niwrap-mrtrix 0.5.0__py3-none-any.whl

niwrap_mrtrix/mrtrix/amp2response.py

@@ -0,0 +1,453 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+AMP2RESPONSE_METADATA = Metadata(
+    id="45d8955b40d231d0262470246ab11182cd79fcb5.boutiques",
+    name="amp2response",
+    package="mrtrix",
+    container_image_tag="mrtrix3/mrtrix3:3.0.4",
+)
+
+
+Amp2responseConfigParameters = typing.TypedDict('Amp2responseConfigParameters', {
+    "__STYX_TYPE__": typing.Literal["config"],
+    "key": str,
+    "value": str,
+})
+
+
+Amp2responseParameters = typing.TypedDict('Amp2responseParameters', {
+    "__STYX_TYPE__": typing.Literal["amp2response"],
+    "isotropic": bool,
+    "noconstraint": bool,
+    "directions": typing.NotRequired[InputPathType | None],
+    "shells": typing.NotRequired[list[float] | None],
+    "lmax": typing.NotRequired[list[int] | None],
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[Amp2responseConfigParameters] | None],
+    "help": bool,
+    "version": bool,
+    "amps": InputPathType,
+    "mask": InputPathType,
+    "directions_1": InputPathType,
+    "response": str,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "amp2response": amp2response_cargs,
+        "config": amp2response_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 {
+        "amp2response": amp2response_outputs,
+    }.get(t)
+
+
+def amp2response_config_params(
+    key: str,
+    value: str,
+) -> Amp2responseConfigParameters:
+    """
+    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 amp2response_config_cargs(
+    params: Amp2responseConfigParameters,
+    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 Amp2responseOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `amp2response(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    response: OutputPathType
+    """the output zonal spherical harmonic coefficients"""
+
+
+def amp2response_params(
+    amps: InputPathType,
+    mask: InputPathType,
+    directions_1: InputPathType,
+    response: str,
+    isotropic: bool = False,
+    noconstraint: bool = False,
+    directions: InputPathType | None = None,
+    shells: list[float] | None = None,
+    lmax: list[int] | None = None,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[Amp2responseConfigParameters] | None = None,
+    help_: bool = False,
+    version: bool = False,
+) -> Amp2responseParameters:
+    """
+    Build parameters.
+    
+    Args:
+        amps: the amplitudes image.
+        mask: the mask containing the voxels from which to estimate the\
+            response function.
+        directions_1: a 4D image containing the estimated fibre directions.
+        response: the output zonal spherical harmonic coefficients.
+        isotropic: estimate an isotropic response function (lmax=0 for all\
+            shells).
+        noconstraint: disable the non-negativity and monotonicity constraints.
+        directions: provide an external text file containing the directions\
+            along which the amplitudes are sampled.
+        shells: specify one or more b-values to use during processing, as a\
+            comma-separated list of the desired approximate b-values (b-values are\
+            clustered to allow for small deviations). Note that some commands are\
+            incompatible with multiple b-values, and will report an error if more\
+            than one b-value is provided.\
+            WARNING: note that, even though the b=0 volumes are never referred\
+            to as shells in the literature, they still have to be explicitly\
+            included in the list of b-values as provided to the -shell option!\
+            Several algorithms which include the b=0 volumes in their\
+            computations may otherwise return an undesired result.
+        lmax: specify the maximum harmonic degree of the response function to\
+            estimate (can be a comma-separated list for multi-shell data).
+        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__": "amp2response",
+        "isotropic": isotropic,
+        "noconstraint": noconstraint,
+        "info": info,
+        "quiet": quiet,
+        "debug": debug,
+        "force": force,
+        "help": help_,
+        "version": version,
+        "amps": amps,
+        "mask": mask,
+        "directions_1": directions_1,
+        "response": response,
+    }
+    if directions is not None:
+        params["directions"] = directions
+    if shells is not None:
+        params["shells"] = shells
+    if lmax is not None:
+        params["lmax"] = lmax
+    if nthreads is not None:
+        params["nthreads"] = nthreads
+    if config is not None:
+        params["config"] = config
+    return params
+
+
+def amp2response_cargs(
+    params: Amp2responseParameters,
+    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("amp2response")
+    if params.get("isotropic"):
+        cargs.append("-isotropic")
+    if params.get("noconstraint"):
+        cargs.append("-noconstraint")
+    if params.get("directions") is not None:
+        cargs.extend([
+            "-directions",
+            execution.input_file(params.get("directions"))
+        ])
+    if params.get("shells") is not None:
+        cargs.extend([
+            "-shells",
+            ",".join(map(str, params.get("shells")))
+        ])
+    if params.get("lmax") is not None:
+        cargs.extend([
+            "-lmax",
+            ",".join(map(str, params.get("lmax")))
+        ])
+    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("amps")))
+    cargs.append(execution.input_file(params.get("mask")))
+    cargs.append(execution.input_file(params.get("directions_1")))
+    cargs.append(params.get("response"))
+    return cargs
+
+
+def amp2response_outputs(
+    params: Amp2responseParameters,
+    execution: Execution,
+) -> Amp2responseOutputs:
+    """
+    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 = Amp2responseOutputs(
+        root=execution.output_file("."),
+        response=execution.output_file(params.get("response")),
+    )
+    return ret
+
+
+def amp2response_execute(
+    params: Amp2responseParameters,
+    execution: Execution,
+) -> Amp2responseOutputs:
+    """
+    Estimate response function coefficients based on the DWI signal in single-fibre
+    voxels.
