Examples with ImageDataset cbit.vcell.VirtualMicroscopy.ImageDataset used on opensource projects

Example 21 with ImageDataset

use of cbit.vcell.VirtualMicroscopy.ImageDataset in project vcell by virtualcell.

the class DataSymbolsPanel method addVFrapDerivedImages.

private void addVFrapDerivedImages() {
    // add special (computed) images from vFrap
    AsynchClientTask[] taskArray = new AsynchClientTask[5];
    // select the desired vfrap file
    taskArray[0] = ChooseVFrapFile();
    // load the images from the vfrap file, compute derived images, store them all in memory
    taskArray[1] = new AsynchClientTask("Import images", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

        public void run(Hashtable<String, Object> hashTable) throws Exception {
            File vFrapFile = (File) hashTable.get("vFrapFile");
            Component requesterComponent = DataSymbolsPanel.this;
            DocumentWindow documentWindow = (DocumentWindow) BeanUtils.findTypeParentOfComponent(requesterComponent, DocumentWindow.class);
            DocumentManager documentManager = documentWindow.getTopLevelWindowManager().getRequestManager().getDocumentManager();
            if (documentManager == null) {
                throw new RuntimeException("Not connected to server.");
            }
            // ex  ccc8.vfrap
            String vFrapFileNameExtended = vFrapFile.getName();
            {
                // we want to make sure to reload these strings from the hash later on
                String initialFieldDataName = vFrapFileNameExtended.substring(0, vFrapFileNameExtended.indexOf(".vfrap"));
                // we'll save here the "special" vFrap images (prebleach_avg, ...)
                String mixedFieldDataName = initialFieldDataName + "Mx";
                hashTable.put("initialFieldDataName", initialFieldDataName);
                hashTable.put("mixedFieldDataName", mixedFieldDataName);
            }
            if (vFrapFileNameExtended.indexOf(".vfrap") <= -1) {
                throw new RuntimeException("File extension must be .vfrap");
            }
            // for derived images and ROIs
            checkNameAvailability(hashTable, true, documentManager, requesterComponent);
            // ----- read needed info from Virtual FRAP xml file
            System.out.println("Loading " + vFrapFileNameExtended + " ...");
            String xmlString = XmlUtil.getXMLString(vFrapFile.getAbsolutePath());
            MicroscopyXmlReader xmlReader = new MicroscopyXmlReader(true);
            Element vFrapRoot = XmlUtil.stringToXML(xmlString, null).getRootElement();
            // loading frap images and a ROIs subset for display purposes only (see next task)
            AnnotatedImageDataset annotatedImages = xmlReader.getAnnotatedImageDataset(vFrapRoot, null);
            hashTable.put("annotatedImages", annotatedImages);
            ROI[] rois = xmlReader.getPrimaryROIs(XmlUtil.stringToXML(xmlString, null).getRootElement(), null);
            LoadVFrapDisplayRoi(hashTable, annotatedImages, rois);
            // ------ locate the special images within the vFrap files and load them in memory
            if (!LoadVFrapSpecialImages(hashTable, vFrapRoot)) {
                throw new RuntimeException("Unable to recover derived images from vFrap.");
            }
        // int startingIndexRecovery = xmlReader.getStartindIndexForRecovery(XmlUtil.stringToXML(xmlString, null).getRootElement());
        // vFrapXmlHelper.LoadVFrapSpecialImages(annotatedImages, startingIndexRecovery);	// prebleach average and first postbleach
        // vFrapXmlHelper.LoadVFrapRoiCompositeImages(annotatedImages, rois);
        }
    };
    // show the images from the vfrap file in an OverlayEditorPanelJAI dialog
    taskArray[2] = new AsynchClientTask("Display images", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {

        public void run(Hashtable<String, Object> hashTable) throws Exception {
            String mixedFieldDataName = (String) hashTable.get("mixedFieldDataName");
            if (mixedFieldDataName.equals("")) {
                JOptionPane.showMessageDialog(DataSymbolsPanel.this, "Field Data name " + mixedFieldDataName + " already in use.");
                // prevents the rest of tasks below from running
                throw UserCancelException.CANCEL_GENERIC;
            }
            AnnotatedImageDataset annotatedImages = (AnnotatedImageDataset) hashTable.get("annotatedImages");
            BufferedImage[] displayROI = (BufferedImage[]) hashTable.get("displayROI");
            if (annotatedImages == null || displayROI == null) {
                return;
            }
            // display the images
            OverlayEditorPanelJAI overlayPanel = new OverlayEditorPanelJAI();
            overlayPanel.setAllowAddROI(false);
            ImageDataset imageDataset = annotatedImages.getImageDataset();
            overlayPanel.setImages(imageDataset, 1, 0, new OverlayEditorPanelJAI.AllPixelValuesRange(1, 200));
            overlayPanel.setAllROICompositeImage(displayROI, OverlayEditorPanelJAI.FRAP_DATA_INIT_PROPERTY);
            int choice = DialogUtils.showComponentOKCancelDialog(DataSymbolsPanel.this, overlayPanel, "vFrap Field Data");
            if (choice != JOptionPane.OK_OPTION) {
                throw UserCancelException.CANCEL_GENERIC;
            }
        }
    };
    // save the ROIs, prebleach average and the first postbleach frame from memory to the database as field data
    taskArray[3] = new AsynchClientTask("Saving roi masks, pre-bleach average and first post-bleach", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

        public void run(Hashtable<String, Object> hashTable) throws Exception {
            Component requesterComponent = DataSymbolsPanel.this;
            DocumentWindow documentWindow = (DocumentWindow) BeanUtils.findTypeParentOfComponent(requesterComponent, DocumentWindow.class);
            DocumentManager documentManager = documentWindow.getTopLevelWindowManager().getRequestManager().getDocumentManager();
            if (documentManager == null) {
                throw new RuntimeException("Not connected to server.");
            }
            ExternalDataIdentifier derivedEDI = SaveVFrapSpecialImagesAsFieldData(hashTable, documentManager);
            hashTable.put("derivedEDI", derivedEDI);
        }
    };
    // create the data symbols for the images saved above and display them in the tree/table
    taskArray[4] = new AsynchClientTask("Display Data Symbols", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {

        public void run(Hashtable<String, Object> hashTable) throws Exception {
            ExternalDataIdentifier derivedEDI = (ExternalDataIdentifier) hashTable.get("derivedEDI");
            BioModel bioModel = simulationContext.getBioModel();
            CreateSaveVFrapDataSymbols(hashTable, bioModel, derivedEDI);
        }
    };
    // save the ROIs, prebleach average and the first postbleach frame from memory to the database as field data
    // taskArray[4] = new AsynchClientTask("Saving roi masks, pre-bleach average and first post-bleach", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {
    // public void run(Hashtable<String, Object> hashTable) throws Exception {
    // File vFrapFile = (File)hashTable.get("vFrapFile");
    // if(vFrapFile == null) {
    // return;
    // }
    // AnnotatedImageDataset annotatedImages = (AnnotatedImageDataset)hashTable.get("annotatedImages");
    // String initialFieldDataName = (String)hashTable.get("initialFieldDataName");
    // 
    // DocumentWindow documentWindow = (DocumentWindow)BeanUtils.findTypeParentOfComponent(DataSymbolsPanel.this, DocumentWindow.class);
    // DocumentManager dm = documentWindow.getTopLevelWindowManager().getRequestManager().getDocumentManager();
    // if(dm == null){
    // throw new RuntimeException("not connected to server");
    // }
    // 
    // // mesh
    // ImageDataset imageDataset = annotatedImages.getImageDataset();
    // Extent extent = imageDataset.getExtent();
    // ISize isize = imageDataset.getISize();
    // Origin origin = new Origin(0,0,0);
    // CartesianMesh cartesianMesh = CartesianMesh.createSimpleCartesianMesh(origin, extent,isize,
    // new RegionImage( new VCImageUncompressed(null, new byte[isize.getXYZ()], extent,
    // isize.getX(),isize.getY(),isize.getZ()),0,null,null,RegionImage.NO_SMOOTHING));
    // double[] firstPostBleach = (double[])hashTable.get("firstPostBleach");
    // double[] prebleachAvg = (double[])hashTable.get("prebleachAverage");
    // ROI[] rois = (ROI[])hashTable.get("rois");
    // 
    // int NumTimePoints = 1;
    // int NumChannels = 2+rois.length;  // prebleach, postbleach, roi1, roi2 ... roiN
    // String[] channelNames = new String[NumChannels];
    // VariableType[] channelTypes = new VariableType[NumChannels];
    // DataSymbolType[] channelVFrapImageType = new DataSymbolType[NumChannels];
    // double[][][] pixData = new double[NumTimePoints][NumChannels][];
    // pixData[0][0] = firstPostBleach;
    // channelNames[0] = "firstPostBleach";
    // channelTypes[0] = VariableType.VOLUME;
    // channelVFrapImageType[0] = DataSymbolType.VFRAP_FIRST_POSTBLEACH;
    // pixData[0][1] = prebleachAvg;
    // channelNames[1] = "prebleachAverage";
    // channelTypes[1] = VariableType.VOLUME;
    // channelVFrapImageType[1] = DataSymbolType.VFRAP_PREBLEACH_AVG;
    // int index = 0;
    // for (ROI roi : rois){
    // short[] ushortPixels = roi.getPixelsXYZ();
    // double[] doublePixels = new double[ushortPixels.length];
    // for (int i = 0; i < ushortPixels.length; i++) {
    // doublePixels[i] = ((int)ushortPixels[i])&0xffff;
    // }
    // pixData[0][index+2] = doublePixels;
    // channelNames[index+2] = "roi_"+index;
    // channelTypes[index+2] = VariableType.VOLUME;
    // channelVFrapImageType[index+2] = DataSymbolType.VFRAP_ROI;
    // index++;
    // }
    // double[] times = new double[] { 0.0 };
    // 
    // FieldDataFileOperationSpec vfrapMiscFieldDataOpSpec = new FieldDataFileOperationSpec();
    // vfrapMiscFieldDataOpSpec.opType = FieldDataFileOperationSpec.FDOS_ADD;
    // vfrapMiscFieldDataOpSpec.cartesianMesh = cartesianMesh;
    // vfrapMiscFieldDataOpSpec.doubleSpecData =  pixData;
    // vfrapMiscFieldDataOpSpec.specEDI = null;
    // vfrapMiscFieldDataOpSpec.varNames = channelNames;
    // vfrapMiscFieldDataOpSpec.owner = dm.getUser();
    // vfrapMiscFieldDataOpSpec.times = times;
    // vfrapMiscFieldDataOpSpec.variableTypes = channelTypes;
    // vfrapMiscFieldDataOpSpec.origin = origin;
    // vfrapMiscFieldDataOpSpec.extent = extent;
    // vfrapMiscFieldDataOpSpec.isize = isize;
    // //  localWorkspace.getDataSetControllerImpl().fieldDataFileOperation(fdos);
    // 
    // //			String formattedDate = (String)hashTable.get("formattedDate");
    // //			String fieldDataName = initialFieldDataName + "_vfrapMisc_" + formattedDate;
    // String mixedFieldDataName = (String)hashTable.get("mixedFieldDataName");
    // ExternalDataIdentifier vfrapMisc = dm.saveFieldData(vfrapMiscFieldDataOpSpec, mixedFieldDataName);
    // 
    // hashTable.put("channelNames", channelNames);
    // hashTable.put("channelVFrapImageType", channelVFrapImageType);
    // hashTable.put("vfrapMisc", vfrapMisc);
    // }
    // };
    // create the data symbols for the images saved above and display them in the tree/table
    // taskArray[5] = new AsynchClientTask("Display Data Symbols", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {
    // public void run(Hashtable<String, Object> hashTable) throws Exception {
    // 
    // // --- create the data symbols associated with the time series
    // String initialFieldDataName = (String)hashTable.get("initialFieldDataName");
    // String mixedFieldDataName = (String)hashTable.get("mixedFieldDataName");
    // String formattedDate = (String)hashTable.get("formattedDate");
    // ImageDataset imageDataset = (ImageDataset)hashTable.get("imageDataset");
    // ExternalDataIdentifier timeSeriesEDI = (ExternalDataIdentifier)hashTable.get("timeSeriesEDI");
    // 
    // for (double time : imageDataset.getImageTimeStamps()){
    // //	   			String fluorName = TokenMangler.fixTokenStrict("fluor_"+time+"_");
    // //				while (simulationContext.getDataContext().getDataSymbol(fluorName)!=null){
    // //					fluorName = TokenMangler.getNextEnumeratedToken(fluorName);
    // //	   			}
    // DecimalFormat df = new  DecimalFormat("0.##");
    // //	   			String fluorName = "fluor_" + df.format(time) + "_" + formattedDate;
    // String fluorName = "fluor_" + df.format(time) + "_" + initialFieldDataName;
    // //				FieldFunctionArguments fluorFFArgs = new FieldFunctionArguments(timeSeriesEDI.getName(), fluorName, new Expression(time), VariableType.VOLUME);
    // DataSymbol fluorDataSymbol = new FieldDataSymbol( fluorName, DataSymbolType.VFRAP_TIMEPOINT,
    // simulationContext.getDataContext(), VCUnitDefinition.UNIT_TBD,
    // timeSeriesEDI, fluorName, VariableType.VOLUME.getTypeName(), time);
    // simulationContext.getDataContext().addDataSymbol(fluorDataSymbol);
    // }
    // // --- create the vFrap-specific symbols (ROIs, first postbleach, prebleach average)
    // String[] channelNames = (String[])hashTable.get("channelNames");
    // DataSymbolType[] channelVFrapImageType = (DataSymbolType[])hashTable.get("channelVFrapImageType");
    // ExternalDataIdentifier vfrapMisc = (ExternalDataIdentifier)hashTable.get("vfrapMisc");
    // 
    // for (int i=0; i<channelNames.length; i++) {
    // String dataSymbolID = channelNames[i] + "_" + mixedFieldDataName;
    // //				while (simulationContext.getDataContext().getDataSymbol(dataSymbolID)!=null){
    // //					dataSymbolID = TokenMangler.getNextEnumeratedToken(dataSymbolID);
    // //				}
    // //				FieldFunctionArguments prebleachFFArgs = new FieldFunctionArguments(vfrapMisc.getName(), channelNames[i], new Expression(0.0), VariableType.VOLUME);
    // //				DataSymbol dataSymbol = new FieldDataSymbol(channelNames[i], channelVFrapImageType[i],
    // //				DataSymbol dataSymbol = new FieldDataSymbol(dataSymbolID + "_" + formattedDate, channelVFrapImageType[i],
    // DataSymbol dataSymbol = new FieldDataSymbol(dataSymbolID, channelVFrapImageType[i],
    // simulationContext.getDataContext(), VCUnitDefinition.UNIT_TBD,
    // vfrapMisc, channelNames[i], VariableType.VOLUME.getTypeName(), 0D);
    // simulationContext.getDataContext().addDataSymbol(dataSymbol);
    // }
    // }
    // };
    Hashtable<String, Object> hash = new Hashtable<String, Object>();
    ClientTaskDispatcher.dispatch(this, hash, taskArray, false, true, null);
}

