Commit 9f0c8d98 authored by Andrey Filippov's avatar Andrey Filippov

making grid calculation work for VNIR cameras and large cells

parent cba1fc01
...@@ -375,11 +375,13 @@ public static MatchSimulatedPattern.DistortionParameters DISTORTION =new MatchSi ...@@ -375,11 +375,13 @@ public static MatchSimulatedPattern.DistortionParameters DISTORTION =new MatchSi
8.0, // 3.0, // correlationMaxOffset, // maximal distance between predicted and actual pattern node 8.0, // 3.0, // correlationMaxOffset, // maximal distance between predicted and actual pattern node
3.0, // 2.0, // increase back to .5? was needed with fisheye. 5.0, // double correlationMinContrast, // minimal contrast for the pattern to pass 3.0, // 2.0, // increase back to .5? was needed with fisheye. 5.0, // double correlationMinContrast, // minimal contrast for the pattern to pass
3.5, // 2.5, // correlationMinInitialContrast, // minimal contrast for the pattern of the center (initial point) 3.5, // 2.5, // correlationMinInitialContrast, // minimal contrast for the pattern of the center (initial point)
1.0, //this.correlationMinAbsoluteContrast, // minimal contrast for the pattern to pass, does not compensate for low ligt // Absolute contrast is broken (05.29.2019), disabling it
0.0, // 1.0, //this.correlationMinAbsoluteContrast, // minimal contrast for the pattern to pass, does not compensate for low ligt
// TODO: adjust to a reasonable number // TODO: adjust to a reasonable number
1.0, //this.correlationMinAbsoluteInitialContrast, // minimal contrast for the pattern of the center (initial point) 0.0, // 1.0, //this.correlationMinAbsoluteInitialContrast, // minimal contrast for the pattern of the center (initial point)
0.8, // scaleFirstPassContrast, // Decrease contrast of cells that are too close to the border to be processed in refinement pass 0.8, // scaleFirstPassContrast, // Decrease contrast of cells that are too close to the border to be processed in refinement pass
2.0, // public double contrastSelectSigmaCenter; // Gaussian sigma to select correlation centers (fraction of UV period), 0.02 (center spot)
0.1, // contrastSelectSigma, // Gaussian sigma to select correlation centers (fraction of UV period), 0.1 0.1, // contrastSelectSigma, // Gaussian sigma to select correlation centers (fraction of UV period), 0.1
0.5, //contrastAverageSigma, // Gaussian sigma to average correlation variations (as contrast reference) 0.5 0.5, //contrastAverageSigma, // Gaussian sigma to average correlation variations (as contrast reference) 0.5
...@@ -9486,14 +9488,16 @@ if (MORE_BUTTONS) { ...@@ -9486,14 +9488,16 @@ if (MORE_BUTTONS) {
for (int nfile = 0; nfile < sourceFilesList[nset].length; nfile++) if (sourceFilesList[nset][nfile] != null){ for (int nfile = 0; nfile < sourceFilesList[nset].length; nfile++) if (sourceFilesList[nset][nfile] != null){
long startFileTime=System.nanoTime(); long startFileTime=System.nanoTime();
if (DEBUG_LEVEL>0){ if (DEBUG_LEVEL>0){
System.out.println(IJ.d2s(0.000000001*(System.nanoTime()-startTime),3)+"s: Processing file # "+(this_file+1)+ System.out.println(IJ.d2s(0.000000001*(System.nanoTime()-startTime),3)+"s: Processing set "+(nset+1) +" (of "+
" (of "+ sourceFilesList.length+"): " + numFiles); sourceFilesList.length+"), channel # "+(nfile + 1)+
" (of "+ sourceFilesList[nset].length+"), file " +(this_file + 1)+" (of "+ numFiles+ ") - "+sourceFilesList[nset][nfile]);
} }
String grid_path = null;
if (saveGrids && !overwriteGrids){ // check if result already exists if (saveGrids && !overwriteGrids){ // check if result already exists
i = sourceFilesList[nset][nfile].lastIndexOf('/'); i = sourceFilesList[nset][nfile].lastIndexOf('/');
if (i>0){ if (i>0){
