From eb3b72d5575ad44b3229686068fcf6ceac626b6b Mon Sep 17 00:00:00 2001
From: Laurent Guerard <laurent.guerard@unibas.ch>
Date: Tue, 14 Jan 2025 11:22:52 +0100
Subject: [PATCH] Docstring formatting and refactoring
---
2c_fibertyping.py | 342 +++++++++++++++++++++++++++++-----------------
1 file changed, 219 insertions(+), 123 deletions(-)
diff --git a/2c_fibertyping.py b/2c_fibertyping.py
index bb58eab..e10c3a2 100755
--- a/2c_fibertyping.py
+++ b/2c_fibertyping.py
@@ -1,4 +1,4 @@
-# this is a python rewrite of the original ijm published at
+# 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
@@ -33,37 +33,47 @@ import os
def fix_ij_options():
- """put IJ into a defined state
+ """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
+ # Disable inverting LUT (Look-Up Table) for images
IJ.run("Appearance...", " menu=0 16-bit=Automatic")
- # set foreground color to be white, background black
+
+ # 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")
- # black BG for binary images and pad edges when eroding
+
+ # Enable black background for binary images and pad edges when eroding
IJ.run("Options...", "black pad")
- # set saving format to .txt files
+
+ # Set saving format to .txt files, saving both columns and rows
IJ.run("Input/Output...", "file=.txt save_column save_row")
- # ============= DON’T MOVE UPWARDS =============
- # set "Black Background" in "Binary Options"
+
+ # Set "Black Background" option for binary operations
IJ.run("Options...", "black")
- # scale when converting = checked
+
+ # Enable scaling when converting images between types
IJ.run("Conversions...", "scale")
def fix_ij_dirs(path):
- """use forward slashes in directory paths
+ """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 : string
- a directory path obtained from dialogue or script parameter
+ path : str
+ A directory path
Returns
-------
- string
- a more robust path with forward slashes as separators
+ str
+ A directory path with forward slashes as separators
"""
-
fixed_path = str(path).replace("\\", "/")
# fixed_path = fixed_path + "/"
@@ -71,169 +81,238 @@ def fix_ij_dirs(path):
def open_image_with_BF(path_to_file):
- """ use Bio-Formats to opens the first image from an image file path
+ """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 : string
- path to the image file
+ path_to_file : str
+ The file path to the image file to be opened.
Returns
-------
ImagePlus
- the first imp stored in a give file
+ 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_GRAYSCALE)
+ # Enable autoscaling for the image
options.setAutoscale(True)
+ # Set the file path for the image to be opened
options.setId(path_to_file)
- imps = BF.openImagePlus(options) # is an array of ImagePlus
+ # 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):
- image_title = os.path.basename( imp.getShortTitle() )
+ """
+ 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.
+
+ 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):
- """delete all ROIs from the RoiManager
+ """
+ Clear all ROIs from the RoiManager.
Parameters
----------
- rm : RoiManager
+ 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')
def get_threshold_from_method(imp, channel, method):
- """returns the threshold value of chosen IJ AutoThreshold method in desired channel
+ """Get the threshold value of chosen IJ AutoThreshold method in desired channel.
Parameters
----------
imp : ImagePlus
- the imp from which to get the threshold value
- channel : integer
- the channel in which to get the treshold
- method : string
- the AutoThreshold method to use
+ The imp from which to get the threshold value.
+ channel : int
+ The channel in which to get the threshold.
+ method : str
+ The AutoThreshold method to use.
Returns
-------
list
- the upper and the lower threshold (integer values)
+ 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
+ # Get the processor of the imp
ip = imp.getProcessor()
+ # Set the AutoThreshold method to the desired method
ip.setAutoThreshold(method + " dark")
+ # Get the minimum and maximum threshold values
lower_thr = ip.getMinThreshold()
upper_thr = ip.getMaxThreshold()
+ # Reset the threshold so that the imp is not affected by this function
ip.resetThreshold()
- return lower_thr, upper_thr
+ 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"
+ """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".
Parameters
----------
- imp : ImagePlus
+ imp : ij.ImagePlus
the imp to measure on
- channel : integer
+ channel : int
the channel to measure in. starts at 1.
- rm : RoiManager
+ 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
+def change_all_roi_color(rm, color):
+ """
+ Change the color of all ROIs in the RoiManager.
Parameters
----------
- rm : RoiManager
- a reference of the IJ-RoiManager
- color : string
- the desired color. e.g. "green", "red", "yellow", "magenta" ...
+ rm : ij.plugin.frame.RoiManager
+ A reference to the IJ-RoiManager.
+ color : str
+ The desired color, e.g., "green", "red", "yellow", "magenta".
+
+ Returns
+ -------
+ None
"""
- number_of_rois = rm.getCount()
- for roi in range( number_of_rois ):
- rm.select(roi)
- rm.runCommand("Set Color", color)
+ # Select all ROIs in the RoiManager
+ rm.setSelectedIndexes(range(rm.getCount()))
+ # 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
+
+def change_subset_roi_color(rm, selected_rois, color):
+ """
+ Change the color of selected ROIs in the RoiManager.
