def save_manual_states_to_json(self, filepath: str):
json_data = {
"input_nwb_file": self.nwb_path,
"stimulus_ontology_file": self.ontology_file,
"manual_sweep_states": self.extract_manual_sweep_states(),
"qc_criteria": self._qc_criteria,
"ipfx_version": ipfx.__version__
}
try:
PipelineParameters().load(json_data)
with open(filepath, 'w') as f:
json.dump(json_data, f, indent=4)
except ValidationError as valerr:
exception_message("Unable to save manual states to JSON",
f"Manual states data failed schema validation",
valerr
)
except IOError as ioerr:
exception_message("Unable to write file",
f'Unable to write to file {filepath}',
ioerr
)
def load_data_set_from_nwb(self, path: str):
""" Attempts to read an NWB file describing an experiment. Fails if
qc criteria or stimulus ontology not already present. Otherwise,
attempts to run the pre-fx pipeline.
Parameters
----------
path :
load dataset from here
"""
try:
if self.stimulus_ontology is None:
raise ValueError("must set stimulus ontology before loading a data set!")
elif self.qc_criteria is None:
raise ValueError("must set qc criteria before loading a data set!")
self.status_message.emit("Running extraction and auto qc...")
self.run_extraction_and_auto_qc(path, self.stimulus_ontology, self.qc_criteria, commit=True)
self.status_message.emit("Done running extraction and auto qc")
except Exception as err:
exception_message(
"Unable to load NWB",
f"failed to load NWB file from {path}",
err
)
def load_stimulus_ontology_from_json(self, path: str):
""" Attempts to read a stimulus ontology file from a JSON. If
successful (and other required data are already set), attempts to
run the pre-fx pipeline
Parameters
----------
path :
load ontology from here
"""
try:
with open(path, "r") as ontology_file:
ontology_data = json.load(ontology_file)
ontology = StimulusOntology(ontology_data)
self.ontology_file = path
if self.nwb_path is not None and self.qc_criteria is not None:
self.run_extraction_and_auto_qc(
self.nwb_path,
ontology,
self.qc_criteria,
commit=True
)
else:
self.stimulus_ontology = ontology
except Exception as err:
exception_message(
"StimulusOntology load failed",
f"failed to load stimulus ontology file from {path}",
err
)
def load_qc_criteria_from_json(self, path: str):
""" Attempts to read qc criteria from a JSON. If successful (and other
required data are already set), attempts to run the pre-fx pipeline
Parameters
----------
path :
load criteria from here
"""
try:
with open(path, "r") as criteria_file:
criteria = json.load(criteria_file)
if self.nwb_path is not None and self.stimulus_ontology is not None:
self.run_extraction_and_auto_qc(
self.nwb_path,
self.stimulus_ontology,
criteria,
commit=True
)
else:
self.qc_criteria = criteria
except Exception as err:
exception_message(
"QC criteria load failure",
f"failed to load qc criteria file from {path}",
err
)
def run_feature_extraction(self):
self.status_message.emit("Computing features, please wait.")
drop_failed_sweeps(self.sweep_info)
data_set = create_ephys_data_set(sweep_info=self.sweep_info,
nwb_file=self.input_nwb_file,
ontology=self.ontology)
try:
cell_features, sweep_features, cell_record, sweep_records,\
cell_state, feature_states = extract_data_set_features(data_set)
self.feature_data = {'cell_features': cell_features,
'sweep_features': sweep_features,
'cell_record': cell_record,
'sweep_records': sweep_records,
'cell_state': cell_state,
'feature_states': feature_states
}
self.new_state()
self.status_message.emit("Done computing features!")
except (FeatureError, IndexError) as ferr:
exception_message("Feature extraction error",
f"failed feature extraction",
ferr
)