niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/make_color_map.py

@@ -0,0 +1,417 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+MAKE_COLOR_MAP_METADATA = Metadata(
+    id="20feab346cace5f8666142aaf08be813c7020806.boutiques",
+    name="MakeColorMap",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+MakeColorMapParameters = typing.TypedDict('MakeColorMapParameters', {
+    "__STYX_TYPE__": typing.Literal["MakeColorMap"],
+    "fiducials_ncol": typing.NotRequired[InputPathType | None],
+    "fiducials": typing.NotRequired[InputPathType | None],
+    "num_colors": typing.NotRequired[float | None],
+    "std_mapname": typing.NotRequired[str | None],
+    "palette_file": typing.NotRequired[InputPathType | None],
+    "cmap_name": typing.NotRequired[str | None],
+    "fscolut_labels": typing.NotRequired[list[float] | None],
+    "fscolut_file": typing.NotRequired[InputPathType | None],
+    "afni_hex": typing.NotRequired[str | None],
+    "afni_hex_complete": typing.NotRequired[str | None],
+    "suma_colormap": typing.NotRequired[str | None],
+    "user_colut_file": typing.NotRequired[InputPathType | None],
+    "sdset": typing.NotRequired[InputPathType | None],
+    "sdset_prefix": typing.NotRequired[str | None],
+    "flipupdown": bool,
+    "skip_last": bool,
+    "show_fscolut": bool,
+    "help_flag": bool,
+    "help_full_flag": bool,
+    "flip_map_updside_down": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "MakeColorMap": make_color_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 {
+        "MakeColorMap": make_color_map_outputs,
+    }.get(t)
+
+
+class MakeColorMapOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `make_color_map(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    afni_hex_output_prefix: OutputPathType | None
+    """Prefix for individual color values in AFNI Hex format."""
+    palette_file_output: OutputPathType
+    """Example palette file output."""
+
+
+def make_color_map_params(
+    fiducials_ncol: InputPathType | None = None,
+    fiducials: InputPathType | None = None,
+    num_colors: float | None = None,
+    std_mapname: str | None = None,
+    palette_file: InputPathType | None = None,
+    cmap_name: str | None = None,
+    fscolut_labels: list[float] | None = None,
+    fscolut_file: InputPathType | None = None,
+    afni_hex: str | None = None,
+    afni_hex_complete: str | None = None,
+    suma_colormap: str | None = None,
+    user_colut_file: InputPathType | None = None,
+    sdset: InputPathType | None = None,
+    sdset_prefix: str | None = None,
+    flipupdown: bool = False,
+    skip_last: bool = False,
+    show_fscolut: bool = False,
+    help_flag: bool = False,
+    help_full_flag: bool = False,
+    flip_map_updside_down: bool = False,
+) -> MakeColorMapParameters:
+    """
+    Build parameters.
+    
+    Args:
+        fiducials_ncol: Fiducial colors and their indices in the color map are\
+            listed in file Fiducials_Ncol.
+        fiducials: Fiducial colors are listed in an ascii file Fiducials.
+        num_colors: Total number of colors in the color map.
+        std_mapname: Returns one of SUMA's standard colormaps.
+        palette_file: Specify the palette file for colormap.
+        cmap_name: Specify the colormap name.
+        fscolut_labels: Get AFNI/SUMA colormaps of FreeSurfer colors indexed\
+            between lbl0 and lbl1.
+        fscolut_file: Use color LUT file FS_COL_LUT.
+        afni_hex: Afni Hex format. Use this option if you want a color map\
+            formatted to fit in AFNI's .afnirc file.
+        afni_hex_complete: Afni Hex format, ready to go into pbardefs.h.
+        suma_colormap: Write colormap in SUMA's format.
+        user_colut_file: Provide a user's own color lookup file.
+        sdset: Add colormap to surface-based dataset DSET, making it a labeled\
+            dataset.
+        sdset_prefix: Prefix of dset for writing labeled version of DSET.
+        flipupdown: Flip the map upside down.
+        skip_last: If used, the last color in the Fiducial list is omitted.
+        show_fscolut: Show all of the FreeSurfer LUT.
+        help_flag: Displays the help message.
