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Commit 3272bf8a authored by Andrey Filippov's avatar Andrey Filippov
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X-cam alignment calculation

parent 739921ca
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Showing with 1562 additions and 1349 deletions
src/main/java/Aberration_Calibration.java
View file @ 3272bf8a
......@@ -25,27 +25,59 @@
**
*/
import ij.*;
import ij.io.*;
import ij.process.*;
import ij.gui.*;
import ij.plugin.frame.*;
import ij.text.TextWindow;
import java.awt.*;
import java.awt.event.*;
import java.io.*; // FIle
import java.util.Properties;
import javax.swing.*; // TODO: modify methods that depend on it, use class CalibrationFileManagement
import java.util.*;
import java.awt.Button;
import java.awt.Color;
import java.awt.Frame;
import java.awt.GridLayout;
import java.awt.Panel;
import java.awt.Rectangle;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.awt.event.WindowEvent;
// FIle
import java.io.BufferedReader;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.FileOutputStream;
import java.io.FileReader;
import java.io.FilenameFilter;
import java.io.IOException;
import java.io.InputStream;
import java.io.OutputStream;
import java.io.PrintWriter;
import java.io.StringWriter;
import java.util.ArrayList;
import java.util.List;
import java.util.Map;
import java.util.Properties;
import java.util.TreeMap;
import java.util.concurrent.atomic.AtomicInteger;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
// TODO: modify methods that depend on it, use class CalibrationFileManagement
import javax.swing.JFileChooser;
import Jama.Matrix; // Download here: http://math.nist.gov/javanumerics/jama/
import ij.IJ;
import ij.ImageJ;
import ij.ImagePlus;
import ij.ImageStack;
import ij.Prefs;
import ij.WindowManager;
import ij.gui.GUI;
import ij.gui.GenericDialog;
import ij.gui.Overlay;
import ij.gui.Roi;
import ij.io.FileSaver;
import ij.io.OpenDialog;
import ij.io.Opener;
import ij.plugin.frame.PlugInFrame;
import ij.process.FloatProcessor;
import ij.process.ImageConverter;
import ij.process.ImageProcessor;
import ij.text.TextWindow;
public class Aberration_Calibration extends PlugInFrame implements ActionListener {
private static final long serialVersionUID = 1040236897357482595L;
......@@ -707,6 +739,7 @@ public static MatchSimulatedPattern.DistortionParameters DISTORTION =new MatchSi
addButton("Configure Distortion/Location",panelLens,color_configure);
addButton("Configure Eyesis4pi",panelLens,color_configure);
addButton("List Eyesis4pi",panelLens,color_report);
addButton("List X-cam",panelLens,color_report);
addButton("Process Lens Distortion",panelLens);
addButton("Configure Lasers",panelLens,color_configure);
addButton("Manual laser pointers",panelLens,color_debug);
......@@ -997,6 +1030,7 @@ if (MORE_BUTTONS) {
b.addKeyListener(IJ.getInstance());
panel.add(b);
}
@Override
public void processWindowEvent(WindowEvent e) {
super.processWindowEvent(e);
if (e.getID()==WindowEvent.WINDOW_CLOSING) {
......@@ -1004,6 +1038,7 @@ if (MORE_BUTTONS) {
}
}
@Override
public void actionPerformed(ActionEvent e) {
String label = e.getActionCommand();
if (label.equals("Abort")) {
......@@ -1133,13 +1168,6 @@ if (MORE_BUTTONS) {
UPDATE_STATUS,
DEBUG_LEVEL
);
/*// Not needed, controlled by parameters
if (ABERRATIONS_PARAMETERS.autoLoadPaths()[3]!=null) {
// Re-read configuration file to overwrite camera parameters restored with calibration files
if (DEBUG_LEVEL>0) System.out.println("Re-reading configuration to overwrite camera parameters restored from the sensor calibration files");
loadProperties(confPath,PROCESS_PARAMETERS.kernelsDirectory,PROCESS_PARAMETERS.useXML, PROPERTIES);
}
*/
if (dcdUpdated) DISTORTION_CALIBRATION_DATA=LENS_DISTORTIONS.fittingStrategy.distortionCalibrationData;
if (ABERRATIONS_PARAMETERS.autoReCalibrate){
if (LENS_DISTORTIONS.fittingStrategy==null) {
......@@ -1243,8 +1271,6 @@ if (MORE_BUTTONS) {
imp_sel); // reuse the same image window
// Remove for old method?
