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AddBlurFunctionAndCleanUp
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@hansenjn
hansenjn committed Sep 20, 2020
1 parent e57ad64 commit 3ccf3c2
Showing 1 changed file with 73 additions and 11 deletions.
84 changes: 73 additions & 11 deletions src/main/java/ciliaQ_Prep_jnh/CiliaQPrepMain.java
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Original file line number Diff line number Diff line change
Expand Up @@ -91,6 +91,10 @@ public class CiliaQPrepMain implements PlugIn, Measurements {
boolean includeDuplicateChannel [] = new boolean [] {true,true,true};
double subtractBGRadius [] = new double [] {10.0, 10.0, 10.0};
double divideBGRadius [] = new double [] {3.0, 3.0, 3.0};

boolean additionalBlur [] = new boolean [] {false,false,false};
double additionalBlurRadius [] = new double [] {0.5, 0.5, 0.5};

boolean separateTimesteps [] = new boolean [] {false, false, false};
String [] algorithm = {"Default", "IJ_IsoData", "Huang", "Intermodes", "IsoData", "Li", "MaxEntropy", "Mean",
"MinError", "Minimum", "Moments", "Otsu", "Percentile", "RenyiEntropy", "Shanbhag", "Triangle",
Expand Down Expand Up @@ -495,13 +499,17 @@ public void windowClosing(WindowEvent winEvt) {
}
if(divideBackground [c]){
progress.updateBarText("Divide by background for channel " + channelIDs [c] + " ...");
tempImp.duplicate().show();
tempImp = divideByBackground(tempImp, divideBGRadius [c]);
//TODO verify
}
if(additionalBlur [c]) {
progress.updateBarText("Blur " + channelIDs [c] + " ...");
tempImp.duplicate().show();
tempImp = blurGaussian(tempImp, additionalBlurRadius [c]);
//TODO verify
tempImp.show();
new WaitForUserDialog("check tempImp").show();
tempImp.hide();
}
}
if(chosenAlgorithms [c].equals("CANNY 3D")){
progress.updateBarText("Segment channel " + channelIDs [c] + " with CANNY 3D ...");

Expand Down Expand Up @@ -853,6 +861,13 @@ private boolean importSettings() {
divideBGRadius [actualC] = Double.parseDouble(tempString);
IJ.log("C" + actualC + ": dbg rad = " + divideBGRadius [actualC]);
}
if(line.contains("Additional blur with Gaussian")){
additionalBlur [actualC] = true;
tempString = line.substring(line.lastIndexOf(" ")+1);
if(tempString.contains(",") && !tempString.contains(".")) tempString = tempString.replace(",", ".");
additionalBlurRadius [actualC] = Double.parseDouble(tempString);
IJ.log("C" + actualC + ": blur rad = " + additionalBlurRadius [actualC]);
}
if(line.contains("Every time step separately segmented.")) {
separateTimesteps [actualC]= true;
IJ.log("C" + actualC + ": time steps separately");
Expand All @@ -873,7 +888,7 @@ private boolean importSettings() {
tempString = line.substring(line.lastIndexOf(" ")+1);
if(tempString.contains(",") && !tempString.contains(".")) tempString = tempString.replace(",", ".");
cannySettings [actualC].setGaussSigma(Double.parseDouble(tempString));
IJ.log("C" + actualC + ": Gauss" + cannySettings [actualC].getGaussSigma());
IJ.log("C" + actualC + ": Gauss " + cannySettings [actualC].getGaussSigma());

line = br.readLine();
if(!line.equals("") && line.equals(null)){IJ.error("Reading problem"); break reading;}
Expand All @@ -884,7 +899,7 @@ private boolean importSettings() {
tempString = line.substring(line.lastIndexOf(" ")+1);
if(tempString.contains(",") && !tempString.contains(".")) tempString = tempString.replace(",", ".");
cannySettings [actualC].setCannyAlpha(Double.parseDouble(tempString));
IJ.log("C" + actualC + ": Alpha" + cannySettings [actualC].getCannyAlpha());
IJ.log("C" + actualC + ": Alpha " + cannySettings [actualC].getCannyAlpha());

line = br.readLine();
if(!line.equals("") && line.equals(null)){IJ.error("Reading problem"); break reading;}
Expand All @@ -908,7 +923,7 @@ private boolean importSettings() {
if(tempString.contains(",") && !tempString.contains(".")) tempString = tempString.replace(",", ".");
cannySettings [actualC].setLowThr(Double.parseDouble(tempString));
}
IJ.log("C" + actualC + ": low Thr" + cannySettings [actualC].getLowThresholdAlgorithm());
IJ.log("C" + actualC + ": low Thr " + cannySettings [actualC].getLowThresholdAlgorithm());

line = br.readLine();
if(!line.contains("High threshold method")) {
Expand All @@ -931,7 +946,7 @@ private boolean importSettings() {
if(tempString.contains(",") && !tempString.contains(".")) tempString = tempString.replace(",", ".");
cannySettings [actualC].setHighThr(Double.parseDouble(tempString));
}
IJ.log("C" + actualC + ": High Thr" + cannySettings [actualC].getHighThresholdAlgorithm());
IJ.log("C" + actualC + ": High Thr " + cannySettings [actualC].getHighThresholdAlgorithm());

