New downsample method #606

chris-langfield · 2022-04-05T16:04:55Z

The final stage of adding the new downsampling method.

This relates to issues

The method uses the new crop_pad_2d method in the frequency domain and is tested by new downsampling tests that do not rely on hardcoded results

codecov · 2022-04-07T21:37:03Z

Codecov Report

Merging #606 (f559ecb) into develop (2806e3d) will decrease coverage by 0.01%.
The diff coverage is 100.00%.

@@             Coverage Diff             @@
##           develop     #606      +/-   ##
===========================================
- Coverage    86.53%   86.52%   -0.02%     
===========================================
  Files          109      109              
  Lines         8296     8287       -9     
===========================================
- Hits          7179     7170       -9     
  Misses        1117     1117

Impacted Files	Coverage Δ
src/aspire/image/image.py	`89.38% <100.00%> (-0.51%)`	⬇️

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chris-langfield · 2022-04-25T17:39:57Z

Using centered_fft2 fixes the issues from #608. The new downsampling method now passes the logical tests introduced in #567

It is worth noting that Volume.downsample() is not currently replaced with this new method.
It uses the related but not identical method aspire.image.downsample().

Although this method uses a similar strategy, I believe there is a conversation to be had about how to best go about vetting and possibly improving this 3D downsampling method. (I made an issue: #617)

j-c-c

Looks good! Couple small things.

j-c-c · 2022-04-25T18:12:18Z

src/aspire/image/image.py

-
-        return Image(im_ds)
+        # compute FT with centered 0-frequency
+        fx = np.array([fft.centered_fft2(self.data[i]) for i in range(self.n_images)])


Should be able to just do fx = fft.centered_fft2(self.data). I don't think the loop is necessary. Same below for ifft.

j-c-c · 2022-04-25T18:14:02Z

src/aspire/image/image.py

+            np.array([fft.centered_ifft2(crop_fx[i]) for i in range(self.n_images)])
+        ) * (ds_res**2 / self.res**2)


Maybe just out = np.real(fft.centered_ifft2(crop_fx)) * (ds_res**2 / self.res**2)?

I prefer the current set up (the return Image(out) echoes the pattern used in other parts of the code)

This was just in reference to the unnecessary list comprehension. Agree with matching other parts of the code for returning an Image.

Oh totally misunderstood. Your comment is absolutely right and I made the change thanks!

j-c-c

Looks good! Couple small things.

j-c-c

Looks good!

janden

Looks good.

* dropped in new ds method * adjust tests temporarily * some imports * change to centered_fft2 and allow gridpoint checks * format * remove debug show() * comment * simplify centered_fft2 and centered_ifft2

