Skip to content

Commit

Permalink
Introduce Padding to Wide Table Export
Browse files Browse the repository at this point in the history 
Allow uneven images to be exported and still retain their correct position within the data matrix.
  • Loading branch information
@AvocadoMoon
AvocadoMoon committed Nov 18, 2024
1 parent 609cebe commit 1b4557d
Show file tree
Hide file tree
Showing 3 changed files with 80 additions and 31 deletions.
107 changes: 78 additions & 29 deletions view-simulation-results/src/main/java/org/vcell/N5/reduction/DataReductionWriter.java
View file
Original file line number Diff line number Diff line change
@@ -1,6 +1,5 @@
package org.vcell.N5.reduction;

import com.amazonaws.AbortedException;
import com.google.gson.internal.LinkedTreeMap;
import com.opencsv.CSVWriter;
import ij.ImagePlus;
Expand Down Expand Up @@ -30,7 +29,7 @@ public class DataReductionWriter implements SimLoadingListener {
private final Object metaDataLock = new Object();
private final File file;

private int numOfImagesToBeOpened;
private int numOfCalculationsTimesNumImages;
private final ReductionCalculations calculations;

public final DataReductionGUI.DataReductionSubmission submission;
Expand All @@ -53,15 +52,24 @@ public class DataReductionWriter implements SimLoadingListener {

private final ArrayList<SelectMeasurements.AvailableMeasurements> selectedMeasurements;

private int maxZ;
private int maxT;

// Per Image
static class ReducedData{
public final double[][] data;
public final ArrayList<String> columnHeaders;
public final SelectMeasurements.AvailableMeasurements measurementType;
public ReducedData(int rowLen, int colLen, SelectMeasurements.AvailableMeasurements measurementType){
data = new double[rowLen][colLen];
public final RangeOfImage rangeOfImage;
public final int colLen;
public ReducedData(RangeOfImage rangeOfImage, int colLen, SelectMeasurements.AvailableMeasurements measurementType){
int nFrames = rangeOfImage.timeEnd - rangeOfImage.timeStart + 1;
int nSlices = rangeOfImage.zEnd - rangeOfImage.zStart + 1;
data = new double[nFrames * nSlices][colLen]; // row - col
columnHeaders = new ArrayList<>();
this.measurementType = measurementType;
this.colLen = colLen;
this.rangeOfImage = rangeOfImage;
}
}

Expand All @@ -73,13 +81,9 @@ public DataReductionWriter(DataReductionGUI.DataReductionSubmission submission){
N5ImageHandler.loadingManager.addSimLoadingListener(this);
this.submission = submission;
this.selectedMeasurements = submission.selectedMeasurements;
synchronized (csvMatrixLock){
synchronized (metaDataLock){
initializeDataSheets();
}
}

this.arrayOfSimRois = submission.arrayOfSimRois;
this.numOfImagesToBeOpened = (submission.numOfSimImages + 1) * submission.selectedMeasurements.size(); // Plus one for the lab image
this.numOfCalculationsTimesNumImages = (submission.numOfSimImages + 1) * submission.selectedMeasurements.size(); // Plus one for the lab image
this.file = submission.fileToSaveResultsTo;
this.calculations = new ReductionCalculations(submission.normalizeMeasurementsBool);

Expand All @@ -92,16 +96,15 @@ public DataReductionWriter(DataReductionGUI.DataReductionSubmission submission){
threadPool.remove("Lab");
}
}, "Processing Lab Image");
ThreadStruct threadStruct = new ThreadStruct(null, new AtomicBoolean(true), processLabResults);
ThreadStruct threadStruct = new ThreadStruct(submission.labResults, new AtomicBoolean(true), processLabResults);
synchronized (threadPoolLock){
threadPool.put("Lab", threadStruct);
}
processLabResults.start();
}

private void initializeDataSheets(){
ArrayList<String> headers = new ArrayList<String>(){{add("Time Frame");}};
boolean is3D = submission.labResults.getNSlices() > 1;
boolean is3D = maxZ > 1;
if (is3D){
headers.add("Z Index");
}
Expand Down Expand Up @@ -129,8 +132,8 @@ private void initializeDataSheets(){

