Add MRI report generator application with Docker support

This commit includes:
- Updated Dockerfiles for all containers (ETL, Jupyter, PhysioNet, Streamlit, Train)
- Updated requirements.txt for Streamlit and Train containers
- Docker Compose configuration for orchestrating services
- Streamlit application for MRI report generation
- Setup scripts for virtual environment and application startup
- Project dependencies and requirements

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude <noreply@anthropic.com>

containers/etl/Dockerfile

@@ -1,8 +1,7 @@
-FROM python:3.9-buster
+FROM python:3.9-slim
 
 RUN \
     apt-get update && \
-    apt-get -y upgrade && \
     apt-get clean && \
     rm -rf /var/lib/apt/lists/*
 
@@ -24,14 +23,10 @@ RUN \
     chown app:app /home/app/common.py && \
     chmod 0755 /home/app/common.py
 
-USER app
-
-ENV VIRTUAL_ENV=/home/app/venv
-RUN python3 -m venv $VIRTUAL_ENV
-ENV PATH="$VIRTUAL_ENV/bin:$PATH"
-
 RUN \
     pip install --upgrade pip && \
     pip install -r requirements.txt
 
+USER app
+
 CMD ["python", "run.py", "worker", "-l", "info"]

containers/jupyter/Dockerfile

@@ -1,8 +1,7 @@
-FROM python:3.9-buster
+FROM python:3.9-slim
 
 RUN \
     apt-get update && \
-    apt-get -y upgrade && \
     apt-get clean && \
     rm -rf /var/lib/apt/lists/*
 
@@ -15,14 +14,10 @@ RUN \
     chown app:app /home/app/requirements.txt && \
     chmod 0755 /home/app/requirements.txt
 
-USER app
-
-ENV VIRTUAL_ENV=/home/app/venv
-RUN python3 -m venv $VIRTUAL_ENV
-ENV PATH="$VIRTUAL_ENV/bin:$PATH"
-
 RUN \
     pip install --upgrade pip && \
     pip install -r requirements.txt
 
+USER app
+
 CMD ["jupyter", "notebook", "--notebook-dir=/opt/notebooks", "--ip='*'", "--port=8888", "--no-browser"]

containers/physionet/Dockerfile

@@ -1,4 +1,4 @@
-FROM debian:buster
+FROM debian:bookworm
 
 RUN apt-get update -y && \
     apt-get -y install parallel wget && \

containers/streamlit/Dockerfile

@@ -1,8 +1,7 @@
-FROM python:3.9-buster
+FROM python:3.9-slim
 
 RUN \
     apt-get update && \
-    apt-get -y upgrade && \
     apt-get clean && \
     rm -rf /var/lib/apt/lists/*
 
@@ -15,17 +14,18 @@ RUN \
     chown app:app /home/app/requirements.txt && \
     chmod 0755 /home/app/requirements.txt && \
     chown app:app /home/app/app.py && \
-    chmod 0755 /home/app/app.py    
+    chmod 0755 /home/app/app.py
 
-USER app
-WORKDIR /home/app
+RUN \
+    pip install --upgrade pip
 
-ENV VIRTUAL_ENV=/home/app/venv
-RUN python3 -m venv $VIRTUAL_ENV
-ENV PATH="$VIRTUAL_ENV/bin:$PATH"
+# Install PyTorch separately from CPU index
+RUN pip install --index-url https://download.pytorch.org/whl/cpu torch>=2.0.0
 
-RUN \
-    pip install --upgrade pip && \
-    pip install -r requirements.txt
+# Install other requirements from default PyPI
+RUN pip install streamlit>=1.28.0 transformers>=4.36.0 pillow>=10.0.0
+
+USER app
+WORKDIR /home/app
 
 CMD ["streamlit", "run", "app.py"]

containers/streamlit/requirements.txt

@@ -1,3 +1,5 @@
-streamlit>=1.17.0,<1.18
-transformers[torch]>=4.26.0,<4.27
-pillow>=9.4.0,<9.5
+streamlit>=1.28.0
+transformers>=4.36.0
+pillow>=10.0.0
+regex>=2023.0.0
+torch>=2.0.0 --index-url https://download.pytorch.org/whl/cpu

containers/train/Dockerfile

@@ -1,8 +1,7 @@
-FROM python:3.9-buster
+FROM python:3.9-slim
 
 RUN \
     apt-get update && \
-    apt-get -y upgrade && \
     apt-get clean && \
     rm -rf /var/lib/apt/lists/*
 
@@ -18,14 +17,15 @@ RUN \
     chown app:app /home/app/run.py && \
     chmod 0755 /home/app/run.py
 
-USER app
+RUN \
+    pip install --upgrade pip
 
-ENV VIRTUAL_ENV=/home/app/venv
-RUN python3 -m venv $VIRTUAL_ENV
-ENV PATH="$VIRTUAL_ENV/bin:$PATH"
+# Install PyTorch separately from CPU index
+RUN pip install --index-url https://download.pytorch.org/whl/cpu torch>=2.0.0
 
