niwrap-mrtrix 0.8.0__py3-none-any.whl

niwrap_mrtrix/mrtrix/sh2peaks.py

@@ -0,0 +1,632 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+SH2PEAKS_METADATA = Metadata(
+    id="1cf460ab2a2a452d9f75103cade5ef23706312a1.boutiques",
+    name="sh2peaks",
+    package="mrtrix",
+    container_image_tag="mrtrix3/mrtrix3:3.0.4",
+)
+
+
+_Sh2peaksDirectionParamsDictNoTag = typing.TypedDict('_Sh2peaksDirectionParamsDictNoTag', {
+    "phi": float,
+    "theta": float,
+})
+Sh2peaksDirectionParamsDictTagged = typing.TypedDict('Sh2peaksDirectionParamsDictTagged', {
+    "@type": typing.Literal["direction"],
+    "phi": float,
+    "theta": float,
+})
+Sh2peaksDirectionParamsDict = _Sh2peaksDirectionParamsDictNoTag | Sh2peaksDirectionParamsDictTagged
+
+
+_Sh2peaksConfigParamsDictNoTag = typing.TypedDict('_Sh2peaksConfigParamsDictNoTag', {
+    "key": str,
+    "value": str,
+})
+Sh2peaksConfigParamsDictTagged = typing.TypedDict('Sh2peaksConfigParamsDictTagged', {
+    "@type": typing.Literal["config"],
+    "key": str,
+    "value": str,
+})
+Sh2peaksConfigParamsDict = _Sh2peaksConfigParamsDictNoTag | Sh2peaksConfigParamsDictTagged
+
+
+_Sh2peaksParamsDictNoTag = typing.TypedDict('_Sh2peaksParamsDictNoTag', {
+    "num": typing.NotRequired[int | None],
+    "direction": typing.NotRequired[list[Sh2peaksDirectionParamsDict] | None],
+    "peaks": typing.NotRequired[InputPathType | None],
+    "threshold": typing.NotRequired[float | None],
+    "seeds": typing.NotRequired[InputPathType | None],
+    "mask": typing.NotRequired[InputPathType | None],
+    "fast": bool,
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[Sh2peaksConfigParamsDict] | None],
+    "help": bool,
+    "version": bool,
+    "SH": InputPathType,
+    "output": str,
+})
+Sh2peaksParamsDictTagged = typing.TypedDict('Sh2peaksParamsDictTagged', {
+    "@type": typing.Literal["mrtrix/sh2peaks"],
+    "num": typing.NotRequired[int | None],
+    "direction": typing.NotRequired[list[Sh2peaksDirectionParamsDict] | None],
+    "peaks": typing.NotRequired[InputPathType | None],
+    "threshold": typing.NotRequired[float | None],
+    "seeds": typing.NotRequired[InputPathType | None],
+    "mask": typing.NotRequired[InputPathType | None],
+    "fast": bool,
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[Sh2peaksConfigParamsDict] | None],
+    "help": bool,
+    "version": bool,
+    "SH": InputPathType,
+    "output": str,
+})
+Sh2peaksParamsDict = _Sh2peaksParamsDictNoTag | Sh2peaksParamsDictTagged
+
+
+def sh2peaks_direction(
+    phi: float,
+    theta: float,
+) -> Sh2peaksDirectionParamsDictTagged:
+    """
+    Build parameters.
+    
+    Args:
+        phi: the direction of a peak to estimate. The algorithm will attempt to\
+            find the same number of peaks as have been specified using this option.
+        theta: the direction of a peak to estimate. The algorithm will attempt\
+            to find the same number of peaks as have been specified using this\
+            option.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "@type": "direction",
+        "phi": phi,
+        "theta": theta,
+    }
+    return params
+
+
+def sh2peaks_direction_validate(
+    params: typing.Any,
+) -> None:
+    """
+    Validate parameters. Throws an error if `params` is not a valid
+    `Sh2peaksDirectionParamsDict` 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("phi", None) is None:
+        raise StyxValidationError("`phi` must not be None")
+    if not isinstance(params["phi"], (float, int)):
+        raise StyxValidationError(f'`phi` has the wrong type: Received `{type(params.get("phi", None))}` expected `float`')
+    if params.get("theta", None) is None:
+        raise StyxValidationError("`theta` must not be None")
+    if not isinstance(params["theta"], (float, int)):
+        raise StyxValidationError(f'`theta` has the wrong type: Received `{type(params.get("theta", None))}` expected `float`')
+
+
+def sh2peaks_direction_cargs(
+    params: Sh2peaksDirectionParamsDict,
+    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("-direction")
+    cargs.append(str(params.get("phi", None)))
+    cargs.append(str(params.get("theta", None)))
+    return cargs
+
+
+def sh2peaks_config(
+    key: str,
+    value: str,
+) -> Sh2peaksConfigParamsDictTagged:
+    """
+    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 sh2peaks_config_validate(
+    params: typing.Any,
+) -> None:
+    """
+    Validate parameters. Throws an error if `params` is not a valid
+    `Sh2peaksConfigParamsDict` 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 sh2peaks_config_cargs(
+    params: Sh2peaksConfigParamsDict,
+    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 Sh2peaksOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `Sh2peaksParamsDict(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output: OutputPathType
+    """the output image. Each volume corresponds to the x, y & z component of
+    each peak direction vector in turn."""
