Add motor-position stacking and stitching pipeline#88
Closed
FIrgolitsch wants to merge 3 commits intomainfrom
Closed
Add motor-position stacking and stitching pipeline#88FIrgolitsch wants to merge 3 commits intomainfrom
FIrgolitsch wants to merge 3 commits intomainfrom
Conversation
Introduces stitching/motor.py (ideal grid positions, seam refinement) and stitching/stacking.py (Z-overlap detection, cross-slice stacking). New scripts: linum_stack_motor_only.py, linum_stack_slices_motor.py, linum_stitch_motor_only.py (fast baseline) and linum_stitch_3d_refined.py (motor + registration refinement). Includes unit tests for both modules.
… handling, removing black speckles.
Contributor
Author
|
Closing in favour of #98 (recreated with squashed commits as part of the PR split plan refresh). |
This file contains hidden or 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
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
1 participant
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Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be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.
Summary
Provides a fast, registration-free stitching and stacking path that uses motor/stage positions recorded during acquisition as the sole source of tile placement — plus an optional refinement step using image registration.
Key Changes
New
linumpy/stitching/motor.py:compute_motor_positions: ideal grid positions from scale/rotation parameterscompute_registration_refinements: phase-correlation seam refinementapply_blend_shift_refinement: blend shift correctionscompare_motor_vs_registration: diagnostic comparison utilityNew
linumpy/stitching/stacking.py:find_z_overlap: cross-correlation Z-overlap searchcompute_z_offsets: per-slice Z-offset calculationstack_slices_with_shifts: full stacking with optional re-homing correctionNew scripts:
linum_stitch_motor_only.py— fast 2D stitching baseline, no phase correlationlinum_stitch_3d_refined.py— motor initialisation + registration refinementlinum_stack_motor_only.py— stack slices using only motor positionslinum_stack_slices_motor.py— full-featured motor + registration stacking with Z-overlap detection, per-slice normalisation, optional accumulationNew tests:
linumpy/tests/test_stitching_motor.pyandtest_stitching_stacking.pyDependencies
Depends on PR #85 (thread config module).