Commit 3e7f255e authored by Andrey Filippov's avatar Andrey Filippov

aberration correction with clt

parent 2e50bfb7
...@@ -2076,8 +2076,53 @@ public class EyesisCorrections { ...@@ -2076,8 +2076,53 @@ public class EyesisCorrections {
outStack.addSlice(chnNames[chn], outPixels[chn]); outStack.addSlice(chnNames[chn], outPixels[chn]);
} }
return outStack; return outStack;
} }
// return 2-d double array instead of the stack
public double [][]bayerToDoubleStack(ImagePlus imp, // source bayer image, linearized, 32-bit (float))
EyesisCorrectionParameters.SplitParameters splitParameters){ // if null - no margins, no oversample
if (imp==null) return null;
boolean adv = splitParameters != null;
int oversample = adv? splitParameters.oversample : 1;
int addTop= adv?splitParameters.addTop: 0;
int addLeft= adv?splitParameters.addLeft: 0;
int addBottom= adv?splitParameters.addBottom: 0;
int addRight= adv?splitParameters.addRight: 0;
String [] chnNames={"Red","Blue","Green"}; //Different sequence than RGB!!
int nChn=chnNames.length;
ImageProcessor ip=imp.getProcessor();
int inWidth=imp.getWidth();
int inHeight=imp.getHeight();
int outHeight=inHeight*oversample + addTop + addBottom;
int outWidth= inWidth* oversample + addLeft + addRight;
int outLength=outWidth*outHeight;
double [][] outPixels=new double[nChn][outLength];
float [] pixels = (float[]) ip.getPixels();
int chn,y,x,i,index;
int bayerPeriod=2*oversample;
int ovrWidth= inWidth * oversample;
int ovrHeight= inHeight * oversample;
for (chn=0;chn<nChn;chn++) for (i=0;i<outPixels[chn].length;i++) outPixels[chn][i]=0.0f;
/* Can be optimized - now it calculate input address for all those 0-es */
for (index=0; index<outLength; index++) {
y=(index / outWidth) - addTop;
x=(index % outWidth) - addLeft;
if (y<0) y= (bayerPeriod-((-y) % bayerPeriod))%bayerPeriod;
else if (y>=ovrHeight) y= ovrHeight-bayerPeriod +((y-ovrHeight) % bayerPeriod);
if (x<0) x= (bayerPeriod-((-x) % bayerPeriod))%bayerPeriod;
else if (x>=ovrWidth) x= ovrWidth-bayerPeriod +((x-ovrWidth) % bayerPeriod);
if (((y% oversample)==0) && ((x% oversample)==0)) {
x/=oversample;
y/=oversample;
chn=((x&1)==(y&1))?2:(((x&1)!=0)?0:1);
outPixels[chn][index]=pixels[y*inWidth+x];
}
}
return outPixels;
}
//double [] DENOISE_MASK=null; //double [] DENOISE_MASK=null;
......
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...@@ -2890,16 +2890,7 @@ private Panel panel1, ...@@ -2890,16 +2890,7 @@ private Panel panel1,
int numChannels=EYESIS_CORRECTIONS.getNumChannels(); int numChannels=EYESIS_CORRECTIONS.getNumChannels();
NONLIN_PARAMETERS.modifyNumChannels(numChannels); NONLIN_PARAMETERS.modifyNumChannels(numChannels);
CHANNEL_GAINS_PARAMETERS.modifyNumChannels(numChannels); CHANNEL_GAINS_PARAMETERS.modifyNumChannels(numChannels);
/*
if (CORRECTION_PARAMETERS.deconvolve && (NONLIN_PARAMETERS.noiseGainPower!=0)) {
EYESIS_CORRECTIONS.updateImageNoiseGains(
NONLIN_PARAMETERS, //EyesisCorrectionParameters.NonlinParameters nonlinParameters,
CONVOLVE_FFT_SIZE, //int fftSize, // 128 - fft size, kernel size should be size/2
THREADS_MAX, // int threadsMax, // maximal number of threads to launch
UPDATE_STATUS, // boolean updateStatus,
DEBUG_LEVEL); //int globalDebugLevel){
}
*/
if (!EYESIS_DCT.DCTKernelsAvailable()){ if (!EYESIS_DCT.DCTKernelsAvailable()){
if (DEBUG_LEVEL > 0){ if (DEBUG_LEVEL > 0){
System.out.println("Reading/converting DCT kernels"); System.out.println("Reading/converting DCT kernels");
...@@ -2914,11 +2905,7 @@ private Panel panel1, ...@@ -2914,11 +2905,7 @@ private Panel panel1,
EYESIS_DCT.showKernels(); // show restored kernels EYESIS_DCT.showKernels(); // show restored kernels
} }
} }
// EYESIS_CORRECTIONS.processChannelImages(
EYESIS_DCT.processDCTChannelImages( EYESIS_DCT.processDCTChannelImages(
// SPLIT_PARAMETERS, // EyesisCorrectionParameters.SplitParameters splitParameters,
