niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/surf_info.py

@@ -0,0 +1,288 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+SURF_INFO_METADATA = Metadata(
+    id="91fa2904287da85a4df485d2f8c7ffbc9ba1a073.boutiques",
+    name="SurfInfo",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+SurfInfoParameters = typing.TypedDict('SurfInfoParameters', {
+    "__STYX_TYPE__": typing.Literal["SurfInfo"],
+    "surface": InputPathType,
+    "com": bool,
+    "debug_level": typing.NotRequired[float | None],
+    "detail_level": typing.NotRequired[float | None],
+    "quiet": bool,
+    "separator": typing.NotRequired[str | None],
+    "input_surface": typing.NotRequired[str | None],
+    "surface_state": typing.NotRequired[str | None],
+    "surface_volume": typing.NotRequired[InputPathType | None],
+    "spec_file": typing.NotRequired[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 {
+        "SurfInfo": surf_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 {
+        "SurfInfo": surf_info_outputs,
+    }.get(t)
+
+
+class SurfInfoOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `surf_info(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    metrics_output: OutputPathType
+    """Output file containing calculated surface metrics."""
+
+
+def surf_info_params(
+    surface: InputPathType,
+    com: bool = False,
+    debug_level: float | None = None,
+    detail_level: float | None = None,
+    quiet: bool = False,
+    separator: str | None = None,
+    input_surface: str | None = None,
+    surface_state: str | None = None,
+    surface_volume: InputPathType | None = None,
+    spec_file: InputPathType | None = None,
+) -> SurfInfoParameters:
+    """
+    Build parameters.
+    
+    Args:
+        surface: Input surface file.
+        com: Output the center of mass.
+        debug_level: Debugging level (2 turns LocalHead ON).
+        detail_level: Calculate surface metrics. 1=yes, 0=no.
+        quiet: Do not include the name of the parameter in output.
+        separator: Use string SEP to separate parameter values. Default is ' ;\
+            '.
+        input_surface: Specify the input surface type and file.
+        surface_state: Specify surface type, state, and name.
+        surface_volume: Specify a surface volume file.
+        spec_file: Specify a surface specification (spec) file.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "SurfInfo",
+        "surface": surface,
+        "com": com,
+        "quiet": quiet,
+    }
+    if debug_level is not None:
+        params["debug_level"] = debug_level
+    if detail_level is not None:
+        params["detail_level"] = detail_level
+    if separator is not None:
+        params["separator"] = separator
+    if input_surface is not None:
+        params["input_surface"] = input_surface
+    if surface_state is not None:
+        params["surface_state"] = surface_state
+    if surface_volume is not None:
+        params["surface_volume"] = surface_volume
+    if spec_file is not None:
+        params["spec_file"] = spec_file
+    return params
+
+
+def surf_info_cargs(
+    params: SurfInfoParameters,
+    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("SurfInfo")
+    cargs.append("[options]")
+    cargs.append(execution.input_file(params.get("surface")))
+    if params.get("com"):
+        cargs.append("-COM")
+    if params.get("debug_level") is not None:
+        cargs.extend([
+            "-debug",
+            str(params.get("debug_level"))
+        ])
+    if params.get("detail_level") is not None:
+        cargs.extend([
+            "-detail",
+            str(params.get("detail_level"))
+        ])
+    if params.get("quiet"):
+        cargs.append("-quiet")
+    if params.get("separator") is not None:
+        cargs.extend([
+            "-sep",
+            params.get("separator")
+        ])
+    if params.get("input_surface") is not None:
+        cargs.extend([
+            "-i_TYPE",
+            params.get("input_surface")
+        ])
+    if params.get("surface_state") is not None:
+        cargs.extend([
+            "-tsn",
+            params.get("surface_state")
+        ])
+    if params.get("surface_volume") is not None:
+        cargs.extend([
+            "-sv",
+            execution.input_file(params.get("surface_volume"))
+        ])
+    if params.get("spec_file") is not None:
+        cargs.extend([
+            "-spec",
+            execution.input_file(params.get("spec_file"))
+        ])
+    return cargs
+
+
+def surf_info_outputs(
+    params: SurfInfoParameters,
+    execution: Execution,
+) -> SurfInfoOutputs:
+    """
+    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 = SurfInfoOutputs(
+        root=execution.output_file("."),
+        metrics_output=execution.output_file(pathlib.Path(params.get("surface")).name + "_metrics.txt"),
+    )
+    return ret
+
+
+def surf_info_execute(
+    params: SurfInfoParameters,
+    execution: Execution,
+) -> SurfInfoOutputs:
+    """
+    Tool to gather information about surface files.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `SurfInfoOutputs`).
