Examples with VCImage cbit.image.VCImage used on opensource projects

Example 21 with VCImage

use of cbit.image.VCImage in project vcell by virtualcell.

the class DisplayImageOp method displayImage.

public void displayImage(final Image image, String title, WindowListener listener) {
    final ImagePlaneManagerPanel imagePanel = new ImagePlaneManagerPanel();
    double[] doublePixels = image.getDoublePixels();
    double minPixel = Double.MAX_VALUE;
    double maxPixel = -Double.MAX_VALUE;
    for (int i = 0; i < doublePixels.length; i++) {
        double pixel = doublePixels[i];
        doublePixels[i] = pixel;
        minPixel = Math.min(minPixel, pixel);
        maxPixel = Math.max(maxPixel, pixel);
    }
    Range newRange = new Range(minPixel, maxPixel);
    SourceDataInfo source = new SourceDataInfo(SourceDataInfo.RAW_VALUE_TYPE, doublePixels, image.getExtent(), image.getOrigin(), newRange, 0, image.getNumX(), 1, image.getNumY(), image.getNumX(), image.getNumZ(), image.getNumX() * image.getNumY());
    imagePanel.setDisplayAdapterServicePanelVisible(true);
    imagePanel.setCurveValueProvider(new CurveValueProvider() {

        @Override
        public void curveAdded(Curve curve) {
            System.out.println("called curveAdded(" + curve + "), do nothing for now");
        }

        @Override
        public void curveRemoved(Curve curve) {
            System.out.println("called curveRemoved(" + curve + ")");
        }

        @Override
        public String getCurveValue(CurveSelectionInfo csi) {
            System.out.println("called getCurveValue(CurveSelectionInfo " + csi);
            return null;
        }

        @Override
        public CurveSelectionInfo getInitalCurveSelection(int tool, Coordinate wc) {
            System.out.println("called getInitialCurveSelection(tool=" + tool + ", coord=" + wc + ")");
            return null;
        }

        @Override
        public boolean isAddControlPointOK(int tool, Coordinate wc, Curve addedToThisCurve) {
            System.out.println("called isAddControlPointOK");
            return true;
        }

        @Override
        public boolean providesInitalCurve(int tool, Coordinate wc) {
            System.out.println("called providesInitialCurve(tool=" + tool + " (TOOL_LINE=" + CurveEditorTool.TOOL_LINE + "), coord=" + wc);
            return false;
        }

        @Override
        public void setDescription(Curve curve) {
            System.out.println("called setDescription(" + curve + ")");
            curve.setDescription(CurveValueProvider.DESCRIPTION_VOLUME);
        }

        @Override
        public CurveSelectionInfo findChomboCurveSelectionInfoForPoint(CoordinateIndex ci) {
            System.out.println("called find ChomboCurveSelectionInfoForPoint(coord=" + ci + ")");
            return null;
        }
    });
    DisplayAdapterService das = imagePanel.getDisplayAdapterServicePanel().getDisplayAdapterService();
    das.setValueDomain(null);
    das.addColorModelForValues(DisplayAdapterService.createGrayColorModel(), DisplayAdapterService.createGraySpecialColors(), DisplayAdapterService.GRAY);
    das.addColorModelForValues(DisplayAdapterService.createBlueRedColorModel(), DisplayAdapterService.createBlueRedSpecialColors(), DisplayAdapterService.BLUERED);
    das.setActiveColorModelID(DisplayAdapterService.BLUERED);
    final JFrame jframe = new JFrame();
    jframe.setTitle(title);
    JPanel panel = new JPanel();
    panel.setLayout(new GridBagLayout());
    GridBagConstraints imageConstraints = new GridBagConstraints();
    imageConstraints.gridx = 0;
    imageConstraints.gridy = 0;
    imageConstraints.weightx = 1.0;
    imageConstraints.weighty = 1.0;
    imageConstraints.fill = GridBagConstraints.BOTH;
    panel.add(imagePanel, imageConstraints);
    JButton plotButton = new JButton("plot");
    plotButton.addActionListener(new ActionListener() {

