niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/v__surf_smooth_heat_07_examples.py

@@ -0,0 +1,172 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V__SURF_SMOOTH_HEAT_07_EXAMPLES_METADATA = Metadata(
+    id="dc0b150ee17a89e1651ca52dbda01cc2f717b438.boutiques",
+    name="@SurfSmooth.HEAT_07.examples",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+VSurfSmoothHeat07ExamplesParameters = typing.TypedDict('VSurfSmoothHeat07ExamplesParameters', {
+    "__STYX_TYPE__": typing.Literal["@SurfSmooth.HEAT_07.examples"],
+    "path_to_suma_demo": str,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "@SurfSmooth.HEAT_07.examples": v__surf_smooth_heat_07_examples_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 VSurfSmoothHeat07ExamplesOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v__surf_smooth_heat_07_examples(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def v__surf_smooth_heat_07_examples_params(
+    path_to_suma_demo: str,
+) -> VSurfSmoothHeat07ExamplesParameters:
+    """
+    Build parameters.
+    
+    Args:
+        path_to_suma_demo: Path to SUMA demo directory.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "@SurfSmooth.HEAT_07.examples",
+        "path_to_suma_demo": path_to_suma_demo,
+    }
+    return params
+
+
+def v__surf_smooth_heat_07_examples_cargs(
+    params: VSurfSmoothHeat07ExamplesParameters,
+    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("@SurfSmooth.HEAT_07.examples")
+    cargs.append(params.get("path_to_suma_demo"))
+    return cargs
+
+
+def v__surf_smooth_heat_07_examples_outputs(
+    params: VSurfSmoothHeat07ExamplesParameters,
+    execution: Execution,
+) -> VSurfSmoothHeat07ExamplesOutputs:
+    """
+    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 = VSurfSmoothHeat07ExamplesOutputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def v__surf_smooth_heat_07_examples_execute(
+    params: VSurfSmoothHeat07ExamplesParameters,
+    execution: Execution,
+) -> VSurfSmoothHeat07ExamplesOutputs:
+    """
+    A script to illustrate controlled blurring of data on the surface.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `VSurfSmoothHeat07ExamplesOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v__surf_smooth_heat_07_examples_cargs(params, execution)
+    ret = v__surf_smooth_heat_07_examples_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v__surf_smooth_heat_07_examples(
+    path_to_suma_demo: str,
+    runner: Runner | None = None,
+) -> VSurfSmoothHeat07ExamplesOutputs:
+    """
+    A script to illustrate controlled blurring of data on the surface.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        path_to_suma_demo: Path to SUMA demo directory.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `VSurfSmoothHeat07ExamplesOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__SURF_SMOOTH_HEAT_07_EXAMPLES_METADATA)
+    params = v__surf_smooth_heat_07_examples_params(
+        path_to_suma_demo=path_to_suma_demo,
+    )
+    return v__surf_smooth_heat_07_examples_execute(params, execution)
+
+
+__all__ = [
+    "VSurfSmoothHeat07ExamplesOutputs",
+    "VSurfSmoothHeat07ExamplesParameters",
+    "V__SURF_SMOOTH_HEAT_07_EXAMPLES_METADATA",
+    "v__surf_smooth_heat_07_examples",
+    "v__surf_smooth_heat_07_examples_params",
+]

niwrap_afni/afni/v__surf_to_vol_spackle.py

@@ -0,0 +1,322 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V__SURF_TO_VOL_SPACKLE_METADATA = Metadata(
+    id="b0444f30cf6b3a9a0996f5b8c66a1134d87d5052.boutiques",
+    name="@surf_to_vol_spackle",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+VSurfToVolSpackleParameters = typing.TypedDict('VSurfToVolSpackleParameters', {
+    "__STYX_TYPE__": typing.Literal["@surf_to_vol_spackle"],
+    "maskset": InputPathType,
+    "spec": InputPathType,
+    "surfA": str,
+    "surfB": typing.NotRequired[str | None],
+    "surfset": InputPathType,
+    "prefix": str,
+    "normal_vector_length": typing.NotRequired[float | None],
+    "search_radius": typing.NotRequired[float | None],
+    "num_steps": typing.NotRequired[float | None],
+    "keep_temp_files": bool,
+    "max_iters": typing.NotRequired[float | None],
+    "use_mode": bool,
+    "datum_type": typing.NotRequired[str | None],
+    "ignore_unknown_options": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "@surf_to_vol_spackle": v__surf_to_vol_spackle_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 {
+        "@surf_to_vol_spackle": v__surf_to_vol_spackle_outputs,
+    }.get(t)
+
+
+class VSurfToVolSpackleOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v__surf_to_vol_spackle(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_volume: OutputPathType
+    """The primary output volume file with surface measures projected."""