String grid_name = prefix+sourceFilesList[nset][nfile].substring(i+1); String grid_name = prefix+sourceFilesList[nset][nfile].substring(i+1);
String grid_path = gridSetPath + Prefs.getFileSeparator() + grid_name; grid_path = gridSetPath + Prefs.getFileSeparator() + grid_name;
if ((new File(grid_path)).exists()){ if ((new File(grid_path)).exists()){
if (DEBUG_LEVEL>0) System.out.println("-->>> Skipping existing "+grid_path+" (as requested in \"Configure Process Distortions\")"); if (DEBUG_LEVEL>0) System.out.println("-->>> Skipping existing "+grid_path+" (as requested in \"Configure Process Distortions\")");
continue; continue;
...@@ -9543,6 +9547,10 @@ if (MORE_BUTTONS) { ...@@ -9543,6 +9547,10 @@ if (MORE_BUTTONS) {
imp_sel, // image to process imp_sel, // image to process
THREADS_MAX); THREADS_MAX);
ImagePlus imp_calibrated=matchSimulatedPattern.getCalibratedPatternAsImage(imp_sel,prefix, numAbsolutePoints); ImagePlus imp_calibrated=matchSimulatedPattern.getCalibratedPatternAsImage(imp_sel,prefix, numAbsolutePoints);
if (imp_calibrated == null) {
if (DEBUG_LEVEL> -1) System.out.println("Grid is empty !");
continue;
}
if (DISTORTION_PROCESS_CONFIGURATION.showGridImages) imp_calibrated.show(); if (DISTORTION_PROCESS_CONFIGURATION.showGridImages) imp_calibrated.show();
if (saveGrids){ if (saveGrids){
FileSaver fs=new FileSaver(imp_calibrated); FileSaver fs=new FileSaver(imp_calibrated);
...@@ -9550,10 +9558,11 @@ if (MORE_BUTTONS) { ...@@ -9550,10 +9558,11 @@ if (MORE_BUTTONS) {
if (srcDir==null){ if (srcDir==null){
saveGrids=false; // do not ask about the next ones too saveGrids=false; // do not ask about the next ones too
} else { } else {
String path=DISTORTION_PROCESS_CONFIGURATION.gridDirectory+Prefs.getFileSeparator()+imp_calibrated.getTitle(); // String path=DISTORTION_PROCESS_CONFIGURATION.gridDirectory+Prefs.getFileSeparator()+imp_calibrated.getTitle();
if (UPDATE_STATUS) IJ.showStatus("Saving "+path); // String path = gridDir + Prefs.getFileSeparator() + set_name+Prefs.getFileSeparator()+imp_calibrated.getTitle();
if (DEBUG_LEVEL>0) System.out.println("-->>> Saving "+path+" - using "+numAbsolutePoints+" laser pointer references"); if (UPDATE_STATUS) IJ.showStatus("Saving "+grid_path);
fs.saveAsTiffStack(path); if (DEBUG_LEVEL>0) System.out.println("-->>> Saving "+grid_path+" - using "+numAbsolutePoints+" laser pointer references");
fs.saveAsTiffStack(grid_path);
} }
} }
} }
...@@ -9657,7 +9666,7 @@ if (MORE_BUTTONS) { ...@@ -9657,7 +9666,7 @@ if (MORE_BUTTONS) {
COMPONENTS.equalizeGreens, COMPONENTS.equalizeGreens,
imp_sel, // image to process imp_sel, // image to process
THREADS_MAX); THREADS_MAX);
ImagePlus imp_calibrated=matchSimulatedPattern.getCalibratedPatternAsImage(imp_sel,prefix, numAbsolutePoints); ImagePlus imp_calibrated=matchSimulatedPattern.getCalibratedPatternAsImage(imp_sel,prefix, numAbsolutePoints); //----
if (DISTORTION_PROCESS_CONFIGURATION.showGridImages) imp_calibrated.show(); if (DISTORTION_PROCESS_CONFIGURATION.showGridImages) imp_calibrated.show();
if (saveGrids){ if (saveGrids){
FileSaver fs=new FileSaver(imp_calibrated); FileSaver fs=new FileSaver(imp_calibrated);
...@@ -17224,8 +17233,10 @@ private double [][] jacobianByJacobian(double [][] jacobian, boolean [] mask) { ...@@ -17224,8 +17233,10 @@ private double [][] jacobianByJacobian(double [][] jacobian, boolean [] mask) {
pixels[4], pixels[4],
WVgreens, // wave vectors (same units as the pixels array) WVgreens, // wave vectors (same units as the pixels array)
// patternDetectParameters.corrRingWidth, // ring (around r=0.5 dist to opposite corr) width // patternDetectParameters.corrRingWidth, // ring (around r=0.5 dist to opposite corr) width
