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imagej-elphel
Commit 367449b7 authored by Andrey Filippov's avatar Andrey Filippov
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Working on the model of the PSF dependence on the distance, height, 

color channel and direction (S,T) to match measurements. And to
simultaneously determine mechanical properties of the setup.
parent 37ef16f3
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Showing with 2455 additions and 31 deletions
src/main/java/Aberration_Calibration.java
View file @ 367449b7
This diff is collapsed.
src/main/java/CalibrationHardwareInterface.java
View file @ 367449b7
......@@ -31,9 +31,12 @@ import ij.process.FloatProcessor;
import ij.process.ImageProcessor;
import ij.text.TextWindow;
import java.io.BufferedWriter;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.FileOutputStream;
import java.io.FileWriter;
import java.io.IOException;
import java.io.InputStream;
import java.io.OutputStream;
......@@ -50,6 +53,8 @@ import javax.xml.parsers.DocumentBuilder;
import javax.xml.parsers.DocumentBuilderFactory;
import javax.xml.parsers.ParserConfigurationException;
import org.apache.commons.configuration.ConfigurationException;
import org.apache.commons.configuration.XMLConfiguration;
import org.w3c.dom.Document;
import org.w3c.dom.Node;
import org.xml.sax.SAXException;
......@@ -2513,7 +2518,7 @@ public class CalibrationHardwareInterface {
public FocusingSharpness focusingSharpness=new FocusingSharpness(1000);
public int debugLevel=1;
public String motorsStatePath="lensAdjustmentMotorPosition.xml"; // will be saved in ~/.imagej/
public String prefsDirectory=Prefs.getPrefsDir()+Prefs.getFileSeparator(); // "~/.imagej/"
public String prefsDirectory=null; // prefs.getPrefsDir()+Prefs.getFileSeparator(); // "~/.imagej/" - too early !!!
private Properties motorProperties=new Properties();
public boolean interactiveRestore=true; // ask for confirmation to restore motor position
public boolean stateValid=false;
......@@ -2528,6 +2533,12 @@ public class CalibrationHardwareInterface {
public double getMicronsPerStep(){return 1000.0*this.threadPitch*this.linearReductionRatio/stepsPerRevolution;}
public void setLinearReductionRatio(double lrr){this.linearReductionRatio=lrr;}
public String getPrefsDir(){
if (prefsDirectory==null) prefsDirectory=Prefs.getPrefsDir();
if (prefsDirectory!=null) prefsDirectory+=Prefs.getFileSeparator(); // "~/.imagej/"
return prefsDirectory;
}
public boolean isInitialized(){
return this.stateValid;
}
......@@ -2568,7 +2579,7 @@ public class CalibrationHardwareInterface {
public void saveMotorState() throws IOException{
if (!this.stateValid) return; // do not save until allowed
for (int i=0;i<curpos.length;i++) this.motorProperties.setProperty("motor"+(i+1),this.curpos[i]+"");
String path=this.prefsDirectory+this.motorsStatePath;
String path=this.getPrefsDir()+this.motorsStatePath;
OutputStream os;
try {
os = new FileOutputStream(path);
......@@ -2600,7 +2611,7 @@ public class CalibrationHardwareInterface {
}
public int [] loadMotorState() throws IOException{
String path=this.prefsDirectory+this.motorsStatePath;
String path=this.getPrefsDir()+this.motorsStatePath;
InputStream is;
try {
is = new FileInputStream(path);
......@@ -2756,7 +2767,7 @@ public class CalibrationHardwareInterface {
if (this.debugLevel>2) System.out.println("--savedPosition="+((savedPosition==null)?"null":("{"+savedPosition[0]+","+savedPosition[1]+","+savedPosition[2]+"}")));
if (this.interactiveRestore){
gd = new GenericDialog("Missing motor position file");
gd.addMessage("No motor position file ("+this.prefsDirectory+this.motorsStatePath+") found.");
gd.addMessage("No motor position file ("+this.getPrefsDir()+this.motorsStatePath+") found.");
gd.addMessage("If you run the program for the first time it is normal, you may click \"OK\" and the new file will be created");
gd.addMessage("If you select \"Cancel\" the current command will be aborted, you may check the file and restart the program.");
gd.showDialog();
......@@ -3056,6 +3067,28 @@ public class CalibrationHardwareInterface {
result_lastKT,
result_allHistoryKT);
}
public void saveHistoryXML(
String path,
String serialNumber,
String lensSerial, // if null - do not add average
String comment,
double pX0,
double pY0,
double [][][] sampleCoord){ // x,y,r
this.focusingHistory.saveXML(
path,
serialNumber,
lensSerial, // if null - do not add average
comment,
pX0,
pY0,
sampleCoord);
}
public void addCurrentHistoryToFocusingField(FocusingField focusingField){
this.focusingHistory.addCurrentHistory(focusingField);
}
public int historySize(){
return this.focusingHistory.history.size();
}
......@@ -5437,7 +5470,94 @@ if (debugLevel>=debugThreshold) System.out.println(i+" "+diff[0]+" "+diff[1]+" "
Double.NaN);
}
public void addCurrentHistory(
FocusingField focusingField)
{
for (int i=0;i<this.history.size();i++){
