niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/v__animal_warper.py

@@ -0,0 +1,602 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V__ANIMAL_WARPER_METADATA = Metadata(
+    id="4c704ce05525848e08865cb268e84925dc07c58a.boutiques",
+    name="@animal_warper",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+VAnimalWarperParameters = typing.TypedDict('VAnimalWarperParameters', {
+    "__STYX_TYPE__": typing.Literal["@animal_warper"],
+    "input_file": InputPathType,
+    "base_template": InputPathType,
+    "output_dir": str,
+    "brainmask": typing.NotRequired[InputPathType | None],
+    "atlases": typing.NotRequired[list[InputPathType] | None],
+    "atlas_followers": typing.NotRequired[list[InputPathType] | None],
+    "seg_followers": typing.NotRequired[list[InputPathType] | None],
+    "template_followers": typing.NotRequired[list[InputPathType] | None],
+    "dset_followers": typing.NotRequired[list[InputPathType] | None],
+    "roidset_followers": typing.NotRequired[list[InputPathType] | None],
+    "input_abbrev": typing.NotRequired[str | None],
+    "base_abbrev": typing.NotRequired[str | None],
+    "atlas_abbrevs": typing.NotRequired[list[str] | None],
+    "template_abbrevs": typing.NotRequired[list[str] | None],
+    "seg_abbrevs": typing.NotRequired[list[str] | None],
+    "dset_abbrevs": typing.NotRequired[list[str] | None],
+    "roidset_abbrevs": typing.NotRequired[list[str] | None],
+    "align_centers_meth": typing.NotRequired[str | None],
+    "aff_move_opt": typing.NotRequired[str | None],
+    "cost": typing.NotRequired[str | None],
+    "maxlev": typing.NotRequired[float | None],
+    "no_surfaces": bool,
+    "feature_size": typing.NotRequired[float | None],
+    "supersize": bool,
+    "init_scale": typing.NotRequired[float | None],
+    "mode_smooth_size": typing.NotRequired[float | None],
+    "mode_smooth_replacement_off": bool,
+    "center_out": typing.NotRequired[str | None],
+    "align_type": typing.NotRequired[str | None],
+    "extra_qw_opts": typing.NotRequired[str | None],
+    "keep_temp": bool,
+    "version": bool,
+    "ok_to_exist": 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 {
+        "@animal_warper": v__animal_warper_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 {
+        "@animal_warper": v__animal_warper_outputs,
+    }.get(t)
+
+
+class VAnimalWarperOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v__animal_warper(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    warp2std: OutputPathType
+    """input dataset nonlinearly warped to template"""
+    qc_image_initial: OutputPathType
+    """initial QC image montage showing overlap of source and base dataset"""
+    qc_image_initial_sh: OutputPathType
+    """initial QC image montage after shifting centers of source and base
+    dataset"""
+    dset_followers_out: OutputPathType
+    """copy(s) of -dset_followers mapped to template space"""
+    roidset_followers_out: OutputPathType
+    """copy(s) of -roidset_followers mapped to template space"""
+    animal_outs_guide: OutputPathType
+    """guide to data in output directory"""
+
+
+def v__animal_warper_params(
+    input_file: InputPathType,
+    base_template: InputPathType,
+    output_dir: str,
+    brainmask: InputPathType | None = None,
+    atlases: list[InputPathType] | None = None,
+    atlas_followers: list[InputPathType] | None = None,
+    seg_followers: list[InputPathType] | None = None,
+    template_followers: list[InputPathType] | None = None,
+    dset_followers: list[InputPathType] | None = None,
+    roidset_followers: list[InputPathType] | None = None,
+    input_abbrev: str | None = None,
+    base_abbrev: str | None = None,
+    atlas_abbrevs: list[str] | None = None,
+    template_abbrevs: list[str] | None = None,
+    seg_abbrevs: list[str] | None = None,
+    dset_abbrevs: list[str] | None = None,
+    roidset_abbrevs: list[str] | None = None,
+    align_centers_meth: str | None = None,
+    aff_move_opt: str | None = None,
+    cost: str | None = None,
+    maxlev: float | None = None,
+    no_surfaces: bool = False,
+    feature_size: float | None = None,
+    supersize: bool = False,
+    init_scale: float | None = None,
+    mode_smooth_size: float | None = None,
+    mode_smooth_replacement_off: bool = False,
+    center_out: str | None = None,
+    align_type: str | None = None,
+    extra_qw_opts: str | None = None,
+    keep_temp: bool = False,
+    version: bool = False,
+    ok_to_exist: bool = False,
+    echo: bool = False,
+) -> VAnimalWarperParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_file: input dataset to align to base template.
