From 5f704ad5acd38be5432f0f00f5fe6a20f06046f2 Mon Sep 17 00:00:00 2001
From: Laurent Guerard <laurent.guerard@unibas.ch>
Date: Wed, 8 Jan 2025 14:38:47 +0100
Subject: [PATCH] Update docstrings
---
1_identify_fibers.py | 242 +++++++++++++++----------------------------
1 file changed, 86 insertions(+), 156 deletions(-)
diff --git a/1_identify_fibers.py b/1_identify_fibers.py
index bb73a5a..2debeef 100755
--- a/1_identify_fibers.py
+++ b/1_identify_fibers.py
@@ -28,47 +28,19 @@ from fiji.plugin.trackmate.providers import (
SpotMorphologyAnalyzerProvider,
)
from fiji.plugin.trackmate.tracking.jaqaman import SparseLAPTrackerFactory
+from ij import IJ
+from ij import WindowManager as wm
+from ij.measure import ResultsTable
+from ij.plugin import Duplicator, ImageCalculator, RoiEnlarger
+from imcflibs import pathtools
+from imcflibs.imagej import bioformats as bf
+from imcflibs.imagej import misc
-from java.lang import Double
-
-from ch.epfl.biop.ij2command import Labels2Rois
-
-
-#@ String (visibility=MESSAGE, value="<html><b> Welcome to Myosoft - identify fibers! </b></html>") msg1
-#@ File (label="Select directory for output", style="directory") output_dir
-#@ File (label="Select image file", description="select your image") path_to_image
-#@ File(label="Cellpose environment folder", style="directory", description="Folder with the cellpose env") cellpose_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> Morphometric Gates </b></html>") msg2
-#@ Integer (label="Min Area [um²]", value=10) minAr
-#@ Integer (label="Max Area [um²]", value=6000) maxAr
-#@ Double (label="Min Circularity", value=0.5) minCir
-#@ Double (label="Max Circularity", value=1) maxCir
-#@ Double (label="Min solidity", value=0.0) minSol
-#@ Double (label="Max solidity", value=1) maxSol
-#@ Integer (label="Min perimeter [um]", value=5) minPer
-#@ Integer (label="Max perimeter [um]", value=300) maxPer
-#@ Integer (label="Min min ferret [um]", value=0.1) minMinFer
-#@ Integer (label="Max min ferret [um]", value=100) maxMinFer
-#@ Integer (label="Min ferret AR", value=0) minFAR
-#@ Integer (label="Max ferret AR", value=8) maxFAR
-#@ Double (label="Min roundess", value=0.2) minRnd
-#@ Double (label="Max roundess", value=1) maxRnd
-#@ String (visibility=MESSAGE, value="<html><b> Expand ROIS to match fibers </b></html>") msg3
-#@ Double (label="ROI expansion [microns]", value=1) enlarge
-#@ String (visibility=MESSAGE, value="<html><b> channel positions in the hyperstack </b></html>") msg5
-#@ Integer (label="Membrane staining channel number", style="slider", min=1, max=5, value=1) membrane_channel
-#@ Integer (label="Fiber staining (MHC) channel number (0=skip)", style="slider", min=0, max=5, value=3) fiber_channel
-#@ Integer (label="minimum fiber intensity (0=auto)", description="0 = automatic threshold detection", value=0) min_fiber_intensity
-#@ Integer (label="sub-tiling to economize RAM", style="slider", min=1, max=8, value=4) tiling_factor
-
-#@ RoiManager rm
-#@ ResultsTable rt
+# ─── Functions ────────────────────────────────────────────────────────────────
def fix_ij_options():
- """put IJ into a defined state
- """
+ """Put IJ into a defined state."""
# disable inverting LUT
IJ.run("Appearance...", " menu=0 16-bit=Automatic")
# set foreground color to be white, background black
@@ -85,7 +57,7 @@ def fix_ij_options():
def fix_ij_dirs(path):
- """use forward slashes in directory paths
+ """use forward slashes in directory paths.
Parameters
----------
@@ -104,34 +76,32 @@ def fix_ij_dirs(path):
return fixed_path
-def open_image_with_BF(path_to_file):
- """ use Bio-Formats to opens the first image from an image file path
+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
----------
- path_to_file : string
- path to the image file
+ imp : ij.ImagePlus
+ The image to be processed.
Returns
-------
- ImagePlus
- the first imp stored in a give file
+ string
+ The modified title of the image.
