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

Example 1 with TimeSpecs

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

the class PDEDataViewer method sendTimeSeriesImageJ.

// private Hashtable<String, JLabel> sendTimeSeriesLabels = new Hashtable<>();
// @Override
// public void exportMessage(ExportEvent event) {
// super.exportMessage(event);
// if(sendTimeSeriesLabels.size() > 0){
// JLabel messgLabel = sendTimeSeriesLabels.values().iterator().next();
// SwingUtilities.invokeLater(new Runnable() {
// @Override
// public void run() {
// messgLabel.setText(event.getMessageData().toString());
// }
// });
// }
// }
private void sendTimeSeriesImageJ() {
    final JPanel mainJPanel = new JPanel();
    BoxLayout mainBL = new BoxLayout(mainJPanel, BoxLayout.Y_AXIS);
    mainJPanel.setLayout(mainBL);
    final boolean[] response = new boolean[] { false };
    MiniTimePanel timeJPanel = new MiniTimePanel();
    final JLabel messgLabel = new JLabel("time points to export:" + (timeJPanel.jcb_time_end.getSelectedIndex() - timeJPanel.jcb_time_begin.getSelectedIndex() + 1));
    JRadioButton slicebtn = new JRadioButton("Slice " + getPDEDataContextPanel1().getSlice() + " only");
    slicebtn.setSelected(true);
    JPanel messageAndSlicePanel = null;
    if (getPdeDataContext().getCartesianMesh().getGeometryDimension() == 3) {
        messageAndSlicePanel = new JPanel();
        ((FlowLayout) messageAndSlicePanel.getLayout()).setAlignment(FlowLayout.LEFT);
        ButtonGroup buttonGroup = new ButtonGroup();
        JRadioButton allslicebtn = new JRadioButton("All slices");
        buttonGroup.add(slicebtn);
        buttonGroup.add(allslicebtn);
        messageAndSlicePanel.add(messgLabel);
        messageAndSlicePanel.add(slicebtn);
        messageAndSlicePanel.add(allslicebtn);
    }
    ActionListener okAction = new ActionListener() {

        @Override
        public void actionPerformed(ActionEvent e) {
            if (((Double) timeJPanel.jcb_time_begin.getSelectedItem()).compareTo((Double) timeJPanel.jcb_time_end.getSelectedItem()) > 0) {
                PopupGenerator.showErrorDialog(PDEDataViewer.this, "Selected 'Begin Time' must be less than or equal to 'End Time'");
                return;
            }
            response[0] = true;
            BeanUtils.disposeParentWindow(mainJPanel);
        }
    };
    ActionListener cancelAction = new ActionListener() {

        @Override
        public void actionPerformed(ActionEvent e) {
            BeanUtils.disposeParentWindow(mainJPanel);
        }
    };
    final OkCancelSubPanel okCancelJPanel = new OkCancelSubPanel(okAction, cancelAction);
    ActionListener rangeListener = new ActionListener() {

        @Override
        public void actionPerformed(ActionEvent e) {
            int range = timeJPanel.jcb_time_end.getSelectedIndex() - timeJPanel.jcb_time_begin.getSelectedIndex() + 1;
            okCancelJPanel.okButton.setEnabled(range > 0);
            messgLabel.setText((range < 0 ? "Error: begin time must be < end time" : "time points to export:" + (range)));
        }
    };
    timeJPanel.jcb_time_end.addActionListener(rangeListener);
    timeJPanel.jcb_time_begin.addActionListener(rangeListener);
    okCancelJPanel.okButton.setEnabled(true);
    mainJPanel.add(timeJPanel);
    mainJPanel.add((messageAndSlicePanel == null ? messgLabel : messageAndSlicePanel));
    mainJPanel.add(okCancelJPanel);
    Frame dialogOwner = JOptionPane.getFrameForComponent(this);
    JOptionPane inputDialog = new JOptionPane(mainJPanel, JOptionPane.PLAIN_MESSAGE, 0, null, new Object[0]);
    final JDialog d = inputDialog.createDialog(dialogOwner, "'" + getSimulationModelInfo().getContextName() + "':'" + getSimulationModelInfo().getSimulationName() + "':'" + getPdeDataContext().getVariableName() + "'");
    d.setResizable(true);
    d.setModal(true);
    d.pack();
    d.setVisible(true);
    // }
    if (!response[0]) {
        return;
    }
    ExportSpecs exportSpecs = new ExportSpecs(getPdeDataContext().getVCDataIdentifier(), ExportFormat.IMAGEJ, new VariableSpecs(new String[] { getPdeDataContext().getDataIdentifier().getName() }, ExportConstants.VARIABLE_MULTI), new TimeSpecs(timeJPanel.jcb_time_begin.getSelectedIndex(), timeJPanel.jcb_time_end.getSelectedIndex(), getPdeDataContext().getTimePoints(), ExportConstants.TIME_RANGE), new GeometrySpecs(null, getPDEDataContextPanel1().getNormalAxis(), getPDEDataContextPanel1().getSlice(), (slicebtn.isSelected() ? ExportConstants.GEOMETRY_SLICE : ExportConstants.GEOMETRY_FULL)), new RasterSpecs(ExportConstants.NRRD_BY_VARIABLE, false), getSimulationModelInfo().getSimulationName(), getSimulationModelInfo().getContextName());
    getDataViewerManager().startExport(this, ((ClientPDEDataContext) getPdeDataContext()).getDataManager().getOutputContext(), exportSpecs);
}

