Examples with PDEDataContext cbit.vcell.simdata.PDEDataContext used on opensource projects

Example 1 with PDEDataContext

use of cbit.vcell.simdata.PDEDataContext in project vcell by virtualcell.

the class PDEDataContextPanel method setPdeDataContext.

/**
 * Sets the pdeDataContext property (cbit.vcell.simdata.PDEDataContext) value.
 * @param pdeDataContext The new value for the property.
 * @see #getPdeDataContext
 */
public void setPdeDataContext(PDEDataContext pdeDataContext) {
    PDEDataContext oldValue = fieldPdeDataContext;
    if (oldValue != null) {
        oldValue.removePropertyChangeListener(ivjEventHandler);
    }
    fieldPdeDataContext = pdeDataContext;
    if (getPdeDataContext() != null) {
        getPdeDataContext().addPropertyChangeListener(ivjEventHandler);
    }
    if (!PDEDataViewer.isParameterScan(oldValue, getPdeDataContext())) {
        initMeshDisplayAdapter();
        if (ivjImagePlaneManagerPanel != null && ivjImagePlaneManagerPanel.getCurveRenderer() != null && getPdeDataContext() != null) {
            ivjImagePlaneManagerPanel.getCurveRenderer().setCartesianMesh(getPdeDataContext().getCartesianMesh());
        }
        if (getPdeDataContext() != null) {
            recodeDataForDomain();
        }
    }
}

Example 2 with PDEDataContext

use of cbit.vcell.simdata.PDEDataContext 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 3 with PDEDataContext

use of cbit.vcell.simdata.PDEDataContext in project vcell by virtualcell.

the class ClientRequestManager method createNewGeometryTasks.

public AsynchClientTask[] createNewGeometryTasks(final TopLevelWindowManager requester, final VCDocument.DocumentCreationInfo documentCreationInfo, final AsynchClientTask[] afterTasks, final String okButtonText) {
    if (!isImportGeometryType(documentCreationInfo)) {
        throw new IllegalArgumentException("Analytic geometry not implemented.");
    }
    final String IMPORT_SOURCE_NAME = "IMPORT_SOURCE_NAME";
    // Get image from file
    AsynchClientTask selectImageFileTask = new AsynchClientTask("select image file", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            File imageFile = DatabaseWindowManager.showFileChooserDialog(requester, null, getUserPreferences(), JFileChooser.FILES_AND_DIRECTORIES);
            hashTable.put("imageFile", imageFile);
            hashTable.put(IMPORT_SOURCE_NAME, "File: " + imageFile.getName());
        }
    };
    final String FDFOS = "FDFOS";
    final String INITIAL_ANNOTATION = "INITIAL_ANNOTATION";
    final String ORIG_IMAGE_SIZE_INFO = "ORIG_IMAGE_SIZE_INFO";
    final String NEW_IMAGE_SIZE_INFO = "NEW_IMAGE_SIZE_INFO";
    final String DIR_FILES = "DIR_FILES";
    final String FD_MESH = "FD_MESH";
    final String FD_MESHISIZE = "FD_MESHISIZE";
    final String FD_TIMEPOINTS = "FD_TIMEPOINTS";
    AsynchClientTask parseImageTask = new AsynchClientTask("read and parse image file", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

