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

parents 01246a62 b759e500
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Showing with 1635 additions and 1089 deletions
src/main/java/Aberration_Correction.java
View file @ d531d201
......@@ -2514,8 +2514,8 @@ if (PROCESS_PARAMETERS.saveSettings) saveProperties(FILE_PARAMETERS.resultsDirec
tileY = nTile /tilesX;
tileX = nTile % tilesX;
if (tileX==0) {
if (updateStatus) IJ.showStatus("Reducing sampling aliases, row "+(tileY+1)+" of "+tilesY);
if (MASTER_DEBUG_LEVEL>2) System.out.println("Reducing sampling aliases, row "+(tileY+1)+" of "+tilesY+" : "+IJ.d2s(0.000000001*(System.nanoTime()-startTime),3));
if (updateStatus) IJ.showStatus("(3)Reducing sampling aliases, row "+(tileY+1)+" of "+tilesY);
if (MASTER_DEBUG_LEVEL>2) System.out.println("(3)Reducing sampling aliases, row "+(tileY+1)+" of "+tilesY+" : "+IJ.d2s(0.000000001*(System.nanoTime()-startTime),3));
}
if ((tileY==yTileDebug) && (tileX==xTileDebug)) DEBUG_LEVEL=4;
......
src/main/java/DebayerScissors.java
View file @ d531d201
This diff is collapsed.
src/main/java/DenseCorrespondence.java
View file @ d531d201
......@@ -39,7 +39,7 @@ public class DenseCorrespondence {
private void disparitySweepTile (
public void disparitySweepTile ( // never used so far
int tileX,
int tileY,
CyclopeanTile [][] allCyclopeanMap,
......
src/main/java/Distortions.java
View file @ d531d201
......@@ -5989,6 +5989,8 @@ List calibration
imp.setProperty("channel", ""+numSensor);
imp.setProperty("comment_subcamera", "number of the subcamera with individual IP, starting with 0");
imp.setProperty("subcamera", ""+camerasInterface.getSubCamera(numSensor));
imp.setProperty("sensor_port",""+camerasInterface.getSensorPort(numSensor));
imp.setProperty("comment_subchannel", "number of the sensor port on a subcamera (0..2)");
imp.setProperty("subchannel", ""+camerasInterface.getSubChannel(numSensor));
imp.setProperty("comment_entrancePupilForward", "entrance pupil distance from the azimuth/radius/height, outwards in mm");
......
src/main/java/EyesisAberrations.java
View file @ d531d201
......@@ -2213,7 +2213,7 @@ public class EyesisAberrations {
public double [][][][] createPSFMap(
final MatchSimulatedPattern commonMatchSimulatedPattern, // to be cloned in threads, using common data
final ImagePlus imp_sel, // linearized Bayer mosaic image form the camera, GR/BG
final ImagePlus imp_sel, // linearized Bayer mosaic image from the camera, GR/BG
final int [][][] sampleList, // optional (or null) 2-d array: list of coordinate pairs (2d - to match existent pdfKernelMap structure)
final double overexposedAllowed, // fraction of pixels OK to be overexposed
final SimulationPattern.SimulParameters simulParameters,
......@@ -2400,7 +2400,7 @@ public class EyesisAberrations {
};
}
startAndJoin(threads);
if (globalDebugLevel>1) System.out.println("Threads done at "+IJ.d2s(0.000000001*(System.nanoTime()-startTime),3));
if (globalDebugLevel>1) System.out.println("Threads done at "+IJ.d2s(0.000000001*(System.nanoTime()-startTime),3));
// globalDebugLevel=saved_globalDebugLevel;
if (debugLateralShifts) {
boolean [] debugUsedColors=new boolean [debugNumColors];
......
src/main/java/EyesisCorrections.java
View file @ d531d201
This diff is collapsed.
