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BlueBrain / Ultraliser

Reconstruction of watertight meshes, annotated volumes and center line skeletons of neuroscience spatial structures from non-watertight inputs, segmented masks, skeletons of NGV morphologies and volumes.
https://portal.bluebrain.epfl.ch
GNU General Public License v3.0
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Segmentation fault during volume projection #15

Open marwan-abdellah opened 2 years ago

marwan-abdellah commented 2 years ago

When I requested the three projections of the volume reconstructed from an input mesh, the XY projection was computed and saved to disk, but the XZ projection failed and caused a segmentation fault. This issue occured on macOSX with the demo neuron1 mesh.

./bin/ultraMesh2Mesh --mesh neuron-1.obj --output-directory testing-datasets/demo4 --export-obj-mesh --ignore-marching-cubes-mesh --ignore-laplacian-mesh --project-xy --project-xz --project-zy --resolution 1024

----------------------------------------------------------------------------------
 ------------------------------| Creating Context |------------------------------
----------------------------------------------------------------------------------

    WARNING: The bounding box of the volume will be computed on the fly

----------------------------------------------------------------------------------
 --------------------------------| Ultralizing |--------------------------------
----------------------------------------------------------------------------------

    NOTE: Output Directory [ /Volumes/Computer/testing-datasets/demo4 ]

    NOTE: Volume resolution [1024], Largest dimension [344.103149]

----------------------------------------------------------------------------------
 ----------------------------| Creating Volume Grid |----------------------------
----------------------------------------------------------------------------------

    NOTE: Volume Dimenions [ 798 x 513 x 1024 ] : [ 295.102295 x 189.448395 x 378.513428 ]

----------------------------------------------------------------------------------
 ----------------------------| Surface Voxelization |----------------------------
----------------------------------------------------------------------------------

    Creating Volume Shell [798 x 513 x 1024]
    Parallel Rasterization
    * Progress │▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒│ (100.00 %)
    * Time     | 0.347741 Seconds

    Rasterization Stats.
    * Time     | 0.34776 Seconds

----------------------------------------------------------------------------------
 -----------------------------| Projecting Volume |-----------------------------
----------------------------------------------------------------------------------

    Compositing Projection(s)
    XY Projection
    * Progress │▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒│ (100.00 %)
    * Time     | 7.19442 Seconds

    XZ Projection
    * Progress │▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒│ (100.00 %)
[1]    42550 segmentation fault  ./bin/ultraMesh2Mesh --mesh /Volumes/Computer/testing-datasets/neuron-1.obj
marwan-abdellah commented 2 years ago

Note that this issue happens only when the volume resolution is set to 1024, but it works fine for 512, 1023, and 1025. There is some magic in the value of 1024. It might be related to the volume resolution [798 x 513 x 1024], but this needs investigation.