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Commit 56b7ed16 authored by Andrey Filippov's avatar Andrey Filippov
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combining with vignetting correction

parent f96b0aec
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Showing with 483 additions and 110 deletions
src/main/java/EyesisCorrectionParameters.java
View file @ 56b7ed16
...@@ -1801,6 +1801,9 @@ public class EyesisCorrectionParameters { ...@@ -1801,6 +1801,9 @@ public class EyesisCorrectionParameters {
public boolean skip_sym = false; // do not apply symmetrical correction public boolean skip_sym = false; // do not apply symmetrical correction
public boolean convolve_direct = false; // do not apply symmetrical correction public boolean convolve_direct = false; // do not apply symmetrical correction
public double vignetting_max = 0.4; // value in vignetting data to correspond to 1x in the kernel
public double vignetting_range = 3.0; // do not try to correct vignetting less than vignetting_max/vignetting_range
public DCTParameters( public DCTParameters(
int dct_size, int dct_size,
int asym_size, int asym_size,
...@@ -1852,6 +1855,8 @@ public class EyesisCorrectionParameters { ...@@ -1852,6 +1855,8 @@ public class EyesisCorrectionParameters {
properties.setProperty(prefix+"normalize", this.normalize+""); properties.setProperty(prefix+"normalize", this.normalize+"");
properties.setProperty(prefix+"skip_sym", this.skip_sym+""); properties.setProperty(prefix+"skip_sym", this.skip_sym+"");
properties.setProperty(prefix+"convolve_direct", this.convolve_direct+""); properties.setProperty(prefix+"convolve_direct", this.convolve_direct+"");
properties.setProperty(prefix+"vignetting_max", this.vignetting_max+"");
properties.setProperty(prefix+"vignetting_range", this.vignetting_range+"");
} }
public void getProperties(String prefix,Properties properties){ public void getProperties(String prefix,Properties properties){
...@@ -1887,6 +1892,8 @@ public class EyesisCorrectionParameters { ...@@ -1887,6 +1892,8 @@ public class EyesisCorrectionParameters {
if (properties.getProperty(prefix+"normalize")!=null) this.normalize=Boolean.parseBoolean(properties.getProperty(prefix+"normalize")); if (properties.getProperty(prefix+"normalize")!=null) this.normalize=Boolean.parseBoolean(properties.getProperty(prefix+"normalize"));
if (properties.getProperty(prefix+"skip_sym")!=null) this.skip_sym=Boolean.parseBoolean(properties.getProperty(prefix+"skip_sym")); if (properties.getProperty(prefix+"skip_sym")!=null) this.skip_sym=Boolean.parseBoolean(properties.getProperty(prefix+"skip_sym"));
if (properties.getProperty(prefix+"convolve_direct")!=null) this.convolve_direct=Boolean.parseBoolean(properties.getProperty(prefix+"convolve_direct")); if (properties.getProperty(prefix+"convolve_direct")!=null) this.convolve_direct=Boolean.parseBoolean(properties.getProperty(prefix+"convolve_direct"));
if (properties.getProperty(prefix+"vignetting_max")!=null) this.vignetting_max=Double.parseDouble(properties.getProperty(prefix+"vignetting_max"));
if (properties.getProperty(prefix+"vignetting_range")!=null) this.vignetting_range=Double.parseDouble(properties.getProperty(prefix+"vignetting_range"));
} }
public boolean showDialog() { public boolean showDialog() {
...@@ -1923,7 +1930,10 @@ public class EyesisCorrectionParameters { ...@@ -1923,7 +1930,10 @@ public class EyesisCorrectionParameters {
gd.addCheckbox ("Normalize both sym and asym kernels ", this.normalize); gd.addCheckbox ("Normalize both sym and asym kernels ", this.normalize);
gd.addCheckbox ("Do not apply symmetrical (DCT) correction ", this.skip_sym); gd.addCheckbox ("Do not apply symmetrical (DCT) correction ", this.skip_sym);
gd.addCheckbox ("Convolve directly with symmetrical kernel (debug feature) ", this.convolve_direct); gd.addCheckbox ("Convolve directly with symmetrical kernel (debug feature) ", this.convolve_direct);
gd.addNumericField("Value (max) in vignetting data to correspond to 1x in the kernel",this.vignetting_max, 3);
gd.addNumericField("Do not try to correct vignetting smaller than this fraction of max",this.vignetting_range, 3);
WindowTools.addScrollBars(gd);
gd.showDialog(); gd.showDialog();
if (gd.wasCanceled()) return false; if (gd.wasCanceled()) return false;
...@@ -1959,6 +1969,8 @@ public class EyesisCorrectionParameters { ...@@ -1959,6 +1969,8 @@ public class EyesisCorrectionParameters {
this.normalize= gd.getNextBoolean(); this.normalize= gd.getNextBoolean();
this.skip_sym= gd.getNextBoolean(); this.skip_sym= gd.getNextBoolean();
this.convolve_direct= gd.getNextBoolean(); this.convolve_direct= gd.getNextBoolean();
this.vignetting_max= gd.getNextNumber();
this.vignetting_range= gd.getNextNumber();
// MASTER_DEBUG_LEVEL= (int) gd.getNextNumber(); // MASTER_DEBUG_LEVEL= (int) gd.getNextNumber();
return true; return true;
} }
......