        @Override
        public void actionPerformed(ActionEvent e) {
            try {
                Curve curve = imagePanel.getCurveRenderer().getSelection().getCurve();
                VariableType variableType = VariableType.VOLUME;
                Curve samplerCurve = curve.getSampledCurve();
                samplerCurve.setDescription(curve.getDescription());
                VCImage vcImage = new VCImageUncompressed(null, new byte[image.getISize().getXYZ()], image.getExtent(), image.getISize().getX(), image.getISize().getY(), image.getISize().getZ());
                int dimension = 1 + (image.getISize().getY() > 0 ? 1 : 0) + (image.getISize().getZ() > 0 ? 1 : 0);
                RegionImage regionImage = new RegionImage(vcImage, dimension, image.getExtent(), image.getOrigin(), RegionImage.NO_SMOOTHING);
                CartesianMesh mesh = CartesianMesh.createSimpleCartesianMesh(image.getOrigin(), image.getExtent(), image.getISize(), regionImage);
                SpatialSelectionVolume ssVolume = new SpatialSelectionVolume(new CurveSelectionInfo(samplerCurve), variableType, mesh);
                String varName = "var";
                SymbolTableEntry[] symbolTableEntries = new SymbolTableEntry[] { new VolVariable(varName, null) };
                PlotData plotData = getLineScan(ssVolume, image, mesh);
                PlotPane plotPane = new PlotPane();
                DataSymbolMetadataResolver resolver = null;
                Plot2D plot2D = new Plot2D(symbolTableEntries, resolver, new String[] { varName }, new PlotData[] { plotData }, new String[] { "Values along curve", "Distance (\u00b5m)", "[" + varName + "]" });
                plotPane.setPlot2D(plot2D);
                DialogUtils.showComponentCloseDialog(jframe, plotPane, "plot");
            } catch (ImageException | IOException | DataAccessException | MathException e1) {
                e1.printStackTrace();
            }
        }
    });
    GridBagConstraints plotButtonConstraints = new GridBagConstraints();
    plotButtonConstraints.gridx = 0;
    plotButtonConstraints.gridy = 1;
    panel.add(plotButton, plotButtonConstraints);
    jframe.getContentPane().add(panel);
    jframe.setSize(500, 500);
    jframe.addWindowListener(listener);
    jframe.setVisible(true);
    imagePanel.setSourceDataInfo(source);
}

Example 22 with VCImage

use of cbit.image.VCImage in project vcell by virtualcell.

the class DisplayTimeSeriesOp method getDataSetControllerProvider.

private DataSetControllerProvider getDataSetControllerProvider(final ImageTimeSeries<? extends Image> imageTimeSeries, final PDEDataViewer pdeDataViewer) throws ImageException, IOException {
    ISize size = imageTimeSeries.getISize();
    int dimension = (size.getZ() > 0) ? (3) : (2);
    Extent extent = imageTimeSeries.getExtent();
    Origin origin = imageTimeSeries.getAllImages()[0].getOrigin();
    // don't care ... no surfaces
    double filterCutoffFrequency = 0.5;
    VCImage vcImage = new VCImageUncompressed(null, new byte[size.getXYZ()], extent, size.getX(), size.getY(), size.getZ());
    RegionImage regionImage = new RegionImage(vcImage, dimension, extent, origin, filterCutoffFrequency);
    final CartesianMesh mesh = CartesianMesh.createSimpleCartesianMesh(origin, extent, size, regionImage);
    final DataIdentifier dataIdentifier = new DataIdentifier("var", VariableType.VOLUME, new Domain("domain"), false, "var");
    final DataSetController dataSetController = new DataSetController() {

        @Override
        public ExportEvent makeRemoteFile(OutputContext outputContext, ExportSpecs exportSpecs) throws DataAccessException, RemoteProxyException {
            throw new RuntimeException("not yet implemented");
        }

