niwrap-mrtrix 0.8.0__py3-none-any.whl

niwrap_mrtrix/mrtrix/fixelconnectivity.py

@@ -0,0 +1,477 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+FIXELCONNECTIVITY_METADATA = Metadata(
+    id="00a3b63e9ba975a20fec13986503b3adc2b7f0f5.boutiques",
+    name="fixelconnectivity",
+    package="mrtrix",
+    container_image_tag="mrtrix3/mrtrix3:3.0.4",
+)
+
+
+_FixelconnectivityConfigParamsDictNoTag = typing.TypedDict('_FixelconnectivityConfigParamsDictNoTag', {
+    "key": str,
+    "value": str,
+})
+FixelconnectivityConfigParamsDictTagged = typing.TypedDict('FixelconnectivityConfigParamsDictTagged', {
+    "@type": typing.Literal["config"],
+    "key": str,
+    "value": str,
+})
+FixelconnectivityConfigParamsDict = _FixelconnectivityConfigParamsDictNoTag | FixelconnectivityConfigParamsDictTagged
+
+
+_FixelconnectivityParamsDictNoTag = typing.TypedDict('_FixelconnectivityParamsDictNoTag', {
+    "threshold": typing.NotRequired[float | None],
+    "angle": typing.NotRequired[float | None],
+    "mask": typing.NotRequired[InputPathType | None],
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[FixelconnectivityConfigParamsDict] | None],
+    "help": bool,
+    "version": bool,
+    "fixel_directory": InputPathType,
+    "tracks": InputPathType,
+    "matrix": str,
+})
+FixelconnectivityParamsDictTagged = typing.TypedDict('FixelconnectivityParamsDictTagged', {
+    "@type": typing.Literal["mrtrix/fixelconnectivity"],
+    "threshold": typing.NotRequired[float | None],
+    "angle": typing.NotRequired[float | None],
+    "mask": typing.NotRequired[InputPathType | None],
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[FixelconnectivityConfigParamsDict] | None],
+    "help": bool,
+    "version": bool,
+    "fixel_directory": InputPathType,
+    "tracks": InputPathType,
+    "matrix": str,
+})
+FixelconnectivityParamsDict = _FixelconnectivityParamsDictNoTag | FixelconnectivityParamsDictTagged
+
+
+def fixelconnectivity_config(
+    key: str,
+    value: str,
+) -> FixelconnectivityConfigParamsDictTagged:
+    """
+    Build parameters.
+    
+    Args:
+        key: temporarily set the value of an MRtrix config file entry.
+        value: temporarily set the value of an MRtrix config file entry.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "@type": "config",
+        "key": key,
+        "value": value,
+    }
+    return params
+
+
+def fixelconnectivity_config_validate(
+    params: typing.Any,
+) -> None:
+    """
+    Validate parameters. Throws an error if `params` is not a valid
+    `FixelconnectivityConfigParamsDict` object.
+    
+    Args:
+        params: The parameters object to validate.
+    """
+    if params is None or not isinstance(params, dict):
+        raise StyxValidationError(f'Params object has the wrong type \'{type(params)}\'')
+    if params.get("key", None) is None:
+        raise StyxValidationError("`key` must not be None")
+    if not isinstance(params["key"], str):
+        raise StyxValidationError(f'`key` has the wrong type: Received `{type(params.get("key", None))}` expected `str`')
+    if params.get("value", None) is None:
+        raise StyxValidationError("`value` must not be None")
+    if not isinstance(params["value"], str):
+        raise StyxValidationError(f'`value` has the wrong type: Received `{type(params.get("value", None))}` expected `str`')
+
+
+def fixelconnectivity_config_cargs(
+    params: FixelconnectivityConfigParamsDict,
+    execution: Execution,
+) -> list[str]:
+    """
+    Build command-line arguments from parameters.
+    
+    Args:
+        params: The parameters.
+        execution: The execution object for resolving input paths.
+    Returns:
+        Command-line arguments.
