niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/surf_dist.py

@@ -0,0 +1,208 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+SURF_DIST_METADATA = Metadata(
+    id="4b7fc8f067afc394968ebdfef5be6b16641eee5b.boutiques",
+    name="SurfDist",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+SurfDistParameters = typing.TypedDict('SurfDistParameters', {
+    "__STYX_TYPE__": typing.Literal["SurfDist"],
+    "surface": InputPathType,
+    "nodepairs": InputPathType,
+    "node_path_do": typing.NotRequired[str | None],
+    "graph": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "SurfDist": surf_dist_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 {
+        "SurfDist": surf_dist_outputs,
+    }.get(t)
+
+
+class SurfDistOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `surf_dist(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    distances: OutputPathType
+    """File containing the distances between nodes"""
+
+
+def surf_dist_params(
+    surface: InputPathType,
+    nodepairs: InputPathType,
+    node_path_do: str | None = None,
+    graph: bool = False,
+) -> SurfDistParameters:
+    """
+    Build parameters.
+    
+    Args:
+        surface: Surface on which distances are computed.
+        nodepairs: Specify node pairs for distance computation.
+        node_path_do: Output the shortest path between each node pair as a SUMA\
+            Displayable object.
+        graph: Calculate distance along the mesh (default).
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "SurfDist",
+        "surface": surface,
+        "nodepairs": nodepairs,
+        "graph": graph,
+    }
+    if node_path_do is not None:
+        params["node_path_do"] = node_path_do
+    return params
+
+
+def surf_dist_cargs(
+    params: SurfDistParameters,
+    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("SurfDist")
+    cargs.append(execution.input_file(params.get("surface")))
+    cargs.append(execution.input_file(params.get("nodepairs")))
+    if params.get("node_path_do") is not None:
+        cargs.extend([
+            "-node_path_do",
+            params.get("node_path_do")
+        ])
+    if params.get("graph"):
+        cargs.append("-graph")
+    return cargs
+
+
+def surf_dist_outputs(
+    params: SurfDistParameters,
+    execution: Execution,
+) -> SurfDistOutputs:
+    """
+    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 = SurfDistOutputs(
+        root=execution.output_file("."),
+        distances=execution.output_file("example.1D"),
+    )
+    return ret
+
+
+def surf_dist_execute(
+    params: SurfDistParameters,
+    execution: Execution,
+) -> SurfDistOutputs:
+    """
+    Calculate shortest distance between node pairs on a surface mesh.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `SurfDistOutputs`).
+    """
+    params = execution.params(params)
+    cargs = surf_dist_cargs(params, execution)
+    ret = surf_dist_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def surf_dist(
+    surface: InputPathType,
+    nodepairs: InputPathType,
+    node_path_do: str | None = None,
+    graph: bool = False,
+    runner: Runner | None = None,
+) -> SurfDistOutputs:
+    """
+    Calculate shortest distance between node pairs on a surface mesh.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        surface: Surface on which distances are computed.
+        nodepairs: Specify node pairs for distance computation.
+        node_path_do: Output the shortest path between each node pair as a SUMA\
+            Displayable object.
+        graph: Calculate distance along the mesh (default).