+
+
+def sh2peaks_params(
+    sh: InputPathType,
+    output: str,
+    num: int | None = None,
+    direction: list[Sh2peaksDirectionParamsDict] | None = None,
+    peaks: InputPathType | None = None,
+    threshold: float | None = None,
+    seeds: InputPathType | None = None,
+    mask: InputPathType | None = None,
+    fast: bool = False,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[Sh2peaksConfigParamsDict] | None = None,
+    help_: bool = False,
+    version: bool = False,
+) -> Sh2peaksParamsDictTagged:
+    """
+    Build parameters.
+    
+    Args:
+        sh: the input image of SH coefficients.
+        output: the output image. Each volume corresponds to the x, y & z\
+            component of each peak direction vector in turn.
+        num: the number of peaks to extract (default: 3).
+        direction: the direction of a peak to estimate. The algorithm will\
+            attempt to find the same number of peaks as have been specified using\
+            this option.
+        peaks: the program will try to find the peaks that most closely match\
+            those in the image provided.
+        threshold: only peak amplitudes greater than the threshold will be\
+            considered.
+        seeds: specify a set of directions from which to start the multiple\
+            restarts of the optimisation (by default, the built-in 60 direction set\
+            is used).
+        mask: only perform computation within the specified binary brain mask\
+            image.
+        fast: use lookup table to compute associated Legendre polynomials\
+            (faster, but approximate).
+        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/sh2peaks",
+        "fast": fast,
+        "info": info,
+        "quiet": quiet,
+        "debug": debug,
+        "force": force,
+        "help": help_,
+        "version": version,
+        "SH": sh,
+        "output": output,
+    }
+    if num is not None:
+        params["num"] = num
+    if direction is not None:
+        params["direction"] = direction
+    if peaks is not None:
+        params["peaks"] = peaks
+    if threshold is not None:
+        params["threshold"] = threshold
+    if seeds is not None:
+        params["seeds"] = seeds
+    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 sh2peaks_validate(
+    params: typing.Any,
+) -> None:
+    """
+    Validate parameters. Throws an error if `params` is not a valid
+    `Sh2peaksParamsDict` 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("num", None) is not None:
+        if not isinstance(params["num"], int):
+            raise StyxValidationError(f'`num` has the wrong type: Received `{type(params.get("num", None))}` expected `int | None`')
+    if params.get("direction", None) is not None:
+        if not isinstance(params["direction"], list):
+            raise StyxValidationError(f'`direction` has the wrong type: Received `{type(params.get("direction", None))}` expected `list[Sh2peaksDirectionParamsDict] | None`')
+        for e in params["direction"]:
+            sh2peaks_direction_validate(e)
+    if params.get("peaks", None) is not None:
+        if not isinstance(params["peaks"], (pathlib.Path, str)):
+            raise StyxValidationError(f'`peaks` has the wrong type: Received `{type(params.get("peaks", None))}` expected `InputPathType | None`')
+    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("seeds", None) is not None:
+        if not isinstance(params["seeds"], (pathlib.Path, str)):
+            raise StyxValidationError(f'`seeds` has the wrong type: Received `{type(params.get("seeds", None))}` expected `InputPathType | 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("fast", False) is None:
+        raise StyxValidationError("`fast` must not be None")
+    if not isinstance(params["fast"], bool):
+        raise StyxValidationError(f'`fast` has the wrong type: Received `{type(params.get("fast", 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[Sh2peaksConfigParamsDict] | None`')
+        for e in params["config"]:
+            sh2peaks_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("SH", None) is None:
+        raise StyxValidationError("`SH` must not be None")
+    if not isinstance(params["SH"], (pathlib.Path, str)):
+        raise StyxValidationError(f'`SH` has the wrong type: Received `{type(params.get("SH", None))}` expected `InputPathType`')
+    if params.get("output", None) is None:
+        raise StyxValidationError("`output` must not be None")
+    if not isinstance(params["output"], str):
+        raise StyxValidationError(f'`output` has the wrong type: Received `{type(params.get("output", None))}` expected `str`')
+
+
+def sh2peaks_cargs(
+    params: Sh2peaksParamsDict,
+    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("sh2peaks")
+    if params.get("num", None) is not None:
+        cargs.extend([
+            "-num",
+            str(params.get("num", None))
+        ])
+    if params.get("direction", None) is not None:
+        cargs.extend([a for c in [sh2peaks_direction_cargs(s, execution) for s in params.get("direction", None)] for a in c])
+    if params.get("peaks", None) is not None:
+        cargs.extend([
+            "-peaks",
+            execution.input_file(params.get("peaks", None))
+        ])
+    if params.get("threshold", None) is not None:
+        cargs.extend([
+            "-threshold",
+            str(params.get("threshold", None))
+        ])
+    if params.get("seeds", None) is not None:
+        cargs.extend([
+            "-seeds",
+            execution.input_file(params.get("seeds", None))
+        ])
+    if params.get("mask", None) is not None:
+        cargs.extend([
+            "-mask",
+            execution.input_file(params.get("mask", None))
+        ])
+    if params.get("fast", False):
+        cargs.append("-fast")
+    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 [sh2peaks_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("SH", None)))
+    cargs.append(params.get("output", None))
+    return cargs
+
+
+def sh2peaks_outputs(
+    params: Sh2peaksParamsDict,
+    execution: Execution,
+) -> Sh2peaksOutputs:
+    """
+    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 = Sh2peaksOutputs(
+        root=execution.output_file("."),
+        output=execution.output_file(params.get("output", None)),
+    )
+    return ret
+
+
+def sh2peaks_execute(
+    params: Sh2peaksParamsDict,
+    runner: Runner | None = None,
+) -> Sh2peaksOutputs:
+    """
+    sh2peaks
+    
+    Extract the peaks of a spherical harmonic function in each voxel.
