Updated - Installing Apache, QGIS Server, and Lizmap Web Client on Windows OS

Part 1: QGIS Server and Lizmap

This is an updated version of my previous blog post on installing Apache, QGIS Server, and Lizweb Map on Windows OS - this time using Apache 2.4.33, QGIS Server LTR 2.18.21 and Lizmap Web Client 3.1.12. I just updated my Windows Server 2016 and needed to redo my GIS server. This post includes screenshots so hopefully it will be more helpful with details. This shows the process on my Windows 10 Pro laptop but should be the same for a Windows Server 2016 (which I've done at my work). If this helps you or if you find any errors or have any suggestions, let me know in the comments section.

For my test on my Windows 10 Pro laptop, I have everything on the same machine. But on the Windows Server 2016 machine, I have QGIS Desktop with Lizmap Web Plugin on a different machine. For my installation I put Apache and Lizmap side-by-side inside a C:/webserver directory. You can however, put your installations inside of Apache root directory (e.g. C:/Apache24/Lizmap) or inside Apache htdocs directory (e.g. C:/Apache24/htdocs/lizmap). If installation of Lizmap and Apache are side by side or Lizmap is inside Apache root directory then you need to properly configure the virtual hosts.

Software Used/Requirements:

  • Lizmap and QGIS Server must be on same machine

  • QGIS Server LTR 2.18.21 (installed via OSGeo4W x64)

  • QGIS Desktop (installed via OSGeo4W x64)

  • Lizmap Web Plugin (installed via QGIS Desktop plugin manager)

  • Lizmap Web Client 3.1.12

  • Apache 2.4.33

    • mod fcgid

    • C++ Redistributable VS 2015

    • PHP 7.2.7

Part 1: Set up workspace

You can choose how you set up your workspace environment, but for this guide the following setup is used.      

1. Optional - turn off IIS if enabled in Windows. I have it enabled so I turned if off so I can use the default port 80.

2. Set up a home workspace on your local drive - for simplicity sake, I have a directory called webserver on my drive that I will use as my workspace (e.g. C:\webserver)

Part 2: Install and Configure Apache

For more info on using Apache for Windows - see this link: https://httpd.apache.org/docs/2.4/platform/windows.html

1. Download Apache and needed components

Go to apachelounge.com/download page and download the appropriate software for your Windows OS. Here's what I'm using:

Note: The Visual C Redistributable Package is needed to run Apache HTTPD as a Windows Service but the version required will depend on which binary you are installing: If you are installing Apache 2.4 VC15 then you need Microsoft Visual Studio C 2017 Redistributable.

Be sure !! that you have installed the latest C++ Redistributable Visual Studio 2017 -  Install this package first if you don't already have it installed : vc_redist_x64 or vc_redist_x86

2. Install the C++ VS 2017 redistributable that you downloaded first if you don't have it installed already

3. Extract from httpd-2.4.33-win64-VC15.zip the Apache24 folder and put into your webserver directory (e.g. C:\webserver\Apache24)

4. Extract mod_fcgid-2.3.9-win64-VC15.zip\mod_fcgid-2.3.9 folder then copy mod_fcgid.so and put into your \Apache24\modules folder (e.g. C:\webserver\Apache24\modules)

5. Change configuration in \Apache24\conf\httpd.conf file (e.g. C:\webserver\Apache24\conf\httpd.conf). In a text editor (I use notepad++) open the httpd.conf file and edit it

a. Replace all occurrences of c:/Apache24 to c:/webserver/Apache24 or where ever you have your Apache24 folder.

b. Find where it says “ServerName” – this should be ServerName localhost:80 (if using default port 80) or if not using default port then it should be ServerName localhost:port (e.g. ServerName localhost:90).

