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MotiQ3D-OutputFilePath-LengthReduction
To decrease the length of output directory paths, the automatically generated filenames of output files in the created results folder was reduced to a minimum prefix ("M3D"). Additionally, the thickness of scale bars in 3D output images was unified for all three dimensions.
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+28
-23
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+28
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‎3D Analyzer/pom.xml

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@@ -18,7 +18,7 @@
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<artifactId>MotiQ_3D</artifactId>
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<groupId>JNH</groupId>
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<version>0.1.1-SNAPSHOT</version>
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<version>0.1.3-SNAPSHOT</version>
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<!-- Plugin Information -->
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<name>MotiQ 3D Analyzer</name>

‎3D Analyzer/src/main/java/motiQ3D/ImPoint.java

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/***===============================================================================
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*
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* MotiQ_3D Version plugin for ImageJ, Version v0.1.1
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* MotiQ_3D Version plugin for ImageJ, Version v0.1.3
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*
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* Copyright (C) 2014-2017 Jan Niklas Hansen
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* First version: July 28, 2014
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* This Version: May 03, 2017
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* This Version: December 1, 2017
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*
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* This program is free software; you can redistribute it and/or
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* modify it under the terms of the GNU General Public License

‎3D Analyzer/src/main/java/motiQ3D/MotiQ_3D.java

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/***===============================================================================
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*
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* MotiQ_3D Version plugin for ImageJ, Version v0.1.1
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* MotiQ_3D Version plugin for ImageJ, Version v0.1.3
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*
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* Copyright (C) 2014-2017 Jan Niklas Hansen
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* First version: July 28, 2014
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* This Version: May 03, 2017
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* This Version: December 1, 2017
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*
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* This program is free software; you can redistribute it and/or
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* modify it under the terms of the GNU General Public License
@@ -42,7 +42,7 @@
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public class MotiQ_3D implements PlugIn, Measurements{
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//Name variables
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static final String pluginName = "MotiQ 3D Analyzer";
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static final String pluginVersion = "v0.1.1";
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static final String pluginVersion = "v0.1.3";
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DecimalFormat dformat6 = new DecimalFormat("#0.000000");
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DecimalFormat dformat3 = new DecimalFormat("#0.000");
@@ -610,7 +610,7 @@ public void windowClosing(WindowEvent winEvt) {
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}
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}
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//write points in save collection back to image
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//write points in saveCollection back to image
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pointSaveCollection.trimToSize();
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for(int i = 0; i < pointSaveCollection.size(); i++){
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imp.getStack().setVoxel(pointSaveCollection.get(i).x, pointSaveCollection.get(i).y,
@@ -855,7 +855,7 @@ public void windowClosing(WindowEvent winEvt) {
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if(saveDate) filePrefix += "_" + NameDateFormatter.format(currentDate);
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//Create subfolder to save additional files
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String subfolderPrefix = "" + dir [task] + filePrefix + System.getProperty("file.separator") + filePrefix;
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String subfolderPrefix = "" + dir [task] + filePrefix + System.getProperty("file.separator") + "M3D";
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try{
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new File(dir [task] + filePrefix).mkdirs();
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}catch(Exception e){

‎3D Analyzer/src/main/java/motiQ3D/OpenFilesDialog.java

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/***===============================================================================
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*
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* MotiQ_3D Version plugin for ImageJ, Version v0.1.1
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* MotiQ_3D Version plugin for ImageJ, Version v0.1.3
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*
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* Copyright (C) 2014-2017 Jan Niklas Hansen
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* First version: July 28, 2014
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* This Version: May 03, 2017
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* This Version: December 1, 2017
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*
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* This program is free software; you can redistribute it and/or
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* modify it under the terms of the GNU General Public License

‎3D Analyzer/src/main/java/motiQ3D/Point3D.java

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@@ -1,10 +1,10 @@
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/***===============================================================================
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*
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* MotiQ_3D Version plugin for ImageJ, Version v0.1.1
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* MotiQ_3D Version plugin for ImageJ, Version v0.1.3
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*
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* Copyright (C) 2014-2017 Jan Niklas Hansen
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* First version: July 28, 2014
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* This Version: May 03, 2017
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* This Version: December 1, 2017
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*
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* This program is free software; you can redistribute it and/or
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* modify it under the terms of the GNU General Public License

