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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;
......@@ -675,11 +676,18 @@ import org.apache.commons.configuration.XMLConfiguration;
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");
}
double [][] cameraPars=new double [numSubCameras][];
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);
// 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
......@@ -29,6 +29,14 @@ import org.apache.commons.configuration.XMLConfiguration;
public class EyesisCameraParameters{
final public String [] distortionModelDescriptions= {
"Radial model",
"Non radial with shift/elongation, non cummulative",
"Non radial with shift/elongation, cummulative",
"With non-radial polynomial terms"
};
final int [] distortionModels={0,100,101,200};
public int defaultLensDistortionModel=200;
public double [] goniometerHorizontal; // goniometer rotation around "horizontal" axis (tilting from the target - positive)
public double [] goniometerAxial; // goniometer rotation around Eyesis axis (clockwise in plan - positive
public EyesisSubCameraParameters [][] eyesisSubCameras=null;
......@@ -274,6 +282,13 @@ import org.apache.commons.configuration.XMLConfiguration;
}
public int getNumStations() {return this.numStations;}
public int getNumChannels() {
return getNumChannels(0);
}
public int getNumChannels(int numStation) {
return this.eyesisSubCameras[numStation].length;
}
// this.eyesisSubCameras[numStation].length
public EyesisCameraParameters () {} // just create new instance, all parameters data will be provided additionally
public EyesisCameraParameters (
int numStations,
......@@ -685,7 +700,7 @@ import org.apache.commons.configuration.XMLConfiguration;
if (numSubCameras>0) {
initSubCameras(numStation, numSubCameras); // set array with default parameters
for (int i=0;i<numSubCameras;i++){
this.eyesisSubCameras[numStation][i].getProperties(prefix+numStation+"_subCamera_"+i+'.',properties);
this.eyesisSubCameras[numStation][i].getProperties(prefix+numStation+"_subCamera_"+i+'.',properties,i);
}
}
}
......@@ -741,7 +756,11 @@ import org.apache.commons.configuration.XMLConfiguration;
GenericDialog gd = new GenericDialog(title);
// public double goniometerHorizontal; // goniometer rotation around "horizontal" axis (tilting from the target - positive)
// public double goniometerAxial; // goniometer rotation around Eyesis axis (clockwise in plan - positive
//this.isTripod
//this.isTripod
String [] modelChoice=new String [distortionModelDescriptions.length+1];
modelChoice[0]="--- keep current ---";
for (int i=0;i<distortionModelDescriptions.length;i++) modelChoice[i+1]=distortionModelDescriptions[i];
gd.addChoice("Change camera distortion model for all channels", modelChoice, modelChoice[0]);
gd.addCheckbox("Tripod mode (first vertical axis, then horizontal), changes meaning of the next 2 fields",this.isTripod);
gd.addMessage("=== Camera parameters to be fitted ===");
for (int numStation=0;numStation<this.numStations;numStation++) {
......@@ -801,6 +820,15 @@ import org.apache.commons.configuration.XMLConfiguration;
WindowTools.addScrollBars(gd);
gd.showDialog();
if (gd.wasCanceled()) return -1;
int modelIndex=gd.getNextChoiceIndex()-1;
if (modelIndex>=0){
for (EyesisSubCameraParameters [] esps:this.eyesisSubCameras){
for (EyesisSubCameraParameters esp:esps){
esp.lensDistortionModel=distortionModels[modelIndex];
}
}
}
this.isTripod= gd.getNextBoolean();
for (int numStation=0;numStation<this.numStations;numStation++) {
if (this.numStations>1){
......@@ -861,6 +889,8 @@ import org.apache.commons.configuration.XMLConfiguration;
gd.addNumericField("Channel "+numSubCam+" default weight", subCam.channelWeightDefault, 5,8,"");
}
if (this.numStations>1) gd.addMessage("--- Station number "+numStation+" ---");
gd.addNumericField("Subcamera lens distortion model", subCam.lensDistortionModel, 5,0,"");
gd.addCheckbox ("Enable matching w/o laser pointers", subCam.enableNoLaser);
