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imagej-elphel
Commit 3f9c52b0 authored by Andrey Filippov's avatar Andrey Filippov
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merged with lwir

parents 13959a97 047fdb5e
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Inline Side-by-side
Showing with 12103 additions and 10299 deletions
src/main/java/JP46_Reader_camera0.java
View file @ 3f9c52b0
......@@ -55,6 +55,8 @@ import org.w3c.dom.NodeList;
import org.xml.sax.InputSource;
import org.xml.sax.SAXException;
import com.elphel.imagej.readers.ImagejJp4Tiff;
import ij.IJ;
import ij.ImageJ;
import ij.ImagePlus;
......@@ -69,6 +71,7 @@ import ij.plugin.frame.PlugInFrame;
import ij.process.ImageConverter;
import ij.process.ImageProcessor;
import ij.text.TextWindow;
import loci.formats.FormatException;
......@@ -87,6 +90,8 @@ public class JP46_Reader_camera0 extends PlugInFrame implements ActionListener {
static File dir;
ImagejJp4Tiff imagejJp4Tiff = new ImagejJp4Tiff();
public String camera_url = "http://192.168.0.236:8081/";
public String camera_img = "bimg";
public String camera_img_new = "towp/wait/bimg"; // will always wait for the next image (repetitive acquisitions get new images)
......@@ -109,8 +114,9 @@ public class JP46_Reader_camera0 extends PlugInFrame implements ActionListener {
panel1 = new Panel();
panel1.setLayout(new GridLayout(6, 1, 50, 5));
panel1.setLayout(new GridLayout(8, 1, 50, 5));
addButton("Open JP4/Tiff...",panel1);
addButton("Open JP4/JP46...",panel1);
addButton("Open JP4/JP46 from camera",panel1);
addButton("Configure...",panel1);
......@@ -137,8 +143,8 @@ public class JP46_Reader_camera0 extends PlugInFrame implements ActionListener {
panel1 = new Panel();
panel1.setLayout(new GridLayout(6, 1, 50, 5));
panel1.setLayout(new GridLayout(8, 1, 50, 5));
addButton("Open JP4/Tiff...",panel1);
addButton("Open JP4/JP46...",panel1);
addButton("Open JP4/JP46 from camera",panel1);
addButton("Configure...",panel1);
......@@ -169,7 +175,11 @@ public class JP46_Reader_camera0 extends PlugInFrame implements ActionListener {
if (label==null) return;
/* button */
if (label.equals("Open JP4/JP46...")) {
if (label.equals("Open JP4/Tiff...")) {
read_jp4Tiff(arg,true);
}else if (label.equals("Open JP4/Tiff (no scale)...")) {
read_jp4Tiff(arg,false);
}else if (label.equals("Open JP4/JP46...")) {
read_jp46(arg,true);
}else if (label.equals("Open JP4/JP46 (no scale)...")) {
read_jp46(arg,false);
......@@ -227,7 +237,54 @@ public class JP46_Reader_camera0 extends PlugInFrame implements ActionListener {
imp_stack.getProcessor().resetMinAndMax();
imp_stack.show();
}
public void read_jp4Tiff(String arg, // not used?
