niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/uber_align_test_py.py

@@ -0,0 +1,266 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+UBER_ALIGN_TEST_PY_METADATA = Metadata(
+    id="1cdb35a694ecfd6f154d70ecf75d0b5138262e0f.boutiques",
+    name="uber_align_test.py",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+UberAlignTestPyParameters = typing.TypedDict('UberAlignTestPyParameters', {
+    "__STYX_TYPE__": typing.Literal["uber_align_test.py"],
+    "no_gui": bool,
+    "print_script": bool,
+    "save_script": typing.NotRequired[str | None],
+    "user_variable": typing.NotRequired[list[str] | None],
+    "qt_opts": typing.NotRequired[str | None],
+    "help": bool,
+    "help_gui": bool,
+    "history": bool,
+    "show_valid_opts": bool,
+    "version": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "uber_align_test.py": uber_align_test_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 UberAlignTestPyOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `uber_align_test_py(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def uber_align_test_py_params(
+    no_gui: bool = False,
+    print_script: bool = False,
+    save_script: str | None = None,
+    user_variable: list[str] | None = None,
+    qt_opts: str | None = None,
+    help_: bool = False,
+    help_gui: bool = False,
+    history: bool = False,
+    show_valid_opts: bool = False,
+    version: bool = False,
+) -> UberAlignTestPyParameters:
+    """
+    Build parameters.
+    
+    Args:
+        no_gui: Run without the graphical user interface (GUI).
+        print_script: Print the generated script to standard output.
+        save_script: Save the generated script to the specified file.
+        user_variable: Specify user variables for alignment.
+        qt_opts: Pass PyQt4 options directly to the GUI.
+        help_: Show help information.
+        help_gui: Show help information for the GUI.
+        history: Show command history.
+        show_valid_opts: Show valid options.
+        version: Show version information.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "uber_align_test.py",
+        "no_gui": no_gui,
+        "print_script": print_script,
+        "help": help_,
+        "help_gui": help_gui,
+        "history": history,
+        "show_valid_opts": show_valid_opts,
+        "version": version,
+    }
+    if save_script is not None:
+        params["save_script"] = save_script
+    if user_variable is not None:
+        params["user_variable"] = user_variable
+    if qt_opts is not None:
+        params["qt_opts"] = qt_opts
+    return params
+
+
+def uber_align_test_py_cargs(
+    params: UberAlignTestPyParameters,
+    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("uber_align_test.py")
+    if params.get("no_gui"):
+        cargs.append("-no_gui")
+    if params.get("print_script"):
+        cargs.append("-print_script")
+    if params.get("save_script") is not None:
+        cargs.extend([
+            "-save_script",
+            params.get("save_script")
+        ])
+    if params.get("user_variable") is not None:
+        cargs.extend([
+            "-uvar",
+            *params.get("user_variable")
+        ])
+    if params.get("qt_opts") is not None:
+        cargs.extend([
+            "-qt_opts",
+            params.get("qt_opts")
+        ])
+    if params.get("help"):
+        cargs.append("-help")
+    if params.get("help_gui"):
+        cargs.append("-help_gui")
+    if params.get("history"):
+        cargs.append("-hist")
+    if params.get("show_valid_opts"):
+        cargs.append("-show_valid_opts")
+    if params.get("version"):
+        cargs.append("-ver")
+    return cargs
+
+
+def uber_align_test_py_outputs(
+    params: UberAlignTestPyParameters,
+    execution: Execution,
+) -> UberAlignTestPyOutputs:
+    """
+    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 = UberAlignTestPyOutputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def uber_align_test_py_execute(
+    params: UberAlignTestPyParameters,
+    execution: Execution,
+) -> UberAlignTestPyOutputs:
+    """
+    Generate script to test anatomical/EPI alignment.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `UberAlignTestPyOutputs`).
+    """
+    params = execution.params(params)
+    cargs = uber_align_test_py_cargs(params, execution)
+    ret = uber_align_test_py_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def uber_align_test_py(
+    no_gui: bool = False,
+    print_script: bool = False,
+    save_script: str | None = None,
+    user_variable: list[str] | None = None,
+    qt_opts: str | None = None,
+    help_: bool = False,
+    help_gui: bool = False,
+    history: bool = False,
+    show_valid_opts: bool = False,
+    version: bool = False,
+    runner: Runner | None = None,
+) -> UberAlignTestPyOutputs:
+    """
+    Generate script to test anatomical/EPI alignment.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        no_gui: Run without the graphical user interface (GUI).
+        print_script: Print the generated script to standard output.
+        save_script: Save the generated script to the specified file.
