niwrap-mrtrix 0.5.0__py3-none-any.whl

niwrap_mrtrix/mrtrix/sh2peaks.py

@@ -0,0 +1,505 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+SH2PEAKS_METADATA = Metadata(
+    id="dc59048f9a978e195396202a13dd54ccebc30173.boutiques",
+    name="sh2peaks",
+    package="mrtrix",
+    container_image_tag="mrtrix3/mrtrix3:3.0.4",
+)
+
+
+Sh2peaksDirectionParameters = typing.TypedDict('Sh2peaksDirectionParameters', {
+    "__STYX_TYPE__": typing.Literal["direction"],
+    "phi": float,
+    "theta": float,
+})
+
+
+Sh2peaksConfigParameters = typing.TypedDict('Sh2peaksConfigParameters', {
+    "__STYX_TYPE__": typing.Literal["config"],
+    "key": str,
+    "value": str,
+})
+
+
+Sh2peaksParameters = typing.TypedDict('Sh2peaksParameters', {
+    "__STYX_TYPE__": typing.Literal["sh2peaks"],
+    "num": typing.NotRequired[int | None],
+    "direction": typing.NotRequired[list[Sh2peaksDirectionParameters] | 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[Sh2peaksConfigParameters] | None],
+    "help": bool,
+    "version": bool,
+    "SH": InputPathType,
+    "output": str,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "sh2peaks": sh2peaks_cargs,
+        "direction": sh2peaks_direction_cargs,
+        "config": sh2peaks_config_cargs,
+    }.get(t)
+
+
+def dyn_outputs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build outputs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build outputs function.
+    """
+    return {
+        "sh2peaks": sh2peaks_outputs,
+    }.get(t)
+
+
+def sh2peaks_direction_params(
+    phi: float,
+    theta: float,
+) -> Sh2peaksDirectionParameters:
+    """
+    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 = {
+        "__STYXTYPE__": "direction",
+        "phi": phi,
+        "theta": theta,
+    }
+    return params
+
+
+def sh2peaks_direction_cargs(
+    params: Sh2peaksDirectionParameters,
+    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")))
+    cargs.append(str(params.get("theta")))
+    return cargs
+
+
+def sh2peaks_config_params(
+    key: str,
+    value: str,
+) -> Sh2peaksConfigParameters:
+    """
+    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 = {
+        "__STYXTYPE__": "config",
+        "key": key,
+        "value": value,
+    }
+    return params
+
+
+def sh2peaks_config_cargs(
+    params: Sh2peaksConfigParameters,
+    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"))
+    cargs.append(params.get("value"))
+    return cargs
+
+
+class Sh2peaksOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `sh2peaks(...)`.
+    """
+    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[Sh2peaksDirectionParameters] | 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[Sh2peaksConfigParameters] | None = None,
+    help_: bool = False,
+    version: bool = False,
+) -> Sh2peaksParameters:
+    """
+    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 = {
+        "__STYXTYPE__": "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_cargs(
+    params: Sh2peaksParameters,
+    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") is not None:
+        cargs.extend([
+            "-num",
+            str(params.get("num"))
+        ])
+    if params.get("direction") is not None:
+        cargs.extend([a for c in [dyn_cargs(s["__STYXTYPE__"])(s, execution) for s in params.get("direction")] for a in c])
+    if params.get("peaks") is not None:
+        cargs.extend([
+            "-peaks",
+            execution.input_file(params.get("peaks"))
+        ])
+    if params.get("threshold") is not None:
+        cargs.extend([
+            "-threshold",
+            str(params.get("threshold"))
+        ])
+    if params.get("seeds") is not None:
+        cargs.extend([
+            "-seeds",
+            execution.input_file(params.get("seeds"))
+        ])
+    if params.get("mask") is not None:
+        cargs.extend([
+            "-mask",
+            execution.input_file(params.get("mask"))
+        ])
+    if params.get("fast"):
+        cargs.append("-fast")
+    if params.get("info"):
+        cargs.append("-info")
+    if params.get("quiet"):
+        cargs.append("-quiet")
+    if params.get("debug"):
+        cargs.append("-debug")
+    if params.get("force"):
+        cargs.append("-force")
+    if params.get("nthreads") is not None:
+        cargs.extend([
+            "-nthreads",
+            str(params.get("nthreads"))
+        ])
+    if params.get("config") is not None:
+        cargs.extend([a for c in [dyn_cargs(s["__STYXTYPE__"])(s, execution) for s in params.get("config")] for a in c])
+    if params.get("help"):
+        cargs.append("-help")
+    if params.get("version"):
+        cargs.append("-version")
+    cargs.append(execution.input_file(params.get("SH")))
+    cargs.append(params.get("output"))
+    return cargs
+
+
+def sh2peaks_outputs(
+    params: Sh2peaksParameters,
+    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")),
+    )
+    return ret
+
+
+def sh2peaks_execute(
+    params: Sh2peaksParameters,
+    execution: Execution,
+) -> Sh2peaksOutputs:
+    """
+    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.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `Sh2peaksOutputs`).
+    """
+    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[Sh2peaksDirectionParameters] | 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[Sh2peaksConfigParameters] | None = None,
+    help_: bool = False,
+    version: bool = False,
+    runner: Runner | None = None,
+) -> Sh2peaksOutputs:
+    """
+    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`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(SH2PEAKS_METADATA)
+    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, execution)
+
+
+__all__ = [
+    "SH2PEAKS_METADATA",
+    "Sh2peaksConfigParameters",
+    "Sh2peaksDirectionParameters",
+    "Sh2peaksOutputs",
+    "Sh2peaksParameters",
+    "sh2peaks",
+    "sh2peaks_config_params",
+    "sh2peaks_direction_params",
+    "sh2peaks_params",
+]