To convert snirf file to bids format.
Project description
module snirf2bids
Module for converting snirf file into bids format
Maintained by the Boston University Neurophotonics Center
function snirf_to_bids
snirf_to_bids(inputpath: str, outputpath: str, participants: dict = None)
Creates a BIDS-compliant folder structure (right now, just the metadata files) from a SNIRF file
Args:
inputpath: The file path to the reference SNIRF fileoutputpath: The file path/directory for the created BIDS metadata filesparticipants: A dictionary with participant information Example ={participant_id: 'sub-01',age: 34,sex: 'M'}scans: A dictionary with SNIRF/run information and its acquisition time
class Field
Class which encapsulates fields inside a Metadata class
Attributes:
_value: The value of the field
method __init__
__init__(val)
Generic constructor for a Field class
It stores a specific value declared in the class initialization in _value
property value
Value Getter for Field class
class String
Subclass which encapsulates fields with string values inside a Metadata class
Attributes:
_value: The value of the fieldtype: Data type of the field - in this case, it's "str"
method __init__
__init__(val)
Generic constructor for a String Field class inherited from the Field class
Additionally, it stores the datatype which in this case, it is string
property value
Value Getter for Field class
method get_type
get_type()
Datatype getter for the String class
method validate
validate(val)
Datatype Validation function for String class
class Number
Subclass which encapsulates fields with numerical values inside a Metadata class
Attributes:
_value: The value of the fieldtype: Data type of the field - in this case, it's "int"
method __init__
__init__(val)
Generic constructor for a Number Field class inherited from the Field class
Additionally, it stores the datatype which in this case, it is integer
property value
Value Getter for Field class
method get_type
get_type()
Datatype getter for the Number class
method validate
validate(val)
Datatype Validation function for Number class
class Metadata
Metadata File Class
Class object that encapsulates the JSON and TSV Metadata File Class
Attributes:
_fields: A dictionary of the fields and the values contained in it for a specific Metadata class_source_snirf: The filepath to the reference SNIRF file to create the specific Metadata class
method __init__
__init__()
Generic constructor for a Metadata class
Most importantly, it constructs the default fields with empty values within _fields in a dictionary format
method change_type
change_type(name)
Change the data type restriction for a field (from a String class to a Number class or vice versa)
Args:
name: The field name
Raises:
TypeError: If it's an invalid/undeclared field
method default_fields
default_fields()
Obtain the default fields and their data type for a specific metadata file/class
Returns: The list of default fields for a specific metadata class and the data type
default_list: List of default field names for a specific metadata classdefault_type: List of default field data types for a specific metadata class
method get_class_name
get_class_name()
Obtains the name of the specific metadata class
Returns: The name of the (specific metadata) class
method get_column
get_column(name)
Obtains the value of a specified field/'column' of a Metadata class
Args:
name: Name of the field/'column'
Returns: The value of a specified field/'column' - similar to getattr
method get_column_names
get_column_names()
Get the names of the field in a specific metadata class/file that has a value(s)
Returns: A list of field names that have a value in a specific metadata file
class JSON
JSON Class
Class object that encapsulates subclasses that create and contain BIDS JSON files
method __init__
__init__()
Generic constructor for JSON class - uses the one inherited from the Metadata class
method change_type
change_type(name)
Change the data type restriction for a field (from a String class to a Number class or vice versa)
Args:
name: The field name
Raises:
TypeError: If it's an invalid/undeclared field
method default_fields
default_fields()
Obtain the default fields and their data type for a specific metadata file/class
Returns: The list of default fields for a specific metadata class and the data type
default_list: List of default field names for a specific metadata classdefault_type: List of default field data types for a specific metadata class
method get_class_name
get_class_name()
Obtains the name of the specific metadata class
