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Draft: v3 tissue

Joe Knapperrequested to merge
v3_tissue into v3

This branch itself will never be merged we need to split up these changes into mergeable chunks. The list below shows what features are on this branch that will need to go into master and we can tick them off when they are merged.

A full list:

  • Adds a single static path to server/serve_static_files.py instead of searching multiple options (!263 (merged) and !265 (merged))
  • MPJEG streams and stream resolution as camera properties
  • Image processing in camera instead of smart_scan.py !246 (merged)
  • RawIsArrayCamera added to init, simulation and openCV camera files
  • Backlash added to fast_autofocus() !237
  • Type changes in autofocus
  • Backlash added to looping_autofocus() !237
  • Produces an autofocus report !210
  • Camera stage mapping certify_move_in_image_coordinates() to perform closed-loop moves !262
  • Camera stage mapping split_certified_move_in_image_coordinates() to perform multiple closed loop moves if the distance is too large for a single move to be reliable !262
  • Camera stage mapping get_displacement_between_images() to get the cross correlation between two images, based on the fft !262
  • An almost full rewrite of smart_scan() !239 (merged) !240 (merged) !242 (merged) These MRs are merged but further checks that all functionality is ported should be done
  • New tests/test_camera.py file
  • Smart scan, background detect and recentering Things added to tests/test_dummy_server.py
  • Aesthetic margin + border changes to webapp/src/assets/less/themes.less
  • Inverse colour button has a colour set to avoid merging with background !236 (merged)
  • Wider side panel in webapp/src/components/genericComponents/tabIcon.vue to see all text !231 (merged)
  • Narrower action button in webapp/src/components/labThingsComponents/actionButton.vue
  • Property changes in GUI no longer confirm new value - shorter message and no long floats covering the screen #456 (closed)
  • CSM in the GUI shows the results of the latest calibration !261 (merged)
  • Reset CCM to standard values in GUI and camera Thing
  • Show limits of exposure time in GUI (!225 (merged))
  • Set CCM in camera tab of GUI
  • USB storage button in Scan List in GUI
  • No scans available screen in Scan List in GUI
  • Thumbnails of scans in GUI, generated by smart_scan.py !250 (merged)
  • Save all settings button in Settings in GUI - already included
  • Stacking parameters in scanning GUI tab
  • Smaller log window in scanning tab
  • Reorder windows in GUI to match the workflow order !231 (merged)
  • Disabled v2 tour in webapp/src/App.vue !238 (merged)
  • Dependency updates in pyproject.toml - ongoing as we make changes
  • Added requirements.txt
Edited by Joe Knapper

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