niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/v__sswarper.py

@@ -0,0 +1,465 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V__SSWARPER_METADATA = Metadata(
+    id="197ce8d754dd8af8616a9982ec614230700e19aa.boutiques",
+    name="@SSwarper",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+VSswarperParameters = typing.TypedDict('VSswarperParameters', {
+    "__STYX_TYPE__": typing.Literal["@SSwarper"],
+    "input_file": InputPathType,
+    "base_template": InputPathType,
+    "subject_id": str,
+    "output_dir": typing.NotRequired[str | None],
+    "min_patch_size": typing.NotRequired[float | None],
+    "no_lite": bool,
+    "skip_warp": bool,
+    "unifize_off": bool,
+    "init_skullstr_off": bool,
+    "extra_qc_off": bool,
+    "jump_to_extra_qc": bool,
+    "cost_nl_init": typing.NotRequired[str | None],
+    "cost_nl_final": typing.NotRequired[str | None],
+    "deoblique": bool,
+    "deoblique_refitly": bool,
+    "warp_scale": typing.NotRequired[float | None],
+    "ssopt_flag": typing.NotRequired[str | None],
+    "aniso_off": bool,
+    "ceil_off": bool,
+    "tmp_name_nice": bool,
+    "echo": bool,
+    "verbose": bool,
+    "noclean": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "@SSwarper": v__sswarper_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 {
+        "@SSwarper": v__sswarper_outputs,
+    }.get(t)
+
+
+class VSswarperOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v__sswarper(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    anat_do: OutputPathType
+    """Deobliqued version of original dataset"""
+    anat_u: OutputPathType
+    """Intensity uniform-ized original dataset"""
+    anat_ua: OutputPathType
+    """Anisotropically smoothed version of the uniformized dataset"""
+    anat_uac: OutputPathType
+    """Ceiling-capped version of the anisotropically smoothed dataset"""
+    anat_s: OutputPathType
+    """First pass skull-stripped original dataset"""
+    anat_ss: OutputPathType
+    """Second pass skull-stripped original dataset"""
+    anat_qq: OutputPathType
+    """Skull-stripped dataset nonlinearly warped to the base template space"""
+    anat_qq_affine: OutputPathType
+    """Affine matrix to transform original dataset to base template space"""
+    anat_qq_warp: OutputPathType
+    """Incremental warp from affine transformation to nonlinearly aligned
+    dataset"""
+    am_snapshot: OutputPathType
+    """3x3 snapshot image of the nonlinearly warped dataset with edges from the
+    base template overlaid"""
+    ma_snapshot: OutputPathType
+    """Similar to AM_snapshot, but with roles of the template and anatomical
+    dataset reversed"""
+    qc_anat_qq: OutputPathType
+    """3 rows of 8 slices snapshot image for checking alignment"""
+    qc_anat_ss: OutputPathType
+    """Snapshot image to check skullstripping in original space"""
+    init_overlap_qc: OutputPathType
+    """Montage to check initial overlap of source and base datasets"""
+
+
+def v__sswarper_params(
+    input_file: InputPathType,
+    base_template: InputPathType,
+    subject_id: str,
+    output_dir: str | None = None,
+    min_patch_size: float | None = None,
+    no_lite: bool = False,
+    skip_warp: bool = False,
+    unifize_off: bool = False,
+    init_skullstr_off: bool = False,
+    extra_qc_off: bool = False,
+    jump_to_extra_qc: bool = False,
+    cost_nl_init: str | None = None,
+    cost_nl_final: str | None = None,
+    deoblique: bool = False,
+    deoblique_refitly: bool = False,
+    warp_scale: float | None = None,
+    ssopt_flag: str | None = None,
+    aniso_off: bool = False,
+    ceil_off: bool = False,
+    tmp_name_nice: bool = False,
+    echo: bool = False,
+    verbose: bool = False,
+    noclean: bool = False,
+) -> VSswarperParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_file: An anatomical dataset, not skull-stripped, with about 1 mm\
+            resolution.
+        base_template: A base template dataset with similar contrast to the\
+            input dataset.
+        subject_id: Name code for output datasets (e.g., 'sub007').
+        output_dir: Output directory for all files from this program.
+        min_patch_size: Minimum patch size on final 3dQwarp.
+        no_lite: Do not use the '-lite' option with 3dQwarp.
+        skip_warp: Do not compute past the output of anatSS.<subid>.nii.
+        unifize_off: Do not start with a 3dUnifize command.
+        init_skullstr_off: Do not preprocess with a 3dSkullstrip command.