        @Override
        public TimeSeriesJobResults getTimeSeriesValues(OutputContext outputContext, VCDataIdentifier vcdataID, TimeSeriesJobSpec timeSeriesJobSpec) throws RemoteProxyException, DataAccessException {
            pdeDataViewer.dataJobMessage(new DataJobEvent(timeSeriesJobSpec.getVcDataJobID(), MessageEvent.DATA_START, vcdataID.getDataKey(), vcdataID.getID(), new Double(0)));
            if (!timeSeriesJobSpec.isCalcSpaceStats() && !timeSeriesJobSpec.isCalcTimeStats()) {
                int[][] indices = timeSeriesJobSpec.getIndices();
                double[] timeStamps = imageTimeSeries.getImageTimeStamps();
                // [var][dataindex+1][timeindex]
                double[][][] dataValues = new double[1][indices[0].length + 1][timeStamps.length];
                for (int timeIndex = 0; timeIndex < timeStamps.length; timeIndex++) {
                    // index 0 is time
                    dataValues[0][0][timeIndex] = timeStamps[timeIndex];
                }
                for (int timeIndex = 0; timeIndex < timeStamps.length; timeIndex++) {
                    float[] pixelValues = imageTimeSeries.getAllImages()[timeIndex].getFloatPixels();
                    for (int samplePointIndex = 0; samplePointIndex < indices[0].length; samplePointIndex++) {
                        int pixelIndex = indices[0][samplePointIndex];
                        dataValues[0][samplePointIndex + 1][timeIndex] = pixelValues[pixelIndex];
                    }
                }
                TSJobResultsNoStats timeSeriesJobResults = new TSJobResultsNoStats(new String[] { "var" }, indices, timeStamps, dataValues);
                pdeDataViewer.dataJobMessage(new DataJobEvent(timeSeriesJobSpec.getVcDataJobID(), MessageEvent.DATA_COMPLETE, vcdataID.getDataKey(), vcdataID.getID(), new Double(0)));
                return timeSeriesJobResults;
            }
            return null;
        }

        @Override
        public SimDataBlock getSimDataBlock(OutputContext outputContext, VCDataIdentifier vcdataID, String varName, double time) throws RemoteProxyException, DataAccessException {
            double timePoint = time;
            double[] timePoints = getDataSetTimes(vcdataID);
            int index = -1;
            for (int i = 0; i < timePoints.length; i++) {
                if (timePoint == timePoints[i]) {
                    index = i;
                    break;
                }
            }
            double[] data = imageTimeSeries.getAllImages()[index].getDoublePixels();
            PDEDataInfo pdeDataInfo = new PDEDataInfo(null, null, varName, time, 0);
            VariableType varType = VariableType.VOLUME;
            return new SimDataBlock(pdeDataInfo, data, varType);
        }

        @Override
        public boolean getParticleDataExists(VCDataIdentifier vcdataID) throws DataAccessException, RemoteProxyException {
            return false;
        }

        @Override
        public ParticleDataBlock getParticleDataBlock(VCDataIdentifier vcdataID, double time) throws DataAccessException, RemoteProxyException {
            return null;
        }

        @Override
        public ODESimData getODEData(VCDataIdentifier vcdataID) throws DataAccessException, RemoteProxyException {
            return null;
        }

        @Override
        public CartesianMesh getMesh(VCDataIdentifier vcdataID) throws RemoteProxyException, DataAccessException {
            return mesh;
        }

        @Override
        public PlotData getLineScan(OutputContext outputContext, VCDataIdentifier vcdataID, String variable, double time, SpatialSelection spatialSelection) throws RemoteProxyException, DataAccessException {
            throw new RuntimeException("not yet implemented");
        }

        @Override
        public AnnotatedFunction[] getFunctions(OutputContext outputContext, VCDataIdentifier vcdataID) throws DataAccessException, RemoteProxyException {
            return new AnnotatedFunction[0];
        }

        @Override
        public double[] getDataSetTimes(VCDataIdentifier vcdataID) throws RemoteProxyException, DataAccessException {
            return imageTimeSeries.getImageTimeStamps();
        }

        @Override
        public DataSetTimeSeries getDataSetTimeSeries(VCDataIdentifier vcdataID, String[] variableNames) throws DataAccessException, RemoteProxyException {
            throw new RuntimeException("not yet implemented");
        }

