Added remaining files

README.md

@@ -1,2 +1,12 @@
-# coc_ui
-UI for the cumulus expansion computer
+# COC Area Measurement
+
+UI showing how to measure the area of the Cumulus Oocyte Complex.
+
+## Local installation
+
+1. Clone the [cumulus_expansion repo from the IIIA gitlab](https://gitlab.iiia.csic.es/eurova/cumulus_expansion)
+2. Clone this repo and change directory into it.
+3. `source bin/init-local.sh`
+4. `streamlit run area_measurement.py`
+
+

area_measurement.py

@@ -15,7 +15,7 @@ st.write("Upload the photograph of your oocyte here:")
 if 'image_path' not in sess:
     sess.image_path = None
 if 'last_image_path' not in sess:
-        sess.last_image_path = None
+    sess.last_image_path = None
 if 'model' not in sess:
     sess.model = AreaModel()
 if 'image' not in sess:

bin/init-local.sh

@@ -6,5 +6,7 @@ fi
 source .venv/bin/activate
 pip install -U pip
 pip install -r requirements.txt
-export PYTHONPATH=$PYTHONPATH:${PWD}/src:${PWD}/../cumulus_expansion/src
-#export LD_LIBRARY_PATH=/home/arcos/miniconda3/envs/aix/lib/
+#if [[ ! -e src ]]; then
+#    cp -r ../cumulus_expansion/src src
+#fi
+export PYTHONPATH=$PYTHONPATH:${PWD}/src

model/majority_roi_production.keras

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:b5a3927c1c6506550019a9845b672f6ddc63272943b1173560240bf0ca65cdb7
+size 23444897

utils.py

@@ -13,7 +13,7 @@ from aix.utils import hardened_dice_coef
 from aix.losses import dice_loss
 
 class AreaModel:
-    def __init__(self, model_path="../cumulus_expansion/models/majority_roi_production/majority_roi_production.keras"):
+    def __init__(self, model_path="model/majority_roi_production.keras"):
         self.model_path = model_path
         self.model = load_model(model_path)
         self.IMG_SIZE = (192, 240)