niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/v__suma_acknowledge.py

@@ -0,0 +1,259 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V__SUMA_ACKNOWLEDGE_METADATA = Metadata(
+    id="a8f4715fa5105c4c0609bd564b7d507bb058f088.boutiques",
+    name="@suma_acknowledge",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+VSumaAcknowledgeParameters = typing.TypedDict('VSumaAcknowledgeParameters', {
+    "__STYX_TYPE__": typing.Literal["@suma_acknowledge"],
+    "input_file": InputPathType,
+    "surface_file": InputPathType,
+    "output_prefix": str,
+    "center_flag": bool,
+    "subsurface_file": typing.NotRequired[str | None],
+    "scale_factor": typing.NotRequired[float | None],
+    "reduce_factor": 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 {
+        "@suma_acknowledge": v__suma_acknowledge_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 {
+        "@suma_acknowledge": v__suma_acknowledge_outputs,
+    }.get(t)
+
+
+class VSumaAcknowledgeOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v__suma_acknowledge(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_file: OutputPathType
+    """Output graph dataset"""
+
+
+def v__suma_acknowledge_params(
+    input_file: InputPathType,
+    surface_file: InputPathType,
+    output_prefix: str,
+    center_flag: bool = False,
+    subsurface_file: str | None = None,
+    scale_factor: float | None = None,
+    reduce_factor: float | None = None,
+) -> VSumaAcknowledgeParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_file: Required input text file with format for each line: first\
+            last groupname.
+        surface_file: Required surface to place nodes.
+        output_prefix: Output prefix for graph dataset.
+        center_flag: Put center coord at x,y,z=0,0,0. Otherwise, uses average\
+            xyz in surface.
+        subsurface_file: Surface for surrounding members of group (use ld2,\
+            ld4, ld5, ld6, .... default is ld5).
+        scale_factor: Scale xyz for group nodes (default is 1.0).
+        reduce_factor: Scale xyz offsets for member nodes (xyz/r), default is\
+            10.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "@suma_acknowledge",
+        "input_file": input_file,
+        "surface_file": surface_file,
+        "output_prefix": output_prefix,
+        "center_flag": center_flag,
+    }
+    if subsurface_file is not None:
+        params["subsurface_file"] = subsurface_file
+    if scale_factor is not None:
+        params["scale_factor"] = scale_factor
+    if reduce_factor is not None:
+        params["reduce_factor"] = reduce_factor
+    return params
+
+
+def v__suma_acknowledge_cargs(
+    params: VSumaAcknowledgeParameters,
+    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("@suma_acknowledge")
+    cargs.extend([
+        "-input",
+        execution.input_file(params.get("input_file"))
+    ])
+    cargs.extend([
+        "-surf",
+        execution.input_file(params.get("surface_file"))
+    ])
+    cargs.extend([
+        "-prefix",
+        params.get("output_prefix")
+    ])
+    if params.get("center_flag"):
+        cargs.append("-center")
+    if params.get("subsurface_file") is not None:
+        cargs.extend([
+            "-subsurf",
+            params.get("subsurface_file")
+        ])
+    if params.get("scale_factor") is not None:
+        cargs.extend([
+            "-scalefactor",
+            str(params.get("scale_factor"))
+        ])
+    if params.get("reduce_factor") is not None:
+        cargs.extend([
+            "-reducefactor",
+            str(params.get("reduce_factor"))
+        ])
+    return cargs
+
+
+def v__suma_acknowledge_outputs(
+    params: VSumaAcknowledgeParameters,
+    execution: Execution,
+) -> VSumaAcknowledgeOutputs:
+    """
+    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 = VSumaAcknowledgeOutputs(
+        root=execution.output_file("."),
+        output_file=execution.output_file(params.get("output_prefix") + "_graph_dataset"),
+    )
+    return ret
+
+
+def v__suma_acknowledge_execute(
+    params: VSumaAcknowledgeParameters,
+    execution: Execution,
+) -> VSumaAcknowledgeOutputs:
+    """
+    Demo script to create a graph dataset to show names of individuals and groups,
+    potentially useful for acknowledgements in a talk.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `VSumaAcknowledgeOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v__suma_acknowledge_cargs(params, execution)
+    ret = v__suma_acknowledge_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v__suma_acknowledge(
+    input_file: InputPathType,
+    surface_file: InputPathType,
+    output_prefix: str,
+    center_flag: bool = False,
+    subsurface_file: str | None = None,
+    scale_factor: float | None = None,
+    reduce_factor: float | None = None,
+    runner: Runner | None = None,
+) -> VSumaAcknowledgeOutputs:
+    """
+    Demo script to create a graph dataset to show names of individuals and groups,
+    potentially useful for acknowledgements in a talk.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        input_file: Required input text file with format for each line: first\
+            last groupname.
