/** Returns true if the provided axes correspond to a complete image plane */
public static boolean wholePlane(
final int imageIndex, final Metadata meta, final long[] planeMin, final long[] planeMax) {
final boolean wholePlane = wholeRow(imageIndex, meta, planeMin, planeMax);
final int yIndex = meta.get(imageIndex).getAxisIndex(Axes.Y);
return wholePlane
&& planeMin[yIndex] == 0
&& planeMax[yIndex] == meta.get(imageIndex).getAxisLength(Axes.Y);
}
/**
* Iterates over the provided Metadata's planar axes, replacing any instances of axes with the
* paired values.
*/
public static long[] modifyPlanar(
final int imageIndex, final Metadata meta, final AxisValue... axes) {
final long[] planarAxes = meta.get(imageIndex).getAxesLengthsPlanar();
for (final AxisValue v : axes) {
planarAxes[meta.get(imageIndex).getAxisIndex(v.getType())] = v.getLength();
}
return planarAxes;
}
/** Returns true if the provided axes correspond to a complete image row */
public static boolean wholeRow(
final int imageIndex, final Metadata meta, final long[] planeMin, final long[] planeMax) {
boolean wholeRow = true;
final int yIndex = meta.get(imageIndex).getAxisIndex(Axes.Y);
for (int i = 0; wholeRow && i < planeMin.length; i++) {
if (i == yIndex) continue;
if (planeMin[i] != 0 || planeMax[i] != meta.get(imageIndex).getAxisLength(i))
wholeRow = false;
}
return wholeRow;
}
@Override
public void populateImageMetadata() {
// clears existing metadata
createImageMetadata(0);
// copies the delegate's image metadata
for (final ImageMetadata meta : metadata.getAll()) add(meta);
}
/** Replaces the first values.length of the provided Metadata's planar axes with the values. */
public static long[] modifyPlanar(
final int imageIndex, final Metadata meta, final long... values) {
final AxisValue[] axes = new AxisValue[values.length];
final List<CalibratedAxis> axisTypes = meta.get(imageIndex).getAxes();
for (int i = 0; i < axes.length && i < axisTypes.size(); i++) {
axes[i] = new AxisValue(axisTypes.get(i).type(), values[i]);
}
return modifyPlanar(imageIndex, meta, axes);
}
/**
* Checks whether the given metadata object has the minimum metadata populated to successfully
* describe the nth Image.
*
* @throws FormatException if there is a missing metadata field, or the metadata object is
* uninitialized
*/
public static void verifyMinimumPopulated(
final Metadata src, final RandomAccessOutputStream out, final int imageIndex)
throws FormatException {
if (src == null) {
throw new FormatException("Metadata object is null; " + "call Writer.setMetadata() first");
}
if (out == null) {
throw new FormatException(
"RandomAccessOutputStream object is null; "
+ "call Writer.setSource(<String/File/RandomAccessOutputStream>) first");
}
if (src.get(imageIndex).getAxes().size() == 0) {
throw new FormatException("Axiscount #" + imageIndex + " is 0");
}
}
@Override
public void close(final boolean fileOnly) throws IOException {
for (final String name : mappedFiles) {
final IRandomAccess handle = locationService.getMappedFile(name);
locationService.mapFile(name, null);
if (handle != null) {
handle.close();
}
}
mappedFiles.clear();
super.close(fileOnly);
if (metadata != null) metadata.close(fileOnly);
if (!fileOnly) metadata = null;
mappedFiles = new ArrayList<String>();
}
public void setMetadata(final io.scif.Metadata m) throws IOException {
if (metadata != null) metadata.close();
metadata = m;
}
@Override
public ColorTable getColorTable(final int imageIndex, final long planeIndex) {
if (HasColorTable.class.isAssignableFrom(metadata.getClass()))
return ((HasColorTable) metadata).getColorTable(imageIndex, planeIndex);
return null;
}