a7904491be
Added a function to allow for deletion of translation positions with logical indexing ( #16 )
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* 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
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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
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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
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
Anastasiia Kutakh
eb64770258
.
2021-08-03 02:25:29 -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
Abe Levitan
ad1a2e77b7
Update the exit_wave_geometry to handle paralellogram detectors
2020-04-23 17:39:16 -04:00
Abe Levitan
d8486306f7
Fix a bug with oversampling in the measurement functions
2020-02-11 15:20:55 -05:00
Abe Levitan
e987d40df8
Remove last of t.tensor usage from dataset loading
2019-10-04 17:00:43 -04:00
Abe Levitan
69be77cc09
Update installation instructions for simplicity and also fix the tests to reflect new usage
2019-10-02 15:56:48 -04:00
Abe Levitan
40998908f1
refactor datasets, wrote more docs, added one more test dataset
2019-09-09 14:16:42 -04:00
levita_a