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This commit is contained in:
gobbo_a
2016-09-08 17:54:48 +02:00
parent 4df26d6ddd
commit e7e3521da5
3 changed files with 360 additions and 408 deletions
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357
plugins/Cameras.java
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@@ -12,25 +12,18 @@ import ch.psi.pshell.imaging.ImageListener;
import ch.psi.utils.State;
import ch.psi.utils.IO;
import ch.psi.utils.swing.SwingUtils;
import ch.psi.utils.swing.ConfigDialog;
import ch.psi.utils.swing.StandardDialog;
import ch.psi.utils.swing.TextEditor;
import ch.psi.pshell.epics.PsiCamera;
import ch.psi.pshell.epics.Camtool;
import ch.psi.pshell.core.JsonSerializer;
import ch.psi.pshell.device.Device;
import ch.psi.pshell.epics.ArraySource;
import ch.psi.pshell.epics.ChannelDouble;
import ch.psi.pshell.epics.ChannelDoubleArray;
import ch.psi.pshell.epics.ChannelInteger;
import ch.psi.pshell.epics.ChannelIntegerArray;
import ch.psi.pshell.ui.App;
import ch.psi.pshell.imaging.Data;
import ch.psi.pshell.imaging.Overlay;
import ch.psi.pshell.imaging.Overlays;
import ch.psi.pshell.imaging.Pen;
import ch.psi.pshell.imaging.Renderer;
import ch.psi.pshell.imaging.PointDouble;
import ch.psi.pshell.imaging.Renderer.Profile;
import ch.psi.pshell.imaging.RendererListener;
import ch.psi.pshell.imaging.Source;
import ch.psi.pshell.imaging.Utils;
import ch.psi.pshell.scripting.InterpreterResult;
@@ -42,7 +35,7 @@ import ch.psi.utils.swing.Editor.EditorDialog;
import java.awt.Color;
import java.awt.Component;
import java.awt.Dimension;
import java.awt.Frame;
import java.awt.Point;
import java.awt.image.BufferedImage;
import java.nio.file.Files;
import java.nio.file.Path;
@@ -52,12 +45,10 @@ import java.util.HashMap;
import java.util.List;
import java.util.logging.Level;
import java.util.logging.Logger;
import java.util.stream.IntStream;
import javax.script.ScriptException;
import static javax.swing.WindowConstants.DISPOSE_ON_CLOSE;
import org.apache.commons.math3.analysis.function.Gaussian;
import org.apache.commons.math3.fitting.GaussianCurveFitter;
import org.apache.commons.math3.fitting.WeightedObservedPoint;
import org.apache.commons.math3.stat.descriptive.DescriptiveStatistics;
/**
*
*/
@@ -66,12 +57,32 @@ public class Cameras extends Panel {
public Cameras() {
initComponents();
renderer.setPersistenceFile(Paths.get(getController().getSetup().getContextPath(), "Renderer_Cameras.bin"));
renderer.setProfileFactor(4);
setPersistedComponents(new Component[]{checkCamtool});
comboCameras.setEnabled(false);
if (App.hasArgument("ct")) {
checkCamtool.setSelected(! App.getArgumentValue("ct").equals("0"));
}
if (App.hasArgument("poll")) {
try{
polling = Integer.valueOf(App.getArgumentValue("poll"));
} catch (Exception ex){
ex.printStackTrace();
}
}
if (App.hasArgument("zoom")) {
try{
renderer.setDefaultZoom(Double.valueOf(App.getArgumentValue("zoom")));
} catch (Exception ex){
ex.printStackTrace();
}
}
}
@Override
public void onStart() {
super.onStart();
if (App.hasArgument("ct")) {
checkCamtool.setSelected(!App.getArgumentValue("ct").equals("0") && !App.getArgumentValue("ct").equalsIgnoreCase("false"));
}
}
final String configFolder = "/afs/psi.ch/intranet/SF/Applications/config/camtool";
File[] cameraConfigFiles = new File[0];
@@ -79,6 +90,7 @@ public class Cameras extends Panel {
