niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/afni.py

@@ -0,0 +1,428 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+AFNI_METADATA = Metadata(
+    id="40dab3442f2e18227072a94a9827898d65dc4372.boutiques",
+    name="afni",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+AfniParameters = typing.TypedDict('AfniParameters', {
+    "__STYX_TYPE__": typing.Literal["afni"],
+    "session_directories": typing.NotRequired[str | None],
+    "bysub": typing.NotRequired[list[str] | None],
+    "all_dsets": bool,
+    "purge": bool,
+    "posfunc": bool,
+    "recursive": bool,
+    "no1D": bool,
+    "nocsv": bool,
+    "notsv": bool,
+    "unique": bool,
+    "orient": typing.NotRequired[str | None],
+    "noplugins": bool,
+    "seehidden": bool,
+    "allow_all_plugins": bool,
+    "yesplugouts": bool,
+    "debug_plugouts": bool,
+    "noplugouts": bool,
+    "skip_afnirc": bool,
+    "layout": typing.NotRequired[InputPathType | None],
+    "niml": bool,
+    "np": typing.NotRequired[int | None],
+    "npq": typing.NotRequired[int | None],
+    "npb": typing.NotRequired[int | None],
+    "com": typing.NotRequired[str | None],
+    "comsep": 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": afni_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": afni_outputs,
+    }.get(t)
+
+
+class AfniOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `afni_(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    session_output: OutputPathType
+    """Output file for the session data"""
+
+
+def afni_params(
+    session_directories: str | None = None,
+    bysub: list[str] | None = None,
+    all_dsets: bool = False,
+    purge: bool = False,
+    posfunc: bool = False,
+    recursive: bool = False,
+    no1_d: bool = False,
+    nocsv: bool = False,
+    notsv: bool = False,
+    unique: bool = False,
+    orient: str | None = None,
+    noplugins: bool = False,
+    seehidden: bool = False,
+    allow_all_plugins: bool = False,
+    yesplugouts: bool = False,
+    debug_plugouts: bool = False,
+    noplugouts: bool = False,
+    skip_afnirc: bool = False,
+    layout: InputPathType | None = None,
+    niml: bool = False,
+    np: int | None = None,
+    npq: int | None = None,
+    npb: int | None = None,
+    com: str | None = None,
+    comsep: str | None = None,
+) -> AfniParameters:
+    """
+    Build parameters.
+    
+    Args:
+        session_directories: Input session directories containing the datasets.
+        bysub: Gather all datasets corresponding to a single subject identifier.
+        all_dsets: Read in all datasets from all listed folders together.
+        purge: Conserve memory by purging unused datasets.
+        posfunc: Start up the color 'pbar' to use only positive function values.
+        recursive: Recursively search each session_directory for more session\
+            subdirectories.
+        no1_d: Tells AFNI not to read *.1D timeseries files.
+        nocsv: Tells AFNI not to read *.csv files.
+        notsv: Tells AFNI not to read *.tsv files.
+        unique: Create a unique set of colors for each AFNI controller window.
+        orient: Orientation code for displaying x-y-z coordinates.
+        noplugins: Do not load plugins.
+        seehidden: Show hidden plugins.
+        allow_all_plugins: Do not hide plugins.
+        yesplugouts: Listen for plugouts.
+        debug_plugouts: Plugout code prints lots of messages (for debugging).
+        noplugouts: Do not listen for plugouts.
+        skip_afnirc: Do not read .afnirc file.
+        layout: Read initial windows layout from a file.
+        niml: Turn on listening for NIML-formatted data from SUMA.
+        np: Provide a port offset for multiple instances.
+        npq: Like -np but quieter in case of errors.
+        npb: Provide a block of port numbers.
+        com: Specify command strings to drive AFNI on startup.
