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

Example 1 with TiffReader

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

the class TiffWriterTest method testSaveBytesTiling.

@Test(dataProvider = "tiling")
public void testSaveBytesTiling(int tileSize, boolean littleEndian, boolean interleaved, int rgbChannels, int seriesCount, int sizeT, String compression, int pixelType, boolean bigTiff) throws Exception {
    if (percentageOfTilingTests == 0)
        return;
    File tmp = File.createTempFile("tiffWriterTest_Tiling", ".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());
    int expectedTileSize = tileSize;
    if (tileSize < TILE_GRANULARITY) {
        expectedTileSize = TILE_GRANULARITY;
    } else {
        expectedTileSize = Math.round((float) tileSize / TILE_GRANULARITY) * TILE_GRANULARITY;
    }
    IFD tileIFd = reader.getIFDs().get(0);
    assertEquals(tileIFd.getIFDIntValue(IFD.TILE_LENGTH), expectedTileSize);
    assertEquals(tileIFd.getIFDIntValue(IFD.TILE_WIDTH), expectedTileSize);
    WriterUtilities.checkImage(reader, originalPlane, interleaved, rgbChannels, seriesCount, sizeT, compression);
    tmp.delete();
    reader.close();
}

Example 2 with TiffReader

use of loci.formats.in.TiffReader 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 3 with TiffReader

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

the class TiffWriterTest method assertTiles.

/**
 * Tests the writing of the tiles.
 * @param output The output where to write the data.
 * @param compression The compression to use.
 * @param n The value by which to divide the width of the image.
 * @param m The value by which to divide the height of the image.
 * @param bigTiff Pass <code>true</code> to set the <code>bigTiff</code> flag,
 *                <code>false</code> otherwise.
 */
private void assertTiles(String output, String compression, int n, int m, 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 series = reader.getSeriesCount();
    String[][][] tileMD5s = new String[series][][];
    for (int s = 0; s < series; s++) {
        reader.setSeries(s);
        w = reader.getSizeX() / n;
        h = reader.getSizeY() / m;
        rowPerStrip = new long[1];
        rowPerStrip[0] = h;
        count = reader.getImageCount();
        tileMD5s[s] = new String[count][m * n];
        for (int k = 0; k < count; k++) {
            ifd = new IFD();
            ifd.put(IFD.TILE_WIDTH, w);
            ifd.put(IFD.TILE_LENGTH, h);
            ifd.put(IFD.ROWS_PER_STRIP, rowPerStrip);
            for (int i = 0; i < m; i++) {
                y = h * i;
                for (int j = 0; j < n; j++) {
                    x = w * j;
                    tile = reader.openBytes(k, x, y, w, h);
                    tileMD5s[s][k][(i * n) + j] = TestTools.md5(tile);
                    writer.saveBytes(k, 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();
        h = outputReader.getSizeY() / m;
        w = outputReader.getSizeX() / n;
        for (int k = 0; k < count; k++) {
            for (int i = 0; i < m; i++) {
                y = h * i;
                for (int j = 0; j < n; j++) {
                    x = w * j;
                    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 4 with TiffReader

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

the class OMETiffWriterTest method testSaveBytesTiling.

@Test(dataProvider = "tiling")
public void testSaveBytesTiling(int tileSize, boolean littleEndian, boolean interleaved, int rgbChannels, int seriesCount, int sizeT, String compression, int pixelType, boolean bigTiff) throws Exception {
    if (percentageOfTilingTests == 0)
        return;
    File tmp = File.createTempFile("OMETiffWriterTest_Tiling", ".ome.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());
    int expectedTileSize = tileSize;
    if (tileSize < TILE_GRANULARITY) {
        expectedTileSize = TILE_GRANULARITY;
    } else {
        expectedTileSize = Math.round((float) tileSize / TILE_GRANULARITY) * TILE_GRANULARITY;
    }
    IFD tileIFd = reader.getIFDs().get(0);
    assertEquals(tileIFd.getIFDIntValue(IFD.TILE_LENGTH), expectedTileSize);
    assertEquals(tileIFd.getIFDIntValue(IFD.TILE_WIDTH), expectedTileSize);
    WriterUtilities.checkImage(reader, originalPlane, interleaved, rgbChannels, seriesCount, sizeT, compression);
    tmp.delete();
    reader.close();
}

Example 5 with TiffReader

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

the class OMETiffWriterTest 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("OMETiffWriterTest", ".ome.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();
}