alg-dev branch merge to main (#121)

* 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]>
mehta-lab · Jul 25, 2023 · 43aace8 · 43aace8
1 parent 4473462
commit 43aace8
Show file tree

Hide file tree

Showing 49 changed files with 2,621 additions and 1,422 deletions.
diff --git a/docs/valuable-prs/2023-02-27.110.pr.open.md b/docs/valuable-prs/2023-02-27.110.pr.open.md
diff --git a/examples/3D_PODT_phase_simulation/3D_PODT_Phase_forward.py b/examples/3D_PODT_phase_simulation/3D_PODT_Phase_forward.py
diff --git a/examples/3D_PODT_phase_simulation/3D_PODT_Phase_recon.py b/examples/3D_PODT_phase_simulation/3D_PODT_Phase_recon.py
diff --git a/examples/README.md b/examples/README.md
@@ -1,12 +1,7 @@
-This folder of examples consists of:
+`waveorder` is undergoing a significant refactor, and this `examples/` folder serves as a good place to understand the current state of the repository.
 
-1) A set of simulations that will run as is. Any of the files in these folders 
-can be run with `python <script-name>.py`, and these files are included in 
-`waveorder`'s automated testing.  
-- `/2D_QLIPP_simulation/`
-- `/3D_PODT_Phase_simulation/`
-- `/PTI_simulation/`
+The `models/` folder demonstrates the latest functionality of `waveorder`. These scripts will run as is in an environment with `waveorder` and `napari` installed. Each script demonstrates a simulation and reconstruction with a **model**: a specific set of assumptions about the sample and the data being acquired. 
 
-2) A set of data-dependent reconstructions in `/experimental_reconstructions/`. 
-These files serve as a form of documentation for the types of reconstructions
-that `waveorder` can perform. 
+The `maintenance/` folder demonstrates the functionality of `waveorder` that we plan to move to `models/`. These scripts can be run as is, and they are being maintained with tests.
+
+The `documentation/` folder consists of examples that demonstrate reconstruction with real data. These examples require access to the complete datasets, so they are not being actively maintained and serve primarily as documentation.
diff --git a/...nt_Recon3D_anisotropic_target_small.ipynb → ...nt_Recon3D_anisotropic_target_small.ipynb b/...nt_Recon3D_anisotropic_target_small.ipynb → ...nt_Recon3D_anisotropic_target_small.ipynb
diff --git a/...ent/PTI_full_FOV_anisotropic_target.ipynb → ...ent/PTI_full_FOV_anisotropic_target.ipynb b/...ent/PTI_full_FOV_anisotropic_target.ipynb → ...ent/PTI_full_FOV_anisotropic_target.ipynb
diff --git a/...eriment/PTI_full_FOV_cardiac_muscle.ipynb → ...eriment/PTI_full_FOV_cardiac_muscle.ipynb b/...eriment/PTI_full_FOV_cardiac_muscle.ipynb → ...eriment/PTI_full_FOV_cardiac_muscle.ipynb
diff --git a/...I_full_FOV_cardiomyocyte_infected_1.ipynb → ...I_full_FOV_cardiomyocyte_infected_1.ipynb b/...I_full_FOV_cardiomyocyte_infected_1.ipynb → ...I_full_FOV_cardiomyocyte_infected_1.ipynb
diff --git a/...I_full_FOV_cardiomyocyte_infected_2.ipynb → ...I_full_FOV_cardiomyocyte_infected_2.ipynb b/...I_full_FOV_cardiomyocyte_infected_2.ipynb → ...I_full_FOV_cardiomyocyte_infected_2.ipynb
diff --git a/...ent/PTI_full_FOV_cardiomyocyte_mock.ipynb → ...ent/PTI_full_FOV_cardiomyocyte_mock.ipynb b/...ent/PTI_full_FOV_cardiomyocyte_mock.ipynb → ...ent/PTI_full_FOV_cardiomyocyte_mock.ipynb
diff --git a/...xperiment/PTI_full_FOV_human_uterus.ipynb → ...xperiment/PTI_full_FOV_human_uterus.ipynb b/...xperiment/PTI_full_FOV_human_uterus.ipynb → ...xperiment/PTI_full_FOV_human_uterus.ipynb
diff --git a/...riment/PTI_full_FOV_mouse_brain_aco.ipynb → ...riment/PTI_full_FOV_mouse_brain_aco.ipynb b/...riment/PTI_full_FOV_mouse_brain_aco.ipynb → ...riment/PTI_full_FOV_mouse_brain_aco.ipynb
diff --git a/...xperiment/2D_QLIPP_recon_experiment.ipynb → ...xperiment/2D_QLIPP_recon_experiment.ipynb b/...xperiment/2D_QLIPP_recon_experiment.ipynb → ...xperiment/2D_QLIPP_recon_experiment.ipynb
diff --git a/...xperiment/3D_QLIPP_recon_experiment.ipynb → ...xperiment/3D_QLIPP_recon_experiment.ipynb b/...xperiment/3D_QLIPP_recon_experiment.ipynb → ...xperiment/3D_QLIPP_recon_experiment.ipynb
diff --git a/examples/documentation/README.md b/examples/documentation/README.md
@@ -0,0 +1 @@
+This folder of `documentation` examples consists of a set of data-dependent reconstructions in `/experimental_reconstructions/`. 
diff --git a/...e_deconvolution/fluorescence_deconv.ipynb → ...e_deconvolution/fluorescence_deconv.ipynb b/...e_deconvolution/fluorescence_deconv.ipynb → ...e_deconvolution/fluorescence_deconv.ipynb
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1 @@
		This folder of `documentation` examples consists of a set of data-dependent reconstructions in `/experimental_reconstructions/`.