Phy gui is blank apart from cluster view and similarity view--if using python 3.12

[AbhiSwamiUConn]

When I open the gui using the command phy template-gui params.py, the gui opens but apart from what is listed in the title, nothing shows up. I am on a windows 10 machine with an intel x-series processor.

[zm711]

If you run:

phy template-gui params.py --debug

What appears?

[AbhiSwamiUConn]

This is what appears: 11:33:28.470 [D] init:68 Start capturing exceptions. 11:33:28.594 [D] model:619 Loading spike clusters. 11:33:28.711 [D] model:569 No channel shank file found. 11:33:28.712 [D] model:692 Loading templates. 11:33:28.715 [D] model:720 Templates are sparse. 11:33:28.720 [W] model:667 Skipping spike waveforms that do not exist, they will be extracted on the fly from the raw data as needed. 11:33:28.720 [D] model:730 Loading the whitening matrix. 11:33:28.720 [D] model:434 Whitening matrix file not found. 11:33:28.721 [D] model:737 Loading the inverse of the whitening matrix. 11:33:28.721 [D] model:440 Whitening matrix inverse file not found, computing it. 11:33:28.721 [D] model:744 Inversing the whitening matrix (3, 3). 11:33:28.725 [D] model:766 Loading features. 11:33:28.727 [D] model:781 Features are sparse. 11:33:28.727 [D] model:803 Loading template features. 11:33:28.728 [D] model:504 Load cluster_channel_group.tsv. 11:33:28.729 [D] model:504 Load cluster_group.tsv. 11:33:28.730 [D] model:504 Load cluster_si_unit_ids.tsv. 11:33:29.365 [D] context:80 Create cache directory C:\Users\User\Desktop\Abhinav\files3\.phy. 11:33:29.412 [D] context:100 Initialize joblib cache dir at C:\Users\User\Desktop\Abhinav\files3\.phy. 11:33:29.413 [D] context:101 Reducing the size of the cache if needed. 11:33:29.415 [D] base:102 Add filter high_pass. 11:33:29.416 [D] config:31 Load config file C:\Users\User\.phy\phy_config.py. 11:33:29.417 [D] plugin:145 Loading 0 plugins. 11:33:29.423 [D] context:209 The file C:\Users\User\Desktop\Abhinav\files3\.phy\new_cluster_id.pkl doesn't exist. 11:33:29.423 [D] context:209 The file C:\Users\User\Desktop\Abhinav\files3\.phy\spikes_per_cluster.pkl doesn't exist. 11:33:29.443 [D] clustering:237 Recompute spikes_per_cluster manually: this might take a while. 11:33:29.651 [D] context:185 Save data to C:\Users\User\Desktop\Abhinav\files3\.phy\spikes_per_cluster.pkl. 11:33:29.666 [D] gui:463 Creating GUI. 11:33:29.691 [D] state:46 Load C:\Users\User.phy\TemplateGUI\state.json for GUIState. 11:33:30.195 [D] gui:718 Add view ClusterView to GUI. 11:33:30.209 [D] gui:718 Add view SimilarityView to GUI. 11:33:30.245 [D] gui:718 Add view WaveformView to GUI. 11:33:30.513 [D] base:337 Set state for WaveformView. 11:33:30.543 [D] gui:718 Add view WaveformView to GUI. 11:33:30.546 [D] base:337 Set state for WaveformView (1). 11:33:30.555 [D] gui:718 Add view TraceImageView to GUI. 11:33:30.557 [D] base:337 Set state for TraceImageView. 11:33:30.557 [D] base:494 Set color scheme to random. 11:33:30.562 [D] base:1626 Adding default color schemes to TraceImageView. 11:33:31.046 [D] gui:519 Load the geometry state. dict_keys([<class 'numpy.ndarray'>, <class 'bytes'>, <class 'OpenGL.converters.c_long_Array_1'>]) 11:33:31.217 [D] base:702 Exception in paintGL: ("No array-type handler for type _ctypes.CArgObject (value: <cparam 'P' (0x000001F4366CD098)>) registered", 'Failure in cConverter <OpenGL.converters.OutputOrInput object at 0x000001F42B70E990>', (3, 0, 32, <cparam 'P' (0x000001F4366CD098)>, <cparam 'P' (0x000001F4366CD118)>, <cparam 'P' (0x000001F4366CCC18)>, <ctypes.c_char_Array_32 object at 0x000001F4366CD150>), 3, <OpenGL.platform.baseplatform.glGetActiveAttrib object at 0x000001F429B807D0>)

[zm711]

So your install is busted :(

Now we need to figure out why. How did you install?

