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imagej-elphel
Commit 4ffb8a32 authored by Andrey Filippov's avatar Andrey Filippov
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working on calculating grids for low frequency pattern

parent 78aea970
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Showing with 2675 additions and 1560 deletions
src/main/java/JP46_Reader_camera0.java
View file @ 4ffb8a32
......@@ -1413,9 +1413,13 @@ Exception in thread "Thread-3564" java.lang.ArrayIndexOutOfBoundsException: 8970
NodeList allNodes=doc.getDocumentElement().getElementsByTagName("*");
for (int i=0;i<allNodes.getLength();i++) {
String name= allNodes.item(i).getNodeName();
String value=allNodes.item(i).getFirstChild().getNodeValue();
imp.setProperty(name, value);
String value="";
try {
value=allNodes.item(i).getFirstChild().getNodeValue();
} catch(Exception e) {
}
imp.setProperty(name, value);
}
return true;
......
src/main/java/com/elphel/imagej/calibration/DistortionProcessConfiguration.java
View file @ 4ffb8a32
......@@ -23,15 +23,16 @@ package com.elphel.imagej.calibration;
**
*/
import ij.IJ;
import ij.Prefs;
import ij.gui.GenericDialog;
import java.io.File;
import java.io.FilenameFilter;
import java.util.Properties;
import com.elphel.imagej.common.WindowTools;
import ij.IJ;
import ij.Prefs;
import ij.gui.GenericDialog;
public class DistortionProcessConfiguration{
public String sourceDirectory="";
......@@ -207,4 +208,25 @@ import com.elphel.imagej.common.WindowTools;
return sourceFiles;
}
public String[] selectSourceSets() {
File dir= new File (this.sourceDirectory);
if (this.debugLevel>1) System.out.println("selectSourceSets, dir="+this.sourceDirectory);
if (!dir.exists()) {
String error="Source directory "+this.sourceDirectory+" does not exist.";
IJ.showMessage("No files selected");
if (this.debugLevel>1) System.out.println("selectSourceFiles() ERROR:"+error);
return null;
}
File [] sourceFileSets = dir.listFiles(new FilenameFilter() {
@Override
public boolean accept(File current, String name) {
return new File(current, name).isDirectory();
}
});
String [] sourceSets = new String[sourceFileSets.length];
for (int i=0;i<sourceSets.length;i++) sourceSets[i]=sourceFileSets[i].getPath();
return sourceSets;
}
}
src/main/java/com/elphel/imagej/calibration/EyesisAberrations.java
View file @ 4ffb8a32
package com.elphel.imagej.calibration;
import ij.IJ;
import ij.ImagePlus;
import ij.ImageStack;
import ij.Prefs;
import ij.gui.GenericDialog;
import ij.io.FileSaver;
import ij.io.Opener;
import ij.process.FloatProcessor;
import ij.process.ImageProcessor;
import java.awt.Rectangle;
import java.io.File;
import java.util.ArrayList;
......@@ -19,14 +9,22 @@ import java.util.concurrent.atomic.AtomicInteger;
import javax.swing.SwingUtilities;
import com.elphel.imagej.calibration.CalibrationFileManagement.MultipleExtensionsFileFilter;
import com.elphel.imagej.calibration.SimulationPattern.SimulParameters;
import com.elphel.imagej.common.DoubleFHT;
import com.elphel.imagej.common.DoubleGaussianBlur;
import com.elphel.imagej.common.ShowDoubleFloatArrays;
import com.elphel.imagej.common.WindowTools;
import com.elphel.imagej.jp4.JP46_Reader_camera;
import ij.IJ;
import ij.ImagePlus;
import ij.ImageStack;
import ij.Prefs;
import ij.gui.GenericDialog;
import ij.io.FileSaver;
import ij.io.Opener;
import ij.process.FloatProcessor;
import ij.process.ImageProcessor;
public class EyesisAberrations {
public double [][][][] pdfKernelMap=null;
JP46_Reader_camera JP4_INSTANCE= new JP46_Reader_camera(false);
......@@ -181,6 +179,7 @@ public class EyesisAberrations {
final int numberOfKernelsInChn=tilesY*tilesX;
for (int ithread = 0; ithread < threads.length; ithread++) {
threads[ithread] = new Thread() {
@Override
public void run() {
float [] pixels=null;
double [] kernel= new double[inverseParameters.dSize*inverseParameters.dSize];
