Vector-optics birefringence reconstruction prototype #170
Conversation
* fix bug finding focus in stack with only one slice * refactor for clarify * formatting * print -> warnings.warn * test single-slice case * fix test bugs * z-scale-invariant test object * no rescaling on output * forward simulation takes a "brightness" - simulating real microscope * fix example script * add background parameter for fluorescence forward model * test voxel-size invariance * rename I_norm -> direct_intensity * refactor to clarify discretization factor * remove comment * fix fluorescence example bug * improved docsring --------- Co-authored-by: Ivan Ivanov <[email protected]>
|
Overall I think at least the core public API needs some documentation, even just type hints will help with future maintenance. |
There was a problem hiding this comment.
The PR looks great to me! I reviewed two READMEs (main and examples) and the new example: inplane_oriented_thick_pol3d_vector.py.
Minor input on example: label the spatial and channel axes in napari viewer, e.g., first axis when data is displayed is z and second axis is c. For transfer functions, the axes seem to be y, d (for data), s (for object).
|
Thank you both! @mattersoflight I've addressed your comments and added axis labels (great idea). @ziw-liu I've addressed your comments and added docstrings and type hints in the most-used APIs throughout |
This PR supports the waveOrder arXiv preprint and will precede a
2.2.0release. It includes:inplane_oriented_thick_pol3d_vectormodel,waveorder/examples/models/inplane_oriented_thick_pol3d_vector.py,waveorder/examples/visuals/folder with scripts that generate Green's tensor and vector transfer function visuals,/examples/README.md, with a new table of example types,README.md, with new badges (matching VisCy's), a new title figure, and new links to the preprint and PTI manuscript.