+        extra_qc_off: Do not make extra QC images.
+        jump_to_extra_qc: Just make the two QC*jpg images from a previous run.
+        cost_nl_init: Specify cost function for initial nonlinear (3dQwarp)\
+            part of alignment.
+        cost_nl_final: Specify cost function for final nonlinear (3dQwarp)\
+            parts of alignment.
+        deoblique: Apply obliquity information to deoblique the input volume.
+        deoblique_refitly: Purge obliquity information to deoblique the input\
+            volume.
+        warp_scale: Control flexibility of warps in 3dQwarp.
+        ssopt_flag: Append a string of options for 3dSkullStrip.
+        aniso_off: Do not preprocess with a 3danisosmooth command.
+        ceil_off: Turn off capping on values after anisosmoothing.
+        tmp_name_nice: Use nicer, non-random intermediate file prefix for\
+            temporary files.
+        echo: Run the script with 'set echo' for extra verbosity in the\
+            terminal output.
+        verbose: Apply the '-verb' option to 3dQwarp for verbose progress\
+            information.
+        noclean: Do not delete the 'junk' files at the end of computations.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "@SSwarper",
+        "input_file": input_file,
+        "base_template": base_template,
+        "subject_id": subject_id,
+        "no_lite": no_lite,
+        "skip_warp": skip_warp,
+        "unifize_off": unifize_off,
+        "init_skullstr_off": init_skullstr_off,
+        "extra_qc_off": extra_qc_off,
+        "jump_to_extra_qc": jump_to_extra_qc,
+        "deoblique": deoblique,
+        "deoblique_refitly": deoblique_refitly,
+        "aniso_off": aniso_off,
+        "ceil_off": ceil_off,
+        "tmp_name_nice": tmp_name_nice,
+        "echo": echo,
+        "verbose": verbose,
+        "noclean": noclean,
+    }
+    if output_dir is not None:
+        params["output_dir"] = output_dir
+    if min_patch_size is not None:
+        params["min_patch_size"] = min_patch_size
+    if cost_nl_init is not None:
+        params["cost_nl_init"] = cost_nl_init
+    if cost_nl_final is not None:
+        params["cost_nl_final"] = cost_nl_final
+    if warp_scale is not None:
+        params["warp_scale"] = warp_scale
+    if ssopt_flag is not None:
+        params["ssopt_flag"] = ssopt_flag
+    return params
+
+
+def v__sswarper_cargs(
+    params: VSswarperParameters,
+    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("@SSwarper")
+    cargs.extend([
+        "-input",
+        execution.input_file(params.get("input_file"))
+    ])
+    cargs.extend([
+        "-base",
+        execution.input_file(params.get("base_template"))
+    ])
+    cargs.extend([
+        "-subid",
+        params.get("subject_id")
+    ])
+    if params.get("output_dir") is not None:
+        cargs.extend([
+            "-odir",
+            params.get("output_dir")
+        ])
+    if params.get("min_patch_size") is not None:
+        cargs.extend([
+            "-minp",
+            str(params.get("min_patch_size"))
+        ])
+    if params.get("no_lite"):
+        cargs.append("-nolite")
+    if params.get("skip_warp"):
+        cargs.append("-skipwarp")
+    if params.get("unifize_off"):
+        cargs.append("-unifize_off")
+    if params.get("init_skullstr_off"):
+        cargs.append("-init_skullstr_off")
+    if params.get("extra_qc_off"):
+        cargs.append("-extra_qc_off")
+    if params.get("jump_to_extra_qc"):
+        cargs.append("-jump_to_extra_qc")
+    if params.get("cost_nl_init") is not None:
+        cargs.extend([
+            "-cost_nl_init",
+            params.get("cost_nl_init")
+        ])
+    if params.get("cost_nl_final") is not None:
+        cargs.extend([
+            "-cost_nl_final",
+            params.get("cost_nl_final")
+        ])
+    if params.get("deoblique"):
+        cargs.append("-deoblique")
+    if params.get("deoblique_refitly"):
+        cargs.append("-deoblique_refitly")
+    if params.get("warp_scale") is not None:
+        cargs.extend([
+            "-warpscale",
+            str(params.get("warp_scale"))
+        ])
+    if params.get("ssopt_flag") is not None:
+        cargs.extend([
+            "-SSopt",
+            params.get("ssopt_flag")
+        ])
+    if params.get("aniso_off"):
+        cargs.append("-aniso_off")
+    if params.get("ceil_off"):
+        cargs.append("-ceil_off")
+    if params.get("tmp_name_nice"):
