bluepyemodel.tools.utils¶

Utils

Functions

`are_same_protocol`(name_a, name_b)	Check if two protocol names or list are equal.
`checkpoint_path_exists`(checkpoint_path)	Returns True if checkpoint path exists, False if not.
`existing_checkpoint_paths`(emodel_metadata[, ...])	Returns a list of existing checkpoint paths conforming to metadata.
`format_protocol_name_to_list`(protocol_name)	Make sure that the name of a protocol is a list [protocol_name, amplitude]
`get_amplitude_from_feature_key`(feat_key)	Get amplitude from a key of the EModel.feature dict.
`get_checkpoint_path`(metadata[, seed])	Get checkpoint path.
`get_curr_name`(feature_name)	Extracts the current name from the feature name or response key.
`get_legacy_checkpoint_path`(checkpoint_path)	Get legacy checkpoint path from checkpoint path
`get_loc_name`(feature_name)	Extracts the location name from the feature name or response key.
`get_mapped_protocol_name`(protocol_name, ...)	Returns the mapped protocol name from protocols_mapping if available; otherwise, returns the original name.
`get_protocol_name`(feature_name)	Extracts the protocol name from the feature name or response key.
`get_seed_from_checkpoint_path`(path)	Get seed from checkpoint path name.
`make_dir`(path_dir)	Creates directory if it does not exist
`parse_feature_name_parts`(feature_name)	Splits the feature name into its respective parts, handling cases where the protocol name contains a dot.
`read_checkpoint`(checkpoint_path)	Reads a BluePyOpt checkpoint file
`select_rec_for_thumbnail`(rec_names[, ...])	Select a recording for thumbnail.
`yesno`(question)	Ask a Yes/No question

are_same_protocol(name_a, name_b)¶: Check if two protocol names or list are equal. Eg: is IV_0.0 the same as IV_0 and the same as [“IV”, 0.0].

checkpoint_path_exists(checkpoint_path)¶

Returns True if checkpoint path exists, False if not.

Parameters:: checkpoint_path (str or Path) – checkpoint path

existing_checkpoint_paths(emodel_metadata, checkpoint_paths=None)¶

Returns a list of existing checkpoint paths conforming to metadata.

Parameters:

emodel_metadata (EModelMetadata) – contains emodel and iteration that should be present in each returned checkpoint path
checkpoint_paths (list) – list of existing checkpoint paths to be filtered using metadata. If None, will be created on the spot.

format_protocol_name_to_list(protocol_name)¶: Make sure that the name of a protocol is a list [protocol_name, amplitude]

get_amplitude_from_feature_key(feat_key)¶

Get amplitude from a key of the EModel.feature dict.

Parameters:: feat_key (str) – feature key, e.g. IV_40.soma.maximum_voltage_from_voltagebase

get_checkpoint_path(metadata, seed=None)¶: Get checkpoint path. Use legacy format if any is found, else use latest format.

get_curr_name(feature_name)¶

Extracts the current name from the feature name or response key.

This function works with both a full feature name string (e.g., “IV_40.0.soma.v.voltage_base”) and a response key (e.g., “IV_40.0.soma.v”). It returns the third part of the input, which is the current name, correctly handling cases where the protocol contains a dot.

Parameters:: feature_name (str) – The full feature name string or response key.
Returns:: The current name part of the feature name.
Return type:: str
Raises:: IndexError – If the current name cannot be determined from the input.

Examples

>>> get_curr_name("IV_40.0.soma.v.voltage_base")
'v'

>>> get_curr_name("IV_40.0.soma.v")
'v'

get_legacy_checkpoint_path(checkpoint_path)¶: Get legacy checkpoint path from checkpoint path

get_loc_name(feature_name)¶

Extracts the location name from the feature name or response key.

This function works with both a full feature name string (e.g., “IV_40.0.soma.v.voltage_base”) and a response key (e.g., “IV_40.0.soma.v”). It returns the second part of the input, which is the location name, correctly handling cases where the protocol contains a dot.

Parameters:: feature_name (str) – The full feature name string or response key.
Returns:: The location name part of the feature name.
Return type:: str
Raises:: IndexError – If the location name cannot be determined from the input.

Examples

>>> get_loc_name("IV_40.0.soma.v.voltage_base")
'soma'

>>> get_loc_name("IV_40.0.soma.v")
'soma'

get_mapped_protocol_name(protocol_name, protocols_mapping)¶: Returns the mapped protocol name from protocols_mapping if available; otherwise, returns the original name.

get_protocol_name(feature_name)¶

Extracts the protocol name from the feature name or response key.

This function works with both a full feature name string (e.g., “IV_40.0.soma.v.voltage_base”) and a response key (e.g., “IV_40.0.soma.v”). It returns the first part of the input, which is the protocol name, correctly handling cases where the protocol contains a dot.

Parameters:: feature_name (str) – The full feature name string or response key.
Returns:: The protocol name part of the feature name.
Return type:: str

Examples

>>> get_protocol_name("IV_40.0.soma.v.voltage_base")
'IV_40.0'

>>> get_protocol_name("IV_40.0.soma.v")
'IV_40.0'

get_seed_from_checkpoint_path(path)¶: Get seed from checkpoint path name. default seed is 0 if not found.

make_dir(path_dir)¶: Creates directory if it does not exist

parse_feature_name_parts(feature_name)¶

Splits the feature name into its respective parts, handling cases where the protocol name contains a dot.

This function works with both a full feature name string (e.g., “IV_40.0.soma.v.voltage_base”) and a response key (e.g., “IV_40.0.soma.v”). It splits the input into a list of parts, combining the first two parts if the protocol name contains a dot and is followed by a numeric component.

Parameters:: feature_name (str) – The full feature name string or response key to be parsed.
Returns:: A list of strings representing the correctly parsed parts of the feature name.
Return type:: list

Examples

>>> parse_feature_name_parts("IV_40.0.soma.v.voltage_base")
['IV_40.0', 'soma', 'v', 'voltage_base']

>>> parse_feature_name_parts("IV_40.0.soma.v")
['IV_40.0', 'soma', 'v']

read_checkpoint(checkpoint_path)¶: Reads a BluePyOpt checkpoint file

select_rec_for_thumbnail(rec_names, additional_step_prots=None, thumbnail_rec=None)¶

Select a recording for thumbnail.

Select the step protocol with lowest positive amplitude, so that delay is visible if present.

Parameters:

rec_names (set) – the names of the recordings, following this naming convention: protocol_name_amplitude.location.variable
additional_step_prots (list) – step protocol names to look for (other than defaults ones)
thumbnail_rec (str) – recording name to use for thumbnail if present

yesno(question)¶: Ask a Yes/No question