mapillary_GVI_googlecolab.ipynb

{"cells":[{"attachments":{},"cell_type":"markdown","metadata":{"id":"c_YUWN49hnem"},"source":["# Automated Street View Index Calculation Pipeline using Mapillary Street Images"]},{"attachments":{},"cell_type":"markdown","metadata":{"id":"bU6Obvi9dZem"},"source":["Before running this Jupyter Notebook, it is recommended to configure it to use a GPU. Follow these steps:\n","\n","1. Go to the \"Runtime\" menu at the top.\n","2. Select \"Change runtime type\" from the dropdown menu.\n","3. In the \"Runtime type\" section, choose \"Python 3\".\n","4. In the \"Hardware accelerator\" section, select \"GPU\".\n","5. In the \"GPU type\" section, choose \"T4\" if available.\n","6. In the \"Runtime shape\" section, select \"High RAM\".\n","\n","Save the notebook settings after making these selections."]},{"cell_type":"code","execution_count":null,"metadata":{"id":"6S7YfDVGb_6Y"},"outputs":[],"source":["# Step 1: Install required libraries\n","# The following libraries are not installed by default in Google Colab, so run these commands:\n","%pip install transformers==4.30.1\n","%pip install geopandas==0.13.2\n","%pip install torch==1.13.1\n","%pip install vt2geojson==0.2.1\n","%pip install mercantile==1.2.1\n","%pip install osmnx==1.4.0\n","%pip install pygam==0.8.0\n","%pip install rasterio==1.3.4\n","%pip install rioxarray==0.13.3\n","%pip install xarray-spatial==0.3.5\n","%pip install rasterio==1.3.4\n","%pip install shapely==2.0.1\n","%pip install pystac-client==0.6.0\n","%pip install planetary-computer==0.4.9\n","%pip install odc-stac==0.3.6\n","%pip install matplotlib==3.7.1\n","%pip install numpy==1.23.0\n","%pip install folium==0.14.0"]},{"cell_type":"code","execution_count":null,"metadata":{"id":"yQKWm-_bcCOg"},"outputs":[],"source":["# Mount Google Drive to Google Colab\n","# This step allows you to store the scripts from GitHub and the resulting files in your Google Drive.\n","\n","# Import the necessary library to mount Google Drive\n","from google.colab import drive\n","\n","# Prompt for permission to connect Google Drive\n","# When running this code, Google Colab will ask for permission to access your Google Drive.\n","# Follow the provided instructions and grant the necessary permissions.\n","# Mount Google Drive to '/content/drive' directory\n","drive.mount('/content/drive')"]},{"cell_type":"code","execution_count":null,"metadata":{"id":"iTMpUOenXLtn"},"outputs":[],"source":["# Change the current directory to your Google Drive's root folder\n","%cd /content/drive/MyDrive"]},{"cell_type":"code","execution_count":null,"metadata":{"id":"_cdVoOuTX3UP"},"outputs":[],"source":["import os\n","\n","# Check if the GitHub repository is cloned in your Google Drive\n","# If the 'StreetView-NatureVisibility' folder doesn't exist, this block of code will clone the repository from GitHub\n","if not os.path.isdir('StreetView-NatureVisibility'):\n","    # Clone the GitHub repository to your Google Drive\n","    !git clone https://github.com/Spatial-Data-Science-and-GEO-AI-Lab/StreetView-NatureVisibility.git"]},{"cell_type":"code","execution_count":null,"metadata":{"id":"G54gRyUgXyq3"},"outputs":[],"source":["# Change the current directory to the cloned project folder ('StreetView-NatureVisibility')\n","%cd StreetView-NatureVisibility"]},{"cell_type":"code","execution_count":1,"metadata":{"id":"YyMASr7JZ5SQ"},"outputs":[],"source":["# Set the desired values for the analysis parameters\n","place = \"Amsterdam, Netherlands\"    # Specify the location for the analysis\n","distance = 50                       # Set the distance parameter for the analysis\n","cut_by_road_centres = 0             # Determine if panoramic images are going to be cropped using the road centres\n","access_token = 'MLY|'              # Enter the access token for data retrieval\n","file_name = 'amsterdam-gvi'         # Set the desired filename for the analysis results\n","max_workers = 6                     # Specify