niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/afni_open.py

@@ -0,0 +1,304 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+AFNI_OPEN_METADATA = Metadata(
+    id="011cf64aad17ae870a6340e6c6714d18cd8c6e43.boutiques",
+    name="afni_open",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+AfniOpenParameters = typing.TypedDict('AfniOpenParameters', {
+    "__STYX_TYPE__": typing.Literal["afni_open"],
+    "files": list[InputPathType],
+    "method": typing.NotRequired[str | None],
+    "editor": bool,
+    "downloader": bool,
+    "examinexmat": bool,
+    "browser": bool,
+    "readme": bool,
+    "afniweb": bool,
+    "global_help": bool,
+    "gopts_help": bool,
+    "help": bool,
+    "mini_help": bool,
+    "extreme_help": bool,
+    "h_view": bool,
+    "h_web": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "afni_open": afni_open_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 AfniOpenOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `afni_open(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def afni_open_params(
+    files: list[InputPathType],
+    method: str | None = None,
+    editor: bool = False,
+    downloader: bool = False,
+    examinexmat: bool = False,
+    browser: bool = False,
+    readme: bool = False,
+    afniweb: bool = False,
+    global_help: bool = False,
+    gopts_help: bool = False,
+    help_: bool = False,
+    mini_help: bool = False,
+    extreme_help: bool = False,
+    h_view: bool = False,
+    h_web: bool = False,
+) -> AfniOpenParameters:
+    """
+    Build parameters.
+    
+    Args:
+        files: Input file(s) to be opened.
+        method: Method to open files (editor, downloader, browser, afni, suma,\
+            1dplot, ExamineXmat, iviewer, afniweb, readme).
+        editor: Same as -w editor.
+        downloader: Same as -w downloader.
+        examinexmat: Same as -w ExamineXmat.
+        browser: Same as -w browser.
+        readme: Same as -w readme.
+        afniweb: Same as -w afniweb.
+        global_help: Show help for global options.
+        gopts_help: Show help for global options.
+        help_: The entire help output.
+        mini_help: Mini help.
+        extreme_help: Extreme help.
+        h_view: Open help in text editor.
+        h_web: Open help in web browser.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "afni_open",
+        "files": files,
+        "editor": editor,
+        "downloader": downloader,
+        "examinexmat": examinexmat,
+        "browser": browser,
+        "readme": readme,
+        "afniweb": afniweb,
+        "global_help": global_help,
+        "gopts_help": gopts_help,
+        "help": help_,
+        "mini_help": mini_help,
+        "extreme_help": extreme_help,
+        "h_view": h_view,
+        "h_web": h_web,
+    }
+    if method is not None:
+        params["method"] = method
+    return params
+
+
+def afni_open_cargs(
+    params: AfniOpenParameters,
+    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_open")
+    cargs.extend([execution.input_file(f) for f in params.get("files")])
+    if params.get("method") is not None:
+        cargs.extend([
+            "-w",
+            params.get("method")
+        ])
+    if params.get("editor"):
+        cargs.append("-e")
+    if params.get("downloader"):
+        cargs.append("-d")
+    if params.get("examinexmat"):
+        cargs.append("-x")
+    if params.get("browser"):
+        cargs.append("-b")
+    if params.get("readme"):
+        cargs.append("-r")
+    if params.get("afniweb"):
+        cargs.append("-aw")
+    if params.get("global_help"):
+        cargs.append("-global_help")
+    if params.get("gopts_help"):
+        cargs.append("-gopts_help")
+    if params.get("help"):
+        cargs.append("-help")
+    if params.get("mini_help"):
+        cargs.append("-h")
+    if params.get("extreme_help"):
+        cargs.append("-HELP")
+    if params.get("h_view"):
+        cargs.append("-h_view")
+    if params.get("h_web"):
+        cargs.append("-h_web")
+    return cargs
+
+
+def afni_open_outputs(
+    params: AfniOpenParameters,
+    execution: Execution,
+) -> AfniOpenOutputs:
+    """
+    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 = AfniOpenOutputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def afni_open_execute(
+    params: AfniOpenParameters,
+    execution: Execution,
+) -> AfniOpenOutputs:
+    """
+    A program to open various AFNI/SUMA files.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `AfniOpenOutputs`).
+    """
+    params = execution.params(params)
+    cargs = afni_open_cargs(params, execution)
+    ret = afni_open_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def afni_open(
+    files: list[InputPathType],
+    method: str | None = None,
+    editor: bool = False,
+    downloader: bool = False,
+    examinexmat: bool = False,
+    browser: bool = False,
+    readme: bool = False,
+    afniweb: bool = False,
+    global_help: bool = False,
+    gopts_help: bool = False,
+    help_: bool = False,
+    mini_help: bool = False,
+    extreme_help: bool = False,
+    h_view: bool = False,
+    h_web: bool = False,
+    runner: Runner | None = None,
+) -> AfniOpenOutputs:
+    """
+    A program to open various AFNI/SUMA files.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        files: Input file(s) to be opened.
