Examples with RegionImage cbit.vcell.geometry.RegionImage used on opensource projects

Example 1 with RegionImage

use of cbit.vcell.geometry.RegionImage in project vcell by virtualcell.

the class RunRefSimulationOp method saveExternalData.

private static void saveExternalData(Image image, String varName, ExternalDataIdentifier newROIExtDataID, LocalWorkspace localWorkspace) throws ObjectNotFoundException, ImageException, IOException {
    Extent extent = image.getExtent();
    Origin origin = image.getOrigin();
    ISize isize = image.getISize();
    VCImage vcImage = new VCImageUncompressed(null, new byte[isize.getXYZ()], extent, isize.getX(), isize.getY(), isize.getZ());
    RegionImage regionImage = new RegionImage(vcImage, 0, null, null, RegionImage.NO_SMOOTHING);
    CartesianMesh simpleCartesianMesh = CartesianMesh.createSimpleCartesianMesh(origin, extent, isize, regionImage);
    int NumTimePoints = 1;
    int NumChannels = 1;
    // dimensions: time points, channels, whole image ordered by z slices.
    double[][][] pixData = new double[NumTimePoints][NumChannels][];
    pixData[0][0] = image.getDoublePixels();
    FieldDataFileOperationSpec fdos = new FieldDataFileOperationSpec();
    fdos.opType = FieldDataFileOperationSpec.FDOS_ADD;
    fdos.cartesianMesh = simpleCartesianMesh;
    fdos.doubleSpecData = pixData;
    fdos.specEDI = newROIExtDataID;
    fdos.varNames = new String[] { varName };
    fdos.owner = LocalWorkspace.getDefaultOwner();
    fdos.times = new double[] { 0.0 };
    fdos.variableTypes = new VariableType[] { VariableType.VOLUME };
    fdos.origin = origin;
    fdos.extent = extent;
    fdos.isize = isize;
    localWorkspace.getDataSetControllerImpl().fieldDataFileOperation(fdos);
}

Example 2 with RegionImage

use of cbit.vcell.geometry.RegionImage in project vcell by virtualcell.

the class VFrapXmlHelper method LoadVFrapSpecialImages.

// // load and compute prebleach average and first postbleach images
// public void LoadVFrapSpecialImages(AnnotatedImageDataset annotatedImages, int startingIndexRecovery)
// {
// // unnormalized prebleach average
// prebleachAvg = new double[annotatedImages.getImageDataset().getImage(0, 0, startingIndexRecovery).getNumXYZ()];
// for(int j = 0; j < prebleachAvg.length; j++)
// {
// double pixelTotal = 0;
// for(int i = 0 ; i < startingIndexRecovery; i++)
// {
// pixelTotal = pixelTotal + (annotatedImages.getImageDataset().getImage(0, 0, i).getPixels()[j] & 0x0000FFFF);
// }
// prebleachAvg[j] = pixelTotal/startingIndexRecovery;
// }
// 
// // unnormalized first post bleach
// firstPostBleach = new double[annotatedImages.getImageDataset().getImage(0, 0, startingIndexRecovery).getNumXYZ()];
// short[] pixels = annotatedImages.getImageDataset().getImage(0, 0, startingIndexRecovery).getPixels();
// for(int i = 0; i< pixels.length; i++)
// {
// firstPostBleach[i] = pixels[i] & 0x0000FFFF;
// }
// }
// 
// Locate the special images within the vFrap files and load them in memory
// 
public static boolean LoadVFrapSpecialImages(Hashtable<String, Object> hashTable, Element vFrapRoot) throws IOException, DataAccessException, MathException, ImageException {
    // ------ parse the vfrap file and the log/zip files referred within -----
    // many channels of 1 timepoint each
    int NumTimePoints = 1;
    // the channels: prebleach, postbleach, roi1, roi2 ... roiN
    int NumChannels = tokenNames.length;
    String[] channelNames = new String[NumChannels];
    VariableType[] channelTypes = new VariableType[NumChannels];
    DataSymbolType[] channelVFrapImageType = new DataSymbolType[NumChannels];
    double[][][] pixData = new double[NumTimePoints][NumChannels][];
    // get the path of the file tagged with "ROIExternalDataInfoTag" and open it
    Element roiExternalDataInfoElement = vFrapRoot.getChild(MicroscopyXMLTags.ROIExternalDataInfoTag);
    if (roiExternalDataInfoElement == null) {
        // can't load FieldData for some reason, fall back to importing the biomodel only
        return false;
    }
    // <ROIExternalDataInfo Filename="c:\vFrap\VirtualMicroscopy\SimulationData\SimID_1282941232246_0_.log">
    // <ExternalDataIdentifier Name="timeData" KeyValue="1282941232246" OwnerName="SimulationData" OwnerKey="0" />
    // </ImageDatasetExternalDataInfo>
    // c:\VirtualMicroscopy\SimulationData\SimID_1284149203811_0_.log
    String filename = (roiExternalDataInfoElement).getAttributeValue("Filename");
    Element childElement = (roiExternalDataInfoElement).getChild("ExternalDataIdentifier");
    if (childElement == null) {
        // can't load FieldData for some reason, fall back to importing the biomodel only
        return false;
    }
    StringTokenizer tokens = new StringTokenizer(filename, "/\\.");
    final ArrayList<String> tokenArray = new ArrayList<String>();
    while (tokens.hasMoreElements()) {
        tokenArray.add(tokens.nextToken());
    }
    final String dataID = tokenArray.get(tokenArray.size() - 2);
    final String userName = tokenArray.get(tokenArray.size() - 3);
    VCDataIdentifier vcDataIdentifier = new VCDataIdentifier() {

        public String getID() {
            return dataID;
        }

        public KeyValue getDataKey() {
            return null;
        }

        public User getOwner() {
            return new User(userName, new KeyValue("123345432334"));
        }
    };
    // ------- recover simulation data for this user name, load the images in memory ------------
    // ex  c:\\VirtualMicroscopy\\SimulationData
    String userDirName = filename.substring(0, filename.indexOf(dataID) - 1);
    File userDir = new File(userDirName);
    SimulationData.SimDataAmplistorInfo simDataAmplistorInfo = AmplistorUtils.getSimDataAmplistorInfoFromPropertyLoader();
    SimulationData simData = new SimulationData(vcDataIdentifier, userDir, null, simDataAmplistorInfo);
    // build a valid mesh in 2 steps, what we have in simData is incomplete
    CartesianMesh incompleteMesh = simData.getMesh();
    Extent extent = incompleteMesh.getExtent();
    ISize isize = new ISize(incompleteMesh.getSizeX(), incompleteMesh.getSizeY(), incompleteMesh.getSizeZ());
    Origin origin = new Origin(0, 0, 0);
    CartesianMesh mesh = CartesianMesh.createSimpleCartesianMesh(origin, extent, isize, new RegionImage(new VCImageUncompressed(null, new byte[isize.getXYZ()], extent, isize.getX(), isize.getY(), isize.getZ()), 0, null, null, RegionImage.NO_SMOOTHING));
    DataIdentifier[] dataIdentifiers = simData.getVarAndFunctionDataIdentifiers(null);
    double[] times = simData.getDataTimes();
    for (int i = 0; i < dataIdentifiers.length; i++) {
        // ex: prebleach_avg, postbleach_first, postbleach_last, bleached_mask, cell_mask, ring1_mask,... ring8_mask
        System.out.println(dataIdentifiers[i].getName());
        for (double time : times) {
            // this loops only once, we have just 1 timepoint for each "special" image
            SimDataBlock simDataBlock = simData.getSimDataBlock(null, dataIdentifiers[i].getName(), time);
            channelNames[i] = dataIdentifiers[i].getName();
            channelTypes[i] = VariableType.VOLUME;
            channelVFrapImageType[i] = SymbolEquivalence.typeFromToken(dataIdentifiers[i].getName());
            pixData[0][i] = simDataBlock.getData();
            // var = prebleach_avg, time = 0.0, data = { 1.0832530361887216 1.0832530361887216 1.0832530361887216 1.0 .... }
            System.out.print("var = " + dataIdentifiers[i].getName() + ", time = " + time + ", data = { ");
            // show a few
            for (int j = 0; j < 5; j++) {
                System.out.print(pixData[0][i][j] + " ");
            }
            // show a few
            ;
            // show a few
            System.out.println(" ... ");
        }
    }
    hashTable.put("mesh", mesh);
    hashTable.put("pixData", pixData);
    hashTable.put("channelNames", channelNames);
    hashTable.put("channelTypes", channelTypes);
    hashTable.put("channelVFrapImageType", channelVFrapImageType);
    return true;
}