[AbhiSwamiUConn]

I installed using a yml file containing the following text: name: phy2 channels:

• conda-forge
• defaults dependencies:
• python
• pip
• git
• numpy
• matplotlib
• scipy
• h5py
• pyqt
• pyopengl
• pyqtwebengine
• pytest
• qtconsole
• requests
• responses
• traitlets
• dask
• cython
• pillow
• scikit-learn
• joblib
• pip:
  • git+https://github.com/cortex-lab/phy.git

[zm711]

could you do

conda list

inside of the environment you created ?

[AbhiSwamiUConn]

packages in environment at C:\Users\User\anaconda3\envs\phy2:

Name Version Build Channel

asttokens 2.4.1 pyhd8ed1ab_0 conda-forge aws-c-auth 0.7.22 ha390a07_2 conda-forge aws-c-cal 0.6.14 h750c3ff_1 conda-forge aws-c-common 0.9.19 h2466b09_0 conda-forge aws-c-compression 0.2.18 h750c3ff_6 conda-forge aws-c-event-stream 0.4.2 he05106e_12 conda-forge aws-c-http 0.8.1 h55c4ea9_17 conda-forge aws-c-io 0.14.8 ha255af7_5 conda-forge aws-c-mqtt 0.10.4 heb8cf2b_4 conda-forge aws-c-s3 0.5.9 haf5e0f7_3 conda-forge aws-c-sdkutils 0.1.16 h750c3ff_2 conda-forge aws-checksums 0.1.18 h750c3ff_6 conda-forge aws-crt-cpp 0.26.9 hb2f7e64_0 conda-forge aws-sdk-cpp 1.11.329 h752cf48_3 conda-forge bokeh 3.4.1 pyhd8ed1ab_0 conda-forge brotli 1.1.0 hcfcfb64_1 conda-forge brotli-bin 1.1.0 hcfcfb64_1 conda-forge brotli-python 1.1.0 py312h53d5487_1 conda-forge bzip2 1.0.8 hcfcfb64_5 conda-forge c-ares 1.28.1 hcfcfb64_0 conda-forge ca-certificates 2024.6.2 h56e8100_0 conda-forge cached-property 1.5.2 hd8ed1ab_1 conda-forge cached_property 1.5.2 pyha770c72_1 conda-forge certifi 2024.2.2 pyhd8ed1ab_0 conda-forge charset-normalizer 3.3.2 pyhd8ed1ab_0 conda-forge click 8.1.7 win_pyh7428d3b_0 conda-forge cloudpickle 3.0.0 pyhd8ed1ab_0 conda-forge colorama 0.4.6 pyhd8ed1ab_0 conda-forge colorcet 3.1.0 pypi_0 pypi comm 0.2.2 pyhd8ed1ab_0 conda-forge contourpy 1.2.1 py312h0d7def4_0 conda-forge cycler 0.12.1 pyhd8ed1ab_0 conda-forge cython 3.0.10 py312h53d5487_0 conda-forge cytoolz 0.12.3 py312he70551f_0 conda-forge dask 2024.5.2 pyhd8ed1ab_0 conda-forge dask-core 2024.5.2 pyhd8ed1ab_0 conda-forge dask-expr 1.1.2 pyhd8ed1ab_0 conda-forge debugpy 1.8.1 py312h53d5487_0 conda-forge decorator 5.1.1 pyhd8ed1ab_0 conda-forge distributed 2024.5.2 pyhd8ed1ab_0 conda-forge exceptiongroup 1.2.0 pyhd8ed1ab_2 conda-forge executing 2.0.1 pyhd8ed1ab_0 conda-forge fonttools 4.53.0 py312h4389bb4_0 conda-forge freetype 2.12.1 hdaf720e_2 conda-forge freetype-py 2.4.0 pypi_0 pypi fsspec 2024.5.0 pyhff2d567_0 conda-forge gettext 0.22.5 h5728263_2 conda-forge