}else if(line.contains("HYSTERESIS threshold")) {
chosenAlgorithms [actualC] = algorithm [19];
Expand Down Expand Up @@ -959,7 +974,7 @@ private boolean importSettings() {
tempString = line.substring(line.lastIndexOf(" ")+1);
if(tempString.contains(",") && !tempString.contains(".")) tempString = tempString.replace(",", ".");
customLowThr [actualC] = (Double.parseDouble(tempString));
IJ.log("C" + actualC + ": Low Thr" + customLowThr [actualC]);
IJ.log("C" + actualC + ": Low Thr " + customLowThr [actualC]);
}

line = br.readLine();
Expand All @@ -983,7 +998,7 @@ private boolean importSettings() {
tempString = line.substring(line.lastIndexOf(" ")+1);
if(tempString.contains(",") && !tempString.contains(".")) tempString = tempString.replace(",", ".");
customHighThr [actualC] = (Double.parseDouble(tempString));
IJ.log("C" + actualC + ": High Thr" + customHighThr [actualC]);
IJ.log("C" + actualC + ": High Thr " + customHighThr [actualC]);
}

if(chosenHighAlg [actualC].equals(hystAlgorithms[0]) && chosenLowAlg [actualC].equals(hystAlgorithms[0])){
Expand Down Expand Up @@ -1062,6 +1077,8 @@ private boolean enterSettings() {
gd.setInsets(-23,100,0); gd.addNumericField("", subtractBGRadius[0], 2);
gd.setInsets(0,10,0); gd.addCheckbox("Divide by Background before segmentation - radius", divideBackground [0]);
gd.setInsets(-23,100,0); gd.addNumericField("", divideBGRadius[0], 2);
gd.setInsets(0,10,0); gd.addCheckbox("Smooth with Gaussian blur - radius", additionalBlur [0]);
gd.setInsets(-23,100,0); gd.addNumericField("", additionalBlurRadius[0], 2);
gd.setInsets(0,10,0); gd.addChoice("Segmentation method", algorithm, chosenAlgorithms[0]);
gd.setInsets(0,0,0); gd.addMessage("If selecting the methods CANNY 3D or HYSTERESIS Threshold"
+ "another dialog for entering additional preferences will open after pressing OK.", InstructionsFont);
Expand All @@ -1088,6 +1105,8 @@ private boolean enterSettings() {
double subtractBGRadiusTemp = (double) gd.getNextNumber();
boolean divideBackgroundTemp = gd.getNextBoolean();
double divideBGRadiusTemp = (double) gd.getNextNumber();
boolean additionalBlurTemp = gd.getNextBoolean();
double additionalBlurRadiusTemp = (double) gd.getNextNumber();
String chosenAlgorithmsTemp = gd.getNextChoice();
double customThrTemp = gd.getNextNumber();
String chosenStackMethodsTemp = gd.getNextChoice();
Expand All @@ -1104,6 +1123,10 @@ private boolean enterSettings() {
includeDuplicateChannel = new boolean [nChannels];
subtractBackground = new boolean [nChannels];
subtractBGRadius = new double [nChannels];
divideBackground = new boolean [nChannels];
divideBGRadius = new double [nChannels];
additionalBlur = new boolean [nChannels];
additionalBlurRadius = new double [nChannels];
chosenAlgorithms = new String [nChannels];
customThr = new double [nChannels];
chosenStackMethods = new String [nChannels];
Expand All @@ -1115,6 +1138,8 @@ private boolean enterSettings() {
subtractBGRadius [0] = subtractBGRadiusTemp;
divideBackground [0] = divideBackgroundTemp;
divideBGRadius [0] = divideBGRadiusTemp;
additionalBlur [0] = additionalBlurTemp;
additionalBlurRadius [0] = additionalBlurRadiusTemp;
chosenAlgorithms [0] = chosenAlgorithmsTemp;
customThr [0] = customThrTemp;
chosenStackMethods [0] = chosenStackMethodsTemp;
Expand All @@ -1138,10 +1163,12 @@ private boolean enterSettings() {
gd2.setInsets(-23,100,0); gd2.addNumericField("", subtractBGRadius[0], 2);
gd2.setInsets(0,10,0); gd2.addCheckbox("Divide by Background before segmentation - radius", divideBackground [0]);
gd2.setInsets(-23,100,0); gd2.addNumericField("", divideBGRadius[0], 2);
gd2.setInsets(0,10,0); gd2.addCheckbox("Smooth with Gaussian blur - radius", additionalBlur [0]);
gd2.setInsets(-23,100,0); gd2.addNumericField("", additionalBlurRadius[0], 2);
gd2.setInsets(0,10,0); gd2.addChoice("Segmentation method", algorithm, chosenAlgorithms[0]);
gd.setInsets(0,0,0); gd.addMessage("If selecting the methods CANNY 3D or HYSTERESIS Threshold"
gd2.setInsets(0,0,0); gd2.addMessage("If selecting the methods CANNY 3D or HYSTERESIS Threshold"
+ "another dialog for entering additional preferences will open after pressing OK.", InstructionsFont);
gd.setInsets(0,0,0); gd.addNumericField("If 'CUSTOM threshold' was selected, specify threshold here", customThr[0], 2);
gd2.setInsets(0,0,0); gd2.addNumericField("If 'CUSTOM threshold' was selected, specify threshold here", customThr[0], 2);
gd2.setInsets(0,10,0); gd2.addChoice("Stack handling (obsolete for segmentation method 'CANNY 3D'): ", stackMethod, chosenStackMethods[0]);
gd2.setInsets(0,10,0); gd2.addCheckbox("Threshold every time step independently (obsolete for segmentation method 'CANNY 3D')", separateTimesteps [0]);

