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imagej-elphel
Commit d811fafa authored by Andrey Filippov's avatar Andrey Filippov
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implemented distorrtion model selection, image selection editor, different... 

implemented distorrtion model selection, image selection editor, different maximal radius for grid match and adjustment
parent ae245e9a
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Showing with 693 additions and 29 deletions
src/main/java/Aberration_Calibration.java
View file @ d811fafa
......@@ -404,6 +404,7 @@ public static MatchSimulatedPattern.DistortionParameters DISTORTION =new MatchSi
1296.0, // double px0 // lens axis from sensor, horizontal, from left (pixels)
968.0, // double py0 // lens axis from sensor, vertical, from top (pixels)
true, // boolean flipVertical // acquired image is mirrored vertically (mirror used)
-1, // lensDistortionModel (use default)
null, // double [][] r_xy,
null // double [][] r_od
);
......@@ -1169,7 +1170,8 @@ if (MORE_BUTTONS) {
System.out.println("Number of enabled grid images: "+numImages[0]+
", of them new: "+numImages[1]+
", disabled without vignetting info: "+numImages[2]+
", disabled having less than "+minGridsNoPointer+" nodes and no matched pointers: "+numImages[3]);
", disabled having less than "+minGridsNoPointer+" nodes and no matched pointers: "+numImages[3]+
", disabled with no lasers and enableNoLaser==false (like 2 bottom cameras):" +numImages[4]);
if (DISTORTION_CALIBRATION_DATA.gIS==null) {
int numImageSets=DISTORTION_CALIBRATION_DATA.buildImageSets(false); // from scratch
......@@ -6062,7 +6064,7 @@ if (MORE_BUTTONS) {
gd.addNumericField("Minimal registered grid period as a fraction of maximal (to filter reflections)", 0.4,2); //was 0.7
gd.addCheckbox ("Reset orientation from the image with most pointers (false - only if it was not set yet)", overwriteAll);
gd.addCheckbox ("Disable (old) images without vignetting information", true);
gd.addNumericField("Minimal number of grids in no-pointer images and estimated orientation", 1000,0);
gd.addNumericField("Minimal number of grid nodes in no-pointer images and estimated orientation", 1000,0);
gd.showDialog();
if (gd.wasCanceled()) return;
boolean resetHinted= gd.getNextBoolean();
......@@ -6081,7 +6083,8 @@ if (MORE_BUTTONS) {
System.out.println("Number of enabled grid images: "+numImages[0]+
", of them new: "+numImages[1]+
", disabled without vignetting info: "+numImages[2]+
", disabled having less than "+minGridsNoPointer+" nodes and no matched pointers: "+numImages[3]);
", disabled having less than "+minGridsNoPointer+" nodes and no matched pointers: "+numImages[3]+
", disabled with no lasers and enableNoLaser==false (like 2 bottom cameras):" +numImages[4]);
if (DISTORTION_CALIBRATION_DATA.gIS==null) {
int numImageSets=DISTORTION_CALIBRATION_DATA.buildImageSets(false); // from scratch
if (DEBUG_LEVEL>0) System.out.println("Image set was empty, built a new one with "+numImageSets+" image sets (\"panoramas\"): ");
......
