diff --git a/2c_fibertyping.py b/2c_fibertyping.py
index cc43e624329573dd4b31fc13c2b918dbea98718a..d57919d9450c73bd818db8cbb742b7c074dac5bc 100644
--- a/2c_fibertyping.py
+++ b/2c_fibertyping.py
@@ -1,24 +1,6 @@
-# this is a python rewrite of the original ijm published at
-# https://github.com/Hyojung-Choo/Myosoft/blob/Myosoft-hub/Scripts/central%20nuclei%20counter.ijm
-
-# IJ imports
-# TODO: are the imports RoiManager and ResultsTable needed when using the services?
-from ij import IJ, WindowManager as wm
-from ij.plugin import Duplicator, RoiEnlarger, RoiScaler
-from trainableSegmentation import WekaSegmentation
-from de.biovoxxel.toolbox import Extended_Particle_Analyzer
-
-# Bio-formats imports
-from loci.plugins import BF
-from loci.plugins.in import ImporterOptions
-
-# python imports
-import time
-import os
-
-#@ 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
+# @ 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
@@ -28,134 +10,26 @@ import os
#@ 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
-
-
-def fix_ij_options():
- """Configure ImageJ (IJ) to a predefined state.
-
- This function sets various options in ImageJ to ensure a consistent
- environment for image processing tasks. It includes settings for appearance,
- color management, binary image options, and file output format.
- """
- # Disable inverting LUT (Look-Up Table) for images
- IJ.run("Appearance...", " menu=0 16-bit=Automatic")
-
- # Set foreground color to be white and background color to be black, with red for selections
- IJ.run("Colors...", "foreground=white background=black selection=red")
-
- # Enable black background for binary images and pad edges when eroding
- IJ.run("Options...", "black pad")
-
- # Set saving format to .txt files, saving both columns and rows
- IJ.run("Input/Output...", "file=.txt save_column save_row")
+# @ ResultsTable rt
+# @ RoiManager rm
- # Set "Black Background" option for binary operations
- IJ.run("Options...", "black")
-
- # Enable scaling when converting images between types
- IJ.run("Conversions...", "scale")
-
-
-def fix_ij_dirs(path):
- """Replace backslashes with forward slashes in directory paths.
-
- This function takes a directory path obtained from a dialogue or script
- parameter and returns a more robust path with forward slashes as separators.
-
- Parameters
- ----------
- path : str
- A directory path
-
- Returns
- -------
- str
- A directory path with forward slashes as separators
- """
- fixed_path = str(path).replace("\\", "/")
- # fixed_path = fixed_path + "/"
+# ─── Requirements ─────────────────────────────────────────────────────────────
- return fixed_path
+# List of update sites needed for the code
+# * IMCF
+# ─── Imports ──────────────────────────────────────────────────────────────────
-def open_image_with_BF(path_to_file):
- """Open the first image from a file using Bio-Formats.
- This function utilizes Bio-Formats to open an image file and returns
- the first image contained within the file. The image is opened in
- grayscale mode with autoscaling enabled.
-
- Parameters
- ----------
- path_to_file : str
- The file path to the image file to be opened.
-
- Returns
- -------
- ImagePlus
- The first image contained in the specified file.
- """
- # Create an ImporterOptions object for configuring the import process
- options = ImporterOptions()
- # Set the color mode to 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
- options.setId(path_to_file)
- # Open the image(s) using Bio-Formats and store them in an array
- imps = BF.openImagePlus(options)
-
- # Return the first image in the array
- return imps[0]
-
-
-def fix_BF_czi_imagetitle(imp):
- """
- Fix the title of an image read using the bio-formats importer.
-
- The title is modified to remove the ".czi" extension and replace
- spaces with underscores.
-
- Parameters
- ----------
- imp : ij.ImagePlus
- The image to be processed.
+import time
- Returns
- -------
- str
- The modified title of the image.
- """
- # Get the short title of the image (without path)
- image_title = os.path.basename(imp.getShortTitle())
- # Remove the ".czi" extension
- image_title = image_title.replace(".czi", "")
- # Replace spaces with underscores
- image_title = image_title.replace(" ", "_")
- # Remove any double underscores
- image_title = image_title.replace("_-_", "")
- # Remove any double underscores
- image_title = image_title.replace("__", "_")
- # Remove any "#" characters
- image_title = image_title.replace("#", "Series")
-
- return image_title
-
-
-def clear_ij_roi_manager(rm):
- """
- Clear all ROIs from the RoiManager.
