diff --git a/backend/config.yaml b/backend/config.yaml index 19b5208..3892524 100644 --- a/backend/config.yaml +++ b/backend/config.yaml @@ -1,4 +1,5 @@ model: + save_dir: models data: root_dir: . diff --git a/backend/cp_run.py b/backend/cp_run.py index 37b40f6..68e9b91 100644 --- a/backend/cp_run.py +++ b/backend/cp_run.py @@ -1,8 +1,7 @@ -from cellpose import models, plot -from cellpose.io import imread, save_masks +import os from PIL import Image import numpy as np -import os, datetime +import datetime import time from omegaconf import OmegaConf from pathlib import Path @@ -14,6 +13,12 @@ BASE_DIR = cfg.data.root_dir UPLOAD_DIR = cfg.data.upload_dir OUTPUT_DIR = cfg.data.run.output_dir OUTPUT_TEST_DIR = cfg.data.run.test_output_dir +MODELS_DIR = str((CONFIG_PATH.parent / cfg.model.save_dir).resolve()) +os.makedirs(MODELS_DIR, exist_ok=True) +os.environ["CELLPOSE_LOCAL_MODELS_PATH"] = MODELS_DIR + +from cellpose import models, plot +from cellpose.io import imread, save_masks class Cprun: