cSAXS/cdtools
0
0
Fork 0
mirror of https://github.com/cdtools-developers/cdtools.git synced 2026-09-09 21:12:42 +02:00
Code Issues Packages Projects Releases Wiki Activity

Added heirarchy of surface_normal definition in Bragg2DPtycho from_dataset

Browse Source
This commit is contained in:
yoshikisd
2025-12-01 22:20:28 +00:00
parent bac95b7636
commit 7286bad264
1 changed files with 27 additions and 12 deletions
Download Patch File Download Diff File Expand all files Collapse all files
src/cdtools/models/bragg_2d_ptycho.py
+27 -12
View File
@@ -258,7 +258,7 @@ class Bragg2DPtycho(CDIModel):
obj_padding=200,
obj_view_crop=None,
units='um',
surface_normal=np.array([0., 0., 1.])
surface_normal=None
):
wavelength = dataset.wavelength
det_basis = dataset.detector_geometry['basis']
@@ -280,20 +280,35 @@ class Bragg2DPtycho(CDIModel):
oversampling=oversampling)
# Now we define the surface normal
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)
else:
# If the scattering_mode has not been defined, we grab
# this from the cxi file if its present.
if hasattr(dataset, 'sample_info') and \
# 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 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.])
# and we use that to generate the probe basis