String cameraName;
String cameraConfigJson;
CameraConfig config;
int polling = 1000;
//Overridable callbacks
@Override
@@ -89,7 +101,7 @@ public class Cameras extends Panel {
renderer.setAutoScroll(true);
((Source)getDevice("image")).addListener(new ImageListener() {
@Override
public void onImage(Object o, BufferedImage bi, Data data) {
public void onImage(Object o, BufferedImage bi, Data data) {
if (bi == null) {
fitOv = null;
} else {
@@ -129,7 +141,7 @@ public class Cameras extends Panel {
}
}
}
startTimer(2000);
startTimer(1000);
}
@Override
@@ -220,6 +232,7 @@ public class Cameras extends Panel {
camera.close();
camera = null;
renderer.setDevice(null);
renderer.setShowReticle(false);
renderer.clear();
}
try {
@@ -229,8 +242,14 @@ public class Cameras extends Panel {
//SwingUtils.showMessage(null, "", json);
try {
if (checkCamtool.isSelected()) {
camera = new Camtool("CurrentCamera", cameraName, false, true);
camera = new Camtool("CurrentCamera", cameraName, false, true);
camera.getConfig().flipHorizontally = false;
camera.getConfig().flipVertically = false;
camera.getConfig().rotation = 0.0;
camera.getConfig().roiX = 0;
camera.getConfig().roiY = 0;
camera.getConfig().roiWidth = -1;
camera.getConfig().roiHeight = -1;
} else {
camera = new PsiCamera("CurrentCamera", cameraName);
config = (CameraConfig) JsonSerializer.decode(cameraConfigJson, CameraConfig.class);
@@ -262,31 +281,50 @@ public class Cameras extends Panel {
}
camera.initialize();
if (camera instanceof Camtool){
try{
camera.getConfig().spatialCalOffsetX = ((Camtool)camera).calOffX.read();
camera.getConfig().spatialCalOffsetY = ((Camtool)camera).calOffY.read();
camera.getConfig().spatialCalScaleX = ((Camtool)camera).calScaleX.read();
camera.getConfig().spatialCalScaleY = ((Camtool)camera).calScaleY.read();
} catch (Exception ex){
ex.printStackTrace();
camera.getConfig().spatialCalOffsetX = 0.0;
camera.getConfig().spatialCalOffsetY = 0.0;
camera.getConfig().spatialCalScaleX = 1.0;
camera.getConfig().spatialCalScaleY = 1.0;
}
/*
double[] origin = ((Camtool)camera).origin.read();
if (origin.length>=2){
camera.getConfig().spatialCalOffsetX = origin[0];
camera.getConfig().spatialCalOffsetY = origin[1];
}
*/
}
camera.getConfig().save();
camera.setPolling(-2000);
camera.setMonitored(false);
renderer.setDevice(camera);
renderer.setShowReticle(true);
if (polling<=0){
camera.setMonitored(true);
} else {
camera.setPolling(-polling);
}
renderer.setDevice(camera);
renderer.setAutoScroll(true);
camera.addListener(new ImageListener() {
@Override
public void onImage(Object o, BufferedImage bi, Data data) {
if (bi == null) {
renderer.removeOverlays(fitOv);
fitOv = null;
} else {
if (renderer.getReticle() != null) {
renderer.getReticle().setSize(new Dimension(bi.getWidth(), bi.getHeight()));
}
//if (renderer.getReticle() != null) {
// renderer.getReticle().setSize(new Dimension(bi.getWidth(), bi.getHeight()));
//}
//long start = System.currentTimeMillis();
Overlay[] profile = renderer.getProfileOverlays();
//System.out.println(System.currentTimeMillis() - start);
profile = ((profile != null) && (profile.length==4)) ? getFitOverlays(bi) : null;
renderer.updateOverlays(profile, fitOv);
fitOv = profile;
@@ -300,6 +338,21 @@ public class Cameras extends Panel {
});
} finally {
if (renderer.getZoom() > 1.0){
renderer.resetZoom();
}
