niwrap-mrtrix 0.5.0__py3-none-any.whl

niwrap_mrtrix/mrtrix/amp2sh.py

@@ -0,0 +1,656 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+AMP2SH_METADATA = Metadata(
+    id="739c6dd01d401b453eb41eade05065e6c9fd17b3.boutiques",
+    name="amp2sh",
+    package="mrtrix",
+    container_image_tag="mrtrix3/mrtrix3:3.0.4",
+)
+
+
+Amp2shFslgradParameters = typing.TypedDict('Amp2shFslgradParameters', {
+    "__STYX_TYPE__": typing.Literal["fslgrad"],
+    "bvecs": InputPathType,
+    "bvals": InputPathType,
+})
+
+
+Amp2shVariousStringParameters = typing.TypedDict('Amp2shVariousStringParameters', {
+    "__STYX_TYPE__": typing.Literal["VariousString"],
+    "obj": str,
+})
+
+
+Amp2shVariousFileParameters = typing.TypedDict('Amp2shVariousFileParameters', {
+    "__STYX_TYPE__": typing.Literal["VariousFile"],
+    "obj": InputPathType,
+})
+
+
+Amp2shConfigParameters = typing.TypedDict('Amp2shConfigParameters', {
+    "__STYX_TYPE__": typing.Literal["config"],
+    "key": str,
+    "value": str,
+})
+
+
+Amp2shParameters = typing.TypedDict('Amp2shParameters', {
+    "__STYX_TYPE__": typing.Literal["amp2sh"],
+    "lmax": typing.NotRequired[int | None],
+    "normalise": bool,
+    "directions": typing.NotRequired[InputPathType | None],
+    "rician": typing.NotRequired[InputPathType | None],
+    "grad": typing.NotRequired[InputPathType | None],
+    "fslgrad": typing.NotRequired[Amp2shFslgradParameters | None],
+    "shells": typing.NotRequired[list[float] | None],
+    "strides": typing.NotRequired[typing.Union[Amp2shVariousStringParameters, Amp2shVariousFileParameters] | None],
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[Amp2shConfigParameters] | None],
+    "help": bool,
+    "version": bool,
+    "amp": InputPathType,
+    "SH": str,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "amp2sh": amp2sh_cargs,
+        "fslgrad": amp2sh_fslgrad_cargs,
+        "VariousString": amp2sh_various_string_cargs,
+        "VariousFile": amp2sh_various_file_cargs,
+        "config": amp2sh_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 {
+        "amp2sh": amp2sh_outputs,
+    }.get(t)
+
+
+def amp2sh_fslgrad_params(
+    bvecs: InputPathType,
+    bvals: InputPathType,
+) -> Amp2shFslgradParameters:
+    """
+    Build parameters.
+    
+    Args:
+        bvecs: Provide the diffusion-weighted gradient scheme used in the\
+            acquisition in FSL bvecs/bvals format files. If a diffusion gradient\
+            scheme is present in the input image header, the data provided with\
+            this option will be instead used.
+        bvals: Provide the diffusion-weighted gradient scheme used in the\
+            acquisition in FSL bvecs/bvals format files. If a diffusion gradient\
+            scheme is present in the input image header, the data provided with\
+            this option will be instead used.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "fslgrad",
+        "bvecs": bvecs,
+        "bvals": bvals,
+    }
+    return params
+
+
+def amp2sh_fslgrad_cargs(
+    params: Amp2shFslgradParameters,
+    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("-fslgrad")
+    cargs.append(execution.input_file(params.get("bvecs")))
+    cargs.append(execution.input_file(params.get("bvals")))
+    return cargs
+
+
+def amp2sh_various_string_params(
+    obj: str,
+) -> Amp2shVariousStringParameters:
+    """
+    Build parameters.
+    
+    Args:
+        obj: String object.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "VariousString",
+        "obj": obj,
+    }
+    return params
+
+
+def amp2sh_various_string_cargs(
+    params: Amp2shVariousStringParameters,
+    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(params.get("obj"))
+    return cargs
+
+
+def amp2sh_various_file_params(
+    obj: InputPathType,
+) -> Amp2shVariousFileParameters:
+    """
+    Build parameters.
+    
+    Args:
+        obj: File object.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "VariousFile",
+        "obj": obj,
+    }
+    return params
+
+
+def amp2sh_various_file_cargs(
+    params: Amp2shVariousFileParameters,
+    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(execution.input_file(params.get("obj")))
+    return cargs
+
+
+def amp2sh_config_params(
+    key: str,
+    value: str,
+) -> Amp2shConfigParameters:
+    """
+    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 amp2sh_config_cargs(
+    params: Amp2shConfigParameters,
+    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 Amp2shOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `amp2sh(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    sh: OutputPathType
+    """the output spherical harmonics coefficients image."""
