Merge pull request #4 from health-data-science-OR/2024

2024 update ( v4.0.0)
health-data-science-OR · Dec 11, 2023 · 5f3dfff · 5f3dfff
2 parents e88f336 + 71516c8
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diff --git a/binder/environment.yml b/binder/environment.yml
@@ -2,18 +2,17 @@ name: hds_logistics
 channels:
   - conda-forge
 dependencies:
-  - contextily=1.2.0
-  - folium=0.13.0
-  - geopandas=0.12.1
+  - contextily=1.4.0
+  - folium=0.15.1
+  - geopandas=0.14.1
   - geoplot=0.5.1
-  - jupyterlab=3.4.6
-  - jupyterlab-spellchecker=0.7.2
-  - mapclassify=2.4.3
-  - matplotlib=3.5.3
-  - numpy=1.23.2
-  - pandas=1.4.4
-  - pip=22.2.2
-  - pysal=2.7.0
-  - python=3.8.12
-  - scipy=1.9.1
-  - seaborn=0.11.1
+  - jupyterlab=4.0.9
+  - jupyterlab-spellchecker=0.8.4
+  - matplotlib=3.8.2
+  - numpy=1.26.2
+  - pandas=2.1.4
+  - pip=23.3.1
+  - pysal=23.7
+  - python=3.10.13
+  - scipy=1.11.4
+  - seaborn=0.13.0
diff --git a/changes.md b/changes.md
@@ -1,5 +1,12 @@
 # Changes
 
+# v4.0.0
+* Updated conda environment.yml to Python 3.10 and latest versions of libraries Dec 2023.
+* Updated Lab1
+    * removed stamin base maps as these are no longer supported
+    * Update inset map code to use new version of `matplotlib` API
+
+
 # v3.0.0
 * Tested for Academic Year 2022/23
 * Updated conda environment.yml to latest versions of libraries
diff --git a/mapping/01_geospatial_analysis.ipynb b/mapping/01_geospatial_analysis.ipynb
@@ -51,9 +51,7 @@
     "import pandas as pd\n",
     "import numpy as np\n",
     "import matplotlib.pyplot as plt\n",
-    "from mpl_toolkits.axes_grid1.inset_locator import (inset_axes, \n",
-    "                                                   InsetPosition,\n",
-    "                                                   mark_inset)\n",
+    "\n",
     "import geopandas as gpd\n",
     "import contextily as ctx\n",
     "import folium"
@@ -497,11 +495,12 @@
     "```python\n",
     "\n",
     "# convert your data to a flat projection\n",
-    "gdf_exeter_admit_flat = gdf_exeter_admit.to_crs(epsg=3857)\n",
+    "gdf_exeter_admit = gdf_exeter_admit.to_crs(epsg=3857)\n",
+    "sw_acute = sw_acute.to_crs(epsg=3857)\n",
     "\n",
     "# create map of IMD deciles\n",
-    "ax = gdf_exeter_admit_flat.plot(column='IMD_Decile',  cmap='autumn',\n",
-    "                           legend=True, figsize=(15,9))\n",
+    "ax = gdf_exeter_admit.plot(column='IMD_Decile',  cmap='autumn',\n",
+    "                       legend=True, figsize=(15,9))\n",
     "\n",
     "#add base map using contextily\n",
     "ctx.add_basemap(ax, \n",
@@ -516,8 +515,12 @@
     "* \"OpenStreetMap.Mapnik\"\n",
     "* \"CartoDB.Positron\"\n",
     "* \"CartoDB.Voyager\"\n",
-    "* \"Stamen.Toner\"\n",
-    "* \"Stamen.TonerLines\"\n",
+    "\n",
+    "you can see all provider by running\n",
+    "\n",
+    "```python\n",
+    "ctx.providers\n",
+    "```\n",
     "\n",
     "# Exercise 8\n",
     "\n",
@@ -572,10 +575,13 @@
     "                                                   facecolor='r', \n",
     "                                                   markersize=200, \n",
     "                                                   marker='*')\n",
+    "\n",
+    "#### CODE UPDATED 2024. all stamen tiles deprecated.\n",
     "# base map using contextily\n",
     "ctx.add_basemap(ax,\n",
-    "                source=ctx.providers.Stamen.Watercolor,\n",
+    "                source=ctx.providers.OpenStreetMap.Mapnik,\n",
     "                zoom=10)\n",
+    "#####\n",
     "\n",
     "ax.set_axis_off()\n",
     "ax.set_title('IMD Decile by LSOA')\n",
@@ -862,14 +868,12 @@
    "source": [
     "## Step 3: Creating an inset map\n",
     "\n",
-    "Matplotlib makes this relatively straight forward using the `axes_grid1.inset_locator` module.  You have already imported what is need at the start of this notebook using the code:\n",
