Model development (#19)

* add model blocks and tests

* add model and tests

* add torch to setup

* add torch to requirements

* update workflow

* add data loader and tests

* add opencv to requirements

* add opencv to requirements and setup

* update opencv version

* implement attention mechanism in unet

* add network visualisations

* update readme

* add visualisations

* update requirements

* devcontainer tweaks

* tweak devcontainer

* minor changes to setup.sh- add safe directory

* add utils func to make images to npy

* update dockerfile

Author: ioannispol

.devcontainer/devcontainer.json

@@ -61,5 +61,5 @@
 	// "customizations": {},
 
 	// Uncomment to connect as an existing user other than the container default. More info: https://aka.ms/dev-containers-non-root.
-	// "remoteUser": "devcontainer"
+	//"remoteUser": "devuser"
 }

Dockerfile

@@ -1,11 +1,27 @@
 
 FROM nvcr.io/nvidia/pytorch:22.11-py3
 
+# Install miniconda
+ENV CONDA_DIR /opt/miniconda/
+
+RUN apt clean && \
+    rm -rf /var/lib/apt/lists/* && \
+    apt-get update && \
+    apt-get install -y wget  \
+    git -y && \
+    wget --quiet https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O ~/miniconda.sh && \
+     /bin/bash ~/miniconda.sh -b -p /opt/miniconda
+
+# Add conda to path
+ENV PATH=$CONDA_DIR/bin:$PATH
+RUN conda create -n uw-unet python=3.8
+
 RUN rm -rf /workspace/*
 WORKDIR /workspace/uw-unet
 
 COPY requirements.txt requirements.txt
-RUN pip3 install -r requirements.txt
+RUN echo "source activate uw-unet" >~/.bashrc && \
+    /opt/miniconda/envs/uw-unet/bin/pip install -r requirements.txt
 
 COPY . .