src/main/java/EyesisCorrections.java
View file @ 56b7ed16
...@@ -2234,7 +2234,8 @@ public class EyesisCorrections { ...@@ -2234,7 +2234,8 @@ public class EyesisCorrections {
return mask; return mask;
} }
/* ======================================================================== */ /* ======================================================================== */
private void saveAndShow( // private void saveAndShow(
public void saveAndShow(
ImagePlus imp, ImagePlus imp,
EyesisCorrectionParameters.CorrectionParameters correctionsParameters){ EyesisCorrectionParameters.CorrectionParameters correctionsParameters){
saveAndShowEnable( imp, correctionsParameters , true, true); saveAndShowEnable( imp, correctionsParameters , true, true);
...@@ -2254,6 +2255,7 @@ public class EyesisCorrections { ...@@ -2254,6 +2255,7 @@ public class EyesisCorrections {
} }
private void saveAndShow( private void saveAndShow(
// public void saveAndShow(
ImagePlus imp, ImagePlus imp,
EyesisCorrectionParameters.CorrectionParameters correctionsParameters, EyesisCorrectionParameters.CorrectionParameters correctionsParameters,
boolean save, boolean save,
......
src/main/java/EyesisDCT.java
View file @ 56b7ed16
...@@ -35,6 +35,8 @@ public class EyesisDCT { ...@@ -35,6 +35,8 @@ public class EyesisDCT {
public EyesisCorrectionParameters.DCTParameters dctParameters = null; public EyesisCorrectionParameters.DCTParameters dctParameters = null;
public DCTKernels [] kernels = null; public DCTKernels [] kernels = null;
public ImagePlus eyesisKernelImage = null; public ImagePlus eyesisKernelImage = null;
public long startTime;
public EyesisDCT( public EyesisDCT(
EyesisCorrections eyesisCorrections, EyesisCorrections eyesisCorrections,
EyesisCorrectionParameters.CorrectionParameters correctionsParameters, EyesisCorrectionParameters.CorrectionParameters correctionsParameters,
...@@ -72,8 +74,15 @@ public class EyesisDCT { ...@@ -72,8 +74,15 @@ public class EyesisDCT {
return eyesisKernelImage != null; return eyesisKernelImage != null;
} }
public boolean DCTKernelsAvailable(){
return kernels != null;
}
public boolean createDCTKernels( public boolean createDCTKernels(
EyesisCorrectionParameters.DCTParameters dct_parameters, EyesisCorrectionParameters.DCTParameters dct_parameters,
/*
PixelMapping pixelMapping,
*/
int srcKernelSize, int srcKernelSize,
int threadsMax, // maximal number of threads to launch int threadsMax, // maximal number of threads to launch
boolean updateStatus, boolean updateStatus,
...@@ -94,9 +103,31 @@ public class EyesisDCT { ...@@ -94,9 +103,31 @@ public class EyesisDCT {
} }
} }
showDoubleFloatArrays sdfa_instance = new showDoubleFloatArrays(); // just for debugging? showDoubleFloatArrays sdfa_instance = new showDoubleFloatArrays(); // just for debugging?
// String [] sensor_files = correctionsParameters.selectSensorFiles(eyesisCorrections.debugLevel);
for (int chn=0;chn<eyesisCorrections.usedChannels.length;chn++){ for (int chn=0;chn<eyesisCorrections.usedChannels.length;chn++){
if (eyesisCorrections.usedChannels[chn] && (sharpKernelPaths[chn]!=null) && (kernels[chn]==null)){ if (eyesisCorrections.usedChannels[chn] && (sharpKernelPaths[chn]!=null) && (kernels[chn]==null)){
// if ((sensor_files!= null) && (sensor_files.length > chn) && (sensor_files[chn]!=null)){
/*
double [][] vignetting = null;
int vign_width = 0;
int vign_height = 0;
int vign_decimation = 1;
if ((pixelMapping != null) &&
(pixelMapping.sensors != null) &&
(pixelMapping.sensors[chn] != null) &&
(pixelMapping.sensors[chn].pixelCorrection != null) &&
(pixelMapping.sensors[chn].pixelCorrection.length >=6)){
vignetting = new double[3][];
vignetting[0] = pixelMapping.sensors[chn].pixelCorrection[3]; // red
vignetting[2] = pixelMapping.sensors[chn].pixelCorrection[4]; // green
vignetting[1] = pixelMapping.sensors[chn].pixelCorrection[5]; // blue
vign_width = pixelMapping.sensors[chn].pixelCorrectionWidth;
vign_height = pixelMapping.sensors[chn].pixelCorrectionHeight;
vign_decimation = pixelMapping.sensors[chn].pixelCorrectionDecimation;
}
*/
ImagePlus imp_kernel_sharp=new ImagePlus(sharpKernelPaths[chn]); ImagePlus imp_kernel_sharp=new ImagePlus(sharpKernelPaths[chn]);
if (imp_kernel_sharp.getStackSize()<3) { if (imp_kernel_sharp.getStackSize()<3) {
System.out.println("Need a 3-layer stack with kernels"); System.out.println("Need a 3-layer stack with kernels");
