From e21f1d513faf43c6cfbddb88b6d1b0cf8d190e6c Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Anna=20B=C3=B8gevang=20Ekner?= <s193396@dtu.dk>
Date: Tue, 4 Feb 2025 15:58:09 +0100
Subject: [PATCH] draft for 3D UNet notebook
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docs/notebooks/UNet.ipynb | 366 ++++++++++++++++++++++++++++++++++++++
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+{
+ "cells": [
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "# **Deep Learning Volume Segmentation (3D UNet)**\n",
+ "\n",
+ "Authors: Anna Ekner (s193396@dtu.dk)\n",
+ "\n",
+ "This notebook aims to demonstrate the feasibility of implementing a comprehensive deep learning segmentation pipeline solely leveraging the capabilities offered by the `qim3d` library. Specifically, it highlights the use of the synthetic data generation functionalities to create a volumetric dataset with associated labels, and walks through the process of creating and training a 3D UNet model using this synthetic dataset."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 13,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "import qim3d\n",
+ "import glob\n",
+ "import os\n",
+ "import numpy as np"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "### **1. Generate synthetic dataset**"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "#### 1.1 Example of data sample (probably should be after creating the dataset??)"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "Synthetic dataset and associated labels."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 6,
+ "metadata": {},
+ "outputs": [
+ {
+ "data": {
+ "application/vnd.jupyter.widget-view+json": {
+ "model_id": "d9b9bb97fe7d4828b5b7f359cb8ac50a",
+ "version_major": 2,
+ "version_minor": 0
+ },
+ "text/plain": [
+ "Objects placed: 0%| | 0/5 [00:00<?, ?it/s]"
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ }
+ ],
+ "source": [
+ "num_objects = 5\n",
+ "vol, labels = qim3d.generate.noise_object_collection(\n",
+ " num_objects = num_objects,\n",
+ " collection_shape = (128, 128, 128),\n",
+ " min_object_noise = 0.03, \n",
+ " max_object_noise = 0.08,\n",
+ " )"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 10,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "# Visualize synthetic collection\n",
+ "# qim3d.viz.volumetric(vol)"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 30,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "# Visualize slices\n",
+ "# qim3d.viz.slicer(vol)"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "There will be $N + 1$ unique labels, because one extra for background.\n",
+ "But we want only 2 labels: foreground and background."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 3,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "# Convert N + 1 labels into 2 labels (background and object)\n",
+ "labels = (labels > 0).astype(int)"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 29,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "# Visualize labels\n",
+ "# qim3d.viz.slicer(labels)"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "#### 1.2 Create folder structure"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 12,
+ "metadata": {},
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "Creating directories:\n",
+ "C:\\Users\\s193396/dataset\\train\\images\n",
+ "C:\\Users\\s193396/dataset\\train\\labels\n",
+ "C:\\Users\\s193396/dataset\\test\\images\n",
+ "C:\\Users\\s193396/dataset\\test\\labels\n"
+ ]
+ }
+ ],
+ "source": [
+ "# Base path for the training data\n",
+ "base_path = os.path.expanduser(\"~/dataset\")\n",
+ "\n",
+ "# Create directories\n",
+ "print(\"Creating directories:\")\n",
+ "for folder_split in [\"train\", \"test\"]:\n",
+ " for folder_type in [\"images\", \"labels\"]:\n",
+ " path = os.path.join(base_path, folder_split, folder_type)\n",
+ " os.makedirs(path, exist_ok=True)\n",
+ " print(path)\n",
+ "\n",
+ "# Here we have the option to remove any previous files\n",
+ "clean_files = True\n",
+ "if clean_files:\n",
+ " for root, dirs, files in os.walk(base_path):\n",
+ " for file in files:\n",
+ " file_path = os.path.join(root, file)\n",
+ " os.remove(file_path)"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "#### 1.3 Create dataset"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "We need to create a dataset of multiple volumes"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "num_samples = 5\n",
+ "\n",
+ "for idx in range(num_samples):\n",
+ " # TODO: Figure out whether or not the seed makes it such that all volumes are identical?\n",
+ "\n",
+ " vol, label = qim3d.generate.noise_object_collection(\n",
+ " num_objects = num_objects,\n",
+ " collection_shape = (128, 128, 128),\n",
+ " min_object_noise = 0.03, \n",
+ " max_object_noise = 0.08,\n",
+ " )\n",
+ "\n",
+ " # Convert N + 1 labels into 2 labels (background and object)\n",
+ " label = (labels > 0).astype(int)\n",
+ "\n",
+ " # Save volume\n",
+ " qim3d.io.save(os.path.join(base_path, folder_split, \"images\", f\"{idx}.nii.gz\"), vol, replace = True)\n",
+ "\n",
+ " # Save label\n",
+ " qim3d.io.save(os.path.join(base_path, folder_split, \"labels\", f\"{idx}.nii.gz\"), label, replace = True)"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "# volumes = sorted(glob.glob(os.path.join(base_path, \"im*.nii.gz\")))\n",
+ "# labels = sorted(glob.glob(os.path.join(base_path, \"seg*.nii.gz\")))"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "### **2. Build 3D UNet model**"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "#### 2.1 Instantiate UNet model"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 4,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "model = qim3d.ml.models.UNet(size = 'small', dropout = 0.25)"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "#### 2.2 Define augmentations"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 5,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "augmentation = qim3d.ml.Augmentation(resize = 'crop', transform_train = 'light')"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "#### 2.3 Divide dataset into train and test splits"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "# datasets and dataloaders\n",
+ "train_set, val_set, test_set = qim3d.ml.prepare_datasets(path = base_path,\n",
+ " val_fraction = 0.5,\n",
+ " model = model,\n",
+ " augmentation = augmentation)\n",
+ "\n",
+ "\n",
+ "train_loader, val_loader, test_loader = qim3d.ml.prepare_dataloaders(train_set, \n",
+ " val_set,\n",
+ " test_set,\n",
+ " batch_size = 1)"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "### **3. Train model**"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "#### 3.1 Define training hyperparameters"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "# hyperparameters\n",
+ "hyperparameters = qim3d.ml.Hyperparameters(model, n_epochs=10, \n",
+ " learning_rate = 5e-3, loss_function='DiceCE',\n",
+ " weight_decay=1e-3)"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "#### 3.2 Train model"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "# training model\n",
+ "qim3d.ml.train_model(model, hyperparameters, train_loader, val_loader, plot=True)"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "### **4. Test model**"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": []
+ }
+ ],
+ "metadata": {
+ "kernelspec": {
+ "display_name": "qim3d",
+ "language": "python",
+ "name": "python3"
+ },
+ "language_info": {
+ "codemirror_mode": {
+ "name": "ipython",
+ "version": 3
+ },
+ "file_extension": ".py",
+ "mimetype": "text/x-python",
+ "name": "python",
+ "nbconvert_exporter": "python",
+ "pygments_lexer": "ipython3",
+ "version": "3.10.14"
+ }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}
--
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