for (SelectMeasurements.AvailableMeasurements measurement : selectedMeasurements){
ArrayList<ArrayList<String>> dataSheet = sheetsAvailable.get(measurement);
for (int t = submission.experimentImageRange.timeStart; t <= submission.experimentImageRange.timeEnd; t++){
for (int z = submission.experimentImageRange.zStart; z <= submission.experimentImageRange.zEnd; z++){
for (int t = 1; t <= maxT; t++){
for (int z = 1; z <= maxZ; z++){
ArrayList<String> pointRow = new ArrayList<>();
pointRow.add(0, String.valueOf(t));
if (is3D){
Expand All @@ -155,45 +158,53 @@ private void calculateAndAddResults(ImagePlus imagePlus, RangeOfImage normRange,
normValue = calculations.calculateNormalValue(imagePlus, normRange, rois, imageRange);
}

int nFrames = imageRange.timeEnd - imageRange.timeStart + 1;
int nSlices = imageRange.zEnd - imageRange.zStart + 1;
int nChannels = imageRange.channelEnd - imageRange.channelStart + 1;

ArrayList<ReducedData> reducedDataArrayList = new ArrayList<>();
for (SelectMeasurements.AvailableMeasurements measurement : submission.selectedMeasurements){
ReducedData reducedData = new ReducedData(nFrames * nSlices, nChannels * arrayOfSimRois.size(), measurement);
ReducedData reducedData = new ReducedData(imageRange, nChannels * arrayOfSimRois.size(), measurement);
reducedDataArrayList.add(reducedData);
calculations.addAppropriateHeaders(imagePlus, rois, imageRange, reducedData, channelInfo);
}
AtomicBoolean continueOperation = threadPool.get(threadName).continueOperation;
calculations.calculateStatistics(imagePlus, rois, normValue, reducedDataArrayList, imageRange, continueOperation);
for (ReducedData reducedData: reducedDataArrayList){
if (continueOperation.get()){
addValuesToCSVMatrix(reducedData);
addValuesToWideCSVMatrix(reducedData);
}
}
}

private void addValuesToCSVMatrix(ReducedData reducedData){
private void addValuesToWideCSVMatrix(ReducedData reducedData){
synchronized (csvMatrixLock){
ArrayList<ArrayList<String>> dataSheet = sheetsAvailable.get(reducedData.measurementType);
int colIndex = columnsForSheets.get(reducedData.measurementType);
fillWithEmptySpace(dataSheet.get(0), colIndex);
for (int c = 0; c < reducedData.columnHeaders.size(); c++){
dataSheet.get(0).add(colIndex, reducedData.columnHeaders.get(c));
}
for (int i = 0; i < reducedData.data.length; i++){
for (int c = 0; c < reducedData.data[i].length; c++){
ArrayList<String> row = dataSheet.get(i + 1);
RangeOfImage rangeOfImage = reducedData.rangeOfImage;
int tzCounter = 1;
for (int t = 1; t <= maxT; t++){
for (int z = 1; z <= maxZ; z++){
boolean inBetweenTime = t <= rangeOfImage.timeEnd && rangeOfImage.timeStart <= t;
boolean inBetweenZ = z <= rangeOfImage.zEnd && rangeOfImage.zStart <= z;
ArrayList<String> row = dataSheet.get(tzCounter);
fillWithEmptySpace(row, colIndex);
double mean = reducedData.data[i][c];
row.add(String.valueOf(mean));
for (int c = 0; c < reducedData.colLen; c++){
if (inBetweenTime && inBetweenZ){
int dataRow = ((t - rangeOfImage.timeStart) * (z - rangeOfImage.zStart)) + (z - rangeOfImage.zStart);
double mean = reducedData.data[dataRow][c];
row.add(String.valueOf(mean));
}
}
tzCounter += 1;
}
}
numOfImagesToBeOpened -= 1;
numOfCalculationsTimesNumImages -= 1;
colIndex += 1 + reducedData.data[0].length;
columnsForSheets.replace(reducedData.measurementType, colIndex);
if (numOfImagesToBeOpened == 0){
if (numOfCalculationsTimesNumImages == 0){
writeCSVMatrix();
}
}
Expand Down Expand Up @@ -237,6 +248,19 @@ private void fillWithEmptySpace(ArrayList<String> arrayList, int col){
}
}