Example 22 with ImageDataset

use of cbit.vcell.VirtualMicroscopy.ImageDataset in project vcell by virtualcell.

the class VFrap_OverlayEditorPanelJAI method getImportROIMaskButton.

public JButton getImportROIMaskButton() {
    if (importROIMaskButton == null) {
        importROIMaskButton = new JButton(new ImageIcon(getClass().getResource("/images/importROI.gif")));
        importROIMaskButton.setPreferredSize(new Dimension(32, 32));
        importROIMaskButton.setMargin(new Insets(2, 2, 2, 2));
        importROIMaskButton.setToolTipText("Import ROI mask from file");
        importROIMaskButton.addActionListener(new ActionListener() {

            public void actionPerformed(final ActionEvent e) {
                File inputFile = null;
                try {
                    int option = openJFileChooser.showOpenDialog(VFrap_OverlayEditorPanelJAI.this);
                    if (option == JFileChooser.APPROVE_OPTION) {
                        inputFile = openJFileChooser.getSelectedFile();
                    } else {
                        throw UserCancelException.CANCEL_GENERIC;
                    }
                    if (!customROIImport.importROI(inputFile)) {
                        ImageDataset importImageDataset = ImageDatasetReaderService.getInstance().getImageDatasetReader().readImageDataset(inputFile.getAbsolutePath(), null);
                        if (importImageDataset.getISize().getX() * importImageDataset.getISize().getY() != getImagePane().getHighlightImage().getWidth() * getImagePane().getHighlightImage().getHeight()) {
                            throw new Exception("Imported ROI mask size (" + importImageDataset.getISize().getX() + "," + importImageDataset.getISize().getY() + ")" + " does not match current Frap DataSet size (" + getImagePane().getHighlightImage().getWidth() + "," + getImagePane().getHighlightImage().getHeight() + ")");
                        }
                        // BufferedImage roiMaskImage = BufferedImageReader.makeBufferedImageReader(iFormatReader).openImage(0);
                        UShortImage roiMaskImage = importImageDataset.getImage(0, 0, 0);
                        int maskColor = highlightColor.getRGB();
                        for (int y = 0; y < importImageDataset.getISize().getY(); y++) {
                            for (int x = 0; x < importImageDataset.getISize().getX(); x++) {
                                if ((roiMaskImage.getPixel(x, y, 0) & 0xFFFF) != 0) {
                                    getImagePane().getHighlightImage().setRGB(x, y, maskColor);
                                }
                            }
                        }
                        getImagePane().refreshImage();
                    }
                } catch (UserCancelException uce) {
                // Do Nothing
                } catch (Exception e1) {
                    e1.printStackTrace();
                    DialogUtils.showErrorDialog(VFrap_OverlayEditorPanelJAI.this, "Error importing ROI" + e1.getMessage());
                }
            }
        });
    }
    return importROIMaskButton;
}