  • Uncomment the ServerName line - that is remove the # character

  • Change from ServerName www.example.com:80 to ServerName localhost:80

Fig0003.png

c. Optional - Find where it says “Listen 80” to and change the port number if not using the default 80 (e.g. Listen 90). You need to use a port that is not already in used by another service.

d. Find where it says “DirectoryIndex index.html” and add index.php (e.g. DirectoryIndex index.html index.php)

Fig0004.png

e. Save your changes. You can keep the configuration file open

6. Check to see if Apache will start. To quickly check to see Apache configurations work and to see if Apache starts up correctly you can run the httpd.exe as a console application. You can use the command window (CMD) to run the httpd.exe or go into the directory where httpd.exe is located and run as admin.

a. Go to \Apache24\bin folder (e.g. C:\webserver\Apache24\bin) and right click on httpd.exe and run as administrator

b. If you get a pop up, allow the app to run - you should then get a console window (black window) that pops up - keep this window open (if you close it, Apache will stop)

Fig0005.png

c. Then in a web browser type in http://localhost or http:localhost:port and you should see a webpage with "It Works!" This means Apache is installed correctly

d. To stop Apache you can just close the console window (black window above)

7. Run Apache as a Windows Service rather than as a console application. Running as a service should be preferred because this lets Apache end any current operations and clean up gracefully. See https://httpd.apache.org/docs/2.4/platform/windows.html#winsvc for more info.

a. Optional - Append Apache to your Windows System Path so you can directly access Apache by just typing httpd.exe instead of the full pathname to it.

Fig0006.png

b. Start Apache as Windows Service:

  • Go to the Command Prompt (CMD) and run as administrator

  • Install Apache as a service: httpd.exe -k install

Fig0008.png
  • Open your Windows Services Manager: you should see Apache as a listed service.

    • Select Apache service and start it

    • Then in web browser, try http://localhost or http://localhost:port and you should get "It Works!"

    • Stop the Apache service for now as you'll do more configuration - you can keep the services window open

Note: If you would rather start, stop, restart Apache in the Command Prompt window: use httpd.exe -k restart, httpd.exe -k shutdown

Fig0010.png

8. Edit Apache configuration (httpd.conf) to enable needed modules. Open Apache24\conf\httpd.conf  (e.g. C:\webserver\Apache24\conf\httpd.conf) and edit it.

a. Remove the # character in front of each of the following module to enable it.

Note: If you don't see the module already in the file then you need to type it in - for example I had to insert mod_fcgid.so module

  • LoadModule actions_module modules/mod_actions.so

  • LoadModule deflate_module modules/mod_deflate.so

  • LoadModule expires_module modules/mod_expires.so

  • LoadModule ext_filter_module modules/mod_ext_filter.so

  • LoadModule fcgid_module modules/mod_fcgid.so

  • LoadModule headers_module modules/mod_headers.so

  • LoadModule ident_module modules/mod_ident.so

  • LoadModule rewrite_module modules/mod_rewrite.so

  • LoadModule ssl_module modules/mod_ssl.so

Note: If you are using a different port than the default 80 then you need to also enable these modules as well.

  • LoadModule cache_module modules/mod_cache.so

  • LoadModule cache_disk_module modules/mod_cache_disk.so

  • LoadModule proxy_module modules/mod_proxy.so

  • LoadModule proxy_connect_module modules/mod_proxy_connect.so

  • LoadModule proxy_fcgi_module modules/mod_proxy_fcgi.so

  • LoadModule proxy_http_module modules/mod_proxy_http.so

b. Add the following code to the end of the httpd configuration file:

<IfModule mod_deflate.c>
SetOutputFilter DEFLATE
BrowserMatch ^Mozilla/4 gzip-only-text/html
BrowserMatch ^Mozilla/4\\.0[678] no-gzip
BrowserMatch \\bMSIE !no-gzip !gzip-only-text/html
SetEnvIfNoCase Reuqest_URI \\.(?:gif|jpe?g|png|rar|zip)$ no-gzip dont-vary
Header append Vary User-Agent env=!dont-vary
</IfModule>

9. Save your changes to the configuration file and restart Apache service. See if you can still access Apache on localhost or localhost:port. I like to restart and check after each set of configuration changes so it's easy to keep track of errors should something not work.

Part 3: Install and Configure PHP

1. Go to PHP download page and download the appropriate file for your OS and Apache version installed from Part 2. I am using PHP 7.2 (7.2.7) VC15 x64 Non Thread Safe 

2. Create a new php folder, called php72 or whatever you want. Extract the zipped file contents to your PHP folder inside your main webserver directory (e.g. C:\webserver\php72).

3. In the php folder there is a php-ini-production file, make a copy of this and rename the copy to php-ini - this will be the php configuration file you edit

Fig0012.png

4. Open php.ini file (e.g. C:\webserver\php72\php.ini) in a text editor and make the following changes

a. Find where it says ;extension_dir = "ext" and remove the ; character and replace "ext" with the path to your php ext folder (e.g. "C:/webserver/php72/ext")

Fig0013.png

b. Enable the following php modules by removing the ; character

  • extension=php_curl

  • extension=php_fileinfo.