boolean scale) {
String LOG_LEVEL = ABSOLUTELY_SILENT? "OFF" : (IS_SILENT?"ERROR":"INFO");
boolean LOG_LEVEL_SET = loci.common.DebugTools.enableLogging(LOG_LEVEL);
if (!LOG_LEVEL_SET) { // only first time true
loci.common.DebugTools.setRootLevel(LOG_LEVEL);
}
JFileChooser fc=null;
//try {fc = new JFileChooser();}
fc = new JFileChooser();
//catch (Throwable e) {IJ.error("This plugin requires Java 2 or Swing."); return;}
fc.setMultiSelectionEnabled(true);
if (dir==null) {
String sdir = OpenDialog.getDefaultDirectory();
if (sdir!=null)
dir = new File(sdir);
}
if (dir!=null)
fc.setCurrentDirectory(dir);
int returnVal = fc.showOpenDialog(IJ.getInstance());
if (returnVal!=JFileChooser.APPROVE_OPTION)
return;
File[] files = fc.getSelectedFiles();
if (files.length==0) { // getSelectedFiles does not work on some JVMs
files = new File[1];
files[0] = fc.getSelectedFile();
}
String path = fc.getCurrentDirectory().getPath()+Prefs.getFileSeparator();
dir = fc.getCurrentDirectory();
for (int i=0; i<files.length; i++) {
try {
ImagePlus imp = imagejJp4Tiff.readTiffJp4(path + files[i].getName(), scale);
// imp.updateAndDraw();
imp.show();
} catch (IOException | FormatException e) {
// TODO Auto-generated catch block
e.printStackTrace();
} // throws IOException, FormatException { // std - include non-elphel properties with prefix std
// open(path, files[i].getName(), arg, scale);
}
}
public void read_jp46(String arg, boolean scale) {
JFileChooser fc=null;
//try {fc = new JFileChooser();}
......@@ -274,6 +331,7 @@ public class JP46_Reader_camera0 extends PlugInFrame implements ActionListener {
confpanel = new Panel();
gd.addPanel(confpanel);
addButton("Open JP4/Tiff (no scale)...", confpanel);
addButton("Open JP4/JP46 (no scale)...", confpanel);
addButton("Open JP4/JP46 from camera (no scale)", confpanel);
......@@ -1413,9 +1471,13 @@ Exception in thread "Thread-3564" java.lang.ArrayIndexOutOfBoundsException: 8970
NodeList allNodes=doc.getDocumentElement().getElementsByTagName("*");
for (int i=0;i<allNodes.getLength();i++) {
String name= allNodes.item(i).getNodeName();
String value=allNodes.item(i).getFirstChild().getNodeValue();
imp.setProperty(name, value);
String value="";
try {
value=allNodes.item(i).getFirstChild().getNodeValue();
} catch(Exception e) {
}
imp.setProperty(name, value);
}
return true;
......
src/main/java/com/elphel/imagej/calibration/DistortionProcessConfiguration.java
View file @ 3f9c52b0
......@@ -23,15 +23,16 @@ package com.elphel.imagej.calibration;
**
*/
import ij.IJ;
import ij.Prefs;
import ij.gui.GenericDialog;
import java.io.File;
import java.io.FilenameFilter;
import java.util.Properties;
import com.elphel.imagej.common.WindowTools;
import ij.IJ;
import ij.Prefs;
import ij.gui.GenericDialog;
public class DistortionProcessConfiguration{
public String sourceDirectory="";
......@@ -207,4 +208,25 @@ import com.elphel.imagej.common.WindowTools;
return sourceFiles;
}
public String[] selectSourceSets() {
File dir= new File (this.sourceDirectory);
if (this.debugLevel>1) System.out.println("selectSourceSets, dir="+this.sourceDirectory);
if (!dir.exists()) {
String error="Source directory "+this.sourceDirectory+" does not exist.";
IJ.showMessage("No files selected");
if (this.debugLevel>1) System.out.println("selectSourceFiles() ERROR:"+error);
return null;
}
File [] sourceFileSets = dir.listFiles(new FilenameFilter() {
@Override
public boolean accept(File current, String name) {
return new File(current, name).isDirectory();
}
});
String [] sourceSets = new String[sourceFileSets.length];
