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

Example 1 with DisplayPreferences

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

the class IMGExporter method makeMedia.

// private ParticleInfo checkParticles_unused(final ExportSpecs exportSpecs,User user,DataServerImpl dataServerImpl,final long jobID) throws Exception{
// int particleMode = FormatSpecificSpecs.PARTICLE_NONE;
// if(exportSpecs.getFormatSpecificSpecs() instanceof ImageSpecs){
// particleMode = ((ImageSpecs)exportSpecs.getFormatSpecificSpecs()).getParticleMode();
// }else if (exportSpecs.getFormatSpecificSpecs() instanceof MovieSpecs){
// particleMode = ((MovieSpecs)exportSpecs.getFormatSpecificSpecs()).getParticleMode();
// }
// if(particleMode == FormatSpecificSpecs.PARTICLE_NONE){
// return null;
// }
// 
// final VCDataIdentifier vcdID = exportSpecs.getVCDataIdentifier();
// CartesianMesh cartesianMesh = dataServerImpl.getMesh(user, vcdID);
// int dimension = cartesianMesh.getGeometryDimension();
// 
// String[] variableNames = exportSpecs.getVariableSpecs().getVariableNames();
// 
// File visitExeLocation =
// new File(PropertyLoader.getRequiredProperty(PropertyLoader.visitSmoldynVisitExecutableProperty));
// File visitSmoldynScriptLocation =
// new File(PropertyLoader.getRequiredProperty(PropertyLoader.visitSmoldynScriptPathProperty));
// final File visitSmoldynScriptTempDir = PropertyLoader.getSystemTemporaryDirectory();
// 
// //-----Get all data (from archive if necessary)
// SimulationData.SimDataAmplistorInfo simDataAmplistorInfo = AmplistorUtils.getSimDataAmplistorInfoFromPropertyLoader();
// SimulationData simData = new SimulationData(vcdID,
// new File(PropertyLoader.getRequiredProperty(PropertyLoader.primarySimDataDirInternalProperty),vcdID.getOwner().getName()),
// new File(PropertyLoader.getProperty(PropertyLoader.primarySimDataDirInternalProperty,null),vcdID.getOwner().getName()),
// simDataAmplistorInfo);
// 
// File logFile = simData.getLogFile();
// if(!logFile.exists()){
// throw new Exception("ImgExport particle, Couldn't find Log file "+logFile.getAbsolutePath());
// }
// simData.getMesh();//gets mesh and meshmetrics files from archive if necessary
// simData.getSubdomainFile();
// simData.getFunctionsFile(false);
// int timeIndex = 1;//smoldyn always begins at timeindex 1
// while(true){
// if(!simData.getSmoldynOutputFile(timeIndex).exists()){//get smoldynOutput files
// break;
// }
// timeIndex++;
// }
// //-----
// 
// File visitDataPathFragment = new File(logFile.getParent(),vcdID.getID()+"_");
// System.out.println(visitExeLocation.getAbsolutePath());
// System.out.println(visitSmoldynScriptLocation.getAbsolutePath());
// System.out.println(visitSmoldynScriptTempDir.getAbsolutePath());
// System.out.println(visitDataPathFragment.getAbsolutePath());
// 
// //if(true){return new ParticleInfo(visitSmoldynScriptTempDir);}
// if(exportSpecs.getTimeSpecs().getAllTimes().length == 1){
// throw new IllegalArgumentException("Time zero not valid for smoldyn particle data");
// }
// int beginIndexTime = exportSpecs.getTimeSpecs().getBeginTimeIndex();
// int endIndexTime = exportSpecs.getTimeSpecs().getEndTimeIndex();
// 
// System.out.println("beginIndexTime="+beginIndexTime+" endIndexTime="+endIndexTime);
// 
// ArrayList<String> args = new ArrayList<String>();
// args.add(visitExeLocation.getAbsolutePath());//location of visit
// args.add("-nowin");
// args.add("-cli");
// args.add("-s");
// 
// args.add(visitSmoldynScriptLocation.getAbsolutePath());//location of the script
// args.add(visitDataPathFragment.getAbsolutePath()); //location of the SimID
// args.add(visitSmoldynScriptTempDir.getAbsolutePath());  // where frames are dumped
// args.add(dimension+""); //dimension
// args.add(beginIndexTime+"");
// args.add(endIndexTime+"");
// args.add(4+"");//particle sphere size
// args.add(FormatSpecificSpecs.SMOLDYN_DEFAULT_FRAME_SIZE.width+"");//frame size X
// args.add(FormatSpecificSpecs.SMOLDYN_DEFAULT_FRAME_SIZE.height+"");//frame size Y
// args.add(variableNames.length+""); // 0 = show all the particles.  >0 == show n different particles, to be listed below
// for (int i = 0; i < variableNames.length; i++) {
// args.add(variableNames[i]);
// }
// 
// final String tempFilePrefix = vcdID.getID()+"_p3d";
// 
// //Monitor progress of smoldyn script
// exportServiceImpl.fireExportProgress(jobID, vcdID, "MEDIA", 0.0);
// final boolean[] finishedFlag = new boolean[] {false};
// final int numTimePoints = exportSpecs.getTimeSpecs().getEndTimeIndex()-exportSpecs.getTimeSpecs().getBeginTimeIndex()+1;
// Thread progressThread = new Thread(new Runnable() {
// public void run() {
// System.out.println("smoldyn progress monitor started");
// while(!finishedFlag[0]){
// int count = 0;
// File[] tempFiles = visitSmoldynScriptTempDir.listFiles();
// for (int i = 0; i < tempFiles.length; i++) {
// if(tempFiles[i].getName().startsWith(tempFilePrefix) ||
// (tempFiles[i].getName().startsWith(vcdID.getID()) &&
// tempFiles[i].getName().endsWith(".jpeg"))){
// count+= 1;
// }
// }
// double progress = .5 * (double)count / (double)(2*numTimePoints);
// exportServiceImpl.fireExportProgress(jobID, vcdID, "MEDIA", progress);
// //System.out.println("All files read="+tempFiles.length+" Files counted="+count+" progress="+progress);
// try {
// Thread.sleep(1000);