+        help_full_flag: Displays the help message.
+        flip_map_updside_down: Flip the map upside down.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "MakeColorMap",
+        "flipupdown": flipupdown,
+        "skip_last": skip_last,
+        "show_fscolut": show_fscolut,
+        "help_flag": help_flag,
+        "help_full_flag": help_full_flag,
+        "flip_map_updside_down": flip_map_updside_down,
+    }
+    if fiducials_ncol is not None:
+        params["fiducials_ncol"] = fiducials_ncol
+    if fiducials is not None:
+        params["fiducials"] = fiducials
+    if num_colors is not None:
+        params["num_colors"] = num_colors
+    if std_mapname is not None:
+        params["std_mapname"] = std_mapname
+    if palette_file is not None:
+        params["palette_file"] = palette_file
+    if cmap_name is not None:
+        params["cmap_name"] = cmap_name
+    if fscolut_labels is not None:
+        params["fscolut_labels"] = fscolut_labels
+    if fscolut_file is not None:
+        params["fscolut_file"] = fscolut_file
+    if afni_hex is not None:
+        params["afni_hex"] = afni_hex
+    if afni_hex_complete is not None:
+        params["afni_hex_complete"] = afni_hex_complete
+    if suma_colormap is not None:
+        params["suma_colormap"] = suma_colormap
+    if user_colut_file is not None:
+        params["user_colut_file"] = user_colut_file
+    if sdset is not None:
+        params["sdset"] = sdset
+    if sdset_prefix is not None:
+        params["sdset_prefix"] = sdset_prefix
+    return params
+
+
+def make_color_map_cargs(
+    params: MakeColorMapParameters,
+    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("MakeColorMap")
+    if params.get("fiducials_ncol") is not None:
+        cargs.extend([
+            "-fn",
+            execution.input_file(params.get("fiducials_ncol"))
+        ])
+    if params.get("fiducials") is not None:
+        cargs.extend([
+            "-f",
+            execution.input_file(params.get("fiducials"))
+        ])
+    if params.get("num_colors") is not None:
+        cargs.extend([
+            "-nc",
+            str(params.get("num_colors"))
+        ])
+    if params.get("std_mapname") is not None:
+        cargs.extend([
+            "-std",
+            params.get("std_mapname")
+        ])
+    if params.get("palette_file") is not None:
+        cargs.extend([
+            "-cmapdb",
+            execution.input_file(params.get("palette_file"))
+        ])
+    if params.get("cmap_name") is not None:
+        cargs.extend([
+            "-cmap",
+            params.get("cmap_name")
+        ])
+    if params.get("fscolut_labels") is not None:
+        cargs.extend([
+            "-fscolut",
+            *map(str, params.get("fscolut_labels"))
+        ])
+    if params.get("fscolut_file") is not None:
+        cargs.extend([
+            "-fscolutfile",
+            execution.input_file(params.get("fscolut_file"))
+        ])
+    if params.get("afni_hex") is not None:
+        cargs.extend([
+            "-ah",
+            params.get("afni_hex")
+        ])
+    if params.get("afni_hex_complete") is not None:
+        cargs.extend([
+            "-ahc",
+            params.get("afni_hex_complete")
+        ])
+    if params.get("suma_colormap") is not None:
+        cargs.extend([
+            "-suma_cmap",
+            params.get("suma_colormap")
+        ])
+    if params.get("user_colut_file") is not None:
+        cargs.extend([
+            "-usercolutfile",
+            execution.input_file(params.get("user_colut_file"))
+        ])
+    if params.get("sdset") is not None:
+        cargs.extend([
+            "-sdset",
+            execution.input_file(params.get("sdset"))
+        ])
+    if params.get("sdset_prefix") is not None:
+        cargs.extend([
+            "-sdset_prefix",
+            params.get("sdset_prefix")
+        ])
+    if params.get("flipupdown"):
+        cargs.append("-flipud")
+    if params.get("skip_last"):
+        cargs.append("-sl")
+    if params.get("show_fscolut"):
+        cargs.append("-show_fscolut")
+    if params.get("help_flag"):
+        cargs.append("-h")
+    if params.get("help_full_flag"):
+        cargs.append("-help")
+    if params.get("flip_map_updside_down"):
+        cargs.append("-flipud")
+    return cargs
+
+
+def make_color_map_outputs(
+    params: MakeColorMapParameters,
+    execution: Execution,
+) -> MakeColorMapOutputs:
+    """
+    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 = MakeColorMapOutputs(
+        root=execution.output_file("."),
+        afni_hex_output_prefix=execution.output_file(params.get("afni_hex") + "_01") if (params.get("afni_hex") is not None) else None,
+        palette_file_output=execution.output_file("TestPalette.pal"),
+    )
+    return ret
+
+
+def make_color_map_execute(
+    params: MakeColorMapParameters,
+    execution: Execution,
+) -> MakeColorMapOutputs:
+    """
+    Utility for creating and modifying colormaps with various formats and fiducial
+    points.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `MakeColorMapOutputs`).
