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

Example 1 with DisplayAdapterService

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

the class PDEDataViewer method makeSurfaceMovie.

private void makeSurfaceMovie(final SurfaceCanvas surfaceCanvas, final int varTotalNumIndices, final String movieDataVarName, final DisplayAdapterService movieDAS, final VCDataIdentifier movieVCDataIdentifier) {
    final SurfaceMovieSettingsPanel smsp = new SurfaceMovieSettingsPanel();
    final double[] timePoints = getPdeDataContext().getTimePoints();
    final int surfaceWidth = surfaceCanvas.getWidth();
    final int surfaceHeight = surfaceCanvas.getHeight();
    smsp.init(surfaceWidth, surfaceHeight, timePoints);
    while (true) {
        if (PopupGenerator.showComponentOKCancelDialog(this, smsp, "Movie Settings for var " + movieDataVarName) != JOptionPane.OK_OPTION) {
            return;
        }
        long movieSize = (smsp.getTotalFrames() * surfaceWidth * surfaceHeight * 3);
        // raw data size;
        long rawDataSize = (smsp.getTotalFrames() * varTotalNumIndices * 8);
        if (movieSize + rawDataSize > 50000000) {
            final String YES_RESULT = "Yes";
            String result = PopupGenerator.showWarningDialog(this, "Movie processing will require at least " + (movieSize + rawDataSize) / 1000000 + " mega-bytes of memory.\nMovie size will be " + (movieSize >= 1000000 ? movieSize / 1000000 + " mega-bytes." : movieSize / 1000.0 + " kilo-bytes.") + " Continue?", new String[] { YES_RESULT, "No" }, YES_RESULT);
            if (result != null && result.equals(YES_RESULT)) {
                break;
            }
        } else {
            break;
        }
    }
    final int beginTimeIndex = smsp.getBeginTimeIndex();
    final int endTimeIndex = smsp.getEndTimeIndex();
    final int step = smsp.getSkipParameter() + 1;
    final String[] varNames = new String[] { movieDataVarName };
    int[] allIndices = new int[varTotalNumIndices];
    for (int i = 0; i < allIndices.length; i++) {
        allIndices[i] = i;
    }
    final TimeSeriesJobSpec timeSeriesJobSpec = new TimeSeriesJobSpec(varNames, new int[][] { allIndices }, null, timePoints[beginTimeIndex], step, timePoints[endTimeIndex], VCDataJobID.createVCDataJobID(getDataViewerManager().getUser(), true));
    Hashtable<String, Object> hash = new Hashtable<String, Object>();
    hash.put(StringKey_timeSeriesJobSpec, timeSeriesJobSpec);
    AsynchClientTask task1 = new TimeSeriesDataRetrievalTask("Retrieving data for variable '" + movieDataVarName + "'", PDEDataViewer.this, getPdeDataContext());
    AsynchClientTask task2 = new AsynchClientTask("select a file", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            VCFileChooser fileChooser = new VCFileChooser();
            fileChooser.setFileSelectionMode(JFileChooser.FILES_ONLY);
            fileChooser.setMultiSelectionEnabled(false);
            fileChooser.addChoosableFileFilter(FileFilters.FILE_FILTER_MOV);
            // Set the default file filter...
            fileChooser.setFileFilter(FileFilters.FILE_FILTER_MOV);
            // remove all selector
            fileChooser.removeChoosableFileFilter(fileChooser.getAcceptAllFileFilter());
            fileChooser.setDialogTitle("Saving surface movie");
            File selectedFile = null;
            while (true) {
                if (fileChooser.showSaveDialog(PDEDataViewer.this) != JFileChooser.APPROVE_OPTION) {
                    return;
                }
                selectedFile = fileChooser.getSelectedFile();
                if (!selectedFile.getName().endsWith(".mov")) {
                    selectedFile = new File(selectedFile.getAbsolutePath() + ".mov");
                }
                if (selectedFile.exists()) {
                    final String YES_RESULT = "Yes";
                    String result = PopupGenerator.showWarningDialog(PDEDataViewer.this, "Overwrite exisitng file:\n" + selectedFile.getAbsolutePath() + "?", new String[] { YES_RESULT, "No" }, YES_RESULT);
                    if (result != null && result.equals(YES_RESULT)) {
                        break;
                    }
                } else {
                    break;
                }
            }
            hashTable.put("selectedFile", selectedFile);
        }
    };
    AsynchClientTask task3 = new AsynchClientTask("create movie", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            File selectedFile = (File) hashTable.get("selectedFile");
            if (selectedFile == null) {
                return;
            }
            TSJobResultsNoStats tsJobResultsNoStats = (TSJobResultsNoStats) hashTable.get(StringKey_timeSeriesJobResults);
            double[][] timeSeries = tsJobResultsNoStats.getTimesAndValuesForVariable(movieDataVarName);
            int[] singleFrame = new int[surfaceWidth * surfaceHeight];
            BufferedImage bufferedImage = new BufferedImage(surfaceWidth, surfaceHeight, BufferedImage.TYPE_3BYTE_BGR);
            Graphics2D g2D = bufferedImage.createGraphics();