+        user_variable: Specify user variables for alignment.
+        qt_opts: Pass PyQt4 options directly to the GUI.
+        help_: Show help information.
+        help_gui: Show help information for the GUI.
+        history: Show command history.
+        show_valid_opts: Show valid options.
+        version: Show version information.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `UberAlignTestPyOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(UBER_ALIGN_TEST_PY_METADATA)
+    params = uber_align_test_py_params(
+        no_gui=no_gui,
+        print_script=print_script,
+        save_script=save_script,
+        user_variable=user_variable,
+        qt_opts=qt_opts,
+        help_=help_,
+        help_gui=help_gui,
+        history=history,
+        show_valid_opts=show_valid_opts,
+        version=version,
+    )
+    return uber_align_test_py_execute(params, execution)
+
+
+__all__ = [
+    "UBER_ALIGN_TEST_PY_METADATA",
+    "UberAlignTestPyOutputs",
+    "UberAlignTestPyParameters",
+    "uber_align_test_py",
+    "uber_align_test_py_params",
+]

niwrap_afni/afni/uber_proc_py.py

@@ -0,0 +1,176 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+UBER_PROC_PY_METADATA = Metadata(
+    id="810164b90b5470d8a01aa9ff880068dc2dfc8cc0.boutiques",
+    name="uber_proc.py",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+UberProcPyParameters = typing.TypedDict('UberProcPyParameters', {
+    "__STYX_TYPE__": typing.Literal["uber_proc.py"],
+    "results_dir": 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 {
+        "uber_proc.py": uber_proc_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 UberProcPyOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `uber_proc_py(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def uber_proc_py_params(
+    results_dir: str | None = None,
+) -> UberProcPyParameters:
+    """
+    Build parameters.
+    
+    Args:
+        results_dir: Directory where results will be placed. Default is a new\
+            'uber_results' directory in the current working directory.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "uber_proc.py",
+    }
+    if results_dir is not None:
+        params["results_dir"] = results_dir
+    return params
+
+
+def uber_proc_py_cargs(
+    params: UberProcPyParameters,
+    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("uber_proc.py")
+    if params.get("results_dir") is not None:
+        cargs.append(params.get("results_dir"))
+    return cargs
+
+
+def uber_proc_py_outputs(
+    params: UberProcPyParameters,
+    execution: Execution,
+) -> UberProcPyOutputs:
+    """
+    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 = UberProcPyOutputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def uber_proc_py_execute(
+    params: UberProcPyParameters,
+    execution: Execution,
+) -> UberProcPyOutputs:
+    """
+    Uber processing tool - work in progress.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `UberProcPyOutputs`).
+    """
+    params = execution.params(params)
+    cargs = uber_proc_py_cargs(params, execution)
+    ret = uber_proc_py_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def uber_proc_py(
+    results_dir: str | None = None,
+    runner: Runner | None = None,
+) -> UberProcPyOutputs:
+    """
+    Uber processing tool - work in progress.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        results_dir: Directory where results will be placed. Default is a new\
+            'uber_results' directory in the current working directory.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `UberProcPyOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(UBER_PROC_PY_METADATA)
+    params = uber_proc_py_params(
+        results_dir=results_dir,
+    )
+    return uber_proc_py_execute(params, execution)
+
+
+__all__ = [
+    "UBER_PROC_PY_METADATA",
+    "UberProcPyOutputs",
+    "UberProcPyParameters",
+    "uber_proc_py",
+    "uber_proc_py_params",
+]

niwrap_afni/afni/uber_skel.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 *
+
+UBER_SKEL_METADATA = Metadata(
+    id="d77a80fc9ecd09ed285b440328c53e4f45eb7735.boutiques",
+    name="uber_skel",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+UberSkelParameters = typing.TypedDict('UberSkelParameters', {
+    "__STYX_TYPE__": typing.Literal["uber_skel"],
+    "qt_options": typing.NotRequired[str | None],
+    "no_gui_flag": bool,
+    "print_script": bool,
+    "save_script": typing.NotRequired[str | None],
+    "user_var": typing.NotRequired[list[str] | None],
+    "help_howto_program": bool,
+    "help": bool,
+    "help_gui": bool,
+    "history": bool,
+    "show_valid_opts": bool,
+    "version": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "uber_skel": uber_skel_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 UberSkelOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `uber_skel(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def uber_skel_params(
+    qt_options: str | None = None,
+    no_gui_flag: bool = False,
+    print_script: bool = False,
+    save_script: str | None = None,
+    user_var: list[str] | None = None,
+    help_howto_program: bool = False,
+    help_: bool = False,
+    help_gui: bool = False,
+    history: bool = False,
+    show_valid_opts: bool = False,
+    version: bool = False,
+) -> UberSkelParameters:
+    """
+    Build parameters.
