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Example 36 with VCImage

use of cbit.image.VCImage 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]);
}
Also used : BngUnitOrigin(org.vcell.model.bngl.BngUnitSystem.BngUnitOrigin) Origin(org.vcell.util.Origin) VCPixelClass(cbit.image.VCPixelClass) FieldDataFileOperationSpec(cbit.vcell.field.io.FieldDataFileOperationSpec) ArrayList(java.util.ArrayList) BufferedInputStream(java.io.BufferedInputStream) SubVolume(cbit.vcell.geometry.SubVolume) AnalyticSubVolume(cbit.vcell.geometry.AnalyticSubVolume) Vector(java.util.Vector) VCDocument(org.vcell.util.document.VCDocument) ROIMultiPaintManager(cbit.vcell.geometry.gui.ROIMultiPaintManager) FileInputStream(java.io.FileInputStream) ImageSizeInfo(cbit.image.ImageSizeInfo) CartesianMesh(cbit.vcell.solvers.CartesianMesh) ChooseFile(cbit.vcell.client.task.ChooseFile) File(java.io.File) PDEDataContext(cbit.vcell.simdata.PDEDataContext) AsynchClientTask(cbit.vcell.client.task.AsynchClientTask) ImageDataset(cbit.vcell.VirtualMicroscopy.ImageDataset) Extent(org.vcell.util.Extent) ISize(org.vcell.util.ISize) VCImage(cbit.image.VCImage) GZIPInputStream(java.util.zip.GZIPInputStream) GeometryThumbnailImageFactoryAWT(cbit.vcell.geometry.GeometryThumbnailImageFactoryAWT) Component(java.awt.Component) Enumeration(java.util.Enumeration) Hashtable(java.util.Hashtable) DataInputStream(java.io.DataInputStream) ProgrammingException(org.vcell.util.ProgrammingException) GeometryException(cbit.vcell.geometry.GeometryException) IOException(java.io.IOException) DataAccessException(org.vcell.util.DataAccessException) PropertyVetoException(java.beans.PropertyVetoException) ImageException(cbit.image.ImageException) UtilCancelException(org.vcell.util.UtilCancelException) DataFormatException(java.util.zip.DataFormatException) UserCancelException(org.vcell.util.UserCancelException) Geometry(cbit.vcell.geometry.Geometry) StringTokenizer(java.util.StringTokenizer) CommentStringTokenizer(org.vcell.util.CommentStringTokenizer) DataFormatException(java.util.zip.DataFormatException)

Example 37 with VCImage

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

the class ClientRequestManager method createFDOSFromSurfaceFile.

public static FieldDataFileOperationSpec createFDOSFromSurfaceFile(File surfaceFile) throws Exception {
    SurfaceCollection surfaceCollection = createSurfaceCollectionFromSurfaceFile(surfaceFile);
    if (surfaceCollection != null) {
        Geometry geometry = RayCaster.createGeometryFromSTL(new GeometryThumbnailImageFactoryAWT(), surfaceCollection, 1000000);
        FieldDataFileOperationSpec fdfos = new FieldDataFileOperationSpec();
        fdfos.origin = geometry.getOrigin();
        fdfos.extent = geometry.getExtent();
        VCImage image = geometry.getGeometrySpec().getImage();
        if (image.getNumPixelClasses() == 1) {
            throw new Exception("STL import failed during processing, pixelclass count=1");
        }
        fdfos.isize = new ISize(image.getNumX(), image.getNumY(), image.getNumZ());
        byte[] pixels = image.getPixels();
        short[] dataToSegment = new short[image.getNumXYZ()];
        for (int i = 0; i < pixels.length; i++) {
            dataToSegment[i] = pixels[i];
        }
        fdfos.shortSpecData = new short[][][] { { dataToSegment } };
        return fdfos;
    }
    return null;
}
Also used : SurfaceCollection(cbit.vcell.geometry.surface.SurfaceCollection) Geometry(cbit.vcell.geometry.Geometry) GeometryThumbnailImageFactoryAWT(cbit.vcell.geometry.GeometryThumbnailImageFactoryAWT) FieldDataFileOperationSpec(cbit.vcell.field.io.FieldDataFileOperationSpec) ISize(org.vcell.util.ISize) VCImage(cbit.image.VCImage) ProgrammingException(org.vcell.util.ProgrammingException) GeometryException(cbit.vcell.geometry.GeometryException) IOException(java.io.IOException) DataAccessException(org.vcell.util.DataAccessException) PropertyVetoException(java.beans.PropertyVetoException) ImageException(cbit.image.ImageException) UtilCancelException(org.vcell.util.UtilCancelException) DataFormatException(java.util.zip.DataFormatException) UserCancelException(org.vcell.util.UserCancelException)

Example 38 with VCImage

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

the class GeometrySummaryPanel method createIcon.