            VideoMediaChunk[] chunks = new VideoMediaChunk[tsJobResultsNoStats.getTimes().length];
            VideoMediaSample sample;
            int sampleDuration = 0;
            int timeScale = smsp.getFramesPerSecond();
            int bitsPerPixel = 32;
            DisplayAdapterService das = new DisplayAdapterService(movieDAS);
            int[][] origSurfacesColors = surfaceCanvas.getSurfacesColors();
            DataInfoProvider dataInfoProvider = getPDEDataContextPanel1().getDataInfoProvider();
            FileDataContainerManager fileDataContainerManager = new FileDataContainerManager();
            try {
                try {
                    for (int t = 0; t < tsJobResultsNoStats.getTimes().length; t++) {
                        getClientTaskStatusSupport().setMessage("Creating Movie... Progress " + NumberUtils.formatNumber(100.0 * ((double) t / (double) tsJobResultsNoStats.getTimes().length), 3) + "%");
                        double min = Double.POSITIVE_INFINITY;
                        double max = Double.NEGATIVE_INFINITY;
                        for (int index = 1; index < timeSeries.length; index++) {
                            double v = timeSeries[index][t];
                            if ((dataInfoProvider == null || dataInfoProvider.isDefined(index - 1)) && !Double.isNaN(v) && !Double.isInfinite(v)) {
                                min = Math.min(min, v);
                                max = Math.max(max, v);
                            }
                        }
                        das.setValueDomain(new Range(min, max));
                        if (das.getAutoScale()) {
                            das.setActiveScaleRange(new Range(min, max));
                        }
                        int[][] surfacesColors = new int[surfaceCanvas.getSurfaceCollection().getSurfaceCount()][];
                        for (int i = 0; i < surfaceCanvas.getSurfaceCollection().getSurfaceCount(); i += 1) {
                            Surface surface = surfaceCanvas.getSurfaceCollection().getSurfaces(i);
                            surfacesColors[i] = new int[surface.getPolygonCount()];
                            for (int j = 0; j < surface.getPolygonCount(); j += 1) {
                                int membIndex = meshRegionSurfaces.getMembraneIndexForPolygon(i, j);
                                surfacesColors[i][j] = das.getColorFromValue(timeSeries[membIndex + 1][t]);
                            }
                        }
                        surfaceCanvas.setSurfacesColors(surfacesColors);
                        surfaceCanvas.paintImmediately(0, 0, surfaceWidth, surfaceHeight);
                        surfaceCanvas.paint(g2D);
                        bufferedImage.getRGB(0, 0, surfaceWidth, surfaceHeight, singleFrame, 0, surfaceWidth);
                        sampleDuration = 1;
                        sample = FormatSpecificSpecs.getVideoMediaSample(surfaceWidth, surfaceHeight * varNames.length, sampleDuration, false, FormatSpecificSpecs.CODEC_JPEG, 1.0f, singleFrame);
                        chunks[t] = new VideoMediaChunk(sample, fileDataContainerManager);
                    }
                } finally {
                    surfaceCanvas.setSurfacesColors(origSurfacesColors);
                    surfaceCanvas.paintImmediately(0, 0, surfaceWidth, surfaceHeight);
                }
                MediaTrack videoTrack = new MediaTrack(chunks);
                MediaMovie newMovie = new MediaMovie(videoTrack, videoTrack.getDuration(), timeScale);
                newMovie.addUserDataEntry(new UserDataEntry("cpy", "\u00A9" + (new GregorianCalendar()).get(Calendar.YEAR) + ", UCHC"));
                newMovie.addUserDataEntry(new UserDataEntry("des", "Dataset name: " + movieVCDataIdentifier.getID()));
                newMovie.addUserDataEntry(new UserDataEntry("cmt", "Time range: " + timePoints[beginTimeIndex] + " - " + timePoints[endTimeIndex]));
                for (int k = 0; k < varNames.length; k++) {
                    // pad with 0 if k < 10
                    String entryType = "v" + (k < 10 ? "0" : "") + k;
                    UserDataEntry entry = new UserDataEntry(entryType, "Variable name: " + varNames[k] + " min: " + das.getValueDomain().getMin() + " max: " + das.getValueDomain().getMax());
                    newMovie.addUserDataEntry(entry);
                }
                getClientTaskStatusSupport().setMessage("Writing Movie to disk...");
                FileOutputStream fos = new FileOutputStream(selectedFile);
                DataOutputStream movieOutput = new DataOutputStream(new BufferedOutputStream(fos));
                MediaMethods.writeMovie(movieOutput, newMovie);
                movieOutput.close();
                fos.close();
            } finally {
                fileDataContainerManager.closeAllAndDelete();
            }
        }
    };
    ClientTaskDispatcher.dispatch(this, hash, new AsynchClientTask[] { task1, task2, task3 }, true, true, null);
}

