niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/surf_clust.py

@@ -0,0 +1,611 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+SURF_CLUST_METADATA = Metadata(
+    id="2346425eb197f04f33322dea847636dd74a3b8a3.boutiques",
+    name="SurfClust",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+SurfClustParameters = typing.TypedDict('SurfClustParameters', {
+    "__STYX_TYPE__": typing.Literal["SurfClust"],
+    "specfile": typing.NotRequired[InputPathType | None],
+    "input_surface": typing.NotRequired[str | None],
+    "input_surf_name": typing.NotRequired[InputPathType | None],
+    "input_dataset": list[InputPathType],
+    "rmm": float,
+    "amm2": typing.NotRequired[float | None],
+    "min_nodes": typing.NotRequired[float | None],
+    "prefix": typing.NotRequired[str | None],
+    "out_clusterdset": bool,
+    "out_roidset": bool,
+    "out_fulllist": bool,
+    "sort_none": bool,
+    "sort_n_nodes": bool,
+    "sort_area": bool,
+    "thresh_col": typing.NotRequired[float | None],
+    "thresh": typing.NotRequired[float | None],
+    "athresh": typing.NotRequired[float | None],
+    "ir_range": typing.NotRequired[list[float] | None],
+    "ex_range": typing.NotRequired[list[float] | None],
+    "prepend_node_index": bool,
+    "update": typing.NotRequired[float | None],
+    "no_cent": bool,
+    "cent": bool,
+    "novolreg": bool,
+    "noxform": bool,
+    "set_env": typing.NotRequired[str | None],
+    "trace": bool,
+    "trace_extreme": bool,
+    "no_memory_trace": bool,
+    "yes_memory_trace": bool,
+    "mini_help": bool,
+    "help": bool,
+    "extreme_help": bool,
+    "view_help": bool,
+    "web_help": bool,
+    "find_help": typing.NotRequired[str | None],
+    "raw_help": bool,
+    "spx_help": bool,
+    "aspx_help": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "SurfClust": surf_clust_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 {
+        "SurfClust": surf_clust_outputs,
+    }.get(t)
+
+
+class SurfClustOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `surf_clust(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    cluster_table: OutputPathType | None
+    """Cluster table output"""
+    clustered_dataset: OutputPathType | None
+    """Clustered version of input dataset"""
+    roi_dataset: OutputPathType | None
+    """ROI dataset with rank of clusters"""
+
+
+def surf_clust_params(
+    input_dataset: list[InputPathType],
+    rmm: float,
+    specfile: InputPathType | None = None,
+    input_surface: str | None = None,
+    input_surf_name: InputPathType | None = None,
+    amm2: float | None = None,
+    min_nodes: float | None = None,
+    prefix: str | None = None,
+    out_clusterdset: bool = False,
+    out_roidset: bool = False,
+    out_fulllist: bool = False,
+    sort_none: bool = False,
+    sort_n_nodes: bool = False,
+    sort_area: bool = False,
+    thresh_col: float | None = None,
+    thresh: float | None = None,
+    athresh: float | None = None,
+    ir_range: list[float] | None = None,
+    ex_range: list[float] | None = None,
+    prepend_node_index: bool = False,
+    update_: float | None = None,
+    no_cent: bool = False,
+    cent: bool = False,
+    novolreg: bool = False,
+    noxform: bool = False,
+    set_env: str | None = None,
+    trace_: bool = False,
+    trace_extreme: bool = False,
+    no_memory_trace: bool = False,
+    yes_memory_trace: bool = False,
+    mini_help: bool = False,
+    help_: bool = False,
+    extreme_help: bool = False,
+    view_help: bool = False,
+    web_help: bool = False,
+    find_help: str | None = None,
+    raw_help: bool = False,
+    spx_help: bool = False,
+    aspx_help: bool = False,
+) -> SurfClustParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_dataset: The input dataset and the index of the datacolumn to use\
+            (index 0 for 1st column). Values of 0 indicate inactive nodes.
