Examples with DataIdentifier cbit.vcell.simdata.DataIdentifier used on opensource projects

Example 1 with DataIdentifier

use of cbit.vcell.simdata.DataIdentifier in project vcell by virtualcell.

the class PDEDataViewer method roiAction.

private void roiAction() {
    BeanUtils.setCursorThroughout(this, Cursor.getPredefinedCursor(Cursor.WAIT_CURSOR));
    try {
        final String[] ROI_COLUMN_NAMES = new String[] { "ROI source", "ROI source name", "ROI Description" };
        final Vector<Object> auxInfoV = new Vector<Object>();
        final DataIdentifier dataIdentifier = getPdeDataContext().getDataIdentifier();
        VariableType variableType = dataIdentifier.getVariableType();
        final boolean isVolume = variableType.equals(VariableType.VOLUME) || variableType.equals(VariableType.VOLUME_REGION);
        DefaultTableModel tableModel = new DefaultTableModel() {

            public boolean isCellEditable(int row, int column) {
                return false;
            }
        };
        for (int i = 0; i < ROI_COLUMN_NAMES.length; i++) {
            tableModel.addColumn(ROI_COLUMN_NAMES[i]);
        }
        // Add Snapshot ROI
        if ((isVolume ? volumeSnapshotROI : membraneSnapshotROI) != null) {
            tableModel.addRow(new Object[] { (isVolume ? "Volume" : "Membrane") + " Variables and Functions", "Snapshot", (isVolume ? volumeSnapshotROIDescription : membraneSnapshotROIDescription) + ", (values = 1.0)" });
            auxInfoV.add((isVolume ? volumeSnapshotROI : membraneSnapshotROI));
        }
        // Add user ROIs
        SpatialSelection[] userROIArr = getPDEDataContextPanel1().fetchSpatialSelections(true, false);
        for (int i = 0; userROIArr != null && i < userROIArr.length; i += 1) {
            String descr = null;
            boolean bPoint = false;
            if (isVolume) {
                if (userROIArr[i] instanceof SpatialSelectionVolume) {
                    Curve curve = ((SpatialSelectionVolume) userROIArr[i]).getCurveSelectionInfo().getCurve();
                    descr = curve.getDescription();
                    if (curve instanceof SinglePoint) {
                        bPoint = true;
                    }
                }
            } else {
                if (userROIArr[i] instanceof SpatialSelectionMembrane) {
                    SampledCurve selectionSource = ((SpatialSelectionMembrane) userROIArr[i]).getSelectionSource();
                    descr = selectionSource.getDescription();
                    if (selectionSource instanceof SinglePoint) {
                        bPoint = true;
                    }
                }
            }
            // Add Area User ROI
            BitSet fillBitSet = null;
            if (userROIArr[i] instanceof SpatialSelectionVolume) {
                fillBitSet = getFillROI((SpatialSelectionVolume) userROIArr[i]);
                if (fillBitSet != null) {
                    tableModel.addRow(new Object[] { "User Defined", descr, "Area Enclosed Volume ROI" });
                    auxInfoV.add(fillBitSet);
                }
            }
            // Add Point and Line User ROI
            if (fillBitSet == null) {
                tableModel.addRow(new Object[] { "User Defined", descr, (bPoint ? "Point" : "Line") + (isVolume ? " Volume" : " Membrane") + " ROI " });
                auxInfoV.add(userROIArr[i]);
            }
        }
        // Add sorted Geometry ROI
        final CartesianMesh cartesianMesh = getPdeDataContext().getCartesianMesh();
        HashMap<Integer, ?> regionMapSubvolumesHashMap = (isVolume ? cartesianMesh.getVolumeRegionMapSubvolume() : cartesianMesh.getMembraneRegionMapSubvolumesInOut());
        Set<?> regionMapSubvolumesEntrySet = regionMapSubvolumesHashMap.entrySet();
        Iterator<?> regionMapSubvolumesEntryIter = regionMapSubvolumesEntrySet.iterator();
        TreeSet<Object[]> sortedGeomROITreeSet = new TreeSet<Object[]>(new Comparator<Object[]>() {

            public int compare(Object[] o1, Object[] o2) {
                int result = ((String) ((Object[]) o1[0])[1]).compareToIgnoreCase((String) ((Object[]) o2[0])[1]);
                if (result == 0) {
                    result = (((Entry<Integer, ?>) o1[1]).getKey()).compareTo(((Entry<Integer, ?>) o2[1]).getKey());
                }
                return result;
            }
        });
        while (regionMapSubvolumesEntryIter.hasNext()) {
            Entry<Integer, ?> regionMapSubvolumesEntry = (Entry<Integer, ?>) regionMapSubvolumesEntryIter.next();
            sortedGeomROITreeSet.add(new Object[] { new Object[] { "Geometry", (isVolume ? getSimulationModelInfo().getVolumeNamePhysiology(((Integer) regionMapSubvolumesEntry.getValue())) : getSimulationModelInfo().getMembraneName(((int[]) regionMapSubvolumesEntry.getValue())[0], ((int[]) regionMapSubvolumesEntry.getValue())[1], false)), (isVolume ? "(svID=" + regionMapSubvolumesEntry.getValue() + " " : "(") + "vrID=" + regionMapSubvolumesEntry.getKey() + ") Predefined " + (isVolume ? "volume" : "membrane") + " region" }, regionMapSubvolumesEntry });
        }
        Iterator<Object[]> sortedGeomROIIter = sortedGeomROITreeSet.iterator();
        while (sortedGeomROIIter.hasNext()) {
            Object[] sortedGeomROIObjArr = (Object[]) sortedGeomROIIter.next();
            tableModel.addRow((Object[]) sortedGeomROIObjArr[0]);
            auxInfoV.add(sortedGeomROIObjArr[1]);
        }
        final ScrollTable roiTable = new ScrollTable();
        roiTable.setModel(tableModel);
        roiTable.setSelectionMode(ListSelectionModel.MULTIPLE_INTERVAL_SELECTION);
        roiTable.setPreferredScrollableViewportSize(new Dimension(500, 200));
        final JPanel mainJPanel = new JPanel();
        BoxLayout mainBL = new BoxLayout(mainJPanel, BoxLayout.Y_AXIS);
        mainJPanel.setLayout(mainBL);
        MiniTimePanel timeJPanel = new MiniTimePanel();
        ActionListener okAction = new ActionListener() {

