- 29 May, 2020 4 commits
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Philipp Schubert authored
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Philipp Schubert authored
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Philipp Schubert authored
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Philipp Schubert authored
Add optional cache usage of object properties in `SegmentationDataset` via `cache_properties` kwarg (see docs/api.md) * Add first example to api.md: Usage of the SegmentationDataset property caches * Property cache can be passed on to `SuperSegmentationDataset` via `sd_lookup`, which is also available for `SuperSegmentationObject` retrieved through `SuperSegmentationDataset.get_supersegmentation_object` (see docs/api.md) * code coverage is now computed correctly for the master branch tests by using a specific pytest config (full_run.ini) * continued: code adaption to line width of 120
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- 28 May, 2020 6 commits
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Philipp Schubert authored
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Philipp Schubert authored
ignore missing config.yml warning in test_models_e3.py; install open3d via conda; exclude tests from setup.py packages
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Philipp Schubert authored
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Philipp Schubert authored
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Philipp Schubert authored
Multi-view pipeline refactoring and object segmentation feature See merge request pschuber/SyConn!34
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Philipp Schubert authored
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- 27 May, 2020 3 commits
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Philipp Schubert authored
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Philipp Schubert authored
fix scaling in batchjob for sample location caching in case of SegmentationObjects with zero vertices
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Philipp Schubert authored
* add cython method for relabeling 3D arrays based on an ID->ID map * make per-chunk object IDs in `_gauss_threshold_connected_components` contiguous when filtering small object seeds during watershed * add `min_seed_vx` parameter for minimum watershed seed size * code clean-up
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- 26 May, 2020 2 commits
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Philipp Schubert authored
improve cache re-usage and performance of loading SuperSegmentationObject meshes ('sv', 'sj', 'syn_ssv', ..); ssv.load_mesh('syn_ssv') and subsequent typedsyns2mesh call in `map_synssv_objects_thread` re-use meshes of 'syn_ssv' objects
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Philipp Schubert authored
refactor meshing - now sparse and dense meshing are based on zmesh and use the same parameters; add model and loader kwarg parser method
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- 20 May, 2020 2 commits
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Philipp Schubert authored
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Philipp Schubert authored
- add on the fly view rendering for spines, cell types and morphology embedding - remove support for cell type inference with large views - improve speed and quality of meshing (isotropic downsampling) - add a more flexible image processing during object extraction (e.g. morphology operation and watershed) - remove unused code - implement initial frame work for point based models TODO: - generate syn_ssv meshes densely, based on a yet to be implemented syn_ssv segmentation KD - use syn_ssv channel instead of sj for views - on the fly rendering for glia separation - support point based models
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- 16 May, 2020 5 commits
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Philipp Schubert authored
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Philipp Schubert authored
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Joergen Kornfeld authored
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Philipp Schubert authored
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Joergen Kornfeld authored
Conflicts: tests/test_run.py
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- 15 May, 2020 1 commit
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Philipp Schubert authored
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- 14 May, 2020 1 commit
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Philipp Schubert authored
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- 03 May, 2020 1 commit
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Philipp Schubert authored
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- 02 May, 2020 1 commit
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Philipp Schubert authored
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- 01 May, 2020 4 commits
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Philipp Schubert authored
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Philipp Schubert authored
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Philipp Schubert authored
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Philipp Schubert authored
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- 30 Apr, 2020 2 commits
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Philipp Schubert authored
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Philipp Schubert authored
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- 28 Apr, 2020 1 commit
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Philipp Schubert authored
* add bulk loader for meshes of SegmentationObjects * [WIP] add glia loader for inference * improve speed of synapse object mapping * refactored view rendering of large neurons
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- 23 Apr, 2020 2 commits
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Philipp Schubert authored
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Philipp Schubert authored
* improve dataset_analysis speed by better data handling. * write syconn version during installation and use it in data set config files. * fix #29 freeze issue which appeared during rendering in environments (environment.yml) recently built from scratch; caused by sklearn.decompostion.PCA called multiple times within short time intervals; fixed by using a custom numpy PCA implementation (`_calc_pca_components` in meshes.py). * change dependency restrictions. * * [WIP] remove elektronn2 model support. * [WIP] transition to pytorch script, currently missing: sub-cellular structures (in training), mylein (in training). * [WIP] collect results of dataset_analysis with batch jobs via SLURM.
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- 22 Apr, 2020 1 commit
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Philipp Schubert authored
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- 21 Apr, 2020 1 commit
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Philipp Schubert authored
* add variation to number of target points in glia prediction training * improve `combine_and_split_syn` by ~8fold with the use of 2-stage kd-trees
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- 18 Apr, 2020 2 commits
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Philipp Schubert authored
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Philipp Schubert authored
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- 15 Apr, 2020 1 commit
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Philipp Schubert authored
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