...@@ -110,6 +141,12 @@ public class EyesisDCT { ...@@ -110,6 +141,12 @@ public class EyesisDCT {
kernel_sharp_stack, // final ImageStack kernelStack, // first stack with 3 colors/slices convolution kernels kernel_sharp_stack, // final ImageStack kernelStack, // first stack with 3 colors/slices convolution kernels
srcKernelSize, // final int kernelSize, // 64 srcKernelSize, // final int kernelSize, // 64
dct_parameters, // final double blurSigma, dct_parameters, // final double blurSigma,
/*
vignetting,
vign_width,
vign_height,
vign_decimation,
*/
threadsMax, // maximal number of threads to launch threadsMax, // maximal number of threads to launch
updateStatus, updateStatus,
debugLevel); // update status info debugLevel); // update status info
...@@ -130,6 +167,12 @@ public class EyesisDCT { ...@@ -130,6 +167,12 @@ public class EyesisDCT {
final ImageStack kernelStack, // first stack with 3 colors/slices convolution kernels final ImageStack kernelStack, // first stack with 3 colors/slices convolution kernels
final int kernelSize, // 64 final int kernelSize, // 64
final EyesisCorrectionParameters.DCTParameters dct_parameters, final EyesisCorrectionParameters.DCTParameters dct_parameters,
/*
final double [][] vignetting,
int vign_width,
int vign_height,
int vign_decimation,
*/
final int threadsMax, // maximal number of threads to launch final int threadsMax, // maximal number of threads to launch
final boolean updateStatus, final boolean updateStatus,
final int globalDebugLevel) // update status info final int globalDebugLevel) // update status info
...@@ -155,9 +198,17 @@ public class EyesisDCT { ...@@ -155,9 +198,17 @@ public class EyesisDCT {
final int preTargetSize = 4 * dct_size; final int preTargetSize = 4 * dct_size;
final int targetSize = 2 * dct_size; // normally 16 final int targetSize = 2 * dct_size; // normally 16
final double [] anitperiodic_window = createAntiperiodicWindow(dct_size); final double [] anitperiodic_window = createAntiperiodicWindow(dct_size);
/*
final int vgn_step = dct_kernel.img_step/vign_decimation;
final int vgn_width = vign_width/vign_decimation;
final int vgn_height = vign_height/vign_decimation;
final int vgn_left = (vign_width - (dct_kernel.img_step * (kernelNumHor-1)))/(2* vign_decimation); // in decimated pixels
final int vgn_top = (vign_height -(dct_kernel.img_step * (kernelNumVert-1)))/(2* vign_decimation); // in decimated pixels
final double vgn_max = dct_parameters.vignetting_max;
final double vgn_min = vgn_max/dct_parameters.vignetting_range;
*/
final int chn_green = 2; // all others multiply by 4 as there 1 in 4 Bayer for those, green - by 2
final long startTime = System.nanoTime(); final long startTime = System.nanoTime();
System.out.println("calculateDCTKernel():numberOfKernels="+numberOfKernels); System.out.println("calculateDCTKernel():numberOfKernels="+numberOfKernels);
for (int ithread = 0; ithread < threads.length; ithread++) { for (int ithread = 0; ithread < threads.length; ithread++) {
threads[ithread] = new Thread() { threads[ithread] = new Thread() {
...@@ -182,6 +233,7 @@ public class EyesisDCT { ...@@ -182,6 +233,7 @@ public class EyesisDCT {
factorConvKernel.setDCWeight (dct_parameters.dc_weight); factorConvKernel.setDCWeight (dct_parameters.dc_weight);
int chn,tileY,tileX; int chn,tileY,tileX;
double kscale;
// int chn0=-1; // int chn0=-1;
// int i; // int i;
// double sum; // double sum;
...@@ -189,6 +241,21 @@ public class EyesisDCT { ...@@ -189,6 +241,21 @@ public class EyesisDCT {
chn=nTile/numberOfKernelsInChn; chn=nTile/numberOfKernelsInChn;
tileY =(nTile % numberOfKernelsInChn)/kernelNumHor; tileY =(nTile % numberOfKernelsInChn)/kernelNumHor;
tileX = nTile % kernelNumHor; tileX = nTile % kernelNumHor;
kscale = 1.0;
/*
if (vignetting != null){
int vh = vgn_left + vgn_step * tileX;
if (vh < 0) vh = 0;
if (vh >= vgn_width) vh = vgn_width -1;
int vv = vgn_top + vgn_step * tileY;
if (vv < 0) vv = 0;
if (vv >= vgn_height) vh = vgn_height -1;
kscale = vignetting[chn][vv*vgn_width+vh];
if (kscale < vgn_min) kscale = vgn_min;
}
kscale = vgn_max/kscale * ((chn == chn_green)? 2:4);
*/
kscale = (chn == chn_green)? 2:4;
if (tileX==0) { if (tileX==0) {
if (updateStatus) IJ.showStatus("Processing kernels, channel "+(chn+1)+" of "+nChn+", row "+(tileY+1)+" of "+kernelNumVert); if (updateStatus) IJ.showStatus("Processing kernels, channel "+(chn+1)+" of "+nChn+", row "+(tileY+1)+" of "+kernelNumVert);