src/main/java/DistortionCalibrationData.java
View file @ d811fafa
......@@ -38,6 +38,7 @@ import java.io.File;
import java.io.FileWriter;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
import org.apache.commons.configuration.ConfigurationException;
......@@ -679,7 +680,14 @@ import org.apache.commons.configuration.XMLConfiguration;
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);
// parameters same order as in this
for (int n=0;n<cameraPars[0].length;n++) if (isSubcameraParameter(n) && isIntrinsicParameter(n)){
......@@ -935,8 +943,10 @@ import org.apache.commons.configuration.XMLConfiguration;
}
}
int numNoVignetting=0;
int disabledNoLaser=0;
for (int i=0;i<this.gIP.length;i++){
int stationNumber=this.gIP[i].getStationNumber();
boolean enableNoLaser=this.eyesisCameraParameters.getEnableNoLaser(stationNumber,this.gIP[i].channel);
boolean wasEnabled=this.gIP[i].enabled;
if (resetHinted) this.gIP[i].hintedMatch=-1; // undefined
if (Double.isNaN(this.gIP[i].gridPeriod) ||
......@@ -949,15 +959,17 @@ import org.apache.commons.configuration.XMLConfiguration;
if (
(this.gIP[i].matchedPointers>=minPointers) ||
((this.gIP[i].matchedPointers>0) && (this.gIP[i].hintedMatch>0)) || // orientation and one pointer
(this.gIP[i].hintedMatch>1)) {
((this.gIP[i].hintedMatch>1) && enableNoLaser)) { // do not use bottom images w/o matched pointers
// before enabling - copy orientation from gIS
if (!this.gIP[i].enabled && (gIS_index[i]>=0)){
if (!Double.isNaN(this.gIS[gIS_index[i]].goniometerTilt)) setGH(i,this.gIS[gIS_index[i]].goniometerTilt );
if (!Double.isNaN(this.gIS[gIS_index[i]].goniometerAxial)) setGA(i,this.gIS[gIS_index[i]].goniometerAxial );
}
this.gIP[i].enabled=true;
} else this.gIP[i].enabled=false;
if ((this.gIP[i].hintedMatch>1) && !enableNoLaser && (this.gIP[i].matchedPointers==0)){
disabledNoLaser++;
}
else this.gIP[i].enabled=false;
}
if (disableNoVignetting) {
......@@ -977,7 +989,7 @@ import org.apache.commons.configuration.XMLConfiguration;
if (this.gIP[i].newEnabled) newEnabled++;
}
// may need buildImageSets
int [] result={numEnabled,newEnabled,numNoVignetting,notEnoughNodes};
int [] result={numEnabled,newEnabled,numNoVignetting,notEnoughNodes,disabledNoLaser};
return result;
}
// TODO:
......@@ -1277,7 +1289,26 @@ import org.apache.commons.configuration.XMLConfiguration;
return numEnabled;
}
int [] getStations(){
int [] result = new int [this.gIP.length];
for (int i=0;i<result.length;i++) result[i]=(this.gIP[i]!=null)?this.gIP[i].stationNumber:-1;
return result;
}
int [] getChannels(){
int [] result = new int [this.gIP.length];
for (int i=0;i<result.length;i++) result[i]=(this.gIP[i]!=null)?this.gIP[i].channel:-1;
return result;
}
int [] getMatchedPointers(){
int [] result = new int [this.gIP.length];
for (int i=0;i<result.length;i++) result[i]=(this.gIP[i]!=null)?this.gIP[i].matchedPointers:0;
return result;
}
int [] getHintedMatch(){
int [] result = new int [this.gIP.length];
for (int i=0;i<result.length;i++) result[i]=(this.gIP[i]!=null)?this.gIP[i].hintedMatch:-1;
return result;
}
boolean [] selectNewEnabled () {
boolean [] newEnabled=new boolean [this.gIP.length] ;
......@@ -1285,14 +1316,22 @@ import org.apache.commons.configuration.XMLConfiguration;
return newEnabled;
}
boolean [] selectEnabled () {
boolean [] enabled=new boolean [this.gIP.length] ;
for (int i=0;i<this.gIP.length;i++) enabled[i]= (this.gIP[i]!=null) && this.gIP[i].enabled;
return enabled;
}
boolean [] selectEstimated (boolean enabledOnly) {
boolean [] estimated=new boolean [getNumImages()];
if (this.gIS==null) {
String msg="Image sets are not initialized";
IJ.showMessage("Error",msg);
throw new IllegalArgumentException (msg);
// throw new IllegalArgumentException (msg);
Arrays.fill(estimated, true);
return estimated;
}
boolean [] estimated=new boolean [getNumImages()];
for (int i=0;i<estimated.length;i++) estimated[i]=false;
for (int i=0;i<this.gIS.length;i++) if (this.gIS[i].imageSet!=null){
for (int j=0;j<this.gIS[i].imageSet.length;j++) if (this.gIS[i].imageSet[j]!=null) {
......
src/main/java/Distortions.java
View file @ d811fafa
......@@ -50,6 +50,7 @@ import Jama.Matrix;
// 1 - put commons-configuration-1.7.jar under ImageJ plugins directory (I used ImageJ-Elphel)
// 2 - in Eclipse project properties -> Build Path -> Libraries -> Add External jar
public class Distortions {
final public double hintedMaxRelativeRadius=1.2; // make adjustable?
private showDoubleFloatArrays SDFA_INSTANCE=new showDoubleFloatArrays(); // just for debugging?
