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Update geometry metadata for masks #297

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Update geometry metadata for masks #297

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9cc8eda
Preserve metadata when moving panels.
turkot Jul 3, 2024
8f69a49
Update mask metadata read from and written to crystfel geometry.
turkot Jul 4, 2024
e928310
Don't try to write mask data if it is not provided.
turkot Jul 4, 2024
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40 changes: 30 additions & 10 deletions extra_geom/base.py
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Original file line number Diff line number Diff line change
Expand Up @@ -297,10 +297,25 @@ def from_crystfel_geom(cls, filename):
# It's possible for these to have different values for different panels,
# but it seems to be common to use them like headers, describing all
# panels, and we're assuming that's the case here.
cfel_md_keys = ('data', 'mask', 'adu_per_eV', 'clen')
cfel_md_keys = ('data', 'adu_per_eV', 'clen')
cfel_md_new_mask_keys = tuple(
f"mask{i}_{suf}" for i in range(8) \
for suf in ["file", "data", "goodbits", "badbits"]
)
d1 = panels_by_data_coord[0, 0, 0]
metadata = {'crystfel': {k: d1.get(k) for k in cfel_md_keys}}
metadata['crystfel']['photon_energy'] = cfel_geom.beam['photon_energy']
metadata = {
'crystfel': {
'photon_energy': cfel_geom.beam['photon_energy'],
**{k: d1.get(k) for k in cfel_md_keys},
'mask_info': {
'mask_file': d1.get('mask_file'),
'mask': d1.get('mask'),
'mask_good': cfel_geom.detector['mask_good'],
'mask_bad': cfel_geom.detector['mask_bad'],
**{k: d1.get(k) for k in cfel_md_new_mask_keys}
}
}
}

# Normalise description of bad regions, so we can output it correctly.
# - Change panel names to uniform pNaM (panel N asic M) format
Expand Down Expand Up @@ -340,7 +355,7 @@ def from_crystfel_geom(cls, filename):

def write_crystfel_geom(self, filename, *,
data_path=None,
mask_path=None, dims=('frame', 'modno', 'ss', 'fs'),
mask_info=None, dims=('frame', 'modno', 'ss', 'fs'),
nquads=None, adu_per_ev=None, clen=None,
photon_energy=None):
"""Write this geometry to a CrystFEL format (.geom) geometry file.
Expand All @@ -357,8 +372,13 @@ def write_crystfel_geom(self, filename, *,
data_path : str
Path to the group that contains the data array in the hdf5 file.
Default: ``'/entry_1/instrument_1/detector_1/data'``.
mask_path : str
Path to the group that contains the mask array in the hdf5 file.
mask_info : dict
Dictionary with information on masks in either old or new style:
Old style: {'mask_file': <file>, 'mask': <path>,
'mask_good': 0x0, 'mask_bad': 0xffff}
New style: {'mask{i}_file': <file>, 'mask{i}_data': <path>,
'mask{i}_goodbits': 0x0, 'mask{i}_badbits': 0xffff}
with {i} in an inclusive range [0, 7].
dims : tuple
Dimensions of the data. Extra dimensions, except for the defaults,
should be added by their index, e.g.
Expand All @@ -380,8 +400,8 @@ def write_crystfel_geom(self, filename, *,
cfelmeta = self.metadata.get('crystfel', {})
if data_path is None:
data_path = cfelmeta.get('data') or '/entry_1/instrument_1/detector_1/data'
if mask_path is None:
mask_path = cfelmeta.get('mask')
if mask_info is None:
mask_info = cfelmeta.get('mask_info')
if adu_per_ev is None:
adu_per_ev = cfelmeta.get('adu_per_eV')
if clen is None:
Expand All @@ -390,7 +410,7 @@ def write_crystfel_geom(self, filename, *,
photon_energy = cfelmeta.get('photon_energy')

write_crystfel_geom(
self, filename, data_path=data_path, mask_path=mask_path, dims=dims,
self, filename, data_path=data_path, mask_info=mask_info, dims=dims,
bad_regions=cfelmeta.get('bad', {}),
nquads=nquads, adu_per_ev=adu_per_ev, clen=clen,
photon_energy=photon_energy,
Expand Down Expand Up @@ -873,7 +893,7 @@ def offset(self, shift, *, modules=np.s_[:], tiles=np.s_[:]):
tile.offset(all_shifts[m, t])
for t, tile in enumerate(module)
] for m, module in enumerate(self.modules)
])
], metadata=self.metadata)

def rotate(self, angles, center=None, modules=np.s_[:], tiles=np.s_[:],
degrees=True):
Expand Down
20 changes: 17 additions & 3 deletions extra_geom/crystfel_fmt.py
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Original file line number Diff line number Diff line change
Expand Up @@ -97,7 +97,7 @@ def motors_to_geom(positions):
def write_crystfel_geom(
self, filename, *,
data_path='/entry_1/instrument_1/detector_1/data',
mask_path=None, dims=('frame', 'modno', 'ss', 'fs'), bad_regions={},
mask_info=None, dims=('frame', 'modno', 'ss', 'fs'), bad_regions={},
nquads=4, adu_per_ev=None, clen=None, photon_energy=None,
):
"""Write this geometry to a CrystFEL format (.geom) geometry file.
Expand Down Expand Up @@ -159,8 +159,22 @@ def write_crystfel_geom(
resolution = 1.0 / self.pixel_size # Pixels per metre

paths = dict(data=data_path)
if mask_path:
paths['mask'] = mask_path
if mask_info is not None:
# Old-style mask data:
if mask_info['mask']:
if mask_info['mask_file']:
paths['mask_file'] = mask_info['mask_file']
paths['mask'] = mask_info['mask']
paths['mask_good'] = mask_info['mask_good']
paths['mask_bad'] = mask_info['mask_bad']
# New-style (CrystFEL v0.10+) mask data:
for i in range(8):
if mask_info[f"mask{i}_data"]:
if mask_info[f"mask{i}_file"]:
paths[f"mask{i}_file"] = mask_info[f"mask{i}_file"]
paths[f"mask{i}_data"] = mask_info[f"mask{i}_data"]
paths[f"mask{i}_goodbits"] = mask_info[f"mask{i}_goodbits"]
paths[f"mask{i}_badbits"] = mask_info[f"mask{i}_badbits"]
path_str = '\n'.join('{} = {} ;'.format(i, j) for i, j in paths.items())

with open(filename, 'w') as f:
Expand Down
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