/** 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;
}
public static double[] readImageInfo(String id) {
try {
reader.setId(id);
} catch (FormatException e) {
// TODO Auto-generated catch block
e.printStackTrace();
} catch (IOException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
// ORDERING: 0 little, 1 seriesCount, 2 pixelType, 3 bpp, 4 itkComponentType, 5 sizeX,
// 6 sizeY, 7 sizeZ, 8 sizeT, 9 sizeC, 10 effSizeC, 11 rgbChannelCount, 12 imageCount
// 13 physX, 14 physY, 15 physZ, 16 timeIncrement
double[] returnValues = new double[17];
// return this and use SetByteOrderToLittleEndian or SetByteOrderToBigEndian in C++ land
boolean little = reader.isLittleEndian();
if (little) {
returnValues[0] = 1;
} else {
returnValues[0] = 0;
}
returnValues[1] = reader.getSeriesCount();
// return bpp and set an IOComponent based on it
int pixelType = reader.getPixelType();
returnValues[2] = (double) pixelType;
returnValues[3] = (double) FormatTools.getBytesPerPixel((int) returnValues[2]);
// 0 UCHAR, 1 CHAR, 2 USHORT, 3 SHORT, 4 UINT, 5 INT, 6 FLOAT, 7 DOUBLE, 8 UNKNOWN
if (pixelType == FormatTools.UINT8) returnValues[4] = (double) 0;
else if (pixelType == FormatTools.INT8) returnValues[4] = (double) 1;
else if (pixelType == FormatTools.UINT16) returnValues[4] = (double) 2;
else if (pixelType == FormatTools.INT16) returnValues[4] = (double) 3;
else if (pixelType == FormatTools.UINT32) returnValues[4] = (double) 4;
else if (pixelType == FormatTools.INT32) returnValues[4] = (double) 5;
else if (pixelType == FormatTools.FLOAT) returnValues[4] = (double) 6;
else if (pixelType == FormatTools.DOUBLE) returnValues[4] = (double) 7;
else returnValues[4] = (double) 8;
// return these
returnValues[5] = (double) reader.getSizeX();
returnValues[6] = (double) reader.getSizeY();
returnValues[7] = (double) reader.getSizeZ();
returnValues[8] = (double) reader.getSizeT();
returnValues[9] = (double) reader.getSizeC();
returnValues[10] = (double) reader.getEffectiveSizeC();
returnValues[11] = (double) reader.getRGBChannelCount();
returnValues[12] = (double) reader.getImageCount();
MetadataRetrieve retrieve = MetadataTools.asRetrieve(reader.getMetadataStore());
Double d = retrieve.getPixelsPhysicalSizeX(0).getValue();
double d2 = d == null ? 1.0 : d.doubleValue();
returnValues[13] = d2;
d = retrieve.getPixelsPhysicalSizeY(0).getValue();
d2 = d == null ? 1.0 : d.doubleValue();
returnValues[14] = d2;
d = retrieve.getPixelsPhysicalSizeZ(0).getValue();
d2 = d == null ? 1.0 : d.doubleValue();
returnValues[15] = d2;
d = retrieve.getPixelsTimeIncrement(0);
d2 = d == null ? 1.0 : d.doubleValue();
returnValues[16] = d2;
return returnValues;
}
