//
// OmeroOpenBytesTest.java
//
/*
LOCI software automated test suite for TestNG. Copyright (C) 2007-@year@
Chris Allan. All rights reserved.
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:
* Redistributions of source code must retain the above copyright
notice, this list of conditions and the following disclaimer.
* Redistributions in binary form must reproduce the above copyright
notice, this list of conditions and the following disclaimer in the
documentation and/or other materials provided with the distribution.
* Neither the name of the UW-Madison LOCI nor the names of its
contributors may be used to endorse or promote products derived from
this software without specific prior written permission.
THIS SOFTWARE IS PROVIDED BY THE UW-MADISON LOCI ``AS IS'' AND ANY
EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS BE LIABLE FOR ANY
DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
*/
package loci.tests.testng;
import static org.testng.AssertJUnit.*;
import org.testng.annotations.AfterClass;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.Parameters;
import org.testng.annotations.Test;
import loci.formats.ChannelFiller;
import loci.formats.ChannelSeparator;
import loci.formats.FormatTools;
import loci.formats.IFormatReader;
import loci.formats.ImageReader;
import loci.formats.MinMaxCalculator;
/**
* Tests various permutations of <code>openBytes()</code> in an OMERO like
* manner.
*
* <dl><dt><b>Source code:</b></dt>
* <dd><a href="http://trac.openmicroscopy.org.uk/ome/browser/bioformats.git/components/test-suite/src/loci/tests/testng/OmeroOpenBytesTest.java">Trac</a>,
* <a href="http://git.openmicroscopy.org/?p=bioformats.git;a=blob;f=components/test-suite/src/loci/tests/testng/OmeroOpenBytesTest.java;hb=HEAD">Gitweb</a></dd></dl>
*
* @author Chris Allan <callan at blackcat dot ca>
*/
public class OmeroOpenBytesTest
{
private IFormatReader reader;
private int imageCount;
private int seriesCount;
private int sizeX;
private int sizeY;
private int sizeZ;
private int sizeC;
private int sizeT;
private int bpp;
private int planeSize;
private int topHalfSize;
private int bottomHalfSize;
private int topLeftQuarterSize;
private int topRightQuarterSize;
private int bottomLeftQuarterSize;
private int bottomRightQuarterSize;
@Parameters({"id"})
@BeforeClass
public void parse(String id) throws Exception {
reader = new ImageReader();
reader = new ChannelFiller(reader);
reader = new ChannelSeparator(reader);
reader = new MinMaxCalculator(reader);
reader.setId(id);
seriesCount = reader.getSeriesCount();
}
private void assertBlock(int blockSize, int posX, int posY,
int width, int height) throws Exception {
byte[] plane = new byte[planeSize];
byte[] buf = new byte[blockSize];
String planeDigest, bufDigest;
for (int i = 0; i < imageCount; i++) {
// Read the data as a full plane
reader.openBytes(i, plane);
// Read the data as a block
try {
reader.openBytes(i, buf, posX, posY, width, height);
}
catch (Exception e) {
throw new RuntimeException(String.format(
"openBytes(series:%d i:%d, buf.length:%d, x:%d, y:%d, w:%d, h:%d) " +
"[sizeX: %d sizeY:%d bpp:%d] threw exception!",
reader.getSeries(), i, buf.length, posX, posY, width, height,
sizeX, sizeY, bpp), e);
}
// Compare hash digests
planeDigest = TestTools.md5(
plane, sizeX, sizeY, posX, posY, width, height, bpp);
bufDigest = TestTools.md5(buf, 0, width * height * bpp);
if (!planeDigest.equals(bufDigest)) {
fail(String.format("MD5:%d;%d len:%d %s != %s",
reader.getSeries(), i, blockSize, planeDigest, bufDigest));
}
}
}
private void assertRows(int blockSize) throws Exception {
for (int series = 0; series < seriesCount; series++) {
assertSeries(series);
byte[] plane = new byte[planeSize];
byte[] buf = new byte[blockSize];
int maximumRowCount = buf.length / bpp / sizeX;
String planeDigest, bufDigest;
int pixelsToRead = sizeX * sizeY;
int width = sizeX, height, posX = 0, posY = 0, actualBufSize;
for (int i = 0; i < imageCount; i++) {
// Read the data as a full plane
reader.openBytes(i, plane);
int offset = 0;
while(pixelsToRead > 0) {
// Prepare our read metadata
height = maximumRowCount;
if ((posY + height) > sizeY)
{
height = sizeY - posY;
}
actualBufSize = bpp * height * width;
// Read the data as a block
try {
reader.openBytes(i, buf, posX, posY, width, height);
}
catch (Exception e) {
throw new RuntimeException(String.format(
"openBytes(series:%d i:%d, buf.length:%d, x:%d, y:%d, w:%d, " +
"h:%d) [sizeX: %d sizeY:%d bpp:%d] threw exception!",
series, i, buf.length, posX, posY, width, height, sizeX, sizeY,
bpp), e);
}
// Compare hash digests
planeDigest = TestTools.md5(plane, offset, actualBufSize);
bufDigest = TestTools.md5(buf, 0, actualBufSize);
if (!planeDigest.equals(bufDigest)) {
fail(String.format("MD5:%s;%d offset:%d len:%d %s != %s",
series, i, offset, actualBufSize, planeDigest, bufDigest));
}
// Update offsets, etc.
