From f48f139be57d77f2e0e11bc0b8b74e67518eac90 Mon Sep 17 00:00:00 2001
From: Harry Carey <38996929+PolarBean@users.noreply.github.com>
Date: Tue, 25 Apr 2023 21:13:27 +0200
Subject: [PATCH] restructured package
---
PyNutil.py => PyNutil/PyNutil.py | 3 ++-
basic_workflow.py => workflows/basic_workflow.py | 6 +++++-
2 files changed, 7 insertions(+), 2 deletions(-)
rename PyNutil.py => PyNutil/PyNutil.py (98%)
rename basic_workflow.py => workflows/basic_workflow.py (84%)
diff --git a/PyNutil.py b/PyNutil/PyNutil.py
similarity index 98%
rename from PyNutil.py
rename to PyNutil/PyNutil.py
index 9ed2f15..d0df0b9 100644
--- a/PyNutil.py
+++ b/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
+
diff --git a/basic_workflow.py b/workflows/basic_workflow.py
similarity index 84%
rename from basic_workflow.py
rename to workflows/basic_workflow.py
index e4912d2..61e4a9f 100644
--- a/basic_workflow.py
+++ b/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/"
--
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