+    """
+    cargs = []
+    cargs.append("-config")
+    cargs.append(params.get("key", None))
+    cargs.append(params.get("value", None))
+    return cargs
+
+
+class FixelconnectivityOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `FixelconnectivityParamsDict(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    matrix: OutputPathType
+    """the output fixel-fixel connectivity matrix directory path"""
+
+
+def fixelconnectivity_params(
+    fixel_directory: InputPathType,
+    tracks: InputPathType,
+    matrix: str,
+    threshold: float | None = None,
+    angle: float | None = None,
+    mask: InputPathType | None = None,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[FixelconnectivityConfigParamsDict] | None = None,
+    help_: bool = False,
+    version: bool = False,
+) -> FixelconnectivityParamsDictTagged:
+    """
+    Build parameters.
+    
+    Args:
+        fixel_directory: the directory containing the fixels between which\
+            connectivity will be quantified.
+        tracks: the tracks used to determine fixel-fixel connectivity.
+        matrix: the output fixel-fixel connectivity matrix directory path.
+        threshold: a threshold to define the required fraction of shared\
+            connections to be included in the neighbourhood (default: 0.01).
+        angle: the max angle threshold for assigning streamline tangents to\
+            fixels (Default: 45 degrees).
+        mask: provide a fixel data file containing a mask of those fixels to be\
+            computed; fixels outside the mask will be empty in the output matrix.
+        info: display information messages.
+        quiet: do not display information messages or progress status;\
+            alternatively, this can be achieved by setting the MRTRIX_QUIET\
+            environment variable to a non-empty string.
+        debug: display debugging messages.
+        force: force overwrite of output files (caution: using the same file as\
+            input and output might cause unexpected behaviour).
+        nthreads: use this number of threads in multi-threaded applications\
+            (set to 0 to disable multi-threading).
+        config: temporarily set the value of an MRtrix config file entry.
+        help_: display this information page and exit.
+        version: display version information and exit.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "@type": "mrtrix/fixelconnectivity",
+        "info": info,
+        "quiet": quiet,
+        "debug": debug,
+        "force": force,
+        "help": help_,
+        "version": version,
+        "fixel_directory": fixel_directory,
+        "tracks": tracks,
+        "matrix": matrix,
+    }
+    if threshold is not None:
+        params["threshold"] = threshold
+    if angle is not None:
+        params["angle"] = angle
+    if mask is not None:
+        params["mask"] = mask
+    if nthreads is not None:
+        params["nthreads"] = nthreads
+    if config is not None:
+        params["config"] = config
+    return params
+
+
+def fixelconnectivity_validate(
+    params: typing.Any,
+) -> None:
+    """
+    Validate parameters. Throws an error if `params` is not a valid
+    `FixelconnectivityParamsDict` object.
+    
+    Args:
+        params: The parameters object to validate.
+    """
+    if params is None or not isinstance(params, dict):
+        raise StyxValidationError(f'Params object has the wrong type \'{type(params)}\'')
+    if params.get("threshold", None) is not None:
+        if not isinstance(params["threshold"], (float, int)):
+            raise StyxValidationError(f'`threshold` has the wrong type: Received `{type(params.get("threshold", None))}` expected `float | None`')
+    if params.get("angle", None) is not None:
+        if not isinstance(params["angle"], (float, int)):
+            raise StyxValidationError(f'`angle` has the wrong type: Received `{type(params.get("angle", None))}` expected `float | None`')
+    if params.get("mask", None) is not None:
+        if not isinstance(params["mask"], (pathlib.Path, str)):
+            raise StyxValidationError(f'`mask` has the wrong type: Received `{type(params.get("mask", None))}` expected `InputPathType | None`')
+    if params.get("info", False) is None:
+        raise StyxValidationError("`info` must not be None")
+    if not isinstance(params["info"], bool):
+        raise StyxValidationError(f'`info` has the wrong type: Received `{type(params.get("info", False))}` expected `bool`')
+    if params.get("quiet", False) is None:
+        raise StyxValidationError("`quiet` must not be None")
+    if not isinstance(params["quiet"], bool):
+        raise StyxValidationError(f'`quiet` has the wrong type: Received `{type(params.get("quiet", False))}` expected `bool`')