Returns: The name of the (specific metadata) class
method get_column
get_column(name)
Obtains the value of a specified field/'column' of a Metadata class
Args:
name: Name of the field/'column'
Returns: The value of a specified field/'column' - similar to getattr
method get_column_names
get_column_names()
Get the names of the field in a specific metadata class/file that has a value(s)
Returns: A list of field names that have a value in a specific metadata file
method load_from_json
load_from_json(fpath)
Create the JSON metadata class from a JSON file
Args:
fpath: The file path to the reference JSON file
Raises:
TypeError: Incorrect data type for a specific field based on data loaded from the JSON file
method save_to_json
save_to_json(info, fpath)
Save a JSON inherited class into an output JSON file with a BIDS-compliant name in the file directory designated by the user
Args:
info: Subject info field from the Subject classfpath: The file path that points to the folder where we intend to save the metadata file in
Returns: Outputs a metadata JSON file with a BIDS-compliant name in the specified file path
class TSV
TSV Class
Class object that encapsulates subclasses that create and contain BIDS TSV files
Attributes:
_sidecar: Contains the field names and descriptions for each field for the Sidecar JSON file
method __init__
__init__()
Generic Constructor for TSV class - uses the one inherited from the Metadata class
Additionally, added the sidecar property for the Sidecar JSON files
method change_type
change_type(name)
Change the data type restriction for a field (from a String class to a Number class or vice versa)
Args:
name: The field name
Raises:
TypeError: If it's an invalid/undeclared field
method default_fields
default_fields()
Obtain the default fields and their data type for a specific metadata file/class
Returns: The list of default fields for a specific metadata class and the data type
default_list: List of default field names for a specific metadata classdefault_type: List of default field data types for a specific metadata class
method export_sidecar
export_sidecar(info, fpath)
Exports sidecar as a json file
method get_class_name
get_class_name()
Obtains the name of the specific metadata class
Returns: The name of the (specific metadata) class
method get_column
get_column(name)
Obtains the value of a specified field/'column' of a Metadata class
Args:
name: Name of the field/'column'
Returns: The value of a specified field/'column' - similar to getattr
method get_column_names
get_column_names()
Get the names of the field in a specific metadata class/file that has a value(s)
Returns: A list of field names that have a value in a specific metadata file
method load_from_tsv
load_from_tsv(fpath)
Create the TSV metadata class from a TSV file
Args:
fpath: The file path to the reference TSV file
method make_sidecar
make_sidecar()
Makes a dictionary with the default description noted in BIDS specification into the Sidecar dictionary
Returns: Dictionary with correct fields(that have values) with description of each field within TSV file filled out
method save_to_tsv
save_to_tsv(info, fpath)
Save a TSV inherited class into an output TSV file with a BIDS-compliant name in the file directory designated by the user
Args:
- <b>`info`</b>: Subject info field from the Subject class
- <b>`fpath`</b>: The file path that points to the folder where we intend to save the metadata file in
Returns: Outputs a metadata TSV file with BIDS-compliant name in the specified file path
class Coordsystem
Coordinate System Metadata Class
Class object that mimics and contains the data for the coordsystem.JSON metadata file
method __init__
__init__(fpath=None)
Inherited constructor for the Coordsystem class
Args:
fpath: The file path to a reference SNIRF file
method change_type
change_type(name)
Change the data type restriction for a field (from a String class to a Number class or vice versa)
Args:
name: The field name
Raises:
TypeError: If it's an invalid/undeclared field
method default_fields
default_fields()
Obtain the default fields and their data type for a specific metadata file/class
Returns: The list of default fields for a specific metadata class and the data type
default_list: List of default field names for a specific metadata classdefault_type: List of default field data types for a specific metadata class
method get_class_name
get_class_name()
Obtains the name of the specific metadata class
Returns: The name of the (specific metadata) class
method get_column
get_column(name)
Obtains the value of a specified field/'column' of a Metadata class
