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Tiff stack implementation #1

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7530183
immer gleiche Bildposition
FrankHerrmannsdoerferPrivat Aug 26, 2015
017d039
fixed STORM simulation
FrankHerrmannsdoerferPrivat Aug 27, 2015
0109531
seed set to 2
FrankHerrmannsdoerferPrivat Aug 29, 2015
3fbba05
changesmadetoday-grenzen und random number glaube ich
FrankHerrmannsdoerferPrivat Aug 29, 2015
e88110a
new Branch
FrankHerrmannsdoerferPrivat Oct 6, 2015
4924f0d
batch processing
FrankHerrmannsdoerferPrivat Oct 7, 2015
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212 changes: 212 additions & 0 deletions STORMVis/src/main/java/batchProcessing/startBatchProcessing.java
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@@ -0,0 +1,212 @@
package batchProcessing;

import gui.DataTypeDetector;
import gui.ParserWrapper;
import gui.DataTypeDetector.DataType;
import inout.FileManager;

import java.io.File;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
import java.util.Random;

import javax.swing.JProgressBar;

import calc.Calc;
import calc.STORMCalculator;
import model.DataSet;
import model.LineDataSet;
import model.TriangleDataSet;

public class startBatchProcessing {
static List<DataSet> allDataSets = new ArrayList<DataSet>();
private static Random random;
private static String EXTENSIONIMAGEOUTPUT = ".tif";

public static void main(String[] args) {
File file = new File("C:\\Users\\herrmannsdoerfer\\Desktop\\OLD\\Models\\Microtubule-CrossingSiterescaled.wimp");
proceedFileImport(file);
SimulationParameter params = new SimulationParameter();
params.backgroundPerMicroMeterCubed = 50;
params.coupleSigmaIntensity = true;
params.detectionEfficiency = 100;
params.epitopeDensity = (float) 1.625;
params.fluorophoresPerLabel = 1;
params.kOff = 2000;
params.kOn = 1;
params.labelEpitopeDistance = 16;
params.labelingEfficiency = 10;
params.makeItReproducible = true;
params.MeanPhotonNumber = 3000;
params.radiusOfFilament = 10;
params.recordedFrames = 10000;
params.sigmaXY = 4;
params.sigmaZ = 8;
params.viewStatus = 1;
ArrayList<Float> sigmas = new ArrayList(Arrays.asList(1.f,4.f,8.f,12.f));
ArrayList<Float> le = new ArrayList(Arrays.asList(1.f,5.f,10.f,50.f));
int counter = 0;
for (int i =0; i<sigmas.size(); i++){
for (int j = 0;j< le.size(); j++){
counter += 1;
params.labelingEfficiency = le.get(j);
params.sigmaXY = sigmas.get(i);
params.sigmaZ = 2*sigmas.get(i);
calculate(params);
params.borders = getBorders();
exportData("c:\\testoutput\\",counter+"", params);
}
}



}

private static String getFilename(SimulationParameter params){
String filename;
filename = "sigXY"+(params.sigmaXY)+"sigZ"+params.sigmaZ+"frames"+params.recordedFrames+"radOfFil"+params.radiusOfFilament+
"meanPhotons"+params.MeanPhotonNumber+"reproducible"+params.makeItReproducible+"labEff"+params.labelingEfficiency+"labEpiDist"+params.labelEpitopeDistance+
"kon"+params.kOn+"koff"+params.kOff+"fluorPerLabel"+params.fluorophoresPerLabel+"epiDens"+params.epitopeDensity+
"detEff"+params.detectionEfficiency+"coupleSigmaInt"+params.coupleSigmaIntensity+"bgpermm3"+params.backgroundPerMicroMeterCubed;

return filename;
}

private static ArrayList<Float> getBorders(){
DataSet thisDataSet = allDataSets.get(0);
ArrayList<Float> retList = new ArrayList<Float>();
retList.add(Calc.min(thisDataSet.stormData,0));
retList.add(Calc.max(thisDataSet.stormData,0));
retList.add(Calc.min(thisDataSet.stormData,1));
retList.add(Calc.max(thisDataSet.stormData,1));
retList.add(Calc.min(thisDataSet.stormData,2));
retList.add(Calc.max(thisDataSet.stormData,2));

return retList;

}

private static void furtherProceedFileImport(DataSet data, DataType type){
if(data.dataType.equals(DataType.TRIANGLES)) {
System.out.println("Triangles parsed correctly.");
}
else if(type.equals(DataType.LINES)) {
System.out.println("Lines parsed correctly.");
}
else if(type.equals(DataType.PLY)){
System.out.println("PLY file parsed.");
}

allDataSets.add(data);

LineDataSet lines = (LineDataSet) allDataSets.get(allDataSets.size()-1);



}
private static void calculate(SimulationParameter params) {
setUpRandomNumberGenerator(params.makeItReproducible) ;
int currentRow= 0;
allDataSets.get(currentRow).getParameterSet().setPabs((float) (params.labelingEfficiency/100.));//Labeling efficiency
allDataSets.get(currentRow).getParameterSet().setAoa((float) ((90)/180*Math.PI));
allDataSets.get(currentRow).getParameterSet().setDeff((float) (params.detectionEfficiency/100)); //detection efficiency
allDataSets.get(currentRow).getParameterSet().setIlpmm3(params.backgroundPerMicroMeterCubed); //background per cubic micro meter
allDataSets.get(currentRow).getParameterSet().setLoa(params.labelEpitopeDistance); //label epitope distance
allDataSets.get(currentRow).getParameterSet().setFpab(params.fluorophoresPerLabel);//fluorophores per label
allDataSets.get(currentRow).getParameterSet().setKOn(params.kOn);
allDataSets.get(currentRow).getParameterSet().setKOff(params.kOff);
allDataSets.get(currentRow).getParameterSet().setBleachConst((float) 0);
allDataSets.get(currentRow).getParameterSet().setFrames(params.recordedFrames); // recorded frames
allDataSets.get(currentRow).getParameterSet().setSxy(params.sigmaXY);
allDataSets.get(currentRow).getParameterSet().setSz(params.sigmaZ);
allDataSets.get(currentRow).getParameterSet().setPsfwidth((float) 380);
allDataSets.get(currentRow).getParameterSet().setMeanPhotonNumber(params.MeanPhotonNumber);
if(allDataSets.get(currentRow).dataType == DataType.LINES) {
allDataSets.get(currentRow).getParameterSet().setBspnm(params.epitopeDensity);
allDataSets.get(currentRow).getParameterSet().setRof(params.radiusOfFilament);
}
else {
allDataSets.get(currentRow).getParameterSet().setBspsnm(params.epitopeDensity);
}
allDataSets.get(currentRow).getParameterSet().setMergedPSF(false);
allDataSets.get(currentRow).getParameterSet().setApplyBleaching(false);
allDataSets.get(currentRow).getParameterSet().setCoupleSigmaIntensity(params.coupleSigmaIntensity);
STORMCalculator calc = new STORMCalculator(allDataSets.get(currentRow), random);
calc = new STORMCalculator(allDataSets.get(currentRow),random);
//calc = new STORMCalculator(allDataSets.get(currentRow));
calc.execute();
while(!calc.isDone()){
try {
Thread.sleep(100);
//System.out.println(calc.isCancelled()+" "+calc.isDone());
} catch (InterruptedException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
}
// When calc has finished, grab the new dataset
//allDataSets.set(currentRow, calc.getCurrentDataSet());
//visualizeAllSelectedData();
}
private static void proceedFileImport(File file) {
System.out.println("Path: " + file.getAbsolutePath());
DataType type = DataType.UNKNOWN;
try {
type = DataTypeDetector.getDataType(file.getAbsolutePath());
System.out.println(type.toString());
} catch (IOException e1) {
// TODO Auto-generated catch block
e1.printStackTrace();
}
DataSet data = ParserWrapper.parseFileOfType(file.getAbsolutePath(), type);
data.setName(file.getName());
data.setProgressBar(new JProgressBar());
furtherProceedFileImport(data,type);
}

private static void setUpRandomNumberGenerator(boolean makeItReproducible) {
if (makeItReproducible){
random = new Random(2);
} else {
random = new Random(System.currentTimeMillis());
}
}

private static void exportData(String path, String name, SimulationParameter params){
if (!path.endsWith(EXTENSIONIMAGEOUTPUT)) {
path += EXTENSIONIMAGEOUTPUT;
}
if(name.endsWith(EXTENSIONIMAGEOUTPUT)){
name = name.substring(0, name.length()-4);
}
System.out.println("Path to write project: " + path);
System.out.println("project name: " + name);
FileManager.ExportToFile(allDataSets.get(0), path, params.viewStatus,params.borders);
}
}


class SimulationParameter{
float labelingEfficiency;
float detectionEfficiency;
float backgroundPerMicroMeterCubed;
float labelEpitopeDistance;
float fluorophoresPerLabel;
int recordedFrames;
float kOn;
float kOff;
float sigmaXY;
float sigmaZ;
int MeanPhotonNumber;
float radiusOfFilament;
float epitopeDensity;
boolean coupleSigmaIntensity;
boolean makeItReproducible;
ArrayList<Float> borders;
int viewStatus = 0;
SimulationParameter(){

