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Trying to accelerate PET algebra tests for larger data #1027

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Trying to accelerate PET algebra tests for larger data #1027

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56 changes: 43 additions & 13 deletions src/xSTIR/pSTIR/tests/test_algebra.py
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Original file line number Diff line number Diff line change
Expand Up @@ -41,16 +41,30 @@ def tearDown(self):
class TestSTIRAcquisitionDataAlgebraFile(unittest.TestCase, TestDataContainerAlgebra):

def setUp(self):
path = os.path.join(
examples_data_path('PET'), 'thorax_single_slice', 'template_sinogram.hs')
self.set_storage_scheme()
sirf_path = os.environ.get('SIRF_PATH')
data_path = os.path.join(sirf_path, 'tests', 'data.hs')
if os.path.exists(data_path):
print('reading data from %s' % data_path)
data = pet.AcquisitionData(data_path)
self.image1 = data.get_uniform_copy(0)
self.image2 = data.get_uniform_copy(0)
self.set_storage_scheme()
return
path = os.path.join(examples_data_path('PET'),
'mMR', 'mMR_template_span11_small.hs')
# 'thorax_single_slice', 'template_sinogram.hs')
if os.path.exists(path):
template = pet.AcquisitionData(path)
self.image1 = template.get_uniform_copy(0)
self.image2 = template.get_uniform_copy(0)
# assert False
self.set_storage_scheme()


print(template.dimensions())
data = template.get_uniform_copy(0)
data = data.rebin(3, num_views_to_combine=6, num_tang_poss_to_trim=200)
print('rebinned to ', data.dimensions())
self.image1 = data
self.image2 = data.get_uniform_copy(0)
print('saving data to %s' % data_path)
self.image1.write(data_path)

def tearDown(self):
pass

Expand All @@ -63,16 +77,32 @@ def test_division_by_datacontainer_zero(self):


class TestSTIRAcquisitionDataAlgebraMemory(unittest.TestCase, TestDataContainerAlgebra):

def setUp(self):
pet.AcquisitionData.set_storage_scheme('file')
path = os.path.join(
examples_data_path('PET'), 'thorax_single_slice', 'template_sinogram.hs')
sirf_path = os.environ.get('SIRF_PATH')
data_path = os.path.join(sirf_path, 'tests', 'data.hs')
if os.path.exists(data_path):
print('reading data from %s' % data_path)
data = pet.AcquisitionData(data_path)
self.image1 = data.get_uniform_copy(0)
self.image2 = data.get_uniform_copy(0)
return
path = os.path.join(examples_data_path('PET'),
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not used?

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looks good. I didn't check current run-time.

Where does tests/data.hs sit? Is it checked in ? (I didn't check)

testing time is now 14 sec

data.hs and data.s are created, if not present, in SIRF/tests by the first test - do not know how to delete them after all tests finished (CMake can, I presume?)

not used?

sorry, do not get what you refer to

'mMR', 'mMR_template_span11_small.hs')
# 'thorax_single_slice', 'template_sinogram.hs')
if os.path.exists(path):
template = pet.AcquisitionData(path)
self.image1 = template.get_uniform_copy(0)
self.image2 = template.get_uniform_copy(0)
# assert False
print(template.dimensions())
data = template.get_uniform_copy(0)
data = data.rebin(3, num_views_to_combine=6, num_tang_poss_to_trim=200)
print('rebinned to ', data.dimensions())
self.image1 = data.get_uniform_copy(0)
self.image2 = data.get_uniform_copy(0)
pet.AcquisitionData.set_storage_scheme('memory')
print('saving data to %s' % data_path)
self.image1.write(data_path)

def test_division_by_datacontainer_zero(self):
# skip this test as currently cSIRF doesn't throw
pass