        @Override
        public DataSetMetadata getDataSetMetadata(VCDataIdentifier vcdataID) throws DataAccessException, RemoteProxyException {
            throw new RuntimeException("not yet implemented");
        }

        @Override
        public DataIdentifier[] getDataIdentifiers(OutputContext outputContext, VCDataIdentifier vcdataID) throws RemoteProxyException, DataAccessException {
            return new DataIdentifier[] { dataIdentifier };
        }

        @Override
        public FieldDataFileOperationResults fieldDataFileOperation(FieldDataFileOperationSpec fieldDataFileOperationSpec) throws RemoteProxyException, DataAccessException {
            throw new RuntimeException("not yet implemented");
        }

        @Override
        public DataOperationResults doDataOperation(DataOperation dataOperation) throws DataAccessException, RemoteProxyException {
            throw new RuntimeException("not yet implemented");
        }

        @Override
        public VtuFileContainer getEmptyVtuMeshFiles(VCDataIdentifier vcdataID, int timeIndex) throws RemoteProxyException, DataAccessException {
            throw new RuntimeException("not yet implemented");
        }

        @Override
        public double[] getVtuTimes(VCDataIdentifier vcdataID) throws RemoteProxyException, DataAccessException {
            throw new RuntimeException("not yet implemented");
        }

        @Override
        public double[] getVtuMeshData(OutputContext outputContext, VCDataIdentifier vcdataID, VtuVarInfo var, double time) throws RemoteProxyException, DataAccessException {
            // TODO Auto-generated method stub
            return null;
        }

        @Override
        public VtuVarInfo[] getVtuVarInfos(OutputContext outputContext, VCDataIdentifier vcDataIdentifier) throws DataAccessException, RemoteProxyException {
            // TODO Auto-generated method stub
            return null;
        }

        @Override
        public NFSimMolecularConfigurations getNFSimMolecularConfigurations(VCDataIdentifier vcdataID) throws RemoteProxyException, DataAccessException {
            // TODO Auto-generated method stub
            return null;
        }
    };
    DataSetControllerProvider dataSetControllerProvider = new DataSetControllerProvider() {

        @Override
        public DataSetController getDataSetController() throws DataAccessException {
            return dataSetController;
        }
    };
    return dataSetControllerProvider;
}

Example 23 with VCImage

use of cbit.image.VCImage 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 24 with VCImage

use of cbit.image.VCImage in project vcell by virtualcell.

the class ROIMultiPaintManager method checkAll.

