niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/surf_qual.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 *
+
+SURF_QUAL_METADATA = Metadata(
+    id="26998942504c3f8916ff5647525cc6689776bf8d.boutiques",
+    name="SurfQual",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+SurfQualParameters = typing.TypedDict('SurfQualParameters', {
+    "__STYX_TYPE__": typing.Literal["SurfQual"],
+    "spec_file": InputPathType,
+    "surface_a": list[InputPathType],
+    "sphere_flag": bool,
+    "summary_flag": bool,
+    "self_intersect_flag": bool,
+    "output_prefix": 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 {
+        "SurfQual": surf_qual_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 {
+        "SurfQual": surf_qual_outputs,
+    }.get(t)
+
+
+class SurfQualOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `surf_qual(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    dist_output: OutputPathType | None
+    """File containing distances of nodes from the surface's center."""
+    dist_color_output: OutputPathType | None
+    """Colorized file containing distances of nodes from the surface's
+    center."""
+    bad_nodes_output: OutputPathType | None
+    """File containing nodes with bad dot product values."""
+    bad_nodes_color_output: OutputPathType | None
+    """Colorized file containing nodes with bad dot product values."""
+    dotprod_output: OutputPathType | None
+    """File containing dot product values for all nodes."""
+    dotprod_color_output: OutputPathType | None
+    """Colorized file containing dot product values for all nodes."""
+    intersect_nodes_output: OutputPathType | None
+    """File containing indices of nodes forming segments that intersect the
+    surface."""
+
+
+def surf_qual_params(
+    spec_file: InputPathType,
+    surface_a: list[InputPathType],
+    sphere_flag: bool = False,
+    summary_flag: bool = False,
+    self_intersect_flag: bool = False,
+    output_prefix: str | None = None,
+) -> SurfQualParameters:
+    """
+    Build parameters.
+    
+    Args:
+        spec_file: Spec file containing input surfaces.
+        surface_a: Name of input surface A.
+        sphere_flag: Indicates that surfaces read are spherical.
+        summary_flag: Provide summary of results to stdout.
+        self_intersect_flag: Check if surface is self intersecting.
+        output_prefix: Prefix of output files. Default is the surface's label.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "SurfQual",
+        "spec_file": spec_file,
+        "surface_a": surface_a,
+        "sphere_flag": sphere_flag,
+        "summary_flag": summary_flag,
+        "self_intersect_flag": self_intersect_flag,
+    }
+    if output_prefix is not None:
+        params["output_prefix"] = output_prefix
+    return params
+
+
+def surf_qual_cargs(
+    params: SurfQualParameters,
+    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("SurfQual")
+    cargs.extend([
+        "-spec",
+        execution.input_file(params.get("spec_file"))
+    ])
+    cargs.extend([
+        "-surf_A",
+        *[execution.input_file(f) for f in params.get("surface_a")]
+    ])
+    if params.get("sphere_flag"):
+        cargs.append("-sphere")
+    if params.get("summary_flag"):
+        cargs.append("-summary")
+    if params.get("self_intersect_flag"):
+        cargs.append("-self_intersect")
+    if params.get("output_prefix") is not None:
+        cargs.extend([
+            "-prefix",
+            params.get("output_prefix")
+        ])
+    return cargs
+
+
+def surf_qual_outputs(
+    params: SurfQualParameters,
+    execution: Execution,
+) -> SurfQualOutputs:
+    """
+    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 = SurfQualOutputs(
+        root=execution.output_file("."),
+        dist_output=execution.output_file(params.get("output_prefix") + "_Dist.1D.dset") if (params.get("output_prefix") is not None) else None,
+        dist_color_output=execution.output_file(params.get("output_prefix") + "_Dist.1D.col") if (params.get("output_prefix") is not None) else None,
+        bad_nodes_output=execution.output_file(params.get("output_prefix") + "_BadNodes.1D.dset") if (params.get("output_prefix") is not None) else None,
+        bad_nodes_color_output=execution.output_file(params.get("output_prefix") + "_BadNodes.1D.col") if (params.get("output_prefix") is not None) else None,
+        dotprod_output=execution.output_file(params.get("output_prefix") + "_dotprod.1D.dset") if (params.get("output_prefix") is not None) else None,
+        dotprod_color_output=execution.output_file(params.get("output_prefix") + "_dotprod.1D.col") if (params.get("output_prefix") is not None) else None,
+        intersect_nodes_output=execution.output_file(params.get("output_prefix") + "_IntersNodes.1D.dset") if (params.get("output_prefix") is not None) else None,
+    )
+    return ret
+
+
+def surf_qual_execute(
+    params: SurfQualParameters,
+    execution: Execution,
+) -> SurfQualOutputs:
+    """
+    A program to check the quality of surfaces.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `SurfQualOutputs`).
+    """
+    params = execution.params(params)
+    cargs = surf_qual_cargs(params, execution)
+    ret = surf_qual_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def surf_qual(
+    spec_file: InputPathType,
+    surface_a: list[InputPathType],
+    sphere_flag: bool = False,
+    summary_flag: bool = False,
+    self_intersect_flag: bool = False,
+    output_prefix: str | None = None,
+    runner: Runner | None = None,
+) -> SurfQualOutputs:
+    """
+    A program to check the quality of surfaces.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        spec_file: Spec file containing input surfaces.
+        surface_a: Name of input surface A.
+        sphere_flag: Indicates that surfaces read are spherical.
+        summary_flag: Provide summary of results to stdout.