for (int i=0;i<sourceSets.length;i++) sourceSets[i]=sourceFileSets[i].getPath();
return sourceSets;
}
}
src/main/java/com/elphel/imagej/calibration/EyesisAberrations.java
View file @ 3f9c52b0
package com.elphel.imagej.calibration;
import ij.IJ;
import ij.ImagePlus;
import ij.ImageStack;
import ij.Prefs;
import ij.gui.GenericDialog;
import ij.io.FileSaver;
import ij.io.Opener;
import ij.process.FloatProcessor;
import ij.process.ImageProcessor;
import java.awt.Rectangle;
import java.io.File;
import java.util.ArrayList;
......@@ -19,14 +9,22 @@ import java.util.concurrent.atomic.AtomicInteger;
import javax.swing.SwingUtilities;
import com.elphel.imagej.calibration.CalibrationFileManagement.MultipleExtensionsFileFilter;
import com.elphel.imagej.calibration.SimulationPattern.SimulParameters;
import com.elphel.imagej.common.DoubleFHT;
import com.elphel.imagej.common.DoubleGaussianBlur;
import com.elphel.imagej.common.ShowDoubleFloatArrays;
import com.elphel.imagej.common.WindowTools;
import com.elphel.imagej.jp4.JP46_Reader_camera;
import ij.IJ;
import ij.ImagePlus;
import ij.ImageStack;
import ij.Prefs;
import ij.gui.GenericDialog;
import ij.io.FileSaver;
import ij.io.Opener;
import ij.process.FloatProcessor;
import ij.process.ImageProcessor;
public class EyesisAberrations {
public double [][][][] pdfKernelMap=null;
JP46_Reader_camera JP4_INSTANCE= new JP46_Reader_camera(false);
......@@ -181,6 +179,7 @@ public class EyesisAberrations {
final int numberOfKernelsInChn=tilesY*tilesX;
for (int ithread = 0; ithread < threads.length; ithread++) {
threads[ithread] = new Thread() {
@Override
public void run() {
float [] pixels=null;
double [] kernel= new double[inverseParameters.dSize*inverseParameters.dSize];
......@@ -555,7 +554,7 @@ public class EyesisAberrations {
iy=-iy;
}
ix= (ix+size) % size;
floatPixels[i]=(float) clusterMap[iy][ix];
floatPixels[i]=clusterMap[iy][ix];
}
ip.setPixels(floatPixels);
ip.resetMinAndMax();
......@@ -639,8 +638,8 @@ public class EyesisAberrations {
row2=(fftsize-row1) %fftsize;
for (col1=0;col1 < fftsize;col1++) {
col2=(fftsize-col1) %fftsize;
fht_pixels[row1*fftsize+col1]=(double) (fft[row1][col1][0]-fft[row1][col1][1]);
fht_pixels[row2*fftsize+col2]=(double) (fft[row1][col1][0]+fft[row1][col1][1]);
fht_pixels[row1*fftsize+col1]=fft[row1][col1][0]-fft[row1][col1][1];
fht_pixels[row2*fftsize+col2]=fft[row1][col1][0]+fft[row1][col1][1];
}
}
return fht_pixels;
......@@ -1279,8 +1278,11 @@ public class EyesisAberrations {
}
int rslt=matchSimulatedPattern.calculateDistortions(
null, // LwirReaderParameters lwirReaderParameters, // null is OK
distortionParameters, //
patternDetectParameters,
// patternDetectParameters.minGridPeriod/2,
// patternDetectParameters.maxGridPeriod/2,
simulParameters,
colorComponents.equalizeGreens,
imp,
......@@ -2313,6 +2315,7 @@ public class EyesisAberrations {
for (int ithread = 0; ithread < threads.length; ithread++) {
// Concurrently run in as many threads as CPUs
threads[ithread] = new Thread() {
@Override
public void run() {
// Each thread processes a few items in the total list
......@@ -2399,6 +2402,7 @@ public class EyesisAberrations {
}
final int numFinished=tilesFinishedAtomic.getAndIncrement();
SwingUtilities.invokeLater(new Runnable() {
@Override
public void run() {
IJ.showProgress(numFinished,patternCells);
}
......@@ -2679,6 +2683,8 @@ public class EyesisAberrations {
if (matchSimulatedPattern.PATTERN_GRID==null) {
double[][] distortedPattern= matchSimulatedPattern.findPatternDistorted(input_bayer, // pixel array to process (no windowing!)
