niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/v__add_edge.py

@@ -0,0 +1,344 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V__ADD_EDGE_METADATA = Metadata(
+    id="e1c15db21c7ca3b4679541ce445b80838292b240.boutiques",
+    name="@AddEdge",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+VAddEdgeParameters = typing.TypedDict('VAddEdgeParameters', {
+    "__STYX_TYPE__": typing.Literal["@AddEdge"],
+    "input_files": list[InputPathType],
+    "examine_list": typing.NotRequired[str | None],
+    "ax_mont": typing.NotRequired[str | None],
+    "ax_geom": typing.NotRequired[str | None],
+    "sag_geom": typing.NotRequired[str | None],
+    "layout_file": typing.NotRequired[str | None],
+    "no_layout": bool,
+    "edge_percentile": typing.NotRequired[int | None],
+    "single_edge": bool,
+    "opacity": typing.NotRequired[int | None],
+    "keep_temp": bool,
+    "no_deoblique": bool,
+    "auto_record": bool,
+    "auto": bool,
+    "no_auto": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "@AddEdge": v__add_edge_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 {
+        "@AddEdge": v__add_edge_outputs,
+    }.get(t)
+
+
+class VAddEdgeOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v__add_edge(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    dset_nn_ec: OutputPathType
+    """Edge composite image of dataset with its own edges"""
+    base_dset_dset_nn_ec: OutputPathType
+    """Edge composite image of base dataset together with the edges of the input
+    dset_nn dataset"""
+    base_dset_e3: OutputPathType
+    """Edge-only datasets - used in single edge display option"""
+    dset_nn_e3: OutputPathType
+    """Edge-only input datasets - used in single edge display option"""
+
+
+def v__add_edge_params(
+    input_files: list[InputPathType],
+    examine_list: str | None = None,
+    ax_mont: str | None = None,
+    ax_geom: str | None = None,
+    sag_geom: str | None = None,
+    layout_file: str | None = None,
+    no_layout: bool = False,
+    edge_percentile: int | None = None,
+    single_edge: bool = False,
+    opacity: int | None = None,
+    keep_temp: bool = False,
+    no_deoblique: bool = False,
+    auto_record: bool = False,
+    auto: bool = False,
+    no_auto: bool = False,
+) -> VAddEdgeParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_files: Input datasets.
+        examine_list: Use list of paired datasets from file.
+        ax_mont: Axial montage string (default='2x2:24').
+        ax_geom: Axial image window geometry (default='777x702+433+334').
+        sag_geom: Sagittal image window geometry (default='540x360+4+436').
+        layout_file: Use AFNI layout file for display.
+        no_layout: Do not use layout. Use AFNI as it is open.
+        edge_percentile: Specify edge threshold value (default=30%).
+        single_edge: Show only a single edge in composite image.
+        opacity: Set opacity of overlay (default=9 opaque).
+        keep_temp: Do not remove temporary files.
+        no_deoblique: Do not deoblique any data to show overlap.
+        auto_record: Save JPEG files of current slices without prompting.
+        auto: Closes old AFNI sessions and relaunches a new one ready to listen\
+            to @AddEdge in review mode.
+        no_auto: Opposite of -auto.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "@AddEdge",
+        "input_files": input_files,
+        "no_layout": no_layout,
+        "single_edge": single_edge,
+        "keep_temp": keep_temp,
+        "no_deoblique": no_deoblique,
+        "auto_record": auto_record,
+        "auto": auto,
+        "no_auto": no_auto,
+    }
+    if examine_list is not None:
+        params["examine_list"] = examine_list
+    if ax_mont is not None:
+        params["ax_mont"] = ax_mont
+    if ax_geom is not None:
+        params["ax_geom"] = ax_geom
+    if sag_geom is not None:
+        params["sag_geom"] = sag_geom
+    if layout_file is not None:
+        params["layout_file"] = layout_file
+    if edge_percentile is not None:
+        params["edge_percentile"] = edge_percentile
+    if opacity is not None:
+        params["opacity"] = opacity
+    return params
+
+
+def v__add_edge_cargs(
+    params: VAddEdgeParameters,
+    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("@AddEdge")
+    cargs.extend([execution.input_file(f) for f in params.get("input_files")])
+    if params.get("examine_list") is not None:
+        cargs.extend([
+            "-examinelist",
+            params.get("examine_list")
+        ])
+    if params.get("ax_mont") is not None:
+        cargs.extend([
+            "-ax_mont",
+            params.get("ax_mont")
+        ])
+    if params.get("ax_geom") is not None:
+        cargs.extend([
+            "-ax_geom",
+            params.get("ax_geom")
+        ])
+    if params.get("sag_geom") is not None:
+        cargs.extend([
+            "-sag_geom",
+            params.get("sag_geom")
+        ])
+    if params.get("layout_file") is not None:
+        cargs.extend([
+            "-layout",
+            params.get("layout_file")
+        ])
+    if params.get("no_layout"):
+        cargs.append("-no_layout")
+    if params.get("edge_percentile") is not None:
+        cargs.extend([
+            "-edge_percentile",
+            str(params.get("edge_percentile"))
+        ])
+    if params.get("single_edge"):