+    """
+    params = execution.params(params)
+    cargs = make_color_map_cargs(params, execution)
+    ret = make_color_map_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def make_color_map(
+    fiducials_ncol: InputPathType | None = None,
+    fiducials: InputPathType | None = None,
+    num_colors: float | None = None,
+    std_mapname: str | None = None,
+    palette_file: InputPathType | None = None,
+    cmap_name: str | None = None,
+    fscolut_labels: list[float] | None = None,
+    fscolut_file: InputPathType | None = None,
+    afni_hex: str | None = None,
+    afni_hex_complete: str | None = None,
+    suma_colormap: str | None = None,
+    user_colut_file: InputPathType | None = None,
+    sdset: InputPathType | None = None,
+    sdset_prefix: str | None = None,
+    flipupdown: bool = False,
+    skip_last: bool = False,
+    show_fscolut: bool = False,
+    help_flag: bool = False,
+    help_full_flag: bool = False,
+    flip_map_updside_down: bool = False,
+    runner: Runner | None = None,
+) -> MakeColorMapOutputs:
+    """
+    Utility for creating and modifying colormaps with various formats and fiducial
+    points.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        fiducials_ncol: Fiducial colors and their indices in the color map are\
+            listed in file Fiducials_Ncol.
+        fiducials: Fiducial colors are listed in an ascii file Fiducials.
+        num_colors: Total number of colors in the color map.
+        std_mapname: Returns one of SUMA's standard colormaps.
+        palette_file: Specify the palette file for colormap.
+        cmap_name: Specify the colormap name.
+        fscolut_labels: Get AFNI/SUMA colormaps of FreeSurfer colors indexed\
+            between lbl0 and lbl1.
+        fscolut_file: Use color LUT file FS_COL_LUT.
+        afni_hex: Afni Hex format. Use this option if you want a color map\
+            formatted to fit in AFNI's .afnirc file.
+        afni_hex_complete: Afni Hex format, ready to go into pbardefs.h.
+        suma_colormap: Write colormap in SUMA's format.
+        user_colut_file: Provide a user's own color lookup file.
+        sdset: Add colormap to surface-based dataset DSET, making it a labeled\
+            dataset.
+        sdset_prefix: Prefix of dset for writing labeled version of DSET.
+        flipupdown: Flip the map upside down.
+        skip_last: If used, the last color in the Fiducial list is omitted.
+        show_fscolut: Show all of the FreeSurfer LUT.
+        help_flag: Displays the help message.
+        help_full_flag: Displays the help message.
