niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/v_3d_surf_mask.py

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+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3D_SURF_MASK_METADATA = Metadata(
+    id="55dc0c4e1d7ff3d126a0dfcd22e6d94d6ee4130c.boutiques",
+    name="3dSurfMask",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dSurfMaskParameters = typing.TypedDict('V3dSurfMaskParameters', {
+    "__STYX_TYPE__": typing.Literal["3dSurfMask"],
+    "surface_type": str,
+    "surface_file": InputPathType,
+    "prefix": str,
+    "grid_parent": InputPathType,
+    "fill_method": typing.NotRequired[str | None],
+    "surface_volume": typing.NotRequired[InputPathType | None],
+    "mask_only": bool,
+    "flip_orientation": bool,
+    "no_distance": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "3dSurfMask": v_3d_surf_mask_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 {
+        "3dSurfMask": v_3d_surf_mask_outputs,
+    }.get(t)
+
+
+class V3dSurfMaskOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_surf_mask(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_mask: OutputPathType
+    """Main output mask dataset."""
+    distance_dataset: OutputPathType
+    """Dataset reflecting voxel shortest distances to the surface."""
+
+
+def v_3d_surf_mask_params(
+    surface_type: str,
+    surface_file: InputPathType,
+    prefix: str,
+    grid_parent: InputPathType,
+    fill_method: str | None = None,
+    surface_volume: InputPathType | None = None,
+    mask_only: bool = False,
+    flip_orientation: bool = False,
+    no_distance: bool = False,
+) -> V3dSurfMaskParameters:
+    """
+    Build parameters.
+    
+    Args:
+        surface_type: Specify input surface.
+        surface_file: Specify input surface filename.
+        prefix: Prefix of output dataset.
+        grid_parent: Specifies the grid for the output volume.
+        fill_method: Fill method: SLOW or FAST (default: FAST).
+        surface_volume: Specify the surface volume.
+        mask_only: Produce an output dataset where voxels are 1 inside the\
+            surface and 0 outside.
+        flip_orientation: Flip triangle winding of surface mesh.
+        no_distance: Do not compute the distances, just the mask from the first\
+            step.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dSurfMask",
+        "surface_type": surface_type,
+        "surface_file": surface_file,
+        "prefix": prefix,
+        "grid_parent": grid_parent,
+        "mask_only": mask_only,
+        "flip_orientation": flip_orientation,
+        "no_distance": no_distance,
+    }
+    if fill_method is not None:
+        params["fill_method"] = fill_method
+    if surface_volume is not None:
+        params["surface_volume"] = surface_volume
+    return params
+
+
+def v_3d_surf_mask_cargs(
+    params: V3dSurfMaskParameters,
+    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("3dSurfMask")
+    cargs.append(params.get("surface_type"))
+    cargs.append(execution.input_file(params.get("surface_file")))
+    cargs.append(params.get("prefix"))
+    cargs.append(execution.input_file(params.get("grid_parent")))
+    if params.get("fill_method") is not None:
+        cargs.extend([
+            "-fill_method",
+            params.get("fill_method")
+        ])
+    if params.get("surface_volume") is not None:
+        cargs.extend([
+            "-sv",
+            execution.input_file(params.get("surface_volume"))
+        ])
+    if params.get("mask_only"):
+        cargs.append("-mask_only")
+    if params.get("flip_orientation"):
+        cargs.append("-flip_orientation")
+    if params.get("no_distance"):
+        cargs.append("-no_dist")
+    return cargs
+
+
+def v_3d_surf_mask_outputs(
+    params: V3dSurfMaskParameters,
+    execution: Execution,
+) -> V3dSurfMaskOutputs:
+    """
+    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 = V3dSurfMaskOutputs(
+        root=execution.output_file("."),
+        output_mask=execution.output_file(params.get("prefix") + ".m+orig.BRIK"),
+        distance_dataset=execution.output_file(params.get("prefix") + ".d+orig.BRIK"),
+    )
+    return ret
+
+
+def v_3d_surf_mask_execute(
+    params: V3dSurfMaskParameters,
+    execution: Execution,
+) -> V3dSurfMaskOutputs:
+    """
+    Creates volumetric datasets marking voxels based on their location relative to a
+    surface.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dSurfMaskOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_surf_mask_cargs(params, execution)
+    ret = v_3d_surf_mask_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_surf_mask(
+    surface_type: str,
+    surface_file: InputPathType,
+    prefix: str,
+    grid_parent: InputPathType,
+    fill_method: str | None = None,
+    surface_volume: InputPathType | None = None,
+    mask_only: bool = False,
+    flip_orientation: bool = False,
+    no_distance: bool = False,
+    runner: Runner | None = None,
+) -> V3dSurfMaskOutputs:
+    """
+    Creates volumetric datasets marking voxels based on their location relative to a
+    surface.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        surface_type: Specify input surface.