src/main/java/Eyesis_Correction.java
View file @ d531d201
......@@ -3464,7 +3464,7 @@ private Panel panel1,panel2,panel3,panel4,panel5,panel5a, panel6,panel7,panelPos
continue;
}
convolutionKernelStack=imp_kernels.getStack();
if (DEBUG_LEVEL>1) System.out.println("Using kernel stack "+kernelPath+" for convolution with "+result[nFile][nChn][nSubChn].getTitle());
if (DEBUG_LEVEL>1) System.out.println("(1)Using kernel stack "+kernelPath+" for convolution with "+result[nFile][nChn][nSubChn].getTitle());
stack_d= convolveStackWithKernelStack(
stack, // stack with 3 colors/slices with the image
convolutionKernelStack, // stack with 3 colors/slices convolution kernels
......@@ -3492,7 +3492,7 @@ private Panel panel1,panel2,panel3,panel4,panel5,panel5a, panel6,panel7,panelPos
continue;
}
convolutionKernelStack=imp_kernels.getStack();
if (DEBUG_LEVEL>1) System.out.println("Using Gaussian stack "+kernelPath+" for convolution with "+result[nFile][nChn][nSubChn].getTitle());
if (DEBUG_LEVEL>1) System.out.println("(2)Using Gaussian stack "+kernelPath+" for convolution with "+result[nFile][nChn][nSubChn].getTitle());
stack_g= convolveStackWithKernelStack(
stack, // stack with 3 colors/slices with the image
convolutionKernelStack, // stack with 3 colors/slices convolution kernels
......@@ -3592,7 +3592,7 @@ private Panel panel1,panel2,panel3,panel4,panel5,panel5a, panel6,panel7,panelPos
continue;
}
convolutionKernelStack=imp_kernels.getStack();
if (DEBUG_LEVEL>1) System.out.println("Using Gaussian stack "+kernelPath+" for convolution with "+result[nFile][nChn][nSubChn].getTitle());
if (DEBUG_LEVEL>1) System.out.println("(3)Using Gaussian stack "+kernelPath+" for convolution with "+result[nFile][nChn][nSubChn].getTitle());
stack_g= convolveStackWithKernelStack(
stack, // stack with 3 colors/slices with the image
convolutionKernelStack, // stack with 3 colors/slices convolution kernels
......@@ -3977,7 +3977,6 @@ private Panel panel1,panel2,panel3,panel4,panel5,panel5a, panel6,panel7,panelPos
final int tilesY=imgHeight/step-1; // vertical number of overlapping tiles in the source image (should be expanded from the registerd one by "step" in each direction)
final int kernelWidth=kernelStack.getWidth();
final int kernelNumHor=kernelWidth/(size/2);
final int nChn=imageStack.getSize();
final float [][] outPixels=new float[nChn][length]; // GLOBAL same as input
// float [][] outPixels=new float[nChn][length]; // same as input
......@@ -3988,6 +3987,21 @@ private Panel panel1,panel2,panel3,panel4,panel5,panel5a, panel6,panel7,panelPos
final AtomicInteger ai = new AtomicInteger(0);
final int numberOfKernels= tilesY*tilesX*nChn;
final int numberOfKernelsInChn=tilesY*tilesX;
if (MASTER_DEBUG_LEVEL>1)
System.out.println("Eyesis_Correction:convolveStackWithKernelStack :\n"+
"MASTER_DEBUG_LEVEL="+MASTER_DEBUG_LEVEL+"\n"+
"imgWidth="+imgWidth+"\n"+
"imgHeight="+imgHeight+"\n"+
"tilesX="+tilesX+"\n"+
"tilesY="+tilesY+"\n"+
"step="+step+"\n"+
"kernelSize="+kernelSize+"\n"+
"tilesX="+tilesX+"\n"+
"tilesY="+tilesY+"\n"+
"kernelWidth="+kernelWidth+"\n"+
"kernelNumHor="+kernelNumHor+"\n"+
"numberOfKernelsInChn="+numberOfKernelsInChn+"\n");
final long startTime = System.nanoTime();
for (int ithread = 0; ithread < threads.length; ithread++) {
threads[ithread] = new Thread() {
......@@ -4153,8 +4167,8 @@ private Panel panel1,panel2,panel3,panel4,panel5,panel5a, panel6,panel7,panelPos
tileY = nTile /tilesX;
tileX = nTile % tilesX;
if (tileX==0) {
if (updateStatus) IJ.showStatus("Reducing sampling aliases, row "+(tileY+1)+" of "+tilesY);
if (MASTER_DEBUG_LEVEL>2) System.out.println("Reducing sampling aliases, row "+(tileY+1)+" of "+tilesY+" : "+IJ.d2s(0.000000001*(System.nanoTime()-startTime),3));
if (updateStatus) IJ.showStatus("(2)Reducing sampling aliases, row "+(tileY+1)+" of "+tilesY);
if (MASTER_DEBUG_LEVEL>1) System.out.println("(2)Reducing sampling aliases, row "+(tileY+1)+" of "+tilesY+" : "+IJ.d2s(0.000000001*(System.nanoTime()-startTime),3));
}
if ((tileY==yTileDebug) && (tileX==xTileDebug)) DEBUG_LEVEL=4;
......
