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imagej-elphel
Commit d531d201 authored by Andrey Filippov's avatar Andrey Filippov
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merged with nc393 branch

parents 01246a62 b759e500
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Showing with 1635 additions and 1089 deletions
src/main/java/Aberration_Correction.java
View file @ d531d201
......@@ -2514,8 +2514,8 @@ if (PROCESS_PARAMETERS.saveSettings) saveProperties(FILE_PARAMETERS.resultsDirec
tileY = nTile /tilesX;
tileX = nTile % tilesX;
if (tileX==0) {
if (updateStatus) IJ.showStatus("Reducing sampling aliases, row "+(tileY+1)+" of "+tilesY);
if (MASTER_DEBUG_LEVEL>2) System.out.println("Reducing sampling aliases, row "+(tileY+1)+" of "+tilesY+" : "+IJ.d2s(0.000000001*(System.nanoTime()-startTime),3));
if (updateStatus) IJ.showStatus("(3)Reducing sampling aliases, row "+(tileY+1)+" of "+tilesY);
if (MASTER_DEBUG_LEVEL>2) System.out.println("(3)Reducing sampling aliases, row "+(tileY+1)+" of "+tilesY+" : "+IJ.d2s(0.000000001*(System.nanoTime()-startTime),3));
}
if ((tileY==yTileDebug) && (tileX==xTileDebug)) DEBUG_LEVEL=4;
......
src/main/java/DebayerScissors.java
View file @ d531d201
......@@ -30,6 +30,8 @@ import ij.ImageStack;
import java.util.concurrent.atomic.AtomicInteger;
import javax.swing.SwingUtilities;
public class DebayerScissors {
// showDoubleFloatArrays SDFA_INSTANCE= new showDoubleFloatArrays();
......@@ -96,7 +98,29 @@ public class DebayerScissors {
final Thread[] threads = newThreadArray(threadsMax);
final AtomicInteger ai = new AtomicInteger(0);
final int numberOfKernels=tilesY*tilesX;
int indx,dx,dy,tx,ty,li;
final int [] nonOverlapSeq = new int[numberOfKernels];
int [] nextFirstFindex=new int[4];
indx = 0;
li=0;
for (dy=0;dy<2;dy++) for (dx=0;dx<2;dx++) {
for (ty=dy; ty < tilesY; ty+=2) for (tx=dx; tx < tilesX; tx+=2){
nonOverlapSeq[indx++] = ty*tilesX + tx;
}
nextFirstFindex[li++] = indx;
}
final AtomicInteger aStopIndex = new AtomicInteger(0);
final long startTime = System.nanoTime();
final AtomicInteger tilesFinishedAtomic = new AtomicInteger(1); // first finished will be 1
if (updateStatus) IJ.showStatus("Reducing sampling aliases, "+tilesY+" rows, threadsMax="+threadsMax);
if (updateStatus) System.out.println("Reducing sampling aliases, "+tilesY+" rows, threadsMax="+threadsMax);
for (li = 0; li < nextFirstFindex.length; li++){
aStopIndex.set(nextFirstFindex[li]);
if (li>0){
ai.set(nextFirstFindex[li-1]);
}
for (int ithread = 0; ithread < threads.length; ithread++) {
threads[ithread] = new Thread() {
public void run() {
......@@ -114,17 +138,19 @@ public class DebayerScissors {
debayerParameters.debayerRelativeWidthRedblue, // result red/blue mask mpy by scaled default (square)
debayerParameters.debayerRelativeWidthRedblueMain, // green mask when applied to red/blue, main (center)
debayerParameters.debayerRelativeWidthRedblueClones);// green mask when applied to red/blue, clones
// for (int nTile0 = ai.getAndIncrement(); nTile0 < numberOfKernels; nTile0 = ai.getAndIncrement()) {
for (int nTile0 = ai.getAndIncrement(); nTile0 < aStopIndex.get(); nTile0 = ai.getAndIncrement()) {
for (int nTile = ai.getAndIncrement(); nTile < numberOfKernels; nTile = ai.getAndIncrement()) {
int nTile = nonOverlapSeq[nTile0];
tileY = nTile /tilesX;
tileX = nTile % tilesX;
if (tileX==0) {
if (updateStatus) IJ.showStatus("Reducing sampling aliases, row "+(tileY+1)+" of "+tilesY);