Expand All @@ -1154,6 +1181,8 @@ private boolean enterSettings() {
subtractBGRadius [c] = (double) gd2.getNextNumber();
divideBackground [c] = gd2.getNextBoolean();
divideBGRadius [c] = (double) gd2.getNextNumber();
additionalBlur [c] = gd2.getNextBoolean();
additionalBlurRadius [c] = (double) gd2.getNextNumber();
chosenAlgorithms [c] = gd2.getNextChoice();
customThr [c] = gd2.getNextNumber();
chosenStackMethods [c] = gd2.getNextChoice();
Expand Down Expand Up @@ -1191,6 +1220,36 @@ static ImagePlus divideByBackground(ImagePlus imp, double radius) {
}
return outImp;
}

static ImagePlus blurGaussian(ImagePlus imp, double radius) {
ImagePlus outImp = IJ.createHyperStack("divided image", imp.getWidth(), imp.getHeight(),
imp.getNChannels(), imp.getNSlices(), imp.getNFrames(), imp.getBitDepth());
outImp.setCalibration(imp.getCalibration());
outImp.setOverlay(imp.getOverlay());
ImagePlus tempImp;
for(int c = 0; c < imp.getNChannels(); c++) {
for(int s = 0; s < imp.getNSlices(); s++) {
for(int t = 0; t < imp.getNFrames(); t++) {
tempImp = IJ.createHyperStack("temp", imp.getWidth(), imp.getHeight(), 1, 1, 1, imp.getBitDepth());
for(int x = 0; x < imp.getWidth(); x++) {
for(int y = 0; y < imp.getHeight(); y++) {
tempImp.getStack().setVoxel(x, y, 0, imp.getStack().getVoxel(x, y, imp.getStackIndex(c+1 , s+1, t+1)-1));
}
}
tempImp.getProcessor().blurGaussian(radius);
for(int x = 0; x < imp.getWidth(); x++) {
for(int y = 0; y < imp.getHeight(); y++) {
outImp.getStack().setVoxel(x, y, outImp.getStackIndex(c+1, s+1, t+1)-1,
tempImp.getStack().getVoxel(x, y, 0));
}
}
}
}
}

return outImp;
}

private void addFooter(TextPanel tp, Date currentDate){
tp.append("");
tp.append("Datafile was generated on " + FullDateFormatter2.format(currentDate) + " by '"
Expand Down Expand Up @@ -1587,6 +1646,9 @@ private void addSettingsBlockToPanel(TextPanel tp, Date startDate, String name,
if(divideBackground [i]){
tp.append(" Divide By Background: " + df3.format(divideBGRadius[i]));
}else{tp.append("");}
if(additionalBlur [i]){
tp.append(" Additional blur with Gaussian: " + df3.format(additionalBlurRadius[i]));
}else{tp.append("");}
if(chosenAlgorithms [i] == "CANNY 3D"){
tp.append(" Segmentation method: " + "Canny 3D Thresholder, a plugin by Sebastian Rassmann,"
+ " see https://github.com/sRassmann/canny3d-thresholder for a descriptions.");
Expand Down

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