+from ij import IJ
+from ij import WindowManager as wm
+from imcflibs import pathtools
+from imcflibs.imagej import bioformats as bf
+from imcflibs.imagej import misc, prefs, resultstable, roimanager
- Parameters
- ----------
- rm : ij.plugin.frame.RoiManager
- a reference of the IJ-RoiManager
- """
- # Run the "reset" command in the RoiManager to clear all ROIs
- rm.runCommand('reset')
+# ─── Functions ────────────────────────────────────────────────────────────────
def get_threshold_from_method(imp, channel, method):
@@ -190,136 +64,47 @@ def get_threshold_from_method(imp, channel, method):
return [lower_thr, upper_thr]
-def measure_in_all_rois( imp, channel, rm ):
- """Measures in all ROIs on a given channel of imp all parameters that are set in IJ "Set Measurements".
-
- This function takes an ImagePlus (imp), a channel (integer, starts at 1), and a RoiManager (rm) as
- parameters. It then sets the channel of the imp to the desired channel, deselects all ROIs in the
- RoiManager, and measures in all ROIs of the RoiManager on the channel of the imp. The parameters
- that are measured are the ones that are set in IJ "Set Measurements".
+def enhance_contrast(imp):
+ """Use "Auto" Contrast & Brightness settings in each channel of imp.
Parameters
----------
imp : ij.ImagePlus
- the imp to measure on
- channel : int
- the channel to measure in. starts at 1.
- rm : ij.plugin.frame.RoiManager
- a reference of the IJ-RoiManager
- """
- # Set the channel of the imp to the desired channel
- imp.setC(channel)
- # Deselect all ROIs in the RoiManager
- rm.runCommand(imp,"Deselect")
- # Measure in all ROIs of the RoiManager on the channel of the imp
- rm.runCommand(imp,"Measure")
-
-
-def change_all_roi_color(rm, color):
- """
- Change the color of all ROIs in the RoiManager.
-
- Parameters
- ----------
- rm : ij.plugin.frame.RoiManager
- A reference to the IJ-RoiManager.
- color : str
- The desired color, e.g., "green", "red", "yellow", "magenta".
-
- Returns
- -------
- None
- """
- # Select all ROIs in the RoiManager
- #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")
-
-
-def change_subset_roi_color(rm, selected_rois, color):
- """
- Change the color of selected ROIs in the RoiManager.
-
- Parameters
- ----------
- rm : ij.plugin.frame.RoiManager
- A reference to the IJ-RoiManager.
- selected_rois : list of int
- Indices of ROIs in the RoiManager to change.
- 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
- rm.setSelectedIndexes(selected_rois)
- # Change the color of the selected ROIs to the specified color
- rm.runCommand("Set Color", color)
- # Deselect all ROIs again to finalize changes
- rm.runCommand("Deselect")
-
-
-def show_all_rois_on_image(rm, imp):
+ The imp on which to change C&B.
"""
- Display all ROIs on the given image using the ROI Manager.
+ for channel in range(imp.getDimensions()[2]):
+ imp.setC(channel + 1) # IJ channels start at 1
+ IJ.run(imp, "Enhance Contrast", "saturated=0.35")
- Parameters
- ----------
- rm : ij.plugin.frame.RoiManager
- A reference to the IJ-RoiManager.
- imp : ij.ImagePlus
- The image on which to display the ROIs.
- """
- # Show the image in the ImageJ window
- imp.show()
- # Use the ROI Manager to show all ROIs on the image
- rm.runCommand(imp, "Show All")
+def setup_defined_ij(rm, rt):
+ """Set up a clean and defined Fiji user environment.
-def save_all_rois(rm, target):
- """Save all ROIs in the RoiManager as a zip file to the given target path.
+ This function configures the ImageJ environment to a predefined state by
+ resetting the RoiManager and ResultsTable, and clearing the IJ log.
Parameters
----------
rm : ij.plugin.frame.RoiManager
A reference to the IJ-RoiManager.
