Gv/final/features2#444
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* Update README (#442) * Update README Added links to the tutorials for creating custom scatterers. * Update README * Update README.md --------- Co-authored-by: Alex <95913221+Pwhsky@users.noreply.github.com> * Auto-update README-pypi.md * removed Image * ok * removed Image from optics and scatterers * Daniel's Mie scatterer. * u * fixed upscale with field scatterers * u * rolled back momentarily removed changed to MieScatetterer suggested by Daniel. Now Upscale doesn't work with MieScatterers * added contrast type included objective attribute (contrast_type) to decide wether to use intensity or refractive index * u * rebased ok * u * fixed sampletomask * u * sampletomask torch compatible * unified field and volume wrapper * u * u * u * u * u * implemented BackendDispatched * u * u * eliminated dispatcher --------- Co-authored-by: Mirja Granfors <95694095+mirjagranfors@users.noreply.github.com> Co-authored-by: Alex <95913221+Pwhsky@users.noreply.github.com> Co-authored-by: github-actions <github-actions@github.com> Co-authored-by: Giovanni Volpe <46021832+giovannivolpe@users.noreply.github.com>
Basically renamed the method to _action to prevent shadowing the attribute in DeepTrackNode.
* created optical, changed imports * init * u * u * bind optical submodules * u * dt_math * issue with python > 3.12 * index order for compatibility with python 3.9 * imageio cleanup * indexing * verbose install * force * lightning check * more checks * roll back * Rename DTEx206_cell_counting.ipynb to DTEx215_cell_counting.ipynb * Revert "Rename DTEx206_cell_counting.ipynb to DTEx215_cell_counting.ipynb" This reverts commit 453a099. * updated: DTEx215_cell_counting (#451) * Add files via upload * Update README.md * renamed to DTEx215 * moved tests, added cv2 * meshgrid indexing for torch * solve issue with multiple volumes solve issue with multiple volumes with different intensities or refractive indexes by introducing _merge_placed_volumes() * test_dlcc corrected --------- Co-authored-by: Alex <95913221+Pwhsky@users.noreply.github.com> Co-authored-by: Alex <lechal.pierre@gmail.com>
* Add torch Mie backend support * Move Mie array API polynomials to backend * Test torch Mie backend autodiff * Simplify Mie backend xp usage * converted Mie scatterer setup, grids, masks, polarization math, FFTs, propagation use, and stratified coefficients to preserve torch tensors/autograd * made get_propagation_matrix backend-aware * torch regression tests for Mie sphere autodiff, multi-field brightfield summation, propagation matrix autodiff, and Zernike coefficient gradients * the derivative through torch.arccos(cos_theta) blowed up for zero illumination angle; this now uses the equivalent cos_theta branch * Pint triggers some numpy conversion. Added a path for tensors so that they don't go through Pint. * modifications for learnable x, y, resolution, na, magnification, wavelength * only bypass Pint for torch tensors that actually require grad * differentiable paths use explicit kwargs["voxel_size"], so we must scale that explicit value * tutorial for position optimization --------- Co-authored-by: edudc <eduard.duta.costache@physics.gu.se>
Updated Python version compatibility and improved text clarity.
…ch (#482) * Update README (#442) * Update README Added links to the tutorials for creating custom scatterers. * Update README * Update README.md --------- Co-authored-by: Alex <95913221+Pwhsky@users.noreply.github.com> * Auto-update README-pypi.md * Rename DTEx206_cell_counting.ipynb to DTEx215_cell_counting.ipynb * Revert "Rename DTEx206_cell_counting.ipynb to DTEx215_cell_counting.ipynb" This reverts commit 453a099. * updated: DTEx215_cell_counting (#451) * Add files via upload * Update README.md * renamed to DTEx215 * Auto-update README-pypi.md * created optical, changed imports * init * u * u * bind optical submodules * u * dt_math * issue with python > 3.12 * index order for compatibility with python 3.9 * imageio cleanup * indexing * verbose install * force * lightning check * more checks * roll back * Rename DTEx206_cell_counting.ipynb to DTEx215_cell_counting.ipynb * Revert "Rename DTEx206_cell_counting.ipynb to DTEx215_cell_counting.ipynb" This reverts commit 453a099. * updated: DTEx215_cell_counting (#451) * Add files via upload * Update README.md * renamed to DTEx215 * moved tests, added cv2 * meshgrid indexing for torch * solve issue with multiple volumes solve issue with multiple volumes with different intensities or refractive indexes by introducing _merge_placed_volumes() * test_dlcc corrected * fix issue with Python 3.9 * u * u * u * nu * back * nu * back * _pad_volume * optics * preserve autograd * remove += * in-place index * test * tests * u * mie * tests * common_setup * _asarray_vector * _process_properties * convert * properties * properties * properties * Revert "u" This reverts commit 4f3bf3f. * skip tests * ok * revert changes to properties * u * revert changes to mie --------- Co-authored-by: Mirja Granfors <95694095+mirjagranfors@users.noreply.github.com> Co-authored-by: Alex <95913221+Pwhsky@users.noreply.github.com> Co-authored-by: github-actions <github-actions@github.com> Co-authored-by: Alex <lechal.pierre@gmail.com>
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