def __init__(self, app, detector_id = None, detector = None, **kwargs):
assert [detector_id, detector].count(None) == 1
if detector is not None:
kwargs['distance'] = flex.mean(flex.double([p.get_distance() for p in detector]))
db_proxy.__init__(self, app, "%s_detector" % app.params.experiment_tag, id=detector_id, **kwargs)
self.detector_id = self.id
def __init__(self, app, tag_id=None, **kwargs):
db_proxy.__init__(self,
app,
"%s_tag" % app.params.experiment_tag,
id=tag_id,
**kwargs)
self.tag_id = self.id
def __init__(self, app, isoform_id=None, **kwargs):
db_proxy.__init__(self,
app,
"%s_isoform" % app.params.experiment_tag,
id=isoform_id,
**kwargs)
self.isoform_id = self.id
def __init__(self, app, rungroup_id=None, **kwargs):
db_proxy.__init__(self,
app,
"%s_rungroup" % app.params.experiment_tag,
id=rungroup_id,
**kwargs)
self.rungroup_id = self.id
def __init__(self, app, experiment_id=None, experiment=None, **kwargs):
assert [experiment_id, experiment].count(None) == 1
if experiment is not None:
self.imageset = Imageset(app)
self.beam = Beam(app, beam=experiment.beam)
self.detector = Detector(app, detector=experiment.detector)
self.crystal = Crystal(app, crystal=experiment.crystal)
kwargs['imageset_id'] = self.imageset.id
kwargs['beam_id'] = self.beam.id
kwargs['detector_id'] = self.detector.id
kwargs['crystal_id'] = self.crystal.id
kwargs['crystal_cell_id'] = self.crystal.cell_id
db_proxy.__init__(self,
app,
"%s_experiment" % app.params.experiment_tag,
id=experiment_id,
**kwargs)
self.experiment_id = self.id
if experiment is None:
self.imageset = Imageset(app, imageset_id=self.imageset_id)
self.beam = Beam(app, beam_id=self.beam_id)
self.detector = Detector(app, self.detector_id)
self.crystal = Crystal(app, self.crystal_id)
def __init__(self, app, dataset_id=None, **kwargs):
db_proxy.__init__(self,
app,
"%s_dataset" % app.params.experiment_tag,
id=dataset_id,
**kwargs)
self.dataset_id = self.id
def __init__(self, app, cell_bin_id=None, **kwargs):
db_proxy.__init__(self,
app,
"%s_cell_bin" % app.params.experiment_tag,
id=cell_bin_id,
**kwargs)
self.cell_bin_id = self.id
def __init__(self, app, crystal_id = None, crystal = None, **kwargs):
assert [crystal_id, crystal].count(None) == 1
if crystal is not None:
u = crystal.get_U() # orientation matrix
for i in xrange(len(u)):
kwargs['ori_%d' % (i + 1)] = u[i]
kwargs['mosaic_block_rotation'] = crystal._ML_half_mosaicity_deg
kwargs['mosaic_block_size'] = crystal._ML_domain_size_ang
try:
isoform_name = crystal.identified_isoform
except AttributeError:
self.cell = Cell(app, crystal=crystal, isoform_id = None)
else:
tag = app.params.experiment_tag
query = """SELECT cell.id from `%s_cell` cell
JOIN `%s_isoform` isoform ON cell.isoform_id = isoform.id
JOIN `%s_trial` trial ON isoform.trial_id = trial.id
WHERE isoform.name = '%s' AND trial.trial = %d""" % (
tag, tag, tag, isoform_name, app.params.input.trial)
cursor = app.execute_query(query)
results = cursor.fetchall()
assert len(results) == 1
self.cell = Cell(app, cell_id = results[0][0])
kwargs['cell_id'] = self.cell.id
db_proxy.__init__(self, app, "%s_crystal" % app.params.experiment_tag, id=crystal_id, **kwargs)
self.crystal_id = self.id
if crystal is None:
self.cell = Cell(app, cell_id = self.cell_id)
def __init__(self, app, imageset_id=None, **kwargs):
db_proxy.__init__(self,
app,
"%s_imageset" % app.params.experiment_tag,
id=imageset_id,
**kwargs)
self.imageset_id = self.id
def __init__(self, app, event_id=None, **kwargs):
db_proxy.__init__(self,
app,
"%s_event" % app.params.experiment_tag,
id=event_id,
**kwargs)
self.event_id = self.id
def __init__(self, app, detector_id = None, detector = None, **kwargs):
assert [detector_id, detector].count(None) == 1
if detector is not None:
kwargs['distance'] = flex.mean(flex.double([p.get_distance() for p in detector]))