- target : str
- The file path in which to save the ROIs, e.g., /my-images/resulting_rois.zip
+ rt : ij.measure.ResultsTable
+ A reference to the IJ-ResultsTable.
"""
- # Save all ROIs in the RoiManager to the given target path
- rm.runCommand("Save", target)
+ # Configure IJ options to a predefined state
+ prefs.set_default_ij_options()
+ # Reset the RoiManager to remove all existing ROIs
+ rm.runCommand("reset")
-def save_selected_rois(rm, selected_rois, target):
- """
- Save selected ROIs in the RoiManager as a zip file to the given target path.
+ # Reset the ResultsTable to clear all previous results
+ rt.reset()
- Parameters
- ----------
- rm : ij.plugin.frame.RoiManager
- A reference to the IJ-RoiManager.
- selected_rois : list of int
- Indices of ROIs in the RoiManager to save.
- target : str
- The file path in which to save the ROIs, e.g., /my-images/resulting_rois_subset.zip
- """
- # Deselect all currently selected ROIs in the RoiManager to ensure a clean start
- rm.runCommand("Deselect")
- # Select the specified ROIs by their indices
- rm.setSelectedIndexes(selected_rois)
- # Save the selected ROIs to the given target path as a zip file
- rm.runCommand("save selected", target)
- # Deselect all ROIs again to finalize changes and maintain a clean state
- rm.runCommand("Deselect")
+ # Clear the IJ log to ensure a fresh output window
+ IJ.log("\\Clear")
-def select_positive_fibers( imp, channel, rm, min_intensity ):
- """For all ROIs in the RoiManager, select ROIs based on intensity measurement in given channel of imp.
- See https://imagej.nih.gov/ij/developer/api/ij/process/ImageStatistics.html
+def measure_mean_of_rois(imp, channel, rm):
+ """Measure the mean intensity of all ROIs in the given channel of imp.
Parameters
----------
@@ -339,149 +124,35 @@ def select_positive_fibers( imp, channel, rm, min_intensity ):
"""
imp.setC(channel)
all_rois = rm.getRoisAsArray()
- selected_rois = []
for i, roi in enumerate(all_rois):
imp.setRoi(roi)
stats = imp.getStatistics()
- if stats.mean > min_intensity:
- selected_rois.append(i)
-
- return selected_rois
-
-
-def open_rois_from_zip(rm, path):
- """
- Open ROIs from a zip file and add them to the RoiManager.
-
- Parameters
- ----------
- rm : ij.plugin.frame.RoiManager
- A reference to the IJ-RoiManager.
- path : str
- The file path to the ROI zip file.
- """
- rm.runCommand("Open", path)
-
-
-def preset_results_column( rt, column, value):
- """Pre-set all rows in given column of the IJ-ResultsTable with desired value.
-
- Parameters
- ----------
- rt : ij.measure.ResultsTable
- A reference of the IJ-ResultsTable
- column : str
- The desired column. Will be created if it does not yet exist
- value : str or float or int
- The value to be set
- """
- for i in range( rt.size() ):
- rt.setValue(column, i, value)
-
- rt.show("Results")
-
-
-def add_results(rt, column, row, value):
- """Add a value in specified rows of a given column.
-
- Parameters
- ----------
- rt : ij.measure.ResultsTable
- A reference to the IJ-ResultsTable.
- column : str
- The column in which to add the values.
- row : list of int
- The row numbers in which to add the values.
- value : str, float, or int
- The value to be set.
- """
- # Iterate over each row index in the row list
- for i in range(len(row)):
- # Set the specified value in the given column and row
- rt.setValue(column, row[i], value)
-
- # Display the updated ResultsTable
- rt.show("Results")
-
-def enhance_contrast(imp):
- """Use "Auto" Contrast & Brightness settings in each channel of imp.
-
- Parameters
- ----------
- imp : ij.ImagePlus
- The imp on which to change C&B.
- """
- for channel in range(imp.getDimensions()[2]):
- imp.setC(channel + 1) # IJ channels start at 1
- IJ.run(imp, "Enhance Contrast", "saturated=0.35")
-
-
-def renumber_rois(rm):
- """Rename all ROIs in the RoiManager according to their number.
-
- The RoiManager uses 0-based indexing, so the first ROI is at index 0.