// } catch (InterruptedException e) {
// e.printStackTrace();
// return;//This shouldn't happen but if so just quit
// }
// }
// System.out.println("smoldyn progress monitor finished");
// }
// });
// progressThread.start();
// 
// 
// try{
// final long TIME_OUT = 1200000; //20 minutes
// Executable executable = new Executable(args.toArray(new String[0]),TIME_OUT);
// executable.start();//blocking, internal monitoring, return after timeout
// if(!executable.getStatus().equals(ExecutableStatus.COMPLETE)){
// System.out.println(executable.getStderrString());
// System.out.println(executable.getStdoutString());
// throw new Exception("Particle data exporter did not complete normally. "+(executable.getStatus()==null?"":executable.getStatus().toString()));
// }
// }finally{
// finishedFlag[0] = true;
// //Remove temp files created by smoldyn script
// File[] tempFiles = visitSmoldynScriptTempDir.listFiles();
// for (int i = 0; i < tempFiles.length; i++) {
// if(tempFiles[i].getName().startsWith(tempFilePrefix)){
// tempFiles[i].delete();
// }
// }
// }
// return new ParticleInfo(visitSmoldynScriptTempDir);
// }
private static ExportOutput[] makeMedia(ExportServiceImpl exportServiceImpl, OutputContext outputContext, long jobID, User user, DataServerImpl dataServerImpl, ExportSpecs exportSpecs, ClientTaskStatusSupport clientTaskStatusSupport, ParticleInfo particleInfo, FileDataContainerManager fileDataContainerManager) throws RemoteException, IOException, GIFFormatException, DataAccessException, Exception {
    boolean bOverLay = false;
    int sliceIndicator = 0;
    if (particleInfo == null) {
        sliceIndicator = (exportSpecs.getGeometrySpecs().getModeID() == ExportConstants.GEOMETRY_FULL ? FULL_MODE_ALL_SLICES : exportSpecs.getGeometrySpecs().getSliceNumber());
    }
    int imageScale = 0;
    int meshMode = 0;
    int mirroringType = 0;
    int membraneScale = 0;
    double duration = 1.0;
    DisplayPreferences[] displayPreferences = null;
    int volVarMembrOutlineThickness = 1;
    if (exportSpecs.getFormatSpecificSpecs() instanceof ImageSpecs) {
        bOverLay = ((ImageSpecs) exportSpecs.getFormatSpecificSpecs()).getOverlayMode();
        imageScale = ((ImageSpecs) exportSpecs.getFormatSpecificSpecs()).getImageScaling();
        volVarMembrOutlineThickness = ((ImageSpecs) exportSpecs.getFormatSpecificSpecs()).getVolVarMembrOutlineThickness();
        meshMode = ((ImageSpecs) exportSpecs.getFormatSpecificSpecs()).getMeshMode();
        mirroringType = ((ImageSpecs) exportSpecs.getFormatSpecificSpecs()).getMirroringType();
        membraneScale = ((ImageSpecs) exportSpecs.getFormatSpecificSpecs()).getMembraneScaling();
        displayPreferences = ((ImageSpecs) exportSpecs.getFormatSpecificSpecs()).getDisplayPreferences();
        // convert from milliseconds to seconds
        duration = (double) ((ImageSpecs) exportSpecs.getFormatSpecificSpecs()).getDuration() / 1000.0;
    } else if (exportSpecs.getFormatSpecificSpecs() instanceof MovieSpecs) {
        bOverLay = ((MovieSpecs) exportSpecs.getFormatSpecificSpecs()).getOverlayMode();
        imageScale = ((MovieSpecs) exportSpecs.getFormatSpecificSpecs()).getImageScaling();
        volVarMembrOutlineThickness = ((MovieSpecs) exportSpecs.getFormatSpecificSpecs()).getVolVarMembrOutlineThickness();
        meshMode = ((MovieSpecs) exportSpecs.getFormatSpecificSpecs()).getMeshMode();
        mirroringType = ((MovieSpecs) exportSpecs.getFormatSpecificSpecs()).getMirroringType();
        membraneScale = ((MovieSpecs) exportSpecs.getFormatSpecificSpecs()).getMembraneScaling();
        displayPreferences = ((MovieSpecs) exportSpecs.getFormatSpecificSpecs()).getDisplayPreferences();
        // convert from milliseconds to seconds
        duration = ((MovieSpecs) exportSpecs.getFormatSpecificSpecs()).getDuration() / 1000.0;
    } else {
        throw new DataFormatException("Unknown FormatSpecificSpec " + exportSpecs.getFormatSpecificSpecs().getClass().getName());
    }
    Vector<ExportOutput> exportOutputV = new Vector<ExportOutput>();
    VCDataIdentifier vcdID = exportSpecs.getVCDataIdentifier();
    int beginTimeIndex = exportSpecs.getTimeSpecs().getBeginTimeIndex();
    int endTimeIndex = exportSpecs.getTimeSpecs().getEndTimeIndex();
    boolean bSingleTimePoint = beginTimeIndex == endTimeIndex;
    String[] varNames = (particleInfo == null ? exportSpecs.getVariableSpecs().getVariableNames() : new String[] { "smoldynParticleDummy" });
    double[] allTimes = dataServerImpl.getDataSetTimes(user, vcdID);
    int startSlice = (sliceIndicator == FULL_MODE_ALL_SLICES ? 0 : sliceIndicator);
    int sliceCount = FormatSpecificSpecs.getSliceCount(sliceIndicator == FULL_MODE_ALL_SLICES, exportSpecs.getGeometrySpecs().getAxis(), dataServerImpl.getMesh(user, vcdID));
    double progressIncr = 1.0 / (sliceCount * (endTimeIndex - beginTimeIndex + 1) * varNames.length);
    double progress = 0.0;
    MovieHolder movieHolder = new MovieHolder();
    Dimension imageDimension = FormatSpecificSpecs.getImageDimension(meshMode, imageScale, dataServerImpl.getMesh(user, vcdID), exportSpecs.getGeometrySpecs().getAxis());
    int originalWidth = (int) imageDimension.getWidth();
    int originalHeight = (int) imageDimension.getHeight();
    ExportRenderInfo exportRenderInfo = null;
    try {
