oxytcmri.infrastructure.cli

Command line interface.

Classes:

Name	Description
CLIOptionFactory	Factory class for creating Typer CLI options with consistent parameters.
DatabaseSetup	Utility class for database configuration.
CLIArgumentParser	Parser for CLI arguments with support for various data types.
ControllerFactory	Factory for creating controllers with appropriate configurations.
BaseDTICommand	Abstract base class defining the common workflow for DTI commands.
ComputeDTINormativeValuesCommand	Command to compute DTI normative values.
SegmentDTILesionsCommand	Command to segment DTI lesions.
ComputeBrainLesionsVolumesCommand	Command to compute brain lesions volumes.
LoadData	Command to load data into the database.

Functions:

Name	Description
load_data	Load data into the database from configured importers.
compute_dti_normative_values	Compute DTI normative values for all centers and store the results in the database.
segment_dti_lesions	Segment DTI lesions based on normative values.
compute_brain_lesions_volumes	Compute brain lesions volumes for specified DTI metrics and MRI exam.

Attributes:

Name	Type	Description
command_line_interface

command_line_interface = typer.Typer(add_completion=False) module-attribute

CLIOptionFactory

Factory class for creating Typer CLI options with consistent parameters.

Methods:

Name	Description
settings_option	Create a standard settings file option.
dti_metrics_option	Create a standard DTI metrics option.
statistics_strategies_option	Create a statistics strategies option.
mri_exam_id_option	Create a standard MRI exam ID option.
regions_of_interest_option	Create a regions of interest option.

settings_option() staticmethod

Create a standard settings file option.

Returns:

Type	Description
Option	Option for settings file path

Source code in oxytcmri/infrastructure/cli.py

@staticmethod
def settings_option():
    """Create a standard settings file option.

    Returns
    -------
    typer.Option
        Option for settings file path
    """
    return typer.Option(
        ...,
        "--settings",
        "-s",
        help="Path to the settings file"
    )

dti_metrics_option() staticmethod

Create a standard DTI metrics option.

Returns:

Type	Description
Option	Option for DTI metrics

Source code in oxytcmri/infrastructure/cli.py

@staticmethod
def dti_metrics_option():
    """Create a standard DTI metrics option.

    Returns
    -------
    typer.Option
        Option for DTI metrics
    """
    return typer.Option(
        None,
        "--dti-metrics",
        "-dti",
        help="Comma-separated list of DTI metrics to include in computations (e.g. 'FA,MD')"
    )

statistics_strategies_option() staticmethod

Create a statistics strategies option.

Returns:

Type	Description
Option	Option for statistics strategies

Source code in oxytcmri/infrastructure/cli.py

@staticmethod
def statistics_strategies_option():
    """Create a statistics strategies option.

    Returns
    -------
    typer.Option
        Option for statistics strategies
    """
    return typer.Option(
        None,
        "--statistics-strategies",
        "-stats",
        help="Comma-separated list of statistical strategies to include in computations (e.g. 'mean,std_dev')"
    )

mri_exam_id_option() classmethod

Create a standard MRI exam ID option.

Returns:

Type	Description
Option	Option for MRI exam ID

Source code in oxytcmri/infrastructure/cli.py

@classmethod
def mri_exam_id_option(cls):
    """
    Create a standard MRI exam ID option.

    Returns
    -------
    typer.Option
        Option for MRI exam ID
    """
    return typer.Option(
        None,
        "--mri-exam-id",
        "-mri",
        help="MRI exam ID to segment lesions"
    )

regions_of_interest_option() classmethod

Create a regions of interest option.

Returns:

Type	Description
Option	Option for regions of interest

Source code in oxytcmri/infrastructure/cli.py

@classmethod
def regions_of_interest_option(cls):
    """Create a regions of interest option.

    Returns
    -------
    typer.Option
        Option for regions of interest
    """
    return typer.Option(
        None,
        "--regions-of-interest",
        "-roi",
        help="Comma-separated list of regions of interest for volume computation (e.g. 'thalamus,corpus_callosum')"
    )

DatabaseSetup

Utility class for database configuration.

Methods:

Name	Description
create_database_gateway	Configure and return a database gateway.

create_database_gateway(settings) staticmethod

Configure and return a database gateway.