/**
 * Comment
 */
public javax.swing.Icon createIcon(VCImage sampledImage, Geometry geom) throws cbit.image.GifParsingException, ImageException {
    if (sampledImage == null) {
        return null;
    } else {
        VCImage sampledGeometryHandles = null;
        if (geom.getDimension() > 0) {
            // project and scale geometry
            int SAMPLED_GEOM_SIZE = 150;
            sampledGeometryHandles = cbit.image.DitherIndexImage.dither(sampledImage, SAMPLED_GEOM_SIZE, SAMPLED_GEOM_SIZE);
            if (sampledGeometryHandles.getNumPixelClasses() != sampledImage.getNumPixelClasses()) {
                throw new RuntimeException("DitherIndexImage.dither()-->image.numPixelClasses = " + sampledGeometryHandles.getNumPixelClasses() + ", and Geometry.getSampledImage()-->image.numPixelClasses = " + sampledImage.getNumPixelClasses());
            }
        } else {
            // Make bogus box for compartmental geometries
            int COMPARTMENT_SIZE_X = 10;
            int COMPARTMENT_SIZE_Y = 10;
            int compartmentalXY = COMPARTMENT_SIZE_X * COMPARTMENT_SIZE_Y;
            byte[] compartmentalPixels = new byte[compartmentalXY];
            for (int c = 0; c < compartmentalXY; c += 1) {
                compartmentalPixels[c] = ((byte[]) (sampledImage.getPixels()))[0];
            }
            sampledGeometryHandles = new cbit.image.VCImageUncompressed(null, compartmentalPixels, new org.vcell.util.Extent(1, 1, 1), COMPARTMENT_SIZE_X, COMPARTMENT_SIZE_Y, 1);
        }
        MemoryImageSource mis = new MemoryImageSource(sampledGeometryHandles.getNumX(), sampledGeometryHandles.getNumY(), DisplayAdapterService.getHandleColorMap(), sampledGeometryHandles.getPixels(), 0, sampledGeometryHandles.getNumX());
        java.awt.Image sampledGeometryImage = java.awt.Toolkit.getDefaultToolkit().createImage(mis);
        return new javax.swing.ImageIcon(sampledGeometryImage, "preview of Geometry");
    }
}
Also used : Extent(org.vcell.util.Extent) VCImage(cbit.image.VCImage) MemoryImageSource(java.awt.image.MemoryImageSource)

Example 39 with VCImage

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

the class GeometryViewer method resample.

private void resample() {
    AsynchClientTask precomputeCurrentGeometryTask = new AsynchClientTask("computing surfaces for existing geometry", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            if (getGeometry().getGeometrySurfaceDescription().getRegionImage() == null) {
                getGeometry().precomputeAll(new GeometryThumbnailImageFactoryAWT(), true, true);
            }
        }
    };
    AsynchClientTask sampleSizeTask = new AsynchClientTask("specify sample size", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {

        public void run(Hashtable<String, Object> hashTable) throws Exception {
            VCImage currSampledImage = getGeometry().getGeometrySpec().getSampledImage().getCurrentValue();
            int currNumSamples = currSampledImage.getNumXYZ();
            ISize currSize = new ISize(currSampledImage.getNumX(), currSampledImage.getNumY(), currSampledImage.getNumZ());
            ISize sampleSize_times_ten = GeometrySpec.calulateResetSamplingSize(3, getGeometry().getExtent(), currNumSamples * 10);
            ISize sampleSize_div_ten = GeometrySpec.calulateResetSamplingSize(3, getGeometry().getExtent(), currNumSamples / 10);
            ISize sampleSize_1e2 = GeometrySpec.calulateResetSamplingSize(3, getGeometry().getExtent(), (int) 1e2);
            ISize sampleSize_1e3 = GeometrySpec.calulateResetSamplingSize(3, getGeometry().getExtent(), (int) 1e3);
            ISize sampleSize_1e4 = GeometrySpec.calulateResetSamplingSize(3, getGeometry().getExtent(), (int) 1e4);
            ISize sampleSize_1e5 = GeometrySpec.calulateResetSamplingSize(3, getGeometry().getExtent(), (int) 1e5);
            ISize sampleSize_1e6 = GeometrySpec.calulateResetSamplingSize(3, getGeometry().getExtent(), (int) 1e6);
            ISize sampleSize_1e7 = GeometrySpec.calulateResetSamplingSize(3, getGeometry().getExtent(), (int) 1e7);
            ISize sampleSize_1e8 = GeometrySpec.calulateResetSamplingSize(3, getGeometry().getExtent(), (int) 1e8);
            String[] columnNames = new String[] { "description", "num samples", "(X,Y,Z)" };
            Object[][] rowData = new Object[][] { new Object[] { "same size", new Integer(currSize.getXYZ()), currSize }, new Object[] { "10 times smaller", new Integer(sampleSize_div_ten.getXYZ()), sampleSize_div_ten }, new Object[] { "10 times bigger", new Integer(sampleSize_times_ten.getXYZ()), sampleSize_times_ten }, new Object[] { "        100 samples", new Integer(sampleSize_1e2.getXYZ()), sampleSize_1e2 }, new Object[] { "      1,000 samples", new Integer(sampleSize_1e3.getXYZ()), sampleSize_1e3 }, new Object[] { "     10,000 samples", new Integer(sampleSize_1e4.getXYZ()), sampleSize_1e4 }, new Object[] { "    100,000 samples", new Integer(sampleSize_1e5.getXYZ()), sampleSize_1e5 }, new Object[] { "  1,000,000 samples", new Integer(sampleSize_1e6.getXYZ()), sampleSize_1e6 }, new Object[] { " 10,000,000 samples", new Integer(sampleSize_1e7.getXYZ()), sampleSize_1e7 }, new Object[] { "100,000,000 samples", new Integer(sampleSize_1e8.getXYZ()), sampleSize_1e8 } };
            int[] selectedRows = DialogUtils.showComponentOKCancelTableList(GeometryViewer.this, "sample size", columnNames, rowData, ListSelectionModel.SINGLE_SELECTION);
            ISize sampleSize = (ISize) rowData[selectedRows[0]][2];
            hashTable.put("sampleSize", sampleSize);
        }
    };
    AsynchClientTask resampleTask = new AsynchClientTask("resample geometry", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            ISize sampleSize = (ISize) hashTable.get("sampleSize");
            Geometry newGeometry = RayCaster.resampleGeometry(new GeometryThumbnailImageFactoryAWT(), getGeometry(), sampleSize);
            hashTable.put("newGeometry", newGeometry);
        }
    };
    AsynchClientTask setGeometryTask = new AsynchClientTask("loading geometry", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            Geometry newGeometry = (Geometry) hashTable.get("newGeometry");
            if (getGeometryOwner() instanceof SimulationContext) {
                ((SimulationContext) getGeometryOwner()).setGeometry(newGeometry);
            } else if (getGeometryOwner() instanceof MathModel) {
                ((MathModel) getGeometryOwner()).getMathDescription().setGeometry(newGeometry);
            } else {
                throw new RuntimeException("unexpected geometry owner, could not set resampled geometry");
            }
        }
    };
    ClientTaskDispatcher.dispatch(this, new Hashtable<String, Object>(), new AsynchClientTask[] { precomputeCurrentGeometryTask, sampleSizeTask, resampleTask, setGeometryTask }, false);
}
Also used : AsynchClientTask(cbit.vcell.client.task.AsynchClientTask) MathModel(cbit.vcell.mathmodel.MathModel) Hashtable(java.util.Hashtable) ISize(org.vcell.util.ISize) VCImage(cbit.image.VCImage) SimulationContext(cbit.vcell.mapping.SimulationContext) Geometry(cbit.vcell.geometry.Geometry) GeometryThumbnailImageFactoryAWT(cbit.vcell.geometry.GeometryThumbnailImageFactoryAWT)

Example 40 with VCImage

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

the class ImageAttributePanel method setImage.

