Merge remote-tracking branch 'origin/EV_updates' into EV_updates

Dockerfile

@@ -0,0 +1,26 @@
+# Use a base image with Conda pre-installed
+FROM continuumio/miniconda3
+
+# Copy the directory containing environment.yml into the Docker image
+COPY ./ /app
+
+# Change the working directory
+WORKDIR /app
+
+# Install Conda and create a new environment from environment.yml
+RUN conda update -n base -c defaults conda && \
+    conda env create -f environment.yml
+
+# Activate the created environment
+RUN echo "conda activate b2p" >> ~/.bashrc
+ENV PATH /opt/conda/envs/b2p/bin:$PATH
+ENV PYTHONPATH /app:$PYTHONPATH
+# Install JupyterLab
+RUN conda install -n b2p jupyterlab
+
+# Expose the port for JupyterLab
+EXPOSE 8888
+
+# Start JupyterLab
+RUN chmod +x /app/entrypoint.sh
+ENTRYPOINT ["/app/entrypoint.sh"]

config.yaml

@@ -3,4 +3,4 @@ aws:
 torch:
   inference:
     batch_size: 100
-    num_workers: 12
+    num_workers: 5

entrypoint.sh

@@ -0,0 +1,2 @@
+#!/bin/bash
+jupyter lab --ip=0.0.0.0 --port=8888 --no-browser --NotebookApp.token=$JUPYTER_TOKEN --allow-root

environment.yml

@@ -145,6 +145,7 @@ dependencies:
   - zipp=3.15.0=pyhd8ed1ab_0
   - zlib=1.2.13=h166bdaf_4
   - zstd=1.5.2=h3eb15da_6
+  - gdal==3.6.4
   - pip:
     - affine==2.4.0
     - attrs==23.1.0
@@ -159,12 +160,12 @@ dependencies:
     - cmake==3.26.3
     - contourpy==1.0.7
     - cycler==0.11.0
+    - chardet
     - debugpy==1.6.7
     - filelock==3.12.0
     - fiona==1.9.3
     - fonttools==4.39.3
     - numpy==1.24.3
-    - gdal==3.6.4
     - geographiclib==2.0
     - geojson==3.0.1
     - geopandas==0.13.0
@@ -235,3 +236,4 @@ dependencies:
     - tzdata==2023.3
     - urllib3==1.26.15
     - xarray==2023.4.2
+      #prefix: /home/ec2-user/anaconda3/envs/b2p

src/ml/inference.py

@@ -102,7 +102,7 @@ def inference_torch(model_file: TrainedModel, tile_match_file: Union[SingleRegio
             output = model(data)
             probs = torch.softmax(output, dim=1)
             conf, pred = torch.max(probs, 1)
-
+            print(data.shape)
             print(pred)
 
             # store res to file