Parameters:

Name	Type	Description	Default
settings	Settings	The application settings	required

Returns:

Type	Description
SQLModelSQLiteDataGateway	Configured database gateway

Raises:

Type	Description
FileExistsError	If database file exists and overwrite_database_file is False

Source code in oxytcmri/infrastructure/cli.py

@staticmethod
def create_database_gateway(settings: Settings) -> SQLModelSQLiteDataGateway:
    """Configure and return a database gateway.

    Parameters
    ----------
    settings: Settings
        The application settings

    Returns
    -------
    SQLModelSQLiteDataGateway
        Configured database gateway

    Raises
    ------
    FileExistsError
        If database file exists and overwrite_database_file is False
    """
    sqlite_database_path = settings.database.path
    overwrite_database_file = settings.database.overwrite_data
    # Delete the existing database file if it exists and overwrite option is set to True
    if Path(sqlite_database_path).exists():
        if overwrite_database_file:
            Path(sqlite_database_path).unlink()
    else:
        # Create the database file if it does not exist
        Path(sqlite_database_path).touch()
    return SQLModelSQLiteDataGateway(sqlite_database_path)

CLIArgumentParser

Parser for CLI arguments with support for various data types.

This class centralizes the parsing logic for different types of CLI arguments, providing consistent error handling and format conversion.

Methods:

Name	Description
parse_dti_metrics	Parse DTI metrics input and return a typed list.
parse_statistics_strategies	Parse statistics strategies input and return a typed list.
parse_mri_exam_id	Parse MRI exam ID input.

parse_dti_metrics(metrics_input) staticmethod

Parse DTI metrics input and return a typed list.

Parameters:

Name	Type	Description	Default
metrics_input	Optional[List[str]]	Raw input from CLI for DTI metrics	required

Returns:

Type	Description
List[DTIMetric]	Parsed DTI metrics

Raises:

Type	Description
ValueError	If invalid metrics are provided

Source code in oxytcmri/infrastructure/cli.py

@staticmethod
def parse_dti_metrics(metrics_input: Optional[List[str]]) -> List[DTIMetric]:
    """Parse DTI metrics input and return a typed list.

    Parameters
    ----------
    metrics_input: Optional[List[str]]
        Raw input from CLI for DTI metrics

    Returns
    -------
    List[DTIMetric]
        Parsed DTI metrics

    Raises
    ------
    ValueError
        If invalid metrics are provided
    """
    if not metrics_input:
        return []

    try:
        acronyms_list = metrics_input[0].split(',')
        return [DTIMetric.from_acronym(acronym) for acronym in acronyms_list]
    except KeyError:
        valid_options = ', '.join([m.name for m in DTIMetric])
        raise ValueError(f"Invalid DTI metrics. Valid options are: {valid_options}")

parse_statistics_strategies(strategies_input) staticmethod

Parse statistics strategies input and return a typed list.

Parameters:

Name	Type	Description	Default
strategies_input	Optional[List[str]]	Raw input from CLI for statistics strategies	required

Returns:

Type	Description
List[StatisticStrategy]	List of statistics strategies

Raises:

Type	Description
ValueError	If invalid strategies are provided

Source code in oxytcmri/infrastructure/cli.py

@staticmethod
def parse_statistics_strategies(strategies_input: Optional[List[str]]) -> List[StatisticStrategy]:
    """Parse statistics strategies input and return a typed list.

    Parameters
    ----------
    strategies_input: Optional[List[str]]
        Raw input from CLI for statistics strategies

    Returns
    -------
    List[StatisticStrategy]
        List of statistics strategies

    Raises
    ------
    ValueError
        If invalid strategies are provided
    """
    if not strategies_input:
        return list(StatisticsStrategies.all())

    try:
        stats_names_list = strategies_input[0].split(',')
        # Replace underscores with spaces in statistical strategy names
        stats_names_list_without_underscores = [name.replace('_', ' ') for name in stats_names_list]
        return [StatisticsStrategies.get_by_name(stat_name)
                for stat_name in stats_names_list_without_underscores]
    except ValueError:
        valid_strategies = [s.name.replace(' ', '_') for s in StatisticsStrategies.all()]
        raise ValueError(f"Invalid statistical strategies. Valid options are: {', '.join(valid_strategies)}")

parse_mri_exam_id(mri_exam_id) classmethod

Parse MRI exam ID input.

Parameters:

Name	Type	Description	Default
mri_exam_id	Optional[str]	Raw input from CLI for MRI exam ID	required

Returns:

Type	Description
Optional[str]	Parsed MRI exam ID

Source code in oxytcmri/infrastructure/cli.py

@classmethod
def parse_mri_exam_id(cls, mri_exam_id: Optional[str]) -> Optional[MRIExamId]:
    """Parse MRI exam ID input.