        for (int sliceNumber = startSlice; sliceNumber < startSlice + sliceCount; sliceNumber++) {
            if (particleInfo == null) {
                PDEOffscreenRenderer offScreenRenderer = new PDEOffscreenRenderer(outputContext, user, dataServerImpl, vcdID);
                offScreenRenderer.setNormalAxis(exportSpecs.getGeometrySpecs().getAxis());
                offScreenRenderer.setSlice(sliceNumber);
                exportRenderInfo = new ExportRenderInfo(offScreenRenderer);
            } else {
                exportRenderInfo = new ExportRenderInfo(particleInfo, allTimes, vcdID, beginTimeIndex);
                Dimension particleImageSize = particleInfo.getImageFrameSize(vcdID);
                originalWidth = particleImageSize.width;
                originalHeight = particleImageSize.height;
            }
            int varNameIndex0 = 0;
            int timeIndex0 = beginTimeIndex;
            int[] overLayPixels = null;
            // set default time if only 1 timepoint
            movieHolder.setSampleDurationSeconds(duration);
            boolean bEndslice = sliceNumber == (startSlice + sliceCount - 1);
            while (true) {
                if (clientTaskStatusSupport != null) {
                    clientTaskStatusSupport.setProgress((int) (progress * 100));
                    if (clientTaskStatusSupport.isInterrupted()) {
                        throw UserCancelException.CANCEL_GENERIC;
                    }
                }
                exportServiceImpl.fireExportProgress(jobID, vcdID, "MEDIA", (particleInfo == null ? progress : .5 + (progress / 2.0)));
                progress += progressIncr;
                MirrorInfo currentSliceTimeMirrorInfo = renderAndMirrorSliceTimePixels(exportRenderInfo, varNames[varNameIndex0], allTimes[timeIndex0], displayPreferences[varNameIndex0], imageScale, membraneScale, meshMode, volVarMembrOutlineThickness, originalWidth, originalHeight, mirroringType);
                if (bOverLay) {
                    if (varNames.length == 1) {
                        overLayPixels = currentSliceTimeMirrorInfo.getPixels();
                    } else {
                        // Overlay append in Y-direction
                        if (overLayPixels == null) {
                            overLayPixels = new int[currentSliceTimeMirrorInfo.getPixels().length * varNames.length];
                        }
                        int appendIndex = currentSliceTimeMirrorInfo.getPixels().length * varNameIndex0;
                        System.arraycopy(currentSliceTimeMirrorInfo.getPixels(), 0, overLayPixels, appendIndex, currentSliceTimeMirrorInfo.getPixels().length);
                    }
                }
                if (timeIndex0 != endTimeIndex) {
                    // calculate duration for each timepoint
                    movieHolder.setSampleDurationSeconds((allTimes[timeIndex0 + 1] - allTimes[timeIndex0]) / (allTimes[endTimeIndex + (endTimeIndex == allTimes.length - 1 ? 0 : 1)] - allTimes[beginTimeIndex]) * duration);
                } else {
                    // when last or only 1 timepoint, use last duration set
                    movieHolder.setSampleDurationSeconds(movieHolder.getSampleDurationSeconds());
                }
                // Index var and time properly
                boolean bBegintime = timeIndex0 == beginTimeIndex;
                boolean bEndTime = timeIndex0 == endTimeIndex;
                if (bOverLay) {
                    varNameIndex0++;
                    if (varNameIndex0 == varNames.length) {
                        String dataID = createDataID(exportSpecs, sliceNumber, "overlay", timeIndex0);
                        createMedia(exportOutputV, vcdID, dataID, exportSpecs, true, bEndslice, bBegintime, bEndTime, bSingleTimePoint, varNames, displayPreferences, movieHolder, overLayPixels, currentSliceTimeMirrorInfo.getMirrorWidth(), currentSliceTimeMirrorInfo.getMirrorHeight() * varNames.length, fileDataContainerManager);
                        varNameIndex0 = 0;
                        timeIndex0++;
                        if (timeIndex0 > endTimeIndex) {
                            break;
                        }
                    }
                } else {
                    String dataID = createDataID(exportSpecs, sliceNumber, varNames[varNameIndex0], timeIndex0);
                    boolean bEndVars = varNameIndex0 == varNames.length - 1;
                    createMedia(exportOutputV, vcdID, dataID, exportSpecs, bEndVars, bEndslice, bBegintime, bEndTime, bSingleTimePoint, new String[] { varNames[varNameIndex0] }, new DisplayPreferences[] { displayPreferences[varNameIndex0] }, movieHolder, currentSliceTimeMirrorInfo.getPixels(), currentSliceTimeMirrorInfo.getMirrorWidth(), currentSliceTimeMirrorInfo.getMirrorHeight(), fileDataContainerManager);
                    timeIndex0++;
                    if (timeIndex0 > endTimeIndex) {
                        timeIndex0 = beginTimeIndex;
                        varNameIndex0++;
                        if (varNameIndex0 == varNames.length) {
                            break;
                        }
                    }
                }
            }
        }
    } finally {
        if (exportRenderInfo != null) {
            exportRenderInfo.cleanup();
        }
    }
    return exportOutputV.toArray(new ExportOutput[0]);
}