+    
+    This command uses the image data from all selected single-fibre voxels
+    concurrently, rather than simply averaging their individual spherical
+    harmonic coefficients. It also ensures that the response function is
+    non-negative, and monotonic (i.e. its amplitude must increase from the fibre
+    direction out to the orthogonal plane).
+    
+    If multi-shell data are provided, and one or more b-value shells are not
+    explicitly requested, the command will generate a response function for
+    every b-value shell (including b=0 if present).
+    
+    References:
+    
+    Smith, R. E.; Dhollander, T. & Connelly, A. Constrained linear least squares
+    estimation of anisotropic response function for spherical deconvolution.
+    ISMRM Workshop on Breaking the Barriers of Diffusion MRI, 23.
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `Amp2responseOutputs`).
+    """
+    params = execution.params(params)
+    cargs = amp2response_cargs(params, execution)
+    ret = amp2response_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def amp2response(
+    amps: InputPathType,
+    mask: InputPathType,
+    directions_1: InputPathType,
+    response: str,
+    isotropic: bool = False,
+    noconstraint: bool = False,
+    directions: InputPathType | None = None,
+    shells: list[float] | None = None,
+    lmax: list[int] | None = None,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[Amp2responseConfigParameters] | None = None,
+    help_: bool = False,
+    version: bool = False,
+    runner: Runner | None = None,
+) -> Amp2responseOutputs:
+    """
+    Estimate response function coefficients based on the DWI signal in single-fibre
+    voxels.
+    
+    This command uses the image data from all selected single-fibre voxels
+    concurrently, rather than simply averaging their individual spherical
+    harmonic coefficients. It also ensures that the response function is
+    non-negative, and monotonic (i.e. its amplitude must increase from the fibre
+    direction out to the orthogonal plane).
+    
+    If multi-shell data are provided, and one or more b-value shells are not
+    explicitly requested, the command will generate a response function for
+    every b-value shell (including b=0 if present).
+    
+    References:
+    
+    Smith, R. E.; Dhollander, T. & Connelly, A. Constrained linear least squares
+    estimation of anisotropic response function for spherical deconvolution.
+    ISMRM Workshop on Breaking the Barriers of Diffusion MRI, 23.
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        amps: the amplitudes image.
+        mask: the mask containing the voxels from which to estimate the\
+            response function.
+        directions_1: a 4D image containing the estimated fibre directions.
+        response: the output zonal spherical harmonic coefficients.
+        isotropic: estimate an isotropic response function (lmax=0 for all\
+            shells).
+        noconstraint: disable the non-negativity and monotonicity constraints.
+        directions: provide an external text file containing the directions\
+            along which the amplitudes are sampled.
+        shells: specify one or more b-values to use during processing, as a\
+            comma-separated list of the desired approximate b-values (b-values are\
+            clustered to allow for small deviations). Note that some commands are\
+            incompatible with multiple b-values, and will report an error if more\
+            than one b-value is provided.\
+            WARNING: note that, even though the b=0 volumes are never referred\
+            to as shells in the literature, they still have to be explicitly\
+            included in the list of b-values as provided to the -shell option!\
+            Several algorithms which include the b=0 volumes in their\
+            computations may otherwise return an undesired result.
+        lmax: specify the maximum harmonic degree of the response function to\
+            estimate (can be a comma-separated list for multi-shell data).
+        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 `Amp2responseOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(AMP2RESPONSE_METADATA)
+    params = amp2response_params(
+        isotropic=isotropic,
+        noconstraint=noconstraint,
+        directions=directions,
+        shells=shells,
+        lmax=lmax,
+        info=info,
+        quiet=quiet,
+        debug=debug,
+        force=force,
+        nthreads=nthreads,
+        config=config,
+        help_=help_,
+        version=version,
+        amps=amps,
+        mask=mask,
+        directions_1=directions_1,
+        response=response,
+    )
+    return amp2response_execute(params, execution)
+
+
+__all__ = [
+    "AMP2RESPONSE_METADATA",
+    "Amp2responseConfigParameters",
+    "Amp2responseOutputs",
+    "Amp2responseParameters",
+    "amp2response",
+    "amp2response_config_params",
+    "amp2response_params",
+]