niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/auto_warp_py.py

@@ -0,0 +1,527 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+AUTO_WARP_PY_METADATA = Metadata(
+    id="a6e140162bdb60ac7b3f82c488330c94eee4e2ab.boutiques",
+    name="auto_warp.py",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+AutoWarpPyParameters = typing.TypedDict('AutoWarpPyParameters', {
+    "__STYX_TYPE__": typing.Literal["auto_warp.py"],
+    "base": InputPathType,
+    "input": InputPathType,
+    "skull_strip_input": bool,
+    "qblur": typing.NotRequired[str | None],
+    "qworkhard": typing.NotRequired[str | None],
+    "qw_opts": typing.NotRequired[str | None],
+    "keep_rm_files": bool,
+    "prep_only": bool,
+    "help": bool,
+    "hview": bool,
+    "limited_help": bool,
+    "option_help": bool,
+    "version": bool,
+    "ver": bool,
+    "verb": bool,
+    "save_script": bool,
+    "skip_affine": bool,
+    "skull_strip_base": bool,
+    "ex_mode": typing.NotRequired[str | None],
+    "overwrite": bool,
+    "suffix": typing.NotRequired[str | None],
+    "child_anat": typing.NotRequired[str | None],
+    "warp_dxyz": typing.NotRequired[float | None],
+    "affine_dxyz": typing.NotRequired[float | None],
+    "affine_input_xmat": typing.NotRequired[str | None],
+    "smooth_anat": bool,
+    "smooth_base": bool,
+    "unifize_input": bool,
+    "output_dir": typing.NotRequired[str | None],
+    "followers": typing.NotRequired[str | None],
+    "affine_followers_xmat": typing.NotRequired[str | None],
+    "skullstrip_opts": typing.NotRequired[str | None],
+    "at_opts": 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 {
+        "auto_warp.py": auto_warp_py_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 {
+    }.get(t)
+
+
+class AutoWarpPyOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `auto_warp_py(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def auto_warp_py_params(
+    base: InputPathType,
+    input_: InputPathType,
+    skull_strip_input: bool = False,
+    qblur: str | None = None,
+    qworkhard: str | None = None,
+    qw_opts: str | None = None,
+    keep_rm_files: bool = False,
+    prep_only: bool = False,
+    help_: bool = False,
+    hview: bool = False,
+    limited_help: bool = False,
+    option_help: bool = False,
+    version: bool = False,
+    ver: bool = False,
+    verb: bool = False,
+    save_script: bool = False,
+    skip_affine: bool = False,
+    skull_strip_base: bool = False,
+    ex_mode: str | None = None,
+    overwrite: bool = False,
+    suffix: str | None = None,
+    child_anat: str | None = None,
+    warp_dxyz: float | None = None,
+    affine_dxyz: float | None = None,
+    affine_input_xmat: str | None = None,
+    smooth_anat: bool = False,
+    smooth_base: bool = False,
+    unifize_input: bool = False,
+    output_dir: str | None = None,
+    followers: str | None = None,
+    affine_followers_xmat: str | None = None,
+    skullstrip_opts: str | None = None,
+    at_opts: str | None = None,
+) -> AutoWarpPyParameters:
+    """
+    Build parameters.
+    
+    Args:
+        base: Name of reference or template volume.
+        input_: Name of dataset to be registered.
+        skull_strip_input: Do not skullstrip input dataset.
+        qblur: Specify 3dQwarp blurs for base and source volumes.
+        qworkhard: Set the two values for 3dQwarp's -workhard option.
+        qw_opts: Pass all of OPTS as extra options directly to 3dQwarp.
+        keep_rm_files: Don't delete any of the temporary files created.
+        prep_only: Do preprocessing steps only without alignment.
+        help_: Display help message.
+        hview: Display help message in a text editor.
+        limited_help: Display limited help message.
+        option_help: Display help for all available options.
+        version: Show version number and exit.
+        ver: Show version number and exit.
+        verb: Be verbose in messages and options.
