niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/v__atlasize.py

@@ -0,0 +1,402 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V__ATLASIZE_METADATA = Metadata(
+    id="5fc4c62439ac62644ef483caa2fc7a4ea1cb35f0.boutiques",
+    name="@Atlasize",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+VAtlasizeParameters = typing.TypedDict('VAtlasizeParameters', {
+    "__STYX_TYPE__": typing.Literal["@Atlasize"],
+    "dset": typing.NotRequired[InputPathType | None],
+    "space": typing.NotRequired[str | None],
+    "lab_file": typing.NotRequired[list[str] | None],
+    "lab_file_delim": typing.NotRequired[str | None],
+    "longnames": typing.NotRequired[float | None],
+    "last_longname_col": typing.NotRequired[float | None],
+    "atlas_type": typing.NotRequired[str | None],
+    "atlas_description": typing.NotRequired[str | None],
+    "atlas_name": typing.NotRequired[str | None],
+    "auto_backup": bool,
+    "centers": bool,
+    "centertype": typing.NotRequired[str | None],
+    "centermask": typing.NotRequired[InputPathType | None],
+    "skip_novoxels": bool,
+    "h_web": bool,
+    "h_view": bool,
+    "all_opts": bool,
+    "h_find": 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 {
+        "@Atlasize": v__atlasize_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 {
+        "@Atlasize": v__atlasize_outputs,
+    }.get(t)
+
+
+class VAtlasizeOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v__atlasize(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    niml_file: OutputPathType | None
+    """Generated NIML file for the atlas"""
+
+
+def v__atlasize_params(
+    dset: InputPathType | None = None,
+    space: str | None = None,
+    lab_file: list[str] | None = None,
+    lab_file_delim: str | None = None,
+    longnames: float | None = None,
+    last_longname_col: float | None = None,
+    atlas_type: str | None = None,
+    atlas_description: str | None = None,
+    atlas_name: str | None = None,
+    auto_backup: bool = False,
+    centers: bool = False,
+    centertype: str | None = None,
+    centermask: InputPathType | None = None,
+    skip_novoxels: bool = False,
+    h_web: bool = False,
+    h_view: bool = False,
+    all_opts: bool = False,
+    h_find: str | None = None,
+) -> VAtlasizeParameters:
+    """
+    Build parameters.
+    
+    Args:
+        dset: Make DSET an atlas.
+        space: Mark DSET as being in space SPACE.
+        lab_file: Labels and keys are in text file FILE. cLAB is the index of\
+            column containing labels, vVAL is the index of column containing keys\
+            (1st column is indexed at 0).
+        lab_file_delim: Set column delimiter for -lab_file option. Default is '\
+            ' (space), but you can set your own. ';' for example.
+        longnames: Additionally, allow for another column of long names for\
+            regions, e.g., amygdala for AMY. cLONGNAME is the starting column for\
+            the long name continuing to the last name of the output.
+        last_longname_col: Limit long names to nth column.
+        atlas_type: Set the atlas type where TP is 'S' for subject-based and\
+            'G' for group-based atlases, respectively.
+        atlas_description: A description for the atlas. Default is 'My Atlas'.
+        atlas_name: Name for the atlas. Default name is based on prefix of\
+            DSET.
+        auto_backup: Back up the dataset if it already exists in the custom\
+            atlas directory and allows an overwrite.
+        centers: Add center of mass coordinates to atlas.
+        centertype: Choose Icent, Dcent, or cm for different ways to compute\
+            centers.
+        centermask: Calculate center of mass locations for each ROI using a\
+            subset of voxels. Useful for atlases with identical labels in both\
+            hemispheres.
+        skip_novoxels: Skip regions without any voxels in the dataset.
+        h_web: Open webpage with help for this program.
+        h_view: Open -help output in a GUI editor.
+        all_opts: List all of the options for this script.
+        h_find: Search for lines containing WORD in -help output. Search is\
+            approximate.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "@Atlasize",
+        "auto_backup": auto_backup,
+        "centers": centers,
+        "skip_novoxels": skip_novoxels,
+        "h_web": h_web,
+        "h_view": h_view,
+        "all_opts": all_opts,
+    }
+    if dset is not None:
+        params["dset"] = dset
+    if space is not None:
+        params["space"] = space
+    if lab_file is not None:
+        params["lab_file"] = lab_file
+    if lab_file_delim is not None:
+        params["lab_file_delim"] = lab_file_delim
+    if longnames is not None:
+        params["longnames"] = longnames
+    if last_longname_col is not None:
+        params["last_longname_col"] = last_longname_col
+    if atlas_type is not None:
+        params["atlas_type"] = atlas_type
+    if atlas_description is not None:
+        params["atlas_description"] = atlas_description
+    if atlas_name is not None:
+        params["atlas_name"] = atlas_name
+    if centertype is not None:
+        params["centertype"] = centertype
+    if centermask is not None:
+        params["centermask"] = centermask
+    if h_find is not None:
+        params["h_find"] = h_find
+    return params
+
+
+def v__atlasize_cargs(
+    params: VAtlasizeParameters,
+    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("@Atlasize")
+    if params.get("dset") is not None:
+        cargs.extend([
+            "-dset",
+            execution.input_file(params.get("dset"))
+        ])
+    if params.get("space") is not None:
+        cargs.extend([
+            "-space",
+            params.get("space")
+        ])
+    if params.get("lab_file") is not None:
+        cargs.extend([
+            "-lab_file",
+            *params.get("lab_file")
+        ])
+    if params.get("lab_file_delim") is not None:
+        cargs.extend([
+            "-lab_file_delim",
+            params.get("lab_file_delim")
+        ])
+    if params.get("longnames") is not None:
+        cargs.extend([
+            "-longnames",
+            str(params.get("longnames"))
+        ])
+    if params.get("last_longname_col") is not None:
+        cargs.extend([
+            "-last_longname_col",
+            str(params.get("last_longname_col"))
+        ])
+    if params.get("atlas_type") is not None:
+        cargs.extend([
+            "-atlas_type",
+            params.get("atlas_type")
+        ])
+    if params.get("atlas_description") is not None:
+        cargs.extend([
+            "-atlas_description",
+            params.get("atlas_description")
+        ])
+    if params.get("atlas_name") is not None:
+        cargs.extend([
+            "-atlas_name",
+            params.get("atlas_name")
+        ])
+    if params.get("auto_backup"):
+        cargs.append("-auto_backup")
+    if params.get("centers"):
+        cargs.append("-centers")
+    if params.get("centertype") is not None:
+        cargs.extend([
+            "-centertype",
+            params.get("centertype")
+        ])
+    if params.get("centermask") is not None:
+        cargs.extend([
+            "-centermask",
+            execution.input_file(params.get("centermask"))
+        ])
+    if params.get("skip_novoxels"):
+        cargs.append("-skip_novoxels")
+    if params.get("h_web"):
+        cargs.append("-h_web")
+    if params.get("h_view"):
+        cargs.append("-h_view")
+    if params.get("all_opts"):
+        cargs.append("-all_opts")
+    if params.get("h_find") is not None:
+        cargs.extend([
+            "-h_find",
+            params.get("h_find")
+        ])
+    return cargs
+
+
+def v__atlasize_outputs(
+    params: VAtlasizeParameters,
+    execution: Execution,
+) -> VAtlasizeOutputs:
+    """
+    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 = VAtlasizeOutputs(
+        root=execution.output_file("."),
+        niml_file=execution.output_file(pathlib.Path(params.get("dset")).name + ".niml") if (params.get("dset") is not None) else None,
+    )
+    return ret
+
+
+def v__atlasize_execute(
+    params: VAtlasizeParameters,
+    execution: Execution,
+) -> VAtlasizeOutputs:
+    """
+    Script to turn a volumetric dataset into an AFNI atlas.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `VAtlasizeOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v__atlasize_cargs(params, execution)
+    ret = v__atlasize_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v__atlasize(
+    dset: InputPathType | None = None,
+    space: str | None = None,
+    lab_file: list[str] | None = None,
+    lab_file_delim: str | None = None,
+    longnames: float | None = None,
+    last_longname_col: float | None = None,
+    atlas_type: str | None = None,
+    atlas_description: str | None = None,
+    atlas_name: str | None = None,
+    auto_backup: bool = False,
+    centers: bool = False,
+    centertype: str | None = None,
+    centermask: InputPathType | None = None,
+    skip_novoxels: bool = False,
+    h_web: bool = False,
+    h_view: bool = False,
+    all_opts: bool = False,
+    h_find: str | None = None,
+    runner: Runner | None = None,
+) -> VAtlasizeOutputs:
+    """
+    Script to turn a volumetric dataset into an AFNI atlas.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        dset: Make DSET an atlas.
+        space: Mark DSET as being in space SPACE.
+        lab_file: Labels and keys are in text file FILE. cLAB is the index of\
+            column containing labels, vVAL is the index of column containing keys\
+            (1st column is indexed at 0).
+        lab_file_delim: Set column delimiter for -lab_file option. Default is '\
+            ' (space), but you can set your own. ';' for example.
+        longnames: Additionally, allow for another column of long names for\
+            regions, e.g., amygdala for AMY. cLONGNAME is the starting column for\
+            the long name continuing to the last name of the output.
+        last_longname_col: Limit long names to nth column.
+        atlas_type: Set the atlas type where TP is 'S' for subject-based and\
+            'G' for group-based atlases, respectively.
+        atlas_description: A description for the atlas. Default is 'My Atlas'.
+        atlas_name: Name for the atlas. Default name is based on prefix of\
+            DSET.
+        auto_backup: Back up the dataset if it already exists in the custom\
+            atlas directory and allows an overwrite.
+        centers: Add center of mass coordinates to atlas.
+        centertype: Choose Icent, Dcent, or cm for different ways to compute\
+            centers.
+        centermask: Calculate center of mass locations for each ROI using a\
+            subset of voxels. Useful for atlases with identical labels in both\
+            hemispheres.
+        skip_novoxels: Skip regions without any voxels in the dataset.
+        h_web: Open webpage with help for this program.
+        h_view: Open -help output in a GUI editor.
+        all_opts: List all of the options for this script.
+        h_find: Search for lines containing WORD in -help output. Search is\
+            approximate.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `VAtlasizeOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__ATLASIZE_METADATA)
+    params = v__atlasize_params(
+        dset=dset,
+        space=space,
+        lab_file=lab_file,
+        lab_file_delim=lab_file_delim,
+        longnames=longnames,
+        last_longname_col=last_longname_col,
+        atlas_type=atlas_type,
+        atlas_description=atlas_description,
+        atlas_name=atlas_name,
+        auto_backup=auto_backup,
+        centers=centers,
+        centertype=centertype,
+        centermask=centermask,
+        skip_novoxels=skip_novoxels,
+        h_web=h_web,
+        h_view=h_view,
+        all_opts=all_opts,
+        h_find=h_find,
+    )
+    return v__atlasize_execute(params, execution)
+
+
+__all__ = [
+    "VAtlasizeOutputs",
+    "VAtlasizeParameters",
+    "V__ATLASIZE_METADATA",
+    "v__atlasize",
+    "v__atlasize_params",
+]