From ffca4070728c75ca2c178fcd34717d7ae5a5cf16 Mon Sep 17 00:00:00 2001
From: Panos Mavrogiorgos <pmav99@gmail.com>
Date: Fri, 5 May 2023 15:22:01 +0300
Subject: [PATCH] notebooks: Update notebooks/API.ipynb

---
 notebooks/API.ipynb | 100 ++++++++++++++++++++++++++++++++++----------
 1 file changed, 78 insertions(+), 22 deletions(-)

diff --git a/notebooks/API.ipynb b/notebooks/API.ipynb
index a129cd3..05475b7 100644
--- a/notebooks/API.ipynb
+++ b/notebooks/API.ipynb
@@ -1,9 +1,19 @@
 {
  "cells": [
+  {
+   "cell_type": "markdown",
+   "id": "2b140634-be0f-40c4-8928-6ae5b04e35e3",
+   "metadata": {
+    "tags": []
+   },
+   "source": [
+    "## Imports"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "f3e4d71b-357e-45e2-aa3e-9e89b1b662ab",
+   "id": "5c7e57bd-c71d-4dc0-83aa-3bbb397fc4d4",
    "metadata": {
     "tags": []
    },
@@ -18,29 +28,29 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "768d9e0a-0ff5-4720-98a0-7d1b5d116042",
+   "id": "21da8e29-2fa0-4250-abaf-f952cdd71349",
    "metadata": {
     "tags": []
    },
    "outputs": [],
    "source": [
-    "%load_ext autoreload\n",
-    "%autoreload 2"
+    "# debug\n",
+    "import sys\n",
+    "\n",
+    "print(sys.executable)\n",
+    "print(sys.version_info)"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "d3538025-3dab-4ce1-b080-e9c70d32914b",
+   "id": "4e8dad1d-f5e5-498b-bc2c-063670fc2e83",
    "metadata": {
     "tags": []
    },
    "outputs": [],
    "source": [
-    "import os\n",
-    "\n",
-    "os.environ['USE_PYGEOS'] = '0'  # remove geopandas warnings\n",
-    "\n",
+    "# main imports\n",
     "import holoviews as hv\n",
     "import numpy as np\n",
     "import pandas as pd\n",
@@ -49,26 +59,46 @@
     "hv.extension(\"bokeh\")"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "id": "9f6cbedd-e4f7-43bc-bf06-a531826c14a5",
+   "metadata": {
+    "tags": []
+   },
+   "source": [
+    "## Open a dataset\n",
+    "\n",
+    "Thalassa supports the output of several solvers (e.g. Schism, ADCIRC). \n",
+    "In order to do so, it converts the output of these files to a common \"schema\".\n",
+    "This process is called \"normalization\".\n",
+    "\n",
+    "> \"normalization\" == Renaming of dimensions and variables\n",
+    "\n",
+    "The most convenient way to apply this normalization process is to use the `api.open_dataset()` function which is a wrapper around `xr.open_dataset()`."
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "1779d199-055f-47f6-a296-f823cec4329c",
+   "id": "c34a0afe-9394-4f49-8edc-90418609a280",
    "metadata": {
     "tags": []
    },
    "outputs": [],
    "source": [
     "%%bash\n",
-    "pushd /tmp\n",
-    "wget --quiet https://github.com/ec-jrc/Thalassa/files/10867068/fort.63.zip \n",
-    "unzip -o fort.63.zip\n",
-    "popd"
+    "if [[ ! -f /tmp/fort.63.nc ]]; then\n",
+    "    pushd /tmp\n",
+    "    wget --quiet https://github.com/ec-jrc/Thalassa/files/10867068/fort.63.zip \n",
+    "    unzip -o fort.63.zip\n",
+    "    popd\n",
+    "fi"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "73965237-0675-49d1-ae01-e45a67bd77d4",
+   "id": "d1da964f-7982-47d2-862c-bdc4edd165b1",
    "metadata": {
     "tags": []
    },
@@ -76,6 +106,18 @@
    "source": [
     "from thalassa import api\n",
     "\n",
+    "api.open_dataset?"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "8c0e749f-2b45-4244-944c-f8419133d43a",
+   "metadata": {
+    "tags": []
+   },
+   "outputs": [],
+   "source": [
     "filename = \"/tmp/fort.63.nc\"\n",
     "ds = api.open_dataset(filename)\n",
     "ds"
@@ -92,7 +134,7 @@
     "\n",
     "`thalassa` supports several types of graphs, including:\n",
     "    \n",
-    "- A visualization of the variables at various timestamps and or layers.\n",
+    "- A visualization of the variables at various timestamps and/or layers.\n",
     "- A visualization of the mesh\n",
     "- Extraction of timeseries from specific points\n",
     "\n",
@@ -145,23 +187,37 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "f42fc4d5-37ff-4195-8cb2-03986c2bcfaa",
+   "id": "43e0da2f-27ea-4bee-b3d1-6d6a9d800a2f",
    "metadata": {
     "tags": []
    },
    "outputs": [],
    "source": [
-    "layout = tiles * raster.opts(width=600, cmap=\"viridis\") \n",
-    "layout\n",
+    "raster_layout = tiles * raster.opts(width=600, cmap=\"viridis\") \n",
+    "raster_layout\n",
+    "\n",
     "(pointer_dmap + tap_dmap).opts(shared_axes=False)"
    ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "bac88601-c15e-4b74-841d-4e8f0d184566",
+   "metadata": {
+    "tags": []
+   },
+   "outputs": [],
+   "source": [
+    "mesh_layout = tiles * wireframe.opts(width=600)\n",
+    "mesh_layout"
+   ]
   }
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "thalassa",
+   "display_name": "python3",
    "language": "python",
-   "name": "thalassa"
+   "name": "python3"
   },
   "language_info": {
    "codemirror_mode": {
@@ -173,7 +229,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.16"
+   "version": "3.11.3"
   }
  },
  "nbformat": 4,