the maximum number of workers for parallel processing\n","num_sample_images= 0                # Number of images with their segmentations that are going to be stored\n","\n","# Modify the values of 'begin' and 'end' to analyze a specific subset of the dataset\n","# It's recommended to analyze the dataset in batches considering the available session time for your Google Colab account\n","# Using the GPU T4, it takes approximately 40 minutes to analyze 2,000 points\n","\n","begin = 0                        # Write None or set 'begin' to a specific value to start the analysis from a particular point in the dataset\n","end = 5                        # Write None or set 'end' to a specific value to end the analysis at a particular point in the dataset"]},{"cell_type":"code","execution_count":3,"metadata":{"id":"7o4odFShcDIG"},"outputs":[{"name":"stdout","output_type":"stream","text":["Downloading images: 100%|█████████████████████████| 5/5 [00:26<00:00,  5.29s/it]\n","Running time: 0:00:28.454943\n"]}],"source":["# Run the script to obtain Green View Index (GVI) values\n","command = f\"python main_script.py '{place}' {distance} {cut_by_road_centres} '{access_token}' {file_name} {max_workers} {num_sample_images} {begin if begin is not None else ''} {end if end is not None else ''}\"\n","!{command}"]},{"cell_type":"markdown","metadata":{},"source":["After running the analysis, you can access the generated results in your Google Drive. Navigate to the 'results' folder, where you will find a subfolder named after the analyzed place. Inside this folder, you will find the following directories:\n","\n","- **roads**: Contains the GeoPackage (GPKG) file with the road network of the analyzed place.\n","- **points**: Contains the GeoPackage (GPKG) file with the sampled points.\n","- **gvi**: Currently, this directory contains the CSV file generated in the previous step.\n","\n","To obtain the GeoPackage (GPKG) file with the points and their calculated Green View Index (GVI) values, run the following cell."]},{"cell_type":"code","execution_count":4,"metadata":{},"outputs":[],"source":["# Generate GeoPackage files from the CSV files obtained in the previous step\n","# The GeoPackage file will be stored in the following location: StreetView-NatureVisibility/results/{place}/gvi/gvi-points.gpkg\n","command = f\"python scripts/get_gvi_gpkg.py '{place}'\"\n","!{command}"]},{"cell_type":"code","execution_count":5,"metadata":{},"outputs":[],"source":["import matplotlib.colors as colors\n","import matplotlib.cm as cm\n","import geopandas as gpd\n","import numpy as np\n","import folium\n","\n","def plot_gvi_points(gpkg_file):\n","    # Load the GeoPackage file\n","    gdf = gpd.read_file(gpkg_file)\n","\n","    centroid = gdf.dissolve().centroid\n","\n","    # Step 1: Create a Folium map object\n","    m = folium.Map(location=[centroid.y, centroid.x], zoom_start=15)\n","\n","    # Step 2: Define the color map and normalization\n","    cmap = cm.get_cmap('Greens')  # Choose a colormap, e.g., 'Greens'\n","    gvi_values = gdf['GVI'].values\n","    valid_values = gvi_values[~np.isnan(gvi_values)]  # Exclude null values\n","    normalize = colors.Normalize(vmin=np.min(valid_values), vmax=np.max(valid_values))  # Normalize non-null GVI values\n","\n","    # Step 3: Iterate over the GeoDataFrame and add points to the map\n","    for index, row in gdf.iterrows():\n","        point = row['geometry']\n","        gvi = row['GVI']\n","        coordinates = (point.y, point.x)  # Swap lat and lon order\n","\n","        if not np.isnan(gvi):\n","            # Map the non-null GVI value to a color in the colormap\n","            color = colors.rgb2hex(cmap(normalize(gvi)))\n","            marker =  folium.CircleMarker(location=coordinates, color=color, radius=5, fill=True, fill_color=color, fill_opacity=1).add_to(m)\n","            marker.add_child(folium.Popup(f\"ID: {row['id']} / GVI: {gvi}\"))  # Add the GVI value to the pop-up