niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/v_3d_extract_group_in_corr.py

@@ -0,0 +1,195 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3D_EXTRACT_GROUP_IN_CORR_METADATA = Metadata(
+    id="589ed658ff74e91ed944c55e458a7888b478c333.boutiques",
+    name="3dExtractGroupInCorr",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dExtractGroupInCorrParameters = typing.TypedDict('V3dExtractGroupInCorrParameters', {
+    "__STYX_TYPE__": typing.Literal["3dExtractGroupInCorr"],
+    "group_in_corr_file": InputPathType,
+    "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 {
+        "3dExtractGroupInCorr": v_3d_extract_group_in_corr_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 {
+        "3dExtractGroupInCorr": v_3d_extract_group_in_corr_outputs,
+    }.get(t)
+
+
+class V3dExtractGroupInCorrOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_extract_group_in_corr(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_dataset: OutputPathType | None
+    """Output dataset reconstructed from GroupInCorr data"""
+
+
+def v_3d_extract_group_in_corr_params(
+    group_in_corr_file: InputPathType,
+    prefix: str | None = None,
+) -> V3dExtractGroupInCorrParameters:
+    """
+    Build parameters.
+    
+    Args:
+        group_in_corr_file: GroupInCorr file to extract datasets from (e.g.\
+            AAA.grpincorr.niml).
+        prefix: Prefix to prepend to dataset labels. Use 'NULL' to skip the use\
+            of the prefix.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dExtractGroupInCorr",
+        "group_in_corr_file": group_in_corr_file,
+    }
+    if prefix is not None:
+        params["prefix"] = prefix
+    return params
+
+
+def v_3d_extract_group_in_corr_cargs(
+    params: V3dExtractGroupInCorrParameters,
+    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("3dExtractGroupInCorr")
+    cargs.append(execution.input_file(params.get("group_in_corr_file")))
+    if params.get("prefix") is not None:
+        cargs.extend([
+            "-prefix",
+            params.get("prefix")
+        ])
+    return cargs
+
+
+def v_3d_extract_group_in_corr_outputs(
+    params: V3dExtractGroupInCorrParameters,
+    execution: Execution,
+) -> V3dExtractGroupInCorrOutputs:
+    """
+    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 = V3dExtractGroupInCorrOutputs(
+        root=execution.output_file("."),
+        output_dataset=execution.output_file(params.get("prefix") + "_[DATASET_LABEL].nii") if (params.get("prefix") is not None) else None,
+    )
+    return ret
+
+
+def v_3d_extract_group_in_corr_execute(
+    params: V3dExtractGroupInCorrParameters,
+    execution: Execution,
+) -> V3dExtractGroupInCorrOutputs:
+    """
+    This program breaks the collection of images from a GroupInCorr file back into
+    individual AFNI 3D+time datasets.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dExtractGroupInCorrOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_extract_group_in_corr_cargs(params, execution)
+    ret = v_3d_extract_group_in_corr_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_extract_group_in_corr(
+    group_in_corr_file: InputPathType,
+    prefix: str | None = None,
+    runner: Runner | None = None,
+) -> V3dExtractGroupInCorrOutputs:
+    """
+    This program breaks the collection of images from a GroupInCorr file back into
+    individual AFNI 3D+time datasets.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        group_in_corr_file: GroupInCorr file to extract datasets from (e.g.\
+            AAA.grpincorr.niml).
