niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/v_3d_tqual.py

@@ -0,0 +1,261 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3D_TQUAL_METADATA = Metadata(
+    id="a5953b420d22f8f6c2b20824e280582d44af991c.boutiques",
+    name="3dTqual",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dTqualParameters = typing.TypedDict('V3dTqualParameters', {
+    "__STYX_TYPE__": typing.Literal["3dTqual"],
+    "dataset": InputPathType,
+    "spearman": bool,
+    "quadrant": bool,
+    "autoclip": bool,
+    "automask": bool,
+    "clip": typing.NotRequired[float | None],
+    "mask": typing.NotRequired[InputPathType | None],
+    "range": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "3dTqual": v_3d_tqual_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 {
+        "3dTqual": v_3d_tqual_outputs,
+    }.get(t)
+
+
+class V3dTqualOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_tqual(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    time_series: OutputPathType
+    """The 1D time series with the quality index for each sub-brick"""
+
+
+def v_3d_tqual_params(
+    dataset: InputPathType,
+    spearman: bool = False,
+    quadrant: bool = False,
+    autoclip: bool = False,
+    automask: bool = False,
+    clip: float | None = None,
+    mask: InputPathType | None = None,
+    range_: bool = False,
+) -> V3dTqualParameters:
+    """
+    Build parameters.
+    
+    Args:
+        dataset: Input 3D+time dataset.
+        spearman: Quality index is 1 minus the Spearman (rank) correlation\
+            coefficient of each sub-brick with the median sub-brick (default\
+            method).
+        quadrant: Quality index is 1 minus the quadrant correlation coefficient\
+            as the quality index.
+        autoclip: Clip off low-intensity regions in the median sub-brick, only\
+            compute correlation between high-intensity voxels.
+        automask: Automatically mask and compute correlation only across\
+            high-intensity (presumably brain) voxels.
+        clip: Clip off values below given threshold in the median sub-brick.
+        mask: Compute correlation only across masked voxels from the given\
+            dataset.
+        range_: Print the median-3.5*MAD and median+3.5*MAD values with each\
+            quality index for plotting.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dTqual",
+        "dataset": dataset,
+        "spearman": spearman,
+        "quadrant": quadrant,
+        "autoclip": autoclip,
+        "automask": automask,
+        "range": range_,
+    }
+    if clip is not None:
+        params["clip"] = clip
+    if mask is not None:
+        params["mask"] = mask
+    return params
+
+
+def v_3d_tqual_cargs(
+    params: V3dTqualParameters,
+    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("3dTqual")
+    cargs.append(execution.input_file(params.get("dataset")))
+    if params.get("spearman"):
+        cargs.append("-spearman")
+    if params.get("quadrant"):
+        cargs.append("-quadrant")
+    if params.get("autoclip"):
+        cargs.append("-autoclip")
+    if params.get("automask"):
+        cargs.append("-automask")
+    if params.get("clip") is not None:
+        cargs.extend([
+            "-clip",
+            str(params.get("clip"))
+        ])
+    if params.get("mask") is not None:
+        cargs.extend([
+            "-mask",
+            execution.input_file(params.get("mask"))
+        ])
+    if params.get("range"):
+        cargs.append("-range")
+    return cargs
+
+
+def v_3d_tqual_outputs(
+    params: V3dTqualParameters,
+    execution: Execution,
+) -> V3dTqualOutputs:
+    """
+    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 = V3dTqualOutputs(
+        root=execution.output_file("."),
+        time_series=execution.output_file("stdout"),
+    )
+    return ret
+
+
+def v_3d_tqual_execute(
+    params: V3dTqualParameters,
+    execution: Execution,
+) -> V3dTqualOutputs:
+    """
+    Computes a quality index for each sub-brick in a 3D+time dataset.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dTqualOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_tqual_cargs(params, execution)
+    ret = v_3d_tqual_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_tqual(
+    dataset: InputPathType,
+    spearman: bool = False,
+    quadrant: bool = False,
+    autoclip: bool = False,
+    automask: bool = False,
+    clip: float | None = None,
+    mask: InputPathType | None = None,
+    range_: bool = False,
+    runner: Runner | None = None,
+) -> V3dTqualOutputs:
+    """
+    Computes a quality index for each sub-brick in a 3D+time dataset.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        dataset: Input 3D+time dataset.
+        spearman: Quality index is 1 minus the Spearman (rank) correlation\
+            coefficient of each sub-brick with the median sub-brick (default\
+            method).
+        quadrant: Quality index is 1 minus the quadrant correlation coefficient\
+            as the quality index.
+        autoclip: Clip off low-intensity regions in the median sub-brick, only\
+            compute correlation between high-intensity voxels.
+        automask: Automatically mask and compute correlation only across\
+            high-intensity (presumably brain) voxels.
+        clip: Clip off values below given threshold in the median sub-brick.
+        mask: Compute correlation only across masked voxels from the given\
+            dataset.
+        range_: Print the median-3.5*MAD and median+3.5*MAD values with each\
+            quality index for plotting.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dTqualOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_TQUAL_METADATA)
+    params = v_3d_tqual_params(
+        dataset=dataset,
+        spearman=spearman,
+        quadrant=quadrant,
+        autoclip=autoclip,
+        automask=automask,
+        clip=clip,
+        mask=mask,
+        range_=range_,
+    )
+    return v_3d_tqual_execute(params, execution)
+
+
+__all__ = [
+    "V3dTqualOutputs",
+    "V3dTqualParameters",
+    "V_3D_TQUAL_METADATA",
+    "v_3d_tqual",
+    "v_3d_tqual_params",
+]