    Parameters
    ----------
    mri_exam_id: Optional[str]
        Raw input from CLI for MRI exam ID

    Returns
    -------
    Optional[str]
        Parsed MRI exam ID
    """
    if not mri_exam_id:
        return None
    return MRIExamId(mri_exam_id)

ControllerFactory

Factory for creating controllers with appropriate configurations.

Methods:

Name	Description
create_dti_controller	Create and configure a controller for DTI operations.

create_dti_controller(settings, database_gateway) staticmethod

Create and configure a controller for DTI operations.

Source code in oxytcmri/infrastructure/cli.py

@staticmethod
def create_dti_controller(settings: Settings,
                          database_gateway: DataBaseGateway) -> Controller:
    """Create and configure a controller for DTI operations."""
    importers = []
    if settings.database.overwrite_data:
        importers = ControllerFactory._get_configured_importers(settings)

    return Controller(
        persistence_gateway=database_gateway,
        importers=importers,
        listeners=[
            TqdmProgressListener(),
        ],
        overwrite_database=settings.database.overwrite_data
    )

BaseDTICommand(settings_filepath)

Bases: ABC

Abstract base class defining the common workflow for DTI commands.

Initialize the command with common parameters.

Parameters:

Name	Type	Description	Default
settings_filepath	str	Path to settings file	required

Methods:

Name	Description
execute	Template method defining the workflow.

Attributes:

Name	Type	Description
controller

Source code in oxytcmri/infrastructure/cli.py

def __init__(self,
             settings_filepath: str):
    """
    Initialize the command with common parameters.

    Parameters
    ----------
    settings_filepath: str
        Path to settings file
    """
    settings = Settings(settings_filepath)
    Logger(settings).setup()

    # Database setup
    database_gateway = DatabaseSetup.create_database_gateway(settings)

    # Controller setup
    self.controller = ControllerFactory.create_dti_controller(settings, database_gateway)

controller = ControllerFactory.create_dti_controller(settings, database_gateway) instance-attribute

execute() abstractmethod

Template method defining the workflow.

Source code in oxytcmri/infrastructure/cli.py

@abstractmethod
def execute(self) -> None:
    """
    Template method defining the workflow.
    """

ComputeDTINormativeValuesCommand(settings_filepath, dti_metrics=None, statistics_strategies=None)

Bases: BaseDTICommand

Command to compute DTI normative values.

Initialize the command with specific parameters.

Parameters:

Name	Type	Description	Default
settings_filepath	str	Path to settings file	required
dti_metrics	Optional[List[str]]	List of DTI metrics to compute	None
statistics_strategies	Optional[List[str]]	List of statistics strategies to use	None

Methods:

Name	Description
execute	Process the compute DTI normative values command.

Attributes:

Name	Type	Description
dti_metric_list
statistics_strategies

Source code in oxytcmri/infrastructure/cli.py

def __init__(self,
             settings_filepath: str,
             dti_metrics: Optional[List[str]] = None,
             statistics_strategies: Optional[List[str]] = None):
    """
    Initialize the command with specific parameters.

    Parameters
    ----------
    settings_filepath: str
        Path to settings file
    dti_metrics: Optional[List[str]]
        List of DTI metrics to compute
    statistics_strategies: Optional[List[str]]
        List of statistics strategies to use
    """
    super().__init__(settings_filepath)
    self.dti_metric_list = CLIArgumentParser.parse_dti_metrics(dti_metrics)
    self.statistics_strategies = CLIArgumentParser.parse_statistics_strategies(statistics_strategies)

dti_metric_list = CLIArgumentParser.parse_dti_metrics(dti_metrics) instance-attribute

statistics_strategies = CLIArgumentParser.parse_statistics_strategies(statistics_strategies) instance-attribute

execute()

Process the compute DTI normative values command.

Source code in oxytcmri/infrastructure/cli.py

def execute(self) -> None:
    """Process the compute DTI normative values command.
    """
    self.controller.compute_normative_dti_values(
        dti_metrics=self.dti_metric_list,
        statistics_strategies=self.statistics_strategies
    )

SegmentDTILesionsCommand(settings_filepath, dti_metrics=None, mri_exam_id=None)

Bases: BaseDTICommand

Command to segment DTI lesions.

Initialize the command with specific parameters.