offset += actualBufSize;
posY += height;
pixelsToRead -= height * width;
}
}
}
}
private void assertSeries(int series) {
reader.setSeries(series);
sizeX = reader.getSizeX();
sizeY = reader.getSizeY();
sizeZ = reader.getSizeZ();
sizeC = reader.getSizeC();
sizeT = reader.getSizeT();
imageCount = reader.getImageCount();
bpp = FormatTools.getBytesPerPixel(reader.getPixelType());
planeSize = sizeX * sizeY * bpp;
topHalfSize = (sizeY / 2) * sizeX * bpp;
bottomHalfSize = (sizeY - (sizeY / 2)) * sizeX * bpp;
topLeftQuarterSize = (sizeY / 2) * (sizeX / 2) * bpp;
topRightQuarterSize = (sizeY / 2) * (sizeX - (sizeX / 2)) * bpp;
bottomLeftQuarterSize = (sizeY - (sizeY / 2)) * (sizeX / 2) * bpp;
bottomRightQuarterSize =
(sizeY - (sizeY / 2)) * (sizeX - (sizeX / 2)) * bpp;
}
@AfterClass
public void tearDown() throws Exception {
reader.close();
}
@Test
public void testOpenBytesPlane() throws Exception {
for (int series = 0; series < seriesCount; series++) {
assertSeries(series);
byte[] plane = new byte[planeSize];
for (int i = 0; i < reader.getImageCount(); i++) {
reader.openBytes(i, plane);
}
}
}
@Test
public void testOpenBytesHalfPlane() throws Exception {
for (int series = 0; series < seriesCount; series++) {
assertSeries(series);
byte[] plane = new byte[planeSize];
byte[] topHalfPlane = new byte[topHalfSize];
byte[] bottomHalfPlane = new byte[bottomHalfSize];
String planeDigest, halfPlaneDigest;
for (int i = 0; i < imageCount; i++) {
// Check the digest for the first half of the plane against a full
// plane
reader.openBytes(i, plane);
reader.openBytes(i, topHalfPlane, 0, 0, sizeX, sizeY / 2);
planeDigest = TestTools.md5(plane, 0, topHalfSize);
halfPlaneDigest = TestTools.md5(topHalfPlane, 0, topHalfSize);
if (!planeDigest.equals(halfPlaneDigest)) {
fail(String.format("First half MD5:%d;%d %s != %s",
series, i, planeDigest, halfPlaneDigest));
}
// Check the digest for the second half of the plane against a full
// plane
reader.openBytes(i, bottomHalfPlane, 0, sizeY / 2, sizeX,
sizeY - (sizeY / 2));
planeDigest = TestTools.md5(plane, topHalfSize, bottomHalfSize);
halfPlaneDigest = TestTools.md5(bottomHalfPlane, 0, bottomHalfSize);
if (!planeDigest.equals(halfPlaneDigest)) {
fail(String.format("Second half MD5:%d;%d %s != %s",
series, i, planeDigest, halfPlaneDigest));
}
}
}
}
@Test
public void testQuartersActualSize() throws Exception {
for (int series = 0; series < seriesCount; series++) {
assertSeries(series);
assertBlock(topLeftQuarterSize, 0, 0, sizeX / 2, sizeY / 2);
assertBlock(topRightQuarterSize, sizeX / 2, 0,
sizeX - (sizeX / 2), sizeY / 2);
assertBlock(bottomLeftQuarterSize, 0, sizeY / 2,
sizeX / 2, (sizeY - (sizeY / 2)));
assertBlock(bottomRightQuarterSize, sizeX / 2, sizeY / 2,
sizeX - (sizeX / 2), sizeY - (sizeY / 2));
}
}
@Test
public void testQuartersTwiceActualSize() throws Exception {
for (int series = 0; series < seriesCount; series++) {
assertSeries(series);
assertBlock(topLeftQuarterSize * 2, 0, 0, sizeX / 2, sizeY / 2);
assertBlock(topRightQuarterSize * 2, sizeX / 2, 0,
sizeX - (sizeX / 2), sizeY / 2);
assertBlock(bottomLeftQuarterSize * 2, 0, sizeY / 2,
sizeX / 2, (sizeY - (sizeY / 2)));
assertBlock(bottomRightQuarterSize * 2, sizeX / 2, sizeY / 2,
sizeX - (sizeX / 2), sizeY - (sizeY / 2));
}
}
@Test
public void testOpenBytesBlocksByRow512KB() throws Exception {
assertRows(524288);
}
@Test
public void testOpenBytesBlocksByRow1MB() throws Exception {
assertRows(1048576);
}
@Test
public void testOpenBytesBlocksByRowPlaneSize() throws Exception {
assertRows(sizeX * sizeY * bpp);
}
}