Examples with ImageWriter loci.formats.ImageWriter used on opensource projects

Example 1 with ImageWriter

use of loci.formats.ImageWriter in project bioformats by openmicroscopy.

the class OMETiffWriterLargeImageWidthTest method testImageWidthWrittenCorrectly.

@Test
public void testImageWidthWrittenCorrectly() throws Exception {
    ImageWriter writer = new ImageWriter();
    writer.setMetadataRetrieve(ms);
    writer.setId(target.getAbsolutePath());
    writer.saveBytes(0, buf, 0, 0, buf.length, 1);
    writer.close();
    TiffReader reader = new TiffReader();
    reader.setId(target.getAbsolutePath());
    assertEquals(SIZE_X, reader.getSizeX());
    assertEquals(SIZE_Y, reader.getSizeY());
}

Example 2 with ImageWriter

use of loci.formats.ImageWriter in project bioformats by openmicroscopy.

the class ImageConverter method testConvert.

// -- Utility methods --
/**
 * A utility method for converting a file from the command line.
 */
public boolean testConvert(IFormatWriter writer, String[] args) throws FormatException, IOException {
    nextOutputIndex.clear();
    options.setValidate(validate);
    writer.setMetadataOptions(options);
    firstTile = true;
    boolean success = parseArgs(args);
    if (!success) {
        return false;
    }
    if (printVersion) {
        CommandLineTools.printVersion();
        return true;
    }
    CommandLineTools.runUpgradeCheck(args);
    if (in == null || out == null) {
        printUsage();
        return false;
    }
    if (new Location(out).exists()) {
        if (overwrite == null) {
            LOGGER.warn("Output file {} exists.", out);
            LOGGER.warn("Do you want to overwrite it? ([y]/n)");
            BufferedReader r = new BufferedReader(new InputStreamReader(System.in, Constants.ENCODING));
            String choice = r.readLine().trim().toLowerCase();
            overwrite = !choice.startsWith("n");
        }
        if (!overwrite) {
            LOGGER.warn("Exiting; next time, please specify an output file that " + "does not exist.");
            return false;
        } else {
            new Location(out).delete();
        }
    }
    if (map != null)
        Location.mapId(in, map);
    long start = System.currentTimeMillis();
    LOGGER.info(in);
    reader = new ImageReader();
    if (stitch) {
        reader = new FileStitcher(reader);
        Location f = new Location(in);
        String pat = null;
        if (!f.exists()) {
            pat = in;
        } else {
            pat = FilePattern.findPattern(f);
        }
        if (pat != null)
            in = pat;
    }
    if (separate)
        reader = new ChannelSeparator(reader);
    if (merge)
        reader = new ChannelMerger(reader);
    if (fill)
        reader = new ChannelFiller(reader);
    minMax = null;
    if (autoscale) {
        reader = new MinMaxCalculator(reader);
        minMax = (MinMaxCalculator) reader;
    }
    reader.setMetadataOptions(options);
    reader.setGroupFiles(group);
    reader.setMetadataFiltered(true);
    reader.setOriginalMetadataPopulated(true);
    OMEXMLService service = null;
    try {
        ServiceFactory factory = new ServiceFactory();
        service = factory.getInstance(OMEXMLService.class);
        reader.setMetadataStore(service.createOMEXMLMetadata());
    } catch (DependencyException de) {
        throw new MissingLibraryException(OMEXMLServiceImpl.NO_OME_XML_MSG, de);
    } catch (ServiceException se) {
        throw new FormatException(se);
    }
    reader.setId(in);
    MetadataStore store = reader.getMetadataStore();
    MetadataTools.populatePixels(store, reader, false, false);
    boolean dimensionsSet = true;
    if (width == 0 || height == 0) {
        // otherwise default to series 0
        if (series >= 0) {
            reader.setSeries(series);
        }
        width = reader.getSizeX();
