Created
January 14, 2020 10:09
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Add ROIs to ImageJ roiManager from an image with labels.
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// adapted from https://gist.github.com/NicoKiaru/ae00117cd6d33fea500d2867a5e669d9 | |
// | |
// = CODE DESCRIPTION = | |
// Add ROIs to ImageJ roiManager from an image with labels. | |
// | |
// == INPUTS == | |
// A label image, grey or RGB. | |
// | |
// == OUTPUTS == | |
// Rois in ImageJ roiManager. | |
// | |
// = DEPENDENCIES = | |
// FIJI 1.52p | |
// | |
// = INSTALLATION = | |
// Open the Script in QuPath, Run (work with Run for Project) | |
// | |
// = AUTHOR INFORMATION = | |
// Code written by Nico Chiarutinni, Olivier Burri, Romain Guiet, EPFL - SV -PTECH - BIOP | |
// 2020 | |
// | |
// = COPYRIGHT = | |
// © All rights reserved. ECOLE POLYTECHNIQUE FEDERALE DE LAUSANNE, Switzerland, BioImaging And Optics Platform (BIOP), 2020 | |
// | |
// Licensed under the BSD-3-Clause License: | |
// Redistribution and use in source and binary forms, with or without modification, are permitted provided | |
// that the following conditions are met: | |
// 1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. | |
// 2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer | |
// in the documentation and/or other materials provided with the distribution. | |
// 3. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products | |
// derived from this software without specific prior written permission. | |
// | |
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, | |
// BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. | |
// IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, | |
// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; | |
// LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, | |
// STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF | |
// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. | |
// | |
// | |
// TO DO : improvement would be to : don't get the ImagePlus nor open it to get the ROIs | |
#@ImagePlus imp | |
#@Boolean(label="split objects with same labels value", value = true) splitObjects | |
#@Boolean(label="exclude on edges", value = true) excludeOnEdges | |
import ij.* | |
import ij.IJ.* | |
import ij.ImagePlus; | |
import ij.gui.Roi; | |
import java.util.HashSet; | |
import ij.process.ImageProcessor; | |
import ij.plugin.filter.ThresholdToSelection; | |
import ij.plugin.frame.RoiManager; | |
import ij.process.FloatProcessor | |
import ij.measure.ResultsTable | |
import ij.plugin.filter.ParticleAnalyzer | |
import ij.plugin.frame.RoiManager | |
// reset RoiManager | |
def rm = new RoiManager() | |
rm = rm.getRoiManager() | |
rm.reset() | |
if ( splitObjects ) labelsImageToRois( imp , excludeOnEdges ) | |
else { | |
rois = labelsImageToRoiArray(imp) | |
putRoisToRoiManager(rois,false); | |
} | |
//------------- HELPERS | |
public void labelsImageToRois(ImagePlus imp, Boolean excludeOnEdges ) { | |
def bitDepth = imp.getBitDepth() | |
ImageProcessor ip = imp.getProcessor(); | |
float[][] pixels = ip.getFloatArray(); | |
HashSet<Float> existingPixelValues = new HashSet<>(); | |
for (int x=0;x<ip.getWidth();x++) { | |
for (int y=0;y<ip.getHeight();y++) { | |
existingPixelValues.add((pixels[x][y])); | |
} | |
} | |
// Converts data in case thats a RGB Image | |
fp = new FloatProcessor(ip.getWidth(), ip.getHeight()) | |
fp.setFloatArray(pixels) | |
imgFloatCopy = new ImagePlus("FloatLabel",fp) | |
//imgFloatCopy.show() | |
// Create a ParticleAnalyzer, with options | |
int options = ParticleAnalyzer.SHOW_PROGRESS + ParticleAnalyzer.ADD_TO_MANAGER | |
if (excludeOnEdges) options += ParticleAnalyzer.EXCLUDE_EDGE_PARTICLES | |
def pa = new ParticleAnalyzer( options, 0 , new ResultsTable(), 0.0, Double.POSITIVE_INFINITY , 0.0, 1.0) | |
existingPixelValues.each { v -> | |
if ( v != 0 ){ | |
if ( ( bitDepth == 24) && ( v != -16777216 ) ){// not perfect , | |
IJ.setRawThreshold( imgFloatCopy, v, v, "No Update") // "Red", "No Update" | |
pa.analyze( imgFloatCopy ) | |
} | |
} | |
} | |
} | |
public ArrayList<Roi> labelsImageToRoiArray(ImagePlus imp) { | |
ArrayList<Roi> roiArray = new ArrayList<>(); | |
ImageProcessor ip = imp.getProcessor(); | |
float[][] pixels = ip.getFloatArray(); | |
HashSet<Float> existingPixelValues = new HashSet<>(); | |
for (int x=0;x<ip.getWidth();x++) { | |
for (int y=0;y<ip.getHeight();y++) { | |
existingPixelValues.add((pixels[x][y])); | |
} | |
} | |
// Converts data in case thats a RGB Image | |
fp = new FloatProcessor(ip.getWidth(), ip.getHeight()) | |
fp.setFloatArray(pixels) | |
imgFloatCopy = new ImagePlus("FloatLabel",fp) | |
existingPixelValues.each { v -> | |
fp.setThreshold( v,v,ImageProcessor.NO_LUT_UPDATE); | |
Roi roi = ThresholdToSelection.run(imgFloatCopy); | |
roi.setName(Integer.toString((int) (double) v)); | |
roiArray.add(roi); | |
} | |
return roiArray; | |
} | |
public static void putRoisToRoiManager(ArrayList<Roi> rois, boolean keepROISName) { | |
RoiManager roiManager = RoiManager.getRoiManager(); | |
if (roiManager==null) { | |
roiManager = new RoiManager(); | |
} | |
roiManager.reset(); | |
for (int i = 0; i < rois.size(); i++) { | |
if (!keepROISName) { | |
rois.get(i).setName(""+i); | |
} | |
roiManager.addRoi(rois.get(i)); | |
} | |
roiManager.runCommand("Show All"); | |
} |
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