......@@ -555,7 +554,7 @@ public class EyesisAberrations {
iy=-iy;
}
ix= (ix+size) % size;
floatPixels[i]=(float) clusterMap[iy][ix];
floatPixels[i]=clusterMap[iy][ix];
}
ip.setPixels(floatPixels);
ip.resetMinAndMax();
......@@ -639,8 +638,8 @@ public class EyesisAberrations {
row2=(fftsize-row1) %fftsize;
for (col1=0;col1 < fftsize;col1++) {
col2=(fftsize-col1) %fftsize;
fht_pixels[row1*fftsize+col1]=(double) (fft[row1][col1][0]-fft[row1][col1][1]);
fht_pixels[row2*fftsize+col2]=(double) (fft[row1][col1][0]+fft[row1][col1][1]);
fht_pixels[row1*fftsize+col1]=fft[row1][col1][0]-fft[row1][col1][1];
fht_pixels[row2*fftsize+col2]=fft[row1][col1][0]+fft[row1][col1][1];
}
}
return fht_pixels;
......@@ -1281,6 +1280,8 @@ public class EyesisAberrations {
int rslt=matchSimulatedPattern.calculateDistortions(
distortionParameters, //
patternDetectParameters,
patternDetectParameters.minGridPeriod/2,
patternDetectParameters.maxGridPeriod/2,
simulParameters,
colorComponents.equalizeGreens,
imp,
......@@ -2313,6 +2314,7 @@ public class EyesisAberrations {
for (int ithread = 0; ithread < threads.length; ithread++) {
// Concurrently run in as many threads as CPUs
threads[ithread] = new Thread() {
@Override
public void run() {
// Each thread processes a few items in the total list
......@@ -2399,6 +2401,7 @@ public class EyesisAberrations {
}
final int numFinished=tilesFinishedAtomic.getAndIncrement();
SwingUtilities.invokeLater(new Runnable() {
@Override
public void run() {
IJ.showProgress(numFinished,patternCells);
}
......@@ -2679,6 +2682,8 @@ public class EyesisAberrations {
if (matchSimulatedPattern.PATTERN_GRID==null) {
double[][] distortedPattern= matchSimulatedPattern.findPatternDistorted(input_bayer, // pixel array to process (no windowing!)
patternDetectParameters,
patternDetectParameters.minGridPeriod/2,
patternDetectParameters.maxGridPeriod/2,
true, //(greensToProcess==4), // boolean greens, // this is a pattern for combined greens (diagonal), adjust results accordingly
title); // title prefix to use for debug images
......@@ -4148,7 +4153,7 @@ if (globalDebugLevel>2)globalDebugLevel=0; //***********************************
ImageProcessor ip = new FloatProcessor(size,size);
float [] floatPixels = new float [size*size];
for (i=0;i<floatPixels.length;i++) {
floatPixels[i]=(float) clusterMap[i/size][i%size];
floatPixels[i]=clusterMap[i/size][i%size];
}
ip.setPixels(floatPixels);
ip.resetMinAndMax();
......@@ -4404,11 +4409,11 @@ if (globalDebugLevel>2)globalDebugLevel=0; //***********************************
if (debug) {
SDFA_INSTANCE.showArrays(debugPixels, title+"_mask_PSF");
double [] doublePixelsPSFCount=new double [pixelsPSF.length];
for (j=0;j<doublePixelsPSFCount.length;j++) doublePixelsPSFCount[j]=(double)pixelsPSFCount[j];
for (j=0;j<doublePixelsPSFCount.length;j++) doublePixelsPSFCount[j]=pixelsPSFCount[j];
SDFA_INSTANCE.showArrays(doublePixelsPSFCount, title+"_PSF_bin_count");
SDFA_INSTANCE.showArrays(pixelsPSFWeight, title+"_PSF_bin_weight");
double [] doubleContrastCache=new double [contrastCache.length];
for (j=0;j<doubleContrastCache.length;j++) doubleContrastCache[j]=(double)((contrastCache[j]>=0.0)?contrastCache[j]:-0.00001);
for (j=0;j<doubleContrastCache.length;j++) doubleContrastCache[j]=(contrastCache[j]>=0.0)?contrastCache[j]:-0.00001;
SDFA_INSTANCE.showArrays(doubleContrastCache, title+"_ContrastCache");
}
return pixelsPSF;
......@@ -4988,6 +4993,7 @@ if (globalDebugLevel>2)globalDebugLevel=0; //***********************************
this.thresholdHigh = thresholdHigh;
this.thresholdLow = thresholdLow;
}
@Override
public OTFFilterParameters clone() {
return new OTFFilterParameters(
this.deconvInvert,
......@@ -5076,6 +5082,7 @@ if (globalDebugLevel>2)globalDebugLevel=0; //***********************************
}
@Override
public PSFParameters clone(){
return new PSFParameters(
this.minContrast,
......