            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;
                }
                int[] selectedRows = roiTable.getSelectedRows();
                if (selectedRows != null) {
                    try {
                        BitSet dataBitSet = new BitSet(getPdeDataContext().getDataValues().length);
                        for (int i = 0; i < selectedRows.length; i++) {
                            Object auxInfo = auxInfoV.elementAt(selectedRows[i]);
                            if (auxInfo instanceof BitSet) {
                                dataBitSet.or((BitSet) auxInfo);
                            } else if (auxInfo instanceof SpatialSelectionMembrane) {
                                int[] roiIndexes = ((SpatialSelectionMembrane) auxInfo).getIndexSamples().getSampledIndexes();
                                for (int j = 0; j < roiIndexes.length; j += 1) {
                                    dataBitSet.set(roiIndexes[j], true);
                                }
                            } else if (auxInfo instanceof SpatialSelectionVolume) {
                                int[] roiIndexes = ((SpatialSelectionVolume) auxInfo).getIndexSamples(0, 1).getSampledIndexes();
                                for (int j = 0; j < roiIndexes.length; j += 1) {
                                    dataBitSet.set(roiIndexes[j], true);
                                }
                            } else if (auxInfo instanceof Entry) {
                                Entry<Integer, Integer> entry = (Entry<Integer, Integer>) auxInfo;
                                if (isVolume) {
                                    int volumeRegionID = entry.getKey();
                                    dataBitSet.or(cartesianMesh.getVolumeROIFromVolumeRegionID(volumeRegionID));
                                } else {
                                    int membraneRegionID = entry.getKey();
                                    dataBitSet.or(cartesianMesh.getMembraneROIFromMembraneRegionID(membraneRegionID));
                                }
                            } else if (auxInfo instanceof BitSet) {
                                dataBitSet.or((BitSet) auxInfo);
                            } else {
                                throw new Exception("ROI table, Unknown data type: " + auxInfo.getClass().getName());
                            }
                        }
                        TimeSeriesJobSpec timeSeriesJobSpec = new TimeSeriesJobSpec(new String[] { dataIdentifier.getName() }, new BitSet[] { dataBitSet }, ((Double) timeJPanel.jcb_time_begin.getSelectedItem()).doubleValue(), 1, ((Double) timeJPanel.jcb_time_end.getSelectedItem()).doubleValue(), true, false, VCDataJobID.createVCDataJobID(getDataViewerManager().getUser(), true));
                        Hashtable<String, Object> hash = new Hashtable<String, Object>();
                        hash.put(StringKey_timeSeriesJobSpec, timeSeriesJobSpec);
                        AsynchClientTask task1 = new TimeSeriesDataRetrievalTask("Retrieve data for '" + dataIdentifier + "'", PDEDataViewer.this, getPdeDataContext());
                        AsynchClientTask task2 = new AsynchClientTask("Showing stat for '" + dataIdentifier + "'", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {

                            @Override
                            public void run(Hashtable<String, Object> hashTable) throws Exception {
                                TSJobResultsSpaceStats tsJobResultsSpaceStats = (TSJobResultsSpaceStats) hashTable.get(StringKey_timeSeriesJobResults);
                                plotSpaceStats(tsJobResultsSpaceStats);
                            }
                        };
                        ClientTaskDispatcher.dispatch(PDEDataViewer.this, hash, new AsynchClientTask[] { task1, task2 }, true, true, null);
                    } catch (Exception e1) {
                        e1.printStackTrace();
                        PopupGenerator.showErrorDialog(PDEDataViewer.this, "ROI Error.\n" + e1.getMessage(), e1);
                    }
                }
                BeanUtils.disposeParentWindow(mainJPanel);
            }
        };
        ActionListener cancelAction = new ActionListener() {

            public void actionPerformed(ActionEvent e) {
                BeanUtils.disposeParentWindow(mainJPanel);
            }
        };
        OkCancelSubPanel okCancelJPanel = new OkCancelSubPanel(okAction, cancelAction);
        roiTable.getSelectionModel().addListSelectionListener(new ListSelectionListener() {