  • extension=php_gd2

  • extension=php_mbstring

  • extension=php_pdo_pgsql

  • extension=php_pdo_sqlite.

  • extension=php_pgsql

  • extension=php_sqlite3

Fig0014.png

c. Find where it says "upload_max filesize" and change it to 15M

d. Find where it says "post_max_size" and change it to 15M

Fig0015.png

e. Save your configuration changes to the php.ini file

5. Add PHP to your Windows System Path (e.g. add C:\webserver\php72 to your Windows system path - same as in Part 2, step 7)

6. Open Command Prompt and check to see if PHP is correctly declared in system path: run CMD as admin, then type in php -m. You should get a list of php modules back.

Fig0016.png

Part 4: Configure Apache for Using PHP

1. Open a new file in a text editor then put in the following code - save the file as php72.conf in \Apache24\conf\extra folder (e.g. C:\webserver\Apache24\conf\extra\php72.conf)

FcgidInitialEnv PHPRC "C:\\webserver\\php72"
 <FilesMatch \\.php$>
  AddHandler fcgid-script .php
  FcgidWrapper "C:/webserver/php72/php-cgi.exe" .php
 </FilesMatch>
Fig0017.png

2. Open and edit Apache httpd.conf file (e.g. C:\webserver\Apache24\conf\httpd.conf)

  • Uncomment or remove the # character: Include conf/extra/httpd-vhosts.conf

  • Save changes to file

Fig0018.png

3. Open and edit httpd-vhosts.conf file (e.g. C:\webserver\Apache\Conf\extra\httpd-vhosts.conf ) for use with Lizmap

a. Delete the two examples that are included in the file and insert the following code. Note: don't forget to change the port if you're using something other then default 80

<VirtualHost *:80>
  Include conf/extra/php72.conf
  ServerName localhost
  DocumentRoot "C:/webserver/lizmap/"

  <Directory "C:/webserver/lizmap">
      Options -Indexes +FollowSymLinks +ExecCGI
      AllowOverride All
      Require all granted
  </Directory>

  CustomLog "logs/lizmap-access.log" common
  ErrorLog "logs/lizmap-error.log"
</VirtualHost>

4. Create a lizmap folder inside the main webserver directory (e.g. C:\webserver\lizmap)

5. Create a text file with following code and save it as index.php inside the lizmap folder (e.g. C:\webserver\lizmap\index.php)

<?php 
    phpinfo(); 
?>

6. Restart Apache service

7. Check to see if PHP works. In a web browser, type in http://localhost/index.php (or http://localhost:port/index.php if not using default 80)

Fig0021.png

Part 5: Install and Configure QGIS Server

I installed QGIS Server using OSGeo4W installer x64 version – download on QGIS site or on OSGeo4W site. Lizmap Web Client doesn’t work properly with the QGIS Server 3.0 , so you must use the LTR 2.18.21. I did try with QGIS Server 3.x but it didn’t work. Note: I have both QGIS dekstop 3.2 and 2.18.21 and QGIS Server 2.18.21 on my machine and they both work fine so far.

If you don't already have QGIS desktop then you have the option to install it via Express install using the OSGeo4W installer (this is easier) or through the advance option.

1. Run the OSGeo4W installer: Select Advance Setup

a. Install from Internet

b. Keep Root Directory default and install for all users

c. Keep default Local Package Directory and Start Menu Name

d. Select these Packages:

  • Commandline_Utilities: GDAL

  • Desktop: QGIS LTR 2.18.21 full (if needed)

  • Libs: fcgi

  • Optional Lib: filegdb (only if you want to be able to use ESRI file gdb)

  • Web: QGIS Server LTR 2.18.21

e. Resolve Un-met Dependencies: Install the required dependencies, accept license agreements, and allow installation to complete

Fig0022.png

2. After installation completes, check in C:\OSGeo4W64\apps\qgis-ltr\bin folder to make sure these files are in there.

  • qgis_mapserv.fcgi.exe

  • qgis_server.dll

  • wms_metadata.xml

3. Configure QGIS server to be accessible as fcgi. Open httpd-vhosts.conf file (e.g. C:\webserver\Apache\Conf\extra\httpd-vhosts.conf ) and edit it to contain the following code. Save the file when done.

<VirtualHost *:80>
  Include conf/extra/php72.conf
  ServerName localhost

# Lizmap Production
DocumentRoot "C:/webserver/lizmap/prod/"
<Directory "C:/webserver/lizmap/prod">
    Options -Indexes +FollowSymLinks +ExecCGI
    AllowOverride All
    Require all granted
</Directory>

# LizMap Pre-production
Alias /preprod/ "C:/webserver/lizmap/preprod/"
<Directory "C:/webserver/lizmap/preprod">
    Options -Indexes +FollowSymLinks +ExecCGI
    AllowOverride All
    Require all granted
</Directory>

Alias /qgis/ "C:/OSGeo4W64/apps/qgis-ltr/bin/"
<Directory "C:/OSGeo4W64/apps/qgis-ltr/bin/">
    SetHandler fcgid-script
    Options +ExecCGI
    AllowOverride All
    Require all granted
</Directory>

Alias /document/ "C:/webserver/data/document/"
<Directory "C:/webserver/data/document">
    Options -Indexes +FollowSymLinks
    AllowOverride All
    Require all granted
</Directory>

CustomLog "logs/lizmap-access.log" common
ErrorLog "logs/lizmap-error.log"
</VirtualHost>

4. Open php72.conf that you created earlier (e.g. C:\webserver\Apache24\conf\extra\php72.conf) and modify it to include the following code. Save your changes to the file.

FcgidInitialEnv PHPRC "C:\\webserver\\php72"

FcgidInitialEnv PATH "C:\OSGeo4W64\bin;C:\OSGeo4W64\apps\qgis-ltr\bin;C:\OSGeo4W64\apps\grass\grass-6.4.3\lib;C:\OSGeo4W64\apps\grass\grass-6.4.3\bin;C:\Windows\system32;C:\Windows;C:\Windows\System32\WBem"
 FcgidInitialEnv QT_PLUGIN_PATH "C:\OSGeo4W64\apps\qgis-ltr\qtplugins;C:\OSGeo4W64\apps\Qt4\plugins"
 FcgidInitialEnv PYTHONHOME "C:\OSGeo4W64\apps\Python27"
 FcgidInitialEnv PYTHONPATH "C:\OSGeo4W64\apps\qgis-ltr\.\python;C:\OSGeo4W64\apps\qgis-ltr\.\python\plugins;C:\OSGeo4W64\apps\Python27\DLLs;C:\OSGeo4W64\apps\Python27\lib;C:\OSGeo4W64\bin;C:\OSGeo4W64\apps\Python27;C:\OSGeo4W64\apps\Python27\lib\site-packages"

FcgidInitialEnv QGIS_SERVER_LOG_LEVEL 0
FcgidInitialEnv QGIS_SERVER_LOG_FILE "C:\\webserver\\Apache24\\logs\\qgis_server.log"

FcgidIOTimeout 120
      FcgidInitialEnv LC_ALL "en_US.UTF-8"
      FcgidInitialEnv PYTHONIOENCODING UTF-8
      FcgidInitialEnv LANG "en_US.UTF-8"
      FcgidInitialEnv QGIS_DEBUG 1
      FcgidInitialEnv QGIS_SERVER_LOG_FILE "C:\\webserver\Apache24\logs\\qgis_server.log"
      FcgidInitialEnv QGIS_SERVER_LOG_LEVEL 0
      FcgidInitialEnv QGIS_PLUGINPATH "C:\OSGeo4W64\apps\qgis-ltr\python\plugins"

SetEnvIf Request_URI ^/qgis QGIS_PREFIX_PATH "C:\OSGeo4W64\apps\qgis-ltr"
SetEnvIf Request_URI ^/qgis TEMP "C:\Windows\Temp"

SetEnvIf Request_URI ^/qgis GDAL_DATA "C:\OSGeo4W64\share\gdal"
SetEnvIf Request_URI ^/qgis GDAL_DRIVER_PATH "C:\OSGeo4W64\bin"
SetEnvIf Request_URI ^/qgis PDAL_DRIVER_PATH "C:\OSGeo4W64\bin"
SetEnvIf Request_URI ^/qgis GDAL_SKIP "JP2ECW"
SetEnvIf Request_URI ^/qgis PROJ_LIB "C:\OSGeo4W64\share\proj"