Example 23 with ImageDataset

use of cbit.vcell.VirtualMicroscopy.ImageDataset 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 24 with ImageDataset

use of cbit.vcell.VirtualMicroscopy.ImageDataset in project vcell by virtualcell.

the class BioformatsImageDatasetReader method readImageDatasetFromMultiFiles.

@Override
public ImageDataset readImageDatasetFromMultiFiles(File[] files, ClientTaskStatusSupport status, boolean isTimeSeries, double timeInterval) throws Exception {
    try (TTransport transport = new TSocket("localhost", port)) {
        transport.open();
        TProtocol protocol = new TBinaryProtocol(transport);
        ImageDatasetService.Client client = new ImageDatasetService.Client(protocol);
        ArrayList<String> fileList = new ArrayList<String>();
        for (File f : files) {
            fileList.add(f.getAbsolutePath());
        }
        org.vcell.imagedataset.ImageDataset t_imageDataset = client.readImageDatasetFromMultiFiles(fileList, isTimeSeries, timeInterval);
        ImageDataset imageDataset = getImageDataset(t_imageDataset);
        return imageDataset;
    }
}

Example 25 with ImageDataset

use of cbit.vcell.VirtualMicroscopy.ImageDataset in project vcell by virtualcell.

the class ClientRequestManager method createFDOSFromImageFile.

// public void prepareDocumentToLoad(VCDocument doc) throws Exception {
// Simulation[] simulations = null;
// if (doc instanceof MathModel) {
// Geometry geometry = ((MathModel)doc).getMathDescription().getGeometry();
// geometry.precomputeAll();
// simulations = ((MathModel)doc).getSimulations();
// } else if (doc instanceof Geometry) {
// ((Geometry)doc).precomputeAll();
// } else if (doc instanceof BioModel) {
// BioModel bioModel = (BioModel)doc;
// SimulationContext[] simContexts = bioModel.getSimulationContexts();
// for (SimulationContext simContext : simContexts) {
// simContext.getGeometry().precomputeAll();
// }
// simulations = ((BioModel)doc).getSimulations();
// }
// if (simulations != null) {
// // preload simulation status
// VCSimulationIdentifier simIDs[] = new VCSimulationIdentifier[simulations.length];
// for (int i = 0; i < simulations.length; i++){
// simIDs[i] = simulations[i].getSimulationInfo().getAuthoritativeVCSimulationIdentifier();
// }
// getDocumentManager().preloadSimulationStatus(simIDs);
// }
// }
public static FieldDataFileOperationSpec createFDOSFromImageFile(File imageFile, boolean bCropOutBlack, Integer saveOnlyThisTimePointIndex) throws DataFormatException, ImageException {
    try {
        ImageDatasetReader imageDatasetReader = ImageDatasetReaderService.getInstance().getImageDatasetReader();
        ImageDataset[] imagedataSets = imageDatasetReader.readImageDatasetChannels(imageFile.getAbsolutePath(), null, false, saveOnlyThisTimePointIndex, null);
        if (imagedataSets != null && bCropOutBlack) {
            for (int i = 0; i < imagedataSets.length; i++) {
                Rectangle nonZeroRect = imagedataSets[i].getNonzeroBoundingRectangle();
                if (nonZeroRect != null) {
                    imagedataSets[i] = imagedataSets[i].crop(nonZeroRect);
                }
            }
        }
        return createFDOSWithChannels(imagedataSets, null);
    } catch (Exception e) {
        e.printStackTrace(System.out);
        throw new DataFormatException(e.getMessage());
    }
}