),
-        "triplets": pointsDict[name],
-        "r": str(infoFile["r"].values[infoFile["allenID"]==name][0]),
-        "g": str(infoFile["g"].values[infoFile["allenID"]==name][0]),
-        "b": str(infoFile["b"].values[infoFile["allenID"]==name][0])
-    }
-    for name, idx in zip(pointsDict.keys(), range(len(pointsDict.keys())))
-    ]
-    #write meshview json
-    with open(filename, "w") as f:
-        json.dump(meshview, f)
-
-
-
-# related to read and write: WritePointsToMeshview
-def WritePointsToMeshview(points, pointNames, filename, infoFile):
-    regionDict = createRegionDict(points, pointNames)
-    WritePoints(regionDict, filename, infoFile)
-
-
-
-# related to counting_and_load: labelPoints.
-# this has been moved successfully. 
-
-# related to counting_and_load: PixelCountPerRegion
-# This has been moved successfully.

PyNutil/folder_of_segmentations_to_meshview_multithreaded.py

@@ -9,14 +9,14 @@ import json
 
 from datetime import datetime
 
-#import json into "input" variable, use to define input parameters
+#import json, use to define input parameters
 with open('../test/test2.json', 'r') as f:
   input = json.load(f)
 #print(input)
 
 #import our function for converting a folder of segmentations to points
-from coordinate_extraction import FolderToAtlasSpace, WritePointsToMeshview, FolderToAtlasSpaceMultiThreaded
-from read_and_write import SaveDataframeasCSV
+from coordinate_extraction import FolderToAtlasSpace, FolderToAtlasSpaceMultiThreaded
+from read_and_write import SaveDataframeasCSV, WritePointsToMeshview
 from counting_and_load import PixelCountPerRegion, labelPoints
 
 startTime = datetime.now()
@@ -35,14 +35,13 @@ label_df = pd.read_csv(input["label_path"])
 data, header = nrrd.read(input["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, input["points_json_path"], label_df)
 
 df_counts_per_label_name = PixelCountPerRegion(labels, input["allen_colours"])
-
 SaveDataframeasCSV(df_counts_per_label_name, input["counts_per_label_name"])
 
-
 time_taken = datetime.now() - startTime
 
 print(f"overall time taken was: {time_taken}")

PyNutil/read_and_write.py

 import json
+import numpy as np
 
 
-#related to read and write: loadVisuAlignJson
+#related to read and write
+# this function reads a VisuAlign JSON and returns the slices
 def loadVisuAlignJson(filename):
     with open(filename) as f:
         vafile = json.load(f)
@@ -9,10 +11,18 @@ def loadVisuAlignJson(filename):
     return slices
 
 
+#related to read_and_write, used in WritePointsToMeshview
+# this function returns a dictionary of region names
+def createRegionDict(points, regions):
+    """points is a list of points and regions is an id for each point"""
+    regionDict = {region:points[regions==region].flatten().tolist() for region in np.unique(regions)}
+    return regionDict
+
+
 #related to read and write: WritePoints
+# this function writes the region dictionary to a meshview json
 def WritePoints(pointsDict, filename, infoFile):
-    """write a series of points to a meshview json file. pointsDict is a dictionary with the points.
-    pointsDict is created by createRegionDict. infoFile is a csv file with the information about the regions"""
+
     meshview = [
     {
         "idx": idx,
@@ -31,9 +41,8 @@ def WritePoints(pointsDict, filename, infoFile):
 
 
 # related to read and write: WritePointsToMeshview
-# this uses createRegionDict in coordinate_extraction.py
+# this function combines createRegionDict and WritePoints functions
 def WritePointsToMeshview(points, pointNames, filename, infoFile):
-    """this is the function you call more often as it combines the other functions for writing meshview"""
     regionDict = createRegionDict(points, pointNames)
     WritePoints(regionDict, filename, infoFile)