niwrap-mrtrix 0.8.0__py3-none-any.whl

niwrap_mrtrix/mrtrix/shbasis.py

@@ -0,0 +1,445 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+SHBASIS_METADATA = Metadata(
+    id="8d1c3a9e142d8ac3b0cfbca9e0fcd6b3d41e317e.boutiques",
+    name="shbasis",
+    package="mrtrix",
+    container_image_tag="mrtrix3/mrtrix3:3.0.4",
+)
+
+
+_ShbasisConfigParamsDictNoTag = typing.TypedDict('_ShbasisConfigParamsDictNoTag', {
+    "key": str,
+    "value": str,
+})
+ShbasisConfigParamsDictTagged = typing.TypedDict('ShbasisConfigParamsDictTagged', {
+    "@type": typing.Literal["config"],
+    "key": str,
+    "value": str,
+})
+ShbasisConfigParamsDict = _ShbasisConfigParamsDictNoTag | ShbasisConfigParamsDictTagged
+
+
+_ShbasisParamsDictNoTag = typing.TypedDict('_ShbasisParamsDictNoTag', {
+    "convert": typing.NotRequired[str | None],
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[ShbasisConfigParamsDict] | None],
+    "help": bool,
+    "version": bool,
+    "SH": list[InputPathType],
+})
+ShbasisParamsDictTagged = typing.TypedDict('ShbasisParamsDictTagged', {
+    "@type": typing.Literal["mrtrix/shbasis"],
+    "convert": typing.NotRequired[str | None],
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[ShbasisConfigParamsDict] | None],
+    "help": bool,
+    "version": bool,
+    "SH": list[InputPathType],
+})
+ShbasisParamsDict = _ShbasisParamsDictNoTag | ShbasisParamsDictTagged
+
+
+def shbasis_config(
+    key: str,
+    value: str,
+) -> ShbasisConfigParamsDictTagged:
+    """
+    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 shbasis_config_validate(
+    params: typing.Any,
+) -> None:
+    """
+    Validate parameters. Throws an error if `params` is not a valid
+    `ShbasisConfigParamsDict` 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 shbasis_config_cargs(
+    params: ShbasisConfigParamsDict,
+    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 ShbasisOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `ShbasisParamsDict(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def shbasis_params(
+    sh: list[InputPathType],
+    convert: str | None = None,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[ShbasisConfigParamsDict] | None = None,
+    help_: bool = False,
+    version: bool = False,
+) -> ShbasisParamsDictTagged:
+    """
+    Build parameters.
+    
+    Args:
+        sh: the input image(s) of SH coefficients.
+        convert: convert the image data in-place to the desired basis; options\
+            are: old,new,force_oldtonew,force_newtoold.
+        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/shbasis",
+        "info": info,
+        "quiet": quiet,
+        "debug": debug,
+        "force": force,
+        "help": help_,
+        "version": version,
+        "SH": sh,
+    }
+    if convert is not None:
+        params["convert"] = convert
+    if nthreads is not None:
+        params["nthreads"] = nthreads
+    if config is not None:
+        params["config"] = config
+    return params
+
+
+def shbasis_validate(
+    params: typing.Any,
+) -> None:
+    """
+    Validate parameters. Throws an error if `params` is not a valid
+    `ShbasisParamsDict` 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("convert", None) is not None:
+        if not isinstance(params["convert"], str):
+            raise StyxValidationError(f'`convert` has the wrong type: Received `{type(params.get("convert", None))}` expected `str | None`')
+    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[ShbasisConfigParamsDict] | None`')
+        for e in params["config"]:
+            shbasis_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"], list):
+        raise StyxValidationError(f'`SH` has the wrong type: Received `{type(params.get("SH", None))}` expected `list[InputPathType]`')
+    for e in params["SH"]:
+        if not isinstance(e, (pathlib.Path, str)):
+            raise StyxValidationError(f'`SH` has the wrong type: Received `{type(params.get("SH", None))}` expected `list[InputPathType]`')
+
+
+def shbasis_cargs(
+    params: ShbasisParamsDict,
+    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("shbasis")
+    if params.get("convert", None) is not None:
+        cargs.extend([
+            "-convert",
+            params.get("convert", None)
+        ])
+    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 [shbasis_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.extend([execution.input_file(f) for f in params.get("SH", None)])
+    return cargs
+
+
+def shbasis_outputs(
+    params: ShbasisParamsDict,
+    execution: Execution,
+) -> ShbasisOutputs:
+    """
+    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 = ShbasisOutputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def shbasis_execute(
+    params: ShbasisParamsDict,
+    runner: Runner | None = None,
+) -> ShbasisOutputs:
+    """
+    shbasis
+    
+    Examine the values in spherical harmonic images to estimate (and optionally
+    change) the SH basis used.