// int numInputs=27; // with A8...// 24; // parameters in subcamera+...
// int numOutputs=16; // with A8...//13; // parameters in a single camera
......@@ -3010,12 +3011,25 @@ For each point in the image
* @param v grid V (signed, 0 in the center)
* @return [7] {pX,pY,grid mask (binary), grid R, grid G, grid B, alpha}
*/
public double [] reprojectGridNode(
LensDistortionParameters lensDistortionParameters,
int numImg,
int u, // grid signed u,v
int v
int v){
double maxRelativeRadius=this.hintedMaxRelativeRadius; // make adjustable
return reprojectGridNode(
lensDistortionParameters,
numImg,
u, // grid signed u,v
v,
maxRelativeRadius);
}
public double [] reprojectGridNode(
LensDistortionParameters lensDistortionParameters,
int numImg,
int u, // grid signed u,v
int v,
double maxRelativeRadius //=2.0;
){
int debugThreshold=1;
int nChn= this.fittingStrategy.distortionCalibrationData.gIP[numImg].channel;
......@@ -3035,6 +3049,7 @@ For each point in the image
XYZMP[0], // target point horizontal, positive - right, mm
XYZMP[1], // target point vertical, positive - down, mm
XYZMP[2], // target point horizontal, positive - away from camera, mm
maxRelativeRadius, //
false); // calculate derivatives, false - values only (NaN for behind points - only when false here)
if (Double.isNaN(pXY[0][0])) {
if (this.debugLevel>debugThreshold){
......@@ -3094,6 +3109,7 @@ For each point in the image
double goniometerAxial, // Axial
int imageSet,
boolean filterBorder){
double maxRelativeRadius=this.hintedMaxRelativeRadius; // make adjustable
int debugThreshold=2;
// Get parameter vector (22) for the selected sensor, current Eyesisparameters and specified orientation angles
double [] parVector=fittingStrategy.distortionCalibrationData.eyesisCameraParameters.getParametersVector(stationNumber,subCamera);
......@@ -3155,6 +3171,7 @@ For each point in the image
XYZM[0], // target point horizontal, positive - right, mm
XYZM[1], // target point vertical, positive - down, mm
XYZM[2], // target point horizontal, positive - away from camera, mm
maxRelativeRadius,
false); // calculate derivatives, false - values only (NaN for behind points - only when false here)
// verify the grid is inside the sensor area (may use sensor mask later too? probably not needed)
// Now NaN if point is behind the sensor
......@@ -5963,6 +5980,10 @@ List calibration
imp.setProperty("comment_entrancePupilForward", "entrance pupil distance from the azimuth/radius/height, outwards in mm");
imp.setProperty("entrancePupilForward", ""+entrancePupilForward); // currently global, decoders will use per-sensor
imp.setProperty("comment_defects", "Sensor hot/cold pixels list as x:y:difference");
imp.setProperty("comment_lensDistortionModel", "Integer specifying lens distrotion model (0 - radial)");
imp.setProperty("lensDistortionModel", ""+subCam.lensDistortionModel);
for (int i=0;i<subCam.r_xy.length;i++){
imp.setProperty("r_xy_"+i+"_x",subCam.r_xy[i][0]+"");
