niwrap-mrtrix 0.5.0__py3-none-any.whl

niwrap_mrtrix/mrtrix/tensor2metric.py

@@ -0,0 +1,544 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+TENSOR2METRIC_METADATA = Metadata(
+    id="ce3b6c1eb5966c84af85ddfef969868689c115fb.boutiques",
+    name="tensor2metric",
+    package="mrtrix",
+    container_image_tag="mrtrix3/mrtrix3:3.0.4",
+)
+
+
+Tensor2metricConfigParameters = typing.TypedDict('Tensor2metricConfigParameters', {
+    "__STYX_TYPE__": typing.Literal["config"],
+    "key": str,
+    "value": str,
+})
+
+
+Tensor2metricParameters = typing.TypedDict('Tensor2metricParameters', {
+    "__STYX_TYPE__": typing.Literal["tensor2metric"],
+    "adc": typing.NotRequired[str | None],
+    "fa": typing.NotRequired[str | None],
+    "ad": typing.NotRequired[str | None],
+    "rd": typing.NotRequired[str | None],
+    "cl": typing.NotRequired[str | None],
+    "cp": typing.NotRequired[str | None],
+    "cs": typing.NotRequired[str | None],
+    "value": typing.NotRequired[str | None],
+    "vector": typing.NotRequired[str | None],
+    "num": typing.NotRequired[list[int] | None],
+    "modulate": typing.NotRequired[str | None],
+    "mask": typing.NotRequired[InputPathType | None],
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[Tensor2metricConfigParameters] | None],
+    "help": bool,
+    "version": bool,
+    "tensor": InputPathType,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "tensor2metric": tensor2metric_cargs,
+        "config": tensor2metric_config_cargs,
+    }.get(t)
+
+
+def dyn_outputs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build outputs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build outputs function.
+    """
+    return {
+        "tensor2metric": tensor2metric_outputs,
+    }.get(t)
+
+
+def tensor2metric_config_params(
+    key: str,
+    value: str,
+) -> Tensor2metricConfigParameters:
+    """
+    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 = {
+        "__STYXTYPE__": "config",
+        "key": key,
+        "value": value,
+    }
+    return params
+
+
+def tensor2metric_config_cargs(
+    params: Tensor2metricConfigParameters,
+    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"))
+    cargs.append(params.get("value"))
+    return cargs
+
+
+class Tensor2metricOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `tensor2metric(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    adc: OutputPathType | None
+    """compute the mean apparent diffusion coefficient (ADC) of the diffusion
+    tensor. (sometimes also referred to as the mean diffusivity (MD)) """
+    fa: OutputPathType | None
+    """compute the fractional anisotropy (FA) of the diffusion tensor. """
+    ad: OutputPathType | None
+    """compute the axial diffusivity (AD) of the diffusion tensor. (equivalent
+    to the principal eigenvalue) """
+    rd: OutputPathType | None
+    """compute the radial diffusivity (RD) of the diffusion tensor. (equivalent
+    to the mean of the two non-principal eigenvalues) """
+    cl: OutputPathType | None
+    """compute the linearity metric of the diffusion tensor. (one of the three
+    Westin shape metrics) """
+    cp: OutputPathType | None
+    """compute the planarity metric of the diffusion tensor. (one of the three
+    Westin shape metrics) """
+    cs: OutputPathType | None
+    """compute the sphericity metric of the diffusion tensor. (one of the three
+    Westin shape metrics) """
+    value: OutputPathType | None
+    """compute the selected eigenvalue(s) of the diffusion tensor. """
+    vector: OutputPathType | None
+    """compute the selected eigenvector(s) of the diffusion tensor. """
+
+
+def tensor2metric_params(
+    tensor: InputPathType,
+    adc: str | None = None,
+    fa: str | None = None,
+    ad: str | None = None,
+    rd: str | None = None,
+    cl: str | None = None,
+    cp: str | None = None,
+    cs: str | None = None,
+    value: str | None = None,
+    vector: str | None = None,
+    num: list[int] | None = None,
+    modulate: str | None = None,
+    mask: InputPathType | None = None,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[Tensor2metricConfigParameters] | None = None,
+    help_: bool = False,
+    version: bool = False,
+) -> Tensor2metricParameters:
+    """
+    Build parameters.
+    
+    Args:
+        tensor: the input tensor image.
+        adc: compute the mean apparent diffusion coefficient (ADC) of the\
+            diffusion tensor. (sometimes also referred to as the mean diffusivity\
+            (MD)).
+        fa: compute the fractional anisotropy (FA) of the diffusion tensor.
+        ad: compute the axial diffusivity (AD) of the diffusion tensor.\
+            (equivalent to the principal eigenvalue).
+        rd: compute the radial diffusivity (RD) of the diffusion tensor.\
+            (equivalent to the mean of the two non-principal eigenvalues).
