Phase 2D + 3D refactor #117
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ziw-liu
reviewed
Apr 20, 2023
ziw-liu
reviewed
Apr 20, 2023
ziw-liu
reviewed
Apr 20, 2023
ziw-liu
reviewed
Apr 20, 2023
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.
I suggest changing this example to be simulation and reconstruction of 2D specimens, thinner than the depth of field of the microscope.
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Thanks for the contributions and in-person chat @mattersoflight. I've made the following changes:
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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 makes the following changes to the "Phase2D" and "Phase3D" reconstructions methods:
waveorder_reconstructorinto their own files in/waveorder/models/phase2D_3D.pyandwaveorder/models/phase3D_3D.py.calculate_transfer_function,visualize_transfer_function(for napari viewing),apply_transfer_function(very simple simulation), andapply_inverse_transfer_function. These methods are in preparation for direct calls from therecOrderCLI.torchoptics,utils, and the newexamplesBirefringence_recon(S1&S2 diffraction-aware reconstruction) inwaveorder_reconstructor. I am now testing several example scripts to alert me to breaking changes.I suggest starting your review by running the new examples scripts in
/examples/PODT_Phase_simulation/. This will demonstrate a simplified form of what I expect on therecOrderside: the TF is calculated (and optionally viewed in napari), saved to a file, then used to reconstruct the data.Next, I suggest you take a look at the (currently under-documented but hopefully much clearer than before) function signatures for
calculate_transfer_functionandapply_inverge_transfer_functioninmodels/phase2D_3D.pyandmodels/phase3D_3D.py. These function signatures have a nearly direct correspondence withrecOrder's GUI parameters.Finally, I'll request your thoughts on my
modelsformat that arose naturally during my refactor. I've temporarily named the three models after our assumption about the sample (phase2D,phase3D,planaranisoND) and the data we acquire (3D,polND). To my eye, this seems to be an extensible way to split up the code since different assumptions about the object and/or different data will lead to different models (and code). I'm also very aware that this could be a good application for an abstract base class (especially since I expect to implementcalculate_transfer_functionandapply_inverse_transfer_functionmethods forplanaranisoND_polND), but I've chosen to delay this for now in fear of premature abstraction.I'm happy to chat in person anytime tomorrow. My immediate focus is on the interface for the "Retardance + Orientation" pipeline which I expect to require about 3/4 of my day tomorrow. After that PR, I am planning to start working on the
recOrderCLI side and link everything up.