niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/roi2dataset.py

@@ -0,0 +1,310 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+ROI2DATASET_METADATA = Metadata(
+    id="5ce644f007ce2ecc979c958450e6f9ce7de594be.boutiques",
+    name="ROI2dataset",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+Roi2datasetParameters = typing.TypedDict('Roi2datasetParameters', {
+    "__STYX_TYPE__": typing.Literal["ROI2dataset"],
+    "prefix": str,
+    "input_rois": list[InputPathType],
+    "keep_separate": bool,
+    "nodelist": typing.NotRequired[str | None],
+    "nodelist_nodups": typing.NotRequired[str | None],
+    "nodelist_with_roival": bool,
+    "label_dset": typing.NotRequired[str | None],
+    "output_format": typing.NotRequired[str | None],
+    "domain_parent_id": typing.NotRequired[str | None],
+    "pad_to_node": typing.NotRequired[float | None],
+    "pad_label": typing.NotRequired[float | None],
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "ROI2dataset": roi2dataset_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 Roi2datasetOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `roi2dataset(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def roi2dataset_params(
+    prefix: str,
+    input_rois: list[InputPathType],
+    keep_separate: bool = False,
+    nodelist: str | None = None,
+    nodelist_nodups: str | None = None,
+    nodelist_with_roival: bool = False,
+    label_dset: str | None = None,
+    output_format: str | None = None,
+    domain_parent_id: str | None = None,
+    pad_to_node: float | None = None,
+    pad_label: float | None = None,
+) -> Roi2datasetParameters:
+    """
+    Build parameters.
+    
+    Args:
+        prefix: Prefix of output dataset.
+        input_rois: ROI files to turn into a data set (space-separated list).\
+            This parameter MUST be the last one on command line.
+        keep_separate: Output one column (sub-brick) for each ROI value.
+        nodelist: Prefix for a set of .1D files that contain a list of node\
+            indices in the order they appear in an ROI.
+        nodelist_nodups: Prefix for a set of .1D files that contain a list of\
+            node indices in the order they appear in an ROI, with duplicate nodes\
+            removed.
+        nodelist_with_roival: Also add the ROI value as a second column in .1D\
+            files output by -nodelist.
+        label_dset: Write a label dataset instead of a simple dataset. Sets\
+            output format to NIML.
+        output_format: Output format of dataset. One of: ni_bi, ni_as, 1D.
+        domain_parent_id: Idcode of domain parent. Only ROIs with the same\
+            domain parent are included in the output.
+        pad_to_node: Output a full dataset from node 0 to node max_index (total\
+            of max_index + 1 nodes).
+        pad_label: Use padding_label (an integer) to label nodes not part of\
+            any ROI. Default is 0.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "ROI2dataset",
+        "prefix": prefix,
+        "input_rois": input_rois,
+        "keep_separate": keep_separate,
+        "nodelist_with_roival": nodelist_with_roival,
+    }
+    if nodelist is not None:
+        params["nodelist"] = nodelist
+    if nodelist_nodups is not None:
+        params["nodelist_nodups"] = nodelist_nodups
+    if label_dset is not None:
+        params["label_dset"] = label_dset
+    if output_format is not None:
+        params["output_format"] = output_format
+    if domain_parent_id is not None:
+        params["domain_parent_id"] = domain_parent_id
+    if pad_to_node is not None:
+        params["pad_to_node"] = pad_to_node
+    if pad_label is not None:
+        params["pad_label"] = pad_label
+    return params
+
+
+def roi2dataset_cargs(
+    params: Roi2datasetParameters,
+    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("ROI2dataset")
+    cargs.extend([
+        "-prefix",
+        params.get("prefix")
+    ])
+    cargs.extend([execution.input_file(f) for f in params.get("input_rois")])
+    if params.get("keep_separate"):
+        cargs.append("-keep_separate")
+    if params.get("nodelist") is not None:
+        cargs.extend([
+            "-nodelist",
+            params.get("nodelist")
+        ])
+    if params.get("nodelist_nodups") is not None:
+        cargs.extend([
+            "-nodelist.nodups",
+            params.get("nodelist_nodups")
+        ])
+    if params.get("nodelist_with_roival"):
+        cargs.append("-nodelist_with_ROIval")
+    if params.get("label_dset") is not None:
+        cargs.extend([
+            "-label_dset",
+            params.get("label_dset")
+        ])
+    if params.get("output_format") is not None:
+        cargs.extend([
+            "-of",
+            params.get("output_format")
+        ])
+    if params.get("domain_parent_id") is not None:
+        cargs.extend([
+            "-dom_par_id",
+            params.get("domain_parent_id")
+        ])
+    if params.get("pad_to_node") is not None:
+        cargs.extend([
+            "-pad_to_node",
+            str(params.get("pad_to_node"))
+        ])
+    if params.get("pad_label") is not None:
+        cargs.extend([
+            "-pad_label",
+            str(params.get("pad_label"))
+        ])
+    return cargs
+
+
+def roi2dataset_outputs(
+    params: Roi2datasetParameters,
+    execution: Execution,
+) -> Roi2datasetOutputs:
+    """
+    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 = Roi2datasetOutputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def roi2dataset_execute(
+    params: Roi2datasetParameters,
+    execution: Execution,
+) -> Roi2datasetOutputs:
+    """
+    Transforms a series of ROI files to a node dataset.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `Roi2datasetOutputs`).