gettext-tools 0.22.5 h7d00a51_2 conda-forge ghp-import 2.1.0 pypi_0 pypi git 2.45.1 h57928b3_0 conda-forge glib 2.80.2 h0df6a38_0 conda-forge glib-tools 2.80.2 h2f9d560_0 conda-forge gst-plugins-base 1.22.9 h001b923_1 conda-forge gstreamer 1.22.9 hb4038d2_1 conda-forge h5py 3.11.0 nompi_py312ha036244_101 conda-forge hdf5 1.14.3 nompi_h2b43c12_103 conda-forge hsluv 5.0.4 pypi_0 pypi icu 73.2 h63175ca_0 conda-forge idna 3.7 pyhd8ed1ab_0 conda-forge importlib-metadata 7.1.0 pyha770c72_0 conda-forge importlib_metadata 7.1.0 hd8ed1ab_0 conda-forge iniconfig 2.0.0 pyhd8ed1ab_0 conda-forge intel-openmp 2024.1.0 h57928b3_966 conda-forge ipykernel 6.29.3 pyha63f2e9_0 conda-forge ipython 8.25.0 pyh7428d3b_0 conda-forge jedi 0.19.1 pyhd8ed1ab_0 conda-forge jinja2 3.1.4 pyhd8ed1ab_0 conda-forge joblib 1.4.2 pyhd8ed1ab_0 conda-forge jupyter_client 8.6.2 pyhd8ed1ab_0 conda-forge jupyter_core 5.7.2 py312h2e8e312_0 conda-forge kiwisolver 1.4.5 py312h0d7def4_1 conda-forge krb5 1.21.2 heb0366b_0 conda-forge lcms2 2.16 h67d730c_0 conda-forge lerc 4.0.0 h63175ca_0 conda-forge libabseil 20240116.2 cxx17_h63175ca_0 conda-forge libaec 1.1.3 h63175ca_0 conda-forge libarrow 16.1.0 h35ad6a0_6_cpu conda-forge libarrow-acero 16.1.0 he0c23c2_6_cpu conda-forge libarrow-dataset 16.1.0 he0c23c2_6_cpu conda-forge libarrow-substrait 16.1.0 h1f0e801_6_cpu conda-forge libasprintf 0.22.5 h5728263_2 conda-forge libasprintf-devel 0.22.5 h5728263_2 conda-forge libblas 3.9.0 22_win64_mkl conda-forge libbrotlicommon 1.1.0 hcfcfb64_1 conda-forge libbrotlidec 1.1.0 hcfcfb64_1 conda-forge libbrotlienc 1.1.0 hcfcfb64_1 conda-forge libcblas 3.9.0 22_win64_mkl conda-forge libclang13 18.1.6 default_hf64faad_0 conda-forge libcrc32c 1.1.2 h0e60522_0 conda-forge libcurl 8.8.0 hd5e4a3a_0 conda-forge libdeflate 1.20 hcfcfb64_0 conda-forge libevent 2.1.12 h3671451_1 conda-forge libexpat 2.6.2 h63175ca_0 conda-forge libffi 3.4.2 h8ffe710_5 conda-forge libgettextpo 0.22.5 h5728263_2 conda-forge libgettextpo-devel 0.22.5 h5728263_2 conda-forge libglib 2.80.2 h0df6a38_0 conda-forge libgoogle-cloud 2.24.0 h5e7cea3_0 conda-forge libgoogle-cloud-storage 2.24.0 hce61461_0 conda-forge libgrpc 1.62.2 h5273850_0 conda-forge libhwloc 2.10.0 default_h8125262_1001 conda-forge libiconv 1.17 hcfcfb64_2 conda-forge libintl 0.22.5 h5728263_2 conda-forge libintl-devel 0.22.5 h5728263_2 conda-forge libjpeg-turbo 3.0.0 hcfcfb64_1 conda-forge liblapack 3.9.0 22_win64_mkl conda-forge libogg 1.3.4 h8ffe710_1 conda-forge libparquet 16.1.0 h178134c_6_cpu