 <FilesMatch \.php$>
  AddHandler fcgid-script .php
  FcgidWrapper "C:/webserver/php72/php-cgi.exe" .php
 </FilesMatch>

5. Restart Apache Service

6. In a web browser, see if you can access the QGIS Server:

Note: Typing in the following as noted in the Lizmap installation documentation: http://localhost/qgis/qgis_mapserv.fcgi.exe will give you an error "Service unknown or unsupported"

Type in this below: you should see the default content of the wms_metadata.xml file - this means QGIS Server was installed correctly and accessed as fcgi.

http://localhost/qgis/qgis_mapserv.fcgi.exe?SERVICE=WMS&VERSION=1.3.0&REQUEST=GetCapabilities

Fig0023.png

Part 6: Install and Configure Lizmap Web Client

1. Download Lizmap Web Client – I used lizmap-web-client-3.1.12.zip.

2. Create in C:\webserver\lizmap directory, 2 new folders for your production and preproduction work. Make sure you have write access to these folders

  • C:\webserver\lizmap\prod

  • C:\webserver\lizmap\preprod

3. Create in C:\webserver directory a new cache directory to hold 2 new subfolders: prod and preprod. Make sure you have write access to these folders

  • C:\webserver\cache\prod

  • C:\webserver\cache\preprod

4. Unzip or extract lizmap-web-client-3.1.12zip to C:\webserver\lizmap\prod directory. So what you end up having is C:\webserver\lizmap\prod\lizmap-web-client-3.1.12

5. Open C:/webserver/Apache24/conf/extra/httpd-vhosts.conf in text editor and modified the section to the virtual host to point to C:/webserver/lizmap/prod/lizmap-web-client-3.1.12/lizmap/www folder - like the content below

<VirtualHost *:80>
  Include conf/extra/php72.conf
  ServerName localhost

# Lizmap Production
DocumentRoot "C:/webserver/lizmap/prod/lizmap-web-client-3.1.12/lizmap/www/"
<Directory "C:/webserver/lizmap/prod/lizmap-web-client-3.1.12/lizmap/www/">
    Options -Indexes +FollowSymLinks +ExecCGI
    AllowOverride All
    Require all granted
</Directory>

# LizMap Pre-production
Alias /preprod/ "C:/webserver/lizmap/preprod/lizmap-web-client-3.1.12/lizmap/www/"
<Directory "C:/webserver/lizmap/preprod/lizmap-web-client-3.1.12/lizmap/www/">
    Options -Indexes +FollowSymLinks +ExecCGI
    AllowOverride All
    Require all granted
</Directory>

Alias /qgis/ "C:/OSGeo4W64/apps/qgis-ltr/bin/"
<Directory "C:/OSGeo4W64/apps/qgis-ltr/bin/">
    SetHandler fcgid-script
    Options +ExecCGI
    AllowOverride All
    Require all granted
</Directory>

Alias /qgis/ "C:/OSGeo4W64/apps/qgis-ltr/bin/"
<Directory "C:/OSGeo4W64/apps/qgis-ltr/bin/">
    SetHandler fcgid-script
    Options +ExecCGI
    AllowOverride All
    Require all granted
</Directory>

# ABP: needed for authentication in Lizmap
<IfModule mod_fcgid.c>
    RewriteEngine on
    RewriteCond %{HTTP:Authorization} .
    RewriteRule .* - [E=HTTP_AUTHORIZATION:%{HTTP:Authorization}]
</IfModule>

CustomLog "logs/lizmap-access.log" common
ErrorLog "logs/lizmap-error.log"

</VirtualHost>

6. Restart Apache Service

7. Open the Command Prompt window (run as Administrator) and type in the following lines - for copying some lizmap files

cd C:\\webserver\\lizmap\\prod\\lizmap-web-client-3.1.12\\
cd lizmap/var/config
copy lizmapConfig.ini.php.dist lizmapConfig.ini.php
copy localconfig.ini.php.dist localconfig.ini.php
copy profiles.ini.php.dist profiles.ini.php
cd ../../..
Fig0025.png

8. Keep your command prompt window open

9. Open Lizmap's localconfig.ini.php file  (e.g. C:\webserver\lizmap\prod\lizmap-web-client-3.1.12\lizmap\var\config\localconfig.ini.php) in a text editor and include the following code if you want to install the Lizmap demo websites – make sure you have admin rights to modify and save this file (e.g. run notepad++ as Administrator then modify and save changes).