            public void valueChanged(ListSelectionEvent e) {
                if (roiTable.getSelectedRows() != null && roiTable.getSelectedRows().length > 0) {
                    okCancelJPanel.okButton.setEnabled(true);
                } else {
                    okCancelJPanel.okButton.setEnabled(false);
                }
            }
        });
        mainJPanel.add(timeJPanel);
        mainJPanel.add(roiTable.getEnclosingScrollPane());
        mainJPanel.add(okCancelJPanel);
        // showComponentInFrame(mainJPanel,
        // "Calculate "+(isVolume?"volume":"membrane")+" statistics for '"+getPdeDataContext().getVariableName()+"'."+
        // "  Choose times and 1 or more ROI(s).");
        Frame dialogOwner = JOptionPane.getFrameForComponent(this);
        JOptionPane inputDialog = new JOptionPane(mainJPanel, JOptionPane.PLAIN_MESSAGE, 0, null, new Object[0]);
        final JDialog d = inputDialog.createDialog(dialogOwner, "Calculate " + (isVolume ? "volume" : "membrane") + " statistics for '" + getPdeDataContext().getVariableName() + "'." + "  Choose times and 1 or more ROI(s).");
        d.setResizable(true);
        try {
            DialogUtils.showModalJDialogOnTop(d, PDEDataViewer.this);
        } finally {
            d.dispose();
        }
    } finally {
        BeanUtils.setCursorThroughout(this, Cursor.getDefaultCursor());
    }
}

Example 2 with DataIdentifier

use of cbit.vcell.simdata.DataIdentifier in project vcell by virtualcell.

the class PDEDataViewerPostProcess method createPostProcessPDEDataContext.

public static PostProcessDataPDEDataContext createPostProcessPDEDataContext(final ClientPDEDataContext parentPDEDataContext) throws Exception {
    final DataOperationResults.DataProcessingOutputInfo dataProcessingOutputInfo = (DataOperationResults.DataProcessingOutputInfo) parentPDEDataContext.doDataOperation(new DataOperation.DataProcessingOutputInfoOP(parentPDEDataContext.getVCDataIdentifier(), false, parentPDEDataContext.getDataManager().getOutputContext()));
    if (dataProcessingOutputInfo == null) {
        return null;
    }
    DataSetControllerProvider dataSetControllerProvider = new DataSetControllerProvider() {

        @Override
        public DataSetController getDataSetController() throws DataAccessException {
            return new DataSetController() {

                // DataIdentifier[] dataIdentifiers;
                @Override
                public ExportEvent makeRemoteFile(OutputContext outputContext, ExportSpecs exportSpecs) throws DataAccessException, RemoteProxyException {
                    throw new DataAccessException("Not implemented");
                }

                @Override
                public TimeSeriesJobResults getTimeSeriesValues(OutputContext outputContext, VCDataIdentifier vcdataID, TimeSeriesJobSpec timeSeriesJobSpec) throws RemoteProxyException, DataAccessException {
                    // return parentPDEDataContext.getDataManager().getTimeSeriesValues(timeSeriesJobSpec);
                    DataOperation.DataProcessingOutputTimeSeriesOP dataProcessingOutputTimeSeriesOP = new DataOperation.DataProcessingOutputTimeSeriesOP(vcdataID, timeSeriesJobSpec, outputContext, getDataSetTimes(vcdataID));
                    DataOperationResults.DataProcessingOutputTimeSeriesValues dataopDataProcessingOutputTimeSeriesValues = (DataOperationResults.DataProcessingOutputTimeSeriesValues) parentPDEDataContext.doDataOperation(dataProcessingOutputTimeSeriesOP);
                    return dataopDataProcessingOutputTimeSeriesValues.getTimeSeriesJobResults();
                }

                @Override
                public SimDataBlock getSimDataBlock(OutputContext outputContext, VCDataIdentifier vcdataID, String varName, double time) throws RemoteProxyException, DataAccessException {
                    // return parentPDEDataContext.getDataManager().getSimDataBlock(varName, time);
                    DataOperationResults.DataProcessingOutputDataValues dataProcessingOutputValues = (DataOperationResults.DataProcessingOutputDataValues) parentPDEDataContext.doDataOperation(new DataOperation.DataProcessingOutputDataValuesOP(vcdataID, varName, TimePointHelper.createSingleTimeTimePointHelper(time), DataIndexHelper.createAllDataIndexesDataIndexHelper(), outputContext, null));
                    PDEDataInfo pdeDataInfo = new PDEDataInfo(vcdataID.getOwner(), vcdataID.getID(), varName, time, Long.MIN_VALUE);
                    SimDataBlock simDataBlock = new SimDataBlock(pdeDataInfo, dataProcessingOutputValues.getDataValues()[0], VariableType.POSTPROCESSING);
                    return simDataBlock;
                }

                @Override
                public boolean getParticleDataExists(VCDataIdentifier vcdataID) throws DataAccessException, RemoteProxyException {
                    // TODO Auto-generated method stub
                    return false;
                }

                @Override
                public ParticleDataBlock getParticleDataBlock(VCDataIdentifier vcdataID, double time) throws DataAccessException, RemoteProxyException {
                    // TODO Auto-generated method stub
                    return null;
                }

                @Override
                public ODESimData getODEData(VCDataIdentifier vcdataID) throws DataAccessException, RemoteProxyException {
                    // TODO Auto-generated method stub
                    return null;
                }

                @Override
                public CartesianMesh getMesh(VCDataIdentifier vcdataID) throws RemoteProxyException, DataAccessException {
                    // throw new DataAccessException("PostProcessData mesh not available at this level");
                    return null;
                }

