Examples with ExportFormat cbit.vcell.export.server.ExportFormat used on opensource projects

Example 1 with ExportFormat

use of cbit.vcell.export.server.ExportFormat in project vcell by virtualcell.

the class ExportSettings method setSelectedFormat.

/**
 * Sets the selectedFormat property (int) value.
 * @param selectedFormat The new value for the property.
 * @see #getSelectedFormat
 */
public void setSelectedFormat(ExportFormat selectedFormat) {
    ExportFormat oldValue = fieldSelectedFormat;
    fieldSelectedFormat = selectedFormat;
    firePropertyChange("selectedFormat", oldValue, selectedFormat);
}

Example 2 with ExportFormat

use of cbit.vcell.export.server.ExportFormat in project vcell by virtualcell.

the class FRAPStudyPanel method showMovie.

private void showMovie() {
    AsynchClientTask createMovieTask = new AsynchClientTask("Buffering movie data...", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

        public void run(Hashtable<String, Object> hashTable) throws Exception {
            FRAPStudy fStudy = getFrapWorkspace().getWorkingFrapStudy();
            if (fStudy == null) {
                return;
            }
            if (fStudy.getMovieURLString() != null && fStudy.getMovieFileString() != null) {
                hashTable.put("FrapStudy", fStudy);
                return;
            }
            // create export specs
            Simulation sim = null;
            if (fStudy.getBioModel() == null || fStudy.getBioModel().getSimulations() == null || fStudy.getBioModel().getSimulations().length < 1) {
                return;
            } else {
                sim = fStudy.getBioModel().getSimulations()[0];
            }
            FieldFunctionArguments[] fieldFunctionArgs = FieldUtilities.getFieldFunctionArguments(sim.getMathDescription());
            FieldDataIdentifierSpec[] fieldDataIdentifierSpecs = new FieldDataIdentifierSpec[fieldFunctionArgs.length];
            for (int i = 0; i < fieldDataIdentifierSpecs.length; i++) {
                fieldDataIdentifierSpecs[i] = new FieldDataIdentifierSpec(fieldFunctionArgs[i], fStudy.getFrapDataExternalDataInfo().getExternalDataIdentifier());
            }
            ExternalDataIdentifier timeSeriesExtDataID = fStudy.getFrapDataExternalDataInfo().getExternalDataIdentifier();
            ExternalDataIdentifier maskExtDataID = fStudy.getRoiExternalDataInfo().getExternalDataIdentifier();
            // add sim
            int jobIndex = 0;
            SimulationJob simJob = new SimulationJob(sim, jobIndex, fieldDataIdentifierSpecs);
            VCDataIdentifier[] dataIDs = new VCDataIdentifier[] { timeSeriesExtDataID, maskExtDataID, simJob.getVCDataIdentifier() };
            VCDataIdentifier vcDataId = new MergedDataInfo(LocalWorkspace.getDefaultOwner(), dataIDs, FRAPStudy.VFRAP_DS_PREFIX);
            PDEDataManager dataManager = new PDEDataManager(null, getLocalWorkspace().getVCDataManager(), vcDataId);
            PDEDataContext pdeDataContext = new ClientPDEDataContext(dataManager);
            ExportFormat format = ExportFormat.QUICKTIME;
            String[] variableNames = new String[] { NORM_FLUOR_VAR, NORM_SIM_VAR };
            VariableSpecs variableSpecs = new VariableSpecs(variableNames, ExportConstants.VARIABLE_MULTI);
            // int endTimeIndex = (int)Math.round(sim.getSolverTaskDescription().getTimeBounds().getEndingTime()/((UniformOutputTimeSpec)sim.getSolverTaskDescription().getOutputTimeSpec()).getOutputTimeStep());
            int endTimeIndex = getFRAPSimDataViewerPanel().getOriginalDataViewer().getPdeDataContext().getTimePoints().length - 1;
            TimeSpecs timeSpecs = new TimeSpecs(0, endTimeIndex, pdeDataContext.getTimePoints(), ExportConstants.TIME_RANGE);
            int geoMode = ExportConstants.GEOMETRY_SLICE;
            GeometrySpecs geometrySpecs = new GeometrySpecs(null, Coordinate.Z_AXIS, 0, geoMode);
            // 10s
            double duration = 10000;
            DisplayPreferences pref1 = new DisplayPreferences("BlueRed", new Range(0.01, 1.1), DisplayAdapterService.createBlueRedSpecialColors());
            DisplayPreferences pref2 = new DisplayPreferences("BlueRed", new Range(0.01, 1.1), DisplayAdapterService.createBlueRedSpecialColors());
            DisplayPreferences[] displayPref = new DisplayPreferences[] { pref1, pref2 };
            int imageScale = 1;
            int membraneScale = 1;
            int scaleMode = ImagePaneModel.MESH_MODE;
            // the default setting in MediaSettingsPanel.
            int volVarMemOutlineThickness = 1;
            MovieSpecs mSpec = new MovieSpecs(duration, true, displayPref, ExportFormat.QUICKTIME, ExportConstants.NO_MIRRORING, volVarMemOutlineThickness, imageScale, membraneScale, scaleMode, FormatSpecificSpecs.CODEC_JPEG, 1.0f, /*lossless*/
            false, FormatSpecificSpecs.PARTICLE_NONE);
            // mSpec.setViewZoom(1);
            ExportSpecs exSpecs = new ExportSpecs(vcDataId, format, variableSpecs, timeSpecs, geometrySpecs, mSpec, fStudy.getName(), null);
            // pass the request
            ExportEvent exportEvt = ((VirtualFrapWindowManager) getFlourDataViewer().getDataViewerManager()).startExportMovie(exSpecs, outputContext, this.getClientTaskStatusSupport());
            hashTable.put("ExportEvt", exportEvt);
            hashTable.put("FrapStudy", fStudy);
        }
    };
    AsynchClientTask showMovieTask = new AsynchClientTask("Showing movie ...", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {

        public void run(Hashtable<String, Object> hashTable) throws Exception {
            ExportEvent exportEvt = (ExportEvent) hashTable.get("ExportEvt");
            FRAPStudy fStudy = (FRAPStudy) hashTable.get("FrapStudy");
            // show movie if successfully exported
            if (exportEvt != null) {
                final String fileURLString = System.getProperty(PropertyLoader.exportBaseURLProperty) + exportEvt.getJobID() + ".mov";
                final String fileString = System.getProperty(PropertyLoader.exportBaseDirInternalProperty) + exportEvt.getJobID() + ".mov";
                fStudy.setMovieURLString(fileURLString);
                fStudy.setMovieFileString(fileString);
            }
            showMovieInDialog(fStudy.getMovieURLString(), fStudy.getMovieFileString());
        }
    };
    ClientTaskDispatcher.dispatch(this, new Hashtable<String, Object>(), new AsynchClientTask[] { createMovieTask, showMovieTask }, true, true, null, true);
}

Example 3 with ExportFormat

use of cbit.vcell.export.server.ExportFormat in project vcell by virtualcell.

the class PDEExportDataPanel method startExport.

/**
 * Comment
 */
private void startExport() {
    if (getExportSettings1().getSelectedFormat() == ExportFormat.QUICKTIME && getJSlider1().getValue() == getJSlider2().getValue()) {
        DialogUtils.showWarningDialog(this, "User selected 'begin' and 'end' export times are the same.  'Movie' export format 'begin' and 'end' times must be different");
        return;
    }
    DisplayPreferences[] displayPreferences = null;
    @SuppressWarnings("deprecation") Object[] variableSelections = getJListVariables().getSelectedValues();
    boolean selectionHasVolumeVariables = false;
    boolean selectionHasMembraneVariables = false;
    switch(getExportSettings1().getSelectedFormat()) {
        case PLY:
        case QUICKTIME:
        case GIF:
        case FORMAT_JPEG:
        case ANIMATED_GIF:
            {
                displayPreferences = new DisplayPreferences[variableSelections.length];
                StringBuffer noScaleInfoNames = new StringBuffer();
                for (int i = 0; i < displayPreferences.length; i++) {
                    BitSet domainValid = null;
                    try {
                        if (dataInfoProvider != null) {
                            DataIdentifier varSelectionDataIdnetDataIdentifier = null;
                            for (int j = 0; j < dataInfoProvider.getPDEDataContext().getDataIdentifiers().length; j++) {
                                if (dataInfoProvider.getPDEDataContext().getDataIdentifiers()[j].getName().equals(variableSelections[i])) {
                                    varSelectionDataIdnetDataIdentifier = dataInfoProvider.getPDEDataContext().getDataIdentifiers()[j];
                                }
                            }
                            if (varSelectionDataIdnetDataIdentifier != null) {
                                selectionHasVolumeVariables = selectionHasVolumeVariables || varSelectionDataIdnetDataIdentifier.getVariableType().equals(VariableType.VOLUME) || varSelectionDataIdnetDataIdentifier.getVariableType().equals(VariableType.POSTPROCESSING) || varSelectionDataIdnetDataIdentifier.getVariableType().equals(VariableType.VOLUME_REGION);
                                selectionHasMembraneVariables = selectionHasMembraneVariables || varSelectionDataIdnetDataIdentifier.getVariableType().equals(VariableType.MEMBRANE) || varSelectionDataIdnetDataIdentifier.getVariableType().equals(VariableType.MEMBRANE_REGION);
                                CartesianMesh cartesianMesh = dataInfoProvider.getPDEDataContext().getCartesianMesh();
                                int dataLength = cartesianMesh.getDataLength(varSelectionDataIdnetDataIdentifier.getVariableType());
                                domainValid = new BitSet(dataLength);
                                domainValid.clear();
                                for (int j = 0; j < dataLength; j++) {
                                    if (dataInfoProvider.isDefined(varSelectionDataIdnetDataIdentifier, j)) {
                                        domainValid.set(j);
                                    }
                                }
                            } else {
                                throw new Exception("No DataIdentifer found for variable name '" + variableSelections[i] + "'");
                            }
                        }
                    } catch (Exception e) {
                        e.printStackTrace();
                        DialogUtils.showErrorDialog(this, "Error during domain evaluation:\n" + e.getMessage());
                        return;
                    }
                    displayPreferences[i] = new DisplayPreferences(getDisplayAdapterService().getDisplayPreferences((String) variableSelections[i]), domainValid);
                    if (!getDisplayAdapterService().hasStateID((String) variableSelections[i])) {
                        noScaleInfoNames.append("--- " + (String) variableSelections[i] + "\n");
