niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/v__electro_grid.py

@@ -0,0 +1,244 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V__ELECTRO_GRID_METADATA = Metadata(
+    id="8d964e948445e43b1078948d73794b4d6f87e09a.boutiques",
+    name="@ElectroGrid",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+VElectroGridParameters = typing.TypedDict('VElectroGridParameters', {
+    "__STYX_TYPE__": typing.Literal["@ElectroGrid"],
+    "strip": typing.NotRequired[int | None],
+    "grid": typing.NotRequired[list[int] | None],
+    "prefix": typing.NotRequired[str | None],
+    "coords": typing.NotRequired[InputPathType | None],
+    "with_markers": bool,
+    "echo": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "@ElectroGrid": v__electro_grid_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 {
+        "@ElectroGrid": v__electro_grid_outputs,
+    }.get(t)
+
+
+class VElectroGridOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v__electro_grid(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_surface: OutputPathType | None
+    """Output surface file"""
+
+
+def v__electro_grid_params(
+    strip: int | None = None,
+    grid: list[int] | None = None,
+    prefix: str | None = None,
+    coords: InputPathType | None = None,
+    with_markers: bool = False,
+    echo: bool = False,
+) -> VElectroGridParameters:
+    """
+    Build parameters.
+    
+    Args:
+        strip: Make an Nx strip (array) of electrodes.
+        grid: Make an Nx by Ny grid of electrodes. A node at (i,j) has a node\
+            ID = i+Nx*j with 0<=i<Nx and 0<=j<=Ny.
+        prefix: Use PREFIX for the output surface.
+        coords: Specify the coordinates of the nodes on the grid, or the array.\
+            XYZ.1D should have three columns, with each row specifying the\
+            coordinates of one node.
+        with_markers: Add markers to the surface at each electrode.
+        echo: Set echo.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "@ElectroGrid",
+        "with_markers": with_markers,
+        "echo": echo,
+    }
+    if strip is not None:
+        params["strip"] = strip
+    if grid is not None:
+        params["grid"] = grid
+    if prefix is not None:
+        params["prefix"] = prefix
+    if coords is not None:
+        params["coords"] = coords
+    return params
+
+
+def v__electro_grid_cargs(
+    params: VElectroGridParameters,
+    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("@ElectroGrid")
+    if params.get("strip") is not None:
+        cargs.extend([
+            "-strip",
+            str(params.get("strip"))
+        ])
+    if params.get("grid") is not None:
+        cargs.extend([
+            "-grid",
+            *map(str, params.get("grid"))
+        ])
+    if params.get("prefix") is not None:
+        cargs.extend([
+            "-prefix",
+            params.get("prefix")
+        ])
+    if params.get("coords") is not None:
+        cargs.extend([
+            "-coords",
+            execution.input_file(params.get("coords"))
+        ])
+    if params.get("with_markers"):
+        cargs.append("-with_markers")
+    if params.get("echo"):
+        cargs.append("-echo")
+    return cargs
+
+
+def v__electro_grid_outputs(
+    params: VElectroGridParameters,
+    execution: Execution,
+) -> VElectroGridOutputs:
+    """
+    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 = VElectroGridOutputs(
+        root=execution.output_file("."),
+        output_surface=execution.output_file(params.get("prefix") + ".gii") if (params.get("prefix") is not None) else None,
+    )
+    return ret
+
+
+def v__electro_grid_execute(
+    params: VElectroGridParameters,
+    execution: Execution,
+) -> VElectroGridOutputs:
+    """
+    Creates a mesh representation of an electrode grid for use with SUMA.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `VElectroGridOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v__electro_grid_cargs(params, execution)
+    ret = v__electro_grid_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v__electro_grid(
+    strip: int | None = None,
+    grid: list[int] | None = None,
+    prefix: str | None = None,
+    coords: InputPathType | None = None,
+    with_markers: bool = False,
+    echo: bool = False,
+    runner: Runner | None = None,
+) -> VElectroGridOutputs:
+    """
+    Creates a mesh representation of an electrode grid for use with SUMA.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        strip: Make an Nx strip (array) of electrodes.