db_proxy.__init__(self, app, "%s_detector" % app.params.experiment_tag, id=detector_id, **kwargs)
self.detector_id = self.id
def __init__(self, app, job_id=None, **kwargs):
db_proxy.__init__(self,
app,
"%s_job" % app.params.experiment_tag,
id=job_id,
**kwargs)
self.job_id = self.id
def __init__(self,
app,
cell_id=None,
crystal=None,
init_bins=False,
**kwargs):
assert [cell_id, crystal].count(None) in [1, 2]
if crystal is not None:
for key, p in zip(['a', 'b', 'c', 'alpha', 'beta', 'gamma'],
crystal.get_unit_cell().parameters()):
kwargs['cell_%s' % key] = p
kwargs['lookup_symbol'] = crystal.get_space_group().type(
).lookup_symbol()
db_proxy.__init__(self,
app,
"%s_cell" % app.params.experiment_tag,
id=cell_id,
**kwargs)
self.cell_id = self.id
assert [self.isoform_id, self.trial_id].count(None) in [1, 2]
if self.isoform_id is not None:
self.isoform = Isoform(app, isoform_id=self.isoform_id)
else:
self.isoform = None
if init_bins:
self._bins = app.get_cell_bins(self.id)
self._bins_set = True
else:
self._bins = []
self._bins_set = False
def __init__(self, app, crystal_id = None, crystal = None, **kwargs):
assert [crystal_id, crystal].count(None) == 1
if crystal is not None:
u = crystal.get_U() # orientation matrix
for i in xrange(len(u)):
kwargs['ori_%d' % (i + 1)] = u[i]
kwargs['mosaic_block_rotation'] = crystal._ML_half_mosaicity_deg
kwargs['mosaic_block_size'] = crystal._ML_domain_size_ang
try:
isoform_name = crystal.identified_isoform
except AttributeError:
self.cell = Cell(app, crystal=crystal, isoform_id = None)
else:
tag = app.params.experiment_tag
query = """SELECT cell.id from `%s_cell` cell
JOIN `%s_isoform` isoform ON cell.isoform_id = isoform.id
JOIN `%s_trial` trial ON isoform.trial_id = trial.id
WHERE isoform.name = '%s' AND trial.trial = %d""" % (
tag, tag, tag, isoform_name, app.params.input.trial)
cursor = app.execute_query(query)
results = cursor.fetchall()
assert len(results) == 1
self.cell = Cell(app, cell_id = results[0][0])
kwargs['cell_id'] = self.cell.id
db_proxy.__init__(self, app, "%s_crystal" % app.params.experiment_tag, id=crystal_id, **kwargs)
self.crystal_id = self.id
if crystal is None:
self.cell = Cell(app, cell_id = self.cell_id)
def __init__(self, app, job_id = None, **kwargs): db_proxy.__init__(self, app, "%s_job" % app.params.experiment_tag, id = job_id, **kwargs) self.job_id = self.id self._run = None self._rungroup = None self._trial = None self._task = None self._dataset = None self._dataset_version = None
def __init__(self, app, beam_id = None, beam = None, **kwargs):
assert [beam_id, beam].count(None) == 1
if beam is not None:
u_s0 = beam.get_unit_s0()
kwargs['direction_1'] = u_s0[0]
kwargs['direction_2'] = u_s0[1]
kwargs['direction_3'] = u_s0[2]
kwargs['wavelength'] = beam.get_wavelength()
db_proxy.__init__(self, app, "%s_beam" % app.params.experiment_tag, id=beam_id, **kwargs)
self.beam_id = self.id
def __init__(self, app, beam_id = None, beam = None, **kwargs):
assert [beam_id, beam].count(None) == 1
if beam is not None:
u_s0 = beam.get_unit_s0()
kwargs['direction_1'] = u_s0[0]
kwargs['direction_2'] = u_s0[1]
kwargs['direction_3'] = u_s0[2]
kwargs['wavelength'] = beam.get_wavelength()
db_proxy.__init__(self, app, "%s_beam" % app.params.experiment_tag, id=beam_id, **kwargs)
self.beam_id = self.id
def __init__(self,
app,
crystal_id=None,
crystal=None,
make_cell=True,
**kwargs):
from scitbx import matrix
assert [crystal_id, crystal].count(None) == 1
if crystal is not None:
u = matrix.sqr(crystal.get_U()) # orientation matrix
for i in range(len(u)):
kwargs['ori_%d' % (i + 1)] = u[i]
try:
kwargs[
'mosaic_block_rotation'] = crystal.get_half_mosaicity_deg(
)
kwargs['mosaic_block_size'] = crystal.get_domain_size_ang()
except AttributeError:
pass
if hasattr(crystal, 'identified_isoform'):
print(
"Warning, isoforms no longer have custom support in the database logger."