if (globalDebugLevel>2) System.out.println("Reducing sampling aliases, row "+(tileY+1)+" of "+tilesY+" : "+IJ.d2s(0.000000001*(System.nanoTime()-startTime),3));
if (tileX < 2) {
int trow=(tileY+((2*(tileY & 1) + (tileX & 1))*tilesY))/4;
if (updateStatus) IJ.showStatus("Reducing sampling aliases, row "+(trow+1)+" of "+tilesY);
// System.out.println("(1)Reducing sampling aliases, row "+(tileY+1)+" of "+tilesY+" ("+nTile+"/"+nTile0+") col="+(tileX+1));
if (globalDebugLevel>2) System.out.println("Reducing sampling aliases, row "+(trow+1)+" of "+tilesY+" : "+IJ.d2s(0.000000001*(System.nanoTime()-startTime),3));
}
// if ((tileY==yTileDebug) && (tileX==xTileDebug)) this.debugLevel=4;
// else this.debugLevel=wasDebugLevel;
for (chn=0;chn<nChn;chn++){
extractSquareTile( pixels[chn], // source pixel array,
tile[chn], // will be filled, should have correct size before call
......@@ -149,8 +175,8 @@ public class DebayerScissors {
debayerParameters.debayerThreshold, // no high frequencies - use default uniform filter
debayerParameters.debayerGamma, // power function applied to the amplitudes before generating spectral masks
debayerParameters.debayerBonus, // scale far pixels as (1.0+bonus*r/rmax)
debayerParameters.mainToAlias,// relative main/alias amplitudes to enable lixels (i.e. 0.5 means that if alias is >0.5*main, the pixel will be masked out)
debayerParameters.debayerMaskBlur, // for both masks sigma for gaussian blur of the binary masks (<0 -do not use "scissors")
debayerParameters.mainToAlias,// relative main/alias amplitudes to enable pixels (i.e. 0.5 means that if alias is >0.5*main, the pixel will be masked out)
debayerParameters.debayerMaskBlur, // for both masks sigma for Gaussian blur of the binary masks (<0 -do not use "scissors")
debayerParameters.debayerUseScissors, // use "scissors", if false - just apply "diamond" ands "square" with DEBAYER_PARAMETERS.debayerRelativeWidthGreen and DEBAYER_PARAMETERS.debayerRelativeWidthRedblue
((tileY==yTileDebug) && (tileX==xTileDebug))?4:1);
// 1); // internal debug level ((this.debugLevel>2) && (yTile==yTile0) && (xTile==xTile0))?3:1;
......@@ -166,11 +192,13 @@ public class DebayerScissors {
fht_instance.inverseTransform(tile[chn]);
fht_instance.swapQuadrants(tile[chn]);
/* accumulate result */
/*This is synchronized method. It is possible to make threads to write to non-overlapping regions of the outPixles, but as the accumulation
* takes just small fraction of severtal FHTs, it should be OK - reasonable number of threads will spread and not "stay in line"
/*This is (now was) a synchronized method. It is possible to make threads to write to non-overlapping regions of the outPixles, but as the accumulation
* takes just small fraction of several FHTs, it should be OK - reasonable number of threads will spread and not "stay in line"
*/
accumulateSquareTile(outPixles[chn], // float pixels array to accumulate tile
//accumulateSquareTile(
nonSyncAccumulateSquareTile (
outPixles[chn], // float pixels array to accumulate tile
tile[chn], // data to accumulate to the pixels array
imgWidth, // width of pixels array
tileX*step, // left corner X
......@@ -178,22 +206,34 @@ public class DebayerScissors {
}
if ((tileY==yTileDebug) && (tileX==xTileDebug) && (SDFA_instance!=null)) SDFA_instance.showArrays (tile.clone(),debayerParameters.size,debayerParameters.size, "B00");
final int numFinished=tilesFinishedAtomic.getAndIncrement();
// final double dprogr= (1.0+numFinished)/numberOfKernels;
if (numFinished % (numberOfKernels/50+1) == 0) {
// System.out.print(numFinished);