matchSimulatedPattern= new MatchSimulatedPattern(DISTORTION.FFTSize);
// matchSimulatedPattern.invalidateFlatFieldForGrid(); //It is already reset, no need to do it again
// matchSimulatedPattern.invalidateFocusMask();
matchSimulatedPattern.calculateDistortions(
DISTORTION, //
......@@ -1263,17 +1289,6 @@ if (MORE_BUTTONS) {
DISTORTION.loop_debug_level, // debug level
noMessageBoxes);
/*
SIM_ARRAY= simulateGridAll (
imp_sel.getWidth(),
imp_sel.getHeight(),
matchSimulatedPattern.getDArray(),
2, // gridFrac, // number of grid steps per pattern full period
SIMUL,
THREADS_MAX,
UPDATE_STATUS,
DISTORTION.loop_debug_level); // debug level
*/
SIM_ARRAY= (new SimulationPattern(SIMUL)).simulateGridAll (
imp_sel.getWidth(),
imp_sel.getHeight(),
......@@ -1288,7 +1303,6 @@ if (MORE_BUTTONS) {
createPSFMap(
matchSimulatedPattern,
matchSimulatedPattern.applyFlatField (imp_sel), // if grid is flat-field calibrated, apply it
// imp_sel, // linearized Bayer mosaic image form the camera, GR/BG
null, // int [][][] sampleList, // optional (or null) 2-d array: list of coordinate pairs (2d - to match existent PSF_KERNEL_MAP structure)
MULTIFILE_PSF.overexposedMaxFraction,
SIMUL, //simulation parameters
......@@ -2295,7 +2309,7 @@ if (MORE_BUTTONS) {
return;
}
/* ======================================================================== */
if (label.equals("List Eyesis4pi")) {
if (label.equals("List Eyesis4pi") || label.equals("List X-cam")) {
DEBUG_LEVEL=MASTER_DEBUG_LEVEL;
System.out.println("DISTORTION_CALIBRATION_DATA="+((DISTORTION_CALIBRATION_DATA==null)?"null":" NOT null"));
System.out.println("+++++++++++ EYESIS_CAMERA_PARAMETERS.numStations="+EYESIS_CAMERA_PARAMETERS.numStations+
......@@ -2309,10 +2323,9 @@ if (MORE_BUTTONS) {
new DistortionCalibrationData(EYESIS_CAMERA_PARAMETERS);
if (DEBUG_LEVEL>1) System.out.println("+++++++++++ dcd.eyesisCameraParameters.numStations="+dcd.eyesisCameraParameters.numStations+
" +dcd.eyesisCameraParameters.goniometerHorizontal.length="+dcd.eyesisCameraParameters.goniometerHorizontal.length);
dcd.listCameraParameters();
dcd.listCameraParameters(label.equals("List X-cam"));
return;
}
/* ======================================================================== */
if (label.equals("Process Lens Distortion")) {
DEBUG_LEVEL=MASTER_DEBUG_LEVEL;
......@@ -12450,7 +12463,7 @@ if (MORE_BUTTONS) {
ImagePlus imp_psf = new ImagePlus(psfTitle, mergedStack);
imp_psf.getProcessor().resetMinAndMax();
imp_psf.setProperty("comment",focusMeasurementParameters.comment);
imp_psf.setProperty("timestamp", (String) imp_sel.getProperty("timestamp"));
imp_psf.setProperty("timestamp", imp_sel.getProperty("timestamp"));
if (!Double.isNaN(focusMeasurementParameters.sensorTemperature))
imp_psf.setProperty("sensorTemperature", ""+focusMeasurementParameters.sensorTemperature);
imp_psf.setProperty("px0", ""+lensDistortionParameters.px0);
......@@ -15744,6 +15757,7 @@ private double [][] jacobianByJacobian(double [][] jacobian, boolean [] mask) {