+    "Matplotlib makes this relatively straight forward.  The inset map API has changed recently and I recommend using the new approach below as the old method will be deprecated in future releases.  \n",
     "\n",
-    "```python\n",
-    "from mpl_toolkits.axes_grid1.inset_locator import (inset_axes, \n",
-    "                                                   InsetPosition,\n",
-    "                                                   mark_inset)\n",
-    "```\n",
+    "The basic logic requires you to create a map and then use `Axes.inset_axes` to create a the inset axis within the main axis.  Full documentation and links to other examples can be found in the [main documentation](https://matplotlib.org/stable/api/_as_gen/matplotlib.axes.Axes.inset_axes.html#matplotlib.axes.Axes.inset_axes)\n",
     "\n",
+    "It is alos possible to add \"zoom lines\" from the main map to the inset.  To do this you need to use the `Axis.indicate_inset_zoom` method.\n",
+    " \n",
     "# Optional Exercise 1\n",
     "The code below generates an inset map of Exeter and includes explanation comments.\n",
     "\n",
@@ -910,13 +914,13 @@
     "                             ax=ax1)\n",
     "\n",
     "\n",
-    "#create the inset\n",
-    "ax2 = plt.axes([0,0,1,1])\n",
+    "#### UPDATED code for 2024. New simpler inset API\n",
+    "# create the inset\n",
+    "# set the lower left x, y location and relative size of the bounding box\n",
+    "# note these are in fractional units.\n",
+    "ax2 = ax1.inset_axes([0.025,0.5,0.45,0.45])\n",
     "\n",
-    "#set the lower left x, y location and relative size of the bounding box\n",
-    "#note these are in fractional units.\n",
-    "ip = InsetPosition(ax1, [0.025,0.5,0.45,0.45])\n",
-    "ax2.set_axes_locator(ip)\n",
+    "#####\n",
     "\n",
     "#plot the exeter LSOA inset\n",
     "ax2 = exeter_city_rate.plot(column='admits_per_1k',\n",
@@ -927,44 +931,45 @@
     "                           ax=ax2)\n",
     "\n",
     "\n",
-    "#manual text within inset\n",
+    "# manual text within inset\n",
     "ax2.text(-3.575, 50.755,'Exeter detail', fontsize='large')\n",
     "\n",
     "\n",
-    "#plot the RDE and only\n",
+    "# plot the RDE and only\n",
     "ax2 = sw_acute.loc[sw_acute['acute'] == 'RDE'].plot(ax=ax2, edgecolor='k', \n",
     "                                                   facecolor='r', \n",
     "                                                   markersize=200, \n",
     "                                                   marker='*')\n",
     "\n",
-    "#formatting tweaks...\n",
+    "# formatting tweaks...\n",
     "\n",
-    "#alight legend left\n",
+    "# align legend left\n",
     "leg = ax1.get_legend()\n",
     "leg._legend_box.align = \"left\"\n",
     "\n",
-    "#set axis 1 limits to provide enough space for exeter\n",
-    "#this might take a bit of trial and error\n",
+    "# set axis 1 limits to provide enough space for exeter\n",
+    "# this might take a bit of trial and error\n",
     "ax1.set_ylim(50.5, 51.6)\n",
     "ax1.set_xlim(-4.5, -2.75)\n",
     "\n",
-    "#hide axis tick marks\n",
+    "# hide axis tick marks\n",
     "ax2.tick_params(axis=u'both', which=u'both',length=0)\n",
     "\n",
-    "#hide axis lat long labels, but keep bounding box\n",
+    "# hide axis lat long labels, but keep bounding box\n",
     "ax2.set_xticklabels([])\n",
     "ax2.set_yticklabels([])\n",
     "\n",
-    "#this draw a box aropund the area where extra detail is needed and\n",
-    "#'zoom out' lines to the detail.\n",
-    "#this is optional and the chart might look better without it.\n",
-    "#try changing loc1 and loc2 between 1 and 4 to see what happens\n",
-    "#ls = line style '-' for solid, '--' for dashed\n",
-    "#ec = edge colour\n",
-    "#fc = face colour \n",
-    "mark_inset(ax1, ax2, loc1=1, loc2=3, ls='--', ec='k', fc='none')\n",
-    "\n",
-    "#hide the box and axis labels\n",
+    "# #### UPDATED CODE 2024 - new interface\n",
