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imagej-elphel
Commit e2086aa9 authored by Andrey Filippov's avatar Andrey Filippov
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more debugging

parent cbbac8c8
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Showing with 39 additions and 17 deletions
src/main/java/EyesisAberrations.java
View file @ e2086aa9
...@@ -1066,7 +1066,7 @@ public class EyesisAberrations { ...@@ -1066,7 +1066,7 @@ public class EyesisAberrations {
MatchSimulatedPattern.PatternDetectParameters patternDetectParameters, MatchSimulatedPattern.PatternDetectParameters patternDetectParameters,
SimulationPattern.SimulParameters simulParameters, SimulationPattern.SimulParameters simulParameters,
ColorComponents colorComponents, ColorComponents colorComponents,
boolean resetBadKernels, // ignore and reset noUsefulKernels mark for seleccted channel boolean resetBadKernels, // ignore and reset noUsefulKernels mark for selected channel
int threadsMax, int threadsMax,
boolean updateStatus, boolean updateStatus,
int loopDebugLevel, // debug level used inside loops int loopDebugLevel, // debug level used inside loops
...@@ -1094,14 +1094,14 @@ public class EyesisAberrations { ...@@ -1094,14 +1094,14 @@ public class EyesisAberrations {
boolean [] selectedChannels=this.aberrationParameters.getChannelSelection(distortions); boolean [] selectedChannels=this.aberrationParameters.getChannelSelection(distortions);
int numSelected=0; int numSelected=0;
int numDeselected=0; int numDeselected=0;
if (debugLevel>1){ if (debugLevel>2){
for (int i=0;i<selectedChannels.length;i++){ for (int i=0;i<selectedChannels.length;i++){
System.out.println("Channel "+i+" is "+(selectedChannels[i]?"Enabled":"Disabled")); System.out.println("Channel "+i+" is "+(selectedChannels[i]?"Enabled":"Disabled"));
} }
} }
for (int imgNum=0;imgNum<selectedImages.length;imgNum++) if (selectedImages[imgNum]) { for (int imgNum=0;imgNum<selectedImages.length;imgNum++) if (selectedImages[imgNum]) {
int numChannel=distortionCalibrationData.gIP[imgNum].channel; int numChannel=distortionCalibrationData.gIP[imgNum].channel;
if (debugLevel>1){ if (debugLevel>2){
System.out.println("Image "+imgNum+" channel "+numChannel+" is "+(selectedChannels[numChannel]?"ENABLED":"DISABLED")); System.out.println("Image "+imgNum+" channel "+numChannel+" is "+(selectedChannels[numChannel]?"ENABLED":"DISABLED"));
} }
if (!selectedChannels[numChannel]){ if (!selectedChannels[numChannel]){
...@@ -1111,7 +1111,7 @@ public class EyesisAberrations { ...@@ -1111,7 +1111,7 @@ public class EyesisAberrations {
distortions.fittingStrategy.setNoUsefulPSFKernels(imgNum,false); // reset noUsefulKernels mark (if it was not set - OK) distortions.fittingStrategy.setNoUsefulPSFKernels(imgNum,false); // reset noUsefulKernels mark (if it was not set - OK)
numSelected++; numSelected++;
} }
} else if (debugLevel>1){ } else if (debugLevel>2){
System.out.println("Skipping disabled image "+imgNum); System.out.println("Skipping disabled image "+imgNum);
} }
if (debugLevel>0)System.out.println("Enabled "+numSelected+" source files ("+numDeselected+") were removed by channel selection"); if (debugLevel>0)System.out.println("Enabled "+numSelected+" source files ("+numDeselected+") were removed by channel selection");
...@@ -1237,9 +1237,9 @@ public class EyesisAberrations { ...@@ -1237,9 +1237,9 @@ public class EyesisAberrations {
int MaxRetries=4; int MaxRetries=4;
int iRetry=0; int iRetry=0;
for (iRetry=0;iRetry<MaxRetries;iRetry++){ for (iRetry=0;iRetry<MaxRetries;iRetry++){ // is this retry needed?
