niwrap-mrtrix 0.8.0__py3-none-any.whl

niwrap_mrtrix/mrtrix/mrmath.py

@@ -0,0 +1,503 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+MRMATH_METADATA = Metadata(
+    id="53ebb217f19a2e0a5175c77890d64115b390d7bd.boutiques",
+    name="mrmath",
+    package="mrtrix",
+    container_image_tag="mrtrix3/mrtrix3:3.0.4",
+)
+
+
+_MrmathConfigParamsDictNoTag = typing.TypedDict('_MrmathConfigParamsDictNoTag', {
+    "key": str,
+    "value": str,
+})
+MrmathConfigParamsDictTagged = typing.TypedDict('MrmathConfigParamsDictTagged', {
+    "@type": typing.Literal["config"],
+    "key": str,
+    "value": str,
+})
+MrmathConfigParamsDict = _MrmathConfigParamsDictNoTag | MrmathConfigParamsDictTagged
+
+
+_MrmathParamsDictNoTag = typing.TypedDict('_MrmathParamsDictNoTag', {
+    "axis": typing.NotRequired[int | None],
+    "keep_unary_axes": bool,
+    "datatype": typing.NotRequired[str | None],
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[MrmathConfigParamsDict] | None],
+    "help": bool,
+    "version": bool,
+    "input": list[InputPathType],
+    "operation": str,
+    "output": str,
+})
+MrmathParamsDictTagged = typing.TypedDict('MrmathParamsDictTagged', {
+    "@type": typing.Literal["mrtrix/mrmath"],
+    "axis": typing.NotRequired[int | None],
+    "keep_unary_axes": bool,
+    "datatype": typing.NotRequired[str | None],
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[MrmathConfigParamsDict] | None],
+    "help": bool,
+    "version": bool,
+    "input": list[InputPathType],
+    "operation": str,
+    "output": str,
+})
+MrmathParamsDict = _MrmathParamsDictNoTag | MrmathParamsDictTagged
+
+
+def mrmath_config(
+    key: str,
+    value: str,
+) -> MrmathConfigParamsDictTagged:
+    """
+    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 mrmath_config_validate(
+    params: typing.Any,
+) -> None:
+    """
+    Validate parameters. Throws an error if `params` is not a valid
+    `MrmathConfigParamsDict` 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 mrmath_config_cargs(
+    params: MrmathConfigParamsDict,
+    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 MrmathOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `MrmathParamsDict(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output: OutputPathType
+    """the output image."""
+
+
+def mrmath_params(
+    input_: list[InputPathType],
+    operation: str,
+    output: str,
+    axis: int | None = None,
+    keep_unary_axes: bool = False,
+    datatype: str | None = None,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[MrmathConfigParamsDict] | None = None,
+    help_: bool = False,
+    version: bool = False,
+) -> MrmathParamsDictTagged:
+    """
+    Build parameters.
+    
+    Args:
+        input_: the input image(s).
+        operation: the operation to apply, one of: mean, median, sum, product,\
+            rms, norm, var, std, min, max, absmax, magmax.
+        output: the output image.
+        axis: perform operation along a specified axis of a single input image.
+        keep_unary_axes: Keep unary axes in input images prior to calculating\
+            the stats. The default is to wipe axes with single elements.
+        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.
+        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/mrmath",
+        "keep_unary_axes": keep_unary_axes,
+        "info": info,
+        "quiet": quiet,
+        "debug": debug,
+        "force": force,
+        "help": help_,
+        "version": version,
+        "input": input_,
+        "operation": operation,
+        "output": output,
+    }
+    if axis is not None:
+        params["axis"] = axis
+    if datatype is not None:
+        params["datatype"] = datatype
+    if nthreads is not None:
+        params["nthreads"] = nthreads
+    if config is not None:
+        params["config"] = config
+    return params
+
+
+def mrmath_validate(
+    params: typing.Any,
+) -> None:
+    """
+    Validate parameters. Throws an error if `params` is not a valid
+    `MrmathParamsDict` 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("axis", None) is not None:
+        if not isinstance(params["axis"], int):
+            raise StyxValidationError(f'`axis` has the wrong type: Received `{type(params.get("axis", None))}` expected `int | None`')
+    if params.get("keep_unary_axes", False) is None:
+        raise StyxValidationError("`keep_unary_axes` must not be None")
+    if not isinstance(params["keep_unary_axes"], bool):
+        raise StyxValidationError(f'`keep_unary_axes` has the wrong type: Received `{type(params.get("keep_unary_axes", False))}` expected `bool`')
+    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("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[MrmathConfigParamsDict] | None`')
+        for e in params["config"]:
+            mrmath_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("input", None) is None:
+        raise StyxValidationError("`input` must not be None")
+    if not isinstance(params["input"], list):
+        raise StyxValidationError(f'`input` has the wrong type: Received `{type(params.get("input", None))}` expected `list[InputPathType]`')
+    for e in params["input"]:
+        if not isinstance(e, (pathlib.Path, str)):
+            raise StyxValidationError(f'`input` has the wrong type: Received `{type(params.get("input", None))}` expected `list[InputPathType]`')
+    if params.get("operation", None) is None:
+        raise StyxValidationError("`operation` must not be None")