* Fix `k` bug in BFSReddyChetterji * restrict corr to a disc * Change `self.L` and `self.n` to `self.src.L` and `self.src.n` for estimators (#550) * changed self.L and self.n to self.src.L and self.src.n for estimators * extraneous comma * Add `aspire.utils.coor_trans.crop_2d` and move `coor_trans` objects to second-level API access (#565) * utils.coor_trans methods accessible from second level * crop_2d method * crop2d test * clarify flooring behavior for centering and add apdding * tests finished * isort shenanigans * fix even to odd n->n+1 padding bug * slightly better comment * better behavior for dtype * remove mistaken characters * fixes after merge * last ensure removed * rect tests * padding tests and fill value test * better comments * even better comments * np.diag * crop_pad_2d * clarifying comment when padding * Logical rather than hardcoded downsample tests (#567) * downsample tests * cleanup and deleting test downsample from preprocess_pipeline * remove hardcoded ds / whiten test * flake8 * 3d volume downsample test * remove redundant test from tests/test_preprocess.py * remove unused import * remove numbered tests for uniformity * typo * skip one of the ds tests * use gaussian_3d to generate test volume * isort * checkCenterPoint * max_resolution -> L_ds * parametrize ds tests * Bessel zero finding cleanup (#596) * docstring for besselj_zeros * rest of docstrings * remove pdb import * second order differences comment * comments and docstring for num_besselj_zeros * formatting * tiny fixes; * docstring fixes * NumPy * NumPy again * sanity check * parentheses inside sentence * `Basis` size fixes (#598) * fix size checking bug * fb2d * fb3d and pswf2d * dirac * fpswf * polar * format * sz -> size * test init with int * docstring * typo * the same typo * Authors page grammar fix. * cmap=gray * Gallery verb tense. Change cmap to gray. * Update gallery/experiments/README.rst header language. * Encode size in 2D FB test * Add test for 2D FB Gaussian expansion * Add eval–expand test for 2D FB * Add adjoint test for 2D FB * Add test for isotropic and modulated in 2D FB * Add test for indices * Add test for specific FB 2D basis element * Make 2D FB tests FFB friendly Cast `Images` to arrays when needed. * Move tests not specific to FB into a mixin * Add mixin to FFB 2D tests * Remove hardcoding from complex conversion tests * First attempt at testElement for FFB2D * Remove hardcoded (F)FB2D tests * Parameterize tests * Pass dtype to gaussian_2d * Expand on comment regarding factor of 1/2 * Fix rtoc bug * Add shape checks To make sure we don't get the same inadvertent broadcasting bug again. * Loop over different indices in 2D (F)FB tests * Fix #604 (#607) * Bump version: 0.9.0 → 0.9.1 * Fourier-Bessel Mixin class (#599) Fourier Bessel Mixin Class: fb.py * New downsample method (#606) * dropped in new ds method * adjust tests temporarily * some imports * change to centered_fft2 and allow gridpoint checks * format * remove debug show() * comment * simplify centered_fft2 and centered_ifft2 * dict of dicts * adjusted tests * Zenodo file with authors and affiliations (#615) * add zenodo file with just creators * name * add zenodo file to manifest * json errors * chris orcid * updated affiliations * update tox.ini to include json.tool check * josh orcid * author ordering * review changes * Remove offending sk import * Explicitly use svd_solver='full' for repro unit test * Fix PIL deprecation warning * sensible defaults * optional saving mrc * populate_unique_filters and read_ctf_file * body of populate_unique_filters * loop var * tests * work around ImageSource.set_metadata * update test * final test * rationalize sample CTF values * readme space * correct metadata test * write_all_star * remove write_one_star * method name * reading from Relion micrograph_ctf.star * format * import_ctf() instead of __init__ option * added tests and clarified import_ctf method * condense ctf args coordinate source * .values() instead of items() * add save image flags to increase test converage * docstrings * rest of docstrings * rename fun to populate_ctf * first pass refactor * refactor 2 * docstring * refactor 3 Co-authored-by: Garrett Wright <[email protected]> Co-authored-by: Garrett Wright <[email protected]> Co-authored-by: Joakim Andén <[email protected]> Co-authored-by: Josh Carmichael <[email protected]> Co-authored-by: Josh Carmichael <[email protected]>

chris-langfield added 3 commits April 5, 2022 12:04

dropped in new ds method

e55d0e5

adjust tests temporarily

02c6d28

some imports

be85d5e

janden mentioned this pull request Apr 21, 2022

Downsampling gridpoint test #608

Closed

chris-langfield added 3 commits April 25, 2022 10:26

Merge remote-tracking branch 'origin/develop' into new_downsample

a65bf53

change to centered_fft2 and allow gridpoint checks

dc5cb01

format

80a8efc

chris-langfield self-assigned this Apr 25, 2022

chris-langfield added the enhancement New feature or request label Apr 25, 2022

chris-langfield added 2 commits April 25, 2022 11:38

remove debug show()

768c749

comment

9253239

chris-langfield mentioned this pull request Apr 25, 2022

3D Downsampling #617

Closed

chris-langfield requested a review from j-c-c April 25, 2022 17:40

j-c-c requested changes Apr 25, 2022

View reviewed changes

simplify centered_fft2 and centered_ifft2

f559ecb

chris-langfield requested a review from j-c-c April 26, 2022 12:27

j-c-c approved these changes Apr 26, 2022

View reviewed changes

chris-langfield marked this pull request as ready for review April 26, 2022 13:31

chris-langfield requested a review from janden as a code owner April 26, 2022 13:31

janden approved these changes Apr 28, 2022

View reviewed changes

chris-langfield merged commit 10f613d into develop Apr 28, 2022

chris-langfield deleted the new_downsample branch April 28, 2022 12:49

chris-langfield mentioned this pull request Jul 6, 2022

Downsample bug #140

Closed

chris-langfield mentioned this pull request Nov 23, 2022

Unify the functions for pre-processing 2D images and 3D volumes #122

Closed

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		np.array([fft.centered_ifft2(crop_fx[i]) for i in range(self.n_images)])
		) * (ds_res2 / self.res2)

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