+        prefix: Prefix to prepend to dataset labels. Use 'NULL' to skip the use\
+            of the prefix.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dExtractGroupInCorrOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_EXTRACT_GROUP_IN_CORR_METADATA)
+    params = v_3d_extract_group_in_corr_params(
+        group_in_corr_file=group_in_corr_file,
+        prefix=prefix,
+    )
+    return v_3d_extract_group_in_corr_execute(params, execution)
+
+
+__all__ = [
+    "V3dExtractGroupInCorrOutputs",
+    "V3dExtractGroupInCorrParameters",
+    "V_3D_EXTRACT_GROUP_IN_CORR_METADATA",
+    "v_3d_extract_group_in_corr",
+    "v_3d_extract_group_in_corr_params",
+]

niwrap_afni/afni/v_3d_extrema.py

@@ -0,0 +1,384 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3D_EXTREMA_METADATA = Metadata(
+    id="0736722868d4ce1e7b5960344c49f43b0a9e4e86.boutiques",
+    name="3dExtrema",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dExtremaParameters = typing.TypedDict('V3dExtremaParameters', {
+    "__STYX_TYPE__": typing.Literal["3dExtrema"],
+    "input_dataset": InputPathType,
+    "output_prefix": typing.NotRequired[str | None],
+    "output_session": typing.NotRequired[str | None],
+    "quiet": bool,
+    "mask_file": typing.NotRequired[InputPathType | None],
+    "mask_threshold": typing.NotRequired[float | None],
+    "data_threshold": typing.NotRequired[float | None],
+    "n_best": typing.NotRequired[float | None],
+    "separation_distance": typing.NotRequired[float | None],
+    "minima": bool,
+    "maxima": bool,
+    "strict": bool,
+    "partial": bool,
+    "interior": bool,
+    "closure": bool,
+    "slice": bool,
+    "volume": bool,
+    "remove": bool,
+    "average": bool,
+    "weight": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "3dExtrema": v_3d_extrema_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 {
+        "3dExtrema": v_3d_extrema_outputs,
+    }.get(t)
+
+
+class V3dExtremaOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_extrema(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_head_file: OutputPathType | None
+    """Output HEAD file"""
+    output_brik_file: OutputPathType | None
+    """Output BRIK file"""
+
+
+def v_3d_extrema_params(
+    input_dataset: InputPathType,
+    output_prefix: str | None = None,
+    output_session: str | None = None,
+    quiet: bool = False,
+    mask_file: InputPathType | None = None,
+    mask_threshold: float | None = None,
+    data_threshold: float | None = None,
+    n_best: float | None = None,
+    separation_distance: float | None = None,
+    minima: bool = False,
+    maxima: bool = False,
+    strict: bool = False,
+    partial: bool = False,
+    interior: bool = False,
+    closure: bool = False,
+    slice_: bool = False,
+    volume: bool = False,
+    remove: bool = False,
+    average: bool = False,
+    weight: bool = False,
+) -> V3dExtremaParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_dataset: Input dataset (e.g. dataset+tlrc'[sub-brick]').
+        output_prefix: Prefix for the output dataset name.
+        output_session: Directory for the output dataset session.
+        quiet: Suppress screen output.
+        mask_file: Mask statistic from file.
+        mask_threshold: Only voxels whose mask statistic is >= m in absolute\
+            value will be considered.
+        data_threshold: Only voxels whose value (intensity) is greater than d\
+            in absolute value will be considered.
+        n_best: Only print the first N extrema.
+        separation_distance: Minimum separation distance (in mm) for distinct\
+            extrema.
+        minima: Find local minima.
+        maxima: Find local maxima (default).
+        strict: Use strict inequality for extrema (default).
+        partial: Use partial inequality for extrema.
+        interior: Extrema must be interior points (default).
+        closure: Extrema may be boundary points.
+        slice_: Consider each slice separately (default).
+        volume: Consider the volume as a whole.
+        remove: Remove all but strongest of neighboring extrema (default).
+        average: Replace neighboring extrema by average.
+        weight: Replace neighboring extrema by weighted average.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dExtrema",
+        "input_dataset": input_dataset,
+        "quiet": quiet,
+        "minima": minima,
+        "maxima": maxima,
+        "strict": strict,
+        "partial": partial,
+        "interior": interior,
+        "closure": closure,
+        "slice": slice_,
+        "volume": volume,
+        "remove": remove,
+        "average": average,
+        "weight": weight,
+    }
+    if output_prefix is not None:
+        params["output_prefix"] = output_prefix
+    if output_session is not None:
+        params["output_session"] = output_session
+    if mask_file is not None:
+        params["mask_file"] = mask_file
+    if mask_threshold is not None:
+        params["mask_threshold"] = mask_threshold
+    if data_threshold is not None:
+        params["data_threshold"] = data_threshold
+    if n_best is not None:
+        params["n_best"] = n_best
+    if separation_distance is not None:
+        params["separation_distance"] = separation_distance
+    return params
+
+
+def v_3d_extrema_cargs(
+    params: V3dExtremaParameters,
+    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("3dExtrema")
+    cargs.append(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("output_session") is not None:
+        cargs.extend([
+            "-session",
+            params.get("output_session")
+        ])
