niwrap-mrtrix 0.8.0__py3-none-any.whl

niwrap_mrtrix/mrtrix/mrstats.py

@@ -0,0 +1,534 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+MRSTATS_METADATA = Metadata(
+    id="28fb063299fa07970bfa62d606e13e87fd3bc94e.boutiques",
+    name="mrstats",
+    package="mrtrix",
+    container_image_tag="mrtrix3/mrtrix3:3.0.4",
+)
+
+
+_MrstatsOutputParamsDictNoTag = typing.TypedDict('_MrstatsOutputParamsDictNoTag', {
+    "field": str,
+})
+MrstatsOutputParamsDictTagged = typing.TypedDict('MrstatsOutputParamsDictTagged', {
+    "@type": typing.Literal["output"],
+    "field": str,
+})
+MrstatsOutputParamsDict = _MrstatsOutputParamsDictNoTag | MrstatsOutputParamsDictTagged
+
+
+_MrstatsConfigParamsDictNoTag = typing.TypedDict('_MrstatsConfigParamsDictNoTag', {
+    "key": str,
+    "value": str,
+})
+MrstatsConfigParamsDictTagged = typing.TypedDict('MrstatsConfigParamsDictTagged', {
+    "@type": typing.Literal["config"],
+    "key": str,
+    "value": str,
+})
+MrstatsConfigParamsDict = _MrstatsConfigParamsDictNoTag | MrstatsConfigParamsDictTagged
+
+
+_MrstatsParamsDictNoTag = typing.TypedDict('_MrstatsParamsDictNoTag', {
+    "output": typing.NotRequired[list[MrstatsOutputParamsDict] | None],
+    "mask": typing.NotRequired[InputPathType | None],
+    "ignorezero": bool,
+    "allvolumes": bool,
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[MrstatsConfigParamsDict] | None],
+    "help": bool,
+    "version": bool,
+    "image": InputPathType,
+})
+MrstatsParamsDictTagged = typing.TypedDict('MrstatsParamsDictTagged', {
+    "@type": typing.Literal["mrtrix/mrstats"],
+    "output": typing.NotRequired[list[MrstatsOutputParamsDict] | None],
+    "mask": typing.NotRequired[InputPathType | None],
+    "ignorezero": bool,
+    "allvolumes": bool,
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[MrstatsConfigParamsDict] | None],
+    "help": bool,
+    "version": bool,
+    "image": InputPathType,
+})
+MrstatsParamsDict = _MrstatsParamsDictNoTag | MrstatsParamsDictTagged
+
+
+def mrstats_output(
+    field: str,
+) -> MrstatsOutputParamsDictTagged:
+    """
+    Build parameters.
+    
+    Args:
+        field: output only the field specified. Multiple such options can be\
+            supplied if required. Choices are: mean, median, std, std_rv, min, max,\
+            count. Useful for use in scripts. Both std options refer to the\
+            unbiased (sample) standard deviation. For complex data, min, max and\
+            std are calculated separately for real and imaginary parts, std_rv is\
+            based on the real valued variance (equals sqrt of sum of variances of\
+            imaginary and real parts).
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "@type": "output",
+        "field": field,
+    }
+    return params
+
+
+def mrstats_output_validate(
+    params: typing.Any,
+) -> None:
+    """
+    Validate parameters. Throws an error if `params` is not a valid
+    `MrstatsOutputParamsDict` 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("field", None) is None:
+        raise StyxValidationError("`field` must not be None")
+    if not isinstance(params["field"], str):
+        raise StyxValidationError(f'`field` has the wrong type: Received `{type(params.get("field", None))}` expected `str`')
+
+
+def mrstats_output_cargs(
+    params: MrstatsOutputParamsDict,
+    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("-output")
+    cargs.append(params.get("field", None))
+    return cargs
+
+
+def mrstats_config(
+    key: str,
+    value: str,
+) -> MrstatsConfigParamsDictTagged:
+    """
+    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 mrstats_config_validate(
+    params: typing.Any,
+) -> None:
+    """
+    Validate parameters. Throws an error if `params` is not a valid
+    `MrstatsConfigParamsDict` 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 mrstats_config_cargs(
+    params: MrstatsConfigParamsDict,
+    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 MrstatsOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `MrstatsParamsDict(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def mrstats_params(
+    image: InputPathType,
+    output: list[MrstatsOutputParamsDict] | None = None,
+    mask: InputPathType | None = None,
+    ignorezero: bool = False,
+    allvolumes: bool = False,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[MrstatsConfigParamsDict] | None = None,
+    help_: bool = False,
+    version: bool = False,
+) -> MrstatsParamsDictTagged:
+    """
+    Build parameters.
+    
+    Args:
+        image: the input image from which statistics will be computed.
+        output: output only the field specified. Multiple such options can be\
+            supplied if required. Choices are: mean, median, std, std_rv, min, max,\
+            count. Useful for use in scripts. Both std options refer to the\
+            unbiased (sample) standard deviation. For complex data, min, max and\
+            std are calculated separately for real and imaginary parts, std_rv is\
+            based on the real valued variance (equals sqrt of sum of variances of\
+            imaginary and real parts).
+        mask: only perform computation within the specified binary mask image.
+        ignorezero: ignore zero values during statistics calculation.
+        allvolumes: generate statistics across all image volumes, rather than\
+            one set of statistics per image volume.
