Skip to content

I
imagej-elphel
Commit d14a3970 authored by Andrey Filippov's avatar Andrey Filippov
Browse files
Options

Implemented simultaneous processing of multiple measurements (averaging, 

thermal scan), fixed adjustment
parent f8e486b9
Expand all Hide whitespace changes
Inline Side-by-side
Showing with 1724 additions and 504 deletions
src/main/java/Aberration_Calibration.java
View file @ d14a3970
This diff is collapsed.
src/main/java/CalibrationHardwareInterface.java
View file @ d14a3970
...@@ -47,6 +47,7 @@ import java.util.ArrayList; ...@@ -47,6 +47,7 @@ import java.util.ArrayList;
import java.util.Iterator; import java.util.Iterator;
import java.util.Properties; import java.util.Properties;
import java.util.Set; import java.util.Set;
import java.util.concurrent.TimeUnit;
import java.util.concurrent.atomic.AtomicInteger; import java.util.concurrent.atomic.AtomicInteger;
import javax.xml.parsers.DocumentBuilder; import javax.xml.parsers.DocumentBuilder;
...@@ -1800,21 +1801,27 @@ public class CalibrationHardwareInterface { ...@@ -1800,21 +1801,27 @@ public class CalibrationHardwareInterface {
} }
public static class PowerControl{ public static class PowerControl{
public boolean [] states={false,false,false};
public String [] groups={"heater","fan","light"};
public int debugLevel=1; public int debugLevel=1;
private String powerIP="192.168.0.80"; private String powerIP="192.168.0.80";
private double lightsDelay=5.0;
private final String urlFormat="http://%s/insteon/index.php?cmd=%s&group=%s"; private final String urlFormat="http://%s/insteon/index.php?cmd=%s&group=%s";
private final String rootElement="Document"; private final String rootElement="Document";
public boolean powerConrtolEnabled=false; public boolean powerConrtolEnabled=false;
public void setProperties(String prefix,Properties properties){ public void setProperties(String prefix,Properties properties){
properties.setProperty(prefix+"powerIP",this.powerIP+""); properties.setProperty(prefix+"powerIP",this.powerIP+"");
properties.setProperty(prefix+"powerConrtolEnabled",this.powerConrtolEnabled+""); properties.setProperty(prefix+"powerConrtolEnabled",this.powerConrtolEnabled+"");
properties.setProperty(prefix+"lightsDelay",this.lightsDelay+"");
} }
//Integer.decode(string) //Integer.decode(string)
public void getProperties(String prefix,Properties properties){ public void getProperties(String prefix,Properties properties){
if (properties.getProperty(prefix+"powerIP")!=null) if (properties.getProperty(prefix+"powerIP")!=null)
this.powerIP=properties.getProperty(prefix+"powerIP"); this.powerIP=properties.getProperty(prefix+"powerIP");
if (properties.getProperty(prefix+"powerConrtolEnabled")!=null) if (properties.getProperty(prefix+"powerConrtolEnabled")!=null)
this.powerConrtolEnabled=Boolean.parseBoolean(properties.getProperty(prefix+"powerConrtolEnabled")); this.powerConrtolEnabled=Boolean.parseBoolean(properties.getProperty(prefix+"powerConrtolEnabled"));
if (properties.getProperty(prefix+"lightsDelay")!=null)
this.lightsDelay=Double.parseDouble(properties.getProperty(prefix+"lightsDelay"));
} }
public boolean setPower (String group, String state){ public boolean setPower (String group, String state){
...@@ -1822,6 +1829,7 @@ public class CalibrationHardwareInterface { ...@@ -1822,6 +1829,7 @@ public class CalibrationHardwareInterface {
System.out.println("=== Power control is disabled ==="); System.out.println("=== Power control is disabled ===");
return false; return false;
} }
System.out.println("=== Power control: "+group+":"+state+" ===");
String url=String.format(urlFormat,this.powerIP,state,group); String url=String.format(urlFormat,this.powerIP,state,group);
if (this.debugLevel>2) System.out.println("setPower: "+url); if (this.debugLevel>2) System.out.println("setPower: "+url);
Document dom=null; Document dom=null;
...@@ -1856,16 +1864,22 @@ public class CalibrationHardwareInterface { ...@@ -1856,16 +1864,22 @@ public class CalibrationHardwareInterface {
se.printStackTrace(); se.printStackTrace();
return false; return false;
} }
for (int i=0;i<this.groups.length;i++) if (this.groups[i].equals(group)){
this.states[i]=state.equals("on");
}
return true; return true;
} }
public boolean showDialog(String title, boolean control) { public boolean showDialog(String title, boolean control) {
GenericDialog gd = new GenericDialog(title); GenericDialog gd = new GenericDialog(title);
boolean heaterOn=false, fanOn=false; boolean heaterOn=false, fanOn=false, lightOn=false;