        height = reader.getSizeY();
        dimensionsSet = false;
    }
    if (channel >= reader.getEffectiveSizeC()) {
        throw new FormatException("Invalid channel '" + channel + "' (" + reader.getEffectiveSizeC() + " channels in source file)");
    }
    if (timepoint >= reader.getSizeT()) {
        throw new FormatException("Invalid timepoint '" + timepoint + "' (" + reader.getSizeT() + " timepoints in source file)");
    }
    if (zSection >= reader.getSizeZ()) {
        throw new FormatException("Invalid Z section '" + zSection + "' (" + reader.getSizeZ() + " Z sections in source file)");
    }
    if (store instanceof MetadataRetrieve) {
        try {
            String xml = service.getOMEXML(service.asRetrieve(store));
            OMEXMLMetadataRoot root = (OMEXMLMetadataRoot) store.getRoot();
            IMetadata meta = service.createOMEXMLMetadata(xml);
            if (series >= 0) {
                Image exportImage = new Image(root.getImage(series));
                Pixels exportPixels = new Pixels(root.getImage(series).getPixels());
                exportImage.setPixels(exportPixels);
                OMEXMLMetadataRoot newRoot = (OMEXMLMetadataRoot) meta.getRoot();
                while (newRoot.sizeOfImageList() > 0) {
                    newRoot.removeImage(newRoot.getImage(0));
                }
                newRoot.addImage(exportImage);
                meta.setRoot(newRoot);
                meta.setPixelsSizeX(new PositiveInteger(width), 0);
                meta.setPixelsSizeY(new PositiveInteger(height), 0);
                if (autoscale) {
                    store.setPixelsType(PixelType.UINT8, 0);
                }
                if (channel >= 0) {
                    meta.setPixelsSizeC(new PositiveInteger(1), 0);
                }
                if (zSection >= 0) {
                    meta.setPixelsSizeZ(new PositiveInteger(1), 0);
                }
                if (timepoint >= 0) {
                    meta.setPixelsSizeT(new PositiveInteger(1), 0);
                }
                writer.setMetadataRetrieve((MetadataRetrieve) meta);
            } else {
                for (int i = 0; i < reader.getSeriesCount(); i++) {
                    meta.setPixelsSizeX(new PositiveInteger(width), 0);
                    meta.setPixelsSizeY(new PositiveInteger(height), 0);
                    if (autoscale) {
                        store.setPixelsType(PixelType.UINT8, i);
                    }
                    if (channel >= 0) {
                        meta.setPixelsSizeC(new PositiveInteger(1), 0);
                    }
                    if (zSection >= 0) {
                        meta.setPixelsSizeZ(new PositiveInteger(1), 0);
                    }
                    if (timepoint >= 0) {
                        meta.setPixelsSizeT(new PositiveInteger(1), 0);
                    }
                }
                writer.setMetadataRetrieve((MetadataRetrieve) meta);
            }
        } catch (ServiceException e) {
            throw new FormatException(e);
        }
    }
    writer.setWriteSequentially(true);
    if (writer instanceof TiffWriter) {
        ((TiffWriter) writer).setBigTiff(bigtiff);
    } else if (writer instanceof ImageWriter) {
        IFormatWriter w = ((ImageWriter) writer).getWriter(out);
        if (w instanceof TiffWriter) {
            ((TiffWriter) w).setBigTiff(bigtiff);
        }
    }
    String format = writer.getFormat();
    LOGGER.info("[{}] -> {} [{}]", new Object[] { reader.getFormat(), out, format });
    long mid = System.currentTimeMillis();
    int total = 0;
    int num = writer.canDoStacks() ? reader.getSeriesCount() : 1;
    long read = 0, write = 0;
    int first = series == -1 ? 0 : series;
    int last = series == -1 ? num : series + 1;
    long timeLastLogged = System.currentTimeMillis();
    for (int q = first; q < last; q++) {