SwingUtilities.invokeLater(new Runnable() {
public void run() {
// System.out.println(" --- "+numFinished+"("+numberOfKernels+"): "+dprogr);
IJ.showProgress(numFinished, numberOfKernels);
}
});
}
}
}
};
}
startAndJoin(threads);
// this.debugLevel=wasDebugLevel;
IJ.showProgress(tilesFinishedAtomic.get(), numberOfKernels);
}
// System.out.println("tilesFinishedAtomic.get()="+tilesFinishedAtomic.get()+", numberOfKernels="+numberOfKernels);
if (updateStatus) IJ.showStatus("Reducing sampling aliases DONE");
IJ.showProgress(1.0);
/* prepare result stack to return */
ImageStack outStack=new ImageStack(imgWidth,imgHeight);
for (chn=0;chn<nChn;chn++) {
outStack.addSlice(imageStack.getSliceLabel(chn+1), outPixles[chn]);
}
debayerEnergyWidth= (debayerEnergy!=null)?tilesX:0; // for the image to be displayed externally
// if (debayerParameters.showEnergy) {
// SDFA_INSTANCE.showArrays (debayerEnergy,tilesX,tilesY, "Debayer-Energy");
// }
if (globalDebugLevel>0) System.out.println("Reducing sampling aliases done in "+IJ.d2s(0.000000001*(System.nanoTime()-startTime),3));
return outStack;
}
......@@ -273,6 +313,31 @@ public class DebayerScissors {
}
}
}
void nonSyncAccumulateSquareTile(
float [] pixels, // float pixels array to accumulate tile
double [] tile, // data to accumulate to the pixels array
int width, // width of pixels array
int x0, // left corner X
int y0) { // top corner Y
int length=tile.length;
int size=(int) Math.sqrt(length);
int i,j,x,y;
int height=pixels.length/width;
int index=0;
for (i=0;i<size;i++) {
y=y0+i;
if ((y>=0) && (y<height)) {
index=i*size;
for (j=0;j<size;j++) {
x=x0+j;
if ((x>=0) && (x<width)) pixels[y*width+x]+=tile [index];
index++;
}
}
}
}
synchronized void accumulateSquareTile(
double [] pixels, // float pixels array to accumulate tile
double [] tile, // data to accumulate to the pixels array
......
src/main/java/DenseCorrespondence.java
View file @ d531d201
......@@ -39,7 +39,7 @@ public class DenseCorrespondence {
private void disparitySweepTile (
public void disparitySweepTile ( // never used so far
int tileX,
int tileY,
CyclopeanTile [][] allCyclopeanMap,
......
src/main/java/Distortions.java
View file @ d531d201
......@@ -5989,6 +5989,8 @@ List calibration
imp.setProperty("channel", ""+numSensor);
imp.setProperty("comment_subcamera", "number of the subcamera with individual IP, starting with 0");
imp.setProperty("subcamera", ""+camerasInterface.getSubCamera(numSensor));
imp.setProperty("sensor_port",""+camerasInterface.getSensorPort(numSensor));
imp.setProperty("comment_subchannel", "number of the sensor port on a subcamera (0..2)");
imp.setProperty("subchannel", ""+camerasInterface.getSubChannel(numSensor));
imp.setProperty("comment_entrancePupilForward", "entrance pupil distance from the azimuth/radius/height, outwards in mm");
......
src/main/java/EyesisAberrations.java
View file @ d531d201
......@@ -2213,7 +2213,7 @@ public class EyesisAberrations {
public double [][][][] createPSFMap(
final MatchSimulatedPattern commonMatchSimulatedPattern, // to be cloned in threads, using common data
final ImagePlus imp_sel, // linearized Bayer mosaic image form the camera, GR/BG
final ImagePlus imp_sel, // linearized Bayer mosaic image from the camera, GR/BG
final int [][][] sampleList, // optional (or null) 2-d array: list of coordinate pairs (2d - to match existent pdfKernelMap structure)
final double overexposedAllowed, // fraction of pixels OK to be overexposed
final SimulationPattern.SimulParameters simulParameters,
......