Example 3 with RegionImage

use of cbit.vcell.geometry.RegionImage in project vcell by virtualcell.

the class ROIMultiPaintManager method createFD.

private void createFD(boolean isFromSimulation, String fieldName, String annotation, Extent extent, Origin origin, String[] varNames, double[] times, ISize isize) throws Exception {
    FieldDataFileOperationSpec fdos = null;
    try {
        // temp-------
        FieldDataDBOperationSpec listExtDataIDSpec = FieldDataDBOperationSpec.createGetExtDataIDsSpec(documentManager.getUser());
        FieldDataDBOperationResults fdDBOperation = documentManager.fieldDataDBOperation(listExtDataIDSpec);
        for (int i = 0; i < fdDBOperation.extDataIDArr.length; i++) {
            if (fdDBOperation.extDataIDArr[i].getName().equals("fd")) {
                FieldDataDBOperationSpec createDeleteExtDataIDSpec = FieldDataDBOperationSpec.createDeleteExtDataIDSpec(fdDBOperation.extDataIDArr[i]);
                documentManager.fieldDataDBOperation(createDeleteExtDataIDSpec);
                break;
            }
        }
        // 
        // -----------
        FieldDataDBOperationSpec newExtDataIDSpec = FieldDataDBOperationSpec.createSaveNewExtDataIDSpec(documentManager.getUser(), fieldName, annotation);
        FieldDataDBOperationResults fieldDataDBOperation = documentManager.fieldDataDBOperation(newExtDataIDSpec);
        fdos = new FieldDataFileOperationSpec();
        fdos.opType = FieldDataFileOperationSpec.FDOS_ADD;
        fdos.variableTypes = new VariableType[] { VariableType.VOLUME };
        fdos.owner = documentManager.getUser();
        fdos.isize = isize;
        fdos.shortSpecData = new short[1][1][fdos.isize.getXYZ()];
        UShortImage[] allImages = initImageDataSetChannels[0].getAllImages();
        for (int i = 0; i < allImages.length; i++) {
            allImages[i].getPixels();
            System.arraycopy(allImages[i].getPixels(), 0, fdos.shortSpecData[0][0], i * allImages[i].getPixels().length, allImages[i].getPixels().length);
        }
        fdos.specEDI = fieldDataDBOperation.extDataID;
        fdos.annotation = annotation;
        if (!isFromSimulation) {
            fdos.extent = extent;
            fdos.origin = origin;
            fdos.varNames = varNames;
            fdos.times = times;
            // 
            // Subvolumes and Regions NOT implemented now
            // 
            fdos.cartesianMesh = CartesianMesh.createSimpleCartesianMesh(fdos.origin, fdos.extent, fdos.isize, new RegionImage(new // empty regions
            VCImageUncompressed(// empty regions
            null, // empty regions
            new byte[fdos.isize.getXYZ()], fdos.extent, fdos.isize.getX(), fdos.isize.getY(), fdos.isize.getZ()), 0, null, null, RegionImage.NO_SMOOTHING));
        }
        // Add to Server Disk
        documentManager.fieldDataFileOperation(fdos);
    // //Update FieldData window
    // Window[] windows = Window.getWindows();
    // for(int i=0;i<windows.length;i++) {
    // if(windows[i] instanceof FieldDataWindow) {
    // ((FieldDataWindow)windows[i]).getFieldDataWindowManger().fieldDataDBEvent(new FieldDataDBEvent(ROIMultiPaintManager.this));
    // break;
    // }
    // }
    } catch (Exception e) {
        try {
            // try to cleanup new ExtDataID
            if (fdos != null && fdos.specEDI != null) {
                documentManager.fieldDataDBOperation(FieldDataDBOperationSpec.createDeleteExtDataIDSpec(fdos.specEDI));
            }
        } catch (Exception e2) {
            e2.printStackTrace();
        }
        throw e;
    }
}

Example 4 with RegionImage

use of cbit.vcell.geometry.RegionImage in project vcell by virtualcell.

the class ROIMultiPaintManager method getImportSTLtasks.

// private File lastImportDir;
private ArrayList<AsynchClientTask> getImportSTLtasks(File[] selectedFiles, Vect3d primarySampleSizes, Vect3d subSampleOffset) {
    // try {
    final RegionImage currRegionImage = regionImage;
    final TreeMap<Integer, String> newROIindexes = new TreeMap<>();
    final TreeMap<BoundingBox, Object[]> regionBounds = new TreeMap<>(new Comparator<BoundingBox>() {