private VCImage checkAll() throws Exception {
    if (!overlayEditorPanelJAI.isHistogramSelectionEmpty()) /*overlayEditorPanelJAI.getHighliteInfo() != null*/
    {
        final String highlightDiscard = "discard, continue";
        final String cancelAssign = "Cancel";
        String result = DialogUtils.showWarningDialog(overlayEditorPanelJAI, "Warning: Selections from the 'Histogram Tool' are present.  Choose an action:\n" + "1.  Discard selection without applying.\n" + "2.  Cancel, go back to Geometry Editor. (hint: Use 'Histogram Tool' apply)", new String[] { highlightDiscard, cancelAssign }, highlightDiscard);
        if (result.equals(highlightDiscard)) {
            overlayEditorPanelJAI.setHighliteInfo(null, OverlayEditorPanelJAI.FRAP_DATA_END_PROPERTY);
        } else {
            throw UserCancelException.CANCEL_GENERIC;
        }
    }
    ComboboxROIName[] roiNamesAndColors = overlayEditorPanelJAI.getAllCompositeROINamesAndColors();
    // Check for unassigned "background" pixels
    boolean bHasUnassignedBackground = false;
    for (int i = 0; i < roiComposite.length; i++) {
        byte[] pixData = ((DataBufferByte) roiComposite[i].getRaster().getDataBuffer()).getData();
        for (int j = 0; j < pixData.length; j++) {
            if (pixData[j] == 0) {
                bHasUnassignedBackground = true;
                break;
            }
        }
        if (bHasUnassignedBackground) {
            break;
        }
    }
    // Create PixelClasses
    VCPixelClass[] vcPixelClassesFromROINames = null;
    boolean bForceAssignBackground = false;
    if (bHasUnassignedBackground) {
        final String assignToBackground = "Assign as default 'background'";
        final String cancelAssign = "Cancel";
        String result = DialogUtils.showWarningDialog(overlayEditorPanelJAI, "Warning: some areas of image segmentation have not been assigned to a Domain.  " + "Choose an action:\n" + "1.  Leave as is, unassigned areas should be treated as 'background'.\n" + "2.  Cancel, back to Geometry Editor. (hint: look at 'Domain Regions' list for 'bkgrnd' entries)", new String[] { assignToBackground, /*assignToNeighbors,*/
        cancelAssign }, assignToBackground);
        if (result.equals(assignToBackground)) {
            bForceAssignBackground = true;
        } else {
            throw UserCancelException.CANCEL_GENERIC;
        }
        if (bForceAssignBackground) {
            vcPixelClassesFromROINames = new VCPixelClass[roiNamesAndColors.length + 1];
            vcPixelClassesFromROINames[0] = new VCPixelClass(null, RESERVED_NAME_BACKGROUND, 0);
        }
    } else {
        vcPixelClassesFromROINames = new VCPixelClass[roiNamesAndColors.length];
    }
    // find pixel indexes corresponding to colors for ROIs
    int index = (bForceAssignBackground ? 1 : 0);
    for (int j = 0; j < roiNamesAndColors.length; j++) {
        String roiNameString = roiNamesAndColors[j].getROIName();
        vcPixelClassesFromROINames[index] = new VCPixelClass(null, roiNameString, roiNamesAndColors[j].getContrastColorIndex());
        index++;
    }
    VCImage initImage = createVCImageFromBufferedImages(ROIMultiPaintManager.DEFAULT_EXTENT, roiComposite);
    // Sanity check VCImage vcPixelClassesFromROINames and new vcPixelClassesFromVCImage found same pixel values
    VCPixelClass[] vcPixelClassesFromVCImage = initImage.getPixelClasses();
    for (int i = 0; i < vcPixelClassesFromVCImage.length; i++) {
        boolean bFound = false;
        for (int j = 0; j < vcPixelClassesFromROINames.length; j++) {
            if (vcPixelClassesFromROINames[j].getPixel() == vcPixelClassesFromVCImage[i].getPixel()) {
                bFound = true;
                break;
            }
        }
        if (!bFound) {
            throw new Exception("Error processing Domain Image.  Pixels found having no matching Domain.");
        }
    }
    Vector<VCPixelClass> missingDomainVCPixelClasses = new Vector<VCPixelClass>();
    Vector<VCPixelClass> foundDomainVCPixelClasses = new Vector<VCPixelClass>();
    StringBuffer missingROISB = new StringBuffer();
    for (int i = 0; i < vcPixelClassesFromROINames.length; i++) {
        boolean bFound = false;
        for (int j = 0; j < vcPixelClassesFromVCImage.length; j++) {
            if (vcPixelClassesFromROINames[i].getPixel() == vcPixelClassesFromVCImage[j].getPixel()) {
                bFound = true;
                break;
            }
        }
        if (!bFound) {
            missingROISB.append((missingDomainVCPixelClasses.size() > 0 ? "," : "") + "'" + vcPixelClassesFromROINames[i].getPixelClassName() + "'");
            missingDomainVCPixelClasses.add(vcPixelClassesFromROINames[i]);
        } else {
            foundDomainVCPixelClasses.add(vcPixelClassesFromROINames[i]);
        }
    }
    if (missingDomainVCPixelClasses.size() > 0) {
        final String removeROI = "Remove Domain" + (missingDomainVCPixelClasses.size() > 1 ? "s" : "") + " and continue";
        final String backtoSegment = "Return to segmentation";
        String result = DialogUtils.showWarningDialog(overlayEditorPanelJAI, "Domain" + (missingDomainVCPixelClasses.size() > 1 ? "s" : "") + " named " + missingROISB.toString() + " have no pixels defined", new String[] { removeROI, backtoSegment }, removeROI);
        if (result.equals(removeROI)) {
            vcPixelClassesFromROINames = foundDomainVCPixelClasses.toArray(new VCPixelClass[0]);
        } else {
            throw UserCancelException.CANCEL_GENERIC;
        }
    }
    // Check borders
    VCImage temp = checkBorders(initImage);
    if (temp != null) {
        initImage = temp;
    }
    // Check if we added a border and don't have a VCPixelClass for background
    boolean bHasBackgroundVCPixel = false;
    for (int j = 0; j < vcPixelClassesFromROINames.length; j++) {
        if (vcPixelClassesFromROINames[j].getPixel() == 0) {
            bHasBackgroundVCPixel = true;
            break;
        }
    }
    if (!bHasBackgroundVCPixel) {
        for (int i = 0; i < initImage.getPixels().length; i++) {
            if (initImage.getPixels()[i] == 0) {
                VCPixelClass[] tempvcp = new VCPixelClass[vcPixelClassesFromROINames.length + 1];
                tempvcp[0] = new VCPixelClass(null, RESERVED_NAME_BACKGROUND, 0);
                System.arraycopy(vcPixelClassesFromROINames, 0, tempvcp, 1, vcPixelClassesFromROINames.length);
                vcPixelClassesFromROINames = tempvcp;
                break;
            }
        }
    }
    initImage.setPixelClasses(vcPixelClassesFromROINames);
    updateExtent(initImage, originalExtent, originalISize);
    return initImage;
}