src/main/java/EyesisCorrections.java
View file @ d531d201
......@@ -39,6 +39,8 @@ import ij.process.ImageProcessor;
import java.io.IOException;
import java.util.concurrent.atomic.AtomicInteger;
import javax.swing.SwingUtilities;
import loci.common.services.DependencyException;
import loci.common.services.ServiceException;
import loci.formats.FormatException;
......@@ -1712,7 +1714,44 @@ public class EyesisCorrections {
final AtomicInteger ai = new AtomicInteger(0);
final int numberOfKernels= tilesY*tilesX*nChn;
final int numberOfKernelsInChn=tilesY*tilesX;
int ichn,indx,dx,dy,tx,ty,li;
final int [] nonOverlapSeq = new int[numberOfKernels];
int [] nextFirstFindex=new int[16*nChn];
indx = 0;
li=0;
for (ichn=0;ichn<nChn;ichn++) for (dy=0;dy<4;dy++) for (dx=0;dx<4;dx++) {
for (ty=dy; ty < tilesY; ty+=4) for (tx=dx; tx < tilesX; tx+=4){
nonOverlapSeq[indx++] = ichn*numberOfKernelsInChn+ ty*tilesX + tx;
}
nextFirstFindex[li++] = indx;
}
final AtomicInteger aStopIndex = new AtomicInteger(0);
final AtomicInteger tilesFinishedAtomic = new AtomicInteger(1); // first finished will be 1
if (globalDebugLevel>1)
System.out.println("Eyesis_Corrections:convolveStackWithKernelStack :\n"+
"globalDebugLevel="+globalDebugLevel+"\n"+
"imgWidth="+imgWidth+"\n"+
"imgHeight="+imgHeight+"\n"+
"tilesX="+tilesX+"\n"+
"tilesY="+tilesY+"\n"+
"nChn="+nChn+"\n"+
"step="+step+"\n"+
"size="+size+"\n"+
"kernelSize="+kernelSize+"\n"+
"kernelWidth="+kernelWidth+"\n"+
"kernelNumHor="+kernelNumHor+"\n"+
"numberOfKernelsInChn="+numberOfKernelsInChn+"\n");
if (updateStatus) IJ.showStatus("Convolving image with kernels, "+nChn+" channels, "+tilesY+" rows");
final long startTime = System.nanoTime();
for (li = 0; li < nextFirstFindex.length; li++){
aStopIndex.set(nextFirstFindex[li]);
if (li>0){
ai.set(nextFirstFindex[li-1]);
}
// System.out.println("\n=== nextFirstFindex["+li+"] =" + nextFirstFindex[li]+" === ");
for (int ithread = 0; ithread < threads.length; ithread++) {
threads[ithread] = new Thread() {
public void run() {
......@@ -1724,16 +1763,20 @@ public class EyesisCorrections {
double [] doubleKernel= new double[size * size];
int chn,tileY,tileX;
int chn0=-1;
// double debug_sum;
// int i;
// double debug_sum;
// int i;
DoubleFHT fht_instance =new DoubleFHT(); // provide DoubleFHT instance to save on initializations (or null)
for (int nTile = ai.getAndIncrement(); nTile < numberOfKernels; nTile = ai.getAndIncrement()) {
// for (int nTile0 = ai.getAndIncrement(); nTile0 < numberOfKernels; nTile0 = ai.getAndIncrement()) {
for (int nTile0 = ai.getAndIncrement(); nTile0 < aStopIndex.get(); nTile0 = ai.getAndIncrement()) {
//aStopIndex
int nTile = nonOverlapSeq[nTile0];
chn=nTile/numberOfKernelsInChn;
tileY =(nTile % numberOfKernelsInChn)/tilesX;
tileX = nTile % tilesX;
if (tileX==0) {
if (updateStatus) IJ.showStatus("Convolving image with kernels, channel "+(chn+1)+" of "+nChn+", row "+(tileY+1)+" of "+tilesY);
if (globalDebugLevel>2) System.out.println("Processing kernels, channel "+(chn+1)+" of "+nChn+", row "+(tileY+1)+" of "+tilesY+" : "+IJ.d2s(0.000000001*(System.nanoTime()-startTime),3));
if (tileX < 4) {
int trow=(tileY+ ((tileY & 3) * tilesY))/4;
if (updateStatus) IJ.showStatus("Convolving image with kernels, channel "+(chn+1)+" of "+nChn+", row "+(trow+1)+" of "+tilesY);
if (globalDebugLevel>2) System.out.println("Processing kernels, channel "+(chn+1)+" of "+nChn+", row "+(trow+1)+" of "+tilesY+" : "+IJ.d2s(0.000000001*(System.nanoTime()-startTime),3));
}
if (chn!=chn0) {
