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

Example 16 with VCImageUncompressed

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

the class DataSymbolsPanel method addVFrapOriginalImages.

private void addVFrapOriginalImages() {
    // add dataset (normal images) from vFrap
    AsynchClientTask[] taskArray = new AsynchClientTask[5];
    // select the desired vfrap file
    taskArray[0] = ChooseVFrapFile();
    taskArray[1] = new AsynchClientTask("Import objects", 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");
            }
            // normal images
            checkNameAvailability(hashTable, false, 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
            AnnotatedImageDataset annotatedImages = xmlReader.getAnnotatedImageDataset(vFrapRoot, null);
            hashTable.put("annotatedImages", annotatedImages);
            // loading ROIs for display purposes only (see next task)
            ROI[] rois = xmlReader.getPrimaryROIs(XmlUtil.stringToXML(xmlString, null).getRootElement(), null);
            LoadVFrapDisplayRoi(hashTable, annotatedImages, rois);
        // Calendar cal = Calendar.getInstance();
        // SimpleDateFormat sdf = new SimpleDateFormat("yyyyMMdd_hhmmss");
        // DocumentWindow documentWindow = (DocumentWindow)BeanUtils.findTypeParentOfComponent(DataSymbolsPanel.this, DocumentWindow.class);
        // DocumentManager documentManager = documentWindow.getTopLevelWindowManager().getRequestManager().getDocumentManager();
        // VFrapXmlHelper vFrapXmlHelper = new VFrapXmlHelper();
        // if(vFrapXmlHelper.isAlreadyImported(vFrapFileName, documentManager)) {
        // throw new RuntimeException("FieldData name already in use.");
        // }
        // //				bioModel.setName(vFrapFileName + "-" + sdf.format(cal.getTime()));
        // bioModel.setName(vFrapFileName);
        // BioModel feedbackModel =  documentManager.save(bioModel, null);
        // BioModelChildSummary  childSummary = BioModelChildSummary.fromDatabaseSerialization(xmlString);
        // BioModelInfo biomodelInfo = new BioModelInfo(feedbackModel.getVersion(), feedbackModel.getVersion().getVersionKey(), childSummary );
        // documentWindow.getTopLevelWindowManager().getRequestManager().openDocument(biomodelInfo, documentWindow.getTopLevelWindowManager(), true);
        }
    };
    // 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 initialFieldDataName = (String) hashTable.get("initialFieldDataName");
            if (initialFieldDataName.equals("")) {
                JOptionPane.showMessageDialog(DataSymbolsPanel.this, "Field Data name " + initialFieldDataName + " 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 timepoints from memory to the database as field data
    taskArray[3] = new AsynchClientTask("Saving time series data", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