+        cargs.append("-single_edge")
+    if params.get("opacity") is not None:
+        cargs.extend([
+            "-opa",
+            str(params.get("opacity"))
+        ])
+    if params.get("keep_temp"):
+        cargs.append("-keep_temp")
+    if params.get("no_deoblique"):
+        cargs.append("-no_deoblique")
+    if params.get("auto_record"):
+        cargs.append("-auto_record")
+    if params.get("auto"):
+        cargs.append("-auto")
+    if params.get("no_auto"):
+        cargs.append("-no_auto")
+    return cargs
+
+
+def v__add_edge_outputs(
+    params: VAddEdgeParameters,
+    execution: Execution,
+) -> VAddEdgeOutputs:
+    """
+    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 = VAddEdgeOutputs(
+        root=execution.output_file("."),
+        dset_nn_ec=execution.output_file("dset_nn_ec"),
+        base_dset_dset_nn_ec=execution.output_file("base_dset_dset_nn_ec"),
+        base_dset_e3=execution.output_file("base_dset_e3"),
+        dset_nn_e3=execution.output_file("dset_nn_e3"),
+    )
+    return ret
+
+
+def v__add_edge_execute(
+    params: VAddEdgeParameters,
+    execution: Execution,
+) -> VAddEdgeOutputs:
+    """
+    A script to create composite edge-enhanced datasets and drive the AFNI interface
+    to display the results.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `VAddEdgeOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v__add_edge_cargs(params, execution)
+    ret = v__add_edge_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v__add_edge(
+    input_files: list[InputPathType],
+    examine_list: str | None = None,
+    ax_mont: str | None = None,
+    ax_geom: str | None = None,
+    sag_geom: str | None = None,
+    layout_file: str | None = None,
+    no_layout: bool = False,
+    edge_percentile: int | None = None,
+    single_edge: bool = False,
+    opacity: int | None = None,
+    keep_temp: bool = False,
+    no_deoblique: bool = False,
+    auto_record: bool = False,
+    auto: bool = False,
+    no_auto: bool = False,
+    runner: Runner | None = None,
+) -> VAddEdgeOutputs:
+    """
+    A script to create composite edge-enhanced datasets and drive the AFNI interface
+    to display the results.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        input_files: Input datasets.
+        examine_list: Use list of paired datasets from file.
+        ax_mont: Axial montage string (default='2x2:24').
+        ax_geom: Axial image window geometry (default='777x702+433+334').
+        sag_geom: Sagittal image window geometry (default='540x360+4+436').
+        layout_file: Use AFNI layout file for display.
+        no_layout: Do not use layout. Use AFNI as it is open.
+        edge_percentile: Specify edge threshold value (default=30%).
+        single_edge: Show only a single edge in composite image.
+        opacity: Set opacity of overlay (default=9 opaque).
+        keep_temp: Do not remove temporary files.
+        no_deoblique: Do not deoblique any data to show overlap.
+        auto_record: Save JPEG files of current slices without prompting.
+        auto: Closes old AFNI sessions and relaunches a new one ready to listen\
+            to @AddEdge in review mode.
+        no_auto: Opposite of -auto.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `VAddEdgeOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__ADD_EDGE_METADATA)
+    params = v__add_edge_params(
+        input_files=input_files,
+        examine_list=examine_list,
+        ax_mont=ax_mont,
+        ax_geom=ax_geom,
+        sag_geom=sag_geom,
+        layout_file=layout_file,
+        no_layout=no_layout,
+        edge_percentile=edge_percentile,
+        single_edge=single_edge,
+        opacity=opacity,
+        keep_temp=keep_temp,
+        no_deoblique=no_deoblique,
+        auto_record=auto_record,
+        auto=auto,
+        no_auto=no_auto,
+    )
+    return v__add_edge_execute(params, execution)
+
+
+__all__ = [
+    "VAddEdgeOutputs",
+    "VAddEdgeParameters",
+    "V__ADD_EDGE_METADATA",
+    "v__add_edge",
+    "v__add_edge_params",
+]

niwrap_afni/afni/v__afni_env.py

@@ -0,0 +1,254 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V__AFNI_ENV_METADATA = Metadata(
+    id="b177bf4393f72d4c785c1458de43a3ef880cfb18.boutiques",
+    name="@AfniEnv",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+VAfniEnvParameters = typing.TypedDict('VAfniEnvParameters', {
+    "__STYX_TYPE__": typing.Literal["@AfniEnv"],
+    "set_flag": typing.NotRequired[list[str] | None],
+    "unset_flag": typing.NotRequired[str | None],
+    "get_flag": typing.NotRequired[str | None],
+    "help_flag": bool,
+    "help_web_flag_alias": bool,
+    "help_view_flag_alias": bool,
+    "all_opts_flag": bool,
+    "help_find_flag": 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 {
+        "@AfniEnv": v__afni_env_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 VAfniEnvOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v__afni_env(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def v__afni_env_params(
+    set_flag: list[str] | None = None,
+    unset_flag: str | None = None,
+    get_flag: str | None = None,
+    help_flag: bool = False,
+    help_web_flag_alias: bool = False,
+    help_view_flag_alias: bool = False,
+    all_opts_flag: bool = False,
+    help_find_flag: str | None = None,
+) -> VAfniEnvParameters:
+    """
+    Build parameters.