+        rmm: Maximum distance between an activated node and the cluster to\
+            which it belongs.
+        specfile: The surface spec file.
+        input_surface: The input surface name.
+        input_surf_name: Full name of the input surface.
+        amm2: Minimum area for clusters.
+        min_nodes: Minimum nodes for clusters.
+        prefix: Prefix for output. Default is the prefix of the input dataset.
+        out_clusterdset: Output a clustered version of input dataset.
+        out_roidset: Output an ROI dataset with the rank of its cluster.
+        out_fulllist: Output a value for all nodes of input surface.
+        sort_none: No sorting of ROI clusters.
+        sort_n_nodes: Sorting based on number of nodes in cluster.
+        sort_area: Sorting based on area of clusters (default).
+        thresh_col: Index of thresholding column. Default is column 0.
+        thresh: Apply thresholding prior to clustering.
+        athresh: Apply absolute thresholding prior to clustering.
+        ir_range: Apply thresholding in range. A node n is considered if\
+            thresh_col[n] >= R0 && thresh_col[n] <= R1.
+        ex_range: Apply thresholding outside of range. A node n is considered\
+            if thresh_col[n] < R0 || thresh_col[n] > R1.
+        prepend_node_index: Force the output dataset to have node indices in\
+            column 0 of output.
+        update_: Pacify me when perc of the data have been processed. perc is\
+            between 1% and 50%. Default is no update.
+        no_cent: Do not find the central nodes.
+        cent: Do find the central nodes (default).
+        novolreg: Ignore any Rotate, Volreg, Tagalign, or WarpDrive\
+            transformations present in the Surface Volume.
+        noxform: Same as -novolreg.
+        set_env: Set environment variable ENVname to be ENVvalue. Quotes are\
+            necessary.
+        trace_: Turns on In/Out debug and Memory tracing.
+        trace_extreme: Turns on extreme tracing.
+        no_memory_trace: Turn off memory tracing.
+        yes_memory_trace: Turn on memory tracing (default).
+        mini_help: Mini help, same as -help in many cases.
+        help_: The entire help output.
+        extreme_help: Extreme help, same as -help in majority of cases.
+        view_help: Open help in text editor. AFNI will try to find a GUI editor\
+            on your machine. You can control which it should use by setting\
+            environment variable AFNI_GUI_EDITOR.
+        web_help: Open help in web browser. AFNI will try to find a browser.\
+            You can control which it should use by setting environment variable\
+            AFNI_GUI_EDITOR.
+        find_help: Look for lines in this program's -help output that match\
+            (approximately) the given word.
+        raw_help: Help string unedited.
+        spx_help: Help string in sphinx format, but do not try to autoformat.
+        aspx_help: Help string in sphinx format with autoformatting of options.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "SurfClust",
+        "input_dataset": input_dataset,
+        "rmm": rmm,
+        "out_clusterdset": out_clusterdset,
+        "out_roidset": out_roidset,
+        "out_fulllist": out_fulllist,
+        "sort_none": sort_none,
+        "sort_n_nodes": sort_n_nodes,
+        "sort_area": sort_area,
+        "prepend_node_index": prepend_node_index,
+        "no_cent": no_cent,
+        "cent": cent,
+        "novolreg": novolreg,
+        "noxform": noxform,
+        "trace": trace_,
+        "trace_extreme": trace_extreme,
+        "no_memory_trace": no_memory_trace,
+        "yes_memory_trace": yes_memory_trace,
+        "mini_help": mini_help,
+        "help": help_,
+        "extreme_help": extreme_help,
+        "view_help": view_help,
+        "web_help": web_help,
+        "raw_help": raw_help,
+        "spx_help": spx_help,
+        "aspx_help": aspx_help,
+    }
+    if specfile is not None:
+        params["specfile"] = specfile
+    if input_surface is not None:
+        params["input_surface"] = input_surface
+    if input_surf_name is not None:
+        params["input_surf_name"] = input_surf_name
+    if amm2 is not None:
+        params["amm2"] = amm2
+    if min_nodes is not None:
+        params["min_nodes"] = min_nodes
+    if prefix is not None:
+        params["prefix"] = prefix
+    if thresh_col is not None:
+        params["thresh_col"] = thresh_col
+    if thresh is not None:
+        params["thresh"] = thresh
+    if athresh is not None:
+        params["athresh"] = athresh
+    if ir_range is not None:
+        params["ir_range"] = ir_range
+    if ex_range is not None:
+        params["ex_range"] = ex_range
+    if update_ is not None:
+        params["update"] = update_
+    if set_env is not None:
+        params["set_env"] = set_env
+    if find_help is not None:
+        params["find_help"] = find_help
+    return params
+
+
+def surf_clust_cargs(
+    params: SurfClustParameters,
+    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("SurfClust")
+    if params.get("specfile") is not None:
+        cargs.extend([
+            "-spec",
+            execution.input_file(params.get("specfile"))
+        ])
+    if params.get("input_surface") is not None:
+        cargs.extend([
+            "-surf_A",
+            params.get("input_surface")
+        ])
+    if params.get("input_surf_name") is not None:
+        cargs.extend([
+            "-i",
+            execution.input_file(params.get("input_surf_name"))
+        ])
+    cargs.extend([
+        "-input",
+        *[execution.input_file(f) for f in params.get("input_dataset")]
+    ])
+    cargs.extend([
+        "-rmm",
+        str(params.get("rmm"))
+    ])
+    if params.get("amm2") is not None:
+        cargs.extend([
+            "-amm2",
+            str(params.get("amm2"))
+        ])
+    if params.get("min_nodes") is not None:
+        cargs.extend([
+            "-n",
+            str(params.get("min_nodes"))
+        ])
+    if params.get("prefix") is not None:
+        cargs.extend([
+            "-prefix",
+            params.get("prefix")
+        ])
+    if params.get("out_clusterdset"):
+        cargs.append("-out_clusterdset")
+    if params.get("out_roidset"):
+        cargs.append("-out_roidset")
+    if params.get("out_fulllist"):
+        cargs.append("-out_fulllist")
+    if params.get("sort_none"):
+        cargs.append("-sort_none")
+    if params.get("sort_n_nodes"):
+        cargs.append("-sort_n_nodes")
+    if params.get("sort_area"):
+        cargs.append("-sort_area")
+    if params.get("thresh_col") is not None:
+        cargs.extend([
+            "-thresh_col",
+            str(params.get("thresh_col"))
+        ])
+    if params.get("thresh") is not None:
+        cargs.extend([
+            "-thresh",
+            str(params.get("thresh"))
+        ])
+    if params.get("athresh") is not None:
+        cargs.extend([
+            "-athresh",
+            str(params.get("athresh"))
+        ])
+    if params.get("ir_range") is not None:
+        cargs.extend([
+            "-ir_range",
+            *map(str, params.get("ir_range"))
+        ])
+    if params.get("ex_range") is not None:
+        cargs.extend([
+            "-ex_range",
+            *map(str, params.get("ex_range"))
+        ])
+    if params.get("prepend_node_index"):
+        cargs.append("-prepend_node_index")
+    if params.get("update") is not None:
+        cargs.extend([
+            "-update",
+            str(params.get("update"))
+        ])
+    if params.get("no_cent"):
+        cargs.append("-no_cent")
+    if params.get("cent"):
+        cargs.append("-cent")
+    if params.get("novolreg"):
+        cargs.append("-novolreg")
+    if params.get("noxform"):
+        cargs.append("-noxform")
+    if params.get("set_env") is not None:
+        cargs.extend([
+            "-setenv",
+            params.get("set_env")
+        ])
+    if params.get("trace"):
+        cargs.append("-trace")
+    if params.get("trace_extreme"):
+        cargs.append("-TRACE")
