optimisations for `ProjDataInMemory` (SWIG still to do)

[KrisThielemans]

C++

ProjData::fill_from and ProjData::copy_to use explicit loops with SegmentByView etc. This is slow.

For ProjDataInMemory we should be able to directly copy via the iterator from/to the buffer. This would currently not work however, as the segments are stored in the wrong order: fill_from and copy_to use order {0,1,-1,2,-2,...}. ProjDataInMemory uses the default order of ProjDataFromStream https://github.com/UCL/STIR/blob/29133a3ffa690b444894b4392aa710e8bb33a42e/src/buildblock/ProjDataFromStream.cxx#L114-L122 which is {....,-2,-1,0,1,2,...}. It seems to me that we should change the constructors https://github.com/UCL/STIR/blob/29133a3ffa690b444894b4392aa710e8bb33a42e/src/buildblock/ProjDataInMemory.cxx#L104-L105 and https://github.com/UCL/STIR/blob/29133a3ffa690b444894b4392aa710e8bb33a42e/src/buildblock/ProjDataInMemory.cxx#L115-L117 to use the {0,1,-1,...} sequence. We can do that by either:

• changing the default order for ProjDataFromStream. probably not a bad idea, but dangerous to rely on a default
• creating a function that returns a std::vector with that sequence (can steal code from https://github.com/UCL/STIR/blob/7dc238f5ec228554f594f1f2228450eb4618472b/src/IO/stir_ecat_common.cxx#L193, but note that this uses {0,-1,1,...}).

Doing this should speed-up SWIG's to_numpy and SIRF's as_array as it calls copy_to here.

SWIG

• We should expose the ProjDataInMemory iterators. That should be easy: copy lines from https://github.com/UCL/STIR/blob/7dc238f5ec228554f594f1f2228450eb4618472b/src/swig/stir.i#L1149-L1153

• to_numpy for ProjData first creates a Array<3,float> https://github.com/UCL/STIR/blob/7dc238f5ec228554f594f1f2228450eb4618472b/src/swig/stirextra.py#L81-82 and then converts to numpy array. If we'd add a shape() to ProjDataInMemory, I believe that the "normal" lines will work already: https://github.com/UCL/STIR/blob/7dc238f5ec228554f594f1f2228450eb4618472b/src/swig/stirextra.py#L75-L77 However, probably Python won't do that if it's passed a ProjData object (even if it's ProjDataInMemory), so possibly we'd have to do a type-cast somehow.

[KrisThielemans]

PR coming

[KrisThielemans]

Everything above except the last item (creating an Array first in SWIG) was addressed in #612