......@@ -1763,9 +1806,9 @@ public class EyesisCorrections {
tileY); // vertical number of kernel to extract
/* zero pad twice the original size*/
doubleKernel=extendFFTInputTo (kernel, size);
// debug_sum=0;
// for (i=0;i<doubleKernel.length;i++) debug_sum+=doubleKernel[i];
// if (globalDebugLevel>1) System.out.println("kernel sum="+debug_sum);
// debug_sum=0;
// for (i=0;i<doubleKernel.length;i++) debug_sum+=doubleKernel[i];
// if (globalDebugLevel>1) System.out.println("kernel sum="+debug_sum);
//if ((tileY==tilesY/2) && (tileX==tilesX/2)) SDFA_INSTANCE.showArrays(doubleKernel,size,size, "doubleKernel-"+chn);
/* FHT transform of the kernel */
......@@ -1779,25 +1822,45 @@ public class EyesisCorrections {
/* accumulate result */
//if ((tileY==tilesY/2) && (tileX==tilesX/2)) SDFA_INSTANCE.showArrays(outTile,size,size, "out-"+chn);
/*This is synchronized method. It is possible to make threads to write to non-overlapping regions of the outPixels, but as the accumulation
* takes just small fraction of severtal FHTs, it should be OK - reasonable number of threads will spread and not "stay in line"
* takes just small fraction of several FHTs, it should be OK - reasonable number of threads will spread and not "stay in line"
*/
accumulateSquareTile(outPixels[chn], // float pixels array to accumulate tile
// Add smart synchronization - wait only if is too far ahead. First test - no synchronization at all
//accumulateSquareTile(
// System.out.print(tileY+":"+tileX+"/"+chn+"("+nTile0+"/"+nTile+") ");
// if (tileX < 4)System.out.println();
nonSyncAccumulateSquareTile(
outPixels[chn], // float pixels array to accumulate tile
outTile, // data to accumulate to the pixels array
imgWidth, // width of pixels array
(tileX-1)*step, // left corner X
(tileY-1)*step); // top corner Y
final int numFinished=tilesFinishedAtomic.getAndIncrement();
if (numFinished % (numberOfKernels/100+1) == 0) {
SwingUtilities.invokeLater(new Runnable() {
public void run() {
IJ.showProgress(numFinished,numberOfKernels);
}
});
}
//numberOfKernels
}
}
};
}
startAndJoin(threads);
if (globalDebugLevel > 1) System.out.println("Threads done at "+IJ.d2s(0.000000001*(System.nanoTime()-startTime),3));
}
if (updateStatus) IJ.showStatus("Convolution DONE");
if (globalDebugLevel > 1) System.out.println("Threads done in "+IJ.d2s(0.000000001*(System.nanoTime()-startTime),3));
IJ.showProgress(1.0);
/* prepare result stack to return */
ImageStack outStack=new ImageStack(imgWidth,imgHeight);
for (i=0;i<nChn;i++) {
outStack.addSlice(imageStack.getSliceLabel(i+1), outPixels[i]);
}
if (globalDebugLevel > 0) System.out.println("Convolution done in "+IJ.d2s(0.000000001*(System.nanoTime()-startTime),3));
return outStack;
}
/* Adds zero pixels around the image, "extending canvas" */
......@@ -1928,6 +1991,32 @@ public class EyesisCorrections {
}
}
}
void nonSyncAccumulateSquareTile(
float [] pixels, // float pixels array to accumulate tile
double [] tile, // data to accumulate to the pixels array
int width, // width of pixels array
int x0, // left corner X
int y0) { // top corner Y
int length=tile.length;
int size=(int) Math.sqrt(length);
int i,j,x,y;
int height=pixels.length/width;
int index=0;
for (i=0;i<size;i++) {
y=y0+i;
if ((y>=0) && (y<height)) {
index=i*size;
for (j=0;j<size;j++) {
x=x0+j;
if ((x>=0) && (x<width)) pixels[y*width+x]+=tile [index];
index++;
}
}
}
}
synchronized void accumulateSquareTile(
double [] pixels, // float pixels array to accumulate tile
double [] tile, // data to accumulate to the pixels array
......
