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Add control by macro (#3) - fix bug in fill holes function
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@hansenjn
hansenjn committed Jul 26, 2024
1 parent 930f517 commit 648382e
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Showing 3 changed files with 263 additions and 83 deletions.
2 changes: 1 addition & 1 deletion Thresholder/pom.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,7 @@

<artifactId>MotiQ_Thresholder</artifactId>
<groupId>JNH</groupId>
<version>0.1.3-SNAPSHOT</version>
<version>0.2.0-SNAPSHOT</version>

<!-- Plugin Information -->
<name>MotiQ thresholder</name>
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338 changes: 259 additions & 79 deletions Thresholder/src/main/java/motiQ_thr/Thresholder.java
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Original file line number Diff line number Diff line change
Expand Up @@ -2,9 +2,9 @@
*
* MotiQ_thresholder plugin for ImageJ
*
* Copyright (C) 2015-2023 Jan N. Hansen
* Copyright (C) 2015-2024 Jan N. Hansen
* First version: January 05, 2015
* This version: January 20, 2023
* This version: July 25, 2024
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU General Public License
Expand Down Expand Up @@ -43,7 +43,7 @@
public class Thresholder implements PlugIn, Measurements{//, DialogListener {
//Name variables
final static String PLUGINNAME = "MotiQ_thresholder";
final static String PLUGINVERSION = "v0.1.3";
final static String PLUGINVERSION = "v0.2.0";

//Fonts
static final Font SuperHeadingFont = new Font("Sansserif", Font.BOLD, 16);
Expand Down Expand Up @@ -105,81 +105,249 @@ public class Thresholder implements PlugIn, Measurements{//, DialogListener {
boolean continueProcessing = true;

public void run(String arg) {
/**&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&& *
* display dialog
* &&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&& */

GenericDialog gd = new GenericDialog(PLUGINNAME + " - Settings");
// gd.setInsets(0,0,0); (top, left, bottom)

gd.setInsets(0,0,0); gd.addMessage(PLUGINNAME + ", version " + PLUGINVERSION
+ " (\u00a9 2015 - " + yearOnly.format(new Date()) + ", Jan Niklas Hansen)", SuperHeadingFont);

gd.setInsets(5,0,0); gd.addChoice("Process ", taskVariant, selectedTaskVariant);
//&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&
//-----------Eventually read settings from macro input------------------------
//&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&

gd.setInsets(5,0,0); gd.addMessage("Reference image", SubHeadingFont);
gd.setInsets(0,0,0); gd.addCheckbox("Use alternate reference image",useAlternateRef);
gd.setInsets(0,20,0); gd.addCheckbox("-> Automatically find alternate reference image in origin directory (via file name)",getImageByName);
gd.setInsets(0,50,0); gd.addStringField("-> Begin of suffix in file name of input image",nameSuffix);
gd.setInsets(0,50,0); gd.addStringField("-> Additional suffix in file name of alternate reference image",parentEnding);
gd.setInsets(0,20,0); gd.addCheckbox("-> Restrict threshold calculation to size and position of input image",restrictToPos);

gd.setInsets(5,0,0); gd.addMessage("Pre-processing", SubHeadingFont);
gd.setInsets(0,0,0); gd.addNumericField("Scale down reference image for calculation - factor: ", scalingFactor, 1);
gd.setInsets(0,0,0); gd.addCheckbox("Convert input and reference image into 8-bit before processing.",conv8Bit); //TODO save into metadata
boolean showDialog = true;
// IJ.log("Macro running? " + IJ.macroRunning() );
// IJ.log(Macro.getOptions());
if (IJ.macroRunning()) {
String macroOptions = Macro.getOptions();
// IJ.log("Macro Options: " + macroOptions);