Args:
name: Name of the field/'column'
Returns: The value of a specified field/'column' - similar to getattr
method get_column_names
get_column_names()
Get the names of the field in a specific metadata class/file that has a value(s)
Returns: A list of field names that have a value in a specific metadata file
method load_from_SNIRF
load_from_SNIRF(fpath)
Creates the Coordsystem class based on information from a reference SNIRF file
Args:
fpath: The file path to the reference SNIRF file
method load_from_json
load_from_json(fpath)
Create the JSON metadata class from a JSON file
Args:
fpath: The file path to the reference JSON file
Raises:
TypeError: Incorrect data type for a specific field based on data loaded from the JSON file
method save_to_json
save_to_json(info, fpath)
Save a JSON inherited class into an output JSON file with a BIDS-compliant name in the file directory designated by the user
Args:
info: Subject info field from the Subject classfpath: The file path that points to the folder where we intend to save the metadata file in
Returns: Outputs a metadata JSON file with a BIDS-compliant name in the specified file path
class Optodes
Optodes Metadata Class
Class object that mimics and contains the data for the optodes.tsv metadata file
method __init__
__init__(fpath=None)
Inherited constructor for the Optodes class
Args:
fpath: The file path to a reference SNIRF file
method change_type
change_type(name)
Change the data type restriction for a field (from a String class to a Number class or vice versa)
Args:
name: The field name
Raises:
TypeError: If it's an invalid/undeclared field
method default_fields
default_fields()
Obtain the default fields and their data type for a specific metadata file/class
Returns: The list of default fields for a specific metadata class and the data type
default_list: List of default field names for a specific metadata classdefault_type: List of default field data types for a specific metadata class
method export_sidecar
export_sidecar(info, fpath)
Exports sidecar as a json file
method get_class_name
get_class_name()
Obtains the name of the specific metadata class
Returns: The name of the (specific metadata) class
method get_column
get_column(name)
Obtains the value of a specified field/'column' of a Metadata class
Args:
name: Name of the field/'column'
Returns: The value of a specified field/'column' - similar to getattr
method get_column_names
get_column_names()
Get the names of the field in a specific metadata class/file that has a value(s)
Returns: A list of field names that have a value in a specific metadata file
method load_from_SNIRF
load_from_SNIRF(fpath)
Creates the Optodes class based on information from a reference SNIRF file
Args:
fpath: The file path to the reference SNIRF file
method load_from_tsv
load_from_tsv(fpath)
Create the TSV metadata class from a TSV file
Args:
fpath: The file path to the reference TSV file
method make_sidecar
make_sidecar()
Makes a dictionary with the default description noted in BIDS specification into the Sidecar dictionary
Returns: Dictionary with correct fields(that have values) with description of each field within TSV file filled out
method save_to_tsv
save_to_tsv(info, fpath)
Save a TSV inherited class into an output TSV file with a BIDS-compliant name in the file directory designated by the user
Args:
- <b>`info`</b>: Subject info field from the Subject class
- <b>`fpath`</b>: The file path that points to the folder where we intend to save the metadata file in
Returns: Outputs a metadata TSV file with BIDS-compliant name in the specified file path
class Channels
Channels Metadata Class
Class object that mimics and contains the data for the channels.tsv metadata file
method __init__
__init__(fpath=None)
Inherited constructor for the Channels class
Args:
fpath: The file path to a reference SNIRF file
method change_type
change_type(name)
Change the data type restriction for a field (from a String class to a Number class or vice versa)
Args:
name: The field name
Raises:
TypeError: If it's an invalid/undeclared field
method default_fields
default_fields()
Obtain the default fields and their data type for a specific metadata file/class
Returns: The list of default fields for a specific metadata class and the data type
default_list: List of default field names for a specific metadata classdefault_type: List of default field data types for a specific metadata class
method export_sidecar
export_sidecar(info, fpath)
Exports sidecar as a json file
method get_class_name
get_class_name()
