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

Example 1 with Range

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

the class KymographPanel method configureMinMax.

/**
 * Insert the method's description here.
 * Creation date: (12/28/2004 10:01:37 AM)
 * @param min double
 * @param max double
 */
private void configureMinMax() {
    getScaleImageModeJLabel().setText((scaleImageMode == SCALE_IMAGE_ALL ? "All" : "") + (scaleImageMode == SCALE_IMAGE_LINESCAN ? "LS" : "") + (scaleImageMode == SCALE_IMAGE_TIMESERIES ? "TS" : "") + (scaleImageMode == SCALE_IMAGE_USERDEFINED ? "User" : ""));
    Range minmaxRange = null;
    switch(scaleImageMode) {
        case SCALE_IMAGE_ALL:
            minmaxRange = (allDataMMMH != null ? allDataMMMH.getRange() : null);
            break;
        case SCALE_IMAGE_LINESCAN:
            minmaxRange = (localDistDataMMMH != null ? localDistDataMMMH.getRange() : null);
            break;
        case SCALE_IMAGE_TIMESERIES:
            minmaxRange = (localTimeDataMMMH != null ? localTimeDataMMMH.getRange() : null);
            break;
        case SCALE_IMAGE_USERDEFINED:
            minmaxRange = (userDefinedMMMH != null ? userDefinedMMMH.getRange() : null);
            break;
    }
    if (minmaxRange == null || minmaxRange.getMin() == minmaxRange.getMax()) {
        getColorMapJLabel().setIcon(null);
        getColorMapJLabel().setText("No Range");
    } else {
        getColorMapJLabel().setIcon(cmapImageIcon);
        getColorMapJLabel().setText(null);
    }
    if (minmaxRange == null) {
        getDisplayAdapterService1().setActiveScaleRange(null);
        getDisplayAdapterService1().setValueDomain(null);
        getMinJLabel().setText("?");
        getMinJLabel().setToolTipText("Unknown");
        getMaxJLabel().setText("?");
        getMaxJLabel().setToolTipText("Unknown");
        // updateColorMapDisplay();
        getimagePaneView1().getImagePaneModel().updateViewPortImage();
    } else if (getDisplayAdapterService1().getActiveScaleRange() == null || getDisplayAdapterService1().getActiveScaleRange().getMin() != minmaxRange.getMin() || getDisplayAdapterService1().getActiveScaleRange().getMax() != minmaxRange.getMax()) {
        getDisplayAdapterService1().setValueDomain((allDataMMMH != null ? allDataMMMH.getRange() : null));
        getDisplayAdapterService1().setActiveScaleRange(minmaxRange);
        java.text.DecimalFormat nf = new java.text.DecimalFormat();
        nf.applyPattern("#.###E0");
        getMinJLabel().setText((("" + minmaxRange.getMin()).length() < 7 ? minmaxRange.getMin() + "" : nf.format(minmaxRange.getMin())));
        getMinJLabel().setToolTipText("" + minmaxRange.getMin());
        getMaxJLabel().setText((("" + minmaxRange.getMax()).length() < 7 ? minmaxRange.getMax() + "" : nf.format(minmaxRange.getMax())));
        getMaxJLabel().setToolTipText("" + minmaxRange.getMax());
        // updateColorMapDisplay();
        getimagePaneView1().getImagePaneModel().updateViewPortImage();
    }
}

Example 2 with Range

use of org.vcell.util.Range 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 Range

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

the class ImageContainer method setDataRange.

/**
 * Sets the dataRange property (cbit.image.Range) value.
 * @param dataRange The new value for the property.
 * @see #getDataRange
 */
public final void setDataRange(Range dataRange) {
    getDisplayAdapter().setDataRange(dataRange);
    Range oldValue = fieldDataRange;
    fieldDataRange = dataRange;
    firePropertyChange("dataRange", oldValue, dataRange);
}

Example 4 with Range

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

the class ImageContainer method setScaleRange.

/**
 * Sets the scaleRange property (cbit.image.Range) value.
 * @param scaleRange The new value for the property.
 * @see #getScaleRange
 */
public final void setScaleRange(Range scaleRange) {
    if (getDisplayAdapter() == null) {
        return;
    }
    getDisplayAdapter().setScaleRange(scaleRange);
    Range oldValue = fieldScaleRange;
    fieldScaleRange = scaleRange;
    firePropertyChange("scaleRange", oldValue, scaleRange);
}

Example 5 with Range

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

the class ScalePanel method setScaleParameters.

/**
 * This method was created in VisualAge.
 * @param minmax int
 * @param inputValue java.lang.String
 */
public void setScaleParameters(String inputMin, String inputMax) {
    try {
        double min = Math.max(0, Double.valueOf(inputMin).doubleValue());
        double max = Math.max(0, Double.valueOf(inputMax).doubleValue());
        if (min > max)
            min = 0;
        setScaleRange(new Range(min, max));
    } catch (NumberFormatException e) {
        // put back existing values
        resetTextFields(getScaleRange());
    }
    return;
}