Examples with UserCancelException org.vcell.util.UserCancelException used on opensource projects

Example 26 with UserCancelException

use of org.vcell.util.UserCancelException in project vcell by virtualcell.

the class ROIAssistPanel method pickKeepRegionInfoFromCurrentROI.

private RegionInfo[] pickKeepRegionInfoFromCurrentROI() throws Exception {
    RegionInfo[] thresholdRegionInfos = calculateRegionInfos(dataToThreshold.getCurrentlyDisplayedROI().getPixelsXYZ());
    Vector<RegionInfo> roiRegionInfoV = new Vector<RegionInfo>();
    for (int i = 0; i < thresholdRegionInfos.length; i++) {
        if (thresholdRegionInfos[i].getPixelValue() == 1) {
            roiRegionInfoV.add(thresholdRegionInfos[i]);
        }
    }
    if (roiRegionInfoV.size() == 0) {
        DialogUtils.showInfoDialog(this, "There are no Regions Of Interest to resolve.");
        return null;
    }
    // Present list to pick from
    final RegionInfo[] regionInfoArr = roiRegionInfoV.toArray(new RegionInfo[0]);
    Arrays.sort(regionInfoArr, new Comparator<RegionInfo>() {

        public int compare(RegionInfo o1, RegionInfo o2) {
            return o2.getNumPixels() - o1.getNumPixels();
        }
    });
    final Object[][] rowData = new Object[regionInfoArr.length][1];
    for (int i = 0; i < regionInfoArr.length; i++) {
        rowData[i][0] = regionInfoArr[i].getNumPixels() + " pixels";
    }
    final ROI beforeROI = new ROI(dataToThreshold.getCurrentlyDisplayedROI());
    int[] resultArr = null;
    ListSelectionListener listSelectionListener = new ListSelectionListener() {

        public void valueChanged(ListSelectionEvent e) {
            if (!e.getValueIsAdjusting()) {
                try {
                    DefaultListSelectionModel defaultListSelectionModel = (DefaultListSelectionModel) e.getSource();
                    Vector<Integer> pickedIndexes = new Vector<Integer>();
                    if (!defaultListSelectionModel.isSelectionEmpty()) {
                        for (int i = defaultListSelectionModel.getMinSelectionIndex(); i <= defaultListSelectionModel.getMaxSelectionIndex(); i++) {
                            if (defaultListSelectionModel.isSelectedIndex(i)) {
                                pickedIndexes.add(i);
                            }
                        }
                    }
                    // beforeROI.getPixelsXYZ();
                    short[] pickedPixels = new short[beforeROI.getISize().getXYZ()];
                    for (int i = 0; i < pickedPixels.length; i++) {
                        for (int j = 0; j < pickedIndexes.size(); j++) {
                            if (regionInfoArr[pickedIndexes.elementAt(j)].isIndexInRegion(i)) {
                                pickedPixels[i] = 1;
                            }
                        }
                    }
                    ROI newCellROI = null;
                    if (pickedIndexes.size() == 0) {
                        newCellROI = beforeROI;
                    } else {
                        UShortImage ushortImage = new UShortImage(pickedPixels, originalROI.getRoiImages()[0].getOrigin(), originalROI.getRoiImages()[0].getExtent(), originalROI.getISize().getX(), originalROI.getISize().getY(), originalROI.getISize().getZ());
                        newCellROI = new ROI(ushortImage, originalROI.getROIName());
                    }
                    dataToThreshold.addReplaceRoi(newCellROI);
                } catch (Exception e2) {
                    e2.printStackTrace();
                    throw new RuntimeException("Error selecting resolved ROI", e2);
                }
            }
        }
    };
    try {
        resultArr = DialogUtils.showComponentOptionsTableList(this, "Select 1 or more pixel regions to keep in ROI", new String[] { "ROI Size (pixel count)" }, rowData, ListSelectionModel.MULTIPLE_INTERVAL_SELECTION, listSelectionListener, null, null, null).selectedTableRows;
    } catch (UserCancelException e) {
        resultArr = null;
    }
    if (resultArr != null && resultArr.length > 0) {
        RegionInfo[] pickedRegions = new RegionInfo[resultArr.length];
        for (int i = 0; i < resultArr.length; i++) {
            pickedRegions[i] = regionInfoArr[resultArr[i]];
        }
        // (resultArr == null?null:regionInfoArr[resultArr]);
        return pickedRegions;
    } else {
        dataToThreshold.addReplaceRoi(beforeROI);
    }
    return null;
}

Example 27 with UserCancelException

use of org.vcell.util.UserCancelException 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 28 with UserCancelException

use of org.vcell.util.UserCancelException in project vcell by virtualcell.

the class VFrap_ROIAssistPanel method pickKeepRegionInfoFromCurrentROI.