patternDetectParameters,
patternDetectParameters.minGridPeriod/2,
patternDetectParameters.maxGridPeriod/2,
true, //(greensToProcess==4), // boolean greens, // this is a pattern for combined greens (diagonal), adjust results accordingly
title); // title prefix to use for debug images
......@@ -2704,7 +2710,8 @@ public class EyesisAberrations {
distortedPattern[2], //
simulParameters.subdiv,
fft_size,
simulParameters.center_for_g2);
simulParameters.center_for_g2,
false);//boolean mono
wVectors[0][0]=2.0*distortedPattern[0][0]/subpixel;
wVectors[0][1]=2.0*distortedPattern[0][1]/subpixel;
wVectors[1][0]=2.0*distortedPattern[1][0]/subpixel;
......@@ -2747,7 +2754,8 @@ public class EyesisAberrations {
simCorr, //
simulParameters.subdiv,
fft_size,
simulParameters.center_for_g2);
simulParameters.center_for_g2,
false);//boolean mono
}
// simul_pixels= simulationPattern.extractSimulPatterns (
simul_pixels= simulationPattern.extractSimulPatterns (
......@@ -4148,7 +4156,7 @@ if (globalDebugLevel>2)globalDebugLevel=0; //***********************************
ImageProcessor ip = new FloatProcessor(size,size);
float [] floatPixels = new float [size*size];
for (i=0;i<floatPixels.length;i++) {
floatPixels[i]=(float) clusterMap[i/size][i%size];
floatPixels[i]=clusterMap[i/size][i%size];
}
ip.setPixels(floatPixels);
ip.resetMinAndMax();
......@@ -4404,11 +4412,11 @@ if (globalDebugLevel>2)globalDebugLevel=0; //***********************************
if (debug) {
SDFA_INSTANCE.showArrays(debugPixels, title+"_mask_PSF");
double [] doublePixelsPSFCount=new double [pixelsPSF.length];
for (j=0;j<doublePixelsPSFCount.length;j++) doublePixelsPSFCount[j]=(double)pixelsPSFCount[j];
for (j=0;j<doublePixelsPSFCount.length;j++) doublePixelsPSFCount[j]=pixelsPSFCount[j];
SDFA_INSTANCE.showArrays(doublePixelsPSFCount, title+"_PSF_bin_count");
SDFA_INSTANCE.showArrays(pixelsPSFWeight, title+"_PSF_bin_weight");
double [] doubleContrastCache=new double [contrastCache.length];
for (j=0;j<doubleContrastCache.length;j++) doubleContrastCache[j]=(double)((contrastCache[j]>=0.0)?contrastCache[j]:-0.00001);
for (j=0;j<doubleContrastCache.length;j++) doubleContrastCache[j]=(contrastCache[j]>=0.0)?contrastCache[j]:-0.00001;
SDFA_INSTANCE.showArrays(doubleContrastCache, title+"_ContrastCache");
}
return pixelsPSF;
......@@ -4988,6 +4996,7 @@ if (globalDebugLevel>2)globalDebugLevel=0; //***********************************
this.thresholdHigh = thresholdHigh;
this.thresholdLow = thresholdLow;
}
@Override
public OTFFilterParameters clone() {
return new OTFFilterParameters(
this.deconvInvert,
......@@ -5076,6 +5085,7 @@ if (globalDebugLevel>2)globalDebugLevel=0; //***********************************
}
@Override
public PSFParameters clone(){
return new PSFParameters(
this.minContrast,
......
src/main/java/com/elphel/imagej/calibration/Goniometer.java
View file @ 3f9c52b0
......@@ -665,9 +665,12 @@ horizontal axis:
boolean noMessageBoxes=true;
int numAbsolutePoints = matchSimulatedPattern.calculateDistortions(
null, // LwirReaderParameters lwirReaderParameters, // null is OK
// allow more of grid around pointers?
distortionParameters, //
this.patternDetectParameters,
// this.patternDetectParameters.minGridPeriod/2,
// this.patternDetectParameters.maxGridPeriod/2,
simulParameters,
equalizeGreens, imp_eq,
this.laserPointers, // null, //LASER_POINTERS, //
......@@ -838,9 +841,12 @@ horizontal axis:
// matchSimulatedPatterns[numSensor].getChannel(images[numSensor])+" ");
int numAbsolutePoints = this.matchSimulatedPatterns[numSensor].calculateDistortions(
null, // LwirReaderParameters lwirReaderParameters, // null is OK
// allow more of grid around pointers?
distortionParameters, //
this.patternDetectParameters,
// this.patternDetectParameters.minGridPeriod/2,
// this.patternDetectParameters.maxGridPeriod/2,
simulParameters,
equalizeGreens, imp_eq,
this.laserPointers, // null, //LASER_POINTERS, //
......
