niwrap-mrtrix 0.8.0__py3-none-any.whl

niwrap_mrtrix/mrtrix/shconv.py

@@ -0,0 +1,661 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+SHCONV_METADATA = Metadata(
+    id="b17c6209ec80f04a818c3feb05bf3e7580772b75.boutiques",
+    name="shconv",
+    package="mrtrix",
+    container_image_tag="mrtrix3/mrtrix3:3.0.4",
+)
+
+
+_ShconvVariousStringParamsDictNoTag = typing.TypedDict('_ShconvVariousStringParamsDictNoTag', {
+    "obj": str,
+})
+ShconvVariousStringParamsDictTagged = typing.TypedDict('ShconvVariousStringParamsDictTagged', {
+    "@type": typing.Literal["VariousString"],
+    "obj": str,
+})
+ShconvVariousStringParamsDict = _ShconvVariousStringParamsDictNoTag | ShconvVariousStringParamsDictTagged
+
+
+_ShconvVariousFileParamsDictNoTag = typing.TypedDict('_ShconvVariousFileParamsDictNoTag', {
+    "obj": InputPathType,
+})
+ShconvVariousFileParamsDictTagged = typing.TypedDict('ShconvVariousFileParamsDictTagged', {
+    "@type": typing.Literal["VariousFile"],
+    "obj": InputPathType,
+})
+ShconvVariousFileParamsDict = _ShconvVariousFileParamsDictNoTag | ShconvVariousFileParamsDictTagged
+
+
+_ShconvConfigParamsDictNoTag = typing.TypedDict('_ShconvConfigParamsDictNoTag', {
+    "key": str,
+    "value": str,
+})
+ShconvConfigParamsDictTagged = typing.TypedDict('ShconvConfigParamsDictTagged', {
+    "@type": typing.Literal["config"],
+    "key": str,
+    "value": str,
+})
+ShconvConfigParamsDict = _ShconvConfigParamsDictNoTag | ShconvConfigParamsDictTagged
+
+
+_ShconvParamsDictNoTag = typing.TypedDict('_ShconvParamsDictNoTag', {
+    "datatype": typing.NotRequired[str | None],
+    "strides": typing.NotRequired[typing.Union[ShconvVariousStringParamsDictTagged, ShconvVariousFileParamsDictTagged] | None],
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[ShconvConfigParamsDict] | None],
+    "help": bool,
+    "version": bool,
+    "odf_response": list[str],
+    "SH_out": str,
+})
+ShconvParamsDictTagged = typing.TypedDict('ShconvParamsDictTagged', {
+    "@type": typing.Literal["mrtrix/shconv"],
+    "datatype": typing.NotRequired[str | None],
+    "strides": typing.NotRequired[typing.Union[ShconvVariousStringParamsDictTagged, ShconvVariousFileParamsDictTagged] | None],
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[ShconvConfigParamsDict] | None],
+    "help": bool,
+    "version": bool,
+    "odf_response": list[str],
+    "SH_out": str,
+})
+ShconvParamsDict = _ShconvParamsDictNoTag | ShconvParamsDictTagged
+
+
+def shconv_strides_cargs_dyn_fn(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "VariousString": shconv_various_string_cargs,
+        "VariousFile": shconv_various_file_cargs,
+    }.get(t)
+
+
+def shconv_strides_validate_dyn_fn(
+    t: str,
+) -> typing.Any:
+    """
+    Get validate params function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Validate params function.
+    """
+    return {
+        "VariousString": shconv_various_string_validate,
+        "VariousFile": shconv_various_file_validate,
+    }.get(t)
+
+
+def shconv_various_string(
+    obj: str,
+) -> ShconvVariousStringParamsDictTagged:
+    """
+    Build parameters.
+    
+    Args:
+        obj: String object.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "@type": "VariousString",
+        "obj": obj,
+    }
+    return params
+
+
+def shconv_various_string_validate(
+    params: typing.Any,
+) -> None:
+    """
+    Validate parameters. Throws an error if `params` is not a valid
+    `ShconvVariousStringParamsDict` 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("obj", None) is None:
+        raise StyxValidationError("`obj` must not be None")
+    if not isinstance(params["obj"], str):
+        raise StyxValidationError(f'`obj` has the wrong type: Received `{type(params.get("obj", None))}` expected `str`')
+
+
+def shconv_various_string_cargs(
+    params: ShconvVariousStringParamsDict,
+    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", None))
+    return cargs
+
+
+def shconv_various_file(
+    obj: InputPathType,
+) -> ShconvVariousFileParamsDictTagged:
+    """
+    Build parameters.
