Examples with VideoMediaChunk cbit.vcell.export.gloworm.quicktime.VideoMediaChunk used on opensource projects

Example 1 with VideoMediaChunk

use of cbit.vcell.export.gloworm.quicktime.VideoMediaChunk 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 2 with VideoMediaChunk

use of cbit.vcell.export.gloworm.quicktime.VideoMediaChunk in project vcell by virtualcell.

the class IMGExporter method createMedia.

private static void createMedia(Vector<ExportOutput> exportOutputV, VCDataIdentifier vcdID, String dataID, ExportSpecs exportSpecs, boolean bEndVars, boolean bEndSlice, boolean bBeginTime, boolean bEndTime, boolean bSingleTimePoint, String[] varNameArr, DisplayPreferences[] displayPreferencesArr, MovieHolder movieHolder, int[] pixels, int mirrorWidth, int mirrorHeight, FileDataContainerManager fileDataContainerManager) throws Exception {
    boolean isGrayScale = true;
    for (int i = 0; i < displayPreferencesArr.length; i++) {
        if (!displayPreferencesArr[i].isGrayScale()) {
            isGrayScale = false;
            break;
        }
    }
    FormatSpecificSpecs formatSpecificSpecs = exportSpecs.getFormatSpecificSpecs();
    if (exportSpecs.getFormat() == ExportFormat.GIF && formatSpecificSpecs instanceof ImageSpecs) /* && ((ImageSpecs)formatSpecificSpecs).getFormat() == ExportConstants.GIF*/
    {
        ByteArrayOutputStream bytesOut = new ByteArrayOutputStream();
        GIFOutputStream gifOut = new GIFOutputStream(bytesOut);
        GIFImage gifImage = new GIFUtils.GIFImage(pixels, mirrorWidth);
        gifImage.write(gifOut);
        gifOut.close();
        byte[] data = bytesOut.toByteArray();
        ExportOutput exportOutput = new ExportOutput(true, ".gif", vcdID.getID(), dataID, fileDataContainerManager);
        fileDataContainerManager.append(exportOutput.getFileDataContainerID(), data);
        exportOutputV.add(exportOutput);
    } else if (exportSpecs.getFormat() == ExportFormat.FORMAT_JPEG && formatSpecificSpecs instanceof ImageSpecs) /* && ((ImageSpecs)formatSpecificSpecs).getFormat() == ExportConstants.JPEG*/
    {
        VideoMediaSample jpegEncodedVideoMediaSample = FormatSpecificSpecs.getVideoMediaSample(mirrorWidth, mirrorHeight, 1, isGrayScale, FormatSpecificSpecs.CODEC_JPEG, ((ImageSpecs) formatSpecificSpecs).getcompressionQuality(), pixels);
        ExportOutput exportOutput = new ExportOutput(true, ".jpg", vcdID.getID(), dataID, fileDataContainerManager);
        fileDataContainerManager.append(exportOutput.getFileDataContainerID(), jpegEncodedVideoMediaSample.getDataBytes());
        exportOutputV.add(exportOutput);
    } else if (exportSpecs.getFormat() == ExportFormat.ANIMATED_GIF && formatSpecificSpecs instanceof ImageSpecs) /* && ((ImageSpecs)formatSpecificSpecs).getFormat() == ExportConstants.ANIMATED_GIF*/
    {
        // 1/100's of a second
        int imageDuration = (int) Math.ceil((movieHolder.getSampleDurationSeconds() * 100));
        if (bEndTime && (((ImageSpecs) formatSpecificSpecs).getLoopingMode() != 0 || bSingleTimePoint)) {
            imageDuration = 0;
        }
        if (bBeginTime) {
            movieHolder.setGifImage(new GIFUtils.GIFImage(pixels, mirrorWidth));
            movieHolder.getGifImage().setDelay(imageDuration);
        } else {
            movieHolder.getGifImage().addImage(pixels, mirrorWidth, true);
            movieHolder.getGifImage().setDelay(movieHolder.getGifImage().countImages() - 1, imageDuration);
        }
        if (bEndTime) {
            movieHolder.getGifImage().setIterationCount(((ImageSpecs) formatSpecificSpecs).getLoopingMode());
            ByteArrayOutputStream bytesOut = new ByteArrayOutputStream();
            GIFOutputStream gifOut = new GIFOutputStream(bytesOut);