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `SurfDistOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(SURF_DIST_METADATA)
+    params = surf_dist_params(
+        surface=surface,
+        nodepairs=nodepairs,
+        node_path_do=node_path_do,
+        graph=graph,
+    )
+    return surf_dist_execute(params, execution)
+
+
+__all__ = [
+    "SURF_DIST_METADATA",
+    "SurfDistOutputs",
+    "SurfDistParameters",
+    "surf_dist",
+    "surf_dist_params",
+]

niwrap_afni/afni/surf_dset_info.py

@@ -0,0 +1,355 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+SURF_DSET_INFO_METADATA = Metadata(
+    id="0eea0d47be8d446fa32a71638d9796998abd8047.boutiques",
+    name="SurfDsetInfo",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+SurfDsetInfoParameters = typing.TypedDict('SurfDsetInfoParameters', {
+    "__STYX_TYPE__": typing.Literal["SurfDsetInfo"],
+    "input_dsets": list[InputPathType],
+    "debug_level": typing.NotRequired[int | None],
+    "novolreg": bool,
+    "noxform": bool,
+    "setenv": typing.NotRequired[str | None],
+    "trace": bool,
+    "extreme_trace": bool,
+    "nomall": bool,
+    "yesmall": bool,
+    "mini_help": bool,
+    "help": bool,
+    "extreme_help": bool,
+    "help_view": bool,
+    "help_web": bool,
+    "help_find": typing.NotRequired[str | None],
+    "help_raw": bool,
+    "help_spx": bool,
+    "help_aspx": bool,
+    "all_opts": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "SurfDsetInfo": surf_dset_info_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 SurfDsetInfoOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `surf_dset_info(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def surf_dset_info_params(
+    input_dsets: list[InputPathType],
+    debug_level: int | None = None,
+    novolreg: bool = False,
+    noxform: bool = False,
+    setenv: str | None = None,
+    trace_: bool = False,
+    extreme_trace: bool = False,
+    nomall: bool = False,
+    yesmall: bool = False,
+    mini_help: bool = False,
+    help_: bool = False,
+    extreme_help: bool = False,
+    help_view: bool = False,
+    help_web: bool = False,
+    help_find: str | None = None,
+    help_raw: bool = False,
+    help_spx: bool = False,
+    help_aspx: bool = False,
+    all_opts: bool = False,
+) -> SurfDsetInfoParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_dsets: Input dataset.
+        debug_level: Debug level. If DBG = 2, show full dataset information in\
+            NIML form.
+        novolreg: Ignore any Rotate, Volreg, Tagalign, or WarpDrive\
+            transformations.
+        noxform: Same as -novolreg.
+        setenv: Set environment variable.
+        trace_: Turns on In/Out debug and Memory tracing.
+        extreme_trace: Turns on extreme tracing.
+        nomall: Turn off memory tracing.
+        yesmall: Turn on memory tracing (default).
+        mini_help: Mini help.
+        help_: Show entire help output.
+        extreme_help: Show extreme help.
+        help_view: Open help in text editor.
+        help_web: Open help in web browser.
+        help_find: Look for lines in help output that match the specified word.
+        help_raw: Show unedited help string.
+        help_spx: Show help string in sphinx format, but do not autoformat.
+        help_aspx: Show help string in sphinx with autoformatting.
+        all_opts: Attempt to identify all options for the program from the help\
+            output.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "SurfDsetInfo",
+        "input_dsets": input_dsets,
+        "novolreg": novolreg,
+        "noxform": noxform,
+        "trace": trace_,
+        "extreme_trace": extreme_trace,
+        "nomall": nomall,
+        "yesmall": yesmall,
+        "mini_help": mini_help,
+        "help": help_,
+        "extreme_help": extreme_help,
+        "help_view": help_view,
+        "help_web": help_web,
+        "help_raw": help_raw,
+        "help_spx": help_spx,
+        "help_aspx": help_aspx,
+        "all_opts": all_opts,
+    }
+    if debug_level is not None:
+        params["debug_level"] = debug_level
+    if setenv is not None:
+        params["setenv"] = setenv
+    if help_find is not None:
+        params["help_find"] = help_find
+    return params
+
+
+def surf_dset_info_cargs(
+    params: SurfDsetInfoParameters,
+    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("SurfDsetInfo")
+    cargs.extend([
+        "-input",
+        *[execution.input_file(f) for f in params.get("input_dsets")]
+    ])
+    if params.get("debug_level") is not None:
+        cargs.extend([
+            "-debug",
+            str(params.get("debug_level"))
+        ])
+    if params.get("novolreg"):
+        cargs.append("-novolreg")
+    if params.get("noxform"):
+        cargs.append("-noxform")
+    if params.get("setenv") is not None:
+        cargs.extend([
+            "-setenv",
+            params.get("setenv")
+        ])
+    if params.get("trace"):
+        cargs.append("-trace")
+    if params.get("extreme_trace"):
+        cargs.append("-TRACE")
+    if params.get("nomall"):
+        cargs.append("-nomall")
+    if params.get("yesmall"):
+        cargs.append("-yesmall")
+    if params.get("mini_help"):
+        cargs.append("-h")
+    if params.get("help"):
+        cargs.append("-help")
+    if params.get("extreme_help"):
+        cargs.append("-HELP")
+    if params.get("help_view"):
+        cargs.append("-h_view")
+    if params.get("help_web"):
+        cargs.append("-h_web")
+    if params.get("help_find") is not None:
+        cargs.extend([
+            "-h_find",
+            params.get("help_find")
+        ])
+    if params.get("help_raw"):
+        cargs.append("-h_raw")
+    if params.get("help_spx"):
+        cargs.append("-h_spx")
+    if params.get("help_aspx"):
+        cargs.append("-h_aspx")
+    if params.get("all_opts"):
+        cargs.append("-all_opts")
+    return cargs
+
+
+def surf_dset_info_outputs(
+    params: SurfDsetInfoParameters,
+    execution: Execution,
+) -> SurfDsetInfoOutputs:
+    """
+    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 = SurfDsetInfoOutputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def surf_dset_info_execute(
+    params: SurfDsetInfoParameters,
+    execution: Execution,
+) -> SurfDsetInfoOutputs:
+    """
+    Provides information about surface datasets (DSET).