Obtains the name of the specific metadata class
Returns: The name of the (specific metadata) class
method get_column
get_column(name)
Obtains the value of a specified field/'column' of a Metadata class
Args:
name: Name of the field/'column'
Returns: The value of a specified field/'column' - similar to getattr
method get_column_names
get_column_names()
Get the names of the field in a specific metadata class/file that has a value(s)
Returns: A list of field names that have a value in a specific metadata file
method load_from_SNIRF
load_from_SNIRF(fpath)
Creates the Channels class based on information from a reference SNIRF file
Args:
fpath: The file path to the reference SNIRF file
method load_from_tsv
load_from_tsv(fpath)
Create the TSV metadata class from a TSV file
Args:
fpath: The file path to the reference TSV file
method make_sidecar
make_sidecar()
Makes a dictionary with the default description noted in BIDS specification into the Sidecar dictionary
Returns: Dictionary with correct fields(that have values) with description of each field within TSV file filled out
method save_to_tsv
save_to_tsv(info, fpath)
Save a TSV inherited class into an output TSV file with a BIDS-compliant name in the file directory designated by the user
Args:
- <b>`info`</b>: Subject info field from the Subject class
- <b>`fpath`</b>: The file path that points to the folder where we intend to save the metadata file in
Returns: Outputs a metadata TSV file with BIDS-compliant name in the specified file path
class Events
Channels Metadata Class
Class object that mimics and contains the data for the events.tsv metadata file
method __init__
__init__(fpath=None)
Inherited constructor for the Events class
Args:
fpath: The file path to a reference SNIRF file
method change_type
change_type(name)
Change the data type restriction for a field (from a String class to a Number class or vice versa)
Args:
name: The field name
Raises:
TypeError: If it's an invalid/undeclared field
method default_fields
default_fields()
Obtain the default fields and their data type for a specific metadata file/class
Returns: The list of default fields for a specific metadata class and the data type
default_list: List of default field names for a specific metadata classdefault_type: List of default field data types for a specific metadata class
method export_sidecar
export_sidecar(info, fpath)
Exports sidecar as a json file
method get_class_name
get_class_name()
Obtains the name of the specific metadata class
Returns: The name of the (specific metadata) class
method get_column
get_column(name)
Obtains the value of a specified field/'column' of a Metadata class
Args:
name: Name of the field/'column'
Returns: The value of a specified field/'column' - similar to getattr
method get_column_names
get_column_names()
Get the names of the field in a specific metadata class/file that has a value(s)
Returns: A list of field names that have a value in a specific metadata file
method load_from_SNIRF
load_from_SNIRF(fpath)
Creates the Events class based on information from a reference SNIRF file
Args:
fpath: The file path to the reference SNIRF file
method load_from_tsv
load_from_tsv(fpath)
Create the TSV metadata class from a TSV file
Args:
fpath: The file path to the reference TSV file
method make_sidecar
make_sidecar()
Makes a dictionary with the default description noted in BIDS specification into the Sidecar dictionary
Returns: Dictionary with correct fields(that have values) with description of each field within TSV file filled out
method save_to_tsv
save_to_tsv(info, fpath)
Save a TSV inherited class into an output TSV file with a BIDS-compliant name in the file directory designated by the user
Args:
- <b>`info`</b>: Subject info field from the Subject class
- <b>`fpath`</b>: The file path that points to the folder where we intend to save the metadata file in
Returns: Outputs a metadata TSV file with BIDS-compliant name in the specified file path
class Sidecar
NIRS Sidecar(_nirs.JSON) Metadata Class
Class object that mimics and contains the data for the _nirs.JSON metadata file
method __init__
__init__(fpath=None)
Inherited constructor for the Sidecar class
Args:
fpath: The file path to a reference SNIRF file
method change_type
change_type(name)
Change the data type restriction for a field (from a String class to a Number class or vice versa)
Args:
name: The field name
Raises:
TypeError: If it's an invalid/undeclared field
method default_fields
default_fields()
Obtain the default fields and their data type for a specific metadata file/class