"""
- options = ImporterOptions()
- options.setColorMode(ImporterOptions.COLOR_MODE_GRAYSCALE)
- options.setAutoscale(True)
- options.setId(path_to_file)
- imps = BF.openImagePlus(options) # is an array of ImagePlus
-
- return imps[0]
-
-
-def fix_BF_czi_imagetitle(imp):
- image_title = os.path.basename( imp.getShortTitle() )
+ 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
@@ -154,11 +124,13 @@ def preprocess_membrane_channel(imp):
def get_threshold_from_method(imp, channel, method):
- """returns the threshold value of chosen IJ AutoThreshold method in desired channel
+ """Get the value of automated threshold method.
+
+ Returns the threshold value of chosen IJ AutoThreshold method in desired channel.
Parameters
----------
- imp : ImagePlus
+ imp : ij.ImagePlus
the imp from which to get the threshold value
channel : integer
the channel in which to get the treshold
@@ -187,21 +159,20 @@ def run_tm(
seg_model,
diam_seg,
channel_sec=0,
- quality_thresh=[0,0],
- intensity_thresh=[0,0],
- circularity_thresh=[0,0],
- perimeter_thresh=[0,0],
- feret_thresh=[0,0],
- area_thresh=[0,0],
+ quality_thresh=[0, 0],
+ intensity_thresh=[0, 0],
+ circularity_thresh=[0, 0],
+ perimeter_thresh=[0, 0],
+ area_thresh=[0, 0],
crop_roi=None,
use_gpu=True,
):
"""
- Function to run TrackMate on open data
+ Function to run TrackMate on open data, applying filters to spots.
Parameters
----------
- implus : ImagePlus
+ implus : ij.ImagePlus
ImagePlus on which to run the function
channel_seg : int
Channel of interest
@@ -214,17 +185,15 @@ def run_tm(
channel_sec : int, optional
Secondary channel to use for segmentation, by default 0
quality_thresh : float, optional
- Threshold for quality filtering, by default 0
+ Threshold for quality filtering, by default None
intensity_thresh : float, optional
- Threshold for intensity filtering, by default 0
+ Threshold for intensity filtering, by default None
circularity_thresh : float, optional
- Threshold for circularity filtering, by default 0
+ Threshold for circularity filtering, by default None
perimeter_thresh : float, optional
- Threshold for perimeter filtering, by default 0
- feret_thresh : float, optional
- Threshold for Feret filtering, by default 0
+ Threshold for perimeter filtering, by default None
area_thresh : float, optional
- Threshold for area filtering, by default 0
+ Threshold for area filtering, by default None
crop_roi : ROI, optional
ROI to crop on the image, by default None
use_gpu : bool, optional
@@ -232,7 +201,7 @@ def run_tm(
Returns
-------
- ImagePlus
+ ij.ImagePlus
Label image with the segmented objects
"""
@@ -346,6 +315,7 @@ def run_tm(
implus.setDimensions(dims[2], dims[3], dims[4])
return label_imp
+
def set_trackmate_filter(settings, filter_name, filter_value):
"""Sets a TrackMate spot filter with specified filter name and values.
@@ -365,12 +335,13 @@ def set_trackmate_filter(settings, filter_name, filter_value):
settings.addSpotFilter(filter)
return settings
+
def delete_channel(imp, channel_number):
- """delete a channel from target imp
+ """Delete a channel from target imp.
Parameters
----------
- imp : ImagePlus
+ imp : ij.ImagePlus
the imp from which to delete target channel
channel_number : integer
the channel number to be deleted. starts at 0.
@@ -379,59 +350,14 @@ def delete_channel(imp, channel_number):
IJ.run(imp, "Delete Slice", "delete=channel")
-def run_extended_particle_analyzer( imp, eda_parameters ):
- """identifies ROIs in target imp using the extended particle analyzer of the BioVoxxel toolbox
- with given parameters
+def measure_in_all_rois(imp, channel, rm):
+ """Gives measurements for all ROIs in ROIManager.
- Parameters
- ----------
- imp : ImagePlus
- the image on which to run the EPA on. Should be 8-bit thresholded
- eda_parameters : array
- all user defined parameters to restrict ROI identification
- """
- epa = Extended_Particle_Analyzer()
- epa.readInputImageParameters(imp)
- epa.setDefaultParameterFields()
-
- # expose all parameters explicitly
- epa.usePixel = False
- epa.usePixelForOutput = False
- epa.Area = str(eda_parameters[0]) + "-" + str(eda_parameters[1])
- epa.Extent = "0.00-1.00"
- epa.Perimeter = str(eda_parameters[2]) + "-" + str(eda_parameters[3])
- epa.Circularity = str(eda_parameters[4]) + "-" + str(eda_parameters[5])
- epa.Roundness = str(eda_parameters[6]) + "-" + str(eda_parameters[7])
- epa.Solidity = str(eda_parameters[8]) + "-" + str(eda_parameters[9])
- epa.Compactness = "0.00-1.00"
- epa.AR = "0-Infinity"
- epa.FeretAR = str(eda_parameters[10]) + "-" + str(eda_parameters[11])
- epa.EllipsoidAngle = "0-180"
- epa.MaxFeret = "0-Infinity"
- epa.MinFeret = str(eda_parameters[12]) + "-" + str(eda_parameters[13])
- epa.FeretAngle = "0-180"
- epa.COV = "0.00-1.00"
- epa.Output = "Nothing"
- epa.Redirect = "None"
- epa.Correction = "None"
- epa.Reset = False
- epa.DisplayResults = False
- epa.ClearResults = False
- epa.Summarize = False
- epa.AddToManager = True
- epa.ExcludeEdges = False
- epa.IncludeHoles = False
-
- epa.defineParticleAnalyzers()
- epa.particleAnalysis( imp.getProcessor(), imp, imp.getTitle() )
-
-
-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".
