Update tutorials (#63)

.gitignore

@@ -105,12 +105,17 @@ venv.bak/
 
 .DS_Store
 
-tutorial/tutorial_outputs/*
-Tutorial/tutorial_data/rek_grid_pop_gravity.cpg
-Tutorial/tutorial_data/rek_grid_pop_gravity.dbf
-Tutorial/tutorial_data/rek_grid_pop_gravity.prj
-Tutorial/tutorial_data/rek_grid_pop_gravity.shp
-Tutorial/tutorial_data/rek_grid_pop_gravity.shx
+Tutorials/tutorial_outputs/*
+Tutorials/tutorial_data/rek_grid_pop_gravity.cpg
+Tutorials/tutorial_data/rek_grid_pop_gravity.dbf
+Tutorials/tutorial_data/rek_grid_pop_gravity.prj
+Tutorials/tutorial_data/rek_grid_pop_gravity.shp
+Tutorials/tutorial_data/rek_grid_pop_gravity.shx
+Tutorials/tutorial_data/rek_grid_pop_gravity2.cpg
+Tutorials/tutorial_data/rek_grid_pop_gravity2.dbf
+Tutorials/tutorial_data/rek_grid_pop_gravity2.prj
+Tutorials/tutorial_data/rek_grid_pop_gravity2.shp
+Tutorials/tutorial_data/rek_grid_pop_gravity2.shx
 
 # ignore the version file
 *_version.py*

Tutorials/EXAMPLE_Finding_links_between_pairs.ipynb

@@ -16,8 +16,7 @@
    "outputs": [],
    "source": [
     "import os\n",
-    "import sys\n",
-    "\n",
+    "import pickle as pkl\n",
     "import networkx as nx\n",
     "import geopandas as gpd\n",
     "import pandas as pd\n",
@@ -31,8 +30,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "# add to your system path the location of the LoadOSM.py and GOSTnet.py scripts\n",
-    "sys.path.append(\"../\")\n",
+    "# import the GOSTnet library\n",
     "import GOSTnets as gn"
    ]
   },
@@ -45,8 +43,8 @@
     "# Define input data\n",
     "pth = \"./\"\n",
     "# Read in cleaned pickle from earlier analysis and convert to time\n",
-    "G = nx.read_gpickle(\n",
-    "    os.path.join(pth, \"tutorial_outputs\", r\"iceland_network_clean.pickle\")\n",
+    "G = pkl.load(\n",
+    "    open(os.path.join(pth, \"tutorial_outputs\", r\"iceland_network_clean.pickle\"), \"rb\")\n",
     ")\n",
     "G_time = gn.convert_network_to_time(\n",
     "    G, distance_tag=\"length\", road_col=\"infra_type\", factor=1000\n",
@@ -117,6 +115,18 @@
     "## Calculate line strings connecting all origins to all destinations"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# for the sake of the example we truncate the number of origins and destinations\n",
+    "# to make the computation faster. We will only use the first 10 of each\n",
+    "origins = origins[:10]\n",
+    "destinations = destinations[:10]"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -153,7 +163,7 @@
    "source": [
     "# Write all connections to file\n",
     "all_results = pd.DataFrame(all_res, columns=[\"O\", \"D\", \"geometry\"])\n",
-    "all_results.to_csv(os.path.join(pth, \"tutorial_data\", \"all_OD_links.csv\"))"
+    "all_results.to_csv(os.path.join(pth, \"tutorial_outputs\", \"all_OD_links.csv\"))"
    ]
   },
   {
@@ -177,7 +187,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "all_connections_first.to_csv(os.path.join(pth, \"tutorial_data\", \"OD_links_usage.csv\"))"
+    "all_connections_first.to_csv(\n",
+    "    os.path.join(pth, \"tutorial_outputs\", \"OD_links_usage.csv\")\n",
+    ")"
    ]
   },
   {

Tutorials/EXAMPLE_Fixing_your_road_network.ipynb

@@ -16,9 +16,9 @@
    "outputs": [],
    "source": [
     "import os\n",
-    "import sys\n",
     "import networkx as nx\n",
-    "import osmnx as ox"
+    "import osmnx as ox\n",
+    "import pickle as pkl"
    ]
   },
   {
@@ -27,8 +27,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "# add to your system path the location of the LoadOSM.py and GOSTnet.py scripts\n",
-    "sys.path.append(\"../\")\n",
+    "# import the GOSTnets library\n",
     "import GOSTnets as gn"
    ]
   },
@@ -41,8 +40,8 @@
     "pth = \"./\"  # change this path to your working folder\n",
     "data_pth = os.path.join(pth, \"tutorial_outputs\")\n",
     "\n",
-    "# read back your graph from step 1 from you saved pickle\n",
-    "G = nx.read_gpickle(os.path.join(data_pth, \"iceland_network_clean.pickle\"))"
+    "# read back your graph from step 2 from you saved pickle\n",
+    "G = pkl.load(open(os.path.join(data_pth, \"iceland_network_clean.pickle\"), \"rb\"))"
    ]
   },
   {
@@ -64,8 +63,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "G_largest = list_of_subgraphs[0]\n",
-    "G_second_largest = list_of_subgraphs[1]"
+    "G_largest = list_of_subgraphs[0]"
    ]
   },
   {
@@ -74,25 +72,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "print(nx.info(G_largest))"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "print(nx.info(G_second_largest))"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "print(nx.info(list_of_subgraphs[2]))"
+    "print(G_largest)"
    ]
   },
   {
@@ -106,20 +86,7 @@
     "G_largest.graph[\"name\"] = \"Iceland\"\n",
     "\n",
     "# largest connected subgraph\n",
-    "ox.plot_graph(G_largest, fig_width=10, edge_linewidth=1, node_size=7)"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "G_second_largest.graph[\"crs\"] = \"epsg:32646\"\n",
-    "G_second_largest.graph[\"name\"] = \"Iceland\"\n",
-    "\n",
-    "# second largest connected subgraph\n",
-    "ox.plot_graph(G_second_largest, fig_width=10, edge_linewidth=1, node_size=7)"
+    "ox.plot_graph(G_largest, figsize=(10, 14), edge_linewidth=1, node_size=7)"
    ]
   },
   {
@@ -132,16 +99,6 @@
     "edges_largest.to_csv(os.path.join(data_pth, \"edges_largest.csv\"))"
    ]
   },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "edges_second = gn.edge_gdf_from_graph(G_second_largest)\n",
-    "edges_second.to_csv(os.path.join(data_pth, \"edges_second.csv\"))"
-   ]
-  },
   {
    "cell_type": "markdown",
    "metadata": {},