Parameters:

Name	Type	Description	Default
settings_filepath	str	Path to settings file	required
dti_metrics	Optional[List[str]]	List of DTI metrics to segment	None
mri_exam_id	Optional[str]	MRI exam ID to segment lesions	None

Methods:

Name	Description
execute	Process the segment DTI lesions command.

Attributes:

Name	Type	Description
dti_metric_list
mri_exam_id

Source code in oxytcmri/infrastructure/cli.py

def __init__(self, settings_filepath: str,
             dti_metrics: Optional[List[str]] = None,
             mri_exam_id: Optional[str] = None):
    """
    Initialize the command with specific parameters.

    Parameters
    ----------
    settings_filepath: str
        Path to settings file
    dti_metrics: Optional[List[str]]
        List of DTI metrics to segment
    mri_exam_id: Optional[str]
        MRI exam ID to segment lesions
    """
    super().__init__(settings_filepath)
    self.dti_metric_list = CLIArgumentParser.parse_dti_metrics(dti_metrics)
    self.mri_exam_id = CLIArgumentParser.parse_mri_exam_id(mri_exam_id)

dti_metric_list = CLIArgumentParser.parse_dti_metrics(dti_metrics) instance-attribute

mri_exam_id = CLIArgumentParser.parse_mri_exam_id(mri_exam_id) instance-attribute

execute()

Process the segment DTI lesions command.

Source code in oxytcmri/infrastructure/cli.py

def execute(self) -> None:
    """
    Process the segment DTI lesions command.
    """
    self.controller.segment_dti_abnormal_values(
        dti_metrics=self.dti_metric_list,
        mri_exam_id=self.mri_exam_id
    )

ComputeBrainLesionsVolumesCommand(settings_filepath, dti_metrics=None, mri_exam_id=None, regions_of_interest=None)

Bases: BaseDTICommand

Command to compute brain lesions volumes.

Initialize the command with specific parameters.

Parameters:

Name	Type	Description	Default
settings_filepath	str	Path to settings file	required
dti_metrics	Optional[List[str]]	List of DTI metrics to compute volumes for	None
mri_exam_id	Optional[str]	MRI exam ID to compute volumes for	None
regions_of_interest	Optional[List[str]]	Regions of interest for volume computation	None

Methods:

Name	Description
execute	Process the compute brain lesions volumes command.

Attributes:

Name	Type	Description
dti_metric_list
mri_exam_id
regions_of_interest

Source code in oxytcmri/infrastructure/cli.py

def __init__(self, settings_filepath: str,
             dti_metrics: Optional[List[str]] = None,
             mri_exam_id: Optional[str] = None,
             regions_of_interest: Optional[List[str]] = None):
    """
    Initialize the command with specific parameters.

    Parameters
    ----------
    settings_filepath: str
        Path to settings file
    dti_metrics: Optional[List[str]]
        List of DTI metrics to compute volumes for
    mri_exam_id: Optional[str]
        MRI exam ID to compute volumes for
    regions_of_interest: Optional[List[str]]
        Regions of interest for volume computation
    """
    super().__init__(settings_filepath)
    self.dti_metric_list = CLIArgumentParser.parse_dti_metrics(dti_metrics)
    self.mri_exam_id = CLIArgumentParser.parse_mri_exam_id(mri_exam_id)
    self.regions_of_interest = regions_of_interest or []

dti_metric_list = CLIArgumentParser.parse_dti_metrics(dti_metrics) instance-attribute

mri_exam_id = CLIArgumentParser.parse_mri_exam_id(mri_exam_id) instance-attribute

regions_of_interest = regions_of_interest or [] instance-attribute

execute()

Process the compute brain lesions volumes command.

Source code in oxytcmri/infrastructure/cli.py

def execute(self) -> None:
    """Process the compute brain lesions volumes command."""
    self.controller.compute_brain_lesions_volumes(
        dti_metrics=self.dti_metric_list,
        mri_exam_id=self.mri_exam_id,
        regions_of_interest=[]  # TODO: Implement regions of interest parsing and handling
    )

LoadData(settings_filepath)

Bases: BaseDTICommand

Command to load data into the database.

Initialize the command with specific parameters.

Parameters:

Name	Type	Description	Default
settings_filepath	str	Path to settings file	required

Methods:

Name	Description
execute	Process the load data command.

Source code in oxytcmri/infrastructure/cli.py

def __init__(self, settings_filepath: str):
    """
    Initialize the command with specific parameters.