+    
+    Args:
+        obj: File object.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "@type": "VariousFile",
+        "obj": obj,
+    }
+    return params
+
+
+def shconv_various_file_validate(
+    params: typing.Any,
+) -> None:
+    """
+    Validate parameters. Throws an error if `params` is not a valid
+    `ShconvVariousFileParamsDict` 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("obj", None) is None:
+        raise StyxValidationError("`obj` must not be None")
+    if not isinstance(params["obj"], (pathlib.Path, str)):
+        raise StyxValidationError(f'`obj` has the wrong type: Received `{type(params.get("obj", None))}` expected `InputPathType`')
+
+
+def shconv_various_file_cargs(
+    params: ShconvVariousFileParamsDict,
+    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", None)))
+    return cargs
+
+
+def shconv_config(
+    key: str,
+    value: str,
+) -> ShconvConfigParamsDictTagged:
+    """
+    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 shconv_config_validate(
+    params: typing.Any,
+) -> None:
+    """
+    Validate parameters. Throws an error if `params` is not a valid
+    `ShconvConfigParamsDict` 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 shconv_config_cargs(
+    params: ShconvConfigParamsDict,
+    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 ShconvOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `ShconvParamsDict(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    sh_out: OutputPathType
+    """the output spherical harmonics coefficients image."""
+
+
+def shconv_params(
+    odf_response: list[str],
+    sh_out: str,
+    datatype: str | None = None,
+    strides: typing.Union[ShconvVariousStringParamsDictTagged, ShconvVariousFileParamsDictTagged] | None = None,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[ShconvConfigParamsDict] | None = None,
+    help_: bool = False,
+    version: bool = False,
+) -> ShconvParamsDictTagged:
+    """
+    Build parameters.
+    
+    Args:
+        odf_response: pairs of input ODF image and corresponding responses.
+        sh_out: the output spherical harmonics coefficients image.
+        datatype: specify output image data type. Valid choices are: float32,\
+            float32le, float32be, float64, float64le, float64be, int64, uint64,\
+            int64le, uint64le, int64be, uint64be, int32, uint32, int32le, uint32le,\
+            int32be, uint32be, int16, uint16, int16le, uint16le, int16be, uint16be,\
+            cfloat32, cfloat32le, cfloat32be, cfloat64, cfloat64le, cfloat64be,\
+            int8, uint8, bit.
+        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 = {
+        "@type": "mrtrix/shconv",
+        "info": info,
+        "quiet": quiet,
+        "debug": debug,
+        "force": force,
+        "help": help_,
+        "version": version,
+        "odf_response": odf_response,
+        "SH_out": sh_out,
+    }
+    if datatype is not None:
+        params["datatype"] = datatype
+    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 shconv_validate(
+    params: typing.Any,
+) -> None:
+    """
+    Validate parameters. Throws an error if `params` is not a valid
+    `ShconvParamsDict` 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("datatype", None) is not None:
+        if not isinstance(params["datatype"], str):
+            raise StyxValidationError(f'`datatype` has the wrong type: Received `{type(params.get("datatype", None))}` expected `str | None`')
+    if params.get("strides", None) is not None:
+        if not isinstance(params["strides"], dict):
+            raise StyxValidationError(f'Params object has the wrong type \'{type(params["strides"])}\'')
+        if "@type" not in params["strides"]:
+            raise StyxValidationError("Params object is missing `@type`")
+        if params["strides"]["@type"] not in ["VariousString", "VariousFile"]:
+            raise StyxValidationError("Parameter `strides`s `@type` must be one of [\"VariousString\", \"VariousFile\"]")
+        shconv_strides_validate_dyn_fn(params["strides"]["@type"])(params["strides"])
+    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[ShconvConfigParamsDict] | None`')
+        for e in params["config"]:
+            shconv_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("odf_response", None) is None:
+        raise StyxValidationError("`odf_response` must not be None")
+    if not isinstance(params["odf_response"], list):
+        raise StyxValidationError(f'`odf_response` has the wrong type: Received `{type(params.get("odf_response", None))}` expected `list[str]`')
+    for e in params["odf_response"]:
+        if not isinstance(e, str):
+            raise StyxValidationError(f'`odf_response` has the wrong type: Received `{type(params.get("odf_response", None))}` expected `list[str]`')
+    if params.get("SH_out", None) is None:
+        raise StyxValidationError("`SH_out` must not be None")
+    if not isinstance(params["SH_out"], str):
+        raise StyxValidationError(f'`SH_out` has the wrong type: Received `{type(params.get("SH_out", None))}` expected `str`')
+
+
+def shconv_cargs(
+    params: ShconvParamsDict,
+    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("shconv")
+    if params.get("datatype", None) is not None:
+        cargs.extend([
+            "-datatype",
+            params.get("datatype", None)
+        ])
+    if params.get("strides", None) is not None:
+        cargs.extend([
+            "-strides",
+            *shconv_strides_cargs_dyn_fn(params.get("strides", None)["@type"])(params.get("strides", None), execution)
+        ])
+    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 [shconv_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(params.get("odf_response", None))
+    cargs.append(params.get("SH_out", None))
+    return cargs
+
+
+def shconv_outputs(
+    params: ShconvParamsDict,
+    execution: Execution,
+) -> ShconvOutputs:
+    """
+    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 = ShconvOutputs(
+        root=execution.output_file("."),
+        sh_out=execution.output_file(params.get("SH_out", None)),
+    )
+    return ret
+
+
+def shconv_execute(
+    params: ShconvParamsDict,
+    runner: Runner | None = None,
+) -> ShconvOutputs:
+    """
+    shconv
+    
+    Perform spherical convolution.
