niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/scale_to_map.py

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+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+SCALE_TO_MAP_METADATA = Metadata(
+    id="2f7e7a834eba315bf3a7ddf886a5f54b169d9aeb.boutiques",
+    name="ScaleToMap",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+ScaleToMapParameters = typing.TypedDict('ScaleToMapParameters', {
+    "__STYX_TYPE__": typing.Literal["ScaleToMap"],
+    "input_file": InputPathType,
+    "icol": float,
+    "vcol": float,
+    "cmap": typing.NotRequired[str | None],
+    "cmapfile": typing.NotRequired[InputPathType | None],
+    "cmapdb": typing.NotRequired[InputPathType | None],
+    "frf": bool,
+    "clp": typing.NotRequired[list[float] | None],
+    "perc_clp": typing.NotRequired[list[float] | None],
+    "apr": typing.NotRequired[float | None],
+    "anr": typing.NotRequired[float | None],
+    "interp": bool,
+    "nointerp": bool,
+    "direct": bool,
+    "msk_zero": bool,
+    "msk": typing.NotRequired[list[float] | None],
+    "msk_col": typing.NotRequired[list[float] | None],
+    "nomsk_col": bool,
+    "br": typing.NotRequired[float | None],
+    "help": bool,
+    "verbose": bool,
+    "showmap": bool,
+    "showdb": bool,
+    "novolreg": bool,
+    "noxform": bool,
+    "setenv": typing.NotRequired[str | None],
+    "TRACE": bool,
+    "TRACE_1": bool,
+    "nomall": bool,
+    "yesmall": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "ScaleToMap": scale_to_map_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 ScaleToMapOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `scale_to_map(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def scale_to_map_params(
+    input_file: InputPathType,
+    icol: float,
+    vcol: float,
+    cmap: str | None = None,
+    cmapfile: InputPathType | None = None,
+    cmapdb: InputPathType | None = None,
+    frf: bool = False,
+    clp: list[float] | None = None,
+    perc_clp: list[float] | None = None,
+    apr: float | None = None,
+    anr: float | None = None,
+    interp: bool = False,
+    nointerp: bool = False,
+    direct: bool = False,
+    msk_zero: bool = False,
+    msk: list[float] | None = None,
+    msk_col: list[float] | None = None,
+    nomsk_col: bool = False,
+    br: float | None = None,
+    help_: bool = False,
+    verbose: bool = False,
+    showmap: bool = False,
+    showdb: bool = False,
+    novolreg: bool = False,
+    noxform: bool = False,
+    setenv: str | None = None,
+    trace_: bool = False,
+    trace_1: bool = False,
+    nomall: bool = False,
+    yesmall: bool = False,
+) -> ScaleToMapParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_file: Input file in 1D formatted ascii containing node values.
+        icol: Index of node index column (-1 if node index is implicit).
+        vcol: Index of node value column.
+        cmap: Choose one of the standard colormaps available with SUMA.
+        cmapfile: Read color map from a Mapfile.
+        cmapdb: Read color maps from an AFNI .pal file.
+        frf: Indicate that the first row in the file is the first color.
+        clp: Clip values in IntVect to specified range.
+        perc_clp: Percentile clip values in IntVect to specified range.
+        apr: Clip values in IntVect to [0 range].
+        anr: Clip values in IntVect to [-range range].
+        interp: Use color interpolation between colors in colormap (default).
+        nointerp: Turn off color interpolation within the colormap.
+        direct: Directly map values to index of color in colormap.
+        msk_zero: Mask values that are 0.
+        msk: Mask values in vcol between specified range.
+        msk_col: Set color of masked voxels.
+        nomsk_col: Do not output nodes that got masked.
+        br: Apply a brightness factor to colormap and mask color.
+        help_: Display help message.
+        verbose: Verbose mode.
+        showmap: Print colormap to screen and quit.
+        showdb: Print colors and colormaps of AFNI along with any loaded from\
+            Palfile.
+        novolreg: Ignore any Rotate, Volreg, Tagalign, or WarpDrive\
+            transformations present in the Surface Volume.
+        noxform: Same as -novolreg.
+        setenv: Set environment variable ENVname to ENVvalue. Quotes are\
+            necessary.
+        trace_: Turn on extreme tracing.
+        trace_1: Turn on extreme tracing.
+        nomall: Turn off memory tracing.
+        yesmall: Turn on memory tracing (default).