if (globalDebugLevel>2) System.out.println("Processing kernels, channel "+(chn+1)+" of "+nChn+", row "+(tileY+1)+" of "+kernelNumVert+" : "+IJ.d2s(0.000000001*(System.nanoTime()-startTime),3)); if (globalDebugLevel>2) System.out.println("Processing kernels, channel "+(chn+1)+" of "+nChn+", row "+(tileY+1)+" of "+kernelNumVert+" : "+IJ.d2s(0.000000001*(System.nanoTime()-startTime),3));
...@@ -224,8 +291,9 @@ public class EyesisDCT { ...@@ -224,8 +291,9 @@ public class EyesisDCT {
for (int i = 0; i < pre_target_kernel.length; i++){ for (int i = 0; i < pre_target_kernel.length; i++){
s+=pre_target_kernel[i]; s+=pre_target_kernel[i];
} }
s = kscale/s;
for (int i = 0; i < pre_target_kernel.length; i++){ for (int i = 0; i < pre_target_kernel.length; i++){
pre_target_kernel[i]/=s; pre_target_kernel[i] *= s;
} }
if (globalDebugLevel > 1){ // was already close to 1.0 if (globalDebugLevel > 1){ // was already close to 1.0
System.out.println(tileX+"/"+tileY+ " s="+s); System.out.println(tileX+"/"+tileY+ " s="+s);
...@@ -289,110 +357,8 @@ public class EyesisDCT { ...@@ -289,110 +357,8 @@ public class EyesisDCT {
// ImageStack outStack=new ImageStack(kernelNumHor,kernelNumVert); // ImageStack outStack=new ImageStack(kernelNumHor,kernelNumVert);
return dct_kernel; return dct_kernel;
} }
/*
* final int kernelNumHor=kernelWidth/kernelSize;
final int kernelNumVert=kernelStack.getHeight()/kernelSize;
final int nChn=kernelStack.getSize();
dct_kernel.sym_kernels = new double [nChn][kernelNumHor*kernelNumVert*dct_parameters.dct_size * dct_parameters.dct_size];
dct_kernel.asym_kernels = new double [nChn][kernelNumHor*kernelNumVert*dct_parameters.asym_size * dct_parameters.asym_size];
*
System.arraycopy(currentfX, 0, convolved, 0, convolved.length);
DCT_PARAMETERS.fact_precision,
DCT_PARAMETERS.asym_pixels,
DCT_PARAMETERS.asym_distance,
DCT_PARAMETERS.seed_size);
*/
//processChannelImage //processChannelImage
//convolveStackWithKernelStack //convolveStackWithKernelStack
// Remove later, copied here as a reference
public ImageStack calculateKernelsNoiseGains (
final ImageStack kernelStack1, // first stack with 3 colors/slices convolution kernels
final ImageStack kernelStack2, // second stack with 3 colors/slices convolution kernels (or null)
final int size, // 128 - fft size, kernel size should be size/2
final double blurSigma,
final int threadsMax, // maximal number of threads to launch
final boolean updateStatus,
final int globalDebugLevel) // update status info
{
if (kernelStack1==null) return null;
final boolean useDiff= (kernelStack2 != null);
final int kernelSize=size/2;
final int kernelWidth=kernelStack1.getWidth();
final int kernelNumHor=kernelWidth/(size/2);
final int kernelNumVert=kernelStack1.getHeight()/(size/2);
final int length=kernelNumHor*kernelNumVert;
final int nChn=kernelStack1.getSize();
final float [][] outPixles=new float[nChn][length]; // GLOBAL same as input
int i,j;
for (i=0;i<nChn;i++) for (j=0;j<length;j++) outPixles[i][j]=0.0f;
final Thread[] threads = ImageDtt.newThreadArray(threadsMax);
final AtomicInteger ai = new AtomicInteger(0);
final int numberOfKernels= kernelNumHor*kernelNumVert*nChn;
final int numberOfKernelsInChn=kernelNumHor*kernelNumVert;
final long startTime = System.nanoTime();
for (int ithread = 0; ithread < threads.length; ithread++) {
threads[ithread] = new Thread() {
public void run() {
DoubleGaussianBlur gb=null;
if (blurSigma>0) gb=new DoubleGaussianBlur();
float [] kernelPixels1= null; // will be initialized at first use
float [] kernelPixels2= null; // will be initialized at first use
double [] kernel1= new double[kernelSize*kernelSize];
double [] kernel2= new double[kernelSize*kernelSize];
int chn,tileY,tileX;
int chn0=-1;
int i;
double sum;
for (int nTile = ai.getAndIncrement(); nTile < numberOfKernels; nTile = ai.getAndIncrement()) {
chn=nTile/numberOfKernelsInChn;
tileY =(nTile % numberOfKernelsInChn)/kernelNumHor;
tileX = nTile % kernelNumHor;
if (tileX==0) {
if (updateStatus) IJ.showStatus("Processing kernels, channel "+(chn+1)+" of "+nChn+", row "+(tileY+1)+" of "+kernelNumVert);
if (globalDebugLevel>2) System.out.println("Processing kernels, channel "+(chn+1)+" of "+nChn+", row "+(tileY+1)+" of "+kernelNumVert+" : "+IJ.d2s(0.000000001*(System.nanoTime()-startTime),3));