+    """
+    params = execution.params(params)
+    cargs = roi2dataset_cargs(params, execution)
+    ret = roi2dataset_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def roi2dataset(
+    prefix: str,
+    input_rois: list[InputPathType],
+    keep_separate: bool = False,
+    nodelist: str | None = None,
+    nodelist_nodups: str | None = None,
+    nodelist_with_roival: bool = False,
+    label_dset: str | None = None,
+    output_format: str | None = None,
+    domain_parent_id: str | None = None,
+    pad_to_node: float | None = None,
+    pad_label: float | None = None,
+    runner: Runner | None = None,
+) -> Roi2datasetOutputs:
+    """
+    Transforms a series of ROI files to a node dataset.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        prefix: Prefix of output dataset.
+        input_rois: ROI files to turn into a data set (space-separated list).\
+            This parameter MUST be the last one on command line.
+        keep_separate: Output one column (sub-brick) for each ROI value.
+        nodelist: Prefix for a set of .1D files that contain a list of node\
+            indices in the order they appear in an ROI.
+        nodelist_nodups: Prefix for a set of .1D files that contain a list of\
+            node indices in the order they appear in an ROI, with duplicate nodes\
+            removed.
+        nodelist_with_roival: Also add the ROI value as a second column in .1D\
+            files output by -nodelist.
+        label_dset: Write a label dataset instead of a simple dataset. Sets\
+            output format to NIML.
+        output_format: Output format of dataset. One of: ni_bi, ni_as, 1D.
+        domain_parent_id: Idcode of domain parent. Only ROIs with the same\
+            domain parent are included in the output.
+        pad_to_node: Output a full dataset from node 0 to node max_index (total\
+            of max_index + 1 nodes).
+        pad_label: Use padding_label (an integer) to label nodes not part of\
+            any ROI. Default is 0.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `Roi2datasetOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(ROI2DATASET_METADATA)
+    params = roi2dataset_params(
+        prefix=prefix,
+        input_rois=input_rois,
+        keep_separate=keep_separate,
+        nodelist=nodelist,
+        nodelist_nodups=nodelist_nodups,
+        nodelist_with_roival=nodelist_with_roival,
+        label_dset=label_dset,
+        output_format=output_format,
+        domain_parent_id=domain_parent_id,
+        pad_to_node=pad_to_node,
+        pad_label=pad_label,
+    )
+    return roi2dataset_execute(params, execution)
+
+
+__all__ = [
+    "ROI2DATASET_METADATA",
+    "Roi2datasetOutputs",
+    "Roi2datasetParameters",
+    "roi2dataset",
+    "roi2dataset_params",
+]

niwrap_afni/afni/roigrow.py

@@ -0,0 +1,276 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+ROIGROW_METADATA = Metadata(
+    id="12bb44f9721e85ea23d86fcfc727735d33f56b50.boutiques",
+    name="ROIgrow",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+RoigrowParameters = typing.TypedDict('RoigrowParameters', {
+    "__STYX_TYPE__": typing.Literal["ROIgrow"],
+    "input_surface": str,
+    "roi_labels": str,
+    "lim_distance": float,
+    "output_prefix": typing.NotRequired[str | None],
+    "full_list": bool,
+    "grow_from_edge": bool,
+    "insphere_diameter": typing.NotRequired[float | None],
+    "inbox_edges": typing.NotRequired[list[float] | None],
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "ROIgrow": roigrow_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 {
+        "ROIgrow": roigrow_outputs,
+    }.get(t)
+
+
+class RoigrowOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `roigrow(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_file: OutputPathType | None
+    """1D output dataset."""
+
+
+def roigrow_params(
+    input_surface: str,
+    roi_labels: str,
+    lim_distance: float,
+    output_prefix: str | None = None,
+    full_list: bool = False,
+    grow_from_edge: bool = False,
+    insphere_diameter: float | None = None,
+    inbox_edges: list[float] | None = None,
+) -> RoigrowParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_surface: Specify input surface. You can also use -t* and -spec\
+            and -surf methods to input surfaces.
+        roi_labels: Data column containing integer labels of ROIs. Each integer\
+            label gets grown separately.
+        lim_distance: Distance to cover from each node. The units of LIM are\
+            those of the surface's node coordinates. Distances are calculated along\
+            the surface's mesh.
