niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/parse_fs_lt_log_py.py

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+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+PARSE_FS_LT_LOG_PY_METADATA = Metadata(
+    id="bc86d7205c69a1f53932715879d366e6a9ef6795.boutiques",
+    name="parse_fs_lt_log.py",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+ParseFsLtLogPyParameters = typing.TypedDict('ParseFsLtLogPyParameters', {
+    "__STYX_TYPE__": typing.Literal["parse_fs_lt_log.py"],
+    "logfile": InputPathType,
+    "labels": list[str],
+    "show_orig": bool,
+    "show_all_orig": bool,
+    "verbosity": 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 {
+        "parse_fs_lt_log.py": parse_fs_lt_log_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 {
+    }.get(t)
+
+
+class ParseFsLtLogPyOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `parse_fs_lt_log_py(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def parse_fs_lt_log_py_params(
+    logfile: InputPathType,
+    labels: list[str],
+    show_orig: bool = False,
+    show_all_orig: bool = False,
+    verbosity: float | None = None,
+) -> ParseFsLtLogPyParameters:
+    """
+    Build parameters.
+    
+    Args:
+        logfile: Specify rank log file.
+        labels: Specify a list of labels to search for.
+        show_orig: Show original label indices.
+        show_all_orig: Show all original label indices.
+        verbosity: Specify verbosity level.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "parse_fs_lt_log.py",
+        "logfile": logfile,
+        "labels": labels,
+        "show_orig": show_orig,
+        "show_all_orig": show_all_orig,
+    }
+    if verbosity is not None:
+        params["verbosity"] = verbosity
+    return params
+
+
+def parse_fs_lt_log_py_cargs(
+    params: ParseFsLtLogPyParameters,
+    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("parse_fs_lt_log.py")
+    cargs.extend([
+        "-logfile",
+        execution.input_file(params.get("logfile"))
+    ])
+    cargs.extend([
+        "-labels",
+        *params.get("labels")
+    ])
+    if params.get("show_orig"):
+        cargs.append("-show_orig")
+    if params.get("show_all_orig"):
+        cargs.append("-show_all_orig")
+    if params.get("verbosity") is not None:
+        cargs.extend([
+            "-verb",
+            str(params.get("verbosity"))
+        ])
+    return cargs
+
+
+def parse_fs_lt_log_py_outputs(
+    params: ParseFsLtLogPyParameters,
+    execution: Execution,
+) -> ParseFsLtLogPyOutputs:
+    """
+    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 = ParseFsLtLogPyOutputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def parse_fs_lt_log_py_execute(
+    params: ParseFsLtLogPyParameters,
+    execution: Execution,
+) -> ParseFsLtLogPyOutputs:
+    """
+    Parses FreeSurfer labeltable log file and retrieves labeltable indices.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `ParseFsLtLogPyOutputs`).
+    """
+    params = execution.params(params)
+    cargs = parse_fs_lt_log_py_cargs(params, execution)
+    ret = parse_fs_lt_log_py_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def parse_fs_lt_log_py(
+    logfile: InputPathType,
+    labels: list[str],
+    show_orig: bool = False,
+    show_all_orig: bool = False,
+    verbosity: float | None = None,
+    runner: Runner | None = None,
+) -> ParseFsLtLogPyOutputs:
+    """
+    Parses FreeSurfer labeltable log file and retrieves labeltable indices.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        logfile: Specify rank log file.
+        labels: Specify a list of labels to search for.
+        show_orig: Show original label indices.
+        show_all_orig: Show all original label indices.
+        verbosity: Specify verbosity level.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `ParseFsLtLogPyOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(PARSE_FS_LT_LOG_PY_METADATA)
+    params = parse_fs_lt_log_py_params(
+        logfile=logfile,
+        labels=labels,
+        show_orig=show_orig,
+        show_all_orig=show_all_orig,
+        verbosity=verbosity,
+    )
+    return parse_fs_lt_log_py_execute(params, execution)
+
+
+__all__ = [
+    "PARSE_FS_LT_LOG_PY_METADATA",
+    "ParseFsLtLogPyOutputs",
+    "ParseFsLtLogPyParameters",
+    "parse_fs_lt_log_py",
+    "parse_fs_lt_log_py_params",
+]

niwrap_afni/afni/plugout_drive.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 *
+
+PLUGOUT_DRIVE_METADATA = Metadata(
+    id="65a44f6f7d92c1ad9ba4ed1d48f6c277a7f935fb.boutiques",
+    name="plugout_drive",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+PlugoutDriveParameters = typing.TypedDict('PlugoutDriveParameters', {
+    "__STYX_TYPE__": typing.Literal["plugout_drive"],
+    "host": typing.NotRequired[str | None],
+    "verbose": bool,
+    "port": typing.NotRequired[float | None],
+    "maxwait": typing.NotRequired[float | None],
+    "name": typing.NotRequired[str | None],
+    "command": typing.NotRequired[list[str] | None],
+    "quit": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "plugout_drive": plugout_drive_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 PlugoutDriveOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `plugout_drive(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def plugout_drive_params(
+    host: str | None = None,
+    verbose: bool = False,
+    port: float | None = None,
+    maxwait: float | None = None,
+    name: str | None = None,
+    command: list[str] | None = None,
+    quit_: bool = False,
+) -> PlugoutDriveParameters:
+    """
+    Build parameters.