message\n","            marker.add_to(m)\n","        else:\n","            # Map the non-null GVI value to a color in the colormap\n","            color = \"red\"\n","            marker =  folium.CircleMarker(location=coordinates, color=color, radius=3, fill=True, fill_color=color, fill_opacity=1).add_to(m)\n","            marker.add_child(folium.Popup(\"GVI: Not known\"))  # Add the GVI value to the pop-up message\n","            marker.add_to(m)\n","\n","    # Step 4: Display the map\n","    return m"]},{"cell_type":"code","execution_count":6,"metadata":{},"outputs":[{"name":"stderr","output_type":"stream","text":["/var/folders/f_/xfklpqfj6kjg8yr6l1byph0h0000gn/T/ipykernel_11040/1628496617.py:11: UserWarning: Geometry is in a geographic CRS. Results from 'centroid' are likely incorrect. Use 'GeoSeries.to_crs()' to re-project geometries to a projected CRS before this operation.\n","\n","  centroid = gdf.dissolve().centroid\n","/var/folders/f_/xfklpqfj6kjg8yr6l1byph0h0000gn/T/ipykernel_11040/1628496617.py:17: MatplotlibDeprecationWarning: The get_cmap function was deprecated in Matplotlib 3.7 and will be removed two minor releases later. Use ``matplotlib.colormaps[name]`` or ``matplotlib.colormaps.get_cmap(obj)`` instead.\n","  cmap = cm.get_cmap('Greens')  # Choose a colormap, e.g., 'Greens'\n"]},{"data":{"text/html":["<div style=\"width:100%;\"><div style=\"position:relative;width:100%;height:0;padding-bottom:60%;\"><span style=\"color:#565656\">Make this Notebook Trusted to load map: File -> Trust Notebook</span><iframe srcdoc=\"&lt;!DOCTYPE html&gt;\n","&lt;html&gt;\n","&lt;head&gt;\n","    \n","    &lt;meta http-equiv=&quot;content-type&quot; content=&quot;text/html; charset=UTF-8&quot; /&gt;\n","    \n","        &lt;script&gt;\n","            L_NO_TOUCH = false;\n","            L_DISABLE_3D = false;\n","        &lt;/script&gt;\n","    \n","    &lt;style&gt;html, body {width: 100%;height: 100%;margin: 0;padding: 0;}&lt;/style&gt;\n","    &lt;style&gt;#map {position:absolute;top:0;bottom:0;right:0;left:0;}&lt;/style&gt;\n","    &lt;script src=&quot;https://cdn.jsdelivr.net/npm/leaflet@1.9.3/dist/leaflet.js&quot;&gt;&lt;/script&gt;\n","    &lt;script src=&quot;https://code.jquery.com/jquery-1.12.4.min.js&quot;&gt;&lt;/script&gt;\n","    &lt;script src=&quot;https://cdn.jsdelivr.net/npm/bootstrap@5.2.2/dist/js/bootstrap.bundle.min.js&quot;&gt;&lt;/script&gt;\n","    &lt;script src=&quot;https://cdnjs.cloudflare.com/ajax/libs/Leaflet.awesome-markers/2.0.2/leaflet.awesome-markers.js&quot;&gt;&lt;/script&gt;\n","    &lt;link rel=&quot;stylesheet&quot; 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It is crucial to change the ESPG code depending on the specific area you are analyzing.\n","\n","Make sure to update the epsg_code variable with the appropriate projection in meters that is suitable for your study area. For example, you can use the same projection as the one used in the roads.gpkg file.\n","\n","Additionally, ensure that you have created the required folder structure: StreetView-NatureVisibility/results/{place}/ndvi. Place the corresponding NDVI file, named ndvi.tif, inside this folder. It is recommended to use an NDVI file that has been consistently generated for the study area over the course of a year. The NDVI file must be in the same chosen projection for your area of study."]},{"cell_type":"code","execution_count":7,"metadata":{},"outputs":[],"source":["# Please modify the code accordingly before executing this cell to ensure accurate results for your specific area of analysis.\n","# Indicate a projection in meters, suitable for the study area\n","\n","epsg_code = 32631\n","file_exists = 0 # Indicates if the file with the calculated ndvi values already exists"]},{"cell_type":"code","execution_count":8,"metadata":{},"outputs":[{"name":"stdout","output_type":"stream","text":["cp: /usr/local/lib/python3.10/dist-packages/pygam/pygam.py: No such file or directory\n"]}],"source":["# Changes a line in pygam library to solve a bug\n","!cp -v pygam/pygam.py /usr/local/lib/python3.10/dist-packages/pygam/pygam.py"]},{"cell_type":"code","execution_count":9,"metadata":{},"outputs":[{"name":"stdout","output_type":"stream","text":["Calculating mean NDVI values...