niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/serial_helper.py

@@ -0,0 +1,298 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+SERIAL_HELPER_METADATA = Metadata(
+    id="4df7ea7f38a6767c1aba72a89599b9e5c022108c.boutiques",
+    name="serial_helper",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+SerialHelperParameters = typing.TypedDict('SerialHelperParameters', {
+    "__STYX_TYPE__": typing.Literal["serial_helper"],
+    "serial_port": str,
+    "sock_num": typing.NotRequired[float | None],
+    "mp_max": typing.NotRequired[float | None],
+    "mp_min": typing.NotRequired[float | None],
+    "num_extra": typing.NotRequired[float | None],
+    "disp_all": typing.NotRequired[float | None],
+    "debug": typing.NotRequired[float | None],
+    "show_times": bool,
+    "help": bool,
+    "hist": bool,
+    "no_serial": 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 {
+        "serial_helper": serial_helper_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 SerialHelperOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `serial_helper(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def serial_helper_params(
+    serial_port: str,
+    sock_num: float | None = None,
+    mp_max: float | None = None,
+    mp_min: float | None = None,
+    num_extra: float | None = None,
+    disp_all: float | None = None,
+    debug: float | None = None,
+    show_times: bool = False,
+    help_: bool = False,
+    hist: bool = False,
+    no_serial: bool = False,
+    version: bool = False,
+) -> SerialHelperParameters:
+    """
+    Build parameters.
+    
+    Args:
+        serial_port: Output serial port filename.
+        sock_num: Specify socket number to serve.
+        mp_max: Limit the maximum value of the MP data.
+        mp_min: Limit the minimum value of the MP data.
+        num_extra: Receive additional floats per TR.
+        disp_all: Receive NVOX*8 extra floats per TR.
+        debug: Set the debugging level (0-3).
+        show_times: Show communication times.
+        help_: Display this help information.
+        hist: Show the module history.
+        no_serial: Turn off serial port output.
+        version: Show the current version number.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "serial_helper",
+        "serial_port": serial_port,
+        "show_times": show_times,
+        "help": help_,
+        "hist": hist,
+        "no_serial": no_serial,
+        "version": version,
+    }
+    if sock_num is not None:
+        params["sock_num"] = sock_num
+    if mp_max is not None:
+        params["mp_max"] = mp_max
+    if mp_min is not None:
+        params["mp_min"] = mp_min
+    if num_extra is not None:
+        params["num_extra"] = num_extra
+    if disp_all is not None:
+        params["disp_all"] = disp_all
+    if debug is not None:
+        params["debug"] = debug
+    return params
+
+
+def serial_helper_cargs(
+    params: SerialHelperParameters,
+    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("serial_helper")
+    cargs.extend([
+        "-serial_port",
+        params.get("serial_port")
+    ])
+    if params.get("sock_num") is not None:
+        cargs.extend([
+            "-sock_num",
+            str(params.get("sock_num"))
+        ])
+    if params.get("mp_max") is not None:
+        cargs.extend([
+            "-mp_max",
+            str(params.get("mp_max"))
+        ])
+    if params.get("mp_min") is not None:
+        cargs.extend([
+            "-mp_min",
+            str(params.get("mp_min"))
+        ])
+    if params.get("num_extra") is not None:
+        cargs.extend([
+            "-num_extra",
+            str(params.get("num_extra"))
+        ])
+    if params.get("disp_all") is not None:
+        cargs.extend([
+            "-disp_all",
+            str(params.get("disp_all"))
+        ])
+    if params.get("debug") is not None:
+        cargs.extend([
+            "-debug",
+            str(params.get("debug"))
+        ])
+    if params.get("show_times"):
+        cargs.append("-show_times")
+    if params.get("help"):
+        cargs.append("-help")
+    if params.get("hist"):
+        cargs.append("-hist")
+    if params.get("no_serial"):
+        cargs.append("-no_serial")
+    if params.get("version"):
+        cargs.append("-version")
+    return cargs
+
+
+def serial_helper_outputs(
+    params: SerialHelperParameters,
+    execution: Execution,
+) -> SerialHelperOutputs:
+    """
+    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 = SerialHelperOutputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def serial_helper_execute(
+    params: SerialHelperParameters,
+    execution: Execution,
+) -> SerialHelperOutputs:
+    """
+    Passes motion parameters from socket to serial port.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `SerialHelperOutputs`).
+    """
+    params = execution.params(params)
+    cargs = serial_helper_cargs(params, execution)
+    ret = serial_helper_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def serial_helper(
+    serial_port: str,
+    sock_num: float | None = None,
+    mp_max: float | None = None,
+    mp_min: float | None = None,
+    num_extra: float | None = None,
+    disp_all: float | None = None,
+    debug: float | None = None,
+    show_times: bool = False,
+    help_: bool = False,
+    hist: bool = False,
+    no_serial: bool = False,
+    version: bool = False,
+    runner: Runner | None = None,
+) -> SerialHelperOutputs:
+    """
+    Passes motion parameters from socket to serial port.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        serial_port: Output serial port filename.
+        sock_num: Specify socket number to serve.
+        mp_max: Limit the maximum value of the MP data.
+        mp_min: Limit the minimum value of the MP data.
+        num_extra: Receive additional floats per TR.
+        disp_all: Receive NVOX*8 extra floats per TR.
+        debug: Set the debugging level (0-3).
+        show_times: Show communication times.
+        help_: Display this help information.
+        hist: Show the module history.
+        no_serial: Turn off serial port output.
+        version: Show the current version number.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `SerialHelperOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(SERIAL_HELPER_METADATA)
+    params = serial_helper_params(
+        serial_port=serial_port,
+        sock_num=sock_num,
+        mp_max=mp_max,
+        mp_min=mp_min,
+        num_extra=num_extra,
+        disp_all=disp_all,
+        debug=debug,
+        show_times=show_times,
+        help_=help_,
+        hist=hist,
+        no_serial=no_serial,
+        version=version,
+    )
+    return serial_helper_execute(params, execution)
+
+
+__all__ = [
+    "SERIAL_HELPER_METADATA",
+    "SerialHelperOutputs",
+    "SerialHelperParameters",
+    "serial_helper",
+    "serial_helper_params",
+]

