Skip to content
GitLab
Projects Groups Topics Snippets
  • /
  • Help
    • Help
    • Support
    • Community forum
    • Submit feedback
    • Contribute to GitLab
  • Sign in
  • N Nabu
  • Project information
    • Project information
    • Activity
    • Labels
    • Members
  • Repository
    • Repository
    • Files
    • Commits
    • Branches
    • Tags
    • Contributor statistics
    • Graph
    • Compare revisions
  • Issues 76
    • Issues 76
    • List
    • Boards
    • Service Desk
    • Milestones
  • Jira
    • Jira
  • Merge requests 11
    • Merge requests 11
  • CI/CD
    • CI/CD
    • Pipelines
    • Jobs
    • Artifacts
    • Schedules
  • Deployments
    • Deployments
    • Environments
    • Releases
  • Packages and registries
    • Packages and registries
    • Container Registry
  • Monitor
    • Monitor
    • Incidents
  • Analytics
    • Analytics
    • Value stream
    • CI/CD
    • Repository
  • Wiki
    • Wiki
  • Snippets
    • Snippets
  • Activity
  • Graph
  • Create a new issue
  • Jobs
  • Commits
  • Issue Boards
Collapse sidebar
  • tomotools
  • Nabu
  • Issues
  • #206
Closed
Open
Issue created Nov 13, 2020 by Pierre Paleo@paleoOwner

Crash with "bamboo_0004" when using binning

Dataset: bamboo_0004

/home/esrf/paleo/.venv/py38_ubuntu20_pow9/lib/python3.8/site-packages/skcuda/cublas.py:284: UserWarning: creating CUBLAS context to get version number
  warnings.warn('creating CUBLAS context to get version number')
Computing final flats/darks for bamboo_0004_0000.nx
Wrote final flats and darks to /tmp/nabu_flatfield_k860k2pd/bamboo_0004_0000_nabu_processes.hdf5
Estimating center of rotation
CenterOfRotationSlidingWindow({})
Estimated center of rotation: 909.39
Overwriting configuration: start_z = 1080 and end_z = 1080
Going to reconstruct slices (1080, 1080)

Processing sub-volume (1080, 1081)
Creating a new pipeline object
Data shape for flatfield is (2300, 1, 1280)
Data shape for take_log is (2300, 1, 1280)
Data shape for build_sino is (2300, 1, 1280)
Allocating sinos: (1, 1150, 1648)
Allocating recs: (1, 1650, 1650)
Estimated center of rotation: 454.50
Data shape for reconstruction is (1150, 1648)
Data shape for flatfield is (2300, 1, 1280)
Reading data
Region = (None, None, 1080, 1081)
End Reading data
Transfering radios to GPU
Allocating radios: (2300, 1, 1280)
Applying flat-field
End Applying flat-field
Taking logarithm
End Taking logarithm
Building sinograms
End Building sinograms
Reconstruction
Traceback (most recent call last):
  File "/home/esrf/paleo/.venv/py38_ubuntu20_pow9/bin/nabu", line 8, in <module>
    sys.exit(main())
  File "/home/esrf/paleo/.venv/py38_ubuntu20_pow9/lib/python3.8/site-packages/nabu/resources/cli/reconstruct.py", line 147, in main
    R.reconstruct()
  File "/home/esrf/paleo/.venv/py38_ubuntu20_pow9/lib/python3.8/site-packages/nabu/app/local_reconstruction.py", line 299, in reconstruct
    self.pipeline.process_chunk(sub_region=task["sub_region"])
  File "/home/esrf/paleo/.venv/py38_ubuntu20_pow9/lib/python3.8/site-packages/nabu/app/fullfield.py", line 706, in process_chunk
    self._process_chunk()
  File "/home/esrf/paleo/.venv/py38_ubuntu20_pow9/lib/python3.8/site-packages/nabu/app/fullfield.py", line 693, in _process_chunk
    self._reconstruct()
  File "/home/esrf/paleo/.venv/py38_ubuntu20_pow9/lib/python3.8/site-packages/nabu/app/utils.py", line 32, in wrapper
    res = func(*args, **kwargs)
  File "/home/esrf/paleo/.venv/py38_ubuntu20_pow9/lib/python3.8/site-packages/nabu/app/fullfield.py", line 649, in _reconstruct
    self.reconstruction.fbp(
  File "/home/esrf/paleo/.venv/py38_ubuntu20_pow9/lib/python3.8/site-packages/nabu/reconstruction/fbp.py", line 323, in filtered_backprojection
    return self.backproj(self._d_sino, output=output)
  File "/home/esrf/paleo/.venv/py38_ubuntu20_pow9/lib/python3.8/site-packages/nabu/reconstruction/fbp.py", line 309, in backproj
    d_slice = self._set_output(output, check=do_checks)
  File "/home/esrf/paleo/.venv/py38_ubuntu20_pow9/lib/python3.8/site-packages/nabu/reconstruction/fbp.py", line 300, in _set_output
    assert output.shape == self.slice_shape, "Expected output shape %s but got %s" % (self.slice_shape, output.shape)
AssertionError: Expected output shape (1648, 1648) but got (1650, 1650)

It seems to occur only when CoR is on the left.

Edited Nov 13, 2020 by Pierre Paleo
Assignee
Assign to
Time tracking