-RUN \
-    pip install --upgrade pip && \
-    pip install -r requirements.txt
+# Install other requirements from default PyPI
+RUN pip install transformers>=4.36.0 pillow>=10.0.0 datasets>=2.14.0
+
+USER app
 
 CMD ["python", "run.py", "worker", "-l", "info"]

containers/train/requirements.txt

@@ -1,3 +1,5 @@
-transformers[torch]>=4.26.0,<4.27
-pillow>=9.4.0,<9.5
-datasets>=2.9.0,<2.10
+transformers>=4.36.0
+pillow>=10.0.0
+datasets>=2.14.0
+regex>=2023.0.0
+torch>=2.0.0 --index-url https://download.pytorch.org/whl/cpu

docker-compose.yaml

@@ -1,4 +1,3 @@
-version: '3'
 services:
 
   # download data

requirements.txt

@@ -0,0 +1,26 @@
+# Prerad Project Root Requirements
+# Main dependencies for the project (CPU-only PyTorch)
+# Updated for Python 3.13 compatibility
+
+# Web Framework
+streamlit>=1.28.0
+
+# Machine Learning & Computer Vision
+transformers>=4.36.0
+pillow>=10.0.0
+regex>=2023.0.0
+
+# PyTorch CPU version (latest stable)
+# Install with: pip install torch --index-url https://download.pytorch.org/whl/cpu
+torch>=2.0.0
+
+# Data Processing
+pandas>=2.0.0
+jsonlines>=4.0.0
+
+# Jupyter & Notebooks
+jupyter>=1.0.0
+ipykernel>=6.25.0
+
+# Additional utilities
+numpy>=1.24.0

setup_venv.py

@@ -0,0 +1,129 @@
+so#!/usr/bin/env python3
+"""
+Setup script to create a virtual environment and install dependencies for the Prerad project.
+This script creates a venv at the project path and installs all necessary packages.
+"""
+
+import os
+import sys
+import subprocess
+import venv
+from pathlib import Path
+
+def main():
+    # Define paths
+    project_path = Path("/run/media/dheena/Leave you files/prerad")
+    venv_path = project_path / "venv"
+    
+    print(f"🚀 Setting up Prerad project environment")
+    print(f"📁 Project path: {project_path}")
+    print(f"📦 Virtual environment path: {venv_path}")
+    print()
+    
+    # Step 1: Create virtual environment
+    print("Step 1: Creating virtual environment...")
+    try:
+        venv.create(venv_path, with_pip=True)
+        print(f"✅ Virtual environment created at {venv_path}")
+    except Exception as e:
+        print(f"❌ Error creating virtual environment: {e}")
+        sys.exit(1)
+    
+    # Step 2: Determine pip executable path
+    if sys.platform == "win32":
+        pip_exe = venv_path / "Scripts" / "pip.exe"
+        python_exe = venv_path / "Scripts" / "python.exe"
+    else:
+        pip_exe = venv_path / "bin" / "pip"
+        python_exe = venv_path / "bin" / "python"
+    
+    print()
+    print("Step 2: Upgrading pip...")
+    try:
+        subprocess.check_call([str(pip_exe), "install", "--upgrade", "pip"])
+        print("✅ Pip upgraded successfully")
+    except Exception as e:
+        print(f"❌ Error upgrading pip: {e}")
+        sys.exit(1)
+    
+    # Step 3: Install requirements for Streamlit (UI application)
+    print()
+    print("Step 3: Installing Streamlit and dependencies...")
+    streamlit_requirements = [
+        "streamlit>=1.28.0",
+        "transformers>=4.36.0",
+        "pillow>=10.0.0",
+        "torch>=2.0.0",  # CPU-only PyTorch
+    ]
+    
+    # Install torch from CPU index first
+    print("  - Installing PyTorch (CPU version)...")
+    try:
+        subprocess.check_call([
+            str(pip_exe), "install", 
+            "--index-url", "https://download.pytorch.org/whl/cpu",
+            "torch>=2.0.0"
+        ])
+        print("  ✅ PyTorch installed")
+    except Exception as e:
+        print(f"  ⚠️  Warning installing PyTorch: {e}")
+    
+    # Install other streamlit packages
+    print("  - Installing other packages...")
+    try:
+        subprocess.check_call([str(pip_exe), "install"] + streamlit_requirements[:-1])
+        print("✅ Streamlit and dependencies installed")
+    except Exception as e:
+        print(f"❌ Error installing Streamlit dependencies: {e}")
+        sys.exit(1)
+    
+    # Step 4: Install ETL dependencies
+    print()
+    print("Step 4: Installing ETL dependencies...")
+    etl_requirements = [
+        "jsonlines>=4.0.0",
+        "pandas>=2.0.0",
+    ]
+    try:
+        subprocess.check_call([str(pip_exe), "install"] + etl_requirements)
+        print("✅ ETL dependencies installed")
+    except Exception as e:
+        print(f"❌ Error installing ETL dependencies: {e}")
+        sys.exit(1)
+    
+    # Step 5: Install Jupyter
+    print()
+    print("Step 5: Installing Jupyter...")
+    try:
+        subprocess.check_call([str(pip_exe), "install", "jupyter>=1.0.0"])
+        print("✅ Jupyter installed")
+    except Exception as e:
+        print(f"❌ Error installing Jupyter: {e}")
+        sys.exit(1)
+    
+    # Step 6: Create activation scripts info
+    print()
+    print("=" * 60)
+    print("✅ Setup Complete!")
+    print("=" * 60)
+    print()
+    print("📌 To activate the virtual environment, run:")
+    print()
+    if sys.platform == "win32":
+        print(f"   {venv_path}\\Scripts\\activate")
+    else:
+        print(f"   source {venv_path}/bin/activate")
+    print()
+    print("🚀 To start the Streamlit application after activation:")
+    print(f"   streamlit run {project_path}/containers/streamlit/app.py")
+    print()
+    print("📓 To start Jupyter Notebook after activation:")
+    print(f"   jupyter notebook --notebook-dir={project_path}/volumes/notebooks")
+    print()
+    print("🔧 Or use Docker Compose for containerized services:")
+    print(f"   cd {project_path}")
+    print("   sudo docker compose up -d jupyter streamlit")
+    print()
+
+if __name__ == "__main__":
+    main()

