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BugfixUseAlternateReferenceImage
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Bugfix for processing without checking "use alternate reference image".
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@hansenjn
hansenjn committed Sep 15, 2017
1 parent 54be6e8 commit aee8e9a
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Showing 3 changed files with 41 additions and 20 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 @@ -18,7 +18,7 @@

<artifactId>MotiQ_Thresholder</artifactId>
<groupId>JNH</groupId>
<version>0.1.1-SNAPSHOT</version>
<version>0.1.2-SNAPSHOT</version>

<!-- Plugin Information -->
<name>MotiQ thresholder</name>
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55 changes: 38 additions & 17 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 @@ -45,7 +45,7 @@
public class Thresholder implements PlugIn, Measurements{//, DialogListener {
//Name variables
final static String PLUGINNAME = "MotiQ_thresholder";
final static String PLUGINVERSION = "v0.1.1";
final static String PLUGINVERSION = "v0.1.2";

//Fonts
static final Font SuperHeadingFont = new Font("Sansserif", Font.BOLD, 16);
Expand All @@ -68,7 +68,7 @@ public class Thresholder implements PlugIn, Measurements{//, DialogListener {
String selectedTaskVariant = taskVariant[1];
int tasks = 1;

boolean useParent = true;
boolean useAlternateRef = true;
boolean getImageByName = true;
String nameSuffix = "_CUT";
String parentEnding = ".tif";
Expand Down Expand Up @@ -120,7 +120,7 @@ public void run(String arg) {
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",useParent);
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);
Expand Down Expand Up @@ -151,20 +151,24 @@ public void run(String arg) {
//get variables
selectedTaskVariant = gd.getNextChoice();

useParent = gd.getNextBoolean();
useAlternateRef = gd.getNextBoolean();
getImageByName = gd.getNextBoolean();
if(useParent == false){getImageByName = false;}
nameSuffix = gd.getNextString();
parentEnding = gd.getNextString();
restrictToPos = gd.getNextBoolean(); //TODO implement method
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(); //TODO implement method!
onlyTimeGroup = gd.getNextBoolean();
startGroup = (int)gd.getNextNumber();
endGroup = (int)gd.getNextNumber();

Expand All @@ -186,7 +190,7 @@ public void run(String arg) {
String parName = "";
String parDir = "";

if(useParent==true&&getImageByName==false){
if(useAlternateRef==true&&getImageByName==false){
//get folder and file name of parent---------------------------------
new WaitForUserDialog("Press OK! -> a dialog will pop up: use it to select the parent image for images to process!").show();
OpenDialog od = new OpenDialog("Open Parent Image", null);
Expand Down Expand Up @@ -319,6 +323,7 @@ public void windowClosing(WindowEvent winEvt) {
break running;
}
}


//open Image
ImagePlus imp;
Expand Down Expand Up @@ -378,9 +383,11 @@ public void windowClosing(WindowEvent winEvt) {

//open reference Image and scale it
ImagePlus primaryParImp;
if(useParent){
if(useAlternateRef){
primaryParImp = IJ.openImage(""+parDir+parName+"");
}else{
parDir = dir[task];
parName = name[task];
primaryParImp = imp.duplicate();
}
primaryParImp.deleteRoi();
Expand Down Expand Up @@ -417,6 +424,7 @@ public void windowClosing(WindowEvent winEvt) {

//eventually convert to 8bit
if(conv8Bit){
progressDialog.updateBarText("converting to 8-bit...");
Thresholder.optimal8BitConversion(imp, parImp);
if(imp.getBitDepth() != 8 || parImp.getBitDepth() != 8){
progressDialog.notifyMessage("Task " + (task+1) + "/" + tasks + ": 8-bit conversion failed!", ProgressDialog.ERROR);
Expand Down Expand Up @@ -571,6 +579,7 @@ else if(chosenStackMethod.equals(stackMethod[3])){
* */
if(separateFrames){
for(int t = startGroup-1; t < endGroup; t++){
progressDialog.updateBarText("generate maximum projection...");
selectedImp = getSelectedTimepoints(imp, t+1, t+1);
selectedImp = maximumProjection(selectedImp, 1, selectedImp.getStackSize());
selectedParImp = getSelectedTimepoints(parImp, (int)((double)zCorr/imp.getNSlices()) + t + 1, (int)((double)zCorr/imp.getNSlices()) + t + 1);
Expand Down Expand Up @@ -908,7 +917,7 @@ else if(chosenStackMethod.equals(stackMethod[4])){
tw1.append("Processing started: " + FullDateFormatter.format(startDate));
tw1.append("");

if(useParent){
if(useAlternateRef){
tw1.append("A REFERENCE IMAGE was used for threshold calculation");
tw1.append(" Reference image name: " + parName);
tw1.append("");
Expand Down Expand Up @@ -1167,9 +1176,11 @@ private static ImagePlus getSelectedTimepoints (ImagePlus imp, int firstTimepoin
* sliceImage range: 1 <= sliceImage <= stacksize
* */
private double getAverageThreshold (ImagePlus imp, ImagePlus parImp, int startSliceImage, int endSliceImage){
progressDialog.updateBarText("get average threshold...");

//initialize
double calculatedThreshold = 0.0;

Roi selection = new Roi(0,0,imp.getWidth(), imp.getHeight());
if(restrictToPos){
selection = this.getPositionRoi(imp, startSliceImage, endSliceImage);
Expand All @@ -1192,12 +1203,13 @@ private double getAverageThreshold (ImagePlus imp, ImagePlus parImp, int startSl
return calculatedThreshold / (double)(endSliceImage-startSliceImage+1);
}