src/main/java/com/elphel/imagej/calibration/LensAdjustment.java
View file @ 3f9c52b0
......@@ -25,7 +25,6 @@ package com.elphel.imagej.calibration;
import java.awt.Rectangle;
import java.util.Properties;
import com.elphel.imagej.calibration.SimulationPattern.SimulParameters;
import com.elphel.imagej.common.ShowDoubleFloatArrays;
import com.elphel.imagej.common.WindowTools;
......@@ -100,6 +99,7 @@ public class LensAdjustment {
ImagePlus imp_eq=matchSimulatedPattern.applyFlatField (imp); // will throw if image size mismatch
if (updating) {
double maxActualCorr= matchSimulatedPattern.refineDistortionCorrelation (
null, // LwirReaderParameters lwirReaderParameters, // null is OK
distortionParameters, //
patternDetectParameters,
simulParameters,
......@@ -133,9 +133,12 @@ public class LensAdjustment {
System.out.println("updateFocusGrid(), number of already defined grid cells (before distortions()) = "+matchSimulatedPattern.numDefinedCells());
}
matchSimulatedPattern.distortions(
null, // is not used in update mode
null, //LwirReaderParameters lwirReaderParameters, // null is OK
null, // final boolean [] triedIndices, // is not used in update mode
distortionParameters, //
patternDetectParameters,
patternDetectParameters.minGridPeriod/2,
patternDetectParameters.maxGridPeriod/2,
simulParameters,
equalizeGreens,
imp_eq, // image to process
......@@ -156,8 +159,11 @@ public class LensAdjustment {
// matchSimulatedPattern.invalidateFlatFieldForGrid(); //Keep these!
// matchSimulatedPattern.invalidateFocusMask();
numAbsolutePoints=matchSimulatedPattern.calculateDistortions( // allow more of grid around pointers?
null, // LwirReaderParameters lwirReaderParameters, // null is OK
distortionParameters, //
patternDetectParameters,
// patternDetectParameters.minGridPeriod/2,
// patternDetectParameters.maxGridPeriod/2,
simulParameters,
equalizeGreens,
imp_eq,
......@@ -806,6 +812,7 @@ public class LensAdjustment {
this.reportTemperature=reportTemperature;
this.showLegacy=showLegacy;
}
@Override
public FocusMeasurementParameters clone(){
return new FocusMeasurementParameters(
this.gridGeometryFile,
......
src/main/java/com/elphel/imagej/common/ShowDoubleFloatArrays.java
View file @ 3f9c52b0
......@@ -112,6 +112,30 @@ import ij.process.ImageProcessor;
return;
} else showArrays(pixels, width, height, titles);
}
public void showComplex(double[][][] cpixels, String title) {
int height = cpixels.length;
int width = cpixels[0].length;
double [][]pixels = new double [height*width][];
int indx = 0;
for (int y = 0; y < height; y++) {
for (int x = 0; x < width; x++) {
pixels[indx++] = cpixels[y][x];
}
}
showComplex(pixels, width, title);
}
public void showComplex(double[][] cpixels, int width, String title) {
int height = cpixels.length/width;
double [][]pixels = new double [2][cpixels.length];
for (int i = 0; i< cpixels.length; i++) {
pixels[0][i]= cpixels[i][0];
pixels[1][i]= cpixels[i][1];
}
String [] titles = {"Re", "Im"};
showArrays(pixels, width, height, true, title, titles);
}
public void showArrays(float[][] pixels, int width, int height, boolean asStack, String title, String [] titles) {
int i,j;
......
src/main/java/com/elphel/imagej/jp4/JP46_Reader_camera.java
View file @ 3f9c52b0
......@@ -1358,7 +1358,11 @@ Exception in thread "Thread-3564" java.lang.ArrayIndexOutOfBoundsException: 8970
itr=set.iterator();
while(itr.hasNext()) {
str = (String) itr.next();
try {
imp_dst.setProperty(str,prop.getProperty(str));
} catch (Exception e) {
imp_dst.setProperty(str,"");
}
}
}
}
......@@ -1407,7 +1411,12 @@ Exception in thread "Thread-3564" java.lang.ArrayIndexOutOfBoundsException: 8970
NodeList allNodes=doc.getDocumentElement().getElementsByTagName("*");
for (int i=0;i<allNodes.getLength();i++) {
String name= allNodes.item(i).getNodeName();
String value=allNodes.item(i).getFirstChild().getNodeValue();
String value="";
try {
value=allNodes.item(i).getFirstChild().getNodeValue();
} catch(Exception e) {
}
imp.setProperty(name, value);
}
......