/**
 * Comment
 */
public void setImage(VCImage vcImage) throws Exception {
    pixelWR = null;
    smallPixelWR = null;
    xSide = 1;
    ySide = 1;
    displayScale = 1.0;
    vcPixelClassArr = null;
    // 
    cbit.image.VCImage oldValue = fieldImage;
    fieldImage = vcImage;
    // 
    if (vcImage != null) {
        getImportJButton().setEnabled(true);
        getPixelSizeXJLabel().setText((getImage() != null ? getImage().getNumX() + "" : null));
        getPixelSizeYJLabel().setText((getImage() != null ? getImage().getNumY() + "" : null));
        getPixelSizeZJLabel().setText((getImage() != null ? getImage().getNumZ() + "" : null));
        getXMicronJTextField().setText((getImage() != null ? getImage().getExtent().getX() + "" : null));
        String yExtent = (getImage() != null ? (getImage().getNumY() > 1 ? getImage().getExtent().getY() + "" : "1.0") : null);
        getYMicronJTextField().setText(yExtent);
        String zExtent = (getImage() != null ? (getImage().getNumZ() > 1 ? getImage().getExtent().getZ() + "" : "1.0") : null);
        getZMicronJTextField().setText(zExtent);
        getYMicronJTextField().setEnabled(vcImage.getNumY() > 1);
        getZMicronJTextField().setEnabled(vcImage.getNumZ() > 1);
        getYPerPixelTextField().setEnabled(vcImage.getNumY() > 1);
        getZPerPixelJextField().setEnabled(vcImage.getNumZ() > 1);
        getAnnotationJTextArea().setText((getImage() != null ? getImage().getDescription() : null));
        if (getImage() != null) {
            cbit.image.VCPixelClass[] orig = getImage().getPixelClasses();
            cbit.image.VCPixelClass[] temp = new cbit.image.VCPixelClass[orig.length];
            for (int i = 0; i < orig.length; i += 1) {
                temp[i] = new cbit.image.VCPixelClass(orig[i].getKey(), orig[i].getPixelClassName(), orig[i].getPixel());
            }
            vcPixelClassArr = temp;
        } else {
            vcPixelClassArr = null;
        }
        final int INIT_REGION = 0;
        setCurrentPixelClassIndex((getImage() != null ? new Integer(INIT_REGION) : null));
        getRegionNameJTextField().setText((getCurrentPixelClassIndex() != null && vcPixelClassArr != null ? vcPixelClassArr[INIT_REGION].getPixelClassName() : null));
        updateRegionCountLabel(INIT_REGION);
        getFullSizeJCheckBox().setSelected(false);
        createRegionImageIcon();
    }
    firePropertyChange("image", oldValue, vcImage);
}
Also used : VCPixelClass(cbit.image.VCPixelClass) VCPixelClass(cbit.image.VCPixelClass) VCImage(cbit.image.VCImage)

Aggregations

VCImage (cbit.image.VCImage)54 Geometry (cbit.vcell.geometry.Geometry)22 Extent (org.vcell.util.Extent)20 ISize (org.vcell.util.ISize)19 VCImageUncompressed (cbit.image.VCImageUncompressed)18 ImageException (cbit.image.ImageException)16 PropertyVetoException (java.beans.PropertyVetoException)15 DataAccessException (org.vcell.util.DataAccessException)15 KeyValue (org.vcell.util.document.KeyValue)15 SubVolume (cbit.vcell.geometry.SubVolume)14 Origin (org.vcell.util.Origin)13 RegionImage (cbit.vcell.geometry.RegionImage)11 SurfaceClass (cbit.vcell.geometry.SurfaceClass)11 ObjectNotFoundException (org.vcell.util.ObjectNotFoundException)11 UserCancelException (org.vcell.util.UserCancelException)11 ImageSubVolume (cbit.vcell.geometry.ImageSubVolume)10 Expression (cbit.vcell.parser.Expression)10 VCPixelClass (cbit.image.VCPixelClass)9 BioModel (cbit.vcell.biomodel.BioModel)8 FieldDataFileOperationSpec (cbit.vcell.field.io.FieldDataFileOperationSpec)8