feat: consolidate Dockerfiles with build arguments (Issue #115 Task #4)

Docker/DOCKERFILE_MERGE.md

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+# Dockerfile Consolidation - Issue #115 Task #4
+
+## Overview
+This document describes the consolidation of two separate Dockerfiles into a single unified Dockerfile that supports both standalone and Kaapana deployment.
+
+## Problem
+Previously maintained two separate Dockerfiles:
+1. `Docker/Dockerfile` - Standalone IVIM fitting
+2. `kaapana_ivim_osipi/.../Dockerfile` - Kaapana deployment
+
+This created:
+- Code duplication
+- Maintenance overhead
+- Inconsistent updates
+
+## Solution
+Created `Docker/Dockerfile.unified` that uses Docker build arguments to support both scenarios.
+
+## Build Arguments
+
+| Argument | Default | Options | Purpose |
+|----------|---------|---------|---------|
+| `BASE_IMAGE` | `python:3.11-slim` | Any valid Docker image | Choose base image |
+| `ENV_TYPE` | `standalone` | `standalone` or `kaapana` | Select environment |
+
+## Building
+
+### Standalone Build
+
+Method 1: Using build script
+./Docker/build-standalone.sh
+
+Method 2: Direct docker command
+docker build
+--build-arg ENV_TYPE=standalone
+-t ivim-fitting:standalone
+-f Docker/Dockerfile.unified .
+### Kaapana Build
+Method 1: Using build script
+./Docker/build-kaapana.sh
+
+Method 2: Direct docker command
+docker build
+--build-arg BASE_IMAGE=local-only/base-python-cpu:latest
+--build-arg ENV_TYPE=kaapana
+-t ivim-fitting:kaapana
+-f Docker/Dockerfile.unified .
+
+## Testing Completed
+
+###  Local Testing (Docker Desktop - Windows)
+- [x] Standalone build succeeds (13.2GB, ID: 75a626d42f0b)
+- [x] Kaapana build succeeds (14GB, ID: f662fb55bfee)
+- [x] Both conditional logic statements work correctly
+- [x] File copying and dependencies install without errors
+- [x] Build scripts execute correctly
+
+###  Integration Testing (Requires Kaapana Platform)
+- [ ] Runtime with actual `local-only/base-python-cpu:latest` base image
+- [ ] Volume mounts work (`OPERATOR_IN_DIR`, `OPERATOR_OUT_DIR`)
+- [ ] MinIO data integration
+- [ ] Airflow DAG execution in Kaapana UI
+- [ ] Workflow submission through web interface
+
+## Files Modified/Added
+
+| File | Change | Type |
+|------|--------|------|
+| `Docker/Dockerfile.unified` | New unified Dockerfile |  New |
+| `Docker/build-standalone.sh` | Build script for standalone |  New |
+| `Docker/build-kaapana.sh` | Build script for Kaapana |  New |
+| `Docker/DOCKERFILE_MERGE.md` | This documentation |  New |
+
+## Notes for Reviewers
+
+### What I Could Test
+ Docker build process for both environments
+ Image creation and basic structure
+ Build argument passing
+ Entry point configuration
+
+### What Needs Your Testing
+ Runtime behavior in actual Kaapana deployment
+ Compatibility with Kaapana base image
+ Workflow execution through Kaapana UI
+ Data pipeline with MinIO
+
+## Related Issues
+- Addresses #115 (Task #4)
+- Related to PR #112

