niwrap-mrtrix 0.8.0__py3-none-any.whl

niwrap_mrtrix/mrtrix/dirgen.py

@@ -0,0 +1,514 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+DIRGEN_METADATA = Metadata(
+    id="cda69ea8a57022773ddb6022ca8ca9caa5cc0e2b.boutiques",
+    name="dirgen",
+    package="mrtrix",
+    container_image_tag="mrtrix3/mrtrix3:3.0.4",
+)
+
+
+_DirgenConfigParamsDictNoTag = typing.TypedDict('_DirgenConfigParamsDictNoTag', {
+    "key": str,
+    "value": str,
+})
+DirgenConfigParamsDictTagged = typing.TypedDict('DirgenConfigParamsDictTagged', {
+    "@type": typing.Literal["config"],
+    "key": str,
+    "value": str,
+})
+DirgenConfigParamsDict = _DirgenConfigParamsDictNoTag | DirgenConfigParamsDictTagged
+
+
+_DirgenParamsDictNoTag = typing.TypedDict('_DirgenParamsDictNoTag', {
+    "power": typing.NotRequired[int | None],
+    "niter": typing.NotRequired[int | None],
+    "restarts": typing.NotRequired[int | None],
+    "unipolar": bool,
+    "cartesian": bool,
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[DirgenConfigParamsDict] | None],
+    "help": bool,
+    "version": bool,
+    "ndir": int,
+    "dirs": str,
+})
+DirgenParamsDictTagged = typing.TypedDict('DirgenParamsDictTagged', {
+    "@type": typing.Literal["mrtrix/dirgen"],
+    "power": typing.NotRequired[int | None],
+    "niter": typing.NotRequired[int | None],
+    "restarts": typing.NotRequired[int | None],
+    "unipolar": bool,
+    "cartesian": bool,
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[DirgenConfigParamsDict] | None],
+    "help": bool,
+    "version": bool,
+    "ndir": int,
+    "dirs": str,
+})
+DirgenParamsDict = _DirgenParamsDictNoTag | DirgenParamsDictTagged
+
+
+def dirgen_config(
+    key: str,
+    value: str,
+) -> DirgenConfigParamsDictTagged:
+    """
+    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 dirgen_config_validate(
+    params: typing.Any,
+) -> None:
+    """
+    Validate parameters. Throws an error if `params` is not a valid
+    `DirgenConfigParamsDict` 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 dirgen_config_cargs(
+    params: DirgenConfigParamsDict,
+    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 DirgenOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `DirgenParamsDict(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    dirs: OutputPathType
+    """the text file to write the directions to, as [ az el ] pairs."""
+
+
+def dirgen_params(
+    ndir: int,
+    dirs: str,
+    power: int | None = None,
+    niter: int | None = None,
+    restarts: int | None = None,
+    unipolar: bool = False,
+    cartesian: bool = False,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[DirgenConfigParamsDict] | None = None,
+    help_: bool = False,
+    version: bool = False,
+) -> DirgenParamsDictTagged:
+    """
+    Build parameters.
+    
+    Args:
+        ndir: the number of directions to generate.
+        dirs: the text file to write the directions to, as [ az el ] pairs.
+        power: specify exponent to use for repulsion power law (default: 1).\
+            This must be a power of 2 (i.e. 1, 2, 4, 8, 16, ...).
+        niter: specify the maximum number of iterations to perform (default:\
+            10000).
+        restarts: specify the number of restarts to perform (default: 10).
+        unipolar: optimise assuming a unipolar electrostatic repulsion model\
+            rather than the bipolar model normally assumed in DWI.
+        cartesian: Output the directions in Cartesian coordinates [x y z]\
+            instead of [az el].
