niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/quickspec.py

@@ -0,0 +1,259 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+QUICKSPEC_METADATA = Metadata(
+    id="0a985ab38a04ef53341c98e04d446660dcd3c0c6.boutiques",
+    name="quickspec",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+QuickspecParameters = typing.TypedDict('QuickspecParameters', {
+    "__STYX_TYPE__": typing.Literal["quickspec"],
+    "tn": list[str],
+    "tsn": list[str],
+    "tsnad": typing.NotRequired[list[str] | None],
+    "tsnadm": typing.NotRequired[list[str] | None],
+    "tsnadl": typing.NotRequired[list[str] | None],
+    "spec": typing.NotRequired[str | None],
+    "help": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "quickspec": quickspec_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 {
+        "quickspec": quickspec_outputs,
+    }.get(t)
+
+
+class QuickspecOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `quickspec(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    out_specfile: OutputPathType | None
+    """The spec file output."""
+
+
+def quickspec_params(
+    tn: list[str],
+    tsn: list[str],
+    tsnad: list[str] | None = None,
+    tsnadm: list[str] | None = None,
+    tsnadl: list[str] | None = None,
+    spec: str | None = None,
+    help_: bool = False,
+) -> QuickspecParameters:
+    """
+    Build parameters.
+    
+    Args:
+        tn: Specify surface type and name.
+        tsn: Specify surface type, state, and name.
+        tsnad: Specify surface type, state, name, anatomical correctness, and\
+            Local Domain Parent.
+        tsnadm: Specify surface type, state, name, anatomical correctness,\
+            Local Domain Parent, and node marker file.
+        tsnadl: Specify surface type, state, name, anatomical correctness,\
+            Local Domain Parent, and label dataset file.
+        spec: Name of spec file output. Default is quick.spec.
+        help_: Display help message.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "quickspec",
+        "tn": tn,
+        "tsn": tsn,
+        "help": help_,
+    }
+    if tsnad is not None:
+        params["tsnad"] = tsnad
+    if tsnadm is not None:
+        params["tsnadm"] = tsnadm
+    if tsnadl is not None:
+        params["tsnadl"] = tsnadl
+    if spec is not None:
+        params["spec"] = spec
+    return params
+
+
+def quickspec_cargs(
+    params: QuickspecParameters,
+    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("quickspec")
+    cargs.extend([
+        "-tn",
+        *params.get("tn")
+    ])
+    cargs.extend([
+        "-tsn",
+        *params.get("tsn")
+    ])
+    if params.get("tsnad") is not None:
+        cargs.extend([
+            "-tsnad",
+            *params.get("tsnad")
+        ])
+    if params.get("tsnadm") is not None:
+        cargs.extend([
+            "-tsnadm",
+            *params.get("tsnadm")
+        ])
+    if params.get("tsnadl") is not None:
+        cargs.extend([
+            "-tsnadl",
+            *params.get("tsnadl")
+        ])
+    if params.get("spec") is not None:
+        cargs.extend([
+            "-spec",
+            params.get("spec")
+        ])
+    if params.get("help"):
+        cargs.append("-h")
+    return cargs
+
+
+def quickspec_outputs(
+    params: QuickspecParameters,
+    execution: Execution,
+) -> QuickspecOutputs:
+    """
+    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 = QuickspecOutputs(
+        root=execution.output_file("."),
+        out_specfile=execution.output_file(params.get("spec")) if (params.get("spec") is not None) else None,
+    )
+    return ret
+
+
+def quickspec_execute(
+    params: QuickspecParameters,
+    execution: Execution,
+) -> QuickspecOutputs:
+    """
+    A quick and dirty way of loading a surface into SUMA or command line programs
+    using a spec file.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `QuickspecOutputs`).
+    """
+    params = execution.params(params)
+    cargs = quickspec_cargs(params, execution)
+    ret = quickspec_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def quickspec(
+    tn: list[str],
+    tsn: list[str],
+    tsnad: list[str] | None = None,
+    tsnadm: list[str] | None = None,
+    tsnadl: list[str] | None = None,
+    spec: str | None = None,
+    help_: bool = False,
+    runner: Runner | None = None,
+) -> QuickspecOutputs:
+    """
+    A quick and dirty way of loading a surface into SUMA or command line programs
+    using a spec file.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        tn: Specify surface type and name.