imp.setProperty("r_xy_"+i+"_y",subCam.r_xy[i][1]+"");
......@@ -6144,6 +6165,7 @@ List calibration
subCam.defectsDiff=null;
}
// non-radial
if (imp.getProperty("lensDistortionModel") !=null) subCam.lensDistortionModel= Integer.parseInt((String) imp.getProperty("lensDistortionModel"));
subCam.setDefaultNonRadial();
for (int i=0;i<subCam.r_xy.length;i++) {
if (imp.getProperty("r_xy_"+i+"_x") !=null) subCam.r_xy[i][0]= Double.parseDouble((String) imp.getProperty("r_xy_"+i+"_x"));
......@@ -9555,6 +9577,7 @@ M * V = B
System.out.println("this.lensDistortionParameters.distortionA="+IJ.d2s(this.lensDistortionParameters.distortionA, 5));
System.out.println("this.lensDistortionParameters.distortionB="+IJ.d2s(this.lensDistortionParameters.distortionB, 5));
System.out.println("this.lensDistortionParameters.distortionC="+IJ.d2s(this.lensDistortionParameters.distortionC, 5));
System.out.println("this.lensDistortionParameters.lensDistortionModel="+this.lensDistortionParameters.lensDistortionModel);
for (int i=0;i<this.lensDistortionParameters.r_xy.length;i++){
System.out.println("this.lensDistortionParameters.r_xy["+i+"][0]="+IJ.d2s(this.lensDistortionParameters.r_xy[i][0], 5));
System.out.println("this.lensDistortionParameters.r_xy["+i+"][1]="+IJ.d2s(this.lensDistortionParameters.r_xy[i][1], 5));
......@@ -9760,6 +9783,7 @@ M * V = B
if (reCenterVertically){
eyesisCameraParameters.recenterVertically(channelMask, stationMask);
for (int i=0;i<channelMask.length;i++) channelMask[i]= true;
parameterMask[distortionCalibrationData.getParameterIndexByName("subcamHeight")] = true;
}
......
src/main/java/EyesisCameraParameters.java
View file @ d811fafa
This diff is collapsed.
src/main/java/EyesisSubCameraParameters.java
View file @ d811fafa
......@@ -25,6 +25,8 @@ import java.util.Properties;
public class EyesisSubCameraParameters{
// origin is on the rotation axis of the tube body closest to the goniometer horizontal axis
public int lensDistortionModel=0;
public boolean enableNoLaser=true; // enable images for this channel w/o matched laser pointer
public double azimuth; // azimuth of the lens entrance pupil center, degrees, clockwise looking from top
public double radius; // mm, distance from the rotation axis
public double height; // mm, up - from the origin point
......@@ -66,6 +68,8 @@ import java.util.Properties;
*/
public EyesisSubCameraParameters(
int lensDistortionModel,
boolean enableNoLaser,
double azimuth, // azimuth of the lens entrance pupil center, degrees, clockwise looking from top
double radius, // mm, distance from the rotation axis
double height, // mm, up from the origin point
......@@ -88,6 +92,8 @@ import java.util.Properties;
double [][] r_od, // elongation for c,b,a,a5,a6,a7,a8
double channelWeightDefault
){
this.lensDistortionModel=lensDistortionModel;
this.enableNoLaser=enableNoLaser;
this.azimuth=azimuth;
this.radius=radius;
this.height=height;
......@@ -121,6 +127,8 @@ import java.util.Properties;
// defects are not cloned!
