allevitan
d8fade9f32
Update the amplitude MSE and intensity MSE loss to act equivalently - currently, the intensity MSE loss was by default a mean, but amplitude was by default a sum. Both functions now have a flag, use_sum=False, which is False by default. This changes the default behavior of amplitude_mse. All models, including the tutorial version of simple_ptycho, are updated accordingly and test coverage was added.
2026-04-13 14:34:23 +02:00
allevitan and Claude Sonnet 4.6
d644782e94
Update poisson_nll test to match sum-based implementation
...
poisson_nll now returns a sum rather than a mean, consistent with the
normalizer pattern. Remove the per-pixel divisions from the numpy
reference calculations accordingly.
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com >
2026-04-03 18:44:04 +02:00
levita_a
f55b35f0dd
Stop stopping at each plot to show it
2026-03-24 16:56:44 +01:00
allevitan and Claude Sonnet 4.6
29e9fddd72
Add test coverage for plot_translations, plot_nanomap, and plot_nanomap_with_images
...
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com >
2026-03-24 16:01:45 +01:00
gnzng
fc5a76ad61
linting test_plotting.py and test_propagators.py
2025-07-07 15:13:11 -07:00
gnzng
65e83753a8
linting test_interactions.py, test_losses.py, and test_measurements.py
2025-07-07 14:58:11 -07:00
gnzng
88df4c0794
linting test_image_processing.py and test_initializers.py
2025-07-07 14:40:17 -07:00
gnzng
b00f39e1fe
linting test_analysis.py and test_data.py
2025-07-07 14:28:23 -07:00
levita_a
4ecc782c28
Reply to Daynes comment's and slightly loosen a tolerance in one test that has been failing
2025-06-10 14:11:01 +02:00
levita_a
2c2f2d2d93
Add a way to save and load the quantum efficiency masks, and add test coverage
2025-05-13 16:05:16 +02:00
levita_a
2fd917350d
response to Dayne's review
2025-03-20 10:46:24 +01:00
levita_a
5b6fd79b28
Add tests for nested_dict_to_numpy and nested_dict_to_torch
2025-03-18 13:13:47 +01:00
levita_a
a30930b082
Fix bug with loading h5 files including strings, and add test coverage for h5_to_nested_dict and nested_dict_to_h5
2025-03-18 11:54:06 +01:00
allevitan
40651eaf54
Remove the various deprication warnings related to converting h5py datasets to arrays with np.array()
2024-10-14 08:30:15 -04:00
levita_a
21b618d2e0
Remove the vestigges of the polarization-dependent code. It belongs in it's own repo
2024-08-30 14:13:36 +02:00
levita_a
47aa3c41e2
Remove a bunch of models that really didn't belong in the main repo, and fix an issue with the RPI interaction conventions
2024-08-30 11:53:20 +02:00
levita_a
35f140d348
Fully replace orthogonalize_probes and update most models
2024-07-25 17:35:48 +02:00
levita_a
943dde13e6
Fix a remaining bug in orthogonalize_probes and also fix some lingering issues with the liveplotting for unified mode fancy ptycho
2024-07-25 16:32:10 +02:00
levita_a
5141320c6f
rewrite the probe orthogonalization for fancy_ptycho, and introduce a new probe orthogonalization tool in analysis. Also, update some tracking plots in fancy_ptycho
2024-07-25 15:46:53 +02:00
levita_a
59d103f6d6
update RPI to work with the latest data saving method, change dependence to latest pytorch for LBFGS to work on complex leaf tensors, and fix an issue with the test for the FRCs
2024-07-01 17:16:07 +02:00
Abe Levitan
5925ee74ab
Checked and fixed the tests, got them all running
2024-02-12 14:55:26 -05:00
Abe Levitan
dd30f58d2d
Start to make the lab bragg ptycho code sane, and fix the bug with probe bases when using probe fourier crop
2024-02-11 17:32:41 -05:00
levita_a
d0a0d12521
Add a normalize reconstruction set function
2024-01-04 16:50:10 +01:00
levita_a
f3b6ac9056
fix the numerical stability issue in the angular spectrum propagator code, but remove the ability to choose whether or not to include an explicit z dependence
2023-12-04 15:29:40 +01:00
levita_a
a9e0157707
Get tests to past and removeopt_for_fft
2023-12-01 15:58:18 +01:00
Abe Levitan
036fa8ea2c
remove dependency on fftpack completely
2022-08-19 10:02:11 -07:00
Abe Levitan
883ac0175a
Changed module name no lowercase because that's really how it should be
2022-06-08 12:52:33 -07:00
Abe Levitan
101e969eda
Fix the failing tests
2022-04-18 17:18:20 -07:00
Abe Levitan
096ec4ff20
Add analysis tools for comparing incoherent wavefields
2021-08-11 14:23:38 -04:00
Anastasiia Kutakh
3db2d0cdf6
.
