/**
* 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;
}
/**
* Shift zero-frequency component to centre of dataset
*
* @param a
* @param axes (if null, then shift all axes)
* @return shifted dataset
*/
public static Dataset ifftshift(final Dataset a, int[] axes) {
int alen;
if (axes == null) {
alen = a.getRank();
axes = new int[alen];
for (int i = 0; i < alen; i++) axes[i] = i;
} else {
alen = axes.length;
for (int i = 0; i < alen; i++) axes[i] = a.checkAxis(axes[i]);
}
Dataset result = a;
int[] indices;
for (int i = 0; i < alen; i++) {
int axis = axes[i];
int n = a.getShapeRef()[axis];
int p = n - (n + 1) / 2;
logger.info("Shift {} by {}", axis, p);
indices = new int[n];
for (int j = 0; j < n; j++) {
if (j < n - p) indices[j] = p + j;
else indices[j] = j - n + p;
}
result = DatasetUtils.take(result, indices, axis);
}
return result;
}
/**
* Create a dataset from an object which could be a PySequence, a Java array (of arrays...) or
* Number. Ragged sequences or arrays are padded with zeros.
*
* @param obj
* @return dataset with contents given by input
*/
public static CompoundIntegerDataset createFromObject(final Object obj) {
IntegerDataset result = IntegerDataset.createFromObject(obj); // CLASS_TYPE
return (CompoundIntegerDataset) DatasetUtils.createCompoundDatasetFromLastAxis(result, true);
}
/**
* Discrete FFT sample frequencies
*
* @param n number of samples
* @param d sample spacing
* @return frequencies
*/
public static Dataset sampleFrequencies(int n, double d) {
int hn = n / 2;
return DatasetUtils.roll(
DoubleDataset.createRange(n).isubtract(hn).imultiply(1 / (d * n)), n - hn, null);
}