Example 2 with DisplayAdapterService

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

the class PDEDataViewer method updateDataValueSurfaceViewer0.

// private AsynchClientTask[] getDataVlaueSurfaceViewerTasks(){
// AsynchClientTask createDataValueSurfaceViewerTask = new AsynchClientTask("Create surface viewer...",AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {
// @Override
// public void run(Hashtable<String, Object> hashTable) throws Exception {
// if(getDataValueSurfaceViewer().getSurfaceCollectionDataInfoProvider() == null){
// createDataValueSurfaceViewer(getClientTaskStatusSupport());
// }
// }
// };
// 
// AsynchClientTask updateDataValueSurfaceViewerTask = new AsynchClientTask("Update surface viewer...",AsynchClientTask.TASKTYPE_SWING_BLOCKING) {
// @Override
// public void run(Hashtable<String, Object> hashTable) throws Exception {
// updateDataValueSurfaceViewer0();
// }
// };
// 
// AsynchClientTask resetDataValueSurfaceViewerTask = new AsynchClientTask("Reset tab...",AsynchClientTask.TASKTYPE_SWING_NONBLOCKING,false,false) {
// @Override
// public void run(Hashtable<String, Object> hashTable) throws Exception {
// if(getDataValueSurfaceViewer().getSurfaceCollectionDataInfoProvider() == null){
// viewDataTabbedPane.setSelectedIndex(0);
// }
// }
// };
// return new AsynchClientTask[] {createDataValueSurfaceViewerTask,updateDataValueSurfaceViewerTask,resetDataValueSurfaceViewerTask};
// }
// private Timer dataValueSurfaceTimer;
// //private boolean bPdeIsParamScan=false;
// private void updateDataValueSurfaceViewer(){
// //	if((dataValueSurfaceTimer = ClientTaskDispatcher.getBlockingTimer(this,getPdeDataContext(),null,dataValueSurfaceTimer,new ActionListener() {@Override public void actionPerformed(ActionEvent e2) {updateDataValueSurfaceViewer();}}))!=null){
// //		return;
// //	}
// if(bSkipSurfaceCalc){
// return;
// }
// if(getDataValueSurfaceViewer().getSurfaceCollectionDataInfoProvider() == null){
// if((dataValueSurfaceTimer = ClientTaskDispatcher.getBlockingTimer(this,getPdeDataContext(),null,dataValueSurfaceTimer,new ActionListener() {@Override public void actionPerformed(ActionEvent e2) {updateDataValueSurfaceViewer();}}))!=null){
// return;
// }
// ClientTaskDispatcher.dispatch(this, new Hashtable<String, Object>(), getDataVlaueSurfaceViewerTasks(),true,true,null);
// }else{
// try{
// updateDataValueSurfaceViewer0();
// }catch(Exception e){
// e.printStackTrace();
// DialogUtils.showErrorDialog(this, e.getMessage());
// }
// }
// }
/**
 * Insert the method's description here.
 * Creation date: (9/25/2005 2:00:05 PM)
 */
private void updateDataValueSurfaceViewer0() {
    // viewDataTabbedPane.addTab(CurrentView.SURFACE_VIEW.title, getDataValueSurfaceViewer());
    if (viewDataTabbedPane.getSelectedIndex() != CurrentView.SURFACE_VIEW.ordinal()) {
        return;
    }
    // SurfaceColors and DataValues
    if (getDataValueSurfaceViewer().getSurfaceCollectionDataInfo() == null) {
        // happens with PostProcessingImageData version of PDEDataViewer
        return;
    }
    SurfaceCollection surfaceCollection = getDataValueSurfaceViewer().getSurfaceCollectionDataInfo().getSurfaceCollection();
    DisplayAdapterService das = getPDEDataContextPanel1().getdisplayAdapterService1();
    final int[][] surfaceColors = new int[surfaceCollection.getSurfaceCount()][];
    final double[][] surfaceDataValues = new double[surfaceCollection.getSurfaceCount()][];
    boolean bMembraneVariable = getPdeDataContext().getDataIdentifier().getVariableType().equals(VariableType.MEMBRANE);
    RecodeDataForDomainInfo recodeDataForDomainInfo = getPDEDataContextPanel1().getRecodeDataForDomainInfo();
    double[] membraneValues = (recodeDataForDomainInfo.isRecoded() ? recodeDataForDomainInfo.getRecodedDataForDomain() : getPdeDataContext().getDataValues());
    for (int i = 0; i < surfaceCollection.getSurfaceCount(); i += 1) {
        Surface surface = surfaceCollection.getSurfaces(i);
        surfaceColors[i] = new int[surface.getPolygonCount()];
        surfaceDataValues[i] = new double[surface.getPolygonCount()];
        for (int j = 0; j < surface.getPolygonCount(); j += 1) {
            int membraneIndexForPolygon = meshRegionSurfaces.getMembraneIndexForPolygon(i, j);
            if (bMembraneVariable) {
                surfaceDataValues[i][j] = membraneValues[membraneIndexForPolygon];
            } else {
                // get membrane region index from membrane index
                surfaceDataValues[i][j] = membraneValues[getPdeDataContext().getCartesianMesh().getMembraneRegionIndex(membraneIndexForPolygon)];
            }
            surfaceColors[i][j] = das.getColorFromValue(surfaceDataValues[i][j]);
        }
    }
    DataValueSurfaceViewer.SurfaceCollectionDataInfoProvider svdp = new DataValueSurfaceViewer.SurfaceCollectionDataInfoProvider() {

