notebooks: Update notebooks/API.ipynb

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",
@@ -49,33 +59,65 @@
  "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": []
  },
  "outputs": [],
  "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,