creanzalab / chipper Goto Github PK

Hi,

I have been trying chipper today, congratulations on what looks like a fantastic tool!
I run into a couple of minor issues when trying to get it to work, and I thought I would let you know in case it's useful:

chipper_v1.0_linux, system info here.

I downloaded the .zip file, extracted its contents and started chipper by running start_chipper, as per the README.md. It started normally, but the audio didn't work:

[INFO   ] Setting up
[INFO   ] Loading file foo.wav
[CRITICAL] [AudioSDL2   ] Unable to open mixer: b'No such audio device'
[WARNING] Deprecated property "<AliasProperty name=filename>" of object "<kivy.core.audio.audio_sdl2.SoundSDL2 object at 0x7f1166f84590>" was accessed, it will be removed in a future version
[WARNING] [AudioSDL2   ] Unable to load foo.wav: b"Audio device hasn't been opened"

See the full output here and a similar issue reported here and possible solutions here. Everything else seems to work ok.

I then tried to install from source. The instructions will not work for a number of reasons (using conda, and for deb based Linux).

The following worked for me:

1. Clone the repository with git clone https://github.com/CreanzaLab/chipper.git

2. Create a new conda environment: conda create -n chipper_env python=3.7 -y

3. Activate the conda environment: conda activate chipper_env and avigate to ./chipper.

4. pip install --no-binary kivy kivy.

Note: Installing kivy from pypi directly by pip install -r requirements.txt resulted in the audio not working. Installing ffpyplayer resulted in the audio playing only once (might be the same issue reported here).

5. Run pip install -r requirements.txt

Note: conda install -r requirements.txt is not a valid conda command. I tried conda install -c conda-forge anaconda --file requirements.txt instead, but soundfile is not available in any conda channels.

conda install pypiwin32 kivy.deps.sdl2 kivy.deps.glew kivy.deps.gstreamer kivy.deps.glew_dev kivy.deps.sdl2_dev kivy.deps.gstreamer_dev or its pip alternative also dont't work—and should't be necessary given that kivy is listed in the requirements file. Also, I'm guessing that pypiwin32 doesn't belong there.

6. Install kivy packages

    garden install --kivy graph
    garden install --kivy filebrowser
    garden install --kivy matplotlib
    garden install --kivy progressspinner
   

7. Next, make the setup.py file that is missing in ./chipper

    from setuptools import find_packages, setup
   
    setup(
        name='chipper',
        packages=find_packages(),
        version='1.0',
    )
   

   and run python setup.py develop

8. Navigate to ./chipper/chipper and run python run_chipper.py

Everything works normally now, but the thresholded sonogram is not binary - i.e. it still has some red and yellow pixels, see example here. It doesn't seem to affect usability, however.

Thank you for putting the time to develop this tool! Will let you know if I run into any other issues.

Nilo