0.1, // contrastSelectSigma 2.0, // distortionParameters.contrastSelectSigmaCenter, // Gaussian sigma to select correlation centers (fraction of UV period), 0.1
0.5, // contrastAverageSigma 0.1, // distortionParameters.contrastSelectSigma, // Gaussian sigma to select correlation centers (fraction of UV period), 0.1
// 0.1, // contrastSelectSigma
// 0.5, // contrastAverageSigma
0.0, // x0, // center coordinates 0.0, // x0, // center coordinates
0.0, //y0, 0.0, //y0,
title)[0]; // title base for optional plots names title)[0]; // title base for optional plots names
...@@ -20320,7 +20331,8 @@ use the result to create a rejectiobn mask - if the energy was high, (multiplica ...@@ -20320,7 +20331,8 @@ use the result to create a rejectiobn mask - if the energy was high, (multiplica
gd.addNumericField("Correlation minimal contrast for initial search (absolute)", distortionParameters.correlationMinAbsoluteInitialContrast, 3); gd.addNumericField("Correlation minimal contrast for initial search (absolute)", distortionParameters.correlationMinAbsoluteInitialContrast, 3);
gd.addNumericField("Decrease contrast of cells that are too close to the border to be processed in refinement pass", distortionParameters.scaleFirstPassContrast, 3); gd.addNumericField("Decrease contrast of cells that are too close to the border to be processed in refinement pass", distortionParameters.scaleFirstPassContrast, 3);
gd.addNumericField("Gaussian sigma to select correlation centers (fraction of UV period), 0.1", distortionParameters.contrastSelectSigma, 3); gd.addNumericField("Gaussian sigma to select correlation center in pixels, 2.0", distortionParameters.contrastSelectSigmaCenter, 3);
gd.addNumericField("Gaussian sigma to select correlation off-centers (fraction of UV period), 0.1", distortionParameters.contrastSelectSigma, 3);
gd.addNumericField("Gaussian sigma to average correlation variations (as contrast reference), 0.5", distortionParameters.contrastAverageSigma, 3); gd.addNumericField("Gaussian sigma to average correlation variations (as contrast reference), 0.5", distortionParameters.contrastAverageSigma, 3);
gd.addNumericField("Minimal initial pattern cluster size (0 - disable retries)", distortionParameters.minimalPatternCluster, 0); gd.addNumericField("Minimal initial pattern cluster size (0 - disable retries)", distortionParameters.minimalPatternCluster, 0);
...@@ -20402,6 +20414,7 @@ use the result to create a rejectiobn mask - if the energy was high, (multiplica ...@@ -20402,6 +20414,7 @@ use the result to create a rejectiobn mask - if the energy was high, (multiplica
distortionParameters.correlationMinAbsoluteInitialContrast= gd.getNextNumber(); distortionParameters.correlationMinAbsoluteInitialContrast= gd.getNextNumber();
distortionParameters.scaleFirstPassContrast= gd.getNextNumber(); distortionParameters.scaleFirstPassContrast= gd.getNextNumber();
distortionParameters.contrastSelectSigmaCenter= gd.getNextNumber();
distortionParameters.contrastSelectSigma= gd.getNextNumber(); distortionParameters.contrastSelectSigma= gd.getNextNumber();
distortionParameters.contrastAverageSigma= gd.getNextNumber(); distortionParameters.contrastAverageSigma= gd.getNextNumber();
...@@ -1358,7 +1358,11 @@ Exception in thread "Thread-3564" java.lang.ArrayIndexOutOfBoundsException: 8970 ...@@ -1358,7 +1358,11 @@ Exception in thread "Thread-3564" java.lang.ArrayIndexOutOfBoundsException: 8970
itr=set.iterator(); itr=set.iterator();
while(itr.hasNext()) { while(itr.hasNext()) {
str = (String) itr.next(); str = (String) itr.next();
try {
imp_dst.setProperty(str,prop.getProperty(str)); imp_dst.setProperty(str,prop.getProperty(str));
} catch (Exception e) {
imp_dst.setProperty(str,"");
}
} }
} }
} }
......
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