src/main/java/Eyesis_Correction.java
View file @ d531d201
......@@ -3464,7 +3464,7 @@ private Panel panel1,panel2,panel3,panel4,panel5,panel5a, panel6,panel7,panelPos
continue;
}
convolutionKernelStack=imp_kernels.getStack();
if (DEBUG_LEVEL>1) System.out.println("Using kernel stack "+kernelPath+" for convolution with "+result[nFile][nChn][nSubChn].getTitle());
if (DEBUG_LEVEL>1) System.out.println("(1)Using kernel stack "+kernelPath+" for convolution with "+result[nFile][nChn][nSubChn].getTitle());
stack_d= convolveStackWithKernelStack(
stack, // stack with 3 colors/slices with the image
convolutionKernelStack, // stack with 3 colors/slices convolution kernels
......@@ -3492,7 +3492,7 @@ private Panel panel1,panel2,panel3,panel4,panel5,panel5a, panel6,panel7,panelPos
continue;
}
convolutionKernelStack=imp_kernels.getStack();
if (DEBUG_LEVEL>1) System.out.println("Using Gaussian stack "+kernelPath+" for convolution with "+result[nFile][nChn][nSubChn].getTitle());
if (DEBUG_LEVEL>1) System.out.println("(2)Using Gaussian stack "+kernelPath+" for convolution with "+result[nFile][nChn][nSubChn].getTitle());
stack_g= convolveStackWithKernelStack(
stack, // stack with 3 colors/slices with the image
convolutionKernelStack, // stack with 3 colors/slices convolution kernels
......@@ -3592,7 +3592,7 @@ private Panel panel1,panel2,panel3,panel4,panel5,panel5a, panel6,panel7,panelPos
continue;
}
convolutionKernelStack=imp_kernels.getStack();
if (DEBUG_LEVEL>1) System.out.println("Using Gaussian stack "+kernelPath+" for convolution with "+result[nFile][nChn][nSubChn].getTitle());
if (DEBUG_LEVEL>1) System.out.println("(3)Using Gaussian stack "+kernelPath+" for convolution with "+result[nFile][nChn][nSubChn].getTitle());
stack_g= convolveStackWithKernelStack(
stack, // stack with 3 colors/slices with the image
convolutionKernelStack, // stack with 3 colors/slices convolution kernels
......@@ -3977,7 +3977,6 @@ private Panel panel1,panel2,panel3,panel4,panel5,panel5a, panel6,panel7,panelPos
final int tilesY=imgHeight/step-1; // vertical number of overlapping tiles in the source image (should be expanded from the registerd one by "step" in each direction)
final int kernelWidth=kernelStack.getWidth();
final int kernelNumHor=kernelWidth/(size/2);
final int nChn=imageStack.getSize();
final float [][] outPixels=new float[nChn][length]; // GLOBAL same as input
// float [][] outPixels=new float[nChn][length]; // same as input
......@@ -3988,6 +3987,21 @@ private Panel panel1,panel2,panel3,panel4,panel5,panel5a, panel6,panel7,panelPos
final AtomicInteger ai = new AtomicInteger(0);
final int numberOfKernels= tilesY*tilesX*nChn;
final int numberOfKernelsInChn=tilesY*tilesX;
if (MASTER_DEBUG_LEVEL>1)
System.out.println("Eyesis_Correction:convolveStackWithKernelStack :\n"+
"MASTER_DEBUG_LEVEL="+MASTER_DEBUG_LEVEL+"\n"+
"imgWidth="+imgWidth+"\n"+
"imgHeight="+imgHeight+"\n"+
"tilesX="+tilesX+"\n"+
"tilesY="+tilesY+"\n"+
"step="+step+"\n"+
"kernelSize="+kernelSize+"\n"+
"tilesX="+tilesX+"\n"+
"tilesY="+tilesY+"\n"+
"kernelWidth="+kernelWidth+"\n"+
"kernelNumHor="+kernelNumHor+"\n"+
"numberOfKernelsInChn="+numberOfKernelsInChn+"\n");
final long startTime = System.nanoTime();
for (int ithread = 0; ithread < threads.length; ithread++) {
threads[ithread] = new Thread() {
......@@ -4153,8 +4167,8 @@ private Panel panel1,panel2,panel3,panel4,panel5,panel5a, panel6,panel7,panelPos
tileY = nTile /tilesX;
tileX = nTile % tilesX;
if (tileX==0) {
if (updateStatus) IJ.showStatus("Reducing sampling aliases, row "+(tileY+1)+" of "+tilesY);
if (MASTER_DEBUG_LEVEL>2) System.out.println("Reducing sampling aliases, row "+(tileY+1)+" of "+tilesY+" : "+IJ.d2s(0.000000001*(System.nanoTime()-startTime),3));
if (updateStatus) IJ.showStatus("(2)Reducing sampling aliases, row "+(tileY+1)+" of "+tilesY);
if (MASTER_DEBUG_LEVEL>1) System.out.println("(2)Reducing sampling aliases, row "+(tileY+1)+" of "+tilesY+" : "+IJ.d2s(0.000000001*(System.nanoTime()-startTime),3));
}
if ((tileY==yTileDebug) && (tileX==xTileDebug)) DEBUG_LEVEL=4;
......