+        save_script: Save executed script in given file.
+        skip_affine: Skip the affine registration process.
+        skull_strip_base: Do not skullstrip base/template dataset.
+        ex_mode: Command execution mode: quiet, echo, dry_run, script.
+        overwrite: Overwrite existing files.
+        suffix: Suffix to add to output files.
+        child_anat: Names of child anatomical datasets.
+        warp_dxyz: Resolution used for computing warp (cubic only).
+        affine_dxyz: Resolution used for computing initial transform (cubic\
+            only).
+        affine_input_xmat: Affine transform to put input in standard space.\
+            Special values are: 'AUTO' to use @auto_tlrc, 'ID' to do nothing,\
+            'FILE.1D' for a pre-computed matrix FILE.1D.
+        smooth_anat: Smooth anatomy before registration.
+        smooth_base: Smooth template before registration.
+        unifize_input: Unifize the input or not.
+        output_dir: Set directory for output datasets.
+        followers: Specify follower datasets.
+        affine_followers_xmat: Specify follower datasets' affine transforms.
+        skullstrip_opts: 3dSkullstrip miscellaneous options.
+        at_opts: @auto_tlrc miscellaneous options.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "auto_warp.py",
+        "base": base,
+        "input": input_,
+        "skull_strip_input": skull_strip_input,
+        "keep_rm_files": keep_rm_files,
+        "prep_only": prep_only,
+        "help": help_,
+        "hview": hview,
+        "limited_help": limited_help,
+        "option_help": option_help,
+        "version": version,
+        "ver": ver,
+        "verb": verb,
+        "save_script": save_script,
+        "skip_affine": skip_affine,
+        "skull_strip_base": skull_strip_base,
+        "overwrite": overwrite,
+        "smooth_anat": smooth_anat,
+        "smooth_base": smooth_base,
+        "unifize_input": unifize_input,
+    }
+    if qblur is not None:
+        params["qblur"] = qblur
+    if qworkhard is not None:
+        params["qworkhard"] = qworkhard
+    if qw_opts is not None:
+        params["qw_opts"] = qw_opts
+    if ex_mode is not None:
+        params["ex_mode"] = ex_mode
+    if suffix is not None:
+        params["suffix"] = suffix
+    if child_anat is not None:
+        params["child_anat"] = child_anat
+    if warp_dxyz is not None:
+        params["warp_dxyz"] = warp_dxyz
+    if affine_dxyz is not None:
+        params["affine_dxyz"] = affine_dxyz
+    if affine_input_xmat is not None:
+        params["affine_input_xmat"] = affine_input_xmat
+    if output_dir is not None:
+        params["output_dir"] = output_dir
+    if followers is not None:
+        params["followers"] = followers
+    if affine_followers_xmat is not None:
+        params["affine_followers_xmat"] = affine_followers_xmat
+    if skullstrip_opts is not None:
+        params["skullstrip_opts"] = skullstrip_opts
+    if at_opts is not None:
+        params["at_opts"] = at_opts
+    return params
+
+
+def auto_warp_py_cargs(
+    params: AutoWarpPyParameters,
+    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("auto_warp.py")
+    cargs.extend([
+        "-base",
+        execution.input_file(params.get("base"))
+    ])
+    cargs.extend([
+        "-input",
+        execution.input_file(params.get("input"))
+    ])
+    if params.get("skull_strip_input"):
+        cargs.append("-skull_strip_input")
+    if params.get("qblur") is not None:
+        cargs.extend([
+            "-qblur",
+            params.get("qblur")
+        ])
+    if params.get("qworkhard") is not None:
+        cargs.extend([
+            "-qworkhard",
+            params.get("qworkhard")
+        ])
+    if params.get("qw_opts") is not None:
+        cargs.extend([
+            "-qw_opts",
+            params.get("qw_opts")
+        ])
+    if params.get("keep_rm_files"):
+        cargs.append("-keep_rm_files")
+    if params.get("prep_only"):
+        cargs.append("-prep_only")
+    if params.get("help"):
+        cargs.append("-help")
+    if params.get("hview"):
+        cargs.append("-hview")
+    if params.get("limited_help"):
+        cargs.append("-limited_help")
+    if params.get("option_help"):
+        cargs.append("-option_help")
+    if params.get("version"):