+        tsn: Specify surface type, state, and name.
+        tsnad: Specify surface type, state, name, anatomical correctness, and\
+            Local Domain Parent.
+        tsnadm: Specify surface type, state, name, anatomical correctness,\
+            Local Domain Parent, and node marker file.
+        tsnadl: Specify surface type, state, name, anatomical correctness,\
+            Local Domain Parent, and label dataset file.
+        spec: Name of spec file output. Default is quick.spec.
+        help_: Display help message.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `QuickspecOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(QUICKSPEC_METADATA)
+    params = quickspec_params(
+        tn=tn,
+        tsn=tsn,
+        tsnad=tsnad,
+        tsnadm=tsnadm,
+        tsnadl=tsnadl,
+        spec=spec,
+        help_=help_,
+    )
+    return quickspec_execute(params, execution)
+
+
+__all__ = [
+    "QUICKSPEC_METADATA",
+    "QuickspecOutputs",
+    "QuickspecParameters",
+    "quickspec",
+    "quickspec_params",
+]

niwrap_afni/afni/quickspec_sl.py

@@ -0,0 +1,282 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+QUICKSPEC_SL_METADATA = Metadata(
+    id="6ad0ef7a3cf68472db5f2c42ec5677d562d0ca24.boutiques",
+    name="quickspecSL",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+QuickspecSlParameters = typing.TypedDict('QuickspecSlParameters', {
+    "__STYX_TYPE__": typing.Literal["quickspecSL"],
+    "surf_A": InputPathType,
+    "surf_B": InputPathType,
+    "surf_intermed_pref": typing.NotRequired[str | None],
+    "infl_surf_A": typing.NotRequired[InputPathType | None],
+    "infl_surf_B": typing.NotRequired[InputPathType | None],
+    "infl_surf_intermed_pref": typing.NotRequired[str | None],
+    "both_lr_flag": bool,
+    "out_spec": 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 {
+        "quickspecSL": quickspec_sl_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 {
+        "quickspecSL": quickspec_sl_outputs,
+    }.get(t)
+
+
+class QuickspecSlOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `quickspec_sl(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_spec_file: OutputPathType | None
+    """Output spec file"""
+
+
+def quickspec_sl_params(
+    surf_a: InputPathType,
+    surf_b: InputPathType,
+    surf_intermed_pref: str | None = None,
+    infl_surf_a: InputPathType | None = None,
+    infl_surf_b: InputPathType | None = None,
+    infl_surf_intermed_pref: str | None = None,
+    both_lr_flag: bool = False,
+    out_spec: str | None = None,
+) -> QuickspecSlParameters:
+    """
+    Build parameters.
+    
+    Args:
+        surf_a: Inner (anatomically-correct) boundary surface dataset (e.g.\
+            smoothwm.gii).
+        surf_b: Outer (anatomically-correct) boundary surface dataset (e.g.\
+            pial.gii).
+        surf_intermed_pref: Prefix for (anatomically-correct) intermediate\
+            surfaces, typically output by SurfLayers (default: isurf).
+        infl_surf_a: Inner (inflated) boundary surface dataset (e.g.\
+            infl.smoothwm.gii).
+        infl_surf_b: Outer (inflated) boundary surface dataset (e.g.\
+            infl.pial.gii).
+        infl_surf_intermed_pref: Prefix for (inflated) intermediate surfaces,\
+            typically output by SurfLayers (default: infl.isurf).
+        both_lr_flag: Specify an output spec for both hemispheres if surfaces\
+            for both exist.
+        out_spec: Name for output *.spec file (default: newspec.spec).