gd.addCheckbox("Enable power control (heater, fan) ", this.powerConrtolEnabled); gd.addCheckbox("Enable power control (heater, fan, lights) ", this.powerConrtolEnabled);
gd.addStringField("IP address of the power control",this.powerIP,15); gd.addStringField("IP address of the power control",this.powerIP,15);
gd.addNumericField("Delay after lights on", this.lightsDelay, 1,4,"sec");
if (control){ if (control){
gd.addCheckbox("Heater On", heaterOn); gd.addCheckbox("Heater On", heaterOn);
gd.addCheckbox("Fan On", fanOn); gd.addCheckbox("Fan On", fanOn);
gd.addCheckbox("Lights On", lightOn);
} }
WindowTools.addScrollBars(gd); WindowTools.addScrollBars(gd);
if (control) gd.enableYesNoCancel("OK", "Control Power"); if (control) gd.enableYesNoCancel("OK", "Control Power");
...@@ -1873,16 +1887,33 @@ public class CalibrationHardwareInterface { ...@@ -1873,16 +1887,33 @@ public class CalibrationHardwareInterface {
if (gd.wasCanceled()) return false; if (gd.wasCanceled()) return false;
this.powerConrtolEnabled=gd.getNextBoolean(); this.powerConrtolEnabled=gd.getNextBoolean();
this.powerIP=gd.getNextString(); this.powerIP=gd.getNextString();
this.lightsDelay=gd.getNextNumber();
if (control){ if (control){
heaterOn=gd.getNextBoolean(); heaterOn=gd.getNextBoolean();
fanOn=gd.getNextBoolean(); fanOn=gd.getNextBoolean();
lightOn=gd.getNextBoolean();
if (!gd.wasOKed()) { if (!gd.wasOKed()) {
setPower("heater",heaterOn?"on":"off"); setPower("heater",heaterOn?"on":"off");
setPower("fan",fanOn?"on":"off"); setPower("fan",fanOn?"on":"off");
setPower("light",lightOn?"on":"off");
} }
} }
return true; return true;
} }
public void lightsOnWithDelay(){
if (this.states[2] || !this.powerConrtolEnabled) return; // already on
setPower("light","on");
System.out.print("Sleeping "+this.lightsDelay+" seconds to let lights stibilize on...");
try {
TimeUnit.MILLISECONDS.sleep((long) (1000*this.lightsDelay));
} catch (InterruptedException e) {
System.out.println("Sleep was interrupted");
// TODO Auto-generated catch block
}
System.out.println(" Done");
}
public boolean isPowerControlEnabled(){ public boolean isPowerControlEnabled(){
return this.powerConrtolEnabled; return this.powerConrtolEnabled;
} }
...@@ -5218,22 +5249,26 @@ if (debugLevel>=debugThreshold) System.out.println(i+" "+diff[0]+" "+diff[1]+" " ...@@ -5218,22 +5249,26 @@ if (debugLevel>=debugThreshold) System.out.println(i+" "+diff[0]+" "+diff[1]+" "
} }
public double [] temperatureLinearApproximation( public double [] temperatureLinearApproximation(
double [][] ZTM, // Z, tXx, tY, m1,m2,m3 found with LMA double [][] ZTT, // Z, tXx, tY, m1,m2,m3 found with LMA - may contain NaN
int numSamples // number of last samples from history to use, 0 - use all int numSamples // number of last samples from history to use, 0 - use all
){ ){
if (numSamples<=0) numSamples=this.history.size(); // if (numSamples<=0) this.history.size();
if (numSamples>this.history.size()) numSamples=this.history.size(); // if (numSamples>this.history.size()) numSamples=this.history.size();
int firstSample=this.history.size()-numSamples; // int firstSample=this.history.size()-numSamples;
if (numSamples<=0) numSamples=ZTT.length;
if (numSamples>ZTT.length) numSamples=ZTT.length;
int firstSample=ZTT.length-numSamples;
int numGoodSamples=0; int numGoodSamples=0;
for (int nSample=0;nSample<numSamples;nSample++){ for (int nSample=0;nSample<numSamples;nSample++){
if (ZTM[firstSample+nSample]!=null) numGoodSamples++; if (ZTT[firstSample+nSample]!=null) numGoodSamples++;
} }
double [][] data =new double [numGoodSamples][2]; // no weights double [][] data =new double [numGoodSamples][2]; // no weights
int index=0; int index=0;
for (int nSample=0;nSample<numSamples;nSample++) if (ZTM[firstSample+nSample]!=null) { for (int nSample=0;nSample<numSamples;nSample++) if (ZTT[firstSample+nSample]!=null) {
data[index][0]=this.history.get(firstSample+nSample).getTemperature(); // data[index][0]=this.history.get(firstSample+nSample).getTemperature();
data[index++][1]=ZTM[firstSample+nSample][0]; // Z data[index][0]=ZTT[firstSample+nSample][3];
data[index++][1]=ZTT[firstSample+nSample][0]; // Z
} }
PolynomialApproximation pa= new PolynomialApproximation(debugLevel); PolynomialApproximation pa= new PolynomialApproximation(debugLevel);
double [] polyCoeff=pa.polynomialApproximation1d(data, 1); // just linear double [] polyCoeff=pa.polynomialApproximation1d(data, 1); // just linear
......
