1. 24 Aug, 2021 3 commits
  2. 23 Aug, 2021 11 commits
  3. 16 Aug, 2021 1 commit
  4. 13 Aug, 2021 1 commit
  5. 12 Aug, 2021 2 commits
  6. 09 Aug, 2021 1 commit
  7. 28 Jul, 2021 1 commit
  8. 26 Jul, 2021 2 commits
  9. 16 Jul, 2021 3 commits
  10. 06 Jul, 2021 1 commit
  11. 05 Jul, 2021 1 commit
  12. 02 Jul, 2021 4 commits
    • Schiffer, Christian's avatar
      [DATALAD RUNCMD] mpirun -n 8 python scripts/tissue_histog... · e74e71bc
      Schiffer, Christian authored
      === Do not change lines below ===
      {
       "chain": [],
       "cmd": "mpirun -n 8 python scripts/tissue_histogram.py /p/project/cjinm16/schiffer1/production/2020_09_08_tissue_segmentation/data/B01/B01_1021_mask.hdf5 data/B01_surface_300_noisecleaned_poisson_left_remeshed_refined.anchor_points.hdf5 data/B01_surface_300_noisecleaned_poisson_right_remeshed_refined.anchor_points.hdf5 data/B03_surface_300_noisecleaned_poisson_left_remeshed_refined.anchor_points.hdf5 data/B03_surface_300_noisecleaned_poisson_right_remeshed_refined.anchor_points.hdf5 data/B04_surface_300_noisecleaned_poisson_left_remeshed_refined.anchor_points.hdf5 data/B04_surface_300_noisecleaned_poisson_right_remeshed_refined.anchor_points.hdf5 data/B05_surface_300_noisecleaned_poisson_left_remeshed_refined.anchor_points.hdf5 data/B05_surface_300_noisecleaned_poisson_right_remeshed_refined.anchor_points.hdf5 data/B06_surface_300_noisecleaned_poisson_left_remeshed_refined.anchor_points.hdf5 data/B06_surface_300_noisecleaned_poisson_right_remeshed_refined.anchor_points.hdf5 data/B07_surface_300_noisecleaned_poisson_left_remeshed_refined.anchor_points.hdf5 data/B07_surface_300_noisecleaned_poisson_right_remeshed_refined.anchor_points.hdf5 data/B10_surface_300_noisecleaned_poisson_left_remeshed_refined.anchor_points.hdf5 data/B10_surface_300_noisecleaned_poisson_right_remeshed_refined.anchor_points.hdf5 data/B12_surface_300_noisecleaned_poisson_left_remeshed_refined.anchor_points.hdf5 data/B12_surface_300_noisecleaned_poisson_right_remeshed_refined.anchor_points.hdf5 data/B06_surface_300_noisecleaned_poisson_left_remeshed_refined_histograms.anchor_points.hdf5 --patch-size 64 --patch-spacing 64 --max-value 2",
       "dsid": "c04d43c2-d593-11ea-a8bb-f832e4bcbbfb",
       "exit": 0,
       "extra_inputs": [],
       "inputs": [
        "data/B*refined.anchor_points.hdf5"
       ],
       "outputs": [
        "data/B*refined_histograms.anchor_points.hdf5"
       ],
       "pwd": "."
      }
      ^^^ Do not change lines above ^^^
      e74e71bc
    • Schiffer, Christian's avatar
      [DATALAD RUNCMD] mpirun -n 8 python scripts/tissue_histog... · 92880fa8
      Schiffer, Christian authored
      === Do not change lines below ===
      {
       "chain": [],
       "cmd": "mpirun -n 8 python scripts/tissue_histogram.py /p/project/cjinm16/schiffer1/production/2020_09_08_tissue_segmentation/data/B01/B01_1021_mask.hdf5 data/B01_surface_300_noisecleaned_poisson_left_remeshed_refined.anchor_points.hdf5 data/B01_surface_300_noisecleaned_poisson_right_remeshed_refined.anchor_points.hdf5 data/B03_surface_300_noisecleaned_poisson_left_remeshed_refined.anchor_points.hdf5 data/B03_surface_300_noisecleaned_poisson_right_remeshed_refined.anchor_points.hdf5 data/B04_surface_300_noisecleaned_poisson_left_remeshed_refined.anchor_points.hdf5 data/B04_surface_300_noisecleaned_poisson_right_remeshed_refined.anchor_points.hdf5 data/B05_surface_300_noisecleaned_poisson_left_remeshed_refined.anchor_points.hdf5 data/B05_surface_300_noisecleaned_poisson_right_remeshed_refined.anchor_points.hdf5 data/B06_surface_300_noisecleaned_poisson_left_remeshed_refined.anchor_points.hdf5 data/B06_surface_300_noisecleaned_poisson_right_remeshed_refined.anchor_points.hdf5 data/B07_surface_300_noisecleaned_poisson_left_remeshed_refined.anchor_points.hdf5 data/B07_surface_300_noisecleaned_poisson_right_remeshed_refined.anchor_points.hdf5 data/B10_surface_300_noisecleaned_poisson_left_remeshed_refined.anchor_points.hdf5 data/B10_surface_300_noisecleaned_poisson_right_remeshed_refined.anchor_points.hdf5 data/B12_surface_300_noisecleaned_poisson_left_remeshed_refined.anchor_points.hdf5 data/B12_surface_300_noisecleaned_poisson_right_remeshed_refined.anchor_points.hdf5 data/B06_surface_300_noisecleaned_poisson_left_remeshed_refined_histograms.anchor_points.hdf5 --patch-size 64 --patch-spacing 64 --max-value 3",
       "dsid": "c04d43c2-d593-11ea-a8bb-f832e4bcbbfb",
       "exit": 0,
       "extra_inputs": [],
       "inputs": [
        "data/B*refined.anchor_points.hdf5"
       ],
       "outputs": [
        "data/B*refined_histograms.anchor_points.hdf5"
       ],
       "pwd": "."
      }
      ^^^ Do not change lines above ^^^
      92880fa8
    • Schiffer, Christian's avatar
      Added tissue histogram computation · 1c79fc8c
      Schiffer, Christian authored
      1c79fc8c
    • Schiffer, Christian's avatar
  13. 01 Jul, 2021 3 commits
  14. 30 Jun, 2021 5 commits
  15. 28 Jun, 2021 1 commit
    • Schiffer, Christian's avatar
      [DATALAD RUNCMD] bash scripts/compute_anchor_points_from_... · 6869e3a6
      Schiffer, Christian authored
      === Do not change lines below ===
      {
       "chain": [],
       "cmd": "bash scripts/compute_anchor_points_from_mesh.sh",
       "dsid": "c04d43c2-d593-11ea-a8bb-f832e4bcbbfb",
       "exit": 0,
       "extra_inputs": [],
       "inputs": [
        "data/B*noisecleaned*remeshed.ply"
       ],
       "outputs": [
        "data/B*noisecleaned*remeshed.anchor_points.hdf5"
       ],
       "pwd": "."
      }
      ^^^ Do not change lines above ^^^
      6869e3a6