Moved to notebooks/ to improve repo organization

notebooks/example_workflow_metadata_annotation.ipynb

@@ -0,0 +1,146 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Metadata Annotation Process\n",
+    "\n",
+    "In this notebook, we will go through a simple metadata annotation process. This involves the following steps:\n",
+    "\n",
+    "1. Define an HDF5 file.\n",
+    "2. Create a YAML representation of the HDF5 file.\n",
+    "3. Edit and augment the YAML with metadata.\n",
+    "4. Update the original file based on the edited YAML.\n",
+    "\n",
+    "\n",
+    "## Import libraries and modules\n",
+    "\n",
+    "* Excecute (or Run) the Cell below"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import src.metadata_review_lib as metadata_annotation\n",
+    "import src.hdf5_vis as hdf5_vis\n",
+    "import os"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Step 1: Define an HDF5 file\n",
+    "\n",
+    "* Set up the string variable `hdf5_file_path` with the path to the HDF5 file of interest.\n",
+    "* Excecute Cell."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "hdf5_file_path = \"output_files/kinetic_flowtube_study_2023-06-29_LuciaI.h5\""
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Step 2: Create a YAML Representation of the File\n",
+    "\n",
+    "We now convert HDF5 file structure and existing metadata into a YAML format. This will be used to add and edit metadata attributes.\n",
+    "\n",
+    "* Excecute Cell."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "yaml_file_path = hdf5_vis.take_yml_snapshot_of_hdf5_file(hdf5_file_path)\n",
+    "\n",
+    "if os.path.exists(yaml_file_path):\n",
+    "    print(f'The YAML file representation {yaml_file_path} of the HDF5 file {hdf5_file_path} was created successfully.')"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Step 3: Edit and Augment YAML with Metadata\n",
+    "\n",
+    "We can now manually edit the YAML file to add metadata.\n",
+    "* (Optional) automate your metadata annotation process by creating a program that takes the YAMl file and returns the modified version of it.\n",
+    "* Excecute Cell."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "def metadata_annotation_process(yaml_file_path):\n",
+    "\n",
+    "    # Include metadata annotation logic, e.g., load yaml file and modify its content accordingly\n",
+    "\n",
+    "    print(f'Ensure your edits to {yaml_file_path} have been properly incorporated and saved.')\n",
+    "\n",
+    "    return yaml_file_path\n",
+    "\n",
+    "yaml_file_path = metadata_annotation_process(yaml_file_path)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Step 4: Update the Original File Based on the Edited YAML\n",
+    "\n",
+    "Lastly, we will update the original file with the metadata from the YAML file.\n",
+    "\n",
+    "* Excecute Cell."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "\n",
+    "metadata_annotation.update_hdf5_file_with_review(hdf5_file_path,yaml_file_path)"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "multiphase_chemistry_env",
+   "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": "3.11.9"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}