+        method: Method to open files (editor, downloader, browser, afni, suma,\
+            1dplot, ExamineXmat, iviewer, afniweb, readme).
+        editor: Same as -w editor.
+        downloader: Same as -w downloader.
+        examinexmat: Same as -w ExamineXmat.
+        browser: Same as -w browser.
+        readme: Same as -w readme.
+        afniweb: Same as -w afniweb.
+        global_help: Show help for global options.
+        gopts_help: Show help for global options.
+        help_: The entire help output.
+        mini_help: Mini help.
+        extreme_help: Extreme help.
+        h_view: Open help in text editor.
+        h_web: Open help in web browser.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `AfniOpenOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(AFNI_OPEN_METADATA)
+    params = afni_open_params(
+        files=files,
+        method=method,
+        editor=editor,
+        downloader=downloader,
+        examinexmat=examinexmat,
+        browser=browser,
+        readme=readme,
+        afniweb=afniweb,
+        global_help=global_help,
+        gopts_help=gopts_help,
+        help_=help_,
+        mini_help=mini_help,
+        extreme_help=extreme_help,
+        h_view=h_view,
+        h_web=h_web,
+    )
+    return afni_open_execute(params, execution)
+
+
+__all__ = [
+    "AFNI_OPEN_METADATA",
+    "AfniOpenOutputs",
+    "AfniOpenParameters",
+    "afni_open",
+    "afni_open_params",
+]

niwrap_afni/afni/afni_proc_py.py

@@ -0,0 +1,283 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+AFNI_PROC_PY_METADATA = Metadata(
+    id="a4908cc703567652b0ff66dd10430d6df6144142.boutiques",
+    name="afni_proc.py",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+AfniProcPyParameters = typing.TypedDict('AfniProcPyParameters', {
+    "__STYX_TYPE__": typing.Literal["afni_proc.py"],
+    "dsets": list[InputPathType],
+    "subj_id": str,
+    "out_dir": typing.NotRequired[str | None],
+    "blocks": typing.NotRequired[list[str] | None],
+    "anat": InputPathType,
+    "echo_times": typing.NotRequired[list[float] | None],
+    "stim_times": typing.NotRequired[list[InputPathType] | None],
+    "stim_files": typing.NotRequired[list[InputPathType] | None],
+    "copy_files": typing.NotRequired[list[InputPathType] | None],
+    "copy_anat": typing.NotRequired[InputPathType | None],
+    "regress_params": typing.NotRequired[list[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_proc.py": afni_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 {
+        "afni_proc.py": afni_proc_py_outputs,
+    }.get(t)
+
+
+class AfniProcPyOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `afni_proc_py(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_files: OutputPathType | None
+    """All output files stored in the specified output directory."""
+
+
+def afni_proc_py_params(
+    dsets: list[InputPathType],
+    subj_id: str,
+    anat: InputPathType,
+    out_dir: str | None = None,
+    blocks: list[str] | None = None,
+    echo_times: list[float] | None = None,
+    stim_times: list[InputPathType] | None = None,
+    stim_files: list[InputPathType] | None = None,
+    copy_files: list[InputPathType] | None = None,
+    copy_anat: InputPathType | None = None,
+    regress_params: list[str] | None = None,
+) -> AfniProcPyParameters:
+    """
+    Build parameters.
+    
+    Args:
+        dsets: Specify the EPI dataset files. (e.g. epi_run1+orig,\
+            epi_run2+orig).
+        subj_id: Specify the subject ID for the script.
+        anat: Specify the anatomical dataset.
+        out_dir: Specify the output directory for the script.
+        blocks: Specify the processing blocks to apply (e.g. tshift volreg blur\
+            mask scale regress).
+        echo_times: Specify echo times for multi-echo data processing.
+        stim_times: Specify files used for stimulus timing in -stim_times.
+        stim_files: Specify TR-locked stim files for 3dDeconvolve -stim_file\
+            instead of -stim_times.
+        copy_files: Specify additional files to be copied to the results\
+            directory.
+        copy_anat: Copy the anatomical dataset(s) to the results directory.
