From a70b76b6bc0fd44dc80be3fe25415eb0482cad5a Mon Sep 17 00:00:00 2001
From: Laurent Guerard <laurent.guerard@unibas.ch>
Date: Thu, 13 Feb 2025 12:00:36 +0100
Subject: [PATCH] Fix resizing threshold and add log
---
1_identify_fibers.py | 31 +++++++++++++++++++++++++------
1 file changed, 25 insertions(+), 6 deletions(-)
diff --git a/1_identify_fibers.py b/1_identify_fibers.py
index cae2423..74d312b 100755
--- a/1_identify_fibers.py
+++ b/1_identify_fibers.py
@@ -47,7 +47,7 @@ import sys
# python imports
import time
-from ch.epfl.biop.ij2command import Labels2CompositeRois
+from ch.epfl.biop.ij2command import Labels2Rois
# TrackMate imports
from fiji.plugin.trackmate import Logger, Model, Settings, TrackMate
@@ -743,21 +743,25 @@ if __name__ == "__main__":
# image (pre)processing and segmentation (-> ROIs)# imp, firstC, lastC, firstZ,
# lastZ, firstT, lastT
+ misc.timed_log("Getting the membrane channel")
membrane = Duplicator().run(
raw, membrane_channel, membrane_channel, 1, 1, 1, 1
)
- if (membrane.getWidth() * membrane.getHeight()) > 100000:
+ while (membrane.getWidth() * membrane.getHeight()) > 100000000:
misc.timed_log("Image is too large, resizing to speed up processing")
membrane = membrane.resize(
membrane.getWidth() / 2,
membrane.getHeight() / 2,
"none",
)
+
+ misc.timed_log("Pre processing the image for segmentation")
imp_bgd_corrected = do_background_correction(membrane)
IJ.run("Conversions...", "scale")
IJ.run(imp_bgd_corrected, "16-bit", "")
+ misc.timed_log("Running the segmentation")
imp_result = run_tm(
imp_bgd_corrected,
1,
@@ -769,25 +773,31 @@ if __name__ == "__main__":
perimeter_thresh=[minPer, maxPer],
)
+ misc.timed_log("Resizing the segmentation results (if needed)")
imp_result = imp_result.resize(
raw.getWidth(),
raw.getHeight(),
"none",
)
+ misc.timed_log("Saving the segmentation results")
IJ.saveAs(
imp_result,
"Tiff",
os.path.join(
output_dir,
- raw_image_title + "_" + str(serie_index) + "_all_fibers_binary",
+ raw_image_title + "_" + str(serie_index) + "_all_fibers_labels",
),
)
- command.run(Labels2CompositeRois, True, "rm", rm, "imp", imp_result).get()
+ misc.timed_log("Getting the ROIs")
+ command.run(Labels2Rois, True, "rm", rm, "imp", imp_result).get()
+ misc.timed_log("Enlarging and renumbering the ROIs")
enlarge_all_rois(enlarge_radius, rm, raw_image_calibration.pixelWidth)
renumber_rois(rm)
+
+ misc.timed_log("Saving the ROIs")
save_all_rois(
rm,
os.path.join(
@@ -798,11 +808,12 @@ if __name__ == "__main__":
# check for positive fibers
if fiber_channel > 0:
+ misc.timed_log("Checking for positive fibers")
if min_fiber_intensity == 0:
min_fiber_intensity = get_threshold_from_method(
raw, fiber_channel, "Mean"
)[0]
- IJ.log("automatic intensity threshold detection: True")
+ misc.timed_log("automatic intensity threshold detection: True")
IJ.log("fiber intensity threshold: " + str(min_fiber_intensity))
change_all_roi_color(rm, "blue")
@@ -810,6 +821,7 @@ if __name__ == "__main__":
raw, fiber_channel, rm, min_fiber_intensity
)
change_subset_roi_color(rm, positive_fibers, "magenta")
+ misc.timed_log("Saving positive fibers")
save_selected_rois(
rm,
positive_fibers,
@@ -823,6 +835,7 @@ if __name__ == "__main__":
)
# measure size & shape, save
+ misc.timed_log("Measuring the ROIs")
IJ.run(
"Set Measurements...",
"area perimeter shape feret's redirect=None decimal=4",
@@ -841,6 +854,7 @@ if __name__ == "__main__":
add_results(rt, "MHC Positive Fibers (magenta)", positive_fibers, "YES")
# print(rt.size())
+ misc.timed_log("Saving the measurements")
rt.save(
os.path.join(
output_dir,
@@ -851,7 +865,11 @@ if __name__ == "__main__":
)
)
# print("saved the all_fibers_results.csv")
- # dress up the original image, save a overlay-png, present original to the user
+ # dress up the original image, save a overlay-png, present original
+ # to the user
+ misc.timed_log(
+ "Improve the contrast and show the results to save an overlay image"
+ )
rm.show()
raw.show()
show_all_rois_on_image(rm, raw)
@@ -877,6 +895,7 @@ if __name__ == "__main__":
raw.setDisplayMode(IJ.GRAYSCALE)
show_all_rois_on_image(rm, raw)
+ misc.timed_log("Save log")
IJ.selectWindow("Log")
IJ.saveAs(
"Text",
--
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