        @Override
        public void run(final Hashtable<String, Object> hashTable) throws Exception {
            final Component guiParent = (Component) hashTable.get(ClientRequestManager.GUI_PARENT);
            try {
                FieldDataFileOperationSpec fdfos = null;
                if (documentCreationInfo.getOption() == VCDocument.GEOM_OPTION_FIJI_IMAGEJ) {
                    hashTable.put("imageFile", ImageJHelper.vcellWantImage(getClientTaskStatusSupport(), "Image for new VCell geometry"));
                }
                if (documentCreationInfo.getOption() == VCDocument.GEOM_OPTION_BLENDER) {
                    hashTable.put("imageFile", ImageJHelper.vcellWantSurface(getClientTaskStatusSupport(), "Image for new VCell geometry"));
                }
                if (documentCreationInfo.getOption() == VCDocument.GEOM_OPTION_FILE || documentCreationInfo.getOption() == VCDocument.GEOM_OPTION_FIJI_IMAGEJ || documentCreationInfo.getOption() == VCDocument.GEOM_OPTION_BLENDER) {
                    File imageFile = (File) hashTable.get("imageFile");
                    if (imageFile == null) {
                        throw new Exception("No file selected");
                    }
                    if (ExtensionFilter.isMatchingExtension(imageFile, ".nrrd")) {
                        DataInputStream dis = null;
                        try {
                            dis = new DataInputStream(new BufferedInputStream(new FileInputStream(imageFile)));
                            int xsize = 1;
                            int ysize = 1;
                            int zsize = 1;
                            double xspace = 1.0;
                            double yspace = 1.0;
                            double zspace = 1.0;
                            NRRDTYPE type = null;
                            NRRDENCODING encoding = null;
                            int dimension = -1;
                            // read header lines
                            while (true) {
                                @SuppressWarnings("deprecation") String line = dis.readLine();
                                if (line == null || line.length() == 0) {
                                    break;
                                }
                                StringTokenizer stringTokenizer = new StringTokenizer(line, ": ");
                                String headerParam = stringTokenizer.nextToken();
                                // System.out.println(headerParam);
                                if (headerParam.equals("sizes")) {
                                    if (dimension != -1) {
                                        xsize = Integer.parseInt(stringTokenizer.nextToken());
                                        if (dimension >= 2) {
                                            ysize = Integer.parseInt(stringTokenizer.nextToken());
                                        }
                                        if (dimension >= 3) {
                                            zsize = Integer.parseInt(stringTokenizer.nextToken());
                                        }
                                        for (int i = 4; i < dimension; i++) {
                                            if (Integer.parseInt(stringTokenizer.nextToken()) != 1) {
                                                throw new Exception("Dimensions > 3 not supported");
                                            }
                                        }
                                    } else {
                                        throw new Exception("dimension expected to be set before reading sizes");
                                    }
                                } else if (headerParam.equals("spacings")) {
                                    if (dimension != -1) {
                                        xspace = Double.parseDouble(stringTokenizer.nextToken());
                                        if (dimension >= 2) {
                                            yspace = Double.parseDouble(stringTokenizer.nextToken());
                                        }
                                        if (dimension >= 3) {
                                            zspace = Double.parseDouble(stringTokenizer.nextToken());
                                        }
                                    // ignore other dimension spacings
                                    } else {
                                        throw new Exception("dimension expected to be set before reading spacings");
                                    }
                                } else if (headerParam.equals("type")) {
                                    String nextToken = stringTokenizer.nextToken();
                                    if (nextToken.equalsIgnoreCase("double")) {
                                        type = NRRDTYPE.DOUBLE;
                                    } else if (nextToken.equalsIgnoreCase("float")) {
                                        type = NRRDTYPE.FLOAT;
                                    } else if (nextToken.equalsIgnoreCase("unsigned")) {
                                        nextToken = stringTokenizer.nextToken();
                                        if (nextToken.equalsIgnoreCase("char")) {
                                            type = NRRDTYPE.UNSIGNEDCHAR;
                                        } else {
                                            throw new Exception("Unknown nrrd data type=" + nextToken);
                                        }
                                    } else {
                                        throw new Exception("Unknown nrrd data type=" + nextToken);
                                    }
                                } else if (headerParam.equals("dimension")) {
                                    dimension = Integer.parseInt(stringTokenizer.nextToken());
                                    if (dimension < 1) {
                                        throw new Exception("unexpected dimension=" + dimension);
                                    }
                                } else if (headerParam.equals("encoding")) {
                                    encoding = NRRDENCODING.valueOf(stringTokenizer.nextToken().toUpperCase());
                                }
                            }
                            BufferedInputStream bis = null;
                            if (encoding == NRRDENCODING.GZIP) {
                                dis.close();
                                bis = new BufferedInputStream(new FileInputStream(imageFile));
                                boolean bnewLine = false;
                                while (true) {
                                    int currentChar = bis.read();
                                    if (currentChar == '\n') {
                                        if (bnewLine) {
                                            // 2 newlines end header
                                            break;
                                        }
                                        bnewLine = true;
                                    } else {
                                        bnewLine = false;
                                    }
                                }
                                GZIPInputStream gzipInputStream = new GZIPInputStream(bis);
                                dis = new DataInputStream(gzipInputStream);
                            }
                            double[] data = new double[xsize * ysize * zsize];
                            double minValue = Double.POSITIVE_INFINITY;
                            double maxValue = Double.NEGATIVE_INFINITY;
                            for (int i = 0; i < data.length; i++) {
                                if (i % 262144 == 0) {
                                    if (getClientTaskStatusSupport() != null) {
                                        getClientTaskStatusSupport().setMessage("Reading " + encoding + " " + type + " NRRD data " + (((long) i * (long) 100) / (long) data.length) + " % done.");
                                    }
                                }
                                if (type == NRRDTYPE.DOUBLE) {
                                    data[i] = dis.readDouble();
                                } else if (type == NRRDTYPE.FLOAT) {
                                    data[i] = dis.readFloat();
                                } else if (type == NRRDTYPE.UNSIGNEDCHAR) {
                                    data[i] = dis.readUnsignedByte();
                                } else {
                                    throw new Exception("Unexpected data type=" + type.toString());
                                }
                                minValue = Math.min(minValue, data[i]);
                                maxValue = Math.max(maxValue, data[i]);
                            }
                            dis.close();
                            if (getClientTaskStatusSupport() != null) {
                                getClientTaskStatusSupport().setMessage("Scaling " + encoding + " " + type + " NRRD data.");
                            }
                            short[] dataToSegment = new short[data.length];
                            double scaleShort = Math.pow(2, Short.SIZE) - 1;
                            for (int i = 0; i < data.length; i++) {
                                dataToSegment[i] |= (int) ((data[i] - minValue) / (maxValue - minValue) * scaleShort);
                            }
                            fdfos = new FieldDataFileOperationSpec();
                            fdfos.origin = new Origin(0, 0, 0);
                            fdfos.extent = new Extent((xsize == 1 ? .5 : (xsize) * xspace), (ysize == 1 ? .5 : (ysize) * yspace), (zsize == 1 ? .5 : (zsize) * zspace));
                            fdfos.isize = new ISize(xsize, ysize, zsize);
                            fdfos.shortSpecData = new short[][][] { { dataToSegment } };
                        } finally {
                            if (dis != null) {
                                try {
                                    dis.close();
                                } catch (Exception e) {
                                    e.printStackTrace();
                                }
                            }
                        }
                    } else if ((fdfos = createFDOSFromSurfaceFile(imageFile)) != null) {
                    // try surface file formats
                    // work already done at this point
                    } else {
                        File[] dirFiles = null;
                        ImageSizeInfo origImageSizeInfo = null;
                        if (imageFile.isDirectory()) {
                            dirFiles = imageFile.listFiles(new java.io.FileFilter() {

