niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/make_stim_times_py.py

@@ -0,0 +1,304 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+MAKE_STIM_TIMES_PY_METADATA = Metadata(
+    id="3d965a39cc5a0128cd3ea1f9b990c124e0c42cd3.boutiques",
+    name="make_stim_times.py",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+MakeStimTimesPyParameters = typing.TypedDict('MakeStimTimesPyParameters', {
+    "__STYX_TYPE__": typing.Literal["make_stim_times.py"],
+    "files": list[InputPathType],
+    "prefix": str,
+    "tr": float,
+    "nruns": float,
+    "nt": float,
+    "run_trs": typing.NotRequired[list[float] | None],
+    "offset": typing.NotRequired[float | None],
+    "labels": typing.NotRequired[list[str] | None],
+    "no_consec_events": bool,
+    "amplitudes": bool,
+    "show_valid_opts": bool,
+    "verbose": 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 {
+        "make_stim_times.py": make_stim_times_py_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 {
+        "make_stim_times.py": make_stim_times_py_outputs,
+    }.get(t)
+
+
+class MakeStimTimesPyOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `make_stim_times_py(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    out_stim_times_01: OutputPathType
+    """Output stim_times file for first stimulus class"""
+    out_stim_times_02: OutputPathType
+    """Output stim_times file for second stimulus class"""
+    out_stim_times_03: OutputPathType
+    """Output stim_times file for third stimulus class"""
+
+
+def make_stim_times_py_params(
+    files: list[InputPathType],
+    prefix: str,
+    tr: float,
+    nruns: float,
+    nt_: float,
+    run_trs: list[float] | None = None,
+    offset: float | None = None,
+    labels: list[str] | None = None,
+    no_consec_events: bool = False,
+    amplitudes: bool = False,
+    show_valid_opts: bool = False,
+    verbose: float | None = None,
+) -> MakeStimTimesPyParameters:
+    """
+    Build parameters.
+    
+    Args:
+        files: Specify stim files.
+        prefix: Output prefix for files.
+        tr: TR time, in seconds.
+        nruns: Number of runs.
+        nt_: Number of TRs per run.
+        run_trs: Specify TRs per run, if they differ.
+        offset: Add OFFSET to all output times.
+        labels: Provide labels for filenames.
+        no_consec_events: Do not allow consecutive events.
+        amplitudes: Marry times with amplitudes.
+        show_valid_opts: Output all options.
+        verbose: Provide verbose output.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "make_stim_times.py",
+        "files": files,
+        "prefix": prefix,
+        "tr": tr,
+        "nruns": nruns,
+        "nt": nt_,
+        "no_consec_events": no_consec_events,
+        "amplitudes": amplitudes,
+        "show_valid_opts": show_valid_opts,
+    }
+    if run_trs is not None:
+        params["run_trs"] = run_trs
+    if offset is not None:
+        params["offset"] = offset
+    if labels is not None:
+        params["labels"] = labels
+    if verbose is not None:
+        params["verbose"] = verbose
+    return params
+
+
+def make_stim_times_py_cargs(
+    params: MakeStimTimesPyParameters,
+    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("make_stim_times.py")
+    cargs.extend([execution.input_file(f) for f in params.get("files")])
+    cargs.extend([
+        "-prefix",
+        params.get("prefix")
+    ])
+    cargs.extend([
+        "-tr",
+        str(params.get("tr"))
+    ])
+    cargs.extend([
+        "-nruns",
+        str(params.get("nruns"))
+    ])
+    cargs.extend([
+        "-nt",
+        str(params.get("nt"))
+    ])
+    if params.get("run_trs") is not None:
+        cargs.extend(map(str, params.get("run_trs")))
+    if params.get("offset") is not None:
+        cargs.extend([
+            "-offset",
+            str(params.get("offset"))
+        ])
+    if params.get("labels") is not None:
+        cargs.extend([
+            "-labels",
+            *params.get("labels")
+        ])
+    if params.get("no_consec_events"):
+        cargs.append("-no_consec")
+    if params.get("amplitudes"):
+        cargs.append("-amplitudes")
+    if params.get("show_valid_opts"):
+        cargs.append("-show_valid_opts")
+    if params.get("verbose") is not None:
+        cargs.extend([
+            "-verb",
+            str(params.get("verbose"))
+        ])
+    return cargs
+
+
+def make_stim_times_py_outputs(
+    params: MakeStimTimesPyParameters,
+    execution: Execution,
+) -> MakeStimTimesPyOutputs:
+    """
+    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 = MakeStimTimesPyOutputs(
+        root=execution.output_file("."),
+        out_stim_times_01=execution.output_file(params.get("prefix") + ".01.1D"),
+        out_stim_times_02=execution.output_file(params.get("prefix") + ".02.1D"),
+        out_stim_times_03=execution.output_file(params.get("prefix") + ".03.1D"),
+    )
+    return ret
+
+
+def make_stim_times_py_execute(
+    params: MakeStimTimesPyParameters,
+    execution: Execution,
+) -> MakeStimTimesPyOutputs:
+    """
+    Convert a set of 0/1 stim files into a set of stim_times files, or convert
+    real-valued files into those for use with -stim_times_AM2.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `MakeStimTimesPyOutputs`).
