oliviergimenez / lynx-id

Re-identify individuals and estimate population density from eurasian lynx population by Deep Learning and Spatial Capture Recapture (Python & R)

DP-SCR_Identify-and-estimate-density-lynx-population

Running code outside the lynx_id module

To run code outside lynx_id folder that uses this module (for example, files in the test folder), you need to install the project locally in editable mode.
On Jean-Zay, first load the module like that :

• module load pytorch-gpu/py3/2.2.0 Then run a command similar to this one at the root of the project:
• pip install --editable . --user --no-cache-dir

You can then run code that does from lynx_id. ... import ....

Preprocess

To prepare the data, perform the following instructions in the following order:

• Running the notebook ./lynx_id/preprocess/preprocess_dataset.ipynb with a V100 GPU