gd.addNumericField("Subcamera azimuth", subCam.azimuth, 5,9,"degrees");
gd.addNumericField("Subcamera distance from the axis", subCam.radius, 5,9,"mm");
gd.addNumericField("Subcamera height from the 'equator'", subCam.height, 5,9,"mm");
......@@ -930,6 +960,8 @@ import org.apache.commons.configuration.XMLConfiguration;
channelWeightDefault=gd.getNextNumber();
}
subCam.channelWeightDefault= channelWeightDefault; // assign to all stations
subCam.lensDistortionModel= (int) gd.getNextNumber();
subCam.enableNoLaser = gd.getNextBoolean();
subCam.azimuth= gd.getNextNumber();
subCam.radius= gd.getNextNumber();
subCam.height= gd.getNextNumber();
......@@ -998,6 +1030,26 @@ import org.apache.commons.configuration.XMLConfiguration;
}
return true;
}
public int getLensDistortionModel(int stationNumber,int subCamNumber){
if (
(this.eyesisSubCameras==null) ||
(this.numStations<=stationNumber) ||
(this.eyesisSubCameras.length<=stationNumber) ||
(this.eyesisSubCameras[stationNumber].length<=subCamNumber)) throw new IllegalArgumentException
("Nonexistent subcamera "+subCamNumber+ " and/or station number="+stationNumber+" this.numStations="+this.numStations+" this.eyesisSubCameras.length="+this.eyesisSubCameras.length);
EyesisSubCameraParameters subCam=this.eyesisSubCameras[stationNumber][subCamNumber];
return subCam.lensDistortionModel;
}
boolean getEnableNoLaser(int stationNumber,int subCamNumber){
if (
(this.eyesisSubCameras==null) ||
(this.numStations<=stationNumber) ||
(this.eyesisSubCameras.length<=stationNumber) ||
(this.eyesisSubCameras[stationNumber].length<=subCamNumber)) throw new IllegalArgumentException
("Nonexistent subcamera "+subCamNumber+ " and/or station number="+stationNumber+" this.numStations="+this.numStations+" this.eyesisSubCameras.length="+this.eyesisSubCameras.length);
EyesisSubCameraParameters subCam=this.eyesisSubCameras[stationNumber][subCamNumber];
return subCam.enableNoLaser;
}
/**
*
* @param eyesisCameraParameters current parameters of the Eyesis camera, subcameras and goniometer
......@@ -1191,6 +1243,8 @@ import org.apache.commons.configuration.XMLConfiguration;
for (int i=0;i<numSubCameras;i++) this.eyesisSubCameras[numStation][i]=null;
if (numSubCameras==3) {
this.eyesisSubCameras[numStation][0]=new EyesisSubCameraParameters( //TODO: modify for lens adjustment defaults?
defaultLensDistortionModel,
true,
0.0, // double azimuth, // azimuth of the lens entrance pupil center, degrees, clockwise looking from top
52.53, // double radius, // mm, distance from the rotation axis
34.64, // double height, // mm, up (was downwards) - from the origin point
......@@ -1213,6 +1267,8 @@ import org.apache.commons.configuration.XMLConfiguration;
null, // elongation for c,b,a,a5,a6,a7,a8
1.0); //channelWeightDefault
this.eyesisSubCameras[numStation][1]=new EyesisSubCameraParameters( //TODO: modify for lens adjustment defaults?
defaultLensDistortionModel,
true,
30.0, // double azimuth, // azimuth of the lens entrance pupil center, degrees, clockwise looking from top
60.0, // double radius, // mm, distance from the rotation axis
-17.32, // double height, // mm, up (was downwards) - from the origin point
......@@ -1235,6 +1291,8 @@ import org.apache.commons.configuration.XMLConfiguration;
null, // elongation for c,b,a,a5,a6,a7,a8
1.0); //channelWeightDefault
this.eyesisSubCameras[numStation][2]=new EyesisSubCameraParameters( //TODO: modify for lens adjustment defaults?
defaultLensDistortionModel,
true,
-30.0, // double azimuth, // azimuth of the lens entrance pupil center, degrees, clockwise looking from top
60.0, // double radius, // mm, distance from the rotation axis
-17.32, // double height, // mm, up (was downwards) - from the origin point
......@@ -1258,6 +1316,8 @@ import org.apache.commons.configuration.XMLConfiguration;
1.0); //channelWeightDefault
} else if (numSubCameras==1) {
this.eyesisSubCameras[numStation][0]=new EyesisSubCameraParameters( //TODO: modify for lens adjustment defaults?