2021-08-05 22:55:43 -04:00
Anastasiia Kutakh
894a5c697e
modified polarization and polarization tests
2021-08-05 18:47:46 -04:00
Abe Levitan
3e6072acb7
Finally remove the scourge of from __future__ import ... and remove any lingering suggestion that this code is python 2 compatible
2021-08-05 11:08:13 -04:00
Abe Levitan
960740f39f
Go over Anastasia's polarization tests and clean up repo a bit
2021-08-05 10:44:32 -04:00
Abe Levitan
14114f2bd4
Add tests to confirm that that the generation of angular spectrum propagators works with AD (and fix gasp so it indeed is)
2021-08-04 22:32:58 -04:00
Abe Levitan
b3e45af06e
Move the polarized ptycho dataset class back to loading data from the actual stored motor positions, and fix the test for the gaussian probe
2021-08-04 19:43:20 -04:00
Abe Levitan
e7d7323e50
Added a polarization dependent ptychography dataset class so we can save and load data!
2021-07-26 14:46:02 -04:00
Abe Levitan
76e6d5efae
get tests working
2021-06-21 16:55:34 -04:00
Abe Levitan
8f58242efe
Changed basic near field propagator to use the generalized function internally, and fixed band-limiting
2021-06-18 18:06:05 -04:00
Abe Levitan
e4a521656d
Changed how I implement the generalized propagator and (I believe) FIX the sign problems with propagation directiongit add --all!
2021-06-18 17:41:38 -04:00
Abe Levitan
c2b8f2fe1b
Bring all the tools to the point where they pass the tests
2021-06-18 14:01:39 -04:00
Abe Levitan
a3765e9097
remove all reference to cmath, get code and tests to the point where they run at least.
2021-06-17 16:47:24 -04:00
Abe Levitan
a536e3bdb4
Maybe last time it didn't actually commit?
2021-01-25 13:38:38 -05:00
Abe Levitan
936b203aac
Fix the issue with odd-sized probes & objs in RPI functions, still not fully tested
2020-12-28 22:09:20 -05:00
Abe Levitan
32a8a8179d
Fix an issue with the test for the poisson NLL function
2020-12-28 21:45:01 -05:00
Abe Levitan
0d484c0ac3
Fix sign error in generalized near field and associated test
2020-05-07 12:13:36 -04:00
Abe Levitan
31cc45da70
One more try to fix the off axis near field propagation
2020-05-04 16:53:50 -04:00
Abe Levitan
9771634551
Implement test for separate propagation and offset vectors
2020-04-29 20:11:03 -04:00
Abe Levitan
a5b2337293
Further develop the 2D Bragg ptychography code and edit some tests to work with a newer version of h5py
2020-04-29 13:50:13 -04:00
Abe Levitan
d586ed914e
Debug and test the off-axis propagation code
2020-04-24 14:16:44 -04:00
Abe Levitan
071eebd37b
Finish first pass of off-axis propagation, still needs to be tested off-axis
2020-04-23 20:37:13 -04:00
allevitan
levita_a