src/main/java/com/elphel/imagej/calibration/Goniometer.java
View file @ 4ffb8a32
......@@ -668,6 +668,8 @@ horizontal axis:
// allow more of grid around pointers?
distortionParameters, //
this.patternDetectParameters,
this.patternDetectParameters.minGridPeriod/2,
this.patternDetectParameters.maxGridPeriod/2,
simulParameters,
equalizeGreens, imp_eq,
this.laserPointers, // null, //LASER_POINTERS, //
......@@ -841,6 +843,8 @@ horizontal axis:
// allow more of grid around pointers?
distortionParameters, //
this.patternDetectParameters,
this.patternDetectParameters.minGridPeriod/2,
this.patternDetectParameters.maxGridPeriod/2,
simulParameters,
equalizeGreens, imp_eq,
this.laserPointers, // null, //LASER_POINTERS, //
......
src/main/java/com/elphel/imagej/calibration/LensAdjustment.java
View file @ 4ffb8a32
......@@ -25,7 +25,6 @@ package com.elphel.imagej.calibration;
import java.awt.Rectangle;
import java.util.Properties;
import com.elphel.imagej.calibration.SimulationPattern.SimulParameters;
import com.elphel.imagej.common.ShowDoubleFloatArrays;
import com.elphel.imagej.common.WindowTools;
......@@ -136,6 +135,8 @@ public class LensAdjustment {
null, // is not used in update mode
distortionParameters, //
patternDetectParameters,
patternDetectParameters.minGridPeriod/2,
patternDetectParameters.maxGridPeriod/2,
simulParameters,
equalizeGreens,
imp_eq, // image to process
......@@ -158,6 +159,8 @@ public class LensAdjustment {
numAbsolutePoints=matchSimulatedPattern.calculateDistortions( // allow more of grid around pointers?
distortionParameters, //
patternDetectParameters,
patternDetectParameters.minGridPeriod/2,
patternDetectParameters.maxGridPeriod/2,
simulParameters,
equalizeGreens,
imp_eq,
......@@ -806,6 +809,7 @@ public class LensAdjustment {
this.reportTemperature=reportTemperature;
this.showLegacy=showLegacy;
}
@Override
public FocusMeasurementParameters clone(){
return new FocusMeasurementParameters(
this.gridGeometryFile,
......
src/main/java/com/elphel/imagej/common/DoubleFHT.java
View file @ 4ffb8a32
......@@ -124,15 +124,7 @@ public class DoubleFHT {
public boolean transform(double [] data, boolean inverse) {
//IJ.log("transform: "+maxN+" "+inverse);
updateMaxN(data);
// maxN = (int) Math.sqrt(data.length);
// if ((S==null) || (S.length!=(maxN/4))) {
// makeSinCosTables(maxN);
// makeBitReverseTable(maxN);
// tempArr = new double[maxN];
// }
// float[] fht = (float[])getPixels();
rc2DFHT(data, inverse, this.maxN);
// isFrequencyDomain = !inverse;
return true;
}
......@@ -141,13 +133,7 @@ public class DoubleFHT {
double lowPass){
return createFrequencyFilter(null,highPass,lowPass);
}
/* public double []createFrequencyFilter(
double [] data,
double highPass,
double lowPass){
return createFrequencyFilter(data.length,highPass,lowPass);
}
*/
public double [] createFrequencyFilter(
double [] data, //int n,
double highPass,
......@@ -155,7 +141,7 @@ public class DoubleFHT {
if (data !=null) updateMaxN(data);
// int n;
if ((this.freqMask!=null) && (this.freqPass[0]==highPass) && (this.freqPass[0]==lowPass)) return this.freqMask;
if ((this.freqMask!=null) && (this.freqPass[0]==highPass) && (this.freqPass[1]==lowPass)) return this.freqMask;
this.freqMask= new double [(this.maxN+1)*this.maxN/2+1];
double [] lo=new double[this.maxN];
double [] hi=new double[this.maxN];
......@@ -177,12 +163,9 @@ public class DoubleFHT {
if (j>this.maxN/2) j=this.maxN-j;
this.freqMask[index]=(1.0-hi[i]*hi[j])*lo[i]*lo[j];
}
// this.freqMaskN=n;
this.freqPass=new double[2];
this.freqPass[0]=highPass;
this.freqPass[1]=lowPass;
// this.freqMask_cache[this.ln2]=this.freqMask;
// this.freqPass_cache[this.ln2]=this.freqPass;
return this.freqMask;
}
/**
......@@ -195,49 +178,6 @@ public class DoubleFHT {
*/
public double [] shift(double [] data, double dx, double dy){
return shift(data, 1, dx, dy);
/*
updateMaxN(data);
double sX=2*Math.PI*dx/this.maxN;
double sY=2*Math.PI*dy/this.maxN;
int halfN=this.maxN/2;
double [] cosDX = new double[this.maxN];
double [] sinDX = new double[this.maxN];
double [] cosDY = new double[halfN+1];
double [] sinDY = new double[halfN+1];
for (int i=0;i<=halfN;i++){ // need less?