Example 2 with TimeSpecs

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

the class PDEExportDataPanel method getExportSpecs.

/**
 * This method was created in VisualAge.
 * @return cbit.vcell.export.server.ExportSpecs
 */
private ExportSpecs getExportSpecs() {
    @SuppressWarnings("deprecation") Object[] variableSelections = getJListVariables().getSelectedValues();
    String[] variableNames = new String[variableSelections.length];
    for (int i = 0; i < variableSelections.length; i++) {
        variableNames[i] = (String) variableSelections[i];
    }
    VariableSpecs variableSpecs = new VariableSpecs(variableNames, ExportConstants.VARIABLE_MULTI);
    TimeSpecs timeSpecs = new TimeSpecs(getJSlider1().getValue(), getJSlider2().getValue(), getPdeDataContext().getTimePoints(), ExportConstants.TIME_RANGE);
    int geoMode = ExportConstants.GEOMETRY_SELECTIONS;
    if (getJRadioButtonSlice().isSelected()) {
        geoMode = ExportConstants.GEOMETRY_SLICE;
    } else if (getJRadioButtonFull().isSelected()) {
        geoMode = ExportConstants.GEOMETRY_FULL;
    }
    Object[] selectionsArr = getROISelections().getSelectedValuesList().toArray();
    SpatialSelection[] selections = new SpatialSelection[selectionsArr.length];
    for (int i = 0; i < selections.length; i++) {
        selections[i] = (SpatialSelection) selectionsArr[i];
    }
    GeometrySpecs geometrySpecs = new GeometrySpecs(selections, getNormalAxis(), getSlice(), geoMode);
    return new ExportSpecs(getPdeDataContext().getVCDataIdentifier(), getExportSettings1().getSelectedFormat(), variableSpecs, timeSpecs, geometrySpecs, getExportSettings1().getFormatSpecificSpecs(), dataInfoProvider.getSimulationModelInfo().getSimulationName(), dataInfoProvider.getSimulationModelInfo().getContextName());
}

Example 3 with TimeSpecs

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

the class ClientRequestManager method downloadExportedData.

/**
 * Comment
 */
public static void downloadExportedData(final Component requester, final UserPreferences userPrefs, final ExportEvent evt) {
    AsynchClientTask task1 = new AsynchClientTask("Retrieving data from '" + evt.getLocation() + "'", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            final Exception[] excArr = new Exception[] { null };
            final boolean[] bFlagArr = new boolean[] { false };
            final ByteArrayOutputStream[] baosArr = new ByteArrayOutputStream[1];
            final HttpGet[] httpGetArr = new HttpGet[1];
            final ImageJConnection[] imagejConnetArr = new ImageJConnection[1];
            // Start download of exported file in separate thread that is interruptible (apache HTTPClient)
            Thread interruptible = new Thread(new Runnable() {