}
if (chn!=chn0) {
kernelPixels1=(float[]) kernelStack1.getPixels(chn+1);
if (useDiff) kernelPixels2=(float[]) kernelStack2.getPixels(chn+1);
chn0=chn;
}
/* read convolution kernel */
extractOneKernel(kernelPixels1, // array of combined square kernels, each
kernel1, // will be filled, should have correct size before call
kernelNumHor, // number of kernels in a row
tileX, // horizontal number of kernel to extract
tileY); // vertical number of kernel to extract
/* optionally read the second convolution kernel */
if (useDiff) {extractOneKernel(kernelPixels2, // array of combined square kernels, each
kernel2, // will be filled, should have correct size before call
kernelNumHor, // number of kernels in a row
tileX, // horizontal number of kernel to extract
tileY); // vertical number of kernel to extract
for (i=0; i<kernel1.length;i++) kernel1[i]-=kernel2[i];
}
if (blurSigma>0) gb.blurDouble(kernel1, kernelSize, kernelSize, blurSigma, blurSigma, 0.01);
/* Calculate sum of squared kernel1 elements */
sum=0.0;
for (i=0; i<kernel1.length;i++) sum+=kernel1[i]*kernel1[i];
outPixles[chn][tileY*kernelNumHor+tileX]= (float) (Math.sqrt(sum));
// System.out.println("Processing kernels, channel "+(chn+1)+" of "+nChn+", row "+(tileY+1)+" of "+kernelNumVert+" sum="+sum);
}
}
};
}
ImageDtt.startAndJoin(threads);
if (globalDebugLevel > 1) System.out.println("Threads done at "+IJ.d2s(0.000000001*(System.nanoTime()-startTime),3));
/* prepare result stack to return */
ImageStack outStack=new ImageStack(kernelNumHor,kernelNumVert);
for (i=0;i<nChn;i++) {
outStack.addSlice(kernelStack1.getSliceLabel(i+1), outPixles[i]);
}
return outStack;
}
// mostly for testing // mostly for testing
//eyesisKernelImage //eyesisKernelImage
...@@ -915,4 +881,290 @@ public class EyesisDCT { ...@@ -915,4 +881,290 @@ public class EyesisDCT {
kernels[chn].asym_kernels = null; // not needed anymore kernels[chn].asym_kernels = null; // not needed anymore
kernels[chn].sym_direct = null; // not needed anymore kernels[chn].sym_direct = null; // not needed anymore
} }
// public boolean isChannelEnabled(int channel){
// return ((channel>=0) && (channel<this.usedChannels.length) && this.usedChannels[channel]);
// }
public void processDCTChannelImages(
// EyesisCorrectionParameters.SplitParameters splitParameters,
EyesisCorrectionParameters.DCTParameters dct_parameters,
EyesisCorrectionParameters.DebayerParameters debayerParameters,
EyesisCorrectionParameters.NonlinParameters nonlinParameters,
EyesisCorrectionParameters.ColorProcParameters colorProcParameters,
CorrectionColorProc.ColorGainsParameters channelGainParameters,
EyesisCorrectionParameters.RGBParameters rgbParameters,
EyesisCorrectionParameters.EquirectangularParameters equirectangularParameters,
int convolveFFTSize, // 128 - fft size, kernel size should be size/2
final int threadsMax, // maximal number of threads to launch
final boolean updateStatus,
final int debugLevel)
{
this.startTime=System.nanoTime();
String [] sourceFiles=correctionsParameters.getSourcePaths();
boolean [] enabledFiles=new boolean[sourceFiles.length];
for (int i=0;i<enabledFiles.length;i++) enabledFiles[i]=false;
int numFilesToProcess=0;
int numImagesToProcess=0;
for (int nFile=0;nFile<enabledFiles.length;nFile++){
if ((sourceFiles[nFile]!=null) && (sourceFiles[nFile].length()>1)) {
int [] channels={correctionsParameters.getChannelFromSourceTiff(sourceFiles[nFile])};
if (correctionsParameters.isJP4()){
int subCamera= channels[0]- correctionsParameters.firstSubCamera; // to match those in the sensor files
channels=this.eyesisCorrections.pixelMapping.channelsForSubCamera(subCamera);
}
if (channels!=null){
for (int i=0;i<channels.length;i++) if (eyesisCorrections.isChannelEnabled(channels[i])){
if (!enabledFiles[nFile]) numFilesToProcess++;
enabledFiles[nFile]=true;
numImagesToProcess++;
}
}
}
}
if (numFilesToProcess==0){
System.out.println("No files to process (of "+sourceFiles.length+")");
return;
} else {
if (debugLevel>0) System.out.println(numFilesToProcess+ " files to process (of "+sourceFiles.length+"), "+numImagesToProcess+" images to process");
}
double [] referenceExposures=eyesisCorrections.calcReferenceExposures(debugLevel); // multiply each image by this and divide by individual (if not NaN)
int [][] fileIndices=new int [numImagesToProcess][2]; // file index, channel number