defaultLensDistortionModel,
true,
0.0, // double azimuth, // azimuth of the lens entrance pupil center, degrees, clockwise looking from top
0.0, // double radius, // mm, distance from the rotation axis
0.0, // double height, // mm, up (was downwards) - from the origin point
......@@ -1282,6 +1342,8 @@ import org.apache.commons.configuration.XMLConfiguration;
} else {
// default setup for the 26 sub-cameras
for (int i=0;i<8;i++) if (i<numSubCameras) this.eyesisSubCameras[numStation][i]=new EyesisSubCameraParameters( // top 8 cameras
defaultLensDistortionModel,
true,
45.0*i, // double azimuth, // azimuth of the lens entrance pupil center, degrees, clockwise looking from top
41.540, // double radius, // mm, distance from the rotation axis
42.883, // double height, // mm, up (was downwards?) - from the origin point
......@@ -1304,6 +1366,8 @@ import org.apache.commons.configuration.XMLConfiguration;
null, // elongation for c,b,a,a5,a6,a7,a8
1.0); //channelWeightDefault
for (int i=8;i<16;i++) if (i<numSubCameras) this.eyesisSubCameras[numStation][i]=new EyesisSubCameraParameters( // middle 8 cameras
defaultLensDistortionModel,
true,
45.0*(i-8), // double azimuth, // azimuth of the lens entrance pupil center, degrees, clockwise looking from top
54.525, // double radius, // mm, distance from the rotation axis
0.0, // double height, // mm, up (was downwards) - from the origin point
......@@ -1326,6 +1390,8 @@ import org.apache.commons.configuration.XMLConfiguration;
null, // elongation for c,b,a,a5,a6,a7,a8
1.0); //channelWeightDefault
for (int i=16;i<24;i++) if (i<numSubCameras) this.eyesisSubCameras[numStation][i]=new EyesisSubCameraParameters( // bottom eight cameras
defaultLensDistortionModel,
true,
45.0*(i-16), // double azimuth, // azimuth of the lens entrance pupil center, degrees, clockwise looking from top
41.540, // double radius, // mm, distance from the rotation axis
-42.883, // double height, // mm, up (was downwards?) - from the origin point
......@@ -1348,6 +1414,8 @@ import org.apache.commons.configuration.XMLConfiguration;
null, // elongation for c,b,a,a5,a6,a7,a8
1.0); //channelWeightDefault
if (24<numSubCameras) this.eyesisSubCameras[numStation][24]=new EyesisSubCameraParameters(
defaultLensDistortionModel,
false,
90, // double azimuth, // azimuth of the lens entrance pupil center, degrees, clockwise looking from top
12.025, // double radius, // mm, distance from the rotation axis
-807.0, // double height, // mm, up - from the origin point
......@@ -1370,6 +1438,8 @@ import org.apache.commons.configuration.XMLConfiguration;
null, // elongation for c,b,a,a5,a6,a7,a8
8.0); //channelWeightDefault (was 4)
if (25<numSubCameras) this.eyesisSubCameras[numStation][25]=new EyesisSubCameraParameters(
defaultLensDistortionModel,
false,
270, // double azimuth, // azimuth of the lens entrance pupil center, degrees, clockwise looking from top
12.025, // double radius, // mm, distance from the rotation axis
-841.0, // double height, // mm, up - from the origin point
......
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
......@@ -30,7 +30,12 @@ import java.io.File;
import java.io.FileWriter;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
import java.util.Set;
import org.apache.commons.configuration.ConfigurationException;
import org.apache.commons.configuration.XMLConfiguration;
......@@ -1394,6 +1399,448 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit
for (int i=0;i<this.parameterList.length;i++) if ((this.parameterList[i][0]==nSub) && (this.parameterList[i][1]==index)) return i;
return -1;
}
private int [] arrayToSortedInt(int [] srcArray){
Set<Integer> set = new HashSet<Integer>();
for (Integer data:srcArray) set.add(data);
int [] array = new int [set.size()];
int i=0;
for (Integer val:set) array[i++]= val;
Arrays.sort(array);
return array;
}
public boolean selectIndividualImages(
boolean [] selection,
boolean allImages,
int startIndex,
int perPage){
boolean [] enabled= this.distortionCalibrationData.selectEnabled();
int [] hintedMatch=this.distortionCalibrationData.getHintedMatch();
if (selection.length!=enabled.length){
System.out.println("BUG: selectIndividualImages(): selection.length!=enabled.length!");