        @Override
        public int compare(BoundingBox arg0, BoundingBox arg1) {
            if (arg1 == arg0) {
                return 0;
            }
            if (arg0.getLoX() == arg1.getLoX() && arg0.getLoY() == arg1.getLoY() && arg0.getLoZ() == arg1.getLoZ() && arg0.getHiX() == arg1.getHiX() && arg0.getHiY() == arg1.getHiY() && arg0.getHiZ() == arg1.getHiZ()) {
                return 0;
            }
            return (arg0.getLoX() >= arg1.getLoX() && arg0.getLoY() >= arg1.getLoY() && arg0.getLoZ() >= arg1.getLoZ() && arg0.getHiX() <= arg1.getHiX() && arg0.getHiY() <= arg1.getHiY() && arg0.getHiZ() <= arg1.getHiZ() ? -1 : +1);
        }
    });
    AsynchClientTask sampleSTLtask = new AsynchClientTask("importSTLtask", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            StatsHelper statsHelper = calcMinMax(selectedFiles);
            Vect3d worldOrigin = new Vect3d(statsHelper.xmin, statsHelper.ymin, statsHelper.zmin);
            Vect3d worldCollapsedBoundingBox = new Vect3d(statsHelper.xmax - statsHelper.xmin, statsHelper.ymax - statsHelper.ymin, statsHelper.zmax - statsHelper.zmin);
            Vect3d scale = new Vect3d(worldCollapsedBoundingBox.getX() / (2.0 * primarySampleSizes.getX()), worldCollapsedBoundingBox.getY() / (2.0 * primarySampleSizes.getY()), worldCollapsedBoundingBox.getZ() / (2.0 * primarySampleSizes.getZ()));
            // }
            if (scale.getX() != 0 && scale.getX() <= (scale.getY() == 0 ? scale.getX() : scale.getY()) && scale.getX() <= (scale.getZ() == 0 ? scale.getX() : scale.getZ())) {
                scale = new Vect3d(scale.getX(), scale.getX(), scale.getX());
            } else if (scale.getY() != 0 && scale.getY() <= (scale.getX() == 0 ? scale.getY() : scale.getX()) && scale.getY() <= (scale.getZ() == 0 ? scale.getY() : scale.getZ())) {
                scale = new Vect3d(scale.getY(), scale.getY(), scale.getY());
            } else if (scale.getZ() != 0 && scale.getZ() <= (scale.getY() == 0 ? scale.getZ() : scale.getY()) && scale.getZ() <= (scale.getX() == 0 ? scale.getZ() : scale.getX())) {
                scale = new Vect3d(scale.getZ(), scale.getZ(), scale.getZ());
            }
            for (int j = 0; j < selectedFiles.length; j++) {
                // ClientRequestManager.createSurfaceCollectionFromSurfaceFile(selectedFile);
                SurfaceCollection surfaceCollection = statsHelper.recalSurfs.get(j);
                for (int i = 0; i < surfaceCollection.getSurfaceCount(); i++) {
                    Surface surface = surfaceCollection.getSurfaces(i);
                    // System.out.println("surface "+i);
                    // Vect3d xyzLow = new Vect3d(surface.getPolygons(0).getNodes(0).getX(),surface.getPolygons(0).getNodes(1).getX(),surface.getPolygons(0).getNodes(2).getX());
                    // Vect3d xyzHigh = new Vect3d(xyzLow);
                    ComboboxROIName[] existingRoiNames = overlayEditorPanelJAI.getAllCompositeROINamesAndColors();
                    int newIndex = getUnusedROIColorIndex(existingRoiNames, newROIindexes.keySet());
                    newROIindexes.put(newIndex, selectedFiles[j].getName());
                    byte value = (byte) newIndex;
                    // overlayEditorPanelJAI.addROIName(roiName, true, roiName, true, value);
                    for (int k = 0; k < surface.getPolygonCount(); k++) {
                        Polygon polygon = surface.getPolygons(k);
                        // for (Node pnode:polygon.getNodes()) {
                        // xyzLow.set(Math.min(xyzLow.getX(), pnode.getX()),Math.min(xyzLow.getY(), pnode.getY()),Math.min(xyzLow.getZ(), pnode.getZ()));
                        // xyzHigh.set(Math.max(xyzHigh.getX(), pnode.getX()),Math.max(xyzHigh.getY(), pnode.getY()),Math.max(xyzHigh.getZ(), pnode.getZ()));
                        // }
                        // if(k%10000 == 0){
                        // System.out.println("progress= file "+(j+1)+" of "+selectedFiles.length+" "+((k*100)/surface.getPolygonCount())+"%");
                        // }
                        // System.out.println("  polygon "+j+" "+polygon.getNodes(0)+" "+polygon.getNodes(1)+" "+polygon.getNodes(2));
                        Vect3d line1 = new Vect3d(polygon.getNodes(0));
                        Vect3d end1 = new Vect3d(polygon.getNodes(2));
                        Vect3d incr1 = Vect3d.sub(end1, line1);
                        incr1.unit();
                        incr1.set(incr1.getX() * scale.getX(), incr1.getY() * scale.getY(), incr1.getZ() * scale.getZ());
                        Vect3d line2 = new Vect3d(line1);
                        Vect3d end2 = new Vect3d(polygon.getNodes(1));
                        Vect3d incr2 = Vect3d.sub(end2, line2);
                        incr2.unit();
                        incr2.set(incr2.getX() * scale.getX(), incr2.getY() * scale.getY(), incr2.getZ() * scale.getZ());
                        while (true) {
                            Vect3d line3 = new Vect3d(line1);
                            Vect3d end3 = new Vect3d(line2);
                            Vect3d incr3 = Vect3d.sub(end3, line3);
                            if (incr3.length() != 0) {
                                incr3.unit();
                                incr3.set(incr3.getX() * scale.getX(), incr3.getY() * scale.getY(), incr3.getZ() * scale.getZ());
                            }
                            while (true) {
                                calcXYZ(line3, worldOrigin, worldCollapsedBoundingBox, primarySampleSizes, subSampleOffset, value);
                                line3.add(incr3);
                                Vect3d check = Vect3d.sub(end3, line3);
                                if ((check.length() == 0) || Math.signum(check.getX()) != Math.signum(incr3.getX()) || Math.signum(check.getY()) != Math.signum(incr3.getY()) || Math.signum(check.getZ()) != Math.signum(incr3.getZ())) {
                                    calcXYZ(end3, worldOrigin, worldCollapsedBoundingBox, primarySampleSizes, subSampleOffset, value);
                                    break;
                                }
                            }
                            if (line1.equals(end1) && line2.equals(end2)) {
                                break;
                            }
                            line1.add(incr1);
                            Vect3d check = Vect3d.sub(end1, line1);
                            if (check.length() == 0 || Math.signum(check.getX()) != Math.signum(incr1.getX()) || Math.signum(check.getY()) != Math.signum(incr1.getY()) || Math.signum(check.getZ()) != Math.signum(incr1.getZ())) {
                                line1 = new Vect3d(end1);
                            }
                            line2.add(incr2);
                            check = Vect3d.sub(end2, line2);
                            if (check.length() == 0 || Math.signum(check.getX()) != Math.signum(incr2.getX()) || Math.signum(check.getY()) != Math.signum(incr2.getY()) || Math.signum(check.getZ()) != Math.signum(incr2.getZ())) {
                                line2 = new Vect3d(end2);
                            }
                        }
                    }
                // regionBounds.put(new BoundingBox(xyzLow.getX(), xyzHigh.getX(),xyzLow.getY(), xyzHigh.getY(),xyzLow.getZ(), xyzHigh.getZ()),new Object[] {new int[] {j,i},roiName});
                }
            }
            // for(BoundingBox bb:regionBounds.keySet()){
            // System.out.println(((int[])regionBounds.get(bb)[0])[0]+","+((int[])regionBounds.get(bb)[0])[1]+" name="+((String)regionBounds.get(bb)[1])+" bound="+bb.getLoX()+","+bb.getHiX()+" "+bb.getLoY()+","+bb.getHiY()+" "+bb.getLoZ()+","+bb.getHiZ());
            // }
            updateAuxiliaryInfo(originalISize, getClientTaskStatusSupport());
        // }
        }
    };
    final int[] checkHolder = new int[1];
    final String[] cleanupHolder = new String[1];
    final String YES = "Yes";
    final ComboboxROIName[] cbxHolder = new ComboboxROIName[1];
    final String CHECK = "check";
    AsynchClientTask addROInamesTask = new AsynchClientTask("Add new ROI names...", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            int i = 0;
            for (Integer newIndex : newROIindexes.keySet()) {
                String roiName = FilenameUtils.getBaseName(newROIindexes.get(newIndex));
                roiName = TokenMangler.fixTokenStrict(roiName, 6);
                roiName += "_" + i++;
                overlayEditorPanelJAI.addROIName(roiName, true, roiName, true, newIndex);
            }
            cleanupHolder[0] = DialogUtils.showWarningDialog(overlayEditorPanelJAI, "Cleanup imported geometry?", new String[] { YES, "No" }, YES);
            if (!YES.equals(cleanupHolder[0])) {
                return;
            }
            checkHolder[0] = getUnusedROIColorIndex(overlayEditorPanelJAI.getAllCompositeROINamesAndColors(), null);
            overlayEditorPanelJAI.addROIName(CHECK, true, CHECK, true, checkHolder[0]);
            ComboboxROIName[] temp = overlayEditorPanelJAI.getAllCompositeROINamesAndColors();
            for (ComboboxROIName cbx : temp) {
                if (cbx.getROIName().equals(CHECK)) {
                    cbxHolder[0] = cbx;
                    break;
                }
            }
        }
    };
    // AsynchClientTask removeCheckROI = new AsynchClientTask("Remove check...",AsynchClientTask.TASKTYPE_SWING_BLOCKING) {
    // 
    // @Override
    // public void run(Hashtable<String, Object> hashTable) throws Exception {
    // ComboboxROIName[] regNames = overlayEditorPanelJAI.getAllCompositeROINamesAndColors();
    // for(ComboboxROIName cbx:regNames){
    // if(cbx.get)
    // }
    // }
    // };
    final AsynchClientTask mergeBackgroundRegions = new AsynchClientTask("Merge background regions...", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            if (!YES.equals(cleanupHolder[0])) {
                return;
            }
            // long start = System.currentTimeMillis();
            // while(currRegionImage == regionImage){
            // int dur = (int)((System.currentTimeMillis()-start)/1000);
            // if(dur > 10){
            // return;
            // }
            // System.out.println("trying..."+dur);
            // Thread.sleep(1000);
            // }
            final TreeMap<RegionInfo, Vect3d[]> regTobb = new TreeMap<>(new Comparator<RegionInfo>() {