+
+
+def v__surf_to_vol_spackle_params(
+    maskset: InputPathType,
+    spec: InputPathType,
+    surf_a: str,
+    surfset: InputPathType,
+    prefix: str,
+    surf_b: str | None = None,
+    normal_vector_length: float | None = None,
+    search_radius: float | None = None,
+    num_steps: float | None = None,
+    keep_temp_files: bool = False,
+    max_iters: float | None = None,
+    use_mode: bool = False,
+    datum_type: str | None = None,
+    ignore_unknown_options: bool = False,
+) -> VSurfToVolSpackleParameters:
+    """
+    Build parameters.
+    
+    Args:
+        maskset: Mask dataset in which to project surface measures.
+        spec: Surface specification file with list of surfaces.
+        surf_a: Name of the first surface, e.g., smoothwm, pial, etc.
+        surfset: Dataset of surface measures.
+        prefix: Basename of output. Final name used is prefix.nii.gz.
+        surf_b: Name of the second surface. If not included, computes using\
+            normal vector.
+        normal_vector_length: Normal vector length if only using a single\
+            surface (default 2 mm).
+        search_radius: Radius for search for mean to fill holes (default 2 mm).
+        num_steps: Number of steps on line segments (default 10).
+        keep_temp_files: Do not remove any of the temporary files (default is\
+            to remove them).
+        max_iters: Maximum number of smoothing and filling iterations (default\
+            is 4).
+        use_mode: Use mode instead of non-zero median (appropriate for ROIs).
+        datum_type: Set datum type to byte, short, or float instead of maskset\
+            type. Mode triggers -datum short.
+        ignore_unknown_options: Ignore additional options that are not needed.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "@surf_to_vol_spackle",
+        "maskset": maskset,
+        "spec": spec,
+        "surfA": surf_a,
+        "surfset": surfset,
+        "prefix": prefix,
+        "keep_temp_files": keep_temp_files,
+        "use_mode": use_mode,
+        "ignore_unknown_options": ignore_unknown_options,
+    }
+    if surf_b is not None:
+        params["surfB"] = surf_b
+    if normal_vector_length is not None:
+        params["normal_vector_length"] = normal_vector_length
+    if search_radius is not None:
+        params["search_radius"] = search_radius
+    if num_steps is not None:
+        params["num_steps"] = num_steps
+    if max_iters is not None:
+        params["max_iters"] = max_iters
+    if datum_type is not None:
+        params["datum_type"] = datum_type
+    return params
+
+
+def v__surf_to_vol_spackle_cargs(
+    params: VSurfToVolSpackleParameters,
+    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("@surf_to_vol_spackle")
+    cargs.append(execution.input_file(params.get("maskset")))
+    cargs.append(execution.input_file(params.get("spec")))
+    cargs.append(params.get("surfA"))
+    if params.get("surfB") is not None:
+        cargs.append(params.get("surfB"))
+    cargs.append(execution.input_file(params.get("surfset")))
+    cargs.append(params.get("prefix"))
+    if params.get("normal_vector_length") is not None:
+        cargs.extend([
+            "-f_pn_mm",
+            str(params.get("normal_vector_length"))
+        ])
+    if params.get("search_radius") is not None:
+        cargs.extend([
+            "-meanrad",
+            str(params.get("search_radius"))
+        ])
+    if params.get("num_steps") is not None:
+        cargs.extend([
+            "-nsteps",
+            str(params.get("num_steps"))
+        ])
+    if params.get("keep_temp_files"):
+        cargs.append("-keep_temp_files")
+    if params.get("max_iters") is not None:
+        cargs.extend([
+            "-maxiters",
+            str(params.get("max_iters"))
+        ])
+    if params.get("use_mode"):
+        cargs.append("-mode")
+    if params.get("datum_type") is not None:
+        cargs.extend([
+            "-datum",
