@Test
public final void testErosionCubicMeshC6() {
ImageStack mask = createCubicMeshImage();
invertGray8Stack(mask);
ImageStack marker = ImageStack.create(20, 20, 20, 8);
marker.setVoxel(5, 5, 5, 255);
invertGray8Stack(marker);
GeodesicReconstruction3DHybrid0Gray8 algo = new GeodesicReconstruction3DHybrid0Gray8();
algo.setReconstructionType(GeodesicReconstructionType.BY_EROSION);
algo.setConnectivity(6);
ImageStack result = algo.applyTo(marker, mask);
assertEquals(0, result.getVoxel(5, 15, 5), .01);
assertEquals(255, result.getVoxel(0, 0, 0), .01);
int sizeX = mask.getWidth();
int sizeY = mask.getHeight();
int sizeZ = mask.getSize();
for (int z = 0; z < sizeZ; z++) {
for (int y = 0; y < sizeY; y++) {
for (int x = 0; x < sizeX; x++) {
assertEquals(result.getVoxel(x, y, z), mask.getVoxel(x, y, z), .01);
}
}
}
}
/**
* Creates an image of cube edges, similar to this:
*
* <p>*---------* ** ** * * * * *********** * | * | * | *------|--* | / | * |/ |* ***********
*
* <p>Typical planes are as follow: z = 0 z=1,2,3 z = 4 X * * * * . . . . . * * * * * . . . . * .
* . . . . * . . . * . . . . * . . . . . * . . . * . . . . * . . . . . * . . . * Z . . . * * . . .
* * * . . . *
*
* <p>(reconstruction starts from the X, and terminates at the Z)
*/
private ImageStack createThinCubicMeshImage() {
int sizeX = 5;
int sizeY = 5;
int sizeZ = 5;
int bitDepth = 8;
// create empty stack
ImageStack stack = ImageStack.create(sizeX, sizeY, sizeZ, bitDepth);
// First, the edges in the x direction
for (int x = 0; x < 5; x++) {
stack.setVoxel(x, 0, 0, 255);
stack.setVoxel(x, 0, 4, 255);
}
// then, the edges in the y direction
for (int y = 0; y < 5; y++) {
stack.setVoxel(4, y, 0, 255);
stack.setVoxel(0, y, 4, 255);
stack.setVoxel(4, y, 4, 255);
}
// Finally, the edges in the z direction
for (int z = 0; z < 5; z++) {
stack.setVoxel(0, 4, z, 255);
stack.setVoxel(4, 4, z, 255);
}
return stack;
}
@Test
public final void testDilationCochleaVolumeC6() {
String fileName = getClass().getResource("/files/bat-cochlea-volume.tif").getFile();
ImagePlus imagePlus = IJ.openImage(fileName);
assertNotNull(imagePlus);
assertTrue(imagePlus.getStackSize() > 0);
ImageStack mask = imagePlus.getStack();
// Ensure regularity of the mask
mask = Morphology.opening(mask, CubeStrel.fromRadius(1));
int width = mask.getWidth();
int height = mask.getHeight();
int depth = mask.getSize();
int bitDepth = mask.getBitDepth();
ImageStack marker = ImageStack.create(width, height, depth, bitDepth);
marker.setVoxel(20, 80, 50, 255);
GeodesicReconstruction3DHybrid0Gray8 algo = new GeodesicReconstruction3DHybrid0Gray8();
algo.setConnectivity(6);
algo.verbose = false;
ImageStack result = algo.applyTo(marker, mask);
for (int z = 0; z < depth; z++) {
for (int y = 0; y < height; y++) {
for (int x = 0; x < width; x++) {
assertEquals(result.getVoxel(x, y, z), mask.getVoxel(x, y, z), .01);
}
}
}
}
@Test
public final void testDilationHilbertCurveC26() {
String fileName = getClass().getResource("/files/hilbert3d.tif").getFile();
ImagePlus imagePlus = IJ.openImage(fileName);
assertNotNull(imagePlus);
assertTrue(imagePlus.getStackSize() > 0);
ImageStack mask = imagePlus.getStack();
int width = mask.getWidth();
int height = mask.getHeight();
int depth = mask.getSize();
int bitDepth = mask.getBitDepth();
ImageStack marker = ImageStack.create(width, height, depth, bitDepth);
marker.setVoxel(3, 0, 0, 255);
GeodesicReconstruction3DHybrid0Gray8 algo = new GeodesicReconstruction3DHybrid0Gray8();
algo.setConnectivity(26);
algo.verbose = false;
ImageStack result = algo.applyTo(marker, mask);
for (int z = 0; z < depth; z++) {
for (int y = 0; y < height; y++) {
for (int x = 0; x < width; x++) {
assertEquals(result.getVoxel(x, y, z), mask.getVoxel(x, y, z), .01);
}
}
}
}
@Test
public final void testApplyTo() {
GeodesicReconstructionByDilation3DGray8 algo = new GeodesicReconstructionByDilation3DGray8();
String fileName = getClass().getResource("/files/bat-cochlea-volume.tif").getFile();
ImagePlus imagePlus = IJ.openImage(fileName);
assertNotNull(imagePlus);
assertTrue(imagePlus.getStackSize() > 0);
ImageStack mask = imagePlus.getStack();
int width = mask.getWidth();
int height = mask.getHeight();
int depth = mask.getSize();
int bitDepth = mask.getBitDepth();
ImageStack marker = ImageStack.create(width, height, depth, bitDepth);
marker.setVoxel(20, 80, 50, 255);
ImageStack result = algo.applyTo(marker, mask);
for (int z = 0; z < depth; z++) {
for (int y = 0; y < height; y++) {
for (int x = 0; x < width; x++) {
assertEquals(result.getVoxel(x, y, z), mask.getVoxel(x, y, z), .01);
}
}
}
}
/**
* Resizes the current array to the given dimensions.