return false;
}
int endIndex=startIndex;
int numImg=0;
for (endIndex=startIndex; (endIndex<enabled.length) && (numImg<perPage);endIndex++) if (allImages || enabled[endIndex]) numImg++;
for (;(endIndex<enabled.length) && !allImages && !enabled[endIndex];endIndex++); // advance over disabled images
GenericDialog gd=new GenericDialog("Select images "+startIndex+"..."+(endIndex-1));
for (int i=startIndex;i<endIndex;i++) if (allImages || enabled[i]){
gd.addCheckbox (i+" - "+(this.distortionCalibrationData.gIP[i].enabled?"":"(disabled) ")+
IJ.d2s(this.distortionCalibrationData.gIP[i].timestamp,6)+
": "+this.distortionCalibrationData.gIP[i].channel+
" matched "+this.distortionCalibrationData.gIP[i].matchedPointers+" pointers"+
", hinted state: "+((hintedMatch[i]<0)?"undefined":((hintedMatch[i]==0)?"failed":((hintedMatch[i]==1)?"orientation":"orientation and translation"))),
selection[i]);
}
if (endIndex<enabled.length){
gd.enableYesNoCancel("Done", "Next");
}
WindowTools.addScrollBars(gd);
gd.showDialog();
if (gd.wasCanceled()) return false;
for (int i=startIndex;i<endIndex;i++) if (allImages || enabled[i]){
selection[i]=gd.getNextBoolean();
}
if (gd.wasOKed()) return true;
return selectIndividualImages(
selection,
allImages,
endIndex,
perPage);
}
public boolean selectImageSets(
boolean [] selection,
boolean allImages,
int startIndex,
int perPage){
boolean [] enabled= this.distortionCalibrationData.selectEnabled();
int [] imageStations=this.distortionCalibrationData.getStations();
int [] imageChannels=this.distortionCalibrationData.getChannels();
if (selection.length!=enabled.length){
System.out.println("BUG: selectIndividualImages(): selection.length!=enabled.length!");
return false;
}
int [][] imageSets=this.distortionCalibrationData.listImages(!allImages); // true - only enabled images
boolean [] enabledSets=new boolean [imageSets.length];
boolean [] selectedSets=new boolean [imageSets.length]; // at least one image selected in the series
for (int i=0;i<imageSets.length;i++){
enabledSets[i]=false;
selectedSets[i]=false;
if (imageSets[i]!=null) for (int j=0;j<imageSets[i].length;j++){
enabledSets[i] |= enabled[imageSets[i][j]];
selectedSets[i] |= selection[imageSets[i][j]];
}
}
int endIndex=startIndex;
int numSet=0;
for (endIndex=startIndex; (endIndex<enabledSets.length) && (numSet<perPage);endIndex++) if (enabledSets[endIndex]) numSet++;
for (;(endIndex<enabledSets.length) && !enabledSets[endIndex];endIndex++); // advance over disabled sets
GenericDialog gd=new GenericDialog("Select image Sets "+startIndex+"..."+(endIndex-1));
for (int i=startIndex;i<endIndex;i++) if (enabledSets[i]){
int station=-1;
String sImgList="";
int l=0;
for (int j=0;j<imageSets[i].length;j++) if (enabled[imageSets[i][j]]) {
station=imageStations[imageSets[i][j]];
int channel=imageChannels[imageSets[i][j]];
if (l > 0) sImgList+=", ";
sImgList+=imageSets[i][j]+" ["+channel+"] ";
l++;
}
gd.addCheckbox (i+" ("+sImgList+") === Station_"+(station+1), selectedSets[i]);
}
if (endIndex<enabledSets.length){
gd.enableYesNoCancel("Done", "Next");
}
WindowTools.addScrollBars(gd);
gd.showDialog();
if (gd.wasCanceled()) return false;
// Arrays.fill(selection, false);
for (int i=startIndex;i<endIndex;i++) if (enabledSets[i]){
selectedSets[i]=gd.getNextBoolean();
for (int j=0;j<imageSets[i].length;j++) {
selection[imageSets[i][j]]=selectedSets[i];
}
}
if (gd.wasOKed()) return true;
return selectImageSets(
selection,
allImages,
endIndex,
perPage);
}
/**
* Manage image selection for the current series
* @param numSeries series number to manage
* @return -1 - cancel, 0 - repeat again, 1 - Done,
*/
public int manageSelection(
int numSeries){
// String [] firstOperand= {"Current","Inverted current","None","All"};
// String [] SecondOperand={"Selection","Inverted selection","None","All"};
// String [] operation={"And","Or"};
String [] actions={
"Replace current with new selection",
"Add selection to current",
"Add inverted selection to current",
"And selection with current",
"Remove selection from current",
"Invert current selection, disregard other settings"};
String [] selectionType={
"Select from all enabled images", // 0
"Select from new enabled images", // 1