[modules]
lizmap.installparam=demo
Fig0026.png

10. Back in the Command Prompt, launch Lizmap installation by typing in the following lines. After installation completes, close the command prompt window.

cd C:\webserver\lizmap\prod\lizmap-web-client-3.1.12\
php lizmap/install/installer.php
Fig0027.png

11. In  web browser, type in http://localhost/index.php - you should see the Lizmap demo page

Fig0028.png

The Lizmap Web Client Dashboard

1. In the Lizmap home page (see above image), click the Connect button in the top right or go to http://localhost/admin.php to access the login page:

  • Login with default username = admin, password = admin

2. Once you log in you can see the Admin dashboard, don't forget to change password (in My Account). Notice there is an additional intranet demo in the dashboard

Fig0030.png

3. Lizmap Configuration menu: Modify the Lizmap generic configuration - input as follows and then save new configuration.

  • QGIS server version: >= 2.18

  • WMS Server URL: http://127.0.0.1/qgis/qgis_mapserv.fcgi.exe

  • Cache root directory: C:/webserver/cache/prod/

Note: if you get a error when trying to update the cache root directory to the folder that you created earlier - make sure you have write access to the location first then reload Lizmap demo again.

Fig0033.png

4. Click over to PROJECTS (top right corner) and you can view the metadata of the demo or load the demo map

Here is the Montpellier Demo web app.

Fig0032.png

Part  7: SVG and QGIS Bug

I’m not sure if this still hold true or not, but not a bad idea to do it. In Apache you need to Add a vhost to publish SVG and images files via HTTP this will avoid the bug in QGIS Server under Windows which cannot display SVG icon when you have a relative path.

1. Create a folder to contain the svg files  (e.g. C:/webserver/data/document/svg)

2. Then modify C:/webserver/Apache24/conf/extra/httpd-vhosts.conf . Add the codes before the CustomLog portion.

Alias /document/ "C:/webserver/data/document/"
<Directory "C:/webserver/data/document/">
    Options -Indexes +FollowSymLinks
    AllowOverride All
    Require all granted
</Directory>

3. Save and restart Apache service.

4. Check if you can add svg file in the folder C:/webserver/webapp/document/svg then access it via http://localhost/document/svg/my_icon.svg and use it as the SVG path in the style properties of a vector layer.

That's it for this post. I hope this helps you get your GIS server running. See Lizmap Documentation for more info on configuration and user/publisher manual.

See Part 2 - on how to use the Lizmap plugin for QGIS to prepare and publish a QGIS project. If you've read this entire post then thank you for reading and I hope it worked out for you. Until next time.

Flood Mapping with Sentinel-1 Data using SNAP and QGIS

I haven't done remote sensing work in a long while and have been wanting to get back into. Remote sensing is a great complement to GIS, and I've been looking for a case study to do a short tutorial. I thought the recent flooding on Kauai Island on April 14-15, 2018 would be a good case to do some flood mapping using remote sensing techniques.

Background:

The Island of Kauai is not called the Garden Isle for no reason - it is one of the rainiest place on Earth. On April 14-15, 2018 unprecedented rains caused major flooding and a series of landslides on Kauai. The National Weather Service recorded 27.52 inches (685 mm) of rainfall in the Hanalei area during the 24-hour period from April 14 to the 15. After the flooding, the County of Kauai was declared a state of emergency.

More info of the flooding event can be found here: http://floodlist.com/america/usa/record-rainfall-floods-hawaii0april-2018

Workflow/Requirements:

Here is the work flow plan and requirements for this tutorial:

  1. Download Sentinel-1 data - require registration/sign up (free)
  2. Download and install SNAP software (if you don't already have it)
  3. Pre-processing - calibrate and speckle filtering of data
  4. Determine flooded areas - threshold binning (binarization, unsupervised classification)
  5. Post-processing - geometric correction of data (apply map projection)
  6. View resulting flood areas in GIS (e.g. QGIS, Google Earth, or ArcGIS  assuming you have a GIS software already)

Step 1: Download Sentinel-1 Imagery

Assessment of flooded areas can be done using radar data, such as the Sentinel-1 SAR imagery provided by the European Space Agency (ESA). For this example, I'm using Sentinel-1 Level-1 Ground Range Detected (GRD) data which already has some basic pre-processing done on it. More info about the Sentinel missions, products, and uses can be found on the Sentinel Online Website. Access to the Sentinel data is provided through the Copernicus Open Access Hub. Although the data is free to use, you will need to register or sign up first before you can download the data.