)
#tag = app.params.experiment_tag
#query = """SELECT cell.id from `%s_cell` cell
# JOIN `%s_isoform` isoform ON cell.isoform_id = isoform.id
# JOIN `%s_trial` trial ON isoform.trial_id = trial.id
# WHERE isoform.name = '%s' AND trial.trial = %d""" % (
# tag, tag, tag, isoform_name, app.params.input.trial)
#cursor = app.execute_query(query)
#results = cursor.fetchall()
#assert len(results) == 1
#self.cell = Cell(app, cell_id = results[0][0])
if make_cell:
self.cell = Cell(app, crystal=crystal, isoform_id=None)
kwargs['cell_id'] = self.cell.id
else:
self.cell = None
db_proxy.__init__(self,
app,
"%s_crystal" % app.params.experiment_tag,
id=crystal_id,
**kwargs)
self.crystal_id = self.id
if crystal is None:
self.cell = Cell(app, cell_id=self.cell_id)
def __init__(self, app, cell_id = None, crystal = None, **kwargs):
assert [cell_id, crystal].count(None) in [1,2]
if crystal is not None:
for key, p in zip(['a', 'b', 'c', 'alpha', 'beta', 'gamma'], crystal.get_unit_cell().parameters()):
kwargs['cell_%s'%key] = p
kwargs['lookup_symbol'] = crystal.get_space_group().type().lookup_symbol()
db_proxy.__init__(self, app, "%s_cell" % app.params.experiment_tag, id=cell_id, **kwargs)
self.cell_id = self.id
if self.isoform_id is not None:
self.isoform = Isoform(app, isoform_id = self.isoform_id)
self.bins = app.get_cell_bins(self.id)
else:
self.isoform = None
self.bins = []
def __init__(self, app, experiment_id = None, experiment = None, **kwargs):
assert [experiment_id, experiment].count(None) == 1
if experiment is not None:
self.imageset = Imageset(app)
self.beam = Beam(app, beam = experiment.beam)
self.detector = Detector(app, detector = experiment.detector)
self.crystal = Crystal(app, crystal = experiment.crystal)
kwargs['imageset_id'] = self.imageset.id
kwargs['beam_id'] = self.beam.id
kwargs['detector_id'] = self.detector.id
kwargs['crystal_id'] = self.crystal.id
kwargs['crystal_cell_id'] = self.crystal.cell_id
db_proxy.__init__(self, app, "%s_experiment" % app.params.experiment_tag, id = experiment_id, **kwargs)
self.experiment_id = self.id
if experiment is None:
self.imageset = Imageset(app, imageset_id=self.imageset_id)
self.beam = Beam(app, beam_id=self.beam_id)
self.detector = Detector(app, self.detector_id)
self.crystal = Crystal(app, self.crystal_id)
def __init__(self, app, cell_bin_id = None, **kwargs): db_proxy.__init__(self, app, "%s_cell_bin" % app.params.experiment_tag, id=cell_bin_id, **kwargs) self.cell_bin_id = self.id
def __init__(self, app, trial_id = None, **kwargs): db_proxy.__init__(self, app, "%s_trial" % app.params.experiment_tag, id = trial_id, **kwargs) self.trial_id = self.id
def __init__(self, app, rungroup_id = None, **kwargs): db_proxy.__init__(self, app, "%s_rungroup" % app.params.experiment_tag, id = rungroup_id, **kwargs) self.rungroup_id = self.id
def __init__(self, app, imageset_id = None, **kwargs): db_proxy.__init__(self, app, "%s_imageset" % app.params.experiment_tag, id=imageset_id, **kwargs) self.imageset_id = self.id
def __init__(self, app, event_id = None, **kwargs): db_proxy.__init__(self, app, "%s_event" % app.params.experiment_tag, id = event_id, **kwargs) self.event_id = self.id
def __init__(self, app, isoform_id=None, **kwargs): db_proxy.__init__(self, app, "%s_isoform" % app.params.experiment_tag, id=isoform_id, **kwargs) self.isoform_id = self.id
def __init__(self, app, job_id = None, **kwargs): db_proxy.__init__(self, app, "%s_job" % app.params.experiment_tag, id = job_id, **kwargs) self.job_id = self.id
