niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/v__align_partial_oblique.py

@@ -0,0 +1,285 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V__ALIGN_PARTIAL_OBLIQUE_METADATA = Metadata(
+    id="8266c2389908e7353d0356e57b5059a88cdc6548.boutiques",
+    name="@align_partial_oblique",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+VAlignPartialObliqueParameters = typing.TypedDict('VAlignPartialObliqueParameters', {
+    "__STYX_TYPE__": typing.Literal["@align_partial_oblique"],
+    "base": InputPathType,
+    "input": InputPathType,
+    "suffix": typing.NotRequired[str | None],
+    "keep_tmp": bool,
+    "clean": bool,
+    "dxyz": typing.NotRequired[float | None],
+    "dx": typing.NotRequired[float | None],
+    "dy": typing.NotRequired[float | None],
+    "dz": typing.NotRequired[float | None],
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "@align_partial_oblique": v__align_partial_oblique_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 {
+        "@align_partial_oblique": v__align_partial_oblique_outputs,
+    }.get(t)
+
+
+class VAlignPartialObliqueOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v__align_partial_oblique(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    aligned_output: OutputPathType
+    """Aligned partial coverage T1 weighted dataset"""
+
+
+def v__align_partial_oblique_params(
+    base: InputPathType,
+    input_: InputPathType,
+    suffix: str | None = None,
+    keep_tmp: bool = False,
+    clean: bool = False,
+    dxyz: float | None = None,
+    dx: float | None = None,
+    dy: float | None = None,
+    dz: float | None = None,
+) -> VAlignPartialObliqueParameters:
+    """
+    Build parameters.
+    
+    Args:
+        base: Reference anatomical full coverage volume.
+        input_: Partial coverage T1 weighted non-oblique dataset.
+        suffix: Output dataset name is formed by adding SUF to the prefix of\
+            the base dataset. The default suffix is _alnd_PartialCoverageObliqueT1.
+        keep_tmp: Keep temporary files.
+        clean: Clean all temp files, likely left from -keep_tmp option then\
+            exit.
+        dxyz: Cubic voxel size of output dataset in TLRC space Default MM is 1.
+        dx: Size of voxel in the x direction (Right-Left). Default is 1mm.
+        dy: Size of voxel in the y direction (Anterior-Posterior). Default is\
+            1mm.
+        dz: Size of voxel in the z direction (Inferior-Superior). Default is\
+            1mm.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "@align_partial_oblique",
+        "base": base,
+        "input": input_,
+        "keep_tmp": keep_tmp,
+        "clean": clean,
+    }
+    if suffix is not None:
+        params["suffix"] = suffix
+    if dxyz is not None:
+        params["dxyz"] = dxyz
+    if dx is not None:
+        params["dx"] = dx
+    if dy is not None:
+        params["dy"] = dy
+    if dz is not None:
+        params["dz"] = dz
+    return params
+
+
+def v__align_partial_oblique_cargs(
+    params: VAlignPartialObliqueParameters,
+    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("@align_partial_oblique")
+    cargs.extend([
+        "-base",
+        execution.input_file(params.get("base"))
+    ])
+    cargs.extend([
+        "-input",
+        execution.input_file(params.get("input"))
+    ])
+    if params.get("suffix") is not None:
+        cargs.extend([
+            "-suffix",
+            params.get("suffix")
+        ])
+    if params.get("keep_tmp"):
+        cargs.append("-keep_tmp")
+    if params.get("clean"):
+        cargs.append("-clean")
+    if params.get("dxyz") is not None:
+        cargs.extend([
+            "-dxyz",
+            str(params.get("dxyz"))
+        ])
+    if params.get("dx") is not None:
+        cargs.extend([
+            "-dx",
+            str(params.get("dx"))
+        ])
+    if params.get("dy") is not None:
+        cargs.extend([
+            "-dy",
+            str(params.get("dy"))
+        ])
+    if params.get("dz") is not None:
+        cargs.extend([
+            "-dz",
+            str(params.get("dz"))
+        ])
+    return cargs
+
+
+def v__align_partial_oblique_outputs(
+    params: VAlignPartialObliqueParameters,
+    execution: Execution,
+) -> VAlignPartialObliqueOutputs:
+    """
+    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 = VAlignPartialObliqueOutputs(
+        root=execution.output_file("."),
+        aligned_output=execution.output_file(pathlib.Path(params.get("base")).name + "_alnd_" + pathlib.Path(params.get("input")).name + ".nii.gz"),
+    )
+    return ret
+
+
+def v__align_partial_oblique_execute(
+    params: VAlignPartialObliqueParameters,
+    execution: Execution,
+) -> VAlignPartialObliqueOutputs:
+    """
+    A script to align a full coverage T1 weighted non-oblique dataset to match a
+    partial coverage T1 weighted non-oblique dataset. Alignment is done with a
+    rotation and shift (6 parameters) transform only.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `VAlignPartialObliqueOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v__align_partial_oblique_cargs(params, execution)
+    ret = v__align_partial_oblique_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v__align_partial_oblique(
+    base: InputPathType,
+    input_: InputPathType,
+    suffix: str | None = None,
+    keep_tmp: bool = False,
+    clean: bool = False,
+    dxyz: float | None = None,
+    dx: float | None = None,
+    dy: float | None = None,
+    dz: float | None = None,
+    runner: Runner | None = None,
+) -> VAlignPartialObliqueOutputs:
+    """
+    A script to align a full coverage T1 weighted non-oblique dataset to match a
+    partial coverage T1 weighted non-oblique dataset. Alignment is done with a
+    rotation and shift (6 parameters) transform only.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        base: Reference anatomical full coverage volume.