+        cargs.append("-version")
+    if params.get("ver"):
+        cargs.append("-ver")
+    if params.get("verb"):
+        cargs.append("-verb")
+    if params.get("save_script"):
+        cargs.append("-save_script")
+    if params.get("skip_affine"):
+        cargs.append("-skip_affine")
+    if params.get("skull_strip_base"):
+        cargs.append("-skull_strip_base")
+    if params.get("ex_mode") is not None:
+        cargs.extend([
+            "-ex_mode",
+            params.get("ex_mode")
+        ])
+    if params.get("overwrite"):
+        cargs.append("-overwrite")
+    if params.get("suffix") is not None:
+        cargs.extend([
+            "-suffix",
+            params.get("suffix")
+        ])
+    if params.get("child_anat") is not None:
+        cargs.extend([
+            "-child_anat",
+            params.get("child_anat")
+        ])
+    if params.get("warp_dxyz") is not None:
+        cargs.extend([
+            "-warp_dxyz",
+            str(params.get("warp_dxyz"))
+        ])
+    if params.get("affine_dxyz") is not None:
+        cargs.extend([
+            "-affine_dxyz",
+            str(params.get("affine_dxyz"))
+        ])
+    if params.get("affine_input_xmat") is not None:
+        cargs.extend([
+            "-affine_input_xmat",
+            params.get("affine_input_xmat")
+        ])
+    if params.get("smooth_anat"):
+        cargs.append("-smooth_anat")
+    if params.get("smooth_base"):
+        cargs.append("-smooth_base")
+    if params.get("unifize_input"):
+        cargs.append("-unifize_input")
+    if params.get("output_dir") is not None:
+        cargs.extend([
+            "-output_dir",
+            params.get("output_dir")
+        ])
+    if params.get("followers") is not None:
+        cargs.extend([
+            "-followers",
+            params.get("followers")
+        ])
+    if params.get("affine_followers_xmat") is not None:
+        cargs.extend([
+            "-affine_followers_xmat",
+            params.get("affine_followers_xmat")
+        ])
+    if params.get("skullstrip_opts") is not None:
+        cargs.extend([
+            "-skullstrip_opts",
+            params.get("skullstrip_opts")
+        ])
+    if params.get("at_opts") is not None:
+        cargs.extend([
+            "-at_opts",
+            params.get("at_opts")
+        ])
+    return cargs
+
+
+def auto_warp_py_outputs(
+    params: AutoWarpPyParameters,
+    execution: Execution,
+) -> AutoWarpPyOutputs:
+    """
+    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 = AutoWarpPyOutputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def auto_warp_py_execute(
+    params: AutoWarpPyParameters,
+    execution: Execution,
+) -> AutoWarpPyOutputs:
+    """
+    Nonlinear registration tool.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `AutoWarpPyOutputs`).
+    """
+    params = execution.params(params)
+    cargs = auto_warp_py_cargs(params, execution)
+    ret = auto_warp_py_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def auto_warp_py(
+    base: InputPathType,
+    input_: InputPathType,
+    skull_strip_input: bool = False,
+    qblur: str | None = None,
+    qworkhard: str | None = None,
+    qw_opts: str | None = None,
+    keep_rm_files: bool = False,
+    prep_only: bool = False,
+    help_: bool = False,
+    hview: bool = False,
+    limited_help: bool = False,
+    option_help: bool = False,
+    version: bool = False,
+    ver: bool = False,
+    verb: bool = False,
+    save_script: bool = False,
+    skip_affine: bool = False,
+    skull_strip_base: bool = False,
+    ex_mode: str | None = None,
+    overwrite: bool = False,
+    suffix: str | None = None,
+    child_anat: str | None = None,
+    warp_dxyz: float | None = None,
+    affine_dxyz: float | None = None,
+    affine_input_xmat: str | None = None,
+    smooth_anat: bool = False,
+    smooth_base: bool = False,
+    unifize_input: bool = False,
+    output_dir: str | None = None,
+    followers: str | None = None,
+    affine_followers_xmat: str | None = None,
+    skullstrip_opts: str | None = None,
+    at_opts: str | None = None,
+    runner: Runner | None = None,
+) -> AutoWarpPyOutputs:
+    """
+    Nonlinear registration tool.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        base: Name of reference or template volume.