+    
+    Args:
+        host: Connect to AFNI running on the specified host using TCP/IP.\
+            Default is 'localhost'.
+        verbose: Verbose mode.
+        port: Use TCP/IP port number. Default is 8099.
+        maxwait: Maximum wait time in seconds for AFNI to connect. Default is 9\
+            seconds.
+        name: Name that AFNI assigns to this plugout. Default is a pre-defined\
+            name.
+        command: Command to be executed on AFNI. Example: '-com "SET_FUNCTION\
+            SomeFunction"'.
+        quit_: Quit after executing all -com commands. Default is to wait for\
+            more commands.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "plugout_drive",
+        "verbose": verbose,
+        "quit": quit_,
+    }
+    if host is not None:
+        params["host"] = host
+    if port is not None:
+        params["port"] = port
+    if maxwait is not None:
+        params["maxwait"] = maxwait
+    if name is not None:
+        params["name"] = name
+    if command is not None:
+        params["command"] = command
+    return params
+
+
+def plugout_drive_cargs(
+    params: PlugoutDriveParameters,
+    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("plugout_drive")
+    if params.get("host") is not None:
+        cargs.extend([
+            "-host",
+            params.get("host")
+        ])
+    if params.get("verbose"):
+        cargs.append("-v")
+    if params.get("port") is not None:
+        cargs.extend([
+            "-port",
+            str(params.get("port"))
+        ])
+    if params.get("maxwait") is not None:
+        cargs.extend([
+            "-maxwait",
+            str(params.get("maxwait"))
+        ])
+    if params.get("name") is not None:
+        cargs.extend([
+            "-name",
+            params.get("name")
+        ])
+    if params.get("command") is not None:
+        cargs.extend([
+            "-com",
+            *params.get("command")
+        ])
+    if params.get("quit"):
+        cargs.append("-quit")
+    return cargs
+
+
+def plugout_drive_outputs(
+    params: PlugoutDriveParameters,
+    execution: Execution,
+) -> PlugoutDriveOutputs:
+    """
+    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 = PlugoutDriveOutputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def plugout_drive_execute(
+    params: PlugoutDriveParameters,
+    execution: Execution,
+) -> PlugoutDriveOutputs:
+    """
+    This program connects to AFNI and sends commands that the user specifies
+    interactively or on command line over to AFNI to be executed.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `PlugoutDriveOutputs`).
+    """
+    params = execution.params(params)
+    cargs = plugout_drive_cargs(params, execution)
+    ret = plugout_drive_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def plugout_drive(
+    host: str | None = None,
+    verbose: bool = False,
+    port: float | None = None,
+    maxwait: float | None = None,
+    name: str | None = None,
+    command: list[str] | None = None,
+    quit_: bool = False,
+    runner: Runner | None = None,
+) -> PlugoutDriveOutputs:
+    """
+    This program connects to AFNI and sends commands that the user specifies
+    interactively or on command line over to AFNI to be executed.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        host: Connect to AFNI running on the specified host using TCP/IP.\
+            Default is 'localhost'.
+        verbose: Verbose mode.
+        port: Use TCP/IP port number. Default is 8099.
+        maxwait: Maximum wait time in seconds for AFNI to connect. Default is 9\
+            seconds.
+        name: Name that AFNI assigns to this plugout. Default is a pre-defined\
+            name.
+        command: Command to be executed on AFNI. Example: '-com "SET_FUNCTION\
+            SomeFunction"'.
+        quit_: Quit after executing all -com commands. Default is to wait for\
+            more commands.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `PlugoutDriveOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(PLUGOUT_DRIVE_METADATA)
+    params = plugout_drive_params(
+        host=host,
+        verbose=verbose,
+        port=port,
+        maxwait=maxwait,
+        name=name,
+        command=command,
+        quit_=quit_,
+    )
+    return plugout_drive_execute(params, execution)
+
+
+__all__ = [
+    "PLUGOUT_DRIVE_METADATA",
+    "PlugoutDriveOutputs",
+    "PlugoutDriveParameters",
+    "plugout_drive",
+    "plugout_drive_params",
+]