int index=0;
for (int nFile=0;nFile<enabledFiles.length;nFile++){
if ((sourceFiles[nFile]!=null) && (sourceFiles[nFile].length()>1)) {
int [] channels={correctionsParameters.getChannelFromSourceTiff(sourceFiles[nFile])};
if (correctionsParameters.isJP4()){
int subCamera= channels[0]- correctionsParameters.firstSubCamera; // to match those in the sensor files
channels=eyesisCorrections.pixelMapping.channelsForSubCamera(subCamera);
}
if (channels!=null){
for (int i=0;i<channels.length;i++) if (eyesisCorrections.isChannelEnabled(channels[i])){
fileIndices[index ][0]=nFile;
fileIndices[index++][1]=channels[i];
}
}
}
}
for (int iImage=0;iImage<fileIndices.length;iImage++){
int nFile=fileIndices[iImage][0];
ImagePlus imp_src=null;
// int srcChannel=correctionsParameters.getChannelFromSourceTiff(sourceFiles[nFile]);
int srcChannel=fileIndices[iImage][1];
if (correctionsParameters.isJP4()){
int subchannel=eyesisCorrections.pixelMapping.getSubChannel(srcChannel);
if (this.correctionsParameters.swapSubchannels01) {
switch (subchannel){
case 0: subchannel=1; break;
case 1: subchannel=0; break;
}
}
if (debugLevel>0) System.out.println("Processing channel "+fileIndices[iImage][1]+" - subchannel "+subchannel+" of "+sourceFiles[nFile]);
ImagePlus imp_composite=eyesisCorrections.JP4_INSTANCE.open(
"", // path,
sourceFiles[nFile],
"", //arg - not used in JP46 reader
true, // un-apply camera color gains
null, // new window
false); // do not show
imp_src=eyesisCorrections.JP4_INSTANCE.demuxImage(imp_composite, subchannel);
if (imp_src==null) imp_src=imp_composite; // not a composite image
// do we need to add any properties?
} else {
imp_src=new ImagePlus(sourceFiles[nFile]);
// (new JP46_Reader_camera(false)).decodeProperiesFromInfo(imp_src); // decode existent properties from info
eyesisCorrections.JP4_INSTANCE.decodeProperiesFromInfo(imp_src); // decode existent properties from info
if (debugLevel>0) System.out.println("Processing "+sourceFiles[nFile]);
}
double scaleExposure=1.0;
if (!Double.isNaN(referenceExposures[nFile]) && (imp_src.getProperty("EXPOSURE")!=null)){
scaleExposure=referenceExposures[nFile]/Double.parseDouble((String) imp_src.getProperty("EXPOSURE"));
// imp_src.setProperty("scaleExposure", scaleExposure); // it may already have channel
if (debugLevel>0) System.out.println("Will scale intensity (to compensate for exposure) by "+scaleExposure);
}
imp_src.setProperty("name", correctionsParameters.getNameFromSourceTiff(sourceFiles[nFile]));
imp_src.setProperty("channel", srcChannel); // it may already have channel
imp_src.setProperty("path", sourceFiles[nFile]); // it may already have channel
// ImagePlus result=processChannelImage( // returns ImagePlus, but it already should be saved/shown
processDCTChannelImage( // returns ImagePlus, but it already should be saved/shown
imp_src, // should have properties "name"(base for saving results), "channel","path"
// splitParameters,
dct_parameters,
debayerParameters,
nonlinParameters,
colorProcParameters,
channelGainParameters,
rgbParameters,
convolveFFTSize, // 128 - fft size, kernel size should be size/2
scaleExposure,
threadsMax, // maximal number of threads to launch
updateStatus,
debugLevel);
// warp result (add support for different color modes)
if (this.correctionsParameters.equirectangular){
if (equirectangularParameters.clearFullMap) eyesisCorrections.pixelMapping.deleteEquirectangularMapFull(srcChannel); // save memory? //removeUnusedSensorData - no, use equirectangular specific settings
if (equirectangularParameters.clearAllMaps) eyesisCorrections.pixelMapping.deleteEquirectangularMapAll(srcChannel); // save memory? //removeUnusedSensorData - no, use equirectangular specific settings
}
//pixelMapping
Runtime.getRuntime().gc();
if (debugLevel>0) System.out.println("Processing image "+(iImage+1)+" (of "+fileIndices.length+") finished at "+
IJ.d2s(0.000000001*(System.nanoTime()-this.startTime),3)+" sec, --- Free memory="+Runtime.getRuntime().freeMemory()+" (of "+Runtime.getRuntime().totalMemory()+")");
if (eyesisCorrections.stopRequested.get()>0) {
System.out.println("User requested stop");
return;
}
}
}
public ImagePlus processDCTChannelImage(
ImagePlus imp_src, // should have properties "name"(base for saving results), "channel","path"
// EyesisCorrectionParameters.SplitParameters splitParameters, // will not be used !