+        comsep: Character to use as a separator for commands.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "afni",
+        "all_dsets": all_dsets,
+        "purge": purge,
+        "posfunc": posfunc,
+        "recursive": recursive,
+        "no1D": no1_d,
+        "nocsv": nocsv,
+        "notsv": notsv,
+        "unique": unique,
+        "noplugins": noplugins,
+        "seehidden": seehidden,
+        "allow_all_plugins": allow_all_plugins,
+        "yesplugouts": yesplugouts,
+        "debug_plugouts": debug_plugouts,
+        "noplugouts": noplugouts,
+        "skip_afnirc": skip_afnirc,
+        "niml": niml,
+    }
+    if session_directories is not None:
+        params["session_directories"] = session_directories
+    if bysub is not None:
+        params["bysub"] = bysub
+    if orient is not None:
+        params["orient"] = orient
+    if layout is not None:
+        params["layout"] = layout
+    if np is not None:
+        params["np"] = np
+    if npq is not None:
+        params["npq"] = npq
+    if npb is not None:
+        params["npb"] = npb
+    if com is not None:
+        params["com"] = com
+    if comsep is not None:
+        params["comsep"] = comsep
+    return params
+
+
+def afni_cargs(
+    params: AfniParameters,
+    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")
+    if params.get("session_directories") is not None:
+        cargs.append(params.get("session_directories"))
+    if params.get("bysub") is not None:
+        cargs.extend([
+            "-bysub",
+            *params.get("bysub")
+        ])
+    if params.get("all_dsets"):
+        cargs.append("-all_dsets")
+    if params.get("purge"):
+        cargs.append("-purge")
+    if params.get("posfunc"):
+        cargs.append("-posfunc")
+    if params.get("recursive"):
+        cargs.append("-R")
+    if params.get("no1D"):
+        cargs.append("-no1D")
+    if params.get("nocsv"):
+        cargs.append("-nocsv")
+    if params.get("notsv"):
+        cargs.append("-notsv")
+    if params.get("unique"):
+        cargs.append("-unique")
+    if params.get("orient") is not None:
+        cargs.extend([
+            "-orient",
+            params.get("orient")
+        ])
+    if params.get("noplugins"):
+        cargs.append("-noplugins")
+    if params.get("seehidden"):
+        cargs.append("-seehidden")
+    if params.get("allow_all_plugins"):
+        cargs.append("-DAFNI_ALLOW_ALL_PLUGINS=YES")
+    if params.get("yesplugouts"):
+        cargs.append("-yesplugouts")
+    if params.get("debug_plugouts"):
+        cargs.append("-YESplugouts")
+    if params.get("noplugouts"):
+        cargs.append("-noplugouts")
+    if params.get("skip_afnirc"):
+        cargs.append("-skip_afnirc")
+    if params.get("layout") is not None:
+        cargs.extend([
+            "-layout",
+            execution.input_file(params.get("layout"))
+        ])
+    if params.get("niml"):
+        cargs.append("-niml")
+    if params.get("np") is not None:
+        cargs.extend([
+            "-np",
+            str(params.get("np"))
+        ])
+    if params.get("npq") is not None:
+        cargs.extend([
+            "-npq",
+            str(params.get("npq"))
+        ])
+    if params.get("npb") is not None:
+        cargs.extend([
+            "-npb",
+            str(params.get("npb"))
+        ])
+    if params.get("com") is not None:
+        cargs.extend([
+            "-com",
+            params.get("com")
+        ])
+    if params.get("comsep") is not None:
+        cargs.extend([
+            "-comsep",
+            params.get("comsep")
+        ])
+    return cargs
+
+
+def afni_outputs(
+    params: AfniParameters,
+    execution: Execution,
+) -> AfniOutputs:
+    """
+    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 = AfniOutputs(
+        root=execution.output_file("."),
+        session_output=execution.output_file("output_session.nii.gz"),
+    )
+    return ret
+
+
+def afni_execute(
+    params: AfniParameters,
+    execution: Execution,
+) -> AfniOutputs:
+    """
+    Tool for reading in sessions of 3D datasets and visualizing them.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `AfniOutputs`).
+    """
+    params = execution.params(params)
+    cargs = afni_cargs(params, execution)
+    ret = afni_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def afni_(
+    session_directories: str | None = None,
+    bysub: list[str] | None = None,
+    all_dsets: bool = False,
+    purge: bool = False,
+    posfunc: bool = False,
+    recursive: bool = False,
+    no1_d: bool = False,
+    nocsv: bool = False,
+    notsv: bool = False,
+    unique: bool = False,
+    orient: str | None = None,
+    noplugins: bool = False,
+    seehidden: bool = False,
+    allow_all_plugins: bool = False,
+    yesplugouts: bool = False,
+    debug_plugouts: bool = False,
+    noplugouts: bool = False,
+    skip_afnirc: bool = False,
+    layout: InputPathType | None = None,
+    niml: bool = False,
+    np: int | None = None,
+    npq: int | None = None,
+    npb: int | None = None,
+    com: str | None = None,
+    comsep: str | None = None,
+    runner: Runner | None = None,
+) -> AfniOutputs:
+    """
+    Tool for reading in sessions of 3D datasets and visualizing them.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        session_directories: Input session directories containing the datasets.
+        bysub: Gather all datasets corresponding to a single subject identifier.
+        all_dsets: Read in all datasets from all listed folders together.
+        purge: Conserve memory by purging unused datasets.
+        posfunc: Start up the color 'pbar' to use only positive function values.
+        recursive: Recursively search each session_directory for more session\
+            subdirectories.
+        no1_d: Tells AFNI not to read *.1D timeseries files.
+        nocsv: Tells AFNI not to read *.csv files.
+        notsv: Tells AFNI not to read *.tsv files.
+        unique: Create a unique set of colors for each AFNI controller window.
+        orient: Orientation code for displaying x-y-z coordinates.
+        noplugins: Do not load plugins.
+        seehidden: Show hidden plugins.
+        allow_all_plugins: Do not hide plugins.
+        yesplugouts: Listen for plugouts.
+        debug_plugouts: Plugout code prints lots of messages (for debugging).
+        noplugouts: Do not listen for plugouts.
+        skip_afnirc: Do not read .afnirc file.
+        layout: Read initial windows layout from a file.
+        niml: Turn on listening for NIML-formatted data from SUMA.
+        np: Provide a port offset for multiple instances.
+        npq: Like -np but quieter in case of errors.
+        npb: Provide a block of port numbers.