src/main/java/JP46_Reader_camera.java
View file @ d531d201
......@@ -346,6 +346,7 @@ public class JP46_Reader_camera implements PlugIn, ActionListener {
boolean showDemux=showImage && demux;
if (demux) showImage=false;
double [] xtraExif=new double[1]; // ExposureTime
// System.out.println("imp_src is "+((imp_src!=null)?"not ":"")+"null");
try {
......
src/main/java/PixelMapping.java
View file @ d531d201
......@@ -25,10 +25,14 @@
**
*/
import java.awt.Point;
import java.awt.Rectangle;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.BitSet;
import java.util.Collections;
import java.util.Comparator;
import java.util.List;
import java.util.concurrent.atomic.AtomicInteger;
......@@ -135,10 +139,19 @@ public class PixelMapping {
if ((channel<0) || (channel>=this.sensors.length)) return -1;
return this.sensors[channel].getSubCamera();
}
/*
public int getSensorPort(int channel ){
if ((channel<0) || (channel>=this.sensors.length)) return -1;
return this.sensors[channel].getSensorPort();
}
*/
public boolean isChannelAvailable(int channel){
return (this.sensors != null) && (channel>=0) && (channel<this.sensors.length) && (this.sensors[channel]!=null);
}
/*
public int [] channelsForSubCamera(int subCamera){
if (this.sensors == null) return null;
......@@ -149,6 +162,50 @@ public class PixelMapping {
for (int i=0;i<this.sensors.length;i++) if ((this.sensors[i]!=null) &&(this.sensors[i].subcamera==subCamera)) result[numChannels++]=i;
return result;
}
*/
// Updating for nc393. subCamera here is 0..9 for Eyesis4pi393 - 0-based index of the file, so it combines physical camera (separate IP)
// as stored in "subcamera" field of the calibration file and "sensor_port". sensor_port may start from non-0, so we need to count all combinations
public int [] channelsForSubCamera(int subCamera){
// ArrayList<ArrayList<ArrayList<Integer>>> camera_IPs = new ArrayList<ArrayList<ArrayList<Integer>>>();
ArrayList<Point> cam_port = new ArrayList<Point>();
for (int i=0;i<this.sensors.length;i++) if (this.sensors[i]!=null) {
Point cp = new Point(this.sensors[i].subcamera, this.sensors[i].sensor_port);
if (!cam_port.contains(cp)){
cam_port.add(cp);
}
}
Point [] cam_port_arr = cam_port.toArray(new Point[0]);
Arrays.sort(cam_port_arr, new Comparator<Point>() {
@Override
public int compare(Point o1, Point o2) {
return (o1.x>o2.x)? 1:((o1.x < o2.x)?-1:(o1.y > o2.y)? 1:((o1.y < o2.y)?-1:0));
}
});
// for (int i=0; i<cam_port_arr.length;i++){
// System.out.println("----- physical camera #"+cam_port_arr[i].x+", sensor_port="+cam_port_arr[i].y);
// }
System.out.println("----- This filename subcamera "+subCamera+": physical camera "+cam_port_arr[subCamera].x+", sensor_port "+cam_port_arr[subCamera].y);
if (subCamera >= cam_port_arr.length) {
System.out.println("Error: Subcamera "+subCamera+" > that total namera of sensor ports in the system = "+cam_port_arr.length);
return null;
}
if (this.sensors == null) return null;
int numChannels=0;
for (int i=0;i<this.sensors.length;i++) if (this.sensors[i]!=null) {
if (new Point(this.sensors[i].subcamera, this.sensors[i].sensor_port).equals(cam_port_arr[subCamera])) numChannels++;
}
int [] result=new int [numChannels];
numChannels=0;
for (int i=0;i<this.sensors.length;i++) if (this.sensors[i]!=null){
if (new Point(this.sensors[i].subcamera, this.sensors[i].sensor_port).equals(cam_port_arr[subCamera])) result[numChannels++]=i;
}
return result;
}
public void removeChannel(int channel){
if ((this.sensors != null) && (channel>=0) && (channel<this.sensors.length)) this.sensors[channel]=null;
}
......@@ -9403,7 +9460,8 @@ public class PixelMapping {
private BitSet innerMask=null;
private int []borderMask=null;
public int getNumberOfPlanes(){return this.maximums.length;}
public int getForegroundPlane(){return this.foregroundIndex;}
@SuppressWarnings("unused")
public int getForegroundPlane(){return this.foregroundIndex;}
public double getPlaneDisparity (int plane){return this.maximums[plane][0];}