        public void run(Hashtable<String, Object> hashTable) throws Exception {
            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.");
            }
            User owner = null;
            Version version = simulationContext.getVersion();
            if (version == null) {
                // new document, so the owner is the user
                owner = dm.getUser();
            } else {
                owner = simulationContext.getVersion().getOwner();
            }
            // 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));
            // save field data
            int NumTimePoints = imageDataset.getImageTimeStamps().length;
            int NumChannels = 1;
            double[][][] pixData = new double[NumTimePoints][NumChannels][];
            for (int i = 0; i < NumTimePoints; i++) {
                // images according to zIndex at specific time points(tIndex)
                short[] originalData = imageDataset.getPixelsZ(0, i);
                double[] doubleData = new double[originalData.length];
                for (int j = 0; j < originalData.length; j++) {
                    doubleData[j] = 0x0000ffff & originalData[j];
                }
                pixData[i][NumChannels - 1] = doubleData;
            }
            FieldDataFileOperationSpec timeSeriesFieldDataOpSpec = new FieldDataFileOperationSpec();
            timeSeriesFieldDataOpSpec.opType = FieldDataFileOperationSpec.FDOS_ADD;
            timeSeriesFieldDataOpSpec.cartesianMesh = cartesianMesh;
            timeSeriesFieldDataOpSpec.doubleSpecData = pixData;
            timeSeriesFieldDataOpSpec.specEDI = null;
            timeSeriesFieldDataOpSpec.varNames = new String[] { SimulationContext.FLUOR_DATA_NAME };
            timeSeriesFieldDataOpSpec.owner = owner;
            timeSeriesFieldDataOpSpec.times = imageDataset.getImageTimeStamps();
            timeSeriesFieldDataOpSpec.variableTypes = new VariableType[] { VariableType.VOLUME };
            timeSeriesFieldDataOpSpec.origin = origin;
            timeSeriesFieldDataOpSpec.extent = extent;
            timeSeriesFieldDataOpSpec.isize = isize;
            // realignment for the case when first timepoint is not zero
            if (timeSeriesFieldDataOpSpec.times[0] != 0) {
                double shift = timeSeriesFieldDataOpSpec.times[0];
                for (int i = 0; i < NumTimePoints; i++) {
                    timeSeriesFieldDataOpSpec.times[i] -= shift;
                }
            }
            Calendar cal = Calendar.getInstance();
            SimpleDateFormat sdf = new SimpleDateFormat("yyMMMdd_hhmmss");
            String formattedDate = sdf.format(cal.getTime());
            hashTable.put("formattedDate", formattedDate);
            // ExternalDataIdentifier timeSeriesEDI = dm.saveFieldData(timeSeriesFieldDataOpSpec,
            // initialFieldDataName + "_" + formattedDate);
            ExternalDataIdentifier timeSeriesEDI = dm.saveFieldData(timeSeriesFieldDataOpSpec, initialFieldDataName);
            hashTable.put("imageDataset", imageDataset);
            hashTable.put("timeSeriesEDI", timeSeriesEDI);
        }
    };
    // 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 {
            // --- create the data symbols associated with the time series
            String initialFieldDataName = (String) hashTable.get("initialFieldDataName");
            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);
                // }
                // max time interval we can display is about 11 days
                DecimalFormat df = new DecimalFormat("###000.00");
                // String fluorName = "fluor_" + df.format(time) + "_" + formattedDate;
                String fluorName = "fluor_" + df.format(time).substring(0, df.format(time).indexOf(".")) + "s" + df.format(time).substring(1 + df.format(time).indexOf(".")) + "_" + initialFieldDataName;
                // FieldFunctionArguments fluorFFArgs = new FieldFunctionArguments(timeSeriesEDI.getName(), fluorName, new Expression(time), VariableType.VOLUME);
                DataSymbol fluorDataSymbol = new FieldDataSymbol(fluorName, DataSymbolType.VFRAP_TIMEPOINT, simulationContext.getDataContext(), simulationContext.getModel().getUnitSystem().getInstance_TBD(), timeSeriesEDI, SimulationContext.FLUOR_DATA_NAME, VariableType.VOLUME.getTypeName(), time);
                simulationContext.getDataContext().addDataSymbol(fluorDataSymbol);
            }
        }
    };
    Hashtable<String, Object> hash = new Hashtable<String, Object>();
    ClientTaskDispatcher.dispatch(this, hash, taskArray, false, true, null);
// String name = null;
// try {
// getNewDataSymbolPanel().setSymbolName("");
// getNewDataSymbolPanel().setSymbolExpression("vcField(dataset1,var1,0.0,Volume)");
// int newSettings = org.vcell.util.gui.DialogUtils.showComponentOKCancelDialog(this, getNewDataSymbolPanel(), "New DataSymbol");
// if (newSettings == JOptionPane.OK_OPTION) {
// name = getNewDataSymbolPanel().getSymbolName();
// String expression = getNewDataSymbolPanel().getSymbolExpression();
// Expression exp = new Expression(expression);
// FunctionInvocation[] functionInvocations = exp.getFunctionInvocations(null);
// //			DataSymbol ds = new FieldDataSymbol(DataSymbolType.GENERIC_SYMBOL, name, "",
// //					simulationContext.getDataContext(), VCUnitDefinition.UNIT_TBD,
// //					new FieldFunctionArguments(functionInvocations[0]));
// DataSymbol ds = new FieldDataSymbol(name, DataSymbolType.GENERIC_SYMBOL,
// simulationContext.getDataContext(), VCUnitDefinition.UNIT_TBD);
// simulationContext.getDataContext().addDataSymbol(ds);
// }
// } catch (java.lang.Throwable ivjExc) {
// DialogUtils.showErrorDialog(this, "Data symbol " + name + " already exists");
// }
}

Example 17 with VCImageUncompressed

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

the class GeomDbDriver method insertBrowseImageDataSQL.

/**
 * This method was created in VisualAge.
 * @param vcimage cbit.image.VCImage
 * @param userid java.lang.String
 * @exception java.rmi.RemoteException The exception description.
 */
private void insertBrowseImageDataSQL(Connection con, KeyValue key, KeyValue imageKey, VCImage image) throws SQLException, DataAccessException, ImageException, GifParsingException {
    String sql;
    sql = "INSERT INTO " + browseImageDataTable.getTableName() + " " + browseImageDataTable.getSQLColumnList() + " VALUES " + browseImageDataTable.getSQLValueList(key, imageKey, dbSyntax);
    // System.out.println(sql);
    byte[] gifEncodedImage = null;
    try {
        if (image != null) {
            if (image.getNumZ() > 1) {
                byte[] sliceBytes = new byte[image.getNumX() * image.getNumY()];
                System.arraycopy(image.getPixels(), 0, sliceBytes, 0, sliceBytes.length);
                gifEncodedImage = BrowseImage.makeBrowseGIFImage(new VCImageUncompressed(null, sliceBytes, new Extent(1, 1, 1), image.getNumX(), image.getNumY(), 1)).getGifEncodedData();
            } else {
                gifEncodedImage = BrowseImage.makeBrowseGIFImage(image).getGifEncodedData();
            }
        }
    } catch (Exception e) {
        e.printStackTrace();
    }
    if (gifEncodedImage == null) {
        gifEncodedImage = BrowseImage.makeBrowseGIFImage(new VCImageUncompressed(null, new byte[BrowseImage.BROWSE_XSIZE * BrowseImage.BROWSE_YSIZE], new Extent(1, 1, 1), BrowseImage.BROWSE_XSIZE, BrowseImage.BROWSE_YSIZE, 1)).getGifEncodedData();
    }
    switch(dbSyntax) {
        case ORACLE:
            {
                updateCleanSQL(con, sql);
                updateCleanLOB(con, browseImageDataTable.id.toString(), key, browseImageDataTable.tableName, browseImageDataTable.data, gifEncodedImage, dbSyntax);
                break;
            }
        case POSTGRES:
            {
                updatePreparedCleanSQL(con, sql, gifEncodedImage);
                break;
            }
        default:
            {
                throw new RuntimeException("unexpected DatabaseSyntax " + dbSyntax);
            }
    }
}