+        grid: Make an Nx by Ny grid of electrodes. A node at (i,j) has a node\
+            ID = i+Nx*j with 0<=i<Nx and 0<=j<=Ny.
+        prefix: Use PREFIX for the output surface.
+        coords: Specify the coordinates of the nodes on the grid, or the array.\
+            XYZ.1D should have three columns, with each row specifying the\
+            coordinates of one node.
+        with_markers: Add markers to the surface at each electrode.
+        echo: Set echo.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `VElectroGridOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__ELECTRO_GRID_METADATA)
+    params = v__electro_grid_params(
+        strip=strip,
+        grid=grid,
+        prefix=prefix,
+        coords=coords,
+        with_markers=with_markers,
+        echo=echo,
+    )
+    return v__electro_grid_execute(params, execution)
+
+
+__all__ = [
+    "VElectroGridOutputs",
+    "VElectroGridParameters",
+    "V__ELECTRO_GRID_METADATA",
+    "v__electro_grid",
+    "v__electro_grid_params",
+]

niwrap_afni/afni/v__examine_gen_feat_dists.py

@@ -0,0 +1,277 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V__EXAMINE_GEN_FEAT_DISTS_METADATA = Metadata(
+    id="60ac2c94312fce85a0d90163607df55149e2869d.boutiques",
+    name="@ExamineGenFeatDists",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+VExamineGenFeatDistsParameters = typing.TypedDict('VExamineGenFeatDistsParameters', {
+    "__STYX_TYPE__": typing.Literal["@ExamineGenFeatDists"],
+    "features_dir": str,
+    "wildcards": typing.NotRequired[list[str] | None],
+    "output_suffix": typing.NotRequired[str | None],
+    "exclude_features": typing.NotRequired[list[str] | None],
+    "exclude_classes": typing.NotRequired[list[str] | None],
+    "output_dir": typing.NotRequired[str | None],
+    "panels_horizontal": typing.NotRequired[float | None],
+    "echo": 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 {
+        "@ExamineGenFeatDists": v__examine_gen_feat_dists_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 VExamineGenFeatDistsOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v__examine_gen_feat_dists(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def v__examine_gen_feat_dists_params(
+    features_dir: str,
+    wildcards: list[str] | None = None,
+    output_suffix: str | None = None,
+    exclude_features: list[str] | None = None,
+    exclude_classes: list[str] | None = None,
+    output_dir: str | None = None,
+    panels_horizontal: float | None = None,
+    echo: bool = False,
+    help_: bool = False,
+) -> VExamineGenFeatDistsParameters:
+    """
+    Build parameters.
+    
+    Args:
+        features_dir: Output directory of 3dGenFeatDists.
+        wildcards: Wildcards used to select feature histograms under the\
+            directory.
+        output_suffix: Output suffix, added to output images. Default is\
+            'nosuff'.
+        exclude_features: Exclude following features. String matching is\
+            partial.
+        exclude_classes: Exclude following classes. String matching is partial.
+        output_dir: Output directory, default is the same as -fdir.
+        panels_horizontal: Set number of panels along the horizontal direction.
+        echo: Set echo.