conda-forge libpng 1.6.43 h19919ed_0 conda-forge libprotobuf 4.25.3 h503648d_0 conda-forge libre2-11 2023.09.01 hf8d8778_2 conda-forge libsodium 1.0.18 h8d14728_1 conda-forge libsqlite 3.45.3 hcfcfb64_0 conda-forge libssh2 1.11.0 h7dfc565_0 conda-forge libthrift 0.19.0 ha2b3283_1 conda-forge libtiff 4.6.0 hddb2be6_3 conda-forge libutf8proc 2.8.0 h82a8f57_0 conda-forge libvorbis 1.3.7 h0e60522_0 conda-forge libwebp 1.4.0 h2466b09_0 conda-forge libwebp-base 1.4.0 hcfcfb64_0 conda-forge libxcb 1.15 hcd874cb_0 conda-forge libxml2 2.12.7 h73268cd_0 conda-forge libzlib 1.3.1 h2466b09_1 conda-forge locket 1.0.0 pyhd8ed1ab_0 conda-forge lz4 4.3.3 py312h594ca44_0 conda-forge lz4-c 1.9.4 hcfcfb64_0 conda-forge m2w64-gcc-libgfortran 5.3.0 6 conda-forge m2w64-gcc-libs 5.3.0 7 conda-forge m2w64-gcc-libs-core 5.3.0 7 conda-forge m2w64-gmp 6.1.0 2 conda-forge m2w64-libwinpthread-git 5.0.0.4634.697f757 2 conda-forge markdown 3.6 pypi_0 pypi markupsafe 2.1.5 py312he70551f_0 conda-forge matplotlib 3.8.4 py312h2e8e312_2 conda-forge matplotlib-base 3.8.4 py312hfee7060_2 conda-forge matplotlib-inline 0.1.7 pyhd8ed1ab_0 conda-forge mergedeep 1.3.4 pypi_0 pypi mkdocs 1.6.0 pypi_0 pypi mkdocs-get-deps 0.2.0 pypi_0 pypi mkl 2024.1.0 h66d3029_692 conda-forge msgpack-python 1.0.8 py312hd5eb7cc_0 conda-forge msys2-conda-epoch 20160418 1 conda-forge mtscomp 1.0.2 pypi_0 pypi munkres 1.1.4 pyh9f0ad1d_0 conda-forge nest-asyncio 1.6.0 pyhd8ed1ab_0 conda-forge numpy 1.26.4 py312h8753938_0 conda-forge openjpeg 2.5.2 h3d672ee_0 conda-forge openssl 3.3.0 h2466b09_3 conda-forge orc 2.0.1 h7e885a9_1 conda-forge packaging 24.0 pyhd8ed1ab_0 conda-forge pandas 2.2.2 py312h72972c8_1 conda-forge parso 0.8.4 pyhd8ed1ab_0 conda-forge partd 1.4.2 pyhd8ed1ab_0 conda-forge pathspec 0.12.1 pypi_0 pypi pcre2 10.43 h17e33f8_0 conda-forge phy 2.0b5 pypi_0 pypi phylib 2.5.0 pypi_0 pypi pickleshare 0.7.5 py_1003 conda-forge pillow 10.3.0 py312h6f6a607_0 conda-forge pip 24.0 pyhd8ed1ab_0 conda-forge platformdirs 4.2.2 pyhd8ed1ab_0 conda-forge pluggy 1.5.0 pyhd8ed1ab_0 conda-forge ply 3.11 pyhd8ed1ab_2 conda-forge prompt-toolkit 3.0.42 pyha770c72_0 conda-forge psutil 5.9.8 py312he70551f_0 conda-forge pthread-stubs 0.4 hcd874cb_1001 conda-forge pthreads-win32 2.9.1 hfa6e2cd_3 conda-forge pure_eval 0.2.2 pyhd8ed1ab_0 conda-forge pyarrow 16.1.0 py312hd42ba9a_1 conda-forge pyarrow-core 16.1.0 py312h78844f3_1_cpu conda-forge pyarrow-hotfix 0.6 pyhd8ed1ab_0 conda-forge pygments 2.18.0 pyhd8ed1ab_0 conda-forge pyopengl 3.1.6 pyhd8ed1ab_1 