"Select from images with estimated orientation", // 2
"Individual images, start from empty selection", // 3
"Individual images, start from current selection",// 4
"Image sets, start from empty selection", // 5
"Image sets, start from current selection" // 6
};
int numStations=this.distortionCalibrationData.eyesisCameraParameters.getNumStations();
int numChannels=this.distortionCalibrationData.eyesisCameraParameters.getNumChannels(0); // for station 0
boolean [] selected= this.selectedImages[numSeries];
boolean [] enabled= this.distortionCalibrationData.selectEnabled();
boolean [] newEnabled= this.distortionCalibrationData.selectNewEnabled ();
boolean [] estimated= this.distortionCalibrationData.selectEstimated(true); //boolean enabledOnly);
boolean [] estimatedAll= this.distortionCalibrationData.selectEstimated(false); //boolean enabledOnly);
if (selected.length!=enabled.length){
System.out.println("WARNING: manageSelection(): lengths (strategy and images) mismatch selected.length="+selected.length+" available images: "+enabled.length);
boolean [] newSelection=new boolean[enabled.length];
for (int i=0;i<newSelection.length;i++) newSelection[i]=(i<enabled.length)?enabled[i]:false;
selected=newSelection;
this.selectedImages[numSeries]=selected;
}
int numSelected=0;
int [] numSelectedPerStation=new int [numStations];
Arrays.fill(numSelectedPerStation, 0);
int numEnabled = 0; // this.distortionCalibrationData.getNumEnabled();
int [] numEnabledPerStation=new int [numStations];
Arrays.fill(numEnabledPerStation, 0);
int [] totalPerStation=new int [numStations];
Arrays.fill(totalPerStation, 0);
int [] imageStations=this.distortionCalibrationData.getStations();
int [] imageChannels=this.distortionCalibrationData.getChannels();
int numNewEnabled=0;
int [] numNewEnabledPerStation=new int [numStations];
Arrays.fill(numNewEnabledPerStation, 0);
int numNewEnabledSelected=0;
int [] numNewEnabledSelectedPerStation=new int [numStations];
Arrays.fill(numNewEnabledSelectedPerStation, 0);
int numEstimatedSelected=0;
int [] numEstimatedSelectedPerStation=new int [numStations];
Arrays.fill(numEstimatedSelectedPerStation, 0);
int numEstimated=0;
int [] numEstimatedPerStation=new int [numStations];
Arrays.fill(numEstimatedPerStation, 0);
int numEstimatedAll=0;
int [] numEstimatedAllPerStation=new int [numStations];
Arrays.fill(numEstimatedAllPerStation, 0);
int [] matchedPointers=this.distortionCalibrationData.getMatchedPointers();
int [] matchedPointersIndex=arrayToSortedInt(matchedPointers);
int [] hintedMatch=this.distortionCalibrationData.getHintedMatch();
int [] hintedMatchIndex=arrayToSortedInt(hintedMatch);
Map <Integer,Integer> mapMP=new HashMap<Integer,Integer>();
Map <Integer,Integer> mapHM=new HashMap<Integer,Integer>();
for (Integer index=0;index<matchedPointersIndex.length;index++) mapMP.put(new Integer(matchedPointersIndex[index]),index);
for (Integer index=0;index<hintedMatchIndex.length;index++) mapHM.put(new Integer(hintedMatchIndex[index]),index);
int [] numMatchedPointers= new int [matchedPointersIndex.length];
int [] numMatchedPointersSelected=new int [matchedPointersIndex.length];
int [] numMatchedPointersEnabled= new int [matchedPointersIndex.length];
int [][] numMatchedPointersPerStation= new int [matchedPointersIndex.length][];
int [][] numMatchedPointersSelectedPerStation=new int [matchedPointersIndex.length][];
int [][] numMatchedPointersEnabledPerStation= new int [matchedPointersIndex.length][];
for (int n=0;n<numMatchedPointers.length;n++){
numMatchedPointers[n]=0;
numMatchedPointersSelected[n]=0;
numMatchedPointersEnabled[n]=0;
numMatchedPointersPerStation[n]=new int [numStations];
numMatchedPointersSelectedPerStation[n]=new int [numStations];
numMatchedPointersEnabledPerStation[n]=new int [numStations];
Arrays.fill(numMatchedPointersPerStation[n], 0);
Arrays.fill(numMatchedPointersSelectedPerStation[n], 0);
Arrays.fill(numMatchedPointersEnabledPerStation[n], 0);
}
int [] numHintedMatch= new int [matchedPointersIndex.length];
int [] numHintedMatchSelected=new int [matchedPointersIndex.length];
int [] numHintedMatchEnabled= new int [matchedPointersIndex.length];
int [][] numHintedMatchPerStation= new int [matchedPointersIndex.length][];