src/main/java/com/elphel/imagej/lwir/LwirReaderParameters.java
View file @ 3f9c52b0
......@@ -26,10 +26,15 @@
*/
package com.elphel.imagej.lwir;
import java.io.File;
import java.io.FilenameFilter;
import java.util.Properties;
import com.elphel.imagej.common.GenericJTabbedDialog;
import ij.ImagePlus;
import ij.Prefs;
public class LwirReaderParameters {
private boolean parameters_updated = false;
protected int avg_number = 4; // number of measurements to average
......@@ -49,6 +54,8 @@ public class LwirReaderParameters {
protected double vnir_gain_g = 2.0;
protected double vnir_gain_rg = 0.7705; // 1.116; halogen/fluorescent
protected double vnir_gain_bg = 2.401; // 1.476;
protected boolean [] selected_channels = {true, true, true, true, true, true, true, true};
protected int max_lwir_width = 1024; //
/*
protected double [] vnir_exp_corr = {1.0, 1.0, 1.0, 1.0};
......@@ -73,11 +80,19 @@ public class LwirReaderParameters {
protected int debug_level = 0;//-3: OFF, -2:Fatal, -1:ERROR, 0:WARN, 1:INFO,2:DEBUG
protected boolean show_images = false;
// --- interface methods
public boolean is_LWIR(int width) {
return width <= max_lwir_width;
}
public boolean is_LWIR(ImagePlus imp){
return is_LWIR(imp.getWidth());
}
public int getDebugLevel() {
return this.debug_level;
}
public void setDebugLevel(int level) {
this.debug_level = level;
}
......@@ -110,9 +125,9 @@ public class LwirReaderParameters {
properties.setProperty(prefix+"max_mismatch_ms", this.max_mismatch_ms+"");
properties.setProperty(prefix+"max_frame_diff", this.max_frame_diff+"");
properties.setProperty(prefix+"debug_level", this.debug_level+"");
properties.setProperty(prefix+"selected_channels", arr_to_str(this.selected_channels));
properties.setProperty(prefix+"show_images", this.show_images+"");
}
public void getProperties(String prefix,Properties properties){
......@@ -140,8 +155,8 @@ public class LwirReaderParameters {
if (properties.getProperty(prefix+"max_mismatch_ms")!=null) this.max_mismatch_ms=Double.parseDouble(properties.getProperty(prefix+"max_mismatch_ms"));
if (properties.getProperty(prefix+"max_frame_diff")!=null) this.max_frame_diff=Integer.parseInt(properties.getProperty(prefix+"max_frame_diff"));
if (properties.getProperty(prefix+"debug_level")!=null) this.debug_level=Integer.parseInt(properties.getProperty(prefix+"debug_level"));
if (properties.getProperty(prefix+"selected_channels")!=null) this.selected_channels=str_to_barr(properties.getProperty(prefix+"selected_channels"));
if (properties.getProperty(prefix+"show_images")!=null) this.show_images= Boolean.parseBoolean(properties.getProperty(prefix+"show_images"));
parameters_updated = true;
}
@Override
......@@ -171,6 +186,7 @@ public class LwirReaderParameters {
lrp.max_mismatch_ms= this.max_mismatch_ms;
lrp.max_frame_diff= this.max_frame_diff;
lrp.debug_level= this.debug_level;
lrp.selected_channels = this.selected_channels.clone();
lrp.show_images = this.show_images;
return lrp;
}
......@@ -208,6 +224,7 @@ public class LwirReaderParameters {
(lrp.max_mismatch_ms == this.max_mismatch_ms) &&
(lrp.max_frame_diff == this.max_frame_diff) &&
(lrp.debug_level == this.debug_level) &&
(java.util.Arrays.equals(lrp.selected_channels, this.selected_channels)) &&
(lrp.show_images == this.show_images);
}
......@@ -235,6 +252,7 @@ public class LwirReaderParameters {
result = prime * result + arr_to_str(vnir_exp_corr).hashCode();
result = prime * result + arr_to_str(vnir_gcorr_rbgb).hashCode();
result = prime * result + (new Integer(lwir_trig_dly)).hashCode();
