/*-
* #%L
* Fiji's plugin for colocalization analysis.
* %%
* Copyright (C) 2009 - 2017 Fiji developers.
* %%
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as
* published by the Free Software Foundation, either version 3 of the
* License, or (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public
* License along with this program. If not, see
* <http://www.gnu.org/licenses/gpl-3.0.html>.
* #L%
*/
package sc.fiji.coloc.tests;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertTrue;
import java.util.Arrays;
import net.imglib2.Cursor;
import net.imglib2.PredicateCursor;
import net.imglib2.RandomAccess;
import net.imglib2.RandomAccessibleInterval;
import net.imglib2.TwinCursor;
import net.imglib2.algorithm.math.ImageStatistics;
import net.imglib2.img.ImgFactory;
import net.imglib2.img.array.ArrayImgFactory;
import net.imglib2.predicate.MaskPredicate;
import net.imglib2.predicate.Predicate;
import net.imglib2.roi.RectangleRegionOfInterest;
import net.imglib2.type.logic.BitType;
import net.imglib2.type.numeric.integer.UnsignedByteType;
import net.imglib2.view.Views;
import org.junit.Test;
import sc.fiji.coloc.algorithms.MissingPreconditionException;
import sc.fiji.coloc.gadgets.MaskFactory;
/**
* This class contains JUnit 4 test cases for the ROI and masks
* implementation.
*
* @author Dan White
* @author Tom Kazimiers
*/
public class MaskAndRoiTest extends ColocalisationTest {
/**
* Tests if a masked walk over an image refers to the correct data
* by copying the data to a separate image and then compare it with
* the original image data. The position data in the original image
* is calculated based on the ROI offset and the relative position
* in the copied ROI image.
* @throws MissingPreconditionException
*/
@Test
public void maskContentTest() throws MissingPreconditionException {
// load a 3D test image
final RandomAccessibleInterval<UnsignedByteType> img = positiveCorrelationImageCh1;
final long[] roiOffset = createRoiOffset(img);
final long[] roiSize = createRoiSize(img);
final long[] dim = new long[ img.numDimensions() ];
img.dimensions(dim);
final RandomAccessibleInterval<BitType> mask =
MaskFactory.createMask(dim, roiOffset, roiSize);
// create cursor to walk an image with respect to a mask
TwinCursor<UnsignedByteType> cursor = new TwinCursor<UnsignedByteType>(
img.randomAccess(), img.randomAccess(),
Views.iterable(mask).localizingCursor());
// create an image for the "clipped ROI"
ImgFactory<UnsignedByteType> maskFactory =
new ArrayImgFactory<UnsignedByteType>();
RandomAccessibleInterval<UnsignedByteType> clippedRoiImage =
maskFactory.create( roiSize, new UnsignedByteType() ); // "Clipped ROI" );
RandomAccess<UnsignedByteType> outputCursor =
clippedRoiImage.randomAccess();
// copy ROI data to new image
long[] pos = new long[ clippedRoiImage.numDimensions() ];
while (cursor.hasNext()) {
cursor.fwd();
cursor.localize(pos);
// shift position by offset
for (int i=0; i<pos.length; i++) {
pos[i] = pos[i] - roiOffset[i];
}
outputCursor.setPosition(pos);
outputCursor.get().set( cursor.getFirst() );
}
/* go through the clipped ROI and compare the date to offset values
* of the original data.
*/
Cursor<UnsignedByteType> roiCopyCursor =
Views.iterable(clippedRoiImage).localizingCursor();
RandomAccess<UnsignedByteType> imgCursor =
img.randomAccess();
// create variable for summing up and set it to zero
double sum = 0;
pos = new long [ clippedRoiImage.numDimensions() ];
while (roiCopyCursor.hasNext()) {
roiCopyCursor.fwd();
roiCopyCursor.localize(pos);
// shift position by offset
for (int i=0; i<pos.length; i++) {
pos[i] = pos[i] + roiOffset[i];
}
// set position in original image
imgCursor.setPosition(pos);
// get ROI and original image data
double roiData = roiCopyCursor.get().getRealDouble();
double imgData = imgCursor.get().getRealDouble();
// sum up the difference
double diff = roiData - imgData;
sum += diff * diff;
}
// check if sum is zero
assertTrue("The sum of squared differences was " + sum + ".", Math.abs(sum) < 0.00001);
}
/**
* Tests a PredicateCursor by checking if all visited values are "true".