                @Override
                public PlotData getLineScan(OutputContext outputContext, VCDataIdentifier vcdataID, String variable, double time, SpatialSelection spatialSelection) throws RemoteProxyException, DataAccessException {
                    throw new DataAccessException("Remote getLineScan method should not be called for PostProcess");
                }

                @Override
                public AnnotatedFunction[] getFunctions(OutputContext outputContext, VCDataIdentifier vcdataID) throws DataAccessException, RemoteProxyException {
                    return outputContext.getOutputFunctions();
                }

                @Override
                public double[] getDataSetTimes(VCDataIdentifier vcdataID) throws RemoteProxyException, DataAccessException {
                    return dataProcessingOutputInfo.getVariableTimePoints();
                }

                @Override
                public DataSetTimeSeries getDataSetTimeSeries(VCDataIdentifier vcdataID, String[] variableNames) throws DataAccessException, RemoteProxyException {
                    // TODO Auto-generated method stub
                    return null;
                }

                @Override
                public DataSetMetadata getDataSetMetadata(VCDataIdentifier vcdataID) throws DataAccessException, RemoteProxyException {
                    // TODO Auto-generated method stub
                    return null;
                }

                @Override
                public DataIdentifier[] getDataIdentifiers(OutputContext outputContext, VCDataIdentifier vcdataID) throws RemoteProxyException, DataAccessException {
                    // return parentPDEDataContext.getDataIdentifiers();
                    ArrayList<DataIdentifier> postProcessDataIDs = new ArrayList<DataIdentifier>();
                    if (outputContext != null && outputContext.getOutputFunctions() != null) {
                        for (int i = 0; i < outputContext.getOutputFunctions().length; i++) {
                            if (outputContext.getOutputFunctions()[i].isPostProcessFunction()) {
                                postProcessDataIDs.add(new DataIdentifier(outputContext.getOutputFunctions()[i].getName(), VariableType.POSTPROCESSING, null, false, outputContext.getOutputFunctions()[i].getDisplayName()));
                            }
                        }
                    }
                    // get 'state' variables
                    for (int i = 0; i < dataProcessingOutputInfo.getVariableNames().length; i++) {
                        if (dataProcessingOutputInfo.getPostProcessDataType(dataProcessingOutputInfo.getVariableNames()[i]).equals(PostProcessDataType.image)) {
                            DataIdentifier dataIdentifier = new DataIdentifier(dataProcessingOutputInfo.getVariableNames()[i], VariableType.POSTPROCESSING, null, false, dataProcessingOutputInfo.getVariableNames()[i]);
                            postProcessDataIDs.add(dataIdentifier);
                        }
                    }
                    if (postProcessDataIDs.size() > 0) {
                        return postProcessDataIDs.toArray(new DataIdentifier[0]);
                    }
                    return null;
                }

                @Override
                public FieldDataFileOperationResults fieldDataFileOperation(FieldDataFileOperationSpec fieldDataFileOperationSpec) throws RemoteProxyException, DataAccessException {
                    // TODO Auto-generated method stub
                    return null;
                }

                @Override
                public DataOperationResults doDataOperation(DataOperation dataOperation) throws DataAccessException, RemoteProxyException {
                    // TODO Auto-generated method stub
                    return parentPDEDataContext.doDataOperation(dataOperation);
                }

                @Override
                public VtuFileContainer getEmptyVtuMeshFiles(VCDataIdentifier vcdataID, int timeIndex) throws DataAccessException {
                    // TODO Auto-generated method stub
                    return null;
                }

                @Override
                public double[] getVtuMeshData(OutputContext outputContext, VCDataIdentifier vcdataID, VtuVarInfo var, double time) throws RemoteProxyException, DataAccessException {
                    // TODO Auto-generated method stub
                    return null;
                }

                @Override
                public VtuVarInfo[] getVtuVarInfos(OutputContext outputContext, VCDataIdentifier vcDataIdentifier) {
                    // TODO Auto-generated method stub
                    return null;
                }

                @Override
                public double[] getVtuTimes(VCDataIdentifier vcdataID) throws RemoteProxyException, DataAccessException {
                    // TODO Auto-generated method stub
                    return null;
                }

                @Override
                public NFSimMolecularConfigurations getNFSimMolecularConfigurations(VCDataIdentifier vcdataID) throws RemoteProxyException, DataAccessException {
                    // TODO Auto-generated method stub
                    return null;
                }
            };
        }
    };
    VCDataManager postProcessVCDataManager = new VCDataManager(dataSetControllerProvider);
    PDEDataManager postProcessPDEDataManager = new PDEDataManager(((ClientPDEDataContext) parentPDEDataContext).getDataManager().getOutputContext(), postProcessVCDataManager, parentPDEDataContext.getVCDataIdentifier());
    PostProcessDataPDEDataContext postProcessDataPDEDataContext = new PostProcessDataPDEDataContext(postProcessPDEDataManager);
    return postProcessDataPDEDataContext;
}

Example 3 with DataIdentifier

use of cbit.vcell.simdata.DataIdentifier in project vcell by virtualcell.

the class FrapDataUtils method importFRAPDataFromVCellSimulationData.

