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Refactor Data Reduction Manager into It's Own Class
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view-simulation-results/src/main/java/org/vcell/N5/reduction/DataReductionManager.java
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| package org.vcell.N5.reduction; | ||
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| import com.google.gson.internal.LinkedTreeMap; | ||
| import ij.ImagePlus; | ||
| import ij.WindowManager; | ||
| import ij.gui.Roi; | ||
| import org.vcell.N5.N5ImageHandler; | ||
| import org.vcell.N5.UI.ControlButtonsPanel; | ||
| import org.vcell.N5.UI.MainPanel; | ||
| import org.vcell.N5.reduction.DTO.RangeOfImage; | ||
| import org.vcell.N5.retrieving.SimLoadingListener; | ||
| import org.vcell.N5.retrieving.SimResultsLoader; | ||
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| import java.io.IOException; | ||
| import java.util.ArrayList; | ||
| import java.util.HashMap; | ||
| import java.util.concurrent.ConcurrentHashMap; | ||
| import java.util.concurrent.atomic.AtomicBoolean; | ||
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| public class DataReductionManager implements SimLoadingListener { | ||
| private final ArrayList<Roi> arrayOfSimRois; | ||
| private final Object csvMatrixLock = new Object(); | ||
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| private int numOfCalculationsTimesNumImages; | ||
| private final ReductionCalculations calculations; | ||
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| public final DataReductionGUI.DataReductionSubmission submission; | ||
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| private final ConcurrentHashMap<String, ThreadStruct> threadPool = new ConcurrentHashMap<>(); | ||
| private final Object threadPoolLock = new Object(); | ||
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| private DataReductionWriter dataReductionWriter; | ||
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| // Per Image | ||
| public static class ReducedData{ | ||
| public final double[][] data; | ||
| public final ArrayList<String> columnHeaders; | ||
| public final SelectMeasurements.AvailableMeasurements measurementType; | ||
| 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; | ||
| } | ||
| } | ||
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| public DataReductionManager(DataReductionGUI.DataReductionSubmission submission){ | ||
| N5ImageHandler.loadingManager.addSimLoadingListener(this); | ||
| this.submission = submission; | ||
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| this.arrayOfSimRois = submission.arrayOfSimRois; | ||
| this.numOfCalculationsTimesNumImages = (submission.numOfSimImages + 1) * submission.selectedMeasurements.size(); // Plus one for the lab image | ||
| this.calculations = new ReductionCalculations(submission.normalizeMeasurementsBool); | ||
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| Thread processLabResults = new Thread(() -> { | ||
| calculateAndAddResults(submission.labResults, submission.experiementNormRange, submission.experimentImageRange, | ||
| submission.arrayOfLabRois, null, "Lab"); | ||
| synchronized (threadPoolLock){ | ||
| threadPool.remove("Lab"); | ||
| } | ||
| }, "Processing Lab Image"); | ||
| ThreadStruct threadStruct = new ThreadStruct(submission.labResults, new AtomicBoolean(true), processLabResults); | ||
| synchronized (threadPoolLock){ | ||
| threadPool.put("Lab", threadStruct); | ||
| } | ||
| } | ||
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| //////////////////////// | ||
| // General Functions // | ||
| ////////////////////// | ||
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| private void calculateAndAddResults(ImagePlus imagePlus, RangeOfImage normRange, | ||
| RangeOfImage imageRange, ArrayList<Roi> rois, | ||
| LinkedTreeMap<String, LinkedTreeMap<String, String>> channelInfo, | ||
| String threadName){ | ||
| HashMap<String, Double> normValue = null; | ||
| if (submission.normalizeMeasurementsBool){ | ||
| normValue = calculations.calculateNormalValue(imagePlus, normRange, rois, imageRange); | ||
| } | ||
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| int nChannels = imageRange.channelEnd - imageRange.channelStart + 1; | ||