if (camera != null) {
if (camera.getConfig().isCalibrated()){
System.out.println("Calibrated");
renderer.setCalibration(camera.getCalibration());
renderer.configureReticle(new Dimension(800,800), 200);
renderer.setShowReticle(true);
} else{
System.out.println("Not Calibrated");
}
}
onTimer();
}
}
@@ -309,7 +362,6 @@ public class Cameras extends Panel {
textState.setText((camera == null) ? "" : camera.getState().toString());
buttonConfig.setEnabled(camera != null);
if (App.hasArgument("s")){
System.out.println("Refresh");
try {
((Source)getDevice("image")).initialize();
} catch (IOException ex) {
@@ -320,30 +372,42 @@ public class Cameras extends Panel {
}
}
Pen fitPen = new Pen(new Color(0, 192, 0), 2);
Pen fitPen = new Pen(new Color(192, 105, 0), 1);
Pen crossPen = new Pen(new Color(192, 105, 0), 1);
Overlay[] getFitOverlays(BufferedImage img){
Overlays.Polyline hpoly = null;
Overlays.Polyline vpoly = null;
int factor = 2;
Double xMean = null; Double xSigma = null;
Double yMean = null; Double ySigma = null;
Profile profile = renderer.getProfile();
if ((profile != Profile.None) && (img != null)) {
img = Utils.grayscale(img);
if (profile.hasVertical()) {
try {
int[] sum = Utils.integrateVertically(img);
int[] x = Arr.indexesInt(sum.length);
double[] sum = (double[]) Convert.toDouble(Utils.integrateVertically(img));
int[] x = Arr.indexesInt(sum.length);
DescriptiveStatistics stats = new DescriptiveStatistics(sum);
double min = stats.getMin();
for (int i=0; i< sum.length; i++){
sum[i] = sum[i] - min;
}
double[] gaussian = fitGaussian(sum, x);
if (gaussian!=null){
System.out.println("Norm: " + gaussian[0] + " Mean: " + gaussian[1] + " Sigma: " + gaussian[2]);
double[] fit = getFitFunction(gaussian, x);
int[] y = new int[x.length];
for (int i = 0; i < x.length; i++) {
y[i] = (int) (img.getHeight() - 1 - (((double) fit[i]) / 255 / factor));
}
vpoly = new Overlays.Polyline(fitPen, x, y);
// System.out.println("Norm: " + gaussian[0] + " Mean: " + gaussian[1] + " Sigma: " + gaussian[2]+ " Min: " + min);
//Only aknowledge beam fully inside the image and peak over 3% of min
if ((gaussian[2] < sum.length * 0.45) && (gaussian[0] > min * 0.03)){
xMean = gaussian[1];
xSigma = gaussian[2];
gaussian[0]+=min;
double[] fit = getFitFunction(gaussian, x);
int[] y = new int[x.length];
for (int i = 0; i < x.length; i++) {
y[i] = (int) (img.getHeight() - 1 - (((double) fit[i]) / 255 / renderer.getProfileFactor()));
}
vpoly = new Overlays.Polyline(fitPen, x, y);
}
} else {
System.out.println("Fit failure");
//System.out.println("Fit failure");
}
} catch (Exception ex) {
@@ -352,53 +416,67 @@ public class Cameras extends Panel {
}
if (profile.hasHorizontal()) {
try {
int[] sum = Utils.integrateHorizontally(img);
double[] sum = (double[]) Convert.toDouble(Utils.integrateHorizontally(img));
int[] x = Arr.indexesInt(sum.length);
DescriptiveStatistics stats = new DescriptiveStatistics(sum);
double min = stats.getMin();
for (int i=0; i< sum.length; i++){
sum[i] = sum[i] - min;
}
double[] gaussian = fitGaussian(sum, x);
if (gaussian!=null){
double[] fit = getFitFunction(gaussian, x);
int[] y = new int[x.length];
for (int i = 0; i < x.length; i++) {
y[i] = (int) (((double) fit[i]) / 255 / factor);
}
hpoly = new Overlays.Polyline(fitPen, y, x);
//Only aknowledge beam fully inside the image and peak over 3% of min