FocusingState focusingState=this.history.get(i);
focusingField.addSample(
focusingState.getTimestamp(),
focusingState.getTemperature(),
focusingState.motorsPos,
focusingState.getSamples());
}
}
public void saveXML(
String path,
String serialNumber,
String lensSerial, // if null - do not add average
String comment,
double pX0,
double pY0,
double [][][] sampleCoord){ // x,y,r
String sep=" "; //",";
ArrayList<String> nodeList=new ArrayList<String>();
XMLConfiguration hConfig=new XMLConfiguration();
hConfig.setRootElementName("focusingHistory");
if (comment!=null) hConfig.addProperty("comment",comment);
if (serialNumber!=null) hConfig.addProperty("serialNumber",serialNumber);
if (lensSerial!=null) hConfig.addProperty("lensSerial",lensSerial);
hConfig.addProperty("lens_center_x",pX0);
hConfig.addProperty("lens_center_y",pY0);
if ((sampleCoord!=null) && (sampleCoord.length>0) && (sampleCoord[0] != null) && (sampleCoord[0].length>0)){
hConfig.addProperty("samples_x",sampleCoord[0].length);
hConfig.addProperty("samples_y",sampleCoord.length);
for (int i=0;i<sampleCoord.length;i++)
for (int j=0;j<sampleCoord[i].length;j++){
// double coord[] = {sampleCoord[i][j][0],sampleCoord[i][j][1]};
hConfig.addProperty("sample_"+i+"_"+j,sampleCoord[i][j][0]+sep+sampleCoord[i][j][1]);
}
}
hConfig.addProperty("measurements",this.history.size());
for (int i=0;i<this.history.size();i++){
FocusingState focusingState=this.history.get(i);
String prefix="measurement_"+i+".";
if (focusingState.getTimestamp()!=null)
hConfig.addProperty(prefix+"timestamp",focusingState.getTimestamp());
hConfig.addProperty(prefix+"temperature",focusingState.getTemperature());
hConfig.addProperty(prefix+"motors",focusingState.motorsPos[0]+sep+focusingState.motorsPos[1]+sep+focusingState.motorsPos[2]); // array of 3
double [][][][] samples=focusingState.getSamples();
nodeList.clear();
if ((samples!=null) && (samples.length>0) && (samples[0]!=null) && (samples[0].length>0)){
for (int ii=0;ii<samples.length;ii++) for (int jj=0;jj<samples[ii].length;jj++){
if ((samples[ii][jj]!=null) && (samples[ii][jj].length>0)) {
String sdata=ii+sep+jj;
for (int cc=0;cc<samples[ii][jj].length;cc++) {
double rt=samples[ii][jj][cc][0]/Math.sqrt((1+samples[ii][jj][cc][1]*samples[ii][jj][cc][1])/2.0); // tangential;
double rs=rt*samples[ii][jj][cc][1]; // saggital
sdata += sep+rs+ // saggital
sep+rt; // tangential
// double [] samples_st={
// samples[ii][jj][cc][0], // saggital
// samples[ii][jj][cc][0]/samples[ii][jj][cc][1] // tangential (was ratio)
// };
if ((samples[ii][jj]!=null) && (samples[ii][jj][cc]!=null)) {
// hConfig.addProperty(prefix+"y"+ii+".x"+jj+".c"+cc,samples_st); // array of 2
// nodeList.add(sdata);
}
}
nodeList.add(sdata);
}
}
hConfig.addProperty(prefix+"sample",nodeList);
}
}
File file=new File (path);
BufferedWriter writer;
try {
writer = new BufferedWriter(new FileWriter(file));
hConfig.save(writer);
} catch (IOException e) {
// TODO Auto-generated catch block
e.printStackTrace();
} catch (ConfigurationException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
}
public void list(
String path,
String serialNumber,
......
src/main/java/FocusingField.java 0 → 100644
View file @ 367449b7
This diff is collapsed.
src/main/java/MatchSimulatedPattern.java
View file @ 367449b7
......@@ -5332,6 +5332,7 @@ java.lang.ArrayIndexOutOfBoundsException: -3566
if (mask[i]<maskCutOff) mask[i]=0.0;
int size = (int) Math.sqrt(psf.length);
int hsize=size/2;
// int nn=0;
double S0=0.0, SR=0.0, ST=0.0,SR2=0.0,ST2=0.0; //,SRT=0.0;
for (int i=0;i<mask.length;i++) if (mask[i]>0.0) {
double x=(i % size) - hsize;
......@@ -5344,10 +5345,12 @@ java.lang.ArrayIndexOutOfBoundsException: -3566
ST+=d*tc;
SR2+=d*rc*rc;
ST2+=d*tc*tc;
// SRT+=d*rc*tc;
// nn++;
}
if (S0==0.0) return null; // make sure it is OK
double [] result={ Math.sqrt(ST2*S0 - ST*ST)/S0, Math.sqrt(SR2*S0 - SR*SR)/S0};
// System.out.println(" mask.length="+mask.length+" nn="+nn+" S0="+S0+" SR="+SR+" ST="+ST+" SR2="+SR2+" ST2="+ST2+
// " result={"+result[0]+","+result[1]+"}");
return result;
}
......
src/main/resources/plugins.config
View file @ 367449b7
......@@ -8,9 +8,9 @@
#
# If something like ("<arg>") is appended to the class name, the setup() method
# will get that as arg parameter; otherwise arg is simply the empty string.
Process, "Process Pixels", Process_Pixels
#Process, "Process Pixels", Process_Pixels
Process, "Aberration Calibration", Aberration_Calibration
#Plugins, "Aberration Calibration", Aberration_Calibration
#Process, "Aberration Correction", Aberration_Correction
#Process, "Eyesis Correction", Eyesis_Correction
#Process, "JP46 Reader camera", JP46_Reader_camera
Plugins, "Aberration Calibration", Aberration_Calibration
Process, "Aberration Correction", Aberration_Correction
Process, "Eyesis Correction", Eyesis_Correction
Process, "JP46 Reader camera", JP46_Reader_camera
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