diff --git a/PyNutil/coordinate_extraction.py b/PyNutil/coordinate_extraction.py
index 232d4f3c698f12f4c3a41fba360a675e1d7c12d3..607d5da05f1bf8f65aae6a88cb0df7a434466784 100644
--- a/PyNutil/coordinate_extraction.py
+++ b/PyNutil/coordinate_extraction.py
@@ -28,7 +28,7 @@ def getCentroidsAndArea(Segmentation, pixelCutOff=0):
# get the area of the objects
area = np.array([label.area for label in labelsInfo])
# get the coordinates for all the pixels in each object
- coords = np.array([label.coords for label in labelsInfo])
+ coords = np.array([label.coords for label in labelsInfo], dtype=object)
return centroids, area, coords
@@ -79,19 +79,17 @@ def transformToAtlasSpace(anchoring, Y, X, RegHeight, RegWidth):
return (O + XYZU + XYZV).T
-
-
-
-
# points.append would make list of lists, keeping sections separate.
# related to coordinate extraction
# this function returns an array of points
def FolderToAtlasSpace(
- folder, QUINT_alignment, pixelID=[0, 0, 0], nonLinear=True
+ folder, QUINT_alignment, pixelID=[0, 0, 0], nonLinear=True, method="all"
):
"apply Segmentation to atlas space to all segmentations in a folder"
+
+ # this should be loaded above and passed as an argument
slices = loadVisuAlignJson(QUINT_alignment)
segmentationFileTypes = [".png", ".tif", ".tiff", ".jpg", ".jpeg"]
@@ -100,7 +98,6 @@ def FolderToAtlasSpace(
for file in glob(folder + "/*")
if any([file.endswith(type) for type in segmentationFileTypes])
]
- SectionNumbers = number_sections(Segmentations)
# order segmentations and sectionNumbers
# Segmentations = [x for _,x in sorted(zip(SectionNumbers,Segmentations))]
# SectionNumbers.sort()
@@ -119,6 +116,7 @@ def FolderToAtlasSpace(
nonLinear,
pointsList,
index,
+ method,
),
)
threads.append(x)
@@ -135,12 +133,22 @@ def FolderToAtlasSpace(
# related to coordinate extraction
# this function returns an array of points
def SegmentationToAtlasSpace(
- slice, SegmentationPath, pixelID="auto", nonLinear=True, pointsList=None, index=None
+ slice,
+ SegmentationPath,
+ pixelID="auto",
+ nonLinear=True,
+ pointsList=None,
+ index=None,
+ method="per_pixel",
):
"""combines many functions to convert a segmentation to atlas space. It takes care
of deformations"""
Segmentation = cv2.imread(SegmentationPath)
-
+ if method in ["per_object", "all"]:
+ # this function returns the centroids, area and coordinates of all the objects in the segmentation
+ # right now we only use centroids
+ centroids, area, coords = getCentroidsAndArea(Segmentation, pixelCutOff=0)
+ print("number of objects: ", len(centroids))
if pixelID == "auto":
# remove the background from the segmentation
SegmentationNoBackGround = Segmentation[~np.all(Segmentation == 255, axis=2)]
@@ -166,7 +174,9 @@ def SegmentationToAtlasSpace(
triangulation = triangulate(RegWidth, RegHeight, slice["markers"])
newX, newY = transform_vec(triangulation, scaledX, scaledY)
else:
- print(f"no markers found for {slice['filename']}, result for section will be linear")
+ print(
+ f"no markers found for {slice['filename']}, result for section will be linear"
+ )
newX, newY = scaledX, scaledY
else:
newX, newY = scaledX, scaledY
diff --git a/PyNutil/folder_of_segmentations_to_meshview_multithreaded.py b/PyNutil/folder_of_segmentations_to_meshview_multithreaded.py
index ea6f0e3d9a1b8aec00fd5368c8e53dbc04fba8ef..4face1fc061d66275cac8f8a1e06549a1efb4229 100644
--- a/PyNutil/folder_of_segmentations_to_meshview_multithreaded.py
+++ b/PyNutil/folder_of_segmentations_to_meshview_multithreaded.py
@@ -15,14 +15,14 @@ with open("../test/test5_NOP_s037.json", "r") as f:
# print(input)
# import our function for converting a folder of segmentations to points
-from coordinate_extraction import FolderToAtlasSpace, FolderToAtlasSpaceMultiThreaded
+from coordinate_extraction import FolderToAtlasSpace, FolderToAtlasSpace
from read_and_write import SaveDataframeasCSV, WritePointsToMeshview, FilesinDirectory
from counting_and_load import PixelCountPerRegion, labelPoints
startTime = datetime.now()
# now we can use our function to convert the folder of segmentations to points
-points = FolderToAtlasSpaceMultiThreaded(
+points = FolderToAtlasSpace(
input["segmentation_folder"],
input["alignment_json"],
pixelID=input["colour"],
diff --git a/PyNutil/main.py b/PyNutil/main.py
index 4de8f3e1e657d07776d5f8f8149b42178fdf1bf1..6334ab2db7a9db035e514ee45cf4a045f34fe83f 100644
--- a/PyNutil/main.py
+++ b/PyNutil/main.py
@@ -6,6 +6,7 @@ import json
import pandas as pd
from datetime import datetime
