niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/rtfeedme.py

@@ -0,0 +1,308 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+RTFEEDME_METADATA = Metadata(
+    id="32964e0c08bfc25e6c4f6eca5347bfc95b91dd98.boutiques",
+    name="rtfeedme",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+RtfeedmeParameters = typing.TypedDict('RtfeedmeParameters', {
+    "__STYX_TYPE__": typing.Literal["rtfeedme"],
+    "datasets": list[InputPathType],
+    "host": typing.NotRequired[str | None],
+    "interval_ms": typing.NotRequired[float | None],
+    "send_3d": bool,
+    "buffer_mb": typing.NotRequired[float | None],
+    "verbose": bool,
+    "swap_bytes": bool,
+    "nz_fake": typing.NotRequired[float | None],
+    "drive_cmd": typing.NotRequired[list[str] | None],
+    "note": typing.NotRequired[list[str] | None],
+    "yrange": typing.NotRequired[float | None],
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "rtfeedme": rtfeedme_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 RtfeedmeOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `rtfeedme(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def rtfeedme_params(
+    datasets: list[InputPathType],
+    host: str | None = None,
+    interval_ms: float | None = None,
+    send_3d: bool = False,
+    buffer_mb: float | None = None,
+    verbose: bool = False,
+    swap_bytes: bool = False,
+    nz_fake: float | None = None,
+    drive_cmd: list[str] | None = None,
+    note: list[str] | None = None,
+    yrange: float | None = None,
+) -> RtfeedmeParameters:
+    """
+    Build parameters.
+    
+    Args:
+        datasets: List of datasets to send to AFNI, specified as paths to\
+            dataset files. Multiple datasets can be specified.
+        host: Send data via TCP/IP to AFNI running on the specified computer\
+            system 'sname'. Default is the current system using shared memory. Use\
+            'localhost' to send on the current system using TCP/IP.
+        interval_ms: Inter-transmit interval in milliseconds. Default is to\
+            send data as fast as possible.
+        send_3d: Send data in 3D bricks. Default is 2D slices.
+        buffer_mb: Set the interprocess communications buffer size in megabytes\
+            when using shared memory. Has no effect if using TCP/IP. Default is 1\
+            MB; if set to 0, a 50 KB buffer is used.
+        verbose: Be talkative about actions.
+        swap_bytes: Swap byte pairs before sending data.
+        nz_fake: Send 'nz' as the value of nzz for debugging purposes.
+        drive_cmd: Send 'cmd' as a DRIVE_AFNI command. If 'cmd' contains\
+            spaces, it must be quoted. Multiple -drive options can be used.
+        note: Send 'sss' as a NOTE to the realtime plugin. Multiple -note\
+            options can be used.
+        yrange: Send value 'v' as the y-range for realtime motion estimation\
+            graphing.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "rtfeedme",
+        "datasets": datasets,
+        "send_3d": send_3d,
+        "verbose": verbose,
+        "swap_bytes": swap_bytes,
+    }
+    if host is not None:
+        params["host"] = host
+    if interval_ms is not None:
+        params["interval_ms"] = interval_ms
+    if buffer_mb is not None:
+        params["buffer_mb"] = buffer_mb
+    if nz_fake is not None:
+        params["nz_fake"] = nz_fake
+    if drive_cmd is not None:
+        params["drive_cmd"] = drive_cmd
+    if note is not None:
+        params["note"] = note
+    if yrange is not None:
+        params["yrange"] = yrange
+    return params
+
+
+def rtfeedme_cargs(
+    params: RtfeedmeParameters,
+    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("rtfeedme")
+    cargs.extend([execution.input_file(f) for f in params.get("datasets")])
+    if params.get("host") is not None:
+        cargs.extend([
+            "-host",
+            params.get("host")
+        ])
+    if params.get("interval_ms") is not None:
+        cargs.extend([
+            "-dt",
+            str(params.get("interval_ms"))
+        ])
+    if params.get("send_3d"):
+        cargs.append("-3D")
+    if params.get("buffer_mb") is not None:
+        cargs.extend([
+            "-buf",
+            str(params.get("buffer_mb"))
+        ])
+    if params.get("verbose"):
+        cargs.append("-verbose")
+    if params.get("swap_bytes"):
+        cargs.append("-swap2")
+    if params.get("nz_fake") is not None:
+        cargs.extend([
+            "-nzfake",
+            str(params.get("nz_fake"))
+        ])
+    if params.get("drive_cmd") is not None:
+        cargs.extend([
+            "-drive",
+            *params.get("drive_cmd")
+        ])
+    if params.get("note") is not None:
+        cargs.extend([
+            "-note",
+            *params.get("note")
+        ])
+    if params.get("yrange") is not None:
+        cargs.extend([
+            "-gyr",
+            str(params.get("yrange"))
+        ])
+    return cargs
+
+
+def rtfeedme_outputs(
+    params: RtfeedmeParameters,
+    execution: Execution,
+) -> RtfeedmeOutputs:
+    """
+    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 = RtfeedmeOutputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def rtfeedme_execute(
+    params: RtfeedmeParameters,
+    execution: Execution,
+) -> RtfeedmeOutputs:
+    """
+    Test the real-time plugin by sending all the bricks in 'dataset' to AFNI.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `RtfeedmeOutputs`).
+    """
+    params = execution.params(params)
+    cargs = rtfeedme_cargs(params, execution)
+    ret = rtfeedme_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def rtfeedme(
+    datasets: list[InputPathType],
+    host: str | None = None,
+    interval_ms: float | None = None,
+    send_3d: bool = False,
+    buffer_mb: float | None = None,
+    verbose: bool = False,
+    swap_bytes: bool = False,
+    nz_fake: float | None = None,
+    drive_cmd: list[str] | None = None,
+    note: list[str] | None = None,
+    yrange: float | None = None,
+    runner: Runner | None = None,
+) -> RtfeedmeOutputs:
+    """
+    Test the real-time plugin by sending all the bricks in 'dataset' to AFNI.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        datasets: List of datasets to send to AFNI, specified as paths to\
+            dataset files. Multiple datasets can be specified.
+        host: Send data via TCP/IP to AFNI running on the specified computer\
+            system 'sname'. Default is the current system using shared memory. Use\
+            'localhost' to send on the current system using TCP/IP.
+        interval_ms: Inter-transmit interval in milliseconds. Default is to\
+            send data as fast as possible.
+        send_3d: Send data in 3D bricks. Default is 2D slices.
+        buffer_mb: Set the interprocess communications buffer size in megabytes\
+            when using shared memory. Has no effect if using TCP/IP. Default is 1\
+            MB; if set to 0, a 50 KB buffer is used.
+        verbose: Be talkative about actions.
+        swap_bytes: Swap byte pairs before sending data.
+        nz_fake: Send 'nz' as the value of nzz for debugging purposes.
+        drive_cmd: Send 'cmd' as a DRIVE_AFNI command. If 'cmd' contains\
+            spaces, it must be quoted. Multiple -drive options can be used.
+        note: Send 'sss' as a NOTE to the realtime plugin. Multiple -note\
+            options can be used.
+        yrange: Send value 'v' as the y-range for realtime motion estimation\
+            graphing.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `RtfeedmeOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(RTFEEDME_METADATA)
+    params = rtfeedme_params(
+        datasets=datasets,
+        host=host,
+        interval_ms=interval_ms,
+        send_3d=send_3d,
+        buffer_mb=buffer_mb,
+        verbose=verbose,
+        swap_bytes=swap_bytes,
+        nz_fake=nz_fake,
+        drive_cmd=drive_cmd,
+        note=note,
+        yrange=yrange,
+    )
+    return rtfeedme_execute(params, execution)
+
+
+__all__ = [
+    "RTFEEDME_METADATA",
+    "RtfeedmeOutputs",
+    "RtfeedmeParameters",
+    "rtfeedme",
+    "rtfeedme_params",
+]

niwrap_afni/afni/samp_bias.py

@@ -0,0 +1,245 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+SAMP_BIAS_METADATA = Metadata(
+    id="6e470934bf7282b84b4830d0577fb44d56bf39e3.boutiques",
+    name="SampBias",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+SampBiasParameters = typing.TypedDict('SampBiasParameters', {
+    "__STYX_TYPE__": typing.Literal["SampBias"],
+    "specfile": InputPathType,
+    "surfname": str,
+    "plimit": typing.NotRequired[float | None],
+    "dlimit": typing.NotRequired[float | None],
+    "outfile": str,
+    "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 {
+        "SampBias": samp_bias_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 {
+        "SampBias": samp_bias_outputs,
+    }.get(t)
+
+
+class SampBiasOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `samp_bias(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    out_1_d: OutputPathType
+    """Output results in .1D format"""
+    out_prefix: OutputPathType | None
+    """Output results in a proper surface-based dataset."""