+        surface_file: Specify input surface filename.
+        prefix: Prefix of output dataset.
+        grid_parent: Specifies the grid for the output volume.
+        fill_method: Fill method: SLOW or FAST (default: FAST).
+        surface_volume: Specify the surface volume.
+        mask_only: Produce an output dataset where voxels are 1 inside the\
+            surface and 0 outside.
+        flip_orientation: Flip triangle winding of surface mesh.
+        no_distance: Do not compute the distances, just the mask from the first\
+            step.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dSurfMaskOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_SURF_MASK_METADATA)
+    params = v_3d_surf_mask_params(
+        surface_type=surface_type,
+        surface_file=surface_file,
+        prefix=prefix,
+        grid_parent=grid_parent,
+        fill_method=fill_method,
+        surface_volume=surface_volume,
+        mask_only=mask_only,
+        flip_orientation=flip_orientation,
+        no_distance=no_distance,
+    )
+    return v_3d_surf_mask_execute(params, execution)
+
+
+__all__ = [
+    "V3dSurfMaskOutputs",
+    "V3dSurfMaskParameters",
+    "V_3D_SURF_MASK_METADATA",
+    "v_3d_surf_mask",
+    "v_3d_surf_mask_params",
+]

niwrap_afni/afni/v_3d_synthesize.py

@@ -0,0 +1,251 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3D_SYNTHESIZE_METADATA = Metadata(
+    id="814a030fd63ed19fbe9b03dd6aaaa8fcb42ba91b.boutiques",
+    name="3dSynthesize",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dSynthesizeParameters = typing.TypedDict('V3dSynthesizeParameters', {
+    "__STYX_TYPE__": typing.Literal["3dSynthesize"],
+    "c_bucket": InputPathType,
+    "matrix": InputPathType,
+    "select": str,
+    "prefix": str,
+    "dry_flag": bool,
+    "tr": typing.NotRequired[float | None],
+    "cenfill": typing.NotRequired[typing.Literal["zero", "nbhr", "none"] | None],
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "3dSynthesize": v_3d_synthesize_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 V3dSynthesizeOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_synthesize(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def v_3d_synthesize_params(
+    c_bucket: InputPathType,
+    matrix: InputPathType,
+    select_: str,
+    prefix: str,
+    dry_flag: bool = False,
+    tr: float | None = None,
+    cenfill: typing.Literal["zero", "nbhr", "none"] | None = None,
+) -> V3dSynthesizeParameters:
+    """
+    Build parameters.
+    
+    Args:
+        c_bucket: Input dataset from 3dDeconvolve via the '-cbucket' option.
+        matrix: Matrix file from 3dDeconvolve via the '-x1D' option.
+        select_: Select columns from the matrix and corresponding sub-bricks\
+            from the cbucket. Can use forms like 'baseline', 'polort', 'allfunc',\
+            'allstim', 'all', 'something', or numbers/ranges.
+        prefix: Output result into dataset with the specified name.
+        dry_flag: Don't compute the output, just check the inputs.