src/main/java/FocusingField.java
View file @ d14a3970
This source diff could not be displayed because it is too large. You can view the blob instead.
src/main/java/LensAdjustment.java
View file @ d14a3970
...@@ -226,13 +226,14 @@ public class LensAdjustment { ...@@ -226,13 +226,14 @@ public class LensAdjustment {
public int lensSerialLength=4; public int lensSerialLength=4;
public String lensSerial=""; // Lens serial number public String lensSerial=""; // Lens serial number
public boolean askLensSerial=true; // Ask lens serial on camera power cycle public boolean askLensSerial=true; // Ask lens serial on camera power cycle
public double reportTemperature=50; // temperature to report focal length
public boolean includeLensSerial=true; // add lens serial to config filename public boolean includeLensSerial=true; // add lens serial to config filename
public double centerDeltaX=0.0; // required X-difference between lens center and sensor center public double centerDeltaX=0.0; // required X-difference between lens center and sensor center
public double centerDeltaY=0.0; // required Y-difference between lens center and sensor center public double centerDeltaY=0.0; // required Y-difference between lens center and sensor center
// with the seam in the middle - make even # of samples horizontally // with the seam in the middle - make even # of samples horizontally
public Rectangle margins=new Rectangle (100,100,2392,1736) ; // maximal height 1816 (1936-120) public Rectangle margins=new Rectangle (100,100,2392,1736) ; // maximal height 1816 (1936-120)
public int [] numSamples={4,3}; // number of samples in x and y directions public int [] numSamples={8,5}; // number of samples in x and y directions
public int sampleSize=256;// 512; // size of square (2^n), in sensor pixels (twice FFT size) public int sampleSize=256;// 512; // size of square (2^n), in sensor pixels (twice FFT size)
public int numInCenter=(numSamples[0]-2)*(numSamples[1]-2);// 2 - number of "center" samples public int numInCenter=(numSamples[0]-2)*(numSamples[1]-2);// 2 - number of "center" samples
public boolean centerSamples=true; // Select samples in the WOI symmetrical around the lens center public boolean centerSamples=true; // Select samples in the WOI symmetrical around the lens center
...@@ -583,7 +584,8 @@ public class LensAdjustment { ...@@ -583,7 +584,8 @@ public class LensAdjustment {
int numIterations, // maximal number of iterations int numIterations, // maximal number of iterations
boolean cameraIsConfigured, boolean cameraIsConfigured,
int [] motorPos, int [] motorPos,
double [] ampsSeconds // cumulative Amps*seconds (read only, but will be saved/restored) double [] ampsSeconds, // cumulative Amps*seconds (read only, but will be saved/restored)
double reportTemperature // temperature to report focal length
){ ){
this.gridGeometryFile=gridGeometryFile; this.gridGeometryFile=gridGeometryFile;
this.initialCalibrationFile=initialCalibrationFile; this.initialCalibrationFile=initialCalibrationFile;
...@@ -734,7 +736,7 @@ public class LensAdjustment { ...@@ -734,7 +736,7 @@ public class LensAdjustment {
this.cameraIsConfigured=cameraIsConfigured; this.cameraIsConfigured=cameraIsConfigured;
this.motorPos=motorPos; this.motorPos=motorPos;
this.ampsSeconds=ampsSeconds; // cumulative Amps*seconds (read only, but will be saved/restored) this.ampsSeconds=ampsSeconds; // cumulative Amps*seconds (read only, but will be saved/restored)
this.reportTemperature=reportTemperature;
} }
public FocusMeasurementParameters clone(){ public FocusMeasurementParameters clone(){
...@@ -887,7 +889,8 @@ public class LensAdjustment { ...@@ -887,7 +889,8 @@ public class LensAdjustment {
this.numIterations, this.numIterations,
this.cameraIsConfigured, this.cameraIsConfigured,
