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* BSD implementations of Bio-Formats readers and writers
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package loci.formats.utests;
import static org.testng.AssertJUnit.*;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
import loci.common.Location;
import loci.formats.FormatException;
import loci.formats.FormatTools;
import loci.formats.MinMaxCalculator;
import loci.formats.in.FakeReader;
import loci.formats.meta.IMinMaxStore;
import org.testng.annotations.AfterMethod;
import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
/**
* Test case which outlines the problems seen in omero:#3599.
*
* @author Chris Allan <callan at blackcat dot ca>
*/
public class MinMaxCalculatorTest {
private static final String TEST_FILE =
"test&pixelType=int8&sizeX=20&sizeY=20&sizeC=1&sizeZ=1&sizeT=1.fake";
private MinMaxCalculatorTestReader reader;
private MinMaxCalculator minMaxCalculator;
private TestMinMaxStore minMaxStore;
private static int fullPlaneCallIndex;
private int sizeX;
private int sizeY;
private int bpp;
private int planeSize;
@BeforeMethod
public void setUp() throws Exception {
fullPlaneCallIndex = 1;
Location.mapId(TEST_FILE, TEST_FILE);
reader = new MinMaxCalculatorTestReader();
reader.setId(TEST_FILE);
minMaxStore = new TestMinMaxStore();
minMaxCalculator = new MinMaxCalculator(reader);
minMaxCalculator.setMinMaxStore(minMaxStore);
sizeX = reader.getSizeX();
sizeY = reader.getSizeY();
bpp = FormatTools.getBytesPerPixel(reader.getPixelType());
planeSize = sizeY * sizeY * bpp;
}
@AfterMethod
public void tearDown() throws Exception {
minMaxCalculator.close();
reader.close();
}
private void assertMinMax(double minimum, double maximum) throws Exception {
Double[] min = minMaxCalculator.getPlaneMinimum(0);
Double[] max = minMaxCalculator.getPlaneMaximum(0);
Double globalMin = minMaxCalculator.getChannelGlobalMinimum(0);
Double globalMax = minMaxCalculator.getChannelGlobalMaximum(0);
Double knownGlobalMin = minMaxCalculator.getChannelKnownMinimum(0);
Double knownGlobalMax = minMaxCalculator.getChannelKnownMaximum(0);
assertTrue(minMaxCalculator.isMinMaxPopulated());
assertNotNull(min);
assertNotNull(max);
assertNotNull(globalMin);
assertNotNull(globalMax);
assertNotNull(knownGlobalMin);
assertNotNull(knownGlobalMax);
assertEquals(1, min.length);
assertEquals(1, max.length);
assertEquals(minimum, min[0]);
assertEquals(maximum, max[0]);
assertEquals(minimum, globalMin);
assertEquals(maximum, globalMax);
assertEquals(minimum, knownGlobalMin);
assertEquals(maximum, knownGlobalMax);
List<List<double[]>> seriesGlobalMinimaMaxima =
minMaxStore.seriesGlobalMinimaMaxima;
assertEquals(1, seriesGlobalMinimaMaxima.size());
List<double[]> channelGlobalMinimaMaxima =
seriesGlobalMinimaMaxima.get(0);
assertEquals(1, channelGlobalMinimaMaxima.size());
double[] channelGlobalMinMax = channelGlobalMinimaMaxima.get(0);
channelGlobalMinMax[0] = minimum;
channelGlobalMinMax[1] = maximum;
}
@Test
public void testValidOpenBytes() throws Exception {
byte[] a = new byte[planeSize / 2];
byte[] b = new byte[planeSize / 2];
int halfway = sizeY / 2;
reader.openBytes(0, a, 0, 0, sizeX, halfway);
reader.openBytes(0, b, 0, halfway, sizeX, halfway);
assertEquals(-1, a[sizeX / 2]);
assertEquals(1, a[sizeX / 2 + 1]);
assertEquals(-2, b[sizeX / 2]);
assertEquals(2, b[sizeX / 2 + 1]);
}
@Test
public void testValidMinMax() throws Exception {
minMaxCalculator.openBytes(0);
assertMinMax(-2.0, 101.0);
}
@Test
public void testValidMinMaxNoOutOfBufferInspection() throws Exception {
byte[] buf = new byte[planeSize * 2];
buf[buf.length - 1] = 120; // This should not be calculated against
minMaxCalculator.openBytes(0, buf, 0, 0, sizeX, sizeY);
assertMinMax(-2.0, 101.0);
}
@Test
public void testValidMinMaxDoesntRecalculateOnFullPlane() throws Exception {
minMaxCalculator.openBytes(0);