EyesisCorrectionParameters.DCTParameters dct_parameters,
EyesisCorrectionParameters.DebayerParameters debayerParameters,
EyesisCorrectionParameters.NonlinParameters nonlinParameters,
EyesisCorrectionParameters.ColorProcParameters colorProcParameters,
CorrectionColorProc.ColorGainsParameters channelGainParameters,
EyesisCorrectionParameters.RGBParameters rgbParameters,
int convolveFFTSize, // 128 - fft size, kernel size should be size/2
double scaleExposure,
final int threadsMax, // maximal number of threads to launch
final boolean updateStatus,
final int debugLevel){
boolean advanced=this.correctionsParameters.zcorrect || this.correctionsParameters.equirectangular;
boolean crop= advanced? true: this.correctionsParameters.crop;
boolean rotate= advanced? false: this.correctionsParameters.rotate;
double JPEG_scale= advanced? 1.0: this.correctionsParameters.JPEG_scale;
boolean toRGB= advanced? true: this.correctionsParameters.toRGB;
// may use this.StartTime to report intermediate steps execution times
String name=(String) imp_src.getProperty("name");
// int channel= Integer.parseInt((String) imp_src.getProperty("channel"));
int channel= (Integer) imp_src.getProperty("channel");
String path= (String) imp_src.getProperty("path");
if (this.correctionsParameters.pixelDefects && (eyesisCorrections.defectsXY!=null)&& (eyesisCorrections.defectsXY[channel]!=null)){
// apply pixel correction
int numApplied= eyesisCorrections.correctDefects(
imp_src,
channel,
debugLevel);
if ((debugLevel>0) && (numApplied>0)) { // reduce verbosity after verified defect correction works
System.out.println("Corrected "+numApplied+" pixels in "+path);
}
}
if (this.correctionsParameters.vignetting){
if ((eyesisCorrections.channelVignettingCorrection==null) || (channel<0) || (channel>=eyesisCorrections.channelVignettingCorrection.length) || (eyesisCorrections.channelVignettingCorrection[channel]==null)){
System.out.println("No vignetting data for channel "+channel);
return null;
}
float [] pixels=(float []) imp_src.getProcessor().getPixels();
if (pixels.length!=eyesisCorrections.channelVignettingCorrection[channel].length){
System.out.println("Vignetting data for channel "+channel+" has "+eyesisCorrections.channelVignettingCorrection[channel].length+" pixels, image "+path+" has "+pixels.length);
return null;
}
for (int i=0;i<pixels.length;i++){
pixels[i]*=eyesisCorrections.channelVignettingCorrection[channel][i];
}
}
String title=name+"-"+String.format("%02d", channel);
ImagePlus result=imp_src;
if (debugLevel>1) System.out.println("processing: "+path);
result.setTitle(title+"RAW");
if (!this.correctionsParameters.split){
eyesisCorrections.saveAndShow(result, this.correctionsParameters);
return result;
}
// Generate split parameters for DCT processing mode
EyesisCorrectionParameters.SplitParameters splitParameters = new EyesisCorrectionParameters.SplitParameters(
(dct_parameters.decimation == 2)?1:2, // oversample; // currently source kernels are oversampled
dct_parameters.dct_size/2, // addLeft
dct_parameters.dct_size/2, // addTop
dct_parameters.dct_size/2, // addRight
dct_parameters.dct_size/2 // addBottom
);
// Split into Bayer components, oversample, increase canvas
ImageStack stack= eyesisCorrections.bayerToStack(
result, // source Bayer image, linearized, 32-bit (float))
splitParameters);
String titleFull=title+"-SPLIT";
if (!this.correctionsParameters.debayer) {
result= new ImagePlus(titleFull, stack);
eyesisCorrections.saveAndShow(result, this.correctionsParameters);
return result;
}
// =================
ImageDtt image_dtt = new ImageDtt();
showDoubleFloatArrays sdfa_instance = new showDoubleFloatArrays(); // just for debugging?