}
}
19 changes: 11 additions & 8 deletions STORMVis/src/main/java/calc/Calc.java
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Expand Up @@ -642,7 +642,8 @@ public static ArrayList<float[][]> addFilteredPoints3D(ArrayList<float[][]> colo
float yMax = dims.get(3);
float zMin = dims.get(4);
float zMax = dims.get(5);

zMax = borders.get(5) ;
zMin = borders.get(4) ;
zMax = zMax - zMin;

System.out.println("zMax: "+zMax+" zMin: "+zMin);
Expand All @@ -657,8 +658,8 @@ public static ArrayList<float[][]> addFilteredPoints3D(ArrayList<float[][]> colo
double posZ = 0;
switch (mode){
case 1:
posX = (sl[0]-xMin)/pixelsize; //position of current localization
posY = (sl[1]-yMin)/pixelsize;
posX = (sl[0]+5000)/pixelsize; //position of current localization
posY = (sl[1]+5000)/pixelsize;
posZ = (sl[2])-zMin;
break;
case 2:
Expand All @@ -683,7 +684,9 @@ public static ArrayList<float[][]> addFilteredPoints3D(ArrayList<float[][]> colo
try{

float weight = (float) (factor*intensity* Math.exp(factor2*(Math.pow((k-posX),2)+Math.pow((l-posY),2))));
redChannel[k][l] = redChannel[k][l] + getColor(posZ,zMax,0) * weight;
float tmp = getColor(posZ,zMax,0) * weight;
//System.out.println(tmp);
redChannel[k][l] = redChannel[k][l] + tmp;
greenChannel[k][l] = greenChannel[k][l] +getColor(posZ,zMax,1) * weight;
blueChannel[k][l] = blueChannel[k][l] +getColor(posZ,zMax,2) * weight;

Expand Down Expand Up @@ -722,13 +725,13 @@ public static ArrayList<float[][]> addFilteredPoints3D(ArrayList<float[][]> colo

private static float getColor(double posZ, float zMax, int color) {

if (posZ < 0.25* zMax){
if (posZ < 0.25* zMax&& posZ>0){
//blue rises from 0 to 1
if (color == 2){
return (float) (4*posZ / zMax);
}
}
else if (posZ < 0.5* zMax){
else if (posZ < 0.5* zMax&& posZ>0){
//green rises from 0 to 1 blue stays one
if (color == 1){
return (float)(4*posZ/zMax - 1);
Expand All @@ -737,7 +740,7 @@ else if (posZ < 0.5* zMax){
return (float) 1;//(2 - 4*posZ/zMax) ;
}
}
else if (posZ < 0.75* zMax){
else if (posZ < 0.75* zMax&& posZ>0){
//green stays one, blue goes to zero again
if (color == 1){
return (float) 1;//(4*posZ/zMax - 2);
Expand All @@ -746,7 +749,7 @@ else if (posZ < 0.75* zMax){
return (float) (3 - 4*posZ/zMax);
}
}
else {
else if (posZ<zMax&&posZ>0) {
//green goes to zero red rises
if (color == 0){
return (float) (4*posZ/zMax - 3);
Expand Down
24 changes: 12 additions & 12 deletions STORMVis/src/main/java/calc/StormPointFinder.java
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Expand Up @@ -115,14 +115,14 @@ private static float[][] createStormPoints(float[][] listEndPoints, ParameterSet
frame[k1] = (int) (calc.random.nextDouble()*frames);
idxList.add(k1);
if (ps.getCoupleSigmaIntensity()){
x[k1] = (float) (listEndPointsTranspose[0][idxArray.get(k1).intValue()] + calc.random.nextFloat()*(sxy/Math.sqrt(intensity[k1]/meanPhotonNumber)));
y[k1] = (float) (listEndPointsTranspose[1][idxArray.get(k1).intValue()] + calc.random.nextFloat()*(sxy/Math.sqrt(intensity[k1]/meanPhotonNumber)));
z[k1] = (float) (listEndPointsTranspose[2][idxArray.get(k1).intValue()] + calc.random.nextFloat()*(sz/Math.sqrt(intensity[k1]/meanPhotonNumber)));
x[k1] = (float) (listEndPointsTranspose[0][idxArray.get(k1).intValue()] + calc.random.nextGaussian()*(sxy/Math.sqrt(intensity[k1]/meanPhotonNumber)));
y[k1] = (float) (listEndPointsTranspose[1][idxArray.get(k1).intValue()] + calc.random.nextGaussian()*(sxy/Math.sqrt(intensity[k1]/meanPhotonNumber)));
z[k1] = (float) (listEndPointsTranspose[2][idxArray.get(k1).intValue()] + calc.random.nextGaussian()*(sz/Math.sqrt(intensity[k1]/meanPhotonNumber)));
}
else {
x[k1] = (listEndPointsTranspose[0][idxArray.get(k1).intValue()] + calc.random.nextFloat()*(sxy));
y[k1] = (listEndPointsTranspose[1][idxArray.get(k1).intValue()] + calc.random.nextFloat()*(sxy));
z[k1] = (listEndPointsTranspose[2][idxArray.get(k1).intValue()] + calc.random.nextFloat()*(sz));
x[k1] = (float) (listEndPointsTranspose[0][idxArray.get(k1).intValue()] + calc.random.nextGaussian()*(sxy));
y[k1] = (float) (listEndPointsTranspose[1][idxArray.get(k1).intValue()] + calc.random.nextGaussian()*(sxy));
z[k1] = (float) (listEndPointsTranspose[2][idxArray.get(k1).intValue()] + calc.random.nextGaussian()*(sz));
}