+        output_prefix: Prefix of 1D output dataset. Default is ROIgrow.
+        full_list: Output a row for each node on the surface. Nodes not in the\
+            grown ROI, receive a 0 for a label. This option is ONLY for use with\
+            -roi_labels.
+        grow_from_edge: Grow ROIs from their edges rather than the brute force\
+            default. This might make the program faster on large ROIs and large\
+            surfaces.
+        insphere_diameter: Diameter of the sphere inside which nodes are added\
+            instead of growing along the surface.
+        inbox_edges: Use a box of edge widths E1, E2, E3 instead of DIA.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "ROIgrow",
+        "input_surface": input_surface,
+        "roi_labels": roi_labels,
+        "lim_distance": lim_distance,
+        "full_list": full_list,
+        "grow_from_edge": grow_from_edge,
+    }
+    if output_prefix is not None:
+        params["output_prefix"] = output_prefix
+    if insphere_diameter is not None:
+        params["insphere_diameter"] = insphere_diameter
+    if inbox_edges is not None:
+        params["inbox_edges"] = inbox_edges
+    return params
+
+
+def roigrow_cargs(
+    params: RoigrowParameters,
+    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("ROIgrow")
+    cargs.extend([
+        "-i_TYPE",
+        params.get("input_surface")
+    ])
+    cargs.extend([
+        "-roi_labels",
+        params.get("roi_labels")
+    ])
+    cargs.extend([
+        "-lim",
+        str(params.get("lim_distance"))
+    ])
+    if params.get("output_prefix") is not None:
+        cargs.extend([
+            "-prefix",
+            params.get("output_prefix")
+        ])
+    if params.get("full_list"):
+        cargs.append("-full_list")
+    if params.get("grow_from_edge"):
+        cargs.append("-grow_from_edge")
+    if params.get("insphere_diameter") is not None:
+        cargs.extend([
+            "-insphere",
+            str(params.get("insphere_diameter"))
+        ])
+    if params.get("inbox_edges") is not None:
+        cargs.extend([
+            "-inbox",
+            *map(str, params.get("inbox_edges"))
+        ])
+    return cargs
+
+
+def roigrow_outputs(
+    params: RoigrowParameters,
+    execution: Execution,
+) -> RoigrowOutputs:
+    """
+    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 = RoigrowOutputs(
+        root=execution.output_file("."),
+        output_file=execution.output_file(params.get("output_prefix") + ".1D") if (params.get("output_prefix") is not None) else None,
+    )
+    return ret
+
+
+def roigrow_execute(
+    params: RoigrowParameters,
+    execution: Execution,
+) -> RoigrowOutputs:
+    """
+    A program to expand an ROI on the surface.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `RoigrowOutputs`).
+    """
+    params = execution.params(params)
+    cargs = roigrow_cargs(params, execution)
+    ret = roigrow_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def roigrow(
+    input_surface: str,
+    roi_labels: str,
+    lim_distance: float,
+    output_prefix: str | None = None,
+    full_list: bool = False,
+    grow_from_edge: bool = False,
+    insphere_diameter: float | None = None,
+    inbox_edges: list[float] | None = None,
+    runner: Runner | None = None,
+) -> RoigrowOutputs:
+    """
+    A program to expand an ROI on the surface.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        input_surface: Specify input surface. You can also use -t* and -spec\
+            and -surf methods to input surfaces.
+        roi_labels: Data column containing integer labels of ROIs. Each integer\
+            label gets grown separately.
+        lim_distance: Distance to cover from each node. The units of LIM are\
+            those of the surface's node coordinates. Distances are calculated along\
+            the surface's mesh.
+        output_prefix: Prefix of 1D output dataset. Default is ROIgrow.
+        full_list: Output a row for each node on the surface. Nodes not in the\
+            grown ROI, receive a 0 for a label. This option is ONLY for use with\
+            -roi_labels.
+        grow_from_edge: Grow ROIs from their edges rather than the brute force\
+            default. This might make the program faster on large ROIs and large\
+            surfaces.
+        insphere_diameter: Diameter of the sphere inside which nodes are added\
+            instead of growing along the surface.
+        inbox_edges: Use a box of edge widths E1, E2, E3 instead of DIA.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `RoigrowOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(ROIGROW_METADATA)
+    params = roigrow_params(
+        input_surface=input_surface,
+        roi_labels=roi_labels,
+        lim_distance=lim_distance,
+        output_prefix=output_prefix,
+        full_list=full_list,
+        grow_from_edge=grow_from_edge,
+        insphere_diameter=insphere_diameter,
+        inbox_edges=inbox_edges,
+    )
+    return roigrow_execute(params, execution)
+
+
+__all__ = [
+    "ROIGROW_METADATA",
+    "RoigrowOutputs",
+    "RoigrowParameters",
+    "roigrow",
+    "roigrow_params",
+]