                @Override
                public int compare(RegionInfo arg0, RegionInfo arg1) {
                    return arg0.getRegionIndex() - arg1.getRegionIndex();
                }
            });
            Hashtable<String, Object> newRegionImgHolder = new Hashtable<>();
            createRegionImageTask.run(newRegionImgHolder);
            RegionImage newRegionImage = (RegionImage) newRegionImgHolder.get(LOCAL_REGION_IMAGE);
            // ArrayList<RegionInfo> remainingRegionInfos = new ArrayList<>(Arrays.asList(newRegionImage.getRegionInfos()));
            // BoundingBox bb = new BoundingBox(0, newRegionImage.getNumX()-1, 0, newRegionImage.getNumY()-1, 0, newRegionImage.getNumZ()-1);
            // int currIndex = 0;
            // for (int z = 0; z <= bb.getHiZ(); z++) {
            // for (int y = 0; y <= bb.getHiY(); y++) {
            // for (int x = 0; x <= bb.getHiX(); x++) {
            // ArrayList<RegionInfo> tempRegionInfos = (ArrayList<RegionInfo>)remainingRegionInfos.clone();
            // if(x==0 || x == bb.getHiX() || y==0 || y == bb.getHiY() || z==0 || z == bb.getHiZ()){
            // for(RegionInfo reg:tempRegionInfos){
            // if(reg.getPixelValue() == 0 && reg.isIndexInRegion(currIndex)){
            // remainingRegionInfos.remove(reg);
            // break;
            // }
            // }
            // }else{
            // for(RegionInfo reg:tempRegionInfos){
            // if(reg.getPixelValue() == 0 && reg.isIndexInRegion(currIndex)){
            // remainingRegionInfos.remove(reg);
            // break;
            // }
            // }
            // }
            // currIndex++;
            // }
            // }
            // }
            // Remove unfilled regions (background) that touch the whole region border
            int allPixCnt = 0;
            ArrayList<RegionInfo> excluded = new ArrayList<>();
            for (int z = 0; z < newRegionImage.getNumZ(); z++) {
                for (int y = 0; y < newRegionImage.getNumY(); y++) {
                    for (int x = 0; x < newRegionImage.getNumX(); x++) {
                        RegionInfo regInfo = newRegionImage.getRegionInfoFromOffset(allPixCnt);
                        allPixCnt += 1;
                        if (excluded.contains(regInfo)) {
                            continue;
                        }
                        if (regInfo.getPixelValue() == 0 && (x == 0 || x == newRegionImage.getNumX() - 1 || y == 0 || y == newRegionImage.getNumY() - 1 || z == 0 || z == newRegionImage.getNumZ() - 1)) {
                            excluded.add(regInfo);
                            if (regTobb.containsKey(regInfo)) {
                                regTobb.remove(regInfo);
                            }
                            continue;
                        }
                        Vect3d[] bounds = regTobb.get(regInfo);
                        if (bounds == null) {
                            bounds = new Vect3d[] { new Vect3d(Double.POSITIVE_INFINITY, Double.POSITIVE_INFINITY, Double.POSITIVE_INFINITY), new Vect3d(Double.NEGATIVE_INFINITY, Double.NEGATIVE_INFINITY, Double.NEGATIVE_INFINITY) };
                            regTobb.put(regInfo, bounds);
                        }
                        bounds[0].set(Math.min(bounds[0].getX(), x), Math.min(bounds[0].getY(), y), Math.min(bounds[0].getZ(), z));
                        bounds[1].set(Math.max(bounds[1].getX(), x), Math.max(bounds[1].getY(), y), Math.max(bounds[1].getZ(), z));
                    }
                }
            }
            // ArrayList<Object[]> tree = new ArrayList<>();//arraylist<object[]>,regionInfo
            // ArrayList<RegionInfo> bucket = new ArrayList<>(regTobb.keySet());
            // tree.add(new Object[] {null,regTobb.firstKey()});
            // //				ArrayList<Object[]> stack = new ArrayList<>();
            // //				stack.add(tree.get(0));
            // while(bucket.size() > 0){
            // //					Object[] next = stack.remove(0);
            // RegionInfo next = bucket.remove(0);
            // Vect3d[] o2v = (Vect3d[])regTobb.get(regTobb.get(next));
            // for(Object[] objArr:tree){
            // //						if(((RegionInfo)next[1]).getRegionIndex() != reg.getRegionIndex()){
            // //								for(RegionInfo bucketReg:bucket){
            // Vect3d[] o1v = (Vect3d[])regTobb.get(objArr[1]);
            // if(	o1v[0].getX() >= o2v[0].getX() && o1v[0].getX() <= o2v[1].getX() &&
            // o1v[0].getY() >= o2v[0].getY() && o1v[0].getY() <= o2v[1].getY() &&
            // o1v[0].getZ() >= o2v[0].getZ() && o1v[0].getZ() <= o2v[1].getZ()
            // ){
            // 
            // }
            // //								}
            // //						}
            // }
            // }
            // Sort filled/unfilled regions by boundingbox
            ArrayList<RegionInfo> sortedRegionInfos = new ArrayList<>(Arrays.asList(regTobb.keySet().toArray(new RegionInfo[0])));
            Collections.sort(sortedRegionInfos, new Comparator<RegionInfo>() {