+
+
+def amp2sh_params(
+    amp: InputPathType,
+    sh: str,
+    lmax: int | None = None,
+    normalise: bool = False,
+    directions: InputPathType | None = None,
+    rician: InputPathType | None = None,
+    grad: InputPathType | None = None,
+    fslgrad: Amp2shFslgradParameters | None = None,
+    shells: list[float] | None = None,
+    strides: typing.Union[Amp2shVariousStringParameters, Amp2shVariousFileParameters] | None = None,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[Amp2shConfigParameters] | None = None,
+    help_: bool = False,
+    version: bool = False,
+) -> Amp2shParameters:
+    """
+    Build parameters.
+    
+    Args:
+        amp: the input amplitude image.
+        sh: the output spherical harmonics coefficients image.
+        lmax: set the maximum harmonic order for the output series. By default,\
+            the program will use the highest possible lmax given the number of\
+            diffusion-weighted images, up to a maximum of 8.
+        normalise: normalise the DW signal to the b=0 image.
+        directions: the directions corresponding to the input amplitude image\
+            used to sample AFD. By default this option is not required providing\
+            the direction set is supplied in the amplitude image. This should be\
+            supplied as a list of directions [az el], as generated using the dirgen\
+            command, or as a list of [ x y z ] Cartesian coordinates.
+        rician: correct for Rician noise induced bias, using noise map supplied.
+        grad: Provide the diffusion-weighted gradient scheme used in the\
+            acquisition in a text file. This should be supplied as a 4xN text file\
+            with each line is in the format [ X Y Z b ], where [ X Y Z ] describe\
+            the direction of the applied gradient, and b gives the b-value in units\
+            of s/mm^2. If a diffusion gradient scheme is present in the input image\
+            header, the data provided with this option will be instead used.
+        fslgrad: Provide the diffusion-weighted gradient scheme used in the\
+            acquisition in FSL bvecs/bvals format files. If a diffusion gradient\
+            scheme is present in the input image header, the data provided with\
+            this option will be instead used.
+        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.
+        strides: specify the strides of the output data in memory; either as a\
+            comma-separated list of (signed) integers, or as a template image from\
+            which the strides shall be extracted and used. The actual strides\
+            produced will depend on whether the output image format can support it.
+        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__": "amp2sh",
+        "normalise": normalise,
+        "info": info,
+        "quiet": quiet,
+        "debug": debug,
+        "force": force,
+        "help": help_,
+        "version": version,
+        "amp": amp,
+        "SH": sh,
+    }
+    if lmax is not None:
+        params["lmax"] = lmax
+    if directions is not None:
+        params["directions"] = directions
+    if rician is not None:
+        params["rician"] = rician
+    if grad is not None:
+        params["grad"] = grad
+    if fslgrad is not None:
+        params["fslgrad"] = fslgrad
+    if shells is not None:
+        params["shells"] = shells
+    if strides is not None:
+        params["strides"] = strides
+    if nthreads is not None:
+        params["nthreads"] = nthreads
+    if config is not None:
+        params["config"] = config
+    return params
+
+
+def amp2sh_cargs(
+    params: Amp2shParameters,
+    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("amp2sh")
+    if params.get("lmax") is not None:
+        cargs.extend([
+            "-lmax",
+            str(params.get("lmax"))
+        ])
+    if params.get("normalise"):
+        cargs.append("-normalise")
+    if params.get("directions") is not None:
+        cargs.extend([
+            "-directions",
+            execution.input_file(params.get("directions"))
+        ])
+    if params.get("rician") is not None:
+        cargs.extend([
+            "-rician",
+            execution.input_file(params.get("rician"))
+        ])
+    if params.get("grad") is not None:
+        cargs.extend([
+            "-grad",
+            execution.input_file(params.get("grad"))
+        ])
+    if params.get("fslgrad") is not None:
+        cargs.extend(dyn_cargs(params.get("fslgrad")["__STYXTYPE__"])(params.get("fslgrad"), execution))
+    if params.get("shells") is not None:
+        cargs.extend([
+            "-shells",
+            ",".join(map(str, params.get("shells")))
+        ])
+    if params.get("strides") is not None:
+        cargs.extend([
+            "-strides",
+            *dyn_cargs(params.get("strides")["__STYXTYPE__"])(params.get("strides"), execution)
+        ])
+    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("amp")))
+    cargs.append(params.get("SH"))
+    return cargs
+
+
+def amp2sh_outputs(
+    params: Amp2shParameters,
+    execution: Execution,
+) -> Amp2shOutputs:
+    """
+    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 = Amp2shOutputs(
+        root=execution.output_file("."),
+        sh=execution.output_file(params.get("SH")),
+    )
+    return ret
+
+
+def amp2sh_execute(
+    params: Amp2shParameters,
+    execution: Execution,
+) -> Amp2shOutputs:
+    """
+    Convert a set of amplitudes (defined along a set of corresponding directions) to
+    their spherical harmonic representation.