int [][] numHintedMatchSelectedPerStation=new int [matchedPointersIndex.length][];
int [][] numHintedMatchEnabledPerStation= new int [matchedPointersIndex.length][];
for (int n=0;n<numHintedMatch.length;n++){
numHintedMatch[n]=0;
numHintedMatchSelected[n]=0;
numHintedMatchEnabled[n]=0;
numHintedMatchPerStation[n]=new int [numStations];
numHintedMatchSelectedPerStation[n]=new int [numStations];
numHintedMatchEnabledPerStation[n]=new int [numStations];
Arrays.fill(numHintedMatchPerStation[n], 0);
Arrays.fill(numHintedMatchSelectedPerStation[n], 0);
Arrays.fill(numHintedMatchEnabledPerStation[n], 0);
}
for (int i=0;i<selected.length;i++) if (imageStations[i]>=0){
int mpi=mapMP.get(new Integer(matchedPointers[i]));
int hmi=mapHM.get(new Integer(hintedMatch[i]));
if (enabled[i]) {
numEnabledPerStation[imageStations[i]]++;
numEnabled++;
if (selected[i]) {
numSelectedPerStation[imageStations[i]]++;
numSelected++;
numMatchedPointersSelectedPerStation[mpi][imageStations[i]]++;
numMatchedPointersSelected[mpi]++;
numHintedMatchSelectedPerStation[hmi][imageStations[i]]++;
numHintedMatchSelected[hmi]++;
}
if (newEnabled[i]){
numNewEnabledPerStation[imageStations[i]]++;
numNewEnabled++;
if (selected[i]) {
numNewEnabledSelectedPerStation[imageStations[i]]++;
numNewEnabledSelected++;
}
}
if (estimated[i]){
numEstimatedPerStation[imageStations[i]]++;
numEstimated++;
if (selected[i]) {
numEstimatedSelectedPerStation[imageStations[i]]++;
numEstimatedSelected++;
}
}
numMatchedPointersEnabledPerStation[mpi][imageStations[i]]++;
numMatchedPointersEnabled[mpi]++;
numHintedMatchEnabledPerStation[hmi][imageStations[i]]++;
numHintedMatchEnabled[hmi]++;
}
if (estimatedAll[i]){
numEstimatedAllPerStation[imageStations[i]]++;
numEstimatedAll++;
}
numMatchedPointersPerStation[mpi][imageStations[i]]++;
numMatchedPointers[mpi]++;
numHintedMatchPerStation[hmi][imageStations[i]]++;
numHintedMatch[hmi]++;
totalPerStation[imageStations[i]]++;
}
String sAvailable="["+numSelected+"/"+numEnabled+"/"+selected.length+"] ";
String sNewEnabled="["+numNewEnabledSelected+"/"+numNewEnabled+"] ";
String sEstimated="["+numEstimatedSelected+"/"+numEstimated+"/"+numEstimatedAll+"] ";
String [] sMatchedPointers=new String [matchedPointersIndex.length];
String [] sHintedMatch=new String [hintedMatchIndex.length];
for (int n=0;n<sMatchedPointers.length;n++){
sMatchedPointers[n]="["+numMatchedPointersSelected[n]+"/"+numMatchedPointersEnabled[n]+"/"+numMatchedPointers[n]+"] ";
}
for (int n=0;n<sHintedMatch.length;n++){
sHintedMatch[n]="["+numHintedMatchSelected[n]+" / "+numHintedMatchEnabled[n]+" / "+numHintedMatch[n]+"] ";
}
if (numStations>1) for (int i=0;i<numStations;i++) {
sAvailable+= " station_"+(i+1)+": ["+numSelectedPerStation[i]+" / "+numEnabledPerStation[i]+" / "+totalPerStation[i]+"]";
sNewEnabled+=" station_"+(i+1)+": ["+numNewEnabledSelectedPerStation[i]+" / "+numNewEnabledPerStation[i]+"]";
sEstimated+=" station_"+(i+1)+": ["+numEstimatedSelectedPerStation[i]+" / "+numEstimatedPerStation[i]+" / "+numEstimatedAllPerStation[i]+"]";
for (int n=0;n<sMatchedPointers.length;n++){
sMatchedPointers[n]+=" station_"+(i+1)+": ["+numMatchedPointersSelectedPerStation[n][i]+" / "+
numMatchedPointersEnabledPerStation[n][i]+" / "+numMatchedPointersPerStation[n][i]+"]";
}
for (int n=0;n<sHintedMatch.length;n++){
sHintedMatch[n]+=" station_"+(i+1)+": ["+numHintedMatchSelectedPerStation[n][i]+" / "+
numHintedMatchEnabledPerStation[n][i]+" / "+numHintedMatchPerStation[n][i]+"]";
}
}
int operIndex=0,selectionTypeIndex=0;
// boolean selectEstimated=false;
// boolean selectNewEnabled=false;
boolean [] requiredMatchedPointers=new boolean [matchedPointersIndex.length];
boolean [] requiredHintedMatch=new boolean [hintedMatchIndex.length];
boolean [] requiredStations=new boolean [numStations];
boolean [] requiredChannels=new boolean [numChannels];
Arrays.fill(requiredMatchedPointers,true);
Arrays.fill(requiredHintedMatch,true);
Arrays.fill(requiredStations,true);
Arrays.fill(requiredChannels,true);
selectionType[0]+=" ("+numEnabled+")";
selectionType[1]+=" ("+numNewEnabled+")";
selectionType[2]+=" ("+numEstimated+")";
if (this.debugLevel>0){