+        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/mrstats",
+        "ignorezero": ignorezero,
+        "allvolumes": allvolumes,
+        "info": info,
+        "quiet": quiet,
+        "debug": debug,
+        "force": force,
+        "help": help_,
+        "version": version,
+        "image": image,
+    }
+    if output is not None:
+        params["output"] = output
+    if mask is not None:
+        params["mask"] = mask
+    if nthreads is not None:
+        params["nthreads"] = nthreads
+    if config is not None:
+        params["config"] = config
+    return params
+
+
+def mrstats_validate(
+    params: typing.Any,
+) -> None:
+    """
+    Validate parameters. Throws an error if `params` is not a valid
+    `MrstatsParamsDict` 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("output", None) is not None:
+        if not isinstance(params["output"], list):
+            raise StyxValidationError(f'`output` has the wrong type: Received `{type(params.get("output", None))}` expected `list[MrstatsOutputParamsDict] | None`')
+        for e in params["output"]:
+            mrstats_output_validate(e)
+    if params.get("mask", None) is not None:
+        if not isinstance(params["mask"], (pathlib.Path, str)):
+            raise StyxValidationError(f'`mask` has the wrong type: Received `{type(params.get("mask", None))}` expected `InputPathType | None`')
+    if params.get("ignorezero", False) is None:
+        raise StyxValidationError("`ignorezero` must not be None")
+    if not isinstance(params["ignorezero"], bool):
+        raise StyxValidationError(f'`ignorezero` has the wrong type: Received `{type(params.get("ignorezero", False))}` expected `bool`')
+    if params.get("allvolumes", False) is None:
+        raise StyxValidationError("`allvolumes` must not be None")
+    if not isinstance(params["allvolumes"], bool):
+        raise StyxValidationError(f'`allvolumes` has the wrong type: Received `{type(params.get("allvolumes", False))}` expected `bool`')
+    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[MrstatsConfigParamsDict] | None`')
+        for e in params["config"]:
+            mrstats_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("image", None) is None:
+        raise StyxValidationError("`image` must not be None")
+    if not isinstance(params["image"], (pathlib.Path, str)):
+        raise StyxValidationError(f'`image` has the wrong type: Received `{type(params.get("image", None))}` expected `InputPathType`')
+
+
+def mrstats_cargs(
+    params: MrstatsParamsDict,
+    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("mrstats")
+    if params.get("output", None) is not None:
+        cargs.extend([a for c in [mrstats_output_cargs(s, execution) for s in params.get("output", None)] for a in c])
+    if params.get("mask", None) is not None:
+        cargs.extend([
+            "-mask",
+            execution.input_file(params.get("mask", None))
+        ])
+    if params.get("ignorezero", False):
+        cargs.append("-ignorezero")
+    if params.get("allvolumes", False):
+        cargs.append("-allvolumes")
+    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 [mrstats_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.append(execution.input_file(params.get("image", None)))
+    return cargs
+
+
+def mrstats_outputs(
+    params: MrstatsParamsDict,
+    execution: Execution,
+) -> MrstatsOutputs:
+    """
+    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 = MrstatsOutputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def mrstats_execute(
+    params: MrstatsParamsDict,
+    runner: Runner | None = None,
+) -> MrstatsOutputs:
+    """
+    mrstats
+    
+    Compute images statistics.
+    
+    
+    
+    References:
+    
+    .
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        params: The parameters.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `MrstatsOutputs`).
+    """
+    mrstats_validate(params)
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRSTATS_METADATA)
+    params = execution.params(params)
+    cargs = mrstats_cargs(params, execution)
+    ret = mrstats_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def mrstats(
+    image: InputPathType,
+    output: list[MrstatsOutputParamsDict] | None = None,
+    mask: InputPathType | None = None,
+    ignorezero: bool = False,
+    allvolumes: bool = False,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[MrstatsConfigParamsDict] | None = None,
+    help_: bool = False,
+    version: bool = False,
+    runner: Runner | None = None,
+) -> MrstatsOutputs:
+    """
+    mrstats
+    
+    Compute images statistics.
+    
+    
+    
+    References:
+    
+    .
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        image: the input image from which statistics will be computed.
+        output: output only the field specified. Multiple such options can be\
+            supplied if required. Choices are: mean, median, std, std_rv, min, max,\
+            count. Useful for use in scripts. Both std options refer to the\
+            unbiased (sample) standard deviation. For complex data, min, max and\
+            std are calculated separately for real and imaginary parts, std_rv is\
+            based on the real valued variance (equals sqrt of sum of variances of\
+            imaginary and real parts).
+        mask: only perform computation within the specified binary mask image.
+        ignorezero: ignore zero values during statistics calculation.
+        allvolumes: generate statistics across all image volumes, rather than\
+            one set of statistics per image volume.
+        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 `MrstatsOutputs`).
+    """
+    params = mrstats_params(
+        output=output,
+        mask=mask,
+        ignorezero=ignorezero,
+        allvolumes=allvolumes,
+        info=info,
+        quiet=quiet,
+        debug=debug,
+        force=force,
+        nthreads=nthreads,
+        config=config,
+        help_=help_,
+        version=version,
+        image=image,
+    )
+    return mrstats_execute(params, runner)
+
+
+__all__ = [
+    "MRSTATS_METADATA",
+    "MrstatsConfigParamsDict",
+    "MrstatsConfigParamsDictTagged",
+    "MrstatsOutputParamsDict",
+    "MrstatsOutputParamsDictTagged",
+    "MrstatsOutputs",
+    "MrstatsParamsDict",
+    "MrstatsParamsDictTagged",
+    "mrstats",
+    "mrstats_config",
+    "mrstats_execute",
+    "mrstats_output",
+    "mrstats_params",
+]