+        surface_file: Required surface to place nodes.
+        output_prefix: Output prefix for graph dataset.
+        center_flag: Put center coord at x,y,z=0,0,0. Otherwise, uses average\
+            xyz in surface.
+        subsurface_file: Surface for surrounding members of group (use ld2,\
+            ld4, ld5, ld6, .... default is ld5).
+        scale_factor: Scale xyz for group nodes (default is 1.0).
+        reduce_factor: Scale xyz offsets for member nodes (xyz/r), default is\
+            10.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `VSumaAcknowledgeOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__SUMA_ACKNOWLEDGE_METADATA)
+    params = v__suma_acknowledge_params(
+        input_file=input_file,
+        surface_file=surface_file,
+        output_prefix=output_prefix,
+        center_flag=center_flag,
+        subsurface_file=subsurface_file,
+        scale_factor=scale_factor,
+        reduce_factor=reduce_factor,
+    )
+    return v__suma_acknowledge_execute(params, execution)
+
+
+__all__ = [
+    "VSumaAcknowledgeOutputs",
+    "VSumaAcknowledgeParameters",
+    "V__SUMA_ACKNOWLEDGE_METADATA",
+    "v__suma_acknowledge",
+    "v__suma_acknowledge_params",
+]

niwrap_afni/afni/v__suma_align_to_experiment.py

@@ -0,0 +1,421 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V__SUMA_ALIGN_TO_EXPERIMENT_METADATA = Metadata(
+    id="8f81484159017f8749f8211125315dcfa8d64e88.boutiques",
+    name="@SUMA_AlignToExperiment",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+VSumaAlignToExperimentParameters = typing.TypedDict('VSumaAlignToExperimentParameters', {
+    "__STYX_TYPE__": typing.Literal["@SUMA_AlignToExperiment"],
+    "exp_anat": InputPathType,
+    "surf_anat": InputPathType,
+    "dxyz": typing.NotRequired[float | None],
+    "out_dxyz": typing.NotRequired[float | None],
+    "wd": bool,
+    "al": bool,
+    "al_opt": typing.NotRequired[str | None],
+    "ok_change_view": bool,
+    "strip_skull": typing.NotRequired[str | None],
+    "skull_strip_opt": typing.NotRequired[str | None],
+    "align_centers": bool,
+    "init_xform": typing.NotRequired[InputPathType | None],
+    "EA_clip_below": typing.NotRequired[float | None],
+    "prefix": typing.NotRequired[str | None],
+    "surf_anat_followers": typing.NotRequired[str | None],
+    "followers_interp": typing.NotRequired[str | None],
+    "atlas_followers": bool,
+    "echo": bool,
+    "keep_tmp": bool,
+    "overwrite_resp": typing.NotRequired[str | None],
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "@SUMA_AlignToExperiment": v__suma_align_to_experiment_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 {
+        "@SUMA_AlignToExperiment": v__suma_align_to_experiment_outputs,
+    }.get(t)
+
+
+class VSumaAlignToExperimentOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v__suma_align_to_experiment(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    aligned_volume: OutputPathType | None
+    """Output volume after alignment."""