+        base_template: base dataset (template) to align with.
+        output_dir: output directory where all processing will be performed.
+        brainmask: provide a brainmask in the base template space.
+        atlases: one or more atlas datasets in the base volume space.
+        atlas_followers: one or more atlas datasets in the base volume space.
+        seg_followers: one or more segmentation datasets in the base volume\
+            space.
+        template_followers: one or more datasets in the template volume space.
+        dset_followers: one or more datasets in the input volume space.
+        roidset_followers: one or more (int-valued) datasets in the input\
+            volume space.
+        input_abbrev: specify abbreviation for input dataset.
+        base_abbrev: specify abbreviation for base dataset.
+        atlas_abbrevs: specify an abbreviation for each atlas follower dataset.
+        template_abbrevs: specify an abbreviation for each template follower\
+            dataset.
+        seg_abbrevs: specify an abbreviation for each segmentation follower\
+            dataset.
+        dset_abbrevs: specify an abbreviation for each dataset follower dataset.
+        roidset_abbrevs: specify an abbreviation for each ROI dataset follower\
+            dataset.
+        align_centers_meth: center alignment method to use.
+        aff_move_opt: alignment movement options for affine alignment step.
+        cost: cost function for affine and nonlinear alignment.
+        maxlev: Max level for nonlinear warping. Final patch size is determined\
+            based on this value.
+        no_surfaces: Do not make surfaces for atlas regions in native space.
+        feature_size: Set feature size for affine alignment (in mm).
+        supersize: Allow up to 50% size difference between subject and template.
+        init_scale: Approximate length ratio of input to template for initial\
+            scaling.
+        mode_smooth_size: Modal smoothing kernel size in voxels.
+        mode_smooth_replacement_off: Turn off replacement in modal smoothing.
+        center_out: Center native-space output to native original space or\
+            template space center-shifted.
+        align_type: Specify level of alignment.
+        extra_qw_opts: Additional options to add to existing options for\
+            3dQwarp.
+        keep_temp: Keep temporary files including awpy directory and other\
+            intermediate datasets.
+        version: Display the program version.
+        ok_to_exist: Reuse and do not overwrite existing datasets.
+        echo: Copy all commands being run into the terminal.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "@animal_warper",
+        "input_file": input_file,
+        "base_template": base_template,
+        "output_dir": output_dir,
+        "no_surfaces": no_surfaces,
+        "supersize": supersize,
+        "mode_smooth_replacement_off": mode_smooth_replacement_off,
+        "keep_temp": keep_temp,
+        "version": version,
+        "ok_to_exist": ok_to_exist,
+        "echo": echo,
+    }
+    if brainmask is not None:
+        params["brainmask"] = brainmask
+    if atlases is not None:
+        params["atlases"] = atlases
+    if atlas_followers is not None:
+        params["atlas_followers"] = atlas_followers
+    if seg_followers is not None:
+        params["seg_followers"] = seg_followers
+    if template_followers is not None:
+        params["template_followers"] = template_followers
+    if dset_followers is not None:
+        params["dset_followers"] = dset_followers
+    if roidset_followers is not None:
+        params["roidset_followers"] = roidset_followers
+    if input_abbrev is not None:
+        params["input_abbrev"] = input_abbrev
+    if base_abbrev is not None:
+        params["base_abbrev"] = base_abbrev
+    if atlas_abbrevs is not None:
+        params["atlas_abbrevs"] = atlas_abbrevs
+    if template_abbrevs is not None:
+        params["template_abbrevs"] = template_abbrevs
+    if seg_abbrevs is not None:
+        params["seg_abbrevs"] = seg_abbrevs
+    if dset_abbrevs is not None:
+        params["dset_abbrevs"] = dset_abbrevs
+    if roidset_abbrevs is not None:
+        params["roidset_abbrevs"] = roidset_abbrevs