        private DisplayAdapterService updatedDAS = new DisplayAdapterService(getPDEDataContextPanel1().getdisplayAdapterService1());

        private String updatedVariableName = getPdeDataContext().getVariableName();

        private double updatedTimePoint = getPdeDataContext().getTimePoint();

        private double[] updatedVariableValues = getPdeDataContext().getDataValues();

        private VCDataIdentifier updatedVCDataIdentifier = getPdeDataContext().getVCDataIdentifier();

        public void makeMovie(SurfaceCanvas surfaceCanvas) {
            makeSurfaceMovie(surfaceCanvas, updatedVariableValues.length, updatedVariableName, updatedDAS, updatedVCDataIdentifier);
        }

        public double getValue(int surfaceIndex, int polygonIndex) {
            return updatedVariableValues[meshRegionSurfaces.getMembraneIndexForPolygon(surfaceIndex, polygonIndex)];
        }

        public String getValueDescription(int surfaceIndex, int polygonIndex) {
            return updatedVariableName;
        }

        public int[][] getSurfacePolygonColors() {
            return surfaceColors;
        }

        public Coordinate getCentroid(int surfaceIndex, int polygonIndex) {
            return getPdeDataContext().getCartesianMesh().getMembraneElements()[meshRegionSurfaces.getMembraneIndexForPolygon(surfaceIndex, polygonIndex)].getCentroid();
        }

        public float getArea(int surfaceIndex, int polygonIndex) {
            return getPdeDataContext().getCartesianMesh().getMembraneElements()[meshRegionSurfaces.getMembraneIndexForPolygon(surfaceIndex, polygonIndex)].getArea();
        }