public static FRAPData importFRAPDataFromVCellSimulationData(File vcellSimLogFile, String variableName, String bleachedMaskVarName, Double maxIntensity, boolean bNoise, final ClientTaskStatusSupport progressListener) throws Exception {
    // bleachedMaskVarName = "laserMask_cell";
    VCSimulationIdentifier vcSimulationIdentifier = getVCSimulationIdentifierFromVCellSimulationData(vcellSimLogFile);
    VCSimulationDataIdentifier vcSimulationDataIdentifier = new VCSimulationDataIdentifier(vcSimulationIdentifier, 0);
    DataSetControllerImpl dataSetControllerImpl = getDataSetControllerImplFromVCellSimulationData(vcellSimLogFile);
    final DataJobEvent[] bStatus = new DataJobEvent[] { null };
    DataJobListener dataJobListener = new DataJobListener() {

        public void dataJobMessage(DataJobEvent event) {
            bStatus[0] = event;
            if (progressListener != null) {
                progressListener.setProgress((int) (event.getProgress() / 100.0 * .75));
            }
        }
    };
    dataSetControllerImpl.addDataJobListener(dataJobListener);
    DataIdentifier[] dataIdentifiers = getDataIdentiferListFromVCellSimulationData(vcellSimLogFile, 0);
    DataIdentifier variableNameDataIdentifier = null;
    for (int i = 0; i < dataIdentifiers.length; i++) {
        if (dataIdentifiers[i].getName().equals(variableName)) {
            variableNameDataIdentifier = dataIdentifiers[i];
            break;
        }
    }
    if (variableNameDataIdentifier == null) {
        throw new IllegalArgumentException("Variable " + variableName + " not found.");
    }
    if (!variableNameDataIdentifier.getVariableType().equals(VariableType.VOLUME)) {
        throw new IllegalArgumentException("Variable " + variableName + " is not VOLUME type.");
    }
    double[] times = dataSetControllerImpl.getDataSetTimes(vcSimulationDataIdentifier);
    CartesianMesh cartesianMesh = dataSetControllerImpl.getMesh(vcSimulationDataIdentifier);
    BitSet allBitset = new BitSet(cartesianMesh.getNumVolumeElements());
    allBitset.set(0, cartesianMesh.getNumVolumeElements() - 1);
    TimeSeriesJobSpec timeSeriesJobSpec = new TimeSeriesJobSpec(new String[] { variableName }, new BitSet[] { allBitset }, times[0], 1, times[times.length - 1], true, false, VCDataJobID.createVCDataJobID(getDotUser(), true));
    TSJobResultsSpaceStats tsJobResultsSpaceStats = (TSJobResultsSpaceStats) dataSetControllerImpl.getTimeSeriesValues(null, vcSimulationDataIdentifier, timeSeriesJobSpec);
    // wait for job to finish
    while (bStatus[0] == null || bStatus[0].getEventTypeID() != DataJobEvent.DATA_COMPLETE) {
        Thread.sleep(100);
    }
    double allTimesMin = tsJobResultsSpaceStats.getMinimums()[0][0];
    double allTimesMax = allTimesMin;
    for (int i = 0; i < times.length; i++) {
        allTimesMin = Math.min(allTimesMin, tsJobResultsSpaceStats.getMinimums()[0][i]);
        allTimesMax = Math.max(allTimesMax, tsJobResultsSpaceStats.getMaximums()[0][i]);
    }
    // double SCALE_MAX = maxIntensity.doubleValue();/*Math.pow(2,16)-1;*///Scale to 16 bits
    double linearScaleFactor = 1;
    if (maxIntensity != null) {
        linearScaleFactor = maxIntensity.doubleValue() / allTimesMax;
    }
    System.out.println("alltimesMin=" + allTimesMin + " allTimesMax=" + allTimesMax + " linearScaleFactor=" + linearScaleFactor);
    UShortImage[] scaledDataImages = new UShortImage[times.length];
    Random rnd = new Random();
    int shortMax = 65535;
    // set messge to load variable
    if (progressListener != null) {
        progressListener.setMessage("Loading variable " + variableName + "...");
    }
    for (int i = 0; i < times.length; i++) {
        double[] rawData = dataSetControllerImpl.getSimDataBlock(null, vcSimulationDataIdentifier, variableName, times[i]).getData();
        short[] scaledDataShort = new short[rawData.length];
        for (int j = 0; j < scaledDataShort.length; j++) {
            double scaledRawDataJ = rawData[j] * linearScaleFactor;
            if (bNoise) {
                double ran = rnd.nextGaussian();
                double scaledRawDataJ_withNoise = Math.max(0, (scaledRawDataJ + ran * Math.sqrt(scaledRawDataJ)));
                scaledRawDataJ_withNoise = Math.min(shortMax, scaledRawDataJ_withNoise);
                int scaledValue = (int) (scaledRawDataJ_withNoise);
                scaledDataShort[j] &= 0x0000;
                scaledDataShort[j] |= 0x0000FFFF & scaledValue;
            } else {
                int scaledValue = (int) (scaledRawDataJ);
                scaledDataShort[j] &= 0x0000;
                scaledDataShort[j] |= 0x0000FFFF & scaledValue;
            }
        }
        scaledDataImages[i] = new UShortImage(scaledDataShort, cartesianMesh.getOrigin(), cartesianMesh.getExtent(), cartesianMesh.getSizeX(), cartesianMesh.getSizeY(), cartesianMesh.getSizeZ());
        if (progressListener != null) {
            int progress = (int) (((i + 1) * 1.0 / times.length) * 100);
            progressListener.setProgress(progress);
        }
    }
    ImageDataset imageDataSet = new ImageDataset(scaledDataImages, times, cartesianMesh.getSizeZ());
    FRAPData frapData = new FRAPData(imageDataSet, new String[] { FRAPData.VFRAP_ROI_ENUM.ROI_BLEACHED.name(), FRAPData.VFRAP_ROI_ENUM.ROI_CELL.name(), FRAPData.VFRAP_ROI_ENUM.ROI_BACKGROUND.name() });
    // get rois from log file
    if (bleachedMaskVarName != null) {
        // set message to load cell ROI variable
        if (progressListener != null) {
            progressListener.setMessage("Loading ROIs...");
        }
        double[] rawROIBleached = dataSetControllerImpl.getSimDataBlock(null, vcSimulationDataIdentifier, bleachedMaskVarName, 0).getData();
        short[] scaledCellDataShort = new short[rawROIBleached.length];
        short[] scaledBleachedDataShort = new short[rawROIBleached.length];
        short[] scaledBackgoundDataShort = new short[rawROIBleached.length];
        for (int j = 0; j < scaledCellDataShort.length; j++) {
            boolean isCell = cartesianMesh.getCompartmentSubdomainNamefromVolIndex(j).equals("subVolume1");
            boolean isBackground = cartesianMesh.getCompartmentSubdomainNamefromVolIndex(j).equals("subVolume0");
            if (isCell) {
                scaledCellDataShort[j] = 1;
            }
            if (isBackground) {
                scaledBackgoundDataShort[j] = 1;
            }
            if (rawROIBleached[j] > 0.2) {
                scaledBleachedDataShort[j] = 1;
            }
        }
        UShortImage cellImage = new UShortImage(scaledCellDataShort, cartesianMesh.getOrigin(), cartesianMesh.getExtent(), cartesianMesh.getSizeX(), cartesianMesh.getSizeY(), cartesianMesh.getSizeZ());
        UShortImage bleachedImage = new UShortImage(scaledBleachedDataShort, cartesianMesh.getOrigin(), cartesianMesh.getExtent(), cartesianMesh.getSizeX(), cartesianMesh.getSizeY(), cartesianMesh.getSizeZ());
        UShortImage backgroundImage = new UShortImage(scaledBackgoundDataShort, cartesianMesh.getOrigin(), cartesianMesh.getExtent(), cartesianMesh.getSizeX(), cartesianMesh.getSizeY(), cartesianMesh.getSizeZ());
        if (progressListener != null) {
            progressListener.setProgress(100);
        }
        frapData.getRoi(FRAPData.VFRAP_ROI_ENUM.ROI_CELL.name()).setROIImages(new UShortImage[] { cellImage });
        frapData.getRoi(FRAPData.VFRAP_ROI_ENUM.ROI_BLEACHED.name()).setROIImages(new UShortImage[] { bleachedImage });
        frapData.getRoi(FRAPData.VFRAP_ROI_ENUM.ROI_BACKGROUND.name()).setROIImages(new UShortImage[] { backgroundImage });
    }
    return frapData;
}