/**
* Calculates a threshold in the histogram of ImagePlus <parImp> for the image <imp>
* Only the slice images between the indicated <startSliceImage> and <endSliceImage> are included into calculation
* */
private double getHistogramThreshold (ImagePlus imp, ImagePlus parImp){
/**
* Calculates a threshold in the histogram of ImagePlus <parImp> for the image <imp>
* Only the slice images between the indicated <startSliceImage> and <endSliceImage> are included into calculation
* */

progressDialog.updateBarText("get histogram threshold...");

parImp.deleteRoi();
if(restrictToPos){
Roi selection = this.getPositionRoi(imp, 1, imp.getStackSize());
Expand All @@ -1215,8 +1227,10 @@ private double getHistogramThreshold (ImagePlus imp, ImagePlus parImp){
* range: 1 <= z <= stacksize
* */
private double getSingleSliceImageThreshold (ImagePlus imp, ImagePlus parImp, int s){
progressDialog.updateBarText("determine threshold...");
parImp.deleteRoi();
if(restrictToPos){
progressDialog.updateBarText("find position...");
Roi selection = this.getPositionRoi(imp, 1, imp.getStackSize());
selection = scaleRoi(selection, scalingFactor);
parImp.setRoi(selection);
Expand Down Expand Up @@ -1247,6 +1261,7 @@ private double getThresholdOfSelection(ImagePlus parImp, Roi selection, int z){
* @return a threshold for the histogram of ImagePlus <parImp> within the <selection>
* */
private double getHistogramThresholdOfSelection (ImagePlus parImp, Roi selection){
progressDialog.updateBarText("determine histogram threshold...");
parImp.deleteRoi();
parImp.setRoi(selection);

Expand All @@ -1260,6 +1275,7 @@ private void segmentImage(ImagePlus imp, double threshold, int z){
//z=slicenr
int maxValue = getMaxPossibleIntensity(imp);
if(fillHoles){
progressDialog.updateBarText("filling holes...");
//generate a mask image
ImagePlus maskImp = IJ.createImage("Mask", "8-bit", imp.getWidth(), imp.getHeight(), 1);
double imageMax = getMaxPossibleIntensity(maskImp);
Expand All @@ -1276,6 +1292,7 @@ private void segmentImage(ImagePlus imp, double threshold, int z){
IJ.run(maskImp, "Fill Holes", "slice");
IJ.run(maskImp, "Invert", "");

progressDialog.updateBarText("segment image...");
for(int x = 0; x < imp.getWidth(); x++){
for(int y = 0; y < imp.getHeight(); y++){
if(maskImp.getStack().getVoxel(x,y,0) == 0.0){
Expand All @@ -1288,6 +1305,7 @@ private void segmentImage(ImagePlus imp, double threshold, int z){
maskImp.changes = false;
maskImp.close();
}else{
progressDialog.updateBarText("segment image...");
for(int x = 0; x < imp.getWidth(); x++){
for(int y = 0; y < imp.getHeight(); y++){
double pxintensity = imp.getStack().getVoxel(x,y,z);
Expand All @@ -1306,7 +1324,7 @@ private void segmentImageLocally (ImagePlus imp, double thresholdMatrix [][][]){
int maxIntensity = getMaxPossibleIntensity(imp);
if(fillHoles){
//Include fill Holes mechanism

progressDialog.updateBarText("filling holes...");
ImagePlus transImp = IJ.createHyperStack("Trans Imp", imp.getWidth(), imp.getHeight(), 1,
imp.getNSlices(), imp.getNFrames(), imp.getBitDepth());

Expand All @@ -1327,6 +1345,7 @@ private void segmentImageLocally (ImagePlus imp, double thresholdMatrix [][][]){
IJ.run(transImp, "Fill Holes", "slice");
IJ.run(transImp, "Invert", "");

progressDialog.updateBarText("segment image...");
for(int x = 0; x < imp.getWidth(); x++){
for(int y = 0; y < imp.getHeight(); y++){
for(int z = 0; z < imp.getStackSize(); z++){
Expand All @@ -1344,6 +1363,7 @@ private void segmentImageLocally (ImagePlus imp, double thresholdMatrix [][][]){
transImp.changes = false;
transImp.close();
}else{
progressDialog.updateBarText("segment image...");
for(int x = 0; x < imp.getWidth(); x++){
for(int y = 0; y < imp.getHeight(); y++){
for(int z = 0; z < imp.getStackSize(); z++){
Expand Down Expand Up @@ -1377,6 +1397,7 @@ private int getMaxPossibleIntensity(ImagePlus imp){
}

private String getOutputPath(String path, Date d){
progressDialog.updateBarText("determine output path...");
SimpleDateFormat NameDateFormatter = new SimpleDateFormat("yyMMdd_HHmmss");

String name = path.substring(path.lastIndexOf(System.getProperty("file.separator"))+1);
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4 changes: 2 additions & 2 deletions Thresholder/src/main/resources/plugins.config
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Original file line number Diff line number Diff line change
Expand Up @@ -24,8 +24,8 @@
# Belongs to the MotiQ toolbox for analyzing cellular morphology, dynamics, and signaling. MotiQ_thresholder is a automated thresholding tool for image stacks. MotiQ thresholder calculates a threshold in a separate reference image and applies it to the input image. The reference image is optionally processed by MotiQ thresholder prior to threshold calculation, whereby the image histogram used for threshold calculation can be improved.

# Author: Jan Niklas Hansen <Jan.Hansen@caesar.de>
# Version: 0.1.1
# Date: 2017/05/03
# Version: 0.1.2
# Date: 2017/09/15
# Requires: ImageJ

Plugins>MotiQ, "MotiQ Thresholder", motiQ_thr.Thresholder

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