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
gnzng
f8bebd0436
typo, factor -> factors
2025-03-04 14:21:51 -08:00
gnzng
efadaf807e
Rename probe_size parameter to probe_shape in FancyPtycho and MultislicePtycho classes to match the gaussian_probe function
2025-03-04 14:20:09 -08:00
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
---------
Co-authored-by: gnzng <damian@guenzing.de >
Co-authored-by: Clemens Schmid <clemisch@tuta.io >
2025-02-26 06:52:04 +01:00
Dayne Sasaki
0020306dd5
Merge pull request #12 from cdtools-developers/bragg_oversampling
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Fixing oversampling in Bragg2DPtycho
2025-01-06 09:24:20 -08:00
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
levita_a
c03d4284f2
Fix the issue with obj view padding in Bragg2DPtycho not working with a probe fourier crop
2024-12-23 10:10:40 +01:00
levita_a
a22ae1b476
Fix the issue with oversampling in bragg 2d ptycho when correct_tilt=True, and fix one other issue with object sizing in bragg 2d ptycho with oversampling
2024-12-22 16:59:30 +01:00
levita_a
08a77ce5c6
Add the object view crop to Bragg2DPtycho for parity, and add a small fix to obj_view_crop which limits the view expansion to the actual object array size
2024-12-22 15:08:23 +01:00
yoshikisd
02ca31a598
Ptycho2DDataset: Add a function to shrink the range of translate positions to analyze
2024-12-21 00:24:53 +00:00
levita_a
ba7c8a17c6
Add a function to downsample a dataset by an integer factor
2024-12-06 15:59:56 +01:00
Clemens Schmid
eee9ac073b
Pad epoch index
2024-11-11 17:20:49 +01:00
Clemens Schmid
4a3349bbad
CDIModel: Refactor report method
2024-11-11 09:04:31 +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
e9e2fd4bee
Get all tests passing
2024-10-13 13:14:19 -04:00
allevitan
25224d4d44
deal with the string_ related issues
2024-10-13 13:08:17 -04:00
levita_a
30593c9c5c
Get the mean pattern to show up by default with dataset.inspect()
2024-09-20 13:42:12 +02:00
levita_a
6b2358df36
Add a fourier translation to fancy ptycho
2024-09-19 18:09:37 +02:00
levita_a
ad9420c3f2
random things
2024-09-17 14:46:56 +02:00
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
b3b19554d0
Add a phase only constraint to RPI and fancy_ptycho, misc small changes
2024-08-30 11:29:51 +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
a02a0466ae
fix a stupid bug I introduced at the last minute in the last commit
2024-07-02 10:58:17 +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
levita_a
ee0d483f26
excise some old code from the RPI model that was making it fail, re: the old way of cropping out a detector slice
2024-06-26 11:09:43 +02:00
levita_a
29d14c9537
Get a basic version of checkpointing working
2024-04-18 14:22:14 +02:00
levita_a
edc94ec09b
Introducing new multislice model
2024-04-18 09:28:03 +02:00
levita_a
7b2509cfe1
remove useless old examples, and update the examples and docs to be useful for the current version
2024-02-26 17:56:19 +01:00
levita_a
46b00807c8
Fix a bug that I introduced in fancy_ptycho's oversampling, and also update some example scripts
2024-02-26 13:44:46 +01:00
levita_a
d7c7e8f396
start getting the docs back up to date
2024-02-23 16:54:48 +01:00
levita_a
2e6db5517d
get the projected views for bragg_2d_Ptycho working
2024-02-22 15:57:35 +01:00
levita_a
30f9b142b6
Fix up bragg_2d_ptycho a bit and add model.save_on_exception
2024-02-22 14:41:07 +01:00
Abe Levitan
5925ee74ab
Checked and fixed the tests, got them all running
2024-02-12 14:55:26 -05:00
Abe Levitan
1502d567bf
honestly, not sure
2024-02-12 09:49:26 -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
Abe Levitan
44a6fac37a
Add a tool to split ptycho datasets and a context manager to save .mat files, and slightly adjust the save format
2024-02-11 10:29:07 -05:00
Abraham Levitan
e48970f7a9
Add an option for probe fourier crop to Bragg 2D Ptycho
2024-02-10 13:42:22 -05:00
levita_a
d0a0d12521
Add a normalize reconstruction set function
2024-01-04 16:50:10 +01:00
levita_a
7c269cff47
remove an errant print statement
2023-12-04 15:35:05 +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
8ef3411604
Whoops I forgot some files in the last commit
2023-11-08 13:09:54 +01:00
Abe Levitan
1f44fdd57c
Some misc work toward the no analyzer jones matrix model (polarization swept)
2023-11-08 13:09:10 +01:00
Abe Levitan
e8023703a0
Start documenting the models, and change the default FOV on fancy_ptycho reconstruction inspections
2023-10-17 15:38:48 +02:00
levita_a
gnzng