        public Vect3d getNormal(int surfaceIndex, int polygonIndex) {
            return getPdeDataContext().getCartesianMesh().getMembraneElements()[meshRegionSurfaces.getMembraneIndexForPolygon(surfaceIndex, polygonIndex)].getNormal();
        }

        public int getMembraneIndex(int surfaceIndex, int polygonIndex) {
            return meshRegionSurfaces.getMembraneIndexForPolygon(surfaceIndex, polygonIndex);
        }

        public Color getROIHighlightColor() {
            return new Color(getPDEDataContextPanel1().getdisplayAdapterService1().getSpecialColors()[cbit.image.DisplayAdapterService.FOREGROUND_HIGHLIGHT_COLOR_OFFSET]);
        }

        @Override
        public boolean isMembrIndexInVarDomain(int membrIndex) {
            return (getPDEDataContextPanel1().getRecodeDataForDomainInfo() != null ? getPDEDataContextPanel1().getRecodeDataForDomainInfo().isIndexInDomain(membrIndex) : true);
        }

        // public void showComponentInFrame(Component comp,String title){
        // PDEDataViewer.this.showComponentInFrame(comp,title);
        // }
        public void plotTimeSeriesData(int[][] indices, boolean bAllTimes, boolean bTimeStats, boolean bSpaceStats) throws DataAccessException {
            double[] timePoints = getPdeDataContext().getTimePoints();
            double beginTime = (bAllTimes ? timePoints[0] : updatedTimePoint);
            double endTime = (bAllTimes ? timePoints[timePoints.length - 1] : beginTime);
            String[] varNames = new String[indices.length];
            for (int i = 0; i < varNames.length; i += 1) {
                varNames[i] = updatedVariableName;
            }
            TimeSeriesJobSpec timeSeriesJobSpec = new TimeSeriesJobSpec(varNames, indices, beginTime, 1, endTime, bSpaceStats, bTimeStats, VCDataJobID.createVCDataJobID(getDataViewerManager().getUser(), true));
            Hashtable<String, Object> hash = new Hashtable<String, Object>();
            hash.put(StringKey_timeSeriesJobSpec, timeSeriesJobSpec);
            AsynchClientTask task1 = new TimeSeriesDataRetrievalTask("Retrieve data", PDEDataViewer.this, getPdeDataContext());
            AsynchClientTask task2 = new AsynchClientTask("Showing surface", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {

                @Override
                public void run(Hashtable<String, Object> hashTable) throws Exception {
                    TSJobResultsSpaceStats tsJobResultsSpaceStats = (TSJobResultsSpaceStats) hashTable.get(StringKey_timeSeriesJobResults);
                    plotSpaceStats(tsJobResultsSpaceStats);
                }
            };
            ClientTaskDispatcher.dispatch(PDEDataViewer.this, hash, new AsynchClientTask[] { task1, task2 }, true, true, null);
        }
    };
    getDataValueSurfaceViewer().setSurfaceCollectionDataInfoProvider(svdp);
}

Example 3 with DisplayAdapterService

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

the class PDEDataContextPanel method colorMembraneCurvesPrivate.

/**
 * Insert the method's description here.
 * Creation date: (10/26/00 4:49:39 PM)
 */
private void colorMembraneCurvesPrivate(java.util.Hashtable<SampledCurve, int[]> curvesAndMembraneIndexes, MeshDisplayAdapter meshDisplayAdapter) {
    DisplayAdapterService das = getdisplayAdapterService1();
    if (curvesAndMembraneIndexes != null) {
        java.util.Enumeration<SampledCurve> keysEnum = curvesAndMembraneIndexes.keys();
        while (keysEnum.hasMoreElements()) {
            SampledCurve curve = keysEnum.nextElement();
            int[] membraneIndexes = curvesAndMembraneIndexes.get(curve);
            double[] membraneValues = null;
            if (membraneIndexes != null && getPdeDataContext().getDataValues() != null && getPdeDataContext().getDataIdentifier() != null) {
                membraneValues = meshDisplayAdapter.getDataValuesForMembraneIndexes(membraneIndexes, (recodeDataForDomainInfo.isRecoded ? recodeDataForDomainInfo.getRecodedDataForDomain() : getPdeDataContext().getDataValues()), getPdeDataContext().getDataIdentifier().getVariableType());
            }
            if (membraneValues != null) {
                int[] valueColors = new int[membraneValues.length];
                for (int i = 0; i < membraneValues.length; i += 1) {
                    valueColors[i] = das.getColorFromValue(membraneValues[i]);
                }
                getImagePlaneManagerPanel().getCurveRenderer().renderPropertySegmentColors(curve, valueColors);
                getImagePlaneManagerPanel().getCurveRenderer().renderPropertySegmentIndexes(curve, membraneIndexes);
            } else {
                getImagePlaneManagerPanel().getCurveRenderer().renderPropertySegmentColors(curve, null);
                getImagePlaneManagerPanel().getCurveRenderer().renderPropertySegmentIndexes(curve, null);
            }
        }
    }
}

