Volume managment improvements #1798
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All geometries in the back-end are now stored as PostGIS TIN Geometry. This allows for more consistency and a cleaner API. Implemented together with @aschampion, @clbarnes, @Willp24. See #1765 Fixes #1581
Includes: - URL endpoint - API method - Test fixture - Simple test
When exporting, use both the extension of the URL and the HTTP ACCEPT header to determine which format to return. This supports both extensions with multiple formats (e.g., ASCII and binary STL) and extensions without a distinctive media type (e.g., OBJ is `text/plain`).
- Bypass DRF response accent content negotiation - Fix chunking of triangles in STL serialization - Fix accept header in tests
Add an ontology class for volumes, create class instances for all existing volumes, and relate volume class instances to volume rows via a `volume_class_instance` table. Also move the `model_of` relation from the needed classes for the tracing tool to the default project needed classes. Written with @tomka, @clbarnes, and @Willp24. See #1765.
Add front-end and back-end functionality to add annotations to a set of volumes. A new checkbox column has been added to the volume table and an "Annotate" button, that allows to annotate all selected volumes. Worked on together with @aschampion, @clbarnes and @Willp24. See #1765
Note that this also changes the response of the volumes listing endpoint from an array of objects to an array of arrays, with a separate `columns` field.
This is run now by default for the catmaid_check_db_integrity management command. The --tracing [true|false] and --volumes [true|false] command line parameters now allow to explicitly test only some parts of the database. By default all is tested. Please enter the commit message for your changes. Lines starting See #1765
Like before, the triangle check tests if each triangle has four vertices (the line is explicitly closed) and now also checks if the start and end point are actually the same.
If the 'trimesh' library is installed, the 'check_db_integretiy' management command will now also check if all triangles that make up CATMAID volumes have the same orientation (per volume). See #1765
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Does checking the consistency of the handedness of the triangles rule out the handedness as the source of that 3D viewer behaviour where some of it was transparent when seen from the wrong side? Or is it that the meshes could be consistent, but still inside out? |
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If this issue is due to the triangle winding, having a consistent winding should at least make this behavior exist for all triangles in a volume or none. There is in fact still a rendering issue in the 3D Viewer with nearly opaque meshes---inside/outside are not consistent and depend on the light and viewing angle (the third box below is almost opaque): |
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And this is how newly created boxes without this branch look like: |
This adds the main changes that are discussed and referenced in issue #1765 on volume improvements. While all API changes are already noted in the changelog, we need to add some regular changelog entries on volume annotations, volume export and STL file import.