niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/afni_run_r.py

@@ -0,0 +1,180 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+AFNI_RUN_R_METADATA = Metadata(
+    id="c25de8aaab9b4faa0067fa6c9d3361eb1f13f7bf.boutiques",
+    name="afni_run_R",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+AfniRunRParameters = typing.TypedDict('AfniRunRParameters', {
+    "__STYX_TYPE__": typing.Literal["afni_run_R"],
+    "r_script": InputPathType,
+    "r_args": list[str],
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "afni_run_R": afni_run_r_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 AfniRunROutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `afni_run_r(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def afni_run_r_params(
+    r_script: InputPathType,
+    r_args: list[str],
+) -> AfniRunRParameters:
+    """
+    Build parameters.
+    
+    Args:
+        r_script: R script to be executed.
+        r_args: Arguments to be passed to the R script.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "afni_run_R",
+        "r_script": r_script,
+        "r_args": r_args,
+    }
+    return params
+
+
+def afni_run_r_cargs(
+    params: AfniRunRParameters,
+    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("afni_run_R")
+    cargs.append(execution.input_file(params.get("r_script")))
+    cargs.extend(params.get("r_args"))
+    return cargs
+
+
+def afni_run_r_outputs(
+    params: AfniRunRParameters,
+    execution: Execution,
+) -> AfniRunROutputs:
+    """
+    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 = AfniRunROutputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def afni_run_r_execute(
+    params: AfniRunRParameters,
+    execution: Execution,
+) -> AfniRunROutputs:
+    """
+    Run an R script with the specified arguments.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `AfniRunROutputs`).
+    """
+    params = execution.params(params)
+    cargs = afni_run_r_cargs(params, execution)
+    ret = afni_run_r_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def afni_run_r(
+    r_script: InputPathType,
+    r_args: list[str],
+    runner: Runner | None = None,
+) -> AfniRunROutputs:
+    """
+    Run an R script with the specified arguments.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        r_script: R script to be executed.
+        r_args: Arguments to be passed to the R script.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `AfniRunROutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(AFNI_RUN_R_METADATA)
+    params = afni_run_r_params(
+        r_script=r_script,
+        r_args=r_args,
+    )
+    return afni_run_r_execute(params, execution)
+
+
+__all__ = [
+    "AFNI_RUN_R_METADATA",
+    "AfniRunROutputs",
+    "AfniRunRParameters",
+    "afni_run_r",
+    "afni_run_r_params",
+]