Tutorials/EXAMPLE_Gravity_Calculations.ipynb

@@ -7,12 +7,11 @@
    "outputs": [],
    "source": [
     "import os\n",
-    "import sys\n",
     "import rasterio\n",
     "\n",
-    "import networkx as nx\n",
     "import geopandas as gpd\n",
-    "import pandas as pd"
+    "import pandas as pd\n",
+    "import pickle as pkl"
    ]
   },
   {
@@ -21,8 +20,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "# add to your system path the location of the LoadOSM.py and GOSTnet.py scripts\n",
-    "sys.path.append(\"../\")\n",
+    "# import the GOSTnets library\n",
     "import GOSTnets as gn"
    ]
   },
@@ -35,8 +33,11 @@
     "# Define input data\n",
     "pth = \"./\"\n",
     "# Read in cleaned pickle from earlier analysis and convert to time\n",
-    "G = nx.read_gpickle(\n",
-    "    os.path.join(pth, \"tutorial_outputs\", r\"iceland_network_clean.pickle\")\n",
+    "G = pkl.load(\n",
+    "    open(\n",
+    "        os.path.join(pth, \"tutorial_outputs\", r\"iceland_network_clean.pickle\"),\n",
+    "        \"rb\",\n",
+    "    )\n",
     ")\n",
     "G_time = gn.convert_network_to_time(\n",
     "    G, distance_tag=\"length\", road_col=\"infra_type\", factor=1000\n",
@@ -177,9 +178,15 @@
     "OD = gn.calculate_OD(G_time, origins, destinations, fail_value=9999999)\n",
     "gravity = calcOD.calculate_gravity(\n",
     "    OD, oWeight=origins_df[\"Pop\"], dWeight=destinations_df[\"Pop\"]\n",
-    ")"
+    ")\n",
+    "gravity[\"NN\"] = origins"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": []
+  },
   {
    "cell_type": "code",
    "execution_count": null,

Tutorials/Step_1-Extract_From_OSM.ipynb

@@ -1,12 +1,5 @@
 {
  "cells": [
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "## note: As of Jan 21, 2020 This tutorial is using the GOSTnets version from this repo's master branch. Make sure that the GOSTnets version from PyPi is uninstalled and that you are pointing your path to the correct location of the library."
-   ]
-  },
   {
    "cell_type": "markdown",
    "metadata": {},
@@ -23,8 +16,7 @@
    "outputs": [],
    "source": [
     "import geopandas as gpd\n",
-    "import os\n",
-    "import sys"
+    "import os"
    ]
   },
   {
@@ -43,8 +35,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Add to your system path the location of the LoadOSM.py and GOSTnet.py scripts.  \n",
-    "In this case, we use relative paths (\"..\") to locate the parent directory (one level up). One dot (\".\") means current directory."
+    "Import the GOSTnets library as gn."
    ]
   },
   {
@@ -53,7 +44,6 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "sys.path.append(\"../\")\n",
     "import GOSTnets as gn"
    ]
   },
@@ -216,7 +206,7 @@
    "outputs": [],
    "source": [
     "clip_shp = gpd.read_file(os.path.join(pth, \"tutorial_data\", \"rek2.shp\"))\n",
-    "clip_shp = clip_shp.to_crs({\"init\": \"epsg:4326\"})\n",
+    "clip_shp = clip_shp.to_crs(\"epsg:4326\")\n",
     "clip_shp_obj = clip_shp.geometry.iloc[0]"
    ]
   },
@@ -271,7 +261,7 @@
    "outputs": [],
    "source": [
     "iceland.roads_raw = iceland.roads_raw.loc[\n",
-    "    iceland.roads_raw.geometry.intersects(clip_shp_obj) is True\n",
+    "    iceland.roads_raw.geometry.intersects(clip_shp_obj) == True  # noqa: E712\n",
     "]"
    ]
   },
@@ -291,6 +281,16 @@
     "iceland.generateRoadsGDF(verbose=False)"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# view the first 5 rows of the newly created roads GeoDataFrame\n",
+    "iceland.roadsGPD.head()"
+   ]
+  },
   {
    "cell_type": "markdown",
    "metadata": {},