+        input_: Partial coverage T1 weighted non-oblique dataset.
+        suffix: Output dataset name is formed by adding SUF to the prefix of\
+            the base dataset. The default suffix is _alnd_PartialCoverageObliqueT1.
+        keep_tmp: Keep temporary files.
+        clean: Clean all temp files, likely left from -keep_tmp option then\
+            exit.
+        dxyz: Cubic voxel size of output dataset in TLRC space Default MM is 1.
+        dx: Size of voxel in the x direction (Right-Left). Default is 1mm.
+        dy: Size of voxel in the y direction (Anterior-Posterior). Default is\
+            1mm.
+        dz: Size of voxel in the z direction (Inferior-Superior). Default is\
+            1mm.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `VAlignPartialObliqueOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__ALIGN_PARTIAL_OBLIQUE_METADATA)
+    params = v__align_partial_oblique_params(
+        base=base,
+        input_=input_,
+        suffix=suffix,
+        keep_tmp=keep_tmp,
+        clean=clean,
+        dxyz=dxyz,
+        dx=dx,
+        dy=dy,
+        dz=dz,
+    )
+    return v__align_partial_oblique_execute(params, execution)
+
+
+__all__ = [
+    "VAlignPartialObliqueOutputs",
+    "VAlignPartialObliqueParameters",
+    "V__ALIGN_PARTIAL_OBLIQUE_METADATA",
+    "v__align_partial_oblique",
+    "v__align_partial_oblique_params",
+]

niwrap_afni/afni/v__anaticor.py

@@ -0,0 +1,326 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V__ANATICOR_METADATA = Metadata(
+    id="48ef68fd2da1d36a9c97f8ae28f53b818a2fe8ee.boutiques",
+    name="@ANATICOR",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+VAnaticorParameters = typing.TypedDict('VAnaticorParameters', {
+    "__STYX_TYPE__": typing.Literal["@ANATICOR"],
+    "ts": InputPathType,
+    "polort": str,
+    "motion": InputPathType,
+    "aseg": InputPathType,
+    "prefix": str,
+    "radius": typing.NotRequired[float | None],
+    "view": typing.NotRequired[str | None],
+    "nuisance": typing.NotRequired[InputPathType | None],
+    "no_ventricles": bool,
+    "Rsq_WMe": bool,
+    "coverage": bool,
+    "verb": bool,
+    "dirty": bool,
+    "echo": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "@ANATICOR": v__anaticor_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 {
+        "@ANATICOR": v__anaticor_outputs,
+    }.get(t)
+
+
+class VAnaticorOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v__anaticor(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_files: OutputPathType
+    """Output files with the prefix specified by the -prefix option."""
+
+
+def v__anaticor_params(
+    ts: InputPathType,
+    polort: str,
+    motion: InputPathType,
+    aseg: InputPathType,
+    prefix: str,
+    radius: float | None = None,
+    view: str | None = None,
+    nuisance: InputPathType | None = None,
+    no_ventricles: bool = False,
+    rsq_wme: bool = False,
+    coverage: bool = False,
+    verb: bool = False,
+    dirty: bool = False,
+    echo: bool = False,
+) -> VAnaticorParameters:
+    """
+    Build parameters.
+    
+    Args:
+        ts: Time series volume which should have already undergone\
+            preprocessing steps such as despiking, RetroIcor, RVT correction, time\
+            shifting, and volume registration.
+        polort: Polynomial for linear trend removal. Use the same order as for\
+            afni_proc.py.
+        motion: Head motion parameters from 3dvolreg, also created by\
+            afni_proc.py.
+        aseg: Aseg file from FreeSurfer's segmentation. This aseg volume must\
+            be in register with the EPI time series.
+        prefix: Use output (residual time series) for a prefix.
+        radius: The radius of a local sphere mask in mm. Default is 15 mm for\
+            high resolution 1.7x1.7x3mm data.
+        view: Set the view of the output data. Default is +orig. Choose from\
+            +orig, +acpc, or +tlrc.
+        nuisance: Other nuisance regressors. Each regressor is a column in .1D\
+            file.
+        no_ventricles: Do not include LVe regressor.
+        rsq_wme: Produce an explained variance map for WMeLOCAL regressor.
+        coverage: Produce a spatial coverage map of WMeLOCAL regressor.
+        verb: Verbose flag.
+        dirty: Keep temporary files.