niwrap_afni/afni/sfim.py

@@ -0,0 +1,229 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+SFIM_METADATA = Metadata(
+    id="62032460073e6537145dc05bebbde2400a1cbdbc.boutiques",
+    name="sfim",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+SfimParameters = typing.TypedDict('SfimParameters', {
+    "__STYX_TYPE__": typing.Literal["sfim"],
+    "sfint_file": typing.NotRequired[str | None],
+    "baseline_state": typing.NotRequired[str | None],
+    "local_base_option": bool,
+    "output_prefix": 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 {
+        "sfim": sfim_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 {
+        "sfim": sfim_outputs,
+    }.get(t)
+
+
+class SfimOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `sfim(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_files: OutputPathType | None
+    """Output image file for interval 'i' with task state name."""
+
+
+def sfim_params(
+    sfint_file: str | None = None,
+    baseline_state: str | None = None,
+    local_base_option: bool = False,
+    output_prefix: str | None = None,
+) -> SfimParameters:
+    """
+    Build parameters.
+    
+    Args:
+        sfint_file: Filename which contains the interval definitions. Default\
+            is 'sfint'. Example: '3*# 5*rest 4*A 5*rest 4*B 5*rest 4*A 5*rest'.
+        baseline_state: Task state name to use as the baseline. Default is\
+            'rest'.
+        local_base_option: Flag to indicate if each non-base task state\
+            interval should have the mean of the two nearest base intervals\
+            subtracted instead of the grand mean of all the base task intervals.
+        output_prefix: Prefix for output image filenames for all states. The\
+            i'th interval with task state name 'fred' will be written to file\
+            'pname.fred.i'. Default is 'sfim'.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "sfim",
+        "local_base_option": local_base_option,
+    }
+    if sfint_file is not None:
+        params["sfint_file"] = sfint_file
+    if baseline_state is not None:
+        params["baseline_state"] = baseline_state
+    if output_prefix is not None:
+        params["output_prefix"] = output_prefix
+    return params
+
+
+def sfim_cargs(
+    params: SfimParameters,
+    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("sfim")
+    if params.get("sfint_file") is not None:
+        cargs.extend([
+            "-sfint",
+            params.get("sfint_file")
+        ])
+    if params.get("baseline_state") is not None:
+        cargs.extend([
+            "-base",
+            params.get("baseline_state")
+        ])
+    if params.get("local_base_option"):
+        cargs.append("-localbase")
+    if params.get("output_prefix") is not None:
+        cargs.extend([
+            "-prefix",
+            params.get("output_prefix")
+        ])
+    cargs.append("[INPUT_FILES...]")
+    return cargs
+
+
+def sfim_outputs(
+    params: SfimParameters,
+    execution: Execution,
+) -> SfimOutputs:
+    """
+    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 = SfimOutputs(
+        root=execution.output_file("."),
+        output_files=execution.output_file(params.get("output_prefix") + ".*.i") if (params.get("output_prefix") is not None) else None,
+    )
+    return ret
+
+
+def sfim_execute(
+    params: SfimParameters,
+    execution: Execution,
+) -> SfimOutputs:
+    """
+    Stepwise Functional IMages.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `SfimOutputs`).
+    """
+    params = execution.params(params)
+    cargs = sfim_cargs(params, execution)
+    ret = sfim_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def sfim(
+    sfint_file: str | None = None,
+    baseline_state: str | None = None,
+    local_base_option: bool = False,
+    output_prefix: str | None = None,
+    runner: Runner | None = None,
+) -> SfimOutputs:
+    """
+    Stepwise Functional IMages.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        sfint_file: Filename which contains the interval definitions. Default\
+            is 'sfint'. Example: '3*# 5*rest 4*A 5*rest 4*B 5*rest 4*A 5*rest'.
+        baseline_state: Task state name to use as the baseline. Default is\
+            'rest'.
+        local_base_option: Flag to indicate if each non-base task state\
+            interval should have the mean of the two nearest base intervals\
+            subtracted instead of the grand mean of all the base task intervals.
+        output_prefix: Prefix for output image filenames for all states. The\
+            i'th interval with task state name 'fred' will be written to file\
+            'pname.fred.i'. Default is 'sfim'.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `SfimOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(SFIM_METADATA)
+    params = sfim_params(
+        sfint_file=sfint_file,
+        baseline_state=baseline_state,
+        local_base_option=local_base_option,
+        output_prefix=output_prefix,
+    )
+    return sfim_execute(params, execution)
+
+
+__all__ = [
+    "SFIM_METADATA",
+    "SfimOutputs",
+    "SfimParameters",
+    "sfim",
+    "sfim_params",
+]