Format code

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