+    if align_centers_meth is not None:
+        params["align_centers_meth"] = align_centers_meth
+    if aff_move_opt is not None:
+        params["aff_move_opt"] = aff_move_opt
+    if cost is not None:
+        params["cost"] = cost
+    if maxlev is not None:
+        params["maxlev"] = maxlev
+    if feature_size is not None:
+        params["feature_size"] = feature_size
+    if init_scale is not None:
+        params["init_scale"] = init_scale
+    if mode_smooth_size is not None:
+        params["mode_smooth_size"] = mode_smooth_size
+    if center_out is not None:
+        params["center_out"] = center_out
+    if align_type is not None:
+        params["align_type"] = align_type
+    if extra_qw_opts is not None:
+        params["extra_qw_opts"] = extra_qw_opts
+    return params
+
+
+def v__animal_warper_cargs(
+    params: VAnimalWarperParameters,
+    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("@animal_warper")
+    cargs.append(execution.input_file(params.get("input_file")))
+    cargs.append(execution.input_file(params.get("base_template")))
+    cargs.append(params.get("output_dir"))
+    if params.get("brainmask") is not None:
+        cargs.append(execution.input_file(params.get("brainmask")))
+    if params.get("atlases") is not None:
+        cargs.extend([
+            "-atlas",
+            *[execution.input_file(f) for f in params.get("atlases")]
+        ])
+    if params.get("atlas_followers") is not None:
+        cargs.extend([
+            "-atlas_followers",
+            *[execution.input_file(f) for f in params.get("atlas_followers")]
+        ])
+    if params.get("seg_followers") is not None:
+        cargs.extend([
+            "-seg_followers",
+            *[execution.input_file(f) for f in params.get("seg_followers")]
+        ])
+    if params.get("template_followers") is not None:
+        cargs.extend([
+            "-template_followers",
+            *[execution.input_file(f) for f in params.get("template_followers")]
+        ])
+    if params.get("dset_followers") is not None:
+        cargs.extend([
+            "-dset_followers",
+            *[execution.input_file(f) for f in params.get("dset_followers")]
+        ])
+    if params.get("roidset_followers") is not None:
+        cargs.extend([
+            "-roidset_followers",
+            *[execution.input_file(f) for f in params.get("roidset_followers")]
+        ])
+    if params.get("input_abbrev") is not None:
+        cargs.extend([
+            "-input_abbrev",
+            params.get("input_abbrev")
+        ])
+    if params.get("base_abbrev") is not None:
+        cargs.extend([
+            "-base_abbrev",
+            params.get("base_abbrev")
+        ])
+    if params.get("atlas_abbrevs") is not None:
+        cargs.extend([
+            "-atlas_abbrevs",
+            *params.get("atlas_abbrevs")
+        ])
+    if params.get("template_abbrevs") is not None:
+        cargs.extend([
+            "-template_abbrevs",
+            *params.get("template_abbrevs")
+        ])
+    if params.get("seg_abbrevs") is not None:
+        cargs.extend([
+            "-seg_abbrevs",
+            *params.get("seg_abbrevs")
+        ])
+    if params.get("dset_abbrevs") is not None:
+        cargs.extend([
+            "-dset_abbrevs",
+            *params.get("dset_abbrevs")
+        ])
+    if params.get("roidset_abbrevs") is not None:
+        cargs.extend([
+            "-roidset_abbrevs",
+            *params.get("roidset_abbrevs")
+        ])
+    if params.get("align_centers_meth") is not None:
+        cargs.extend([
+            "-align_centers_meth",
+            params.get("align_centers_meth")
+        ])
+    if params.get("aff_move_opt") is not None:
+        cargs.extend([
+            "-aff_move_opt",
+            params.get("aff_move_opt")
+        ])
+    if params.get("cost") is not None:
+        cargs.extend([
+            "-cost",
+            params.get("cost")
+        ])
+    if params.get("maxlev") is not None:
+        cargs.extend([
+            "-maxlev",
+            str(params.get("maxlev"))
+        ])
+    if params.get("no_surfaces"):
+        cargs.append("-no_surfaces")
+    if params.get("feature_size") is not None:
+        cargs.extend([
+            "-feature_size",