Example 4 with DataIdentifier

use of cbit.vcell.simdata.DataIdentifier in project vcell by virtualcell.

the class PdeTimePlotMultipleVariablesPanel method initialize.

private void initialize() {
    VariableType varType = multiTimePlotHelper.getPdeDatacontext().getDataIdentifier().getVariableType();
    String varName = multiTimePlotHelper.getPdeDatacontext().getVariableName();
    String[] plotNames = new String[pointVector.size()];
    final SymbolTableEntry[] symbolTableEntries = new SymbolTableEntry[plotNames.length];
    DefaultListModel<String> pointListModel = new DefaultListModel<String>();
    for (int i = 0; i < pointVector.size(); i++) {
        Coordinate tp = null;
        if (varType.equals(VariableType.VOLUME) || varType.equals(VariableType.VOLUME_REGION) || varType.equals(VariableType.POSTPROCESSING)) {
            SpatialSelectionVolume ssv = (SpatialSelectionVolume) pointVector.get(i);
            tp = ssv.getCurveSelectionInfo().getCurve().getBeginningCoordinate();
        } else if (varType.equals(VariableType.MEMBRANE) || varType.equals(VariableType.MEMBRANE_REGION)) {
            SpatialSelectionMembrane ssm = (SpatialSelectionMembrane) pointVector.get(i);
            double midU = ssm.getCurveSelectionInfo().getCurveUfromSelectionU(.5);
            tp = ((SampledCurve) ssm.getCurveSelectionInfo().getCurve()).coordinateFromNormalizedU(midU);
        }
        plotNames[i] = varName + " at P[" + i + "]";
        String point = "P[" + i + "]  (" + niceCoordinateString(tp) + ")";
        pointListModel.addElement(point);
        if (multiTimePlotHelper.getsimulation() != null) {
            symbolTableEntries[0] = multiTimePlotHelper.getsimulation().getMathDescription().getEntry(varName);
        } else {
            System.out.println("PdeTimePlotMultipleVariablesPanel.initialize() adding artificial symbol table entries for field data");
            SimpleSymbolTable simpleSymbolTable = new SimpleSymbolTable(new String[] { varName });
            symbolTableEntries[0] = simpleSymbolTable.getEntry(varName);
        }
    }
    pointJList.setModel(pointListModel);
    pointJList.setForeground(variableJList.getForeground());
    pointJList.setVisibleRowCount(3);
    pointJList.setBackground(getBackground());
    pointJList.setSelectionBackground(getBackground());
    pointJList.setSelectionForeground(Color.black);
    plotPane = new PlotPane();
    double[][] plotDatas = tsJobResultsNoStats.getTimesAndValuesForVariable(varName);
    Plot2D plot2D = new SingleXPlot2D(symbolTableEntries, multiTimePlotHelper.getDataSymbolMetadataResolver(), ReservedVariable.TIME.getName(), plotNames, plotDatas, new String[] { "Time Plot", ReservedVariable.TIME.getName(), "" });
    plotPane.setPlot2D(plot2D);
    DataIdentifier[] dis = (multiTimePlotHelper.getCopyOfDisplayedDataIdentifiers() != null ? multiTimePlotHelper.getCopyOfDisplayedDataIdentifiers() : DataIdentifier.collectSortedSimilarDataTypes(multiTimePlotHelper.getVariableType(), multiTimePlotHelper.getPdeDatacontext().getDataIdentifiers()));
    Arrays.sort(dis, new Comparator<DataIdentifier>() {