this.motorPos, this.motorPos,
this.ampsSeconds // cumulative Amps*seconds (read only, but will be saved/restored) this.ampsSeconds, // cumulative Amps*seconds (read only, but will be saved/restored)
this.reportTemperature
); );
} }
public void setProperties(String prefix,Properties properties){ public void setProperties(String prefix,Properties properties){
...@@ -1049,6 +1052,7 @@ public class LensAdjustment { ...@@ -1049,6 +1052,7 @@ public class LensAdjustment {
properties.setProperty(prefix+"numIterations",this.numIterations+""); properties.setProperty(prefix+"numIterations",this.numIterations+"");
for (int i=0;i<this.ampsSeconds.length;i++) for (int i=0;i<this.ampsSeconds.length;i++)
properties.setProperty(prefix+"ampsSeconds_"+i,this.ampsSeconds[i]+""); properties.setProperty(prefix+"ampsSeconds_"+i,this.ampsSeconds[i]+"");
properties.setProperty(prefix+"reportTemperature",this.reportTemperature+"");
} }
public void getProperties(String prefix,Properties properties){ public void getProperties(String prefix,Properties properties){
if (properties.getProperty(prefix+"gridGeometryFile")!=null) if (properties.getProperty(prefix+"gridGeometryFile")!=null)
...@@ -1368,9 +1372,10 @@ public class LensAdjustment { ...@@ -1368,9 +1372,10 @@ public class LensAdjustment {
this.thresholdFinish=Double.parseDouble(properties.getProperty(prefix+"thresholdFinish")); this.thresholdFinish=Double.parseDouble(properties.getProperty(prefix+"thresholdFinish"));
if (properties.getProperty(prefix+"numIterations")!=null) if (properties.getProperty(prefix+"numIterations")!=null)
this.numIterations=Integer.parseInt(properties.getProperty(prefix+"numIterations")); this.numIterations=Integer.parseInt(properties.getProperty(prefix+"numIterations"));
for (int i=0;i<this.ampsSeconds.length;i++) if (properties.getProperty(prefix+"ampsSeconds_"+i)!=null) for (int i=0;i<this.ampsSeconds.length;i++) if (properties.getProperty(prefix+"ampsSeconds_"+i)!=null)
this.ampsSeconds[i]=Double.parseDouble(properties.getProperty(prefix+"ampsSeconds_"+i)); this.ampsSeconds[i]=Double.parseDouble(properties.getProperty(prefix+"ampsSeconds_"+i));
if (properties.getProperty(prefix+"reportTemperature")!=null)
this.reportTemperature=Double.parseDouble(properties.getProperty(prefix+"reportTemperature"));
} }
public boolean getLensSerial(){ public boolean getLensSerial(){
while (true) { // loop until OK-ed while (true) { // loop until OK-ed
...@@ -1628,13 +1633,23 @@ public class LensAdjustment { ...@@ -1628,13 +1633,23 @@ public class LensAdjustment {
gd.addNumericField("Expand during extrapolation (relative to the average grid period)", this.flatFieldExpand, 3); gd.addNumericField("Expand during extrapolation (relative to the average grid period)", this.flatFieldExpand, 3);
gd.addNumericField("Threshold RMS to exit LMA", this.thresholdFinish, 7,9,"pix"); gd.addNumericField("Threshold RMS to exit LMA", this.thresholdFinish, 7,9,"pix");
gd.addNumericField("Maximal number of LMA iterations per series",this.numIterations, 0); gd.addNumericField("Maximal number of LMA iterations per series",this.numIterations, 0);
gd.addMessage("-----");
gd.addNumericField("Report focal length at this temperature", this.reportTemperature, 1,5,"C");
if (!Double.isNaN(this.sensorTemperature)) gd.addMessage("Last measured sensor temperature is "+this.sensorTemperature+" C"); if (!Double.isNaN(this.sensorTemperature)) gd.addMessage("Last measured sensor temperature is "+this.sensorTemperature+" C");
if (!Double.isNaN(this.result_lastKT)) gd.addMessage("Temperature focal distance coefficient measured in last run is "+this.result_lastKT+"microns/C"); if (!Double.isNaN(this.result_lastKT)) gd.addMessage("Temperature focal distance coefficient measured in last run is "+this.result_lastKT+"microns/C");