src/main/java/JP46_Reader_camera.java
View file @ d531d201
......@@ -347,6 +347,7 @@ public class JP46_Reader_camera implements PlugIn, ActionListener {
if (demux) showImage=false;
double [] xtraExif=new double[1]; // ExposureTime
// System.out.println("imp_src is "+((imp_src!=null)?"not ":"")+"null");
try {
imp = openJpegOrGifUsingURL(url);
......
src/main/java/PixelMapping.java
View file @ d531d201
......@@ -25,10 +25,14 @@
**
*/
import java.awt.Point;
import java.awt.Rectangle;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.BitSet;
import java.util.Collections;
import java.util.Comparator;
import java.util.List;
import java.util.concurrent.atomic.AtomicInteger;
......@@ -135,11 +139,20 @@ public class PixelMapping {
if ((channel<0) || (channel>=this.sensors.length)) return -1;
return this.sensors[channel].getSubCamera();
}
/*
public int getSensorPort(int channel ){
if ((channel<0) || (channel>=this.sensors.length)) return -1;
return this.sensors[channel].getSensorPort();
}
*/
public boolean isChannelAvailable(int channel){
return (this.sensors != null) && (channel>=0) && (channel<this.sensors.length) && (this.sensors[channel]!=null);
}
/*
public int [] channelsForSubCamera(int subCamera){
if (this.sensors == null) return null;
int numChannels=0;
......@@ -149,6 +162,50 @@ public class PixelMapping {
for (int i=0;i<this.sensors.length;i++) if ((this.sensors[i]!=null) &&(this.sensors[i].subcamera==subCamera)) result[numChannels++]=i;
return result;
}
*/
// Updating for nc393. subCamera here is 0..9 for Eyesis4pi393 - 0-based index of the file, so it combines physical camera (separate IP)
// as stored in "subcamera" field of the calibration file and "sensor_port". sensor_port may start from non-0, so we need to count all combinations
public int [] channelsForSubCamera(int subCamera){
// ArrayList<ArrayList<ArrayList<Integer>>> camera_IPs = new ArrayList<ArrayList<ArrayList<Integer>>>();
ArrayList<Point> cam_port = new ArrayList<Point>();
for (int i=0;i<this.sensors.length;i++) if (this.sensors[i]!=null) {
Point cp = new Point(this.sensors[i].subcamera, this.sensors[i].sensor_port);
if (!cam_port.contains(cp)){
cam_port.add(cp);
}
}
Point [] cam_port_arr = cam_port.toArray(new Point[0]);
Arrays.sort(cam_port_arr, new Comparator<Point>() {
@Override
public int compare(Point o1, Point o2) {
return (o1.x>o2.x)? 1:((o1.x < o2.x)?-1:(o1.y > o2.y)? 1:((o1.y < o2.y)?-1:0));
}
});
// for (int i=0; i<cam_port_arr.length;i++){
// System.out.println("----- physical camera #"+cam_port_arr[i].x+", sensor_port="+cam_port_arr[i].y);
// }
System.out.println("----- This filename subcamera "+subCamera+": physical camera "+cam_port_arr[subCamera].x+", sensor_port "+cam_port_arr[subCamera].y);
if (subCamera >= cam_port_arr.length) {
System.out.println("Error: Subcamera "+subCamera+" > that total namera of sensor ports in the system = "+cam_port_arr.length);
return null;
}
if (this.sensors == null) return null;
int numChannels=0;
for (int i=0;i<this.sensors.length;i++) if (this.sensors[i]!=null) {
if (new Point(this.sensors[i].subcamera, this.sensors[i].sensor_port).equals(cam_port_arr[subCamera])) numChannels++;
}
int [] result=new int [numChannels];
numChannels=0;
for (int i=0;i<this.sensors.length;i++) if (this.sensors[i]!=null){
if (new Point(this.sensors[i].subcamera, this.sensors[i].sensor_port).equals(cam_port_arr[subCamera])) result[numChannels++]=i;
}
return result;
}
public void removeChannel(int channel){
if ((this.sensors != null) && (channel>=0) && (channel<this.sensors.length)) this.sensors[channel]=null;
}
......@@ -9403,6 +9460,7 @@ public class PixelMapping {
private BitSet innerMask=null;