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "ScaleToMap",
+        "input_file": input_file,
+        "icol": icol,
+        "vcol": vcol,
+        "frf": frf,
+        "interp": interp,
+        "nointerp": nointerp,
+        "direct": direct,
+        "msk_zero": msk_zero,
+        "nomsk_col": nomsk_col,
+        "help": help_,
+        "verbose": verbose,
+        "showmap": showmap,
+        "showdb": showdb,
+        "novolreg": novolreg,
+        "noxform": noxform,
+        "TRACE": trace_,
+        "TRACE_1": trace_1,
+        "nomall": nomall,
+        "yesmall": yesmall,
+    }
+    if cmap is not None:
+        params["cmap"] = cmap
+    if cmapfile is not None:
+        params["cmapfile"] = cmapfile
+    if cmapdb is not None:
+        params["cmapdb"] = cmapdb
+    if clp is not None:
+        params["clp"] = clp
+    if perc_clp is not None:
+        params["perc_clp"] = perc_clp
+    if apr is not None:
+        params["apr"] = apr
+    if anr is not None:
+        params["anr"] = anr
+    if msk is not None:
+        params["msk"] = msk
+    if msk_col is not None:
+        params["msk_col"] = msk_col
+    if br is not None:
+        params["br"] = br
+    if setenv is not None:
+        params["setenv"] = setenv
+    return params
+
+
+def scale_to_map_cargs(
+    params: ScaleToMapParameters,
+    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("ScaleToMap")
+    cargs.append(execution.input_file(params.get("input_file")))
+    cargs.append(str(params.get("icol")))
+    cargs.append(str(params.get("vcol")))
+    if params.get("cmap") is not None:
+        cargs.extend([
+            "-cmap",
+            params.get("cmap")
+        ])
+    if params.get("cmapfile") is not None:
+        cargs.extend([
+            "-cmapfile",
+            execution.input_file(params.get("cmapfile"))
+        ])
+    if params.get("cmapdb") is not None:
+        cargs.extend([
+            "-cmapdb",
+            execution.input_file(params.get("cmapdb"))
+        ])
+    if params.get("frf"):
+        cargs.append("-frf")
+    if params.get("clp") is not None:
+        cargs.extend([
+            "-clp",
+            *map(str, params.get("clp"))
+        ])
+    if params.get("perc_clp") is not None:
+        cargs.extend([
+            "-perc_clp",
+            *map(str, params.get("perc_clp"))
+        ])
+    if params.get("apr") is not None:
+        cargs.extend([
+            "-apr",
+            str(params.get("apr"))
+        ])
+    if params.get("anr") is not None:
+        cargs.extend([
+            "-anr",
+            str(params.get("anr"))
+        ])
+    if params.get("interp"):
+        cargs.append("-interp")
+    if params.get("nointerp"):
+        cargs.append("-nointerp")
+    if params.get("direct"):
+        cargs.append("-direct")
+    if params.get("msk_zero"):
+        cargs.append("-msk_zero")
+    if params.get("msk") is not None:
+        cargs.extend([
+            "-msk",
+            *map(str, params.get("msk"))
+        ])
+    if params.get("msk_col") is not None:
+        cargs.extend([
+            "-msk_col",
+            *map(str, params.get("msk_col"))
+        ])
+    if params.get("nomsk_col"):
+        cargs.append("-nomsk_col")
+    if params.get("br") is not None:
+        cargs.extend([
+            "-br",
+            str(params.get("br"))
+        ])
+    if params.get("help"):
+        cargs.append("-h")
+    if params.get("verbose"):
+        cargs.append("-verb")
+    if params.get("showmap"):
+        cargs.append("-showmap")
+    if params.get("showdb"):
+        cargs.append("-showdb")
+    if params.get("novolreg"):
+        cargs.append("-novolreg")
+    if params.get("noxform"):
+        cargs.append("-noxform")
+    if params.get("setenv") is not None:
+        cargs.extend([
+            "-setenv",
+            params.get("setenv")
+        ])
+    if params.get("TRACE"):
+        cargs.append("-TRACE")
+    if params.get("TRACE_1"):
+        cargs.append("-TRACE")
+    if params.get("nomall"):
+        cargs.append("-nomall")
+    if params.get("yesmall"):
+        cargs.append("-yesmall")
+    return cargs
+
+
+def scale_to_map_outputs(
+    params: ScaleToMapParameters,
+    execution: Execution,
+) -> ScaleToMapOutputs:
+    """
+    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 = ScaleToMapOutputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def scale_to_map_execute(
+    params: ScaleToMapParameters,
+    execution: Execution,
+) -> ScaleToMapOutputs:
+    """
+    Tool to scale values to a color map.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `ScaleToMapOutputs`).