+    additional_followers: OutputPathType | None
+    """Output followers dataset after transforming."""
+
+
+def v__suma_align_to_experiment_params(
+    exp_anat: InputPathType,
+    surf_anat: InputPathType,
+    dxyz: float | None = None,
+    out_dxyz: float | None = None,
+    wd: bool = False,
+    al: bool = False,
+    al_opt: str | None = None,
+    ok_change_view: bool = False,
+    strip_skull: str | None = None,
+    skull_strip_opt: str | None = None,
+    align_centers: bool = False,
+    init_xform: InputPathType | None = None,
+    ea_clip_below: float | None = None,
+    prefix: str | None = None,
+    surf_anat_followers: str | None = None,
+    followers_interp: str | None = None,
+    atlas_followers: bool = False,
+    echo: bool = False,
+    keep_tmp: bool = False,
+    overwrite_resp: str | None = None,
+) -> VSumaAlignToExperimentParameters:
+    """
+    Build parameters.
+    
+    Args:
+        exp_anat: Name of high resolution anatomical data set in register with\
+            experimental data.
+        surf_anat: Path and name of high resolution antomical data set used to\
+            create the surface.
+        dxyz: Optional parameter to downsample anatomical volumes to dxyz mm\
+            voxel resolution before registration.
+        out_dxyz: Output the final aligned volume at a cubic voxelsize of\
+            DXYZmm.
+        wd: Use 3dWarpDrive's general affine transform (12 param) instead of\
+            3dvolreg's 6 parameters.
+        al: Use 3dAllineate to do the 12 parameter alignment. Cost function is\
+            'lpa'.
+        al_opt: Specify set of options to pass to 3dAllineate.
+        ok_change_view: Be quiet when view of registered volume is changed to\
+            match that of the Experiment_Anatomy.
+        strip_skull: Use 3dSkullStrip to remove non-brain tissue.
+        skull_strip_opt: Pass the options to 3dSkullStrip.
+        align_centers: Add an additional transformation to align the volume\
+            centers.
+        init_xform: Apply affine transform file to Surface_Anatomy before\
+            beginning registration.
+        ea_clip_below: Set slices below CLPmm in 'Experiment Anatomy' to zero.
+        prefix: Prefix for the output volume.
+        surf_anat_followers: Apply the same alignment transform to additional\
+            datasets.
+        followers_interp: Set the interpolation mode for the follower datasets.
+        atlas_followers: Automatically set the followers to be atlases in the\
+            directory of -surf_anat.
+        echo: Echo all commands to terminal for debugging.
+        keep_tmp: Keep temporary files for debugging.