+            str(params.get("feature_size"))
+        ])
+    if params.get("supersize"):
+        cargs.append("-supersize")
+    if params.get("init_scale") is not None:
+        cargs.extend([
+            "-init_scale",
+            str(params.get("init_scale"))
+        ])
+    if params.get("mode_smooth_size") is not None:
+        cargs.extend([
+            "-mode_smooth_size",
+            str(params.get("mode_smooth_size"))
+        ])
+    if params.get("mode_smooth_replacement_off"):
+        cargs.append("-mode_smooth_replacement_off")
+    if params.get("center_out") is not None:
+        cargs.extend([
+            "-center_out",
+            params.get("center_out")
+        ])
+    if params.get("align_type") is not None:
+        cargs.extend([
+            "-align_type",
+            params.get("align_type")
+        ])
+    if params.get("extra_qw_opts") is not None:
+        cargs.extend([
+            "-extra_qw_opts",
+            params.get("extra_qw_opts")
+        ])
+    if params.get("keep_temp"):
+        cargs.append("-keep_temp")
+    if params.get("version"):
+        cargs.append("-ver")
+    if params.get("ok_to_exist"):
+        cargs.append("-ok_to_exist")
+    if params.get("echo"):
+        cargs.append("-echo")
+    return cargs
+
+
+def v__animal_warper_outputs(
+    params: VAnimalWarperParameters,
+    execution: Execution,
+) -> VAnimalWarperOutputs:
+    """
+    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 = VAnimalWarperOutputs(
+        root=execution.output_file("."),
+        warp2std=execution.output_file("aw_results/" + pathlib.Path(params.get("input_file")).name + "_warp2std.nii.gz"),
+        qc_image_initial=execution.output_file("aw_results/init_qc_00.input+base*.jpg"),
+        qc_image_initial_sh=execution.output_file("aw_results/init_qc_01.input_sh+base*.jpg"),
+        dset_followers_out=execution.output_file("aw_results/DSET_FOLL.nii.gz"),
+        roidset_followers_out=execution.output_file("aw_results/ROIDSET_FOLL.nii.gz"),
+        animal_outs_guide=execution.output_file("aw_results/animal_outs.txt"),
+    )
+    return ret
+
+
+def v__animal_warper_execute(
+    params: VAnimalWarperParameters,
+    execution: Execution,
+) -> VAnimalWarperOutputs:
+    """
+    Align a subject structural dataset to a template and perform several
+    post-alignment operations.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `VAnimalWarperOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v__animal_warper_cargs(params, execution)
+    ret = v__animal_warper_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v__animal_warper(
+    input_file: InputPathType,
+    base_template: InputPathType,
+    output_dir: str,
+    brainmask: InputPathType | None = None,
+    atlases: list[InputPathType] | None = None,
+    atlas_followers: list[InputPathType] | None = None,
+    seg_followers: list[InputPathType] | None = None,
+    template_followers: list[InputPathType] | None = None,
+    dset_followers: list[InputPathType] | None = None,
+    roidset_followers: list[InputPathType] | None = None,
+    input_abbrev: str | None = None,
+    base_abbrev: str | None = None,
+    atlas_abbrevs: list[str] | None = None,
+    template_abbrevs: list[str] | None = None,
+    seg_abbrevs: list[str] | None = None,
+    dset_abbrevs: list[str] | None = None,
+    roidset_abbrevs: list[str] | None = None,
+    align_centers_meth: str | None = None,
+    aff_move_opt: str | None = None,
+    cost: str | None = None,
+    maxlev: float | None = None,
+    no_surfaces: bool = False,
+    feature_size: float | None = None,
+    supersize: bool = False,
+    init_scale: float | None = None,
+    mode_smooth_size: float | None = None,
+    mode_smooth_replacement_off: bool = False,
+    center_out: str | None = None,
+    align_type: str | None = None,
+    extra_qw_opts: str | None = None,
+    keep_temp: bool = False,
+    version: bool = False,
+    ok_to_exist: bool = False,
+    echo: bool = False,
+    runner: Runner | None = None,
+) -> VAnimalWarperOutputs:
+    """
+    Align a subject structural dataset to a template and perform several
+    post-alignment operations.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        input_file: input dataset to align to base template.
