niwrap-mrtrix 0.8.0__py3-none-any.whl

niwrap_mrtrix/mrtrix/warp2metric.py

@@ -0,0 +1,556 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+WARP2METRIC_METADATA = Metadata(
+    id="6239916d39fe990e43c4b408dab7798207712e0c.boutiques",
+    name="warp2metric",
+    package="mrtrix",
+    container_image_tag="mrtrix3/mrtrix3:3.0.4",
+)
+
+
+_Warp2metricFcParamsDictNoTag = typing.TypedDict('_Warp2metricFcParamsDictNoTag', {
+    "template_fixel_directory": InputPathType,
+    "output_fixel_directory": str,
+    "output_fixel_data": str,
+})
+Warp2metricFcParamsDictTagged = typing.TypedDict('Warp2metricFcParamsDictTagged', {
+    "@type": typing.Literal["fc"],
+    "template_fixel_directory": InputPathType,
+    "output_fixel_directory": str,
+    "output_fixel_data": str,
+})
+Warp2metricFcParamsDict = _Warp2metricFcParamsDictNoTag | Warp2metricFcParamsDictTagged
+
+
+_Warp2metricConfigParamsDictNoTag = typing.TypedDict('_Warp2metricConfigParamsDictNoTag', {
+    "key": str,
+    "value": str,
+})
+Warp2metricConfigParamsDictTagged = typing.TypedDict('Warp2metricConfigParamsDictTagged', {
+    "@type": typing.Literal["config"],
+    "key": str,
+    "value": str,
+})
+Warp2metricConfigParamsDict = _Warp2metricConfigParamsDictNoTag | Warp2metricConfigParamsDictTagged
+
+
+_Warp2metricParamsDictNoTag = typing.TypedDict('_Warp2metricParamsDictNoTag', {
+    "fc": typing.NotRequired[Warp2metricFcParamsDict | None],
+    "jmat": typing.NotRequired[str | None],
+    "jdet": typing.NotRequired[str | None],
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[Warp2metricConfigParamsDict] | None],
+    "help": bool,
+    "version": bool,
+    "in": InputPathType,
+})
+Warp2metricParamsDictTagged = typing.TypedDict('Warp2metricParamsDictTagged', {
+    "@type": typing.Literal["mrtrix/warp2metric"],
+    "fc": typing.NotRequired[Warp2metricFcParamsDict | None],
+    "jmat": typing.NotRequired[str | None],
+    "jdet": typing.NotRequired[str | None],
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[Warp2metricConfigParamsDict] | None],
+    "help": bool,
+    "version": bool,
+    "in": InputPathType,
+})
+Warp2metricParamsDict = _Warp2metricParamsDictNoTag | Warp2metricParamsDictTagged
+
+
+def warp2metric_fc(
+    template_fixel_directory: InputPathType,
+    output_fixel_directory: str,
+    output_fixel_data: str,
+) -> Warp2metricFcParamsDictTagged:
+    """
+    Build parameters.
+    
+    Args:
+        template_fixel_directory: use an input template fixel image to define\
+            fibre orientations and output a fixel image describing the change in\
+            fibre cross-section (FC) in the perpendicular plane to the fixel\
+            orientation. e.g. warp2metric warp.mif -fc fixel_template_directory\
+            output_fixel_directory fc.mif.
+        output_fixel_directory: use an input template fixel image to define\
+            fibre orientations and output a fixel image describing the change in\
+            fibre cross-section (FC) in the perpendicular plane to the fixel\
+            orientation. e.g. warp2metric warp.mif -fc fixel_template_directory\
+            output_fixel_directory fc.mif.
