From ab283fec0ae8b276838bacfa7967bc884d083715 Mon Sep 17 00:00:00 2001
From: Mattia Amadio <44863827+matamadio@users.noreply.github.com>
Date: Thu, 8 Feb 2024 11:41:55 +0100
Subject: [PATCH] Add utility merge tiles

---
 docs/_toc.yml                         |  3 ++
 docs/utility.md                       | 11 +++++
 utility/merge_tiles/Merge_tiles.ipynb | 62 +++++++++++++++++++++++++++
 utility/merge_tiles/merge_utils.py    | 13 ++++++
 4 files changed, 89 insertions(+)
 create mode 100644 docs/utility.md
 create mode 100644 utility/merge_tiles/Merge_tiles.ipynb
 create mode 100644 utility/merge_tiles/merge_utils.py

diff --git a/docs/_toc.yml b/docs/_toc.yml
index bd1dff7b..aea9f022 100644
--- a/docs/_toc.yml
+++ b/docs/_toc.yml
@@ -34,6 +34,9 @@ parts:
     chapters:
       - file: docs/tool-setup
       - file: docs/run-baseline
+      - file: docs/utility
+      sections:
+        - file: utility/merge_tiles/Merge_tiles.ipynb
   - caption: External resources
     chapters:
       - file: docs/external-tools
diff --git a/docs/utility.md b/docs/utility.md
new file mode 100644
index 00000000..7219991c
--- /dev/null
+++ b/docs/utility.md
@@ -0,0 +1,11 @@
+# Utilities
+
+Additional tools to help collect, view and process risk data.
+
+## Merge tiles
+
+Large raster datasets often comes as a collection of regular tiles.
+In order to run the raster analysis offered in our tools, they often need to be merged into one file.
+To do that, a simple python script is provided as jupyter notebook.
+
+[TILE MERGE](utility/merge_tiles/Merge_tiles.ipynb)
\ No newline at end of file
diff --git a/utility/merge_tiles/Merge_tiles.ipynb b/utility/merge_tiles/Merge_tiles.ipynb
new file mode 100644
index 00000000..c72eb902
--- /dev/null
+++ b/utility/merge_tiles/Merge_tiles.ipynb
@@ -0,0 +1,62 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "id": "b8bf67f8",
+   "metadata": {},
+   "source": [
+    "# TILE MERGE SCRIPT\n",
+    "\n",
+    "The python script below looks into subfolders of specified directory and merge together all tiff files found, naming the resulting tiff as the folder from which they are generated.\n",
+    "\n",
+    "- The function for merging and exporting is found in merge_utils.py\n",
+    "- GDAL library must be installed in your python environment\n",
+    "- Output is exported in the same format of the original tiles\n",
+    "- The scripts makes use of parallel processing for quicker results"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 26,
+   "id": "e3904d3e",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import os\n",
+    "import concurrent.futures\n",
+    "from merge_utils import merge_tifs\n",
+    "\n",
+    "# Specify the directory to search for .tif files\n",
+    "directory = 'C:/YourWorkDirectory/Fathom3/PL/2020/'\n",
+    "\n",
+    "# Iterate through each subdirectory\n",
+    "subdirs = [os.path.join(directory, subdir) for subdir in os.listdir(directory) if os.path.isdir(os.path.join(directory, subdir))]\n",
+    "\n",
+    "# Process subdirectories in parallel\n",
+    "with concurrent.futures.ProcessPoolExecutor() as executor:\n",
+    "    executor.map(merge_tifs, subdirs)\n"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
+   "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": "3.10.2"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}
diff --git a/utility/merge_tiles/merge_utils.py b/utility/merge_tiles/merge_utils.py
new file mode 100644
index 00000000..8d8f3438
--- /dev/null
+++ b/utility/merge_tiles/merge_utils.py
@@ -0,0 +1,13 @@
+import os
+from osgeo import gdal
+
+def merge_tifs(subdir_path):
+    # Get a list of all .tif files in the subdirectory
+    tif_files = [os.path.join(subdir_path, file) for file in os.listdir(subdir_path) if file.endswith('.tif')]
+    
+    # If there are .tif files in the subdirectory, merge them
+    if tif_files:
+        output_file = os.path.join(subdir_path, f"{os.path.basename(subdir_path)}.tif")
+        vrt = gdal.BuildVRT('', tif_files)
+        gdal.Translate(output_file, vrt, options='-co COMPRESS=DEFLATE -co PREDICTOR=2 -co ZLEVEL=9')
+        vrt = None