+    """
+    params = execution.params(params)
+    cargs = make_stim_times_py_cargs(params, execution)
+    ret = make_stim_times_py_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def make_stim_times_py(
+    files: list[InputPathType],
+    prefix: str,
+    tr: float,
+    nruns: float,
+    nt_: float,
+    run_trs: list[float] | None = None,
+    offset: float | None = None,
+    labels: list[str] | None = None,
+    no_consec_events: bool = False,
+    amplitudes: bool = False,
+    show_valid_opts: bool = False,
+    verbose: float | None = None,
+    runner: Runner | None = None,
+) -> MakeStimTimesPyOutputs:
+    """
+    Convert a set of 0/1 stim files into a set of stim_times files, or convert
+    real-valued files into those for use with -stim_times_AM2.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        files: Specify stim files.
+        prefix: Output prefix for files.
+        tr: TR time, in seconds.
+        nruns: Number of runs.
+        nt_: Number of TRs per run.
+        run_trs: Specify TRs per run, if they differ.
+        offset: Add OFFSET to all output times.
+        labels: Provide labels for filenames.
+        no_consec_events: Do not allow consecutive events.
+        amplitudes: Marry times with amplitudes.
+        show_valid_opts: Output all options.
+        verbose: Provide verbose output.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `MakeStimTimesPyOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MAKE_STIM_TIMES_PY_METADATA)
+    params = make_stim_times_py_params(
+        files=files,
+        prefix=prefix,
+        tr=tr,
+        nruns=nruns,
+        nt_=nt_,
+        run_trs=run_trs,
+        offset=offset,
+        labels=labels,
+        no_consec_events=no_consec_events,
+        amplitudes=amplitudes,
+        show_valid_opts=show_valid_opts,
+        verbose=verbose,
+    )
+    return make_stim_times_py_execute(params, execution)
+
+
+__all__ = [
+    "MAKE_STIM_TIMES_PY_METADATA",
+    "MakeStimTimesPyOutputs",
+    "MakeStimTimesPyParameters",
+    "make_stim_times_py",
+    "make_stim_times_py_params",
+]

niwrap_afni/afni/map_icosahedron.py

@@ -0,0 +1,296 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+MAP_ICOSAHEDRON_METADATA = Metadata(
+    id="29dbfdf370b411c5e1a730bd832837169913b924.boutiques",
+    name="MapIcosahedron",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+MapIcosahedronParameters = typing.TypedDict('MapIcosahedronParameters', {
+    "__STYX_TYPE__": typing.Literal["MapIcosahedron"],
+    "spec_file": InputPathType,
+    "rec_depth": typing.NotRequired[float | None],
+    "lin_depth": typing.NotRequired[float | None],
+    "morph_surf": typing.NotRequired[str | None],
+    "num_it": typing.NotRequired[float | None],
+    "prefix": typing.NotRequired[str | None],
+    "nn_dset": typing.NotRequired[str | None],
+    "dset": typing.NotRequired[str | None],
+    "fix_cut_surfaces": bool,
+    "verbosity": bool,
+    "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 {
+        "MapIcosahedron": map_icosahedron_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 MapIcosahedronOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `map_icosahedron(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def map_icosahedron_params(
+    spec_file: InputPathType,
+    rec_depth: float | None = None,
+    lin_depth: float | None = None,
+    morph_surf: str | None = None,
+    num_it: float | None = None,
+    prefix: str | None = None,
+    nn_dset: str | None = None,
+    dset: str | None = None,
+    fix_cut_surfaces: bool = False,
+    verbosity: bool = False,
+    help_: bool = False,
+) -> MapIcosahedronParameters:
+    """
+    Build parameters.
+    
+    Args:
+        spec_file: Spec file containing original-mesh surfaces.
+        rec_depth: Recursive (binary) tessellation depth for icosahedron\
+            (default: 3).
+        lin_depth: Number of edge divides for linear icosahedron tessellation.
+        morph_surf: Specifies the morphSurf surface.
+        num_it: Number of smoothing iterations.
+        prefix: Prefix for output files (default: 'std.').
+        nn_dset: Map DSET onto the new mesh using Nearest Neighbor\
+            interpolation.
+        dset: Map DSET onto the new mesh using barycentric interpolation.
+        fix_cut_surfaces: Check and fix standard-mesh surfaces with cuts for\
+            cross-cut connections.
+        verbosity: Enable verbose output.
