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Workflow to process PH4 imagery in Pix4Dmapper Pro for vegetation mapping

(Generation of orthomosaics and DSMs)

Technical Report · December 2019

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Ximena Tagle Silvana Di Liberto

Instituto de Investigaciones de la Amazonía Peruana Universidad Nacional Agraria La Molina
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 Workflow to process PH4 imagery in Pix4Dmapper Pro for vegetation mapping (Generation of
orthomosaics and DSMs)

Ximena Tagle, Silvana Di Liberto and Julinho Benavides

This workflow was designed to process Phantom 4 Pro imagery for vegetation mapping during the work
at the MonANPeru project at IIAP, it is based on Pix4Dmapper recommendations and our own tests.

Reference Paper: Tagle Casapia, X.; Falen, L.; Bartholomeus, H.; Cárdenas, R.; Flores, G.; Herold, M.; Coronado,
E.N.H.; Baker, T.R. Identifying and Quantifying the Abundance of Economically Important Palms in Tropical Moist
Forest Using UAV Imagery. Remote Sens. 2020, Vol. 12, Page 9 2019, 12, 9.

1. Open Pix4D Mapper and Select a New project.

2. Create a new project

Before you start, it is recommended to save the project to avoid the loss of information. One way to
save the project could be “Place-Number of plot_Number of mission_Method”.
- Details:
- Place: 3 capital letters.
- Number of plot: 2 digits or more.
- Number of mission (or combination of missions).
- Method: a) _tr for DSM and orthomosaic generation using triangulation.
b) _idw for DSM and orthomosaic generation using interpolation of inverse distance
weighted.
c) _e when a edition of the mosaic is conducted afterwards.
3. Select the working directory to save the project.

4. Add images
- Remove images that do not add value to the mosaic, such as those that the format is
incompatible with the program, blurry images and the take-off and landing images.

5. Select the coordinate system of the images:

- It can appear automatically, but it is better to check if it is the correct one. Otherwise, select Edit
and choose the preferred Coordinate System.
6. Check camera model and groups

- In the case of PH4, it appears automatically. If not, it can be selected. When other images like
the ones from takeoff and landing are included, another camera model will be added with lower
resolution.
7. Select Processing options template
- We have created two customized templates, one used for missions with pure or dense vegetation
named “Forest”, and one for missions containing vegetation with buildings and sand named
“Canteras”. In the case there is not a customized template, select the “Standard: 3D Maps”.
- Do not forget to unclick “Start processing now”, to be able to make some changes in the
processing options and create your own template according to your needs

8. Select processing options

 1. Initial processing:
In the general label:
- Choose “Full” for Keypoint Image Scale, choose this option for more accurate results whe working
with original scale images for alignment.
- Check the box “Generate Orthomosaic Preview in Quality Report” for Quality report in order to see a
preview of the orthomosaic and DSM in the quality report.

In the matching label:

- Select Aerial Grid or Corridor (it depends on the mission plan, in our case is Aerial Grid) for Matching
image Pairs.
- Only check the Use Geometrically Verified Matching box when working with patterns (ex. rows of
plants in a farming field, window corners on a building's facade, etc.)
In the calibration label:
- Check “Automatic” for Targeted Number of keypoints, it could be modified with the custom option if
necessary.
- Select “Standard” for Calibration method and “All” for internal and external parameters optimization.
- Choose “Automatic” for Rematch, in order to compute more matches between the images.
- Finally, Export camera internals and externals, AAT, BBA in order to have the camera parameters in a
folder like this (...\project_name\1_initial\params).
 2. Point Cloud and Mesh
In the point cloud label:
- For the Point cloud densification, Image scale, select ¼ or 1/8 if working with vegetation to get more
points (due to its complexity); otherwise select ½ when working with a farming field, or regular
buildings.
- Check Multiscale to compute additional 3D points on multiple image scales, starting with the chosen
scale from the Image scale drop-down list and going to the 1/8 scale (eighth image size, tolerant).
- Select “High” for Point density and use 3 for Minimum Number of Matches. If you need to edit the
point cloud in external software, check LAS for Export.