        public int compare(DataIdentifier o1, DataIdentifier o2) {
            int bEqualIgnoreCase = o1.getDisplayName().compareToIgnoreCase(o2.getDisplayName());
            if (bEqualIgnoreCase == 0) {
                return o1.getDisplayName().compareTo(o2.getDisplayName());
            }
            return bEqualIgnoreCase;
        }
    });
    variableJList.setListData(dis);
    initVariableListSelected(variableJList, multiTimePlotHelper.getPdeDatacontext().getDataIdentifier());
    variableJList.setCellRenderer(multiTimePlotHelper.getListCellRenderer());
    setLayout(new GridBagLayout());
    JLabel label = new JLabel("Selected Points");
    label.setFont(label.getFont().deriveFont(Font.BOLD));
    GridBagConstraints gbc = new GridBagConstraints();
    gbc.gridx = 0;
    gbc.gridy = 0;
    gbc.anchor = GridBagConstraints.WEST;
    gbc.insets = new java.awt.Insets(15, 10, 4, 4);
    add(label, gbc);
    gbc = new GridBagConstraints();
    gbc.gridx = 1;
    gbc.gridy = 0;
    gbc.fill = java.awt.GridBagConstraints.BOTH;
    gbc.gridheight = 4;
    gbc.weightx = 1;
    gbc.weighty = 1;
    gbc.fill = GridBagConstraints.BOTH;
    gbc.insets = new java.awt.Insets(0, 4, 0, 0);
    add(plotPane, gbc);
    JScrollPane sp = new JScrollPane(pointJList);
    sp.setVerticalScrollBarPolicy(JScrollPane.VERTICAL_SCROLLBAR_ALWAYS);
    sp.setHorizontalScrollBarPolicy(JScrollPane.HORIZONTAL_SCROLLBAR_ALWAYS);
    gbc = new GridBagConstraints();
    gbc.gridx = 0;
    gbc.gridy = 1;
    gbc.anchor = GridBagConstraints.WEST;
    gbc.weighty = 0.5;
    gbc.fill = java.awt.GridBagConstraints.BOTH;
    gbc.insets = new java.awt.Insets(4, 10, 4, 4);
    add(sp, gbc);
    label = new JLabel("Y Axis");
    label.setFont(label.getFont().deriveFont(Font.BOLD));
    gbc = new GridBagConstraints();
    gbc.gridx = 0;
    gbc.gridy = 2;
    gbc.anchor = GridBagConstraints.WEST;
    gbc.insets = new java.awt.Insets(4, 10, 4, 4);
    add(label, gbc);
    sp = new JScrollPane(variableJList);
    sp.setVerticalScrollBarPolicy(JScrollPane.VERTICAL_SCROLLBAR_ALWAYS);
    sp.setHorizontalScrollBarPolicy(JScrollPane.HORIZONTAL_SCROLLBAR_ALWAYS);
    gbc = new GridBagConstraints();
    gbc.gridx = 0;
    gbc.gridy = 3;
    gbc.weightx = 0.2;
    gbc.weighty = 1;
    gbc.insets = new java.awt.Insets(4, 10, 50, 4);
    gbc.fill = java.awt.GridBagConstraints.BOTH;
    add(sp, gbc);
    variableJList.addListSelectionListener(eventHandler);
    multiTimePlotHelper.addPropertyChangeListener(eventHandler);
}

Example 5 with DataIdentifier

use of cbit.vcell.simdata.DataIdentifier in project vcell by virtualcell.

the class PdeTimePlotMultipleVariablesPanel method showTimePlot.

public void showTimePlot() {
    if ((plotChangeTimer = ClientTaskDispatcher.getBlockingTimer(this, multiTimePlotHelper.getPdeDatacontext(), null, plotChangeTimer, new ActionListener() {