+        regress_params: Specify extra options for 3dDeconvolve.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "afni_proc.py",
+        "dsets": dsets,
+        "subj_id": subj_id,
+        "anat": anat,
+    }
+    if out_dir is not None:
+        params["out_dir"] = out_dir
+    if blocks is not None:
+        params["blocks"] = blocks
+    if echo_times is not None:
+        params["echo_times"] = echo_times
+    if stim_times is not None:
+        params["stim_times"] = stim_times
+    if stim_files is not None:
+        params["stim_files"] = stim_files
+    if copy_files is not None:
+        params["copy_files"] = copy_files
+    if copy_anat is not None:
+        params["copy_anat"] = copy_anat
+    if regress_params is not None:
+        params["regress_params"] = regress_params
+    return params
+
+
+def afni_proc_py_cargs(
+    params: AfniProcPyParameters,
+    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_proc.py")
+    cargs.extend([execution.input_file(f) for f in params.get("dsets")])
+    cargs.append(params.get("subj_id"))
+    if params.get("out_dir") is not None:
+        cargs.append(params.get("out_dir"))
+    if params.get("blocks") is not None:
+        cargs.extend(params.get("blocks"))
+    cargs.append(execution.input_file(params.get("anat")))
+    if params.get("echo_times") is not None:
+        cargs.extend(map(str, params.get("echo_times")))
+    if params.get("stim_times") is not None:
+        cargs.extend([execution.input_file(f) for f in params.get("stim_times")])
+    if params.get("stim_files") is not None:
+        cargs.extend([execution.input_file(f) for f in params.get("stim_files")])
+    if params.get("copy_files") is not None:
+        cargs.extend([execution.input_file(f) for f in params.get("copy_files")])
+    if params.get("copy_anat") is not None:
+        cargs.append(execution.input_file(params.get("copy_anat")))
+    if params.get("regress_params") is not None:
+        cargs.extend([
+            "-regress_opts_3dD",
+            *params.get("regress_params")
+        ])
+    return cargs
+
+
+def afni_proc_py_outputs(
+    params: AfniProcPyParameters,
+    execution: Execution,
+) -> AfniProcPyOutputs:
+    """
+    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 = AfniProcPyOutputs(
+        root=execution.output_file("."),
+        output_files=execution.output_file(params.get("out_dir") + "/*") if (params.get("out_dir") is not None) else None,
+    )
+    return ret
+
+
+def afni_proc_py_execute(
+    params: AfniProcPyParameters,
+    execution: Execution,
+) -> AfniProcPyOutputs:
+    """
+    Generate a tcsh script for an AFNI single subject processing stream.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `AfniProcPyOutputs`).
+    """
+    params = execution.params(params)
+    cargs = afni_proc_py_cargs(params, execution)
+    ret = afni_proc_py_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def afni_proc_py(
+    dsets: list[InputPathType],
+    subj_id: str,
+    anat: InputPathType,
+    out_dir: str | None = None,
+    blocks: list[str] | None = None,
+    echo_times: list[float] | None = None,
+    stim_times: list[InputPathType] | None = None,
+    stim_files: list[InputPathType] | None = None,
+    copy_files: list[InputPathType] | None = None,
+    copy_anat: InputPathType | None = None,
+    regress_params: list[str] | None = None,
+    runner: Runner | None = None,
+) -> AfniProcPyOutputs:
+    """
+    Generate a tcsh script for an AFNI single subject processing stream.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        dsets: Specify the EPI dataset files. (e.g. epi_run1+orig,\
+            epi_run2+orig).
+        subj_id: Specify the subject ID for the script.
+        anat: Specify the anatomical dataset.
+        out_dir: Specify the output directory for the script.
+        blocks: Specify the processing blocks to apply (e.g. tshift volreg blur\
+            mask scale regress).
+        echo_times: Specify echo times for multi-echo data processing.
+        stim_times: Specify files used for stimulus timing in -stim_times.
+        stim_files: Specify TR-locked stim files for 3dDeconvolve -stim_file\
+            instead of -stim_times.
+        copy_files: Specify additional files to be copied to the results\
+            directory.
+        copy_anat: Copy the anatomical dataset(s) to the results directory.
+        regress_params: Specify extra options for 3dDeconvolve.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `AfniProcPyOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(AFNI_PROC_PY_METADATA)
+    params = afni_proc_py_params(
+        dsets=dsets,
+        subj_id=subj_id,
+        out_dir=out_dir,
+        blocks=blocks,
+        anat=anat,
+        echo_times=echo_times,
+        stim_times=stim_times,
+        stim_files=stim_files,
+        copy_files=copy_files,
+        copy_anat=copy_anat,
+        regress_params=regress_params,
+    )
+    return afni_proc_py_execute(params, execution)
+
+
+__all__ = [
+    "AFNI_PROC_PY_METADATA",
+    "AfniProcPyOutputs",
+    "AfniProcPyParameters",
+    "afni_proc_py",
+    "afni_proc_py_params",
+]