+        tr: Set TR in the output to the specified value.
+        cenfill: How censored time points from 3dDeconvolve will be filled\
+            (options: 'zero', 'nbhr', 'none').
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dSynthesize",
+        "c_bucket": c_bucket,
+        "matrix": matrix,
+        "select": select_,
+        "prefix": prefix,
+        "dry_flag": dry_flag,
+    }
+    if tr is not None:
+        params["tr"] = tr
+    if cenfill is not None:
+        params["cenfill"] = cenfill
+    return params
+
+
+def v_3d_synthesize_cargs(
+    params: V3dSynthesizeParameters,
+    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("3dSynthesize")
+    cargs.extend([
+        "-cbucket",
+        execution.input_file(params.get("c_bucket"))
+    ])
+    cargs.extend([
+        "-matrix",
+        execution.input_file(params.get("matrix"))
+    ])
+    cargs.extend([
+        "-select",
+        params.get("select")
+    ])
+    cargs.extend([
+        "-prefix",
+        params.get("prefix")
+    ])
+    if params.get("dry_flag"):
+        cargs.append("-dry")
+    if params.get("tr") is not None:
+        cargs.extend([
+            "-TR",
+            str(params.get("tr"))
+        ])
+    if params.get("cenfill") is not None:
+        cargs.extend([
+            "-cenfill",
+            params.get("cenfill")
+        ])
+    return cargs
+
+
+def v_3d_synthesize_outputs(
+    params: V3dSynthesizeParameters,
+    execution: Execution,
+) -> V3dSynthesizeOutputs:
+    """
+    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 = V3dSynthesizeOutputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def v_3d_synthesize_execute(
+    params: V3dSynthesizeParameters,
+    execution: Execution,
+) -> V3dSynthesizeOutputs:
+    """
+    Reads a '-cbucket' dataset and a '.xmat.1D' matrix from 3dDeconvolve, and
+    synthesizes a fit dataset using selected sub-bricks and matrix columns.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dSynthesizeOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_synthesize_cargs(params, execution)
+    ret = v_3d_synthesize_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_synthesize(
+    c_bucket: InputPathType,
+    matrix: InputPathType,
+    select_: str,
+    prefix: str,
+    dry_flag: bool = False,
+    tr: float | None = None,
+    cenfill: typing.Literal["zero", "nbhr", "none"] | None = None,
+    runner: Runner | None = None,
+) -> V3dSynthesizeOutputs:
+    """
+    Reads a '-cbucket' dataset and a '.xmat.1D' matrix from 3dDeconvolve, and
+    synthesizes a fit dataset using selected sub-bricks and matrix columns.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        c_bucket: Input dataset from 3dDeconvolve via the '-cbucket' option.
+        matrix: Matrix file from 3dDeconvolve via the '-x1D' option.
+        select_: Select columns from the matrix and corresponding sub-bricks\
+            from the cbucket. Can use forms like 'baseline', 'polort', 'allfunc',\
+            'allstim', 'all', 'something', or numbers/ranges.
+        prefix: Output result into dataset with the specified name.
+        dry_flag: Don't compute the output, just check the inputs.
+        tr: Set TR in the output to the specified value.
+        cenfill: How censored time points from 3dDeconvolve will be filled\
+            (options: 'zero', 'nbhr', 'none').
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dSynthesizeOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_SYNTHESIZE_METADATA)
+    params = v_3d_synthesize_params(
+        c_bucket=c_bucket,
+        matrix=matrix,
+        select_=select_,
+        prefix=prefix,
+        dry_flag=dry_flag,
+        tr=tr,
+        cenfill=cenfill,
+    )
+    return v_3d_synthesize_execute(params, execution)
+
+
+__all__ = [
+    "V3dSynthesizeOutputs",
+    "V3dSynthesizeParameters",
+    "V_3D_SYNTHESIZE_METADATA",
+    "v_3d_synthesize",
+    "v_3d_synthesize_params",
+]