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
2c5587cacf
Fix an issue for datasets with colinear translations
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
c86e505ae5
Make it possible to add a quantum efficiency mask to a dataset, allow fancy_ptycho to load that and use it in the forward model
2025-05-13 14:06:02 +02:00
levita_a
ac1499f511
get it running in principle, but it is not good
2025-05-12 16:55:26 +02:00
Abe Levitan
d853a141bf
Merge pull request #26 from gnzng/update-doc-link
...
[minor doc fix] update links to automatic docs
2025-04-02 18:32:31 +02:00
Damian Guenzing
a2ec05f63b
Update CITATION.cff
2025-04-01 10:45:07 -07:00
Damian Guenzing
dbd54f310b
Update README.md
2025-04-01 10:43:54 -07:00
Dayne Yoshiki Sasaki
1c434dd277
Merge pull request #25 from cdtools-developers/bugfix/h5_strings
...
Bugfix/h5 strings
2025-03-20 12:03:00 -07:00
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
Dayne Yoshiki Sasaki
fce2add124
Merge pull request #24 from gnzng/fix-doc-deployment
...
[fix] remove environment from github actions for docs deployment
2025-03-07 13:23:00 -08:00
gnzng
48ca3a675a
remove environment from github actions
2025-03-07 08:48:33 -08:00
allevitan
ee7f7eecd4
Merge pull request #21 from gnzng/master
...
Include docs in main repo and automatic deploy using github actions
2025-03-07 16:25:05 +01:00
allevitan
54decc486a
Merge pull request #22 from gnzng/fix-gaussian
...
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
gnzng
e1b76f0959
DOCS: Force-Push due to rebasing unnecessary large commits to just add an extra doc publishing action
2025-03-03 10:11:20 -08:00
gnzng
a097dd50d2
Update .gitignore to include .DS_Store files
2025-03-02 13:05:39 -08:00
allevitan
db2450c5ae
Merge pull request #18 from gnzng/master
...
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 )
...
* 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
Damian Guenzing
5f30990e55
Delete constraints.txt
...
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
...
Fixing oversampling in Bragg2DPtycho
2025-01-06 09:24:20 -08:00
allevitan
1f573370fc
Merge pull request #13 from yoshikisd/crop
...
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
...
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
...
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
...
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
...
Add support for numpy 2.0
2024-11-08 15:17:39 +01:00
allevitan
26f4eb4cd1
Merge pull request #3 from cdtools-developers/citation
...
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
...
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
Abe Levitan