*
* @param input the array to resize
* @param lenX the desired length in x-direction (with, horizontal length)
* @param lenY the desired length in y-direction (height, vertical length)
* @return a new 2d float array with the specified dimensions, and values interpolated from the
* input array.
*/
public static float[][] resize(float[][] input, int lenX, int lenY) {
float[] linearized = linearize2DArray(input);
ImageStack is = ImageStack.create(input.length, input[0].length, 1, 32);
is.setPixels(linearized, 1);
ImageProcessor ip = new ImagePlus("", is).getProcessor();
ip.setInterpolationMethod(ImageProcessor.BICUBIC);
float[] resized = (float[]) ip.resize(lenX, lenY).getPixels();
return linearizedArrayTo2D(resized, lenX, lenY);
}
@Test
public final void testDilationThinCubicMeshC26() {
ImageStack mask = createThinCubicMeshImage();
ImageStack marker = ImageStack.create(5, 5, 5, 8);
marker.setVoxel(0, 0, 0, 255);
GeodesicReconstruction3DHybrid0Gray8 algo = new GeodesicReconstruction3DHybrid0Gray8();
algo.setConnectivity(26);
ImageStack result = algo.applyTo(marker, mask);
assertEquals(255, result.getVoxel(0, 4, 0), .01);
}
private ImageStack loadImages() {
String fileNameNumberRef = new String();
String fileNameNumberCorr = new String();
if (numOfIteration < 9) {
fileNameNumberRef = "000" + numOfIteration;
fileNameNumberCorr = "000" + (numOfIteration + 1);
}
if (numOfIteration == 9) {
fileNameNumberRef = "0009";
fileNameNumberCorr = "0010";
}
if (numOfIteration >= 10 && numOfIteration < 99) {
fileNameNumberRef = "00" + numOfIteration;
fileNameNumberCorr = "00" + (numOfIteration + 1);
}
if (numOfIteration == 99) {
fileNameNumberRef = "0099";
fileNameNumberCorr = "0100";
}
if (numOfIteration >= 100 && numOfIteration < 999) {
fileNameNumberRef = "0" + numOfIteration;
fileNameNumberCorr = "0" + (numOfIteration + 1);
}
if (numOfIteration == 999) {
fileNameNumberRef = "0999";
fileNameNumberCorr = "1000";
}
if (numOfIteration >= 1000) {
fileNameNumberRef = String.valueOf(numOfIteration);
fileNameNumberCorr = String.valueOf(numOfIteration + 1);
}
ImagePlus ref = new ImagePlus(dir + name + fileNameNumberRef + format);
ImagePlus corr = new ImagePlus(dir + name + (fileNameNumberCorr) + format);
ImageStack tmp = ImageStack.create(ref.getWidth(), ref.getHeight(), 2, ref.getBitDepth());
tmp.setPixels(ref.getProcessor().getPixels(), 1);
tmp.setPixels(corr.getProcessor().getPixels(), 2);
return tmp;
}
/**
* Combination of {@link ImageJInterpolation#crop(float[][], float, float, float, float)} and
* {@link ImageJInterpolation#resize(float[][], int, int)}. Crops and resizes the input array into
* a new output array.
