def read_aps_8bm(image_directory,
ind_tomo,
ind_flat,
image_file_pattern='image_00000.xrm',
flat_file_pattern='ref_00000.xrm',
proj=None,
sino=None):
"""
Read APS 8-BM tomography data from a stack of xrm files.
Parameters
----------
image_directory : str
Path to data folder name without indices and extension.
ind_tomo : list of int
Indices of the projection files to read.
ind_flat : list of int
Indices of the flat field files to read.
image_file_pattern: string
Specify how the projection files are named.
flat_file_pattern: string
Specify how the flat reference files are named.
proj : {sequence, int}, optional
Specify projections to read. (start, end, step)
sino : {sequence, int}, optional
Specify sinograms to read. (start, end, step)
Returns
-------
ndarray
3D tomographic data.
ndarray
3D flat field data.
dictionary
Image set metadata.
"""
image_directory = os.path.abspath(image_directory)
tomo_name = os.path.join(image_directory, 'radios', image_file_pattern)
flat_name = os.path.join(image_directory, 'flats', flat_file_pattern)
if proj is not None:
ind_tomo = ind_tomo[slice(*proj)]
tomo, metadata = dxreader.read_xrm_stack(tomo_name,
ind=ind_tomo,
slc=(sino, None))
flat, _ = dxreader.read_xrm_stack(flat_name,
ind=ind_flat,
slc=(sino, None))
return tomo, flat, metadata
def read_aps_8bm(image_directory, ind_tomo, ind_flat,
image_file_pattern='image_00000.xrm',
flat_file_pattern='ref_00000.xrm', proj=None, sino=None):
"""
Read APS 8-BM tomography data from a stack of xrm files.
Parameters
----------
image_directory : str
Path to data folder name without indices and extension.
ind_tomo : list of int
Indices of the projection files to read.
ind_flat : list of int
Indices of the flat field files to read.
image_file_pattern: string
Specify how the projection files are named.
flat_file_pattern: string
Specify how the flat reference files are named.
proj : {sequence, int}, optional
Specify projections to read. (start, end, step)
sino : {sequence, int}, optional
Specify sinograms to read. (start, end, step)
Returns
-------
ndarray
3D tomographic data.
ndarray
3D flat field data.
dictionary
Image set metadata.
"""
image_directory = os.path.abspath(image_directory)
tomo_name = os.path.join(image_directory, 'radios', image_file_pattern)
flat_name = os.path.join(image_directory, 'flats', flat_file_pattern)
if proj is not None:
ind_tomo = ind_tomo[slice(*proj)]
tomo, metadata = dxreader.read_xrm_stack(
tomo_name, ind=ind_tomo, slc=(sino, None))
flat, _ = dxreader.read_xrm_stack(
flat_name, ind=ind_flat, slc=(sino, None))
return tomo, flat, metadata
def test_read_xrm_stack_gets_x_position_set(self):
image_data, metadata = reader.read_xrm_stack(
os.path.join(TEST_DIR, "test_data/test_chip00.xrm"), [0, 1])
self.assertEqual(metadata["x_positions"], [
715.3599853515625,
715.3599853515625,
])
def test_read_xrm_stack_gets_y_position_set(self):
image_data, metadata = reader.read_xrm_stack(
os.path.join(TEST_DIR, "test_data/test_chip00.xrm"), [0, 1])
self.assertEqual(metadata["y_positions"], [
-3761.9892578125,
-3761.9892578125,
])
def test_read_xrm_stack_gets_theta_set(self):
image_data, metadata = reader.read_xrm_stack(
os.path.join(TEST_DIR, "test_data/test_chip00.xrm"), [0, 1])
self.assertEqual(metadata["thetas"], [
-0.06000000238418579,
-0.06000000238418579,
])
def test_read_xrm_stack_gets_y_position_set(self):
image_data, metadata = reader.read_xrm_stack(
os.path.join(TEST_DIR, "test_data/test_chip00.xrm"), [0, 1])
self.assertEqual(
metadata["y_positions"],
[
-3761.9892578125,
-3761.9892578125,
]
)
def test_read_xrm_stack_gets_x_position_set(self):
image_data, metadata = reader.read_xrm_stack(
os.path.join(TEST_DIR, "test_data/test_chip00.xrm"), [0, 1])
self.assertEqual(
metadata["x_positions"],
[
715.3599853515625,
715.3599853515625,
]
)
def test_read_xrm_stack_gets_theta_set(self):
image_data, metadata = reader.read_xrm_stack(
os.path.join(TEST_DIR, "test_data/test_chip00.xrm"), [0, 1])
self.assertEqual(
metadata["thetas"],
[
-0.06000000238418579,
-0.06000000238418579,
]
)
def read_aps_26id(fname, ind_tomo, ind_flat, proj=None, sino=None):
"""
Read APS 26-ID tomography data from a stack of xrm files.
Note: file are renamed as
radios/image_00000.xrm and flats/image_00000.xrm
Parameters
----------
fname : str
Path to data folder name without indices and extension.
ind_tomo : list of int, optional
Indices of the projection files to read.
ind_flat : list of int, optional
Indices of the flat field files to read.
proj : {sequence, int}, optional
Specify projections to read. (start, end, step)
sino : {sequence, int}, optional
Specify sinograms to read. (start, end, step)
Returns
-------
ndarray
3D tomographic data.
ndarray
3D flat field data.
"""
fname = os.path.abspath(fname)
tomo_name = os.path.join(fname, 'radios', 'image_00000.xrm')
flat_name = os.path.join(fname, 'flats', 'image_00000.xrm')
tomo = dxreader.read_xrm_stack(
tomo_name, ind=ind_tomo, digit=5, slc=(sino, proj))
flat = dxreader.read_xrm_stack(
flat_name, ind=ind_flat, digit=5, slc=(sino, None))
return tomo, flat
def test_read_xrm_stack_reads_multiple_xrms(self):
image_data, metadata = reader.read_xrm_stack(
os.path.join(TEST_DIR, "test_data/test_chip00.xrm"), [0, 1])
np.testing.utils.assert_(image_data is not False)
np.testing.utils.assert_(metadata is not False)
def test_read_xrm_stack_reads_multiple_xrms(self):
image_data, metadata = reader.read_xrm_stack(
os.path.join(TEST_DIR, "test_data/test_chip00.xrm"), [0, 1])
np.testing.utils.assert_(image_data is not False)
np.testing.utils.assert_(metadata is not False)