Go to Copernicus Open Access Hub:

  • Register or sign up for a free account then log in
  • On the map, navigate to the Hawaiian Islands and zoom in to the island of Kauai
  • Use the Polygon tool (in the bottom left, box tool doesn't seem to work) and draw an area of interest on Kauai (northern portion of the island)
  • Click the Advance Search menu (in top left) and use the following search parameters
    • Sensing Period: From = 4/15/2018, To = 4/15/2018
    • Mission Sentinel-1: Product Type = GRD
    • Note: there is only 1 image for Kauai taken on the date specified so there's no need to include other parameter criteria
  • Click the Search button when done
  • There should only be 1 result based on the search criteria for the area of interest. Note: when you click the link to download the file, you may be asked again to login (think this might be a time out issue on the Copernicus site).
Fig0001.png
Fig0002.png

Notice the available imagery is Level -1 Ground Range Detected (GRD) Sentinel-1 C-band (SAR-C) data collected in Interferometric Wide (IW) mode, allowing for an image acquisition over a 250km swath with resolution of 10m (5x20m).

Step 2: Download and Install SNAP

SNAP is a application developed by the ESA to work with Sentinel data. You will need to download and install the appropriate software for your computer. I am using the Windows 64bit version of the Sentinel Toolbox.

Fig0003.png

Step 3: Explore the Image and Create Subset

After you've install the SNAP application, you can use it to open and explore the Sentinel-1 image you downloaded previously. The SNAP application can open the zipped file without need to unzip it first.

  • In the SNAP application >> Open Product >> S1A_IW_GRDH_1SDV_20180415.zip (file downloaded earlier) >> Open
  • The Product Explorer Panel on the left shows relevant information/metadata related to the Sentinel data. You can right click on any of the file/item to get a context menu to view properties related to that item.
  • Under Bands, you'll see that for each polarization (VV + VH or HH + HV), there are 2 bands (Amplitude and Intensity). Intensity band is a virtual band and is just a square of the amplitude. To view an image of a Band, double click it and an image will be created for viewing in the left panel. Double click on the Intensity_VV band to view it - this is the band being used.

Note: Although any of the polarization/band can be used to analyze flooding extent, some studies have shown that VV gives a slight advantage when delineate flooding when using Sentinel‐1 data. This article, "Multi‐temporal synthetic aperture radar flood mapping using change detection" provides a good comparison using different polarizations for delineating flooding using Sentinel data.

Fig0004.png
  • To create a subset a portion of the island, first zoom in to the extent of the area you want to subset - which in this case is the northern portion of the island where Hanelei town is located.
Fig0005.png
  • Create the subset, go to Raster Menu >> Subset
  • In the Specify Product Subset window, the lat/long coordinates for the area of interest should already be filled in based on the zoomed in map extent. Click OK to create subset
Fig0006.png

The newly created subset image should show up in the Product Explorer panel and look something like this.

Fig0007.png

Step 4: Pre-Processing - Calibration and Speckle Filtering

Pre-processing calibration and speckle filtering here is done on the subset image you created in step 3 above. The pixel values in a SAR imagery can be related to the radar backscatter of the scene taken - what calibration does is transform the pixel values from the digital values recorded by the sensor into backscatter coefficient values -- essentially calibrated values of the backscatter coefficient. Speckle filtering is just reducing the noise in the image so to obtain higher quality imagery.

  • Calibration Tool: Go to Radar Menu >> Radiometric >> Calibrate
  • In the Calibration window:
    • I/O Parameters tab: source = your subset image from step 3; target product = your output file
    • Processing Parameters tab: Polarizations = VV; check Output sigma0 band >> Run
    • Close the Calibration window when it finished running
    • The resulting output file should be shown in the Product Explorer panel
  • The Calibration tool will create a new image with the backscatter coefficient
Fig0008.png
  • Speckle Filtering Tool: go to Radar Menu >> Speckle Filtering >> Single Product Speckle Filter
  • In the Single Product Speckle Filter window:
    • I/O Parameters tab: source = your calibrated image from the above calibration step; target product = your output file
    • Processing Parameters tab: Source Bands = Sigma0_VV; Filter = Lee; Filter size = 3x3 >> Run
    • Close the window when it finishes running
    • The resulting output file should then be shown in the Product Explorer panel
Fig0009.png

Step 5: Determining Flooded Areas (areas covered by water)

Using a histogram of the filtered backscatter coefficient and applying a threshold, the water pixels can be separated from the non-water pixels. I think of this as a form of unsupervised classification - you apply a threshold value and let the software decide what is considered water and what isn't. After this first pass you could further refine results using a supervised classification method (not covered in this tutorial).