if ((gaussian[2] < sum.length * 0.45) && (gaussian[0] > min * 0.03)){
yMean = gaussian[1];
ySigma = gaussian[2];
gaussian[0]+=min;
double[] fit = getFitFunction(gaussian, x);
int[] y = new int[x.length];
for (int i = 0; i < x.length; i++) {
y[i] = (int) (((double) fit[i]) / 255 / renderer.getProfileFactor());
}
hpoly = new Overlays.Polyline(fitPen, y, x);
}
}
} catch (Exception ex) {
ex.printStackTrace();
}
}
return new Overlay[]{hpoly, vpoly};
Overlays.Crosshairs cross= null;
if ((xMean!=null) && (yMean!=null)){
cross = new Overlays.Crosshairs(crossPen,
new Point(xMean.intValue(), yMean.intValue()),
new Dimension(2*xSigma.intValue(),2*ySigma.intValue()));
}
return new Overlay[]{hpoly, vpoly, cross};
}
return null;
}
double[] fitGaussianScript(int[] y, int[] x){
ScriptManager sm = Controller.getInstance().getScriptManager();
ArrayProperties pY = ArrayProperties.get(y);
sm.setVar("y", y);
sm.setVar("x", x);
//InterpreterResult r = sm.eval("r = fit(y, x)");
System.out.println("-> " + pY.maxIndex);
InterpreterResult r = sm.eval("r = fit_gaussians(y, x, [" + pY.maxIndex+ ",])");
if (r.exception != null){
r.exception .printStackTrace();
} else {
List ret = (List) sm.getVar("r");
System.out.println(ret.size());
if ((ret!=null) && (ret.size()==1)&& (ret.get(0) instanceof List) && (((List)(ret.get(0))).size()==3)){
double norm = (Double) ((List)ret.get(0)).get(0);
double mean = (Double) ((List)ret.get(0)).get(1);
double sigma = (Double) ((List)ret.get(0)).get(2);
System.out.println("! " + norm + " " + mean + " " + sigma) ;
return new double[]{norm, mean, sigma};
}
}
return null;
}
double[]fitGaussian(int[] y, int[] x){
double[]fitGaussian(double[] y, int[] x){
try{
ArrayProperties pY = ArrayProperties.get(y);
GaussianCurveFitter fitter = GaussianCurveFitter.create().withStartPoint(new double[]{(pY.max-pY.min)/2,x[pY.maxIndex],1.0}).withMaxIterations(1000);
@@ -423,174 +501,7 @@ double[]fitGaussian(int[] y, int[] x){
}
return fit;
}
/////////
public class Camtool extends ArraySource {
final String prefix;
final String dataPrefix;
final boolean latch;
final public ChannelInteger channelRun;
final public ChannelInteger channelLatch;
final public ChannelDouble channelTimestamp;
final public ChannelDoubleArray origin;
final public ChannelDouble posX, posY;
final public ChannelDoubleArray profileX, profileY;
final public ChannelIntegerArray shape;
final public ChannelInteger bgEnable, bgCapture, bgCaptureRemain;
//final public CamToolPosX posMeanX;
//final public CamToolPosY posMeanY;
//final public CamToolVarX posVarX;
//final public CamToolVarY posVarY;
public Camtool(String name, String prefix) {
this(name, prefix, false, true);
}
public Camtool(String name, String prefix, boolean latch, boolean roi) {
super(name, prefix + (latch ? ":latch" : ":pipeline") + (roi ? ".roi.output" : ".image"));
this.prefix = prefix + ":";
this.latch = latch;
dataPrefix = this.prefix + (latch ? "latch" : "pipeline") + ".";
channelRun = new ChannelInteger(name + " run", this.prefix + "camera.run");
channelLatch = new ChannelInteger(name + " latch", this.prefix + "latch.capture");
channelTimestamp = new ChannelDouble(name + " timestamp", dataPrefix + "timestamp");
channelTimestamp.setMonitored(true);
//posX = new ChannelDouble(name + " com x", dataPrefix + "x_stats.com");
//posY = new ChannelDouble(name + " com y", dataPrefix + "y_stats.com");
