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Suggested changes: Make surface_normal work with anything castable to an array with np.asarray, change the check for length-3 to cover all cases, and add a check to explicitly fail if the scattering_mode argument is improperly set, instead of silently falling back to default

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levita_a
2025-12-02 15:27:20 +01:00
parent 7286bad264
commit 8f3ad59c6d
1 changed files with 26 additions and 25 deletions
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src/cdtools/models/bragg_2d_ptycho.py
+26 -25
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@@ -283,33 +283,34 @@ class Bragg2DPtycho(CDIModel):
# The surface normal definition is based on the following heirarchy:
# manual surface_normal definition > scattering_mode
# > dataset.sample_info['orientation'] > transmission geometry
# Guard against any surface_normal entries that are not numpy vectors
if surface_normal is not None and \
not isinstance(surface_normal, np.ndarray) or \
(isinstance(surface_normal, np.ndarray)
and not surface_normal.shape == (3,)):
raise RuntimeError(
'surface_normal needs to be a numpy vector with 3 elements.'
if surface_normal is not None:
surface_normal = np.asarray(surface_normal)
elif scattering_mode.strip().lower() in {'t', 'transmission'}:
surface_normal = np.array([0.,0.,1.])
elif scattering_mode.strip().lower() in {'r', 'reflection'}:
outgoing_dir = np.cross(det_basis[:,0], det_basis[:,1])
outgoing_dir /= np.linalg.norm(outgoing_dir)
surface_normal = outgoing_dir + np.array([0.,0.,1.])
surface_normal /= np.linalg.norm(outgoing_dir)
elif scattering_mode is not None:
raise ValueError(
'Scattering mode must be either "transmission" ("t"), "reflection" ("r"), or the default of None.'
)
elif hasattr(dataset, 'sample_info') and \
dataset.sample_info is not None and \
'orientation' in dataset.sample_info:
# If the scattering_mode has not been defined, we grab
# this from the cxi file if its present.
surface_normal = dataset.sample_info['orientation'][2]
else:
surface_normal = np.array([0., 0., 1.])
if surface_normal is None:
if scattering_mode in {'t', 'transmission'}:
surface_normal = np.array([0.,0.,1.])
elif scattering_mode in {'r', 'reflection'}:
outgoing_dir = np.cross(det_basis[:,0], det_basis[:,1])
outgoing_dir /= np.linalg.norm(outgoing_dir)
surface_normal = outgoing_dir + np.array([0.,0.,1.])
surface_normal /= np.linalg.norm(outgoing_dir)
elif hasattr(dataset, 'sample_info') and \
dataset.sample_info is not None and \
'orientation' in dataset.sample_info:
# If the scattering_mode has not been defined, we grab
# this from the cxi file if its present.
surface_normal = dataset.sample_info['orientation'][2]
else:
surface_normal = np.array([0., 0., 1.])
# Guard against any surface_normal entries that are not castable
# to a length-3 numpy vector, with a sensible error message
if not surface_normal.shape == (3,):
raise ValueError(
'`surface_normal` needs to be a numpy vector with 3 elements. If it was set incorrectly from dataset.sample_info, consider explicitly setting it via the `surface_normal` keyword argument.'
)
# and we use that to generate the probe basis
ew_normal = np.cross(np.array(ew_basis)[:,1],