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imagej-elphel
Commit 9f0c8d98 authored by Andrey Filippov's avatar Andrey Filippov
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making grid calculation work for VNIR cameras and large cells

parent cba1fc01
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Showing with 516 additions and 338 deletions
src/main/java/com/elphel/imagej/calibration/Aberration_Calibration.java
View file @ 9f0c8d98
......@@ -375,11 +375,13 @@ public static MatchSimulatedPattern.DistortionParameters DISTORTION =new MatchSi
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
3.5, // 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
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
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
0.5, //contrastAverageSigma, // Gaussian sigma to average correlation variations (as contrast reference) 0.5
......@@ -9486,14 +9488,16 @@ if (MORE_BUTTONS) {
for (int nfile = 0; nfile < sourceFilesList[nset].length; nfile++) if (sourceFilesList[nset][nfile] != null){
long startFileTime=System.nanoTime();
if (DEBUG_LEVEL>0){
System.out.println(IJ.d2s(0.000000001*(System.nanoTime()-startTime),3)+"s: Processing file # "+(this_file+1)+
" (of "+ sourceFilesList.length+"): " + numFiles);
System.out.println(IJ.d2s(0.000000001*(System.nanoTime()-startTime),3)+"s: Processing set "+(nset+1) +" (of "+
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
i = sourceFilesList[nset][nfile].lastIndexOf('/');
if (i>0){
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 (DEBUG_LEVEL>0) System.out.println("-->>> Skipping existing "+grid_path+" (as requested in \"Configure Process Distortions\")");
continue;
......@@ -9543,6 +9547,10 @@ if (MORE_BUTTONS) {
imp_sel, // image to process
THREADS_MAX);
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 (saveGrids){
FileSaver fs=new FileSaver(imp_calibrated);
......@@ -9550,10 +9558,11 @@ if (MORE_BUTTONS) {
if (srcDir==null){
saveGrids=false; // do not ask about the next ones too
} else {
String path=DISTORTION_PROCESS_CONFIGURATION.gridDirectory+Prefs.getFileSeparator()+imp_calibrated.getTitle();
if (UPDATE_STATUS) IJ.showStatus("Saving "+path);
if (DEBUG_LEVEL>0) System.out.println("-->>> Saving "+path+" - using "+numAbsolutePoints+" laser pointer references");
fs.saveAsTiffStack(path);
// String path=DISTORTION_PROCESS_CONFIGURATION.gridDirectory+Prefs.getFileSeparator()+imp_calibrated.getTitle();
// String path = gridDir + Prefs.getFileSeparator() + set_name+Prefs.getFileSeparator()+imp_calibrated.getTitle();
if (UPDATE_STATUS) IJ.showStatus("Saving "+grid_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) {
COMPONENTS.equalizeGreens,
imp_sel, // image to process
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 (saveGrids){
FileSaver fs=new FileSaver(imp_calibrated);
......@@ -17224,8 +17233,10 @@ private double [][] jacobianByJacobian(double [][] jacobian, boolean [] mask) {
pixels[4],
WVgreens, // wave vectors (same units as the pixels array)
// patternDetectParameters.corrRingWidth, // ring (around r=0.5 dist to opposite corr) width
0.1, // contrastSelectSigma
0.5, // contrastAverageSigma
2.0, // distortionParameters.contrastSelectSigmaCenter, // Gaussian sigma to select correlation centers (fraction of UV period), 0.1
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, //y0,
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
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("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("Minimal initial pattern cluster size (0 - disable retries)", distortionParameters.minimalPatternCluster, 0);
......@@ -20401,13 +20413,14 @@ use the result to create a rejectiobn mask - if the energy was high, (multiplica
distortionParameters.correlationMinAbsoluteContrast= gd.getNextNumber();
distortionParameters.correlationMinAbsoluteInitialContrast= gd.getNextNumber();
distortionParameters.scaleFirstPassContrast= gd.getNextNumber();
distortionParameters.contrastSelectSigma= gd.getNextNumber();
distortionParameters.contrastAverageSigma= gd.getNextNumber();
distortionParameters.scaleFirstPassContrast= gd.getNextNumber();
distortionParameters.contrastSelectSigmaCenter= gd.getNextNumber();
distortionParameters.contrastSelectSigma= gd.getNextNumber();
distortionParameters.contrastAverageSigma= gd.getNextNumber();
distortionParameters.minimalPatternCluster=(int) gd.getNextNumber();
distortionParameters.scaleMinimalInitialContrast=gd.getNextNumber();
distortionParameters.searchOverlap= gd.getNextNumber();
distortionParameters.searchOverlap= gd.getNextNumber();
distortionParameters.patternSubdiv= (int) gd.getNextNumber();
distortionParameters.bPatternSigma= gd.getNextNumber();
src/main/java/com/elphel/imagej/jp4/JP46_Reader_camera.java
View file @ 9f0c8d98
......@@ -1358,7 +1358,11 @@ Exception in thread "Thread-3564" java.lang.ArrayIndexOutOfBoundsException: 8970
itr=set.iterator();
while(itr.hasNext()) {
str = (String) itr.next();
imp_dst.setProperty(str,prop.getProperty(str));
try {
imp_dst.setProperty(str,prop.getProperty(str));
} catch (Exception e) {
imp_dst.setProperty(str,"");
}
}
}
}
......
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