niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/dsetstat2p.py

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+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+DSETSTAT2P_METADATA = Metadata(
+    id="b07011bb5bdd8084543d33f9a06e2ddf0d7fd9f2.boutiques",
+    name="dsetstat2p",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+Dsetstat2pParameters = typing.TypedDict('Dsetstat2pParameters', {
+    "__STYX_TYPE__": typing.Literal["dsetstat2p"],
+    "dataset": str,
+    "statval": float,
+    "one_sided": 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 {
+        "dsetstat2p": dsetstat2p_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 {
+        "dsetstat2p": dsetstat2p_outputs,
+    }.get(t)
+
+
+class Dsetstat2pOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `dsetstat2p(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_file: OutputPathType
+    """Output p-value or stat value"""
+
+
+def dsetstat2p_params(
+    dataset: str,
+    statval: float,
+    one_sided: bool = False,
+    quiet: bool = False,
+) -> Dsetstat2pParameters:
+    """
+    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). Note that 'i' can be either a number\
+            of a string label selector.
+        statval: Input stat-value S, which MUST be in the interval [0,\
+            infinity).
+        one_sided: Choose one-sided or bi-sided/two-sided testing.
+        quiet: An optional flag so that output ONLY the final statistic value\
+            output to standard output; this can be then be viewed, redirected to a\
+            text file or saved as a shell variable. (Default: display supplementary\
+            text.).
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "dsetstat2p",
+        "dataset": dataset,
+        "statval": statval,
+        "one_sided": one_sided,
+        "quiet": quiet,
+    }
+    return params
+
+
+def dsetstat2p_cargs(
+    params: Dsetstat2pParameters,
+    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("dsetstat2p")
+    cargs.append(params.get("dataset"))
+    cargs.append(str(params.get("statval")))
+    if params.get("one_sided"):
+        cargs.append("-1sided")
+    if params.get("quiet"):
+        cargs.append("-quiet")
+    return cargs
+
+
+def dsetstat2p_outputs(
+    params: Dsetstat2pParameters,
+    execution: Execution,
+) -> Dsetstat2pOutputs:
+    """
+    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 = Dsetstat2pOutputs(
+        root=execution.output_file("."),
+        output_file=execution.output_file("output.txt"),
+    )
+    return ret
+
+
+def dsetstat2p_execute(
+    params: Dsetstat2pParameters,
+    execution: Execution,
+) -> Dsetstat2pOutputs:
+    """
+    Converts a statistic to a p-value with reference to a particular dataset.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `Dsetstat2pOutputs`).
+    """
+    params = execution.params(params)
+    cargs = dsetstat2p_cargs(params, execution)
+    ret = dsetstat2p_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def dsetstat2p(
+    dataset: str,
+    statval: float,
+    one_sided: bool = False,
+    quiet: bool = False,
+    runner: Runner | None = None,
+) -> Dsetstat2pOutputs:
+    """
+    Converts a statistic to a p-value with reference to a particular 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). Note that 'i' can be either a number\
+            of a string label selector.
+        statval: Input stat-value S, which MUST be in the interval [0,\
+            infinity).
+        one_sided: Choose one-sided or bi-sided/two-sided testing.
+        quiet: An optional flag so that output ONLY the final statistic value\
+            output to standard output; this can be then be viewed, redirected to a\
+            text file or saved as a shell variable. (Default: display supplementary\
+            text.).
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `Dsetstat2pOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(DSETSTAT2P_METADATA)
+    params = dsetstat2p_params(
+        dataset=dataset,
+        statval=statval,
+        one_sided=one_sided,
+        quiet=quiet,
+    )
+    return dsetstat2p_execute(params, execution)
+
+
+__all__ = [
+    "DSETSTAT2P_METADATA",
+    "Dsetstat2pOutputs",
+    "Dsetstat2pParameters",
+    "dsetstat2p",
+    "dsetstat2p_params",
+]

