Example Bmode reconstruction doesn't run

[kwsp]

Trying to run the example but getting a type error in the uff dependency.

Using the latest version of k-wave-python from github on Ubuntu (WSL2).

(sim) ~ python3 bmode_reconstruction_example.py
Traceback (most recent call last):
  File "/home/tnie/code/sim/k-wave-python/examples/bmode_reconstruction_example.py", line 4, in <module>
    from kwave.reconstruction.beamform import beamform
  File "/home/tnie/code/sim/k-wave-python/kwave/reconstruction/beamform.py", line 4, in <module>
    from uff import UFF, ChannelData
  File "/home/tnie/miniconda3/envs/sim/lib/python3.10/site-packages/uff/__init__.py", line 48, in <module>
    from uff import converters, model  # noqa
  File "/home/tnie/miniconda3/envs/sim/lib/python3.10/site-packages/uff/model/__init__.py", line 48, in <module>
    from . import uff_pb2 as uff_pb  # noqa
  File "/home/tnie/miniconda3/envs/sim/lib/python3.10/site-packages/uff/model/uff_pb2.py", line 33, in <module>
    _descriptor.EnumValueDescriptor(
  File "/home/tnie/miniconda3/envs/sim/lib/python3.10/site-packages/google/protobuf/descriptor.py", line 755, in __new__
    _message.Message._CheckCalledFromGeneratedFile()
TypeError: Descriptors cannot not be created directly.
If this call came from a _pb2.py file, your generated code is out of date and must be regenerated with protoc >= 3.19.0.
If you cannot immediately regenerate your protos, some other possible workarounds are:
 1. Downgrade the protobuf package to 3.20.x or lower.
 2. Set PROTOCOL_BUFFERS_PYTHON_IMPLEMENTATION=python (but this will use pure-Python parsing and will be much slower).

More information: https://developers.google.com/protocol-buffers/docs/news/2022-05-06#python-updates

[waltsims]

Thank you for this, I'll look into it!

[waltsims]

Can you share with me the output of pip freeze?

[kwsp]

certifi @ file:///opt/conda/conda-bld/certifi_1655968806487/work/certifi
cycler==0.11.0
fonttools==4.33.3
h5py==3.7.0
-e git+ssh://git@github.com/kwsp/k-wave-python.git@1147462c92c112f3c1ec85e3427adbd020bb16e1#egg=k_Wave_python
kiwisolver==1.4.3
matplotlib==3.5.2
numpy==1.23.0
nvidia-pyindex==1.0.9
opencv-python==4.6.0.66
packaging==21.3
Pillow==9.2.0
protobuf==4.21.2
pyparsing==3.0.9
PyQt5==5.15.7
PyQt5-Qt5==5.15.2
PyQt5-sip==12.11.0
python-dateutil==2.8.2
scipy==1.8.1
six==1.16.0
uff==0.6.9

[waltsims]

It looks like you have installed another package called uff. Currently uff.py, the python port of the ultrasound file format, is not published to PyPi. There is another package called uff from NVIDIA with (currently) the same package name.

things should work if you uninstall uff with

pip uninstall uff
and install uff.py as defined in the requirement files via

pip install git+https://github.com/waltsims/uff.py@a672319b5cfbe3a676837e47c5958a3fdea12fa7

Please let me know if that works for you.

[waltsims]

There was a typo in the uninstall command that I just corrected.

[waltsims]

After testing the solution this should solve your issue. closing for now.