+    if params.get("quiet"):
+        cargs.append("-quiet")
+    if params.get("mask_file") is not None:
+        cargs.extend([
+            "-mask_file",
+            execution.input_file(params.get("mask_file"))
+        ])
+    if params.get("mask_threshold") is not None:
+        cargs.extend([
+            "-mask_thr",
+            str(params.get("mask_threshold"))
+        ])
+    if params.get("data_threshold") is not None:
+        cargs.extend([
+            "-data_thr",
+            str(params.get("data_threshold"))
+        ])
+    if params.get("n_best") is not None:
+        cargs.extend([
+            "-nbest",
+            str(params.get("n_best"))
+        ])
+    if params.get("separation_distance") is not None:
+        cargs.extend([
+            "-sep_dist",
+            str(params.get("separation_distance"))
+        ])
+    if params.get("minima"):
+        cargs.append("-minima")
+    if params.get("maxima"):
+        cargs.append("-maxima")
+    if params.get("strict"):
+        cargs.append("-strict")
+    if params.get("partial"):
+        cargs.append("-partial")
+    if params.get("interior"):
+        cargs.append("-interior")
+    if params.get("closure"):
+        cargs.append("-closure")
+    if params.get("slice"):
+        cargs.append("-slice")
+    if params.get("volume"):
+        cargs.append("-volume")
+    if params.get("remove"):
+        cargs.append("-remove")
+    if params.get("average"):
+        cargs.append("-average")
+    if params.get("weight"):
+        cargs.append("-weight")
+    return cargs
+
+
+def v_3d_extrema_outputs(
+    params: V3dExtremaParameters,
+    execution: Execution,
+) -> V3dExtremaOutputs:
+    """
+    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 = V3dExtremaOutputs(
+        root=execution.output_file("."),
+        output_head_file=execution.output_file(params.get("output_prefix") + ".HEAD") if (params.get("output_prefix") is not None) else None,
+        output_brik_file=execution.output_file(params.get("output_prefix") + ".BRIK") if (params.get("output_prefix") is not None) else None,
+    )
+    return ret
+
+
+def v_3d_extrema_execute(
+    params: V3dExtremaParameters,
+    execution: Execution,
+) -> V3dExtremaOutputs:
+    """
+    Find local extrema (minima or maxima) in 3D datasets.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dExtremaOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_extrema_cargs(params, execution)
+    ret = v_3d_extrema_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_extrema(
+    input_dataset: InputPathType,
+    output_prefix: str | None = None,
+    output_session: str | None = None,
+    quiet: bool = False,
+    mask_file: InputPathType | None = None,
+    mask_threshold: float | None = None,
+    data_threshold: float | None = None,
+    n_best: float | None = None,
+    separation_distance: float | None = None,
+    minima: bool = False,
+    maxima: bool = False,
+    strict: bool = False,
+    partial: bool = False,
+    interior: bool = False,
+    closure: bool = False,
+    slice_: bool = False,
+    volume: bool = False,
+    remove: bool = False,
+    average: bool = False,
+    weight: bool = False,
+    runner: Runner | None = None,
+) -> V3dExtremaOutputs:
+    """
+    Find local extrema (minima or maxima) in 3D datasets.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        input_dataset: Input dataset (e.g. dataset+tlrc'[sub-brick]').
+        output_prefix: Prefix for the output dataset name.
+        output_session: Directory for the output dataset session.
+        quiet: Suppress screen output.
+        mask_file: Mask statistic from file.
+        mask_threshold: Only voxels whose mask statistic is >= m in absolute\
+            value will be considered.
+        data_threshold: Only voxels whose value (intensity) is greater than d\
+            in absolute value will be considered.
+        n_best: Only print the first N extrema.
+        separation_distance: Minimum separation distance (in mm) for distinct\
+            extrema.
+        minima: Find local minima.
+        maxima: Find local maxima (default).
+        strict: Use strict inequality for extrema (default).
+        partial: Use partial inequality for extrema.
+        interior: Extrema must be interior points (default).
+        closure: Extrema may be boundary points.
+        slice_: Consider each slice separately (default).
+        volume: Consider the volume as a whole.
+        remove: Remove all but strongest of neighboring extrema (default).
+        average: Replace neighboring extrema by average.
+        weight: Replace neighboring extrema by weighted average.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dExtremaOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_EXTREMA_METADATA)
+    params = v_3d_extrema_params(
+        input_dataset=input_dataset,
+        output_prefix=output_prefix,
+        output_session=output_session,
+        quiet=quiet,
+        mask_file=mask_file,
+        mask_threshold=mask_threshold,
+        data_threshold=data_threshold,
+        n_best=n_best,
+        separation_distance=separation_distance,
+        minima=minima,
+        maxima=maxima,
+        strict=strict,
+        partial=partial,
+        interior=interior,
+        closure=closure,
+        slice_=slice_,
+        volume=volume,
+        remove=remove,
+        average=average,
+        weight=weight,
+    )
+    return v_3d_extrema_execute(params, execution)
+
+
+__all__ = [
+    "V3dExtremaOutputs",
+    "V3dExtremaParameters",
+    "V_3D_EXTREMA_METADATA",
+    "v_3d_extrema",
+    "v_3d_extrema_params",
+]