Match parameters to simplify recOrder-waveorder interface
#131
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edyoshikun
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Jul 10, 2023
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talonchandler
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Jul 25, 2023
* New Stokes and Mueller module (#110) * Initial fwd and inv w/ tests * Add A-matrix and mueller-from-projection functions * Debug AR_mueller * Add convenience functions * Make 4d transposes nd with moveaxis * Add documentation * Improve module docstring * Change `KeyError` to `ValueError` * Improved docs * Remove unnecessary test * Removed "float" from docs * Revert "Removed "float" from docs" This reverts commit d9dd7e3. * Use `assert_almost_equal` * fixed couple of typos * `A` -> `I2S` & new `S2I` * comprehensive renaming * copy `s0` <-> `tra` * `np.array(s0)` so that it always has `.copy()` * Set default to "inverse" --------- Co-authored-by: Shalin Mehta <[email protected]> * PR docs (#111) * Add .git-blame-ignore-revs (#109) * Add #110 pr doc * Phase 2D + 3D refactor (#117) * black formatting * move 2D-to-3D phase recon to phase.py * convert gen_HZ_stack to ZYX * keep existing gpu handling * add 3D_to_3D phase OTF * improve naming consistency in phase_2D_to_3D_OTF * Add kwargs to recon params * change axes for 2D recon preparation * simplify 2D_to_3D recon with kwargs * handle padding and simplify OTFs * add 3D_to_3D recon with kwargs * temporarily remove docs for rewriting * first dependence on torch * move gen_Hz_stack to torch * convert 2d wotf to torch * move gen_Greens_function_z to torch * move important utils to torch * phase3Dto3D complete overhaul * refactor * optics.py to torch * high-level tests * splitt phase.py into models * clean up 3D script * cleaning and notes * phase2Dto3D placeholders * clean tests * use napari in tests * better skipping * reduce dependencies * update tests * maintiain PTI simulation's compatibility revised optics functions * drop pdb * Preserve birefringence recon * fix transpose bug * transpose bug * phase2Dto3D.py example * support padding * empty model for planaraniso * improved names * broad renaming of phase2D_3D and phase3D_3D * updated 2D phase and absorption recon Return the 2D absorption along with phase. Viewing OTFs in napari is very nice. I changed the axis order to be able to compare phase and absorption OTFs at focal plane. * display OTFs with Z-axis as a slider * changes to 2D phase/absorption simulation I suggest changing this example to be simulation and reconstruction of 2D specimens, thinner than the depth of field of the microscope. * rename models to <object-type>_<object-thickness>_<data_shape> * fix isotropic_thin_3d example, include absorption * 2D -> 2d, 3D -> 3d --------- Co-authored-by: Shalin Mehta <[email protected]> * Prepare polarization algorithms for integration with `recOrder` (#118) * black formatting * move 2D-to-3D phase recon to phase.py * convert gen_HZ_stack to ZYX * keep existing gpu handling * add 3D_to_3D phase OTF * improve naming consistency in phase_2D_to_3D_OTF * Add kwargs to recon params * change axes for 2D recon preparation * simplify 2D_to_3D recon with kwargs * handle padding and simplify OTFs * add 3D_to_3D recon with kwargs * temporarily remove docs for rewriting * first dependence on torch * move gen_Hz_stack to torch * convert 2d wotf to torch * move gen_Greens_function_z to torch * move important utils to torch * phase3Dto3D complete overhaul * refactor * optics.py to torch * high-level tests * splitt phase.py into models * clean up 3D script * cleaning and notes * phase2Dto3D placeholders * clean tests * use napari in tests * better skipping * reduce dependencies * update tests * maintiain PTI simulation's compatibility revised optics functions * drop pdb * Preserve birefringence recon * fix transpose bug * transpose bug * phase2Dto3D.py example * support padding * empty model for planaraniso * improved names * broad renaming of phase2D_3D and phase3D_3D * Rename variables in `stokes.py`. * updated 2D phase and absorption recon Return the 2D absorption along with phase. Viewing OTFs in napari is very nice. I changed the axis order to be able to compare phase and absorption OTFs at focal plane. * display OTFs with Z-axis as a slider * changes to 2D phase/absorption simulation I suggest changing this example to be simulation and reconstruction of 2D specimens, thinner than the depth of field of the microscope. * convert stokes to torch * initial draft of planaraniso model * rename models to <object-type>_<object-thickness>_<data_shape> * fix isotropic_thin_3d example, include absorption * 2D -> 2d, 3D -> 3d * calculate background corrections with transfer function * rearrange examples folder * rearrange examples folder * rearrange `isotropic` and `phase` examples * add `inplane_anisotropic` model and example * fix inplane tests * fix maintenance scripts * remove deprecated * use `np.meshgrid` for consistency * minor bug * integration changes --------- Co-authored-by: Shalin Mehta <[email protected]> * Remove kwargs from reconstructions (#119) * remove kwargs * fix estimated background bug * `illumination_wavelength` -> `wavelength_illumination` (#123) * Remove duplicate test (#125) remove duplicate test * Add option for axial flip of `phase_thick_3d` transfer function (#124) * `illumination_wavelength` -> `wavelength_illumination` * add option for axial flip of transfer function * test axial flip --------- Co-authored-by: Ziwen Liu <[email protected]> * Rename model from `anisotropic_thin` to `oriented_thick` (#127) `anisotropic_thin` -> `oriented_thick` * `isotropic_fluorescent_thick_3d` model (#128) * typo * model outline * prototype transfer function * 3d phantom + visualize transfer function * refactor apply_transfer_function * typo * refactor padding (with gpt docs + tests) * complete example * test apply_inverse_transfer_function * TV reconstructions raise NotImplementedError * `pad_zyx` -> `pad_zyx_along_z` * Simplify `data += 10` * Update tests/test_util.py Co-authored-by: Ziwen Liu <[email protected]> --------- Co-authored-by: Ziwen Liu <[email protected]> * Match parameters to simplify `recOrder`-`waveorder` interface (#131) * add axial_flip to `isotropic_thin_3d` * `illumination` -> `emission` for fluorescence * simplify parameters for usage with recOrder * fix test * pin torch>=2.0.0 * `z_position_list` should accept a list --------- Co-authored-by: Shalin Mehta <[email protected]> Co-authored-by: Ziwen Liu <[email protected]>
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This PR simplifies the parameter names for the
recOrder-waveorderinterface.This PR needs is matched with
recOrder#381. Sorry for the headache @edyoshikun.