niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/v_3d_toutcount.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 *
+
+V_3D_TOUTCOUNT_METADATA = Metadata(
+    id="b726a8742694b4a0acfdfd929608a00118e5b42b.boutiques",
+    name="3dToutcount",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dToutcountParameters = typing.TypedDict('V3dToutcountParameters', {
+    "__STYX_TYPE__": typing.Literal["3dToutcount"],
+    "input_dataset": str,
+    "output_prefix": typing.NotRequired[str | None],
+    "mask_dataset": typing.NotRequired[str | None],
+    "q_threshold": typing.NotRequired[float | None],
+    "autoclip": bool,
+    "automask": bool,
+    "fraction": bool,
+    "range": bool,
+    "polort_order": typing.NotRequired[float | None],
+    "legendre": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "3dToutcount": v_3d_toutcount_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 {
+        "3dToutcount": v_3d_toutcount_outputs,
+    }.get(t)
+
+
+class V3dToutcountOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_toutcount(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_afni_head: OutputPathType | None
+    """Output dataset in AFNI format (HEAD file)."""
+    output_afni_brik: OutputPathType | None
+    """Output dataset in AFNI format (BRIK file)."""
+
+
+def v_3d_toutcount_params(
+    input_dataset: str,
+    output_prefix: str | None = None,
+    mask_dataset: str | None = None,
+    q_threshold: float | None = None,
+    autoclip: bool = False,
+    automask: bool = False,
+    fraction: bool = False,
+    range_: bool = False,
+    polort_order: float | None = None,
+    legendre: bool = False,
+) -> V3dToutcountParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_dataset: Input 3D+time dataset (e.g. dataset+orig).
+        output_prefix: Prefix of the new dataset saved with the outlier Q\
+            values, applicable with the -save option.
+        mask_dataset: Only count voxels in the provided mask dataset.
+        q_threshold: Use 'q' instead of 0.001 in the calculation of alpha. Must\
+            be within range 0 < q < 1.
+        autoclip: Clip off 'small' voxels (as in 3dClipLevel). Cannot use with\
+            -mask.
+        automask: Automatically mask the dataset. Cannot use with -mask.
+        fraction: Output the fraction of (masked) voxels which are outliers at\
+            each time point, instead of the count.
+        range_: Print out median+3.5*MAD of outlier count with each time point.
+        polort_order: Detrend each voxel time series with polynomials of order\
+            'nn'. Default value is 0, which removes the median.
+        legendre: Use Legendre polynomials for detrending (also allows -polort\
+            > 3).
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dToutcount",
+        "input_dataset": input_dataset,
+        "autoclip": autoclip,
+        "automask": automask,
+        "fraction": fraction,
+        "range": range_,
+        "legendre": legendre,
+    }
+    if output_prefix is not None:
+        params["output_prefix"] = output_prefix
+    if mask_dataset is not None:
+        params["mask_dataset"] = mask_dataset
+    if q_threshold is not None:
+        params["q_threshold"] = q_threshold
+    if polort_order is not None:
+        params["polort_order"] = polort_order
+    return params
+
+
+def v_3d_toutcount_cargs(
+    params: V3dToutcountParameters,
+    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("3dToutcount")
+    cargs.append(params.get("input_dataset"))
+    if params.get("output_prefix") is not None:
+        cargs.append(params.get("output_prefix"))
+    if params.get("mask_dataset") is not None:
+        cargs.extend([
+            "-mask",
+            params.get("mask_dataset")
+        ])
+    if params.get("q_threshold") is not None:
+        cargs.extend([
+            "-qthr",
+            str(params.get("q_threshold"))
+        ])
+    if params.get("autoclip"):
+        cargs.append("-autoclip")
+    if params.get("automask"):
+        cargs.append("-automask")
+    if params.get("fraction"):
+        cargs.append("-fraction")
+    if params.get("range"):
+        cargs.append("-range")
+    if params.get("polort_order") is not None:
+        cargs.extend([
+            "-polort",
+            str(params.get("polort_order"))
+        ])
+    if params.get("legendre"):
+        cargs.append("-legendre")
+    return cargs
+
+
+def v_3d_toutcount_outputs(
+    params: V3dToutcountParameters,
+    execution: Execution,
+) -> V3dToutcountOutputs:
+    """
+    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 = V3dToutcountOutputs(
+        root=execution.output_file("."),
+        output_afni_head=execution.output_file(params.get("output_prefix") + ".HEAD") if (params.get("output_prefix") is not None) else None,
+        output_afni_brik=execution.output_file(params.get("output_prefix") + ".BRIK") if (params.get("output_prefix") is not None) else None,
+    )
+    return ret
+
+
+def v_3d_toutcount_execute(
+    params: V3dToutcountParameters,
+    execution: Execution,
+) -> V3dToutcountOutputs:
+    """
+    Calculates the number of 'outliers' in a 3D+time dataset at each time point.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dToutcountOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_toutcount_cargs(params, execution)
+    ret = v_3d_toutcount_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_toutcount(
+    input_dataset: str,
+    output_prefix: str | None = None,
+    mask_dataset: str | None = None,
+    q_threshold: float | None = None,
+    autoclip: bool = False,
+    automask: bool = False,
+    fraction: bool = False,
+    range_: bool = False,
+    polort_order: float | None = None,
+    legendre: bool = False,
+    runner: Runner | None = None,
+) -> V3dToutcountOutputs:
+    """
+    Calculates the number of 'outliers' in a 3D+time dataset at each time point.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        input_dataset: Input 3D+time dataset (e.g. dataset+orig).