                                public boolean accept(File pathname) {
                                    // exclude windows Thumbs.db
                                    return pathname.isFile() && !pathname.isHidden();
                                }
                            });
                            if (dirFiles.length == 0) {
                                throw new Exception("No valid files in selected directory");
                            }
                            String fileExt0 = null;
                            for (int i = 0; i < dirFiles.length; i++) {
                                int lastDot = dirFiles[i].getName().lastIndexOf('.');
                                String fileExt = (lastDot != -1 ? dirFiles[i].getName().substring(lastDot) : null);
                                if (dirFiles[i].isDirectory()) {
                                    fileExt = "dir";
                                }
                                if (i == 0) {
                                    fileExt0 = fileExt;
                                } else if (!Compare.isEqualOrNull(fileExt, fileExt0)) {
                                    String result = DialogUtils.showWarningDialog(requester.getComponent(), "Files in '" + imageFile.getAbsolutePath() + "' have different name extensions, continue?", new String[] { "OK", "Cancel" }, "Cancel");
                                    if (!"OK".equals(result)) {
                                        throw UserCancelException.CANCEL_FILE_SELECTION;
                                    }
                                    break;
                                }
                            }
                            hashTable.put(IMPORT_SOURCE_NAME, "Directory: " + imageFile.getAbsolutePath());
                            origImageSizeInfo = ImageDatasetReaderService.getInstance().getImageDatasetReader().getImageSizeInfoForceZ(dirFiles[0].getAbsolutePath(), dirFiles.length);
                            if (dirFiles.length > 1) {
                                final String importZ = "Import Z-Sections";
                                final String cancelOption = "Cancel";
                                String result = DialogUtils.showWarningDialog(guiParent, "Import all files in directory '" + imageFile.getAbsolutePath() + "' as Z-Sections", new String[] { importZ, cancelOption }, importZ);
                                if (result.equals(cancelOption)) {
                                    throw UserCancelException.CANCEL_GENERIC;
                                }
                            }
                            hashTable.put(DIR_FILES, dirFiles);
                        } else {
                            origImageSizeInfo = ImageDatasetReaderService.getInstance().getImageDatasetReader().getImageSizeInfo(imageFile.getAbsolutePath());
                            hashTable.put(IMPORT_SOURCE_NAME, "File: " + imageFile.getAbsolutePath());
                        }
                        hashTable.put(ORIG_IMAGE_SIZE_INFO, origImageSizeInfo);
                        return;
                    }
                } else if (documentCreationInfo.getOption() == VCDocument.GEOM_OPTION_FIELDDATA) {
                    getClientTaskStatusSupport().setMessage("Reading data from VCell server.");
                    VCDocument.GeomFromFieldDataCreationInfo docInfo = (VCDocument.GeomFromFieldDataCreationInfo) documentCreationInfo;
                    PDEDataContext pdeDataContext = getMdiManager().getFieldDataWindowManager().getPDEDataContext(docInfo.getExternalDataID(), null);
                    ImageSizeInfo newImageSizeInfo = (ImageSizeInfo) hashTable.get(NEW_IMAGE_SIZE_INFO);
                    pdeDataContext.setVariableNameAndTime(docInfo.getVarName(), newImageSizeInfo.getTimePoints()[newImageSizeInfo.getSelectedTimeIndex()]);
                    double[] data = pdeDataContext.getDataValues();
                    hashTable.put(INITIAL_ANNOTATION, hashTable.get(IMPORT_SOURCE_NAME));
                    CartesianMesh mesh = (CartesianMesh) hashTable.get(FD_MESH);
                    ISize meshISize = (ISize) hashTable.get(FD_MESHISIZE);
                    double minValue = Double.POSITIVE_INFINITY;
                    double maxValue = Double.NEGATIVE_INFINITY;