            movieHolder.getGifImage().write(gifOut);
            gifOut.close();
            byte[] data = bytesOut.toByteArray();
            ExportOutput exportOutput = new ExportOutput(true, ".gif", vcdID.getID(), dataID, fileDataContainerManager);
            fileDataContainerManager.append(exportOutput.getFileDataContainerID(), data);
            exportOutputV.add(exportOutput);
        }
    } else if (exportSpecs.getFormat() == ExportFormat.QUICKTIME && formatSpecificSpecs instanceof MovieSpecs) {
        String VIDEOMEDIACHUNKID = (varNameArr.length == 1 ? varNameArr[0] : "OVERLAY");
        // number of units per second in movie
        final int TIMESCALE = 1000;
        boolean bQTVR = ((MovieSpecs) exportSpecs.getFormatSpecificSpecs()).isQTVR();
        int sampleDuration = (bQTVR ? TIMESCALE : (int) (TIMESCALE * movieHolder.getSampleDurationSeconds()));
        VideoMediaSample videoMediaSample = FormatSpecificSpecs.getVideoMediaSample(mirrorWidth, mirrorHeight, sampleDuration, isGrayScale, FormatSpecificSpecs.CODEC_JPEG, ((MovieSpecs) formatSpecificSpecs).getcompressionQuality(), pixels);
        if (bBeginTime && (!bQTVR || movieHolder.getVarNameVideoMediaChunkHash().get(VIDEOMEDIACHUNKID) == null)) {
            movieHolder.getVarNameVideoMediaChunkHash().put(VIDEOMEDIACHUNKID, new Vector<VideoMediaChunk>());
            movieHolder.getVarNameDataIDHash().put(VIDEOMEDIACHUNKID, dataID);
        }
        movieHolder.getVarNameVideoMediaChunkHash().get(VIDEOMEDIACHUNKID).add(new VideoMediaChunk(videoMediaSample, fileDataContainerManager));
        if (bEndTime && !bQTVR) {
            String simID = exportSpecs.getVCDataIdentifier().getID();
            double[] allTimes = exportSpecs.getTimeSpecs().getAllTimes();
            int beginTimeIndex = exportSpecs.getTimeSpecs().getBeginTimeIndex();
            int endTimeIndex = exportSpecs.getTimeSpecs().getEndTimeIndex();
            VideoMediaChunk[] videoMediaChunkArr = movieHolder.getVarNameVideoMediaChunkHash().get(VIDEOMEDIACHUNKID).toArray(new VideoMediaChunk[0]);
            MediaTrack videoTrack = new MediaTrack(videoMediaChunkArr);
            MediaMovie newMovie = new MediaMovie(videoTrack, videoTrack.getDuration(), TIMESCALE);
            newMovie.addUserDataEntry(new UserDataEntry("cpy", "�" + (new GregorianCalendar()).get(Calendar.YEAR) + ", UCHC"));
            newMovie.addUserDataEntry(new UserDataEntry("des", "Dataset name: " + simID));
            newMovie.addUserDataEntry(new UserDataEntry("cmt", "Time range: " + allTimes[beginTimeIndex] + " - " + allTimes[endTimeIndex]));
            for (int i = 0; varNameArr != null && i < varNameArr.length; i++) {
                newMovie.addUserDataEntry(new UserDataEntry("v" + (i < 10 ? "0" : "") + i, "Variable name: " + varNameArr[i] + "\nmin: " + (displayPreferencesArr == null || displayPreferencesArr[i].getScaleSettings() == null ? "default" : displayPreferencesArr[i].getScaleSettings().getMin()) + "\nmax: " + (displayPreferencesArr == null || displayPreferencesArr[i].getScaleSettings() == null ? "default" : displayPreferencesArr[i].getScaleSettings().getMax())));
            }
            FileOutputStream fos = null;
            BufferedOutputStream bos = null;
            DataOutputStream movieos = null;
            try {
                ExportOutput exportOutput = new ExportOutput(true, ".mov", simID, dataID, fileDataContainerManager);
                File tempMovieFile = File.createTempFile("Movie", "temp");
                fileDataContainerManager.manageExistingTempFile(exportOutput.getFileDataContainerID(), tempMovieFile);
                fos = new FileOutputStream(tempMovieFile);
                bos = new BufferedOutputStream(fos);