+    if params.get("no_memory_trace"):
+        cargs.append("-nomall")
+    if params.get("yes_memory_trace"):
+        cargs.append("-yesmall")
+    if params.get("mini_help"):
+        cargs.append("-h")
+    if params.get("help"):
+        cargs.append("-help")
+    if params.get("extreme_help"):
+        cargs.append("-HELP")
+    if params.get("view_help"):
+        cargs.append("-h_view")
+    if params.get("web_help"):
+        cargs.append("-h_web")
+    if params.get("find_help") is not None:
+        cargs.extend([
+            "-h_find",
+            params.get("find_help")
+        ])
+    if params.get("raw_help"):
+        cargs.append("-h_raw")
+    if params.get("spx_help"):
+        cargs.append("-h_spx")
+    if params.get("aspx_help"):
+        cargs.append("-h_aspx")
+    return cargs
+
+
+def surf_clust_outputs(
+    params: SurfClustParameters,
+    execution: Execution,
+) -> SurfClustOutputs:
+    """
+    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 = SurfClustOutputs(
+        root=execution.output_file("."),
+        cluster_table=execution.output_file(params.get("prefix") + "_ClstTable_rXX_aXX.1D") if (params.get("prefix") is not None) else None,
+        clustered_dataset=execution.output_file(params.get("prefix") + "_Clustered_rXX_aXX.dset") if (params.get("prefix") is not None) else None,
+        roi_dataset=execution.output_file(params.get("prefix") + "_ClstMsk_rXX_aXX.dset") if (params.get("prefix") is not None) else None,
+    )
+    return ret
+
+
+def surf_clust_execute(
+    params: SurfClustParameters,
+    execution: Execution,
+) -> SurfClustOutputs:
+    """
+    A program to perform clustering analysis surfaces.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `SurfClustOutputs`).
+    """
+    params = execution.params(params)
+    cargs = surf_clust_cargs(params, execution)
+    ret = surf_clust_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def surf_clust(
+    input_dataset: list[InputPathType],
+    rmm: float,
+    specfile: InputPathType | None = None,
+    input_surface: str | None = None,
+    input_surf_name: InputPathType | None = None,
+    amm2: float | None = None,
+    min_nodes: float | None = None,
+    prefix: str | None = None,
+    out_clusterdset: bool = False,
+    out_roidset: bool = False,
+    out_fulllist: bool = False,
+    sort_none: bool = False,
+    sort_n_nodes: bool = False,
+    sort_area: bool = False,
+    thresh_col: float | None = None,
+    thresh: float | None = None,
+    athresh: float | None = None,
+    ir_range: list[float] | None = None,
+    ex_range: list[float] | None = None,
+    prepend_node_index: bool = False,
+    update_: float | None = None,
+    no_cent: bool = False,
+    cent: bool = False,
+    novolreg: bool = False,
+    noxform: bool = False,
+    set_env: str | None = None,
+    trace_: bool = False,
+    trace_extreme: bool = False,
+    no_memory_trace: bool = False,
+    yes_memory_trace: bool = False,
+    mini_help: bool = False,
+    help_: bool = False,
+    extreme_help: bool = False,
+    view_help: bool = False,
+    web_help: bool = False,
+    find_help: str | None = None,
+    raw_help: bool = False,
+    spx_help: bool = False,
+    aspx_help: bool = False,
+    runner: Runner | None = None,
+) -> SurfClustOutputs:
+    """
+    A program to perform clustering analysis surfaces.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        input_dataset: The input dataset and the index of the datacolumn to use\
+            (index 0 for 1st column). Values of 0 indicate inactive nodes.
+        rmm: Maximum distance between an activated node and the cluster to\
+            which it belongs.
+        specfile: The surface spec file.
+        input_surface: The input surface name.
+        input_surf_name: Full name of the input surface.
+        amm2: Minimum area for clusters.
+        min_nodes: Minimum nodes for clusters.
+        prefix: Prefix for output. Default is the prefix of the input dataset.
+        out_clusterdset: Output a clustered version of input dataset.