Returns: The list of default fields for a specific metadata class and the data type
default_list: List of default field names for a specific metadata classdefault_type: List of default field data types for a specific metadata class
method get_class_name
get_class_name()
Obtains the name of the specific metadata class
Returns: The name of the (specific metadata) class
method get_column
get_column(name)
Obtains the value of a specified field/'column' of a Metadata class
Args:
name: Name of the field/'column'
Returns: The value of a specified field/'column' - similar to getattr
method get_column_names
get_column_names()
Get the names of the field in a specific metadata class/file that has a value(s)
Returns: A list of field names that have a value in a specific metadata file
method load_from_SNIRF
load_from_SNIRF(fpath)
Creates the Sidecar class based on information from a reference SNIRF file
Args:
fpath: The file path to the reference SNIRF file
method load_from_json
load_from_json(fpath)
Create the JSON metadata class from a JSON file
Args:
fpath: The file path to the reference JSON file
Raises:
TypeError: Incorrect data type for a specific field based on data loaded from the JSON file
method save_to_json
save_to_json(info, fpath)
Save a JSON inherited class into an output JSON file with a BIDS-compliant name in the file directory designated by the user
Args:
info: Subject info field from the Subject classfpath: The file path that points to the folder where we intend to save the metadata file in
Returns: Outputs a metadata JSON file with a BIDS-compliant name in the specified file path
class Subject
'Subject' Class
Class object that encapsulates a single 'run' (for now) with fields containing the metadata and 'subject'/run information
Attributes:
coordsystem: Contains a Coordsystem class object for a specific 'subject'/runoptodes: Contains an Optodes class object for a specific 'subject'/runchannel: Contains a Channels class object for a specific 'subject'/runsidecar: Contains a Sidecar (_nirs.JSON) class object for a specific 'subject'/runevents: Contains an Events class object for a specific 'subject'/runsubinfo: Contains the 'subject'/run information related to the data stored in a 'Subject' objectparticipants: Contains the metadata related to the participants.tsv file
method __init__
__init__(fpath=None)
Constructor for the 'Subject' class
method export
export(outputFormat: str = 'Folder', fpath: str = None)
Exports/creates the BIDS-compliant metadata files based on information stored in the 'subject' class object
Args:
outputFormat: The target destination and indirectly, the output format of the metadata file The default value is 'Folder', which outputs the metadata file to a specific file directory specified by the user The other option is 'Text', which outputs the files and data as a string (JSON-like format)fpath: The file path that points to the folder where we intend to save the metadata files in
Returns: A string containing the metadata file names and its content if the user chose the 'Text' output format or a set of metadata files in a specified folder if the user chose the default or 'Folder' output format
method get_ses
get_ses()
Obtains the session ID/number for a particular 'subject'/run
Returns: The session ID/number (returns an empty string if there is no information)
method get_subj
get_subj()
Obtains the subject ID/number for a particular 'subject'/run
Returns: The subject ID/number (returns an empty string if there is no information)
method load_from_snirf
load_from_snirf(fpath)
Loads the metadata from a reference SNIRF file
Args:
fpath: The file path to the reference SNIRF file
method pull_fnames
pull_fnames()
Check directory for files (not folders)
Returns: A dictionary of file names for specific metadata files based on the existence of a session label (different nomenclature) that are split into subject-level and session-level metadata files
subj_fnames: Contains a dictionary of metadata filenames that are on the subject levelses_fnames: Contains a dictionary of metadata filenames that are on the session level
Notes:
Have to figure out how to do this based on the database structure In the case of the test snirf file, there is no presence of: 1. session number 2. run number
method pull_task
pull_task(fpath=None)
Pull the Task label from either the SNIRF file name or from the Sidecar class (if available)
Args:
fpath: The file path to the reference SNIRF file
Returns: The task label/name
This file was automatically generated via lazydocs.
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