+        cargs.append("-tmp_name_nice")
+    if params.get("echo"):
+        cargs.append("-echo")
+    if params.get("verbose"):
+        cargs.append("-verb")
+    if params.get("noclean"):
+        cargs.append("-noclean")
+    return cargs
+
+
+def v__sswarper_outputs(
+    params: VSswarperParameters,
+    execution: Execution,
+) -> VSswarperOutputs:
+    """
+    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 = VSswarperOutputs(
+        root=execution.output_file("."),
+        anat_do=execution.output_file("anatDO." + params.get("subject_id") + ".nii"),
+        anat_u=execution.output_file("anatU." + params.get("subject_id") + ".nii"),
+        anat_ua=execution.output_file("anatUA." + params.get("subject_id") + ".nii"),
+        anat_uac=execution.output_file("anatUAC." + params.get("subject_id") + ".nii"),
+        anat_s=execution.output_file("anatS." + params.get("subject_id") + ".nii"),
+        anat_ss=execution.output_file("anatSS." + params.get("subject_id") + ".nii"),
+        anat_qq=execution.output_file("anatQQ." + params.get("subject_id") + ".nii"),
+        anat_qq_affine=execution.output_file("anatQQ." + params.get("subject_id") + ".aff12.1D"),
+        anat_qq_warp=execution.output_file("anatQQ." + params.get("subject_id") + "_WARP.nii"),
+        am_snapshot=execution.output_file("AM" + params.get("subject_id") + ".jpg"),
+        ma_snapshot=execution.output_file("MA" + params.get("subject_id") + ".jpg"),
+        qc_anat_qq=execution.output_file("QC_anatQQ." + params.get("subject_id") + ".jpg"),
+        qc_anat_ss=execution.output_file("QC_anatSS." + params.get("subject_id") + ".jpg"),
+        init_overlap_qc=execution.output_file("init_qc_00_overlap_uinp_obase.jpg"),
+    )
+    return ret
+
+
+def v__sswarper_execute(
+    params: VSswarperParameters,
+    execution: Execution,
+) -> VSswarperOutputs:
+    """
+    Dual purposes for processing a given subject's anatomical volume: skull-strip
+    the brain and calculate the warp to a reference template/standard space.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `VSswarperOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v__sswarper_cargs(params, execution)
+    ret = v__sswarper_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v__sswarper(
+    input_file: InputPathType,
+    base_template: InputPathType,
+    subject_id: str,
+    output_dir: str | None = None,
+    min_patch_size: float | None = None,
+    no_lite: bool = False,
+    skip_warp: bool = False,
+    unifize_off: bool = False,
+    init_skullstr_off: bool = False,
+    extra_qc_off: bool = False,
+    jump_to_extra_qc: bool = False,
+    cost_nl_init: str | None = None,
+    cost_nl_final: str | None = None,
+    deoblique: bool = False,
+    deoblique_refitly: bool = False,
+    warp_scale: float | None = None,
+    ssopt_flag: str | None = None,
+    aniso_off: bool = False,
+    ceil_off: bool = False,
+    tmp_name_nice: bool = False,
+    echo: bool = False,
+    verbose: bool = False,
+    noclean: bool = False,
+    runner: Runner | None = None,
+) -> VSswarperOutputs:
+    """
+    Dual purposes for processing a given subject's anatomical volume: skull-strip
+    the brain and calculate the warp to a reference template/standard space.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        input_file: An anatomical dataset, not skull-stripped, with about 1 mm\
+            resolution.
+        base_template: A base template dataset with similar contrast to the\
+            input dataset.
+        subject_id: Name code for output datasets (e.g., 'sub007').
+        output_dir: Output directory for all files from this program.
+        min_patch_size: Minimum patch size on final 3dQwarp.
+        no_lite: Do not use the '-lite' option with 3dQwarp.
+        skip_warp: Do not compute past the output of anatSS.<subid>.nii.
+        unifize_off: Do not start with a 3dUnifize command.
+        init_skullstr_off: Do not preprocess with a 3dSkullstrip command.
+        extra_qc_off: Do not make extra QC images.
+        jump_to_extra_qc: Just make the two QC*jpg images from a previous run.
+        cost_nl_init: Specify cost function for initial nonlinear (3dQwarp)\
+            part of alignment.
+        cost_nl_final: Specify cost function for final nonlinear (3dQwarp)\
+            parts of alignment.
+        deoblique: Apply obliquity information to deoblique the input volume.