posX = new ChannelDouble(name + " com x", dataPrefix + "x_stats.com_egu");
posY = new ChannelDouble(name + " com y", dataPrefix + "y_stats.com_egu");
profileX = new ChannelDoubleArray(name + " profile x", dataPrefix + "profile.x");
profileY = new ChannelDoubleArray(name + " profile y", dataPrefix + "profile.y");
shape = new ChannelIntegerArray(name + " shape", dataPrefix + (roi ? "roi.output.shape" : "image.shape"));
origin = new ChannelDoubleArray(name + " origin X", roi ? (dataPrefix + "roi.origin_out") : (prefix+"origin"));
bgEnable = new ChannelInteger(name + " bg enable", this.prefix + "pipeline.bg.enabled");
bgCapture = new ChannelInteger(name + " bg capture", this.prefix + "pipeline.bg.capture");
bgCaptureRemain = new ChannelInteger(name + " bg capture remain", this.prefix + "pipeline.bg.capture_remain");
//posMeanX = new CamToolPosX();
//posMeanY = new CamToolPosY();
//posVarX = new CamToolVarX();
//posVarY = new CamToolVarY();
}
@Override
public void doSetMonitored(boolean value) {
super.doSetMonitored(value);
getDevice().setMonitored(value);
}
@Override
public void doUpdate() throws IOException, InterruptedException {
super.doUpdate();
getDevice().update();
}
void safeInitialize(Device dev, int timeout) throws IOException, InterruptedException{
for (int retries = 0; retries < 10; retries ++){
try{
dev.initialize();
break;
} catch (IOException ex){
if (retries==9){
throw ex;
}
Thread.sleep(timeout / 10);
}
}
}
@Override
protected void doInitialize() throws IOException, InterruptedException {
try {
safeInitialize (channelRun,3000);
channelLatch.initialize();
if (latch){
start();
latch();
}
safeInitialize (channelTimestamp,2000);
posX.initialize();
posY.initialize();
profileX.initialize();
profileY.initialize();
shape.initialize();
origin.initialize();
bgEnable.initialize();
bgCapture.initialize();
bgCaptureRemain.initialize();
int[] s = shape.read();
getConfig().imageHeight = s[0];
getConfig().imageWidth = s[1];
getConfig().save();
getDevice().setSize(s[0] * s[1]);
super.doInitialize();
} catch (InterruptedException ex) {
throw ex;
} catch (Exception ex) {
throw new IOException(ex);
}
}
int numImages = 1;
public int getNumImages() {
return numImages;
}
public void setNumImages(int value) {
numImages = value;
}
double grabTimeout = 3.0;
public double getGrabTimeout() {
return grabTimeout;
}
public void setGrabTimeou(double value) {
grabTimeout = value;
}
public void capture() throws IOException, InterruptedException {
}
public void start() throws IOException, InterruptedException {
channelRun.write(-1);
}
public void stop() throws IOException, InterruptedException {
channelRun.write(0);
}
public void grabSingle() throws IOException, InterruptedException {
channelRun.write(1);
}
public void latch() throws IOException, InterruptedException {
System.out.println("LATCH");
channelLatch.write(1);
System.out.println("Ret:" + channelLatch.read());
}
public void enableBackground(boolean value) throws IOException, InterruptedException {
bgEnable.write(value ? 1 : 0);
}
public void captureBackground(int images) throws IOException, InterruptedException {
start();
bgCapture.write(images);
Thread.sleep(200);
while (bgCaptureRemain.read() > 0) {
Thread.sleep(10);
}
}
}
////////
@SuppressWarnings("unchecked")
// <editor-fold defaultstate="collapsed" desc="Generated Code">//GEN-BEGIN:initComponents