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

Example 1 with DataInfoProvider

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

the class PDEDataViewer method setupDataInfoProvider.

private void setupDataInfoProvider() throws Exception {
    // }
    if (getPdeDataContext() != null && getSimulationModelInfo() != null) {
        getPDEDataContextPanel1().setDataInfoProvider(new DataInfoProvider(getPdeDataContext(), getSimulationModelInfo()));
        getPDEExportPanel1().setDataInfoProvider(getPDEDataContextPanel1().getDataInfoProvider());
        if (getSimulationModelInfo() instanceof SimulationWorkspaceModelInfo && ((SimulationWorkspaceModelInfo) getSimulationModelInfo()).getDataSymbolMetadataResolver().getUniqueFilterCategories() != null) {
            DefaultDataIdentifierFilter newFilter = new DefaultDataIdentifierFilter(((SimulationWorkspaceModelInfo) getSimulationModelInfo()).getDataSymbolMetadataResolver());
            if (ivjJTabbedPane1.getTabCount() < 4) {
                newFilter.setPostProcessingMode(true);
            }
            getPDEPlotControlPanel1().setDataIdentifierFilter(newFilter);
        }
    } else {
        getPDEDataContextPanel1().setDataInfoProvider(null);
        getPDEExportPanel1().setDataInfoProvider(null);
    }
}

Example 2 with DataInfoProvider

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

the class PDEDataViewer method makeSurfaceMovie.