+        com: Specify command strings to drive AFNI on startup.
+        comsep: Character to use as a separator for commands.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `AfniOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(AFNI_METADATA)
+    params = afni_params(
+        session_directories=session_directories,
+        bysub=bysub,
+        all_dsets=all_dsets,
+        purge=purge,
+        posfunc=posfunc,
+        recursive=recursive,
+        no1_d=no1_d,
+        nocsv=nocsv,
+        notsv=notsv,
+        unique=unique,
+        orient=orient,
+        noplugins=noplugins,
+        seehidden=seehidden,
+        allow_all_plugins=allow_all_plugins,
+        yesplugouts=yesplugouts,
+        debug_plugouts=debug_plugouts,
+        noplugouts=noplugouts,
+        skip_afnirc=skip_afnirc,
+        layout=layout,
+        niml=niml,
+        np=np,
+        npq=npq,
+        npb=npb,
+        com=com,
+        comsep=comsep,
+    )
+    return afni_execute(params, execution)
+
+
+__all__ = [
+    "AFNI_METADATA",
+    "AfniOutputs",
+    "AfniParameters",
+    "afni_",
+    "afni_params",
+]

niwrap_afni/afni/afni_batch_r.py

@@ -0,0 +1,215 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+AFNI_BATCH_R_METADATA = Metadata(
+    id="78789aab686dc723a7f6543875033396e8a4b97c.boutiques",
+    name="AFNI_Batch_R",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+AfniBatchRParameters = typing.TypedDict('AfniBatchRParameters', {
+    "__STYX_TYPE__": typing.Literal["AFNI_Batch_R"],
+    "no_restore": bool,
+    "save_workspace": bool,
+    "no_readline": bool,
+    "vanilla_mode": bool,
+    "help": 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_Batch_R": afni_batch_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 AfniBatchROutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `afni_batch_r(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def afni_batch_r_params(
+    no_restore: bool = False,
+    save_workspace: bool = False,
+    no_readline: bool = False,
+    vanilla_mode: bool = False,
+    help_: bool = False,
+) -> AfniBatchRParameters:
+    """
+    Build parameters.
+    
+    Args:
+        no_restore: Do not restore anything in the R workspace at startup.
+        save_workspace: Save the workspace at the end of the script execution.
+        no_readline: Disable reading input from the command line.
+        vanilla_mode: Run R without saving the workspace at the end, restoring\
+            anything, reading the site file, or acting on startup files.
+        help_: Display this help message and exit.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "AFNI_Batch_R",
+        "no_restore": no_restore,
+        "save_workspace": save_workspace,
+        "no_readline": no_readline,
+        "vanilla_mode": vanilla_mode,
+        "help": help_,
+    }
+    return params
+
+
+def afni_batch_r_cargs(
+    params: AfniBatchRParameters,
+    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_Batch_R")
+    cargs.append("R")
+    cargs.append("CMD")
+    cargs.append("BATCH")
+    if params.get("no_restore"):
+        cargs.append("--no-restore")
+    if params.get("save_workspace"):
+        cargs.append("--save")
+    if params.get("no_readline"):
+        cargs.append("--no-readline")
+    if params.get("vanilla_mode"):
+        cargs.append("--vanilla")
+    cargs.append("--args")
+    if params.get("help"):
+        cargs.append("-help")
+    return cargs
+
+
+def afni_batch_r_outputs(
+    params: AfniBatchRParameters,
+    execution: Execution,
+) -> AfniBatchROutputs:
+    """
+    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 = AfniBatchROutputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def afni_batch_r_execute(
+    params: AfniBatchRParameters,
+    execution: Execution,
+) -> AfniBatchROutputs:
+    """
+    Batch mode for executing R scripts in the AFNI environment.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `AfniBatchROutputs`).
+    """
+    params = execution.params(params)
+    cargs = afni_batch_r_cargs(params, execution)
+    ret = afni_batch_r_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def afni_batch_r(
+    no_restore: bool = False,
+    save_workspace: bool = False,
+    no_readline: bool = False,
+    vanilla_mode: bool = False,
+    help_: bool = False,
+    runner: Runner | None = None,
+) -> AfniBatchROutputs:
+    """
+    Batch mode for executing R scripts in the AFNI environment.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        no_restore: Do not restore anything in the R workspace at startup.
+        save_workspace: Save the workspace at the end of the script execution.
+        no_readline: Disable reading input from the command line.
+        vanilla_mode: Run R without saving the workspace at the end, restoring\
+            anything, reading the site file, or acting on startup files.
+        help_: Display this help message and exit.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `AfniBatchROutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(AFNI_BATCH_R_METADATA)
+    params = afni_batch_r_params(
+        no_restore=no_restore,
+        save_workspace=save_workspace,
+        no_readline=no_readline,
+        vanilla_mode=vanilla_mode,
+        help_=help_,
+    )
+    return afni_batch_r_execute(params, execution)
+
+
+__all__ = [
+    "AFNI_BATCH_R_METADATA",
+    "AfniBatchROutputs",
+    "AfniBatchRParameters",
+    "afni_batch_r",
+    "afni_batch_r_params",
+]