- This function renames each ROI with its index (starting from 1).
-
- Parameters
- ----------
- rm : ij.plugin.frame.RoiManager
- A reference to the IJ-RoiManager.
- """
- number_of_rois = rm.getCount()
- for roi in range( number_of_rois ):
- rm.rename( roi, str(roi + 1) )
-
-
-def setup_defined_ij(rm, rt):
- """Set up a clean and defined Fiji user environment.
-
- This function configures the ImageJ environment to a predefined state by
- resetting the RoiManager and ResultsTable, and clearing the IJ log.
-
- Parameters
- ----------
- rm : ij.plugin.frame.RoiManager
- A reference to the IJ-RoiManager.
- rt : ij.measure.ResultsTable
- A reference to the IJ-ResultsTable.
- """
- # Configure IJ options to a predefined state
- fix_ij_options()
- # Reset the RoiManager to remove all existing ROIs
- rm.runCommand('reset')
-
- # Reset the ResultsTable to clear all previous results
- rt.reset()
-
- # Clear the IJ log to ensure a fresh output window
- IJ.log("\\Clear")
execution_start_time = time.time()
-setup_defined_ij(rm, rt)
+ misc.timed_log("Script starting")
+ setup_defined_ij(rm, rt)
+ image_file_info = pathtools.parse_path(path_to_image)
# open image using Bio-Formats
-path_to_image = fix_ij_dirs(path_to_image)
-raw = open_image_with_BF(path_to_image)
-raw.hide()
+ raw = bf.import_image(image_file_info["full"])
+ raw.hide()
-# get image info
-raw_image_calibration = raw.getCalibration()
-raw_image_title = fix_BF_czi_imagetitle(raw)
+ # get image info
+ raw_image_calibration = raw.getCalibration()
+ raw_image_title = misc.sanitize_image_title(raw)
-# take care of paths and directories
-input_rois_path = fix_ij_dirs( roi_zip )
-output_dir = fix_ij_dirs(output_dir) + "/2c_fibertyping"
+ roi_file_info = pathtools.parse_path(roi_zip)
-if not os.path.exists( str(output_dir) ):
- os.makedirs( str(output_dir) )
+ # take care of paths and directories
+ input_rois_path = roi_file_info["full"]
+ output_dir = pathtools.join2(output_dir, "2c_fibertyping")
+ pathtools.create_directory(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 )
+ 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) )
@@ -498,6 +169,7 @@ IJ.log( " -- settings used -- ")
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 )
+ 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]
@@ -505,18 +177,65 @@ all_min_fiber_intensities = [min_fiber_intensity_1, min_fiber_intensity_2, min_f
roi_colors = ["green", "orange", "red"]
all_fiber_subsets =[ [], [], [] ]
-for index, fiber_channel in enumerate(all_fiber_channels):
- if fiber_channel > 0:
- preset_results_column( rt, "channel " + str(fiber_channel) + " positive (" + roi_colors[index] + ")", "NO" )
- if all_min_fiber_intensities[index] == 0:
- all_min_fiber_intensities[index] = get_threshold_from_method(raw, fiber_channel, "Mean")[0]
- IJ.log( "fiber channel " + str(fiber_channel) + " intensity threshold: " + str(all_min_fiber_intensities[index]) )
- positive_fibers = select_positive_fibers( raw, fiber_channel, rm, all_min_fiber_intensities[index] )
- all_fiber_subsets[index] = positive_fibers
- if len(positive_fibers) > 0:
- change_subset_roi_color(rm, positive_fibers, roi_colors[index])
- save_selected_rois( rm, positive_fibers, output_dir + "/" + raw_image_title + "_positive_fiber_rois_c" + str( fiber_channel ) + ".zip")
- add_results( rt, "channel " + str(fiber_channel) + " positive (" + roi_colors[index] + ")", positive_fibers, "YES")
+ for index, fiber_channel in enumerate(all_fiber_channels):
+ if fiber_channel > 0:
+ resultstable.preset_results_column(
