/*
* Makes sure calculation of IJ1 channels is correctly invertible
*/
@Test
public void testRasterization() {
final long[][] dimsList = {{1, 1, 1}, {1, 2, 3}, {2, 3, 4}, {5, 4, 3}, {4, 2, 7}};
final AxisType[] axes = {Axes.CHANNEL, SCIFIOAxes.SPECTRA, SCIFIOAxes.FREQUENCY};
for (long[] dims : dimsList) {
// setup
long numChannels = 1;
for (long dim : dims) numChannels *= dim;
// test from long index back to long index
for (long channel = 0; channel < numChannels; channel++) {
long[] channelPositions = new long[dims.length];
LegacyUtils.fillChannelIndices(dims, axes, channel, channelPositions);
long ij1Pos = LegacyUtils.calcIJ1ChannelPos(dims, axes, channelPositions);
assertEquals(channel, ij1Pos);
}
// test from long[] index back to long[] index
long[] channelPositions1 = new long[dims.length];
long[] channelPositions2 = new long[dims.length];
Extents extents = new Extents(dims);
Position pos = extents.createPosition();
while (pos.hasNext()) {
pos.fwd();
pos.localize(channelPositions1);
long ij1Channel = LegacyUtils.calcIJ1ChannelPos(dims, axes, channelPositions1);
LegacyUtils.fillChannelIndices(dims, axes, ij1Channel, channelPositions2);
for (int i = 0; i < channelPositions1.length; i++)
assertEquals(channelPositions1[i], channelPositions2[i]);
}
}
}
/**
* Makes a color {@link Dataset} from an {@link ImagePlus}. Color Datasets have isRgbMerged()
* true, channels == 3, and bitsperPixel == 8. Does not populate the data of the returned Dataset.
* That is left to other utility methods. Does not set metadata of Dataset. Throws exceptions if
* input ImagePlus is not single channel RGB.
*/
private Dataset makeColorDataset(final ImagePlus imp, final AxisType[] preferredOrder) {
final int x = imp.getWidth();
final int y = imp.getHeight();
final int c = imp.getNChannels();
final int z = imp.getNSlices();
final int t = imp.getNFrames();
if (imp.getType() != ImagePlus.COLOR_RGB) {
throw new IllegalArgumentException("can't make a color Dataset from a nonRGB ImagePlus");
}
if (c != 1) {
throw new IllegalArgumentException(
"can't make a color Dataset from a multichannel ColorProcessor stack");
}
final int[] inputDims = new int[] {x, y, 3, z, t};
final AxisType[] axes = LegacyUtils.orderedAxes(preferredOrder, inputDims);
final long[] dims = LegacyUtils.orderedDims(axes, inputDims);
final String name = imp.getTitle();
final int bitsPerPixel = 8;
final boolean signed = false;
final boolean floating = false;
final boolean virtual = imp.getStack().isVirtual();
final Dataset ds =
datasetService.create(dims, name, axes, bitsPerPixel, signed, floating, virtual);
ds.setRGBMerged(true);
DatasetUtils.initColorTables(ds);
return ds;
}
/**
* Makes a color {@link ImagePlus} from a color {@link Dataset}. The ImagePlus will have the same
* X, Y, Z, & T dimensions. C will be 1. The data values and metadata are not assigned. Throws an
* exception if the dataset is not color compatible.
*/
private ImagePlus makeColorImagePlus(final Dataset ds) {
if (!LegacyUtils.isColorCompatible(ds)) {
throw new IllegalArgumentException("Dataset is not color compatible");
}
final int[] dimIndices = new int[5];
final int[] dimValues = new int[5];
LegacyUtils.getImagePlusDims(ds, dimIndices, dimValues);
final int w = dimValues[0];
final int h = dimValues[1];
final int c = dimValues[2] / 3;
final int z = dimValues[3];
final int t = dimValues[4];
final ImageStack stack = new ImageStack(w, h, c * z * t);
for (int i = 0; i < c * z * t; i++) stack.setPixels(new int[w * h], i + 1);
final ImagePlus imp = new ImagePlus(ds.getName(), stack);
imp.setDimensions(c, z, t);
return imp;
}
/**
* Assigns the data values of a {@link Dataset} from a paired {@link ImagePlus}. Assumes the
* Dataset and ImagePlus have compatible dimensions and that the data planes are not directly
* mapped. Gets values via {@link ImageProcessor}::getf(). In cases where there is a narrowing of
* data into modern ImageJ types the data is range clamped. Does not change the Dataset's
* metadata.
*/
@Override
public void updateDataset(final Dataset ds, final ImagePlus imp) {
final RealType<?> type = ds.getType();
final double typeMin = type.getMinValue();
final double typeMax = type.getMaxValue();
final boolean signed16BitData = type instanceof ShortType;
final RandomAccess<? extends RealType<?>> accessor = ds.getImgPlus().randomAccess();
final long[] dims = ds.getDims();
final AxisType[] axes = ds.getAxes();
final int xIndex = ds.getAxisIndex(Axes.X);
final int yIndex = ds.getAxisIndex(Axes.Y);
final int zIndex = ds.getAxisIndex(Axes.Z);
final int tIndex = ds.getAxisIndex(Axes.TIME);
final int xSize = imp.getWidth();
final int ySize = imp.getHeight();
final int zSize = imp.getNSlices();
final int tSize = imp.getNFrames();
final int cSize = imp.getNChannels();
final ImageStack stack = imp.getStack();
int planeNum = 1;
final long[] pos = new long[dims.length];
for (int t = 0; t < tSize; t++) {
if (tIndex >= 0) pos[tIndex] = t;
for (int z = 0; z < zSize; z++) {
if (zIndex >= 0) pos[zIndex] = z;
for (int c = 0; c < cSize; c++) {
LegacyUtils.fillChannelIndices(dims, axes, c, pos);
final ImageProcessor proc = stack.getProcessor(planeNum++);
for (int x = 0; x < xSize; x++) {
if (xIndex >= 0) pos[xIndex] = x;
for (int y = 0; y < ySize; y++) {
if (yIndex >= 0) pos[yIndex] = y;
accessor.setPosition(pos);
double value = proc.getf(x, y);
if (signed16BitData) value -= 32768.0;
if (value < typeMin) value = typeMin;
else if (value > typeMax) value = typeMax;
accessor.get().setReal(value);
}
}
}
}
}
ds.update();
}
/**
* Creates a {@link ImageDisplay} from an {@link ImagePlus}. Shares planes of data when possible.
*/
@Override
public ImageDisplay createDisplay(final ImagePlus imp) {
return createDisplay(imp, LegacyUtils.getPreferredAxisOrder());
}