                    for (int i = 0; i < data.length; i++) {
                        minValue = Math.min(minValue, data[i]);
                        maxValue = Math.max(maxValue, data[i]);
                    }
                    short[] dataToSegment = new short[data.length];
                    double scaleShort = Math.pow(2, Short.SIZE) - 1;
                    for (int i = 0; i < data.length; i++) {
                        dataToSegment[i] |= (int) ((data[i] - minValue) / (maxValue - minValue) * scaleShort);
                    }
                    fdfos = new FieldDataFileOperationSpec();
                    fdfos.origin = mesh.getOrigin();
                    fdfos.extent = mesh.getExtent();
                    fdfos.isize = meshISize;
                    fdfos.shortSpecData = new short[][][] { { dataToSegment } };
                } else if (documentCreationInfo.getOption() == VCDocument.GEOM_OPTION_FROM_SCRATCH) {
                    ISize isize = getISizeFromUser(guiParent, new ISize(256, 256, 8), "Enter # of pixels for  x,y,z (e.g. 3D{256,256,8}, 2D{256,256,1}, 1D{256,1,1})");
                    fdfos = new FieldDataFileOperationSpec();
                    fdfos.origin = new Origin(0, 0, 0);
                    fdfos.extent = new Extent(1, 1, 1);
                    fdfos.isize = isize;
                    hashTable.put(IMPORT_SOURCE_NAME, "Scratch: New Geometry");
                // final int SCRATCH_SIZE_LIMIT = 512*512*20;
                // if(isize.getXYZ() > (SCRATCH_SIZE_LIMIT)){
                // throw new Exception("Total pixels (x*y*z) cannot be >"+SCRATCH_SIZE_LIMIT+".");
                // }
                } else if (documentCreationInfo.getOption() == VCDocument.GEOM_OPTION_FROM_WORKSPACE_ANALYTIC) {
                    if (hashTable.get(ClientRequestManager.GEOM_FROM_WORKSPACE) != null) {
                        Geometry workspaceGeom = (Geometry) hashTable.get(ClientRequestManager.GEOM_FROM_WORKSPACE);
                        ISize defaultISize = workspaceGeom.getGeometrySpec().getDefaultSampledImageSize();
                        ISize isize = getISizeFromUser(guiParent, defaultISize, "Warning: converting analytic expression geometry into an image based geometry\nwill remove analytic expressions after new image is created.\n\n" + "Enter size (x,y,z) for new geometry image (e.g. " + defaultISize.getX() + "," + defaultISize.getY() + "," + defaultISize.getZ() + ")");
                        hashTable.put(IMPORT_SOURCE_NAME, "Workspace from Analytic Geometry");
                        VCImage img = workspaceGeom.getGeometrySpec().createSampledImage(isize);
                        Enumeration<SubVolume> enumSubvolume = workspaceGeom.getGeometrySpec().getAnalyticOrCSGSubVolumes();
                        ArrayList<VCPixelClass> vcPixelClassArrList = new ArrayList<VCPixelClass>();
                        while (enumSubvolume.hasMoreElements()) {
                            SubVolume subVolume = enumSubvolume.nextElement();
                            vcPixelClassArrList.add(new VCPixelClass(null, subVolume.getName(), subVolume.getHandle()));
                        }
                        if (vcPixelClassArrList.size() > img.getPixelClasses().length) {
                            String result = DialogUtils.showOKCancelWarningDialog(requester.getComponent(), null, "Warning: sampling size is too small to include all subvolumes.");
                            if (result == null || !result.equals(SimpleUserMessage.OPTION_OK)) {
                                throw UserCancelException.CANCEL_GENERIC;
                            }
                        }
                        hashTable.put(VCPIXELCLASSES, vcPixelClassArrList.toArray(new VCPixelClass[0]));
                        fdfos = createFDOSFromVCImage(img);
                    } else {
                        throw new Exception("Expecting image source for GEOM_OPTION_FROM_WORKSPACE_ANALYTIC");
                    }
                } else if (documentCreationInfo.getOption() == VCDocument.GEOM_OPTION_FROM_WORKSPACE_IMAGE) {
                    if (hashTable.get(ClientRequestManager.GEOM_FROM_WORKSPACE) != null) {
                        Geometry workspaceGeom = (Geometry) hashTable.get(ClientRequestManager.GEOM_FROM_WORKSPACE);
                        hashTable.put(IMPORT_SOURCE_NAME, "Workspace Image");