Example 25 with VCImage

use of cbit.image.VCImage in project vcell by virtualcell.

the class GeomDbDriver method getGeometry.

/**
 * This method was created in VisualAge.
 * @return cbit.vcell.model.Model
 * @param rset java.sql.ResultSet
 */
private Geometry getGeometry(QueryHashtable dbc, Connection con, User user, ResultSet rset) throws SQLException, DataAccessException {
    // 
    // get Image reference
    // 
    java.math.BigDecimal bigD = rset.getBigDecimal(geomTable.imageRef.toString());
    KeyValue imageRef = null;
    if (!rset.wasNull()) {
        imageRef = new KeyValue(bigD);
    }
    // 
    // get geometry object
    // 
    Geometry tempGeometry = null;
    try {
        tempGeometry = geomTable.getGeometry(rset, con);
    } catch (PropertyVetoException e) {
        throw new DataAccessException(e.getMessage());
    }
    Geometry geom = null;
    // 
    // get image for this geometry
    // 
    VCImage vcImage = null;
    if (imageRef != null) {
        // permission checking for the image is disabled because it is a child of this geometry
        vcImage = getVCImage(dbc, con, user, imageRef, false);
    }
    if (vcImage != null) {
        geom = new Geometry(tempGeometry, vcImage);
    } else {
        geom = tempGeometry;
    }
    // 
    // get SubVolumes for this geometry
    // 
    SubVolume[] subVolumes = getSubVolumesFromGeometry(dbc, con, geom.getVersion().getVersionKey());
    if (subVolumes != null) {
        try {
            geom.getGeometrySpec().setSubVolumes(subVolumes);
        } catch (java.beans.PropertyVetoException e) {
            lg.error(e.getMessage(), e);
            throw new DataAccessException(e.getMessage());
        }
    }
    // 
    if (geom.getDimension() > 0) {
        getSurfaceDescription(con, geom);
    }
    // 
    if (geom.getDimension() > 0) {
        getFilaments(con, geom);
    }
    // 
    // get SurfaceClasses for this geometry
    // 
    SurfaceClass[] surfaceClasses = getSurfaceClassesFromGeometry(dbc, con, geom.getVersion().getVersionKey());
    if (surfaceClasses != null) {
        try {
            geom.getGeometrySurfaceDescription().setSurfaceClasses(surfaceClasses);
        } catch (java.beans.PropertyVetoException e) {
            lg.error(e.getMessage(), e);
            throw new DataAccessException(e.getMessage());
        }
    }
    return geom;
}