+        overwrite_resp: Answer 'overwrite' questions automatically.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "@SUMA_AlignToExperiment",
+        "exp_anat": exp_anat,
+        "surf_anat": surf_anat,
+        "wd": wd,
+        "al": al,
+        "ok_change_view": ok_change_view,
+        "align_centers": align_centers,
+        "atlas_followers": atlas_followers,
+        "echo": echo,
+        "keep_tmp": keep_tmp,
+    }
+    if dxyz is not None:
+        params["dxyz"] = dxyz
+    if out_dxyz is not None:
+        params["out_dxyz"] = out_dxyz
+    if al_opt is not None:
+        params["al_opt"] = al_opt
+    if strip_skull is not None:
+        params["strip_skull"] = strip_skull
+    if skull_strip_opt is not None:
+        params["skull_strip_opt"] = skull_strip_opt
+    if init_xform is not None:
+        params["init_xform"] = init_xform
+    if ea_clip_below is not None:
+        params["EA_clip_below"] = ea_clip_below
+    if prefix is not None:
+        params["prefix"] = prefix
+    if surf_anat_followers is not None:
+        params["surf_anat_followers"] = surf_anat_followers
+    if followers_interp is not None:
+        params["followers_interp"] = followers_interp
+    if overwrite_resp is not None:
+        params["overwrite_resp"] = overwrite_resp
+    return params
+
+
+def v__suma_align_to_experiment_cargs(
+    params: VSumaAlignToExperimentParameters,
+    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("@SUMA_AlignToExperiment")
+    cargs.extend([
+        "-exp_anat",
+        execution.input_file(params.get("exp_anat"))
+    ])
+    cargs.extend([
+        "-surf_anat",
+        execution.input_file(params.get("surf_anat"))
+    ])
+    if params.get("dxyz") is not None:
+        cargs.extend([
+            "-dxyz",
+            str(params.get("dxyz"))
+        ])
+    if params.get("out_dxyz") is not None:
+        cargs.extend([
+            "-out_dxyz",
+            str(params.get("out_dxyz"))
+        ])
+    if params.get("wd"):
+        cargs.append("-wd")
+    if params.get("al"):
+        cargs.append("-al")
+    if params.get("al_opt") is not None:
+        cargs.extend([
+            "-al_opt",
+            params.get("al_opt")
+        ])
+    if params.get("ok_change_view"):
+        cargs.append("-ok_change_view")
+    if params.get("strip_skull") is not None:
+        cargs.extend([
+            "-strip_skull",
+            params.get("strip_skull")
+        ])
+    if params.get("skull_strip_opt") is not None:
+        cargs.extend([
+            "-skull_strip_opt",
+            params.get("skull_strip_opt")
+        ])
+    if params.get("align_centers"):
+        cargs.append("-align_centers")
+    if params.get("init_xform") is not None:
+        cargs.extend([
+            "-init_xform",
+            execution.input_file(params.get("init_xform"))
+        ])
+    if params.get("EA_clip_below") is not None:
+        cargs.extend([
+            "-EA_clip_below",
+            str(params.get("EA_clip_below"))
+        ])
+    if params.get("prefix") is not None:
+        cargs.extend([
+            "-prefix",
+            params.get("prefix")
+        ])
+    if params.get("surf_anat_followers") is not None:
+        cargs.extend([
+            "-surf_anat_followers",
+            params.get("surf_anat_followers")
+        ])
+    if params.get("followers_interp") is not None:
+        cargs.extend([
+            "-followers_interp",
+            params.get("followers_interp")
+        ])
+    if params.get("atlas_followers"):
+        cargs.append("-atlas_followers")
+    if params.get("echo"):
+        cargs.append("-echo")
+    if params.get("keep_tmp"):
+        cargs.append("-keep_tmp")
+    if params.get("overwrite_resp") is not None:
+        cargs.extend([
+            "-overwrite_resp",
+            params.get("overwrite_resp")
+        ])
+    return cargs
+
+
+def v__suma_align_to_experiment_outputs(
+    params: VSumaAlignToExperimentParameters,
+    execution: Execution,
+) -> VSumaAlignToExperimentOutputs:
+    """
+    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 = VSumaAlignToExperimentOutputs(
+        root=execution.output_file("."),
+        aligned_volume=execution.output_file(params.get("prefix") + "_Alnd_Exp.nii.gz") if (params.get("prefix") is not None) else None,
+        additional_followers=execution.output_file(params.get("prefix") + "_Alnd_Exp_Fdset.nii.gz") if (params.get("prefix") is not None) else None,
+    )
+    return ret
+
+
+def v__suma_align_to_experiment_execute(
+    params: VSumaAlignToExperimentParameters,
+    execution: Execution,
+) -> VSumaAlignToExperimentOutputs:
+    """
+    Creates a version of Surface Anatomy that is registered to Experiment Anatomy.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `VSumaAlignToExperimentOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v__suma_align_to_experiment_cargs(params, execution)
+    ret = v__suma_align_to_experiment_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v__suma_align_to_experiment(
+    exp_anat: InputPathType,
+    surf_anat: InputPathType,
+    dxyz: float | None = None,
+    out_dxyz: float | None = None,
+    wd: bool = False,
+    al: bool = False,
+    al_opt: str | None = None,
+    ok_change_view: bool = False,
+    strip_skull: str | None = None,
+    skull_strip_opt: str | None = None,
+    align_centers: bool = False,
+    init_xform: InputPathType | None = None,
+    ea_clip_below: float | None = None,
+    prefix: str | None = None,
+    surf_anat_followers: str | None = None,
+    followers_interp: str | None = None,
+    atlas_followers: bool = False,
+    echo: bool = False,
+    keep_tmp: bool = False,
+    overwrite_resp: str | None = None,
+    runner: Runner | None = None,
+) -> VSumaAlignToExperimentOutputs:
+    """
+    Creates a version of Surface Anatomy that is registered to Experiment Anatomy.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        exp_anat: Name of high resolution anatomical data set in register with\
+            experimental data.
