From d693f307b6a619e86f95c4e55cdd4a20e487228d Mon Sep 17 00:00:00 2001
From: Laurent Guerard <laurent.guerard@unibas.ch>
Date: Tue, 14 Jan 2025 14:05:32 +0100
Subject: [PATCH] Improve speed by hiding the image during processing
---
2c_fibertyping.py | 22 ++++++++++++----------
1 file changed, 12 insertions(+), 10 deletions(-)
mode change 100755 => 100644 2c_fibertyping.py
diff --git a/2c_fibertyping.py b/2c_fibertyping.py
old mode 100755
new mode 100644
index ffc1520..cc43e62
--- a/2c_fibertyping.py
+++ b/2c_fibertyping.py
@@ -100,7 +100,7 @@ def open_image_with_BF(path_to_file):
# Create an ImporterOptions object for configuring the import process
options = ImporterOptions()
# Set the color mode to grayscale
- options.setColorMode(ImporterOptions.COLOR_MODE_GRAYSCALE)
+ options.setColorMode(ImporterOptions.COLOR_MODE_COMPOSITE )
# Enable autoscaling for the image
options.setAutoscale(True)
# Set the file path for the image to be opened
@@ -231,12 +231,12 @@ def change_all_roi_color(rm, color):
None
"""
# Select all ROIs in the RoiManager
- rm.setSelectedIndexes(range(rm.getCount()))
-
+ #rm.setSelectedIndexes(range(rm.getCount()))
+ rm.runCommand("Deselect")
# Change the color of all ROIs to the desired color
rm.runCommand("Set Color", color)
- # Deselect all ROIs again to finalize changes
- rm.runCommand("Deselect")
+ # # Deselect all ROIs again to finalize changes
+ # rm.runCommand("Deselect")
def change_subset_roi_color(rm, selected_rois, color):
@@ -252,6 +252,7 @@ def change_subset_roi_color(rm, selected_rois, color):
color : str
The desired color, e.g., "green", "red", "yellow", "magenta", etc.
"""
+
# Deselect all currently selected ROIs in the RoiManager
rm.runCommand("Deselect")
# Select the specified ROIs by their indices
@@ -464,6 +465,7 @@ setup_defined_ij(rm, rt)
# open image using Bio-Formats
path_to_image = fix_ij_dirs(path_to_image)
raw = open_image_with_BF(path_to_image)
+raw.hide()
# get image info
raw_image_calibration = raw.getCalibration()
@@ -479,7 +481,7 @@ if not os.path.exists( str(output_dir) ):
# open ROIS and show on image
open_rois_from_zip( rm, str(input_rois_path) )
change_all_roi_color(rm, "blue")
-show_all_rois_on_image( rm, raw )
+# show_all_rois_on_image( rm, raw )
# update the log for the user
IJ.log( "Now working on " + str(raw_image_title) )
@@ -551,16 +553,16 @@ rt.save(output_dir + "/" + raw_image_title + "_fibertyping_results.csv")
# dress up the original image, save a overlay-png, present original to the user
raw.show()
show_all_rois_on_image( rm, raw )
-raw.setDisplayMode(IJ.COMPOSITE)
+# raw.setDisplayMode(IJ.COMPOSITE)
enhance_contrast( raw )
IJ.run("From ROI Manager", "") # ROIs -> overlays so they show up in the saved png
qc_duplicate = raw.duplicate()
IJ.saveAs(qc_duplicate, "PNG", output_dir + "/" + raw_image_title + "_fibertyping")
qc_duplicate.close()
wm.toFront( raw.getWindow() )
-IJ.run("Remove Overlay", "")
-raw.setDisplayMode(IJ.GRAYSCALE)
-show_all_rois_on_image( rm, raw )
+# IJ.run("Remove Overlay", "")
+# raw.setDisplayMode(IJ.GRAYSCALE)
+# show_all_rois_on_image( rm, raw )
total_execution_time_min = (time.time() - execution_start_time) / 60.0
IJ.log("total time in minutes: " + str(total_execution_time_min))
IJ.log( "~~ all done ~~" )
--
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