Example 2 with DisplayPreferences

use of cbit.image.DisplayPreferences 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 3 with DisplayPreferences

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

the class FRAPStudyPanel method showMovie.

private void showMovie() {
    AsynchClientTask createMovieTask = new AsynchClientTask("Buffering movie data...", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

        public void run(Hashtable<String, Object> hashTable) throws Exception {
            FRAPStudy fStudy = getFrapWorkspace().getWorkingFrapStudy();
            if (fStudy == null) {
                return;
            }
            if (fStudy.getMovieURLString() != null && fStudy.getMovieFileString() != null) {
                hashTable.put("FrapStudy", fStudy);
                return;
            }
            // create export specs
            Simulation sim = null;
            if (fStudy.getBioModel() == null || fStudy.getBioModel().getSimulations() == null || fStudy.getBioModel().getSimulations().length < 1) {
                return;
            } else {
                sim = fStudy.getBioModel().getSimulations()[0];
            }
            FieldFunctionArguments[] fieldFunctionArgs = FieldUtilities.getFieldFunctionArguments(sim.getMathDescription());
            FieldDataIdentifierSpec[] fieldDataIdentifierSpecs = new FieldDataIdentifierSpec[fieldFunctionArgs.length];
            for (int i = 0; i < fieldDataIdentifierSpecs.length; i++) {
                fieldDataIdentifierSpecs[i] = new FieldDataIdentifierSpec(fieldFunctionArgs[i], fStudy.getFrapDataExternalDataInfo().getExternalDataIdentifier());
            }
            ExternalDataIdentifier timeSeriesExtDataID = fStudy.getFrapDataExternalDataInfo().getExternalDataIdentifier();
            ExternalDataIdentifier maskExtDataID = fStudy.getRoiExternalDataInfo().getExternalDataIdentifier();
            // add sim
            int jobIndex = 0;
            SimulationJob simJob = new SimulationJob(sim, jobIndex, fieldDataIdentifierSpecs);
            VCDataIdentifier[] dataIDs = new VCDataIdentifier[] { timeSeriesExtDataID, maskExtDataID, simJob.getVCDataIdentifier() };
            VCDataIdentifier vcDataId = new MergedDataInfo(LocalWorkspace.getDefaultOwner(), dataIDs, FRAPStudy.VFRAP_DS_PREFIX);
            PDEDataManager dataManager = new PDEDataManager(null, getLocalWorkspace().getVCDataManager(), vcDataId);
            PDEDataContext pdeDataContext = new ClientPDEDataContext(dataManager);
            ExportFormat format = ExportFormat.QUICKTIME;
            String[] variableNames = new String[] { NORM_FLUOR_VAR, NORM_SIM_VAR };
            VariableSpecs variableSpecs = new VariableSpecs(variableNames, ExportConstants.VARIABLE_MULTI);
            // int endTimeIndex = (int)Math.round(sim.getSolverTaskDescription().getTimeBounds().getEndingTime()/((UniformOutputTimeSpec)sim.getSolverTaskDescription().getOutputTimeSpec()).getOutputTimeStep());
            int endTimeIndex = getFRAPSimDataViewerPanel().getOriginalDataViewer().getPdeDataContext().getTimePoints().length - 1;
            TimeSpecs timeSpecs = new TimeSpecs(0, endTimeIndex, pdeDataContext.getTimePoints(), ExportConstants.TIME_RANGE);
            int geoMode = ExportConstants.GEOMETRY_SLICE;
            GeometrySpecs geometrySpecs = new GeometrySpecs(null, Coordinate.Z_AXIS, 0, geoMode);
            // 10s
            double duration = 10000;
            DisplayPreferences pref1 = new DisplayPreferences("BlueRed", new Range(0.01, 1.1), DisplayAdapterService.createBlueRedSpecialColors());
            DisplayPreferences pref2 = new DisplayPreferences("BlueRed", new Range(0.01, 1.1), DisplayAdapterService.createBlueRedSpecialColors());
            DisplayPreferences[] displayPref = new DisplayPreferences[] { pref1, pref2 };
            int imageScale = 1;
            int membraneScale = 1;
            int scaleMode = ImagePaneModel.MESH_MODE;
            // the default setting in MediaSettingsPanel.
            int volVarMemOutlineThickness = 1;
            MovieSpecs mSpec = new MovieSpecs(duration, true, displayPref, ExportFormat.QUICKTIME, ExportConstants.NO_MIRRORING, volVarMemOutlineThickness, imageScale, membraneScale, scaleMode, FormatSpecificSpecs.CODEC_JPEG, 1.0f, /*lossless*/
            false, FormatSpecificSpecs.PARTICLE_NONE);
            // mSpec.setViewZoom(1);
            ExportSpecs exSpecs = new ExportSpecs(vcDataId, format, variableSpecs, timeSpecs, geometrySpecs, mSpec, fStudy.getName(), null);
            // pass the request
            ExportEvent exportEvt = ((VirtualFrapWindowManager) getFlourDataViewer().getDataViewerManager()).startExportMovie(exSpecs, outputContext, this.getClientTaskStatusSupport());
            hashTable.put("ExportEvt", exportEvt);
            hashTable.put("FrapStudy", fStudy);
        }
    };
    AsynchClientTask showMovieTask = new AsynchClientTask("Showing movie ...", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {

        public void run(Hashtable<String, Object> hashTable) throws Exception {
            ExportEvent exportEvt = (ExportEvent) hashTable.get("ExportEvt");
            FRAPStudy fStudy = (FRAPStudy) hashTable.get("FrapStudy");
            // show movie if successfully exported
            if (exportEvt != null) {
                final String fileURLString = System.getProperty(PropertyLoader.exportBaseURLProperty) + exportEvt.getJobID() + ".mov";
                final String fileString = System.getProperty(PropertyLoader.exportBaseDirInternalProperty) + exportEvt.getJobID() + ".mov";
                fStudy.setMovieURLString(fileURLString);
                fStudy.setMovieFileString(fileString);
            }
            showMovieInDialog(fStudy.getMovieURLString(), fStudy.getMovieFileString());
        }
    };
    ClientTaskDispatcher.dispatch(this, new Hashtable<String, Object>(), new AsynchClientTask[] { createMovieTask, showMovieTask }, true, true, null, true);
}

Example 4 with DisplayPreferences

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

the class IMGExporter method main.