String temp;
selectedTaskVariant = taskVariant[0];

temp = "";
if(macroOptions.contains("use-alternate")) {
useAlternateRef = true;

if(macroOptions.contains("automatically-find")) {
getImageByName = true;
// IJ.log("detected getImageByName: " + getImageByName);
}

temp = "";
if(macroOptions.contains("begin-of-suffix=")){
temp = macroOptions.substring(macroOptions.indexOf("begin-of-suffix="));
temp = temp.substring(temp.indexOf("=")+1);
if(temp.startsWith("[") || temp.startsWith("//[")) {
temp = temp.substring(1,temp.indexOf("]"));
}else {
temp = temp.substring(0,temp.indexOf(" "));
}
nameSuffix = temp;
// IJ.log("detected suffixbegin: " + nameSuffix);
}

if(macroOptions.contains("additional-suffix=")){
temp = macroOptions.substring(macroOptions.indexOf("additional-suffix="));
temp = temp.substring(temp.indexOf("=")+1);
if(temp.startsWith("[") || temp.startsWith("//[")) {
temp = temp.substring(1,temp.indexOf("]"));
}else {
temp = temp.substring(0,temp.indexOf(" "));
}
parentEnding = temp;
// IJ.log("detected parentEnding: " + parentEnding);
}

if(macroOptions.contains("restrict")) {
restrictToPos = true;
// IJ.log("detected restrictToPos: " + restrictToPos);
}
}else {
useAlternateRef = false;
getImageByName = false;
restrictToPos = false;
}

if(macroOptions.contains("scale=")){
temp = macroOptions.substring(macroOptions.indexOf("scale="));
temp = temp.substring(temp.indexOf("=")+1,temp.indexOf(" "));
scalingFactor = Double.parseDouble(temp);
// IJ.log("detected scalingFactor: " + scalingFactor);
}

if(macroOptions.contains("convert")) {
conv8Bit = true;
// IJ.log("detected conv8Bit: " + conv8Bit);
}

if(macroOptions.contains("threshold=")){
temp = macroOptions.substring(macroOptions.indexOf("threshold="));
temp = temp.substring(temp.indexOf("=")+1,temp.indexOf(" "));
selectedAlgorithm = temp;

boolean thresholdFits = false;
for(int i = 0; i < algorithm.length; i++) {
if(selectedAlgorithm.equals(algorithm[i])) {
thresholdFits = true;
break;
}
}
if(thresholdFits == false) {
IJ.error("Unknown threshold algorithm specified!\nSelect a threshold algorithm available in MotiQ Thresholder!");
}

// IJ.log("detected selectedAlgorithm: " + selectedAlgorithm);
}

if(macroOptions.contains("stack-handling=")){
temp = macroOptions.substring(macroOptions.indexOf("stack-handling="));
temp = temp.substring(temp.indexOf("=")+1);

for(int i = 0; i < algorithm.length; i++) {
if(temp.contains(stackMethod[i])) {
chosenStackMethod = stackMethod[i];
break;
}
if(i == algorithm.length-1) {
IJ.error("Stack handling method was not correctly specified!");
}
}
// IJ.log("detected chosenStackMethod: " + chosenStackMethod);
}

if(macroOptions.contains("threshold-every-time-step")) {
separateFrames = true;
// IJ.log("detected separateFrames: " + separateFrames);
}

if(macroOptions.contains("threshold-only-distinct-times")) {
onlyTimeGroup = true;
// IJ.log("detected onlyTimeGroup: " + onlyTimeGroup);

if(macroOptions.contains("start-time=")){
temp = macroOptions.substring(macroOptions.indexOf("start-time="));
temp = temp.substring(temp.indexOf("=")+1,temp.indexOf(" "));
startGroup = Integer.parseInt(temp);
// IJ.log("detected startGroup: " + startGroup);
}

if(macroOptions.contains("end-time=")){
temp = macroOptions.substring(macroOptions.indexOf("end-time="));
temp = temp.substring(temp.indexOf("=")+1,temp.indexOf(" "));
endGroup = Integer.parseInt(temp);
// IJ.log("detected endGroup: " + endGroup);
}
}

if(macroOptions.contains("local-threshold")) {
localThreshold = true;
// IJ.log("detected localThreshold: " + localThreshold);

if(macroOptions.contains("local-threshold-radius=")){
temp = macroOptions.substring(macroOptions.indexOf("local-threshold-radius="));
temp = temp.substring(temp.indexOf("=")+1,temp.indexOf(" "));
locThrRadius = Integer.parseInt(temp);
// IJ.log("detected locThrRadius: " + locThrRadius);
}
}

if(macroOptions.contains("fill-holes")) {
fillHoles = true;
// IJ.log("detected fillHoles: " + fillHoles);
}

if(macroOptions.contains("keep-intensities")) {
keepIntensities = true;
// IJ.log("detected keepIntensities: " + keepIntensities);
}

if(macroOptions.contains("automatically-save")) {
autoSaveImage = true;
// IJ.log("detected autoSaveImage: " + autoSaveImage);
}

if(macroOptions.contains("include-date")){
saveDate = true;
// IJ.log("detected saveDate: " + saveDate);
}

showDialog = false;
}

if(showDialog) {
/**&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&& *
* display dialog
* &&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&& */