niwrap_afni/afni/dtistudio_fiberto_segments.py

@@ -0,0 +1,198 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+DTISTUDIO_FIBERTO_SEGMENTS_METADATA = Metadata(
+    id="3f18eb1cd61025f3b6f243c49c95ab75c9ad86a9.boutiques",
+    name="DTIStudioFibertoSegments",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+DtistudioFibertoSegmentsParameters = typing.TypedDict('DtistudioFibertoSegmentsParameters', {
+    "__STYX_TYPE__": typing.Literal["DTIStudioFibertoSegments"],
+    "dataset": InputPathType,
+    "output_file": typing.NotRequired[str | None],
+    "swap_flag": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "DTIStudioFibertoSegments": dtistudio_fiberto_segments_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 {
+        "DTIStudioFibertoSegments": dtistudio_fiberto_segments_outputs,
+    }.get(t)
+
+
+class DtistudioFibertoSegmentsOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `dtistudio_fiberto_segments(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_segment_file: OutputPathType | None
+    """Output SUMA segment file"""
+
+
+def dtistudio_fiberto_segments_params(
+    dataset: InputPathType,
+    output_file: str | None = None,
+    swap_flag: bool = False,
+) -> DtistudioFibertoSegmentsParameters:
+    """
+    Build parameters.
+    
+    Args:
+        dataset: Input dataset file.
+        output_file: Name of the output file (default is rawxyzseg.dat).
+        swap_flag: Swap bytes in data.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "DTIStudioFibertoSegments",
+        "dataset": dataset,
+        "swap_flag": swap_flag,
+    }
+    if output_file is not None:
+        params["output_file"] = output_file
+    return params
+
+
+def dtistudio_fiberto_segments_cargs(
+    params: DtistudioFibertoSegmentsParameters,
+    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("DTIStudioFibertoSegments")
+    cargs.append(execution.input_file(params.get("dataset")))
+    if params.get("output_file") is not None:
+        cargs.extend([
+            "-output",
+            params.get("output_file")
+        ])
+    if params.get("swap_flag"):
+        cargs.append("-swap")
+    return cargs
+
+
+def dtistudio_fiberto_segments_outputs(
+    params: DtistudioFibertoSegmentsParameters,
+    execution: Execution,
+) -> DtistudioFibertoSegmentsOutputs:
+    """
+    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 = DtistudioFibertoSegmentsOutputs(
+        root=execution.output_file("."),
+        output_segment_file=execution.output_file(params.get("output_file")) if (params.get("output_file") is not None) else None,
+    )
+    return ret
+
+
+def dtistudio_fiberto_segments_execute(
+    params: DtistudioFibertoSegmentsParameters,
+    execution: Execution,
+) -> DtistudioFibertoSegmentsOutputs:
+    """
+    Convert a DTIStudio Fiber file to a SUMA segment file.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `DtistudioFibertoSegmentsOutputs`).
+    """
+    params = execution.params(params)
+    cargs = dtistudio_fiberto_segments_cargs(params, execution)
+    ret = dtistudio_fiberto_segments_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def dtistudio_fiberto_segments(
+    dataset: InputPathType,
+    output_file: str | None = None,
+    swap_flag: bool = False,
+    runner: Runner | None = None,
+) -> DtistudioFibertoSegmentsOutputs:
+    """
+    Convert a DTIStudio Fiber file to a SUMA segment file.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        dataset: Input dataset file.
+        output_file: Name of the output file (default is rawxyzseg.dat).
+        swap_flag: Swap bytes in data.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `DtistudioFibertoSegmentsOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(DTISTUDIO_FIBERTO_SEGMENTS_METADATA)
+    params = dtistudio_fiberto_segments_params(
+        dataset=dataset,
+        output_file=output_file,
+        swap_flag=swap_flag,
+    )
+    return dtistudio_fiberto_segments_execute(params, execution)
+
+
+__all__ = [
+    "DTISTUDIO_FIBERTO_SEGMENTS_METADATA",
+    "DtistudioFibertoSegmentsOutputs",
+    "DtistudioFibertoSegmentsParameters",
+    "dtistudio_fiberto_segments",
+    "dtistudio_fiberto_segments_params",
+]