+        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/dirgen",
+        "unipolar": unipolar,
+        "cartesian": cartesian,
+        "info": info,
+        "quiet": quiet,
+        "debug": debug,
+        "force": force,
+        "help": help_,
+        "version": version,
+        "ndir": ndir,
+        "dirs": dirs,
+    }
+    if power is not None:
+        params["power"] = power
+    if niter is not None:
+        params["niter"] = niter
+    if restarts is not None:
+        params["restarts"] = restarts
+    if nthreads is not None:
+        params["nthreads"] = nthreads
+    if config is not None:
+        params["config"] = config
+    return params
+
+
+def dirgen_validate(
+    params: typing.Any,
+) -> None:
+    """
+    Validate parameters. Throws an error if `params` is not a valid
+    `DirgenParamsDict` 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("power", None) is not None:
+        if not isinstance(params["power"], int):
+            raise StyxValidationError(f'`power` has the wrong type: Received `{type(params.get("power", None))}` expected `int | None`')
+    if params.get("niter", None) is not None:
+        if not isinstance(params["niter"], int):
+            raise StyxValidationError(f'`niter` has the wrong type: Received `{type(params.get("niter", None))}` expected `int | None`')
+    if params.get("restarts", None) is not None:
+        if not isinstance(params["restarts"], int):
+            raise StyxValidationError(f'`restarts` has the wrong type: Received `{type(params.get("restarts", None))}` expected `int | None`')
+    if params.get("unipolar", False) is None:
+        raise StyxValidationError("`unipolar` must not be None")
+    if not isinstance(params["unipolar"], bool):
+        raise StyxValidationError(f'`unipolar` has the wrong type: Received `{type(params.get("unipolar", False))}` expected `bool`')
+    if params.get("cartesian", False) is None:
+        raise StyxValidationError("`cartesian` must not be None")
+    if not isinstance(params["cartesian"], bool):
+        raise StyxValidationError(f'`cartesian` has the wrong type: Received `{type(params.get("cartesian", False))}` expected `bool`')
+    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[DirgenConfigParamsDict] | None`')
+        for e in params["config"]:
+            dirgen_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("ndir", None) is None:
+        raise StyxValidationError("`ndir` must not be None")
+    if not isinstance(params["ndir"], int):
+        raise StyxValidationError(f'`ndir` has the wrong type: Received `{type(params.get("ndir", None))}` expected `int`')
+    if params.get("dirs", None) is None:
+        raise StyxValidationError("`dirs` must not be None")
+    if not isinstance(params["dirs"], str):
+        raise StyxValidationError(f'`dirs` has the wrong type: Received `{type(params.get("dirs", None))}` expected `str`')
+
+
+def dirgen_cargs(
+    params: DirgenParamsDict,
+    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("dirgen")
+    if params.get("power", None) is not None:
+        cargs.extend([
+            "-power",
+            str(params.get("power", None))
+        ])
+    if params.get("niter", None) is not None:
+        cargs.extend([
+            "-niter",
+            str(params.get("niter", None))
+        ])
+    if params.get("restarts", None) is not None:
+        cargs.extend([
+            "-restarts",
+            str(params.get("restarts", None))
+        ])
+    if params.get("unipolar", False):
+        cargs.append("-unipolar")
+    if params.get("cartesian", False):
+        cargs.append("-cartesian")
+    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 [dirgen_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(str(params.get("ndir", None)))
+    cargs.append(params.get("dirs", None))
+    return cargs
+
+
+def dirgen_outputs(
+    params: DirgenParamsDict,
+    execution: Execution,
+) -> DirgenOutputs:
+    """
+    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 = DirgenOutputs(
+        root=execution.output_file("."),
+        dirs=execution.output_file(params.get("dirs", None)),
+    )
+    return ret
+
+
+def dirgen_execute(
+    params: DirgenParamsDict,
+    runner: Runner | None = None,
+) -> DirgenOutputs:
+    """
+    dirgen
+    
+    Generate a set of uniformly distributed directions using a bipolar
+    electrostatic repulsion model.
+    
+    Directions are distributed by analogy to an electrostatic repulsion system,
+    with each direction corresponding to a single electrostatic charge (for
+    -unipolar), or a pair of diametrically opposed charges (for the default
+    bipolar case). The energy of the system is determined based on the Coulomb
+    repulsion, which assumes the form 1/r^power, where r is the distance between
+    any pair of charges, and p is the power assumed for the repulsion law
+    (default: 1). The minimum energy state is obtained by gradient descent.
