diff --git a/PyNutil/coordinate_extraction.py b/PyNutil/coordinate_extraction.py
index 453fa27dc85e9bf598b2635589f0004f806ce707..e1ac91f443da27d78543829323d4f5656644da1b 100644
--- a/PyNutil/coordinate_extraction.py
+++ b/PyNutil/coordinate_extraction.py
@@ -9,6 +9,7 @@ import cv2
from skimage import measure
import threading
+#related to coordinate_extraction
def getCentroidsAndArea(Segmentation, pixelCutOff=0):
"""this function returns the center coordinate of each object in the segmentation.
You can set a pixelCutOff to remove objects that are smaller than that number of pixels"""
@@ -26,18 +27,14 @@ def getCentroidsAndArea(Segmentation, pixelCutOff=0):
coords = np.array([label.coords for label in labelsInfo])
return centroids, area, coords
-
-
-
-
-
+# related to coordinate extraction
def transformToRegistration(SegHeight, SegWidth, RegHeight, RegWidth):
"""this function returns the scaling factors to transform the segmentation to the registration space"""
Yscale = RegHeight/SegHeight
Xscale = RegWidth/SegWidth
return Yscale,Xscale
-
+# related to coordinate extraction
def findMatchingPixels(Segmentation, id):
"""this function returns the Y and X coordinates of all the pixels in the segmentation that match the id provided"""
mask = Segmentation==id
@@ -46,6 +43,7 @@ def findMatchingPixels(Segmentation, id):
idY, idX = id_positions[0], id_positions[1]
return idY,idX
+#related to coordinate extraction
def scalePositions(idY, idX, Yscale, Xscale):
"""this function scales the Y and X coordinates to the registration space.
(the Yscale and Xscale are the output of transformToRegistration)"""
@@ -53,6 +51,7 @@ def scalePositions(idY, idX, Yscale, Xscale):
idX = idX * Xscale
return idY,idX
+#related to coordinate extraction
def transformToAtlasSpace(anchoring, Y, X, RegHeight, RegWidth):
"""transform to atlas space using the QuickNII anchoring vector"""
O = anchoring[0:3]
@@ -71,12 +70,14 @@ def transformToAtlasSpace(anchoring, Y, X, RegHeight, RegWidth):
O = np.reshape(O, (3,1))
return (O+XYZU+XYZV).T
+#related 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
of deformations"""
@@ -114,7 +115,7 @@ def SegmentationToAtlasSpace(slice, SegmentationPath, pixelID='auto', nonLinear=
# points = points.reshape(-1)
return np.array(points)
-
+# related to coordinate extraction
def FolderToAtlasSpace(folder, QUINT_alignment, pixelID=[0, 0, 0], nonLinear=True):
"apply Segmentation to atlas space to all segmentations in a folder"
slices = loadVisuAlignJson(QUINT_alignment)
@@ -133,6 +134,7 @@ def FolderToAtlasSpace(folder, QUINT_alignment, pixelID=[0, 0, 0], nonLinear=Tru
points.extend(SegmentationToAtlasSpace(current_slice, SegmentationPath, pixelID, nonLinear))
return np.array(points)
+#related to coordinate extraction
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)
@@ -160,7 +162,7 @@ def FolderToAtlasSpaceMultiThreaded(folder, QUINT_alignment, pixelID=[0, 0, 0],
points = [item for sublist in pointsList for item in sublist]
return np.array(points)
-
+# related to coordinate extraction
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"""
@@ -198,11 +200,13 @@ def SegmentationToAtlasSpaceMultiThreaded(slice, SegmentationPath, pixelID='auto
# points = points.reshape(-1)
pointsList[index] = np.array(points)
+#related to coordinate extraction
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
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"""
@@ -222,11 +226,14 @@ def WritePoints(pointsDict, filename, infoFile):
with open(filename, "w") as f:
json.dump(meshview, f)
+
+# related to read and write
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)
+# related to object_counting
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.
These regions will just be the values in the regionVolume at the points.
diff --git a/PyNutil/folder_of_segmentations_to_meshview_multithreaded.py b/PyNutil/folder_of_segmentations_to_meshview_multithreaded.py
index 47fc06ab0b53f4c454ac045d1761faccb2d0a304..74d36152aca1d33b6220b86583d369e9b9732e71 100644
--- a/PyNutil/folder_of_segmentations_to_meshview_multithreaded.py
+++ b/PyNutil/folder_of_segmentations_to_meshview_multithreaded.py
@@ -10,17 +10,18 @@ import json
from datetime import datetime
#import json, use to define input parameters
-with open('../input.json', 'r') as f:
+with open('../input/input.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, labelPoints, WritePointsToMeshview, FolderToAtlasSpaceMultiThreaded
+#from read_and_write import
startTime = datetime.now()
#now we can use our function to convert the folder of segmentations to points
-points = FolderToAtlasSpaceMultiThreaded(input["segmentation_folder"],input["alignment_json"], pixelID=[255,0,255], nonLinear=True)
+points = FolderToAtlasSpaceMultiThreaded(input["segmentation_folder"],input["alignment_json"], pixelID=input["colour"], nonLinear=input["nonlinear"])
time_taken = datetime.now() - startTime
diff --git a/input.json b/input.json
deleted file mode 100644
index a3596365e91c1f9c2968b31ea2ceb138be62c940..0000000000000000000000000000000000000000
--- a/input.json
+++ /dev/null
@@ -1,10 +0,0 @@
-{"label_path": "../annotation_volumes//allen2022_colours.csv",
- "colour": "[255, 0, 255]",
- "nonlinear": "True",
- "volume_path": "../annotation_volumes//annotation_10_reoriented.nrrd",
- "points_json_path": "../outputs/points.json",
- "segmentation_folder": "../test_data/oneSection15",
- "alignment_json": "../test_data/C68_nonlinear_no_markers.json",
- "allen_colours": "../annotation_volumes//allen2022_colours.csv",
- "counts_per_label_name": "../outputs/counts_per_allenID.csv"
-}
\ No newline at end of file
diff --git a/input/input.json b/input/input.json
index 68434ceda0d756a31b8998958b8e3e0cb85d53aa..479bdd3228cca9bf88c1b1becb68e60d1ed57b84 100644
--- a/input/input.json
+++ b/input/input.json
@@ -1,10 +1,10 @@
-{"label_path": "../annotation_volumes//allen2022_colours.csv",
- "colour": "[255, 0, 255]",
- "volume_path": "../annotation_volumes//annotation_10_reoriented.nrrd",
- "data, header": "nrrd.read(volume_path)",
- "points_json_path": "../outputs/points.json",
+{ "volume_path": "../annotation_volumes/annotation_10_reoriented.nrrd",
+ "label_path": "../annotation_volumes/allen2022_colours.csv",
+ "allen_colours": "../annotation_volumes/allen2022_colours.csv",
"segmentation_folder": "../test_data/oneSection15",
"alignment_json": "../test_data/C68_nonlinear_no_markers.json",
- "allen_colours": "../annotation_volumes//allen2022_colours.csv",
+ "nonlinear": true,
+ "colour": [255, 0, 255],
+ "points_json_path": "../outputs/points.json",
"counts_per_label_name": "../outputs/counts_per_allenID.csv"
}
\ No newline at end of file