private int []borderMask=null;
public int getNumberOfPlanes(){return this.maximums.length;}
@SuppressWarnings("unused")
public int getForegroundPlane(){return this.foregroundIndex;}
public double getPlaneDisparity (int plane){return this.maximums[plane][0];}
public void setPlaneDisparity (double disparity, int plane){this.maximums[plane][0]=disparity;}
......@@ -9441,6 +9499,7 @@ public class PixelMapping {
this.auxData=new float[n][];
for (int i=0;i<n;i++) this.auxData[i]=null;
}
@SuppressWarnings("unused")
public void resetAux(){
this.auxData=null;
}
......@@ -9448,6 +9507,7 @@ public class PixelMapping {
if (this.auxData==null) initAux(n+1);
this.auxData[n]=data;
}
@SuppressWarnings("unused")
public float [][] getAux (){
return this.auxData;
}
......@@ -9460,16 +9520,20 @@ public class PixelMapping {
this.likely=new float[this.numPlanes][];
for (int i=0;i<this.numPlanes;i++) this.likely[i]=null;
}
@SuppressWarnings("unused")
public void resetLikely(){
this.likely=null;
}
@SuppressWarnings("unused")
public void setLikely(int n, float [] data){
if (this.likely==null) initLikely();
this.likely[n]=data;
}
@SuppressWarnings("unused")
public float [][] getLikely (){
return this.likely;
}
@SuppressWarnings("unused")
public float [] getLikely (int n){
if ((this.likely==null) || (this.likely.length<=n)) return null;
return this.likely[n];
......@@ -9479,16 +9543,20 @@ public class PixelMapping {
this.unlikely=new float[this.numPlanes][];
for (int i=0;i<this.numPlanes;i++) this.unlikely[i]=null;
}
@SuppressWarnings("unused")
public void resetUnlikely(){
this.unlikely=null;
}
@SuppressWarnings("unused")
public void setUnlikely(int n, float [] data){
if (this.unlikely==null) initUnlikely();
this.unlikely[n]=data;
}
@SuppressWarnings("unused")
public float [][] getUnlikely(){
return this.unlikely;
}
@SuppressWarnings("unused")
public float [] getUnlikely(int n){
if ((this.unlikely==null) || (this.unlikely.length<=n)) return null;
return this.unlikely[n];
......@@ -9577,6 +9645,7 @@ public class PixelMapping {
* @param disparityTolerance - consider "this" as being withing disparityTolerance of disparity. NaN - do not filter by this
* @return
*/
@SuppressWarnings("unused")
public boolean [] getEnabledNonOccluded(
double disparityFG,
double disparity,
......@@ -15527,6 +15596,7 @@ public class PixelMapping {
public int channel= -1;
public int subcamera= -1;
public int subchannel=-1;
public int sensor_port=-1;
// TODO: add serial# (and temperature?)
public double azimuth; // azimuth of the lens entrance pupil center, degrees, clockwise looking from top
public double radius; // mm, distance from the rotation axis
......@@ -16094,6 +16164,9 @@ public class PixelMapping {
public int getChannel(){return this.channel;}
public int getSubChannel(){return this.subchannel;}
public int getSubCamera(){return this.subcamera;}
public int getSensorPort(){return this.sensor_port;}
public void setSensorDataFromImageStack(ImagePlus imp){
// int corrX=0,corrY=1,corrMask=2;
if (imp == null){
......@@ -16170,6 +16243,9 @@ public class PixelMapping {
// older files do not have these properties
if (imp.getProperty("subcamera")!=null) this.subcamera= Integer.parseInt((String) imp.getProperty("subcamera"));
if (imp.getProperty("subchannel")!=null) this.subchannel=Integer.parseInt((String) imp.getProperty("subchannel"));
if (imp.getProperty("sensor_port")!=null) this.sensor_port=Integer.parseInt((String) imp.getProperty("sensor_port"));
// now read the calibration data and mask
this.pixelCorrection=null;
......
src/main/java/deBayerScissors.java
View file @ d531d201
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