        reader.setSeries(q);
        firstTile = true;
        if (!dimensionsSet) {
            width = reader.getSizeX();
            height = reader.getSizeY();
        }
        int writerSeries = series == -1 ? q : 0;
        writer.setSeries(writerSeries);
        writer.setInterleaved(reader.isInterleaved() && !autoscale);
        writer.setValidBitsPerPixel(reader.getBitsPerPixel());
        int numImages = writer.canDoStacks() ? reader.getImageCount() : 1;
        int startPlane = (int) Math.max(0, firstPlane);
        int endPlane = (int) Math.min(numImages, lastPlane);
        numImages = endPlane - startPlane;
        if (channel >= 0) {
            numImages /= reader.getEffectiveSizeC();
        }
        if (zSection >= 0) {
            numImages /= reader.getSizeZ();
        }
        if (timepoint >= 0) {
            numImages /= reader.getSizeT();
        }
        total += numImages;
        int count = 0;
        for (int i = startPlane; i < endPlane; i++) {
            int[] coords = reader.getZCTCoords(i);
            if ((zSection >= 0 && coords[0] != zSection) || (channel >= 0 && coords[1] != channel) || (timepoint >= 0 && coords[2] != timepoint)) {
                continue;
            }
            String outputName = FormatTools.getFilename(q, i, reader, out, zeroPadding);
            if (outputName.equals(FormatTools.getTileFilename(0, 0, 0, outputName))) {
                writer.setId(outputName);
                if (compression != null)
                    writer.setCompression(compression);
            } else {
                int tileNum = outputName.indexOf(FormatTools.TILE_NUM);
                int tileX = outputName.indexOf(FormatTools.TILE_X);
                int tileY = outputName.indexOf(FormatTools.TILE_Y);
                if (tileNum < 0 && (tileX < 0 || tileY < 0)) {
                    throw new FormatException("Invalid file name pattern; " + FormatTools.TILE_NUM + " or both of " + FormatTools.TILE_X + " and " + FormatTools.TILE_Y + " must be specified.");
                }
            }
            int outputIndex = 0;
            if (nextOutputIndex.containsKey(outputName)) {
                outputIndex = nextOutputIndex.get(outputName);
            }
            long s = System.currentTimeMillis();
            long m = convertPlane(writer, i, outputIndex, outputName);
            long e = System.currentTimeMillis();
            read += m - s;
            write += e - m;
            nextOutputIndex.put(outputName, outputIndex + 1);
            if (i == endPlane - 1) {
                nextOutputIndex.remove(outputName);
            }
            // log number of planes processed every second or so
            if (count == numImages - 1 || (e - timeLastLogged) / 1000 > 0) {
                int current = (count - startPlane) + 1;
                int percent = 100 * current / numImages;
                StringBuilder sb = new StringBuilder();
                sb.append("\t");
                int numSeries = last - first;
                if (numSeries > 1) {
                    sb.append("Series ");
                    sb.append(q);
                    sb.append(": converted ");
                } else
                    sb.append("Converted ");
                LOGGER.info(sb.toString() + "{}/{} planes ({}%)", new Object[] { current, numImages, percent });
                timeLastLogged = e;
            }
            count++;
        }
    }
    writer.close();
    long end = System.currentTimeMillis();
    LOGGER.info("[done]");
    // output timing results
    float sec = (end - start) / 1000f;
    long initial = mid - start;
    float readAvg = (float) read / total;
    float writeAvg = (float) write / total;
    LOGGER.info("{}s elapsed ({}+{}ms per plane, {}ms overhead)", new Object[] { sec, readAvg, writeAvg, initial });
    return true;
}

