niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/v__check_for_afni_dset.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__CHECK_FOR_AFNI_DSET_METADATA = Metadata(
+    id="36d93d7fee0a8f5033359b79ea1fc2a9f56b9766.boutiques",
+    name="@CheckForAfniDset",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+VCheckForAfniDsetParameters = typing.TypedDict('VCheckForAfniDsetParameters', {
+    "__STYX_TYPE__": typing.Literal["@CheckForAfniDset"],
+    "dataset_name": str,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "@CheckForAfniDset": v__check_for_afni_dset_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 {
+        "@CheckForAfniDset": v__check_for_afni_dset_outputs,
+    }.get(t)
+
+
+class VCheckForAfniDsetOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v__check_for_afni_dset(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_status: OutputPathType
+    """Text file containing the status code of the dataset"""
+
+
+def v__check_for_afni_dset_params(
+    dataset_name: str,
+) -> VCheckForAfniDsetParameters:
+    """
+    Build parameters.
+    
+    Args:
+        dataset_name: Path to the AFNI dataset (e.g.,\
+            /Data/stuff/Hello+orig.HEAD).
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "@CheckForAfniDset",
+        "dataset_name": dataset_name,
+    }
+    return params
+
+
+def v__check_for_afni_dset_cargs(
+    params: VCheckForAfniDsetParameters,
+    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("@CheckForAfniDset")
+    cargs.append(params.get("dataset_name"))
+    return cargs
+
+
+def v__check_for_afni_dset_outputs(
+    params: VCheckForAfniDsetParameters,
+    execution: Execution,
+) -> VCheckForAfniDsetOutputs:
+    """
+    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 = VCheckForAfniDsetOutputs(
+        root=execution.output_file("."),
+        output_status=execution.output_file(params.get("dataset_name") + "_status.txt"),
+    )
+    return ret
+
+
+def v__check_for_afni_dset_execute(
+    params: VCheckForAfniDsetParameters,
+    execution: Execution,
+) -> VCheckForAfniDsetOutputs:
+    """
+    Check for the existence of AFNI datasets.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `VCheckForAfniDsetOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v__check_for_afni_dset_cargs(params, execution)
+    ret = v__check_for_afni_dset_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v__check_for_afni_dset(
+    dataset_name: str,
+    runner: Runner | None = None,
+) -> VCheckForAfniDsetOutputs:
+    """
+    Check for the existence of AFNI datasets.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        dataset_name: Path to the AFNI dataset (e.g.,\
+            /Data/stuff/Hello+orig.HEAD).
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `VCheckForAfniDsetOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__CHECK_FOR_AFNI_DSET_METADATA)
+    params = v__check_for_afni_dset_params(
+        dataset_name=dataset_name,
+    )
+    return v__check_for_afni_dset_execute(params, execution)
+
+
+__all__ = [
+    "VCheckForAfniDsetOutputs",
+    "VCheckForAfniDsetParameters",
+    "V__CHECK_FOR_AFNI_DSET_METADATA",
+    "v__check_for_afni_dset",
+    "v__check_for_afni_dset_params",
+]

niwrap_afni/afni/v__clip_volume.py

@@ -0,0 +1,388 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V__CLIP_VOLUME_METADATA = Metadata(
+    id="7bfb440cf4d5cd2d5ca3418b3dc2ad19927c0963.boutiques",
+    name="@clip_volume",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+VClipVolumeParameters = typing.TypedDict('VClipVolumeParameters', {
+    "__STYX_TYPE__": typing.Literal["@clip_volume"],
+    "input_volume": InputPathType,
+    "below_zmm": typing.NotRequired[float | None],
+    "above_zmm": typing.NotRequired[float | None],
+    "left_xmm": typing.NotRequired[float | None],
+    "right_xmm": typing.NotRequired[float | None],
+    "anterior_ymm": typing.NotRequired[float | None],
+    "posterior_ymm": typing.NotRequired[float | None],
+    "box": typing.NotRequired[list[float] | None],
+    "mask_box": typing.NotRequired[list[float] | None],
+    "and_logic": bool,
+    "or_logic": bool,
+    "verbosity": bool,
+    "crop_allzero": bool,
+    "crop_greedy": bool,
+    "crop": bool,
+    "crop_npad": typing.NotRequired[float | None],
+    "output_prefix": typing.NotRequired[str | None],
+    "followers": typing.NotRequired[list[InputPathType] | None],
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "@clip_volume": v__clip_volume_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 {
+        "@clip_volume": v__clip_volume_outputs,
+    }.get(t)
+
+
+class VClipVolumeOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v__clip_volume(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_clipped_volume: OutputPathType | None
+    """Output clipped or cropped volume"""
+    output_followers: OutputPathType | None
+    """Output for follower datasets after clipping/cropping"""
+
+
+def v__clip_volume_params(
+    input_volume: InputPathType,
+    below_zmm: float | None = None,
+    above_zmm: float | None = None,
+    left_xmm: float | None = None,
+    right_xmm: float | None = None,
+    anterior_ymm: float | None = None,
+    posterior_ymm: float | None = None,
+    box: list[float] | None = None,
+    mask_box: list[float] | None = None,
+    and_logic: bool = False,
+    or_logic: bool = False,
+    verbosity: bool = False,
+    crop_allzero: bool = False,
+    crop_greedy: bool = False,
+    crop: bool = False,
+    crop_npad: float | None = None,
+    output_prefix: str | None = None,
+    followers: list[InputPathType] | None = None,
+) -> VClipVolumeParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_volume: Volume to clip.
