import fails with OSError on headless system

[thawn]

importing napari_simpleitk_image_processing fails with errors about missing GL libraries (see below). I assume this means that this plugin needs a working display?

is there a workaround to make this plugin work without gl support?

Cheers,

Till

`napari_simpleitk_image_processing` import errors

---------------------------------------------------------------------------

OSError Traceback (most recent call last)
Input In [6], in <cell line: 7>()
5 import numpy as np
6 #import napari_segment_blobs_and_things_with_membranes as nsbatwm
----> 7 import napari_simpleitk_image_processing as nsitk

File /app/env/lib/python3.9/site-packages/napari_simpleitk_image_processing/init.py:9, in
3 common_alias = "nsitk"
8 from ._function import napari_experimental_provide_function
----> 9 from ._simpleitk_image_processing import
10 plugin_function,
11 median_filter,
12 gaussian_blur,
13 threshold_otsu,
14 threshold_intermodes,
15 threshold_kittler_illingworth,
16 threshold_li,
17 threshold_moments,
18 threshold_renyi_entropy,
19 threshold_shanbhag,
20 threshold_yen,
21 threshold_isodata,
22 threshold_triangle,
23 threshold_huang,
24 threshold_maximum_entropy,
25 signed_maurer_distance_map,
26 morphological_watershed,
27 morphological_gradient,
28 standard_deviation_filter,
29 simple_linear_iterative_clustering,
30 scalar_image_k_means_clustering,
31 connected_component_labeling,
32 touching_objects_labeling,
33 watershed_otsu_labeling,
34 binary_fill_holes,
35 invert_intensity,
36 bilateral_filter,
37 laplacian_filter,
38 laplacian_of_gaussian_filter,
39 binominal_blur_filter,
40 canny_edge_detection,
41 gradient_magnitude,
42 h_maxima,
43 h_minima,
44 otsu_multiple_thresholds,
45 regional_maxima,
46 regional_minima,
47 richardson_lucy_deconvolution,
48 wiener_deconvolution,
49 tikhonov_deconvolution,
50 rescale_intensity,
51 sobel,
52 black_top_hat,
53 white_top_hat,
54 adaptive_histogram_equalization,
55 curvature_flow_denoise,
56 relabel_component,
57 label_contour,
58 label_statistics,
59 pixel_count_map,
60 elongation_map,
61 feret_diameter_map,
62 roundness_map

File /app/env/lib/python3.9/site-packages/napari_simpleitk_image_processing/_simpleitk_image_processing.py:7, in
5 from toolz import curry
6 import inspect
----> 7 from napari_tools_menu import register_function
8 from napari_time_slicer import time_slicer
9 from napari_skimage_regionprops._all_frames import analyze_all_frames

File /app/env/lib/python3.9/site-packages/napari_tools_menu/init.py:9, in
7 import warnings
8 import napari
----> 9 import napari._qt
10 import numpy as np
11 from qtpy.QtWidgets import QMenu

File /app/env/lib/python3.9/site-packages/napari/qt/init.py:53, in
45 warn_message = trans.(
46 "\n\nnapari was tested with QT library >=5.12.3.\nThe version installed is {version}. Please report any issues with\nthis specific QT version at https://github.com/Napari/napari/issues. style="color:rgb(175,0,0)">",
47 deferred=True,
48 version=QtCore.version,
49 )
50 warn(message=warn_message)
---> 53 from .qt_event_loop import get_app, gui_qt, quit_app, run
54 from .qt_main_window import Window

File /app/env/lib/python3.9/site-packages/napari/_qt/qt_event_loop.py:15, in
12 from qtpy.QtWidgets import QApplication
14 from .. import version
---> 15 from ..settings import get_settings
16 from ..utils import config, perf
17 from ..utils.notifications import (
18 notification_manager,
19 show_console_notification,
20 )

File /app/env/lib/python3.9/site-packages/napari/settings/init.py:6, in
4 from ..utils.translations import trans
5 from ._base import _NOT_SET
----> 6 from ._napari_settings import NapariSettings
8 all = ['NapariSettings', 'get_settings']
11 class _SettingsProxy:

File /app/env/lib/python3.9/site-packages/napari/settings/_napari_settings.py:9, in
7 from ..utils._base import _DEFAULT_CONFIG_PATH
8 from ..utils.translations import trans
----> 9 from ._appearance import AppearanceSettings
10 from ._application import ApplicationSettings
11 from ._base import EventedConfigFileSettings, _remove_empty_dicts

File /app/env/lib/python3.9/site-packages/napari/settings/_appearance.py:4, in
1 from pydantic import Field
3 from ..utils.events.evented_model import EventedModel
----> 4 from ..utils.theme import available_themes
5 from ..utils.translations import trans
6 from ._fields import Theme

File /app/env/lib/python3.9/site-packages/napari/utils/init.py:2, in
1 from ._dask_utils import resize_dask_cache
----> 2 from .colormaps import Colormap
3 from .info import citation_text, sys_info
4 from .notebook_display import nbscreenshot

File /app/env/lib/python3.9/site-packages/napari/utils/colormaps/init.py:2, in
1 from .colorbars import make_colorbar
----> 2 from .colormap import Colormap
3 from .colormap_utils import (
4 ALL_COLORMAPS,
5 AVAILABLE_COLORMAPS,
(...)
16 matplotlib_colormaps,
17 )

File /app/env/lib/python3.9/site-packages/napari/utils/colormaps/colormap.py:11, in
9 from ..translations import trans
10 from .colorbars import make_colorbar
---> 11 from .standardize_color import transform_color
14 class ColormapInterpolationMode(str, Enum):
15 """INTERPOLATION: Interpolation mode for colormaps.
16
17 Selects an interpolation mode for the colormap.
(...)
21 bin between by neighboring controls points.
22 """

File /app/env/lib/python3.9/site-packages/napari/utils/colormaps/standardize_color.py:27, in
24 from typing import Any, Callable, Dict, Sequence
26 import numpy as np
---> 27 from vispy.color import ColorArray, get_color_dict, get_color_names
28 from vispy.color.color_array import _string_to_rgb
30 from ..translations import trans

File /app/env/lib/python3.9/site-packages/vispy/color/init.py:12, in
10 from ._color_dict import get_color_names, get_color_dict # noqa
11 from .color_array import Color, ColorArray
---> 12 from .colormap import (Colormap, BaseColormap, # noqa
13 get_colormap, get_colormaps) # noqa
15 all = ['Color', 'ColorArray', 'Colormap', 'BaseColormap',
16 'get_colormap', 'get_colormaps',
17 'get_color_names', 'get_color_dict']

File /app/env/lib/python3.9/site-packages/vispy/color/colormap.py:14, in
12 from hsluv import hsluv_to_rgb
13 from ..util.check_environment import has_matplotlib
---> 14 import vispy.gloo
16 ###############################################################################
17 # Color maps
18
19 # Length of the texture map used for luminance to RGBA conversion
20 LUT_len = 1024

File /app/env/lib/python3.9/site-packages/vispy/gloo/init.py:47, in
5 """
6 Object oriented interface to OpenGL.
7
(...)
42
43 """
45 from future import division
---> 47 from . import gl # noqa
48 from .wrappers import * # noqa
49 from .context import (GLContext, get_default_config, # noqa
50 get_current_canvas) # noqa

File /app/env/lib/python3.9/site-packages/vispy/gloo/gl/init.py:230, in
228 from . import gl2 as default_backend # noqa
229 if default_backend._lib is None: # Probably Android or RPi
--> 230 from . import es2 as default_backend # noqa
233 # Call use to start using our default backend
234 use_gl()

File /app/env/lib/python3.9/site-packages/vispy/gloo/gl/es2.py:48, in
46 # Else, we failed and exit
47 if es2_file is None:
---> 48 raise OSError('GL ES 2.0 library not found')
49 # Load it
50 _lib = ctypes.CDLL(es2_file)

OSError: GL ES 2.0 library not found

[haesleinhuepf]

HI @thawn ,

this bug should be fixed in the recent release of nsitk. Can you check? If not, please let me know how I can reproduce the issue.

Thanks!
Best,
Robert