// // Z changes the fastest
// private ArrayList<ArrayList<String>> fillWithEmptySpace(ReducedData reducedData){
// int t = 1;
// int z = 1;
// ArrayList<ArrayList<String>> paddedInfo = new ArrayList<>();
// while (reducedData.numFrames != t){
// while (reducedData.numSlices != z){
//
// }
// t += 1;
// }
// }

private void writeCSVMatrix(){

try {
Expand Down Expand Up @@ -276,7 +300,10 @@ public void stopAllThreads(){
if (threadStruct.simResultsLoader != null){
SimResultsLoader loadedResults = threadStruct.simResultsLoader;
MainPanel.n5ExportTable.removeSpecificRowFromLoadingRows(loadedResults.rowNumber);
WindowManager.getImage(loadedResults.getImagePlus().getID()).close();
ImagePlus openImage = WindowManager.getImage(loadedResults.getImagePlus().getID());
if (openImage != null){
openImage.close();
}
}
threadPool.remove(threadName);
}
Expand Down Expand Up @@ -309,19 +336,41 @@ public void simFinishedLoading(SimResultsLoader loadedResults) {
ThreadStruct threadStruct = new ThreadStruct(loadedResults, new AtomicBoolean(true), imageProcessingThread);
synchronized (threadPoolLock){
threadPool.put(loadedResults.exportID, threadStruct);
if (threadPool.size() == (submission.numOfSimImages + 1)){
maxZ = 0;
maxT = 0;
for (String threadName : threadPool.keySet()){
int curZ = threadPool.get(threadName).imagePlus.getNSlices();
int curT = threadPool.get(threadName).imagePlus.getNFrames();
maxZ = Math.max(curZ, maxZ);
maxT = Math.max(curT, maxT);
}
initializeDataSheets();
for (String threadName : threadPool.keySet()){
threadPool.get(threadName).thread.start();
}
}
}
imageProcessingThread.start();
}
}

static class ThreadStruct {
public final SimResultsLoader simResultsLoader;
public final ImagePlus imagePlus;
public final AtomicBoolean continueOperation;
public final Thread thread;
public ThreadStruct(SimResultsLoader simResultsLoader, AtomicBoolean continueOperation, Thread thread){
this.simResultsLoader = simResultsLoader;
this.continueOperation = continueOperation;
this.thread = thread;
this.imagePlus = simResultsLoader.getImagePlus();
}

public ThreadStruct(ImagePlus imagePlus, AtomicBoolean continueOperation, Thread thread){
this.imagePlus = imagePlus;
this.simResultsLoader = null;
this.continueOperation = continueOperation;
this.thread = thread;
}
}

Expand Down
2 changes: 1 addition & 1 deletion view-simulation-results/src/main/java/org/vcell/N5/reduction/ReductionCalculations.java
View file
Original file line number Diff line number Diff line change
Expand Up @@ -23,7 +23,7 @@ public void addAppropriateHeaders(ImagePlus imagePlus, ArrayList<Roi> roiList, R
for (int c = rangeOfImage.channelStart; c <= rangeOfImage.channelEnd; c++){ //Last channel is domain channel, not variable
String stringC = String.valueOf(c - 1);
String channelName = channelInfo != null && channelInfo.containsKey(stringC) ? channelInfo.get(stringC).get("Name") : String.valueOf(c);
reducedData.columnHeaders.add(imagePlus.getTitle() + ":" + roi.getName() + ":" + channelName);
reducedData.columnHeaders.add(0, imagePlus.getTitle() + ":" + roi.getName() + ":" + channelName);
}
}
}
Expand Down
2 changes: 1 addition & 1 deletion view-simulation-results/src/test/java/org/vcell/N5/reduction/ReductionCalculationsTest.java
View file
Original file line number Diff line number Diff line change
Expand Up @@ -49,9 +49,9 @@ private void compareExpectedCalculations(ImagePlus imagePlus, ArrayList<Roi> roi
boolean normalizeMeasurementsBool){
ReductionCalculations reductionCalculations = new ReductionCalculations(normalizeMeasurementsBool);

DataReductionWriter.ReducedData reducedData = new DataReductionWriter.ReducedData(imagePlus.getNFrames() * imagePlus.getNSlices(), imagePlus.getNChannels() * roiList.size(), SelectMeasurements.AvailableMeasurements.AVERAGE);
RangeOfImage entireRange = new RangeOfImage(1, imagePlus.getNFrames(), 1, imagePlus.getNSlices(), 1, imagePlus.getNChannels());
RangeOfImage normRange = new RangeOfImage(1, 1);
DataReductionWriter.ReducedData reducedData = new DataReductionWriter.ReducedData(entireRange, imagePlus.getNChannels() * roiList.size(), SelectMeasurements.AvailableMeasurements.AVERAGE);
ArrayList<DataReductionWriter.ReducedData> reducedDataArrayList = new ArrayList<>();
reducedDataArrayList.add(reducedData);

Expand Down

0 comments on commit 1b4557d

Please sign in to comment.