+        help_: Display the help text.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "MapIcosahedron",
+        "spec_file": spec_file,
+        "fix_cut_surfaces": fix_cut_surfaces,
+        "verbosity": verbosity,
+        "help": help_,
+    }
+    if rec_depth is not None:
+        params["rec_depth"] = rec_depth
+    if lin_depth is not None:
+        params["lin_depth"] = lin_depth
+    if morph_surf is not None:
+        params["morph_surf"] = morph_surf
+    if num_it is not None:
+        params["num_it"] = num_it
+    if prefix is not None:
+        params["prefix"] = prefix
+    if nn_dset is not None:
+        params["nn_dset"] = nn_dset
+    if dset is not None:
+        params["dset"] = dset
+    return params
+
+
+def map_icosahedron_cargs(
+    params: MapIcosahedronParameters,
+    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("MapIcosahedron")
+    cargs.append(execution.input_file(params.get("spec_file")))
+    if params.get("rec_depth") is not None:
+        cargs.extend([
+            "-rd",
+            str(params.get("rec_depth"))
+        ])
+    if params.get("lin_depth") is not None:
+        cargs.extend([
+            "-ld",
+            str(params.get("lin_depth"))
+        ])
+    if params.get("morph_surf") is not None:
+        cargs.extend([
+            "-morph",
+            params.get("morph_surf")
+        ])
+    if params.get("num_it") is not None:
+        cargs.extend([
+            "-it",
+            str(params.get("num_it"))
+        ])
+    if params.get("prefix") is not None:
+        cargs.extend([
+            "-prefix",
+            params.get("prefix")
+        ])
+    if params.get("nn_dset") is not None:
+        cargs.extend([
+            "-NN_dset_map",
+            params.get("nn_dset")
+        ])
+    if params.get("dset") is not None:
+        cargs.extend([
+            "-dset_map",
+            params.get("dset")
+        ])
+    if params.get("fix_cut_surfaces"):
+        cargs.append("-fix_cut_surfaces")
+    if params.get("verbosity"):
+        cargs.append("-verb")
+    if params.get("help"):
+        cargs.append("-help")
+    return cargs
+
+
+def map_icosahedron_outputs(
+    params: MapIcosahedronParameters,
+    execution: Execution,
+) -> MapIcosahedronOutputs:
+    """
+    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 = MapIcosahedronOutputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def map_icosahedron_execute(
+    params: MapIcosahedronParameters,
+    execution: Execution,
+) -> MapIcosahedronOutputs:
+    """
+    Creates new versions of original-mesh surfaces using the mesh of an icosahedron.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `MapIcosahedronOutputs`).
+    """
+    params = execution.params(params)
+    cargs = map_icosahedron_cargs(params, execution)
+    ret = map_icosahedron_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def map_icosahedron(
+    spec_file: InputPathType,
+    rec_depth: float | None = None,
+    lin_depth: float | None = None,
+    morph_surf: str | None = None,
+    num_it: float | None = None,
+    prefix: str | None = None,
+    nn_dset: str | None = None,
+    dset: str | None = None,
+    fix_cut_surfaces: bool = False,
+    verbosity: bool = False,
+    help_: bool = False,
+    runner: Runner | None = None,
+) -> MapIcosahedronOutputs:
+    """
+    Creates new versions of original-mesh surfaces using the mesh of an icosahedron.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        spec_file: Spec file containing original-mesh surfaces.
+        rec_depth: Recursive (binary) tessellation depth for icosahedron\
+            (default: 3).
+        lin_depth: Number of edge divides for linear icosahedron tessellation.
+        morph_surf: Specifies the morphSurf surface.
+        num_it: Number of smoothing iterations.
+        prefix: Prefix for output files (default: 'std.').
+        nn_dset: Map DSET onto the new mesh using Nearest Neighbor\
+            interpolation.
+        dset: Map DSET onto the new mesh using barycentric interpolation.
+        fix_cut_surfaces: Check and fix standard-mesh surfaces with cuts for\
+            cross-cut connections.
+        verbosity: Enable verbose output.
+        help_: Display the help text.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `MapIcosahedronOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MAP_ICOSAHEDRON_METADATA)
+    params = map_icosahedron_params(
+        spec_file=spec_file,
+        rec_depth=rec_depth,
+        lin_depth=lin_depth,
+        morph_surf=morph_surf,
+        num_it=num_it,
+        prefix=prefix,
+        nn_dset=nn_dset,
+        dset=dset,
+        fix_cut_surfaces=fix_cut_surfaces,
+        verbosity=verbosity,
+        help_=help_,
+    )
+    return map_icosahedron_execute(params, execution)
+
+
+__all__ = [
+    "MAP_ICOSAHEDRON_METADATA",
+    "MapIcosahedronOutputs",
+    "MapIcosahedronParameters",
+    "map_icosahedron",
+    "map_icosahedron_params",
+]