                @Override
                public int compare(RegionInfo o1, RegionInfo o2) {
                    Vect3d[] o1v = (Vect3d[]) regTobb.get(o1);
                    Vect3d[] o2v = (Vect3d[]) regTobb.get(o2);
                    // }
                    if (o1v[0].getX() == o2v[0].getX() && o1v[1].getX() == o2v[1].getX() && o1v[0].getY() == o2v[0].getY() && o1v[1].getY() == o2v[1].getY() && o1v[0].getZ() >= o2v[0].getZ() && o1v[1].getZ() == o2v[1].getZ()) {
                        System.out.println(o1.getRegionIndex() + " == " + o2.getRegionIndex());
                        return 0;
                    } else if (o1v[0].getX() >= o2v[0].getX() && o1v[0].getX() <= o2v[1].getX() && // o1v[1].getX() >= o2v[0].getX() && o1v[1].getX() <= o2v[1].getX() &&
                    o1v[0].getY() >= o2v[0].getY() && o1v[0].getY() <= o2v[1].getY() && // o1v[1].getY() >= o2v[0].getY() && o1v[1].getY() <= o2v[1].getY() &&
                    o1v[0].getZ() >= o2v[0].getZ() && o1v[0].getZ() <= o2v[1].getZ()) // && o1v[1].getZ() >= o2v[0].getZ() && o1v[1].getZ() <= o2v[1].getZ()
                    {
                        System.out.println(o1.getRegionIndex() + " > " + o2.getRegionIndex());
                        return 1;
                    } else if (o1v[0].getX() <= o2v[0].getX() && o1v[1].getX() >= o2v[1].getX() && o1v[0].getY() <= o2v[0].getY() && o1v[1].getY() >= o2v[1].getY() && o1v[0].getZ() <= o2v[0].getZ() && o1v[1].getZ() >= o2v[1].getZ()) // (o1v[0].getX() < o2v[0].getX() && o1v[1].getX() < o2v[0].getX()) ||
                    // (o1v[0].getX() > o2v[1].getX() && o1v[1].getX() > o2v[1].getX()) ||
                    // 
                    // (o1v[0].getY() < o2v[0].getY() && o1v[1].getY() < o2v[0].getY()) ||
                    // (o1v[0].getY() > o2v[1].getY() && o1v[1].getY() > o2v[1].getY()) ||
                    // 
                    // (o1v[0].getZ() < o2v[0].getZ() && o1v[1].getZ() < o2v[0].getZ()) ||
                    // (o1v[0].getZ() > o2v[1].getZ() && o1v[1].getZ() > o2v[1].getZ())
                    // 
                    // /*	(o1v[0].getX() < o2v[0].getX() && o1v[0].getX() > o2v[1].getX() &&
                    // o1v[1].getX() < o2v[0].getX() && o1v[1].getX() > o2v[1].getX()) ||
                    // (o1v[0].getY() < o2v[0].getY() && o1v[0].getY() > o2v[1].getY() &&
                    // o1v[1].getY() < o2v[0].getY() && o1v[1].getY() > o2v[1].getY()) ||
                    // (o1v[0].getZ() < o2v[0].getZ() && o1v[0].getZ() > o2v[1].getZ() &&
                    // o1v[1].getZ() < o2v[0].getZ() && o1v[1].getZ() > o2v[1].getZ())*/
                    {
                        System.out.println(o1.getRegionIndex() + " <a " + o2.getRegionIndex());
                        return -1;
                    } else if ((o1v[0].getX() < o2v[0].getX() && o1v[1].getX() < o2v[0].getX()) || (o1v[0].getX() > o2v[1].getX() && o1v[1].getX() > o2v[1].getX()) || (o1v[0].getY() < o2v[0].getY() && o1v[1].getY() < o2v[0].getY()) || (o1v[0].getY() > o2v[1].getY() && o1v[1].getY() > o2v[1].getY()) || (o1v[0].getZ() < o2v[0].getZ() && o1v[1].getZ() < o2v[0].getZ()) || (o1v[0].getZ() > o2v[1].getZ() && o1v[1].getZ() > o2v[1].getZ())) {
                        System.out.println(o1.getRegionIndex() + " <b " + o2.getRegionIndex());
                        return -1;
                    }
                    System.out.println("inconclusive " + o1.getRegionIndex() + " == " + o2.getRegionIndex());
                    return 0;
                // System.out.println("inconclusive "+o1.getRegionIndex()+" "+(o1.getNumPixels() - o2.getNumPixels()<0?"<":(o1.getNumPixels() - o2.getNumPixels()>0?">":"=="))+" "+o2.getRegionIndex());
                // return o1.getNumPixels() - o2.getNumPixels();
                // System.out.println("inconclusive "+o1.getRegionIndex()+" "+(o1.getRegionIndex()-o2.getRegionIndex()<0?"<":(o1.getRegionIndex()-o2.getRegionIndex()>0?">":"=="))+" "+o2.getRegionIndex());
                // return o1.getRegionIndex()-o2.getRegionIndex();
                // if(o1v[0].getZ() != o2v[0].getZ()){
                // return (int)(o1v[0].getZ() - o2v[0].getZ());
                // }else if(o1v[0].getY() != o2v[0].getY()){
                // return (int)(o1v[0].getY() - o2v[0].getY());
                // }else if(o1v[0].getX() != o2v[0].getX()){
                // return (int)(o1v[0].getX() - o2v[0].getX());
                // }else
                // return 0;
                }
            });
            // Convert unfilled regions into parent regions
            int currColorIndex = -1;
            // for (int i = sortedRegionInfos.size()-1; i >= 0; i--) {
            for (int i = 0; i < sortedRegionInfos.size(); i++) {
                RegionInfo regInfo = sortedRegionInfos.get(i);
                Vect3d[] o1v = (Vect3d[]) regTobb.get(regInfo);
                ComboboxROIName cbxroiName = overlayEditorPanelJAI.getComboboxROIName(regInfo);
                // System.out.println(cbxroiName+" colorIndex="+regInfo.getPixelValue()+" regIndex="+regInfo.getRegionIndex()+" pixels="+regInfo.getNumPixels()+" "+o1v[0]+" "+o1v[1]);
                if (cbxroiName != null) {
                    currColorIndex = cbxroiName.getContrastColorIndex();
                    continue;
                }
                allPixCnt = 0;
                for (int z = 0; z < newRegionImage.getNumZ(); z++) {
                    for (int y = 0; y < newRegionImage.getNumY(); y++) {
                        for (int x = 0; x < newRegionImage.getNumX(); x++) {
                            if (regInfo.isIndexInRegion(allPixCnt)) {
                                BufferedImage plane = roiComposite[z];
                                byte[] data = ((DataBufferByte) plane.getRaster().getDataBuffer()).getData();
                                data[x + (plane.getWidth() * y)] = (byte) currColorIndex;
                            }
                            allPixCnt++;
                        }
                    }
                }
            }
            // for(RegionInfo regInfo:regTobb.keySet()){
            // Vect3d[] varr = regTobb.get(regInfo);
            // ComboboxROIName cbxroiName = overlayEditorPanelJAI.getComboboxROIName(regInfo);
            // regionBounds.put(new BoundingBox(varr[0].getX(), varr[1].getX(),varr[0].getY(), varr[1].getY(),varr[0].getZ(), varr[1].getZ()),new Object[] {cbxroiName});
            // }
            // for(BoundingBox bb:regionBounds.keySet()){
            // ComboboxROIName cbxroiName = ((ComboboxROIName)regionBounds.get(bb)[0]);
            // System.out.println(cbxroiName+" bound="+bb.getLoX()+","+bb.getHiX()+" "+bb.getLoY()+","+bb.getHiY()+" "+bb.getLoZ()+","+bb.getHiZ());
            // 
            // }
            // Make sure every pixel has only 1 kind of neighbor
            // createRegionImageTask.run(newRegionImgHolder);
            // newRegionImage = (RegionImage)newRegionImgHolder.get(LOCAL_REGION_IMAGE);
            boolean bHasCheck = false;
            VCImage checkImage = ROIMultiPaintManager.createVCImageFromBufferedImages(ROIMultiPaintManager.DEFAULT_EXTENT, roiComposite);
            newRegionImage = new RegionImage(checkImage, 0, /*0 means generate no surfacecollection*/
            checkImage.getExtent(), ROIMultiPaintManager.DEFAULT_ORIGIN, RegionImage.NO_SMOOTHING, null);
            TreeSet<Integer> diffNeighbors = new TreeSet<>();
            int[][] offsets = new int[][] { { -1, 0, 0 }, { 1, 0, 0 }, { 0, -1, 0 }, { 0, 1, 0 }, { 0, 0, -1 }, { 0, 0, 1 } };
            for (int z = 0; z < newRegionImage.getNumZ(); z++) {
                BufferedImage plane = roiComposite[z];
                byte[] data = ((DataBufferByte) plane.getRaster().getDataBuffer()).getData();
                allPixCnt = 0;
                for (int y = 0; y < newRegionImage.getNumY(); y++) {
                    for (int x = 0; x < newRegionImage.getNumX(); x++) {
                        diffNeighbors.clear();
                        RegionInfo regInfo = newRegionImage.getRegionInfoFromOffset(allPixCnt);
                        if (regInfo.getPixelValue() == 0) {
                            allPixCnt++;
                            continue;
                        }
                        if (x == 19 && y == 15) {
                            System.out.println("here");
                        }
                        for (int i = 0; i < offsets.length; i++) {
                            int tmpx = offsets[i][0] + x;
                            if (tmpx < 0 || tmpx >= newRegionImage.getNumX()) {
                                continue;
                            }
                            int tmpy = offsets[i][1] + y;
                            if (tmpy < 0 || tmpy >= newRegionImage.getNumY()) {
                                continue;
                            }
                            int tmpz = offsets[i][2] + z;
                            if (tmpz < 0 || tmpz >= newRegionImage.getNumZ()) {
                                continue;
                            }
                            BufferedImage plane0 = roiComposite[tmpz];
                            byte[] data0 = ((DataBufferByte) plane.getRaster().getDataBuffer()).getData();
                            byte shiftb = data0[tmpx + (tmpy * newRegionImage.getNumX())];
                            if (shiftb != regInfo.getPixelValue()) {
                                diffNeighbors.add(0x000000FF & shiftb);
                            }
                        }
                        // for (int z0 = -1; z0 <= 1; z0+=2) {
                        // int tmpz = z+z0;
                        // if(tmpz < 0 || tmpz >= newRegionImage.getNumZ()){
                        // continue;
                        // }
                        // //								tmpz = allPixCnt+(z0*newRegionImage.getNumXY());
                        // BufferedImage plane0 = roiComposite[z+z0];
                        // byte[] data0 = ((DataBufferByte)plane.getRaster().getDataBuffer()).getData();
                        // for (int y0 = -1; y0 <= 1; y0+=2) {
                        // int tmpy = y+y0;
                        // if(tmpy < 0 || tmpy >= newRegionImage.getNumY()){
                        // continue;
                        // }
                        // //									tmpy = tmpz+(y0*newRegionImage.getNumX());
                        // for (int x0 = -1; x0 <= 1; x0+=2) {
                        // int tmpx = x+x0;
                        // if(tmpx < 0 || tmpx >= newRegionImage.getNumX()){
                        // continue;
                        // }
                        // //										tmpx = tmpy+(x0);
                        // byte shiftb = data0[tmpx+(tmpy*newRegionImage.getNumX())];
                        // if(shiftb != regInfo.getPixelValue()){
                        // diffNeighbors.add(0x000000FF&shiftb);
                        // }
                        // }
                        // }
                        // }
                        allPixCnt++;
                        if (diffNeighbors.size() > 1) {
                            bHasCheck = true;
                            data[x + y * newRegionImage.getNumX()] = (byte) checkHolder[0];
                        }
                    }
                }
            }
            if (!bHasCheck && cbxHolder[0] != null) {
                SwingUtilities.invokeAndWait(new Runnable() {