public static void main(String[] args) throws Exception {
    if (args.length < 7) {
        System.out.println("Usage: IMGExporter username userkey simulationkey userdatadir beginTimeIndex endTimeIndex {varName1 varName2 ...}");
        System.exit(0);
    }
    String userName = args[0];
    String userKey = args[1];
    String SimulationKey = args[2];
    String primaryDirStr = args[3];
    int beginTimeIndex = Integer.valueOf(args[4]);
    int endTimeIndex = Integer.valueOf(args[5]);
    String[] varNames = new String[args.length - 6];
    if (args.length > 6) {
        for (int i = 6; i < args.length; i++) {
            varNames[i - 6] = args[i];
        }
    }
    PropertyLoader.loadProperties();
    User user = new User(userName, new KeyValue(userKey));
    VCSimulationIdentifier vcSimID = new VCSimulationIdentifier(new KeyValue(SimulationKey), user);
    VCSimulationDataIdentifier vcdID = new VCSimulationDataIdentifier(vcSimID, 0);
    class PrintingExportServiceImpl extends ExportServiceImpl {

        public PrintingExportServiceImpl() {
            super();
        }

        @Override
        protected void fireExportEvent(ExportEvent event) {
            super.fireExportEvent(event);
            System.out.println("Event type=" + event.getEventTypeID() + " JobID=" + event.getJobID() + " progress=" + event.getProgress());
        }
    }
    ExportServiceImpl exportServiceImpl = new PrintingExportServiceImpl();
    Cachetable cachetable = new Cachetable(10 * Cachetable.minute);
    File primaryDir = new File(primaryDirStr);
    DataSetControllerImpl dataSetControllerImpl = new DataSetControllerImpl(cachetable, primaryDir, null);
    DataServerImpl dataServerImpl = new DataServerImpl(dataSetControllerImpl, exportServiceImpl);
    double[] allTimes = dataSetControllerImpl.getDataSetTimes(vcdID);
    TimeSpecs timeSpecs = new TimeSpecs(beginTimeIndex, endTimeIndex, allTimes, ExportConstants.TIME_RANGE);
    VariableSpecs variableSpecs = new VariableSpecs(varNames, ExportConstants.VARIABLE_MULTI);
    GeometrySpecs geometrySpecs = new GeometrySpecs(null, 0, 0, ExportConstants.GEOMETRY_SLICE);
    DisplayPreferences displayPreferences = new DisplayPreferences(DisplayAdapterService.BLUERED, new Range(0, 1), DisplayAdapterService.createBlueRedSpecialColors());
    MovieSpecs movieSpecs = new MovieSpecs(// /
    1000.0, // /
    false, // /
    new DisplayPreferences[] { displayPreferences }, // /
    ExportFormat.FORMAT_JPEG, // /
    0, // /
    1, // /
    1, // /
    1, ImagePaneModel.MESH_MODE, FormatSpecificSpecs.CODEC_JPEG, 1.0f, false, FormatSpecificSpecs.PARTICLE_SELECT);
    ExportSpecs exportSpecs = new ExportSpecs(vcdID, ExportFormat.QUICKTIME, variableSpecs, timeSpecs, geometrySpecs, movieSpecs, "IMGExporterTest", null);
    exportServiceImpl.makeRemoteFile(null, user, dataServerImpl, exportSpecs);
}

Example 5 with DisplayPreferences

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

the class PDEExportDataPanel method startExport.