public EyesisSubCameraParameters clone() {
return new EyesisSubCameraParameters(
this.lensDistortionModel,
this.enableNoLaser,
this.azimuth,
this.radius,
this.height,
......@@ -152,6 +160,8 @@ import java.util.Properties;
}
// TODO: add/restore new properties
public void setProperties(String prefix,Properties properties){
properties.setProperty(prefix+"lensDistortionModel",this.lensDistortionModel+"");
properties.setProperty(prefix+"enableNoLaser",this.enableNoLaser+"");
properties.setProperty(prefix+"azimuth",this.azimuth+"");
properties.setProperty(prefix+"radius",this.radius+"");
properties.setProperty(prefix+"height",this.height+"");
......@@ -181,6 +191,11 @@ import java.util.Properties;
properties.setProperty(prefix+"channelWeightDefault",this.channelWeightDefault+"");
}
public void getProperties(String prefix,Properties properties){
getProperties(prefix,properties, -1);
}
public void getProperties(String prefix,Properties properties, int channel){
if (properties.getProperty(prefix+"lensDistortionModel")!=null)
this.lensDistortionModel=Integer.parseInt(properties.getProperty(prefix+"lensDistortionModel"));
if (properties.getProperty(prefix+"azimuth")!=null)
this.azimuth=Double.parseDouble(properties.getProperty(prefix+"azimuth"));
if (properties.getProperty(prefix+"radius")!=null)
......@@ -231,6 +246,13 @@ import java.util.Properties;
this.channelWeightDefault=Double.parseDouble(properties.getProperty(prefix+"channelWeightDefault"));
this.channelWeightCurrent=this.channelWeightDefault;
}
// /enableNoLaser
if (properties.getProperty(prefix+"enableNoLaser")!=null) {
this.enableNoLaser=Boolean.parseBoolean(properties.getProperty(prefix+"enableNoLaser"));
} else {
this.enableNoLaser=(channel<24);
}
}
public void setChannelWeightCurrent(
double weight){
......
src/main/java/FittingStrategy.java
View file @ d811fafa
This diff is collapsed.
src/main/java/LensDistortionParameters.java
View file @ d811fafa
......@@ -22,6 +22,9 @@ import Jama.Matrix;
final int numOutputs=42; //16; // with A8...//13; // parameters in a single camera
// final
// boolean cummulativeCorrection=true; // r_xy, r_od for higher terms are relative to lower ones
public int defaultLensDistortionModel=200;
public int lensDistortionModel=defaultLensDistortionModel;
public int lensDistortionModelType=0; // set from lensDistortionModel
boolean cummulativeCorrection=false; //true; // r_xy, r_od for higher terms are relative to lower ones
public double focalLength=4.5;
public double pixelSize= 2.2; //um
......@@ -73,7 +76,22 @@ import Jama.Matrix;
// intermediate values
public double phi, theta,psi,cPH,sPH,cTH,sTH,cPS,sPS;
public double [][] rotMatrix=new double[3][3]; // includes mirroring for Y (target coordinates y- down, camera - y up)
public void setDistortionModelParameters(){
if (lensDistortionModel<0){
System.out.println("BUG:setDistortionModelParameters() - lensDistortionModel<0");
lensDistortionModel=defaultLensDistortionModel;
}
this.cummulativeCorrection= (lensDistortionModel==101);
if (lensDistortionModel<100){
lensDistortionModelType=0;
} else if (lensDistortionModel<200){
lensDistortionModelType=1;
} else if (lensDistortionModel<300){
lensDistortionModelType=2;
} else {
lensDistortionModelType=0;
}
}
public LensDistortionParameters(
// LensDistortionParameters lensDistortionParameters,
boolean isTripod,
......@@ -116,6 +134,7 @@ import Jama.Matrix;
double px0, // center of the lens on the sensor, pixels
double py0, // center of the lens on the sensor, pixels
boolean flipVertical, // acquired image is mirrored vertically (mirror used)
int lensDistortionModel,
double [][] r_xy,
double [][] r_od
){
......@@ -140,6 +159,7 @@ import Jama.Matrix;
px0,
py0,
flipVertical,
lensDistortionModel,
r_xy,
r_od);
}
......@@ -166,6 +186,7 @@ import Jama.Matrix;
1296, // px0,
698, // py0,
true, // flipVertical,
-1, // lensDistortionModel
null, // r_xy,
null // r_od,
);
......@@ -192,6 +213,7 @@ import Jama.Matrix;
this.px0,
this.py0,
this.flipVertical,
this.lensDistortionModel,
this.r_xy,
this.r_od
);
......@@ -218,6 +240,7 @@ import Jama.Matrix;
double px0, // center of the lens on the sensor, pixels
double py0, // center of the lens on the sensor, pixels
boolean flipVertical, // acquired image is mirrored vertically (mirror used)
int lensDistortionModel,
double [][] r_xy, // per polynomial term center x,y correction only 6, as for the first term delta x, delta y ==0
double [][] r_od // per polynomial term orthogonal+diagonal elongation
){
......@@ -241,6 +264,7 @@ import Jama.Matrix;
this.px0=px0;
this.py0=py0;
this.flipVertical=flipVertical;
this.lensDistortionModel=(lensDistortionModel>=0)?lensDistortionModel:defaultLensDistortionModel;
if (r_xy==null) r_xy=r_xy_dflt;
if (r_od==null) r_od=r_od_dflt;
this.r_xy=new double [r_xy.length][2];
......@@ -273,6 +297,7 @@ import Jama.Matrix;
pars.px0, // center of the lens on the sensor, pixels
pars.py0, // center of the lens on the sensor, pixels
this.flipVertical, // (keep) acquired image is mirrored vertically (mirror used)
pars.lensDistortionModel,
pars.r_xy, // do not exist yet!