private RegionInfo pickKeepRegionInfoFromCurrentROI() throws Exception {
    if (lastRegionInfos == null) {
        throw new Exception("No regionInfo to resolve");
    }
    final Vector<RegionInfo> roiRegionInfoV2 = new Vector<RegionInfo>();
    for (int i = 0; i < lastRegionInfos.length; i++) {
        if (lastRegionInfos[i].getPixelValue() == 1) {
            roiRegionInfoV2.add(lastRegionInfos[i]);
        }
    }
    if (roiRegionInfoV2.size() <= 1) {
        throw new Exception("No regionInfo to resolve");
    }
    final RegionInfo[] regionInfoArr = roiRegionInfoV2.toArray(new RegionInfo[0]);
    Arrays.sort(regionInfoArr, new Comparator<RegionInfo>() {

        public int compare(RegionInfo o1, RegionInfo o2) {
            return o2.getNumPixels() - o1.getNumPixels();
        }
    });
    final Object[][] rowData = new Object[regionInfoArr.length][1];
    for (int i = 0; i < regionInfoArr.length; i++) {
        rowData[i][0] = regionInfoArr[i].getNumPixels() + " pixels";
    }
    ROI beforeROI = new ROI(frapData.getCurrentlyDisplayedROI());
    int[] resultArr = null;
    // SwingUtilities.invokeAndWait(new Runnable(){public void run(){//}});
    try {
        resultArr = /*DialogUtils.*/
        showComponentOKCancelTableList(this, "Select ROI to Keep", new String[] { "ROI Size (pixel count)" }, rowData, ListSelectionModel.SINGLE_SELECTION, regionInfoArr, beforeROI.getPixelsXYZ());
    } catch (UserCancelException e) {
        resultArr = null;
    }
    // }});
    if (resultArr != null && resultArr.length > 0) {
        return (resultArr == null ? null : regionInfoArr[resultArr[0]]);
    } else {
        // SwingUtilities.invokeAndWait(new Runnable(){public void run(){//}});
        frapData.addReplaceRoi(beforeROI);
        applyROIButton.setEnabled(false);
        resolveROIButton.setEnabled(true);
        fillVoidsButton.setEnabled(false);
    // }});
    }
    return null;
}

Example 29 with UserCancelException

use of org.vcell.util.UserCancelException in project vcell by virtualcell.

the class ImageJHelper method vcellSendImage.

public static void vcellSendImage(final Component requester, final PDEDataContext pdeDataContext, SubVolume subvolume, Hashtable<SampledCurve, int[]>[] membraneTables, String description, double[] timePoints, String[] channelDescriptions, int[] colormap) throws Exception {
    // xyz, 1 time, 1 var
    final ImageJConnection[] imageJConnectionArr = new ImageJConnection[1];
    AsynchClientTask sendImageTask = new AsynchClientTask("Send image to ImageJ...", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            try {
                ImageJConnection imageJConnection = new ImageJConnection(ExternalCommunicator.IMAGEJ);
                imageJConnectionArr[0] = imageJConnection;
                imageJConnection.openConnection(VCellImageJCommands.vcellSendImage, description);
                // send size of the standard 5 dimensions in this order (width, height, nChannels, nSlices, nFrames)
                ISize xyzSize = pdeDataContext.getCartesianMesh().getISize();
                Extent extent = pdeDataContext.getCartesianMesh().getExtent();
                BasicStackDimensions basicStackDimensions = new BasicStackDimensions(xyzSize.getX(), xyzSize.getY(), xyzSize.getZ(), 1, 1);
                sendData0(imageJConnection, new HyperStackHelper(basicStackDimensions, extent, true, Float.class.getSimpleName(), null, new int[] { subvolume.getHandle() }, timePoints, channelDescriptions, colormap), pdeDataContext.getDataValues(), "'" + pdeDataContext.getVariableName() + "'" + pdeDataContext.getTimePoint());
                sendVolumeDomain0(imageJConnection, pdeDataContext.getCartesianMesh(), null, description);
                sendMembraneOutline(imageJConnection, membraneTables);
            } catch (Exception e) {
                if (e instanceof UserCancelException) {
                    throw e;
                }
                e.printStackTrace();
                hashTable.put("imagejerror", e);
            } finally {
                try {
                    if (imageJConnectionArr[0] != null) {
                        imageJConnectionArr[0].closeConnection();
                    }
                } catch (Exception e) {
                    e.printStackTrace();
                }
            }
        }
    };
    ClientTaskDispatcher.dispatch(requester, new Hashtable<>(), new AsynchClientTask[] { sendImageTask }, false, true, new ProgressDialogListener() {

        @Override
        public void cancelButton_actionPerformed(EventObject newEvent) {
            if (imageJConnectionArr[0] != null) {
                imageJConnectionArr[0].closeConnection();
            }
        }
    });
}

Example 30 with UserCancelException

use of org.vcell.util.UserCancelException in project vcell by virtualcell.

the class ExportServiceImpl method makeRemoteFile.