cosDX[i]=Math.cos(sX*i);
sinDX[i]=Math.sin(sX*i);
cosDY[i]=Math.cos(sY*i);
sinDY[i]=Math.sin(sY*i);
}
for (int i=1;i<halfN;i++){ // need less?
cosDX[this.maxN-i]= cosDX[i];
sinDX[this.maxN-i]=-sinDX[i];
}
swapQuadrants(data);
if (!transform(data,false)) return null; // direct FHT
for (int row =0; row<=halfN; row++) {
int rowMod = (this.maxN - row) % this.maxN;
int maxCol=(row<halfN)?(this.maxN-1):halfN;
for (int col=0; col<=maxCol; col++) {
int colMod = (this.maxN - col) % this.maxN;
int index= row * this.maxN + col;
int indexMod=rowMod * this.maxN + colMod;
double re=0.5*(data[index]+data[indexMod]);
double im=0.5*(data[index]-data[indexMod]);
if ((col==halfN) || (row==halfN)) im=0;
double cosDelta= cosDX[col]*cosDY[row] - sinDX[col]*sinDY[row]; // cos(deltaX)*cos(deltaY)-sin(deltaX)*sin(deltaY)
double sinDelta= sinDX[col]*cosDY[row] + cosDX[col]*sinDY[row]; // sin(deltaX)*cos(deltaY)+cos(deltaX)*sin(deltaY)
double reMod=re*cosDelta-im*sinDelta;
double imMod=re*sinDelta+im*cosDelta;
data[index]= reMod+imMod;
data[indexMod]=reMod-imMod;
}
}
if (!transform(data,true)) return null; // inverse FHT
swapQuadrants(data);
return data;
*/
}
/**
* Upsample input array by padding in the frequency domain
......@@ -247,30 +187,6 @@ public class DoubleFHT {
*/
public double [] upsample( double [] first, int scale){
return shift (first, scale, 0.0, 0.0);
/*
if (scale <=1) return first.clone();
updateMaxN(first);
swapQuadrants(first);
if (!transform(first,false)) return null; // direct FHT
int halfN=this.maxN/2;
int shift=this.maxN*(scale-1);
int scaledN=this.maxN*scale;
double [] result =new double [first.length*scale*scale];
for (int i=0;i<result.length;i++) result [i]=0.0;
double scale2=scale*scale;
for (int i=0;i<first.length;i++){
int iy=i/this.maxN;
int ix=i%this.maxN;
if (ix>halfN) ix+=shift;
if (iy>halfN) iy+=shift;
result[scaledN*iy+ix]=scale2*first[i];
}
updateMaxN(result);
if (!transform(result,true)) return null; // inverse FHT
swapQuadrants(result);
return result;
*/
}
/**
......@@ -408,6 +324,54 @@ public class DoubleFHT {
swapQuadrants(first);
return first;
}
public double [] phaseCorrelate (
double [] first,
double phaseCoeff,
double high_pass,
double low_pass) { // high/low pass filtering
return phaseCorrelate(first, phaseCoeff, high_pass, low_pass, null);
}
public double [] phaseCorrelate (
double [] first,
double phaseCoeff,
double high_pass,
double low_pass, // high/low pass filtering
double [] fht_save){ //null-OK
updateMaxN(first);
double [] filter = null;
if ((high_pass >0) || (low_pass > 0)) {
filter = createFrequencyFilter(high_pass, low_pass);
}
return phaseCorrelate(first, phaseCoeff, filter,fht_save);
}
public double [] phaseCorrelate (
double [] first,
double phaseCoeff,
double [] filter) { // high/low pass filtering
return phaseCorrelate(first, phaseCoeff, filter, null);
}
public double [] phaseCorrelate (
double [] first,
double phaseCoeff,
double [] filter, // high/low pass filtering
double [] fht_save){ //null-OK
updateMaxN(first);
swapQuadrants(first);
if (!transform(first,false)) return null; // direct FHT
