Could you try to generate another orthomosaic with the following coordinate system: BD72 / Belgian Lambert 72 - Belgium - EPSG:31370 ? This includes the TOWGS84 parameters for the most precise transformation, which is the same that Pix4Dcloud picks.
Here the instructions on how to use a prj file to define your output coordinate system.
You can then replace the orthomosaic file from the Files > Results section of your project.
I have some updates for you regarding my previous answer.
I actually tried to import your orthomosaic in QGIS with different transformations and changing them doesn’t seem to influence the position of the polygons. Therefore I am considering the fact that your point cloud might have a different coordinate system.
Which are the coordinate systems of the single outputs? Do they all match? Do you have the parameters defining the coordinate systems for all the outputs so that we can ensure the files have the same CS? We don’t support different coordinate systems in the same project.
It also looks like Pix4Dcloud is not able to read the coordinate system from your las file.
How could you check that point cloud and orthomosaic are aligned in QGIS?
I imported the ortho and the annotations and they match with what I see in Pix4Dcloud.
at that time we didn’t saw the difference because the difference was exceptional high, with the latest data (from the citymapper) the error between ortho and pointcloud is smaller and we see the 2 annotations in the same viewer (in 2D we see the annotations we made in 3D, and vice versa)
So, I think that pix4d cloud doesn’t import the las file correctly because the problem occures with data from pix4d mapper and 3th party software…
The case for project 627756 is different. There you are adding the measurements on the 3D Mesh, that is not georeferenced and therefore the coordinates between mesh points and the points belonging to other outputs are different. To align the mesh with the point cloud and the other outputs, I recommend that you read the suggestions for the mesh upload at this link. The annotations already align with the 2D layers with the current outputs if you place them on the point cloud. Uploading the offset file as explained in the linked documentation article, will solve all your problems there.
The project 738451 makes me think that we do not handle las files coming from Leica Citymapper very well. I can investigate a bit more into this but I cannot guarantee that we can add support for this at the moment.
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