diff --git a/2c_fibertyping.py b/2c_fibertyping.py
index 7497a4c78c0b8db3e344743927d6b7c422277bbe..125b99c644eb9b7c33013dd85b7c420d66b3af4c 100644
--- a/2c_fibertyping.py
+++ b/2c_fibertyping.py
@@ -1,15 +1,15 @@
# @ String (visibility=MESSAGE, value="<html><b> Welcome to Myosoft! </b></html>") msg1
# @ File (label="Select fiber-ROIs zip-file", style="file") roi_zip
# @ File (label="Select image file", description="select your image") path_to_image
-#@ File (label="Select directory for output", style="directory") output_dir
-#@ Boolean (label="close image after processing", description="tick this box when using batch mode", value=False) close_raw
-#@ String (visibility=MESSAGE, value="<html><b> channel positions in the hyperstack </b></html>") msg5
-#@ Integer (label="Fiber staining 1 channel number (0=n.a.)", style="slider", min=0, max=5, value=1) fiber_channel_1
-#@ Integer (label="Fiber staining 2 channel number (0=n.a.)", style="slider", min=0, max=5, value=2) fiber_channel_2
-#@ Integer (label="Fiber staining 3 channel number (0=n.a.)", style="slider", min=0, max=5, value=3) fiber_channel_3
-#@ Integer (label="minimum fiber intensity (0=auto)", description="0 = automatic threshold detection", value=0) min_fiber_intensity_1
-#@ Integer (label="minimum fiber intensity (0=auto)", description="0 = automatic threshold detection", value=0) min_fiber_intensity_2
-#@ Integer (label="minimum fiber intensity (0=auto)", description="0 = automatic threshold detection", value=0) min_fiber_intensity_3
+# @ File (label="Select directory for output", style="directory") output_dir
+# @ Boolean (label="close image after processing", description="tick this box when using batch mode", value=False) close_raw
+# @ String (visibility=MESSAGE, value="<html><b> channel positions in the hyperstack </b></html>") msg5
+# @ Integer (label="Fiber staining 1 channel number (0=n.a.)", style="slider", min=0, max=5, value=1) fiber_channel_1
+# @ Integer (label="Fiber staining 2 channel number (0=n.a.)", style="slider", min=0, max=5, value=2) fiber_channel_2
+# @ Integer (label="Fiber staining 3 channel number (0=n.a.)", style="slider", min=0, max=5, value=3) fiber_channel_3
+# @ Integer (label="minimum fiber intensity (0=auto)", description="0 = automatic threshold detection", value=0) min_fiber_intensity_1
+# @ Integer (label="minimum fiber intensity (0=auto)", description="0 = automatic threshold detection", value=0) min_fiber_intensity_2
+# @ Integer (label="minimum fiber intensity (0=auto)", description="0 = automatic threshold detection", value=0) min_fiber_intensity_3
# @ ResultsTable rt
# @ RoiManager rm
@@ -50,7 +50,7 @@ def get_threshold_from_method(imp, channel, method):
A list containing the upper and the lower threshold (integer values).
"""
# Set the channel of the imp to the desired channel
- imp.setC(channel) # starts at 1
+ imp.setC(channel) # starts at 1
# Get the processor of the imp
ip = imp.getProcessor()
# Set the AutoThreshold method to the desired method
@@ -159,28 +159,35 @@ if __name__ == "__main__":
roimanager.load_rois_from_zip(rm, input_rois_path)
roimanager.change_roi_color(rm, "blue")
-# 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( "Selected fiber-ROIs zip-file = " + str(input_rois_path) )
-IJ.log( "Fiber staining 1 channel number = " + str(fiber_channel_1) )
-IJ.log( "Fiber staining 2 channel number = " + str(fiber_channel_2) )
-IJ.log( "Fiber staining 3 channel number = " + str(fiber_channel_3) )
-IJ.log( " -- settings used -- ")
-
-# measure size & shape,
-IJ.run("Set Measurements...", "area perimeter shape feret's redirect=None decimal=4")
-IJ.run("Clear Results", "")
-measure_in_all_rois( raw, fiber_channel_1, rm )
+ # update the log for the user
+ IJ.log("Now working on " + str(raw_image_title))
+ if not raw_image_calibration.scaled():
+ IJ.log(
+ "Your image is not spatially calibrated! Size measurements are only possible in [px]."