+        deoblique_refitly: Purge obliquity information to deoblique the input\
+            volume.
+        warp_scale: Control flexibility of warps in 3dQwarp.
+        ssopt_flag: Append a string of options for 3dSkullStrip.
+        aniso_off: Do not preprocess with a 3danisosmooth command.
+        ceil_off: Turn off capping on values after anisosmoothing.
+        tmp_name_nice: Use nicer, non-random intermediate file prefix for\
+            temporary files.
+        echo: Run the script with 'set echo' for extra verbosity in the\
+            terminal output.
+        verbose: Apply the '-verb' option to 3dQwarp for verbose progress\
+            information.
+        noclean: Do not delete the 'junk' files at the end of computations.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `VSswarperOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__SSWARPER_METADATA)
+    params = v__sswarper_params(
+        input_file=input_file,
+        base_template=base_template,
+        subject_id=subject_id,
+        output_dir=output_dir,
+        min_patch_size=min_patch_size,
+        no_lite=no_lite,
+        skip_warp=skip_warp,
+        unifize_off=unifize_off,
+        init_skullstr_off=init_skullstr_off,
+        extra_qc_off=extra_qc_off,
+        jump_to_extra_qc=jump_to_extra_qc,
+        cost_nl_init=cost_nl_init,
+        cost_nl_final=cost_nl_final,
+        deoblique=deoblique,
+        deoblique_refitly=deoblique_refitly,
+        warp_scale=warp_scale,
+        ssopt_flag=ssopt_flag,
+        aniso_off=aniso_off,
+        ceil_off=ceil_off,
+        tmp_name_nice=tmp_name_nice,
+        echo=echo,
+        verbose=verbose,
+        noclean=noclean,
+    )
+    return v__sswarper_execute(params, execution)
+
+
+__all__ = [
+    "VSswarperOutputs",
+    "VSswarperParameters",
+    "V__SSWARPER_METADATA",
+    "v__sswarper",
+    "v__sswarper_params",
+]

niwrap_afni/afni/v__statauxcode.py

@@ -0,0 +1,178 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V__STATAUXCODE_METADATA = Metadata(
+    id="f6c1767e1a9b29b920fca298ee485697451c9d8a.boutiques",
+    name="@statauxcode",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+VStatauxcodeParameters = typing.TypedDict('VStatauxcodeParameters', {
+    "__STYX_TYPE__": typing.Literal["@statauxcode"],
+    "code": str,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "@statauxcode": v__statauxcode_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 {
+        "@statauxcode": v__statauxcode_outputs,
+    }.get(t)
+
+
+class VStatauxcodeOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v__statauxcode(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output: OutputPathType
+    """Output file containing the result of the conversion"""
+
+
+def v__statauxcode_params(
+    code_: str,
+) -> VStatauxcodeParameters:
+    """
+    Build parameters.
+    
+    Args:
+        code_: The statistical code or its numerical equivalent to be\
+            converted.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "@statauxcode",
+        "code": code_,
+    }
+    return params
+
+
+def v__statauxcode_cargs(
+    params: VStatauxcodeParameters,
+    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("@statauxcode")
+    cargs.append(params.get("code"))
+    return cargs
+
+
+def v__statauxcode_outputs(
+    params: VStatauxcodeParameters,
+    execution: Execution,
+) -> VStatauxcodeOutputs:
+    """
+    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 = VStatauxcodeOutputs(
+        root=execution.output_file("."),
+        output=execution.output_file("output.txt"),
+    )
+    return ret
+
+
+def v__statauxcode_execute(
+    params: VStatauxcodeParameters,
+    execution: Execution,
+) -> VStatauxcodeOutputs:
+    """
+    Returns the name or number of a statistics code based on specified mappings.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `VStatauxcodeOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v__statauxcode_cargs(params, execution)
+    ret = v__statauxcode_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v__statauxcode(
+    code_: str,
+    runner: Runner | None = None,
+) -> VStatauxcodeOutputs:
+    """
+    Returns the name or number of a statistics code based on specified mappings.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        code_: The statistical code or its numerical equivalent to be\
+            converted.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `VStatauxcodeOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__STATAUXCODE_METADATA)
+    params = v__statauxcode_params(
+        code_=code_,
+    )
+    return v__statauxcode_execute(params, execution)
+
+
+__all__ = [
+    "VStatauxcodeOutputs",
+    "VStatauxcodeParameters",
+    "V__STATAUXCODE_METADATA",
+    "v__statauxcode",
+    "v__statauxcode_params",
+]