+        out_roidset: Output an ROI dataset with the rank of its cluster.
+        out_fulllist: Output a value for all nodes of input surface.
+        sort_none: No sorting of ROI clusters.
+        sort_n_nodes: Sorting based on number of nodes in cluster.
+        sort_area: Sorting based on area of clusters (default).
+        thresh_col: Index of thresholding column. Default is column 0.
+        thresh: Apply thresholding prior to clustering.
+        athresh: Apply absolute thresholding prior to clustering.
+        ir_range: Apply thresholding in range. A node n is considered if\
+            thresh_col[n] >= R0 && thresh_col[n] <= R1.
+        ex_range: Apply thresholding outside of range. A node n is considered\
+            if thresh_col[n] < R0 || thresh_col[n] > R1.
+        prepend_node_index: Force the output dataset to have node indices in\
+            column 0 of output.
+        update_: Pacify me when perc of the data have been processed. perc is\
+            between 1% and 50%. Default is no update.
+        no_cent: Do not find the central nodes.
+        cent: Do find the central nodes (default).
+        novolreg: Ignore any Rotate, Volreg, Tagalign, or WarpDrive\
+            transformations present in the Surface Volume.
+        noxform: Same as -novolreg.
+        set_env: Set environment variable ENVname to be ENVvalue. Quotes are\
+            necessary.
+        trace_: Turns on In/Out debug and Memory tracing.
+        trace_extreme: Turns on extreme tracing.
+        no_memory_trace: Turn off memory tracing.
+        yes_memory_trace: Turn on memory tracing (default).
+        mini_help: Mini help, same as -help in many cases.
+        help_: The entire help output.
+        extreme_help: Extreme help, same as -help in majority of cases.
+        view_help: Open help in text editor. AFNI will try to find a GUI editor\
+            on your machine. You can control which it should use by setting\
+            environment variable AFNI_GUI_EDITOR.
+        web_help: Open help in web browser. AFNI will try to find a browser.\
+            You can control which it should use by setting environment variable\
+            AFNI_GUI_EDITOR.
+        find_help: Look for lines in this program's -help output that match\
+            (approximately) the given word.
+        raw_help: Help string unedited.
+        spx_help: Help string in sphinx format, but do not try to autoformat.
+        aspx_help: Help string in sphinx format with autoformatting of options.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `SurfClustOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(SURF_CLUST_METADATA)
+    params = surf_clust_params(
+        specfile=specfile,
+        input_surface=input_surface,
+        input_surf_name=input_surf_name,
+        input_dataset=input_dataset,
+        rmm=rmm,
+        amm2=amm2,
+        min_nodes=min_nodes,
+        prefix=prefix,
+        out_clusterdset=out_clusterdset,
+        out_roidset=out_roidset,
+        out_fulllist=out_fulllist,
+        sort_none=sort_none,
+        sort_n_nodes=sort_n_nodes,
+        sort_area=sort_area,
+        thresh_col=thresh_col,
+        thresh=thresh,
+        athresh=athresh,
+        ir_range=ir_range,
+        ex_range=ex_range,
+        prepend_node_index=prepend_node_index,
+        update_=update_,
+        no_cent=no_cent,
+        cent=cent,
+        novolreg=novolreg,
+        noxform=noxform,
+        set_env=set_env,
+        trace_=trace_,
+        trace_extreme=trace_extreme,
+        no_memory_trace=no_memory_trace,
+        yes_memory_trace=yes_memory_trace,
+        mini_help=mini_help,
+        help_=help_,
+        extreme_help=extreme_help,
+        view_help=view_help,
+        web_help=web_help,
+        find_help=find_help,
+        raw_help=raw_help,
+        spx_help=spx_help,
+        aspx_help=aspx_help,
+    )
+    return surf_clust_execute(params, execution)
+
+
+__all__ = [
+    "SURF_CLUST_METADATA",
+    "SurfClustOutputs",
+    "SurfClustParameters",
+    "surf_clust",
+    "surf_clust_params",
+]