timsainb/avgn_paper

Latent and generative models of animal vocalizations for songbirds, mice, primates, humans, cetaceans, etc.

avgn_paper's Issues

About requirements.txt

Hi Tim,

It seems that the requirements.txt does not specify the versions for each packages, so does it mean that for each package, the latest version is okay? I tried pip install -r requirements .txt and run the tutorials, but there are still bugs related to not installed packages or version incompatibilities between installed packages.

Fix for OS specific files

Some errors are given with invisible files in the tutorial e.g. .ds_store for macs.

this can be filtered e.g. with paths.py:

subdir_list = list((dataset_loc).iterdir())
subdir_list = [i for i in subdir_list if i != '.DS_Store']

AttributeError: 'Tensor' object has no attribute 'numpy'

am trying to run bf-koumura-syllable-df notebook.
this line:

create a dataset object

dataset = DataSet(DATASET_ID, hparams = hparams)

gives me an

AttributeError: 'Tensor' object has no attribute 'numpy'

am running on CPU only, don't have access to GPU right now. maybe related to this?

vocalseg.utils

in /notebooks/00.1-data-exploration/butcherbird-exploration.ipynb

from vocalseg.utils import butter_bandpass_filter, spectrogram, int16tofloat32, plot_spec
gives me

---------------------------------------------------------------------------
ModuleNotFoundError                       Traceback (most recent call last)
<ipython-input-14-f72d2c72aa59> in <module>
----> 1 from vocalseg.utils import butter_bandpass_filter, spectrogram, int16tofloat32, plot_spec

ModuleNotFoundError: No module named 'vocalseg'

a quick search in the sources didn't yield any results for me. i suppose i can just use the one here? https://github.com/timsainb/vocalization-segmentation

circular dependency?

cannot import name most_recent_subdirectory from avgn.utils.paths

def most_recent_subdirectory(dataset_loc):
""" return the subdirectory that has been generated most
recently with the "%Y-%m-%d_%H-%M-%S" time scheme used in AVGN
"""
subdir_list = list((dataset_loc).iterdir())
directory_dates = [
datetime.strptime(i.name, "%Y-%m-%d_%H-%M-%S") for i in subdir_list
]
return subdir_list[np.argsort(directory_dates)[-1]]

Wrong lines in scatter_spec

Hello @timsainb,

Using scatter_spec() I plotted successfully my UMAP's projection, however the lines added by the parameter draw_lines seem to point at the wrong locations.

Any ideas?

Thanks

Invalid file names preventing installation

Hi Tim,
I tried cloning this repo on my windows 10 laptop today, and ran into an error due to the use of invalid characters for windows file paths in the file notebooks/01.1-syllabic-segmentation/fruit-bat/.ipynb_checkpoints/delete?fruit_bat_segment-all-2.0-checkpoint.ipynb. Windows doesn't allow '?' in file paths, so it blocked successful checkout of the repo. I found a work around, but I would imagine that this will be a recurring issue for anyone trying to clone the repo on a windows device. Could you:

• remove the question mark from that file name
• remove the question mark from the corresponding .ipynb checkpoint (or just add the checkpoints folder to your .gitignore)