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| ArrayList<ReducedData> reducedDataArrayList = new ArrayList<>(); | ||
| for (SelectMeasurements.AvailableMeasurements measurement : submission.selectedMeasurements){ | ||
| 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()){ | ||
| synchronized (csvMatrixLock){ | ||
| dataReductionWriter.addValuesToWideCSVMatrix(reducedData); | ||
| numOfCalculationsTimesNumImages -= 1; | ||
| } | ||
| } | ||
| } | ||
| if (numOfCalculationsTimesNumImages == 0){ | ||
| try{ | ||
| dataReductionWriter.writeCSVMatrix(); | ||
| } catch (IOException ioException){ | ||
| throw new RuntimeException(ioException); | ||
| } finally { | ||
| N5ImageHandler.loadingManager.removeFromSimLoadingListener(this); | ||
| MainPanel.controlButtonsPanel.updateButtonsToMatchState(false, ControlButtonsPanel.PanelState.NOTHING_OR_LOADING_IMAGE); | ||
| } | ||
| } | ||
| } | ||
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| public void stopAllThreads(){ | ||
| synchronized (threadPoolLock){ | ||
| for (String threadName: threadPool.keySet()){ | ||
| ThreadStruct threadStruct = threadPool.get(threadName); | ||
| threadStruct.continueOperation.set(false); | ||
| // Experiment image is in thread pool, so trying to retrieve a results loader for it would not work | ||
| if (threadStruct.simResultsLoader != null){ | ||
| SimResultsLoader loadedResults = threadStruct.simResultsLoader; | ||
| MainPanel.n5ExportTable.removeSpecificRowFromLoadingRows(loadedResults.rowNumber); | ||
| ImagePlus openImage = WindowManager.getImage(loadedResults.getImagePlus().getID()); | ||
| if (openImage != null){ | ||
| openImage.close(); | ||
| } | ||
| } | ||
| threadPool.remove(threadName); | ||
| } | ||
| } | ||
| N5ImageHandler.loadingManager.removeFromSimLoadingListener(this); | ||
| MainPanel.controlButtonsPanel.updateButtonsToMatchState(false, ControlButtonsPanel.PanelState.NOTHING_OR_LOADING_IMAGE); | ||
| } | ||
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| @Override | ||
| public void simIsLoading(int itemRow, String exportID) { | ||
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| } | ||
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| @Override | ||
| public void simFinishedLoading(SimResultsLoader loadedResults) { | ||
| if (loadedResults.openTag == SimResultsLoader.OpenTag.DATA_REDUCTION){ | ||
| Thread imageProcessingThread = new Thread(() -> { | ||
| ImagePlus imagePlus = loadedResults.getImagePlus(); | ||
| imagePlus.show(); | ||
| dataReductionWriter.addMetaData(loadedResults); | ||
| calculateAndAddResults(imagePlus, submission.simNormRange, submission.simImageRange, | ||
| submission.arrayOfSimRois, loadedResults.getChannelInfo(), loadedResults.exportID); | ||
| MainPanel.n5ExportTable.removeSpecificRowFromLoadingRows(loadedResults.rowNumber); | ||
| imagePlus.close(); | ||
| synchronized (threadPoolLock){ | ||
| threadPool.remove(loadedResults.exportID); | ||
| } | ||
| }, "Processing Image: " + loadedResults.userSetFileName); | ||
| ThreadStruct threadStruct = new ThreadStruct(loadedResults, new AtomicBoolean(true), imageProcessingThread); | ||
| synchronized (threadPoolLock){ | ||
| threadPool.put(loadedResults.exportID, threadStruct); | ||
| if (threadPool.size() == (submission.numOfSimImages + 1)){ | ||
| int maxZ = 0; | ||
| int 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); | ||
| } | ||
| dataReductionWriter = new DataReductionWriter(submission, maxT, maxZ); | ||
| dataReductionWriter.initializeDataSheets(); | ||
| for (String threadName : threadPool.keySet()){ | ||
| threadPool.get(threadName).thread.start(); | ||
| } | ||
| } | ||
| } | ||
| } | ||
| } | ||
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| 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(); | ||
| } | ||
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| public ThreadStruct(ImagePlus imagePlus, AtomicBoolean continueOperation, Thread thread){ | ||
| this.imagePlus = imagePlus; | ||
| this.simResultsLoader = null; | ||
| this.continueOperation = continueOperation; | ||
| this.thread = thread; | ||
| } | ||
| } | ||
| } |
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