In the 3D Textured Mesh label:

- Unclick Generate 3D Textured Mesh, this process is time-consuming and not required to generate an
orthomosaic and DSM. Only keep it active if really needed for other purposes.
- Choose “Medium resolution (default)” for Settings.
In the Advanced label:
- Matching Windows Size is the size of the grid used to match the densified points in the original images,
for vegetation mapping with the PH4 7x7 pixels is faster. Pix4d suggests it when using aerial nadir images
(90 degrees). When working with oblique images, it is recommended to use 9x9 pixels.
- Check “Use processing Area and Use Annotations” for Point Cloud Filters.
3. DSM, Orthomosaic and Index
In the DSM and Orthomosaic label:
- Check the Automatic box or checking the custom option, the resolution can be defined. Always select a
lower spatial resolution than the one expected (i.e: 5.3 cm/pixel-> 6 cm/pixel) for Resolution.
- Choose “Use noise filtering” to reduce the noise and “Use surface smoothing” and select the Sharp
option to remove drastically outliers for DSM filters.
- In option Raster DSM, check the GeoTIFF box, select triangulation (for dense vegetation)/ IWD (for more
defined structures: palm trees, field crops, buildings, etc.) for Method and “Merge title” (in order to have
the whole DSM in one file).
- In option Orthomosaic, choose the GeoTIFF and Merge tiles boxes.
 4. Resources and notifications
In order to maximize the processing capabilities of Pix4D mapper, the maximum RAM capacity should be
enabled. In the case of having GPU options, the CPU threads is reduced and the GPU is enabled.
- The option “Send me email notification when processing is done” is quite useful to get updates of
the processing.

- Select the option “Save Templates” to save the created template and give it a name. If it is necessary,
select the option “Manage templates” to edit the template.
 - After selecting the options, do not forget to click OK.

- And then to click start.

*** In the case of having GCPs, follow the next steps which are detailed below, otherwise continue with
step 9 “Mosaic edition”.
1. Before start processing, Unclick Steps number 2 “Point Cloud and Mesh” and 3 “DSM,
Orthomosaic and Index, then click on Project -> GCP/MTP manager. Do not forget that is
important to execute step number 1 “Start processing” to continue with the process.

2. Import GCPs.
- Select the option “Import GCPs”.
- Choose the order of the coordinates in the file by displaying the list of the option“Coordinates
Order”.
- Load the Ground Control Points file (.csv or .txt) at the option “Browse” and click OK.
- It is important that all the GCPs have the same coordinate system as the images.
3. Once step 1 “Start processing” has been completed, click “ray CloudEditor”. At the left side you
can see the option “Layers”, display option “Tie Points” and then “GCPs/MTPs”. If you want to
see the properties of any selection, click on the GCP.

4. GCP location
- At the right side you can see the tab “Properties”, there are the options “Selection” and “Images”,
in the last option we can find all the images of the project.
- The GCP location can be found as a blue icon in some of the images.
- Locate the GCP target and select the central position with a yellow cross.
- This process needs to be conducted until we have seen a green cross that show us the correct
position of the GCP.
 Figure 1 Blue icon showing the Figure 2 GCP Target.
GCP position.

Figure 3 Central position of Figure 4 Location of the

the GCP target marked with central position in more
a yellow cross. images, green cross shows
the adjusted position.

5. Then we continue clicking the “Selection” tab and choose the option “Automarking”.
Pix4Dmapper will search for automatic color correlation of the clicked pixels on the rest of the
images. Thereby, the position of the GCP will be optimized in more than the clicked images if the
color correlation is good. The images that have a green cross are taken into account during
processing.
6. Check the rest of the images
− If the green cross indicates the correct GCP position: There is no need to mark the point on
more images.
− If the green cross indicates the wrong GCP position: Mark the GCP on more images. Every
time the GCP is marked on a new image, the green cross gets closer to the correct place.

7. When the green cross is at the correct position in most images, click Apply.

8. Repeat steps 4 to 7 for the rest of the GCPs.

 9. When all the GCPs are marked on the images, click Process -> Reoptimize. This reoptimizes the
reconstruction using the GCPs.

10. The reoptimization with the GCPs has finished.

11. Run steps 2 “Point Cloud and Mesh and 3 “DSM, Orthomosaic and Index”.

******************************************************************************

9. Mosaic edition
- Once the mosaic is generated, if the orthomosaic has artifacts, Open the mosaic editor.
- Zoom in and click on the Draw box to start delineating the area that needs to be edited. The pointer will appear
now with a cross, click several times until delineating the area to edit. To finish delineating, use the right
click once.

- In order to avoid distortions (with planar projection), select ortho projection and choose the images that add
information to the orthomosaic.

- Once the areas are edited. Click Save and then click Export.
- The orthomosaic and DSM will be updated.

****In the case there were more than 2 missions at nearly the same time and light conditions, with
different altitude (i.e AGL of 90m and 65m), the images can be combined by merging the 2 separated
projects.

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