Parameters
----------
- rm : RoiManager
- a reference of the IJ-RoiManager
- selected_rois : array
- ROIs in the RoiManager to change
- color : string
- the desired color. e.g. "green", "red", "yellow", "magenta" ...
+ 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):
- """shows all ROIs in the ROiManager on imp
+ """
+ Display all ROIs on the given image using the ROI Manager.
Parameters
----------
- rm : RoiManager
- a reference of the IJ-RoiManager
- imp : ImagePlus
- the imp on which to show the ROIs
+ 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()
- rm.runCommand(imp,"Show All")
+ # Use the ROI Manager to show all ROIs on the image
+ rm.runCommand(imp, "Show All")
def save_all_rois(rm, target):
- """save all ROIs in the RoiManager as zip to target path
+ """Save all ROIs in the RoiManager as a zip file to the given target path.
Parameters
----------
- rm : RoiManager
- a reference of the IJ-RoiManager
- target : string
- the path in to store the ROIs. e.g. /my-images/resulting_rois.zip
+ 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
"""
+ # Save all ROIs in the RoiManager to the given target path
rm.runCommand("Save", target)
-def save_selected_rois( rm, selected_rois, target ):
- """save selected ROIs in the RoiManager as zip to target path
+def save_selected_rois(rm, selected_rois, target):
+ """
+ Save selected ROIs in the RoiManager as a zip file to the given target path.
Parameters
----------
- rm : RoiManager
- a reference of the IJ-RoiManager
- selected_rois : array
- ROIs in the RoiManager to save
- target : string
- the path in to store the ROIs. e.g. /my-images/resulting_rois_subset.zip
+ 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")
@@ -243,19 +322,19 @@ def select_positive_fibers( imp, channel, rm, min_intensity ):
Parameters
----------
- imp : ImagePlus
- the imp on which to measure
- channel : integer
- the channel on which to measure. starts at 1
- rm : RoiManager
- a reference of the IJ-RoiManager
- min_intensity : integer
- the selection criterion (here: intensity threshold)
-
+ imp : ij.ImagePlus
+ The ImagePlus on which to measure.
+ channel : int
+ The channel on which to measure. starts at 1.
+ rm : ij.plugin.frame.RoiManager
+ A reference of the IJ-RoiManager.
+ min_intensity : int
+ The selection criterion (here: intensity threshold).
+
Returns
-------
- array
- a selection of ROIs which passed the selection criterion (are above the threshold)
+ list
+ A selection of ROIs which passed the selection criterion (are above the threshold).
"""
imp.setC(channel)
all_rois = rm.getRoisAsArray()
@@ -266,33 +345,34 @@ def select_positive_fibers( imp, channel, rm, min_intensity ):
if stats.mean > min_intensity:
selected_rois.append(i)
- return selected_rois
+ return selected_rois
-def open_rois_from_zip( rm, path ):
- """open RoiManager ROIs from zip and adds them to the RoiManager
+def open_rois_from_zip(rm, path):
+ """
+ Open ROIs from a zip file and add them to the RoiManager.
Parameters
----------
- rm : RoiManager
- a reference of the IJ-RoiManager
- path : string
- path to the ROI zip file
+ 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
+ """Pre-set all rows in given column of the IJ-ResultsTable with desired value.
Parameters
----------
- rt : ResultsTable
- a reference of the IJ-ResultsTable
- column : string
- the desired column. will be created if it does not yet exist
- value : string or float or integer
- the value to be set
+ 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)
@@ -300,46 +380,52 @@ def preset_results_column( rt, column, value):
rt.show("Results")
-def add_results( rt, column, row, value ):
- """adds a value in desired rows of a given column
+def add_results(rt, column, row, value):
+ """Add a value in specified rows of a given column.
Parameters
----------
- rt : ResultsTable
- a reference of the IJ-ResultsTable
- column : string
- the column in which to add the values
- row : array
- the row numbers in which too add the values.
- value : string or float or integer
- the value to be set
+ 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.
"""
- for i in range( len( row ) ):
+ # 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
+def enhance_contrast(imp):
+ """Use "Auto" Contrast & Brightness settings in each channel of imp.
Parameters
----------
- imp : ImagePlus
- the imp on which to change C&B
+ 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
+ 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
+ """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 : RoiManager
- a reference of the IJ-RoiManager
+ rm : ij.plugin.frame.RoiManager
+ A reference to the IJ-RoiManager.
"""
number_of_rois = rm.getCount()
for roi in range( number_of_rois ):
@@ -347,18 +433,28 @@ def renumber_rois(rm):
def setup_defined_ij(rm, rt):
- """set up a clean and defined Fiji user environment
+ """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 : RoiManager
- a reference of the IJ-RoiManager
- rt : ResultsTable
- a reference of the IJ-ResultsTable
+ 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")
@@ -412,7 +508,7 @@ for index, fiber_channel in enumerate(all_fiber_channels):
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]) )
+ 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:
--
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