+        self_intersect_flag: Check if surface is self intersecting.
+        output_prefix: Prefix of output files. Default is the surface's label.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `SurfQualOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(SURF_QUAL_METADATA)
+    params = surf_qual_params(
+        spec_file=spec_file,
+        surface_a=surface_a,
+        sphere_flag=sphere_flag,
+        summary_flag=summary_flag,
+        self_intersect_flag=self_intersect_flag,
+        output_prefix=output_prefix,
+    )
+    return surf_qual_execute(params, execution)
+
+
+__all__ = [
+    "SURF_QUAL_METADATA",
+    "SurfQualOutputs",
+    "SurfQualParameters",
+    "surf_qual",
+    "surf_qual_params",
+]

niwrap_afni/afni/surf_retino_map.py

@@ -0,0 +1,225 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+SURF_RETINO_MAP_METADATA = Metadata(
+    id="0a0bd510fbdb86c742b4ce55d2755f1f8650721e.boutiques",
+    name="SurfRetinoMap",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+SurfRetinoMapParameters = typing.TypedDict('SurfRetinoMapParameters', {
+    "__STYX_TYPE__": typing.Literal["SurfRetinoMap"],
+    "surface": str,
+    "polar": str,
+    "eccentricity": str,
+    "prefix": typing.NotRequired[str | None],
+    "node_debug": typing.NotRequired[float | None],
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "SurfRetinoMap": surf_retino_map_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 {
+        "SurfRetinoMap": surf_retino_map_outputs,
+    }.get(t)
+
+
+class SurfRetinoMapOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `surf_retino_map(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    vfr_output: OutputPathType | None
+    """Output Visual Field Ratio (VFR) dataset."""
+    threshold_max_output: OutputPathType | None
+    """Maximum threshold at each node in the input datasets."""
+
+
+def surf_retino_map_params(
+    surface: str,
+    polar: str,
+    eccentricity: str,
+    prefix: str | None = None,
+    node_debug: float | None = None,
+) -> SurfRetinoMapParameters:
+    """
+    Build parameters.
+    
+    Args:
+        surface: Surface on which distances are computed. See 'Specifying input\
+            surfaces' section for syntax.
+        polar: Retinotopic dataset: polar angle dataset.
+        eccentricity: Retinotopic dataset: eccentricity angle dataset.
+        prefix: Prefix for output datasets.
+        node_debug: Index of node number for which debugging information is\
+            output.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "SurfRetinoMap",
+        "surface": surface,
+        "polar": polar,
+        "eccentricity": eccentricity,
+    }
+    if prefix is not None:
+        params["prefix"] = prefix
+    if node_debug is not None:
+        params["node_debug"] = node_debug
+    return params
+
+
+def surf_retino_map_cargs(
+    params: SurfRetinoMapParameters,
+    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("SurfRetinoMap")
+    cargs.append(params.get("surface"))
+    cargs.append(params.get("polar"))
+    cargs.append(params.get("eccentricity"))
+    if params.get("prefix") is not None:
+        cargs.extend([
+            "--prefix",
+            params.get("prefix")
+        ])
+    if params.get("node_debug") is not None:
+        cargs.extend([
+            "--node_dbg",
+            str(params.get("node_debug"))
+        ])
+    return cargs
+
+
+def surf_retino_map_outputs(
+    params: SurfRetinoMapParameters,
+    execution: Execution,
+) -> SurfRetinoMapOutputs:
+    """
+    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 = SurfRetinoMapOutputs(
+        root=execution.output_file("."),
+        vfr_output=execution.output_file(params.get("prefix") + "_VFR.nii.gz") if (params.get("prefix") is not None) else None,
+        threshold_max_output=execution.output_file(params.get("prefix") + "_threshold_max.nii.gz") if (params.get("prefix") is not None) else None,
+    )
+    return ret
+
+
+def surf_retino_map_execute(
+    params: SurfRetinoMapParameters,
+    execution: Execution,
+) -> SurfRetinoMapOutputs:
+    """
+    Tool for retinotopic mapping on cortical surfaces.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `SurfRetinoMapOutputs`).
+    """
+    params = execution.params(params)
+    cargs = surf_retino_map_cargs(params, execution)
+    ret = surf_retino_map_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def surf_retino_map(
+    surface: str,
+    polar: str,
+    eccentricity: str,
+    prefix: str | None = None,
+    node_debug: float | None = None,
+    runner: Runner | None = None,
+) -> SurfRetinoMapOutputs:
+    """
+    Tool for retinotopic mapping on cortical surfaces.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        surface: Surface on which distances are computed. See 'Specifying input\
+            surfaces' section for syntax.
+        polar: Retinotopic dataset: polar angle dataset.
+        eccentricity: Retinotopic dataset: eccentricity angle dataset.
+        prefix: Prefix for output datasets.
+        node_debug: Index of node number for which debugging information is\
+            output.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `SurfRetinoMapOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(SURF_RETINO_MAP_METADATA)
+    params = surf_retino_map_params(
+        surface=surface,
+        polar=polar,
+        eccentricity=eccentricity,
+        prefix=prefix,
+        node_debug=node_debug,
+    )
+    return surf_retino_map_execute(params, execution)
+
+
+__all__ = [
+    "SURF_RETINO_MAP_METADATA",
+    "SurfRetinoMapOutputs",
+    "SurfRetinoMapParameters",
+    "surf_retino_map",
+    "surf_retino_map_params",
+]