conda-forge pyparsing 3.1.2 pyhd8ed1ab_0 conda-forge pyqt 5.15.9 py312he09f080_5 conda-forge pyqt5-sip 12.12.2 py312h53d5487_5 conda-forge pyqtwebengine 5.15.9 py312hca0710b_5 conda-forge pysocks 1.7.1 pyh0701188_6 conda-forge pytest 8.2.1 pyhd8ed1ab_0 conda-forge python 3.12.3 h2628c8c_0_cpython conda-forge python-dateutil 2.9.0 pyhd8ed1ab_0 conda-forge python-tzdata 2024.1 pyhd8ed1ab_0 conda-forge python_abi 3.12 4_cp312 conda-forge pytz 2024.1 pyhd8ed1ab_0 conda-forge pywin32 306 py312h53d5487_2 conda-forge pyyaml 6.0.1 py312he70551f_1 conda-forge pyyaml-env-tag 0.1 pypi_0 pypi pyzmq 26.0.3 py312hd7027bb_0 conda-forge qt-main 5.15.8 h9e85ed6_20 conda-forge qt-webengine 5.15.8 h4bf5c4e_4 conda-forge qtconsole 5.5.2 pyhd8ed1ab_0 conda-forge qtconsole-base 5.5.2 pyha770c72_0 conda-forge qtpy 2.4.1 pyhd8ed1ab_0 conda-forge re2 2023.09.01 hd3b24a8_2 conda-forge requests 2.32.3 pyhd8ed1ab_0 conda-forge responses 0.25.0 pyhd8ed1ab_0 conda-forge scikit-learn 1.5.0 py312h816cc57_1 conda-forge scipy 1.13.1 py312h1f4e10d_0 conda-forge setuptools 70.0.0 pyhd8ed1ab_0 conda-forge sip 6.7.12 py312h53d5487_0 conda-forge six 1.16.0 pyh6c4a22f_0 conda-forge snappy 1.2.0 hfb803bf_1 conda-forge sortedcontainers 2.4.0 pyhd8ed1ab_0 conda-forge stack_data 0.6.2 pyhd8ed1ab_0 conda-forge tbb 2021.12.0 hc790b64_1 conda-forge tblib 3.0.0 pyhd8ed1ab_0 conda-forge threadpoolctl 3.5.0 pyhc1e730c_0 conda-forge tk 8.6.13 h5226925_1 conda-forge toml 0.10.2 pyhd8ed1ab_0 conda-forge tomli 2.0.1 pyhd8ed1ab_0 conda-forge toolz 0.12.1 pyhd8ed1ab_0 conda-forge tornado 6.4 py312he70551f_0 conda-forge tqdm 4.66.4 pypi_0 pypi traitlets 5.14.3 pyhd8ed1ab_0 conda-forge types-pyyaml 6.0.12.20240311 pyhd8ed1ab_0 conda-forge typing_extensions 4.12.1 pyha770c72_0 conda-forge tzdata 2024a h0c530f3_0 conda-forge ucrt 10.0.22621.0 h57928b3_0 conda-forge urllib3 2.2.1 pyhd8ed1ab_0 conda-forge vc 14.3 ha32ba9b_20 conda-forge vc14_runtime 14.38.33135 h835141b_20 conda-forge vispy 0.14.2 pypi_0 pypi vs2015_runtime 14.38.33135 h22015db_20 conda-forge watchdog 4.0.1 pypi_0 pypi wcwidth 0.2.13 pyhd8ed1ab_0 conda-forge wheel 0.43.0 pyhd8ed1ab_1 conda-forge win_inet_pton 1.1.0 pyhd8ed1ab_6 conda-forge xorg-libxau 1.0.11 hcd874cb_0 conda-forge xorg-libxdmcp 1.1.3 hcd874cb_0 conda-forge xyzservices 2024.4.0 pyhd8ed1ab_0 conda-forge xz 5.2.6 h8d14728_0 conda-forge yaml 0.2.5 h8ffe710_2 conda-forge zeromq 4.3.5 he1f189c_4 conda-forge zict 3.0.0 pyhd8ed1ab_0 conda-forge zipp 3.17.0 pyhd8ed1ab_0 conda-forge zstd 1.5.6 h0ea2cb4_0 conda-forge