  • To view the histogram: first make sure you're viewing the filtered sigma0_VV image. In the left side panel (below Product Explorer), select the Color Manipulation tab
  • In the Color Manipulation tab: a histogram is displayed showing one or more peaks. Low values of backscatter will correspond to water and high values to non-water class. You will need to use a threshold value to get the best representation for water.
    • You may need to select the logarithmic display for the histogram
    • Use the threshold slider to see different threshold values -  I am using the value 1.28E-2 for this example
Fig0010.png
  • After determining a good threshold value, the next step is to create a new image - basically a binary image of water (1 = true or 255 = white) and non-water (0 = false or 0 = black). To do this you would use a raster math calculation.
    • Go to Raster Menu >> Band Math..
    • In the Band Maths window: type in a name and uncheck the Virtual file box (if you want to save to disk)
    • Click Edit Expression: then in the window that comes up, type in 255*(sigma0_VV< 1.28E-2). This expression will return a 1 or true for pixel values less than the threshold and 0 or false for values higher than the threshold, this is then multiplied by 255 to get the binary black and white image
    • Click OK to run

Fig0011.png
  • A newly create Water image will be added to your product. An example result is shown below. Notice that since Kauai is surrounded by ocean so it makes it harder to determine flooded areas on land. I guess a quick work around solution would be just to clip the image to the coastline so ocean is seen as "flooded" areas.
Fig0012.png

Step 6: Post-processing - Geometric Correction

The Sentinel-1 image that was downloaded is in the geometry of the sensor, meaning it does not have geographic coordinates so you will need to applying a coordinate system if you want to view it in a GIS with other data.

  • Go to Radar Menu >> Geometric >> Terrain Correction >> Range-Doppler Terrain Correction
  • In the Range-Doppler Terrain Correction window:
    • I/O Parameters tab: source = your filtered image, then input other parameters if needed or use defaults
    • Processing Parameters tab: source bands = Water; DEM = use your own or the default SRTM 3Sec (Auto Download) which requires an internet connection; change other parameters if needed or use defaults
    • Click Run and Close window when completed

Note: If you save as BEAM-DIMAP format the output image will be an *.img format (see optional step 7 below)

Fig0013.png
  • A newly create image will be added to the Product Explorer panel. Double click on the band to open it for viewing. Here is a sample image below
Fig0014.png

Optional Step 7: Export Image for Viewing in GIS or Google Earth

At the point you should be able to use the output result in an GIS - the default output format (from step 6 above) is an *.img format. If you want to export it to other formats or view in Google Earth you can do that as well.

  • Go to File Menu >> Export >> Other >> View as Google Earth KMZ   OR
  • Go to File Menu >> Export >> Choose an export format
Fig0015.png

Here is an example resulting flood image as view in QGIS 3.0. In QGIS just add in your *.img or exported image and use the layer's properties to change color and transparency of the image. Flooded areas are shown in RED in the image.

Fig0016.png

Assessment of the resulting flooded areas

The Dartmouth Flood Observatory at the University of Colorado (previously at Dartmouth College) have mapped the maximum observed extent of the flooding on Kauai - see DFO Flood Event 4601 USA (Kauai, Hawaii). This can be used to assess how well your results are. The snapshots below show the comparison between the more accurate DFO Observed Flooding and the tutorial result. I would say that tutorial result is not bad given that no refinement was applied to the methodology other than using the SNAP geoprocessing defaults. A more accurate result could have been attained by using different thresholds, and doing some post-editing or processing to further refine the flooded areas such as supervised classification to weed out false positives (wrong classification of water).  Also keep in mind that no other supplement data were used except the Sentinel-1 data. Anyway, the point of this tutorial was just to get you thinking about remote sensing application.

Fig0017.png
Fig0018.png

That is it for this tutorial. I hope it got you thinking more about applying or using remote sensing in addition to GIS. As always thanks for reading.