diff --git a/book/_toc.yml b/book/_toc.yml index 771fae1..6231ec7 100644 --- a/book/_toc.yml +++ b/book/_toc.yml @@ -14,3 +14,4 @@ parts: - file: notebooks - file: markdown-notebooks - file: first-figure + - file: ecosystem diff --git a/book/ecosystem.ipynb b/book/ecosystem.ipynb new file mode 100644 index 0000000..57c958d --- /dev/null +++ b/book/ecosystem.ipynb @@ -0,0 +1,266 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "id": "b862b964-62fc-48b7-96db-d7f3b868ced1", + "metadata": { + "tags": [] + }, + "source": [ + "# Integration with the scientific Python ecosystem 🐍\n", + "\n", + "In this tutorial, we'll try out the integration between PyGMT and other common packages in the scientific Python ecosystem.\n", + "\n", + "\n", + "Besides [pygmt](https://www.pygmt.org), we'll also be using:\n", + "\n", + "- [GeoPandas](https://geopandas.org/en/stable/) for managing geospatial tabular data\n", + "- [Panel](https://panel.holoviz.org/index.html) for interactive visualizations\n", + "- [Xarray](https://xarray.dev/) for managing n-dimensional labelled arrays\n" + ] + }, + { + "cell_type": "markdown", + "id": "62d489cd-c901-42a2-b51a-9b21842b34df", + "metadata": {}, + "source": [ + "## Plotting geospatial vector data with GeoPandas and PyGMT\n", + "\n", + "We'll extend the GeoPandas [Mapping and Plotting Tools Examples](https://geopandas.org/en/stable/docs/user_guide/mapping.html) to show how to create choropleth maps using PyGMT.\n", + "\n", + "**References**:\n", + "\n", + " - GeoPandas User Guide - https://geopandas.org/en/stable/docs/user_guide/" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "6436dfbb-be9c-4c2b-901a-a8fc7cde4ae8", + "metadata": {}, + "outputs": [], + "source": [ + "import pygmt\n", + "import geopandas as gpd" + ] + }, + { + "cell_type": "markdown", + "id": "a0f88acb-e463-4193-a7ef-33837b2f5fdf", + "metadata": {}, + "source": [ + "We'll load sample data provided through the GeoPandas package and inspect the GeoDataFrame." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "8cf79e91-8ce0-48ec-8812-1395d3d0eddf", + "metadata": {}, + "outputs": [], + "source": [ + "world = gpd.read_file(gpd.datasets.get_path('naturalearth_lowres'))\n", + "world.head()" + ] + }, + { + "cell_type": "markdown", + "id": "65adae6a-3933-453b-bd4b-4e04e018d02d", + "metadata": {}, + "source": [ + "Following the [GeoPandas example](https://geopandas.org/en/stable/docs/user_guide/mapping.html#choropleth-maps), we'll create a Choropleth map showing world population estimates, but will use PyGMT to plot the data using the [Hammer projection](https://www.pygmt.org/latest/projections/misc/misc_hammer.html#hammer)." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "76b850c4-e5bc-42bd-ba13-7b52b4f60dc2", + "metadata": {}, + "outputs": [], + "source": [ + "# Calculate the populations in millions per capita\n", + "world = world[(world.pop_est>0) & (world.name!=\"Antarctica\")]\n", + "world['pop_est'] = world.pop_est * 1e-6\n", + "\n", + "# Find the range of data values for creating a colormap\n", + "cmap_bounds = pygmt.info(data=world['pop_est'], per_column=True)\n", + "cmap_bounds" + ] + }, + { + "cell_type": "markdown", + "id": "864091e5-85e2-4452-ab44-5cbeaa2ac8a9", + "metadata": {}, + "source": [ + "Now, we'll plot the data on a PyGMT figure, by creating a figure instance, laying down a basemap, plotting the GeoDataFrame, and adding a colorbar!" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "15a21a74-8531-4e74-86e1-a85e6eaef793", + "metadata": {}, + "outputs": [], + "source": [ + "# Create an instance of the pygmt.Figure class\n", + "fig = pygmt.Figure()\n", + "# Create a colormap for the figure\n", + "pygmt.makecpt(cmap=\"bilbao\", series=cmap_bounds)\n", + "# Create a basemap\n", + "fig.basemap(region=\"d\", projection=\"H15c\", frame=True)\n", + "# Plot the GeoDataFrame\n", + "# - Use `close=True` to specify that the polygons should be forced closed\n", + "# - Plot the polygon outlines with a 1 point, black pen\n", + "# - Set that the color should be based on the `pop_est` using the `color, `cmap`, and `aspatial` parameters\n", + "fig.plot(data=world, pen=\"1p,black\", close=True, color=\"+z\", cmap=True, aspatial=\"Z=pop_est\")\n", + "# Add a colorbar\n", + "fig.colorbar(position=\"JMR\", frame='a200+lPopulation (millions)')\n", + "# Display the output\n", + "fig.show()\n" + ] + }, + { + "cell_type": "markdown", + "id": "b73a6666-6c2c-4f49-a92b-995ade576ccc", + "metadata": {}, + "source": [ + "## Interactive data visualization with Xarray, Panel, and PyGMT" + ] + }, + { + "cell_type": "markdown", + "id": "1bf15df6-6a4f-4221-af66-0db1c5b1e328", + "metadata": {}, + "source": [ + "In this section, we'll create some interactive visualizations of oceanographic data!