System.out.println("Image statistics for series "+numSeries+": [currently selected/enabled/total]");
System.out.println("Grid images:"+sAvailable);
System.out.println("New enabled images: "+sNewEnabled);
System.out.println("Estimated orientation: "+sEstimated);
for (int n=0;n<sMatchedPointers.length;n++) System.out.println("Images with "+matchedPointersIndex[n]+" pointers: "+sMatchedPointers[n]);
for (int n=0;n<sHintedMatch.length;n++) System.out.println("Images with hinted match state=\""+hintedMatchIndex[n]+"\": "+sHintedMatch[n]);
System.out.println();
}
GenericDialog gd=new GenericDialog("Manage image selection for series "+numSeries);
gd.addMessage("Image statistics: [currently selected/enabled/total]");
gd.addMessage("Grid images:"+sAvailable);
gd.addMessage("New enabled images: "+sNewEnabled);
gd.addMessage("Estimated orientation: "+sEstimated);
for (int n=0;n<sMatchedPointers.length;n++) gd.addMessage("Images with "+matchedPointersIndex[n]+" pointers: "+sMatchedPointers[n]);
for (int n=0;n<sHintedMatch.length;n++) gd.addMessage("Images with hinted match state=\""+hintedMatchIndex[n]+"\": "+sHintedMatch[n]);
gd.addChoice("Operation on selection", actions, actions[operIndex]);
gd.addChoice("Selection type", selectionType, selectionType[selectionTypeIndex]);
//selectionType
// gd.addCheckbox("Select images with estimated orientation", selectEstimated);
// gd.addCheckbox("Select new enabled images", selectNewEnabled);
gd.addMessage("=== Filter selection by the number of matched laser pointers ===");
for (int i=0;i<matchedPointersIndex.length;i++){
gd.addCheckbox("Select images with "+matchedPointersIndex[i]+" pointers", requiredMatchedPointers[i]);
}
gd.addMessage("=== Filter selection by the hinted match state (-1 - none, 1 - orientation, 2 - position and orientation) ===");
for (int i=0;i<hintedMatchIndex.length;i++){
gd.addCheckbox("Select images hintedMatch="+hintedMatchIndex[i], requiredHintedMatch[i]);
}
gd.addMessage("=== Limit selection by the station ===");
for (int i=0;i<requiredStations.length;i++){
gd.addCheckbox("Select station "+(i+1), requiredStations[i]);
}
gd.addMessage("=== Limit selection by the channel ===");
for (int i=0;i<requiredChannels.length;i++){
gd.addCheckbox("Select channel "+i, requiredChannels[i]);
}
gd.enableYesNoCancel("OK", "More");
WindowTools.addScrollBars(gd);
gd.showDialog();
if (gd.wasCanceled()) return -1;
boolean more=!gd.wasOKed();
operIndex=gd.getNextChoiceIndex();
selectionTypeIndex=gd.getNextChoiceIndex(); // TODO:Implement!
// selectEstimated=gd.getNextBoolean();
// selectNewEnabled=gd.getNextBoolean();
for (int i=0;i<matchedPointersIndex.length;i++) requiredMatchedPointers[i]=gd.getNextBoolean();
for (int i=0;i<hintedMatchIndex.length;i++) requiredHintedMatch[i]= gd.getNextBoolean();
for (int i=0;i<requiredStations.length;i++) requiredStations[i]=gd.getNextBoolean();
for (int i=0;i<requiredChannels.length;i++) requiredChannels[i]=gd.getNextBoolean();
boolean [] selection=new boolean [enabled.length];
Arrays.fill(selection,false);
switch (selectionTypeIndex){
case 0:
selection=enabled.clone();
break;
case 1:
selection=newEnabled.clone();
break;
case 2:
selection=estimated.clone();
break;
case 4: // start from current selection
selection=selected.clone();
case 3: // start from empty selection
if (!selectIndividualImages(
selection,
false, // allImages,
0, // star iIndex
500)) return -1; //perPage))
case 6: // start from current selection
selection=selected.clone();
case 5: // start from empty selection
if (!selectImageSets(
selection,
false, // allImages,
0, // star iIndex
500)) return -1; //perPage))
}
for (int i=0;i<selection.length;i++) selection[i] &= requiredMatchedPointers[mapMP.get(new Integer(matchedPointers[i]))];
for (int i=0;i<selection.length;i++) selection[i] &= requiredHintedMatch[mapHM.get(new Integer(hintedMatch[i]))];
for (int i=0;i<selection.length;i++) if (imageStations[i]>=0) selection[i] &= requiredStations[imageStations[i]];
else selection[i] = false;
for (int i=0;i<selection.length;i++) if (imageChannels[i]>=0) selection[i] &= requiredChannels[imageChannels[i]];
else selection[i] = false;
// now combine new/old selections
switch (operIndex){
case 0: // keep new selection