result = prime * result + arr_to_str(selected_channels).hashCode();
// next are not needed to be programmed to the cameras
// result = prime * result + (new Integer(vnir_lag)).hashCode();
// result = prime * result + (new Double(max_mismatch_ms)).hashCode();
......@@ -251,7 +269,7 @@ public class LwirReaderParameters {
gd.addStringField ("LWIR channels", arr_to_str(this.lwir_channels), 20, "Space-separated list of used LWIR camera channels, such as '0 1 2 3'");
gd.addStringField ("VNIR channels", arr_to_str(this.vnir_channels), 20, "Space-separated list of used visible range camera channels, such as '0 1 2 3'");
gd.addCheckbox ("LWIR telemetry", this.lwir_telemetry, "Set LWIR sesnors to provide telemetry data in the last 2 lines (may become mandatory later)");
gd.addNumericField("VNIR quality", this.vnir_quality, 3,6,"ms", "Visible range camera JPEG compression quality (all channels)");
gd.addNumericField("VNIR quality", this.vnir_quality, 3,6,"%", "Visible range camera JPEG compression quality (all channels)");
gd.addCheckbox ("VNIR undo white balance", this.vnir_scale, "Undo in-camera white balancing");
gd.addCheckbox ("VNIR autoexposure", this.vnir_autoexp, "Enable autoexposure for the visible range camera");
gd.addNumericField("VNIR vnir_max_autoexp_ms", this.vnir_max_autoexp_ms, 3,6,"ms", "Visible range camera maximal exposure in autoexposure mode");
......@@ -267,6 +285,7 @@ public class LwirReaderParameters {
gd.addNumericField("Max mismatch", this.max_mismatch_ms, 3,6,"ms","Maximal mismatch between image timestamps. Larger mismatch requires LWIR sinsor reinitialization");
gd.addNumericField("Max frame diff",this.max_frame_diff, 0,3,"","Maximal difference in frames between simultaneously acquired channels as calculated from the timestamps");
gd.addNumericField("Debug level", this.debug_level, 0,3,"","Image acquisition log level: -3: OFF, -2:FATAL, -1:ERROR, 0:WARN, 1:INFO, 2:DEBUG");
gd.addStringField ("Selected channels", arr_to_str(this.selected_channels), 20, "Space-separated channel selection (1 - selected, 0 - unselected)");
gd.addCheckbox ("Show images", this.show_images, "Show acquired images after averaging)");
}
......@@ -295,8 +314,8 @@ public class LwirReaderParameters {
this.max_mismatch_ms = gd.getNextNumber();
this.max_frame_diff = (int) gd.getNextNumber();
this.debug_level = (int) gd.getNextNumber();
this.selected_channels = str_to_barr(gd.getNextString());
this.show_images = gd.getNextBoolean();
parameters_updated = true;
}
......@@ -320,6 +339,80 @@ public class LwirReaderParameters {
parameters_updated = false;
}
public boolean [] getSelected(){
return selected_channels;
}
public boolean [] getSelectedLwir(){
boolean [] sel = selected_channels.clone();
for (int i = lwir_channels.length; i < sel.length; i++ ) {
sel[i] = false;
}
return sel;
}
public boolean [] getSelectedVnir(){
boolean [] sel = selected_channels.clone();
for (int i = 0; i < lwir_channels.length; i++ ) {
sel[i] = false;
}
return sel;
}
public String [] getSourceFilesFlat(String [] sets, boolean[] channels) {
int num_sel = 0;
for (boolean s: channels) if (s) num_sel++;
String [] files = new String [sets.length * num_sel];
int indx = 0;
for (String set:sets) {
for (int i = 0; i < channels.length; i++) if (channels[i]) {
String file_base = set;
if (set.indexOf(Prefs.getFileSeparator()) >=0) {
file_base = set.substring(set.lastIndexOf(Prefs.getFileSeparator())+1);
}
files[indx++] =set + Prefs.getFileSeparator()+ file_base+"_"+i+".tiff";
}
}
return files;