+        help_: Display help message.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "@ExamineGenFeatDists",
+        "features_dir": features_dir,
+        "echo": echo,
+        "help": help_,
+    }
+    if wildcards is not None:
+        params["wildcards"] = wildcards
+    if output_suffix is not None:
+        params["output_suffix"] = output_suffix
+    if exclude_features is not None:
+        params["exclude_features"] = exclude_features
+    if exclude_classes is not None:
+        params["exclude_classes"] = exclude_classes
+    if output_dir is not None:
+        params["output_dir"] = output_dir
+    if panels_horizontal is not None:
+        params["panels_horizontal"] = panels_horizontal
+    return params
+
+
+def v__examine_gen_feat_dists_cargs(
+    params: VExamineGenFeatDistsParameters,
+    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("@ExamineGenFeatDists")
+    cargs.extend([
+        "-fdir",
+        params.get("features_dir")
+    ])
+    if params.get("wildcards") is not None:
+        cargs.extend([
+            "-fwild",
+            *params.get("wildcards")
+        ])
+    if params.get("output_suffix") is not None:
+        cargs.extend([
+            "-suffix",
+            params.get("output_suffix")
+        ])
+    if params.get("exclude_features") is not None:
+        cargs.extend([
+            "-exfeat",
+            *params.get("exclude_features")
+        ])
+    if params.get("exclude_classes") is not None:
+        cargs.extend([
+            "-exclass",
+            *params.get("exclude_classes")
+        ])
+    if params.get("output_dir") is not None:
+        cargs.extend([
+            "-odir",
+            params.get("output_dir")
+        ])
+    if params.get("panels_horizontal") is not None:
+        cargs.extend([
+            "-nx",
+            str(params.get("panels_horizontal"))
+        ])
+    if params.get("echo"):
+        cargs.append("-echo")
+    if params.get("help"):
+        cargs.append("-help")
+    return cargs
+
+
+def v__examine_gen_feat_dists_outputs(
+    params: VExamineGenFeatDistsParameters,
+    execution: Execution,
+) -> VExamineGenFeatDistsOutputs:
+    """
+    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 = VExamineGenFeatDistsOutputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def v__examine_gen_feat_dists_execute(
+    params: VExamineGenFeatDistsParameters,
+    execution: Execution,
+) -> VExamineGenFeatDistsOutputs:
+    """
+    Examine histograms produced by 3dGenFeatDists.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `VExamineGenFeatDistsOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v__examine_gen_feat_dists_cargs(params, execution)
+    ret = v__examine_gen_feat_dists_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v__examine_gen_feat_dists(
+    features_dir: str,
+    wildcards: list[str] | None = None,
+    output_suffix: str | None = None,
+    exclude_features: list[str] | None = None,
+    exclude_classes: list[str] | None = None,
+    output_dir: str | None = None,
+    panels_horizontal: float | None = None,
+    echo: bool = False,
+    help_: bool = False,
+    runner: Runner | None = None,
+) -> VExamineGenFeatDistsOutputs:
+    """
+    Examine histograms produced by 3dGenFeatDists.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        features_dir: Output directory of 3dGenFeatDists.
+        wildcards: Wildcards used to select feature histograms under the\
+            directory.
+        output_suffix: Output suffix, added to output images. Default is\
+            'nosuff'.
+        exclude_features: Exclude following features. String matching is\
+            partial.
+        exclude_classes: Exclude following classes. String matching is partial.
+        output_dir: Output directory, default is the same as -fdir.
+        panels_horizontal: Set number of panels along the horizontal direction.
+        echo: Set echo.
+        help_: Display help message.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `VExamineGenFeatDistsOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__EXAMINE_GEN_FEAT_DISTS_METADATA)
+    params = v__examine_gen_feat_dists_params(
+        features_dir=features_dir,
+        wildcards=wildcards,
+        output_suffix=output_suffix,
+        exclude_features=exclude_features,
+        exclude_classes=exclude_classes,
+        output_dir=output_dir,
+        panels_horizontal=panels_horizontal,
+        echo=echo,
+        help_=help_,
+    )
+    return v__examine_gen_feat_dists_execute(params, execution)
+
+
+__all__ = [
+    "VExamineGenFeatDistsOutputs",
+    "VExamineGenFeatDistsParameters",
+    "V__EXAMINE_GEN_FEAT_DISTS_METADATA",
+    "v__examine_gen_feat_dists",
+    "v__examine_gen_feat_dists_params",
+]