double [][][][] dctdc_data = image_dtt.mdctDcStack(
stack,
dct_parameters,
this,
threadsMax,
debugLevel,
updateStatus);
for (int chn = 0; chn < dctdc_data.length; chn++) {
image_dtt.dct_lpf(
dct_parameters.dbg_sigma,
dctdc_data[chn],
threadsMax,
debugLevel);
}
int tilesY = stack.getHeight()/dct_parameters.dct_size - 1;
int tilesX = stack.getWidth()/dct_parameters.dct_size - 1;
if (debugLevel>0){
System.out.println("--tilesX="+tilesX);
System.out.println("--tilesY="+tilesY);
}
double [][] dct_dc = new double [dctdc_data.length][];
double [][] dct_ac = new double [dctdc_data.length][];
for (int chn = 0; chn < dct_dc.length; chn++) {
dct_dc[chn] = image_dtt.lapped_dct_dcac(
false, // out_ac, // false - output DC, true - output AC
dctdc_data [chn],
threadsMax,
debugLevel);
dct_ac[chn] = image_dtt.lapped_dct_dcac(
true, // out_ac, // false - output DC, true - output AC
dctdc_data [chn],
threadsMax,
debugLevel);
}
// System.out.println("dct_dc.length="+dct_dc.length+" dct_ac.length="+dct_ac.length);
sdfa_instance.showArrays(dct_ac,
tilesX*dct_parameters.dct_size,
tilesY*dct_parameters.dct_size,
true,
result.getTitle()+"-DCT_AC");
sdfa_instance.showArrays(dct_dc,
tilesX,
tilesY,
true,
result.getTitle()+"-DCT_DC");
double [][] idct_data = new double [dctdc_data.length][];
for (int chn=0; chn<idct_data.length;chn++){
idct_data[chn] = image_dtt.lapped_idctdc(
dctdc_data[chn], // scanline representation of dcd data, organized as dct_size x dct_size tiles
dct_parameters.dct_size, // final int
dct_parameters.dct_window, //window_type
threadsMax,
debugLevel);
}
sdfa_instance.showArrays(idct_data,
(tilesX + 1) * dct_parameters.dct_size,
(tilesY + 1) * dct_parameters.dct_size,
true,
result.getTitle()+"-IDCTDC");
return result;
}
} }
src/main/java/Eyesis_Correction.java
View file @ 56b7ed16
...@@ -462,6 +462,8 @@ private Panel panel1,panel2,panel3,panel4,panel5,panel5a, panel6,panel7,panelPos ...@@ -462,6 +462,8 @@ private Panel panel1,panel2,panel3,panel4,panel5,panel5a, panel6,panel7,panelPos
addButton("Select kernels image", panelDct1, color_configure); addButton("Select kernels image", panelDct1, color_configure);
addButton("Create DCT kernels", panelDct1, color_process); addButton("Create DCT kernels", panelDct1, color_process);
addButton("Read DCT kernels", panelDct1, color_process); addButton("Read DCT kernels", panelDct1, color_process);
addButton("Setup DCT parameters", panelDct1, color_configure);
addButton("DCT process files", panelDct1, color_process);
add(panelDct1); add(panelDct1);
} }
pack(); pack();
...@@ -2781,8 +2783,110 @@ private Panel panel1,panel2,panel3,panel4,panel5,panel5a, panel6,panel7,panelPos ...@@ -2781,8 +2783,110 @@ private Panel panel1,panel2,panel3,panel4,panel5,panel5a, panel6,panel7,panelPos
true, true,
DBG_IMP.getTitle()+"-IDCTDC"); DBG_IMP.getTitle()+"-IDCTDC");
return; return;
/* ======================================================================== */
} else if (label.equals("Setup DCT parameters")) {
DCT_PARAMETERS.showDialog();
return;
/* ======================================================================== */ /* ======================================================================== */
} else if (label.equals("DCT 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 DCT 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 (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 (DEBUG_LEVEL > 0){
System.out.println("Reading/converting DCT kernels");
}
EYESIS_DCT.readDCTKernels(
DCT_PARAMETERS,
CONVOLVE_FFT_SIZE/2,
THREADS_MAX,
UPDATE_STATUS, // update status info
DEBUG_LEVEL);
if (DEBUG_LEVEL > 1){
EYESIS_DCT.showKernels(); // show restored kernels
}
}
// EYESIS_CORRECTIONS.processChannelImages(
EYESIS_DCT.processDCTChannelImages(
// SPLIT_PARAMETERS, // EyesisCorrectionParameters.SplitParameters splitParameters,
DCT_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;
/* ======================================================================== */
} else if (label.equals("DCT test 3")) { } else if (label.equals("DCT test 3")) {
DEBUG_LEVEL=MASTER_DEBUG_LEVEL; DEBUG_LEVEL=MASTER_DEBUG_LEVEL;
int n = 32; int n = 32;
...@@ -3397,6 +3501,9 @@ private Panel panel1,panel2,panel3,panel4,panel5,panel5a, panel6,panel7,panelPos ...@@ -3397,6 +3501,9 @@ private Panel panel1,panel2,panel3,panel4,panel5,panel5a, panel6,panel7,panelPos
EYESIS_DCT.createDCTKernels( EYESIS_DCT.createDCTKernels(
DCT_PARAMETERS, DCT_PARAMETERS,
/*
EYESIS_CORRECTIONS.pixelMapping,
*/
CONVOLVE_FFT_SIZE/2, CONVOLVE_FFT_SIZE/2,
THREADS_MAX, THREADS_MAX,
UPDATE_STATUS, // update status info UPDATE_STATUS, // update status info
......
src/main/java/ImageDtt.java
View file @ 56b7ed16
...@@ -529,7 +529,7 @@ public class ImageDtt { ...@@ -529,7 +529,7 @@ public class ImageDtt {
} }
if ((tileY == debug_tileY) && (tileX == debug_tileX) && (color == 2)) { if ((dct_kernels!=null) && (tileY == debug_tileY) && (tileX == debug_tileX) && (color == 2)) {
double [][] dbg_tile = { double [][] dbg_tile = {
dct_kernels.st_direct[color][kernelTileY][kernelTileX], dct_kernels.st_direct[color][kernelTileY][kernelTileX],
dct_kernels.st_kernels[color][kernelTileY][kernelTileX], dct_kernels.st_kernels[color][kernelTileY][kernelTileX],
......
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