if (fht_save != null) {
System.arraycopy(first, 0, fht_save, 0, first.length);
}
first= phaseMultiplyNorm(first, first, phaseCoeff); // correlation, not convolution
if (filter!=null) multiplyByReal(first, filter);
transform(first,true) ; // inverse transform
swapQuadrants(first);
return first;
}
//
public double [] applyFreqFilter(
double [] first,
double [] filter
......@@ -2024,6 +1988,7 @@ public class DoubleFHT {
return product;
}
public double [] phaseMultiply(double [] h1, double [] h2, double phaseCoeff) {
int rowMod, colMod;
double h2e, h2o,d;
......@@ -2041,6 +2006,54 @@ public class DoubleFHT {
return product;
}
public double [] phaseMultiplyNorm(double [] h1, double [] h2, double phaseCoeff) {
int size = maxN;
int size2 = size >> 1;
int size21 = size*size2;
int rowMod, colMod, base, baseMod;
double h2e, h2o;
double[] product = new double[size*size];
for (int r =0; r<size; r++) {
rowMod = (size - r) % size;
for (int c=0; c<size; c++) {
colMod = (size - c) % size;
h2e = (h2[r * size + c] + h2[rowMod * size + colMod]) / 2;
h2o = (h2[r * size + c] - h2[rowMod * size + colMod]) / 2;
product[r * size + c] = (h1[r * size + c] * h2e - h1[rowMod * size + colMod] * h2o);
}
}
double [] amplitude = calculateAmplitudeHalf(product);
double avg_ampl = 0.0;
for (int row = 1; row < size2; row++) {
base = row*size;
for (int col = 0; col < size; col++) {
avg_ampl += amplitude[col+base];
}
}
avg_ampl *= 2;
for (int col = 0; col < size; col++) {
avg_ampl += amplitude[col] + amplitude[col + size21];
}
avg_ampl /= size*size;
double aoffs = (1.0 - phaseCoeff) * avg_ampl;
double ampl;
for (int row = 0; row <= size2; row++) {
base = row*size;
rowMod = (size - row) % size;
baseMod = rowMod * size;
for (int col = 0; col < size; col++) {
ampl = phaseCoeff * amplitude[col+base] + aoffs;
product[col+base] /= ampl;
if ((row > 0) && (row < size2)) {
colMod = (size - col) % size;
product[colMod + baseMod] /= ampl;
}
}
}
return product;
}
// Multiply by real array (i.e. filtering in frequency domain). Array m length should be at least maxN*maxN/2+1
public void multiplyByReal(double [] h, double [] m) {
......@@ -2094,6 +2107,17 @@ public class DoubleFHT {
swapQuadrants(amp);
return amp;
}
public double [] calculateAmplitudeHalf(double [] fht) {
int size=(int) Math.sqrt(fht.length);
int size2 = (size >>1) +1;
double[] amp = new double[size* size2];
for (int row=0; row<size2; row++) {
amplitude(row, size, fht, amp);
}
return amp;
}
public double [] calculateAmplitude2(double [] fht) {
int size=(int) Math.sqrt(fht.length);
double[] amp = new double[size*size];
......@@ -2133,8 +2157,6 @@ public class DoubleFHT {
row2=(fftsize-row1) %fftsize;
for (col1=0;col1<fftsize;col1++) {
col2=(fftsize-col1) %fftsize;
// fftHalf[row1][col1]= complex( 0.5*(fht_pixels[row1*fftsize+col1] + fht_pixels[row2*fftsize+col2]),
// 0.5*(fht_pixels[row2*fftsize+col2] - fht_pixels[row1*fftsize+col1]));
fftHalf[row1][col1][0]= 0.5*(fht_pixels[row1*fftsize+col1] + fht_pixels[row2*fftsize+col2]);
fftHalf[row1][col1][1]= 0.5*(fht_pixels[row2*fftsize+col2] - fht_pixels[row1*fftsize+col1]);
}
......
