def export(self, experiment):
"""
Export FCS files from an experiment.
Parameters
----------
experiment : Experiment
The :class:`.Experiment` to export
"""
if experiment is None:
raise util.CytoflowViewError('experiment',
"No experiment specified")
if len(experiment) == 0:
raise util.CytoflowViewError('experiment',
"No events in experiment")
if not self.path:
raise util.CytoflowViewError('path',
'Must specify an output directory')
d = Path(self.path)
if not d.is_dir():
raise util.CytoflowViewError('path',
'Output directory {} must exist')
# also tests for good experiment, self.by
for filename in self.enum_files(experiment):
p = d / filename
if p.is_file():
raise util.CytoflowViewError(
'path', 'File {} already exists'.format(p))
if self.subset:
try:
experiment = experiment.query(self.subset)
except util.CytoflowError as e:
raise util.CytoflowViewError('subset', str(e)) from e
except Exception as e:
raise util.CytoflowViewError(
'subset', "Subset string '{0}' isn't valid".format(
self.subset)) from e
if len(experiment) == 0:
raise util.CytoflowViewError(
'subset', "Subset string '{0}' returned no events".format(
self.subset))
tube0, common_metadata = list(
experiment.metadata['fcs_metadata'].items())[0]
common_metadata = copy(common_metadata)
exclude_keywords = [
'$BEGINSTEXT', '$ENDSTEXT', '$BEGINANALYSIS', '$ENDANALYSIS',
'$BEGINDATA', '$ENDDATA', '$BYTEORD', '$DATATYPE', '$MODE',
'$NEXTDATA', '$TOT', '$PAR'
]
common_metadata = {
str(k): str(v)
for k, v in common_metadata.items()
if re.search('^\$P\d+[BENRDSG]$', k) is None
and k not in exclude_keywords
}
for filename, metadata in experiment.metadata['fcs_metadata'].items():
if filename == tube0:
continue
for name, value in metadata.items():
if name not in common_metadata:
continue
if name not in common_metadata or value != common_metadata[
name]:
del common_metadata[name]
for i, channel in enumerate(experiment.channels):
if 'voltage' in experiment.metadata[channel]:
common_metadata['$P{}V'.format(
i + 1)] = experiment.metadata[channel]['voltage']
for group, data_subset in experiment.data.groupby(self.by):
data_subset = data_subset[experiment.channels]
if len(self.by) == 1:
group = [group]
parts = []
kws = copy(self.keywords)
kws.update(common_metadata)
kws = {k: str(v) for k, v in kws.items()}
for i, name in enumerate(self.by):
if self._include_by:
parts.append(name + '_' + str(group[i]))
else:
parts.append(str(group[i]))
kws["CF_" + name] = str(group[i])
if self.base:
filename = self.base + '_' + '_'.join(parts) + '.fcs'
else:
filename = '_'.join(parts) + '.fcs'
full_path = d / filename
util.write_fcs(str(full_path),
experiment.channels, {
c: experiment.metadata[c]['range']
for c in experiment.channels
},
data_subset.values,
compat_chn_names=False,
compat_negative=False,
**kws)
def export(self, experiment):
"""
Export FCS files from an experiment.
Parameters
----------
experiment : Experiment
The :class:`.Experiment` to export
"""
if experiment is None:
raise util.CytoflowViewError('experiment', "No experiment specified")
if not self.path:
raise util.CytoflowOpError('path',
'Must specify an output directory')
d = Path(self.path)
if not d.is_dir():
raise util.CytoflowOpError('path',
'Output directory {} must exist')
# also tests for good experiment, self.by
for filename in self.enum_files(experiment):
p = d / filename
if p.is_file():
raise util.CytoflowOpError('path',
'File {} already exists'
.format(p))
if self.subset:
try:
experiment = experiment.query(self.subset)
except util.CytoflowError as e:
raise util.CytoflowViewError('subset', str(e)) from e
except Exception as e:
raise util.CytoflowViewError('subset',
"Subset string '{0}' isn't valid"
.format(self.subset)) from e
if len(experiment) == 0:
raise util.CytoflowViewError('subset',
"Subset string '{0}' returned no events"
.format(self.subset))
for group, data_subset in experiment.data.groupby(self.by):
data_subset = data_subset[experiment.channels]
if len(self.by) == 1:
group = [group]
parts = []
kws = copy(self.keywords)
for i, name in enumerate(self.by):
if self._include_by:
parts.append(name + '_' + str(group[i]))
else:
parts.append(str(group[i]))
kws["CF_" + name] = str(group[i])
if self.base:
filename = self.base + '_' + '_'.join(parts) + '.fcs'
else:
filename = '_'.join(parts) + '.fcs'
full_path = d / filename
util.write_fcs(str(full_path),
experiment.channels,
data_subset.values,
compat_chn_names = False,
compat_negative = False,
**kws)