if (!Double.isNaN(this.result_lastFD20)) gd.addMessage("Focal distance @20C measured at last run is "+this.result_lastFD20+" microns"); if (!Double.isNaN(this.result_lastFD20)) gd.addMessage("Focal distance @20C measured at last run is "+this.result_lastFD20+" microns");
if (!Double.isNaN(this.result_lastKT) && !Double.isNaN(this.result_lastFD20)){
gd.addMessage("Focal distance @"+this.reportTemperature+"C measured at last run is "+
(this.result_lastFD20+(this.reportTemperature-20.0)*this.result_lastKT)+" microns");
}
if (!Double.isNaN(this.result_allHistoryKT)) gd.addMessage("Temperature focal distance coefficient calculated from all measurements is "+this.result_allHistoryKT+" microns"); if (!Double.isNaN(this.result_allHistoryKT)) gd.addMessage("Temperature focal distance coefficient calculated from all measurements is "+this.result_allHistoryKT+" microns");
if (!Double.isNaN(this.result_allHistoryFD20)) gd.addMessage("Focal distance @20C calculated from all measurements is "+this.result_allHistoryFD20+" microns"); if (!Double.isNaN(this.result_allHistoryFD20)) gd.addMessage("Focal distance @20C calculated from all measurements is "+this.result_allHistoryFD20+" microns");
if (!Double.isNaN(this.result_allHistoryKT) && !Double.isNaN(this.result_allHistoryFD20)){
gd.addMessage("Focal distance @"+this.reportTemperature+"C calculated from all measurements is "+
(this.result_allHistoryFD20+(this.reportTemperature-20.0)*this.result_allHistoryKT)+" microns");
}
if (!Double.isNaN(this.result_fDistance)) gd.addMessage("Focal distance is "+this.result_fDistance+" microns"); if (!Double.isNaN(this.result_fDistance)) gd.addMessage("Focal distance is "+this.result_fDistance+" microns");
if (!Double.isNaN(this.result_tiltX)) gd.addMessage("Horizontal angular/tangential asymmetry "+this.result_tiltX); if (!Double.isNaN(this.result_tiltX)) gd.addMessage("Horizontal angular/tangential asymmetry "+this.result_tiltX);
if (!Double.isNaN(this.result_tiltY)) gd.addMessage("Vertical angular/tangential asymmetry "+this.result_tiltY); if (!Double.isNaN(this.result_tiltY)) gd.addMessage("Vertical angular/tangential asymmetry "+this.result_tiltY);
...@@ -1650,6 +1665,7 @@ public class LensAdjustment { ...@@ -1650,6 +1665,7 @@ public class LensAdjustment {
if (!Double.isNaN(this.result_FocalLength)) gd.addMessage("Lens focal length "+this.result_FocalLength+" mm"); if (!Double.isNaN(this.result_FocalLength)) gd.addMessage("Lens focal length "+this.result_FocalLength+" mm");
gd.addMessage("Cumulative currents that ran through UV LEDs:"); gd.addMessage("Cumulative currents that ran through UV LEDs:");
for (int i=0;i<this.ampsSeconds.length;i++) gd.addMessage("UV LED "+(i+1)+":"+IJ.d2s(this.ampsSeconds[i],3)+" coulombs (amp-seconds)"); for (int i=0;i<this.ampsSeconds.length;i++) gd.addMessage("UV LED "+(i+1)+":"+IJ.d2s(this.ampsSeconds[i],3)+" coulombs (amp-seconds)");
WindowTools.addScrollBars(gd); WindowTools.addScrollBars(gd);
gd.showDialog(); gd.showDialog();
if (gd.wasCanceled()) return false; if (gd.wasCanceled()) return false;
...@@ -1803,6 +1819,7 @@ public class LensAdjustment { ...@@ -1803,6 +1819,7 @@ public class LensAdjustment {
this.flatFieldExpand= gd.getNextNumber(); this.flatFieldExpand= gd.getNextNumber();
this.thresholdFinish= gd.getNextNumber(); this.thresholdFinish= gd.getNextNumber();
this.numIterations= (int) gd.getNextNumber(); this.numIterations= (int) gd.getNextNumber();
this.reportTemperature= gd.getNextNumber();
return true; return true;
} }
/* ======================================================================== */ /* ======================================================================== */
......
Markdown is supported
0% or
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment