niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/convert_dset.py

@@ -0,0 +1,421 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+CONVERT_DSET_METADATA = Metadata(
+    id="844cbaec7e78b76addf8794c6d75de087e117e30.boutiques",
+    name="ConvertDset",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+ConvertDsetParameters = typing.TypedDict('ConvertDsetParameters', {
+    "__STYX_TYPE__": typing.Literal["ConvertDset"],
+    "output_type": list[typing.Literal["niml_asc", "niml_bi", "1D", "1Dp", "1Dpt", "gii", "gii_asc", "gii_b64", "gii_b64gz", "1D_stderr", "1D_stdout", "niml_stderr", "niml_stdout", "1Dp_stdout", "1Dp_stderr", "1Dpt_stdout", "1Dpt_stderr"]],
+    "input_dataset": InputPathType,
+    "input_type": typing.NotRequired[typing.Literal["niml", "1D", "dx"] | None],
+    "output_prefix": typing.NotRequired[str | None],
+    "dset_labels": typing.NotRequired[str | None],
+    "add_node_index": bool,
+    "node_index_file": typing.NotRequired[InputPathType | None],
+    "node_select_file": typing.NotRequired[InputPathType | None],
+    "prepend_node_index": bool,
+    "pad_to_node": typing.NotRequired[str | None],
+    "labelize": typing.NotRequired[InputPathType | None],
+    "graphize": bool,
+    "graph_nodelist": typing.NotRequired[str | None],
+    "graph_full_nodelist": typing.NotRequired[InputPathType | None],
+    "graph_named_nodelist": typing.NotRequired[str | None],
+    "graph_xyz_lpi": bool,
+    "graph_edgelist": typing.NotRequired[InputPathType | None],
+    "onegraph": bool,
+    "multigraph": bool,
+    "split": typing.NotRequired[int | None],
+    "no_history": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "ConvertDset": convert_dset_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 {
+        "ConvertDset": convert_dset_outputs,
+    }.get(t)
+
+
+class ConvertDsetOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `convert_dset(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    converted_dataset: OutputPathType | None
+    """Converted dataset output"""
+
+
+def convert_dset_params(
+    output_type: list[typing.Literal["niml_asc", "niml_bi", "1D", "1Dp", "1Dpt", "gii", "gii_asc", "gii_b64", "gii_b64gz", "1D_stderr", "1D_stdout", "niml_stderr", "niml_stdout", "1Dp_stdout", "1Dp_stderr", "1Dpt_stdout", "1Dpt_stderr"]],
+    input_dataset: InputPathType,
+    input_type: typing.Literal["niml", "1D", "dx"] | None = None,
+    output_prefix: str | None = None,
+    dset_labels: str | None = None,
+    add_node_index: bool = False,
+    node_index_file: InputPathType | None = None,
+    node_select_file: InputPathType | None = None,
+    prepend_node_index: bool = False,
+    pad_to_node: str | None = None,
+    labelize: InputPathType | None = None,
+    graphize: bool = False,
+    graph_nodelist: str | None = None,
+    graph_full_nodelist: InputPathType | None = None,
+    graph_named_nodelist: str | None = None,
+    graph_xyz_lpi: bool = False,
+    graph_edgelist: InputPathType | None = None,
+    onegraph: bool = False,
+    multigraph: bool = False,
+    split: int | None = None,
+    no_history: bool = False,
+) -> ConvertDsetParameters:
+    """
+    Build parameters.
+    
+    Args:
+        output_type: Type of output datasets.
+        input_dataset: Input dataset to be converted.
+        input_type: Type of input datasets.
+        output_prefix: Output prefix for dataset.
+        dset_labels: Label the columns (sub-bricks) of the output dataset.
+        add_node_index: Add a node index element if one does not exist in the\
+            input dataset.
+        node_index_file: File containing node indices.
+        node_select_file: File specifying the nodes to keep in the output.
+        prepend_node_index: Add a node index column to the data.
+        pad_to_node: Output a full dataset from node 0 to MAX_INDEX.
+        labelize: Turn the dataset into a labeled set per the colormap in CMAP.
+        graphize: Turn the dataset into a SUMA graph dataset.
+        graph_nodelist: Two files specifying the indices and the coordinates of\
+            the graph's nodes.
+        graph_full_nodelist: Similar to -graph_nodelist_1D but without need for\
+            NODEINDLIST.1D.
+        graph_named_nodelist: Two files specifying graph node indices, string\
+            labels, and their coordinates.
+        graph_xyz_lpi: Coordinates in NodeList.1D are in LPI instead of RAI.
+        graph_edgelist: Indices of graph nodes defining edge.
+        onegraph: Expect input dataset to be one square matrix defining the\
+            graph (default).
+        multigraph: Expect each column in input dataset to define an entire\
+            graph.
+        split: Split a multi-column dataset into about N output datasets.
+        no_history: Do not include a history element in the output.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "ConvertDset",
+        "output_type": output_type,
+        "input_dataset": input_dataset,
+        "add_node_index": add_node_index,
+        "prepend_node_index": prepend_node_index,
+        "graphize": graphize,
+        "graph_xyz_lpi": graph_xyz_lpi,
+        "onegraph": onegraph,
+        "multigraph": multigraph,
+        "no_history": no_history,
+    }
+    if input_type is not None:
+        params["input_type"] = input_type
+    if output_prefix is not None:
+        params["output_prefix"] = output_prefix
+    if dset_labels is not None:
+        params["dset_labels"] = dset_labels
+    if node_index_file is not None:
+        params["node_index_file"] = node_index_file
+    if node_select_file is not None:
+        params["node_select_file"] = node_select_file
+    if pad_to_node is not None:
+        params["pad_to_node"] = pad_to_node
+    if labelize is not None:
+        params["labelize"] = labelize
+    if graph_nodelist is not None:
+        params["graph_nodelist"] = graph_nodelist
+    if graph_full_nodelist is not None:
+        params["graph_full_nodelist"] = graph_full_nodelist
+    if graph_named_nodelist is not None:
+        params["graph_named_nodelist"] = graph_named_nodelist
+    if graph_edgelist is not None:
+        params["graph_edgelist"] = graph_edgelist
+    if split is not None:
+        params["split"] = split
+    return params
+
+
+def convert_dset_cargs(
+    params: ConvertDsetParameters,
+    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("ConvertDset")
+    cargs.extend([
+        "-o_",
+        *params.get("output_type")
+    ])
+    cargs.extend([
+        "-input",
+        execution.input_file(params.get("input_dataset"))
+    ])
+    if params.get("input_type") is not None:
+        cargs.extend([
+            "-i_",
+            params.get("input_type")
+        ])
+    if params.get("output_prefix") is not None:
+        cargs.extend([
+            "-prefix",
+            params.get("output_prefix")
+        ])
+    if params.get("dset_labels") is not None:
+        cargs.extend([
+            "-dset_labels",
+            params.get("dset_labels")
+        ])
+    if params.get("add_node_index"):
+        cargs.append("-add_node_index")
+    if params.get("node_index_file") is not None:
+        cargs.extend([
+            "-node_index_1D",
+            execution.input_file(params.get("node_index_file"))
+        ])
+    if params.get("node_select_file") is not None:
+        cargs.extend([
+            "-node_select_1D",
+            execution.input_file(params.get("node_select_file"))
+        ])
+    if params.get("prepend_node_index"):
+        cargs.append("-prepend_node_index_1D")
+    if params.get("pad_to_node") is not None:
+        cargs.extend([
+            "-pad_to_node",
+            params.get("pad_to_node")
+        ])
+    if params.get("labelize") is not None:
+        cargs.extend([
+            "-labelize",
+            execution.input_file(params.get("labelize"))
+        ])
+    if params.get("graphize"):
+        cargs.append("-graphize")
+    if params.get("graph_nodelist") is not None:
+        cargs.extend([
+            "-graph_nodelist_1D",
+            params.get("graph_nodelist")
+        ])
+    if params.get("graph_full_nodelist") is not None:
+        cargs.extend([
+            "-graph_full_nodelist_1D",
+            execution.input_file(params.get("graph_full_nodelist"))
+        ])
+    if params.get("graph_named_nodelist") is not None:
+        cargs.extend([
+            "-graph_named_nodelist_txt",
+            params.get("graph_named_nodelist")
+        ])
+    if params.get("graph_xyz_lpi"):
+        cargs.append("-graph_XYZ_LPI")
+    if params.get("graph_edgelist") is not None:
+        cargs.extend([
+            "-graph_edgelist_1D",
+            execution.input_file(params.get("graph_edgelist"))
+        ])
+    if params.get("onegraph"):
+        cargs.append("-onegraph")
+    if params.get("multigraph"):
+        cargs.append("-multigraph")
+    if params.get("split") is not None:
+        cargs.extend([
+            "-split",
+            str(params.get("split"))
+        ])
+    if params.get("no_history"):
+        cargs.append("-no_history")
+    return cargs
+
+
+def convert_dset_outputs(
+    params: ConvertDsetParameters,
+    execution: Execution,
+) -> ConvertDsetOutputs:
+    """
+    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 = ConvertDsetOutputs(
+        root=execution.output_file("."),
+        converted_dataset=execution.output_file(params.get("output_prefix")) if (params.get("output_prefix") is not None) else None,
+    )
+    return ret
+
+
+def convert_dset_execute(
+    params: ConvertDsetParameters,
+    execution: Execution,
+) -> ConvertDsetOutputs:
+    """
+    Converts a surface dataset from one format to another.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `ConvertDsetOutputs`).
+    """
+    params = execution.params(params)
+    cargs = convert_dset_cargs(params, execution)
+    ret = convert_dset_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def convert_dset(
+    output_type: list[typing.Literal["niml_asc", "niml_bi", "1D", "1Dp", "1Dpt", "gii", "gii_asc", "gii_b64", "gii_b64gz", "1D_stderr", "1D_stdout", "niml_stderr", "niml_stdout", "1Dp_stdout", "1Dp_stderr", "1Dpt_stdout", "1Dpt_stderr"]],
+    input_dataset: InputPathType,
+    input_type: typing.Literal["niml", "1D", "dx"] | None = None,
+    output_prefix: str | None = None,
+    dset_labels: str | None = None,
+    add_node_index: bool = False,
+    node_index_file: InputPathType | None = None,
+    node_select_file: InputPathType | None = None,
+    prepend_node_index: bool = False,
+    pad_to_node: str | None = None,
+    labelize: InputPathType | None = None,
+    graphize: bool = False,
+    graph_nodelist: str | None = None,
+    graph_full_nodelist: InputPathType | None = None,
+    graph_named_nodelist: str | None = None,
+    graph_xyz_lpi: bool = False,
+    graph_edgelist: InputPathType | None = None,
+    onegraph: bool = False,
+    multigraph: bool = False,
+    split: int | None = None,
+    no_history: bool = False,
+    runner: Runner | None = None,
+) -> ConvertDsetOutputs:
+    """
+    Converts a surface dataset from one format to another.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        output_type: Type of output datasets.
+        input_dataset: Input dataset to be converted.
+        input_type: Type of input datasets.
+        output_prefix: Output prefix for dataset.
+        dset_labels: Label the columns (sub-bricks) of the output dataset.
+        add_node_index: Add a node index element if one does not exist in the\
+            input dataset.
+        node_index_file: File containing node indices.
+        node_select_file: File specifying the nodes to keep in the output.
+        prepend_node_index: Add a node index column to the data.
+        pad_to_node: Output a full dataset from node 0 to MAX_INDEX.
+        labelize: Turn the dataset into a labeled set per the colormap in CMAP.
+        graphize: Turn the dataset into a SUMA graph dataset.
+        graph_nodelist: Two files specifying the indices and the coordinates of\
+            the graph's nodes.
+        graph_full_nodelist: Similar to -graph_nodelist_1D but without need for\
+            NODEINDLIST.1D.
+        graph_named_nodelist: Two files specifying graph node indices, string\
+            labels, and their coordinates.
+        graph_xyz_lpi: Coordinates in NodeList.1D are in LPI instead of RAI.
+        graph_edgelist: Indices of graph nodes defining edge.
+        onegraph: Expect input dataset to be one square matrix defining the\
+            graph (default).
+        multigraph: Expect each column in input dataset to define an entire\
+            graph.
+        split: Split a multi-column dataset into about N output datasets.
+        no_history: Do not include a history element in the output.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `ConvertDsetOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(CONVERT_DSET_METADATA)
+    params = convert_dset_params(
+        output_type=output_type,
+        input_dataset=input_dataset,
+        input_type=input_type,
+        output_prefix=output_prefix,
+        dset_labels=dset_labels,
+        add_node_index=add_node_index,
+        node_index_file=node_index_file,
+        node_select_file=node_select_file,
+        prepend_node_index=prepend_node_index,
+        pad_to_node=pad_to_node,
+        labelize=labelize,
+        graphize=graphize,
+        graph_nodelist=graph_nodelist,
+        graph_full_nodelist=graph_full_nodelist,
+        graph_named_nodelist=graph_named_nodelist,
+        graph_xyz_lpi=graph_xyz_lpi,
+        graph_edgelist=graph_edgelist,
+        onegraph=onegraph,
+        multigraph=multigraph,
+        split=split,
+        no_history=no_history,
+    )
+    return convert_dset_execute(params, execution)
+
+
+__all__ = [
+    "CONVERT_DSET_METADATA",
+    "ConvertDsetOutputs",
+    "ConvertDsetParameters",
+    "convert_dset",
+    "convert_dset_params",
+]

niwrap_afni/afni/convert_surface.py

@@ -0,0 +1,247 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+CONVERT_SURFACE_METADATA = Metadata(
+    id="2b7452b8bf057bc43ac7efc4c5a01abd5236749c.boutiques",
+    name="ConvertSurface",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+ConvertSurfaceParameters = typing.TypedDict('ConvertSurfaceParameters', {
+    "__STYX_TYPE__": typing.Literal["ConvertSurface"],
+    "input_surface": str,
+    "output_surface": str,
+    "surface_volume": typing.NotRequired[str | None],
+    "transform_tlrc": bool,
+    "mni_lpi": bool,
+    "ixmat_1D": typing.NotRequired[str | None],
+    "native": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "ConvertSurface": convert_surface_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 {
+        "ConvertSurface": convert_surface_outputs,
+    }.get(t)
+
+
+class ConvertSurfaceOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `convert_surface(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_surface_file: OutputPathType
+    """The converted output surface file."""
+
+
+def convert_surface_params(
+    input_surface: str,
+    output_surface: str,
+    surface_volume: str | None = None,
+    transform_tlrc: bool = False,
+    mni_lpi: bool = False,
+    ixmat_1_d: str | None = None,
+    native: bool = False,
+) -> ConvertSurfaceParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_surface: Specifies the input surface.
+        output_surface: Specifies the output surface.
+        surface_volume: Specifies a surface volume.
+        transform_tlrc: Apply Talairach transform.
+        mni_lpi: Turn AFNI tlrc coordinates (RAI) into MNI coord space in LPI.
+        ixmat_1_d: Apply inverse transformation specified in 1D file.
+        native: Write the output surface in the coordinate system native to its\
+            format.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "ConvertSurface",
+        "input_surface": input_surface,
+        "output_surface": output_surface,
+        "transform_tlrc": transform_tlrc,
+        "mni_lpi": mni_lpi,
+        "native": native,
+    }
+    if surface_volume is not None:
+        params["surface_volume"] = surface_volume
+    if ixmat_1_d is not None:
+        params["ixmat_1D"] = ixmat_1_d
+    return params
+
+
+def convert_surface_cargs(
+    params: ConvertSurfaceParameters,
+    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("ConvertSurface")
+    cargs.extend([
+        "-i",
+        params.get("input_surface")
+    ])
+    cargs.extend([
+        "-o",
+        params.get("output_surface")
+    ])
+    if params.get("surface_volume") is not None:
+        cargs.extend([
+            "-sv",
+            params.get("surface_volume")
+        ])
+    if params.get("transform_tlrc"):
+        cargs.append("-tlrc")
+    if params.get("mni_lpi"):
+        cargs.append("-MNI_lpi")
+    if params.get("ixmat_1D") is not None:
+        cargs.extend([
+            "-ixmat_1D",
+            params.get("ixmat_1D")
+        ])
+    if params.get("native"):
+        cargs.append("-native")
+    return cargs
+
+
+def convert_surface_outputs(
+    params: ConvertSurfaceParameters,
+    execution: Execution,
+) -> ConvertSurfaceOutputs:
+    """
+    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 = ConvertSurfaceOutputs(
+        root=execution.output_file("."),
+        output_surface_file=execution.output_file(params.get("output_surface")),
+    )
+    return ret
+
+
+def convert_surface_execute(
+    params: ConvertSurfaceParameters,
+    execution: Execution,
+) -> ConvertSurfaceOutputs:
+    """
+    Reads in a surface and writes it out in another format. Only fields pertinent to
+    SUMA are preserved.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `ConvertSurfaceOutputs`).
+    """
+    params = execution.params(params)
+    cargs = convert_surface_cargs(params, execution)
+    ret = convert_surface_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def convert_surface(
+    input_surface: str,
+    output_surface: str,
+    surface_volume: str | None = None,
+    transform_tlrc: bool = False,
+    mni_lpi: bool = False,
+    ixmat_1_d: str | None = None,
+    native: bool = False,
+    runner: Runner | None = None,
+) -> ConvertSurfaceOutputs:
+    """
+    Reads in a surface and writes it out in another format. Only fields pertinent to
+    SUMA are preserved.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        input_surface: Specifies the input surface.
+        output_surface: Specifies the output surface.
+        surface_volume: Specifies a surface volume.
+        transform_tlrc: Apply Talairach transform.
+        mni_lpi: Turn AFNI tlrc coordinates (RAI) into MNI coord space in LPI.
+        ixmat_1_d: Apply inverse transformation specified in 1D file.
+        native: Write the output surface in the coordinate system native to its\
+            format.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `ConvertSurfaceOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(CONVERT_SURFACE_METADATA)
+    params = convert_surface_params(
+        input_surface=input_surface,
+        output_surface=output_surface,
+        surface_volume=surface_volume,
+        transform_tlrc=transform_tlrc,
+        mni_lpi=mni_lpi,
+        ixmat_1_d=ixmat_1_d,
+        native=native,
+    )
+    return convert_surface_execute(params, execution)
+
+
+__all__ = [
+    "CONVERT_SURFACE_METADATA",
+    "ConvertSurfaceOutputs",
+    "ConvertSurfaceParameters",
+    "convert_surface",
+    "convert_surface_params",
+]