public void setPlaneDisparity (double disparity, int plane){this.maximums[plane][0]=disparity;}
public double getPlaneStrength (int plane){return this.maximums[plane][1];}
......@@ -9441,14 +9499,16 @@ public class PixelMapping {
this.auxData=new float[n][];
for (int i=0;i<n;i++) this.auxData[i]=null;
}
public void resetAux(){
@SuppressWarnings("unused")
public void resetAux(){
this.auxData=null;
}
public void setAux(int n, float [] data){
if (this.auxData==null) initAux(n+1);
this.auxData[n]=data;
}
public float [][] getAux (){
@SuppressWarnings("unused")
public float [][] getAux (){
return this.auxData;
}
public float [] getAux (int n){
......@@ -9460,17 +9520,21 @@ public class PixelMapping {
this.likely=new float[this.numPlanes][];
for (int i=0;i<this.numPlanes;i++) this.likely[i]=null;
}
public void resetLikely(){
@SuppressWarnings("unused")
public void resetLikely(){
this.likely=null;
}
public void setLikely(int n, float [] data){
@SuppressWarnings("unused")
public void setLikely(int n, float [] data){
if (this.likely==null) initLikely();
this.likely[n]=data;
}
public float [][] getLikely (){
@SuppressWarnings("unused")
public float [][] getLikely (){
return this.likely;
}
public float [] getLikely (int n){
@SuppressWarnings("unused")
public float [] getLikely (int n){
if ((this.likely==null) || (this.likely.length<=n)) return null;
return this.likely[n];
}
......@@ -9479,17 +9543,21 @@ public class PixelMapping {
this.unlikely=new float[this.numPlanes][];
for (int i=0;i<this.numPlanes;i++) this.unlikely[i]=null;
}
public void resetUnlikely(){
@SuppressWarnings("unused")
public void resetUnlikely(){
this.unlikely=null;
}
public void setUnlikely(int n, float [] data){
@SuppressWarnings("unused")
public void setUnlikely(int n, float [] data){
if (this.unlikely==null) initUnlikely();
this.unlikely[n]=data;
}
public float [][] getUnlikely(){
@SuppressWarnings("unused")
public float [][] getUnlikely(){
return this.unlikely;
}
public float [] getUnlikely(int n){
@SuppressWarnings("unused")
public float [] getUnlikely(int n){
if ((this.unlikely==null) || (this.unlikely.length<=n)) return null;
return this.unlikely[n];
}
......@@ -9577,7 +9645,8 @@ public class PixelMapping {
* @param disparityTolerance - consider "this" as being withing disparityTolerance of disparity. NaN - do not filter by this
* @return
*/
public boolean [] getEnabledNonOccluded(
@SuppressWarnings("unused")
public boolean [] getEnabledNonOccluded(
double disparityFG,
double disparity,
double disparityTolerance){
......@@ -15527,6 +15596,7 @@ public class PixelMapping {
public int channel= -1;
public int subcamera= -1;
public int subchannel=-1;
public int sensor_port=-1;
// TODO: add serial# (and temperature?)
public double azimuth; // azimuth of the lens entrance pupil center, degrees, clockwise looking from top
public double radius; // mm, distance from the rotation axis
......@@ -16094,6 +16164,9 @@ public class PixelMapping {
public int getChannel(){return this.channel;}
public int getSubChannel(){return this.subchannel;}
public int getSubCamera(){return this.subcamera;}
public int getSensorPort(){return this.sensor_port;}
public void setSensorDataFromImageStack(ImagePlus imp){
// int corrX=0,corrY=1,corrMask=2;
if (imp == null){
......@@ -16170,6 +16243,9 @@ public class PixelMapping {
// older files do not have these properties
if (imp.getProperty("subcamera")!=null) this.subcamera= Integer.parseInt((String) imp.getProperty("subcamera"));
if (imp.getProperty("subchannel")!=null) this.subchannel=Integer.parseInt((String) imp.getProperty("subchannel"));
if (imp.getProperty("sensor_port")!=null) this.sensor_port=Integer.parseInt((String) imp.getProperty("sensor_port"));
// now read the calibration data and mask
this.pixelCorrection=null;
......
src/main/java/deBayerScissors.java
View file @ d531d201
This diff is collapsed.
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