Welcome to Benthic Photo Survey’s documentation!¶

What You Need to use BPS¶

Benthic Photo Survey is designed to work with inexpensive and relatively easy to acquire equipment, partly because that’s all that’s really required and partly because that’s all I can afford. Here’s what you’ll need:

1. A submersible digital camera that produces jpeg images. I use a Panasonic Lumix DMC-TS4 in an Ikelite housing. This camera has a built in compass that records the direction that the camera is facing when the photo is taken and BPS passes the direction into the shapefile that is created. However, this is not a requirement and any camera that produces jpeg images should be compatible with BPS.
2. A GPS that can be towed by a snorkeler or diver. If you’re working with fairly high resolution imagery, you’ll want a GPS receiver with WAAS capability. I am using a Garmin GPS 60 CSX. I tow mine in a small waterproof plastic box on a float. See GPS Photo Transects for Benthic Cover Manual by Roelfsema and Phinn [RP2010] for details on how to build a float. BPS can import NMEA text files and GPX files.
3. A depth logger is optional but if you’re going to spend the time and money to go in the field, it seems worthwhile. BPS is set up to import log files from the Sensus Ultra depth and temperature logger. It should be fairly easy to adapt it to deal with a different logger but that would require a bit of coding.
4. A computer to run BPS. BPS was developed on Ubuntu but is also available for Windows. In theory it will run on Mac as well but has almost no testing there.

What BPS Actually Does¶

There are 4 steps to what BPS does.

1. It imports your GPS and/or depth and temperature logs into a database.
2. It writes data from those logs to the Exif portion of each of your jpeg photos based on the time stamp on each photo and the time stamps in the respective logs.
3. You use BPS to tag each photo with habitat and/or substrate information. This is also written to the Exif portion of each photo.
4. BPS can export a point shapefile with a point at each location where a photo was taken. Each point is attributed with the habitat, substrate, depth, temperature, direction, and file path to the photo.

References

WARNING!¶

Please make sure you back up all your data (photos, GPS, and Depth logs) before using it in BPS. I haven’t seen it happen yet but it is entirely possible that BPS could ruin your files. This is not a commercial product and it does not come with any guarantees.

Tutorial¶

The following instructions will assume that you have followed the Windows Installation instruction on the BPS Installation Page unless otherwise noted. Only the paths will change for the Linux installation. The other instructions will be the same.

These steps will lead you through the process of producing a shapefile from data. We will use a few photos, depths, and positions collected off the coast of Great Barrier Island in New Zealand’s Hauraki Gulf. These data are included with the BPS installation so, if you’ve installed BPS, you already have them. The data consist of a GPS log in gpx format, a csv depth log, and 9 photos.

1. Start BPS by navigating to the bps_gui folder and double clicking bps_gui.exe. If you are using a Linux installation, you’ll navigate to bps_package and run python bps_gui.py in the terminal. When BPS opens, you’ll see something like this:

   

2. Set the general preferences for BPS. Go to the file menu in BPS and select “Preferences”. You’ll see a window with 4 tabs. Each tab will have a help button. Click the help button for information about the options presented in each tab.

   

   1. Set the working directory. Click the ... button. If you followed the Windows Installation instructions on the BPS Installation Page, you should set the working directory to C:bps_guitest_data. If you’re using the Linux install, the test_data directory will be in the bps_package directory and you should set your working directory there.
   2. Set the database path. Use the ... button next to the Database field and set it to use a file called raw_log.db within your working directory. It’s fine if the file you specify doesn’t currently exist. BPS will create it for you.
   3. We’ll come back to the Preferences in a minute but, for now, click the “OK” button to save the changes.

3. Load the GPS log. Go to the file menu and select “Load GPS Log”. If the working directory was set correctly, this should open up a file dialog with the test_datagps directory. Select the file called gb_island_19092012.gpx and click “Open”. A message will be displayed (briefly) in the status bar at the bottom left of the BPS window telling you how many records were written into the database. During this step positions and time codes are read out of the GPS log and written to the database file specified in the preferences.

4. Load the depth / temperature log. Select “Load Depth Log” from the file menu. Assuming the working directory was set correctly, this should open the test_datasensus directory. Select the file called gb_island_19092012.csv. Another message will be displayed in the status bar and the depths, temperatures, and time stamps will be written to the database.

