[perf] Improve spot finding in estimate_grid_orientation_from_img #2987
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
|
Converted to draft, because I forgot to add a test case |
Improved spot finding and grid fitting accuracy in `estimate_grid_orientation_from_img` and `find_spot_positions` by: - Using a configurable minimum distance between spots during local maxima finding. This addresses issues when the intensity difference between spots is high and single bright spots could be detected twice, while less bright spots were not detected. - Splitting `min_distance` and `len_object` parameters in `peak_local_max` and `find_spot_positions` to refine spot size calculation and edge exclusion relative to minimum spot distance.
a2984c5 to
b9d0d4b
Compare
nandishjpatel
approved these changes
Jan 14, 2025
- Add pitch to simulator microscope file - added comment to explain factor 0.75 - added pitch as an input argument to the spot-grid.py script, if not provided it will try to use the detector metadata - Update the lens magnification in the simulated yaml file to match the hardware, this ensures the spot-grid script finds the right spots for the pitch matching the pitch on the hardware
|
@tmoerkerken and @nandishjpatel this is ready for review |
nandishjpatel
approved these changes
Jan 22, 2025
tmoerkerken
requested changes
Jan 24, 2025
- make DEFAULT_PITCH a constant in fastem.py to have a single source of truth - clean up spot-grid.py
tmoerkerken
approved these changes
Jan 28, 2025
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
[perf] Improve spot finding in when distance between spots >> spot size
Improved spot finding and grid fitting accuracy in
estimate_grid_orientation_from_imgandfind_spot_positionsby:min_distanceandlen_objectparameters inpeak_local_maxandfind_spot_positionsto refine spot size calculation and edge exclusion relative to minimum spot distance.