Examples with TiffReader loci.formats.in.TiffReader used on opensource projects

Example 6 with TiffReader

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

the class TiffWriterTest method testSaveBytes.

@Test(dataProvider = "nonTiling")
public void testSaveBytes(int tileSize, boolean littleEndian, boolean interleaved, int rgbChannels, int seriesCount, int sizeT, String compression, int pixelType, boolean bigTiff) throws Exception {
    if (percentageOfSaveBytesTests == 0)
        return;
    File tmp = File.createTempFile("tiffWriterTest", ".tiff");
    tmp.deleteOnExit();
    Plane originalPlane = WriterUtilities.writeImage(tmp, tileSize, littleEndian, interleaved, rgbChannels, seriesCount, sizeT, compression, pixelType, bigTiff);
    TiffReader reader = new TiffReader();
    reader.setId(tmp.getAbsolutePath());
    WriterUtilities.checkImage(reader, originalPlane, interleaved, rgbChannels, seriesCount, sizeT, compression);
    tmp.delete();
    reader.close();
}

Example 7 with TiffReader

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

the class OMETiffWriterBigTiffLargeImageWidthTest method testImageWidthWrittenCorrectly.

@Test
public void testImageWidthWrittenCorrectly() throws Exception {
    OMETiffWriter writer = new OMETiffWriter();
    writer.setBigTiff(true);
    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 8 with TiffReader

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

the class TiffWriterTest method assertUnevenTiles.

/**
 * Tests the writing of the tiles.
 * @param output The output where to write the data.
 * @param compression The compression to use.
 * @param blockWidth The width of block to write.
 * @param blockHeight The height of block to write.
 * @param bigTiff Pass <code>true</code> to set the <code>bigTiff</code> flag,
 *                <code>false</code> otherwise.
 */
private void assertUnevenTiles(String output, String compression, int blockWidth, int blockHeight, boolean bigTiff) throws Exception {
    TiffWriter writer = initializeWriter(output, compression, bigTiff);
    int x, y;
    byte[] tile;
    long[] rowPerStrip;
    int w, h;
    IFD ifd;
    int count;
    int sizeX, sizeY;
    int n, m;
    int diffWidth, diffHeight;
    int series = reader.getSeriesCount();
    String[][][] tileMD5s = new String[series][][];
    for (int s = 0; s < series; s++) {
        reader.setSeries(s);
        sizeX = reader.getSizeX();
        sizeY = reader.getSizeY();
        if (blockWidth <= 0)
            blockWidth = sizeX;
        if (blockHeight <= 0)
            blockHeight = sizeY;
        n = sizeX / blockWidth;
        m = sizeY / blockHeight;
        if (n == 0) {
            blockWidth = sizeX;
            n = 1;
        }
        if (m == 0) {
            blockHeight = sizeY;
            m = 1;
        }
        diffWidth = sizeX - n * blockWidth;
        diffHeight = sizeY - m * blockHeight;
        if (diffWidth > 0)
            n++;
        if (diffHeight > 0)
            m++;
        rowPerStrip = new long[1];
        rowPerStrip[0] = blockHeight;
        count = reader.getImageCount();
        tileMD5s[s] = new String[count][m * n];
        for (int k = 0; k < count; k++) {
            x = 0;
            y = 0;
            ifd = new IFD();
            ifd.put(IFD.TILE_WIDTH, blockWidth);
            ifd.put(IFD.TILE_LENGTH, blockHeight);
            ifd.put(IFD.ROWS_PER_STRIP, rowPerStrip);
            for (int i = 0; i < m; i++) {
                if (diffHeight > 0 && i == (m - 1)) {
                    y = sizeY - diffHeight;
                    h = diffHeight;
                } else {
                    y = blockHeight * i;
                    h = blockHeight;
                }
                for (int j = 0; j < n; j++) {
                    if (diffWidth > 0 && j == (n - 1)) {
                        x = sizeX - diffWidth;
                        w = diffWidth;
                    } else {
                        x = blockWidth * j;
                        w = blockWidth;
                    }
                    tile = reader.openBytes(k, x, y, w, h);
                    tileMD5s[s][k][(i * n) + j] = TestTools.md5(tile);
                    writer.saveBytes(0, tile, ifd, x, y, w, h);
                }
            }
        }
    }
    writer.close();
    // Now going to read the output.
    TiffReader outputReader = new TiffReader();
    outputReader.setId(output);
    // first series.
    String writtenDigest;
    String readDigest;
    for (int s = 0; s < series; s++) {
        outputReader.setSeries(s);
        count = outputReader.getImageCount();
        for (int k = 0; k < count; k++) {
            sizeX = outputReader.getSizeX();
            sizeY = outputReader.getSizeY();
            n = sizeX / blockWidth;
            m = sizeY / blockHeight;
            diffWidth = sizeX - n * blockWidth;
            diffHeight = sizeY - m * blockHeight;
            if (diffWidth > 0)
                n++;
            if (diffHeight > 0)
                m++;
            for (int i = 0; i < m; i++) {
                if (diffHeight > 0 && i == (m - 1)) {
                    y = sizeY - diffHeight;
                    h = diffHeight;
                } else {
                    y = blockHeight * i;
                    h = blockHeight;
                }
                for (int j = 0; j < n; j++) {
                    if (diffWidth > 0 && j == (n - 1)) {
                        x = sizeX - diffWidth;
                        w = diffWidth;
                    } else {
                        x = blockWidth * j;
                        w = blockWidth;
                    }
                    tile = outputReader.openBytes(k, x, y, w, h);
                    writtenDigest = tileMD5s[s][k][(i * n) + j];
                    readDigest = TestTools.md5(tile);
                    if (!writtenDigest.equals(readDigest)) {
                        fail(String.format("Compression:%s MD5:%d;%d;%d;%d;%d; %s != %s", compression, k, x, y, w, h, writtenDigest, readDigest));
                    }
                }
            }
        }
    }
    outputReader.close();
}