5. Load the photos. Select “Load Photos” from the file menu. Navigate into the test_dataimages directory (this should be the directory that opens by default) and click “Select Folder”. On Windows, the actual image files will (annoyingly) be invisible in this dialog but you’re selecting the folder rather than the individual images so that’s okay. Once the images have been loaded, you’ll see something like this:

   

   • You can use the arrow keys or the “Next” and “Previous” buttons to step through the photos.
   • Notice that most of the fields in the “Exif Data” area are initially empty.

6. Tag the images with location and depth. You can tag all the images at once by using the “Actions” menu. Choose “Geo Tag All Photos” to assign positions. Choose “Depth/Temp Tag All” to assign depths and temperatures from the Sensus Ultra records. Alternatively, you can use the “Geo Tag” and “Depth/Temp Tag” buttons on the bottom of the BPS window to operate on just the current photo. Once photos have been tagged with position, depth, and temperature, these values will be displayed in the “Exif Data” section for each photo.

7. Check the depth plot. Select “Depth Plot” from the “Output” menu. This will display a plot with time along the x axis and depth along the y. The stars represent when and and what depth the photos were taken. This can be very useful for making sure the photo and depth log time codes are lining up correctly. In the case of this test data, they were captured while breath hold diving. You can see that all of the photos were taken at the lowest part of the dive. That suggests that the photo capture times lined up well with the depth log. You can zoom and pan the plot using the controls in the plot window.

   

8. Set up habitat and substrate categories. Open the preferences dialog again via the file menu. Click the “Habitats” tab. Add a couple of habitats. Click the Help button in the Habitat preferences if you need more instructions on how to add a habitat. For this example you should end up with categories of Kelp, Turf, and Sand. Click the “Substrates” tab. The default substrate categories should be fine for this tutorial but, if you’d like to change them, this is where to do it. Again, there’s a Help button on this tab that can provide more information. Click “OK” to save your preference changes and notice that the “Habitat” and “Substrate” categories on the bottom right side of the BPS window now match your specifications.

9. Assign Habitats and Substrates to the photos. Step through the photos (using the arrow keys or the “Next” and “Previous” buttons) and assign habitat and substrate values:

   • For habitats, you assign the proportion of each habitat visible in the photo. If, for instance, you’re looking at a photo that is about 30% sand and 70% kelp, you would assign 0.3 to the sand category and 0.7 to the kelp category. To do this, position your cursor over the kelp roll box and turn your mouse wheel until the value is 0.7. Alternatively, you can type a value into the box or click the up and down arrows. The “Save” button will be disabled until the sum of your categories is 1.0. Once your values add to 1.0 and you click the “Save” button, the habitat values will be written to the Exif portion of the image. You will then see the dominant habitat type displayed in the “Exif Data” area. The dominant habitat value is the category with the largest proportion. In the event of a tie, one of the categories with the highest value is randomly chosen as dominant. The dominant habitat is just for convenience of display. All proportions are saved and will be part of the final shapefile output.
   • To assign a substrate to your photo, simply click the “Substrate” tab in the bottom right corner and then double click on the substrate category of your choice. Substrate categorization does not support proportional tagging. It’s a one substrate per photo kind of thing.

10. Export a shapefile. This is the final product that BPS was built to deliver. Choose “Export Shapefile” from the Output menu. Navigate to where you’d like to save your shapefile and enter a file name that ends with ”.shp”. I need to change the code a little bit so that it’s more tolerant but, at the moment, a file name without ”.shp” on the end will not work.

Now that you’ve gone through all that, you should use a GIS program to take a look at your shapefile. If you’re not familiar with GIS, a good place to start is the QGIS website (where you can download QGIS) and the QGIS Documentation page.

Field Work¶

This section will discuss how to prepare for and conduct field work. This text assumes that you are breath-hold diving or using SCUBA. BPS can be used with a drop camera as well. If you’re going to use it that way, just use your imagination to adapt these instructions.

Configuring BPS¶

Configuration is handled through the “Preferences” dialog (found in the BPS file menu). For specific details about the options, click the “Help” buttons found on each tab of the Preferences dialog.

If you are deploying more than one camera / gps / depth logger set up at a time, you will need to take precautions to avoid confusion. You will need to change the db_path in the preferences and keep the logs from the two setups separate.

References