src/main/java/com/elphel/imagej/common/ShowDoubleFloatArrays.java
View file @ 4ffb8a32
......@@ -112,6 +112,30 @@ import ij.process.ImageProcessor;
return;
} else showArrays(pixels, width, height, titles);
}
public void showComplex(double[][][] cpixels, String title) {
int height = cpixels.length;
int width = cpixels[0].length;
double [][]pixels = new double [height*width][];
int indx = 0;
for (int y = 0; y < height; y++) {
for (int x = 0; x < width; x++) {
pixels[indx++] = cpixels[y][x];
}
}
showComplex(pixels, width, title);
}
public void showComplex(double[][] cpixels, int width, String title) {
int height = cpixels.length/width;
double [][]pixels = new double [2][cpixels.length];
for (int i = 0; i< cpixels.length; i++) {
pixels[0][i]= cpixels[i][0];
pixels[1][i]= cpixels[i][1];
}
String [] titles = {"Re", "Im"};
showArrays(pixels, width, height, true, title, titles);
}
public void showArrays(float[][] pixels, int width, int height, boolean asStack, String title, String [] titles) {
int i,j;
......
src/main/java/com/elphel/imagej/jp4/JP46_Reader_camera.java
View file @ 4ffb8a32
......@@ -1407,7 +1407,12 @@ Exception in thread "Thread-3564" java.lang.ArrayIndexOutOfBoundsException: 8970
NodeList allNodes=doc.getDocumentElement().getElementsByTagName("*");
for (int i=0;i<allNodes.getLength();i++) {
String name= allNodes.item(i).getNodeName();
String value=allNodes.item(i).getFirstChild().getNodeValue();
String value="";
try {
value=allNodes.item(i).getFirstChild().getNodeValue();
} catch(Exception e) {
}
imp.setProperty(name, value);
}
......
src/main/java/com/elphel/imagej/lwir/LwirReaderParameters.java
View file @ 4ffb8a32
......@@ -26,10 +26,14 @@
*/
package com.elphel.imagej.lwir;
import java.io.File;
import java.io.FilenameFilter;
import java.util.Properties;
import com.elphel.imagej.common.GenericJTabbedDialog;
import ij.Prefs;
public class LwirReaderParameters {
private boolean parameters_updated = false;
protected int avg_number = 4; // number of measurements to average
......@@ -49,6 +53,7 @@ public class LwirReaderParameters {
protected double vnir_gain_g = 2.0;
protected double vnir_gain_rg = 0.7705; // 1.116; halogen/fluorescent
protected double vnir_gain_bg = 2.401; // 1.476;
protected boolean [] selected_channels = {true, true, true, true, true, true, true, true};
/*
protected double [] vnir_exp_corr = {1.0, 1.0, 1.0, 1.0};
......@@ -106,6 +111,7 @@ public class LwirReaderParameters {
properties.setProperty(prefix+"max_mismatch_ms", this.max_mismatch_ms+"");
properties.setProperty(prefix+"max_frame_diff", this.max_frame_diff+"");
properties.setProperty(prefix+"debug_level", this.debug_level+"");
properties.setProperty(prefix+"selected_channels", arr_to_str(this.selected_channels));
}
......@@ -134,6 +140,7 @@ public class LwirReaderParameters {
if (properties.getProperty(prefix+"max_mismatch_ms")!=null) this.max_mismatch_ms=Double.parseDouble(properties.getProperty(prefix+"max_mismatch_ms"));
if (properties.getProperty(prefix+"max_frame_diff")!=null) this.max_frame_diff=Integer.parseInt(properties.getProperty(prefix+"max_frame_diff"));
if (properties.getProperty(prefix+"debug_level")!=null) this.debug_level=Integer.parseInt(properties.getProperty(prefix+"debug_level"));
if (properties.getProperty(prefix+"selected_channels")!=null) this.selected_channels=str_to_barr(properties.getProperty(prefix+"selected_channels"));
parameters_updated = true;
}
@Override
......@@ -163,6 +170,7 @@ public class LwirReaderParameters {
lrp.max_mismatch_ms= this.max_mismatch_ms;
lrp.max_frame_diff= this.max_frame_diff;
lrp.debug_level= this.debug_level;
lrp.selected_channels = this.selected_channels.clone();
return lrp;
}
......@@ -198,7 +206,8 @@ public class LwirReaderParameters {