Example 18 with VCImageUncompressed

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

the class ROIMultiPaintManager method checkBorders.

private VCImage checkBorders(VCImage checkThisVCImage) throws Exception {
    boolean bAddBorder = false;
    BorderInfo borderInfo = checkBorderInfo(checkThisVCImage);
    if (borderInfo.bXYTouch || borderInfo.bZTouch) {
        boolean b3DTouch = borderInfo.bXYTouch && borderInfo.bZTouch;
        String edgeDescrFrag = "on the " + (b3DTouch ? "XY and Z" : (borderInfo.bXYTouch ? "XY" : "Z")) + " border.";
        final String addBorder = "Add empty border";
        final String keep = "Keep as is";
        final String cancel = "Cancel";
        String result = DialogUtils.showWarningDialog(overlayEditorPanelJAI, "One or more Domain Regions touches the outer boundary " + edgeDescrFrag + "\n" + "Choose an option:\n" + "1. Keep as is, do not change.\n" + "2. Add empty 'background' border around outer boundary so no Domain Region touches an outer edge.", new String[] { keep, addBorder, cancel }, keep);
        if (result.equals(cancel)) {
            throw UserCancelException.CANCEL_GENERIC;
        } else if (result.equals(addBorder)) {
            bAddBorder = true;
            ;
        }
    }
    if (!bAddBorder) {
        return null;
    }
    ISize checkThisVCImageISize = new ISize(checkThisVCImage.getNumX(), checkThisVCImage.getNumY(), checkThisVCImage.getNumZ());
    boolean bxy = borderInfo.bXYTouch;
    boolean bz = borderInfo.bZTouch;
    ROIMultiPaintManager.PaddedInfo paddedInfo = copyToPadded(checkThisVCImage.getPixels(), checkThisVCImageISize, null, checkThisVCImage.getExtent(), new ISize((bxy ? 1 : 0), (bxy ? 1 : 0), (bz ? 1 : 0)), new ISize((bxy ? 1 : 0), (bxy ? 1 : 0), (bz ? 1 : 0)));
    VCImage newVCImage = new VCImageUncompressed(null, (byte[]) paddedInfo.paddedArray, DEFAULT_EXTENT, /*paddedInfo.paddedExtent*/
    paddedInfo.paddedISize.getX(), paddedInfo.paddedISize.getY(), paddedInfo.paddedISize.getZ());
    return newVCImage;
}

Example 19 with VCImageUncompressed

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

the class ROIAssistPanel method calculateRegionInfos.

private RegionInfo[] calculateRegionInfos(short[] validatePixels) throws Exception {
    byte[] roiBytes = new byte[validatePixels.length];
    for (int i = 0; i < roiBytes.length; i++) {
        roiBytes[i] = (byte) (validatePixels[i] == 0 ? 0 : 1);
    }
    VCImageUncompressed roiVCImage = new VCImageUncompressed(null, roiBytes, new Extent(1, 1, 1), originalROI.getISize().getX(), originalROI.getISize().getY(), originalROI.getISize().getZ());
    RegionImage roiRegionImage = new RegionImage(roiVCImage, 0, null, null, RegionImage.NO_SMOOTHING);
    return roiRegionImage.getRegionInfos();
}

Example 20 with VCImageUncompressed

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

the class VFrap_ROIAssistPanel method calculateRegionInfos.

private RegionInfo[] calculateRegionInfos(short[] validatePixels) throws Exception {
    byte[] roiBytes = new byte[validatePixels.length];
    for (int i = 0; i < roiBytes.length; i++) {
        roiBytes[i] = (byte) (validatePixels[i] == 0 ? 0 : 1);
    }
    VCImageUncompressed roiVCImage = new VCImageUncompressed(null, roiBytes, new Extent(1, 1, 1), originalROI.getISize().getX(), originalROI.getISize().getY(), originalROI.getISize().getZ());
    RegionImage roiRegionImage = new RegionImage(roiVCImage, 0, null, null, RegionImage.NO_SMOOTHING);
    return roiRegionImage.getRegionInfos();
}