Java Code Examples for net.imagej.axis.CalibratedAxis#averageScale()

/**
 * Gets the average scale over the specified axis of the given image metadata.
 *
 * @return the average scale over the axis's values, or 1.0 if the desired
 *         axis is null.
 */
public static double getScale(final ImageMetadata imageMeta,
	final AxisType axisType)
{
	final CalibratedAxis axis = imageMeta.getAxis(axisType);
	if (axis == null) return 1.0;
	final long axisLength = imageMeta.getAxisLength(axis);
	return axis.averageScale(0, axisLength - 1);
}
 

@Override
public void setDest(final DataHandle<Location> out, final int imageIndex,
	final SCIFIOConfig config) throws FormatException, IOException
{
	final String currentId = getMetadata().idsId != null ? getMetadata().idsId
		: getMetadata().icsId;

	super.setDest(out, imageIndex, config);

	if (out.length() == 0) {
		out.writeBytes("\t\n");
		if (FormatTools.checkSuffix(currentId, "ids")) {
			out.writeBytes("ics_version\t1.0\n");
		}
		else {
			out.writeBytes("ics_version\t2.0\n");
		}
		out.writeBytes("filename\t" + currentId + "\n");
		out.writeBytes("layout\tparameters\t6\n");

		final Metadata meta = getMetadata();
		// SCIFIOMetadataTools.verifyMinimumPopulated(meta, pixels);

		final int pixelType = meta.get(imageIndex).getPixelType();

		dimensionOffset = out.offset();
		final int[] sizes = overwriteDimensions(meta, imageIndex);
		dimensionLength = (int) (out.offset() - dimensionOffset);

		if (getValidBits() != 0) {
			out.writeBytes("layout\tsignificant_bits\t" + getValidBits() + "\n");
		}

		final boolean signed = FormatTools.isSigned(pixelType);
		final boolean littleEndian = meta.get(imageIndex).isLittleEndian();

		out.writeBytes("representation\tformat\t" +
			(pixelType == FormatTools.FLOAT ? "real\n" : "integer\n"));
		out.writeBytes("representation\tsign\t" + (signed ? "signed\n"
			: "unsigned\n"));
		out.writeBytes("representation\tcompression\tuncompressed\n");
		out.writeBytes("representation\tbyte_order\t");
		for (int i = 0; i < sizes[0] / 8; i++) {
			if ((littleEndian && (sizes[0] < 32 ||
				pixelType == FormatTools.FLOAT)) || (!littleEndian &&
					sizes[0] >= 32 && pixelType != FormatTools.FLOAT))
			{
				out.writeBytes((i + 1) + "\t");
			}
			else {
				out.writeBytes(((sizes[0] / 8) - i) + "\t");
			}
		}

		out.writeBytes("\nparameter\tscale\t1.000000\t");

		final StringBuilder units = new StringBuilder();

		for (final CalibratedAxis axis : meta.get(imageIndex).getAxes()) {
			Number value = 1.0;
			if (axis.type() == Axes.X) {
				value = axis.averageScale(0, 1);
			}
			else if (axis.type() == Axes.Y) {
				value = axis.averageScale(0, 1);
			}
			else if (axis.type() == Axes.Z) {
				value = axis.averageScale(0, 1);
			}
			else if (axis.type() == Axes.TIME) {
				value = axis.averageScale(0, 1);
			}
			units.append(axis.unit() + "\t");
			out.writeBytes(value + "\t");
		}

		out.writeBytes("\nparameter\tunits\tbits\t" + units.toString() + "\n");
		out.writeBytes("\nend\n");
		pixelOffset = out.offset();
	}
	else if (FormatTools.checkSuffix(currentId, "ics")) {
		try (DataHandle<Location> tmpin = dataHandleService.create(out.get())) {
			tmpin.findString("\nend\n");
			pixelOffset = tmpin.offset();
		}
	}

	if (FormatTools.checkSuffix(currentId, "ids")) {
		pixelOffset = 0;
	}

	if (pixels == null) {
		pixels = dataHandleService.create(out.get());
	}
}
 

@Override
public void translateImageMetadata(final List<ImageMetadata> source,
	final Metadata dest)
{
	final ImageMetadata iMeta = source.get(0);

	String name = dest.getDatasetName();

	final String[] axes = new String[iMeta.getAxes().size()];
	final long[] lengths = new long[axes.length];
	final double[] scales = new double[axes.length];
	final String[] units = new String[axes.length];

	int index = 0;
	for (final CalibratedAxis axis : iMeta.getAxes()) {
		axes[index] = axis.type().getLabel();
		lengths[index] = iMeta.getAxisLength(axis);
		scales[index] = axis.averageScale(0, lengths[index]);
		units[index] = axis.unit();
		index++;
	}

	TestImgLocation.Builder b = new Builder();
	b.axes(axes);
	b.lengths(lengths);
	b.scales(scales);
	b.units(units);
	b.planarDims(iMeta.getPlanarAxisCount());
	b.interleavedDims(iMeta.getInterleavedAxisCount());
	b.thumbSizeX((int) iMeta.getThumbSizeX());
	b.thumbSizeY((int) iMeta.getThumbSizeX());
	b.pixelType(FormatTools.getPixelTypeString(iMeta.getPixelType()));
	b.falseColor(iMeta.isFalseColor());
	b.little(iMeta.isLittleEndian());
	b.metadataComplete(iMeta.isMetadataComplete());
	b.thumbnail(iMeta.isThumbnail());

	b.orderCertain(iMeta.isOrderCertain());
	b.images(source.size());

	if (iMeta.isIndexed()) {
		final int lutLength = ((HasColorTable) source).getColorTable(0, 0)
			.getComponentCount();
		b.indexed(iMeta.isIndexed());
		b.lutLength(lutLength);
	}

	try {
		dest.close();
		dest.setSource(dataHandleService.create(b.build()));
	}
	catch (final IOException e) {
		log().debug("Failed to create RAIS: " + name, e);
	}
}