niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/v__make_label_table.py

@@ -0,0 +1,587 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V__MAKE_LABEL_TABLE_METADATA = Metadata(
+    id="20feae505751ac89a0b8a088a83f7ee7d488f8c6.boutiques",
+    name="@MakeLabelTable",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+VMakeLabelTableParameters = typing.TypedDict('VMakeLabelTableParameters', {
+    "__STYX_TYPE__": typing.Literal["@MakeLabelTable"],
+    "labeltable": str,
+    "atlas_pointlist": typing.NotRequired[str | None],
+    "lab_r": typing.NotRequired[list[str] | None],
+    "lab_v": typing.NotRequired[list[str] | None],
+    "lab_file": typing.NotRequired[list[str] | None],
+    "dset": typing.NotRequired[InputPathType | None],
+    "longnames": typing.NotRequired[float | None],
+    "last_longname_col": typing.NotRequired[float | None],
+    "centers": bool,
+    "centertype": typing.NotRequired[str | None],
+    "centermask": typing.NotRequired[str | None],
+    "skip_novoxels": bool,
+    "all_labels": bool,
+    "all_keys": bool,
+    "lkeys": typing.NotRequired[str | None],
+    "rkeys": typing.NotRequired[str | None],
+    "klabel": typing.NotRequired[str | None],
+    "match_label": typing.NotRequired[str | None],
+    "labeltable_of_dset": typing.NotRequired[InputPathType | None],
+    "word_label_match": bool,
+    "quiet_death": bool,
+    "lt_to_atlas_pl": typing.NotRequired[str | None],
+    "dset_lt_to_atlas_pl": typing.NotRequired[list[InputPathType] | None],
+    "lt_to_csv": typing.NotRequired[InputPathType | None],
+    "atlasize_labeled_dset": typing.NotRequired[InputPathType | None],
+    "atlas_file": typing.NotRequired[str | None],
+    "atlas_name": typing.NotRequired[str | None],
+    "atlas_description": typing.NotRequired[str | None],
+    "replace": bool,
+    "add_atlas_dset": typing.NotRequired[InputPathType | None],
+    "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 {
+        "@MakeLabelTable": v__make_label_table_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 {
+        "@MakeLabelTable": v__make_label_table_outputs,
+    }.get(t)
+
+
+class VMakeLabelTableOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v__make_label_table(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_labeltable: OutputPathType
+    """Output label table file"""
+    output_atlas_pointlist: OutputPathType | None
+    """Output atlas point list file"""
+    output_csv: OutputPathType | None
+    """Output CSV file from label table"""
+    output_niml_atlas: OutputPathType | None
+    """Output NIML file after atlasizing labeled dataset"""
+
+
+def v__make_label_table_params(
+    labeltable: str,
+    atlas_pointlist: str | None = None,
+    lab_r: list[str] | None = None,
+    lab_v: list[str] | None = None,
+    lab_file: list[str] | None = None,
+    dset: InputPathType | None = None,
+    longnames: float | None = None,
+    last_longname_col: float | None = None,
+    centers: bool = False,
+    centertype: str | None = None,
+    centermask: str | None = None,
+    skip_novoxels: bool = False,
+    all_labels: bool = False,
+    all_keys: bool = False,
+    lkeys: str | None = None,
+    rkeys: str | None = None,
+    klabel: str | None = None,
+    match_label: str | None = None,
+    labeltable_of_dset: InputPathType | None = None,
+    word_label_match: bool = False,
+    quiet_death: bool = False,
+    lt_to_atlas_pl: str | None = None,
+    dset_lt_to_atlas_pl: list[InputPathType] | None = None,
+    lt_to_csv: InputPathType | None = None,
+    atlasize_labeled_dset: InputPathType | None = None,
+    atlas_file: str | None = None,
+    atlas_name: str | None = None,
+    atlas_description: str | None = None,
+    replace: bool = False,
+    add_atlas_dset: InputPathType | None = None,
+    h_web: bool = False,
+    h_view: bool = False,
+    all_opts: bool = False,
+    h_find: str | None = None,
+) -> VMakeLabelTableParameters:
+    """
+    Build parameters.
+    
+    Args:
+        labeltable: Name of output label table.
+        atlas_pointlist: Instead of a label table, produce an atlas point list.
+        lab_r: Define a label with its minimum and maximum key values.
+        lab_v: Define a label and its value.
+        lab_file: Specify labels and keys from a text file.
+        dset: Attach the label table (or atlas point list) to dataset.
+        longnames: Allow for another column of long names for regions.
+        last_longname_col: Limit long names to nth column.
+        centers: Compute center of mass location for each ROI.
+        centertype: Different ways to compute centers (Icent, Dcent, cm).
+        centermask: Calculate center of mass locations using a subset of voxels.
+        skip_novoxels: Skip regions without voxels.
+        all_labels: Return a listing of all labels.
+        all_keys: Return a listing of all keys.
+        lkeys: Return the keys whose labels match a given label.
+        rkeys: Return the range (min max) of keys whose labels match a given\
+            label.
+        klabel: Return the label associated with a given key.
+        match_label: Return labels matching a given label.
+        labeltable_of_dset: Dump the labeltable from a dataset.
+        word_label_match: Use word matching for labels.
+        quiet_death: Do not give error messages when failing.
+        lt_to_atlas_pl: Transform Label Table to Atlas Point List.
+        dset_lt_to_atlas_pl: Get Label Table in dataset and write as an Atlas\
+            Point List.
+        lt_to_csv: Transform Label Table to CSV format.
+        atlasize_labeled_dset: Transform a labeled ROI dataset into an atlas.
+        atlas_file: Specify the name of the NIML file where atlas attributes\
+            are stored.
+        atlas_name: Name of the Atlas.
+        atlas_description: Description of the Atlas, which appears in AFNI's\
+            whereami window.
+        replace: Replace existing Atlas if the name already exists in the NIML\
+            file.
+        add_atlas_dset: Add an existing atlas to an atlas file.
+        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 a specific word in the help output.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "@MakeLabelTable",
+        "labeltable": labeltable,
+        "centers": centers,
+        "skip_novoxels": skip_novoxels,
+        "all_labels": all_labels,
+        "all_keys": all_keys,
+        "word_label_match": word_label_match,
+        "quiet_death": quiet_death,
+        "replace": replace,
+        "h_web": h_web,
+        "h_view": h_view,
+        "all_opts": all_opts,
+    }
+    if atlas_pointlist is not None:
+        params["atlas_pointlist"] = atlas_pointlist
+    if lab_r is not None:
+        params["lab_r"] = lab_r
+    if lab_v is not None:
+        params["lab_v"] = lab_v
+    if lab_file is not None:
+        params["lab_file"] = lab_file
+    if dset is not None:
+        params["dset"] = dset
+    if longnames is not None:
+        params["longnames"] = longnames
+    if last_longname_col is not None:
+        params["last_longname_col"] = last_longname_col
+    if centertype is not None:
+        params["centertype"] = centertype
+    if centermask is not None:
+        params["centermask"] = centermask
+    if lkeys is not None:
+        params["lkeys"] = lkeys
+    if rkeys is not None:
+        params["rkeys"] = rkeys
+    if klabel is not None:
+        params["klabel"] = klabel
+    if match_label is not None:
+        params["match_label"] = match_label
+    if labeltable_of_dset is not None:
+        params["labeltable_of_dset"] = labeltable_of_dset
+    if lt_to_atlas_pl is not None:
+        params["lt_to_atlas_pl"] = lt_to_atlas_pl
+    if dset_lt_to_atlas_pl is not None:
+        params["dset_lt_to_atlas_pl"] = dset_lt_to_atlas_pl
+    if lt_to_csv is not None:
+        params["lt_to_csv"] = lt_to_csv
+    if atlasize_labeled_dset is not None:
+        params["atlasize_labeled_dset"] = atlasize_labeled_dset
+    if atlas_file is not None:
+        params["atlas_file"] = atlas_file
+    if atlas_name is not None:
+        params["atlas_name"] = atlas_name
+    if atlas_description is not None:
+        params["atlas_description"] = atlas_description
+    if add_atlas_dset is not None:
+        params["add_atlas_dset"] = add_atlas_dset
+    if h_find is not None:
+        params["h_find"] = h_find
+    return params
+
+
+def v__make_label_table_cargs(
+    params: VMakeLabelTableParameters,
+    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("@MakeLabelTable")
+    cargs.extend([
+        "-labeltable",
+        params.get("labeltable")
+    ])
+    if params.get("atlas_pointlist") is not None:
+        cargs.extend([
+            "-atlas_pointlist",
+            params.get("atlas_pointlist")
+        ])
+    if params.get("lab_r") is not None:
+        cargs.extend([
+            "-lab_r",
+            *params.get("lab_r")
+        ])
+    if params.get("lab_v") is not None:
+        cargs.extend([
+            "-lab_v",
+            *params.get("lab_v")
+        ])
+    if params.get("lab_file") is not None:
+        cargs.extend([
+            "-lab_file",
+            *params.get("lab_file")
+        ])
+    if params.get("dset") is not None:
+        cargs.extend([
+            "-dset",
+            execution.input_file(params.get("dset"))
+        ])
+    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("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",
+            params.get("centermask")
+        ])
+    if params.get("skip_novoxels"):
+        cargs.append("-skip_novoxels")
+    if params.get("all_labels"):
+        cargs.append("-all_labels")
+    if params.get("all_keys"):
+        cargs.append("-all_keys")
+    if params.get("lkeys") is not None:
+        cargs.extend([
+            "-lkeys",
+            params.get("lkeys")
+        ])
+    if params.get("rkeys") is not None:
+        cargs.extend([
+            "-rkeys",
+            params.get("rkeys")
+        ])
+    if params.get("klabel") is not None:
+        cargs.extend([
+            "-klabel",
+            params.get("klabel")
+        ])
+    if params.get("match_label") is not None:
+        cargs.extend([
+            "-match_label",
+            params.get("match_label")
+        ])
+    if params.get("labeltable_of_dset") is not None:
+        cargs.extend([
+            "-labeltable_of_dset",
+            execution.input_file(params.get("labeltable_of_dset"))
+        ])
+    if params.get("word_label_match"):
+        cargs.append("-word_label_match")
+    if params.get("quiet_death"):
+        cargs.append("-quiet_death")
+    if params.get("lt_to_atlas_pl") is not None:
+        cargs.extend([
+            "-LT_to_atlas_PL",
+            params.get("lt_to_atlas_pl")
+        ])
+    if params.get("dset_lt_to_atlas_pl") is not None:
+        cargs.extend([
+            "-dset_LT_to_atlas_PL",
+            *[execution.input_file(f) for f in params.get("dset_lt_to_atlas_pl")]
+        ])
+    if params.get("lt_to_csv") is not None:
+        cargs.extend([
+            "-LT_to_CSV",
+            execution.input_file(params.get("lt_to_csv"))
+        ])
+    if params.get("atlasize_labeled_dset") is not None:
+        cargs.extend([
+            "-atlasize_labeled_dset",
+            execution.input_file(params.get("atlasize_labeled_dset"))
+        ])
+    if params.get("atlas_file") is not None:
+        cargs.extend([
+            "-atlas_file",
+            params.get("atlas_file")
+        ])
+    if params.get("atlas_name") is not None:
+        cargs.extend([
+            "-atlas_name",
+            params.get("atlas_name")
+        ])
+    if params.get("atlas_description") is not None:
+        cargs.extend([
+            "-atlas_description",
+            params.get("atlas_description")
+        ])
+    if params.get("replace"):
+        cargs.append("-replace")
+    if params.get("add_atlas_dset") is not None:
+        cargs.extend([
+            "-add_atlas_dset",
+            execution.input_file(params.get("add_atlas_dset"))
+        ])
+    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__make_label_table_outputs(
+    params: VMakeLabelTableParameters,
+    execution: Execution,
+) -> VMakeLabelTableOutputs:
+    """
+    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 = VMakeLabelTableOutputs(
+        root=execution.output_file("."),
+        output_labeltable=execution.output_file(params.get("labeltable") + ".niml.lt"),
+        output_atlas_pointlist=execution.output_file(params.get("atlas_pointlist") + ".niml.atlas") if (params.get("atlas_pointlist") is not None) else None,
+        output_csv=execution.output_file(pathlib.Path(params.get("lt_to_csv")).name + ".csv") if (params.get("lt_to_csv") is not None) else None,
+        output_niml_atlas=execution.output_file(pathlib.Path(params.get("atlasize_labeled_dset")).name + ".niml") if (params.get("atlasize_labeled_dset") is not None) else None,
+    )
+    return ret
+
+
+def v__make_label_table_execute(
+    params: VMakeLabelTableParameters,
+    execution: Execution,
+) -> VMakeLabelTableOutputs:
+    """
+    Script used to create, modify, and transform label tables.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `VMakeLabelTableOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v__make_label_table_cargs(params, execution)
+    ret = v__make_label_table_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v__make_label_table(
+    labeltable: str,
+    atlas_pointlist: str | None = None,
+    lab_r: list[str] | None = None,
+    lab_v: list[str] | None = None,
+    lab_file: list[str] | None = None,
+    dset: InputPathType | None = None,
+    longnames: float | None = None,
+    last_longname_col: float | None = None,
+    centers: bool = False,
+    centertype: str | None = None,
+    centermask: str | None = None,
+    skip_novoxels: bool = False,
+    all_labels: bool = False,
+    all_keys: bool = False,
+    lkeys: str | None = None,
+    rkeys: str | None = None,
+    klabel: str | None = None,
+    match_label: str | None = None,
+    labeltable_of_dset: InputPathType | None = None,
+    word_label_match: bool = False,
+    quiet_death: bool = False,
+    lt_to_atlas_pl: str | None = None,
+    dset_lt_to_atlas_pl: list[InputPathType] | None = None,
+    lt_to_csv: InputPathType | None = None,
+    atlasize_labeled_dset: InputPathType | None = None,
+    atlas_file: str | None = None,
+    atlas_name: str | None = None,
+    atlas_description: str | None = None,
+    replace: bool = False,
+    add_atlas_dset: InputPathType | None = None,
+    h_web: bool = False,
+    h_view: bool = False,
+    all_opts: bool = False,
+    h_find: str | None = None,
+    runner: Runner | None = None,
+) -> VMakeLabelTableOutputs:
+    """
+    Script used to create, modify, and transform label tables.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        labeltable: Name of output label table.