+        flip_map_updside_down: Flip the map upside down.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `MakeColorMapOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MAKE_COLOR_MAP_METADATA)
+    params = make_color_map_params(
+        fiducials_ncol=fiducials_ncol,
+        fiducials=fiducials,
+        num_colors=num_colors,
+        std_mapname=std_mapname,
+        palette_file=palette_file,
+        cmap_name=cmap_name,
+        fscolut_labels=fscolut_labels,
+        fscolut_file=fscolut_file,
+        afni_hex=afni_hex,
+        afni_hex_complete=afni_hex_complete,
+        suma_colormap=suma_colormap,
+        user_colut_file=user_colut_file,
+        sdset=sdset,
+        sdset_prefix=sdset_prefix,
+        flipupdown=flipupdown,
+        skip_last=skip_last,
+        show_fscolut=show_fscolut,
+        help_flag=help_flag,
+        help_full_flag=help_full_flag,
+        flip_map_updside_down=flip_map_updside_down,
+    )
+    return make_color_map_execute(params, execution)
+
+
+__all__ = [
+    "MAKE_COLOR_MAP_METADATA",
+    "MakeColorMapOutputs",
+    "MakeColorMapParameters",
+    "make_color_map",
+    "make_color_map_params",
+]

niwrap_afni/afni/make_pq_script_py.py

@@ -0,0 +1,200 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+MAKE_PQ_SCRIPT_PY_METADATA = Metadata(
+    id="a615a94a90a33ebcd0b428159142b2d1a4947946.boutiques",
+    name="make_pq_script.py",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+MakePqScriptPyParameters = typing.TypedDict('MakePqScriptPyParameters', {
+    "__STYX_TYPE__": typing.Literal["make_pq_script.py"],
+    "dataset": InputPathType,
+    "brick_index": float,
+    "mask": InputPathType,
+    "out_script": str,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "make_pq_script.py": make_pq_script_py_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 {
+        "make_pq_script.py": make_pq_script_py_outputs,
+    }.get(t)
+
+
+class MakePqScriptPyOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `make_pq_script_py(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    script: OutputPathType
+    """Generated output script"""
+
+
+def make_pq_script_py_params(
+    dataset: InputPathType,
+    brick_index: float,
+    mask: InputPathType,
+    out_script: str,
+) -> MakePqScriptPyParameters:
+    """
+    Build parameters.
+    
+    Args:
+        dataset: Input dataset (no sub-brick selectors).
+        brick_index: Volume sub-brick for specific t-stat.
+        mask: Mask volume dataset.
+        out_script: Name for output script to write.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "make_pq_script.py",
+        "dataset": dataset,
+        "brick_index": brick_index,
+        "mask": mask,
+        "out_script": out_script,
+    }
+    return params
+
+
+def make_pq_script_py_cargs(
+    params: MakePqScriptPyParameters,
+    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("make_pq_script.py")
+    cargs.append(execution.input_file(params.get("dataset")))
+    cargs.append(str(params.get("brick_index")))
+    cargs.append(execution.input_file(params.get("mask")))
+    cargs.append(params.get("out_script"))
+    return cargs
+
+
+def make_pq_script_py_outputs(
+    params: MakePqScriptPyParameters,
+    execution: Execution,
+) -> MakePqScriptPyOutputs:
+    """
+    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 = MakePqScriptPyOutputs(
+        root=execution.output_file("."),
+        script=execution.output_file(params.get("out_script")),
+    )
+    return ret
+
+
+def make_pq_script_py_execute(
+    params: MakePqScriptPyParameters,
+    execution: Execution,
+) -> MakePqScriptPyOutputs:
+    """
+    Creates a script to compute p-value and q-value curves.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `MakePqScriptPyOutputs`).
+    """
+    params = execution.params(params)
+    cargs = make_pq_script_py_cargs(params, execution)
+    ret = make_pq_script_py_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def make_pq_script_py(
+    dataset: InputPathType,
+    brick_index: float,
+    mask: InputPathType,
+    out_script: str,
+    runner: Runner | None = None,
+) -> MakePqScriptPyOutputs:
+    """
+    Creates a script to compute p-value and q-value curves.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        dataset: Input dataset (no sub-brick selectors).
+        brick_index: Volume sub-brick for specific t-stat.
+        mask: Mask volume dataset.
+        out_script: Name for output script to write.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `MakePqScriptPyOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MAKE_PQ_SCRIPT_PY_METADATA)
+    params = make_pq_script_py_params(
+        dataset=dataset,
+        brick_index=brick_index,
+        mask=mask,
+        out_script=out_script,
+    )
+    return make_pq_script_py_execute(params, execution)
+
+
+__all__ = [
+    "MAKE_PQ_SCRIPT_PY_METADATA",
+    "MakePqScriptPyOutputs",
+    "MakePqScriptPyParameters",
+    "make_pq_script_py",
+    "make_pq_script_py_params",
+]