                    }
                }
                break;
            }
        case CSV:
            {
                // check for membrane variables... warn for 3D geometry...
                // one gets the whole nine yards by index, not generally useful... except for a few people like Boris :)
                boolean mbVars = false;
                DataIdentifier[] dataIDs = getPdeDataContext().getDataIdentifiers();
                for (int i = 0; i < variableSelections.length; i++) {
                    String varName = (String) variableSelections[i];
                    for (int j = 0; j < dataIDs.length; j++) {
                        if (dataIDs[j].getName().equals(varName) && dataIDs[j].getVariableType().equals(VariableType.MEMBRANE)) {
                            mbVars = true;
                            break;
                        }
                    }
                }
                if (mbVars && getPdeDataContext().getCartesianMesh().getGeometryDimension() == 3 && getJRadioButtonSlice().isSelected()) {
                    String choice = PopupGenerator.showWarningDialog(this, getDataViewerManager().getUserPreferences(), UserMessage.warn_exportMembraneData3D, null);
                    if (choice.equals(UserMessage.OPTION_CANCEL)) {
                        // user canceled
                        return;
                    }
                }
                getExportSettings1().setSimulationSelector(createSimulationSelector());
                getExportSettings1().setIsCSVExport(true);
                break;
            }
        case NRRD:
        case IMAGEJ:
        case UCD:
        case VTK_IMAGE:
        case VTK_UNSTRUCT:
            break;
        default:
            break;
    }
    ;
    if (getJRadioButtonROI().isSelected() && getROISelections().getSelectedIndex() == -1) {
        PopupGenerator.showErrorDialog(this, "To export selections, you must select at least one item from the ROI selection list");
    }
    getExportSettings1().setTimeSpecs(new TimeSpecs(getJSlider1().getValue(), getJSlider2().getValue(), getPdeDataContext().getTimePoints(), ExportConstants.TIME_RANGE));
    getExportSettings1().setDisplayPreferences(displayPreferences, Arrays.asList(variableSelections).toArray(new String[0]), viewZoom);
    getExportSettings1().setSliceCount(FormatSpecificSpecs.getSliceCount(getJRadioButtonFull().isSelected(), getNormalAxis(), getPdeDataContext().getCartesianMesh()));
    getExportSettings1().setImageSizeCalculationInfo(getPdeDataContext().getCartesianMesh(), getNormalAxis());
    getExportSettings1().setIsSmoldyn(isSmoldyn);
    ExportFormat format = getSelectedFormat();
    if (format.equals(ExportFormat.PLY)) {
        getExportSettings1().setFormatSpecificSpecs(new PLYSpecs(true, displayPreferences));
    }
    if (format.requiresFollowOn()) {
        Frame theFrame = JOptionPane.getFrameForComponent(this);
        boolean okToExport = getExportSettings1().showFormatSpecificDialog(theFrame, selectionHasVolumeVariables, selectionHasMembraneVariables);
        if (!okToExport) {
            return;
        }
    }
    if (format.equals(ExportFormat.IMAGEJ)) {
        // export nrrd for imagej direct, the we'll send to imagej from vcell client
        getExportSettings1().setFormatSpecificSpecs(new RasterSpecs(ExportConstants.NRRD_SINGLE, false));
    }
    // determine of sim result is from local (quick) run or on server.
    final OutputContext outputContext = ((ClientPDEDataContext) getPdeDataContext()).getDataManager().getOutputContext();
    final ExportSpecs exportSpecs = getExportSpecs();
    boolean isLocalSimResult = false;
    VCDataIdentifier vcId = exportSpecs.getVCDataIdentifier();
    if (vcId instanceof LocalVCDataIdentifier) {
        isLocalSimResult = true;
    }
    // find out if smoldyn export choice is 'particle' - not available at this time
    boolean isParticle = false;
    if (getExportSettings1().getFormatSpecificSpecs() instanceof ImageSpecs) {
        isParticle = ((ImageSpecs) getExportSettings1().getFormatSpecificSpecs()).getParticleMode() == FormatSpecificSpecs.PARTICLE_SELECT;
    } else if (getExportSettings1().getFormatSpecificSpecs() instanceof MovieSpecs) {
        isParticle = ((MovieSpecs) getExportSettings1().getFormatSpecificSpecs()).getParticleMode() == FormatSpecificSpecs.PARTICLE_SELECT;
    }
    if (isLocalSimResult && isParticle) {
        DialogUtils.showErrorDialog(this, "Particle export for Smoldyn particles unavailable in local data at this time.");
        return;
    }
    // pass the export request down the line; non-blocking call
    if (!isLocalSimResult) {
        // for sims that ran on server, do as before.
        getDataViewerManager().startExport(this, outputContext, exportSpecs);
    } else {
        final String SOURCE_FILE_KEY = "SOURCE_FILE_KEY";
        final String DESTINATION_FILE_KEY = "DEESTINATION_FILE_KEY";
        AsynchClientTask localExportTast = new AsynchClientTask("Start Local Export", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