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "quickspecSL",
+        "surf_A": surf_a,
+        "surf_B": surf_b,
+        "both_lr_flag": both_lr_flag,
+    }
+    if surf_intermed_pref is not None:
+        params["surf_intermed_pref"] = surf_intermed_pref
+    if infl_surf_a is not None:
+        params["infl_surf_A"] = infl_surf_a
+    if infl_surf_b is not None:
+        params["infl_surf_B"] = infl_surf_b
+    if infl_surf_intermed_pref is not None:
+        params["infl_surf_intermed_pref"] = infl_surf_intermed_pref
+    if out_spec is not None:
+        params["out_spec"] = out_spec
+    return params
+
+
+def quickspec_sl_cargs(
+    params: QuickspecSlParameters,
+    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("quickspecSL")
+    cargs.extend([
+        "-surf_A",
+        execution.input_file(params.get("surf_A"))
+    ])
+    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("infl_surf_A") is not None:
+        cargs.extend([
+            "-infl_surf_A",
+            execution.input_file(params.get("infl_surf_A"))
+        ])
+    if params.get("infl_surf_B") is not None:
+        cargs.extend([
+            "-infl_surf_B",
+            execution.input_file(params.get("infl_surf_B"))
+        ])
+    if params.get("infl_surf_intermed_pref") is not None:
+        cargs.extend([
+            "-infl_surf_intermed_pref",
+            params.get("infl_surf_intermed_pref")
+        ])
+    if params.get("both_lr_flag"):
+        cargs.append("-both_lr")
+    if params.get("out_spec") is not None:
+        cargs.extend([
+            "-out_spec",
+            params.get("out_spec")
+        ])
+    return cargs
+
+
+def quickspec_sl_outputs(
+    params: QuickspecSlParameters,
+    execution: Execution,
+) -> QuickspecSlOutputs:
+    """
+    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 = QuickspecSlOutputs(
+        root=execution.output_file("."),
+        output_spec_file=execution.output_file(params.get("out_spec")) if (params.get("out_spec") is not None) else None,
+    )
+    return ret
+
+
+def quickspec_sl_execute(
+    params: QuickspecSlParameters,
+    execution: Execution,
+) -> QuickspecSlOutputs:
+    """
+    This program makes a *.spec file after a set of intermediate surfaces have been
+    generated with SurfLayers. It can also make a *.spec file that relates inflated
+    surfaces to anatomically-correct surfaces.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `QuickspecSlOutputs`).
+    """
+    params = execution.params(params)
+    cargs = quickspec_sl_cargs(params, execution)
+    ret = quickspec_sl_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def quickspec_sl(
+    surf_a: InputPathType,
+    surf_b: InputPathType,
+    surf_intermed_pref: str | None = None,
+    infl_surf_a: InputPathType | None = None,
+    infl_surf_b: InputPathType | None = None,
+    infl_surf_intermed_pref: str | None = None,
+    both_lr_flag: bool = False,
+    out_spec: str | None = None,
+    runner: Runner | None = None,
+) -> QuickspecSlOutputs:
+    """
+    This program makes a *.spec file after a set of intermediate surfaces have been
+    generated with SurfLayers. It can also make a *.spec file that relates inflated
+    surfaces to anatomically-correct surfaces.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        surf_a: Inner (anatomically-correct) boundary surface dataset (e.g.\
+            smoothwm.gii).
+        surf_b: Outer (anatomically-correct) boundary surface dataset (e.g.\
+            pial.gii).
+        surf_intermed_pref: Prefix for (anatomically-correct) intermediate\
+            surfaces, typically output by SurfLayers (default: isurf).
+        infl_surf_a: Inner (inflated) boundary surface dataset (e.g.\
+            infl.smoothwm.gii).
+        infl_surf_b: Outer (inflated) boundary surface dataset (e.g.\
+            infl.pial.gii).
+        infl_surf_intermed_pref: Prefix for (inflated) intermediate surfaces,\
+            typically output by SurfLayers (default: infl.isurf).
+        both_lr_flag: Specify an output spec for both hemispheres if surfaces\
+            for both exist.
+        out_spec: Name for output *.spec file (default: newspec.spec).
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `QuickspecSlOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(QUICKSPEC_SL_METADATA)
+    params = quickspec_sl_params(
+        surf_a=surf_a,
+        surf_b=surf_b,
+        surf_intermed_pref=surf_intermed_pref,
+        infl_surf_a=infl_surf_a,
+        infl_surf_b=infl_surf_b,
+        infl_surf_intermed_pref=infl_surf_intermed_pref,
+        both_lr_flag=both_lr_flag,
+        out_spec=out_spec,
+    )
+    return quickspec_sl_execute(params, execution)
+
+
+__all__ = [
+    "QUICKSPEC_SL_METADATA",
+    "QuickspecSlOutputs",
+    "QuickspecSlParameters",
+    "quickspec_sl",
+    "quickspec_sl_params",
+]