+        output_prefix: Prefix of the new dataset saved with the outlier Q\
+            values, applicable with the -save option.
+        mask_dataset: Only count voxels in the provided mask dataset.
+        q_threshold: Use 'q' instead of 0.001 in the calculation of alpha. Must\
+            be within range 0 < q < 1.
+        autoclip: Clip off 'small' voxels (as in 3dClipLevel). Cannot use with\
+            -mask.
+        automask: Automatically mask the dataset. Cannot use with -mask.
+        fraction: Output the fraction of (masked) voxels which are outliers at\
+            each time point, instead of the count.
+        range_: Print out median+3.5*MAD of outlier count with each time point.
+        polort_order: Detrend each voxel time series with polynomials of order\
+            'nn'. Default value is 0, which removes the median.
+        legendre: Use Legendre polynomials for detrending (also allows -polort\
+            > 3).
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dToutcountOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_TOUTCOUNT_METADATA)
+    params = v_3d_toutcount_params(
+        input_dataset=input_dataset,
+        output_prefix=output_prefix,
+        mask_dataset=mask_dataset,
+        q_threshold=q_threshold,
+        autoclip=autoclip,
+        automask=automask,
+        fraction=fraction,
+        range_=range_,
+        polort_order=polort_order,
+        legendre=legendre,
+    )
+    return v_3d_toutcount_execute(params, execution)
+
+
+__all__ = [
+    "V3dToutcountOutputs",
+    "V3dToutcountParameters",
+    "V_3D_TOUTCOUNT_METADATA",
+    "v_3d_toutcount",
+    "v_3d_toutcount_params",
+]

niwrap_afni/afni/v_3d_toy_prog.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 *
+
+V_3D_TOY_PROG_METADATA = Metadata(
+    id="1311a81e171aae35dd519b54379bb3bfad692a46.boutiques",
+    name="3dToyProg",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dToyProgParameters = typing.TypedDict('V3dToyProgParameters', {
+    "__STYX_TYPE__": typing.Literal["3dToyProg"],
+    "input_dataset": InputPathType,
+    "output_prefix": typing.NotRequired[str | None],
+    "mask_dataset": typing.NotRequired[InputPathType | None],
+    "output_datum": typing.NotRequired[typing.Literal["float", "short"] | None],
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "3dToyProg": v_3d_toy_prog_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 V3dToyProgOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_toy_prog(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def v_3d_toy_prog_params(
+    input_dataset: InputPathType,
+    output_prefix: str | None = None,
+    mask_dataset: InputPathType | None = None,
+    output_datum: typing.Literal["float", "short"] | None = None,
+) -> V3dToyProgParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_dataset: Reference dataset.
+        output_prefix: Prefix of the output datasets.
+        mask_dataset: Restrict analysis to non-zero voxels in the mask dataset.
+        output_datum: Output datum type for one of the datasets. Choose from\
+            'float' or 'short'. Default is 'float'.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dToyProg",
+        "input_dataset": input_dataset,
+    }
+    if output_prefix is not None:
+        params["output_prefix"] = output_prefix
+    if mask_dataset is not None:
+        params["mask_dataset"] = mask_dataset
+    if output_datum is not None:
+        params["output_datum"] = output_datum
+    return params
+
+
+def v_3d_toy_prog_cargs(
+    params: V3dToyProgParameters,
+    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("3dToyProg")
+    cargs.extend([
+        "-input",
+        execution.input_file(params.get("input_dataset"))
+    ])
+    if params.get("output_prefix") is not None:
+        cargs.extend([
+            "-prefix",
+            params.get("output_prefix")
+        ])
+    if params.get("mask_dataset") is not None:
+        cargs.extend([
+            "-mask",
+            execution.input_file(params.get("mask_dataset"))
+        ])
+    if params.get("output_datum") is not None:
+        cargs.extend([
+            "-datum",
+            params.get("output_datum")
+        ])
+    return cargs
+
+
+def v_3d_toy_prog_outputs(
+    params: V3dToyProgParameters,
+    execution: Execution,
+) -> V3dToyProgOutputs:
+    """
+    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 = V3dToyProgOutputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def v_3d_toy_prog_execute(
+    params: V3dToyProgParameters,
+    execution: Execution,
+) -> V3dToyProgOutputs:
+    """
+    A program to illustrate dataset creation and manipulation in C using AFNI's API.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dToyProgOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_toy_prog_cargs(params, execution)
+    ret = v_3d_toy_prog_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_toy_prog(
+    input_dataset: InputPathType,
+    output_prefix: str | None = None,
+    mask_dataset: InputPathType | None = None,
+    output_datum: typing.Literal["float", "short"] | None = None,
+    runner: Runner | None = None,
+) -> V3dToyProgOutputs:
+    """
+    A program to illustrate dataset creation and manipulation in C using AFNI's API.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        input_dataset: Reference dataset.
+        output_prefix: Prefix of the output datasets.
+        mask_dataset: Restrict analysis to non-zero voxels in the mask dataset.
+        output_datum: Output datum type for one of the datasets. Choose from\
+            'float' or 'short'. Default is 'float'.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dToyProgOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_TOY_PROG_METADATA)
+    params = v_3d_toy_prog_params(
+        input_dataset=input_dataset,
+        output_prefix=output_prefix,
+        mask_dataset=mask_dataset,
+        output_datum=output_datum,
+    )
+    return v_3d_toy_prog_execute(params, execution)
+
+
+__all__ = [
+    "V3dToyProgOutputs",
+    "V3dToyProgParameters",
+    "V_3D_TOY_PROG_METADATA",
+    "v_3d_toy_prog",
+    "v_3d_toy_prog_params",
+]