Example 3 with ImageWriter

use of loci.formats.ImageWriter in project bioformats by openmicroscopy.

the class ImageConverter method convertTilePlane.

/**
 * Convert the specified plane as a set of tiles, using the specified writer.
 * @param writer the {@link loci.formats.IFormatWriter} to use for writing the plane
 * @param index the index of the plane to convert in the input file
 * @param outputIndex the index of the plane to convert in the output file
 * @param currentFile the file name or pattern being written to
 * @return the time at which conversion started, in milliseconds
 * @throws FormatException
 * @throws IOException
 */
private long convertTilePlane(IFormatWriter writer, int index, int outputIndex, String currentFile) throws FormatException, IOException {
    int w = reader.getOptimalTileWidth();
    int h = reader.getOptimalTileHeight();
    if (saveTileWidth > 0 && saveTileWidth <= width) {
        w = saveTileWidth;
    }
    if (saveTileHeight > 0 && saveTileHeight <= height) {
        h = saveTileHeight;
    }
    if (firstTile) {
        LOGGER.info("Tile size = {} x {}", w, h);
        firstTile = false;
    }
    int nXTiles = width / w;
    int nYTiles = height / h;
    if (nXTiles * w != width) {
        nXTiles++;
    }
    if (nYTiles * h != height) {
        nYTiles++;
    }
    IFD ifd = new IFD();
    ifd.put(IFD.TILE_WIDTH, w);
    ifd.put(IFD.TILE_LENGTH, h);
    Long m = null;
    for (int y = 0; y < nYTiles; y++) {
        for (int x = 0; x < nXTiles; x++) {
            int tileX = xCoordinate + x * w;
            int tileY = yCoordinate + y * h;
            int tileWidth = x < nXTiles - 1 ? w : width - (w * x);
            int tileHeight = y < nYTiles - 1 ? h : height - (h * y);
            byte[] buf = reader.openBytes(index, tileX, tileY, tileWidth, tileHeight);
            String tileName = FormatTools.getTileFilename(x, y, y * nXTiles + x, currentFile);
            if (!currentFile.equals(tileName)) {
                int nTileRows = getTileRows(currentFile);
                int nTileCols = getTileColumns(currentFile);
                int sizeX = nTileCols == 1 ? width : tileWidth;
                int sizeY = nTileRows == 1 ? height : tileHeight;
                MetadataRetrieve retrieve = writer.getMetadataRetrieve();
                if (retrieve instanceof MetadataStore) {
                    ((MetadataStore) retrieve).setPixelsSizeX(new PositiveInteger(sizeX), reader.getSeries());
                    ((MetadataStore) retrieve).setPixelsSizeY(new PositiveInteger(sizeY), reader.getSeries());
                }
                writer.close();
                writer.setMetadataRetrieve(retrieve);
                writer.setId(tileName);
                if (compression != null)
                    writer.setCompression(compression);
                outputIndex = 0;
                if (nextOutputIndex.containsKey(tileName)) {
                    outputIndex = nextOutputIndex.get(tileName);
                }
                nextOutputIndex.put(tileName, outputIndex + 1);
                if (nTileRows > 1) {
                    tileY = 0;
                }
                if (nTileCols > 1) {
                    tileX = 0;
                }
            }
            autoscalePlane(buf, index);
            applyLUT(writer);
            if (m == null) {
                m = System.currentTimeMillis();
            }
            if (writer instanceof TiffWriter) {
                ((TiffWriter) writer).saveBytes(outputIndex, buf, ifd, tileX, tileY, tileWidth, tileHeight);
            } else if (writer instanceof ImageWriter) {
                IFormatWriter baseWriter = ((ImageWriter) writer).getWriter(out);
                if (baseWriter instanceof TiffWriter) {
                    ((TiffWriter) baseWriter).saveBytes(outputIndex, buf, ifd, tileX, tileY, tileWidth, tileHeight);
                }
            }
        }
    }
    return m;
}

Example 4 with ImageWriter

use of loci.formats.ImageWriter in project bioformats by openmicroscopy.

the class FileConvert method initialize.

/**
 * Set up the file reader and writer, ensuring that the input file is
 * associated with the reader and the output file is associated with the
 * writer.
 *
 * @return true if the reader and writer were successfully set up, or false
 *   if an error occurred
 */
private boolean initialize() {
    Exception exception = null;
    try {
        // construct the object that stores OME-XML metadata
        ServiceFactory factory = new ServiceFactory();
        OMEXMLService service = factory.getInstance(OMEXMLService.class);
        IMetadata omexml = service.createOMEXMLMetadata();
        // set up the reader and associate it with the input file
        reader = new ImageReader();
        reader.setMetadataStore(omexml);
        reader.setId(inputFile);
        // set up the writer and associate it with the output file
        writer = new ImageWriter();
        writer.setMetadataRetrieve(omexml);
        writer.setInterleaved(reader.isInterleaved());
        writer.setId(outputFile);
    } catch (FormatException e) {
        exception = e;
    } catch (IOException e) {
        exception = e;
    } catch (DependencyException e) {
        exception = e;
    } catch (ServiceException e) {
        exception = e;
    }
    if (exception != null) {
        System.err.println("Failed to initialize files.");
        exception.printStackTrace();
    }
    return exception == null;
}

Example 5 with ImageWriter

use of loci.formats.ImageWriter in project bioformats by openmicroscopy.

the class FileExportSPW method initializeWriter.

/**
 * Set up the file writer.
 *
 * @param omexml
 *          the IMetadata object that is to be associated with the writer
 * @return true if the file writer was successfully initialized; false if an
 *         error occurred
 */
private boolean initializeWriter(IMetadata omexml) {
    // create the file writer and associate the OME-XML metadata with it
    writer = new ImageWriter();
    writer.setMetadataRetrieve(omexml);
    Exception exception = null;
    try {
        writer.setId(outputFile);
    } catch (FormatException e) {
        exception = e;
    } catch (IOException e) {
        exception = e;
    }
    if (exception != null) {
        System.err.println("Failed to initialize file writer.");
        exception.printStackTrace();
    }
    return exception == null;
}