restructured package

PyNutil.py → PyNutil/PyNutil.py

@@ -154,7 +154,7 @@ def WritePointsToMeshview(points, pointNames, filename, infoFile):
     WritePoints(regionDict, filename, infoFile)
 
 def labelPoints(points, label_volume, scale_factor=1):
-        """this function takes a list of points and assigns them to a region based on the regionVolume.
+    """this function takes a list of points and assigns them to a region based on the regionVolume.
     These regions will just be the values in the regionVolume at the points.
     it returns a dictionary with the region as the key and the points as the value"""
     #first convert the points to 3 columns
@@ -169,3 +169,4 @@ def labelPoints(points, label_volume, scale_factor=1):
     #get the label value for each point
     labels = label_volume[x,y,z]
     return labels
+

basic_workflow.py → workflows/basic_workflow.py

@@ -2,8 +2,12 @@
 import pandas as pd
 #nrrd just lets us open nrrd files
 import nrrd
+
+#this is a hack to let us import as if we are in the parent directory
+import sys
+sys.path.append('..')
 #import our function for converting a folder of segmentations to points
-from PyNutil import FolderToAtlasSpace, labelPoints, WritePointsToMeshview
+from PyNutil.PyNutil import FolderToAtlasSpace, labelPoints, WritePointsToMeshview
 
 
 segmentation_folder = "test_data/oneSection15/"