GenericDialog gd = new GenericDialog(PLUGINNAME + " - Settings");
// gd.setInsets(0,0,0); (top, left, bottom)

gd.setInsets(5,0,0); gd.addMessage("Threshold determination", SubHeadingFont);
gd.setInsets(0,0,0); gd.addChoice("Threshold algorithm", algorithm, selectedAlgorithm);
gd.setInsets(10,0,0); gd.addChoice("Stack handling: ", stackMethod, chosenStackMethod);
gd.setInsets(5,0,0); gd.addCheckbox("Threshold every time-step separately.", separateFrames);
gd.setInsets(0,0,0); gd.addCheckbox("Threshold only distinct time series. Start / end time-step: ",onlyTimeGroup);
gd.setInsets(-23,0,0); gd.addNumericField("", startGroup, 0);
gd.setInsets(-23,55,0); gd.addNumericField("", endGroup, 0);
gd.setInsets(0,0,0); gd.addCheckbox("Calculate an individual threshold for each pixel - local threshold radius [px]: ",localThreshold);
gd.setInsets(-21,45,0); gd.addNumericField("", locThrRadius, 0);
gd.setInsets(0,0,0); gd.addMessage(PLUGINNAME + ", version " + PLUGINVERSION
+ " (\u00a9 2015 - " + yearOnly.format(new Date()) + ", Jan Niklas Hansen)", SuperHeadingFont);

gd.setInsets(5,0,0); gd.addMessage("Image segmentation and output", SubHeadingFont);
gd.setInsets(0,0,0); gd.addCheckbox("Fill holes in mask (independent for every stack image)",fillHoles);
gd.setInsets(0,0,0); gd.addCheckbox("Keep original intensities in pixels above threshold",keepIntensities);
gd.setInsets(0,0,0); gd.addCheckbox("Automatically save image/metadata into origin directory and close image", autoSaveImage);
gd.setInsets(0,0,0); gd.addCheckbox("Include date in output file names", saveDate);

gd.showDialog();

//get variables
selectedTaskVariant = gd.getNextChoice();

useAlternateRef = gd.getNextBoolean();
getImageByName = gd.getNextBoolean();
nameSuffix = gd.getNextString();
parentEnding = gd.getNextString();
restrictToPos = gd.getNextBoolean();

if(useAlternateRef == false){
getImageByName = false;
restrictToPos = false;
}

scalingFactor = (double)gd.getNextNumber();
conv8Bit = gd.getNextBoolean();

selectedAlgorithm = gd.getNextChoice();
chosenStackMethod = gd.getNextChoice();
separateFrames = gd.getNextBoolean();
onlyTimeGroup = gd.getNextBoolean();
startGroup = (int)gd.getNextNumber();
endGroup = (int)gd.getNextNumber();

localThreshold = gd.getNextBoolean();
locThrRadius = (int)gd.getNextNumber();

fillHoles = gd.getNextBoolean();
keepIntensities = gd.getNextBoolean();
autoSaveImage = gd.getNextBoolean();
saveDate = gd.getNextBoolean();

if (gd.wasCanceled()) return;

gd.setInsets(5,0,0); gd.addChoice("Process ", taskVariant, selectedTaskVariant);

gd.setInsets(5,0,0); gd.addMessage("Reference image", SubHeadingFont);
gd.setInsets(0,0,0); gd.addCheckbox("Use alternate reference image",useAlternateRef);
gd.setInsets(0,20,0); gd.addCheckbox("-> Automatically find alternate reference image in origin directory (via file name)",getImageByName);
gd.setInsets(0,50,0); gd.addStringField("-> Begin of suffix in file name of input image",nameSuffix);
gd.setInsets(0,50,0); gd.addStringField("-> Additional suffix in file name of alternate reference image",parentEnding);
gd.setInsets(0,20,0); gd.addCheckbox("-> Restrict threshold calculation to size and position of input image",restrictToPos);