+    """
+    params = execution.params(params)
+    cargs = surf_info_cargs(params, execution)
+    ret = surf_info_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def surf_info(
+    surface: InputPathType,
+    com: bool = False,
+    debug_level: float | None = None,
+    detail_level: float | None = None,
+    quiet: bool = False,
+    separator: str | None = None,
+    input_surface: str | None = None,
+    surface_state: str | None = None,
+    surface_volume: InputPathType | None = None,
+    spec_file: InputPathType | None = None,
+    runner: Runner | None = None,
+) -> SurfInfoOutputs:
+    """
+    Tool to gather information about surface files.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        surface: Input surface file.
+        com: Output the center of mass.
+        debug_level: Debugging level (2 turns LocalHead ON).
+        detail_level: Calculate surface metrics. 1=yes, 0=no.
+        quiet: Do not include the name of the parameter in output.
+        separator: Use string SEP to separate parameter values. Default is ' ;\
+            '.
+        input_surface: Specify the input surface type and file.
+        surface_state: Specify surface type, state, and name.
+        surface_volume: Specify a surface volume file.
+        spec_file: Specify a surface specification (spec) file.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `SurfInfoOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(SURF_INFO_METADATA)
+    params = surf_info_params(
+        surface=surface,
+        com=com,
+        debug_level=debug_level,
+        detail_level=detail_level,
+        quiet=quiet,
+        separator=separator,
+        input_surface=input_surface,
+        surface_state=surface_state,
+        surface_volume=surface_volume,
+        spec_file=spec_file,
+    )
+    return surf_info_execute(params, execution)
+
+
+__all__ = [
+    "SURF_INFO_METADATA",
+    "SurfInfoOutputs",
+    "SurfInfoParameters",
+    "surf_info",
+    "surf_info_params",
+]

niwrap_afni/afni/surf_layers.py

@@ -0,0 +1,300 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+SURF_LAYERS_METADATA = Metadata(
+    id="e966c2d7b51c012df1e75b107d18f44f83eac9a4.boutiques",
+    name="SurfLayers",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+SurfLayersParameters = typing.TypedDict('SurfLayersParameters', {
+    "__STYX_TYPE__": typing.Literal["SurfLayers"],
+    "spec_dset": typing.NotRequired[InputPathType | None],
+    "outdir": typing.NotRequired[str | None],
+    "states": typing.NotRequired[str | None],
+    "hemi": typing.NotRequired[str | None],
+    "n_intermed_surfs": typing.NotRequired[float | None],
+    "surf_a": typing.NotRequired[InputPathType | None],
+    "surf_b": typing.NotRequired[InputPathType | None],
+    "surf_intermed_pref": typing.NotRequired[str | None],
+    "echo": bool,
+    "no_clean": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "SurfLayers": surf_layers_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 {
+        "SurfLayers": surf_layers_outputs,
+    }.get(t)
+
+
+class SurfLayersOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `surf_layers(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    interpolated_surfaces: OutputPathType | None
+    """Interpolated surfaces files"""
+    additional_spec_files: OutputPathType | None
+    """Additional files if -spec option was used"""
+    run_view_script: OutputPathType | None
+    """Run script to view output directly"""
+
+
+def surf_layers_params(
+    spec_dset: InputPathType | None = None,
+    outdir: str | None = None,
+    states: str | None = None,
+    hemi: str | None = None,
+    n_intermed_surfs: float | None = None,
+    surf_a: InputPathType | None = None,
+    surf_b: InputPathType | None = None,
+    surf_intermed_pref: str | None = None,
+    echo: bool = False,
+    no_clean: bool = False,
+) -> SurfLayersParameters:
+    """
+    Build parameters.
+    
+    Args:
+        spec_dset: Dataset that is the SUMA specification file describing input\
+            surfaces.
+        outdir: New directory for output (default: surflayers).
+        states: Typically smoothwm, pial states to describe inner and outer\
+            surfaces (default: 'smoothwm pial').
+        hemi: Choose hemisphere: 'lh', 'rh', or 'lh rh' (for both).
+        n_intermed_surfs: Total number of intermediate surfaces to create.
+        surf_a: Inner boundary surface by filename (e.g., smoothwm.gii).
+        surf_b: Outer boundary surface by filename (e.g., pial.gii).
+        surf_intermed_pref: Name for interpolated surfaces (default: isurf).
+        echo: Run script with 'set echo' (i.e., verbosely).
+        no_clean: Do not remove temp files (probably just for testing).
