Move internal DiscretisedDensity origin to vendor defined origin

For latest info on this, see:
https://github.com/UCL/STIR/wiki/Proposals-for-new-features-major-changes#vendor-based-coordinate-system

I will attempt to keep it in-line with latest developments and discussion.

The proposal is to move STIR's reference system for images in line with the vendor's system. This would mean that reconstructed images can be directly compared with vendor reconstructions. The main change required is for DiscretisedDensity to be able to express voxel locations in DICOM-standard LPS space. However, this in turn requires that the internal origin for DiscretisedDensity to align with the vendor origin.

Proposed changes

• ProjDataInfo.h

  • Private
    • float bed_position
    • TODO: float bed_height? Or Coordinate bed_position?
  • Public
    • ONE OF:
      • LOR ProjDataInfo::lor_gantry_to_bed(LOR lor) Maps a LOR (i.e., encoded
        via s, ϕ, t, θ) from Gantry space with origin at middle of scanner
        to Bed space with origin at vendor origin.
      • BasicCoordinate ProjDataInfo::point_gantry_to_bed(BasicCoordinate point) Maps a point (i.e., encoded by x, y, z) from Gantry space with
        origin at middle of scanner to Bed space with origin at vendor
        origin.
      • Currently these functions will simply apply an offset to t and
        z based on Scanner::default_vendor_origin_in_gantry_space
        and ProjDataInfo::bed_position.
      • Plus inverse functions.
    • OR
      • float ProjDataInfo::get_s_bed(Bin bin)
      • float ProjDataInfo::get_phi_bed(Bin bin)
      • float ProjDataInfo::get_t_bed(Bin bin)
      • float ProjDataInfo::get_m_bed(Bin bin)
      • float ProjDataInfo::get_theta_bed(Bin bin)
      • etc.
    • OR
      • LOR ProjDataInfo::get_LOR(Bin bin)
      • LOR ProjDataInfo::get_LOR_in_bed_space(Bin bin)
      • float LOR::get_s()
      • etc.

• Everything inheriting will have to be checked for z offsets.

• Scanner.h

  • BasicCoordinate default_vendor_origin_in_gantry_space

• ProjMatrixByBinUsingRayTracing

  • calculate_proj_matrix_elems_for_one_bin()
    • Where s, ϕ, etc. are calculated, we will then convert this into the bed space

• Other ProjMatrixByBin

  • Likely will have to change on a case-by-case basis.

• DiscretisedDensity

  • New member: CartesianCoordinate DiscretisedDensity::get_DICOM_LPS_for_indices(BasicCoordinate idx).

• ScatterEstimationByBin

  • This does its own manual projection in integral_between_2_points
    https://github.com/UCL/STIR/blob/db0b3e9b67ac45bdd250fbaf07257e5a690276b7/src/scatter_buildblock/single_scatter_integrals.cxx#L100-L141
    and uses a z offset. Also
    beforehand in sample_scatter_points()
    https://github.com/UCL/STIR/blob/db0b3e9b67ac45bdd250fbaf07257e5a690276b7/src/scatter_buildblock/sample_scatter_points.cxx#L65-L95
  • These could use something like:
    • proj_data_info_ptr->image_bed_to_gantry(scatter_point)/voxel_size,
    • proj_data_info_ptr->image_bed_to_gantry(detector_coord)/voxel_size,
      eliminating the need for origin.

• Symmetries

  • TODO

• zoom.cxx Zooms around image origin, will have to be changed.