niwrap_afni/afni/afni_system_check_py.py

@@ -0,0 +1,274 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+AFNI_SYSTEM_CHECK_PY_METADATA = Metadata(
+    id="707dd8a3faf114c94899a8373ea46705cdf40480.boutiques",
+    name="afni_system_check.py",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+AfniSystemCheckPyParameters = typing.TypedDict('AfniSystemCheckPyParameters', {
+    "__STYX_TYPE__": typing.Literal["afni_system_check.py"],
+    "check_all": bool,
+    "find_prog": typing.NotRequired[str | None],
+    "exact": typing.NotRequired[str | None],
+    "disp_num_cpu": bool,
+    "disp_ver_matplotlib": bool,
+    "dot_file_list": bool,
+    "dot_file_show": bool,
+    "dot_file_pack": typing.NotRequired[str | None],
+    "casematch": typing.NotRequired[str | None],
+    "data_root": 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 {
+        "afni_system_check.py": afni_system_check_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 AfniSystemCheckPyOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `afni_system_check_py(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def afni_system_check_py_params(
+    check_all: bool = False,
+    find_prog: str | None = None,
+    exact: str | None = None,
+    disp_num_cpu: bool = False,
+    disp_ver_matplotlib: bool = False,
+    dot_file_list: bool = False,
+    dot_file_show: bool = False,
+    dot_file_pack: str | None = None,
+    casematch: str | None = None,
+    data_root: str | None = None,
+) -> AfniSystemCheckPyParameters:
+    """
+    Build parameters.
+    
+    Args:
+        check_all: Perform all system checks.
+        find_prog: Search PATH for PROG.
+        exact: Search for PROG without wildcards in -find_prog.
+        disp_num_cpu: Display number of CPUs available.
+        disp_ver_matplotlib: Display matplotlib version (else 'None').
+        dot_file_list: List all found dot files (startup files).
+        dot_file_show: Display contents of all found dot files.
+        dot_file_pack: Create a NAME.tgz package containing dot files.
+        casematch: Match case in -find_prog.
+        data_root: Search for class data under DDIR.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "afni_system_check.py",
+        "check_all": check_all,
+        "disp_num_cpu": disp_num_cpu,
+        "disp_ver_matplotlib": disp_ver_matplotlib,
+        "dot_file_list": dot_file_list,
+        "dot_file_show": dot_file_show,
+    }
+    if find_prog is not None:
+        params["find_prog"] = find_prog
+    if exact is not None:
+        params["exact"] = exact
+    if dot_file_pack is not None:
+        params["dot_file_pack"] = dot_file_pack
+    if casematch is not None:
+        params["casematch"] = casematch
+    if data_root is not None:
+        params["data_root"] = data_root
+    return params
+
+
+def afni_system_check_py_cargs(
+    params: AfniSystemCheckPyParameters,
+    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("afni_system_check.py")
+    if params.get("check_all"):
+        cargs.append("-check_all")
+    if params.get("find_prog") is not None:
+        cargs.extend([
+            "-find_prog",
+            params.get("find_prog")
+        ])
+    if params.get("exact") is not None:
+        cargs.extend([
+            "-exact",
+            params.get("exact")
+        ])
+    if params.get("disp_num_cpu"):
+        cargs.append("-disp_num_cpu")
+    if params.get("disp_ver_matplotlib"):
+        cargs.append("-disp_ver_matplotlib")
+    if params.get("dot_file_list"):
+        cargs.append("-dot_file_list")
+    if params.get("dot_file_show"):
+        cargs.append("-dot_file_show")
+    if params.get("dot_file_pack") is not None:
+        cargs.extend([
+            "-dot_file_pack",
+            params.get("dot_file_pack")
+        ])
+    if params.get("casematch") is not None:
+        cargs.extend([
+            "-casematch",
+            params.get("casematch")
+        ])
+    if params.get("data_root") is not None:
+        cargs.extend([
+            "-data_root",
+            params.get("data_root")
+        ])
+    return cargs
+
+
+def afni_system_check_py_outputs(
+    params: AfniSystemCheckPyParameters,
+    execution: Execution,
+) -> AfniSystemCheckPyOutputs:
+    """
+    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 = AfniSystemCheckPyOutputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def afni_system_check_py_execute(
+    params: AfniSystemCheckPyParameters,
+    execution: Execution,
+) -> AfniSystemCheckPyOutputs:
+    """
+    Perform various system checks for figuring out AFNI installation issues.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `AfniSystemCheckPyOutputs`).
+    """
+    params = execution.params(params)
+    cargs = afni_system_check_py_cargs(params, execution)
+    ret = afni_system_check_py_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def afni_system_check_py(
+    check_all: bool = False,
+    find_prog: str | None = None,
+    exact: str | None = None,
+    disp_num_cpu: bool = False,
+    disp_ver_matplotlib: bool = False,
+    dot_file_list: bool = False,
+    dot_file_show: bool = False,
+    dot_file_pack: str | None = None,
+    casematch: str | None = None,
+    data_root: str | None = None,
+    runner: Runner | None = None,
+) -> AfniSystemCheckPyOutputs:
+    """
+    Perform various system checks for figuring out AFNI installation issues.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        check_all: Perform all system checks.
+        find_prog: Search PATH for PROG.
+        exact: Search for PROG without wildcards in -find_prog.
+        disp_num_cpu: Display number of CPUs available.
+        disp_ver_matplotlib: Display matplotlib version (else 'None').
+        dot_file_list: List all found dot files (startup files).
+        dot_file_show: Display contents of all found dot files.
+        dot_file_pack: Create a NAME.tgz package containing dot files.
+        casematch: Match case in -find_prog.
+        data_root: Search for class data under DDIR.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `AfniSystemCheckPyOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(AFNI_SYSTEM_CHECK_PY_METADATA)
+    params = afni_system_check_py_params(
+        check_all=check_all,
+        find_prog=find_prog,
+        exact=exact,
+        disp_num_cpu=disp_num_cpu,
+        disp_ver_matplotlib=disp_ver_matplotlib,
+        dot_file_list=dot_file_list,
+        dot_file_show=dot_file_show,
+        dot_file_pack=dot_file_pack,
+        casematch=casematch,
+        data_root=data_root,
+    )
+    return afni_system_check_py_execute(params, execution)
+
+
+__all__ = [
+    "AFNI_SYSTEM_CHECK_PY_METADATA",
+    "AfniSystemCheckPyOutputs",
+    "AfniSystemCheckPyParameters",
+    "afni_system_check_py",
+    "afni_system_check_py_params",
+]