+
+
+def samp_bias_params(
+    specfile: InputPathType,
+    surfname: str,
+    outfile: str,
+    plimit: float | None = None,
+    dlimit: float | None = None,
+    prefix: str | None = None,
+) -> SampBiasParameters:
+    """
+    Build parameters.
+    
+    Args:
+        specfile: Spec file containing input surfaces.
+        surfname: Name of input surface.
+        outfile: Output results in .1D format.
+        plimit: Maximum length of path along surface in mm. Default is 50 mm.
+        dlimit: Maximum length of euclidean distance in mm. Default is 1000 mm.
+        prefix: Output results into a proper surface-based dataset.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "SampBias",
+        "specfile": specfile,
+        "surfname": surfname,
+        "outfile": outfile,
+    }
+    if plimit is not None:
+        params["plimit"] = plimit
+    if dlimit is not None:
+        params["dlimit"] = dlimit
+    if prefix is not None:
+        params["prefix"] = prefix
+    return params
+
+
+def samp_bias_cargs(
+    params: SampBiasParameters,
+    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("SampBias")
+    cargs.extend([
+        "-spec",
+        execution.input_file(params.get("specfile"))
+    ])
+    cargs.extend([
+        "-surf",
+        params.get("surfname")
+    ])
+    if params.get("plimit") is not None:
+        cargs.extend([
+            "-plimit",
+            str(params.get("plimit"))
+        ])
+    if params.get("dlimit") is not None:
+        cargs.extend([
+            "-dlimit",
+            str(params.get("dlimit"))
+        ])
+    cargs.extend([
+        "-out",
+        params.get("outfile")
+    ])
+    if params.get("prefix") is not None:
+        cargs.extend([
+            "-prefix",
+            params.get("prefix")
+        ])
+    return cargs
+
+
+def samp_bias_outputs(
+    params: SampBiasParameters,
+    execution: Execution,
+) -> SampBiasOutputs:
+    """
+    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 = SampBiasOutputs(
+        root=execution.output_file("."),
+        out_1_d=execution.output_file(params.get("outfile") + ".1D"),
+        out_prefix=execution.output_file(params.get("prefix")) if (params.get("prefix") is not None) else None,
+    )
+    return ret
+
+
+def samp_bias_execute(
+    params: SampBiasParameters,
+    execution: Execution,
+) -> SampBiasOutputs:
+    """
+    SampBias is a tool for sampling bias resultant segments between paired nodes on
+    anatomical surfaces.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `SampBiasOutputs`).
+    """
+    params = execution.params(params)
+    cargs = samp_bias_cargs(params, execution)
+    ret = samp_bias_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def samp_bias(
+    specfile: InputPathType,
+    surfname: str,
+    outfile: str,
+    plimit: float | None = None,
+    dlimit: float | None = None,
+    prefix: str | None = None,
+    runner: Runner | None = None,
+) -> SampBiasOutputs:
+    """
+    SampBias is a tool for sampling bias resultant segments between paired nodes on
+    anatomical surfaces.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        specfile: Spec file containing input surfaces.
+        surfname: Name of input surface.
+        outfile: Output results in .1D format.
+        plimit: Maximum length of path along surface in mm. Default is 50 mm.
+        dlimit: Maximum length of euclidean distance in mm. Default is 1000 mm.
+        prefix: Output results into a proper surface-based dataset.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `SampBiasOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(SAMP_BIAS_METADATA)
+    params = samp_bias_params(
+        specfile=specfile,
+        surfname=surfname,
+        plimit=plimit,
+        dlimit=dlimit,
+        outfile=outfile,
+        prefix=prefix,
+    )
+    return samp_bias_execute(params, execution)
+
+
+__all__ = [
+    "SAMP_BIAS_METADATA",
+    "SampBiasOutputs",
+    "SampBiasParameters",
+    "samp_bias",
+    "samp_bias_params",
+]