                @Override
                public void run() {
                    if (getClientTaskStatusSupport() != null) {
                        getClientTaskStatusSupport().setMessage("downloading data...");
                    }
                    CloseableHttpClient httpclient = HttpClients.createDefault();
                    httpGetArr[0] = new HttpGet(evt.getLocation());
                    CloseableHttpResponse response = null;
                    try {
                        response = httpclient.execute(httpGetArr[0]);
                        HttpEntity entity = response.getEntity();
                        if (entity != null) {
                            long size = entity.getContentLength();
                            InputStream instream = entity.getContent();
                            try {
                                // Thread.sleep(60000);
                                if (size > 0) {
                                    baosArr[0] = new ByteArrayOutputStream((int) size);
                                } else {
                                    baosArr[0] = new ByteArrayOutputStream();
                                }
                                IOUtils.copy(instream, baosArr[0]);
                            } finally {
                                instream.close();
                            }
                        }
                    } catch (Exception e) {
                        excArr[0] = e;
                    } finally {
                        if (imagejConnetArr[0] != null) {
                            imagejConnetArr[0].closeConnection();
                        }
                        if (response != null) {
                            try {
                                response.close();
                            } catch (Exception e) {
                            }
                        }
                        if (httpclient != null) {
                            try {
                                httpclient.close();
                            } catch (Exception e) {
                            }
                        }
                        bFlagArr[0] = true;
                    }
                }
            });
            interruptible.start();
            // Wait for download to 1-finish, 2-fail or 3-be cancelled by user
            while (!bFlagArr[0]) {
                if (getClientTaskStatusSupport() != null && getClientTaskStatusSupport().isInterrupted()) {
                    // user cancelled
                    if (httpGetArr[0] != null) {
                        httpGetArr[0].abort();
                    }
                    if (imagejConnetArr[0] != null) {
                        imagejConnetArr[0].closeConnection();
                    }
                    throw UserCancelException.CANCEL_GENERIC;
                }
                try {
                    Thread.sleep(500);
                } catch (InterruptedException e) {
                    // caused by pressing 'cancel' button on progresspopup
                    if (httpGetArr[0] != null) {
                        httpGetArr[0].abort();
                    }
                    if (imagejConnetArr[0] != null) {
                        imagejConnetArr[0].closeConnection();
                    }
                    if (getClientTaskStatusSupport() != null && getClientTaskStatusSupport().isInterrupted()) {
                        throw UserCancelException.CANCEL_GENERIC;
                    }
                }
            }
            if (excArr[0] != null) {
                // download failed
                throw excArr[0];
            }
            // 
            if (evt.getFormat() == null || !evt.getFormat().equals("IMAGEJ")) {
                // save for file save operations
                hashTable.put(BYTES_KEY, baosArr[0].toByteArray());
            } else {
                // NRRD format send to ImageJ
                if (getClientTaskStatusSupport() != null) {
                    getClientTaskStatusSupport().setMessage("unpacking data...");
                }
                ByteArrayInputStream bais = new ByteArrayInputStream(baosArr[0].toByteArray());
                ZipInputStream zis = null;
                BufferedInputStream bis = null;
                try {
                    zis = new ZipInputStream(bais);
                    ZipEntry entry = zis.getNextEntry();
                    // System.out.println("zipfile entry name="+entry.getName()+"zipfile entry size="+entry.getSize());
                    // File tempf = new File("C:\\temp\\tempf.nrrd");
                    // FileOutputStream fos = new FileOutputStream(tempf);
                    // byte[] mybuf = new byte[1000];
                    // int numread = 0;
                    // while((numread = zis.read(mybuf)) != -1){
                    // fos.write(mybuf, 0, numread);
                    // }
                    // fos.close();
                    TimeSpecs timeSpecs = evt.getTimeSpecs();
                    double[] timePoints = new double[timeSpecs.getEndTimeIndex() - timeSpecs.getBeginTimeIndex() + 1];
                    for (int tp = timeSpecs.getBeginTimeIndex(); tp <= timeSpecs.getEndTimeIndex(); tp++) {
                        timePoints[tp - timeSpecs.getBeginTimeIndex()] = timeSpecs.getAllTimes()[tp];
                    }
                    // doesn't open connection until later
                    imagejConnetArr[0] = new ImageJConnection(ImageJHelper.ExternalCommunicator.IMAGEJ);
                    bis = new BufferedInputStream(zis);
