allevitan
54decc486a
Merge pull request #22 from gnzng/fix-gaussian
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Fix use of gaussian_probe() + typo
2025-03-07 16:22:00 +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
allevitan
db2450c5ae
Merge pull request #18 from gnzng/master
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add github workflow using pip installation for python 3.8 - 3.12
2025-02-27 10:34:19 +01:00
Damian Guenzing
b39cd2b705
updated installation.rst for pip installation
2025-02-26 15:24:29 +00:00
Damian Guenzing
165ff8aced
Merge branch 'cdtools-developers:master' into master
2025-02-26 07:19:48 -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
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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
Damian Guenzing
5f30990e55
Delete constraints.txt
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constraints not needed anymore, relict from rebasing
2025-02-25 17:07:30 -08:00
gnzng
9159afa987
add github workflow using pip installation for python 3.8 - 3.12
2025-02-25 16:04:09 -08:00
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
allevitan
1f573370fc
Merge pull request #13 from yoshikisd/crop
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Add a function to shrink the range of translation positions in a dataset
2025-01-06 11:49:42 +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
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
yoshikisd
920f17bc66
Added a test for crop_2D_translations in Ptycho2DDataset.
2024-12-23 04:12:09 +00:00
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
allevitan
41fa25fdef
Merge pull request #7 from cdtools-developers/dataset-downsample
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Add a function to downsample a dataset by an integer factor
2024-12-09 11:10:24 +01:00
levita_a
ba7c8a17c6
Add a function to downsample a dataset by an integer factor
2024-12-06 15:59:56 +01:00
allevitan
93a5083455
Merge pull request #6 from cdtools-developers/report_msg
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CDIModel: Refactor report method
2024-11-19 09:19:58 +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
clemisch
ce16fbcedc
Merge pull request #5 from cdtools-developers/numpy2
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Add support for numpy 2.0
2024-11-08 15:17:39 +01:00
allevitan
26f4eb4cd1
Merge pull request #3 from cdtools-developers/citation
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Added a citation.cff file
2024-10-25 10:05:26 +02:00
allevitan
6097d5549c
Added a citation.cff file
2024-10-25 10:02:30 +02:00
allevitan
a86fe10e1f
Merge pull request #2 from cdtools-developers/license
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Add a license!
2024-10-25 00:42:34 +02:00
levita_a
0cbfb556f5
Add all contributors to the license
2024-10-25 00:39:49 +02:00
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
allevitan
059c253756
Added authorship and copyright info to license for data
2024-10-13 11:46:09 -04:00
levita_a
2ed4802755
Add a CC BY license to the included datasets
2024-10-10 17:41:36 +02:00
levita_a
2f16c43a11
Add an MIT license to the repo to prep for open release
2024-10-10 17:26:28 +02:00
allevitan
7fba211b5d
Merge pull request #1 from cdtools-developers/signal_estimate
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Add the tools to quickly estimate the signal level from raw data
2024-09-20 13:44:51 +02:00
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
levita_a
1052d5bcb6
Move documentation to the new organization
2024-09-02 14:23:59 +02:00
allevitan
3b6b0534af
Merge pull request #1 from allevitan/organization
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Organization
2024-09-02 11:20:37 +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
allevitan
levita_a