(lrp.vnir_lag == this.vnir_lag) &&
(lrp.max_mismatch_ms == this.max_mismatch_ms) &&
(lrp.max_frame_diff == this.max_frame_diff) &&
(lrp.debug_level == this.debug_level);
(lrp.debug_level == this.debug_level) &&
(java.util.Arrays.equals(lrp.selected_channels, this.selected_channels));
}
@Override
......@@ -225,6 +234,7 @@ public class LwirReaderParameters {
result = prime * result + arr_to_str(vnir_exp_corr).hashCode();
result = prime * result + arr_to_str(vnir_gcorr_rbgb).hashCode();
result = prime * result + (new Integer(lwir_trig_dly)).hashCode();
result = prime * result + arr_to_str(selected_channels).hashCode();
// next are not needed to be programmed to the cameras
// result = prime * result + (new Integer(vnir_lag)).hashCode();
// result = prime * result + (new Double(max_mismatch_ms)).hashCode();
......@@ -241,7 +251,7 @@ public class LwirReaderParameters {
gd.addStringField ("LWIR channels", arr_to_str(this.lwir_channels), 20, "Space-separated list of used LWIR camera channels, such as '0 1 2 3'");
gd.addStringField ("VNIR channels", arr_to_str(this.vnir_channels), 20, "Space-separated list of used visible range camera channels, such as '0 1 2 3'");
gd.addCheckbox ("LWIR telemetry", this.lwir_telemetry, "Set LWIR sesnors to provide telemetry data in the last 2 lines (may become mandatory later)");
gd.addNumericField("VNIR quality", this.vnir_quality, 3,6,"ms", "Visible range camera JPEG compression quality (all channels)");
gd.addNumericField("VNIR quality", this.vnir_quality, 3,6,"%", "Visible range camera JPEG compression quality (all channels)");
gd.addCheckbox ("VNIR undo white balance", this.vnir_scale, "Undo in-camera white balancing");
gd.addCheckbox ("VNIR autoexposure", this.vnir_autoexp, "Enable autoexposure for the visible range camera");
gd.addNumericField("VNIR vnir_max_autoexp_ms", this.vnir_max_autoexp_ms, 3,6,"ms", "Visible range camera maximal exposure in autoexposure mode");
......@@ -257,6 +267,7 @@ public class LwirReaderParameters {
gd.addNumericField("Max mismatch", this.max_mismatch_ms, 3,6,"ms","Maximal mismatch between image timestamps. Larger mismatch requires LWIR sinsor reinitialization");
gd.addNumericField("Max frame diff",this.max_frame_diff, 0,3,"","Maximal difference in frames between simultaneously acquired channels as calculated from the timestamps");
gd.addNumericField("Debug level", this.debug_level, 0,3,"","Image acquisition log level: -3: OFF, -2:FATAL, -1:ERROR, 0:WARN, 1:INFO, 2:DEBUG");
gd.addStringField ("Selected channels", arr_to_str(this.selected_channels), 20, "Space-separated channel selection (1 - selected, 0 - unselected)");
}
public void dialogAnswers(GenericJTabbedDialog gd) {
......@@ -284,6 +295,7 @@ public class LwirReaderParameters {
this.max_mismatch_ms = gd.getNextNumber();
this.max_frame_diff = (int) gd.getNextNumber();
this.debug_level = (int) gd.getNextNumber();
this.selected_channels = str_to_barr(gd.getNextString());
parameters_updated = true;
}
......@@ -307,6 +319,80 @@ public class LwirReaderParameters {
parameters_updated = false;
}
public boolean [] getSelected(){
return selected_channels;
}
public boolean [] getSelectedLwir(){
boolean [] sel = selected_channels.clone();
for (int i = lwir_channels.length; i < sel.length; i++ ) {
sel[i] = false;
}
return sel;
}
public boolean [] getSelectedVnir(){
boolean [] sel = selected_channels.clone();
for (int i = 0; i < lwir_channels.length; i++ ) {
sel[i] = false;
}
return sel;
}
public String [] getSourceFilesFlat(String [] sets, boolean[] channels) {
int num_sel = 0;
for (boolean s: channels) if (s) num_sel++;
String [] files = new String [sets.length * num_sel];
int indx = 0;
for (String set:sets) {
for (int i = 0; i < channels.length; i++) if (channels[i]) {