                    @Override
                    public void run() {
                        overlayEditorPanelJAI.deleteROIName(cbxHolder[0]);
                    }
                });
            }
        }
    };
    // }).start();
    return new ArrayList<>(Arrays.asList(new AsynchClientTask[] { sampleSTLtask, addROInamesTask, mergeBackgroundRegions, getUpdateDisplayAfterCropTask() }));
// JFileChooser importJFC = new JFileChooser(ClientRequestManager.getPreferredPath(UserPreferences.getLastUserPreferences()));
// importJFC.setDialogTitle("Choose .stl file to import");
// importJFC.setMultiSelectionEnabled(true);
// int result = importJFC.showOpenDialog(overlayEditorPanelJAI);
// if(result == JFileChooser.APPROVE_OPTION){
// File[] selectedFiles = importJFC.getSelectedFiles();
// if(statsHelper == null){
// statsHelper = calcMinMax(selectedFiles);
// }
// ClientRequestManager.setPreferredPath(UserPreferences.getLastUserPreferences(), selectedFiles[0]);
// 
// Vect3d worldOrigin = new Vect3d(statsHelper.xmin, statsHelper.ymin, statsHelper.zmin);
// Vect3d worldCollapsedBoundingBox = new Vect3d(statsHelper.xmax-statsHelper.xmin, statsHelper.ymax-statsHelper.ymin, statsHelper.zmax-statsHelper.zmin);
// Vect3d scale = new Vect3d(worldCollapsedBoundingBox.getX()/(2.0*primarySampleSizes.getX()), worldCollapsedBoundingBox.getY()/(2.0*primarySampleSizes.getY()), worldCollapsedBoundingBox.getZ()/(2.0*primarySampleSizes.getZ()));
// //				if(scale.getX() !=0 && scale.getX() >= (scale.getY()==0?scale.getX():scale.getY()) && scale.getX() >= (scale.getZ()==0?scale.getX():scale.getZ())){
// //					scale = new Vect3d(scale.getX(), scale.getX(), scale.getX());
// //				}else if(scale.getY() !=0 && scale.getY() >= (scale.getX()==0?scale.getY():scale.getX()) && scale.getY() >= (scale.getZ()==0?scale.getY():scale.getZ())){
// //					scale = new Vect3d(scale.getY(), scale.getY(), scale.getY());
// //				}else if(scale.getZ() !=0 && scale.getZ() >= (scale.getY()==0?scale.getZ():scale.getY()) && scale.getZ() >= (scale.getX()==0?scale.getZ():scale.getX())){
// //					scale = new Vect3d(scale.getZ(), scale.getZ(), scale.getZ());
// //				}
// if(scale.getX() !=0 && scale.getX() <= (scale.getY()==0?scale.getX():scale.getY()) && scale.getX() <= (scale.getZ()==0?scale.getX():scale.getZ())){
// scale = new Vect3d(scale.getX(), scale.getX(), scale.getX());
// }else if(scale.getY() !=0 && scale.getY() <= (scale.getX()==0?scale.getY():scale.getX()) && scale.getY() <= (scale.getZ()==0?scale.getY():scale.getZ())){
// scale = new Vect3d(scale.getY(), scale.getY(), scale.getY());
// }else if(scale.getZ() !=0 && scale.getZ() <= (scale.getY()==0?scale.getZ():scale.getY()) && scale.getZ() <= (scale.getX()==0?scale.getZ():scale.getX())){
// scale = new Vect3d(scale.getZ(), scale.getZ(), scale.getZ());
// }
// TreeMap<BoundingBox,Object[]> regionBounds = new TreeMap<>(new Comparator<BoundingBox>() {
// @Override
// public int compare(BoundingBox arg0, BoundingBox arg1) {
// if(arg1 == arg0){
// return 0;
// }
// if(arg0.getLoX() == arg1.getLoX() &&
// arg0.getLoY() == arg1.getLoY() &&
// arg0.getLoZ() == arg1.getLoZ() &&
// arg0.getHiX() == arg1.getHiX() &&
// arg0.getHiY() == arg1.getHiY() &&
// arg0.getHiZ() == arg1.getHiZ()){
// return 0;
// }
// return (arg0.getLoX() >= arg1.getLoX() &&
// arg0.getLoY() >= arg1.getLoY() &&
// arg0.getLoZ() >= arg1.getLoZ() &&
// arg0.getHiX() <= arg1.getHiX() &&
// arg0.getHiY() <= arg1.getHiY() &&
// arg0.getHiZ() <= arg1.getHiZ()?-1:+1);
// }
// });
// for (int j = 0; j < selectedFiles.length; j++) {
// SurfaceCollection surfaceCollection = statsHelper.recalSurfs.get(j);//ClientRequestManager.createSurfaceCollectionFromSurfaceFile(selectedFile);
// for (int i = 0; i < surfaceCollection.getSurfaceCount(); i++) {
// Surface surface = surfaceCollection.getSurfaces(i);
// System.out.println("surface "+i);
// Vect3d xyzLow = new Vect3d(surface.getPolygons(0).getNodes(0).getX(),surface.getPolygons(0).getNodes(1).getX(),surface.getPolygons(0).getNodes(2).getX());
// Vect3d xyzHigh = new Vect3d(xyzLow);
// ComboboxROIName[] existingRoiNames = overlayEditorPanelJAI.getAllCompositeROINamesAndColors();
// byte value = (byte)getUnusedROIColorIndex(existingRoiNames);
// String roiName = FilenameUtils.getBaseName(selectedFiles[j].getName());
// roiName = TokenMangler.fixTokenStrict(roiName, 6);
// roiName+= "_"+i;
// overlayEditorPanelJAI.addROIName(roiName, true, roiName, true, value);
// for (int k = 0; k < surface.getPolygonCount(); k++){
// Polygon polygon = surface.getPolygons(k);
// //							for (Node pnode:polygon.getNodes()) {
// //								xyzLow.set(Math.min(xyzLow.getX(), pnode.getX()),Math.min(xyzLow.getY(), pnode.getY()),Math.min(xyzLow.getZ(), pnode.getZ()));
// //								xyzHigh.set(Math.max(xyzHigh.getX(), pnode.getX()),Math.max(xyzHigh.getY(), pnode.getY()),Math.max(xyzHigh.getZ(), pnode.getZ()));
