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This reverts commit baeff85. Even with this flag, the transformation doesn't seem to be recognized during matching; try another approach
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This PR adds functionality for correcting stage creep effects in the wafer 60/61 multisem acquisition. The added code is divided into three parts.
Deriving parameters
Parameters for stage creep correction are derived on a per-mfov level: sfovs within an mfov that overlap vertically are aligned pairwise using an affine model. Parameters for this affine model are converted to a creep correction transformation. Only pre-existing matches are used and the correction parameters per mfov may optionally be stored in a csv file.
This step closely follows a python prototype by Ken.
Patching tile specs
A new stack is created with patched tile specs: tile specs that need to be corrected get an additional stage creep transform. Because there is a forward-backward mismatch between how the python prototype and render handle transformations, this transform needs to solve a non-linear equation at any point, which makes it a bit expensive to apply.
Patching matches
Instead of re-deriving point matches, matches are patched by applying the corresponding stage creep correction. A new match collection is created.
@trautmane let me know if this is enough to easily apply the correction to every slab. If not, I'm happy to modify the spark client to handle multi-stack configurations.
The process took about 30min for a full stack on my laptop on a single core, so it shouldn't be too compute intensive.