+        atlas_pointlist: Instead of a label table, produce an atlas point list.
+        lab_r: Define a label with its minimum and maximum key values.
+        lab_v: Define a label and its value.
+        lab_file: Specify labels and keys from a text file.
+        dset: Attach the label table (or atlas point list) to dataset.
+        longnames: Allow for another column of long names for regions.
+        last_longname_col: Limit long names to nth column.
+        centers: Compute center of mass location for each ROI.
+        centertype: Different ways to compute centers (Icent, Dcent, cm).
+        centermask: Calculate center of mass locations using a subset of voxels.
+        skip_novoxels: Skip regions without voxels.
+        all_labels: Return a listing of all labels.
+        all_keys: Return a listing of all keys.
+        lkeys: Return the keys whose labels match a given label.
+        rkeys: Return the range (min max) of keys whose labels match a given\
+            label.
+        klabel: Return the label associated with a given key.
+        match_label: Return labels matching a given label.
+        labeltable_of_dset: Dump the labeltable from a dataset.
+        word_label_match: Use word matching for labels.
+        quiet_death: Do not give error messages when failing.
+        lt_to_atlas_pl: Transform Label Table to Atlas Point List.
+        dset_lt_to_atlas_pl: Get Label Table in dataset and write as an Atlas\
+            Point List.
+        lt_to_csv: Transform Label Table to CSV format.
+        atlasize_labeled_dset: Transform a labeled ROI dataset into an atlas.
+        atlas_file: Specify the name of the NIML file where atlas attributes\
+            are stored.
+        atlas_name: Name of the Atlas.
+        atlas_description: Description of the Atlas, which appears in AFNI's\
+            whereami window.
+        replace: Replace existing Atlas if the name already exists in the NIML\
+            file.
+        add_atlas_dset: Add an existing atlas to an atlas file.
+        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 a specific word in the help output.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `VMakeLabelTableOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__MAKE_LABEL_TABLE_METADATA)
+    params = v__make_label_table_params(
+        labeltable=labeltable,
+        atlas_pointlist=atlas_pointlist,
+        lab_r=lab_r,
+        lab_v=lab_v,
+        lab_file=lab_file,
+        dset=dset,
+        longnames=longnames,
+        last_longname_col=last_longname_col,
+        centers=centers,
+        centertype=centertype,
+        centermask=centermask,
+        skip_novoxels=skip_novoxels,
+        all_labels=all_labels,
+        all_keys=all_keys,
+        lkeys=lkeys,
+        rkeys=rkeys,
+        klabel=klabel,
+        match_label=match_label,
+        labeltable_of_dset=labeltable_of_dset,
+        word_label_match=word_label_match,
+        quiet_death=quiet_death,
+        lt_to_atlas_pl=lt_to_atlas_pl,
+        dset_lt_to_atlas_pl=dset_lt_to_atlas_pl,
+        lt_to_csv=lt_to_csv,
+        atlasize_labeled_dset=atlasize_labeled_dset,
+        atlas_file=atlas_file,
+        atlas_name=atlas_name,
+        atlas_description=atlas_description,
+        replace=replace,
+        add_atlas_dset=add_atlas_dset,
+        h_web=h_web,
+        h_view=h_view,
+        all_opts=all_opts,
+        h_find=h_find,
+    )
+    return v__make_label_table_execute(params, execution)
+
+
+__all__ = [
+    "VMakeLabelTableOutputs",
+    "VMakeLabelTableParameters",
+    "V__MAKE_LABEL_TABLE_METADATA",
+    "v__make_label_table",
+    "v__make_label_table_params",
+]