/**
 * Comment
 */
private void startExport() {
    if (getExportSettings1().getSelectedFormat() == ExportFormat.QUICKTIME && getJSlider1().getValue() == getJSlider2().getValue()) {
        DialogUtils.showWarningDialog(this, "User selected 'begin' and 'end' export times are the same.  'Movie' export format 'begin' and 'end' times must be different");
        return;
    }
    DisplayPreferences[] displayPreferences = null;
    @SuppressWarnings("deprecation") Object[] variableSelections = getJListVariables().getSelectedValues();
    boolean selectionHasVolumeVariables = false;
    boolean selectionHasMembraneVariables = false;
    switch(getExportSettings1().getSelectedFormat()) {
        case PLY:
        case QUICKTIME:
        case GIF:
        case FORMAT_JPEG:
        case ANIMATED_GIF:
            {
                displayPreferences = new DisplayPreferences[variableSelections.length];
                StringBuffer noScaleInfoNames = new StringBuffer();
                for (int i = 0; i < displayPreferences.length; i++) {
                    BitSet domainValid = null;
                    try {
                        if (dataInfoProvider != null) {
                            DataIdentifier varSelectionDataIdnetDataIdentifier = null;
                            for (int j = 0; j < dataInfoProvider.getPDEDataContext().getDataIdentifiers().length; j++) {
                                if (dataInfoProvider.getPDEDataContext().getDataIdentifiers()[j].getName().equals(variableSelections[i])) {
                                    varSelectionDataIdnetDataIdentifier = dataInfoProvider.getPDEDataContext().getDataIdentifiers()[j];
                                }
                            }
                            if (varSelectionDataIdnetDataIdentifier != null) {
                                selectionHasVolumeVariables = selectionHasVolumeVariables || varSelectionDataIdnetDataIdentifier.getVariableType().equals(VariableType.VOLUME) || varSelectionDataIdnetDataIdentifier.getVariableType().equals(VariableType.POSTPROCESSING) || varSelectionDataIdnetDataIdentifier.getVariableType().equals(VariableType.VOLUME_REGION);
                                selectionHasMembraneVariables = selectionHasMembraneVariables || varSelectionDataIdnetDataIdentifier.getVariableType().equals(VariableType.MEMBRANE) || varSelectionDataIdnetDataIdentifier.getVariableType().equals(VariableType.MEMBRANE_REGION);
                                CartesianMesh cartesianMesh = dataInfoProvider.getPDEDataContext().getCartesianMesh();
                                int dataLength = cartesianMesh.getDataLength(varSelectionDataIdnetDataIdentifier.getVariableType());
                                domainValid = new BitSet(dataLength);
                                domainValid.clear();
                                for (int j = 0; j < dataLength; j++) {
                                    if (dataInfoProvider.isDefined(varSelectionDataIdnetDataIdentifier, j)) {
                                        domainValid.set(j);
                                    }
                                }
                            } else {
                                throw new Exception("No DataIdentifer found for variable name '" + variableSelections[i] + "'");
                            }
                        }
                    } catch (Exception e) {
                        e.printStackTrace();
                        DialogUtils.showErrorDialog(this, "Error during domain evaluation:\n" + e.getMessage());
                        return;
                    }
                    displayPreferences[i] = new DisplayPreferences(getDisplayAdapterService().getDisplayPreferences((String) variableSelections[i]), domainValid);
                    if (!getDisplayAdapterService().hasStateID((String) variableSelections[i])) {
                        noScaleInfoNames.append("--- " + (String) variableSelections[i] + "\n");
                    }
                }
                break;
            }
        case CSV:
            {
                // check for membrane variables... warn for 3D geometry...
                // one gets the whole nine yards by index, not generally useful... except for a few people like Boris :)
                boolean mbVars = false;
                DataIdentifier[] dataIDs = getPdeDataContext().getDataIdentifiers();
                for (int i = 0; i < variableSelections.length; i++) {
                    String varName = (String) variableSelections[i];