try { try {
matchSimulatedPattern.calculateDistortions( int rslt=matchSimulatedPattern.calculateDistortions(
distortionParameters, // distortionParameters, //
patternDetectParameters, patternDetectParameters,
simulParameters, simulParameters,
...@@ -1255,7 +1255,10 @@ public class EyesisAberrations { ...@@ -1255,7 +1255,10 @@ public class EyesisAberrations {
debugLevel, debugLevel,
loopDebugLevel, // debug level loopDebugLevel, // debug level
aberrationParameters.noMessageBoxes); aberrationParameters.noMessageBoxes);
if (rslt<0){
if (debugLevel>0) System.out.println("calculateDistortions failed, returned error code "+rslt+" riRetry="+iRetry+" (of "+MaxRetries+")");
continue;
}
correlationSizesUsed=matchSimulatedPattern.getCorrelationSizesUsed(); correlationSizesUsed=matchSimulatedPattern.getCorrelationSizesUsed();
simArray= (new SimulationPattern(simulParameters)).simulateGridAll ( simArray= (new SimulationPattern(simulParameters)).simulateGridAll (
imp.getWidth(), imp.getWidth(),
...@@ -1299,7 +1302,10 @@ public class EyesisAberrations { ...@@ -1299,7 +1302,10 @@ public class EyesisAberrations {
continue; continue;
} }
} }
if (iRetry==MaxRetries) continue; if (iRetry==MaxRetries) {
System.out.println("File "+files[imgNum][1]+ " has problems - finished at "+ IJ.d2s(0.000000001*(System.nanoTime()-startTime),3));
continue;
}
ImageStack stack=mergeKernelsToStack(this.pdfKernelMap); ImageStack stack=mergeKernelsToStack(this.pdfKernelMap);
......
src/main/java/MatchSimulatedPattern.java
View file @ e2086aa9
...@@ -3282,7 +3282,7 @@ public class MatchSimulatedPattern { ...@@ -3282,7 +3282,7 @@ public class MatchSimulatedPattern {
triedIndices[numTries]=true; // all tried triedIndices[numTries]=true; // all tried
} else { } else {
// if (debugLevel>1) System.out.println("Found "+nodes.length+" candidates"); // if (debugLevel>1) System.out.println("Found "+nodes.length+" candidates");
if (debugLevel>1) System.out.println("Found "+nodeQueue.size()+" candidates"); if (debugLevel>1) System.out.println("distortions: Found "+nodeQueue.size()+" candidates");
} }
} else { } else {
if (debugLevel>1) System.out.println("All start points tried before - should not get here"); if (debugLevel>1) System.out.println("All start points tried before - should not get here");
...@@ -3330,15 +3330,23 @@ public class MatchSimulatedPattern { ...@@ -3330,15 +3330,23 @@ public class MatchSimulatedPattern {
nodeQueue.add(new GridNode(node)); // will not be used, any element nodeQueue.add(new GridNode(node)); // will not be used, any element
} }
int numDefinedCells=0; int numDefinedCells=0;
for (GridNode gn:nodeQueue){ int debug_left=nodeQueue.size();
for (GridNode gn:nodeQueue){ // trying candidates as grid seeds - until found or nothing left
if (global_debug_level>1) {
