From 1474c5fea444d094ff83e409a6c0306dc2cb286f Mon Sep 17 00:00:00 2001
From: Harry Carey <38996929+PolarBean@users.noreply.github.com>
Date: Tue, 25 Apr 2023 21:23:13 +0200
Subject: [PATCH] restructuring and adding comments
---
.../visualign_deformations.py | 0
...ow.py => folder_of_segmentations_to_meshview.py} | 13 ++++++++-----
2 files changed, 8 insertions(+), 5 deletions(-)
rename VisuAlignWarpVec.py => PyNutil/visualign_deformations.py (100%)
rename workflows/{basic_workflow.py => folder_of_segmentations_to_meshview.py} (69%)
diff --git a/VisuAlignWarpVec.py b/PyNutil/visualign_deformations.py
similarity index 100%
rename from VisuAlignWarpVec.py
rename to PyNutil/visualign_deformations.py
diff --git a/workflows/basic_workflow.py b/workflows/folder_of_segmentations_to_meshview.py
similarity index 69%
rename from workflows/basic_workflow.py
rename to workflows/folder_of_segmentations_to_meshview.py
index 61e4a9f..d90da81 100644
--- a/workflows/basic_workflow.py
+++ b/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.
+
--
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