prefix= pref;
pattern = str;
}
@Override
public boolean accept (File dir, String name) {
if (prefix!=null) return (name.startsWith(prefix)) && (name.toLowerCase().endsWith(pattern.toLowerCase()));
return name.toLowerCase().endsWith(pattern.toLowerCase());
......@@ -16264,6 +16278,7 @@ private double [][] jacobianByJacobian(double [][] jacobian, boolean [] mask) {
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];
......@@ -16476,6 +16491,7 @@ private double [][] jacobianByJacobian(double [][] jacobian, boolean [] mask) {
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
......@@ -16640,6 +16656,7 @@ private double [][] jacobianByJacobian(double [][] jacobian, boolean [] mask) {
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
......@@ -18541,11 +18558,11 @@ use the result to create a rejectiobn mask - if the energy was high, (multiplica
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;
......@@ -19138,7 +19155,7 @@ if (DEBUG_LEVEL>1) System.out.println("findClusterOnPSF: ix="+ix+" iy="+iy);
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();
......@@ -19368,7 +19385,7 @@ returns integer array (same dimensions as input) with 1 - selected, 0 - not sele
iy=-iy;
}
ix= (ix+size) % size;
floatPixels[i]=(float) clusterMap[iy][ix];
floatPixels[i]=clusterMap[iy][ix];
}
ip.setPixels(floatPixels);
ip.resetMinAndMax();
......@@ -20460,8 +20477,8 @@ use the result to create a rejectiobn mask - if the energy was high, (multiplica
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;
src/main/java/DistortionCalibrationData.java
View file @ 3272bf8a
......@@ -22,17 +22,6 @@
**
*/
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 ij.text.TextWindow;
import java.io.BufferedWriter;
import java.io.File;
import java.io.FileWriter;
......@@ -45,6 +34,17 @@ import org.apache.commons.configuration.ConfigurationException;
import org.apache.commons.configuration.HierarchicalConfiguration;
import org.apache.commons.configuration.XMLConfiguration;
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 ij.text.TextWindow;
//import EyesisCameraParameters;
//import Distortions.EyesisSubCameraParameters;
//import LensDistortionParameters;
......@@ -712,6 +712,22 @@ import org.apache.commons.configuration.XMLConfiguration;
}
public void listCameraParameters(boolean xcam){
int numSubCameras=getNumSubCameras();
if (this.gIP!=null) {
int maxChn=0;
for (int i=0;i<this.gIP.length;i++) if ((this.gIP[i]!=null) && (this.gIP[i].channel>maxChn)){
maxChn=this.gIP[i].channel;
}
numSubCameras=maxChn+1;
}
if (xcam && (numSubCameras == 4)) {
listCameraParametersXcam();
} else {
listCameraParameters();
}
}
public void listCameraParameters(){
int numSubCameras=getNumSubCameras();
if (this.gIP!=null) {
......@@ -778,6 +794,186 @@ import org.apache.commons.configuration.XMLConfiguration;
new TextWindow("Camera parameters", header, sb.toString(), 85*(numSubCameras+3),600);
}
public void listCameraParametersXcam(){ // getNumSubCameras() should be 4!