+        below_zmm: Set to 0 slices below Zmm.
+        above_zmm: Set to 0 slices above Zmm.
+        left_xmm: Set to 0 slices left of Xmm.
+        right_xmm: Set to 0 slices right of Xmm.
+        anterior_ymm: Set to 0 slices anterior to Ymm.
+        posterior_ymm: Set to 0 slices posterior to Ymm.
+        box: Clip the volume to a box centered at Cx, Cy, Cz (RAI mm), and of\
+            dimensions Dx Dy Dz (RAI mm).
+        mask_box: Set all values inside the box to 1. Box centered at Cx, Cy,\
+            Cz (RAI mm), and of dimensions Dx Dy Dz (RAI mm).
+        and_logic: Combine with next clipping planes using 'and'.
+        or_logic: Combine with next clipping planes using 'or'.
+        verbosity: Show command details (verbose output).
+        crop_allzero: Crop the output volume with 3dAutobox -noclust.
+        crop_greedy: Crop the output volume with 3dAutobox.
+        crop: Same as -crop_greedy, kept for backward compatibility.
+        crop_npad: Set 3dAutobox's -npad option to NPAD. NPAD fattens the\
+            volume a little after cropping.
+        output_prefix: Output prefix for the resultant volume. Default is the\
+            input prefix with _clp suffixed to it.
+        followers: Apply the same clipping or cropping treatment to the\
+            follower datasets.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "@clip_volume",
+        "input_volume": input_volume,
+        "and_logic": and_logic,
+        "or_logic": or_logic,
+        "verbosity": verbosity,
+        "crop_allzero": crop_allzero,
+        "crop_greedy": crop_greedy,
+        "crop": crop,
+    }
+    if below_zmm is not None:
+        params["below_zmm"] = below_zmm
+    if above_zmm is not None:
+        params["above_zmm"] = above_zmm
+    if left_xmm is not None:
+        params["left_xmm"] = left_xmm
+    if right_xmm is not None:
+        params["right_xmm"] = right_xmm
+    if anterior_ymm is not None:
+        params["anterior_ymm"] = anterior_ymm
+    if posterior_ymm is not None:
+        params["posterior_ymm"] = posterior_ymm
+    if box is not None:
+        params["box"] = box
+    if mask_box is not None:
+        params["mask_box"] = mask_box
+    if crop_npad is not None:
+        params["crop_npad"] = crop_npad
+    if output_prefix is not None:
+        params["output_prefix"] = output_prefix
+    if followers is not None:
+        params["followers"] = followers
+    return params
+
+
+def v__clip_volume_cargs(
+    params: VClipVolumeParameters,
+    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("@clip_volume")
+    cargs.append(execution.input_file(params.get("input_volume")))
+    if params.get("below_zmm") is not None:
+        cargs.extend([
+            "-below",
+            str(params.get("below_zmm"))
+        ])
+    if params.get("above_zmm") is not None:
+        cargs.extend([
+            "-above",
+            str(params.get("above_zmm"))
+        ])
+    if params.get("left_xmm") is not None:
+        cargs.extend([
+            "-left",
+            str(params.get("left_xmm"))
+        ])
+    if params.get("right_xmm") is not None:
+        cargs.extend([
+            "-right",
+            str(params.get("right_xmm"))
+        ])
+    if params.get("anterior_ymm") is not None:
+        cargs.extend([
+            "-anterior",
+            str(params.get("anterior_ymm"))
+        ])
+    if params.get("posterior_ymm") is not None:
+        cargs.extend([
+            "-posterior",
+            str(params.get("posterior_ymm"))
+        ])
+    if params.get("box") is not None:
+        cargs.extend([
+            "-box",
+            *map(str, params.get("box"))
+        ])
+    if params.get("mask_box") is not None:
+        cargs.extend([
+            "-mask_box",
+            *map(str, params.get("mask_box"))
+        ])
+    if params.get("and_logic"):
+        cargs.append("-and")
+    if params.get("or_logic"):
+        cargs.append("-or")
+    if params.get("verbosity"):
+        cargs.append("-verb")
+    if params.get("crop_allzero"):
+        cargs.append("-crop_allzero")
+    if params.get("crop_greedy"):
+        cargs.append("-crop_greedy")
+    if params.get("crop"):
+        cargs.append("-crop")
+    if params.get("crop_npad") is not None:
+        cargs.extend([
+            "-crop_npad",
+            str(params.get("crop_npad"))
+        ])
+    if params.get("output_prefix") is not None:
+        cargs.extend([
+            "-prefix",
+            params.get("output_prefix")