                        fdfos = createFDOSFromVCImage(workspaceGeom.getGeometrySpec().getImage());
                        if (workspaceGeom.getGeometrySpec().getImage().getDescription() != null) {
                            hashTable.put(INITIAL_ANNOTATION, workspaceGeom.getGeometrySpec().getImage().getDescription());
                        }
                        hashTable.put(VCPIXELCLASSES, workspaceGeom.getGeometrySpec().getImage().getPixelClasses());
                    } else {
                        throw new Exception("Expecting image source for GEOM_OPTION_FROM_WORKSPACE");
                    }
                }
                hashTable.put(FDFOS, fdfos);
            } catch (DataFormatException ex) {
                throw new Exception("Cannot read image file.\n" + ex.getMessage());
            }
        }
    };
    AsynchClientTask getFieldDataImageParams = new AsynchClientTask("Getting DB Image parameters...", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            VCDocument.GeomFromFieldDataCreationInfo docInfo = (VCDocument.GeomFromFieldDataCreationInfo) documentCreationInfo;
            PDEDataContext pdeDataContext = getMdiManager().getFieldDataWindowManager().getPDEDataContext(docInfo.getExternalDataID(), null);
            CartesianMesh mesh = pdeDataContext.getCartesianMesh();
            ISize meshISize = new ISize(mesh.getSizeX(), mesh.getSizeY(), mesh.getSizeZ());
            double[] timePoints = pdeDataContext.getTimePoints();
            hashTable.put(FD_MESH, mesh);
            hashTable.put(FD_MESHISIZE, meshISize);
            hashTable.put(FD_TIMEPOINTS, timePoints);
        }
    };
    AsynchClientTask queryImageResizeTask = new AsynchClientTask("Query File Image Resize...", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            String importSourceName = (String) hashTable.get(IMPORT_SOURCE_NAME);
            if ((ImageSizeInfo) hashTable.get(ORIG_IMAGE_SIZE_INFO) != null) {
                // from file
                ImageSizeInfo newImagesiSizeInfo = queryImageResize(requester.getComponent(), (ImageSizeInfo) hashTable.get(ORIG_IMAGE_SIZE_INFO), true);
                hashTable.put(NEW_IMAGE_SIZE_INFO, newImagesiSizeInfo);
            } else if (documentCreationInfo.getOption() == VCDocument.GEOM_OPTION_FIELDDATA) {
                // from fielddata
                VCDocument.GeomFromFieldDataCreationInfo docInfo = (VCDocument.GeomFromFieldDataCreationInfo) documentCreationInfo;
                double[] fieldDataTimes = (double[]) hashTable.get(FD_TIMEPOINTS);
                hashTable.remove(FD_TIMEPOINTS);
                ISize fieldDataISize = (ISize) hashTable.get(FD_MESHISIZE);
                ImageSizeInfo origImageSizeInfo = new ImageSizeInfo(importSourceName, fieldDataISize, 1, fieldDataTimes, null);
                ImageSizeInfo newImagesiSizeInfo = queryImageResize(requester.getComponent(), origImageSizeInfo, true);
                hashTable.put(NEW_IMAGE_SIZE_INFO, newImagesiSizeInfo);
                hashTable.put(IMPORT_SOURCE_NAME, "FieldData: " + docInfo.getExternalDataID().getName() + " varName=" + docInfo.getVarName() + " timeIndex=" + newImagesiSizeInfo.getTimePoints()[newImagesiSizeInfo.getSelectedTimeIndex()]);
            }
        }
    };
    AsynchClientTask importFileImageTask = new AsynchClientTask("Importing Image from File...", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            if (documentCreationInfo.getOption() == VCDocument.GEOM_OPTION_FILE && hashTable.get(FDFOS) == null) {
                ImageSizeInfo origImageSizeInfo = (ImageSizeInfo) hashTable.get(ORIG_IMAGE_SIZE_INFO);
                ImageSizeInfo newImageSizeInfo = (ImageSizeInfo) hashTable.get(NEW_IMAGE_SIZE_INFO);
                File[] dirFiles = (File[]) hashTable.get(DIR_FILES);
                File imageFile = (File) hashTable.get("imageFile");
                FieldDataFileOperationSpec fdfos = null;
                boolean bMergeChannels = origImageSizeInfo.getNumChannels() != newImageSizeInfo.getNumChannels();
                ISize resize = (origImageSizeInfo.getiSize().compareEqual(newImageSizeInfo.getiSize()) ? null : newImageSizeInfo.getiSize());
                if (dirFiles != null) {
                    Arrays.sort(dirFiles, new Comparator<File>() {