+        input_: Name of dataset to be registered.
+        skull_strip_input: Do not skullstrip input dataset.
+        qblur: Specify 3dQwarp blurs for base and source volumes.
+        qworkhard: Set the two values for 3dQwarp's -workhard option.
+        qw_opts: Pass all of OPTS as extra options directly to 3dQwarp.
+        keep_rm_files: Don't delete any of the temporary files created.
+        prep_only: Do preprocessing steps only without alignment.
+        help_: Display help message.
+        hview: Display help message in a text editor.
+        limited_help: Display limited help message.
+        option_help: Display help for all available options.
+        version: Show version number and exit.
+        ver: Show version number and exit.
+        verb: Be verbose in messages and options.
+        save_script: Save executed script in given file.
+        skip_affine: Skip the affine registration process.
+        skull_strip_base: Do not skullstrip base/template dataset.
+        ex_mode: Command execution mode: quiet, echo, dry_run, script.
+        overwrite: Overwrite existing files.
+        suffix: Suffix to add to output files.
+        child_anat: Names of child anatomical datasets.
+        warp_dxyz: Resolution used for computing warp (cubic only).
+        affine_dxyz: Resolution used for computing initial transform (cubic\
+            only).
+        affine_input_xmat: Affine transform to put input in standard space.\
+            Special values are: 'AUTO' to use @auto_tlrc, 'ID' to do nothing,\
+            'FILE.1D' for a pre-computed matrix FILE.1D.
+        smooth_anat: Smooth anatomy before registration.
+        smooth_base: Smooth template before registration.
+        unifize_input: Unifize the input or not.
+        output_dir: Set directory for output datasets.
+        followers: Specify follower datasets.
+        affine_followers_xmat: Specify follower datasets' affine transforms.
+        skullstrip_opts: 3dSkullstrip miscellaneous options.
+        at_opts: @auto_tlrc miscellaneous options.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `AutoWarpPyOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(AUTO_WARP_PY_METADATA)
+    params = auto_warp_py_params(
+        base=base,
+        input_=input_,
+        skull_strip_input=skull_strip_input,
+        qblur=qblur,
+        qworkhard=qworkhard,
+        qw_opts=qw_opts,
+        keep_rm_files=keep_rm_files,
+        prep_only=prep_only,
+        help_=help_,
+        hview=hview,
+        limited_help=limited_help,
+        option_help=option_help,
+        version=version,
+        ver=ver,
+        verb=verb,
+        save_script=save_script,
+        skip_affine=skip_affine,
+        skull_strip_base=skull_strip_base,
+        ex_mode=ex_mode,
+        overwrite=overwrite,
+        suffix=suffix,
+        child_anat=child_anat,
+        warp_dxyz=warp_dxyz,
+        affine_dxyz=affine_dxyz,
+        affine_input_xmat=affine_input_xmat,
+        smooth_anat=smooth_anat,
+        smooth_base=smooth_base,
+        unifize_input=unifize_input,
+        output_dir=output_dir,
+        followers=followers,
+        affine_followers_xmat=affine_followers_xmat,
+        skullstrip_opts=skullstrip_opts,
+        at_opts=at_opts,
+    )
+    return auto_warp_py_execute(params, execution)
+
+
+__all__ = [
+    "AUTO_WARP_PY_METADATA",
+    "AutoWarpPyOutputs",
+    "AutoWarpPyParameters",
+    "auto_warp_py",
+    "auto_warp_py_params",
+]