+        ])
+    if params.get("followers") is not None:
+        cargs.extend([
+            "-followers",
+            *[execution.input_file(f) for f in params.get("followers")]
+        ])
+    return cargs
+
+
+def v__clip_volume_outputs(
+    params: VClipVolumeParameters,
+    execution: Execution,
+) -> VClipVolumeOutputs:
+    """
+    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 = VClipVolumeOutputs(
+        root=execution.output_file("."),
+        output_clipped_volume=execution.output_file(params.get("output_prefix") + "_clp.nii.gz") if (params.get("output_prefix") is not None) else None,
+        output_followers=execution.output_file(params.get("output_prefix") + "_follow_clp.nii.gz") if (params.get("output_prefix") is not None) else None,
+    )
+    return ret
+
+
+def v__clip_volume_execute(
+    params: VClipVolumeParameters,
+    execution: Execution,
+) -> VClipVolumeOutputs:
+    """
+    A tool to clip regions of a volume in various ways, such as above/below certain
+    coordinates or within a specified box.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `VClipVolumeOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v__clip_volume_cargs(params, execution)
+    ret = v__clip_volume_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v__clip_volume(
+    input_volume: InputPathType,
+    below_zmm: float | None = None,
+    above_zmm: float | None = None,
+    left_xmm: float | None = None,
+    right_xmm: float | None = None,
+    anterior_ymm: float | None = None,
+    posterior_ymm: float | None = None,
+    box: list[float] | None = None,
+    mask_box: list[float] | None = None,
+    and_logic: bool = False,
+    or_logic: bool = False,
+    verbosity: bool = False,
+    crop_allzero: bool = False,
+    crop_greedy: bool = False,
+    crop: bool = False,
+    crop_npad: float | None = None,
+    output_prefix: str | None = None,
+    followers: list[InputPathType] | None = None,
+    runner: Runner | None = None,
+) -> VClipVolumeOutputs:
+    """
+    A tool to clip regions of a volume in various ways, such as above/below certain
+    coordinates or within a specified box.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        input_volume: Volume to clip.
+        below_zmm: Set to 0 slices below Zmm.
+        above_zmm: Set to 0 slices above Zmm.
+        left_xmm: Set to 0 slices left of Xmm.
+        right_xmm: Set to 0 slices right of Xmm.
+        anterior_ymm: Set to 0 slices anterior to Ymm.
+        posterior_ymm: Set to 0 slices posterior to Ymm.
+        box: Clip the volume to a box centered at Cx, Cy, Cz (RAI mm), and of\
+            dimensions Dx Dy Dz (RAI mm).
+        mask_box: Set all values inside the box to 1. Box centered at Cx, Cy,\
+            Cz (RAI mm), and of dimensions Dx Dy Dz (RAI mm).
+        and_logic: Combine with next clipping planes using 'and'.
+        or_logic: Combine with next clipping planes using 'or'.
+        verbosity: Show command details (verbose output).
+        crop_allzero: Crop the output volume with 3dAutobox -noclust.
+        crop_greedy: Crop the output volume with 3dAutobox.
+        crop: Same as -crop_greedy, kept for backward compatibility.
+        crop_npad: Set 3dAutobox's -npad option to NPAD. NPAD fattens the\
+            volume a little after cropping.
+        output_prefix: Output prefix for the resultant volume. Default is the\
+            input prefix with _clp suffixed to it.
+        followers: Apply the same clipping or cropping treatment to the\
+            follower datasets.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `VClipVolumeOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__CLIP_VOLUME_METADATA)
+    params = v__clip_volume_params(
+        input_volume=input_volume,
+        below_zmm=below_zmm,
+        above_zmm=above_zmm,
+        left_xmm=left_xmm,
+        right_xmm=right_xmm,
+        anterior_ymm=anterior_ymm,
+        posterior_ymm=posterior_ymm,
+        box=box,
+        mask_box=mask_box,
+        and_logic=and_logic,
+        or_logic=or_logic,
+        verbosity=verbosity,
+        crop_allzero=crop_allzero,
+        crop_greedy=crop_greedy,
+        crop=crop,
+        crop_npad=crop_npad,
+        output_prefix=output_prefix,
+        followers=followers,
+    )
+    return v__clip_volume_execute(params, execution)
+
+
+__all__ = [
+    "VClipVolumeOutputs",
+    "VClipVolumeParameters",
+    "V__CLIP_VOLUME_METADATA",
+    "v__clip_volume",
+    "v__clip_volume_params",
+]