                    for (int j = 0; j < dataIDs.length; j++) {
                        if (dataIDs[j].getName().equals(varName) && dataIDs[j].getVariableType().equals(VariableType.MEMBRANE)) {
                            mbVars = true;
                            break;
                        }
                    }
                }
                if (mbVars && getPdeDataContext().getCartesianMesh().getGeometryDimension() == 3 && getJRadioButtonSlice().isSelected()) {
                    String choice = PopupGenerator.showWarningDialog(this, getDataViewerManager().getUserPreferences(), UserMessage.warn_exportMembraneData3D, null);
                    if (choice.equals(UserMessage.OPTION_CANCEL)) {
                        // user canceled
                        return;
                    }
                }
                getExportSettings1().setSimulationSelector(createSimulationSelector());
                getExportSettings1().setIsCSVExport(true);
                break;
            }
        case NRRD:
        case IMAGEJ:
        case UCD:
        case VTK_IMAGE:
        case VTK_UNSTRUCT:
            break;
        default:
            break;
    }
    ;
    if (getJRadioButtonROI().isSelected() && getROISelections().getSelectedIndex() == -1) {
        PopupGenerator.showErrorDialog(this, "To export selections, you must select at least one item from the ROI selection list");
    }
    getExportSettings1().setTimeSpecs(new TimeSpecs(getJSlider1().getValue(), getJSlider2().getValue(), getPdeDataContext().getTimePoints(), ExportConstants.TIME_RANGE));
    getExportSettings1().setDisplayPreferences(displayPreferences, Arrays.asList(variableSelections).toArray(new String[0]), viewZoom);
    getExportSettings1().setSliceCount(FormatSpecificSpecs.getSliceCount(getJRadioButtonFull().isSelected(), getNormalAxis(), getPdeDataContext().getCartesianMesh()));
    getExportSettings1().setImageSizeCalculationInfo(getPdeDataContext().getCartesianMesh(), getNormalAxis());
    getExportSettings1().setIsSmoldyn(isSmoldyn);
    ExportFormat format = getSelectedFormat();
    if (format.equals(ExportFormat.PLY)) {
        getExportSettings1().setFormatSpecificSpecs(new PLYSpecs(true, displayPreferences));
    }
    if (format.requiresFollowOn()) {
        Frame theFrame = JOptionPane.getFrameForComponent(this);
        boolean okToExport = getExportSettings1().showFormatSpecificDialog(theFrame, selectionHasVolumeVariables, selectionHasMembraneVariables);
        if (!okToExport) {
            return;
        }
    }
    if (format.equals(ExportFormat.IMAGEJ)) {
        // export nrrd for imagej direct, the we'll send to imagej from vcell client
        getExportSettings1().setFormatSpecificSpecs(new RasterSpecs(ExportConstants.NRRD_SINGLE, false));
    }
    // determine of sim result is from local (quick) run or on server.
    final OutputContext outputContext = ((ClientPDEDataContext) getPdeDataContext()).getDataManager().getOutputContext();
    final ExportSpecs exportSpecs = getExportSpecs();
    boolean isLocalSimResult = false;
    VCDataIdentifier vcId = exportSpecs.getVCDataIdentifier();
    if (vcId instanceof LocalVCDataIdentifier) {
        isLocalSimResult = true;
    }
    // find out if smoldyn export choice is 'particle' - not available at this time
    boolean isParticle = false;
    if (getExportSettings1().getFormatSpecificSpecs() instanceof ImageSpecs) {
        isParticle = ((ImageSpecs) getExportSettings1().getFormatSpecificSpecs()).getParticleMode() == FormatSpecificSpecs.PARTICLE_SELECT;
    } else if (getExportSettings1().getFormatSpecificSpecs() instanceof MovieSpecs) {
        isParticle = ((MovieSpecs) getExportSettings1().getFormatSpecificSpecs()).getParticleMode() == FormatSpecificSpecs.PARTICLE_SELECT;
    }
    if (isLocalSimResult && isParticle) {
        DialogUtils.showErrorDialog(this, "Particle export for Smoldyn particles unavailable in local data at this time.");
        return;
    }
    // pass the export request down the line; non-blocking call
    if (!isLocalSimResult) {
        // for sims that ran on server, do as before.
        getDataViewerManager().startExport(this, outputContext, exportSpecs);
    } else {
        final String SOURCE_FILE_KEY = "SOURCE_FILE_KEY";
        final String DESTINATION_FILE_KEY = "DEESTINATION_FILE_KEY";
        AsynchClientTask localExportTast = new AsynchClientTask("Start Local Export", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