Example 9 with TiffReader

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

the class SewTiffs method main.

public static void main(String[] args) throws Exception {
    if (args.length < 2) {
        System.out.println("Usage: java SewTiffs base_name channel_num [time_count]");
        System.exit(1);
    }
    String base = args[0];
    int c = Integer.parseInt(args[1]);
    int num;
    if (args.length < 3) {
        FilePattern fp = new FilePattern(new Location(base + "_C" + c + "_TP1.tiff"));
        int[] count = fp.getCount();
        num = count[count.length - 1];
    } else
        num = Integer.parseInt(args[2]);
    System.out.println("Fixing " + base + "_C" + c + "_TP<1-" + num + ">.tiff");
    TiffReader in = new TiffReader();
    TiffWriter out = new TiffWriter();
    String outId = base + "_C" + c + ".tiff";
    System.out.println("Writing " + outId);
    out.setId(outId);
    System.out.print("   ");
    boolean comment = false;
    for (int t = 0; t < num; t++) {
        String inId = base + "_C" + c + "_TP" + (t + 1) + ".tiff";
        ServiceFactory factory = new ServiceFactory();
        OMEXMLService service = factory.getInstance(OMEXMLService.class);
        IMetadata meta = service.createOMEXMLMetadata();
        in.setMetadataStore(meta);
        in.setId(inId);
        out.setMetadataRetrieve(meta);
        // read first image plane
        byte[] image = in.openBytes(0);
        in.close();
        if (t == 0) {
            // read first IFD
            RandomAccessInputStream ras = new RandomAccessInputStream(inId);
            TiffParser parser = new TiffParser(ras);
            IFD ifd = parser.getFirstIFD();
            ras.close();
            // preserve TIFF comment
            String desc = ifd.getComment();
            if (desc != null) {
                ifd = new IFD();
                ifd.putIFDValue(IFD.IMAGE_DESCRIPTION, desc);
                comment = true;
                out.saveBytes(t, image, ifd);
                System.out.print(".");
                continue;
            }
        }
        // write image plane
        out.saveBytes(t, image);
        // update status
        System.out.print(".");
        if (t % DOTS == DOTS - 1) {
            System.out.println(" " + (t + 1));
            System.out.print("   ");
        }
    }
    System.out.println();
    if (comment)
        System.out.println("OME-TIFF comment saved.");
    else
        System.out.println("No OME-TIFF comment found.");
}