}
// Image set may have different timestamps, only lwir0 matches
public String [][] getSourceFiles(String [] sets, boolean[] channels) {
String [][] files = new String [sets.length][channels.length];
for (int nset= 0; nset < sets.length; nset++) {
// read all files in the directory
File set_dir = new File(sets[nset]);
File [] channel_files = set_dir.listFiles(new FilenameFilter() {
@Override
public boolean accept(File current, String name) {
if (!(new File(current, name).isFile()) || !name.endsWith(".tiff")) return false;
String base = name.substring(0, name.lastIndexOf(".tiff"));
int undr = base.lastIndexOf("_");
if (undr < 0) return false;
int chn = -1;
try {
chn = Integer.parseInt(base.substring(undr + 1));
} catch (Exception e) {
}
return chn >= 0;
}
});
for (File f: channel_files) {
String base = f.getName().substring(0, f.getName().lastIndexOf(".tiff"));
int undr = base.lastIndexOf("_");
int chn = Integer.parseInt(base.substring(undr + 1));
if ((chn >= 0) && (chn < channels.length) && channels[chn]) {
files[nset][chn] = f.getPath();
}
}
}
return files;
}
// --- internal methods
private String arr_to_str(int [] arr) {
......@@ -334,6 +427,23 @@ public class LwirReaderParameters {
return s.trim();
}
private String arr_to_str(boolean [] arr) {
String s = "";
for (boolean c:arr) s+= (c?1:0)+" ";
return s.trim();
}
private boolean [] str_to_barr(String s) {
int [] iarr = str_to_iarr(s);
if (iarr == null) return null;
boolean [] barr = new boolean [iarr.length];
for (int i = 0; i < barr.length; i++) {
barr[i] = iarr[i] != 0;
}
return barr;
}
private int [] str_to_iarr(String s) {
String [] sa;
if (s.indexOf(",") >= 0) {
......@@ -362,4 +472,22 @@ public class LwirReaderParameters {
return darr;
}
public boolean [] selectSourceChannels(){
return selectSourceChannels(selected_channels);
}
public boolean [] selectSourceChannels(boolean [] sel) {
GenericJTabbedDialog gd = new GenericJTabbedDialog("Set CLT parameters",300,500);
for (int i = 0; i < sel.length; i++) {
gd.addCheckbox ("Channel "+i, sel[i], "Enable processing camera channel "+i);
}
gd.showDialog();
if (gd.wasCanceled()) return null;
for (int i = 0; i < sel.length; i++) {
sel[i] = gd.getNextBoolean();
}
return sel;
}
}
src/main/java/com/elphel/imagej/readers/EyesisTiff.java
View file @ 3f9c52b0
......@@ -640,7 +640,7 @@ the type of pixel data in this file getPixelType()
}
// copied from JP46_Reader_camera.java
public ImagePlus encodeProperiesToInfo(ImagePlus imp){
public static ImagePlus encodeProperiesToInfo(ImagePlus imp){
String info="<?xml version=\"1.0\" encoding=\"UTF-8\"?><properties>";
Set<Object> jp4_set;
Properties jp4_prop;
......@@ -661,7 +661,7 @@ the type of pixel data in this file getPixelType()
return imp;
}
public boolean decodeProperiesFromInfo(ImagePlus imp){
public static boolean decodeProperiesFromInfo(ImagePlus imp){
if (imp.getProperty("Info")==null) return false;
String xml= (String) imp.getProperty("Info");
......@@ -684,11 +684,15 @@ the type of pixel data in this file getPixelType()
NodeList allNodes=doc.getDocumentElement().getElementsByTagName("*");
for (int i=0;i<allNodes.getLength();i++) {
String name= allNodes.item(i).getNodeName();
String value=allNodes.item(i).getFirstChild().getNodeValue();
// System.out.print(name+" -> ");
String value = "";
try {
value=allNodes.item(i).getFirstChild().getNodeValue();
} catch (Exception e) {
}
// System.out.println(value);
imp.setProperty(name, value);
}
return true;
}
......
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