+        output_fixel_data: use an input template fixel image to define fibre\
+            orientations and output a fixel image describing the change in fibre\
+            cross-section (FC) in the perpendicular plane to the fixel orientation.\
+            e.g. warp2metric warp.mif -fc fixel_template_directory\
+            output_fixel_directory fc.mif.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "@type": "fc",
+        "template_fixel_directory": template_fixel_directory,
+        "output_fixel_directory": output_fixel_directory,
+        "output_fixel_data": output_fixel_data,
+    }
+    return params
+
+
+def warp2metric_fc_validate(
+    params: typing.Any,
+) -> None:
+    """
+    Validate parameters. Throws an error if `params` is not a valid
+    `Warp2metricFcParamsDict` 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("template_fixel_directory", None) is None:
+        raise StyxValidationError("`template_fixel_directory` must not be None")
+    if not isinstance(params["template_fixel_directory"], (pathlib.Path, str)):
+        raise StyxValidationError(f'`template_fixel_directory` has the wrong type: Received `{type(params.get("template_fixel_directory", None))}` expected `InputPathType`')
+    if params.get("output_fixel_directory", None) is None:
+        raise StyxValidationError("`output_fixel_directory` must not be None")
+    if not isinstance(params["output_fixel_directory"], str):
+        raise StyxValidationError(f'`output_fixel_directory` has the wrong type: Received `{type(params.get("output_fixel_directory", None))}` expected `str`')
+    if params.get("output_fixel_data", None) is None:
+        raise StyxValidationError("`output_fixel_data` must not be None")
+    if not isinstance(params["output_fixel_data"], str):
+        raise StyxValidationError(f'`output_fixel_data` has the wrong type: Received `{type(params.get("output_fixel_data", None))}` expected `str`')
+
+
+def warp2metric_fc_cargs(
+    params: Warp2metricFcParamsDict,
+    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("-fc")
+    cargs.append(execution.input_file(params.get("template_fixel_directory", None)))
+    cargs.append(params.get("output_fixel_directory", None))
+    cargs.append(params.get("output_fixel_data", None))
+    return cargs
+
+
+def warp2metric_config(
+    key: str,
+    value: str,
+) -> Warp2metricConfigParamsDictTagged:
+    """
+    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 warp2metric_config_validate(
+    params: typing.Any,
+) -> None:
+    """
+    Validate parameters. Throws an error if `params` is not a valid
+    `Warp2metricConfigParamsDict` 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 warp2metric_config_cargs(
+    params: Warp2metricConfigParamsDict,
+    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 Warp2metricOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `Warp2metricParamsDict(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    jmat: OutputPathType | None
+    """output a Jacobian matrix image stored in column-major order along the 4th
+    dimension.Note the output jacobian describes the warp gradient w.r.t the
+    scanner space coordinate system """
+    jdet: OutputPathType | None
+    """output the Jacobian determinant instead of the full matrix """
+
+
+def warp2metric_params(
+    in_: InputPathType,
+    fc: Warp2metricFcParamsDict | None = None,
+    jmat: str | None = None,
+    jdet: str | None = None,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[Warp2metricConfigParamsDict] | None = None,
+    help_: bool = False,
+    version: bool = False,
+) -> Warp2metricParamsDictTagged:
+    """
+    Build parameters.
+    
+    Args:
+        in_: the input deformation field.
+        fc: use an input template fixel image to define fibre orientations and\
+            output a fixel image describing the change in fibre cross-section (FC)\
+            in the perpendicular plane to the fixel orientation. e.g. warp2metric\
+            warp.mif -fc fixel_template_directory output_fixel_directory fc.mif.
+        jmat: output a Jacobian matrix image stored in column-major order along\
+            the 4th dimension.Note the output jacobian describes the warp gradient\
+            w.r.t the scanner space coordinate system.
+        jdet: output the Jacobian determinant instead of the full matrix.
+        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/warp2metric",
+        "info": info,
+        "quiet": quiet,
+        "debug": debug,
+        "force": force,
+        "help": help_,
+        "version": version,
+        "in": in_,
+    }
+    if fc is not None:
+        params["fc"] = fc
+    if jmat is not None:
+        params["jmat"] = jmat
+    if jdet is not None:
+        params["jdet"] = jdet
+    if nthreads is not None:
+        params["nthreads"] = nthreads
+    if config is not None:
+        params["config"] = config
+    return params
+
+
+def warp2metric_validate(
+    params: typing.Any,
+) -> None:
+    """
+    Validate parameters. Throws an error if `params` is not a valid
+    `Warp2metricParamsDict` 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("fc", None) is not None:
+        warp2metric_fc_validate(params["fc"])
+    if params.get("jmat", None) is not None:
+        if not isinstance(params["jmat"], str):