+
class PyNutil:
def __init__(
self,
@@ -37,7 +38,7 @@ class PyNutil:
raise ValueError(
f"Atlas {volume_path} not found in config file, valid atlases are: \n{' , '.join(list(self.config['annotation_volumes'].keys()))}"
)
-
+
self.segmentation_folder = segmentation_folder
self.alignment_json = alignment_json
self.colour = colour
@@ -45,7 +46,7 @@ class PyNutil:
# load the metadata json as well as the path to stored data files
def build_quantifier(self):
- # do all the expensive computations
+ # this could potentially be moved into init
atlas_root_path = self.config["annotation_volume_directory"]
current_atlas_path = self.config["annotation_volumes"][self.atlas]["volume"]
print("loading atlas volume")
@@ -57,48 +58,59 @@ class PyNutil:
print("loading atlas labels")
self.atlas_labels = pd.read_csv(atlas_root_path + atlas_label_path)
print("atlas labels loaded")
-
def get_coordinates(self, nonLinear=True, method="all"):
if not hasattr(self, "atlas_volume"):
- raise ValueError("Please run build_quantifier before running get_coordinates")
+ raise ValueError(
+ "Please run build_quantifier before running get_coordinates"
+ )
if method not in ["per_pixel", "per_object", "all"]:
- raise ValueError(f"method {method} not recognised, valid methods are: per_pixel, per_object, or all")
+ raise ValueError(
+ f"method {method} not recognised, valid methods are: per_pixel, per_object, or all"
+ )
print("extracting coordinates")
- points = FolderToAtlasSpace(
+ pixel_points = FolderToAtlasSpace(
self.segmentation_folder,
self.alignment_json,
pixelID=self.colour,
- nonLinear=nonLinear
+ nonLinear=nonLinear,
+ method=method,
)
- self.points = points
-
+ self.pixel_points = pixel_points
def quantify_coordinates(self):
- if not hasattr(self, "points"):
- raise ValueError("Please run get_coordinates before running quantify_coordinates")
+ if not hasattr(self, "pixel_points"):
+ raise ValueError(
+ "Please run get_coordinates before running quantify_coordinates"
+ )
print("quantifying coordinates")
- labeled_points = labelPoints(self.points, self.atlas_volume, scale_factor=2.5)
+ labeled_points = labelPoints(
+ self.pixel_points, self.atlas_volume, scale_factor=2.5
+ )
self.label_df = PixelCountPerRegion(labeled_points, self.atlas_labels)
self.labeled_points = labeled_points
print("quantification complete")
def save_analysis(self, output_folder):
- if not hasattr(self, "points"):
+ if not hasattr(self, "pixel_points"):
raise ValueError("Please run get_coordinates before running save_analysis")
+
+ self.label_df.to_csv(
+ output_folder + "/counts.csv", sep=";", na_rep="", index=False
+ )
+
if not hasattr(self, "label_df"):
print("no quantification found so we will only save the coordinates")
- print("if you want to save the quantification please run quantify_coordinates")
- self.label_df.to_csv(output_folder + '/counts.csv', sep=";", na_rep="", index=False)
+ print(
+ "if you want to save the quantification please run quantify_coordinates"
+ )
else:
- self.label_df.to_csv(output_folder + '/counts.csv', sep=";", na_rep="", index=False)
WritePointsToMeshview(
- self.points,
+ self.pixel_points,
self.labeled_points,
- output_folder + '/pixels_meshview.json',
- self.atlas_labels
+ output_folder + "/pixels_meshview.json",
+ self.atlas_labels,
)
-
-
+ print("analysis saved")
diff --git a/PyNutil/read_and_write.py b/PyNutil/read_and_write.py
index bbb67301ee23c759395ad04dca302fa25bec979c..9e1849061cf376fdc8130c6547acef6a0812ffb7 100644
--- a/PyNutil/read_and_write.py
+++ b/PyNutil/read_and_write.py
@@ -53,7 +53,8 @@ def WritePointsToMeshview(points, pointNames, filename, infoFile):
regionDict = createRegionDict(points, pointNames)
WritePoints(regionDict, filename, infoFile)
-# I think this might not need to be its own function :)
+
+# I think this might not need to be its own function :)
def SaveDataframeasCSV(df_to_save, output_csv):
"""Function for saving a df as a CSV file"""
df_to_save.to_csv(output_csv, sep=";", na_rep="", index=False)
diff --git a/testOOP.py b/testOOP.py
index 9c19e0055f031685e8d599cf5af8c4dd5b32d6d0..7f415c7c8f36162d765b7da0af29036dbe272b43 100644
--- a/testOOP.py
+++ b/testOOP.py
@@ -1,12 +1,10 @@
from PyNutil import PyNutil
-pnt = PyNutil(
- settings_file=r"test/test4_2017.json"
- )
+pnt = PyNutil(settings_file=r"test/test4_2017.json")
pnt.build_quantifier()
pnt.get_coordinates()
pnt.quantify_coordinates()
-pnt.save_analysis('outputs/test4_2017')
\ No newline at end of file
+pnt.save_analysis("outputs/test4_2017")