* @throws MissingPreconditionException
*/
@Test
public void predicateCursorTest() throws MissingPreconditionException {
// load a 3D test image
RandomAccessibleInterval<UnsignedByteType> img = positiveCorrelationImageCh1;
long[] roiOffset = createRoiOffset(img);
long[] roiSize = createRoiSize(img);
long[] dim = new long[ img.numDimensions() ];
img.dimensions(dim);
RandomAccessibleInterval<BitType> mask = MaskFactory.createMask(dim,
roiOffset, roiSize);
// create cursor to walk an image with respect to a mask
final Predicate<BitType> predicate = new MaskPredicate();
Cursor<BitType> roiCursor
= new PredicateCursor<BitType>(
Views.iterable(mask).localizingCursor(), predicate);
// test if all visited voxels are "true"
while (roiCursor.hasNext()) {
roiCursor.fwd();
assertTrue(roiCursor.get().get());
}
}
/**
* This test test if a regular mask is created by the MaskFactory
* correctly. First, the dimensions are checked, they must be the
* same as the original images ones. Then it is checked if all
* values in the mask image have the value they should have. For
* a regular ROI this is easy to tell as one can calculate it out
* of the position.
*/
@Test
public void regularMaskCreationTest() throws MissingPreconditionException {
// load a 3D test image
RandomAccessibleInterval<UnsignedByteType> img = positiveCorrelationImageCh1;
final long[] roiOffset = createRoiOffset(img);
final long[] roiSize = createRoiSize(img);
final long[] dim = new long[ img.numDimensions() ];
img.dimensions(dim);
RandomAccessibleInterval<BitType> mask = MaskFactory.createMask(dim,
roiOffset, roiSize);
// is the number of dimensions the same as in the image?
final long[] dimMask = new long[ mask.numDimensions() ];
mask.dimensions(dimMask);
assertTrue( Arrays.equals(dim, dimMask) );
// go through the mask and check if all valid points are in the ROI
long[] pos = new long[ img.numDimensions() ];
final Cursor<BitType> cursor = Views.iterable(mask).localizingCursor();
while ( cursor.hasNext() ) {
cursor.fwd();
cursor.localize(pos);
// get values in mask image
boolean onInMask = cursor.get().get();
// calculate value that the current point *should* have
boolean onInROI = true;
for(int i=0; i<pos.length; ++i)
onInROI &= pos[i] >= roiOffset[i] && pos[i] < (roiOffset[i] + roiSize[i]);
// both values must match
assertTrue(onInMask == onInROI);
}
/* go once more trough the image wrt. the mask to build a
* bounding box
*/
// create cursor to walk an image with respect to a mask
final Predicate<BitType> predicate = new MaskPredicate();
Cursor<BitType> roiCursor
= new PredicateCursor<BitType>(
Views.iterable(mask).localizingCursor(), predicate);
long[] min = new long[ mask.numDimensions() ];
long[] max = new long[ mask.numDimensions() ];
Arrays.fill(min, Integer.MAX_VALUE);
Arrays.fill(max, Integer.MIN_VALUE);
while (roiCursor.hasNext()) {
roiCursor.fwd();
roiCursor.localize(pos);
for (int i=0; i<pos.length; i++) {
if (pos[i] < min[i])
min[i] = pos[i];
if (pos[i] > max[i])
max[i] = pos[i];
}
}
// the bounding box min should equal the ROI offset
assertTrue(Arrays.equals(min, roiOffset));
// create theoretical bounding box max and check it
long[] roiMax = roiOffset.clone();
for (int i=0; i<roiMax.length; i++)
roiMax[i] += roiSize[i] - 1;
assertTrue(Arrays.equals(max, roiMax));
}
/**
* This test creates first an "always true" mask and count the data
* values. There should be as many as the number of vocels in total.
* After that an "always false" mask is created. The predicate cursor
* there should not return any values.
*/
@Test
public void simpleMaskCreationTest() {
final RandomAccessibleInterval<UnsignedByteType> img = positiveCorrelationImageCh1;
// first, create an always true mask
final long[] dim = new long[ img.numDimensions() ];
img.dimensions(dim);
RandomAccessibleInterval<BitType> mask = MaskFactory.createMask(dim, true);
final Predicate<BitType> predicate = new MaskPredicate();
Cursor<BitType> cursor
= new PredicateCursor<BitType>(
Views.iterable(mask).localizingCursor(), predicate);
// iterate over mask and count values
long count = 0;
while (cursor.hasNext()) {
cursor.fwd();
count++;
assertTrue(cursor.get().get());
}
assertEquals(ImageStatistics.getNumPixels(mask), count);
// second, create an always false mask
mask = MaskFactory.createMask(dim, false);
cursor = new PredicateCursor<BitType>(
Views.iterable(mask).localizingCursor(), predicate);
// iterate over mask and count values
count = 0;
while (cursor.hasNext()) {
cursor.fwd();
count++;
}
assertEquals(0, count);
}
/**
* Tests against the implementation of irregular ROIs alias
* masks. Masks can also be produced by mask images open in
* another Fiji window.