            @Override
            public void run(Hashtable<String, Object> hashTable) throws Exception {
                try {
                    File primaryDir = ResourceUtil.getLocalRootDir();
                    User usr = User.tempUser;
                    File usrDir = new File(primaryDir.getAbsolutePath(), usr.getName());
                    System.setProperty(PropertyLoader.exportBaseDirInternalProperty, usrDir.getAbsolutePath() + File.separator);
                    System.setProperty(PropertyLoader.exportBaseURLProperty, usrDir.toURI().toURL().toString());
                    DataSetControllerImpl dataSetControllerImpl = new DataSetControllerImpl(null, primaryDir, null);
                    ExportServiceImpl localExportServiceImpl = new ExportServiceImpl();
                    DataServerImpl dataServerImpl = new DataServerImpl(dataSetControllerImpl, localExportServiceImpl);
                    ExportEvent localExportEvent = dataServerImpl.makeRemoteFile(outputContext, usr, exportSpecs);
                    File sourceFile = new File(usrDir, new File((new URL(localExportEvent.getLocation()).getPath())).getName());
                    hashTable.put(SOURCE_FILE_KEY, sourceFile);
                } catch (Exception e) {
                    throw new Exception("Unable to export local sim results data : " + e.getMessage(), e);
                }
            }
        };
        AsynchClientTask localSaveTask = new AsynchClientTask("Start Local Export", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {

            @Override
            public void run(Hashtable<String, Object> hashTable) throws Exception {
                File sourceFile = (File) hashTable.get(SOURCE_FILE_KEY);
                JFileChooser jFileChooser = new JFileChooser();
                jFileChooser.setSelectedFile(new File(sourceFile.getName()));
                if (jFileChooser.showSaveDialog(PDEExportDataPanel.this) == JFileChooser.APPROVE_OPTION) {
                    File destinationFile = jFileChooser.getSelectedFile();
                    if (destinationFile.exists()) {
                        final String OVERWRITE = "Overwrite";
                        final String CANCEL = "Cancel";
                        String response = DialogUtils.showWarningDialog(PDEExportDataPanel.this, "OK to Overwrite " + destinationFile.getAbsolutePath() + "?", new String[] { OVERWRITE, CANCEL }, OVERWRITE);
                        if (response == null || !response.equals(OVERWRITE)) {
                            return;
                        }
                    }
                    hashTable.put(DESTINATION_FILE_KEY, destinationFile);
                }
            }
        };
        AsynchClientTask localDeleteTempTask = new AsynchClientTask("Start Local Export", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING, false, false) {

            @Override
            public void run(Hashtable<String, Object> hashTable) throws Exception {
                File sourceFile = (File) hashTable.get(SOURCE_FILE_KEY);
                File destinationFile = (File) hashTable.get(DESTINATION_FILE_KEY);
                if (sourceFile != null && sourceFile.exists()) {
                    try {
                        if (destinationFile != null) {
                            copyFile(sourceFile, destinationFile);
                        }
                    } finally {
                        sourceFile.delete();
                    }
                }
            }
        };
        ClientTaskDispatcher.dispatch(this, new Hashtable<String, Object>(), new AsynchClientTask[] { localExportTast, localSaveTask, localDeleteTempTask }, false, true, null);
    }
}

Example 4 with ExportFormat

use of cbit.vcell.export.server.ExportFormat in project vcell by virtualcell.

the class ExportSettings method showFormatSpecificDialog.

/**
 * Comment
 */
@SuppressWarnings("incomplete-switch")
public boolean showFormatSpecificDialog(Frame reference, boolean selectionHasVolumeVars, boolean selectionHasMembraneVars) {
    JDialog dialogToShow = null;
    setClosedOK(false);
    ExportFormat format = getSelectedFormat();
    VCAssert.assertTrue(format.requiresFollowOn(), "Follow on dialog required");
    switch(format) {
        case CSV:
            dialogToShow = getJDialogASCIISettings(reference);
            break;
        case QUICKTIME:
        case ANIMATED_GIF:
            dialogToShow = getJDialogMediaSettings(reference, getSelectedFormat(), selectionHasVolumeVars, selectionHasMembraneVars, "Movie");
            break;
        case GIF:
        case FORMAT_JPEG:
            dialogToShow = getJDialogMediaSettings(reference, getSelectedFormat(), selectionHasVolumeVars, selectionHasMembraneVars, "Image");
            break;
        case NRRD:
            dialogToShow = getJDialogRasterSettings(reference);
            break;
    }
    dialogToShow.pack();
    BeanUtils.centerOnComponent(dialogToShow, reference);
    LWJDialogDecorator.decoratorFor(dialogToShow);
    // modal; blocks until OK'd or closed
    dialogToShow.setVisible(true);
    return isClosedOK();
}