levita_a
fcd0b31b2c
Fix a bug with the mask implementation for the normalizers conflicting with SimplePtycho, and update the thresholds to accomodate the new normalization with masks and for intensity_MSE
2026-04-13 15:44:52 +02:00
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
levita_a
3d10f36739
Fix a bug where the normalizers stopped the loss history from being saved as a numpy scalar, and added test coverage
2026-04-05 22:23:23 +02:00
levita_a
388d1669f3
Final checks to ensure all tests pass with the new scaling
2026-04-05 21:52:14 +02:00
levita_a
8ee8bf9237
Fix bug where fancyptycho test was not being run on GPU
2026-04-03 18:59:09 +02:00
levita_a
b6553fd522
Update the example near field ptycho code to use Poisson NLL
2026-04-03 18:48:35 +02:00
allevitan and Claude Sonnet 4.6
3ccdc24d3f
Restructure loss coverage in reconstruction tests
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- Revert test_Adam_gold_balls to default amplitude_mse
- Add new test_intensity_MSE test (gold balls + AdamReconstructor)
- Update near_field threshold to 17 (poisson_nll scale)
Thresholds for test_intensity_MSE to be tuned after GPU run.
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com >
2026-04-03 18:46:27 +02:00
allevitan and Claude Sonnet 4.6
178e9a4e4e
Add loss function coverage to slow reconstruction tests
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Use poisson_nll in test_near_field_ptycho and intensity_mse in
test_Adam_gold_balls to exercise these loss paths end-to-end.
Thresholds left as-is pending re-running on a GPU machine.
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com >
2026-04-03 18:45:29 +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
d2c09acd44
Get all tests passing by updating the loss thresholds for the new normalizations, and add the new normalization to all models
2026-04-03 18:38:11 +02:00
Abe Levitan
3f028e2fbf
Merge pull request #72 from cdtools-developers/feature/betterplots
...
A bunch of long overdue updates to the plotting system
2026-04-03 18:23:41 +02:00
levita_a
f55b35f0dd
Stop stopping at each plot to show it
2026-03-24 16:56:44 +01:00
allevitan
603486e824
Change the default colormap for exponentiated objects to match that for un-exponentiated objects, and also update test_fancy_ptycho to show all the plots (not just plot level 2)
2026-03-24 16:55:56 +01:00
allevitan
ad2b09f2f0
Update the tests to work better when checking the model plotting, and make sure to cover panel_plot_mode=False
2026-03-24 16:19:26 +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
allevitan
4c89b3e46b
Fix the bug with loading from datasets with intensity info when OPRP is on and add test coverage
2026-03-19 22:45:57 +01:00
levita_a
a97e4cdf39
Add licensed near-field ptycho data to enable testing
2026-01-14 17:01:11 +01:00
gnzng
f79836bfc2
Add tests for version existence and semantic format
2025-10-29 21:40:12 -07:00
levita_a
e38ebd7372
Fix a high priority bug with the masking system which was introduced in the switch to reconstructors classes
2025-10-24 15:11:46 +02:00
levita_a
7d39015719
response to dayne's review
2025-10-17 23:41:08 +02:00
levita_a
f022b5e2c4
Get the tests passing again after the change of the optimization functions in the model classes
2025-10-16 15:58:28 +02:00
yoshikisd
82ce845385
Changed the names of the reconstructors and updated the old optimizer class documentation
2025-08-04 16:51:24 +00:00
yoshikisd
1e7fe2eb5f
Added pytests for reconstructors
2025-08-01 22:31:40 +00:00
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
gnzng
96d8b10792
linting test_fancy_ptycho.py
2025-07-07 14:11:50 -07:00
gnzng
ecb8ee4864
linting test_simple_ptycho.py
2025-07-07 13:59:35 -07:00
gnzng
745f7b73e6
Fix background calculation in test_Ptycho2DDataset_downsample
2025-07-07 13:55:54 -07:00
gnzng
f463144347
linting test_datasets.py
2025-07-07 13:49:46 -07:00
gnzng
4d812db68a
restructured conftest.py imports
2025-07-07 13:39:44 -07:00
gnzng
38be347a18
lint conftest.py
2025-07-07 13:38:52 -07:00
yoshikisd
36de44565b
Set fixed RNG seed for reconstruction pytests
2025-07-07 15:16:12 +00:00
gnzng
b189c3c2af
Add warning for 64-bit float conversion in Ptycho2DDataset and added to tests
2025-06-17 11:01:30 -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
b6bc7d95cc
Change the behavior of FancyPtycho.center_probes to center the probe in real space even when fourier_probe is set to True
2025-06-10 13:57:03 +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
a7904491be
Added a function to allow for deletion of translation positions with logical indexing ( #16 )
...
* Added a function to allow for deletion of translation positions via logical indexing
In ptycho_2d_dataset.py
- Created remove_translations_mask. This handles logical-indexing-based deletion of translation points
- Refactored crop_translations to be dependent on remove_translations_mask
* Add validation and tests for remove_translations_mask method in Ptycho2DDataset
* Switch mask to mask_remove
---------
Co-authored-by: gnzng <damian@guenzing.de >
Co-authored-by: Clemens Schmid <clemisch@tuta.io >
2025-02-26 06:52:04 +01:00
yoshikisd
1da20c8427
improvements: Implemented requested changes for PR13
...
For crop_translations in ptycho_2d_dataset.py
- crop_2d_translations is now crop_translations
- roi is now order-insensitive within the first and last pairs of elements.
- the definition of top, bottom, left, and right, are now consistent with figures generated by matplotlib.pyplot.imshow
- self.intensities is now updated
For tests_datasets.py
- the order-insensitivity of roi in crop_translation is tested, and tests for specific ordering of values in roi are removed.
2024-12-30 01:36:54 +00:00
yoshikisd
920f17bc66
Added a test for crop_2D_translations in Ptycho2DDataset.
2024-12-23 04:12:09 +00:00
levita_a
ba7c8a17c6
Add a function to downsample a dataset by an integer factor
2024-12-06 15:59:56 +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
allevitan
25224d4d44
deal with the string_ related issues
2024-10-13 13:08:17 -04:00
Abe Levitan
13a2ba86df
Make big changes to docs to update the tutorial section, and also to finally autoload the documentation of the models and datasets
2024-09-01 13:04:28 +02:00
levita_a
30a989fe3e
Add first tests for models, and replace t.tensor with t.as_tensor in models
2024-08-30 16:10:26 +02:00
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
allevitan