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Example 16 with ImageDataset

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

the class PointSpreadFunctionManagement method importPointSpreadFunction.

public void importPointSpreadFunction() {
    AsynchClientTask[] taskArray = new AsynchClientTask[3];
    // select the desired PSF file
    taskArray[0] = new AsynchClientTask("Select a file", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {

        public void run(Hashtable<String, Object> hashTable) throws Exception {
            ChoosePSFFile(hashTable);
        }
    };
    // create and save the field data object
    taskArray[1] = new AsynchClientTask("Import objects", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

        public void run(Hashtable<String, Object> hashTable) throws Exception {
            Component requesterComponent = parentWindow;
            DocumentWindow documentWindow = (DocumentWindow) BeanUtils.findTypeParentOfComponent(requesterComponent, DocumentWindow.class);
            DocumentManager documentManager = documentWindow.getTopLevelWindowManager().getRequestManager().getDocumentManager();
            if (documentManager == null) {
                throw new RuntimeException("Not connected to server.");
            }
            // the following line of code may modify initialFieldDataName
            // normal file name
            checkNameAvailability(hashTable, false, documentManager, requesterComponent);
            File filePSF = (File) hashTable.get("filePSF");
            String initialFieldDataName = (String) hashTable.get("initialFieldDataName");
            ImageDataset imageDataset = ImageDatasetReaderService.getInstance().getImageDatasetReader().readImageDataset(filePSF.getAbsolutePath(), null);
            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 fdos = new FieldDataFileOperationSpec();
            // try {
            // fdos = ClientRequestManager.createFDOSFromImageFile(filePSF, false, null);
            // } catch (DataFormatException ex) {
            // throw new Exception("Cannot read image " + filePSF.getAbsolutePath()+"\n"+ex.getMessage());
            // }
            fdos.owner = documentManager.getUser();
            fdos.opType = FieldDataFileOperationSpec.FDOS_ADD;
            fdos.cartesianMesh = cartesianMesh;
            fdos.doubleSpecData = pixData;
            fdos.specEDI = null;
            fdos.varNames = new String[] { SimulationContext.FLUOR_DATA_NAME };
            fdos.times = imageDataset.getImageTimeStamps();
            fdos.variableTypes = new VariableType[] { VariableType.VOLUME };
            fdos.origin = origin;
            fdos.extent = extent;
            fdos.isize = isize;
            ExternalDataIdentifier pSFImageEDI = documentManager.saveFieldData(fdos, initialFieldDataName);
            hashTable.put("pSFImageEDI", pSFImageEDI);
        }
    };
    // create a data symbol for the PSF image saved above as field data
    taskArray[2] = 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");
            ExternalDataIdentifier pSFImageEDI = (ExternalDataIdentifier) hashTable.get("pSFImageEDI");
            String fluorName = "psf_" + initialFieldDataName;
            DataSymbol fluorDataSymbol = new FieldDataSymbol(fluorName, DataSymbolType.POINT_SPREAD_FUNCTION, simulationContext.getDataContext(), simulationContext.getModel().getUnitSystem().getInstance_TBD(), pSFImageEDI, SimulationContext.FLUOR_DATA_NAME, VariableType.VOLUME.getTypeName(), 0D);
            simulationContext.getDataContext().addDataSymbol(fluorDataSymbol);
        }
    };
    Hashtable<String, Object> hash = new Hashtable<String, Object>();
    ClientTaskDispatcher.dispatch(parentWindow, hash, taskArray, false, true, null);
}
Also used : Origin(org.vcell.util.Origin) AsynchClientTask(cbit.vcell.client.task.AsynchClientTask) ImageDataset(cbit.vcell.VirtualMicroscopy.ImageDataset) VariableType(cbit.vcell.math.VariableType) Extent(org.vcell.util.Extent) ISize(org.vcell.util.ISize) FieldDataFileOperationSpec(cbit.vcell.field.io.FieldDataFileOperationSpec) Hashtable(java.util.Hashtable) DocumentManager(cbit.vcell.clientdb.DocumentManager) VCImageUncompressed(cbit.image.VCImageUncompressed) ImageException(cbit.image.ImageException) IOException(java.io.IOException) UserCancelException(org.vcell.util.UserCancelException) DocumentWindow(cbit.vcell.client.desktop.DocumentWindow) FieldDataSymbol(cbit.vcell.data.FieldDataSymbol) DataSymbol(cbit.vcell.data.DataSymbol) CartesianMesh(cbit.vcell.solvers.CartesianMesh) RegionImage(cbit.vcell.geometry.RegionImage) ExternalDataIdentifier(org.vcell.util.document.ExternalDataIdentifier) Component(java.awt.Component) ImageFile(cbit.image.ImageFile) File(java.io.File) FieldDataSymbol(cbit.vcell.data.FieldDataSymbol)