    Parameters
    ----------
    settings_filepath: str
        Path to settings file
    """
    super().__init__(settings_filepath)

execute()

Process the load data command.

Source code in oxytcmri/infrastructure/cli.py

def execute(self) -> None:
    """Process the load data command."""
    getLogger().info("Data loaded successfully.")

load_data(settings_filepath=CLIOptionFactory.settings_option())

Load data into the database from configured importers.

This command initializes the database and imports data from CSV files and NIfTI folders as specified in the settings.

Source code in oxytcmri/infrastructure/cli.py

@command_line_interface.command()
def load_data(
        settings_filepath: str = CLIOptionFactory.settings_option(),
):
    """Load data into the database from configured importers.

    This command initializes the database and imports data from CSV files
    and NIfTI folders as specified in the settings.
    """
    command = LoadData(settings_filepath=settings_filepath)
    command.execute()

compute_dti_normative_values(settings_filepath=CLIOptionFactory.settings_option(), dti_metrics=CLIOptionFactory.dti_metrics_option(), statistics_strategies=CLIOptionFactory.statistics_strategies_option())

Compute DTI normative values for all centers and store the results in the database.

This command processes DTI data to calculate normative values across centers for specified metrics and statistical strategies.

Source code in oxytcmri/infrastructure/cli.py

@command_line_interface.command()
def compute_dti_normative_values(
        settings_filepath: str = CLIOptionFactory.settings_option(),
        dti_metrics: Optional[List[str]] = CLIOptionFactory.dti_metrics_option(),
        statistics_strategies: Optional[List[str]] = CLIOptionFactory.statistics_strategies_option(),
):
    """Compute DTI normative values for all centers and store the results in the database.

    This command processes DTI data to calculate normative values across centers
    for specified metrics and statistical strategies.
    """
    command = ComputeDTINormativeValuesCommand(
        settings_filepath=settings_filepath,
        dti_metrics=dti_metrics,
        statistics_strategies=statistics_strategies
    )
    command.execute()

segment_dti_lesions(settings_filepath=CLIOptionFactory.settings_option(), dti_metrics=CLIOptionFactory.dti_metrics_option(), mri_exam_id=CLIOptionFactory.mri_exam_id_option())

Segment DTI lesions based on normative values.

This command uses previously computed normative values to identify and segment abnormal regions in DTI data.

Source code in oxytcmri/infrastructure/cli.py

@command_line_interface.command()
def segment_dti_lesions(
        settings_filepath: str = CLIOptionFactory.settings_option(),
        dti_metrics: Optional[List[str]] = CLIOptionFactory.dti_metrics_option(),
        mri_exam_id: Optional[str] = CLIOptionFactory.mri_exam_id_option(),
):
    """Segment DTI lesions based on normative values.

    This command uses previously computed normative values to identify
    and segment abnormal regions in DTI data.
    """
    command = SegmentDTILesionsCommand(
        settings_filepath=settings_filepath,
        dti_metrics=dti_metrics,
        mri_exam_id=mri_exam_id
    )
    command.execute()

compute_brain_lesions_volumes(settings_filepath=CLIOptionFactory.settings_option(), dti_metrics=CLIOptionFactory.dti_metrics_option(), mri_exam_id=CLIOptionFactory.mri_exam_id_option(), regions_of_interest=CLIOptionFactory.regions_of_interest_option())

Compute brain lesions volumes for specified DTI metrics and MRI exam.

This command calculates the volumes of brain lesions based on DTI metrics and specified regions of interest.

Source code in oxytcmri/infrastructure/cli.py

@command_line_interface.command()
def compute_brain_lesions_volumes(
        settings_filepath: str = CLIOptionFactory.settings_option(),
        dti_metrics: Optional[List[str]] = CLIOptionFactory.dti_metrics_option(),
        mri_exam_id: Optional[str] = CLIOptionFactory.mri_exam_id_option(),
        regions_of_interest: Optional[List[str]] = CLIOptionFactory.regions_of_interest_option(),
):
    """Compute brain lesions volumes for specified DTI metrics and MRI exam.

    This command calculates the volumes of brain lesions based on DTI metrics
    and specified regions of interest.
    """
    command = ComputeBrainLesionsVolumesCommand(
        settings_filepath=settings_filepath,
        dti_metrics=dti_metrics,
        mri_exam_id=mri_exam_id,
        regions_of_interest=regions_of_interest
    )
    command.execute()