                        public int compare(File o1, File o2) {
                            return o1.getName().compareToIgnoreCase(o2.getName());
                        }
                    });
                    hashTable.put(INITIAL_ANNOTATION, dirFiles[0].getAbsolutePath() + "\n.\n.\n.\n" + dirFiles[dirFiles.length - 1].getAbsolutePath());
                    short[][] dataToSegment = null;
                    ISize isize = null;
                    Origin origin = null;
                    Extent extent = null;
                    int sizeXY = 0;
                    ISize firstImageISize = null;
                    for (int i = 0; i < dirFiles.length; i++) {
                        ImageDataset[] imageDatasets = ImageDatasetReaderService.getInstance().getImageDatasetReader().readImageDatasetChannels(dirFiles[i].getAbsolutePath(), null, bMergeChannels, null, resize);
                        for (int c = 0; c < imageDatasets.length; c++) {
                            if (imageDatasets[c].getSizeZ() != 1 || imageDatasets[c].getSizeT() != 1) {
                                throwImportWholeDirectoryException(imageFile, dirFiles[i].getAbsolutePath() + " has Z=" + imageDatasets[c].getSizeZ() + " T=" + imageDatasets[c].getSizeT());
                            }
                            if (isize == null) {
                                firstImageISize = imageDatasets[c].getISize();
                                sizeXY = imageDatasets[c].getISize().getX() * imageDatasets[c].getISize().getY();
                                dataToSegment = new short[imageDatasets.length][sizeXY * dirFiles.length];
                                isize = new ISize(imageDatasets[c].getISize().getX(), imageDatasets[c].getISize().getY(), dirFiles.length);
                                origin = imageDatasets[c].getAllImages()[0].getOrigin();
                                extent = imageDatasets[c].getExtent();
                            }
                            if (!firstImageISize.compareEqual(imageDatasets[c].getISize())) {
                                throwImportWholeDirectoryException(imageFile, dirFiles[0].getAbsolutePath() + " " + firstImageISize + " does not equal " + dirFiles[i].getAbsolutePath() + " " + imageDatasets[c].getISize());
                            }
                            System.arraycopy(imageDatasets[c].getImage(0, 0, 0).getPixels(), 0, dataToSegment[c], sizeXY * i, sizeXY);
                        }
                    }
                    fdfos = new FieldDataFileOperationSpec();
                    fdfos.origin = origin;
                    fdfos.extent = extent;
                    fdfos.isize = isize;
                    fdfos.shortSpecData = new short[][][] { dataToSegment };
                } else {
                    hashTable.put(INITIAL_ANNOTATION, imageFile.getAbsolutePath());
                    Integer userPreferredTimeIndex = null;
                    if (origImageSizeInfo.getTimePoints().length > 1) {
                        userPreferredTimeIndex = newImageSizeInfo.getSelectedTimeIndex();
                    }
                    getClientTaskStatusSupport().setMessage("Reading file...");
                    ImageDataset[] imageDatasets = ImageDatasetReaderService.getInstance().getImageDatasetReader().readImageDatasetChannels(imageFile.getAbsolutePath(), null, bMergeChannels, userPreferredTimeIndex, resize);
                    fdfos = ClientRequestManager.createFDOSWithChannels(imageDatasets, null);
                }
                hashTable.put(FDFOS, fdfos);
                hashTable.remove(NEW_IMAGE_SIZE_INFO);
                hashTable.remove(ORIG_IMAGE_SIZE_INFO);
                hashTable.remove(DIR_FILES);
            }
        }
    };
    AsynchClientTask resizeImageTask = new AsynchClientTask("Resizing Image...", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            ImageSizeInfo newImageSizeInfo = (ImageSizeInfo) hashTable.get(NEW_IMAGE_SIZE_INFO);
            FieldDataFileOperationSpec fdfos = (FieldDataFileOperationSpec) hashTable.get(FDFOS);
            if (newImageSizeInfo != null && fdfos != null && !fdfos.isize.compareEqual(newImageSizeInfo.getiSize())) {
                resizeImage((FieldDataFileOperationSpec) hashTable.get(FDFOS), newImageSizeInfo.getiSize(), documentCreationInfo.getOption());
            }
        }
    };
    AsynchClientTask finishTask = new AsynchClientTask("Finishing...", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