\n","Done, running time: 0:00:01.624598 \n","\n","<----- Linear Regression ----->\n","R2 value: -0.14012519531811482\n","RMSE: 0.08051354209591755\n","AIC value: -237.8556688555344\n","100% (20 of 20) |########################| Elapsed Time: 0:00:00 Time:  0:00:00\n","<----- Linear GAM ----->\n","RMSE: 0.09846157437967826\n","AIC value: -218.53653581470112\n"]}],"source":["# Compute missing GVI points using NDVI values\n","# The estimation for the missing points will be stored in the following path: StreetView-NatureVisibility/results/{place}/ndvi/calculated_missing_values_linreg.gpkg and StreetView-NatureVisibility/results/{place}/ndvi/calculated_missing_values_gam.gpkg \n"," \n","command = f\"python predict_missing_gvi.py '{place}' {file_exists} {epsg_code} {distance}\"\n","!{command}"]},{"cell_type":"code","execution_count":10,"metadata":{},"outputs":[{"name":"stderr","output_type":"stream","text":["/var/folders/f_/xfklpqfj6kjg8yr6l1byph0h0000gn/T/ipykernel_11040/1628496617.py:11: UserWarning: Geometry is in a geographic CRS. Results from 'centroid' are likely incorrect. Use 'GeoSeries.to_crs()' to re-project geometries to a projected CRS before this operation.\n","\n","  centroid = gdf.dissolve().centroid\n","/var/folders/f_/xfklpqfj6kjg8yr6l1byph0h0000gn/T/ipykernel_11040/1628496617.py:17: MatplotlibDeprecationWarning: The get_cmap function was deprecated in Matplotlib 3.7 and will be removed two minor releases later. Use ``matplotlib.colormaps[name]`` or ``matplotlib.colormaps.get_cmap(obj)`` instead.\n","  cmap = cm.get_cmap('Greens')  # Choose a colormap, e.g., 'Greens'\n"]},{"data":{"text/html":["<div style=\"width:100%;\"><div style=\"position:relative;width:100%;height:0;padding-bottom:60%;\"><span style=\"color:#565656\">Make this Notebook Trusted to load map: File -> Trust Notebook</span><iframe srcdoc=\"&lt;!DOCTYPE html&gt;\n","&lt;html&gt;\n","&lt;head&gt;\n","    \n","    &lt;meta http-equiv=&quot;content-type&quot; content=&quot;text/html; charset=UTF-8&quot; /&gt;\n","    \n","        &lt;script&gt;\n","            L_NO_TOUCH = false;\n","            L_DISABLE_3D = false;\n","        &lt;/script&gt;\n","    \n","    &lt;style&gt;html, body {width: 100%;height: 100%;margin: 0;padding: 0;}&lt;/style&gt;\n","    &lt;style&gt;#map {position:absolute;top:0;bottom:0;right:0;left:0;}&lt;/style&gt;\n","    &lt;script src=&quot;https://cdn.jsdelivr.net/npm/leaflet@1.9.3/dist/leaflet.js&quot;&gt;&lt;/script&gt;\n","    &lt;script src=&quot;https://code.jquery.com/jquery-1.12.4.min.js&quot;&gt;&lt;/script&gt;\n","    &lt;script src=&quot;https://cdn.jsdelivr.net/npm/bootstrap@5.2.2/dist/js/bootstrap.bundle.min.js&quot;&gt;&lt;/script&gt;\n","    &lt;script src=&quot;https://cdnjs.cloudflare.com/ajax/libs/Leaflet.awesome-markers/2.0.2/leaflet.awesome-markers.js&quot;&gt;&lt;/script&gt;\n","    &lt;link rel=&quot;stylesheet&quot; 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Results from 'centroid' are likely incorrect. Use 'GeoSeries.to_crs()' to re-project geometries to a projected CRS before this operation.\n","\n","  centroid = gdf.dissolve().centroid\n","/var/folders/f_/xfklpqfj6kjg8yr6l1byph0h0000gn/T/ipykernel_11040/1628496617.py:17: MatplotlibDeprecationWarning: The get_cmap function was deprecated in Matplotlib 3.7 and will be removed two minor releases later. Use ``matplotlib.colormaps[name]`` or ``matplotlib.colormaps.get_cmap(obj)`` instead.