From 06c407b9891e6a7128e7e66f54efbba014e45725 Mon Sep 17 00:00:00 2001
From: Laurent Guerard <laurent.guerard@unibas.ch>
Date: Wed, 8 Jan 2025 14:41:40 +0100
Subject: [PATCH] Format code
---
1_identify_fibers.py | 50 ++------------------------------------------
1 file changed, 2 insertions(+), 48 deletions(-)
diff --git a/1_identify_fibers.py b/1_identify_fibers.py
index 46ca49c..186b492 100755
--- a/1_identify_fibers.py
+++ b/1_identify_fibers.py
@@ -318,7 +318,6 @@ def run_tm(
settings.trackerSettings["GAP_CLOSING_MAX_DISTANCE"] = 3.0
settings.trackerSettings["MAX_FRAME_GAP"] = 2
-
# Initialize TrackMate with model and settings
trackmate = TrackMate(model, settings)
trackmate.computeSpotFeatures(True)
@@ -578,7 +577,7 @@ def add_results(rt, column, row, value):
value : string or float or integer
the value to be set
"""
- for i in range( len( row ) ):
+ for i in range(len(row)):
rt.setValue(column, row[i], value)
rt.show("Results")
@@ -621,7 +620,7 @@ def setup_defined_ij(rm, rt):
a reference of the IJ-ResultsTable
"""
fix_ij_options()
- rm.runCommand('reset')
+ rm.runCommand("reset")
rt.reset()
IJ.log("\\Clear")
@@ -633,57 +632,12 @@ if __name__ == "__main__":
IJ.log("\\Clear")
misc.timed_log("Script starting")
setup_defined_ij(rm, rt)
-path_to_image = fix_ij_dirs(path_to_image)
-raw = open_image_with_BF(path_to_image)
-
-# get image info
-raw_image_calibration = raw.getCalibration()
-raw_image_title = fix_BF_czi_imagetitle(raw)
-print("raw image title: ", str(raw_image_title))
-
-# take care of paths and directories
-output_dir = fix_ij_dirs(output_dir) + "/" + str(raw_image_title) + "/1_identify_fibers"
-print("output_dir: ", str(output_dir))
-
-if not os.path.exists( str(output_dir) ):
- os.makedirs( str(output_dir) )
-
-# update the log for the user
-IJ.log( "Now working on " + str(raw_image_title) )
-if raw_image_calibration.scaled() == False:
- IJ.log("Your image is not spatially calibrated! Size measurements are only possible in [px].")
-IJ.log( " -- settings used -- ")
-IJ.log( "area = " + str(minAr) + "-" + str(maxAr) )
-IJ.log( "perimeter = " + str(minPer) + "-" + str(maxPer) )
-IJ.log( "circularity = " + str(minCir) + "-" + str(maxCir) )
-IJ.log( "roundness = " + str(minRnd) + "-" + str(maxRnd) )
-IJ.log( "solidity = " + str(minSol) + "-" + str(maxSol) )
-IJ.log( "feret_ar = " + str(minFAR) + "-" + str(maxFAR) )
-IJ.log( "min_feret = " + str(minMinFer) + "-" + str(maxMinFer) )
-IJ.log( "ROI expansion [microns] = " + str(enlarge) )
-IJ.log( "Membrane channel = " + str(membrane_channel) )
-IJ.log( "MHC positive fiber channel = " + str(fiber_channel) )
-IJ.log( "sub-tiling = " + str(tiling_factor) )
-IJ.log( " -- settings used -- ")
-
-# image (pre)processing and segmentation (-> ROIs)# imp, firstC, lastC, firstZ,
-# lastZ, firstT, lastT
-membrane = Duplicator().run(raw, membrane_channel, membrane_channel, 1, 1, 1, 1)
-preprocess_membrane_channel(membrane)
-imp_result = run_tm(membrane, 1, cellpose_dir.getPath(), PretrainedModel.CYTO2, 30.0, area_thresh=[minAr, maxAr], circularity_thresh=[minCir, maxCir],
- perimeter_thresh=[minPer, maxPer],
- # feret_thresh=[minMinFer, maxMinFer],
- )
-IJ.saveAs(imp_result, "Tiff", output_dir + "/" + raw_image_title + "_all_fibers_binary")
-sys.exit()
file_list = pathtools.listdir_matching(
src_dir.getPath(), filename_filter, fullpath=True
)
out_dir_info = pathtools.parse_path(output_dir)
-rm.hide()
-raw.hide()
for index, file in enumerate(file_list):
# open image using Bio-Formats
--
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