\n", + "\n", + "We'll use [Panel](https://panel.holoviz.org/index.html), which is a Python library\n", + "for connecting interactive widgets with plots! We'll use Panel with\n", + "[PyGMT](https://www.pygmt.org) and [xarray](https://www.xarray.dev) to visualize\n", + "the objectively interpolated mean field for in-situ temperature from the World Ocean Atlas.\n", + "\n", + "**References**:\n", + "\n", + "- Temperature visualization based on https://rabernat.github.io/intro_to_physical_oceanography/02-c_ocean_temperature_salinity_stratification.html\n", + "- Interactive setup based on https://github.com/weiji14/30DayMapChallenge2021/blob/main/day25_interactive.py\n", + "- Data from the NOAA World Ocean Atlas, stored on the IRI Data Library at http://iridl.ldeo.columbia.edu/SOURCES/.NOAA/.NODC/.WOA09/." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "dbcff01f-fac0-4c1d-bb66-89dcb2e7711b", + "metadata": {}, + "outputs": [], + "source": [ + "import panel as pn\n", + "import xarray as xr\n", + "import pygmt\n", + "pn.extension()\n" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "7b2f9cb8-add6-45c2-9f54-8e33ed9e6f02", + "metadata": {}, + "outputs": [], + "source": [ + "# Download the dataset from the IRI Data Library\n", + "url = 'https://iridl.ldeo.columbia.edu/SOURCES/.NOAA/.NODC/.WOA09/.Grid-1x1/.Annual/.temperature/.t_an/data.nc'\n", + "netcdf_file = pygmt.which(fname=url, download=True)\n", + "woa_temp = xr.open_dataset(netcdf_file).isel(time=0)\n", + "woa_temp" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "1c72a673", + "metadata": {}, + "outputs": [], + "source": [ + "# Make a static plot of sea surface temperature\n", + "fig = pygmt.Figure()\n", + "fig.grdimage(grid=woa_temp.t_an.sel(depth=0), cmap=\"vik\", projection=\"R15c\", frame=True)\n", + "fig.show()" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "b11ea510-7540-475e-9217-be4204cb1ea3", + "metadata": {}, + "outputs": [], + "source": [ + "# Make a panel widget for controlling the depth plotted\n", + "depth_slider = pn.widgets.DiscreteSlider(name='Depth (m)', options=woa_temp.depth.values.astype(int).tolist(), value=0)" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "3496d4db-92d9-45ee-9d48-6b4f00a19361", + "metadata": {}, + "outputs": [], + "source": [ + "# Make a function for plotting the depth slice with PyGMT\n", + "\n", + "@pn.depends(depth=depth_slider)\n", + "def view(depth: int):\n", + " fig = pygmt.Figure()\n", + " pygmt.makecpt(cmap=\"vik\", series=[-2,30])\n", + " fig.grdimage(grid=woa_temp.t_an.sel(depth=depth), cmap=True, projection=\"R15c\", frame=True)\n", + " fig.colorbar(frame=\"a5\")\n", + " return fig" + ] + }, + { + "cell_type": "markdown", + "id": "d339433c-1c7a-4769-8986-edfb2a9897ed", + "metadata": {}, + "source": [ + "### Make the interactive dashboard!\n", + "\n", + "Now to put everything together! The 'dashboard' will be very simple.\n", + "The 'depth' slider is placed next to the map using `panel.Column`.\n", + "Selecting different depths will update the data plotted! Find out more at\n", + "https://panel.holoviz.org/getting_started/index.html#using-panel.\n", + "\n", + "Note: This is meant to run in a Jupyter lab/notebook environment.\n", + "The grdinfo warning can be ignored." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "cc8d2f88-6e37-4ca4-9ebc-4bdf1e00ec8e", + "metadata": {}, + "outputs": [], + "source": [ + "pn.Column(depth_slider, view)" + ] + } + ], + "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": "3.9.12" + } + }, + "nbformat": 4, + "nbformat_minor": 5 +} diff --git a/environment.yml b/environment.yml index 3c11948..57f1719 100644 --- a/environment.yml +++ b/environment.yml @@ -9,6 +9,7 @@ dependencies: - python=3.9 - pip=22 # Optional dependencies + - panel=0.13.0 - geopandas=0.10.2 - jupyter-book=0.12.3 - laspy=2.1.2