double rollDegPerTurn = -0.45/33.5*180/Math.PI; // -0.769644799429464 deg/turn, CW screw increases roll, degrees per 1 screw turn
double headDegPerTurn = 0.45/34.5*180/Math.PI; // 0.7473362545184652 deg/turn, both screws CW decreases heading (degree/turn)
double elevDegPerTurn = 0.45/14*180/Math.PI; // 1.8416500557776463 deg/turn, top CW, bottom CCW decreases elevation (degree/turn)
int numSubCameras=getNumSubCameras();
if (this.gIP!=null) {
int maxChn=0;
for (int i=0;i<this.gIP.length;i++) if ((this.gIP[i]!=null) && (this.gIP[i].channel>maxChn)){
maxChn=this.gIP[i].channel;
}
numSubCameras=maxChn+1;
}
String header="Name\tUnits";
StringBuffer sb = new StringBuffer();
for (int i=0;i<numSubCameras;i++) header+="\t"+i;
for (int stationNumber=0;stationNumber<this.eyesisCameraParameters.numStations;stationNumber++){
if (this.eyesisCameraParameters.numStations>1){
sb.append("Station "+stationNumber+" W="+(100*this.eyesisCameraParameters.stationWeight[stationNumber])+"%"); for (int i=-1;i<numSubCameras;i++) sb.append("\t==="); sb.append("\n");
}
int [] lensDistortionModels=new int [numSubCameras];
for (int i=0;i<numSubCameras;i++) lensDistortionModels[i]=eyesisCameraParameters.getLensDistortionModel(stationNumber,i);
// sb.append("Lens Distortion Model\t");
// for (int i=0;i<numSubCameras;i++) sb.append("\t"+lensDistortionModels[i]);
// sb.append("\n");
double [][] cameraPars=new double [numSubCameras][];
for (int i=0;i<numSubCameras;i++) cameraPars[i]=eyesisCameraParameters.getParametersVector(stationNumber,i);
// calculate average height average right
double [] subcamRight = new double[numSubCameras];
double [] subcamHeight = new double[numSubCameras];
double [] subcamCorrRight = new double[numSubCameras]; // in rotated C.S.
double [] subcamCorrHeight = new double[numSubCameras]; // in rotated C.S.
double [] subcamHeading = new double[numSubCameras];
double [] subcamElevation = new double[numSubCameras];
double subcamRightCenter = 0.0;
double subcamHeightCenter = 0.0;
double subcamHeadingCenter = 0.0;
double subcamElevationCenter = 0.0;
double [] subcamRelRot = new double[numSubCameras];
double [] subcamRelHeading = new double[numSubCameras];
double [] subcamRelElevation = new double[numSubCameras];
double [] rollCorrTurns = new double[numSubCameras];
double [] topCorrTurns = new double[numSubCameras];
double [] botCorrTurns = new double[numSubCameras];
for (int i=0;i<numSubCameras;i++) {
subcamRight[i] = cameraPars[i][getParameterIndexByName("subcamRight")];
subcamHeight[i] = cameraPars[i][getParameterIndexByName("subcamHeight")];
subcamHeading[i] = cameraPars[i][getParameterIndexByName("subcamHeading")];
subcamElevation[i] = cameraPars[i][getParameterIndexByName("subcamElevation")];
subcamRightCenter += subcamRight[i];
subcamHeightCenter += subcamHeight[i];
subcamHeadingCenter += subcamHeading[i];
subcamElevationCenter += subcamElevation[i];
}
subcamRightCenter /= numSubCameras;
subcamHeightCenter /= numSubCameras;
subcamHeadingCenter /= numSubCameras;
subcamElevationCenter /= numSubCameras;
double [] subcamNominalDirs = {135.0,45.0, -135.0, -45.0};