+    
+    References:
+    
+    Jones, D.; Horsfield, M. & Simmons, A. Optimal strategies for measuring
+    diffusion in anisotropic systems by magnetic resonance imaging. Magnetic
+    Resonance in Medicine, 1999, 42: 515-525
+    
+    Papadakis, N. G.; Murrills, C. D.; Hall, L. D.; Huang, C. L.-H. & Adrian
+    Carpenter, T. Minimal gradient encoding for robust estimation of diffusion
+    anisotropy. Magnetic Resonance Imaging, 2000, 18: 671-679.
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        params: The parameters.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `DirgenOutputs`).
+    """
+    dirgen_validate(params)
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(DIRGEN_METADATA)
+    params = execution.params(params)
+    cargs = dirgen_cargs(params, execution)
+    ret = dirgen_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def dirgen(
+    ndir: int,
+    dirs: str,
+    power: int | None = None,
+    niter: int | None = None,
+    restarts: int | None = None,
+    unipolar: bool = False,
+    cartesian: bool = False,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[DirgenConfigParamsDict] | None = None,
+    help_: bool = False,
+    version: bool = False,
+    runner: Runner | None = None,
+) -> DirgenOutputs:
+    """
+    dirgen
+    
+    Generate a set of uniformly distributed directions using a bipolar
+    electrostatic repulsion model.
+    
+    Directions are distributed by analogy to an electrostatic repulsion system,
+    with each direction corresponding to a single electrostatic charge (for
+    -unipolar), or a pair of diametrically opposed charges (for the default
+    bipolar case). The energy of the system is determined based on the Coulomb
+    repulsion, which assumes the form 1/r^power, where r is the distance between
+    any pair of charges, and p is the power assumed for the repulsion law
+    (default: 1). The minimum energy state is obtained by gradient descent.
+    
+    References:
+    
+    Jones, D.; Horsfield, M. & Simmons, A. Optimal strategies for measuring
+    diffusion in anisotropic systems by magnetic resonance imaging. Magnetic
+    Resonance in Medicine, 1999, 42: 515-525
+    
+    Papadakis, N. G.; Murrills, C. D.; Hall, L. D.; Huang, C. L.-H. & Adrian
+    Carpenter, T. Minimal gradient encoding for robust estimation of diffusion
+    anisotropy. Magnetic Resonance Imaging, 2000, 18: 671-679.
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        ndir: the number of directions to generate.
+        dirs: the text file to write the directions to, as [ az el ] pairs.
+        power: specify exponent to use for repulsion power law (default: 1).\
+            This must be a power of 2 (i.e. 1, 2, 4, 8, 16, ...).
+        niter: specify the maximum number of iterations to perform (default:\
+            10000).
+        restarts: specify the number of restarts to perform (default: 10).
+        unipolar: optimise assuming a unipolar electrostatic repulsion model\
+            rather than the bipolar model normally assumed in DWI.
+        cartesian: Output the directions in Cartesian coordinates [x y z]\
+            instead of [az el].
+        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 `DirgenOutputs`).
+    """
+    params = dirgen_params(
+        power=power,
+        niter=niter,
+        restarts=restarts,
+        unipolar=unipolar,
+        cartesian=cartesian,
+        info=info,
+        quiet=quiet,
+        debug=debug,
+        force=force,
+        nthreads=nthreads,
+        config=config,
+        help_=help_,
+        version=version,
+        ndir=ndir,
+        dirs=dirs,
+    )
+    return dirgen_execute(params, runner)
+
+
+__all__ = [
+    "DIRGEN_METADATA",
+    "DirgenConfigParamsDict",
+    "DirgenConfigParamsDictTagged",
+    "DirgenOutputs",
+    "DirgenParamsDict",
+    "DirgenParamsDictTagged",
+    "dirgen",
+    "dirgen_config",
+    "dirgen_execute",
+    "dirgen_params",
+]