start_app.bat

@@ -0,0 +1,55 @@
+@echo off
+REM Prerad Setup and Launch Script for Windows
+REM This script creates a virtual environment and starts the Streamlit application
+
+setlocal enabledelayedexpansion
+
+set "PROJECT_PATH=C:\Users\YourUsername\prerad"
+set "VENV_PATH=%PROJECT_PATH%\venv"
+
+echo ====================================
+echo Prerad Environment Setup and Launch
+echo ====================================
+echo.
+
+echo Running setup script...
+python "%PROJECT_PATH%\setup_venv.py"
+
+echo.
+echo ====================================
+echo Environment is ready!
+echo ====================================
+echo.
+
+echo Activating virtual environment...
+call "%VENV_PATH%\Scripts\activate.bat"
+
+echo.
+echo Virtual environment activated
+echo.
+
+echo Choose what to start:
+echo 1) Streamlit application (localhost:8501)
+echo 2) Jupyter Notebook (localhost:8888)
+echo 3) Exit
+echo.
+
+set /p choice="Enter your choice (1-3): "
+
+if "%choice%"=="1" (
+    echo.
+    echo Starting Streamlit application...
+    streamlit run "%PROJECT_PATH%\containers\streamlit\app.py"
+) else if "%choice%"=="2" (
+    echo.
+    echo Starting Jupyter Notebook...
+    jupyter notebook --notebook-dir="%PROJECT_PATH%\volumes\notebooks"
+) else if "%choice%"=="3" (
+    echo Exiting...
+    exit /b 0
+) else (
+    echo Invalid choice. Exiting...
+    exit /b 1
+)
+
+endlocal

start_app.sh

@@ -0,0 +1,70 @@
+#!/bin/bash
+# Prerad Setup and Launch Script
+# This script creates a virtual environment and starts the Streamlit application
+
+set -e
+
+PROJECT_PATH="/run/media/dheena/Leave you files/prerad"
+VENV_PATH="${PROJECT_PATH}/venv"
+
+echo "🎯 Prerad Environment Setup and Launch"
+echo "======================================"
+echo ""
+
+# Run Python setup script
+echo "Running setup script..."
+python3 "${PROJECT_PATH}/setup_venv.py"
+
+echo ""
+echo "======================================"
+echo "🎉 Environment is ready!"
+echo "======================================"
+echo ""
+
+# Activate virtual environment
+echo "Activating virtual environment..."
+source "${VENV_PATH}/bin/activate"
+
+echo ""
+echo "✅ Virtual environment activated"
+echo ""
+
+# Offer options to start services
+echo "Choose what to start:"
+echo "1) Streamlit application (localhost:8501)"
+echo "2) Jupyter Notebook (localhost:8888)"
+echo "3) Both (using Docker Compose with sudo)"
+echo "4) Exit"
+echo ""
+read -p "Enter your choice (1-4): " choice
+
+case $choice in
+    1)
+        echo ""
+        echo "🚀 Starting Streamlit application..."
+        streamlit run "${PROJECT_PATH}/containers/streamlit/app.py"
+        ;;
+    2)
+        echo ""
+        echo "📓 Starting Jupyter Notebook..."
+        jupyter notebook --notebook-dir="${PROJECT_PATH}/volumes/notebooks"
+        ;;
+    3)
+        echo ""
+        echo "🐳 Starting services with Docker Compose..."
+        cd "${PROJECT_PATH}"
+        sudo docker compose up -d jupyter streamlit
+        echo ""
+        echo "✅ Services started!"
+        echo "   Jupyter: http://localhost:8888"
+        echo "   Streamlit: http://localhost:8501"
+        ;;
+    4)
+        echo "Exiting..."
+        exit 0
+        ;;
+    *)
+        echo "Invalid choice. Exiting..."
+        exit 1
+        ;;
+esac