+    
+    Args:
+        qt_options: Pass PyQt4 options directly to the GUI.
+        no_gui_flag: Run without the GUI.
+        print_script: Print the script.
+        save_script: Save the script.
+        user_var: Initialize user variables. Usage: -uvar <name> <value>.
+        help_howto_program: Show programming comments.
+        help_: Show help.
+        help_gui: Show help for the GUI.
+        history: Show history.
+        show_valid_opts: Show valid options.
+        version: Show version.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "uber_skel",
+        "no_gui_flag": no_gui_flag,
+        "print_script": print_script,
+        "help_howto_program": help_howto_program,
+        "help": help_,
+        "help_gui": help_gui,
+        "history": history,
+        "show_valid_opts": show_valid_opts,
+        "version": version,
+    }
+    if qt_options is not None:
+        params["qt_options"] = qt_options
+    if save_script is not None:
+        params["save_script"] = save_script
+    if user_var is not None:
+        params["user_var"] = user_var
+    return params
+
+
+def uber_skel_cargs(
+    params: UberSkelParameters,
+    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("uber_skel.py")
+    if params.get("qt_options") is not None:
+        cargs.extend([
+            "-qt_opts",
+            params.get("qt_options")
+        ])
+    if params.get("no_gui_flag"):
+        cargs.append("-no_gui")
+    if params.get("print_script"):
+        cargs.append("-print_script")
+    if params.get("save_script") is not None:
+        cargs.extend([
+            "-save_script",
+            params.get("save_script")
+        ])
+    if params.get("user_var") is not None:
+        cargs.extend([
+            "-uvar",
+            *params.get("user_var")
+        ])
+    if params.get("help_howto_program"):
+        cargs.append("-help_howto_program")
+    if params.get("help"):
+        cargs.append("-help")
+    if params.get("help_gui"):
+        cargs.append("-help_gui")
+    if params.get("history"):
+        cargs.append("-hist")
+    if params.get("show_valid_opts"):
+        cargs.append("-show_valid_opts")
+    if params.get("version"):
+        cargs.append("-ver")
+    return cargs
+
+
+def uber_skel_outputs(
+    params: UberSkelParameters,
+    execution: Execution,
+) -> UberSkelOutputs:
+    """
+    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 = UberSkelOutputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def uber_skel_execute(
+    params: UberSkelParameters,
+    execution: Execution,
+) -> UberSkelOutputs:
+    """
+    Sample uber processing program for initializing user and control variables, with
+    options for both GUI and non-GUI modes.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `UberSkelOutputs`).
+    """
+    params = execution.params(params)
+    cargs = uber_skel_cargs(params, execution)
+    ret = uber_skel_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def uber_skel(
+    qt_options: str | None = None,
+    no_gui_flag: bool = False,
+    print_script: bool = False,
+    save_script: str | None = None,
+    user_var: list[str] | None = None,
+    help_howto_program: bool = False,
+    help_: bool = False,
+    help_gui: bool = False,
+    history: bool = False,
+    show_valid_opts: bool = False,
+    version: bool = False,
+    runner: Runner | None = None,
+) -> UberSkelOutputs:
+    """
+    Sample uber processing program for initializing user and control variables, with
+    options for both GUI and non-GUI modes.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        qt_options: Pass PyQt4 options directly to the GUI.
+        no_gui_flag: Run without the GUI.
+        print_script: Print the script.
+        save_script: Save the script.
+        user_var: Initialize user variables. Usage: -uvar <name> <value>.
+        help_howto_program: Show programming comments.
+        help_: Show help.
+        help_gui: Show help for the GUI.
+        history: Show history.
+        show_valid_opts: Show valid options.
+        version: Show version.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `UberSkelOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(UBER_SKEL_METADATA)
+    params = uber_skel_params(
+        qt_options=qt_options,
+        no_gui_flag=no_gui_flag,
+        print_script=print_script,
+        save_script=save_script,
+        user_var=user_var,
+        help_howto_program=help_howto_program,
+        help_=help_,
+        help_gui=help_gui,
+        history=history,
+        show_valid_opts=show_valid_opts,
+        version=version,
+    )
+    return uber_skel_execute(params, execution)
+
+
+__all__ = [
+    "UBER_SKEL_METADATA",
+    "UberSkelOutputs",
+    "UberSkelParameters",
+    "uber_skel",
+    "uber_skel_params",
+]