private void makeSurfaceMovie(final SurfaceCanvas surfaceCanvas, final int varTotalNumIndices, final String movieDataVarName, final DisplayAdapterService movieDAS, final VCDataIdentifier movieVCDataIdentifier) {
    final SurfaceMovieSettingsPanel smsp = new SurfaceMovieSettingsPanel();
    final double[] timePoints = getPdeDataContext().getTimePoints();
    final int surfaceWidth = surfaceCanvas.getWidth();
    final int surfaceHeight = surfaceCanvas.getHeight();
    smsp.init(surfaceWidth, surfaceHeight, timePoints);
    while (true) {
        if (PopupGenerator.showComponentOKCancelDialog(this, smsp, "Movie Settings for var " + movieDataVarName) != JOptionPane.OK_OPTION) {
            return;
        }
        long movieSize = (smsp.getTotalFrames() * surfaceWidth * surfaceHeight * 3);
        // raw data size;
        long rawDataSize = (smsp.getTotalFrames() * varTotalNumIndices * 8);
        if (movieSize + rawDataSize > 50000000) {
            final String YES_RESULT = "Yes";
            String result = PopupGenerator.showWarningDialog(this, "Movie processing will require at least " + (movieSize + rawDataSize) / 1000000 + " mega-bytes of memory.\nMovie size will be " + (movieSize >= 1000000 ? movieSize / 1000000 + " mega-bytes." : movieSize / 1000.0 + " kilo-bytes.") + " Continue?", new String[] { YES_RESULT, "No" }, YES_RESULT);
            if (result != null && result.equals(YES_RESULT)) {
                break;
            }
        } else {
            break;
        }
    }
    final int beginTimeIndex = smsp.getBeginTimeIndex();
    final int endTimeIndex = smsp.getEndTimeIndex();
    final int step = smsp.getSkipParameter() + 1;
    final String[] varNames = new String[] { movieDataVarName };
    int[] allIndices = new int[varTotalNumIndices];
    for (int i = 0; i < allIndices.length; i++) {
        allIndices[i] = i;
    }
    final TimeSeriesJobSpec timeSeriesJobSpec = new TimeSeriesJobSpec(varNames, new int[][] { allIndices }, null, timePoints[beginTimeIndex], step, timePoints[endTimeIndex], VCDataJobID.createVCDataJobID(getDataViewerManager().getUser(), true));
    Hashtable<String, Object> hash = new Hashtable<String, Object>();
    hash.put(StringKey_timeSeriesJobSpec, timeSeriesJobSpec);
    AsynchClientTask task1 = new TimeSeriesDataRetrievalTask("Retrieving data for variable '" + movieDataVarName + "'", PDEDataViewer.this, getPdeDataContext());
    AsynchClientTask task2 = new AsynchClientTask("select a file", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            VCFileChooser fileChooser = new VCFileChooser();
            fileChooser.setFileSelectionMode(JFileChooser.FILES_ONLY);
            fileChooser.setMultiSelectionEnabled(false);
            fileChooser.addChoosableFileFilter(FileFilters.FILE_FILTER_MOV);
            // Set the default file filter...
            fileChooser.setFileFilter(FileFilters.FILE_FILTER_MOV);
            // remove all selector
            fileChooser.removeChoosableFileFilter(fileChooser.getAcceptAllFileFilter());
            fileChooser.setDialogTitle("Saving surface movie");
            File selectedFile = null;
            while (true) {
                if (fileChooser.showSaveDialog(PDEDataViewer.this) != JFileChooser.APPROVE_OPTION) {
                    return;
                }
                selectedFile = fileChooser.getSelectedFile();
                if (!selectedFile.getName().endsWith(".mov")) {
                    selectedFile = new File(selectedFile.getAbsolutePath() + ".mov");
                }
                if (selectedFile.exists()) {
                    final String YES_RESULT = "Yes";
                    String result = PopupGenerator.showWarningDialog(PDEDataViewer.this, "Overwrite exisitng file:\n" + selectedFile.getAbsolutePath() + "?", new String[] { YES_RESULT, "No" }, YES_RESULT);
                    if (result != null && result.equals(YES_RESULT)) {
                        break;
                    }
                } else {
                    break;
                }
            }
            hashTable.put("selectedFile", selectedFile);
        }
    };
    AsynchClientTask task3 = new AsynchClientTask("create movie", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            File selectedFile = (File) hashTable.get("selectedFile");
            if (selectedFile == null) {
                return;
            }
            TSJobResultsNoStats tsJobResultsNoStats = (TSJobResultsNoStats) hashTable.get(StringKey_timeSeriesJobResults);
            double[][] timeSeries = tsJobResultsNoStats.getTimesAndValuesForVariable(movieDataVarName);
            int[] singleFrame = new int[surfaceWidth * surfaceHeight];
            BufferedImage bufferedImage = new BufferedImage(surfaceWidth, surfaceHeight, BufferedImage.TYPE_3BYTE_BGR);
            Graphics2D g2D = bufferedImage.createGraphics();
            VideoMediaChunk[] chunks = new VideoMediaChunk[tsJobResultsNoStats.getTimes().length];
            VideoMediaSample sample;
            int sampleDuration = 0;
            int timeScale = smsp.getFramesPerSecond();
            int bitsPerPixel = 32;
            DisplayAdapterService das = new DisplayAdapterService(movieDAS);
            int[][] origSurfacesColors = surfaceCanvas.getSurfacesColors();
            DataInfoProvider dataInfoProvider = getPDEDataContextPanel1().getDataInfoProvider();
            FileDataContainerManager fileDataContainerManager = new FileDataContainerManager();
            try {
                try {
                    for (int t = 0; t < tsJobResultsNoStats.getTimes().length; t++) {
                        getClientTaskStatusSupport().setMessage("Creating Movie... Progress " + NumberUtils.formatNumber(100.0 * ((double) t / (double) tsJobResultsNoStats.getTimes().length), 3) + "%");
                        double min = Double.POSITIVE_INFINITY;
                        double max = Double.NEGATIVE_INFINITY;
                        for (int index = 1; index < timeSeries.length; index++) {
                            double v = timeSeries[index][t];
                            if ((dataInfoProvider == null || dataInfoProvider.isDefined(index - 1)) && !Double.isNaN(v) && !Double.isInfinite(v)) {
                                min = Math.min(min, v);
                                max = Math.max(max, v);
                            }
                        }
                        das.setValueDomain(new Range(min, max));
                        if (das.getAutoScale()) {
                            das.setActiveScaleRange(new Range(min, max));
                        }
                        int[][] surfacesColors = new int[surfaceCanvas.getSurfaceCollection().getSurfaceCount()][];
                        for (int i = 0; i < surfaceCanvas.getSurfaceCollection().getSurfaceCount(); i += 1) {
                            Surface surface = surfaceCanvas.getSurfaceCollection().getSurfaces(i);
                            surfacesColors[i] = new int[surface.getPolygonCount()];
                            for (int j = 0; j < surface.getPolygonCount(); j += 1) {
                                int membIndex = meshRegionSurfaces.getMembraneIndexForPolygon(i, j);
                                surfacesColors[i][j] = das.getColorFromValue(timeSeries[membIndex + 1][t]);
                            }
                        }
                        surfaceCanvas.setSurfacesColors(surfacesColors);
                        surfaceCanvas.paintImmediately(0, 0, surfaceWidth, surfaceHeight);
                        surfaceCanvas.paint(g2D);
                        bufferedImage.getRGB(0, 0, surfaceWidth, surfaceHeight, singleFrame, 0, surfaceWidth);
                        sampleDuration = 1;
                        sample = FormatSpecificSpecs.getVideoMediaSample(surfaceWidth, surfaceHeight * varNames.length, sampleDuration, false, FormatSpecificSpecs.CODEC_JPEG, 1.0f, singleFrame);
                        chunks[t] = new VideoMediaChunk(sample, fileDataContainerManager);
                    }
                } finally {
                    surfaceCanvas.setSurfacesColors(origSurfacesColors);
                    surfaceCanvas.paintImmediately(0, 0, surfaceWidth, surfaceHeight);
                }
                MediaTrack videoTrack = new MediaTrack(chunks);
                MediaMovie newMovie = new MediaMovie(videoTrack, videoTrack.getDuration(), timeScale);
                newMovie.addUserDataEntry(new UserDataEntry("cpy", "\u00A9" + (new GregorianCalendar()).get(Calendar.YEAR) + ", UCHC"));
                newMovie.addUserDataEntry(new UserDataEntry("des", "Dataset name: " + movieVCDataIdentifier.getID()));
                newMovie.addUserDataEntry(new UserDataEntry("cmt", "Time range: " + timePoints[beginTimeIndex] + " - " + timePoints[endTimeIndex]));
                for (int k = 0; k < varNames.length; k++) {
                    // pad with 0 if k < 10
                    String entryType = "v" + (k < 10 ? "0" : "") + k;
                    UserDataEntry entry = new UserDataEntry(entryType, "Variable name: " + varNames[k] + " min: " + das.getValueDomain().getMin() + " max: " + das.getValueDomain().getMax());
                    newMovie.addUserDataEntry(entry);
                }
                getClientTaskStatusSupport().setMessage("Writing Movie to disk...");
                FileOutputStream fos = new FileOutputStream(selectedFile);
                DataOutputStream movieOutput = new DataOutputStream(new BufferedOutputStream(fos));
                MediaMethods.writeMovie(movieOutput, newMovie);
                movieOutput.close();
                fos.close();
            } finally {
                fileDataContainerManager.closeAllAndDelete();
            }
        }
    };
    ClientTaskDispatcher.dispatch(this, hash, new AsynchClientTask[] { task1, task2, task3 }, true, true, null);
}