+    
+    Args:
+        set_flag: Set environment variable NAME to value VALUE.
+        unset_flag: Unset environment variable NAME.
+        get_flag: Get the value of environment variable NAME.
+        help_flag: Display the help message for @AfniEnv script.
+        help_web_flag_alias: Same as -h_web.
+        help_view_flag_alias: Same as -h_view.
+        all_opts_flag: List all of the options for this script.
+        help_find_flag: Search for lines containing WORD in -help output.\
+            Search is approximate.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "@AfniEnv",
+        "help_flag": help_flag,
+        "help_web_flag_alias": help_web_flag_alias,
+        "help_view_flag_alias": help_view_flag_alias,
+        "all_opts_flag": all_opts_flag,
+    }
+    if set_flag is not None:
+        params["set_flag"] = set_flag
+    if unset_flag is not None:
+        params["unset_flag"] = unset_flag
+    if get_flag is not None:
+        params["get_flag"] = get_flag
+    if help_find_flag is not None:
+        params["help_find_flag"] = help_find_flag
+    return params
+
+
+def v__afni_env_cargs(
+    params: VAfniEnvParameters,
+    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("@AfniEnv")
+    if params.get("set_flag") is not None:
+        cargs.extend([
+            "-set",
+            *params.get("set_flag")
+        ])
+    if params.get("unset_flag") is not None:
+        cargs.extend([
+            "-unset",
+            params.get("unset_flag")
+        ])
+    if params.get("get_flag") is not None:
+        cargs.extend([
+            "-get",
+            params.get("get_flag")
+        ])
+    if params.get("help_flag"):
+        cargs.append("-help")
+    if params.get("help_web_flag_alias"):
+        cargs.append("-hweb")
+    if params.get("help_view_flag_alias"):
+        cargs.append("-hview")
+    if params.get("all_opts_flag"):
+        cargs.append("-all_opts")
+    if params.get("help_find_flag") is not None:
+        cargs.extend([
+            "-h_find",
+            params.get("help_find_flag")
+        ])
+    return cargs
+
+
+def v__afni_env_outputs(
+    params: VAfniEnvParameters,
+    execution: Execution,
+) -> VAfniEnvOutputs:
+    """
+    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 = VAfniEnvOutputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def v__afni_env_execute(
+    params: VAfniEnvParameters,
+    execution: Execution,
+) -> VAfniEnvOutputs:
+    """
+    Script to set or unset an AFNI environment variable in your .afnirc file.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `VAfniEnvOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v__afni_env_cargs(params, execution)
+    ret = v__afni_env_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v__afni_env(
+    set_flag: list[str] | None = None,
+    unset_flag: str | None = None,
+    get_flag: str | None = None,
+    help_flag: bool = False,
+    help_web_flag_alias: bool = False,
+    help_view_flag_alias: bool = False,
+    all_opts_flag: bool = False,
+    help_find_flag: str | None = None,
+    runner: Runner | None = None,
+) -> VAfniEnvOutputs:
+    """
+    Script to set or unset an AFNI environment variable in your .afnirc file.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        set_flag: Set environment variable NAME to value VALUE.
+        unset_flag: Unset environment variable NAME.
+        get_flag: Get the value of environment variable NAME.
+        help_flag: Display the help message for @AfniEnv script.
+        help_web_flag_alias: Same as -h_web.
+        help_view_flag_alias: Same as -h_view.
+        all_opts_flag: List all of the options for this script.
+        help_find_flag: Search for lines containing WORD in -help output.\
+            Search is approximate.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `VAfniEnvOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__AFNI_ENV_METADATA)
+    params = v__afni_env_params(
+        set_flag=set_flag,
+        unset_flag=unset_flag,
+        get_flag=get_flag,
+        help_flag=help_flag,
+        help_web_flag_alias=help_web_flag_alias,
+        help_view_flag_alias=help_view_flag_alias,
+        all_opts_flag=all_opts_flag,
+        help_find_flag=help_find_flag,
+    )
+    return v__afni_env_execute(params, execution)
+
+
+__all__ = [
+    "VAfniEnvOutputs",
+    "VAfniEnvParameters",
+    "V__AFNI_ENV_METADATA",
+    "v__afni_env",
+    "v__afni_env_params",
+]