Example 4 with DisplayAdapterService

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

the class RasterExporter method makePLYWithTexData.

public ExportOutput[] makePLYWithTexData(OutputContext outputContext, JobRequest jobRequest, User user, DataServerImpl dataServerImpl, ExportSpecs exportSpecs, FileDataContainerManager fileDataContainerManager) throws Exception {
    String simID = exportSpecs.getVCDataIdentifier().getID();
    VCDataIdentifier vcdID = exportSpecs.getVCDataIdentifier();
    cbit.vcell.solvers.CartesianMesh mesh = dataServerImpl.getMesh(user, vcdID);
    TimeSpecs timeSpecs = exportSpecs.getTimeSpecs();
    VariableSpecs variableSpecs = exportSpecs.getVariableSpecs();
    Vector<ExportOutput> exportOutV = new Vector<ExportOutput>();
    RegionImage regionImage = MeshDisplayAdapter.generateRegionImage(mesh, null);
    PLYSpecs plySpecs = (PLYSpecs) exportSpecs.getFormatSpecificSpecs();
    DisplayPreferences[] displayPreferences = plySpecs.getDisplayPreferences();
    // BitSet bInDomain = null;
    // String variableName = variableSpecs.getVariableNames()[0];
    // Domain varDomain = null;
    // DataIdentifier[] dataIdentifiers = dataServerImpl.getDataIdentifiers(outputContext, user, vcdID);
    // for (int i = 0; i < dataIdentifiers.length; i++) {
    // //dataIdentifier.getDomain();
    // if(dataIdentifiers[i].getName().equals(variableName)){
    // varDomain = dataIdentifiers[i].getDomain();
    // break;
    // }
    // }
    // MembraneElement membraneElement = mesh.getMembraneElements()[faceIndex];
    // String memSubdomainName = (varDomain==null?null:mesh.getMembraneSubdomainNamefromMemIndex(faceIndex));
    // boolean bInDomain = (varDomain==null?true:varDomain.getName().equals(memSubdomainName));
    DisplayAdapterService das = new DisplayAdapterService();
    StringWriter stringWriter = new StringWriter();
    PolyTexHelper imgResults = writeStanfordPolygonTex(regionImage, stringWriter, /*,bInDomain*/
    mesh);
    // mesh
    ExportOutput exportOut = new ExportOutput(true, ".ply", simID.toString(), "_memb", fileDataContainerManager);
    fileDataContainerManager.append(exportOut.getFileDataContainerID(), stringWriter.toString());
    exportOutV.add(exportOut);
    // special neighbor annotation image
    ExportOutput textImagetOut0 = new ExportOutput(true, ".png", simID.toString(), "_membAnnot", fileDataContainerManager);
    fileDataContainerManager.append(textImagetOut0.getFileDataContainerID(), imgResults.specialNeighborImage);
    exportOutV.add(textImagetOut0);
    for (int varNameIndex = 0; varNameIndex < variableSpecs.getVariableNames().length; varNameIndex++) {
        if (das.fetchColorModel(displayPreferences[varNameIndex].getColorMode()) == null) {
            if (displayPreferences[varNameIndex].getColorMode().equals(DisplayAdapterService.GRAY)) {
                das.addColorModelForValues(DisplayAdapterService.createGrayColorModel(), DisplayAdapterService.createBlueRedSpecialColors(), displayPreferences[varNameIndex].getColorMode());
            } else {
                das.addColorModelForValues(DisplayAdapterService.createBlueRedColorModel(), DisplayAdapterService.createGraySpecialColors(), displayPreferences[varNameIndex].getColorMode());
            // das.setActiveColorModelID("Contrast");
            }
        }
        // BitSet domainValid = (displayPreferences[varNameIndex]==null?null:(displayPreferences[varNameIndex].getDomainValid()==null?null:displayPreferences[varNameIndex].getDomainValid()));
        ExportSpecs.setupDisplayAdapterService(displayPreferences[varNameIndex], das, displayPreferences[varNameIndex].getScaleSettings());
        for (int j = timeSpecs.getBeginTimeIndex(); j <= timeSpecs.getEndTimeIndex(); j++) {
            BufferedImage image = createTextureImage(imgResults.imageSideSize);
            int[] imgBuffer = ((DataBufferInt) (image.getRaster().getDataBuffer())).getData();
            Arrays.fill(imgBuffer, Integer.MAX_VALUE);
            SimDataBlock simDataBlock = dataServerImpl.getSimDataBlock(outputContext, user, vcdID, variableSpecs.getVariableNames()[varNameIndex], timeSpecs.getAllTimes()[j]);
            for (int k = 0; k < imgResults.dataIndexes.length; k++) {
                if (imgBuffer[k] != Integer.MAX_VALUE) {
                    System.out.println("texture pixel used twice");
                }
                double avgVal = 0;
                for (int l = 0; l < imgResults.dataIndexes[k].length; l++) {
                    avgVal += simDataBlock.getData()[imgResults.dataIndexes[k][l]];
                }
                imgBuffer[k] = das.getColorFromValue(avgVal / imgResults.dataIndexes[k].length);
            }
            byte[] pngImage = flipPNG(image);
            ExportOutput textImagetOut = new ExportOutput(true, ".png", simID.toString(), "_memb_" + variableSpecs.getVariableNames()[varNameIndex] + "_" + j, fileDataContainerManager);
            fileDataContainerManager.append(textImagetOut.getFileDataContainerID(), pngImage);
            exportOutV.add(textImagetOut);
        }
    }
    ExportOutput[] exportOutputArr = exportOutV.toArray(new ExportOutput[0]);
    return exportOutputArr;
}