gd.setInsets(5,0,0); gd.addMessage("Pre-processing", SubHeadingFont);
gd.setInsets(0,0,0); gd.addNumericField("Scale down reference image for calculation - factor: ", scalingFactor, 1);
gd.setInsets(0,0,0); gd.addCheckbox("Convert input and reference image into 8-bit before processing.",conv8Bit); //TODO save into metadata

gd.setInsets(5,0,0); gd.addMessage("Threshold determination", SubHeadingFont);
gd.setInsets(0,0,0); gd.addChoice("Threshold algorithm", algorithm, selectedAlgorithm);
gd.setInsets(10,0,0); gd.addChoice("Stack handling: ", stackMethod, chosenStackMethod);
gd.setInsets(5,0,0); gd.addCheckbox("Threshold every time-step separately.", separateFrames);
gd.setInsets(0,0,0); gd.addCheckbox("Threshold only distinct time series. Start / end time-step: ",onlyTimeGroup);
gd.setInsets(-23,0,0); gd.addNumericField("", startGroup, 0);
gd.setInsets(-23,55,0); gd.addNumericField("", endGroup, 0);
gd.setInsets(0,0,0); gd.addCheckbox("Calculate an individual threshold for each pixel - local threshold radius [px]: ",localThreshold);
gd.setInsets(-21,45,0); gd.addNumericField("", locThrRadius, 0);

gd.setInsets(5,0,0); gd.addMessage("Image segmentation and output", SubHeadingFont);
gd.setInsets(0,0,0); gd.addCheckbox("Fill holes in mask (independent for every stack image)",fillHoles);
gd.setInsets(0,0,0); gd.addCheckbox("Keep original intensities in pixels above threshold",keepIntensities);
gd.setInsets(0,0,0); gd.addCheckbox("Automatically save image/metadata into origin directory and close image", autoSaveImage);
gd.setInsets(0,0,0); gd.addCheckbox("Include date in output file names", saveDate);

gd.showDialog();

//get variables
selectedTaskVariant = gd.getNextChoice();

useAlternateRef = gd.getNextBoolean();
getImageByName = gd.getNextBoolean();
nameSuffix = gd.getNextString();
parentEnding = gd.getNextString();
restrictToPos = gd.getNextBoolean();

if(useAlternateRef == false){
getImageByName = false;
restrictToPos = false;
}

scalingFactor = (double)gd.getNextNumber();
conv8Bit = gd.getNextBoolean();

selectedAlgorithm = gd.getNextChoice();
chosenStackMethod = gd.getNextChoice();
separateFrames = gd.getNextBoolean();
onlyTimeGroup = gd.getNextBoolean();
startGroup = (int)gd.getNextNumber();
endGroup = (int)gd.getNextNumber();

localThreshold = gd.getNextBoolean();
locThrRadius = (int)gd.getNextNumber();

fillHoles = gd.getNextBoolean();
keepIntensities = gd.getNextBoolean();
autoSaveImage = gd.getNextBoolean();
saveDate = gd.getNextBoolean();

if (gd.wasCanceled()) return;


}

/**&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&
* load image tasks
Expand Down Expand Up @@ -1316,9 +1484,14 @@ private void segmentImage(ImagePlus imp, double threshold, int z){
}
}
}
IJ.run(maskImp, "Invert", "");
imp.setPosition(z+1);
if(!Prefs.blackBackground) {
IJ.run(maskImp, "Invert", "slice");
}
IJ.run(maskImp, "Fill Holes", "slice");
IJ.run(maskImp, "Invert", "");
if(!Prefs.blackBackground) {
IJ.run(maskImp, "Invert", "slice");
}

progressDialog.updateBarText("segment image...");
for(int x = 0; x < imp.getWidth(); x++){
Expand Down Expand Up @@ -1369,9 +1542,16 @@ private void segmentImageLocally (ImagePlus imp, double thresholdMatrix [][][]){
}
}

IJ.run(transImp, "Invert", "");
IJ.run(transImp, "Fill Holes", "slice");
IJ.run(transImp, "Invert", "");

if(!Prefs.blackBackground) {
IJ.run(transImp, "Invert", "stack");
}

IJ.run(transImp, "Fill Holes", "stack");

if(!Prefs.blackBackground) {
IJ.run(transImp, "Invert", "stack");
}

progressDialog.updateBarText("segment image...");
for(int x = 0; x < imp.getWidth(); x++){
Expand Down
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