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `SurfDsetInfoOutputs`).
+    """
+    params = execution.params(params)
+    cargs = surf_dset_info_cargs(params, execution)
+    ret = surf_dset_info_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def surf_dset_info(
+    input_dsets: list[InputPathType],
+    debug_level: int | None = None,
+    novolreg: bool = False,
+    noxform: bool = False,
+    setenv: str | None = None,
+    trace_: bool = False,
+    extreme_trace: bool = False,
+    nomall: bool = False,
+    yesmall: bool = False,
+    mini_help: bool = False,
+    help_: bool = False,
+    extreme_help: bool = False,
+    help_view: bool = False,
+    help_web: bool = False,
+    help_find: str | None = None,
+    help_raw: bool = False,
+    help_spx: bool = False,
+    help_aspx: bool = False,
+    all_opts: bool = False,
+    runner: Runner | None = None,
+) -> SurfDsetInfoOutputs:
+    """
+    Provides information about surface datasets (DSET).
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        input_dsets: Input dataset.
+        debug_level: Debug level. If DBG = 2, show full dataset information in\
+            NIML form.
+        novolreg: Ignore any Rotate, Volreg, Tagalign, or WarpDrive\
+            transformations.
+        noxform: Same as -novolreg.
+        setenv: Set environment variable.
+        trace_: Turns on In/Out debug and Memory tracing.
+        extreme_trace: Turns on extreme tracing.
+        nomall: Turn off memory tracing.
+        yesmall: Turn on memory tracing (default).
+        mini_help: Mini help.
+        help_: Show entire help output.
+        extreme_help: Show extreme help.
+        help_view: Open help in text editor.
+        help_web: Open help in web browser.
+        help_find: Look for lines in help output that match the specified word.
+        help_raw: Show unedited help string.
+        help_spx: Show help string in sphinx format, but do not autoformat.
+        help_aspx: Show help string in sphinx with autoformatting.
+        all_opts: Attempt to identify all options for the program from the help\
+            output.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `SurfDsetInfoOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(SURF_DSET_INFO_METADATA)
+    params = surf_dset_info_params(
+        input_dsets=input_dsets,
+        debug_level=debug_level,
+        novolreg=novolreg,
+        noxform=noxform,
+        setenv=setenv,
+        trace_=trace_,
+        extreme_trace=extreme_trace,
+        nomall=nomall,
+        yesmall=yesmall,
+        mini_help=mini_help,
+        help_=help_,
+        extreme_help=extreme_help,
+        help_view=help_view,
+        help_web=help_web,
+        help_find=help_find,
+        help_raw=help_raw,
+        help_spx=help_spx,
+        help_aspx=help_aspx,
+        all_opts=all_opts,
+    )
+    return surf_dset_info_execute(params, execution)
+
+
+__all__ = [
+    "SURF_DSET_INFO_METADATA",
+    "SurfDsetInfoOutputs",
+    "SurfDsetInfoParameters",
+    "surf_dset_info",
+    "surf_dset_info_params",
+]