        @Override
        public void run(final Hashtable<String, Object> hashTable) throws Exception {
            getClientTaskStatusSupport().setMessage("Initializing...");
            final ROIMultiPaintManager roiMultiPaintManager = new ROIMultiPaintManager();
            roiMultiPaintManager.initROIData((FieldDataFileOperationSpec) hashTable.get(FDFOS));
            final Geometry[] geomHolder = new Geometry[1];
            final VCPixelClass[] postProcessPixelClasses = (VCPixelClass[]) hashTable.get(VCPIXELCLASSES);
            AsynchClientTask task1 = new AsynchClientTask("edit geometry", AsynchClientTask.TASKTYPE_SWING_BLOCKING, false) {

                @Override
                public void run(Hashtable<String, Object> hashTable) throws Exception {
                    geomHolder[0] = roiMultiPaintManager.showGUI(okButtonText, (String) hashTable.get(IMPORT_SOURCE_NAME), (Component) hashTable.get(GUI_PARENT), (String) hashTable.get(INITIAL_ANNOTATION), postProcessPixelClasses, getUserPreferences());
                }
            };
            AsynchClientTask task2 = new AsynchClientTask("update geometry", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

                @Override
                public void run(Hashtable<String, Object> hashTable) throws Exception {
                    // Create default name for image
                    String dateTimeString = BeanUtils.generateDateTimeString();
                    geomHolder[0].getGeometrySpec().getImage().setName("img_" + dateTimeString);
                    geomHolder[0].setName("geom_" + dateTimeString);
                    // cause update in this thread so later swing threads won't be delayed
                    geomHolder[0].precomputeAll(new GeometryThumbnailImageFactoryAWT());
                    hashTable.put("doc", geomHolder[0]);
                }
            };
            AsynchClientTask[] finalTasks = afterTasks;
            if (finalTasks == null) {
                finalTasks = new AsynchClientTask[] { getSaveImageAndGeometryTask() };
            }
            AsynchClientTask[] tasks = new AsynchClientTask[2 + finalTasks.length];
            tasks[0] = task1;
            tasks[1] = task2;
            System.arraycopy(finalTasks, 0, tasks, 2, finalTasks.length);
            ClientTaskDispatcher.dispatch((Component) hashTable.get(GUI_PARENT), hashTable, tasks, false, false, null, true);
        }
    };
    Vector<AsynchClientTask> tasksV = new Vector<AsynchClientTask>();
    if (documentCreationInfo.getOption() == VCDocument.GEOM_OPTION_FROM_SCRATCH) {
        tasksV.addAll(Arrays.asList(new AsynchClientTask[] { parseImageTask, finishTask }));
    } else if (documentCreationInfo.getOption() == VCDocument.GEOM_OPTION_FROM_WORKSPACE_ANALYTIC) {
        tasksV.addAll(Arrays.asList(new AsynchClientTask[] { parseImageTask, finishTask }));
    } else if (documentCreationInfo.getOption() == VCDocument.GEOM_OPTION_FROM_WORKSPACE_IMAGE) {
        tasksV.addAll(Arrays.asList(new AsynchClientTask[] { parseImageTask, finishTask }));
    } else if (documentCreationInfo.getOption() == VCDocument.GEOM_OPTION_FILE) {
        tasksV.addAll(Arrays.asList(new AsynchClientTask[] { selectImageFileTask, parseImageTask, queryImageResizeTask, importFileImageTask, /*resizes*/
        finishTask }));
    } else if (documentCreationInfo.getOption() == VCDocument.GEOM_OPTION_FIJI_IMAGEJ || documentCreationInfo.getOption() == VCDocument.GEOM_OPTION_BLENDER) {
        tasksV.addAll(Arrays.asList(new AsynchClientTask[] { parseImageTask, queryImageResizeTask, importFileImageTask, /*resizes*/
        finishTask }));
    } else if (documentCreationInfo.getOption() == VCDocument.GEOM_OPTION_FIELDDATA) {
        tasksV.addAll(Arrays.asList(new AsynchClientTask[] { getFieldDataImageParams, queryImageResizeTask, parseImageTask, resizeImageTask, finishTask }));
    }
    return tasksV.toArray(new AsynchClientTask[0]);
}

Example 4 with PDEDataContext

use of cbit.vcell.simdata.PDEDataContext in project vcell by virtualcell.

the class PDEDataViewer method setPdeDataContext.