+            params.get("datum_type")
+        ])
+    if params.get("ignore_unknown_options"):
+        cargs.append("-ignore_unknown_options")
+    return cargs
+
+
+def v__surf_to_vol_spackle_outputs(
+    params: VSurfToVolSpackleParameters,
+    execution: Execution,
+) -> VSurfToVolSpackleOutputs:
+    """
+    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 = VSurfToVolSpackleOutputs(
+        root=execution.output_file("."),
+        output_volume=execution.output_file(params.get("prefix") + ".nii.gz"),
+    )
+    return ret
+
+
+def v__surf_to_vol_spackle_execute(
+    params: VSurfToVolSpackleParameters,
+    execution: Execution,
+) -> VSurfToVolSpackleOutputs:
+    """
+    Project data from a surface dataset into a volume primarily using 3dSurf2Vol but
+    then filling any holes with an iterative smoothing procedure.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `VSurfToVolSpackleOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v__surf_to_vol_spackle_cargs(params, execution)
+    ret = v__surf_to_vol_spackle_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v__surf_to_vol_spackle(
+    maskset: InputPathType,
+    spec: InputPathType,
+    surf_a: str,
+    surfset: InputPathType,
+    prefix: str,
+    surf_b: str | None = None,
+    normal_vector_length: float | None = None,
+    search_radius: float | None = None,
+    num_steps: float | None = None,
+    keep_temp_files: bool = False,
+    max_iters: float | None = None,
+    use_mode: bool = False,
+    datum_type: str | None = None,
+    ignore_unknown_options: bool = False,
+    runner: Runner | None = None,
+) -> VSurfToVolSpackleOutputs:
+    """
+    Project data from a surface dataset into a volume primarily using 3dSurf2Vol but
+    then filling any holes with an iterative smoothing procedure.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        maskset: Mask dataset in which to project surface measures.
+        spec: Surface specification file with list of surfaces.
+        surf_a: Name of the first surface, e.g., smoothwm, pial, etc.
+        surfset: Dataset of surface measures.
+        prefix: Basename of output. Final name used is prefix.nii.gz.
+        surf_b: Name of the second surface. If not included, computes using\
+            normal vector.
+        normal_vector_length: Normal vector length if only using a single\
+            surface (default 2 mm).
+        search_radius: Radius for search for mean to fill holes (default 2 mm).
+        num_steps: Number of steps on line segments (default 10).
+        keep_temp_files: Do not remove any of the temporary files (default is\
+            to remove them).
+        max_iters: Maximum number of smoothing and filling iterations (default\
+            is 4).
+        use_mode: Use mode instead of non-zero median (appropriate for ROIs).
+        datum_type: Set datum type to byte, short, or float instead of maskset\
+            type. Mode triggers -datum short.
+        ignore_unknown_options: Ignore additional options that are not needed.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `VSurfToVolSpackleOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__SURF_TO_VOL_SPACKLE_METADATA)
+    params = v__surf_to_vol_spackle_params(
+        maskset=maskset,
+        spec=spec,
+        surf_a=surf_a,
+        surf_b=surf_b,
+        surfset=surfset,
+        prefix=prefix,
+        normal_vector_length=normal_vector_length,
+        search_radius=search_radius,
+        num_steps=num_steps,
+        keep_temp_files=keep_temp_files,
+        max_iters=max_iters,
+        use_mode=use_mode,
+        datum_type=datum_type,
+        ignore_unknown_options=ignore_unknown_options,
+    )
+    return v__surf_to_vol_spackle_execute(params, execution)
+
+
+__all__ = [
+    "VSurfToVolSpackleOutputs",
+    "VSurfToVolSpackleParameters",
+    "V__SURF_TO_VOL_SPACKLE_METADATA",
+    "v__surf_to_vol_spackle",
+    "v__surf_to_vol_spackle_params",
+]