From 07264a86b52c17e37ceb6efa126f12de6691020b Mon Sep 17 00:00:00 2001
From: Harry Carey <harry.carey95@gmail.com>
Date: Thu, 25 May 2023 09:01:31 +0200
Subject: [PATCH] added emoji
---
PyNutil/coordinate_extraction.py | 27 +++++++++++++++++----------
PyNutil/main.py | 8 ++++----
2 files changed, 21 insertions(+), 14 deletions(-)
diff --git a/PyNutil/coordinate_extraction.py b/PyNutil/coordinate_extraction.py
index 607d5da..f218125 100644
--- a/PyNutil/coordinate_extraction.py
+++ b/PyNutil/coordinate_extraction.py
@@ -17,8 +17,8 @@ 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
"""
- SegmentationBinary = ~np.all(Segmentation == 255, axis=2)
- labels = measure.label(SegmentationBinary)
+ # SegmentationBinary = ~np.all(Segmentation == 255, axis=2)
+ labels = measure.label(Segmentation)
# this finds all the objects in the image
labelsInfo = measure.regionprops(labels)
# remove objects that are less than pixelCutOff
@@ -144,11 +144,6 @@ def SegmentationToAtlasSpace(
"""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)]
@@ -157,7 +152,7 @@ def SegmentationToAtlasSpace(
) # remove background
# currently only works for a single label
pixelID = pixelID[0]
- ID_pixels = findMatchingPixels(Segmentation, pixelID)
+
# transform pixels to registration space (the registered image and segmentation have different dimensions)
SegHeight = Segmentation.shape[0]
SegWidth = Segmentation.shape[1]
@@ -166,8 +161,20 @@ def SegmentationToAtlasSpace(
# this calculates reg/seg
Yscale, Xscale = transformToRegistration(SegHeight, SegWidth, RegHeight, RegWidth)
- # scale the seg coordinates to reg/seg
- scaledY, scaledX = scalePositions(ID_pixels[0], ID_pixels[1], Yscale, Xscale)
+ 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
+ binary_seg = Segmentation == pixelID
+ binary_seg = np.all(binary_seg, axis=2)
+ centroids, area, coords = getCentroidsAndArea(binary_seg, pixelCutOff=0)
+ print("number of objects: ", len(centroids))
+ # print(centroids)
+
+ if method in ["per_pixel", "all"]:
+ ID_pixels = findMatchingPixels(Segmentation, pixelID)
+ # scale the seg coordinates to reg/seg
+ scaledY, scaledX = scalePositions(ID_pixels[0], ID_pixels[1], Yscale, Xscale)
+
if nonLinear:
if "markers" in slice:
# this creates a triangulation using the reg width
diff --git a/PyNutil/main.py b/PyNutil/main.py
index 6334ab2..0179f90 100644
--- a/PyNutil/main.py
+++ b/PyNutil/main.py
@@ -53,11 +53,11 @@ class PyNutil:
startTime = datetime.now()
self.atlas_volume = readAtlasVolume(atlas_root_path + current_atlas_path)
time_taken = datetime.now() - startTime
- print(f"atlas volume loaded in: {time_taken}")
+ print(f"atlas volume loaded in: {time_taken} ✅")
atlas_label_path = self.config["annotation_volumes"][self.atlas]["labels"]
print("loading atlas labels")
self.atlas_labels = pd.read_csv(atlas_root_path + atlas_label_path)
- print("atlas labels loaded")
+ print("atlas labels loaded ✅")
def get_coordinates(self, nonLinear=True, method="all"):
if not hasattr(self, "atlas_volume"):
@@ -90,7 +90,7 @@ class PyNutil:
self.label_df = PixelCountPerRegion(labeled_points, self.atlas_labels)
self.labeled_points = labeled_points
- print("quantification complete")
+ print("quantification complete ✅")
def save_analysis(self, output_folder):
if not hasattr(self, "pixel_points"):
@@ -113,4 +113,4 @@ class PyNutil:
output_folder + "/pixels_meshview.json",
self.atlas_labels,
)
- print("analysis saved")
+ print("analysis saved ✅")
--
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