pars.r_od // do not exist yet!
);
......@@ -301,6 +326,7 @@ import Jama.Matrix;
ldp.px0,
ldp.py0,
ldp.flipVertical,
ldp.lensDistortionModel,
ldp.r_xy,
ldp.r_od);
}
......@@ -427,6 +453,7 @@ dPXmmc/dphi=
this.r_xyod[0][1]=0.0; // this.py0;
this.r_xyod[0][2]=this.r_od[0][0];
this.r_xyod[0][3]=this.r_od[0][1];
setDistortionModelParameters();
if (cummulativeCorrection){
for (int i=1;i<this.r_xyod.length;i++){
this.r_xyod[i][0]=this.r_xyod[i-1][0]+this.r_xy[i-1][0];
......@@ -911,13 +938,39 @@ dPXmmc/dphi=
}
}
}
public double [][] calcPartialDerivatives_old(
public double [][] calcPartialDerivatives(
double xp, // target point horizontal, positive - right, mm
double yp, // target point vertical, positive - down, mm
double zp, // target point horizontal, positive - away from camera, mm
boolean calculateAll){ // calculate derivatives, false - values only
double maxRelativeRadius=2.0;
return calcPartialDerivatives(xp,yp,zp,maxRelativeRadius,calculateAll);
}
public double [][] calcPartialDerivatives(
double xp, // target point horizontal, positive - right, mm
double yp, // target point vertical, positive - down, mm
double zp, // target point horizontal, positive - away from camera, mm
double maxRelativeRadius, // make configurable?
boolean calculateAll){ // calculate derivatives, false - values only
switch (this.lensDistortionModelType){
case 0:
case 1:
return calcPartialDerivatives_type1(xp,yp,zp,maxRelativeRadius,calculateAll);
case 2:
return calcPartialDerivatives_type2(xp,yp,zp,maxRelativeRadius,calculateAll);
default:
return calcPartialDerivatives_type1(xp,yp,zp,maxRelativeRadius,calculateAll);
}
}
public double [][] calcPartialDerivatives_type1(
double xp, // target point horizontal, positive - right, mm
double yp, // target point vertical, positive - down, mm
double zp, // target point horizontal, positive - away from camera, mm
double maxRelativeRadius,
boolean calculateAll){ // calculate derivatives, false - values only
// this.cummulativeCorrection=false; // just debugging
final double maxRelativeRadius=2.0; // make configurable?
// TODO - add reduced calculations for less terms?
// final int numDerivatives=44; // 18+6*2+7*2; // 18 for radial and 26 more for non-radial
......@@ -1261,15 +1314,13 @@ dPXmmc/dphi=
return partDeriv;
}
public double [][] calcPartialDerivatives(
public double [][] calcPartialDerivatives_type2(
double xp, // target point horizontal, positive - right, mm
double yp, // target point vertical, positive - down, mm
double zp, // target point horizontal, positive - away from camera, mm
double maxRelativeRadius,
boolean calculateAll){ // calculate derivatives, false - values only
// this.cummulativeCorrection=false; // just debugging
final double maxRelativeRadius=2.0; // make configurable?
// TODO - add reduced calculations for less terms?
// final int numDerivatives=44; // 18+6*2+7*2; // 18 for radial and 26 more for non-radial
......
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