/** Compiles an N-dimensional list of axis lengths from the given reader. */
private int[] getDimLengths(IFormatReader r) {
final int sizeX = r.getSizeX();
final int sizeY = r.getSizeY();
final int sizeZ = r.getSizeZ();
final int sizeT = r.getSizeT();
// final String[] cDimTypes = r.getChannelDimTypes();
final int[] cDimLengths = r.getChannelDimLengths();
final String dimOrder = r.getDimensionOrder();
final List<Integer> dimLengthsList = new ArrayList<Integer>();
// add core dimensions
for (int i = 0; i < dimOrder.length(); i++) {
final char dim = dimOrder.charAt(i);
switch (dim) {
case 'X':
if (sizeX > 1) dimLengthsList.add(sizeX);
break;
case 'Y':
if (sizeY > 1) dimLengthsList.add(sizeY);
break;
case 'Z':
if (sizeZ > 1) dimLengthsList.add(sizeZ);
break;
case 'T':
if (sizeT > 1) dimLengthsList.add(sizeT);
break;
case 'C':
for (int c = 0; c < cDimLengths.length; c++) {
int len = cDimLengths[c];
if (len > 1) dimLengthsList.add(len);
}
break;
}
}
// convert result to primitive array
final int[] dimLengths = new int[dimLengthsList.size()];
for (int i = 0; i < dimLengths.length; i++) {
dimLengths[i] = dimLengthsList.get(i);
}
return dimLengths;
}
@Test(dataProvider = "wrappers")
public void testCoreMetadata(IFormatReader reader) {
assertNotNull(reader.getCurrentFile());
CoreMetadata[] core = reader.getCoreMetadata();
assertEquals(core.length, reader.getSeriesCount());
for (int i = 0; i < reader.getSeriesCount(); i++) {
reader.setSeries(i);
assertEquals(core[i].sizeX, reader.getSizeX());
assertEquals(core[i].sizeY, reader.getSizeY());
assertEquals(core[i].sizeZ, reader.getSizeZ());
assertEquals(core[i].sizeC, reader.getSizeC());
assertEquals(core[i].sizeT, reader.getSizeT());
assertEquals(core[i].pixelType, reader.getPixelType());
assertEquals(core[i].imageCount, reader.getImageCount());
assertEquals(core[i].dimensionOrder, reader.getDimensionOrder());
assertEquals(core[i].littleEndian, reader.isLittleEndian());
assertEquals(core[i].rgb, reader.isRGB());
assertEquals(core[i].interleaved, reader.isInterleaved());
assertEquals(core[i].indexed, reader.isIndexed());
}
}
/** Copies the current dimensional position into the given array. */
private void getPosition(IFormatReader r, int no, int[] pos) {
final int sizeX = r.getSizeX();
final int sizeY = r.getSizeY();
final int sizeZ = r.getSizeZ();
final int sizeT = r.getSizeT();
// final String[] cDimTypes = r.getChannelDimTypes();
final int[] cDimLengths = r.getChannelDimLengths();
final String dimOrder = r.getDimensionOrder();
final int[] zct = r.getZCTCoords(no);
int index = 0;
for (int i = 0; i < dimOrder.length(); i++) {
final char dim = dimOrder.charAt(i);
switch (dim) {
case 'X':
if (sizeX > 1) index++; // NB: Leave X axis position alone.
break;
case 'Y':
if (sizeY > 1) index++; // NB: Leave Y axis position alone.
break;
case 'Z':
if (sizeZ > 1) pos[index++] = zct[0];
break;
case 'T':
if (sizeT > 1) pos[index++] = zct[2];
break;
case 'C':
final int[] cPos = FormatTools.rasterToPosition(cDimLengths, zct[1]);
for (int c = 0; c < cDimLengths.length; c++) {
if (cDimLengths[c] > 1) pos[index++] = cPos[c];
}
break;
}
}
}
/** Retrieves calibration for X,Y,Z,T * */
private float[] getCalibration(final IFormatReader r, final int[] dimensions) {
float[] calibration = new float[dimensions.length];
for (int i = 0; i < calibration.length; ++i) calibration[i] = 1;
try {
final String dimOrder = r.getDimensionOrder().toUpperCase();
final MetadataRetrieve retrieve = (MetadataRetrieve) r.getMetadataStore();
PositiveFloat cal;
final int posX = dimOrder.indexOf('X');
cal = retrieve.getPixelsPhysicalSizeX(0);
if (posX >= 0 && posX < calibration.length && cal != null && cal.getValue() != 0)
calibration[posX] = cal.getValue().floatValue();
final int posY = dimOrder.indexOf('Y');
cal = retrieve.getPixelsPhysicalSizeY(0);
if (posY >= 0 && posY < calibration.length && cal != null && cal.getValue() != 0)
calibration[posY] = cal.getValue().floatValue();
final int posZ = dimOrder.indexOf('Z');
cal = retrieve.getPixelsPhysicalSizeZ(0);
if (posZ >= 0 && posZ < calibration.length && cal != null && cal.getValue() != 0)
calibration[posZ] = cal.getValue().floatValue();
final int posT = dimOrder.indexOf('T');
retrieve.getPixelsTimeIncrement(0);
Double cal1 = retrieve.getPixelsTimeIncrement(0);
if (posT >= 0 && posT < calibration.length && cal1 != null && cal1.floatValue() != 0)
calibration[posT] = cal1.floatValue();
} catch (Exception e) {
// somehow an error occured reading the calibration
}
return calibration;
}
/** Compiles an N-dimensional list of axis types from the given reader. */
private String[] getDimTypes(IFormatReader r) {
final int sizeX = r.getSizeX();
final int sizeY = r.getSizeY();
final int sizeZ = r.getSizeZ();
final int sizeT = r.getSizeT();
final String[] cDimTypes = r.getChannelDimTypes();
final int[] cDimLengths = r.getChannelDimLengths();
final String dimOrder = r.getDimensionOrder();
final List<String> dimTypes = new ArrayList<String>();
// add core dimensions
for (char dim : dimOrder.toCharArray()) {
switch (dim) {
case 'X':
if (sizeX > 1) dimTypes.add(X);
break;
case 'Y':
if (sizeY > 1) dimTypes.add(Y);
break;
case 'Z':
if (sizeZ > 1) dimTypes.add(Z);
break;
case 'T':
if (sizeT > 1) dimTypes.add(TIME);
break;
case 'C':
for (int c = 0; c < cDimTypes.length; c++) {
int len = cDimLengths[c];
if (len > 1) dimTypes.add(cDimTypes[c]);
}
break;
}
}
return dimTypes.toArray(new String[0]);
}