DCT_PARAMETERS, // EyesisCorrectionParameters.DCTParameters dct_parameters, DCT_PARAMETERS, // EyesisCorrectionParameters.DCTParameters dct_parameters,
DEBAYER_PARAMETERS, //EyesisCorrectionParameters.DebayerParameters debayerParameters, DEBAYER_PARAMETERS, //EyesisCorrectionParameters.DebayerParameters debayerParameters,
NONLIN_PARAMETERS, //EyesisCorrectionParameters.NonlinParameters nonlinParameters, NONLIN_PARAMETERS, //EyesisCorrectionParameters.NonlinParameters nonlinParameters,
...@@ -4096,6 +4083,7 @@ private Panel panel1, ...@@ -4096,6 +4083,7 @@ private Panel panel1,
if (EYESIS_DCT != null){ if (EYESIS_DCT != null){
EYESIS_DCT.resetCLTKernels(); EYESIS_DCT.resetCLTKernels();
} }
} else if (label.equals("Read CLT kernels")) { } else if (label.equals("Read CLT kernels")) {
if (!CLT_PARAMETERS.showDialog()) return; if (!CLT_PARAMETERS.showDialog()) return;
if (EYESIS_DCT == null){ if (EYESIS_DCT == null){
...@@ -4145,6 +4133,92 @@ private Panel panel1, ...@@ -4145,6 +4133,92 @@ private Panel panel1,
DEBUG_LEVEL); DEBUG_LEVEL);
} }
return;
} else if (label.equals("CLT process files")) {
DEBUG_LEVEL=MASTER_DEBUG_LEVEL;
EYESIS_CORRECTIONS.setDebug(DEBUG_LEVEL);
if (EYESIS_DCT == null){
EYESIS_DCT = new EyesisDCT (
EYESIS_CORRECTIONS,
CORRECTION_PARAMETERS,
DCT_PARAMETERS);
if (DEBUG_LEVEL > 0){
System.out.println("Created new EyesisDCT instance, will need to read CLT kernels");
}
}
String configPath=null;
if (EYESIS_CORRECTIONS.correctionsParameters.saveSettings) {
configPath=EYESIS_CORRECTIONS.correctionsParameters.selectResultsDirectory(
true,
true);
if (configPath==null){
String msg="No results directory selected, command aborted";
System.out.println("Warning: "+msg);
IJ.showMessage("Warning",msg);
return;
}
configPath+=Prefs.getFileSeparator()+"autoconfig";
try {
saveTimestampedProperties(
configPath, // full path or null
null, // use as default directory if path==null
true,
PROPERTIES);
} catch (Exception e){
String msg="Failed to save configuration to "+configPath+", command aborted";
System.out.println("Error: "+msg);
IJ.showMessage("Error",msg);
return;
}
}
EYESIS_CORRECTIONS.initSensorFiles(DEBUG_LEVEL);
int numChannels=EYESIS_CORRECTIONS.getNumChannels();
NONLIN_PARAMETERS.modifyNumChannels(numChannels);
CHANNEL_GAINS_PARAMETERS.modifyNumChannels(numChannels);
if (!EYESIS_DCT.CLTKernelsAvailable()){
if (DEBUG_LEVEL > 0){
System.out.println("Reading CLT kernels");
}
EYESIS_DCT.readCLTKernels(
CLT_PARAMETERS,
THREADS_MAX,
UPDATE_STATUS, // update status info
DEBUG_LEVEL);
if (DEBUG_LEVEL > 1){
EYESIS_DCT.showCLTKernels(
THREADS_MAX,
UPDATE_STATUS, // update status info
DEBUG_LEVEL);
}
}
///========================================
EYESIS_DCT.processCLTChannelImages(
CLT_PARAMETERS, // EyesisCorrectionParameters.DCTParameters dct_parameters,
DEBAYER_PARAMETERS, //EyesisCorrectionParameters.DebayerParameters debayerParameters,
NONLIN_PARAMETERS, //EyesisCorrectionParameters.NonlinParameters nonlinParameters,
COLOR_PROC_PARAMETERS, //EyesisCorrectionParameters.ColorProcParameters colorProcParameters,
CHANNEL_GAINS_PARAMETERS, //CorrectionColorProc.ColorGainsParameters channelGainParameters,
RGB_PARAMETERS, //EyesisCorrectionParameters.RGBParameters rgbParameters,
EQUIRECTANGULAR_PARAMETERS, // EyesisCorrectionParameters.EquirectangularParameters equirectangularParameters,
CONVOLVE_FFT_SIZE, //int convolveFFTSize, // 128 - fft size, kernel size should be size/2
THREADS_MAX, //final int threadsMax, // maximal number of threads to launch
UPDATE_STATUS, //final boolean updateStatus,
DEBUG_LEVEL); //final int debugLevel);
if (configPath!=null) {
saveTimestampedProperties( // save config again
configPath, // full path or null
null, // use as default directory if path==null
true,
PROPERTIES);
}
return; return;
// End of buttons code // End of buttons code
......
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