+    
+    In previous versions of MRtrix, the convention used for storing spherical
+    harmonic coefficients was a non-orthonormal basis (the m!=0 coefficients
+    were a factor of sqrt(2) too large). This error has been rectified in newer
+    versions of MRtrix, but will cause issues if processing SH data that was
+    generated using an older version of MRtrix (or vice-versa).
+    
+    This command provides a mechanism for testing the basis used in storage of
+    image data representing a spherical harmonic series per voxel, and allows
+    the user to forcibly modify the raw image data to conform to the desired
+    basis.
+    
+    Note that the "force_*" conversion choices should only be used in cases
+    where this command has previously been unable to automatically determine the
+    SH basis from the image data, but the user themselves are confident of the
+    SH basis of the data.
+    
+    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.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `ShbasisOutputs`).
+    """
+    shbasis_validate(params)
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(SHBASIS_METADATA)
+    params = execution.params(params)
+    cargs = shbasis_cargs(params, execution)
+    ret = shbasis_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def shbasis(
+    sh: list[InputPathType],
+    convert: str | None = None,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[ShbasisConfigParamsDict] | None = None,
+    help_: bool = False,
+    version: bool = False,
+    runner: Runner | None = None,
+) -> ShbasisOutputs:
+    """
+    shbasis
+    
+    Examine the values in spherical harmonic images to estimate (and optionally
+    change) the SH basis used.
+    
+    In previous versions of MRtrix, the convention used for storing spherical
+    harmonic coefficients was a non-orthonormal basis (the m!=0 coefficients
+    were a factor of sqrt(2) too large). This error has been rectified in newer
+    versions of MRtrix, but will cause issues if processing SH data that was
+    generated using an older version of MRtrix (or vice-versa).
+    
+    This command provides a mechanism for testing the basis used in storage of
+    image data representing a spherical harmonic series per voxel, and allows
+    the user to forcibly modify the raw image data to conform to the desired
+    basis.
+    
+    Note that the "force_*" conversion choices should only be used in cases
+    where this command has previously been unable to automatically determine the
+    SH basis from the image data, but the user themselves are confident of the
+    SH basis of the data.
+    
+    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:
+        sh: the input image(s) of SH coefficients.
+        convert: convert the image data in-place to the desired basis; options\
+            are: old,new,force_oldtonew,force_newtoold.
+        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 `ShbasisOutputs`).
+    """
+    params = shbasis_params(
+        convert=convert,
+        info=info,
+        quiet=quiet,
+        debug=debug,
+        force=force,
+        nthreads=nthreads,
+        config=config,
+        help_=help_,
+        version=version,
+        sh=sh,
+    )
+    return shbasis_execute(params, runner)
+
+
+__all__ = [
+    "SHBASIS_METADATA",
+    "ShbasisConfigParamsDict",
+    "ShbasisConfigParamsDictTagged",
+    "ShbasisOutputs",
+    "ShbasisParamsDict",
+    "ShbasisParamsDictTagged",
+    "shbasis",
+    "shbasis_config",
+    "shbasis_execute",
+    "shbasis_params",
+]