+ rt, "channel %s mean intensity" % fiber_channel, 0
+ )
+ mean_intensities = measure_mean_of_rois(raw, fiber_channel, rm)
+ resultstable.add_results_to_resultstable(
+ rt,
+ "channel %s mean intensity" % fiber_channel,
+ range(rm.getCount()),
+ mean_intensities,
+ )
+
+ resultstable.preset_results_column(
+ rt,
+ "channel "
+ + str(fiber_channel)
+ + " positive ("
+ + roi_colors[index]
+ + ")",
+ "NO",
+ )
+ if all_min_fiber_intensities[index] == 0:
+ all_min_fiber_intensities[index] = get_threshold_from_method(
+ raw, fiber_channel, "Mean"
+ )[0]
+ IJ.log(
+ "fiber channel "
+ + str(fiber_channel)
+ + " intensity threshold: "
+ + str(all_min_fiber_intensities[index])
+ )
+ positive_fibers = roimanager.select_rois_above_min_intensity(
+ raw, fiber_channel, rm, all_min_fiber_intensities[index]
+ )
+ all_fiber_subsets[index] = positive_fibers
+ if len(positive_fibers) > 0:
+ roimanager.change_roi_color(rm, roi_colors[index], positive_fibers)
+ roimanager.save_rois_to_zip(
+ rm,
+ pathtools.join2(
+ output_dir,
+ raw_image_title
+ + "_positive_fiber_rois_c"
+ + str(fiber_channel)
+ + ".zip",
+ ),
+ positive_fibers,
+ )
+ resultstable.add_results_to_resultstable(
+ rt,
+ "channel "
+ + str(fiber_channel)
+ + " positive ("
+ + roi_colors[index]
+ + ")",
+ positive_fibers,
+ "YES",
+ )
# single positive
positive_c1 = all_fiber_subsets[0]
@@ -537,22 +256,34 @@ channels = [
(positive_c1_c2_c3, [fiber_channel_1, fiber_channel_2, fiber_channel_3], "white")
]
-for positives, ch_nums, color in channels:
- if positives:
- ch_str = ",".join(map(str, ch_nums))
- color_label = "channel %s positive (%s)" % (ch_str, color)
- preset_results_column(rt, color_label.replace(',', '-'), "NO")
- change_subset_roi_color(rm, positives, color)
- save_selected_rois(rm, positives, "%s/%s_positive_fiber_rois_c%s.zip" % (output_dir, raw_image_title, '_c'.join(map(str, ch_nums))))
- add_results(rt, color_label.replace(',', '-'), positives, "YES")
-
-# save all results together
-save_all_rois( rm, output_dir + "/" + raw_image_title + "_all_fiber_type_rois_color-coded.zip" )
-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 )
+ for positives, ch_nums, color in channels:
+ if positives:
+ ch_str = ",".join(map(str, ch_nums))
+ color_label = "channel %s positive (%s)" % (ch_str, color)
+ resultstable.preset_results_column(rt, color_label.replace(",", "-"), "NO")
+ roimanager.change_roi_color(rm, color, positives)
+ roimanager.save_rois_to_zip(
+ rm,
+ "%s/%s_positive_fiber_rois_c%s.zip"
+ % (output_dir, raw_image_title, "_c".join(map(str, ch_nums))),
+ positives,
+ )
+ resultstable.add_results_to_resultstable(
+ rt, color_label.replace(",", "-"), positives, "YES"
+ )
+
+ # save all results together
+ roimanager.save_rois_to_zip(
+ rm,
+ pathtools.join2(
+ output_dir, raw_image_title + "_all_fiber_type_rois_color-coded.zip"
+ ),
+ )
+ rt.save(pathtools.join2(output_dir, raw_image_title + "_fibertyping_results.csv"))
+
+ # 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
@@ -560,13 +291,13 @@ 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 )
-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 ~~" )
-IJ.selectWindow("Log")
-IJ.saveAs("Text", str(output_dir + "/" + raw_image_title + "_fibertyping_Log"))
-if close_raw == True:
- raw.close()
\ No newline at end of file
+
+ IJ.log(
+ "Script finished. Total runtime [HH:MM:SS.ss]: "
+ + misc.elapsed_time_since(execution_start_time)
+ )
+ IJ.log("~~ all done ~~")
+ IJ.selectWindow("Log")
+ IJ.saveAs("Text", str(output_dir + "/" + raw_image_title + "_fibertyping_Log"))
+ if close_raw:
+ raw.close()