+            raise StyxValidationError(f'`jmat` has the wrong type: Received `{type(params.get("jmat", None))}` expected `str | None`')
+    if params.get("jdet", None) is not None:
+        if not isinstance(params["jdet"], str):
+            raise StyxValidationError(f'`jdet` has the wrong type: Received `{type(params.get("jdet", 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[Warp2metricConfigParamsDict] | None`')
+        for e in params["config"]:
+            warp2metric_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("in", None) is None:
+        raise StyxValidationError("`in` must not be None")
+    if not isinstance(params["in"], (pathlib.Path, str)):
+        raise StyxValidationError(f'`in` has the wrong type: Received `{type(params.get("in", None))}` expected `InputPathType`')
+
+
+def warp2metric_cargs(
+    params: Warp2metricParamsDict,
+    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("warp2metric")
+    if params.get("fc", None) is not None:
+        cargs.extend(warp2metric_fc_cargs(params.get("fc", None), execution))
+    if params.get("jmat", None) is not None:
+        cargs.extend([
+            "-jmat",
+            params.get("jmat", None)
+        ])
+    if params.get("jdet", None) is not None:
+        cargs.extend([
+            "-jdet",
+            params.get("jdet", 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 [warp2metric_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("in", None)))
+    return cargs
+
+
+def warp2metric_outputs(
+    params: Warp2metricParamsDict,
+    execution: Execution,
+) -> Warp2metricOutputs:
+    """
+    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 = Warp2metricOutputs(
+        root=execution.output_file("."),
+        jmat=execution.output_file(params.get("jmat", None)) if (params.get("jmat") is not None) else None,
+        jdet=execution.output_file(params.get("jdet", None)) if (params.get("jdet") is not None) else None,
+    )
+    return ret
+
+
+def warp2metric_execute(
+    params: Warp2metricParamsDict,
+    runner: Runner | None = None,
+) -> Warp2metricOutputs:
+    """
+    warp2metric
+    
+    Compute fixel-wise or voxel-wise metrics from a 4D deformation field.
+    
+    
+    
+    References:
+    
+    Raffelt, D.; Tournier, JD/; Smith, RE.; Vaughan, DN.; Jackson, G.; Ridgway,
+    GR. Connelly, A.Investigating White Matter Fibre Density and Morphology
+    using Fixel-Based Analysis. Neuroimage, 2017, 144, 58-73, doi:
+    10.1016/j.neuroimage.2016.09.029.
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        params: The parameters.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `Warp2metricOutputs`).
+    """
+    warp2metric_validate(params)
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(WARP2METRIC_METADATA)
+    params = execution.params(params)
+    cargs = warp2metric_cargs(params, execution)
+    ret = warp2metric_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def warp2metric(
+    in_: InputPathType,
+    fc: Warp2metricFcParamsDict | None = None,
+    jmat: str | None = None,
+    jdet: str | None = None,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[Warp2metricConfigParamsDict] | None = None,
+    help_: bool = False,
+    version: bool = False,
+    runner: Runner | None = None,
+) -> Warp2metricOutputs:
+    """
+    warp2metric
+    
+    Compute fixel-wise or voxel-wise metrics from a 4D deformation field.
+    
+    
+    
+    References:
+    
+    Raffelt, D.; Tournier, JD/; Smith, RE.; Vaughan, DN.; Jackson, G.; Ridgway,
+    GR. Connelly, A.Investigating White Matter Fibre Density and Morphology
+    using Fixel-Based Analysis. Neuroimage, 2017, 144, 58-73, doi:
+    10.1016/j.neuroimage.2016.09.029.
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        in_: the input deformation field.
+        fc: use an input template fixel image to define fibre orientations and\
+            output a fixel image describing the change in fibre cross-section (FC)\
+            in the perpendicular plane to the fixel orientation. e.g. warp2metric\
+            warp.mif -fc fixel_template_directory output_fixel_directory fc.mif.
+        jmat: output a Jacobian matrix image stored in column-major order along\
+            the 4th dimension.Note the output jacobian describes the warp gradient\
+            w.r.t the scanner space coordinate system.
+        jdet: output the Jacobian determinant instead of the full matrix.
+        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 `Warp2metricOutputs`).
+    """
+    params = warp2metric_params(
+        fc=fc,
+        jmat=jmat,
+        jdet=jdet,
+        info=info,
+        quiet=quiet,
+        debug=debug,
+        force=force,
+        nthreads=nthreads,
+        config=config,
+        help_=help_,
+        version=version,
+        in_=in_,
+    )
+    return warp2metric_execute(params, runner)
+
+
+__all__ = [
+    "WARP2METRIC_METADATA",
+    "Warp2metricConfigParamsDict",
+    "Warp2metricConfigParamsDictTagged",
+    "Warp2metricFcParamsDict",
+    "Warp2metricFcParamsDictTagged",
+    "Warp2metricOutputs",
+    "Warp2metricParamsDict",
+    "Warp2metricParamsDictTagged",
+    "warp2metric",
+    "warp2metric_config",
+    "warp2metric_execute",
+    "warp2metric_fc",
+    "warp2metric_params",
+]