synthesis_workflow.utils

Utils functions.

Attributes

_TEMPLATES

Classes

DisableLogger

Context manager to disable logging.

Functions

setup_logging([log_level, log_file, log_file_level, ...])	Setup logging.
create_parameter_diff(param, param_spec)	Create a dataframe with a diff between two parameter dict.
_create_entry(param, entry)	Create a dict entry if it does not exist.
apply_parameter_diff(param, custom_values)	Apply a parameter diff from 'create_parameter_diff' to a parameter dict.
save_planes(planes, path)	Save planes to txt files.
create_circuit_config(nodes_file, morphology_path)	Create simple circuit config.
parse_annotations(filepath)	Parse XML with morphology annotations.
parse_morphdb(filepath)	Parse (ext)neuronDB.dat file.
collect_annotations(annotation_dir, morphdb_path)	Collect annotations from given directory.

Module Contents

_TEMPLATES

class DisableLogger(log_level=logging.CRITICAL, logger=None)

Context manager to disable logging.

log_level

logger

__enter__()

Disabling the logger when entering the context manager.

__exit__(*args)

Enabling the logger when exiting the context manager.

setup_logging(log_level=logging.DEBUG, log_file=None, log_file_level=None, log_format=None, date_format=None, logger=None)

Setup logging.

create_parameter_diff(param, param_spec)

Create a dataframe with a diff between two parameter dict.

_create_entry(param, entry)

Create a dict entry if it does not exist.

apply_parameter_diff(param, custom_values)

Apply a parameter diff from ‘create_parameter_diff’ to a parameter dict.

save_planes(planes, path)

Save planes to txt files.

create_circuit_config(nodes_file, morphology_path)

Create simple circuit config.

parse_annotations(filepath)

Parse XML with morphology annotations.

parse_morphdb(filepath)

Parse (ext)neuronDB.dat file.

collect_annotations(annotation_dir, morphdb_path)

Collect annotations from given directory.