+    
+    Provided with matching pairs of response function and ODF images (containing
+    SH coefficients), perform spherical convolution to provide the corresponding
+    SH coefficients of the signal.
+    
+    If multiple pairs of inputs are provided, their contributions will be summed
+    into a single output.
+    
+    If the responses are multi-shell (with one line of coefficients per shell),
+    the output will be a 5-dimensional image, with the SH coefficients of the
+    signal in each shell stored at different indices along the 5th dimension.
+    
+    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
+    
+    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 `ShconvOutputs`).
+    """
+    shconv_validate(params)
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(SHCONV_METADATA)
+    params = execution.params(params)
+    cargs = shconv_cargs(params, execution)
+    ret = shconv_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def shconv(
+    odf_response: list[str],
+    sh_out: str,
+    datatype: str | None = None,
+    strides: typing.Union[ShconvVariousStringParamsDictTagged, ShconvVariousFileParamsDictTagged] | None = None,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[ShconvConfigParamsDict] | None = None,
+    help_: bool = False,
+    version: bool = False,
+    runner: Runner | None = None,
+) -> ShconvOutputs:
+    """
+    shconv
+    
+    Perform spherical convolution.
+    
+    Provided with matching pairs of response function and ODF images (containing
+    SH coefficients), perform spherical convolution to provide the corresponding
+    SH coefficients of the signal.
+    
+    If multiple pairs of inputs are provided, their contributions will be summed
+    into a single output.
+    
+    If the responses are multi-shell (with one line of coefficients per shell),
+    the output will be a 5-dimensional image, with the SH coefficients of the
+    signal in each shell stored at different indices along the 5th dimension.
+    
+    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
+    
+    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:
+        odf_response: pairs of input ODF image and corresponding responses.
+        sh_out: the output spherical harmonics coefficients image.
+        datatype: specify output image data type. Valid choices are: float32,\
+            float32le, float32be, float64, float64le, float64be, int64, uint64,\
+            int64le, uint64le, int64be, uint64be, int32, uint32, int32le, uint32le,\
+            int32be, uint32be, int16, uint16, int16le, uint16le, int16be, uint16be,\
+            cfloat32, cfloat32le, cfloat32be, cfloat64, cfloat64le, cfloat64be,\
+            int8, uint8, bit.
+        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 `ShconvOutputs`).
+    """
+    params = shconv_params(
+        datatype=datatype,
+        strides=strides,
+        info=info,
+        quiet=quiet,
+        debug=debug,
+        force=force,
+        nthreads=nthreads,
+        config=config,
+        help_=help_,
+        version=version,
+        odf_response=odf_response,
+        sh_out=sh_out,
+    )
+    return shconv_execute(params, runner)
+
+
+__all__ = [
+    "SHCONV_METADATA",
+    "ShconvConfigParamsDict",
+    "ShconvConfigParamsDictTagged",
+    "ShconvOutputs",
+    "ShconvParamsDict",
+    "ShconvParamsDictTagged",
+    "ShconvVariousFileParamsDict",
+    "ShconvVariousFileParamsDictTagged",
+    "ShconvVariousStringParamsDict",
+    "ShconvVariousStringParamsDictTagged",
+    "shconv",
+    "shconv_config",
+    "shconv_execute",
+    "shconv_params",
+    "shconv_various_file",
+    "shconv_various_string",
+]