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "SurfLayers",
+        "echo": echo,
+        "no_clean": no_clean,
+    }
+    if spec_dset is not None:
+        params["spec_dset"] = spec_dset
+    if outdir is not None:
+        params["outdir"] = outdir
+    if states is not None:
+        params["states"] = states
+    if hemi is not None:
+        params["hemi"] = hemi
+    if n_intermed_surfs is not None:
+        params["n_intermed_surfs"] = n_intermed_surfs
+    if surf_a is not None:
+        params["surf_a"] = surf_a
+    if surf_b is not None:
+        params["surf_b"] = surf_b
+    if surf_intermed_pref is not None:
+        params["surf_intermed_pref"] = surf_intermed_pref
+    return params
+
+
+def surf_layers_cargs(
+    params: SurfLayersParameters,
+    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("SurfLayers")
+    if params.get("spec_dset") is not None:
+        cargs.extend([
+            "-spec",
+            execution.input_file(params.get("spec_dset"))
+        ])
+    if params.get("outdir") is not None:
+        cargs.extend([
+            "-outdir",
+            params.get("outdir")
+        ])
+    if params.get("states") is not None:
+        cargs.extend([
+            "-states",
+            params.get("states")
+        ])
+    if params.get("hemi") is not None:
+        cargs.extend([
+            "-hemi",
+            params.get("hemi")
+        ])
+    if params.get("n_intermed_surfs") is not None:
+        cargs.extend([
+            "-n_intermed_surfs",
+            str(params.get("n_intermed_surfs"))
+        ])
+    if params.get("surf_a") is not None:
+        cargs.extend([
+            "-surf_A",
+            execution.input_file(params.get("surf_a"))
+        ])
+    if params.get("surf_b") is not None:
+        cargs.extend([
+            "-surf_B",
+            execution.input_file(params.get("surf_b"))
+        ])
+    if params.get("surf_intermed_pref") is not None:
+        cargs.extend([
+            "-surf_intermed_pref",
+            params.get("surf_intermed_pref")
+        ])
+    if params.get("echo"):
+        cargs.append("-echo")
+    if params.get("no_clean"):
+        cargs.append("-no_clean")
+    return cargs
+
+
+def surf_layers_outputs(
+    params: SurfLayersParameters,
+    execution: Execution,
+) -> SurfLayersOutputs:
+    """
+    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 = SurfLayersOutputs(
+        root=execution.output_file("."),
+        interpolated_surfaces=execution.output_file(params.get("outdir") + "/isurf." + params.get("hemi") + ".*.gii") if (params.get("outdir") is not None and params.get("hemi") is not None) else None,
+        additional_spec_files=execution.output_file(params.get("outdir") + "/*") if (params.get("outdir") is not None) else None,
+        run_view_script=execution.output_file(params.get("outdir") + "/run*tcsh") if (params.get("outdir") is not None) else None,
+    )
+    return ret
+
+
+def surf_layers_execute(
+    params: SurfLayersParameters,
+    execution: Execution,
+) -> SurfLayersOutputs:
+    """
+    Compute intermediate equi-distant surfaces between two boundary surfaces.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `SurfLayersOutputs`).
+    """
+    params = execution.params(params)
+    cargs = surf_layers_cargs(params, execution)
+    ret = surf_layers_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def surf_layers(
+    spec_dset: InputPathType | None = None,
+    outdir: str | None = None,
+    states: str | None = None,
+    hemi: str | None = None,
+    n_intermed_surfs: float | None = None,
+    surf_a: InputPathType | None = None,
+    surf_b: InputPathType | None = None,
+    surf_intermed_pref: str | None = None,
+    echo: bool = False,
+    no_clean: bool = False,
+    runner: Runner | None = None,
+) -> SurfLayersOutputs:
+    """
+    Compute intermediate equi-distant surfaces between two boundary surfaces.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        spec_dset: Dataset that is the SUMA specification file describing input\
+            surfaces.
+        outdir: New directory for output (default: surflayers).
+        states: Typically smoothwm, pial states to describe inner and outer\
+            surfaces (default: 'smoothwm pial').
+        hemi: Choose hemisphere: 'lh', 'rh', or 'lh rh' (for both).
+        n_intermed_surfs: Total number of intermediate surfaces to create.
+        surf_a: Inner boundary surface by filename (e.g., smoothwm.gii).
+        surf_b: Outer boundary surface by filename (e.g., pial.gii).
+        surf_intermed_pref: Name for interpolated surfaces (default: isurf).
+        echo: Run script with 'set echo' (i.e., verbosely).
+        no_clean: Do not remove temp files (probably just for testing).
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `SurfLayersOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(SURF_LAYERS_METADATA)
+    params = surf_layers_params(
+        spec_dset=spec_dset,
+        outdir=outdir,
+        states=states,
+        hemi=hemi,
+        n_intermed_surfs=n_intermed_surfs,
+        surf_a=surf_a,
+        surf_b=surf_b,
+        surf_intermed_pref=surf_intermed_pref,
+        echo=echo,
+        no_clean=no_clean,
+    )
+    return surf_layers_execute(params, execution)
+
+
+__all__ = [
+    "SURF_LAYERS_METADATA",
+    "SurfLayersOutputs",
+    "SurfLayersParameters",
+    "surf_layers",
+    "surf_layers_params",
+]