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avoid copying data to Python but using numpy::frombuffer #717

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avoid copying data to Python but using numpy::frombuffer #717

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14 changes: 14 additions & 0 deletions src/xSTIR/cSTIR/cstir.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -694,6 +694,20 @@ void* cSTIR_get_ProjDataInfo(void* ptr_acq)
CATCH;
}

extern "C"
void* cSTIR_AcquisitionDataInMemory_get_buffer(void* adim_ptr, size_t out_ptr)
{
try {
SPTR_FROM_HANDLE(PETAcquisitionDataInMemory, adim_sptr, adim_ptr);
stir::ProjDataInMemory &pdim =
dynamic_cast<stir::ProjDataInMemory&>(*adim_sptr->data());
float* out_float_ptr = (float*)out_ptr;
out_float_ptr = pdim.begin().base();
return (void*) new DataHandle;
}
CATCH;
}

extern "C"
void* cSTIR_setupFBP2DReconstruction(void* ptr_r, void* ptr_i)
{
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1 change: 1 addition & 0 deletions src/xSTIR/cSTIR/include/sirf/STIR/cstir.h
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Expand Up @@ -102,6 +102,7 @@ extern "C" {
(void* ptr_acq, const void * ptr_from);
void* cSTIR_writeAcquisitionData(void* ptr_acq, const char* filename);
void* cSTIR_get_ProjDataInfo(void* ptr_acq);
void* cSTIR_AcquisitionDataInMemory_get_buffer(void* adim_ptr, PTR_FLOAT out_ptr);

// Reconstruction methods
void* cSTIR_setupFBP2DReconstruction(void* ptr_r, void* ptr_i);
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21 changes: 18 additions & 3 deletions src/xSTIR/pSTIR/STIR.py.in
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Expand Up @@ -722,9 +722,18 @@ class AcquisitionData(DataContainer):
- number of tangential positions.
'''
assert self.handle is not None
array = numpy.ndarray(self.dimensions(), dtype = numpy.float32)
try_calling(pystir.cSTIR_getAcquisitionData\
(self.handle, array.ctypes.data))
# If using file storage scheme, create numpy array and copy data
if self.get_storage_scheme() == "file":
array = numpy.ndarray(self.dimensions(), dtype = numpy.float32)
try_calling(pystir.cSTIR_getAcquisitionData\
(self.handle, array.ctypes.data))
# If using memory, use a buffer and have a shared object
else:
buffer = ?
try_calling(pystir.cSTIR_AcquisitionDataInMemory_get_buffer\
(self.handle, buffer))
array = numpy.frombuffer(buffer, dtype=numpy.float32)
Comment on lines +732 to +735
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I do not see how this can possibly work. However you define buffer, pystir.cSTIR_AcquisitionDataInMemory_get_buffer can only give you an address in memory, but numpy.frombuffer needs to know the size of memory represented by the buffer to be able to handle that memory as numpy array data.

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I haven't done it here, but you can give the number of elements with count:

numpy.frombuffer(buffer, dtype=float, count=-1, offset=0)

And obviously we know how many elements our sinogram contains.

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The problem is that the first argument to frombuffer should be of type buffer_like (see here). I have no idea how to do this, but the address to the first float in C++ somehow needs to be converted to this buffer_like object in Python. Searching online, it looks like it's possible with SWIG, but I'm not sure how to do it in SIRF's setup.

array.shape = self.dimensions()
return array
def fill(self, value):
'''
Expand All @@ -744,6 +753,12 @@ class AcquisitionData(DataContainer):
v = value.astype(numpy.float32)
if not v.flags['C_CONTIGUOUS']:
v = numpy.ascontiguousarray(v)
# If storage_scheme==memory AND numpy array has same address as
# C++ buffer, nothing to do!
# if self.get_storage_scheme() == 'memory' and :
# return

# Else, copy from numpy to c++
try_calling(pystir.cSTIR_setAcquisitionData\
(self.handle, v.ctypes.data))
elif isinstance(value, AcquisitionData):
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