+    "# this draw a box around the area where extra detail is needed and\n",
+    "# 'zoom out' lines to the detail.\n",
+    "# this is optional and the chart might look better without it.\n",
+    "# ls = line style '-' for solid, '--' for dashed\n",
+    "# ec = edge colour\n",
+    "# fc = face colour \n",
+    "ax1.indicate_inset_zoom(ax2, edgecolor=\"black\", ls='--', ec='black', fc=None)\n",
+    "# ####\n",
+    "\n",
+    "# hide the box and axis labels\n",
     "ax1.set_axis_off()\n",
     "\n",
     "fig.savefig('images/insert_image.png', bbox_inches='tight')"
@@ -999,7 +1004,6 @@
     "* “OpenStreetMap”\n",
     "* “Mapbox Bright” (Limited levels of zoom for free tiles)\n",
     "* “Mapbox Control Room” (Limited levels of zoom for free tiles)\n",
-    "* “Stamen” (Terrain, Toner, and Watercolor)\n",
     "* “Cloudmade” (Must pass API key)\n",
     "* “Mapbox” (Must pass API key)\n",
     "* “CartoDB” (positron and dark_matter)\n",
@@ -1008,8 +1012,7 @@
     "\n",
     "```python\n",
     "#add some different background layers\n",
-    "tiles = ['stamenwatercolor', 'cartodbpositron', 'cartodbdark_matter', \n",
-    "         'openstreetmap', 'stamenterrain', 'stamentoner']\n",
+    "tiles = ['cartodbpositron', 'cartodbdark_matter', 'openstreetmap']\n",
     "for tile in tiles:\n",
     "    folium.TileLayer(tile).add_to(stroke_map)\n",
     "\n",
@@ -1073,38 +1076,39 @@
     "stroke_map = folium.Map(location=[50.71671, -3.50668], zoom_start=9, \n",
     "                        tiles='cartodbpositron')\n",
     "\n",
-    "#add some different background layers\n",
-    "tiles = ['stamenwatercolor', 'cartodbpositron', 'cartodbdark_matter', \n",
-    "         'openstreetmap', 'stamenterrain', 'stamentoner']\n",
+    "#### Updated code 2024\n",
+    "# add some different background layers\n",
+    "tiles = ['cartodbpositron', 'cartodbdark_matter', 'openstreetmap']\n",
+    "####\n",
     "\n",
     "for tile in tiles:\n",
     "    folium.TileLayer(tile).add_to(stroke_map)\n",
     "\n",
-    "#filter data to display\n",
+    "# filter data to display\n",
     "fields = ['LSOA11NM', 'admissions', 'admits_per_1k', 'IMD_Decile']\n",
     "lsoa_tia = gdf_exeter_admit[fields]\n",
     "\n",
-    "#field to color; 0 = LSOA11NM; 1 = 'admissions' etc.\n",
+    "# field to color; 0 = LSOA11NM; 1 = 'admissions' etc.\n",
     "field_index = 3\n",
     "\n",
-    "#create and add choropleth map\n",
+    "# create and add choropleth map\n",
     "choropleth = folium.Choropleth(\n",
-    "    #pass the GeoDataFrame\n",
+    "    # pass the GeoDataFrame\n",
     "    geo_data=gdf_exeter_admit,\n",
-    "    #Data for overlaying\n",
+    "    # Data for overlaying\n",
     "    data=lsoa_tia,\n",
-    "    #columns = [key, field to plot]\n",
+    "    #c olumns = [key, field to plot]\n",
     "    columns=['LSOA11NM', fields[field_index]],\n",
     "    key_on='feature.properties.LSOA11NM',\n",
-    "    #choose the fill colour\n",
+    "    # choose the fill colour\n",
     "    fill_color='OrRd',\n",
-    "    #set the legent name\n",
+    "    # set the legent name\n",
     "    legend_name=fields[field_index],\n",
-    "    #highlight the LSOA shape when mouse pointer enters it\n",
+    "    # highlight the LSOA shape when mouse pointer enters it\n",
     "    highlight=True,\n",
     "    smooth_factor=0).add_to(stroke_map)    \n",
     "    \n",
-    "#add layer control to map - make sure you do this after adding choropleth map\n",
+    "# add layer control to map - make sure you do this after adding choropleth map\n",
     "folium.LayerControl().add_to(stroke_map)\n",
     "\n",
     "stroke_map"
@@ -1148,6 +1152,13 @@
    "source": [
     "# your code here ..."
    ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
   }
  ],
  "metadata": {
@@ -1166,7 +1177,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.8"
+   "version": "3.10.13"
   }
  },
  "nbformat": 4,