// //							}
// if(k%10000 == 0){
// System.out.println("progress= file "+(j+1)+" of "+selectedFiles.length+" "+((k*100)/surface.getPolygonCount())+"%");
// }
// //							System.out.println("  polygon "+j+" "+polygon.getNodes(0)+" "+polygon.getNodes(1)+" "+polygon.getNodes(2));
// Vect3d line1 = new Vect3d(polygon.getNodes(0));
// Vect3d end1 = new Vect3d(polygon.getNodes(2));
// Vect3d incr1 = Vect3d.sub(end1,line1);
// incr1.unit();
// incr1.set(incr1.getX()*scale.getX(), incr1.getY()*scale.getY(), incr1.getZ()*scale.getZ());
// Vect3d line2 = new Vect3d(line1);
// Vect3d end2 = new Vect3d(polygon.getNodes(1));
// Vect3d incr2 = Vect3d.sub(end2,line2);
// incr2.unit();
// incr2.set(incr2.getX()*scale.getX(), incr2.getY()*scale.getY(), incr2.getZ()*scale.getZ());
// while(true){
// Vect3d line3 = new Vect3d(line1);
// Vect3d end3 = new Vect3d(line2);
// Vect3d incr3 = Vect3d.sub(end3,line3);
// if(incr3.length() != 0){
// incr3.unit();
// incr3.set(incr3.getX()*scale.getX(), incr3.getY()*scale.getY(), incr3.getZ()*scale.getZ());
// }
// while(true){
// calcXYZ(line3, worldOrigin, worldCollapsedBoundingBox, primarySampleSizes,subSampleOffset,value);
// line3.add(incr3);
// Vect3d check =  Vect3d.sub(end3, line3);
// if((check.length()==0) || Math.signum(check.getX()) != Math.signum(incr3.getX()) || Math.signum(check.getY()) != Math.signum(incr3.getY()) || Math.signum(check.getZ()) != Math.signum(incr3.getZ())){
// calcXYZ(end3, worldOrigin, worldCollapsedBoundingBox, primarySampleSizes,subSampleOffset,value);
// break;
// }
// }
// if(line1.equals(end1) && line2.equals(end2)){
// break;
// }
// 
// line1.add(incr1);
// Vect3d check =  Vect3d.sub(end1, line1);
// if(check.length()==0 || Math.signum(check.getX()) != Math.signum(incr1.getX()) || Math.signum(check.getY()) != Math.signum(incr1.getY()) || Math.signum(check.getZ()) != Math.signum(incr1.getZ())){
// line1 = new Vect3d(end1);
// }
// line2.add(incr2);
// check =  Vect3d.sub(end2, line2);
// if(check.length()==0 || Math.signum(check.getX()) != Math.signum(incr2.getX()) || Math.signum(check.getY()) != Math.signum(incr2.getY()) || Math.signum(check.getZ()) != Math.signum(incr2.getZ())){
// line2 = new Vect3d(end2);
// }
// }
// }
// //						regionBounds.put(new BoundingBox(xyzLow.getX(), xyzHigh.getX(),xyzLow.getY(), xyzHigh.getY(),xyzLow.getZ(), xyzHigh.getZ()),new Object[] {new int[] {j,i},roiName});
// }
// }
// //				for(BoundingBox bb:regionBounds.keySet()){
// //					System.out.println(((int[])regionBounds.get(bb)[0])[0]+","+((int[])regionBounds.get(bb)[0])[1]+" name="+((String)regionBounds.get(bb)[1])+" bound="+bb.getLoX()+","+bb.getHiX()+" "+bb.getLoY()+","+bb.getHiY()+" "+bb.getLoZ()+","+bb.getHiZ());
// //				}
// updateAuxiliaryInfo(originalISize, null);
// getUpdateDisplayAfterCropTask().run(null);
// 
// new Thread(new Runnable() {
// @Override
// public void run() {
// while(ClientTaskDispatcher.isBusy()){
// try {
// Thread.sleep(1000);
// } catch (InterruptedException e) {
// // TODO Auto-generated catch block
// e.printStackTrace();
// }
// }
// TreeMap<RegionInfo, Vect3d[]> regTobb = new TreeMap<>(new Comparator<RegionInfo>() {
// @Override
// public int compare(RegionInfo arg0, RegionInfo arg1) {
// return arg0.getRegionIndex()-arg1.getRegionIndex();
// }
// });
// int allPixCnt = regionImage.getNumX()*regionImage.getNumY()*regionImage.getNumZ();
// for (int z = 0; z < regionImage.getNumZ(); z++) {
// for (int y = 0; y < regionImage.getNumY(); y++) {
// for (int x = 0; x < regionImage.getNumX(); x++) {
// allPixCnt-=1;
// RegionInfo regInfo = regionImage.getRegionInfoFromOffset(allPixCnt);
// Vect3d[] bounds = regTobb.get(regInfo);
// if(bounds == null){
// bounds = new Vect3d[] {new Vect3d(),new Vect3d()};
// regTobb.put(regInfo, bounds);
// }
// bounds[0].set(Math.min(bounds[0].getX(), x),Math.min(bounds[0].getY(), y),Math.min(bounds[0].getZ(), z));
// bounds[1].set(Math.max(bounds[1].getX(), x),Math.max(bounds[1].getY(), y),Math.max(bounds[1].getZ(), z));
// 
// }
// }
// }
// for(RegionInfo regInfo:regTobb.keySet()){
// Vect3d[] varr = regTobb.get(regInfo);
// ComboboxROIName cbxroiName = overlayEditorPanelJAI.getComboboxROIName(regInfo);
// regionBounds.put(new BoundingBox(varr[0].getX(), varr[1].getX(),varr[0].getY(), varr[1].getY(),varr[0].getZ(), varr[1].getZ()),new Object[] {cbxroiName});
// }
// for(BoundingBox bb:regionBounds.keySet()){
// ComboboxROIName cbxroiName = ((ComboboxROIName)regionBounds.get(bb)[0]);
// System.out.println(cbxroiName+" bound="+bb.getLoX()+","+bb.getHiX()+" "+bb.getLoY()+","+bb.getHiY()+" "+bb.getLoZ()+","+bb.getHiZ());
// 
// }
// }
// }).start();
// }
// }catch (Exception e) {
// e.printStackTrace();
// DialogUtils.showErrorDialog(overlayEditorPanelJAI, e.getMessage());
// }
}

