updated readme

Author: vaibhavbahel

src/baseline/v2/inference/docker/readme.md

@@ -0,0 +1,165 @@
+# 🧠 Pseudo-CT Inference Docker
+
+This repository provides a **Dockerized inference pipeline** for generating pseudo-CT images from NAC PET input using a trained 3D U-Net model.
+
+---
+
+## 🚀 Features
+
+* ✅ GPU-accelerated inference (CUDA)
+* ✅ Sliding window inference (overlap = 0.75)
+* ✅ PET-only input
+* ✅ Outputs CT in Hounsfield Units (HU)
+* ✅ Clean CLI interface
+* ✅ Runtime + inference timing logs
+
+---
+
+## 📦 Requirements
+
+* Docker installed
+* NVIDIA GPU + drivers
+* NVIDIA Container Toolkit (`--gpus all` support)
+
+---
+
+## 🏗️ Build Docker Image
+
+Navigate to the docker directory:
+
+```bash
+cd inference/docker
+```
+
+Build the image:
+
+```bash
+docker build -t pseudoct .
+```
+
+---
+
+## ▶️ Run Inference
+
+### 🔹 Basic Usage
+
+```bash
+docker run --rm \
+  --gpus all \
+  --user $(id -u):$(id -g) \
+  -v /absolute/path/to/data:/data \
+  pseudoct \
+  --input /data/sub-XXX/features/nacpet.nii.gz \
+  --output /data/sub-XXX/pseudo_ct.nii.gz
+```
+
+---
+
+## 📁 Input Structure
+
+Your data should follow:
+
+```
+data/
+└── sub-XXX/
+    └── features/
+        └── nacpet.nii.gz
+```
+
+---
+
+## 📁 Output
+
+The output will be saved as:
+
+```
+data/
+└── sub-XXX/
+    └── pseudo_ct.nii.gz
+```
+
+---
+
+## ⚠️ Important Notes
+
+### 🔸 Path Mounting
+
+Docker cannot access host paths directly. You must mount them using `-v`.
+
+Example:
+
+```bash
+-v /home/user/data:/data
+```
+
+---
+
+### 🔸 Permissions Fix
+
+If you get a **permission denied error**, use:
+
+```bash
+--user $(id -u):$(id -g)
+```
+
+---
+
+### 🔸 GPU Usage
+
+Make sure to include:
+
+```bash
+--gpus all
+```
+
+Otherwise inference will run on CPU.
+
+---
+
+## ⏱️ Output Logs
+
+Example output:
+
+```
+Using device: cuda
+Inference time: 3.21 seconds
+Total runtime: 5.12 seconds
+Saved: /data/sub-XXX/pseudo_ct.nii.gz
+```
+
+---
+
+## 🧪 Debugging
+
+### Check mounted data inside container:
+
+```bash
+docker run --rm -it \
+  -v /your/data:/data \
+  pseudoct bash
+
+ls /data
+```
+
+---
+
+## 🛠️ Customization
+
+You can modify:
+
+* Patch size → `PATCH_SIZE`
+* Sliding window batch → `SW_BATCH`
+* Overlap → `OVERLAP`
+
+inside `inference.py`.
+
+---
+
+## 📌 Summary
+
+| Step  | Command                                            |
+| ----- | -------------------------------------------------- |
+| Build | `docker build -t pseudoct .`                       |
+| Run   | `docker run ... pseudoct --input ... --output ...` |
+
+---