niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/niml_feedme.py

@@ -0,0 +1,260 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+NIML_FEEDME_METADATA = Metadata(
+    id="1bac7bbed08a8bb76281f7d7e0ddd7246fef322f.boutiques",
+    name="niml_feedme",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+NimlFeedmeParameters = typing.TypedDict('NimlFeedmeParameters', {
+    "__STYX_TYPE__": typing.Literal["niml_feedme"],
+    "host": typing.NotRequired[str | None],
+    "interval": typing.NotRequired[float | None],
+    "verbose": bool,
+    "accum": bool,
+    "target_dataset": typing.NotRequired[str | None],
+    "drive_cmds": typing.NotRequired[list[str] | None],
+    "dataset": InputPathType,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "niml_feedme": niml_feedme_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 NimlFeedmeOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `niml_feedme(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def niml_feedme_params(
+    dataset: InputPathType,
+    host: str | None = None,
+    interval: float | None = None,
+    verbose: bool = False,
+    accum: bool = False,
+    target_dataset: str | None = None,
+    drive_cmds: list[str] | None = None,
+) -> NimlFeedmeParameters:
+    """
+    Build parameters.
+    
+    Args:
+        dataset: Input dataset to be sent to AFNI.
+        host: Send data, via TCP/IP, to AFNI running on the computer system\
+            'sname'. By default, uses the current system (localhost), if you don't\
+            use this option.
+        interval: Tries to maintain an inter-transmit interval of 'ms'\
+            milliseconds. The default is 1000 msec per volume.
+        verbose: Be (very) talkative about actions.
+        accum: Send sub-bricks so that they accumulate in AFNI. The default is\
+            to create only a 1 volume dataset inside AFNI, and each sub-brick just\
+            replaces that one volume when it is received.
+        target_dataset: Change the dataset name transmitted to AFNI from\
+            'niml_feedme' to 'nam'.
+        drive_cmds: Send 'cmd' as a DRIVE_AFNI command. If cmd contains blanks,\
+            it must be in 'quotes'. Multiple -drive options may be used. These\
+            commands will be sent to AFNI just after the first volume is\
+            transmitted. See file README.driver for a list of commands.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "niml_feedme",
+        "verbose": verbose,
+        "accum": accum,
+        "dataset": dataset,
+    }
+    if host is not None:
+        params["host"] = host
+    if interval is not None:
+        params["interval"] = interval
+    if target_dataset is not None:
+        params["target_dataset"] = target_dataset
+    if drive_cmds is not None:
+        params["drive_cmds"] = drive_cmds
+    return params
+
+
+def niml_feedme_cargs(
+    params: NimlFeedmeParameters,
+    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("niml_feedme")
+    if params.get("host") is not None:
+        cargs.extend([
+            "-host",
+            params.get("host")
+        ])
+    if params.get("interval") is not None:
+        cargs.extend([
+            "-dt",
+            str(params.get("interval"))
+        ])
+    if params.get("verbose"):
+        cargs.append("-verb")
+    if params.get("accum"):
+        cargs.append("-accum")
+    if params.get("target_dataset") is not None:
+        cargs.extend([
+            "-target",
+            params.get("target_dataset")
+        ])
+    if params.get("drive_cmds") is not None:
+        cargs.extend([
+            "-drive",
+            *params.get("drive_cmds")
+        ])
+    cargs.append(execution.input_file(params.get("dataset")))
+    return cargs
+
+
+def niml_feedme_outputs(
+    params: NimlFeedmeParameters,
+    execution: Execution,
+) -> NimlFeedmeOutputs:
+    """
+    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 = NimlFeedmeOutputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def niml_feedme_execute(
+    params: NimlFeedmeParameters,
+    execution: Execution,
+) -> NimlFeedmeOutputs:
+    """
+    Sends volumes from the dataset to AFNI via the NIML socket interface.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `NimlFeedmeOutputs`).
+    """
+    params = execution.params(params)
+    cargs = niml_feedme_cargs(params, execution)
+    ret = niml_feedme_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def niml_feedme(
+    dataset: InputPathType,
+    host: str | None = None,
+    interval: float | None = None,
+    verbose: bool = False,
+    accum: bool = False,
+    target_dataset: str | None = None,
+    drive_cmds: list[str] | None = None,
+    runner: Runner | None = None,
+) -> NimlFeedmeOutputs:
+    """
+    Sends volumes from the dataset to AFNI via the NIML socket interface.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        dataset: Input dataset to be sent to AFNI.
+        host: Send data, via TCP/IP, to AFNI running on the computer system\
+            'sname'. By default, uses the current system (localhost), if you don't\
+            use this option.
+        interval: Tries to maintain an inter-transmit interval of 'ms'\
+            milliseconds. The default is 1000 msec per volume.
+        verbose: Be (very) talkative about actions.
+        accum: Send sub-bricks so that they accumulate in AFNI. The default is\
+            to create only a 1 volume dataset inside AFNI, and each sub-brick just\
+            replaces that one volume when it is received.
+        target_dataset: Change the dataset name transmitted to AFNI from\
+            'niml_feedme' to 'nam'.
+        drive_cmds: Send 'cmd' as a DRIVE_AFNI command. If cmd contains blanks,\
+            it must be in 'quotes'. Multiple -drive options may be used. These\
+            commands will be sent to AFNI just after the first volume is\
+            transmitted. See file README.driver for a list of commands.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `NimlFeedmeOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(NIML_FEEDME_METADATA)
+    params = niml_feedme_params(
+        host=host,
+        interval=interval,
+        verbose=verbose,
+        accum=accum,
+        target_dataset=target_dataset,
+        drive_cmds=drive_cmds,
+        dataset=dataset,
+    )
+    return niml_feedme_execute(params, execution)
+
+
+__all__ = [
+    "NIML_FEEDME_METADATA",
+    "NimlFeedmeOutputs",
+    "NimlFeedmeParameters",
+    "niml_feedme",
+    "niml_feedme_params",
+]