public void setPdeDataContext(ClientPDEDataContext pdeDataContext) {
    if (pdeDataContext != null && pdeDataContext.getVCDataIdentifier() instanceof ExternalDataIdentifier) {
        // getJTabbedPane1().removeTabAt(getJTabbedPane1().indexOfTab(POST_PROCESS_IMAGE_TABNAME));
        // getJTabbedPane1().removeTabAt(getJTabbedPane1().indexOfTab(POST_PROCESS_STATS_TABNAME));
        getJTabbedPane1().setEnabledAt(getJTabbedPane1().indexOfTab(POST_PROCESS_IMAGE_TABNAME), false);
        getJTabbedPane1().setEnabledAt(getJTabbedPane1().indexOfTab(POST_PROCESS_STATS_TABNAME), false);
    }
    getPDEDataContextPanel1().getdisplayAdapterServicePanel1().enableAutoAllTimes(true && !(pdeDataContext instanceof PostProcessDataPDEDataContext));
    PDEDataContext oldValue = fieldPdeDataContext;
    String setVarName = null;
    Integer setTimePoint = null;
    if (oldValue != null) {
        setVarName = oldValue.getVariableName();
        setTimePoint = getPDEPlotControlPanel1().getTimeSliderValue();
        try {
            if (pdeDataContext != null) {
                pdeDataContext.setVariableNameAndTime(setVarName, pdeDataContext.getTimePoints()[setTimePoint]);
            }
        } catch (Exception e) {
            e.printStackTrace();
            setVarName = null;
            setTimePoint = null;
        }
        oldValue.removePropertyChangeListener(ivjEventHandler);
    }
    fieldPdeDataContext = pdeDataContext;
    if (getPdeDataContext() != null && (setVarName == null || setTimePoint == null)) {
        setVarName = getPdeDataContext().getVariableNames()[0];
        setTimePoint = 0;
        try {
            pdeDataContext.setVariableNameAndTime(setVarName, pdeDataContext.getTimePoints()[setTimePoint]);
        } catch (Exception e2) {
            e2.printStackTrace();
            DialogUtils.showErrorDialog(this, "Couldn't set time and variable on pdeDataContext");
            return;
        }
    }
    if (getPdeDataContext() != null) {
        getPdeDataContext().removePropertyChangeListener(ivjEventHandler);
        getPdeDataContext().addPropertyChangeListener(ivjEventHandler);
        try {
            getPDEPlotControlPanel1().removePropertyChangeListener(ivjEventHandler);
            try {
                getPDEPlotControlPanel1().setup(((ClientPDEDataContext) getPdeDataContext()).getDataManager().getOutputContext().getOutputFunctions(), getPdeDataContext().getDataIdentifiers(), getPdeDataContext().getTimePoints(), setVarName, setTimePoint);
            } catch (Exception e) {
                e.printStackTrace();
                DialogUtils.showErrorDialog(this, "Couldn't setup PDEPlotControlPanel, " + e.getMessage());
                return;
            }
        } finally {
            getPDEPlotControlPanel1().addPropertyChangeListener(ivjEventHandler);
        }
    }
    bSkipSurfaceCalc = true;
    firePropertyChange(PDEDataContext.PROP_PDE_DATA_CONTEXT, null, pdeDataContext);
    bSkipSurfaceCalc = false;
    if (ivjJTabbedPane1.getTitleAt(ivjJTabbedPane1.getSelectedIndex()).equals(POST_PROCESS_STATS_TABNAME)) {
        dataProcessingResultsPanel.update(getPdeDataContext());
    }
    postProcessPdeDataViewerPanel.setParentPDEDataContext((ClientPDEDataContext) getPdeDataContext());
    if (ivjJTabbedPane1.getTitleAt(ivjJTabbedPane1.getSelectedIndex()).equals(POST_PROCESS_IMAGE_TABNAME)) {
        postProcessPdeDataViewerPanel.update();
    }
}

Example 5 with PDEDataContext

use of cbit.vcell.simdata.PDEDataContext in project vcell by virtualcell.

the class PDEExportDataPanel method setpdeDataContext1.

/**
 * Set the pdeDataContext1 to a new value.
 * @param newValue cbit.vcell.simdata.PDEDataContext
 */
/* WARNING: THIS METHOD WILL BE REGENERATED. */
private void setpdeDataContext1(PDEDataContext newValue) {
    if (ivjpdeDataContext1 != newValue) {
        try {
            PDEDataContext oldValue = getpdeDataContext1();
            /* Stop listening for events from the current object */
            if (ivjpdeDataContext1 != null) {
                ivjpdeDataContext1.removePropertyChangeListener(ivjEventHandler);
            }
            ivjpdeDataContext1 = newValue;
            /* Listen for events from the new object */
            if (ivjpdeDataContext1 != null) {
                ivjpdeDataContext1.addPropertyChangeListener(ivjEventHandler);
            }
            connPtoP3SetSource();
            connEtoC1(ivjpdeDataContext1);
            firePropertyChange(PDEDataContext.PROP_PDE_DATA_CONTEXT, oldValue, newValue);
        // user code begin {1}
        // user code end
        } catch (java.lang.Throwable ivjExc) {
            // user code begin {2}
            // user code end
            handleException(ivjExc);
        }
    }
    ;
// user code begin {3}
// user code end
}