Example 5 with RegionImage

use of cbit.vcell.geometry.RegionImage in project vcell by virtualcell.

the class ROIMultiPaintManager method mergeResolvedSelections.

private void mergeResolvedSelections(final RegionInfo[] selectedRegionInfos) throws Exception {
    if (selectedRegionInfos == null || selectedRegionInfos.length == 0) {
        return;
    }
    // final String UNUSED_ROI_PIXVAL = "UNUSED_ROI_INDEX";
    // final String MULTI_NEIGHBOR_MERGE = "MultiNeighborMerge";
    AsynchClientTask mergeTask = new AsynchClientTask("Merging " + selectedRegionInfos.length + " regions...", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            // make new RegionImage with all selections converted to a single temporary ROI
            // 
            // if(isROINameUsed(overlayEditorPanelJAI.getAllCompositeROINamesAndColors(), MULTI_NEIGHBOR_MERGE)){
            // throw new Exception(MULTI_NEIGHBOR_MERGE+" exists, they must be reconciled before any new merge");
            // }
            // sort selected region index for fast lookup
            TreeSet<Integer> selectedRegionIndexesTS = new TreeSet<Integer>();
            for (int i = 0; i < selectedRegionInfos.length; i++) {
                selectedRegionIndexesTS.add(selectedRegionInfos[i].getRegionIndex());
            }
            // //find unused index we can use for temporary ROI
            // BitSet usedROIIndexes = new BitSet();
            // for (int i = 0; i < roiComposite.length; i++) {
            // byte[] sliceBytes = ((DataBufferByte)roiComposite[i].getRaster().getDataBuffer()).getData();
            // for (int j = 0; j < sliceBytes.length; j++) {
            // usedROIIndexes.set((int)(sliceBytes[j]&0x000000FF));
            // }
            // }
            int unusedROIPixelValue = getUnusedROIColorIndex(overlayEditorPanelJAI.getAllCompositeROINamesAndColors(), null);
            // if(usedROIIndexes.get(unusedROIPixelValue)){
            // throw new Exception("Error: Found unused color index but that ROI pixel value exists");
            // }
            // find image indexes of selected regions and fill new ROIImage with temporary ROI Index
            byte[] shortEncodedRegionIndexArr = regionImage.getShortEncodedRegionIndexImage();
            BufferedImage[] tempROI = new BufferedImage[roiComposite.length];
            int count = 0;
            for (int i = 0; i < tempROI.length; i++) {
                byte[] roiBytes = ((DataBufferByte) roiComposite[i].getRaster().getDataBuffer()).getData();
                tempROI[i] = new BufferedImage(roiComposite[i].getWidth(), roiComposite[i].getHeight(), BufferedImage.TYPE_BYTE_INDEXED, getContrastIndexColorModel());
                byte[] sliceBytes = ((DataBufferByte) tempROI[i].getRaster().getDataBuffer()).getData();
                System.arraycopy(roiBytes, 0, sliceBytes, 0, roiBytes.length);
                for (int j = 0; j < sliceBytes.length; j++) {
                    int regionIndex = (int) ((0x000000ff & shortEncodedRegionIndexArr[2 * count]) | ((0x000000ff & shortEncodedRegionIndexArr[2 * count + 1]) << 8));
                    if (selectedRegionIndexesTS.contains(regionIndex)) {
                        sliceBytes[j] = (byte) unusedROIPixelValue;
                    }
                    count++;
                }
            }
            if (getClientTaskStatusSupport() != null) {
                getClientTaskStatusSupport().setProgress(10);
            }
            // release memory
            shortEncodedRegionIndexArr = null;
            // get new regionImage and new selectedRegionInfos
            VCImage tempImage = ROIMultiPaintManager.createVCImageFromBufferedImages(ROIMultiPaintManager.DEFAULT_EXTENT, tempROI);
            RegionImage tempRegionImage = new RegionImage(tempImage, 0, /*0 means generate no surfacecollection*/
            tempImage.getExtent(), ROIMultiPaintManager.DEFAULT_ORIGIN, RegionImage.NO_SMOOTHING, null);
            // release memory
            tempImage = null;
            RegionInfo[] tempRegionInfos = tempRegionImage.getRegionInfos();
            if (tempRegionInfos.length == 1) {
                throw new Exception("No unselected neighbors to merge with.");
            }
            if (getClientTaskStatusSupport() != null) {
                getClientTaskStatusSupport().setProgress(20);
            }
            Vector<RegionImage.RegionInfo> tempSelectedRegionInfos = new Vector<RegionImage.RegionInfo>();
            HighlightROIInfo highlightROIInfo = generateHighlightROIInfo((byte) -1, tempROI, tempRegionImage, RegionAction.createCheckNeighborsOnlyRegionAction(tempRegionInfos), null);
            boolean bHasSelectionWithMoreThanOneNeighbor = false;
            for (int i = 0; i < tempRegionInfos.length; i++) {
                if (tempRegionInfos[i].getPixelValue() == unusedROIPixelValue) {
                    tempSelectedRegionInfos.add(tempRegionInfos[i]);
                // if (highlightROIInfo.neighborsForRegionsMap.get(tempRegionInfos[i]).size() > 1) {
                // hashTable.put(UNUSED_ROI_PIXVAL, new Integer(unusedROIPixelValue));
                // bHasSelectionWithMoreThanOneNeighbor = true;
                // } else {
                // tempSelectedRegionInfos.add(tempRegionInfos[i]);
                // }
                }
            }
            if (getClientTaskStatusSupport() != null) {
                getClientTaskStatusSupport().setProgress(50);
            }
            // final merge
            updateUndo(UNDO_INIT.ALLZ);
            generateHighlightROIInfo((byte) unusedROIPixelValue, tempROI, tempRegionImage, RegionAction.createMergeSelectedWithNeighborsRegionAction(tempRegionInfos, tempSelectedRegionInfos, highlightROIInfo.neighborsForRegionsMap), null);
            // copy merged bytes back to ROI
            for (int i = 0; i < tempROI.length; i++) {
                byte[] roiBytes = ((DataBufferByte) roiComposite[i].getRaster().getDataBuffer()).getData();
                byte[] sliceBytes = ((DataBufferByte) tempROI[i].getRaster().getDataBuffer()).getData();
                // for (int j = 0; j < sliceBytes.length; j++) {
                // if(sliceBytes[j] == (byte)unusedROIPixelValue){
                // System.out.println("Bad");
                // }
                // }
                System.arraycopy(sliceBytes, 0, roiBytes, 0, roiBytes.length);
            }
            if (getClientTaskStatusSupport() != null) {
                getClientTaskStatusSupport().setProgress(90);
            }
        }
    };
    AsynchClientTask updateGUITask = new AsynchClientTask("Updating display...", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            // Integer unusedROIIndex = (Integer)hashTable.get(UNUSED_ROI_PIXVAL);
            // if(unusedROIIndex != null){
            // overlayEditorPanelJAI.addROIName(MULTI_NEIGHBOR_MERGE, true, MULTI_NEIGHBOR_MERGE,true,/*true,true,*/OverlayEditorPanelJAI.CONTRAST_COLORS[unusedROIIndex]);
            // }
            overlayEditorPanelJAI.setHighliteInfo(null, OverlayEditorPanelJAI.FRAP_DATA_RESOLVEDMERGE_PROPERTY);
            updateUndoAfterPrivate(true, false);
        }
    };
    Vector<AsynchClientTask> asynchClientTaskV = new Vector<AsynchClientTask>();
    asynchClientTaskV.add(mergeTask);
    asynchClientTaskV.add(updateGUITask);
    asynchClientTaskV.addAll(Arrays.asList(getRefreshObjectsTasks()));
    ClientTaskDispatcher.dispatch(overlayEditorPanelJAI, new Hashtable<String, Object>(), asynchClientTaskV.toArray(new AsynchClientTask[0]), true, false, null, true);
}