+        base_template: base dataset (template) to align with.
+        output_dir: output directory where all processing will be performed.
+        brainmask: provide a brainmask in the base template space.
+        atlases: one or more atlas datasets in the base volume space.
+        atlas_followers: one or more atlas datasets in the base volume space.
+        seg_followers: one or more segmentation datasets in the base volume\
+            space.
+        template_followers: one or more datasets in the template volume space.
+        dset_followers: one or more datasets in the input volume space.
+        roidset_followers: one or more (int-valued) datasets in the input\
+            volume space.
+        input_abbrev: specify abbreviation for input dataset.
+        base_abbrev: specify abbreviation for base dataset.
+        atlas_abbrevs: specify an abbreviation for each atlas follower dataset.
+        template_abbrevs: specify an abbreviation for each template follower\
+            dataset.
+        seg_abbrevs: specify an abbreviation for each segmentation follower\
+            dataset.
+        dset_abbrevs: specify an abbreviation for each dataset follower dataset.
+        roidset_abbrevs: specify an abbreviation for each ROI dataset follower\
+            dataset.
+        align_centers_meth: center alignment method to use.
+        aff_move_opt: alignment movement options for affine alignment step.
+        cost: cost function for affine and nonlinear alignment.
+        maxlev: Max level for nonlinear warping. Final patch size is determined\
+            based on this value.
+        no_surfaces: Do not make surfaces for atlas regions in native space.
+        feature_size: Set feature size for affine alignment (in mm).
+        supersize: Allow up to 50% size difference between subject and template.
+        init_scale: Approximate length ratio of input to template for initial\
+            scaling.
+        mode_smooth_size: Modal smoothing kernel size in voxels.
+        mode_smooth_replacement_off: Turn off replacement in modal smoothing.
+        center_out: Center native-space output to native original space or\
+            template space center-shifted.
+        align_type: Specify level of alignment.
+        extra_qw_opts: Additional options to add to existing options for\
+            3dQwarp.
+        keep_temp: Keep temporary files including awpy directory and other\
+            intermediate datasets.
+        version: Display the program version.
+        ok_to_exist: Reuse and do not overwrite existing datasets.
+        echo: Copy all commands being run into the terminal.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `VAnimalWarperOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__ANIMAL_WARPER_METADATA)
+    params = v__animal_warper_params(
+        input_file=input_file,
+        base_template=base_template,
+        output_dir=output_dir,
+        brainmask=brainmask,
+        atlases=atlases,
+        atlas_followers=atlas_followers,
+        seg_followers=seg_followers,
+        template_followers=template_followers,
+        dset_followers=dset_followers,
+        roidset_followers=roidset_followers,
+        input_abbrev=input_abbrev,
+        base_abbrev=base_abbrev,
+        atlas_abbrevs=atlas_abbrevs,
+        template_abbrevs=template_abbrevs,
+        seg_abbrevs=seg_abbrevs,
+        dset_abbrevs=dset_abbrevs,
+        roidset_abbrevs=roidset_abbrevs,
+        align_centers_meth=align_centers_meth,
+        aff_move_opt=aff_move_opt,
+        cost=cost,
+        maxlev=maxlev,
+        no_surfaces=no_surfaces,
+        feature_size=feature_size,
+        supersize=supersize,
+        init_scale=init_scale,
+        mode_smooth_size=mode_smooth_size,
+        mode_smooth_replacement_off=mode_smooth_replacement_off,
+        center_out=center_out,
+        align_type=align_type,
+        extra_qw_opts=extra_qw_opts,
+        keep_temp=keep_temp,
+        version=version,
+        ok_to_exist=ok_to_exist,
+        echo=echo,
+    )
+    return v__animal_warper_execute(params, execution)
+
+
+__all__ = [
+    "VAnimalWarperOutputs",
+    "VAnimalWarperParameters",
+    "V__ANIMAL_WARPER_METADATA",
+    "v__animal_warper",
+    "v__animal_warper_params",
+]