+        surf_anat: Path and name of high resolution antomical data set used to\
+            create the surface.
+        dxyz: Optional parameter to downsample anatomical volumes to dxyz mm\
+            voxel resolution before registration.
+        out_dxyz: Output the final aligned volume at a cubic voxelsize of\
+            DXYZmm.
+        wd: Use 3dWarpDrive's general affine transform (12 param) instead of\
+            3dvolreg's 6 parameters.
+        al: Use 3dAllineate to do the 12 parameter alignment. Cost function is\
+            'lpa'.
+        al_opt: Specify set of options to pass to 3dAllineate.
+        ok_change_view: Be quiet when view of registered volume is changed to\
+            match that of the Experiment_Anatomy.
+        strip_skull: Use 3dSkullStrip to remove non-brain tissue.
+        skull_strip_opt: Pass the options to 3dSkullStrip.
+        align_centers: Add an additional transformation to align the volume\
+            centers.
+        init_xform: Apply affine transform file to Surface_Anatomy before\
+            beginning registration.
+        ea_clip_below: Set slices below CLPmm in 'Experiment Anatomy' to zero.
+        prefix: Prefix for the output volume.
+        surf_anat_followers: Apply the same alignment transform to additional\
+            datasets.
+        followers_interp: Set the interpolation mode for the follower datasets.
+        atlas_followers: Automatically set the followers to be atlases in the\
+            directory of -surf_anat.
+        echo: Echo all commands to terminal for debugging.
+        keep_tmp: Keep temporary files for debugging.
+        overwrite_resp: Answer 'overwrite' questions automatically.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `VSumaAlignToExperimentOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__SUMA_ALIGN_TO_EXPERIMENT_METADATA)
+    params = v__suma_align_to_experiment_params(
+        exp_anat=exp_anat,
+        surf_anat=surf_anat,
+        dxyz=dxyz,
+        out_dxyz=out_dxyz,
+        wd=wd,
+        al=al,
+        al_opt=al_opt,
+        ok_change_view=ok_change_view,
+        strip_skull=strip_skull,
+        skull_strip_opt=skull_strip_opt,
+        align_centers=align_centers,
+        init_xform=init_xform,
+        ea_clip_below=ea_clip_below,
+        prefix=prefix,
+        surf_anat_followers=surf_anat_followers,
+        followers_interp=followers_interp,
+        atlas_followers=atlas_followers,
+        echo=echo,
+        keep_tmp=keep_tmp,
+        overwrite_resp=overwrite_resp,
+    )
+    return v__suma_align_to_experiment_execute(params, execution)
+
+
+__all__ = [
+    "VSumaAlignToExperimentOutputs",
+    "VSumaAlignToExperimentParameters",
+    "V__SUMA_ALIGN_TO_EXPERIMENT_METADATA",
+    "v__suma_align_to_experiment",
+    "v__suma_align_to_experiment_params",
+]