*
* This test generates a random black/white noise image and
* uses first itself and then an inverted version of it as
* mask. While iterating over it, the pixel values are
* checked. Is the first version only non-zero values should
* be present, while only zeros should be there in the second
* one.
*/
@Test
public void irregularRoiTest() {
// create a random noise 2D image -- set roiWidh/roiSize accordingly
RandomAccessibleInterval<UnsignedByteType> img =
TestImageAccessor.produceSticksNoiseImage(300, 300, 50, 2, 10);
final long[] dim = new long[ img.numDimensions() ];
img.dimensions(dim);
/* first test - using itself as a mask */
RandomAccessibleInterval<BitType> mask = MaskFactory.createMask(dim, img);
TwinCursor<UnsignedByteType> cursor = new TwinCursor<UnsignedByteType>(
img.randomAccess(),
img.randomAccess(),
Views.iterable(mask).localizingCursor());
while (cursor.hasNext()) {
cursor.fwd();
assertTrue( cursor.getFirst().getInteger() != 0 );
}
/* second test - using inverted image */
RandomAccessibleInterval<UnsignedByteType> invImg =
TestImageAccessor.invertImage(img);
RandomAccessibleInterval<BitType> invMask =
MaskFactory.createMask(dim, invImg);
cursor = new TwinCursor<UnsignedByteType>(
img.randomAccess(),
img.randomAccess(),
Views.iterable(invMask).localizingCursor());
while (cursor.hasNext()) {
cursor.fwd();
assertEquals( 0, cursor.getFirst().getInteger() );
}
}
/**
* This test makes sure that a mask that is based on a lower dimension
* image has the correct dimensionality.
*/
@Test
public void irregularRoiDimensionTest() {
// load a 3D test image
RandomAccessibleInterval<UnsignedByteType> img = positiveCorrelationImageCh1;
final long width = img.dimension(0);
final long height = img.dimension(1);
final long slices = img.dimension(2);
final long[] dimImg = new long[ img.numDimensions() ];
img.dimensions(dimImg);
// create a random noise 2D image -- set roiWidh/roiSize accordingly
RandomAccessibleInterval<UnsignedByteType> maskSlice =
TestImageAccessor.produceSticksNoiseImage( (int) width, (int) height, 50, 2, 10);
RandomAccessibleInterval<BitType> mask =
MaskFactory.createMask(dimImg, maskSlice);
final long[] dimMask = new long[ mask.numDimensions() ];
mask.dimensions(dimMask);
// check the dimensions of the mask
org.junit.Assert.assertArrayEquals(dimImg, dimMask);
// make sure the mask actually got the same content on every slice
final double[] offset = new double[ mask.numDimensions() ];
Arrays.fill(offset, 0);
double[] size = new double[ mask.numDimensions() ];
size[0] = width;
size[1] = height;
size[2] = 1;
RandomAccess<BitType> maskCursor = mask.randomAccess();
RectangleRegionOfInterest roi = new RectangleRegionOfInterest( offset, size);
Cursor<BitType> firstSliceCursor = roi.getIterableIntervalOverROI(mask).cursor();
final long[] pos = new long[ mask.numDimensions() ];
while (firstSliceCursor.hasNext()) {
firstSliceCursor.fwd();
firstSliceCursor.localize(pos);
BitType maskValue = firstSliceCursor.get();
// go through all slices
for (int i=1; i<slices; ++i) {
pos[2] = i;
maskCursor.setPosition(pos);
// compare the values and assume they are the same
int cmp = maskCursor.get().compareTo(maskValue);
assertEquals(0, cmp);
}
}
}
@Test
public void regularRoiPixelCountTest() {
// load a 3D test image
RandomAccessibleInterval<UnsignedByteType> img = positiveCorrelationImageCh1;
final long[] roiOffset = createRoiOffset(img);
final long[] roiSize = createRoiSize(img);
final long width = img.dimension(0);
final long height = img.dimension(1);
RandomAccessibleInterval<UnsignedByteType> maskImg
= TestImageAccessor.createRectengularMaskImage(width, height, roiOffset, roiSize);
final long[] dim = new long[ img.numDimensions() ];
img.dimensions(dim);
RandomAccessibleInterval<BitType> mask =
MaskFactory.createMask(dim, maskImg);
TwinCursor<UnsignedByteType> cursor = new TwinCursor<UnsignedByteType>(
img.randomAccess(),
img.randomAccess(),
Views.iterable(mask).localizingCursor());
// calculate volume of mask bounding box
long roiVolume = roiSize[0] * roiSize[1] * img.dimension(2);
long count = 0;
while (cursor.hasNext()) {
cursor.fwd();
count++;
}
assertEquals(roiVolume, count);
}
}