[zm711]

Does openGL work on your Intel x-series? Seems like the error is happening there.

[AbhiSwamiUConn]

How do I check that openGL works correctly?

[zm711]

I would just google. For example Apple deprecated the use of openGL on macOS years ago which makes it very hard/basically impossible at this point to run phy on an M-series Mac. So I would google your exact processor and see if there are any issues with openGL on your processor/ in Windows 10.

I've got Phy working on a Windows ten, but on the standard i-series processors, so I just wasn't sure if the x-series were the problem.

[AbhiSwamiUConn]

From what I see, intel x-series processors themselves do not have graphics support. However, the computer I am using does appear to have a graphics card that supports at least openGL 4.5. Second, when I look in windows settings, hardware accelerated gpu scheduling is off.

[zm711]

name: phy2_test
channels:
  - conda-forge
  - defaults
dependencies:
  - python=3.11
  - pip
  - git
  - numpy
  - matplotlib
  - scipy
  - h5py
  - pyqt
  - pyopengl
  - pyqtwebengine
  - pytest
  - qtconsole
  - requests
  - responses
  - traitlets
  - dask
  - cython
  - pillow
  - scikit-learn
  - joblib
  - pip:
    - git+https://github.com/cortex-lab/phy.git

could you try using this as your yaml instead. We recently tried adding 3.12 support, but I think it might not be fully there yet.

[AbhiSwamiUConn]

That works. Thank you.

[zm711]

Thank you! It helped me discover that there is still an issue with 3.12. I changed the yaml file to automatically just do python 3.11 until I can track down the issue.

[jesusdpa1]

For anyone looking into this, at least on macOS M1 the issue seems to be with opengl

when setting up the startup of phy like this it works, now I am still unable to use manual clustering,

import os
from pathlib import Path

from PyQt5.QtGui import QSurfaceFormat

from phy.apps.template import template_gui

# Set environment variables BEFORE importing QtWebEngine
os.environ['QTWEBENGINE_CHROMIUM_FLAGS'] = (
    '--enable-gpu --use-gl=desktop --enable-features=VaapiVideoDecoder'
)
os.environ['QTWEBENGINE_DISABLE_SANDBOX'] = '1'


# Configure OpenGL for both PyQt5 and QtWebEngine
def setup_opengl_for_webengine():
    # This must be called before QApplication creation
    # QApplication.setAttribute(Qt.AA_ShareOpenGLContexts, True)

    format = QSurfaceFormat()
    format.setVersion(2, 1)  # Mac M1 maximum
    format.setProfile(QSurfaceFormat.CoreProfile)
    format.setDepthBufferSize(24)
    format.setStencilBufferSize(8)
    format.setSamples(4)
    format.setSwapBehavior(QSurfaceFormat.DoubleBuffer)

    QSurfaceFormat.setDefaultFormat(format)


# Apply configuration
setup_opengl_for_webengine()
# Now all OpenGL contexts created will use this format
# %%
HOME_PATH = Path().home()
BASE_PATH = HOME_PATH / 'Documents'
PARAMS_PATH = BASE_PATH / 'ks4_output_2025-06-10_19-27' / 'sorter_output' / 'params.py'

# %%
template_gui(PARAMS_PATH)

An OpenGL surfcace format was requested that is either not version 3.2 or higher or a not Core Profile.
Chromium on macOS will fall back to software rendering in this case.
Hardware acceleration and features such as WebGL will not be available.
Sandboxing disabled by user.