Example 17 with ImageDataset

use of cbit.vcell.VirtualMicroscopy.ImageDataset 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");
// }
}
Also used : Origin(org.vcell.util.Origin) AsynchClientTask(cbit.vcell.client.task.AsynchClientTask) User(org.vcell.util.document.User) AnnotatedImageDataset(cbit.vcell.VirtualMicroscopy.importer.AnnotatedImageDataset) ImageDataset(cbit.vcell.VirtualMicroscopy.ImageDataset) Extent(org.vcell.util.Extent) ISize(org.vcell.util.ISize) FieldDataFileOperationSpec(cbit.vcell.field.io.FieldDataFileOperationSpec) Element(org.jdom.Element) DecimalFormat(java.text.DecimalFormat) BufferedImage(java.awt.image.BufferedImage) Version(org.vcell.util.document.Version) ExternalDataIdentifier(org.vcell.util.document.ExternalDataIdentifier) Component(java.awt.Component) AnnotatedImageDataset(cbit.vcell.VirtualMicroscopy.importer.AnnotatedImageDataset) VariableType(cbit.vcell.math.VariableType) Hashtable(java.util.Hashtable) Calendar(java.util.Calendar) DocumentManager(cbit.vcell.clientdb.DocumentManager) VCImageUncompressed(cbit.image.VCImageUncompressed) UserCancelException(org.vcell.util.UserCancelException) DocumentWindow(cbit.vcell.client.desktop.DocumentWindow) MicroscopyXmlReader(cbit.vcell.VirtualMicroscopy.importer.MicroscopyXmlReader) FieldDataSymbol(cbit.vcell.data.FieldDataSymbol) DataSymbol(cbit.vcell.data.DataSymbol) CartesianMesh(cbit.vcell.solvers.CartesianMesh) RegionImage(cbit.vcell.geometry.RegionImage) File(java.io.File) OverlayEditorPanelJAI(cbit.vcell.geometry.gui.OverlayEditorPanelJAI) SimpleDateFormat(java.text.SimpleDateFormat) FieldDataSymbol(cbit.vcell.data.FieldDataSymbol)

Example 18 with ImageDataset

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

the class ROIMultiPaintManager method smoothImageDataset.