+ )
+ IJ.log(" -- settings used -- ")
+ IJ.log("Selected fiber-ROIs zip-file = " + str(input_rois_path))
+ IJ.log("Fiber staining 1 channel number = " + str(fiber_channel_1))
+ IJ.log("Fiber staining 2 channel number = " + str(fiber_channel_2))
+ IJ.log("Fiber staining 3 channel number = " + str(fiber_channel_3))
+ IJ.log(" -- settings used -- ")
+
+ # measure size & shape,
+ IJ.run(
+ "Set Measurements...", "area perimeter shape feret's redirect=None decimal=4"
+ )
+ IJ.run("Clear Results", "")
roimanager.measure_in_all_rois(raw, fiber_channel_1, rm)
-# loop through the fiber channels, check if positive, add info to results table
-all_fiber_channels = [fiber_channel_1, fiber_channel_2, fiber_channel_3]
-all_min_fiber_intensities = [min_fiber_intensity_1, min_fiber_intensity_2, min_fiber_intensity_3]
-roi_colors = ["green", "orange", "red"]
-all_fiber_subsets =[ [], [], [] ]
+ # loop through the fiber channels, check if positive, add info to results table
+ all_fiber_channels = [fiber_channel_1, fiber_channel_2, fiber_channel_3]
+ all_min_fiber_intensities = [
+ min_fiber_intensity_1,
+ min_fiber_intensity_2,
+ min_fiber_intensity_3,
+ ]
+ roi_colors = ["green", "orange", "red"]
+ all_fiber_subsets = [[], [], []]
for index, fiber_channel in enumerate(all_fiber_channels):
if fiber_channel > 0:
@@ -242,24 +249,28 @@ all_fiber_subsets =[ [], [], [] ]
"YES",
)
-# single positive
-positive_c1 = all_fiber_subsets[0]
-positive_c2 = all_fiber_subsets[1]
-positive_c3 = all_fiber_subsets[2]
-# double positive
-positive_c1_c2 = list( set(all_fiber_subsets[0]).intersection(all_fiber_subsets[1]) )
-positive_c1_c3 = list( set(all_fiber_subsets[0]).intersection(all_fiber_subsets[2]) )
-positive_c2_c3 = list( set(all_fiber_subsets[1]).intersection(all_fiber_subsets[2]) )
-# triple positive
-positive_c1_c2_c3 = list( set(positive_c1_c2).intersection(all_fiber_subsets[2]) )
-
-# update ROI color & results table for double and triple positives
-channels = [
- (positive_c1_c2, [fiber_channel_1, fiber_channel_2], "magenta"),
- (positive_c1_c3, [fiber_channel_1, fiber_channel_3], "yellow"),
- (positive_c2_c3, [fiber_channel_2, fiber_channel_3], "cyan"),
- (positive_c1_c2_c3, [fiber_channel_1, fiber_channel_2, fiber_channel_3], "white")
-]
+ # single positive
+ positive_c1 = all_fiber_subsets[0]
+ positive_c2 = all_fiber_subsets[1]
+ positive_c3 = all_fiber_subsets[2]
+ # double positive
+ positive_c1_c2 = list(set(all_fiber_subsets[0]).intersection(all_fiber_subsets[1]))
+ positive_c1_c3 = list(set(all_fiber_subsets[0]).intersection(all_fiber_subsets[2]))
+ positive_c2_c3 = list(set(all_fiber_subsets[1]).intersection(all_fiber_subsets[2]))
+ # triple positive
+ positive_c1_c2_c3 = list(set(positive_c1_c2).intersection(all_fiber_subsets[2]))
+
+ # update ROI color & results table for double and triple positives
+ channels = [
+ (positive_c1_c2, [fiber_channel_1, fiber_channel_2], "magenta"),
+ (positive_c1_c3, [fiber_channel_1, fiber_channel_3], "yellow"),
+ (positive_c2_c3, [fiber_channel_2, fiber_channel_3], "cyan"),
+ (
+ positive_c1_c2_c3,
+ [fiber_channel_1, fiber_channel_2, fiber_channel_3],
+ "white",
+ ),
+ ]
for positives, ch_nums, color in channels:
if positives:
@@ -289,13 +300,13 @@ channels = [
# dress up the original image, save a overlay-png, present original to the user
raw.show()
roimanager.show_all_rois_on_image(rm, raw)
-# 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() )
+ # 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.log(
"Script finished. Total runtime [HH:MM:SS.ss]: "