+    if params.get("debug", False) is None:
+        raise StyxValidationError("`debug` must not be None")
+    if not isinstance(params["debug"], bool):
+        raise StyxValidationError(f'`debug` has the wrong type: Received `{type(params.get("debug", False))}` expected `bool`')
+    if params.get("force", False) is None:
+        raise StyxValidationError("`force` must not be None")
+    if not isinstance(params["force"], bool):
+        raise StyxValidationError(f'`force` has the wrong type: Received `{type(params.get("force", False))}` expected `bool`')
+    if params.get("nthreads", None) is not None:
+        if not isinstance(params["nthreads"], int):
+            raise StyxValidationError(f'`nthreads` has the wrong type: Received `{type(params.get("nthreads", None))}` expected `int | None`')
+    if params.get("config", None) is not None:
+        if not isinstance(params["config"], list):
+            raise StyxValidationError(f'`config` has the wrong type: Received `{type(params.get("config", None))}` expected `list[FixelconnectivityConfigParamsDict] | None`')
+        for e in params["config"]:
+            fixelconnectivity_config_validate(e)
+    if params.get("help", False) is None:
+        raise StyxValidationError("`help` must not be None")
+    if not isinstance(params["help"], bool):
+        raise StyxValidationError(f'`help` has the wrong type: Received `{type(params.get("help", False))}` expected `bool`')
+    if params.get("version", False) is None:
+        raise StyxValidationError("`version` must not be None")
+    if not isinstance(params["version"], bool):
+        raise StyxValidationError(f'`version` has the wrong type: Received `{type(params.get("version", False))}` expected `bool`')
+    if params.get("fixel_directory", None) is None:
+        raise StyxValidationError("`fixel_directory` must not be None")
+    if not isinstance(params["fixel_directory"], (pathlib.Path, str)):
+        raise StyxValidationError(f'`fixel_directory` has the wrong type: Received `{type(params.get("fixel_directory", None))}` expected `InputPathType`')
+    if params.get("tracks", None) is None:
+        raise StyxValidationError("`tracks` must not be None")
+    if not isinstance(params["tracks"], (pathlib.Path, str)):
+        raise StyxValidationError(f'`tracks` has the wrong type: Received `{type(params.get("tracks", None))}` expected `InputPathType`')
+    if params.get("matrix", None) is None:
+        raise StyxValidationError("`matrix` must not be None")
+    if not isinstance(params["matrix"], str):
+        raise StyxValidationError(f'`matrix` has the wrong type: Received `{type(params.get("matrix", None))}` expected `str`')
+
+
+def fixelconnectivity_cargs(
+    params: FixelconnectivityParamsDict,
+    execution: Execution,
+) -> list[str]:
+    """
+    Build command-line arguments from parameters.
+    
+    Args:
+        params: The parameters.
+        execution: The execution object for resolving input paths.
+    Returns:
+        Command-line arguments.
+    """
+    cargs = []
+    cargs.append("fixelconnectivity")
+    if params.get("threshold", None) is not None:
+        cargs.extend([
+            "-threshold",
+            str(params.get("threshold", None))
+        ])
+    if params.get("angle", None) is not None:
+        cargs.extend([
+            "-angle",
+            str(params.get("angle", None))
+        ])
+    if params.get("mask", None) is not None:
+        cargs.extend([
+            "-mask",
+            execution.input_file(params.get("mask", None))
+        ])
+    if params.get("info", False):
+        cargs.append("-info")
+    if params.get("quiet", False):
+        cargs.append("-quiet")
+    if params.get("debug", False):
+        cargs.append("-debug")
+    if params.get("force", False):
+        cargs.append("-force")
+    if params.get("nthreads", None) is not None:
+        cargs.extend([
+            "-nthreads",
+            str(params.get("nthreads", None))
+        ])
+    if params.get("config", None) is not None:
+        cargs.extend([a for c in [fixelconnectivity_config_cargs(s, execution) for s in params.get("config", None)] for a in c])
+    if params.get("help", False):
+        cargs.append("-help")
+    if params.get("version", False):
+        cargs.append("-version")
+    cargs.append(execution.input_file(params.get("fixel_directory", None)))
+    cargs.append(execution.input_file(params.get("tracks", None)))
+    cargs.append(params.get("matrix", None))
+    return cargs
+
+
+def fixelconnectivity_outputs(
+    params: FixelconnectivityParamsDict,
+    execution: Execution,
+) -> FixelconnectivityOutputs:
+    """
+    Build outputs object containing output file paths and possibly stdout/stderr.