private ImageDataset[] smoothImageDataset(ImageDataset[] origImageDatasetChannels, int enhanceImageAmount, ClientTaskStatusSupport clientTaskStatusSupport) throws Exception {
    if (enhanceImageAmount == ROIMultiPaintManager.ENHANCE_NONE) {
        return null;
    }
    ImageDataset[] smoothedImageDatasetChannels = new ImageDataset[origImageDatasetChannels.length];
    int allCount = origImageDatasetChannels.length * origImageDatasetChannels[0].getSizeZ();
    int progress = 0;
    for (int c = 0; c < origImageDatasetChannels.length; c++) {
        UShortImage[] smoothedZSections = new UShortImage[origImageDatasetChannels[c].getISize().getZ()];
        // *2+1;
        int radius = enhanceImageAmount;
        // int[] divideTable = BoxBlurFilter.createDivideTable(radius);
        short[] intermediateArr = new short[origImageDatasetChannels[c].getAllImages()[0].getPixels().length];
        for (int z = 0; z < origImageDatasetChannels[c].getAllImages().length; z++) {
            smoothedZSections[z] = new UShortImage(new short[origImageDatasetChannels[c].getISize().getX() * origImageDatasetChannels[c].getISize().getY()], ROIMultiPaintManager.DEFAULT_ORIGIN, ROIMultiPaintManager.DEFAULT_EXTENT, origImageDatasetChannels[c].getISize().getX(), origImageDatasetChannels[c].getISize().getY(), 1);
            short[] enhancedData = smoothedZSections[z].getPixels();
            short[] roiSourceData = origImageDatasetChannels[c].getAllImages()[z].getPixels();
            BoxBlurFilter.blur(roiSourceData, intermediateArr, origImageDatasetChannels[c].getISize().getX(), origImageDatasetChannels[c].getISize().getY(), radius);
            BoxBlurFilter.blur(intermediateArr, enhancedData, origImageDatasetChannels[c].getISize().getY(), origImageDatasetChannels[c].getISize().getX(), radius);
            if (clientTaskStatusSupport != null) {
                if (clientTaskStatusSupport.isInterrupted()) {
                    return null;
                }
                progress++;
                clientTaskStatusSupport.setProgress(progress * 100 / allCount);
            }
        }
        ImageDataset smoothedImageDataset = new ImageDataset(smoothedZSections, new double[] { 0 }, origImageDatasetChannels[c].getISize().getZ());
        smoothedImageDatasetChannels[c] = smoothedImageDataset;
    }
    return smoothedImageDatasetChannels;
}
Also used : ImageDataset(cbit.vcell.VirtualMicroscopy.ImageDataset) UShortImage(cbit.vcell.VirtualMicroscopy.UShortImage) Point(java.awt.Point)

Example 19 with ImageDataset

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

the class ROIMultiPaintManager method resizeImpl.

private void resizeImpl(ResizeInfo resizeInfo, ClientTaskStatusSupport clientTaskStatusSupport) throws Exception {
    resizeImpl0(resizeInfo, (bHasOriginalData ? initImageDataSetChannels : null), roiComposite);
    ISize newISize = resizeInfo.getNewSize();
    ISize oldISize = resizeInfo.getOriginalSize();
    Extent resizeExtent = createResizeExtent(originalExtent, oldISize, newISize);
    if (bHasOriginalData) {
        for (int c = 0; c < initImageDataSetChannels.length; c++) {
            UShortImage[] zImageSet = new UShortImage[newISize.getZ()];
            for (int z = 0; z < zImageSet.length; z++) {
                zImageSet[z] = new UShortImage(resizeInfo.underlayC[c][z], originalOrigin, resizeExtent, newISize.getX(), newISize.getY(), 1);
            }
            initImageDataSetChannels[c] = new ImageDataset(zImageSet, new double[] { 0.0 }, newISize.getZ());
        }
    } else {
        initImageDataSet(null, newISize);
    }
    roiComposite = resizeInfo.roiComposite;
    updateAuxiliaryInfo(originalISize, clientTaskStatusSupport);
}
Also used : ImageDataset(cbit.vcell.VirtualMicroscopy.ImageDataset) Extent(org.vcell.util.Extent) ISize(org.vcell.util.ISize) UShortImage(cbit.vcell.VirtualMicroscopy.UShortImage) Point(java.awt.Point)

Example 20 with ImageDataset

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

the class ROIMultiPaintManager method duplicateROIData.

