LPS returns SPL

[KrisThielemans]

@ashgillman I find the following confusing:

CartesianCoordinate3D<float> LPS = image.get_LPS_for_indices();
const float S = LPS[1];
const float L = LPS[3];

i.e. I'd expect that LPS coordinates are in order LPS.

I guess you did this because of the usual STIR z,y,x convention (where z is along the axis of the scanner), but we never call this get_xyz.

This seems quite non-trivial to change however. Moreover, it would also have repercussions for SIRF I guess (@rijobro @evgueni-ovtchinnikov, please confirm).

Not sure what to do with this...

[ashgillman]

Sorry, I missed this.

Hmm, looks like this is handled here:

STIR/src/include/stir/DiscretisedDensity.inl

Lines 218 to 253 in 29133a3

	swap_axes_based_on_orientation(const CartesianCoordinate3D<float>& coords,
	const PatientPosition patient_position)
	{
	CartesianCoordinate3D<float> flip_coords = coords;
	// STIR coordinates run:
	// x: left to right as you face the scanner (as seen from the bed side)
	// y: top to bottom of the scanner
	// z: running from deep in the scanner out along the bed (as seen from the bed
	// side)
	// ITK coordinates are defined w.r.t LPS
	switch (patient_position.get_position())
	{
	case PatientPosition::unknown_position: // If unknown, assume HFS
	case PatientPosition::HFS: // HFS means currently in patient LPI
	flip_coords.z() *= -1;
	break;
	case PatientPosition::HFP: // HFP means currently in patient RAI
	flip_coords.x() *= -1;
	flip_coords.y() *= -1;
	flip_coords.z() *= -1;
	break;
	case PatientPosition::FFS: // FFS means currently in patient RPS
	flip_coords.x() *= -1;
	break;
	case PatientPosition::FFP: // FFP means currently in patient LAS
	flip_coords.y() *= -1;
	break;
	default:
	throw std::runtime_error("Unsupported patient position, can't convert to LPS.");
	}
	return flip_coords;
	}

I use the CartesianCoordinate3D.{x(),y(),z()} interface as opposed to indexing. So it would seem the issue might be with the use of that data type?