/** 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;
}