+        cl: compute the linearity metric of the diffusion tensor. (one of the\
+            three Westin shape metrics).
+        cp: compute the planarity metric of the diffusion tensor. (one of the\
+            three Westin shape metrics).
+        cs: compute the sphericity metric of the diffusion tensor. (one of the\
+            three Westin shape metrics).
+        value: compute the selected eigenvalue(s) of the diffusion tensor.
+        vector: compute the selected eigenvector(s) of the diffusion tensor.
+        num: specify the desired eigenvalue/eigenvector(s). Note that several\
+            eigenvalues can be specified as a number sequence. For example, '1,3'\
+            specifies the principal (1) and minor (3) eigenvalues/eigenvectors\
+            (default = 1).
+        modulate: specify how to modulate the magnitude of the eigenvectors.\
+            Valid choices are: none, FA, eigval (default = FA).
+        mask: only perform computation within the specified binary brain mask\
+            image.
+        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 = {
+        "__STYXTYPE__": "tensor2metric",
+        "info": info,
+        "quiet": quiet,
+        "debug": debug,
+        "force": force,
+        "help": help_,
+        "version": version,
+        "tensor": tensor,
+    }
+    if adc is not None:
+        params["adc"] = adc
+    if fa is not None:
+        params["fa"] = fa
+    if ad is not None:
+        params["ad"] = ad
+    if rd is not None:
+        params["rd"] = rd
+    if cl is not None:
+        params["cl"] = cl
+    if cp is not None:
+        params["cp"] = cp
+    if cs is not None:
+        params["cs"] = cs
+    if value is not None:
+        params["value"] = value
+    if vector is not None:
+        params["vector"] = vector
+    if num is not None:
+        params["num"] = num
+    if modulate is not None:
+        params["modulate"] = modulate
+    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 tensor2metric_cargs(
+    params: Tensor2metricParameters,
+    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("tensor2metric")
+    if params.get("adc") is not None:
+        cargs.extend([
+            "-adc",
+            params.get("adc")
+        ])
+    if params.get("fa") is not None:
+        cargs.extend([
+            "-fa",
+            params.get("fa")
+        ])
+    if params.get("ad") is not None:
+        cargs.extend([
+            "-ad",
+            params.get("ad")
+        ])
+    if params.get("rd") is not None:
+        cargs.extend([
+            "-rd",
+            params.get("rd")
+        ])
+    if params.get("cl") is not None:
+        cargs.extend([
+            "-cl",
+            params.get("cl")
+        ])
+    if params.get("cp") is not None:
+        cargs.extend([
+            "-cp",
+            params.get("cp")
+        ])
+    if params.get("cs") is not None:
+        cargs.extend([
+            "-cs",
+            params.get("cs")
+        ])
+    if params.get("value") is not None:
+        cargs.extend([
+            "-value",
+            params.get("value")
+        ])
+    if params.get("vector") is not None:
+        cargs.extend([
+            "-vector",
+            params.get("vector")
+        ])
+    if params.get("num") is not None:
+        cargs.extend([
+            "-num",
+            *map(str, params.get("num"))
+        ])
+    if params.get("modulate") is not None:
+        cargs.extend([
+            "-modulate",
+            params.get("modulate")
+        ])
+    if params.get("mask") is not None:
+        cargs.extend([
+            "-mask",
+            execution.input_file(params.get("mask"))
+        ])
+    if params.get("info"):
+        cargs.append("-info")
+    if params.get("quiet"):
+        cargs.append("-quiet")
+    if params.get("debug"):
+        cargs.append("-debug")
+    if params.get("force"):
+        cargs.append("-force")
+    if params.get("nthreads") is not None:
+        cargs.extend([
+            "-nthreads",
+            str(params.get("nthreads"))
+        ])
+    if params.get("config") is not None:
+        cargs.extend([a for c in [dyn_cargs(s["__STYXTYPE__"])(s, execution) for s in params.get("config")] for a in c])
+    if params.get("help"):
+        cargs.append("-help")
+    if params.get("version"):
+        cargs.append("-version")
+    cargs.append(execution.input_file(params.get("tensor")))
+    return cargs
+
+
+def tensor2metric_outputs(
+    params: Tensor2metricParameters,
+    execution: Execution,
+) -> Tensor2metricOutputs:
+    """
+    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 = Tensor2metricOutputs(
+        root=execution.output_file("."),
+        adc=execution.output_file(params.get("adc")) if (params.get("adc") is not None) else None,
+        fa=execution.output_file(params.get("fa")) if (params.get("fa") is not None) else None,
+        ad=execution.output_file(params.get("ad")) if (params.get("ad") is not None) else None,
+        rd=execution.output_file(params.get("rd")) if (params.get("rd") is not None) else None,
+        cl=execution.output_file(params.get("cl")) if (params.get("cl") is not None) else None,
+        cp=execution.output_file(params.get("cp")) if (params.get("cp") is not None) else None,
+        cs=execution.output_file(params.get("cs")) if (params.get("cs") is not None) else None,
+        value=execution.output_file(params.get("value")) if (params.get("value") is not None) else None,
+        vector=execution.output_file(params.get("vector")) if (params.get("vector") is not None) else None,
+    )
+    return ret
+
+
+def tensor2metric_execute(
+    params: Tensor2metricParameters,
+    execution: Execution,
+) -> Tensor2metricOutputs:
+    """
+    Generate maps of tensor-derived parameters.
+    
+    
+    
+    References:
+    
+    Basser, P. J.; Mattiello, J. & Lebihan, D. MR diffusion tensor spectroscopy
+    and imaging. Biophysical Journal, 1994, 66, 259-267
+    
+    Westin, C. F.; Peled, S.; Gudbjartsson, H.; Kikinis, R. & Jolesz, F. A.
+    Geometrical diffusion measures for MRI from tensor basis analysis. Proc Intl
+    Soc Mag Reson Med, 1997, 5, 1742.
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `Tensor2metricOutputs`).
+    """
+    params = execution.params(params)
+    cargs = tensor2metric_cargs(params, execution)
+    ret = tensor2metric_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def tensor2metric(
+    tensor: InputPathType,
+    adc: str | None = None,
+    fa: str | None = None,
+    ad: str | None = None,
+    rd: str | None = None,
+    cl: str | None = None,
+    cp: str | None = None,
+    cs: str | None = None,
+    value: str | None = None,
+    vector: str | None = None,
+    num: list[int] | None = None,
+    modulate: str | None = None,
+    mask: InputPathType | None = None,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[Tensor2metricConfigParameters] | None = None,
+    help_: bool = False,
+    version: bool = False,
+    runner: Runner | None = None,
+) -> Tensor2metricOutputs:
+    """
+    Generate maps of tensor-derived parameters.
+    
+    
+    
+    References:
+    
+    Basser, P. J.; Mattiello, J. & Lebihan, D. MR diffusion tensor spectroscopy
+    and imaging. Biophysical Journal, 1994, 66, 259-267
+    
+    Westin, C. F.; Peled, S.; Gudbjartsson, H.; Kikinis, R. & Jolesz, F. A.
+    Geometrical diffusion measures for MRI from tensor basis analysis. Proc Intl
+    Soc Mag Reson Med, 1997, 5, 1742.
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        tensor: the input tensor image.
+        adc: compute the mean apparent diffusion coefficient (ADC) of the\
+            diffusion tensor. (sometimes also referred to as the mean diffusivity\
+            (MD)).
+        fa: compute the fractional anisotropy (FA) of the diffusion tensor.
+        ad: compute the axial diffusivity (AD) of the diffusion tensor.\
+            (equivalent to the principal eigenvalue).
+        rd: compute the radial diffusivity (RD) of the diffusion tensor.\
+            (equivalent to the mean of the two non-principal eigenvalues).
+        cl: compute the linearity metric of the diffusion tensor. (one of the\
+            three Westin shape metrics).
+        cp: compute the planarity metric of the diffusion tensor. (one of the\
+            three Westin shape metrics).
+        cs: compute the sphericity metric of the diffusion tensor. (one of the\
+            three Westin shape metrics).
+        value: compute the selected eigenvalue(s) of the diffusion tensor.
+        vector: compute the selected eigenvector(s) of the diffusion tensor.
+        num: specify the desired eigenvalue/eigenvector(s). Note that several\
+            eigenvalues can be specified as a number sequence. For example, '1,3'\
+            specifies the principal (1) and minor (3) eigenvalues/eigenvectors\
+            (default = 1).
+        modulate: specify how to modulate the magnitude of the eigenvectors.\
+            Valid choices are: none, FA, eigval (default = FA).
+        mask: only perform computation within the specified binary brain mask\
+            image.
+        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 `Tensor2metricOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(TENSOR2METRIC_METADATA)
+    params = tensor2metric_params(
+        adc=adc,
+        fa=fa,
+        ad=ad,
+        rd=rd,
+        cl=cl,
+        cp=cp,
+        cs=cs,
+        value=value,
+        vector=vector,
+        num=num,
+        modulate=modulate,
+        mask=mask,
+        info=info,
+        quiet=quiet,
+        debug=debug,
+        force=force,
+        nthreads=nthreads,
+        config=config,
+        help_=help_,
+        version=version,
+        tensor=tensor,
+    )
+    return tensor2metric_execute(params, execution)
+
+
+__all__ = [
+    "TENSOR2METRIC_METADATA",
+    "Tensor2metricConfigParameters",
+    "Tensor2metricOutputs",
+    "Tensor2metricParameters",
+    "tensor2metric",
+    "tensor2metric_config_params",
+    "tensor2metric_params",
+]