al-recon

[gianthk]

The TomoPy reconstruction GUI. Written in Solara

• [ ] README.md
  • [X] Install instructions
  • [X] provide environment files for integration with ASTRA and TomoPy
  • [ ] gif video
  • [X] gspread integration
    • [X] requirements
    • [X] link video on how to setup Google API
• [ ] Package (?)
• [ ] expert settings
• [ ] check for imagej exe path
• [ ] submit to cluster button
  • [ ] write slurm job
  • [ ] submit slurm job to rum cluster
  • [x] log recon parameters to gspread master
  • [x] sino range enable /api/tomopy.misc.corr.html#tomopy.misc.corr.remove_ring)
• [ ] implement dxchange.reader.readbeats
• [ ] write recon midplanes (test pending)
  • [X] alrecon
  • [X] BEATS_recon.py
• [x] ring-artefact correction
  • [x] remove stripes (sinogram space)
  • [ ] remove stripes in BEATS_recon.py
• [ ] extended FOV clipping (360 to 180deg sino)
• [ ] oauth2client deprecated
• [X] absolute settings path
• [x] log to gspread option
• [x] attempt gpsread load keys
• [x] import touint from recon_utils
• [x] free all processed data at new H5 file load
• [x] directory autocompletion ('recon', 'cor') based on experiment dir and dataset name
• [x] delegate logging
• [x] deactivate napari viewers if napari not installed
• [x] deactivate napari viewers if alrecon is launched as local host app
• [X] move gspread key path to local config file
• [X] launch pages within jupyter notebook
• [x] MultiPage with Settings page
• [x] config and user_config YAML files
• [x] Recon with different algorithms
• [x] phase-retrieval
• [x] Dataset info using reactive input
  • [x] projs size
• [X] circular mask
• [x] 16-bit option
• [x] data range for write
• [x] proj range
• [X] COR range slider
• [x] COR slice input
• [x] COR guess button
• [x] Recon
• [x] write recon to disk
• [x] Napari viewer
  • [X] projs
  • [x] recon
• [x] disable buttons:
  • [x] Load if h5 file not selected
  • [x] COR if data not loaded
  • [x] Recon if data not loaded
  • [x] write recon if data not reconstructed
  • [x] napari proj if data not loaded
  • [x] napari recon if data not reconstructed
• [x] this al-recon instance has reconstructed N datasets

[gianthk]

Transfered to alrecon repository