Example 5 with DisplayAdapterService

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

the class GeometrySummaryPanel method initGeometry.

/**
 * Comment
 */
private void initGeometry(Geometry arg1) {
    final boolean bSpatial = getGeometry() != null && getGeometry().getDimension() > 0;
    getImagePlaneManagerPanel1().setVisible(bSpatial);
    getJPanelOrigin().setVisible(bSpatial);
    getJPanelSize().setVisible(bSpatial);
    if (getGeometry() != null) {
        try {
            if (getGeometry().getGeometrySpec().getSampledImage().isDirty()) {
                return;
            }
            VCImage vcImage = getGeometry().getGeometrySpec().getSampledImage().getCurrentValue();
            byte[] pixels = vcImage.getPixels();
            DisplayAdapterService das = new DisplayAdapterService();
            das.setActiveScaleRange(new org.vcell.util.Range(0, 255));
            das.setValueDomain(new org.vcell.util.Range(0, 255));
            das.addColorModelForValues(DisplayAdapterService.createContrastColorModel(), DisplayAdapterService.createGraySpecialColors(), "Contrast");
            das.setActiveColorModelID("Contrast");
            int[] rgb = new int[pixels.length];
            for (int i = 0; i < rgb.length; i += 1) {
                rgb[i] = das.getColorFromIndex(pixels[i]);
            }
            SourceDataInfo sdi = new SourceDataInfo(SourceDataInfo.INT_RGB_TYPE, rgb, getGeometry().getExtent(), getGeometry().getOrigin(), new org.vcell.util.Range(0, 255), 0, vcImage.getNumX(), 1, vcImage.getNumY(), vcImage.getNumX(), vcImage.getNumZ(), vcImage.getNumX() * vcImage.getNumY());
            getImagePlaneManagerPanel1().setSourceDataInfo(sdi);
        } catch (Exception e) {
            PopupGenerator.showErrorDialog(GeometrySummaryPanel.this, e.getMessage(), e);
        }
    } else {
        getImagePlaneManagerPanel1().setSourceDataInfo(null);
    }
}