Photogrammetry toolkit



In this section we describe step by step how to apply the photogrammetric tools developed to monitor red coral populations within the framework of the Perfect project funded by the TOTAL Foundation. These tools are based in the use of the Arpenteur software www.arpenteur.org

Download the manual PDF version of the photogrammetry toolkit [link-here-soon]

For more information on the photogrammetric methods please visit: [link-here-soon]

Setup Arpenteur’s red coral module

This video tutorial will show you how install the software Arpenteur in your computer.

Download Arpenteur zip file

Computer requirements:

Arpenteur can run on Windows, Mac OS and Linux.
To run Arpenteur on your computer JAVA need to be installed. Arpenteur is running with JAVA Version 8 freely downloadable here

Warning: to run full features of Arpenteur we recommend the following computer configuration:
PC, MAC LINUX: configuration 16 GB RAM with a decent Graphic card
However, in the tests carried out most of Arpenteur’s features can run in PC, Mac and LINUX computers with more standard configurations. In the tests carried out in PC configuration PC and Mac configurations Mac run efficiently Arpenteur

Underwater photography equipment

These are some examples of underwater photography equipment settings that you can use for photogrammetric survey

Recommendation on underwater photography equipment

For photogrammetric analysis you can use a wide array of cameras, housings, electronic strobes and video lights settings. However, since during a standard photogrammetric survey you will obtain hundreds of photos and bottom time is limited, we recommend you to use professional cameras settings guaranteeing high performance and reliability. We usually work with reflex cameras (e.g. Nikon D300, D7000) with 20 mm lenses in housings (Sea & Sea, Aquatica, Issota) and two electronic strobes (e.g. Ikelite DS160) to avoid shadows. However, lighter and less expensive equipment based on compact cameras in housings equipped with video lights can be used as well.

To avoid problems with the autofocus we recommend you to set the focus to manual once you find the focus distance to carry out the red coral surveys. Since the photos have to be taken from similar distances.

Get quadrat for photogrammetric surveys

For photogrammetric surveys you must use a quadrat specifically developed. The quadrat has specific tags. You can print the quadrat using a two color 3D printer using this file [soon]

To carry out the red coral surveys a quadrat we will use a specially designed quadrat 20 x 20 cm with specific tags. The purpose of the tags is to have to be used speed up the image processing required for photogrammetry analysis. In particular, the tags are automatically recognized by Arpenteur in order to create the 3D models from the sets of photos from the same scene taken from different angles and set the scale. You can print the quadrat using a two color 3D printer using this file [soon]

Once you have the quadrat to facilitate the surveys you must glue plastic screws in each corner as well as gluing corks or other material to ensure positive buoyancy. This complements are required to ensure a stable position of the quadrat within the red coral populations during the surveys.

Taking pictures for photogrammetric analysis

In this video tutorial will show you how to carry out photographic surveys for photogrammetric analysis.

You have to place the quadrat within the populations. At each position take two or three photos of the scene ensuring that the quadrat does not move between shoots. If the quadrat moves can affect the final outcomes of the measurements.

Callibration

In this video tutorial will show you how to calibrate your camera a required step to carry out photogrammetric analysis.

For each underwater equipment used (i.e. camera, lenses and housing –dome-) we need to obtain the corresponding calibration file. To do so print the calibration sheet [soon], plasticize and stick it to a slate and take photos underwater following the instructions provided in the video tutorial. Use some diving weight to ensure that slate does not move while you are taking photos for calibration.

Arpenteur installation

This video tutorial will show you how install the software Arpenteur in your computer.

Download Arpenteur zip file

Computer requirements:

Arpenteur can run on Windows, Mac OS and Linux.
To run Arpenteur on your computer JAVA need to be installed. Arpenteur is running with JAVA Version 8 freely downloadable here

Warning: to run full features of Arpenteur we recommend the following computer configuration:
PC, MAC LINUX: configuration 16 GB RAM with a decent Graphic card
However, in the tests carried out most of Arpenteur’s features can run in PC, Mac and LINUX computers with more standard configurations. In the tests carried out in PC configuration PC and Mac configurations Mac run efficiently Arpenteur

Pics preparation

In this video tutorial will show you how to rename the photos to carry photogrammetric analysis.

In order to process the (two or three) photos obtained from each quadrat, the corresponding file must be renamed following a specific pattern that is used by Arpenteur to recognize the photo sets that belong to the same quadrat position.

Models generation

In this video tutorial will show how to use the function Model generation to obtain 3D models from the each set of photos.

Model generation is the step in which we compute the external orientation (EO) of the camera, i.e. the position of the camera, respect to the quadra, when the photo were made. This step is crucial for the measurement (see next step) and an indicator of precision is provided for each model.

Measurements

In this video tutorial will show how to carry out the measurements of red coral colonies.

Once the model are computed (EO) measurement on specific zone of the photograph can be done by identifying homolougous points in two or three photograph. As relevant points are not always easy to identify an automatic approach is not relevant. We offer an interface to identify relevant points on two photograph with a real time precision control using epipolar line display.

Upload data on CorMedNet database

For each red coral population surveyed you will obtain information on colonies sizes as well as density and necrosis rate. The current version of Arpenteur provides the results for individual quadrats. You can use this [Excel Macro -soon] to assemble the Excel files obtained for individual quadrats belonging to the same population.

We encourage you to upload the obtained data to the CorMedNet database in order to update the database providing the most comprehensive view on the red coral population status in the Mediterranean.

Check this section to know more on how to upload the data to the CorMedNet database.