+    
+    Args:
+        params: The parameters.
+        execution: The execution object for resolving input paths.
+    Returns:
+        Outputs object.
+    """
+    ret = FixelconnectivityOutputs(
+        root=execution.output_file("."),
+        matrix=execution.output_file(params.get("matrix", None)),
+    )
+    return ret
+
+
+def fixelconnectivity_execute(
+    params: FixelconnectivityParamsDict,
+    runner: Runner | None = None,
+) -> FixelconnectivityOutputs:
+    """
+    fixelconnectivity
+    
+    Generate a fixel-fixel connectivity matrix.
+    
+    This command will generate a directory containing three images, which
+    encodes the fixel-fixel connectivity matrix. Documentation regarding this
+    format and how to use it will come in the future.
+    
+    References:
+    
+    .
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        params: The parameters.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `FixelconnectivityOutputs`).
+    """
+    fixelconnectivity_validate(params)
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(FIXELCONNECTIVITY_METADATA)
+    params = execution.params(params)
+    cargs = fixelconnectivity_cargs(params, execution)
+    ret = fixelconnectivity_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def fixelconnectivity(
+    fixel_directory: InputPathType,
+    tracks: InputPathType,
+    matrix: str,
+    threshold: float | None = None,
+    angle: float | None = None,
+    mask: InputPathType | None = None,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[FixelconnectivityConfigParamsDict] | None = None,
+    help_: bool = False,
+    version: bool = False,
+    runner: Runner | None = None,
+) -> FixelconnectivityOutputs:
+    """
+    fixelconnectivity
+    
+    Generate a fixel-fixel connectivity matrix.
+    
+    This command will generate a directory containing three images, which
+    encodes the fixel-fixel connectivity matrix. Documentation regarding this
+    format and how to use it will come in the future.
+    
+    References:
+    
+    .
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        fixel_directory: the directory containing the fixels between which\
+            connectivity will be quantified.
+        tracks: the tracks used to determine fixel-fixel connectivity.
+        matrix: the output fixel-fixel connectivity matrix directory path.
+        threshold: a threshold to define the required fraction of shared\
+            connections to be included in the neighbourhood (default: 0.01).
+        angle: the max angle threshold for assigning streamline tangents to\
+            fixels (Default: 45 degrees).
+        mask: provide a fixel data file containing a mask of those fixels to be\
+            computed; fixels outside the mask will be empty in the output matrix.
+        info: display information messages.
+        quiet: do not display information messages or progress status;\
+            alternatively, this can be achieved by setting the MRTRIX_QUIET\
+            environment variable to a non-empty string.
+        debug: display debugging messages.
+        force: force overwrite of output files (caution: using the same file as\
+            input and output might cause unexpected behaviour).
+        nthreads: use this number of threads in multi-threaded applications\
+            (set to 0 to disable multi-threading).
+        config: temporarily set the value of an MRtrix config file entry.
+        help_: display this information page and exit.
+        version: display version information and exit.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `FixelconnectivityOutputs`).
+    """
+    params = fixelconnectivity_params(
+        threshold=threshold,
+        angle=angle,
+        mask=mask,
+        info=info,
+        quiet=quiet,
+        debug=debug,
+        force=force,
+        nthreads=nthreads,
+        config=config,
+        help_=help_,
+        version=version,
+        fixel_directory=fixel_directory,
+        tracks=tracks,
+        matrix=matrix,
+    )
+    return fixelconnectivity_execute(params, runner)
+
+
+__all__ = [
+    "FIXELCONNECTIVITY_METADATA",
+    "FixelconnectivityConfigParamsDict",
+    "FixelconnectivityConfigParamsDictTagged",
+    "FixelconnectivityOutputs",
+    "FixelconnectivityParamsDict",
+    "FixelconnectivityParamsDictTagged",
+    "fixelconnectivity",
+    "fixelconnectivity_config",
+    "fixelconnectivity_execute",
+    "fixelconnectivity_params",
+]