+    if not isinstance(params["operation"], str):
+        raise StyxValidationError(f'`operation` has the wrong type: Received `{type(params.get("operation", None))}` expected `str`')
+    if params.get("output", None) is None:
+        raise StyxValidationError("`output` must not be None")
+    if not isinstance(params["output"], str):
+        raise StyxValidationError(f'`output` has the wrong type: Received `{type(params.get("output", None))}` expected `str`')
+
+
+def mrmath_cargs(
+    params: MrmathParamsDict,
+    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("mrmath")
+    if params.get("axis", None) is not None:
+        cargs.extend([
+            "-axis",
+            str(params.get("axis", None))
+        ])
+    if params.get("keep_unary_axes", False):
+        cargs.append("-keep_unary_axes")
+    if params.get("datatype", None) is not None:
+        cargs.extend([
+            "-datatype",
+            params.get("datatype", 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 [mrmath_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("input", None)])
+    cargs.append(params.get("operation", None))
+    cargs.append(params.get("output", None))
+    return cargs
+
+
+def mrmath_outputs(
+    params: MrmathParamsDict,
+    execution: Execution,
+) -> MrmathOutputs:
+    """
+    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 = MrmathOutputs(
+        root=execution.output_file("."),
+        output=execution.output_file(params.get("output", None)),
+    )
+    return ret
+
+
+def mrmath_execute(
+    params: MrmathParamsDict,
+    runner: Runner | None = None,
+) -> MrmathOutputs:
+    """
+    mrmath
+    
+    Compute summary statistic on image intensities either across images, or
+    along a specified axis of a single image.
+    
+    Supported operations are:
+    
+    mean, median, sum, product, rms (root-mean-square value), norm (vector
+    2-norm), var (unbiased variance), std (unbiased standard deviation), min,
+    max, absmax (maximum absolute value), magmax (value with maximum absolute
+    value, preserving its sign).
+    
+    This command is used to traverse either along an image axis, or across a set
+    of input images, calculating some statistic from the values along each
+    traversal. If you are seeking to instead perform mathematical calculations
+    that are done independently for each voxel, pleaase see the 'mrcalc'
+    command.
+    
+    References:
+    
+    .
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        params: The parameters.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `MrmathOutputs`).
+    """
+    mrmath_validate(params)
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRMATH_METADATA)
+    params = execution.params(params)
+    cargs = mrmath_cargs(params, execution)
+    ret = mrmath_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def mrmath(
+    input_: list[InputPathType],
+    operation: str,
+    output: str,
+    axis: int | None = None,
+    keep_unary_axes: bool = False,
+    datatype: str | None = None,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[MrmathConfigParamsDict] | None = None,
+    help_: bool = False,
+    version: bool = False,
+    runner: Runner | None = None,
+) -> MrmathOutputs:
+    """
+    mrmath
+    
+    Compute summary statistic on image intensities either across images, or
+    along a specified axis of a single image.
+    
+    Supported operations are:
+    
+    mean, median, sum, product, rms (root-mean-square value), norm (vector
+    2-norm), var (unbiased variance), std (unbiased standard deviation), min,
+    max, absmax (maximum absolute value), magmax (value with maximum absolute
+    value, preserving its sign).
+    
+    This command is used to traverse either along an image axis, or across a set
+    of input images, calculating some statistic from the values along each
+    traversal. If you are seeking to instead perform mathematical calculations
+    that are done independently for each voxel, pleaase see the 'mrcalc'
+    command.
+    
+    References:
+    
+    .
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        input_: the input image(s).
+        operation: the operation to apply, one of: mean, median, sum, product,\
+            rms, norm, var, std, min, max, absmax, magmax.
+        output: the output image.
+        axis: perform operation along a specified axis of a single input image.
+        keep_unary_axes: Keep unary axes in input images prior to calculating\
+            the stats. The default is to wipe axes with single elements.
+        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.
+        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 `MrmathOutputs`).
+    """
+    params = mrmath_params(
+        axis=axis,
+        keep_unary_axes=keep_unary_axes,
+        datatype=datatype,
+        info=info,
+        quiet=quiet,
+        debug=debug,
+        force=force,
+        nthreads=nthreads,
+        config=config,
+        help_=help_,
+        version=version,
+        input_=input_,
+        operation=operation,
+        output=output,
+    )
+    return mrmath_execute(params, runner)
+
+
+__all__ = [
+    "MRMATH_METADATA",
+    "MrmathConfigParamsDict",
+    "MrmathConfigParamsDictTagged",
+    "MrmathOutputs",
+    "MrmathParamsDict",
+    "MrmathParamsDictTagged",
+    "mrmath",
+    "mrmath_config",
+    "mrmath_execute",
+    "mrmath_params",
+]