*
* @param input the array to work on
* @param lenX the desired length in x-direction (with, horizontal length)
* @param lenY the desired length in y-direction (height, vertical length)
* @param minX the lower index in x-direction
* @param minY the lower index in y-direction
* @param maxX the higher index in x-direction
* @param maxY the higher index in y-direction
* @return a new cropped and resized version of the input array
*/
public static float[][] cropAndResize(
float[][] input, int lenX, int lenY, float minX, float minY, float maxX, float maxY) {
float[] linearized = linearize2DArray(input);
ImageStack is = ImageStack.create(input[0].length, input.length, 1, 32);
is.setPixels(linearized, 1);
ImageProcessor ip = new ImagePlus("", is).getProcessor();
ip.setInterpolationMethod(ImageProcessor.BICUBIC);
ip.setRoi((int) minX, (int) minY, (int) Math.ceil(maxX - minX), (int) Math.ceil(maxY - minY));
float[] resized = (float[]) ip.crop().resize(lenX, lenY).getPixels();
return linearizedArrayTo2D(resized, lenX, lenY);
}
private ImageStack createCubicMeshImage() {
int sizeX = 20;
int sizeY = 20;
int sizeZ = 20;
int bitDepth = 8;
// create empty stack
ImageStack stack = ImageStack.create(sizeX, sizeY, sizeZ, bitDepth);
// number of voxels between edges and 'tube' borders
int gap = 2;
// First, the edges in the x direction
for (int z = 5 - gap - 1; z <= 5 + gap + 1; z++) {
for (int y = 5 - gap - 1; y <= 5 + gap + 1; y++) {
for (int x = 5 - gap - 1; x <= 15 + gap + 1; x++) {
stack.setVoxel(x, y, z, 255);
stack.setVoxel(x, y, z + 10, 255);
}
}
}
// then, the edges in the y direction
for (int z = 5 - gap - 1; z <= 5 + gap + 1; z++) {
for (int x = 5 - gap - 1; x <= 5 + gap + 1; x++) {
for (int y = 5 - gap - 1; y <= 15 + gap + 1; y++) {
stack.setVoxel(x + 10, y, z, 255);
stack.setVoxel(x, y, z + 10, 255);
stack.setVoxel(x + 10, y, z + 10, 255);
}
}
}
// Finally, the edges in the z direction
for (int y = 5 - gap - 1; y <= 5 + gap + 1; y++) {
for (int x = 5 - gap - 1; x <= 5 + gap + 1; x++) {
for (int z = 5 - gap - 1; z <= 15 + gap + 1; z++) {
stack.setVoxel(x, y + 10, z, 255);
stack.setVoxel(x + 10, y + 10, z, 255);
}
}
}
return stack;
}
@Test
public final void testDilationCubicHollowMesh() {
ImageStack mask = createCubicHollowMeshImage();
ImageStack marker = ImageStack.create(20, 20, 20, 8);
for (int z = 0; z < 20; z++) {
for (int y = 0; y < 20; y++) {
for (int x = 0; x < 20; x++) {
marker.setVoxel(x, y, z, 255);
}
}
}
marker.setVoxel(5, 5, 5, 0);
GeodesicReconstruction3DHybrid0Gray8 algo = new GeodesicReconstruction3DHybrid0Gray8();
ImageStack result = algo.applyTo(marker, mask);
assertEquals(0, result.getVoxel(5, 15, 5), .01);
assertStackEquals(mask, result);
}
@Test
public final void testErosionCochleaVolumeC26() {
String fileName = getClass().getResource("/files/bat-cochlea-volume.tif").getFile();
ImagePlus imagePlus = IJ.openImage(fileName);
assertNotNull(imagePlus);
assertTrue(imagePlus.getStackSize() > 0);
ImageStack mask = imagePlus.getStack();
// Ensure regularity of the mask
mask = Morphology.opening(mask, CubeStrel.fromRadius(1));
invertGray8Stack(mask);
int width = mask.getWidth();
int height = mask.getHeight();
int depth = mask.getSize();
int bitDepth = mask.getBitDepth();
ImageStack marker = ImageStack.create(width, height, depth, bitDepth);
marker.setVoxel(20, 80, 50, 255);
invertGray8Stack(marker);
GeodesicReconstruction3DHybrid0Gray8 algo =
new GeodesicReconstruction3DHybrid0Gray8(GeodesicReconstructionType.BY_EROSION);
algo.setConnectivity(26);
ImageStack result = algo.applyTo(marker, mask);
for (int z = 0; z < depth; z++) {
for (int y = 0; y < height; y++) {
for (int x = 0; x < width; x++) {
if (Math.abs(result.getVoxel(x, y, z) - mask.getVoxel(x, y, z)) > .1) {
System.out.println("x=" + x + " y=" + y + " z=" + z);
System.out.println(" mask = " + (int) mask.getVoxel(x, y, z));
System.out.println(" res = " + (int) result.getVoxel(x, y, z));
assertTrue(false);
}
}
}
}
}
/** Creates a 3D image containing thin cube mesh. */
private ImageStack createCubeGraphImage() {
int sizeX = 11;
int sizeY = 11;
int sizeZ = 11;
int bitDepth = 8;
// create empty stack
ImageStack stack = ImageStack.create(sizeX, sizeY, sizeZ, bitDepth);
// coordinates of the cube edges
int x1 = 1;
int x2 = 9;
int y1 = 1;
int y2 = 9;
int z1 = 1;
int z2 = 9;
// First, the edges in the x direction
for (int x = x1; x <= x2; x++) {
stack.setVoxel(x, y1, z1, 255);
stack.setVoxel(x, y1, z2, 255);
}
// then, the edges in the y direction
for (int y = y1; y <= y2; y++) {
stack.setVoxel(x2, y, z1, 255);
stack.setVoxel(x1, y, z2, 255);
stack.setVoxel(x2, y, z2, 255);
}
// Finally, the edges in the z direction
for (int z = z1; z <= z2; z++) {
stack.setVoxel(x1, y2, z, 255);
stack.setVoxel(x2, y2, z, 255);
}
return stack;
}