+    
+    Peaks of the spherical harmonic function in each voxel are located by
+    commencing a Newton search along each of a set of pre-specified directions
+    
+    The spherical harmonic coefficients are stored according the conventions
+    described the main documentation, which can be found at the following link:
+    https://mrtrix.readthedocs.io/en/3.0.4/concepts/spherical_harmonics.html
+    
+    References:
+    
+    Jeurissen, B.; Leemans, A.; Tournier, J.-D.; Jones, D.K.; Sijbers, J.
+    Investigating the prevalence of complex fiber configurations in white matter
+    tissue with diffusion magnetic resonance imaging. Human Brain Mapping, 2013,
+    34(11), 2747-2766.
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        params: The parameters.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `Sh2peaksOutputs`).
+    """
+    sh2peaks_validate(params)
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(SH2PEAKS_METADATA)
+    params = execution.params(params)
+    cargs = sh2peaks_cargs(params, execution)
+    ret = sh2peaks_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def sh2peaks(
+    sh: InputPathType,
+    output: str,
+    num: int | None = None,
+    direction: list[Sh2peaksDirectionParamsDict] | None = None,
+    peaks: InputPathType | None = None,
+    threshold: float | None = None,
+    seeds: InputPathType | None = None,
+    mask: InputPathType | None = None,
+    fast: bool = False,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[Sh2peaksConfigParamsDict] | None = None,
+    help_: bool = False,
+    version: bool = False,
+    runner: Runner | None = None,
+) -> Sh2peaksOutputs:
+    """
+    sh2peaks
+    
+    Extract the peaks of a spherical harmonic function in each voxel.
+    
+    Peaks of the spherical harmonic function in each voxel are located by
+    commencing a Newton search along each of a set of pre-specified directions
+    
+    The spherical harmonic coefficients are stored according the conventions
+    described the main documentation, which can be found at the following link:
+    https://mrtrix.readthedocs.io/en/3.0.4/concepts/spherical_harmonics.html
+    
+    References:
+    
+    Jeurissen, B.; Leemans, A.; Tournier, J.-D.; Jones, D.K.; Sijbers, J.
+    Investigating the prevalence of complex fiber configurations in white matter
+    tissue with diffusion magnetic resonance imaging. Human Brain Mapping, 2013,
+    34(11), 2747-2766.
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        sh: the input image of SH coefficients.
+        output: the output image. Each volume corresponds to the x, y & z\
+            component of each peak direction vector in turn.
+        num: the number of peaks to extract (default: 3).
+        direction: the direction of a peak to estimate. The algorithm will\
+            attempt to find the same number of peaks as have been specified using\
+            this option.
+        peaks: the program will try to find the peaks that most closely match\
+            those in the image provided.
+        threshold: only peak amplitudes greater than the threshold will be\
+            considered.
+        seeds: specify a set of directions from which to start the multiple\
+            restarts of the optimisation (by default, the built-in 60 direction set\
+            is used).
+        mask: only perform computation within the specified binary brain mask\
+            image.
+        fast: use lookup table to compute associated Legendre polynomials\
+            (faster, but approximate).
+        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 `Sh2peaksOutputs`).
+    """
+    params = sh2peaks_params(
+        num=num,
+        direction=direction,
+        peaks=peaks,
+        threshold=threshold,
+        seeds=seeds,
+        mask=mask,
+        fast=fast,
+        info=info,
+        quiet=quiet,
+        debug=debug,
+        force=force,
+        nthreads=nthreads,
+        config=config,
+        help_=help_,
+        version=version,
+        sh=sh,
+        output=output,
+    )
+    return sh2peaks_execute(params, runner)
+
+
+__all__ = [
+    "SH2PEAKS_METADATA",
+    "Sh2peaksConfigParamsDict",
+    "Sh2peaksConfigParamsDictTagged",
+    "Sh2peaksDirectionParamsDict",
+    "Sh2peaksDirectionParamsDictTagged",
+    "Sh2peaksOutputs",
+    "Sh2peaksParamsDict",
+    "Sh2peaksParamsDictTagged",
+    "sh2peaks",
+    "sh2peaks_config",
+    "sh2peaks_direction",
+    "sh2peaks_execute",
+    "sh2peaks_params",
+]