minMaxCalculator.openBytes(0);
assertMinMax(-2.0, 101.0);
}
@Test
public void testValidMinMaxFirstHalf() throws Exception {
byte[] buf = new byte[planeSize / 2];
int halfway = sizeY / 2;
minMaxCalculator.openBytes(0, buf, 0, 0, sizeX, halfway);
assertMinMax(-1.0, 1.0);
}
@Test
public void testValidMinMaxSecondHalf() throws Exception {
byte[] buf = new byte[planeSize / 2];
int halfway = sizeY / 2;
minMaxCalculator.openBytes(0, buf, 0, halfway, sizeX, halfway);
assertMinMax(-2.0, 2.0);
}
@Test
public void testValidMinMaxBothHalvesLowerFirst() throws Exception {
byte[] buf = new byte[planeSize / 2];
int halfway = sizeY / 2;
minMaxCalculator.openBytes(0, buf, 0, 0, sizeX, halfway);
minMaxCalculator.openBytes(0, buf, 0, halfway, sizeX, halfway);
assertMinMax(-2.0, 2.0);
}
@Test
public void testValidMinMaxBothHalvesUpperFirst() throws Exception {
byte[] buf = new byte[planeSize / 2];
int halfway = sizeY / 2;
minMaxCalculator.openBytes(0, buf, 0, halfway, sizeX, halfway);
minMaxCalculator.openBytes(0, buf, 0, 0, sizeX, halfway);
assertMinMax(-2.0, 2.0);
}
/**
* A testing implementation of {@link loci.formats.meta.IMinMaxStore} that
* we'll use to ensure that the various methods are called with the correct
* parameters.
*
* @author Chris Allan <callan at blackcat dot ca>
*
*/
class TestMinMaxStore implements IMinMaxStore {
public List<List<double[]>> seriesGlobalMinimaMaxima =
new ArrayList<List<double[]>>();
/**
* @see loci.formats.meta.IMinMaxStore#setChannelGlobalMinMax(int, double, double, int)
*/
@Override
public void setChannelGlobalMinMax(int channel, double minimum,
double maximum, int series) {
if (seriesGlobalMinimaMaxima.size() == series) {
seriesGlobalMinimaMaxima.add(new ArrayList<double[]>());
}
List<double[]> channelGlobalMinimaMaxima =
seriesGlobalMinimaMaxima.get(series);
if (channelGlobalMinimaMaxima.size() == channel) {
channelGlobalMinimaMaxima.add(new double[2]);
}
double[] channelGlobalMinMax = channelGlobalMinimaMaxima.get(channel);
channelGlobalMinMax[0] = minimum;
channelGlobalMinMax[1] = maximum;
}
}
/**
* An extension of {@link loci.formats.in.FakeReader} that allows us to
* control exactly what is in the data returned by the <code>openBytes</code>
* class of methods.
*
* @author Chris Allan <callan at blackcat dot ca>
*
*/
class MinMaxCalculatorTestReader extends FakeReader {
/**
* @see loci.formats.IFormatReader#openBytes(int, byte[], int, int, int, int)
*/
@Override
public byte[] openBytes(int no, byte[] buf, int x, int y, int w, int h)
throws FormatException, IOException {
FormatTools.checkPlaneParameters(this, no, buf.length, x, y, w, h);
int bpp = FormatTools.getBytesPerPixel(getPixelType());
int sizeX = getSizeX();
int sizeY = getSizeY();
int planeSize = sizeX * sizeY * bpp;
if (x != 0) {
throw new FormatException("x != 0 not supported by this test!");
}
if (w != sizeX) {
throw new FormatException("Width != sizeX not supported by this test!");
}
// When we're working with the first half of the rows of the image then
// populate with (-1, 1) pixel values. (-2, 2) for the second half. This
// will aid us during testing to ensure that minima and maxima are being
// correctly re-calculated when using block based openBytes() access.
int from, to;
for (int i = 0; i < h; i++) {
from = i * sizeX * bpp;
to = ((i * sizeX) + sizeX - 1) * bpp;
Arrays.fill(buf, from, to, (byte) 0x00);
if (i + y == 0) {
buf[(sizeX / 2) * bpp] = -1;
buf[((sizeX / 2) + 1) * bpp] = 1;
}
if (i + y == 10) {
buf[(sizeX / 2) * bpp] = -2;
buf[((sizeX / 2) + 1) * bpp] = 2;
}
}
// When working with a buffer that is equal to or larger than the plane
// size we're going to place an index in its last pixel so that we can
// check re-calculation and call counts.
if (buf.length >= planeSize) {
buf[planeSize - 1] = (byte) (100 + fullPlaneCallIndex);
fullPlaneCallIndex++;
}
return buf;
}
}
}