Add chla_predict notebook

opengeos · Dec 8, 2024 · 4f276d3 · 4f276d3
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diff --git a/docs/examples/chla_predict.ipynb b/docs/examples/chla_predict.ipynb
@@ -0,0 +1,236 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "[![image](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/opengeos/HyperCoast/blob/main/docs/examples/chla_predict.ipynb)\n",
+    "\n",
+    "# Chlorophyll-a prediction with Deep Learning\n",
+    "\n",
+    "## Install packages\n",
+    "\n",
+    "Uncomment the following cell to install the required packages."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# %pip install \"hypercoast[all]\""
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Import libraries"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import torch\n",
+    "import hypercoast\n",
+    "from hypercoast.chla import *"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Download sample data"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "chla_data_url = \"https://github.com/opengeos/datasets/releases/download/hypercoast/chla_test_data.zip\"\n",
+    "pace_data_url = \"https://github.com/opengeos/datasets/releases/download/hypercoast/PACE_OCI.20241024T182127.L2.OC_AOP.V2_0.NRT.nc\""
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "hypercoast.download_file(chla_data_url, quiet=True)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "pace_filepath = hypercoast.download_file(pace_data_url, quiet=True)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Train the model"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "device = torch.device(\"cuda\" if torch.cuda.is_available() else \"cpu\")\n",
+    "# Load the training dataset\n",
+    "train_real_dl, test_real_dl, input_dim, output_dim = load_real_data(\n",
+    "    \"data/Chl_RC_PACE.csv\", \"data/Rrs_RC_PACE.csv\"\n",
+    ")\n",
+    "# Load the validation dataset\n",
+    "test_real_Sep, _, _ = load_real_test(\n",
+    "    \"data/Chl_RC_PACE_Sep.csv\", \"data/Rrs_RC_PACE_Sep.csv\"\n",
+    ")\n",
+    "# Model output path.\n",
+    "save_dir = \"model/VAE_Chla_PACE\"\n",
+    "os.makedirs(save_dir, exist_ok=True)\n",
+    "\n",
+    "# Create the VAE model and optimizer\n",
+    "model = VAE(input_dim, output_dim).to(device)\n",
+    "opt = torch.optim.Adam(model.parameters(), lr=0.001, weight_decay=1e-3)\n",
+    "\n",
+    "best_model_path = \"model/vae_trans_model_best_Chl_PACE.pth\"\n",
+    "train(model, train_real_dl, epochs=400, best_model_path=best_model_path)\n",
+    "# Load the optimal model\n",
+    "model.load_state_dict(torch.load(best_model_path, map_location=device))\n",
+    "\n",
+    "predictions, actuals = evaluate(model, test_real_dl)\n",
+    "\n",
+    "predictions_Sep, actuals_Sep = evaluate(model, test_real_Sep)\n",
+    "\n",
+    "save_to_csv(predictions, os.path.join(save_dir, \"predictions.csv\"))\n",
+    "save_to_csv(actuals, os.path.join(save_dir, \"actuals.csv\"))"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "plot_results(predictions, actuals, save_dir, mode=\"test\")"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "![image](https://github.com/user-attachments/assets/8766a2a9-8bdf-4348-a544-7115cfb95f63)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "plot_results(predictions_Sep, actuals_Sep, save_dir, mode=\"Sep\")"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "![image](https://github.com/user-attachments/assets/2e16bbc5-9b8c-46ce-88f5-9fb6187fe5af)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Predict chlorophyll-a concentration"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "chla_data_file = pace_filepath.replace(\".nc\", \".npy\")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "chla_predict(pace_filepath, best_model_path, chla_data_file, device)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Visualize the results"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "rgb_image_tif_file = \"data/snapshot-2024-08-10T00_00_00Z.tif\"\n",
+    "output_file = \"20241024-2.png\"\n",
+    "title = \"PACE Chla Prediction\"\n",
+    "figsize = (12, 8)\n",
+    "cmap = \"jet\""
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "chla_viz(rgb_image_tif_file, chla_data_file, output_file, title, figsize, cmap)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "![image](https://github.com/user-attachments/assets/93944a8d-8784-441a-9a51-9050780eb22e)"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "hyper",
+   "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": "3.12.8"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}
diff --git a/mkdocs.yml b/mkdocs.yml
@@ -60,6 +60,7 @@ plugins:
                   "image_slicing.ipynb",
                   "temperature.ipynb",
                   "pace_oci_l1.ipynb",
+                  "chla_predict.ipynb",
               ]
 
 markdown_extensions:
@@ -101,6 +102,7 @@ nav:
           - examples/pace.ipynb
           - examples/ecostress.ipynb
           - examples/chlorophyll_a.ipynb
+          - examples/chla_predict.ipynb
           - examples/temperature.ipynb
           - examples/pace_oci_l1.ipynb
           - examples/pace_oci_l2.ipynb