+        echo: Echo each script command for debugging.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "@ANATICOR",
+        "ts": ts,
+        "polort": polort,
+        "motion": motion,
+        "aseg": aseg,
+        "prefix": prefix,
+        "no_ventricles": no_ventricles,
+        "Rsq_WMe": rsq_wme,
+        "coverage": coverage,
+        "verb": verb,
+        "dirty": dirty,
+        "echo": echo,
+    }
+    if radius is not None:
+        params["radius"] = radius
+    if view is not None:
+        params["view"] = view
+    if nuisance is not None:
+        params["nuisance"] = nuisance
+    return params
+
+
+def v__anaticor_cargs(
+    params: VAnaticorParameters,
+    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("@ANATICOR")
+    cargs.extend([
+        "-ts",
+        execution.input_file(params.get("ts"))
+    ])
+    cargs.extend([
+        "-polort",
+        params.get("polort")
+    ])
+    cargs.extend([
+        "-motion",
+        execution.input_file(params.get("motion"))
+    ])
+    cargs.append(execution.input_file(params.get("aseg")))
+    cargs.extend([
+        "-prefix",
+        params.get("prefix")
+    ])
+    if params.get("radius") is not None:
+        cargs.extend([
+            "-radius",
+            str(params.get("radius"))
+        ])
+    if params.get("view") is not None:
+        cargs.append(params.get("view"))
+    if params.get("nuisance") is not None:
+        cargs.extend([
+            "-nuisance",
+            execution.input_file(params.get("nuisance"))
+        ])
+    if params.get("no_ventricles"):
+        cargs.append("-no_ventricles")
+    if params.get("Rsq_WMe"):
+        cargs.append("-Rsq_WMe")
+    if params.get("coverage"):
+        cargs.append("-coverage")
+    if params.get("verb"):
+        cargs.append("-verb")
+    if params.get("dirty"):
+        cargs.append("-dirty")
+    if params.get("echo"):
+        cargs.append("-echo")
+    return cargs
+
+
+def v__anaticor_outputs(
+    params: VAnaticorParameters,
+    execution: Execution,
+) -> VAnaticorOutputs:
+    """
+    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 = VAnaticorOutputs(
+        root=execution.output_file("."),
+        output_files=execution.output_file(params.get("prefix")),
+    )
+    return ret
+
+
+def v__anaticor_execute(
+    params: VAnaticorParameters,
+    execution: Execution,
+) -> VAnaticorOutputs:
+    """
+    Script to produce a residual time series cleaned by ANATICOR model.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `VAnaticorOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v__anaticor_cargs(params, execution)
+    ret = v__anaticor_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v__anaticor(
+    ts: InputPathType,
+    polort: str,
+    motion: InputPathType,
+    aseg: InputPathType,
+    prefix: str,
+    radius: float | None = None,
+    view: str | None = None,
+    nuisance: InputPathType | None = None,
+    no_ventricles: bool = False,
+    rsq_wme: bool = False,
+    coverage: bool = False,
+    verb: bool = False,
+    dirty: bool = False,
+    echo: bool = False,
+    runner: Runner | None = None,
+) -> VAnaticorOutputs:
+    """
+    Script to produce a residual time series cleaned by ANATICOR model.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        ts: Time series volume which should have already undergone\
+            preprocessing steps such as despiking, RetroIcor, RVT correction, time\
+            shifting, and volume registration.
+        polort: Polynomial for linear trend removal. Use the same order as for\
+            afni_proc.py.
+        motion: Head motion parameters from 3dvolreg, also created by\
+            afni_proc.py.
+        aseg: Aseg file from FreeSurfer's segmentation. This aseg volume must\
+            be in register with the EPI time series.
+        prefix: Use output (residual time series) for a prefix.
+        radius: The radius of a local sphere mask in mm. Default is 15 mm for\
+            high resolution 1.7x1.7x3mm data.
+        view: Set the view of the output data. Default is +orig. Choose from\
+            +orig, +acpc, or +tlrc.
+        nuisance: Other nuisance regressors. Each regressor is a column in .1D\
+            file.
+        no_ventricles: Do not include LVe regressor.
+        rsq_wme: Produce an explained variance map for WMeLOCAL regressor.
+        coverage: Produce a spatial coverage map of WMeLOCAL regressor.
+        verb: Verbose flag.
+        dirty: Keep temporary files.
+        echo: Echo each script command for debugging.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `VAnaticorOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__ANATICOR_METADATA)
+    params = v__anaticor_params(
+        ts=ts,
+        polort=polort,
+        motion=motion,
+        aseg=aseg,
+        prefix=prefix,
+        radius=radius,
+        view=view,
+        nuisance=nuisance,
+        no_ventricles=no_ventricles,
+        rsq_wme=rsq_wme,
+        coverage=coverage,
+        verb=verb,
+        dirty=dirty,
+        echo=echo,
+    )
+    return v__anaticor_execute(params, execution)
+
+
+__all__ = [
+    "VAnaticorOutputs",
+    "VAnaticorParameters",
+    "V__ANATICOR_METADATA",
+    "v__anaticor",
+    "v__anaticor_params",
+]