System.out.println("distortions: nodeQueue has "+(debug_left--)+" candidates left (including this one)");
}
if (!updating){ if (!updating){
double [][] node=gn.getNode(); double [][] node=gn.getNode();
double [] centerXY=node[0]; double [] centerXY=node[0];
if (global_debug_level>1) {
System.out.println("distortions: node X/Y are "+centerXY[0]+"/"+centerXY[1]);
}
// if (debugLevel>1) { // if (debugLevel>1) {
if (global_debug_level>1) { if (global_debug_level>1) {
System.out.println("*** distortions: Center x="+IJ.d2s(centerXY[0],3)+" y="+ IJ.d2s(centerXY[1],3)); System.out.println("*** distortions: Center x="+IJ.d2s(centerXY[0],3)+" y="+ IJ.d2s(centerXY[1],3));
System.out.println("*** distortions: setting debugX="+IJ.d2s(centerXY[0],3)+" debugY="+ IJ.d2s(centerXY[1],3)); System.out.println("*** distortions: setting debugX="+IJ.d2s(centerXY[0],3)+" debugY="+ IJ.d2s(centerXY[1],3));
patternDetectParameters.debugX=centerXY[0]; // patternDetectParameters.debugX=centerXY[0]; // Change debug coordinates to the initial node
patternDetectParameters.debugY=centerXY[1]; //patternDetectParameters.debugRadius); patternDetectParameters.debugY=centerXY[1]; //patternDetectParameters.debugRadius);
} }
debugLevel=debug_level; debugLevel=debug_level;
...@@ -3352,7 +3360,9 @@ public class MatchSimulatedPattern { ...@@ -3352,7 +3360,9 @@ public class MatchSimulatedPattern {
node[2]); node[2]);
waveFrontList.clear(); waveFrontList.clear();
putInWaveList(waveFrontList, centerUV, 0); putInWaveList(waveFrontList, centerUV, 0);
if (global_debug_level>1) {
System.out.println("putInWaveList(waveFrontList, {"+centerUV[0]+","+centerUV[1]+"}, 0);");
}
} }
...@@ -3382,6 +3392,7 @@ public class MatchSimulatedPattern { ...@@ -3382,6 +3392,7 @@ public class MatchSimulatedPattern {
final AtomicInteger debugCellSet= new AtomicInteger(0); // cells added at cleanup stage final AtomicInteger debugCellSet= new AtomicInteger(0); // cells added at cleanup stage
// special case (most common, actually) when initial wave has 1 node. Remove it after processing // special case (most common, actually) when initial wave has 1 node. Remove it after processing
//first cell(s) will need large correction and so may fail during "refine", so trying to recalculate it right after the first layer)
ArrayList<Integer> initialWave=new ArrayList<Integer>(); ArrayList<Integer> initialWave=new ArrayList<Integer>();
for (Integer I:waveFrontList) initialWave.add(I); for (Integer I:waveFrontList) initialWave.add(I);
while (waveFrontList.size()>0) { while (waveFrontList.size()>0) {
...@@ -3430,7 +3441,8 @@ public class MatchSimulatedPattern { ...@@ -3430,7 +3441,8 @@ public class MatchSimulatedPattern {
if (waveFrontList.size()==0) break; // not really needed? if (waveFrontList.size()==0) break; // not really needed?