                movieos = new DataOutputStream(bos);
                MediaMethods.writeMovie(movieos, newMovie);
                movieos.close();
                exportOutputV.add(exportOutput);
                movieHolder.getVarNameVideoMediaChunkHash().clear();
                movieHolder.getVarNameDataIDHash().clear();
            } finally {
                if (movieos != null) {
                    try {
                        movieos.close();
                    } catch (Exception e) {
                        e.printStackTrace();
                    }
                }
                if (bos != null) {
                    try {
                        bos.close();
                    } catch (Exception e) {
                        e.printStackTrace();
                    }
                }
                if (fos != null) {
                    try {
                        fos.close();
                    } catch (Exception e) {
                        e.printStackTrace();
                    }
                }
            }
        } else if (bEndVars && bEndTime && bEndSlice && bQTVR) {
            String simID = exportSpecs.getVCDataIdentifier().getID();
            Enumeration<String> allStoredVarNamesEnum = movieHolder.getVarNameVideoMediaChunkHash().keys();
            while (allStoredVarNamesEnum.hasMoreElements()) {
                String varName = allStoredVarNamesEnum.nextElement();
                String storedDataID = movieHolder.getVarNameDataIDHash().get(varName);
                VideoMediaChunk[] videoMediaChunkArr = movieHolder.getVarNameVideoMediaChunkHash().get(varName).toArray(new VideoMediaChunk[0]);
                int beginTimeIndex = exportSpecs.getTimeSpecs().getBeginTimeIndex();
                int endTimeIndex = exportSpecs.getTimeSpecs().getEndTimeIndex();
                int numTimes = endTimeIndex - beginTimeIndex + 1;
                FileOutputStream fos = null;
                BufferedOutputStream bos = null;
                DataOutputStream movieos = null;
                try {
                    ExportOutput exportOutput = new ExportOutput(true, ".mov", simID, storedDataID, fileDataContainerManager);
                    File tempMovieFile = File.createTempFile("Movie", "temp");
                    fileDataContainerManager.manageExistingTempFile(exportOutput.getFileDataContainerID(), tempMovieFile);
                    fos = new FileOutputStream(tempMovieFile);
                    bos = new BufferedOutputStream(fos);
                    movieos = new DataOutputStream(bos);
                    writeQTVRWorker(movieos, videoMediaChunkArr, numTimes, videoMediaChunkArr.length / numTimes, mirrorWidth, mirrorHeight);
                    movieos.close();
                    exportOutputV.add(exportOutput);
                } finally {
                    if (movieos != null) {
                        try {
                            movieos.close();
                        } catch (Exception e) {
                            e.printStackTrace();
                        }
                    }
                    if (bos != null) {
                        try {
                            bos.close();
                        } catch (Exception e) {
                            e.printStackTrace();
                        }
                    }
                    if (fos != null) {
                        try {
                            fos.close();
                        } catch (Exception e) {
                            e.printStackTrace();
                        }
                    }
                }
            }
            movieHolder.getVarNameVideoMediaChunkHash().clear();
            movieHolder.getVarNameDataIDHash().clear();
        }
    }
}