+    
+    The spherical harmonic decomposition is calculated by least-squares linear
+    fitting to the amplitude data.
+    
+    The directions can be defined either as a DW gradient scheme (for example to
+    compute the SH representation of the DW signal), a set of [az el] pairs as
+    output by the dirgen command, or a set of [ x y z ] directions in Cartesian
+    coordinates. The DW gradient scheme or direction set can be supplied within
+    the input image header or using the -gradient or -directions option. Note
+    that if a direction set and DW gradient scheme can be found, the direction
+    set will be used by default.
+    
+    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:
+    
+    .
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `Amp2shOutputs`).
+    """
+    params = execution.params(params)
+    cargs = amp2sh_cargs(params, execution)
+    ret = amp2sh_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def amp2sh(
+    amp: InputPathType,
+    sh: str,
+    lmax: int | None = None,
+    normalise: bool = False,
+    directions: InputPathType | None = None,
+    rician: InputPathType | None = None,
+    grad: InputPathType | None = None,
+    fslgrad: Amp2shFslgradParameters | None = None,
+    shells: list[float] | None = None,
+    strides: typing.Union[Amp2shVariousStringParameters, Amp2shVariousFileParameters] | None = None,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[Amp2shConfigParameters] | None = None,
+    help_: bool = False,
+    version: bool = False,
+    runner: Runner | None = None,
+) -> Amp2shOutputs:
+    """
+    Convert a set of amplitudes (defined along a set of corresponding directions) to
+    their spherical harmonic representation.
+    
+    The spherical harmonic decomposition is calculated by least-squares linear
+    fitting to the amplitude data.
+    
+    The directions can be defined either as a DW gradient scheme (for example to
+    compute the SH representation of the DW signal), a set of [az el] pairs as
+    output by the dirgen command, or a set of [ x y z ] directions in Cartesian
+    coordinates. The DW gradient scheme or direction set can be supplied within
+    the input image header or using the -gradient or -directions option. Note
+    that if a direction set and DW gradient scheme can be found, the direction
+    set will be used by default.
+    
+    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:
+    
+    .
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        amp: the input amplitude image.
+        sh: the output spherical harmonics coefficients image.
+        lmax: set the maximum harmonic order for the output series. By default,\
+            the program will use the highest possible lmax given the number of\
+            diffusion-weighted images, up to a maximum of 8.
+        normalise: normalise the DW signal to the b=0 image.
+        directions: the directions corresponding to the input amplitude image\
+            used to sample AFD. By default this option is not required providing\
+            the direction set is supplied in the amplitude image. This should be\
+            supplied as a list of directions [az el], as generated using the dirgen\
+            command, or as a list of [ x y z ] Cartesian coordinates.
+        rician: correct for Rician noise induced bias, using noise map supplied.
+        grad: Provide the diffusion-weighted gradient scheme used in the\
+            acquisition in a text file. This should be supplied as a 4xN text file\
+            with each line is in the format [ X Y Z b ], where [ X Y Z ] describe\
+            the direction of the applied gradient, and b gives the b-value in units\
+            of s/mm^2. If a diffusion gradient scheme is present in the input image\
+            header, the data provided with this option will be instead used.
+        fslgrad: Provide the diffusion-weighted gradient scheme used in the\
+            acquisition in FSL bvecs/bvals format files. If a diffusion gradient\
+            scheme is present in the input image header, the data provided with\
+            this option will be instead used.
+        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.
+        strides: specify the strides of the output data in memory; either as a\
+            comma-separated list of (signed) integers, or as a template image from\
+            which the strides shall be extracted and used. The actual strides\
+            produced will depend on whether the output image format can support it.
+        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 `Amp2shOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(AMP2SH_METADATA)
+    params = amp2sh_params(
+        lmax=lmax,
+        normalise=normalise,
+        directions=directions,
+        rician=rician,
+        grad=grad,
+        fslgrad=fslgrad,
+        shells=shells,
+        strides=strides,
+        info=info,
+        quiet=quiet,
+        debug=debug,
+        force=force,
+        nthreads=nthreads,
+        config=config,
+        help_=help_,
+        version=version,
+        amp=amp,
+        sh=sh,
+    )
+    return amp2sh_execute(params, execution)
+
+
+__all__ = [
+    "AMP2SH_METADATA",
+    "Amp2shConfigParameters",
+    "Amp2shFslgradParameters",
+    "Amp2shOutputs",
+    "Amp2shParameters",
+    "Amp2shVariousFileParameters",
+    "Amp2shVariousStringParameters",
+    "amp2sh",
+    "amp2sh_config_params",
+    "amp2sh_fslgrad_params",
+    "amp2sh_params",
+    "amp2sh_various_file_params",
+    "amp2sh_various_string_params",
+]