niwrap_afni/afni/nsize.py

@@ -0,0 +1,184 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+NSIZE_METADATA = Metadata(
+    id="d61eb0714ab51aec00c025a2f54aab55318f6b55.boutiques",
+    name="nsize",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+NsizeParameters = typing.TypedDict('NsizeParameters', {
+    "__STYX_TYPE__": typing.Literal["nsize"],
+    "image_in": InputPathType,
+    "image_out": str,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "nsize": nsize_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 {
+        "nsize": nsize_outputs,
+    }.get(t)
+
+
+class NsizeOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `nsize(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    image_out_file: OutputPathType
+    """Zero padded output image file"""
+
+
+def nsize_params(
+    image_in: InputPathType,
+    image_out: str,
+) -> NsizeParameters:
+    """
+    Build parameters.
+    
+    Args:
+        image_in: Input image file.
+        image_out: Output padded image file.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "nsize",
+        "image_in": image_in,
+        "image_out": image_out,
+    }
+    return params
+
+
+def nsize_cargs(
+    params: NsizeParameters,
+    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("nsize")
+    cargs.append(execution.input_file(params.get("image_in")))
+    cargs.append(params.get("image_out"))
+    return cargs
+
+
+def nsize_outputs(
+    params: NsizeParameters,
+    execution: Execution,
+) -> NsizeOutputs:
+    """
+    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 = NsizeOutputs(
+        root=execution.output_file("."),
+        image_out_file=execution.output_file(params.get("image_out")),
+    )
+    return ret
+
+
+def nsize_execute(
+    params: NsizeParameters,
+    execution: Execution,
+) -> NsizeOutputs:
+    """
+    Zero pads an input image to the nearest larger NxN dimensions.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `NsizeOutputs`).
+    """
+    params = execution.params(params)
+    cargs = nsize_cargs(params, execution)
+    ret = nsize_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def nsize(
+    image_in: InputPathType,
+    image_out: str,
+    runner: Runner | None = None,
+) -> NsizeOutputs:
+    """
+    Zero pads an input image to the nearest larger NxN dimensions.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        image_in: Input image file.
+        image_out: Output padded image file.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `NsizeOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(NSIZE_METADATA)
+    params = nsize_params(
+        image_in=image_in,
+        image_out=image_out,
+    )
+    return nsize_execute(params, execution)
+
+
+__all__ = [
+    "NSIZE_METADATA",
+    "NsizeOutputs",
+    "NsizeParameters",
+    "nsize",
+    "nsize_params",
+]