break;
case 1:
for (int i=0;i<selection.length;i++) selection[i] |= selected[i]; // OR
break;
case 2:
for (int i=0;i<selection.length;i++) selection[i] = selected[i] | !selection[i]; // OR-NOT
break;
case 3:
for (int i=0;i<selection.length;i++) selection[i] = selected[i] && selection[i]; // AND
break;
case 4:
for (int i=0;i<selection.length;i++) selection[i] = selected[i] && !selection[i]; // AND-NOT
break;
case 5:
for (int i=0;i<selection.length;i++) selection[i]= !selected[i];
break;
}
// Remove disabled
for (int i=0;i<selection.length;i++) selection[i] &= enabled[i];
// replace current selection
this.selectedImages[numSeries]=selection;
return more?0:1;
}
/**
*
......@@ -1402,7 +1849,7 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit
* @param fromToImages - limit number of checkboxes, otherwise window does not show the bottom ones
* @param useParameters Select parameters for this series
* @param askNextSeries Ask for next series number
* @param zeroAndOther use 2 channels 0 and "other", propagete settings for channel 1 to all the rest
* @param zeroAndOther use 2 channels 0 and "other", propagate settings for channel 1 to all the rest
* @return -2 - cancel, -1, done, otherwise - number of step to edit
*/
public int selectStrategyStep(
......@@ -1417,6 +1864,7 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit
){
boolean showDirectMap=false;
boolean showReverseMap=false;
boolean showAdvancedImageSelection=false;
// if current series is not valid (probably just started a new one) - look for the last valid (if any)
// and copy it;
int numEstimated=this.distortionCalibrationData.getNumberOfEstimated(true); //(boolean enabledOnly
......@@ -1439,6 +1887,7 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit
}
GenericDialog gd = new GenericDialog("Fitting Strategy Step Configuration, step "+numSeries+" number of enabled images="+this.distortionCalibrationData.getNumEnabled());
gd.addCheckbox("Advanced image selection (disregard other fields)", showAdvancedImageSelection);
gd.addCheckbox("Copy all from the series below, ignore all other fields", false);
gd.addNumericField("Source series to copy from", (numSeries>0)?(numSeries-1):(numSeries+1), 0, 3, "");
gd.addCheckbox("Remove all (but first) images, reopen dialog", false); // remove all will be invalid, copied from the previous
......@@ -1465,8 +1914,8 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit
}
if (useImages) {
gd.addNumericField("Image sepection range, from", fromToImages[0], 0);
gd.addNumericField("Image sepection range, up to (inclufing)", fromToImages[1], 0);
gd.addNumericField("Image selection range, from", fromToImages[0], 0);
gd.addNumericField("Image selection range, up to (including)", fromToImages[1], 0);
gd.addMessage("Select files to include");
for (int i =0; i<this.distortionCalibrationData.getNumImages();i++)
if ((allImages || this.distortionCalibrationData.gIP[i].enabled) && (i>=fromToImages[0]) && (i<=fromToImages[1])){
......@@ -1580,6 +2029,12 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit
WindowTools.addScrollBars(gd);
gd.showDialog();
if (gd.wasCanceled()) return -2;
showAdvancedImageSelection=gd.getNextBoolean();
if (showAdvancedImageSelection){
int rslt=0;
while (rslt==0) rslt=manageSelection(numSeries);
return (rslt<0)?-2:numSeries;
}
boolean copyFromPrevious=gd.getNextBoolean();
int sourceStrategy= (int) gd.getNextNumber();
boolean removeAllImages=gd.getNextBoolean();
......@@ -1822,7 +2277,7 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit
// gd.addNumericField("Number of series in this strategy", (oldLength>0)?oldLength:1, 0); //
gd.addCheckbox ("Select images",selectImages);
gd.addNumericField("Show image checkboxes from", fromToImages[0], 0);
gd.addNumericField("Show image checkboxes up to (inclufing)", fromToImages[1], 0);
gd.addNumericField("Show image checkboxes up to (including)", fromToImages[1], 0);
gd.addCheckbox ("Select from all images (false - only enabled)",allImages);
gd.addCheckbox ("Select parameters",selectParameters);
gd.addCheckbox ("Ask for initial lambda",askLambdas);
......
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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