String file_base = set;
if (set.indexOf(Prefs.getFileSeparator()) >=0) {
file_base = set.substring(set.lastIndexOf(Prefs.getFileSeparator())+1);
}
files[indx++] =set + Prefs.getFileSeparator()+ file_base+"_"+i+".tiff";
}
}
return files;
}
// Image set may have different timestamps, only lwir0 matches
public String [][] getSourceFiles(String [] sets, boolean[] channels) {
String [][] files = new String [sets.length][channels.length];
for (int nset= 0; nset < sets.length; nset++) {
// read all files in the directory
File set_dir = new File(sets[nset]);
File [] channel_files = set_dir.listFiles(new FilenameFilter() {
@Override
public boolean accept(File current, String name) {
if (!(new File(current, name).isFile()) || !name.endsWith(".tiff")) return false;
String base = name.substring(0, name.lastIndexOf(".tiff"));
int undr = base.lastIndexOf("_");
if (undr < 0) return false;
int chn = -1;
try {
chn = Integer.parseInt(base.substring(undr + 1));
} catch (Exception e) {
}
return chn >= 0;
}
});
for (File f: channel_files) {
String base = f.getName().substring(0, f.getName().lastIndexOf(".tiff"));
int undr = base.lastIndexOf("_");
int chn = Integer.parseInt(base.substring(undr + 1));
if ((chn >= 0) && (chn < channels.length) && channels[chn]) {
files[nset][chn] = f.getPath();
}
}
}
return files;
}
// --- internal methods
private String arr_to_str(int [] arr) {
......@@ -321,6 +407,23 @@ public class LwirReaderParameters {
return s.trim();
}
private String arr_to_str(boolean [] arr) {
String s = "";
for (boolean c:arr) s+= (c?1:0)+" ";
return s.trim();
}
private boolean [] str_to_barr(String s) {
int [] iarr = str_to_iarr(s);
if (iarr == null) return null;
boolean [] barr = new boolean [iarr.length];
for (int i = 0; i < barr.length; i++) {
barr[i] = iarr[i] != 0;
}
return barr;
}
private int [] str_to_iarr(String s) {
String [] sa;
if (s.indexOf(",") >= 0) {
......@@ -349,4 +452,22 @@ public class LwirReaderParameters {
return darr;
}
public boolean [] selectSourceChannels(){
return selectSourceChannels(selected_channels);
}
public boolean [] selectSourceChannels(boolean [] sel) {
GenericJTabbedDialog gd = new GenericJTabbedDialog("Set CLT parameters",300,500);
for (int i = 0; i < sel.length; i++) {
gd.addCheckbox ("Channel "+i, sel[i], "Enable processing camera channel "+i);
}
gd.showDialog();
if (gd.wasCanceled()) return null;
for (int i = 0; i < sel.length; i++) {
sel[i] = gd.getNextBoolean();
}
return sel;
}
}
src/main/java/com/elphel/imagej/readers/EyesisTiff.java
View file @ 4ffb8a32
......@@ -640,7 +640,7 @@ the type of pixel data in this file getPixelType()
}
// copied from JP46_Reader_camera.java
public ImagePlus encodeProperiesToInfo(ImagePlus imp){
public static ImagePlus encodeProperiesToInfo(ImagePlus imp){
String info="<?xml version=\"1.0\" encoding=\"UTF-8\"?><properties>";
Set<Object> jp4_set;
Properties jp4_prop;
......@@ -661,7 +661,7 @@ the type of pixel data in this file getPixelType()
return imp;
}
public boolean decodeProperiesFromInfo(ImagePlus imp){
public static boolean decodeProperiesFromInfo(ImagePlus imp){
if (imp.getProperty("Info")==null) return false;
String xml= (String) imp.getProperty("Info");
......@@ -684,11 +684,15 @@ the type of pixel data in this file getPixelType()
NodeList allNodes=doc.getDocumentElement().getElementsByTagName("*");
for (int i=0;i<allNodes.getLength();i++) {
String name= allNodes.item(i).getNodeName();
String value=allNodes.item(i).getFirstChild().getNodeValue();
// System.out.print(name+" -> ");
String value = "";
try {
value=allNodes.item(i).getFirstChild().getNodeValue();
} catch (Exception e) {
}
// System.out.println(value);
imp.setProperty(name, value);
}
return true;
}
......
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