        @Override
        public void actionPerformed(ActionEvent e2) {
            showTimePlot();
        }
    }, "PdeTimePlotMultipleVariablesPanel update...")) != null) {
        return;
    }
    VariableType varType = multiTimePlotHelper.getVariableType();
    Object[] selectedValues = variableJList.getSelectedValues();
    DataIdentifier[] selectedDataIdentifiers = new DataIdentifier[selectedValues.length];
    System.arraycopy(selectedValues, 0, selectedDataIdentifiers, 0, selectedValues.length);
    if (selectedDataIdentifiers.length > 1) {
        for (DataIdentifier selectedDataIdentifier : selectedDataIdentifiers) {
            if (!selectedDataIdentifier.getVariableType().getVariableDomain().equals(varType.getVariableDomain())) {
                PopupGenerator.showErrorDialog(this, "Please choose VOLUME variables or MEMBRANE variables only");
                variableJList.clearSelection();
                variableJList.setSelectedValue(multiTimePlotHelper.getPdeDatacontext().getVariableName(), true);
                return;
            }
        }
    }
    try {
        final int numSelectedVariables = selectedDataIdentifiers.length;
        final int numSelectedSpatialPoints = pointVector.size();
        int[][] indices = new int[numSelectedVariables][numSelectedSpatialPoints];
        // 
        for (int i = 0; i < numSelectedSpatialPoints; i++) {
            for (int v = 0; v < numSelectedVariables; v++) {
                if (selectedDataIdentifiers[v].getVariableType().equals(varType)) {
                    if (varType.equals(VariableType.VOLUME) || varType.equals(VariableType.VOLUME_REGION) || varType.equals(VariableType.POSTPROCESSING)) {
                        SpatialSelectionVolume ssv = (SpatialSelectionVolume) pointVector.get(i);
                        indices[v][i] = ssv.getIndex(0);
                    } else if (varType.equals(VariableType.MEMBRANE) || varType.equals(VariableType.MEMBRANE_REGION)) {
                        SpatialSelectionMembrane ssm = (SpatialSelectionMembrane) pointVector.get(i);
                        indices[v][i] = ssm.getIndex(0);
                    }
                } else {
                    if (varType.equals(VariableType.VOLUME) || varType.equals(VariableType.VOLUME_REGION) || varType.equals(VariableType.POSTPROCESSING)) {
                        SpatialSelectionVolume ssv = (SpatialSelectionVolume) pointVector2.get(i);
                        indices[v][i] = ssv.getIndex(0);
                    } else if (varType.equals(VariableType.MEMBRANE) || varType.equals(VariableType.MEMBRANE_REGION)) {
                        SpatialSelectionMembrane ssm = (SpatialSelectionMembrane) pointVector2.get(i);
                        indices[v][i] = ssm.getIndex(0);
                    }
                }
            }
        }
        final String[] selectedVarNames = new String[numSelectedVariables];
        for (int i = 0; i < selectedVarNames.length; i++) {
            selectedVarNames[i] = selectedDataIdentifiers[i].getName();
        }
        final double[] timePoints = multiTimePlotHelper.getPdeDatacontext().getTimePoints();
        TimeSeriesJobSpec tsjs = new TimeSeriesJobSpec(selectedVarNames, indices, null, timePoints[0], 1, timePoints[timePoints.length - 1], VCDataJobID.createVCDataJobID(multiTimePlotHelper.getUser(), true));
        if (!tsjs.getVcDataJobID().isBackgroundTask()) {
            throw new RuntimeException("Use getTimeSeries(...) if not a background job");
        }
        Hashtable<String, Object> hash = new Hashtable<String, Object>();
        hash.put(PDEDataViewer.StringKey_timeSeriesJobSpec, tsjs);
        AsynchClientTask task1 = new PDEDataViewer.TimeSeriesDataRetrievalTask("Retrieving Data", multiTimePlotHelper, multiTimePlotHelper.getPdeDatacontext());
        AsynchClientTask task2 = new AsynchClientTask("showing time plot", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {

            @Override
            public void run(Hashtable<String, Object> hashTable) throws Exception {
                TSJobResultsNoStats tsJobResultsNoStats = (TSJobResultsNoStats) hashTable.get(PDEDataViewer.StringKey_timeSeriesJobResults);
                int plotCount = numSelectedVariables * numSelectedSpatialPoints;
                SymbolTableEntry[] symbolTableEntries = new SymbolTableEntry[plotCount];
                String[] plotNames = new String[plotCount];
                double[][] plotDatas = new double[1 + plotCount][];
                plotDatas[0] = timePoints;
                int plotIndex = 0;
                for (int v = 0; v < numSelectedVariables; v++) {
                    String varName = selectedVarNames[v];
                    double[][] data = tsJobResultsNoStats.getTimesAndValuesForVariable(varName);
                    for (int i = 1; i < data.length; i++) {
                        symbolTableEntries[plotIndex] = multiTimePlotHelper.getsimulation().getMathDescription().getEntry(varName);
                        plotNames[plotIndex] = varName + " at P[" + (i - 1) + "]";
                        plotDatas[plotIndex + 1] = data[i];
                        plotIndex++;
                    }
                }
                Plot2D plot2D = new SingleXPlot2D(symbolTableEntries, multiTimePlotHelper.getDataSymbolMetadataResolver(), ReservedVariable.TIME.getName(), plotNames, plotDatas, new String[] { "Time Plot", ReservedVariable.TIME.getName(), "" });
                plotPane.setPlot2D(plot2D);
            }
        };
        ClientTaskDispatcher.dispatch(this, hash, new AsynchClientTask[] { task1, task2 }, false, true, true, null, false);
    } catch (Exception e) {
        e.printStackTrace(System.out);
    }
}