public ExportEvent makeRemoteFile(OutputContext outputContext, User user, DataServerImpl dataServerImpl, ExportSpecs exportSpecs, boolean bSaveAsZip, ClientTaskStatusSupport clientTaskStatusSupport) throws DataAccessException {
    // if export completes successfully, we return the generated event for logging
    if (user == null) {
        throw new DataAccessException("ERROR: user is null");
    }
    JobRequest newExportJob = JobRequest.createExportJobRequest(user);
    jobRequestIDs.put(new Long(newExportJob.getJobID()), user);
    if (lg.isTraceEnabled())
        lg.trace("ExportServiceImpl.makeRemoteFile(): " + newExportJob + ", " + exportSpecs);
    String fileFormat = null;
    switch(exportSpecs.getFormat()) {
        case CSV:
            fileFormat = "CSV";
            break;
        case QUICKTIME:
            fileFormat = "MOV";
            break;
        case GIF:
        case ANIMATED_GIF:
            fileFormat = "GIF";
            break;
        case FORMAT_JPEG:
            fileFormat = "JPEG";
            break;
        case NRRD:
            fileFormat = "NRRD";
            break;
        case IMAGEJ:
            fileFormat = "IMAGEJ";
            break;
    }
    fireExportStarted(newExportJob.getJobID(), exportSpecs.getVCDataIdentifier(), fileFormat);
    try {
        String exportBaseURL = PropertyLoader.getRequiredProperty(PropertyLoader.exportBaseURLProperty);
        String exportBaseDir = PropertyLoader.getRequiredProperty(PropertyLoader.exportBaseDirInternalProperty);
        // we need to make new output
        if (lg.isTraceEnabled())
            lg.trace("ExportServiceImpl.makeRemoteFile(): Starting new export job: " + newExportJob);
        FileDataContainerManager fileDataContainerManager = new FileDataContainerManager();
        try {
            ExportOutput[] exportOutputs = null;
            switch(exportSpecs.getFormat()) {
                case CSV:
                    Collection<ExportOutput> asciiOut = asciiExporter.makeASCIIData(outputContext, newExportJob, user, dataServerImpl, exportSpecs, fileDataContainerManager);
                    exportOutputs = asciiOut.toArray(new ExportOutput[asciiOut.size()]);
                    return makeRemoteFile(fileFormat, exportBaseDir, exportBaseURL, exportOutputs, exportSpecs, newExportJob, fileDataContainerManager);
                case QUICKTIME:
                case GIF:
                case FORMAT_JPEG:
                case ANIMATED_GIF:
                    exportOutputs = imgExporter.makeMediaData(outputContext, newExportJob, user, dataServerImpl, exportSpecs, clientTaskStatusSupport, fileDataContainerManager);
                    boolean bOverrideZip = exportOutputs.length == 1;
                    if (bSaveAsZip && !bOverrideZip) {
                        return makeRemoteFile(fileFormat, exportBaseDir, exportBaseURL, exportOutputs, exportSpecs, newExportJob, fileDataContainerManager);
                    } else {
                        return makeRemoteFile_Unzipped(fileFormat, exportBaseDir, exportBaseURL, exportOutputs, exportSpecs, newExportJob, fileDataContainerManager);
                    }
                case NRRD:
                case IMAGEJ:
                    NrrdInfo[] nrrdInfos = rrExporter.makeRasterData(outputContext, newExportJob, user, dataServerImpl, exportSpecs, fileDataContainerManager);
                    return makeRemoteFile(fileFormat, exportBaseDir, exportBaseURL, nrrdInfos, exportSpecs, newExportJob, fileDataContainerManager);
                case UCD:
                    exportOutputs = rrExporter.makeUCDData(outputContext, newExportJob, user, dataServerImpl, exportSpecs, fileDataContainerManager);
                    return makeRemoteFile(fileFormat, exportBaseDir, exportBaseURL, exportOutputs, exportSpecs, newExportJob, fileDataContainerManager);
                case PLY:
                    exportOutputs = rrExporter.makePLYWithTexData(outputContext, newExportJob, user, dataServerImpl, exportSpecs, fileDataContainerManager);
                    return makeRemoteFile(fileFormat, exportBaseDir, exportBaseURL, exportOutputs, exportSpecs, newExportJob, fileDataContainerManager);
                case VTK_IMAGE:
                    exportOutputs = rrExporter.makeVTKImageData(outputContext, newExportJob, user, dataServerImpl, exportSpecs, fileDataContainerManager);
                    return makeRemoteFile(fileFormat, exportBaseDir, exportBaseURL, exportOutputs, exportSpecs, newExportJob, fileDataContainerManager);
                case VTK_UNSTRUCT:
                    exportOutputs = rrExporter.makeVTKUnstructuredData0(outputContext, newExportJob, user, dataServerImpl, exportSpecs, fileDataContainerManager);
                    return makeRemoteFile(fileFormat, exportBaseDir, exportBaseURL, exportOutputs, exportSpecs, newExportJob, fileDataContainerManager);
                default:
                    throw new DataAccessException("Unknown export format requested");
            }
        } finally {
            fileDataContainerManager.closeAllAndDelete();
        }
    } catch (UserCancelException ex) {
        throw ex;
    } catch (Throwable exc) {
        lg.error(exc.getMessage(), exc);
        fireExportFailed(newExportJob.getJobID(), exportSpecs.getVCDataIdentifier(), fileFormat, exc.getMessage());
        throw new DataAccessException(exc.getMessage());
    }
}