niwrap_afni/afni/aiv.py

@@ -0,0 +1,231 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+AIV_METADATA = Metadata(
+    id="75e86933c73fb7bb162a4ffaf0ccf5435ce96089.boutiques",
+    name="aiv",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+AivParameters = typing.TypedDict('AivParameters', {
+    "__STYX_TYPE__": typing.Literal["aiv"],
+    "verbose": bool,
+    "quiet": bool,
+    "title": typing.NotRequired[str | None],
+    "port": typing.NotRequired[float | None],
+    "pad": typing.NotRequired[str | None],
+    "input_images": list[InputPathType],
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "aiv": aiv_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 AivOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `aiv(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def aiv_params(
+    input_images: list[InputPathType],
+    verbose: bool = False,
+    quiet: bool = False,
+    title: str | None = None,
+    port: float | None = None,
+    pad: str | None = None,
+) -> AivParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_images: Input image files (e.g., img1.jpg, img2.bmp).
+        verbose: Print out the image filenames for progress tracking.
+        quiet: Run the program in quiet mode.
+        title: Specify the window title.
+        port: Listen to TCP/IP port for incoming images.
+        pad: Pad all input images to be the same size.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "aiv",
+        "verbose": verbose,
+        "quiet": quiet,
+        "input_images": input_images,
+    }
+    if title is not None:
+        params["title"] = title
+    if port is not None:
+        params["port"] = port
+    if pad is not None:
+        params["pad"] = pad
+    return params
+
+
+def aiv_cargs(
+    params: AivParameters,
+    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("aiv")
+    if params.get("verbose"):
+        cargs.append("-v")
+    if params.get("quiet"):
+        cargs.append("-q")
+    if params.get("title") is not None:
+        cargs.extend([
+            "-title",
+            params.get("title")
+        ])
+    if params.get("port") is not None:
+        cargs.extend([
+            "-p",
+            str(params.get("port"))
+        ])
+    if params.get("pad") is not None:
+        cargs.extend([
+            "-pad",
+            params.get("pad")
+        ])
+    cargs.extend([execution.input_file(f) for f in params.get("input_images")])
+    return cargs
+
+
+def aiv_outputs(
+    params: AivParameters,
+    execution: Execution,
+) -> AivOutputs:
+    """
+    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 = AivOutputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def aiv_execute(
+    params: AivParameters,
+    execution: Execution,
+) -> AivOutputs:
+    """
+    AFNI Image Viewer program. Shows the 2D images on the command line in an
+    AFNI-like image viewer.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `AivOutputs`).
+    """
+    params = execution.params(params)
+    cargs = aiv_cargs(params, execution)
+    ret = aiv_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def aiv(
+    input_images: list[InputPathType],
+    verbose: bool = False,
+    quiet: bool = False,
+    title: str | None = None,
+    port: float | None = None,
+    pad: str | None = None,
+    runner: Runner | None = None,
+) -> AivOutputs:
+    """
+    AFNI Image Viewer program. Shows the 2D images on the command line in an
+    AFNI-like image viewer.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        input_images: Input image files (e.g., img1.jpg, img2.bmp).
+        verbose: Print out the image filenames for progress tracking.
+        quiet: Run the program in quiet mode.
+        title: Specify the window title.
+        port: Listen to TCP/IP port for incoming images.
+        pad: Pad all input images to be the same size.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `AivOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(AIV_METADATA)
+    params = aiv_params(
+        verbose=verbose,
+        quiet=quiet,
+        title=title,
+        port=port,
+        pad=pad,
+        input_images=input_images,
+    )
+    return aiv_execute(params, execution)
+
+
+__all__ = [
+    "AIV_METADATA",
+    "AivOutputs",
+    "AivParameters",
+    "aiv",
+    "aiv_params",
+]