Commits · 561d8bf1847d7374d8f4e974a7fd66bf2c76b012 · ALMF / SVLT

Oct 18, 2023
- Merge remote-tracking branch 'origin/chaeo_pipeline' into chaeo_pipeline · 561d8bf1
  Christopher Randolph Rhodes authored 1 year ago
  
  # Conflicts: # extensions/chaeo/examples/transfer_labels_to_ilastik_object_classifier.py
  561d8bf1
- Renamed a few output files · b8bd1a91
  Christopher Randolph Rhodes authored 1 year ago
  
  b8bd1a91
- Renamed a few output files · d5caf156
  Christopher Randolph Rhodes authored 1 year ago
  
  d5caf156
- Needed to make copy of project file · 5aca68af
  Christopher Randolph Rhodes authored 1 year ago
  
  5aca68af
- Prompt user input and compare results of same model before and after opening in ilastik · 5125d44c
  Christopher Randolph Rhodes authored 1 year ago
  
  5125d44c
Oct 17, 2023
- Corrected problem in labels key where total counts per annotation were misreported · 4bcad216
  Christopher Randolph Rhodes authored 1 year ago
  
  4bcad216
- Wrote comparison table, caught case where ilastik can label multiple fragments of an object · b973846b
  Christopher Randolph Rhodes authored 1 year ago
  
  b973846b
Oct 16, 2023
- Started accuracy quantification part · 9d49942a
  Christopher Randolph Rhodes authored 1 year ago
  
  9d49942a
- Successfully built and inferred with object classification model · 942be790
  Christopher Randolph Rhodes authored 1 year ago
  
  942be790
- Needed to modify model wrapper to handle patch stacks · 6942c044
  Christopher Randolph Rhodes authored 1 year ago
  
  6942c044
- Debugging vigra typing error · 1a60e61d
  Christopher Randolph Rhodes authored 1 year ago
  
  1a60e61d
- Start online validation of autogenerated model; but need to make inference... · 38530833
  Christopher Randolph Rhodes authored 1 year ago
  
  Start online validation of autogenerated model; but need to make inference model that takes binary inputs
  38530833
- Trying to recreate error during inference · 6e315a2b
  Christopher Randolph Rhodes authored 1 year ago
  
  6e315a2b
- Populate input data in object classification model · a91b885d
  Christopher Randolph Rhodes authored 1 year ago
  
  a91b885d
- Populate input data in object classification model · ecf4bdfe
  Christopher Randolph Rhodes authored 1 year ago
  
  ecf4bdfe
- Can set input dataset parameters · f6429ae3
  Christopher Randolph Rhodes authored 1 year ago
  
  f6429ae3
- Start end-to-end transfer method to ilastik object model · ed29f8f6
  Christopher Randolph Rhodes authored 1 year ago
  
  ed29f8f6
Oct 14, 2023
- Harmonized unit index of object class · 9e018533
  Christopher Randolph Rhodes authored 1 year ago
  
  9e018533
- Export test zstacks, too · 68f0f8a9
  Christopher Randolph Rhodes authored 1 year ago
  
  68f0f8a9
Oct 13, 2023
- Apply labels to ilastik project file from training data · 75eacb9f
  Christopher Randolph Rhodes authored 1 year ago
  
  75eacb9f
- Changed label in existing project file · 215a8002
  Christopher Randolph Rhodes authored 1 year ago
  
  215a8002
- Export table of z-stack patch files and annotations · a7d1a717
  Christopher Randolph Rhodes authored 1 year ago
  
  a7d1a717
- Export table of z-stack patch files and annotations · 2a2cb813
  Christopher Randolph Rhodes authored 1 year ago
  
  2a2cb813
- Export binary masks, too · a2ace075
  Christopher Randolph Rhodes authored 1 year ago
  
  a2ace075
- Export patches as z-stack, too · a877929b
  Christopher Randolph Rhodes authored 1 year ago
  
  a877929b
- Implemented training-test split in label mask export · da091a5d
  Christopher Randolph Rhodes authored 1 year ago
  
  da091a5d
Oct 12, 2023
- Export z-stack of masks, encoded with object class from EcoTaxa table · 05af7b71
  Christopher Randolph Rhodes authored 1 year ago
  
  05af7b71
- Working on export zstack of object labels for ilastik ingest · 6f3aae76
  Christopher Randolph Rhodes authored 1 year ago
  
  6f3aae76
- Corrected translational error in mask file output · a2c2fa51
  Christopher Randolph Rhodes authored 1 year ago
  
  a2c2fa51
- Confirmed able to catch failures · f8295af0
  Christopher Randolph Rhodes authored 1 year ago
  
  f8295af0
- Moved more of batch runner into utility methods · cd2fe9b8
  Christopher Randolph Rhodes authored 1 year ago
  
  cd2fe9b8
- Cleaned up batch runner script with filepath utility functions · 7695e1f0
  Christopher Randolph Rhodes authored 1 year ago
  
  7695e1f0
- Exposed export product flags in batch runner · b7738938
  Christopher Randolph Rhodes authored 1 year ago
  
  b7738938
Oct 11, 2023

Maintain DataFrame index throughout workflow, export patch filenames and... · 8fd758a5

Christopher Randolph Rhodes authored 1 year ago

Maintain DataFrame index throughout workflow, export patch filenames and complete source filepaths to workflow DataFrame; prepopulate patch UUID

8fd758a5

Oct 10, 2023
- Cleaned up RGB export work · 8ce0262f
  Christopher Randolph Rhodes authored 1 year ago
  
  8ce0262f
- Corrected slicing mistake that caused error in edge cases · 61130b78
  Christopher Randolph Rhodes authored 1 year ago
  
  61130b78
- Chasing down bug in overlay annotations · aade8740
  Christopher Randolph Rhodes authored 1 year ago
  
  aade8740
- Implemented and tested rendering of contours and mask overlays · 00672758
  Christopher Randolph Rhodes authored 1 year ago
  
  00672758
- Support balanced multichannel overlay as RGB export · dc7d49bb
  Christopher Randolph Rhodes authored 1 year ago
  
  dc7d49bb
- Now test against multichannel TIF that includes chlorophyl · 6364418b
  Christopher Randolph Rhodes authored 1 year ago
  
  6364418b