diff --git a/PyNutil/coordinate_extraction.py b/PyNutil/coordinate_extraction.py
index e1ac91f443da27d78543829323d4f5656644da1b..c3cb1f3a671d88d913c6cafaabed04c5cd58fa2b 100644
--- a/PyNutil/coordinate_extraction.py
+++ b/PyNutil/coordinate_extraction.py
@@ -2,6 +2,8 @@
import numpy as np
from DeepSlice.coord_post_processing.spacing_and_indexing import number_sections
import json
+from read_and_write import loadVisuAlignJson
+from object_counting import labelPoints
from visualign_deformations import triangulate, transform_vec
from glob import glob
from tqdm import tqdm
@@ -27,6 +29,7 @@ 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"""
@@ -34,6 +37,7 @@ def transformToRegistration(SegHeight, SegWidth, RegHeight, RegWidth):
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"""
@@ -43,6 +47,7 @@ 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.
@@ -51,6 +56,7 @@ 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"""
@@ -70,12 +76,17 @@ def transformToAtlasSpace(anchoring, Y, X, RegHeight, RegWidth):
O = np.reshape(O, (3,1))
return (O+XYZU+XYZV).T
-#related to read and write
+
+#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):
@@ -115,6 +126,7 @@ 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"
@@ -134,6 +146,7 @@ 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"
@@ -162,6 +175,7 @@ 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
@@ -200,16 +214,18 @@ def SegmentationToAtlasSpaceMultiThreaded(slice, SegmentationPath, pixelID='auto
# points = points.reshape(-1)
pointsList[index] = np.array(points)
-#related to coordinate extraction
+
+#related to coordinate extraction or object_counting
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
+
+#related to read and write: WritePoints
+
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,
@@ -227,13 +243,16 @@ def WritePoints(pointsDict, filename, infoFile):
json.dump(meshview, f)
-# related to read and write
+
+# related to read and write: WritePointsToMeshview
+
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
+
+
+# related to object_counting: labelPoints
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 74d36152aca1d33b6220b86583d369e9b9732e71..1103e73112f3ee2951fdf61acd791b44c0c873d5 100644
--- a/PyNutil/folder_of_segmentations_to_meshview_multithreaded.py
+++ b/PyNutil/folder_of_segmentations_to_meshview_multithreaded.py
@@ -16,7 +16,7 @@ with open('../input/input.json', 'r') as f:
#import our function for converting a folder of segmentations to points
from coordinate_extraction import FolderToAtlasSpace, labelPoints, WritePointsToMeshview, FolderToAtlasSpaceMultiThreaded
-#from read_and_write import
+#from read_and_write import WritePointsToMeshview
startTime = datetime.now()
diff --git a/PyNutil/object_counting.py b/PyNutil/object_counting.py
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..e237457fc11240e2f6f77e4b57f33de0c2927236 100644
--- a/PyNutil/object_counting.py
+++ b/PyNutil/object_counting.py
@@ -0,0 +1,17 @@
+# related to object_counting: labelPoints
+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.
+ it returns a dictionary with the region as the key and the points as the value"""
+ #first convert the points to 3 columns
+ points = np.reshape(points, (-1,3))
+ #scale the points
+ points = points * scale_factor
+ #round the points to the nearest whole number
+ points = np.round(points).astype(int)
+ x = points[:,0]
+ y = points[:,1]
+ z = points[:,2]
+ #get the label value for each point
+ labels = label_volume[x,y,z]
+ return labels
\ No newline at end of file
diff --git a/PyNutil/read_and_write.py b/PyNutil/read_and_write.py
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..205de7a2d5961de0bd71136bf285e9cde981a7ad 100644
--- a/PyNutil/read_and_write.py
+++ b/PyNutil/read_and_write.py
@@ -0,0 +1,37 @@
+import json
+
+#related to read and write: loadVisuAlignJson
+def loadVisuAlignJson(filename):
+ with open(filename) as f:
+ vafile = json.load(f)
+ slices = vafile["slices"]
+ return slices
+
+
+#related to read and write: WritePoints
+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,
+ "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
+# this uses createRegionDict in coordinate_extraction.py
+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)
\ No newline at end of file