‎3D Analyzer/src/main/java/motiQ3D/ProgressDialog.java

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/***===============================================================================
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*
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* MotiQ_3D Version plugin for ImageJ, Version v0.1.1
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* MotiQ_3D Version plugin for ImageJ, Version v0.1.3
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*
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* Copyright (C) 2014-2017 Jan Niklas Hansen
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* First version: July 28, 2014
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* This Version: May 03, 2017
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* This Version: December 1, 2017
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*
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* This program is free software; you can redistribute it and/or
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* modify it under the terms of the GNU General Public License

‎3D Analyzer/src/main/java/motiQ3D/TimelapseParticle.java

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/***===============================================================================
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*
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* MotiQ_3D Version plugin for ImageJ, Version v0.1.1
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* MotiQ_3D Version plugin for ImageJ, Version v0.1.3
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*
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* Copyright (C) 2014-2017 Jan Niklas Hansen
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* First version: July 28, 2014
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* This Version: May 03, 2017
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* This Version: December 1, 2017
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*
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* This program is free software; you can redistribute it and/or
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* modify it under the terms of the GNU General Public License
@@ -2118,9 +2118,14 @@ private ImagePlus getContained3DScBar(ImagePlus imp2, int pxNrX, int pxNrY, int
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int orX = 0, orY = imp2.getHeight()-1, orZ = imp2.getNSlices()-1;
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ImagePlus imp = imp2.duplicate();
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double maxValue = MotiQ_3D.getMaxIntensity(imp);
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int thicknessX = (int)Math.round(2.0 / imp.getCalibration().pixelHeight),
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thicknessY = (int)Math.round(2.0 / imp.getCalibration().pixelWidth),
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thicknessZ = (int)Math.round(2.0 / imp.getCalibration().pixelDepth);
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double thicknessCal = imp.getCalibration().pixelHeight;
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if(thicknessCal < imp.getCalibration().pixelWidth) thicknessCal = imp.getCalibration().pixelWidth;
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if(thicknessCal < imp.getCalibration().pixelDepth) thicknessCal = imp.getCalibration().pixelDepth;
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int thicknessX = (int)Math.round(thicknessCal / imp.getCalibration().pixelHeight),
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thicknessY = (int)Math.round(thicknessCal / imp.getCalibration().pixelWidth),
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thicknessZ = (int)Math.round(thicknessCal / imp.getCalibration().pixelDepth);
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if(thicknessX < 1) thicknessX = 1;
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if(thicknessY < 1) thicknessY = 1;
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if(thicknessZ < 1) thicknessZ = 1;

‎3D Analyzer/src/main/java/motiQ3D/Visualizer3D.java

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/***===============================================================================
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*
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* MotiQ_3D Version plugin for ImageJ, Version v0.1.1
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* MotiQ_3D Version plugin for ImageJ, Version v0.1.3
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*
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* Copyright (C) 2014-2017 Jan Niklas Hansen
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* First version: July 28, 2014
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* This Version: May 03, 2017
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* This Version: December 1, 2017
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*
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* This program is free software; you can redistribute it and/or
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* modify it under the terms of the GNU General Public License

‎3D Analyzer/src/main/resources/plugins.config

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# Belongs to the MotiQ toolbox for analyzing cellular morphology, dynamics, and signaling. MotiQ 3D analyzer analyzes segmented images that are either background-removed (in which intensity information in foreground pixels is preserved while the intensity of background pixels is set to zero) or binary images. After analysis, MotiQ 3D analyzer outputs a text-file containing many different parameter results and a set of images visualizing the results.
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# Author: Jan Niklas Hansen <Jan.Hansen@caesar.de>
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# Version: 0.1.1
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# Date: 2017/05/03
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# Version: 0.1.3
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# Date: 2017/12/01
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# Requires: ImageJ
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Plugins>MotiQ, "MotiQ 3D Analyzer", motiQ3D.MotiQ_3D

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