Example 3 with DataInfoProvider

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

the class TestingFrameworkWindowManager method getDataInfoProvider.

private DataInfoProvider getDataInfoProvider(VCDocument document, PDEDataContext pdeDataContext, String refSimName) throws ObjectNotFoundException {
    SimulationWorkspaceModelInfo simulationWorkspaceModelInfo = null;
    if (document instanceof MathModel) {
        MathModel mathModel = (MathModel) document;
        Simulation[] sims = mathModel.getSimulations();
        for (int i = 0; i < sims.length; i++) {
            if (refSimName.equals(sims[i].getName())) {
                simulationWorkspaceModelInfo = new SimulationWorkspaceModelInfo(mathModel, sims[i].getName());
                break;
            }
        }
    } else {
        BioModel bioModel = (BioModel) document;
        Simulation[] sims = bioModel.getSimulations();
        for (int i = 0; i < sims.length; i++) {
            if (refSimName.equals(sims[i].getName())) {
                simulationWorkspaceModelInfo = new SimulationWorkspaceModelInfo(bioModel.getSimulationContext(sims[i]), sims[i].getName());
                break;
            }
        }
    }
    DataInfoProvider dataInfoProvider = new DataInfoProvider(pdeDataContext, simulationWorkspaceModelInfo);
    return dataInfoProvider;
}

Example 4 with DataInfoProvider

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

the class PDEDataViewer method updateMetadata.

public void updateMetadata() {
    if (getPdeDataContext() == null) {
        return;
    }
    // check if clienttaskdispatcher is busy, if so schedule this method to run later (workaround spurious threading problem)
    if ((pdeDataViewersetupTimer = ClientTaskDispatcher.getBlockingTimer(PDEDataViewer.this, null, null, pdeDataViewersetupTimer, new ActionListener() {

        @Override
        public void actionPerformed(ActionEvent e2) {
            updateMetadata();
        }
    }, "PDEDataViewer Setup...")) != null) {
        return;
    }
    try {
        updatingMetaData = true;
        AsynchClientTask filterCategoriesTask = new AsynchClientTask("Calculating Filter...", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

            @Override
            public void run(Hashtable<String, Object> hashTable) throws Exception {
                // try {
                if (getSimulationModelInfo() != null) {
                    SimulationModelInfo simulationWorkspaceModelInfo = PDEDataViewer.this.getSimulationModelInfo();
                    simulationWorkspaceModelInfo.getDataSymbolMetadataResolver().populateDataSymbolMetadata(null);
                }
            // }catch (Exception e){
            // e.printStackTrace();
            // }
            }
        };
        AsynchClientTask firePropertyChangeTask = new AsynchClientTask("Fire Property Change...", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {

            @Override
            public void run(Hashtable<String, Object> hashTable) throws Exception {
                SimulationModelInfo simulationModelInfo = PDEDataViewer.this.getSimulationModelInfo();
                DataInfoProvider dataInfoProvider = new DataInfoProvider(getPdeDataContext(), simulationModelInfo);
                getPDEPlotControlPanel1().setDataInfoProvider(dataInfoProvider);
                getPDEDataContextPanel1().setDataInfoProvider(dataInfoProvider);
                getPDEExportPanel1().setDataInfoProvider(getPDEDataContextPanel1().getDataInfoProvider());
                if (getSimulationModelInfo() != null && getSimulationModelInfo().getDataSymbolMetadataResolver().getUniqueFilterCategories() != null) {
                    getPDEPlotControlPanel1().setDataIdentifierFilter(new DefaultDataIdentifierFilter(getSimulationModelInfo().getDataSymbolMetadataResolver()));
                }
            }
        };
        ClientTaskDispatcher.dispatch(PDEDataViewer.this, new Hashtable<String, Object>(), new AsynchClientTask[] { filterCategoriesTask, firePropertyChangeTask }, false, false, false, null, true);
    } finally {
        updatingMetaData = false;
    }
}