+    """
+    params = execution.params(params)
+    cargs = scale_to_map_cargs(params, execution)
+    ret = scale_to_map_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def scale_to_map(
+    input_file: InputPathType,
+    icol: float,
+    vcol: float,
+    cmap: str | None = None,
+    cmapfile: InputPathType | None = None,
+    cmapdb: InputPathType | None = None,
+    frf: bool = False,
+    clp: list[float] | None = None,
+    perc_clp: list[float] | None = None,
+    apr: float | None = None,
+    anr: float | None = None,
+    interp: bool = False,
+    nointerp: bool = False,
+    direct: bool = False,
+    msk_zero: bool = False,
+    msk: list[float] | None = None,
+    msk_col: list[float] | None = None,
+    nomsk_col: bool = False,
+    br: float | None = None,
+    help_: bool = False,
+    verbose: bool = False,
+    showmap: bool = False,
+    showdb: bool = False,
+    novolreg: bool = False,
+    noxform: bool = False,
+    setenv: str | None = None,
+    trace_: bool = False,
+    trace_1: bool = False,
+    nomall: bool = False,
+    yesmall: bool = False,
+    runner: Runner | None = None,
+) -> ScaleToMapOutputs:
+    """
+    Tool to scale values to a color map.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        input_file: Input file in 1D formatted ascii containing node values.
+        icol: Index of node index column (-1 if node index is implicit).
+        vcol: Index of node value column.
+        cmap: Choose one of the standard colormaps available with SUMA.
+        cmapfile: Read color map from a Mapfile.
+        cmapdb: Read color maps from an AFNI .pal file.
+        frf: Indicate that the first row in the file is the first color.
+        clp: Clip values in IntVect to specified range.
+        perc_clp: Percentile clip values in IntVect to specified range.
+        apr: Clip values in IntVect to [0 range].
+        anr: Clip values in IntVect to [-range range].
+        interp: Use color interpolation between colors in colormap (default).
+        nointerp: Turn off color interpolation within the colormap.
+        direct: Directly map values to index of color in colormap.
+        msk_zero: Mask values that are 0.
+        msk: Mask values in vcol between specified range.
+        msk_col: Set color of masked voxels.
+        nomsk_col: Do not output nodes that got masked.
+        br: Apply a brightness factor to colormap and mask color.
+        help_: Display help message.
+        verbose: Verbose mode.
+        showmap: Print colormap to screen and quit.
+        showdb: Print colors and colormaps of AFNI along with any loaded from\
+            Palfile.
+        novolreg: Ignore any Rotate, Volreg, Tagalign, or WarpDrive\
+            transformations present in the Surface Volume.
+        noxform: Same as -novolreg.
+        setenv: Set environment variable ENVname to ENVvalue. Quotes are\
+            necessary.
+        trace_: Turn on extreme tracing.
+        trace_1: Turn on extreme tracing.
+        nomall: Turn off memory tracing.
+        yesmall: Turn on memory tracing (default).
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `ScaleToMapOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(SCALE_TO_MAP_METADATA)
+    params = scale_to_map_params(
+        input_file=input_file,
+        icol=icol,
+        vcol=vcol,
+        cmap=cmap,
+        cmapfile=cmapfile,
+        cmapdb=cmapdb,
+        frf=frf,
+        clp=clp,
+        perc_clp=perc_clp,
+        apr=apr,
+        anr=anr,
+        interp=interp,
+        nointerp=nointerp,
+        direct=direct,
+        msk_zero=msk_zero,
+        msk=msk,
+        msk_col=msk_col,
+        nomsk_col=nomsk_col,
+        br=br,
+        help_=help_,
+        verbose=verbose,
+        showmap=showmap,
+        showdb=showdb,
+        novolreg=novolreg,
+        noxform=noxform,
+        setenv=setenv,
+        trace_=trace_,
+        trace_1=trace_1,
+        nomall=nomall,
+        yesmall=yesmall,
+    )
+    return scale_to_map_execute(params, execution)
+
+
+__all__ = [
+    "SCALE_TO_MAP_METADATA",
+    "ScaleToMapOutputs",
+    "ScaleToMapParameters",
+    "scale_to_map",
+    "scale_to_map_params",
+]