def process_dataset(self, metadata, flags=(), sample=None):
numbers = datatools.frameset_to_list(metadata['frames'])
filename = os.path.join(metadata['directory'], metadata['filename'].format(numbers[0]))
suffix = 'anom' if 'anomalous' in flags else 'native'
params = {
'uuid': str(uuid.uuid4()),
'title': 'MX analysis in progress ...',
'state': self.manager.State.ACTIVE,
'data': metadata,
'sample_id': metadata['sample_id'],
'name': metadata['name'],
'file_names': [filename],
'anomalous': 'anomalous' in flags,
'activity': 'proc-{}'.format(suffix),
'type': metadata['type'],
}
params = datatools.update_for_sample(params, sample, overwrite=False)
self.manager.add_item(params, False)
try:
report = yield self.beamline.dps.process_mx(params, params['directory'], misc.get_project_name())
except Exception as e:
logger.error('MX analysis failed: {}'.format(str(e)))
self.failed(e, params['uuid'], self.ResultType.MX)
returnValue({})
else:
report['data_id'] = [_f for _f in [metadata.get('id')] if _f]
self.save_report(report)
self.succeeded(report, params['uuid'], self.ResultType.MX)
returnValue(report)
def process_powder(self, metadata, flags=(), sample=None):
file_names = [
os.path.join(metadata['directory'], metadata['filename'].format(number))
for number in datatools.frameset_to_list(metadata['frames'])
]
params = {
'uuid': str(uuid.uuid4()),
'title': 'XRD Analysis in progress ...',
'state': self.manager.State.ACTIVE,
'data': metadata,
'sample_id': metadata['sample_id'],
'name': metadata['name'],
'file_names': file_names,
'calib': 'calibrate' in flags,
'activity': 'proc-xrd',
'type': metadata['type'],
}
params = datatools.update_for_sample(params, sample, overwrite=False)
self.manager.add_item(params, False)
try:
report = yield self.beamline.dps.process_xrd(params, params['directory'], misc.get_project_name())
except Exception as e:
logger.error('XRD analysis failed: {}'.format(str(e)))
self.failed(e, params['uuid'], self.ResultType.XRD)
returnValue({})
else:
report['data_id'] = [_f for _f in [metadata.get('id')] if _f]
self.save_report(report)
self.succeeded(report, params['uuid'], self.ResultType.XRD)
returnValue(report)
def resume_sequence(self):
self.paused = False
collected = 0
# reset 'existing' field
for run in self.config['runs']:
existing, resumable = self.beamline.detector.check(
run['directory'], run['name'], first=run['first'])
run['existing'] = datatools.summarize_list(existing)
collected += len(datatools.frameset_to_list(run['existing']))
self.configure(self.config['runs'], take_snapshots=False)
self.beamline.all_shutters.open()
self.start()
def check_runlist(self, runs):
existing = {
run['name']: self.beamline.detector.check(run['directory'], run['name'], first=run['first'])
for run in runs
}
config_data = copy.deepcopy(runs)
success = True
collected = 0
# check for existing files
if any(pair[0] for pair in existing.values()):
details = '\n'.join([
'{}: {}'.format(k, datatools.summarize_list(v[0]))
for k, v in existing.items()
if v[0]
])
header = 'Frames from this sequence already exist!\n'
sub_header = details + (
'\n\n<b>What would you like to? </b>\n'
'NOTE: Starting over will delete existing data!\n'
)
buttons = (
('Cancel', RESPONSE_CANCEL),
('Start Over', RESPONSE_REPLACE_ALL),
)
# Add resume option if resumable
if all(pair[1] for pair in existing.values()):
buttons += (('Resume', RESPONSE_SKIP),)
response = dialogs.warning(header, sub_header, buttons=buttons)
if response == RESPONSE_SKIP:
success = True
collected = 0
for run in config_data:
run['existing'] = datatools.summarize_list(existing.get(run['name'], ([], False))[0])
collected += len(datatools.frameset_to_list(run['existing']))
elif response == RESPONSE_REPLACE_ALL:
success = True
else:
success = False
return success, config_data, collected
def process_multiple(self, *metadatas, **kwargs):
sample = kwargs.get('sample', None)
flags = kwargs.get('flags', ())
file_names = []
names = []
for metadata in metadatas:
numbers = datatools.frameset_to_list(metadata['frames'])
file_names.append(os.path.join(metadata['directory'], metadata['filename'].format(numbers[0])))
names.append(metadata['name'])
metadata = metadatas[0]
suffix = 'mad' if 'mad' in flags else 'merge'
params = {
'uuid': str(uuid.uuid4()),
'title': 'MX {} analysis in progress ...'.format(suffix.upper()),
'state': self.manager.State.ACTIVE,
'data': metadata,
'sample_id': metadata['sample_id'],
'name': '-'.join(names),
'file_names': file_names,
'anomalous': 'anomalous' in flags,
'merge': 'merge' in flags,
'mad': 'mad' in flags,
'activity': 'proc-{}'.format(suffix),
'type': metadata['type'],
}
params = datatools.update_for_sample(params, sample, overwrite=False)
self.manager.add_item(params, False)
try:
report = yield self.beamline.dps.process_mx(params, params['directory'], misc.get_project_name())
except Exception as e:
logger.error('MX analysis failed: {}'.format(str(e)))
self.failed(e, params['uuid'], self.ResultType.MX)
returnValue({})
else:
report['data_id'] = [_f for _f in [metadata.get('id') for metadata in metadatas] if _f]
self.save_report(report)
self.succeeded(report, params['uuid'], self.ResultType.MX)
returnValue(report)