double [] subcamDirsDeg = new double[numSubCameras];
double commonRot = 0.0;
for (int i=0;i<numSubCameras;i++) {
subcamDirsDeg[i]=180.0/Math.PI*Math.atan2(subcamHeight[i]-subcamHeightCenter, subcamRight[i]-subcamRightCenter);
commonRot += subcamNominalDirs[i]-subcamDirsDeg[i];
}
commonRot /= numSubCameras;
for (int i=0;i<numSubCameras;i++) {
subcamRelRot[i] = cameraPars[i][getParameterIndexByName("subcamRoll")] - commonRot;
subcamRelHeading[i] = subcamHeading[i] - subcamHeadingCenter;
subcamRelElevation[i] = subcamElevation[i] - subcamElevationCenter;
double r = Math.sqrt((subcamHeight[i]-subcamHeightCenter)*(subcamHeight[i]-subcamHeightCenter)+
(subcamRight[i]-subcamRightCenter)*(subcamRight[i]-subcamRightCenter));
subcamCorrRight[i] = r*Math.cos(Math.PI/180.0*(subcamDirsDeg[i]+commonRot));
subcamCorrHeight[i] = r*Math.sin(Math.PI/180.0*(subcamDirsDeg[i]+commonRot));
rollCorrTurns[i] = subcamRelRot[i] * rollDegPerTurn;
topCorrTurns[i] = subcamRelHeading[i] * headDegPerTurn + subcamRelElevation[i] * elevDegPerTurn;
botCorrTurns[i] = subcamRelHeading[i] * headDegPerTurn - subcamRelElevation[i] * elevDegPerTurn;
}
/*
// parameters same order as in this
for (int n=0;n<cameraPars[0].length;n++) if (isSubcameraParameter(n) && isIntrinsicParameter(n)){
sb.append(getParameterName(n)+"\t"+getParameterUnits(n));
for (int i=0;i<numSubCameras;i++) sb.append("\t"+IJ.d2s(cameraPars[i][n],3));
sb.append("\n");
}
*/
// sb.append("---"); for (int i=-1;i<numSubCameras;i++) sb.append("\t"); sb.append("\n");
int flindex =getParameterIndexByName("subcamFocalLength");
sb.append(getParameterName(flindex)+"\t"+getParameterUnits(flindex));
for (int i=0;i<numSubCameras;i++) sb.append("\t"+IJ.d2s(cameraPars[i][flindex],3));
sb.append("\n");
sb.append("Camera roll"+"\t"+"degrees"+"\t"+IJ.d2s(commonRot,3));
for (int i=1;i<numSubCameras;i++) sb.append("\t"); sb.append("\n");
sb.append("Camera heading"+"\t"+"degrees"+"\t"+IJ.d2s(subcamHeadingCenter,3));
for (int i=1;i<numSubCameras;i++) sb.append("\t"); sb.append("\n");
sb.append("Camera elevation"+"\t"+"degrees"+"\t"+IJ.d2s(subcamElevationCenter,3));
for (int i=1;i<numSubCameras;i++) sb.append("\t"); sb.append("\n");
sb.append("Rel roll"+"\t"+"degrees");
for (int i=0;i<numSubCameras;i++) sb.append("\t"+IJ.d2s(subcamRelRot[i],3));
sb.append("\n");
sb.append("Rel heading"+"\t"+"degrees");
for (int i=0;i<numSubCameras;i++) sb.append("\t"+IJ.d2s(subcamRelHeading[i],3));
sb.append("\n");
sb.append("Rel elevation"+"\t"+"degrees");
for (int i=0;i<numSubCameras;i++) sb.append("\t"+IJ.d2s(subcamRelElevation[i],3));
sb.append("\n");
sb.append("Corr right"+"\t"+"mm");
for (int i=0;i<numSubCameras;i++) sb.append("\t"+IJ.d2s(subcamCorrRight[i],3));
sb.append("\n");
sb.append("Corr height"+"\t"+"mm");
for (int i=0;i<numSubCameras;i++) sb.append("\t"+IJ.d2s(subcamCorrHeight[i],3));
sb.append("\n");
sb.append("---"); for (int i=-1;i<numSubCameras;i++) sb.append("\t"); sb.append("\n");
sb.append("Screw roll"+"\t"+"turns CW");
for (int i=0;i<numSubCameras;i++) sb.append("\t"+IJ.d2s(rollCorrTurns[i],2));
sb.append("\n");
sb.append("Screw top"+"\t"+"turns CW");