            @Override
            public void run(Hashtable<String, Object> hashTable) throws Exception {
                try {
                    File primaryDir = ResourceUtil.getLocalRootDir();
                    User usr = User.tempUser;
                    File usrDir = new File(primaryDir.getAbsolutePath(), usr.getName());
                    System.setProperty(PropertyLoader.exportBaseDirInternalProperty, usrDir.getAbsolutePath() + File.separator);
                    System.setProperty(PropertyLoader.exportBaseURLProperty, usrDir.toURI().toURL().toString());
                    DataSetControllerImpl dataSetControllerImpl = new DataSetControllerImpl(null, primaryDir, null);
                    ExportServiceImpl localExportServiceImpl = new ExportServiceImpl();
                    DataServerImpl dataServerImpl = new DataServerImpl(dataSetControllerImpl, localExportServiceImpl);
                    ExportEvent localExportEvent = dataServerImpl.makeRemoteFile(outputContext, usr, exportSpecs);
                    File sourceFile = new File(usrDir, new File((new URL(localExportEvent.getLocation()).getPath())).getName());
                    hashTable.put(SOURCE_FILE_KEY, sourceFile);
                } catch (Exception e) {
                    throw new Exception("Unable to export local sim results data : " + e.getMessage(), e);
                }
            }
        };
        AsynchClientTask localSaveTask = new AsynchClientTask("Start Local Export", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {

            @Override
            public void run(Hashtable<String, Object> hashTable) throws Exception {
                File sourceFile = (File) hashTable.get(SOURCE_FILE_KEY);
                JFileChooser jFileChooser = new JFileChooser();
                jFileChooser.setSelectedFile(new File(sourceFile.getName()));
                if (jFileChooser.showSaveDialog(PDEExportDataPanel.this) == JFileChooser.APPROVE_OPTION) {
                    File destinationFile = jFileChooser.getSelectedFile();
                    if (destinationFile.exists()) {
                        final String OVERWRITE = "Overwrite";
                        final String CANCEL = "Cancel";
                        String response = DialogUtils.showWarningDialog(PDEExportDataPanel.this, "OK to Overwrite " + destinationFile.getAbsolutePath() + "?", new String[] { OVERWRITE, CANCEL }, OVERWRITE);
                        if (response == null || !response.equals(OVERWRITE)) {
                            return;
                        }
                    }
                    hashTable.put(DESTINATION_FILE_KEY, destinationFile);
                }
            }
        };
        AsynchClientTask localDeleteTempTask = new AsynchClientTask("Start Local Export", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING, false, false) {

            @Override
            public void run(Hashtable<String, Object> hashTable) throws Exception {
                File sourceFile = (File) hashTable.get(SOURCE_FILE_KEY);
                File destinationFile = (File) hashTable.get(DESTINATION_FILE_KEY);
                if (sourceFile != null && sourceFile.exists()) {
                    try {
                        if (destinationFile != null) {
                            copyFile(sourceFile, destinationFile);
                        }
                    } finally {
                        sourceFile.delete();
                    }
                }
            }
        };
        ClientTaskDispatcher.dispatch(this, new Hashtable<String, Object>(), new AsynchClientTask[] { localExportTast, localSaveTask, localDeleteTempTask }, false, true, null);
    }
}