def test_get_array(mock_fxe_raw_run):
run = RunDirectory(mock_fxe_raw_run)
det = LPD1M(run.select_trains(by_index[:3]))
assert det.detector_name == 'FXE_DET_LPD1M-1'
arr = det.get_array('image.data')
assert arr.shape == (16, 3, 128, 256, 256)
assert arr.dims == ('module', 'train', 'pulse', 'slow_scan', 'fast_scan')
def test_iterate(mock_fxe_raw_run):
run = RunDirectory(mock_fxe_raw_run)
det = LPD1M(run.select_trains(by_index[:2]))
it = iter(det.trains())
tid, d = next(it)
assert d['image.data'].shape == (16, 1, 128, 256, 256)
assert d['image.data'].dims == ('module', 'train', 'pulse', 'slow_scan',
'fast_scan')
tid, d = next(it)
assert d['image.data'].shape == (16, 1, 128, 256, 256)
with pytest.raises(StopIteration):
next(it)
def test_iterate_pulse_index(mock_fxe_raw_run):
run = RunDirectory(mock_fxe_raw_run)
det = LPD1M(run.select_trains(by_index[:3]))
tid, d = next(iter(det.trains(pulses=by_index[0])))
assert d['image.data'].shape == (16, 1, 1, 256, 256)
tid, d = next(iter(det.trains(pulses=by_index[:5])))
assert d['image.data'].shape == (16, 1, 5, 256, 256)
tid, d = next(iter(det.trains(pulses=by_index[122:])))
assert d['image.data'].shape == (16, 1, 6, 256, 256)
tid, d = next(iter(det.trains(pulses=by_index[[1, 7, 22, 23]])))
assert d['image.data'].shape == (16, 1, 4, 256, 256)
assert list(d['image.data'].coords['pulse']) == [1, 7, 22, 23]
def test_write_virtual_cxi(mock_spb_proc_run, tmpdir):
run = RunDirectory(mock_spb_proc_run)
det = AGIPD1M(run)
test_file = osp.join(str(tmpdir), 'test.cxi')
det.write_virtual_cxi(test_file)
assert_isfile(test_file)
with h5py.File(test_file) as f:
det_grp = f['entry_1/instrument_1/detector_1']
ds = det_grp['data']
assert isinstance(ds, h5py.Dataset)
assert ds.is_virtual
assert ds.shape[1:] == (16, 512, 128)
assert 'axes' in ds.attrs
assert len(ds.virtual_sources()) == 16
# Check position of each source file in the modules dimension
for src in ds.virtual_sources():
start, _, block, count = src.vspace.get_regular_hyperslab()
assert block[1] == 1
assert count[1] == 1
expected_file = 'CORR-R0238-AGIPD{:0>2}-S00000.h5'.format(start[1])
assert osp.basename(src.file_name) == expected_file
# Check presence of other datasets
assert 'gain' in det_grp
assert 'mask' in det_grp
assert 'experiment_identifier' in det_grp
def test_write_virtual_cxi_raw_data(mock_fxe_raw_run, tmpdir, caplog):
import logging
caplog.set_level(logging.INFO)
run = RunDirectory(mock_fxe_raw_run)
det = LPD1M(run)
test_file = osp.join(str(tmpdir), 'test.cxi')
det.write_virtual_cxi(test_file)
assert_isfile(test_file)
def test_get_array_pulse_indexes(mock_fxe_raw_run):
run = RunDirectory(mock_fxe_raw_run)
det = LPD1M(run.select_trains(by_index[:3]))
arr = det.get_array('image.data', pulses=by_index[0])
assert arr.shape == (16, 3, 1, 256, 256)
assert (arr.coords['pulse'] == 0).all()
arr = det.get_array('image.data', pulses=by_index[:5])
assert arr.shape == (16, 3, 5, 256, 256)
# Empty selection
arr = det.get_array('image.data', pulses=by_index[:0])
assert arr.shape == (16, 0, 0, 256, 256)
arr = det.get_array('image.data', pulses=by_index[122:])
assert arr.shape == (16, 3, 6, 256, 256)
arr = det.get_array('image.data', pulses=by_index[[1, 7, 22, 23]])
assert arr.shape == (16, 3, 4, 256, 256)
def test_write_virtual_cxi_some_modules(mock_spb_proc_run, tmpdir):
run = RunDirectory(mock_spb_proc_run)
det = AGIPD1M(run, modules=[3, 4, 8, 15])
test_file = osp.join(str(tmpdir), 'test.cxi')
det.write_virtual_cxi(test_file)
assert_isfile(test_file)
with h5py.File(test_file) as f:
det_grp = f['entry_1/instrument_1/detector_1']
ds = det_grp['data']
assert ds.shape[1:] == (16, 512, 128)