                    ImageJHelper.vcellSendNRRD(requester, bis, getClientTaskStatusSupport(), imagejConnetArr[0], "VCell exported data '" + entry.getName() + "'", timePoints, evt.getVariableSpecs().getVariableNames());
                } finally {
                    if (zis != null) {
                        try {
                            zis.closeEntry();
                            zis.close();
                        } catch (Exception e) {
                            e.printStackTrace();
                        }
                    }
                    if (bis != null) {
                        try {
                            bis.close();
                        } catch (Exception e) {
                            e.printStackTrace();
                        }
                    }
                }
                // finished, exit all further tasks
                throw UserCancelException.CANCEL_GENERIC;
            }
        }
    };
    AsynchClientTask task2 = new AsynchClientTask("selecting file to save", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            // user pref could be null if trying local export
            String defaultPath = getPreferredPath(userPrefs);
            final VCFileChooser fileChooser = new VCFileChooser(defaultPath);
            fileChooser.setFileSelectionMode(JFileChooser.FILES_ONLY);
            fileChooser.setMultiSelectionEnabled(false);
            String name = evt.getDataIdString();
            String suffix = null;
            if (evt.getLocation().toLowerCase().endsWith(".mov")) {
                fileChooser.addChoosableFileFilter(FileFilters.FILE_FILTER_MOV);
                fileChooser.setFileFilter(FileFilters.FILE_FILTER_MOV);
                suffix = "_exported.mov";
            } else if (evt.getLocation().toLowerCase().endsWith(".gif")) {
                fileChooser.addChoosableFileFilter(FileFilters.FILE_FILTER_GIF);
                fileChooser.setFileFilter(FileFilters.FILE_FILTER_GIF);
                suffix = "_exported.gif";
            } else if (evt.getLocation().toLowerCase().endsWith(".jpeg")) {
                fileChooser.addChoosableFileFilter(FileFilters.FILE_FILTER_JPEG);
                fileChooser.setFileFilter(FileFilters.FILE_FILTER_JPEG);
                suffix = "_exported.jpeg";
            } else {
                fileChooser.addChoosableFileFilter(FileFilters.FILE_FILTER_ZIP);
                fileChooser.setFileFilter(FileFilters.FILE_FILTER_ZIP);
                suffix = "_exported.zip";
            }
            File file = new File(name + suffix);
            if (file.exists()) {
                int count = 0;
                do {
                    file = new File(name + "_" + count + suffix);
                    count++;
                } while (file.exists());
            }
            fileChooser.setSelectedFile(file);
            fileChooser.setDialogTitle("Save exported dataset...");
            int approve = fileChooser.showSaveDialog(requester);
            if (approve == JFileChooser.APPROVE_OPTION) {
                hashTable.put("selectedFile", fileChooser.getSelectedFile());
            } else {
                fileChooser.setSelectedFile(null);
            }
        }
    };
    AsynchClientTask task3 = new AsynchClientTask("saving to file", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            File selectedFile = (File) hashTable.get("selectedFile");
            if (selectedFile == null) {
                return;
            }
            setPreferredPath(userPrefs, selectedFile);
            // System.out.println("New preferred file path: " + newPath + ", Old preferred file path: " + defaultPath);
            if (selectedFile.exists()) {
                String question = null;
                if (userPrefs != null) {
                    question = PopupGenerator.showWarningDialog(requester, userPrefs, UserMessage.warn_OverwriteFile, selectedFile.getAbsolutePath());
                } else {
                    question = DialogUtils.showWarningDialog(requester, "Overwrite File?", "Overwrite file '" + selectedFile.getAbsolutePath() + "'?", new String[] { UserMessage.OPTION_OVERWRITE_FILE, UserMessage.OPTION_CANCEL }, UserMessage.OPTION_OVERWRITE_FILE);
                }
                if (question != null && question.equals(UserMessage.OPTION_CANCEL)) {
                    return;
                }
            }
            byte[] bytes = (byte[]) hashTable.get(BYTES_KEY);
            FileOutputStream fo = new FileOutputStream(selectedFile);
            fo.write(bytes);
            fo.close();
        }
    };
    ClientTaskDispatcher.dispatch(requester, new Hashtable<String, Object>(), new AsynchClientTask[] { task1, task2, task3 }, false, true, null);
}

Example 4 with TimeSpecs

use of cbit.vcell.export.server.TimeSpecs 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 5 with TimeSpecs

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

the class ExportEvent method fromJsonRep.

public static ExportEvent fromJsonRep(Object eventSource, ExportEventRepresentation rep) {
    User user = new User(rep.username, new KeyValue(rep.userkey));
    TimeSpecs timeSpecs = null;
    if (rep.exportTimeSpecs != null) {
        timeSpecs = TimeSpecs.fromJsonRep(rep.exportTimeSpecs);
    }
    VariableSpecs variableSpecs = null;
    if (rep.exportVariableSpecs != null) {
        variableSpecs = VariableSpecs.fromJsonRep(rep.exportVariableSpecs);
    }
    ExportEvent event = new ExportEvent(eventSource, rep.jobid, user, rep.dataIdString, new KeyValue(rep.dataKey), rep.eventType, rep.format, rep.location, rep.progress, timeSpecs, variableSpecs);
    return event;
}