}
Expand Down Expand Up @@ -193,14 +193,14 @@ private static float[][] createStormPointsRealisticBleaching(float[][] listEndPo
if (blinkingTest <= (kOn/kOff)){
float intensity = intensities.get((int) (calc.random.nextDouble()*intensities.size()-1));
if (ps.getCoupleSigmaIntensity()){
x = (float) (listEndPoints[i][0] + calc.random.nextFloat()*(sxy/Math.sqrt(intensity/meanPhotonNumber)));
y = (float) (listEndPoints[i][1] + calc.random.nextFloat()*(sxy/Math.sqrt(intensity/meanPhotonNumber)));
z = (float) (listEndPoints[i][2] + calc.random.nextFloat()*(sz/Math.sqrt(intensity/meanPhotonNumber)));
x = (float) (listEndPoints[i][0] + calc.random.nextGaussian()*(sxy/Math.sqrt(intensity/meanPhotonNumber)));
y = (float) (listEndPoints[i][1] + calc.random.nextGaussian()*(sxy/Math.sqrt(intensity/meanPhotonNumber)));
z = (float) (listEndPoints[i][2] + calc.random.nextGaussian()*(sz/Math.sqrt(intensity/meanPhotonNumber)));
}
else {
x = (float) (listEndPoints[i][0] + calc.random.nextFloat()*(sxy));
y = (float) (listEndPoints[i][1] + calc.random.nextFloat()*(sxy));
z = (float) (listEndPoints[i][2] + calc.random.nextFloat()*(sz));
x = (float) (listEndPoints[i][0] + calc.random.nextGaussian()*(sxy));
y = (float) (listEndPoints[i][1] + calc.random.nextGaussian()*(sxy));
z = (float) (listEndPoints[i][2] + calc.random.nextGaussian()*(sz));
}
float tmpLoc[] = {x,y,z,frame,intensity};
allStormPoints.add(tmpLoc);
Expand Down
17 changes: 16 additions & 1 deletion STORMVis/src/main/java/inout/FileManager.java
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Original file line number Diff line number Diff line change
Expand Up @@ -274,6 +274,8 @@ private static void writeLogFile(DataSet dataset, String basename,ArrayList<Floa
writer.close();
} catch (IOException e) {e.printStackTrace();}
}



private static void writeLocalizationsToFile(float[][] stormData, String basename) {
try{
Expand All @@ -287,4 +289,17 @@ private static void writeLocalizationsToFile(float[][] stormData, String basenam
writer.close();
} catch (IOException e) {e.printStackTrace();}
}
}
private static void writeLocalizationsToFileForFRC(float[][] stormData, String basename) {
try{
double minx = Calc.min(stormData, 0);
double miny = Calc.min(stormData, 1);
FileWriter writer = new FileWriter(basename+"LocalizationsForFRCAnalysis.txt");
for (int i = 0; i<stormData.length; i++){
float[] tmp = stormData[i];
writer.append((tmp[0]-minx)/106.6666+" "+(tmp[1]-miny)/106.6666+" "+tmp[3]+"\n");
}
writer.flush();
writer.close();
} catch (IOException e) {e.printStackTrace();}
}
}
6 changes: 3 additions & 3 deletions STORMVis/src/main/java/parsing/TriangleObjectParser.java
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Original file line number Diff line number Diff line change
Expand Up @@ -115,9 +115,9 @@ private void importPly() throws IOException {
words.add(line.substring(pos,line.length()));
}
Float[] vertex = new Float[3];
vertex[0] = Float.valueOf(words.get(0));
vertex[1] = Float.valueOf(words.get(1));
vertex[2] = Float.valueOf(words.get(2));
vertex[0] = (float) (Float.valueOf(words.get(0))*1.62);
vertex[1] = (float) (Float.valueOf(words.get(1))*1.62);
vertex[2] = (float) (Float.valueOf(words.get(2))*1.62);
listVertices.add(vertex);
}
else{//create triangles
Expand Down