From 63073f738066d66cb261aa84a45ea2d0f5242d3a Mon Sep 17 00:00:00 2001
From: sharoncy <s.c.yates@medisin.uio.no>
Date: Thu, 11 May 2023 14:36:09 +0200
Subject: [PATCH] Move functions to read_and_write.py
---
PyNutil/coordinate_extraction.py | 53 +------------------
...segmentations_to_meshview_multithreaded.py | 9 ++--
PyNutil/read_and_write.py | 19 +++++--
3 files changed, 20 insertions(+), 61 deletions(-)
diff --git a/PyNutil/coordinate_extraction.py b/PyNutil/coordinate_extraction.py
index 270fc37..088c52f 100644
--- a/PyNutil/coordinate_extraction.py
+++ b/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.
diff --git a/PyNutil/folder_of_segmentations_to_meshview_multithreaded.py b/PyNutil/folder_of_segmentations_to_meshview_multithreaded.py
index 8705412..c7f43cd 100644
--- a/PyNutil/folder_of_segmentations_to_meshview_multithreaded.py
+++ b/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}")
diff --git a/PyNutil/read_and_write.py b/PyNutil/read_and_write.py
index e791c78..574e3e6 100644
--- a/PyNutil/read_and_write.py
+++ b/PyNutil/read_and_write.py
@@ -1,7 +1,9 @@
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)
--
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