Phase reconstruction is invariant to voxel-size #164
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ziw-liu
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Apr 16, 2024
ziw-liu
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Apr 23, 2024
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talonchandler
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Jul 5, 2024
* Phase reconstruction is invariant to voxel-size (#164) * 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]> * np.product -> np.prod --------- Co-authored-by: Ivan Ivanov <[email protected]>
talonchandler
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Dec 22, 2024
* Phase reconstruction is invariant to voxel-size (#164) * 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]> * poster scripting * may 14 poster draft * last-minute poster changes * quick clearning * checkpoint before svd refactor * SVD refactor * pass singular system * update visualization script * fix visualization script scaling * correct phase recon regression, legacy recon assumes axially even green's function * helper functions * fluorescence wrap safety * 3d phase wrap safety * fix axial nyquist bug * 2d phase wrap safety * fix interaction between padding and wrap safety * clean defaults * refactor singular system computation * remove accidental duplicate * refactor visuals * fix warnings from tensoring a tensor * match defaults * readme type * handle napari dependency * Revert "fix warnings from tensoring a tensor" This reverts commit ca4e7c5. * Reapply "fix warnings from tensoring a tensor" This reverts commit 790df57. * revive old version of greens tensor for backwards compatibility * fix tests that fail because of napari on github * wrap-safe vector transfer function * sampling tests * fourier-space oversampling * better visualizations for debugging * complex-valued napari visuals * complex utils * fix colormaps * debugging coherent tfs * formatting * fix rotation matrices * fix dc term * cleaning up * first-pass visuals checkpoint * matplotlib visuals * temporarily turn off rotations * debugging progress * example script to generate matplotlib tf figures * add rose asset * add all assets * plot all stokes * brighter plot for greens * visual improvements * revised rotation-symmetric Green's tensor * ignore * fix green's tensor units * modify circular anisotropy gellman matrices so that all transfer function are hermitian * improved matplotlib visuals * clean up plotting script * fix bug with 3x3 hardcoded shape * update tf components * minor reconstruction updates * refactor greens tensor spectrum * clean test script * clean models * simple memory reduction * clean debug statements * reorder svd for clean i/o * invert phase contrast * formatting * padding warning * revise visuals * visual cleanup * manage large reconstructions * Transfer function visuals (#178) * Bump torch to unpin numpy (#176) * bump torch to unpin numpy * add SPEC-0 conformant numpy requirement * Bump torch to unpin numpy (#176) * bump torch to unpin numpy * add SPEC-0 conformant numpy requirement * first-pass scripts * cleanup greens * clean transfer function support * fix naming issue * Wrap-safe transfer functions (#175) * helper functions * fluorescence wrap safety * 3d phase wrap safety * fix axial nyquist bug * 2d phase wrap safety * fix interaction between padding and wrap safety * green's tensor surfaces * dark theme default --------- Co-authored-by: Ziwen Liu <[email protected]> * matplotlib movie features * cheaper default viz script * move all visuals to /examples/visuals * update examples/README to table * typo * update badges * typo * revise main README * add 10-second slideshow * Clean installation instructions * cleanup vector model example * minor cleanup * remove matplotlib plot example * edits to README * clarify contrast mechanisms in README * simplify example installation w/ `pip install waveorder[examples]` * fix unintended diff * clarify `examples/README.md` * document 3d-to-2d transfer function * test orthonormal bases * fix accidental deletion * add deprecation warnings * remove plotting assets * label transfer function and simulation axes * guard type hint * matplotlib visuals docs and type hints * add type hints throughout models * revert TYPE_CHECKING to strings --------- Co-authored-by: Ivan Ivanov <[email protected]> Co-authored-by: Ziwen Liu <[email protected]> Co-authored-by: Shalin Mehta <[email protected]>
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This PR is paired with a confluence page with more context.
Before: phase reconstructions varied with the square of the z step size.
After: phase density reconstructions are invariant to the z step size.
This PR:
Note: this is a PR to
alg-dev, a new branch from main that I will develop on for the next few PRs. My commit history is not clean (git accident), but this PR's diff is clean.