private void duplicateROIData(final int newZSize) {
    final AsynchClientTask extrudeTask = new AsynchClientTask("Extruding...", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            ISize origSize = getImageDataSetChannel().getISize();
            if (origSize.getZ() != 1 || newZSize < 1) {
                throw new IllegalArgumentException("Extrude assumes starting with 2D and new Z size >= 1.");
            }
            UShortImage[][] newUnderLayImageArr = new UShortImage[initImageDataSetChannels.length][newZSize];
            BufferedImage[] newROICompositeArr = new BufferedImage[newZSize];
            for (int i = 0; i < newZSize; i++) {
                for (int c = 0; c < initImageDataSetChannels.length; c++) {
                    // short[] zslice = new short[initImageDataSetChannels[c].getAllImages()[0].getPixels().length];
                    // System.arraycopy(initImageDataSetChannels[c].getAllImages()[0].getPixels(), 0, zslice, 0, zslice.length);
                    newUnderLayImageArr[c][i] = new UShortImage(// zslice,
                    initImageDataSetChannels[c].getAllImages()[0].getPixels().clone(), DEFAULT_ORIGIN, DEFAULT_EXTENT, initImageDataSetChannels[c].getAllImages()[0].getNumX(), initImageDataSetChannels[c].getAllImages()[0].getNumY(), 1);
                }
                newROICompositeArr[i] = new BufferedImage(roiComposite[0].getWidth(), roiComposite[0].getHeight(), BufferedImage.TYPE_BYTE_INDEXED, getContrastIndexColorModel());
                System.arraycopy((byte[]) ((DataBufferByte) roiComposite[0].getRaster().getDataBuffer()).getData(), 0, (byte[]) ((DataBufferByte) newROICompositeArr[i].getRaster().getDataBuffer()).getData(), 0, origSize.getX() * origSize.getY());
            }
            for (int c = 0; c < initImageDataSetChannels.length; c++) {
                initImageDataSetChannels[c] = new ImageDataset(newUnderLayImageArr[c], null, newZSize);
            }
            roiComposite = newROICompositeArr;
            if (!(enhanceImageAmount == ROIMultiPaintManager.ENHANCE_NONE)) {
                getClientTaskStatusSupport().setMessage("smoothing...");
            }
            updateAuxiliaryInfo(origSize, getClientTaskStatusSupport());
        }
    };
    final AsynchClientTask updatePanelTask = getUpdateDisplayAfterCropTask();
    ClientTaskDispatcher.dispatch(overlayEditorPanelJAI, new Hashtable<String, Object>(), new AsynchClientTask[] { extrudeTask, updatePanelTask }, false, false, null, true);
}
Also used : AsynchClientTask(cbit.vcell.client.task.AsynchClientTask) ImageDataset(cbit.vcell.VirtualMicroscopy.ImageDataset) Hashtable(java.util.Hashtable) ISize(org.vcell.util.ISize) UShortImage(cbit.vcell.VirtualMicroscopy.UShortImage) DataBufferByte(java.awt.image.DataBufferByte) BufferedImage(java.awt.image.BufferedImage) Point(java.awt.Point)

Aggregations

ImageDataset (cbit.vcell.VirtualMicroscopy.ImageDataset)42 UShortImage (cbit.vcell.VirtualMicroscopy.UShortImage)20 ROI (cbit.vcell.VirtualMicroscopy.ROI)9 Extent (org.vcell.util.Extent)9 File (java.io.File)8 Element (org.jdom.Element)8 ISize (org.vcell.util.ISize)8 Origin (org.vcell.util.Origin)7 CartesianMesh (cbit.vcell.solvers.CartesianMesh)6 UserCancelException (org.vcell.util.UserCancelException)6 ImageException (cbit.image.ImageException)5 AsynchClientTask (cbit.vcell.client.task.AsynchClientTask)5 FieldDataFileOperationSpec (cbit.vcell.field.io.FieldDataFileOperationSpec)5 Hashtable (java.util.Hashtable)5 Component (java.awt.Component)4 ArrayList (java.util.ArrayList)4 ImageTimeSeries (org.vcell.vmicro.workflow.data.ImageTimeSeries)4 VCImageUncompressed (cbit.image.VCImageUncompressed)3 AnnotatedImageDataset (cbit.vcell.VirtualMicroscopy.importer.AnnotatedImageDataset)3 MicroscopyXmlReader (cbit.vcell.VirtualMicroscopy.importer.MicroscopyXmlReader)3