for (int i=0;i<numSubCameras;i++) sb.append("\t"+IJ.d2s(topCorrTurns[i],2));
sb.append("\n");
sb.append("Screw bottom"+"\t"+"turns CW");
for (int i=0;i<numSubCameras;i++) sb.append("\t"+IJ.d2s(botCorrTurns[i],2));
sb.append("\n");
sb.append("---"); for (int i=-1;i<numSubCameras;i++) sb.append("\t"); sb.append("\n");
for (int n=0;n<cameraPars[0].length;n++) if (isSubcameraParameter(n) && !isIntrinsicParameter(n)){
sb.append(getParameterName(n)+"\t"+getParameterUnits(n));
for (int i=0;i<numSubCameras;i++) sb.append("\t"+IJ.d2s(cameraPars[i][n],3));
sb.append("\n");
}
sb.append("---"); for (int i=-1;i<numSubCameras;i++) sb.append("\t"); sb.append("\n");
/*
for (int n=0;n<cameraPars[0].length;n++) if (
!isSubcameraParameter(n)&&
!isLocationParameter(n)&&
!isOrientationParameter(n)){
sb.append(getParameterName(n)+"\t"+getParameterUnits(n));
sb.append("\t"+IJ.d2s(cameraPars[0][n],3));
for (int i=1;i<numSubCameras;i++) sb.append("\t---");
sb.append("\n");
}
sb.append("---"); for (int i=-1;i<numSubCameras;i++) sb.append("\t"); sb.append("\n");
for (int n=0;n<cameraPars[0].length;n++) if (isLocationParameter(n)){
sb.append(getParameterName(n)+"\t"+getParameterUnits(n));
sb.append("\t"+IJ.d2s(cameraPars[0][n],3));
for (int i=1;i<numSubCameras;i++) sb.append("\t---");
sb.append("\n");
}
sb.append("---"); for (int i=-1;i<numSubCameras;i++) sb.append("\t"); sb.append("\n");
for (int n=0;n<cameraPars[0].length;n++) if (isOrientationParameter(n)){
sb.append(getParameterName(n)+"\t"+getParameterUnits(n));
sb.append("\t"+IJ.d2s(cameraPars[0][n],3));
for (int i=1;i<numSubCameras;i++) sb.append("\t---");
sb.append("\n");
}
*/
}
new TextWindow("Camera parameters", header, sb.toString(), 85*(numSubCameras+3),600);
}
public void setImages(
ImagePlus [] images, // images in the memory
......@@ -2055,8 +2251,8 @@ import org.apache.commons.configuration.XMLConfiguration;
// int numOfGridNodes=0;
// int numOfGridNodes_extra=0;
for (int i=0;i<pixels[0].length;i++) if ((pixels[0][i]>=0) && (pixels[1][i]>=0) && (pixels[0][i]<sensorWidth) && (pixels[1][i]<sensorHeight)){
int u=(int) Math.round(pixels[2][i]);
int v=(int) Math.round(pixels[3][i]);
int u=Math.round(pixels[2][i]);
int v=Math.round(pixels[3][i]);
int u1= reMap[0][0]*u + reMap[0][1]*v + reMap[0][2]; // u
int v1= reMap[1][0]*u + reMap[1][1]*v + reMap[1][2]; // v;
// if (patternParameters.getXYZM(u,v,this.debugLevel>1)!=null) size++;
......@@ -2079,8 +2275,8 @@ import org.apache.commons.configuration.XMLConfiguration;
// this.gIP[fileNumber].flatFieldAvailable=pixels.length>=8;
// if (disableNoFlatfield && !this.gIP[fileNumber].flatFieldAvailable) this.gIP[fileNumber].enabled=false; // just to use old mixed data
for (int i=0;i<pixels[0].length;i++) if ((pixels[0][i]>=0) && (pixels[1][i]>=0) && (pixels[0][i]<sensorWidth) && (pixels[1][i]<sensorHeight)) {
int u=(int) Math.round(pixels[2][i]);
int v=(int) Math.round(pixels[3][i]);
int u=Math.round(pixels[2][i]);
int v=Math.round(pixels[3][i]);
int u1= reMap[0][0]*u + reMap[0][1]*v + reMap[0][2]; // u
int v1= reMap[1][0]*u + reMap[1][1]*v + reMap[1][2]; // v;
......
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