Docker/Dockerfile.unified

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+
+# Unified Dockerfile for IVIM Fitting Method
+# 
+# Supports both standalone and Kaapana deployment using build arguments.
+#
+# BUILD COMMANDS:
+# ===============
+# 
+# For standalone (default):
+# $ docker build --build-arg ENV_TYPE=standalone \
+#                -t ivim-fitting:standalone \
+#                -f Dockerfile.unified .
+#
+# For Kaapana deployment:
+# $ docker build --build-arg BASE_IMAGE=local-only/base-python-cpu:latest \
+#                --build-arg ENV_TYPE=kaapana \
+#                -t ivim-fitting:kaapana \
+#                -f Dockerfile.unified .
+#
+
+
+# Step 1: Set base image (before FROM)
+ARG BASE_IMAGE=python:3.11-slim
+
+FROM ${BASE_IMAGE}
+
+# Step 2: Define build-time configuration
+ARG ENV_TYPE=standalone
+ARG WORKDIR_PATH=/usr/src/app
+
+# Metadata labels
+LABEL IMAGE="ivim-fitting-method"
+LABEL VERSION="0.2.4"
+LABEL BUILD_IGNORE="False"
+
+
+# COMMON SETUP (applies to both standalone and Kaapana)
+# Install common system dependencies
+RUN apt-get update && apt-get install -y --no-install-recommends \
+    build-essential \
+    libssl-dev \
+    && rm -rf /var/lib/apt/lists/*
+
+
+# ENVIRONMENT-SPECIFIC SETUP
+# Kaapana setup
+RUN if [ "$ENV_TYPE" = "kaapana" ]; then \
+        echo "=== Configuring for KAAPANA ==="; \
+        apt-get update && apt-get install -y --no-install-recommends \
+        texlive-xetex \
+        texlive-fonts-recommended \
+        texlive-plain-generic \
+        git && \
+        apt-get clean && rm -rf /var/lib/apt/lists/*; \
+    fi
+
+# Standalone setup
+RUN if [ "$ENV_TYPE" = "standalone" ]; then \
+        echo "=== Configuring for STANDALONE ==="; \
+    fi
+
+# CODE ACQUISITION
+# For Kaapana: Clone from GitHub and install dependencies
+RUN if [ "$ENV_TYPE" = "kaapana" ]; then \
+        mkdir -p /kaapana/app && \
+        cd /kaapana/app && \
+        git clone https://github.com/OSIPI/TF2.4_IVIM-MRI_CodeCollection.git && \
+        cd TF2.4_IVIM-MRI_CodeCollection && \
+        pip install --no-cache-dir -r requirements.txt; \
+    fi
+
+# For Standalone: Copy requirements and install
+RUN if [ "$ENV_TYPE" = "standalone" ]; then \
+        mkdir -p /usr/src/app; \
+    fi
+
+# Set working directory
+WORKDIR ${WORKDIR_PATH}
+
+
+# COPY FILES AND INSTALL DEPENDENCIES
+# Copy requirements.txt from project root to current working directory
+COPY requirements.txt ./
+
+# Copy source code (WrapImage and other files)
+COPY WrapImage ./WrapImage/
+
+# Install Python dependencies for standalone
+RUN if [ "$ENV_TYPE" = "standalone" ]; then \
+        pip install --no-cache-dir -r requirements.txt; \
+    fi
+
+
+# SET ENTRYPOINT
+# Kaapana entrypoint with verbose output
+RUN if [ "$ENV_TYPE" = "kaapana" ]; then \
+        echo "Kaapana wrapper selected"; \
+    else \
+        echo "Standalone wrapper selected"; \
+    fi
+
+# Use entrypoint script approach for flexibility
+RUN echo '#!/bin/bash' > /entrypoint.sh && \
+    if [ "$ENV_TYPE" = "kaapana" ]; then \
+        echo 'cd /kaapana/app/TF2.4_IVIM-MRI_CodeCollection' >> /entrypoint.sh && \
+        echo 'exec python3 -u -m WrapImage.nifti_wrapper_kaapana "$@"' >> /entrypoint.sh; \
+    else \
+        echo 'cd /usr/src/app' >> /entrypoint.sh && \
+        echo 'exec python3 -m WrapImage.nifti_wrapper "$@"' >> /entrypoint.sh; \
+    fi && \
+    chmod +x /entrypoint.sh
+
+ENTRYPOINT ["/entrypoint.sh"]
+CMD []

Docker/build-kaapana.sh

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+#!/bin/bash
+set -e
+
+echo " Building IVIM Fitting for KAAPANA..."
+echo "━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━"
+
+docker build \
+  --build-arg BASE_IMAGE=local-only/base-python-cpu:latest \
+  --build-arg ENV_TYPE=kaapana \
+  -t ivim-fitting:kaapana \
+  -f Docker/Dockerfile.unified \
+  .
+
+echo ""
+echo " Build successful!"
+echo " Image: ivim-fitting:kaapana"
+docker images | grep "ivim-fitting.*kaapana"

Docker/build-standalone.sh

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+#!/bin/bash
+set -e
+
+echo " Building IVIM Fitting for STANDALONE..."
+echo "━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━"
+
+docker build \
+  --build-arg ENV_TYPE=standalone \
+  -t ivim-fitting:standalone \
+  -f Docker/Dockerfile.unified \
+  .
+
+echo ""
+echo " Build successful!"
+echo " Image: ivim-fitting:standalone"
+docker images | grep "ivim-fitting.*standalone"