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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.

Home Page:https://portal.bluebrain.epfl.ch

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Segmentation fault during volume projection

marwan-abdellah opened this issue · comments

commented

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
commented

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.