niwrap_afni/afni/p2dsetstat.py

@@ -0,0 +1,216 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+P2DSETSTAT_METADATA = Metadata(
+    id="425596bb580582f82bf97f7e288cb9c38b721949.boutiques",
+    name="p2dsetstat",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+P2dsetstatParameters = typing.TypedDict('P2dsetstatParameters', {
+    "__STYX_TYPE__": typing.Literal["p2dsetstat"],
+    "dataset": str,
+    "pvalue": float,
+    "onesided": bool,
+    "quiet": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "p2dsetstat": p2dsetstat_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 {
+        "p2dsetstat": p2dsetstat_outputs,
+    }.get(t)
+
+
+class P2dsetstatOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `p2dsetstat(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    stat_value: OutputPathType
+    """The converted statistic value."""
+
+
+def p2dsetstat_params(
+    dataset: str,
+    pvalue: float,
+    onesided: bool = False,
+    quiet: bool = False,
+) -> P2dsetstatParameters:
+    """
+    Build parameters.
+    
+    Args:
+        dataset: Specify a dataset DDD and, if it has multiple sub-bricks, the\
+            [i]th subbrick with the statistic of interest MUST be selected\
+            explicitly; note the use of quotation marks around the brick selector\
+            (because of the square-brackets). 'i' can be either a number or a\
+            string label selector.
+        pvalue: Input p-value P, which MUST be in the interval [0,1].
+        onesided: One-sided test.
+        quiet: Output only the final statistic value.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "p2dsetstat",
+        "dataset": dataset,
+        "pvalue": pvalue,
+        "onesided": onesided,
+        "quiet": quiet,
+    }
+    return params
+
+
+def p2dsetstat_cargs(
+    params: P2dsetstatParameters,
+    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("p2dsetstat")
+    cargs.extend([
+        "-inset",
+        params.get("dataset")
+    ])
+    cargs.extend([
+        "-pval",
+        str(params.get("pvalue"))
+    ])
+    if params.get("onesided"):
+        cargs.append("-1sided")
+    if params.get("quiet"):
+        cargs.append("-quiet")
+    return cargs
+
+
+def p2dsetstat_outputs(
+    params: P2dsetstatParameters,
+    execution: Execution,
+) -> P2dsetstatOutputs:
+    """
+    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 = P2dsetstatOutputs(
+        root=execution.output_file("."),
+        stat_value=execution.output_file("stdout"),
+    )
+    return ret
+
+
+def p2dsetstat_execute(
+    params: P2dsetstatParameters,
+    execution: Execution,
+) -> P2dsetstatOutputs:
+    """
+    Convert a p-value to a statistic of choice with reference to a specific dataset.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `P2dsetstatOutputs`).
+    """
+    params = execution.params(params)
+    cargs = p2dsetstat_cargs(params, execution)
+    ret = p2dsetstat_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def p2dsetstat(
+    dataset: str,
+    pvalue: float,
+    onesided: bool = False,
+    quiet: bool = False,
+    runner: Runner | None = None,
+) -> P2dsetstatOutputs:
+    """
+    Convert a p-value to a statistic of choice with reference to a specific dataset.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        dataset: Specify a dataset DDD and, if it has multiple sub-bricks, the\
+            [i]th subbrick with the statistic of interest MUST be selected\
+            explicitly; note the use of quotation marks around the brick selector\
+            (because of the square-brackets). 'i' can be either a number or a\
+            string label selector.
+        pvalue: Input p-value P, which MUST be in the interval [0,1].
+        onesided: One-sided test.
+        quiet: Output only the final statistic value.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `P2dsetstatOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(P2DSETSTAT_METADATA)
+    params = p2dsetstat_params(
+        dataset=dataset,
+        pvalue=pvalue,
+        onesided=onesided,
+        quiet=quiet,
+    )
+    return p2dsetstat_execute(params, execution)
+
+
+__all__ = [
+    "P2DSETSTAT_METADATA",
+    "P2dsetstatOutputs",
+    "P2dsetstatParameters",
+    "p2dsetstat",
+    "p2dsetstat_params",
+]