Parameters
----------
- imp : ImagePlus
+ imp : ij.ImagePlus
the imp to measure on
channel : integer
the channel to measure in. starts at 1.
@@ -439,12 +365,12 @@ def measure_in_all_rois( imp, channel, rm ):
a reference of the IJ-RoiManager
"""
imp.setC(channel)
- rm.runCommand(imp,"Deselect")
- rm.runCommand(imp,"Measure")
+ rm.runCommand(imp, "Deselect")
+ 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):
+ """Cchange the color of all ROIs in the RoiManager.
Parameters
----------
@@ -454,13 +380,13 @@ def change_all_roi_color( rm, color ):
the desired color. e.g. "green", "red", "yellow", "magenta" ...
"""
number_of_rois = rm.getCount()
- for roi in range( number_of_rois ):
+ for roi in range(number_of_rois):
rm.select(roi)
rm.runCommand("Set Color", color)
-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
----------
@@ -478,21 +404,21 @@ def change_subset_roi_color( rm, selected_rois, color ):
def show_all_rois_on_image(rm, imp):
- """shows all ROIs in the ROiManager on imp
+ """Shows all ROIs in the ROiManager on imp.
Parameters
----------
rm : RoiManager
a reference of the IJ-RoiManager
- imp : ImagePlus
+ imp : ij.ImagePlus
the imp on which to show the ROIs
"""
imp.show()
- rm.runCommand(imp,"Show All")
+ 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 zip to target path.
Parameters
----------
@@ -504,8 +430,8 @@ def save_all_rois(rm, target):
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 zip to target path.
Parameters
----------
@@ -522,8 +448,8 @@ def save_selected_rois( rm, selected_rois, target ):
rm.runCommand("Deselect")
-def enlarge_all_rois( amount_in_um, rm, pixel_size_in_um ):
- """enlarges all ROIs in the RoiManager by x scaled units
+def enlarge_all_rois(amount_in_um, rm, pixel_size_in_um):
+ """Enlarges all ROIs in the RoiManager by x scaled units.
Parameters
----------
@@ -542,13 +468,15 @@ def enlarge_all_rois( amount_in_um, rm, pixel_size_in_um ):
rm.addRoi(enlarged_roi)
-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.
+def select_positive_fibers(imp, channel, rm, min_intensity):
+ """Select ROIs in ROIManager based on intensity in specific channel.
+
+ 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
Parameters
----------
- imp : ImagePlus
+ imp : ij.ImagePlus
the imp on which to measure
channel : integer
the channel on which to measure. starts at 1
@@ -574,8 +502,10 @@ def select_positive_fibers( imp, channel, rm, min_intensity ):
return selected_rois
-def preset_results_column( rt, column, value):
- """pre-set all rows in given column of the IJ-ResultsTable with desired value
+def preset_results_column(rt, column, value):
+ """Pre-set values in selected column from the ResultsTable.
+
+ Pre-set all rows in given column of the IJ-ResultsTable with desired value.
Parameters
----------
@@ -586,14 +516,14 @@ def preset_results_column( rt, column, value):
value : string or float or integer
the value to be set
"""
- for i in range( rt.size() ):
+ for i in range(rt.size()):
rt.setValue(column, i, 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):
+ """Adds a value in desired rows of a given column.
Parameters
----------
@@ -612,21 +542,21 @@ def add_results( rt, column, row, value ):
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
+ 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.
Parameters
----------
@@ -634,12 +564,12 @@ def renumber_rois(rm):
a reference of the IJ-RoiManager
"""
number_of_rois = rm.getCount()
- for roi in range( number_of_rois ):
- rm.rename( roi, str(roi + 1) )
+ 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
+ """Set up a clean and defined Fiji user environment.
Parameters
----------
--
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