\n","  cmap = cm.get_cmap('Greens')  # Choose a colormap, e.g., 'Greens'\n"]},{"data":{"text/html":["<div style=\"width:100%;\"><div style=\"position:relative;width:100%;height:0;padding-bottom:60%;\"><span style=\"color:#565656\">Make this Notebook Trusted to load map: File -> Trust Notebook</span><iframe srcdoc=\"&lt;!DOCTYPE html&gt;\n","&lt;html&gt;\n","&lt;head&gt;\n","    \n","    &lt;meta http-equiv=&quot;content-type&quot; content=&quot;text/html; charset=UTF-8&quot; /&gt;\n","    \n","        &lt;script&gt;\n","            L_NO_TOUCH = false;\n","            L_DISABLE_3D = false;\n","        &lt;/script&gt;\n","    \n","    &lt;style&gt;html, body {width: 100%;height: 100%;margin: 0;padding: 0;}&lt;/style&gt;\n","    &lt;style&gt;#map {position:absolute;top:0;bottom:0;right:0;left:0;}&lt;/style&gt;\n","    &lt;script src=&quot;https://cdn.jsdelivr.net/npm/leaflet@1.9.3/dist/leaflet.js&quot;&gt;&lt;/script&gt;\n","    &lt;script src=&quot;https://code.jquery.com/jquery-1.12.4.min.js&quot;&gt;&lt;/script&gt;\n","    &lt;script src=&quot;https://cdn.jsdelivr.net/npm/bootstrap@5.2.2/dist/js/bootstrap.bundle.min.js&quot;&gt;&lt;/script&gt;\n","    &lt;script src=&quot;https://cdnjs.cloudflare.com/ajax/libs/Leaflet.awesome-markers/2.0.2/leaflet.awesome-markers.js&quot;&gt;&lt;/script&gt;\n","    &lt;link rel=&quot;stylesheet&quot; 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Roads types with the most missing images\n","2. Missing images\n","3. Panoramic images\n","4. Image Availability Score and Adjusted Image Availability Score\n","5. Image Usability Score and Ajdusted Image Usability Score\n","\n","After running the second code cell, there will be a plot in the results/{place} folder illustrating the roads with the highest amount of missing images in the analysed place."]},{"cell_type":"code","execution_count":12,"metadata":{"id":"dj_YKhykeLRV"},"outputs":[],"source":["# First,we compute the mean Green View Index (GVI) value per street in the road network\n","# The GeoPackage file will be stored in the following location: StreetView-NatureVisibility/results/{place}/gvi/gvi-streets.gpkg\n","command = f\"python scripts/mean_gvi_street.py '{place}'\"\n","!{command}"]},{"cell_type":"code","execution_count":13,"metadata":{},"outputs":[{"name":"stdout","output_type":"stream","text":["Unavailable images per road type for Amsterdam, Netherlands\n","Figure(640x480)\n","                           highway                    city  total_null  \\\n","0                      residential  Amsterdam, Netherlands          35   \n","1                     unclassified  Amsterdam, Netherlands          11   \n","2  ['unclassified', 'residential']  Amsterdam, Netherlands           2   \n","3                         tertiary  Amsterdam, Netherlands           2   \n","\n","   proportion_null  \n","0             0.70  \n","1             0.22  \n","2             0.04  \n","3             0.04  \n","\n","Missing images for Amsterdam, Netherlands\n","   Unavailable  Unsuitable  Total  Proportion  Total Sample Points\n","0            0           2      2        0.04                   50\n","\n","Panoramic images for Amsterdam, Netherlands\n","   Panoramic Images  Total Images  Proportion\n","0                40            50         0.8\n","\n","Image Availability Score and Adjusted Image Availability Score for Amsterdam, Netherlands\n","   GVI Points  Road Length  Total Sample  Availability Score  \\\n","0          50     8.608296            50                 1.0   \n","\n","   Adjusted Availability Score  \n","0                     2.152726  \n","\n","Image Usability Score and Ajdusted Image Usability Score  for Amsterdam, Netherlands\n","   GVI Points  Road Length  Total Sample  Usability Score  \\\n","0          48     8.608296            50             0.96   \n","\n","   Adjusted Usability Score  \n","0                  2.066617  \n"]}],"source":["# Now we can get the statistics for the analysed place\n","command = f\"python scripts/results_metrics.py '{place}'\"\n","!{command}"]}],"metadata":{"colab":{"gpuType":"T4","machine_shape":"hm","provenance":[]},"kernelspec":{"display_name":"Python 3","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":"3.10.9"}},"nbformat":4,"nbformat_minor":0}