layer++; layer++;
if (updateStatus) IJ.showStatus("Correlating patterns, layer "+layer+(cleanup.get()?"(cleanup)":"")+", length "+waveFrontList.size()); if (updateStatus) IJ.showStatus("Correlating patterns, layer "+layer+(cleanup.get()?"(cleanup)":"")+", length "+waveFrontList.size());
if (debugLevel>1) System.out.println("Correlating patterns, layer "+layer+", length "+waveFrontList.size()); // if (debugLevel>1) System.out.println("Correlating patterns, layer "+layer+", length "+waveFrontList.size());
if (global_debug_level>1) System.out.println("Correlating patterns, layer "+layer+", length "+waveFrontList.size());
// starting layer // starting layer
cellNum.set(0); cellNum.set(0);
for (int ithread = 0; ithread < threads.length; ithread++) { for (int ithread = 0; ithread < threads.length; ithread++) {
...@@ -3453,7 +3465,8 @@ public class MatchSimulatedPattern { ...@@ -3453,7 +3465,8 @@ public class MatchSimulatedPattern {
double [][] refCell=PATTERN_GRID[iUVRef[1]][iUVRef[0]]; // should never be null as it is an old one double [][] refCell=PATTERN_GRID[iUVRef[1]][iUVRef[0]]; // should never be null as it is an old one
if (refCell==null){ if (refCell==null){
System.out.println("**** refCell==null - what does it mean?**** u="+iUVRef[0]+" v="+iUVRef[1]); System.out.println("**** refCell==null - what does it mean?**** u="+iUVRef[0]+" v="+iUVRef[1]+
" current="+iUVdir[0]+"/"+iUVdir[1]+" len="+iUVdir.length);
continue; continue;
} else if ((refCell[0]!=null) && (refCell[0].length>3)){ } else if ((refCell[0]!=null) && (refCell[0].length>3)){
System.out.println("**** refCell was deleted ****"); System.out.println("**** refCell was deleted ****");
...@@ -3678,7 +3691,7 @@ public class MatchSimulatedPattern { ...@@ -3678,7 +3691,7 @@ public class MatchSimulatedPattern {
} }
if (global_debug_level>1) System.out.println("***** Starting cleanup, wave length="+waveFrontList.size()); if (global_debug_level>1) System.out.println("***** Starting cleanup, wave length="+waveFrontList.size());
} }
// end of layer // end of layer - it is a hack below, marking initial wave to recalculate it from neighbors
if (initialWave!=null){ // just after the first layer (usually one cell) - delete it and add next time - otherwise first one needs large correction if (initialWave!=null){ // just after the first layer (usually one cell) - delete it and add next time - otherwise first one needs large correction
if (global_debug_level>0) if (global_debug_level>0)
System.out.println("Removing "+initialWave.size()+" initial wave cells"); System.out.println("Removing "+initialWave.size()+" initial wave cells");
...@@ -5415,6 +5428,7 @@ public class MatchSimulatedPattern { ...@@ -5415,6 +5428,7 @@ public class MatchSimulatedPattern {
int [] uv){ int [] uv){
grid[uv[1]][uv[0]]=null; grid[uv[1]][uv[0]]=null;
} }
private void markDeletedPatternGridCell( private void markDeletedPatternGridCell(
double [][][][] grid, double [][][][] grid,
int [] uv){ int [] uv){
...@@ -5426,8 +5440,10 @@ public class MatchSimulatedPattern { ...@@ -5426,8 +5440,10 @@ public class MatchSimulatedPattern {
else else
newXYC[i]=Double.NaN; newXYC[i]=Double.NaN;
} }
grid[uv[1]][uv[0]][0]=newXYC;
} }
grid[uv[1]][uv[0]]=null; // grid[uv[1]][uv[0]]=null;
} }
private boolean isCellNew( //modified, for invalid uv will return "not new" private boolean isCellNew( //modified, for invalid uv will return "not new"
double [][][][] grid, double [][][][] grid,
...@@ -5565,7 +5581,7 @@ public class MatchSimulatedPattern { ...@@ -5565,7 +5581,7 @@ public class MatchSimulatedPattern {
public int gridUVHeight(){return ((this.PATTERN_GRID==null) || (this.PATTERN_GRID.length==0l) ||(this.PATTERN_GRID[0]==null))?0:this.PATTERN_GRID.length;} public int gridUVHeight(){return ((this.PATTERN_GRID==null) || (this.PATTERN_GRID.length==0l) ||(this.PATTERN_GRID[0]==null))?0:this.PATTERN_GRID.length;}
/* ======================================================================== */ /* ======================================================================== */
/** /**
* returns number of laser pointers matched * returns number of laser pointers matched (or negative error)
* if (this.flatFieldForGrid!=null) it should already be applied !! * if (this.flatFieldForGrid!=null) it should already be applied !!
*/ */
public int calculateDistortions( public int calculateDistortions(
......
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