Debug 3D to 2D phase reconstruction #501
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* Add option to automatically choose regularization parameter for single variable Tikhonov deconvolution * Return reconstruction for chosen parameter, and 2 others around it, for user to choose * Avoid computing L curve norm values when unnecessary for better efficiency * Remove repeated computation on H_eff * Reduce GPU memory for L curve and fix padding bug for 3D phase * fix small gpu memory leak when running autotuning * fix small gpu memory leak when running autotuning * add option to output l-curve value * update output to non-log scale Co-authored-by: Tiffany Chien <[email protected]> Co-authored-by: lihaoyeh <[email protected]> Co-authored-by: camfoltz <[email protected]>
OMEZarr HCS Writer
…multipagetiff_optmization
* m1 document installation * remove defunct NVIDIA installation instructions * Update README.md Co-authored-by: Ziwen Liu <[email protected]> --------- Co-authored-by: Ziwen Liu <[email protected]>
* m1 document installation * remove defunct NVIDIA installation instructions * direct link to png * example notebooks -> examples * fix broken link
link BIA next to examples
* update a single example notebook * zarr.open mode to "r" * remove unused imports
* first-pass script and .html * html -> pdf * correct a docstring * remove obsolete waveOrderWriter calls * stub for iohub writer + correcting names of quantities * Save reconstruction to OME zarr for viewing in napari * fix mean/differential permittivity mistake * fix comments * don't track jupyter notebook * clean path * update pdf and readme --------- Co-authored-by: Shalin Mehta <[email protected]>
* fix bug finding focus in stack with only one slice * refactor for clarify * formatting * print -> warnings.warn * test single-slice case * fix test bugs --------- Co-authored-by: Talon Chandler <[email protected]>
* author and release updates * nits --------- Co-authored-by: Shalin Mehta <[email protected]>
* migrate to pyproject.toml * bump python * remove inaccurate topics from pyproject.toml * Revert "remove inaccurate topics from pyproject.toml" This reverts commit 46a5e72500501b9bff3b8d5fb1fe467d44b3bd44. * remove inaccurate topic metadata
* 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]>
pin numpy <2 pytorch/pytorch#128860
* bump torch to unpin numpy * add SPEC-0 conformant numpy requirement
* helper functions * fluorescence wrap safety * 3d phase wrap safety * fix axial nyquist bug * 2d phase wrap safety * fix interaction between padding and wrap safety
* 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 ca4e7c597dcf880d0c2d2b7859ed0e685522308c. * Reapply "fix warnings from tensoring a tensor" This reverts commit 790df573e82311226ca25f7c547c96a0d8fa7175. * 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]>
* stretched_multiply functions & tests * first pass `apply_transfer_function_filter` * check filter inputs * improved comment * test `apply_transfer_function_filter` * pad and multiply instead of iterating over stretched multiply blocks * phase reconstruction uses apply_transfer_function_filter * revised strategy --- prepad, require stretch-multiply to be divisible, then crop * fix tests --- now need divisibility * refactor inverse filter * refactor fluorescence deconvolution to support mismatched PSF and data * refactor to support transfer function banks * refactor phase and fluorescence to use "filter bank" functions * remove transverse_downsample_factor and interpolation * styling * clearer variable names * return real part only and update docs * expect real-valued input arrays * add `isotropic_thin_3d` TODO * update tests * put output on same device as input * comment Ziwen's optimization suggestions
* fix dependencies * move key pieces back to setup.cfg * update imports * move entirely to .toml --- basic working installation
* fix acq test * fix test_reconstruct * need all for tests * fix filename * remove all * copy iohub gh actions; remove tox * revert * all for pr * match recOrder's setup * remove tox dependency * try to match recOrder's test-and-deploy w/o tox * reinstate tox * only style with a single python version * skip example scripts on github actions * don't limit parallelism * no mps test on ghactions * debug ghactions * remove false debug * run subprocess in os.environ * replace python with sys.executable * remove debug * skip examples temporarily
* store .npz files in correct place * reduce clutter from local testing * fix qlipp example bug * clean pti tests
* ignore waveorder/_version.py * update recOrder README figure * updates plugin logo
…into debug-3d-to-2d
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Closing. Moved to (waveorder #441)[https://github.com/mehta-lab/waveorder/pull/441]. |
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I've added some debugging jigs here to start this process:
/hpc/projects/comp.micro/microscope_dev/2025-02-11-3d-to-2d-debugphase_transfer_functionis being saved to zeros (thoughabsorption_transfer_functionis non-zero), so that's certainly a bug, and a place to start.