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• ab30afb10e Update the documentation to reflect the existence of a PyPI package levita_a 2025-07-02 14:21:43 +02:00
• b223011b0f Merge pull request #40 from cdtools-developers/fixpypinaming v0.3.0pypi1 Dayne Yoshiki Sasaki 2025-06-30 10:17:37 -07:00
• 1ecf001ad4 change name from cdtools to cdtools-py to match pypi naming Damian Guenzing 2025-06-29 21:14:49 +00:00
• 99139f59c9 Merge pull request #39 from cdtools-developers/pypirelease v0.3.0pypi Abe Levitan 2025-06-29 11:11:50 +02:00
• 302decd922 remove version increase gnzng 2025-06-23 15:46:32 -07:00
• 2c764d4190 add pypi workflow gnzng 2025-06-23 15:38:44 -07:00
• 8c216aa7e6 Merge pull request #36 from cdtools-developers/version0-3-0 Dayne Yoshiki Sasaki 2025-06-23 09:37:16 -07:00
• 951636e39f pin current version to 0.3.0 v0.3.0 gnzng 2025-06-18 14:09:43 -07:00
• b95bdba1ef Merge pull request #35 from gnzng/float64 Dayne Yoshiki Sasaki 2025-06-17 16:21:56 -07:00
• d7a1ea82c9 adjusted warn msg based on Daynes suggestion gnzng 2025-06-17 15:50:51 -07:00
• b189c3c2af Add warning for 64-bit float conversion in Ptycho2DDataset and added to tests gnzng 2025-06-17 11:01:30 -07:00
• eb19ce3995 Merge pull request #32 from yoshikisd/bugfix/rpi_compare Abe Levitan 2025-06-12 07:50:18 -04:00
• 31318819d0 Merge branch 'cdtools-developers:master' into bugfix/rpi_compare Dayne Yoshiki Sasaki 2025-06-11 17:03:06 -07:00
• 4c784de922 Fixed sim_data shape change in CDIModel.compare for RPI measurements yoshikisd 2025-06-12 00:02:32 +00:00
• b3a70ec325 Merge pull request #30 from cdtools-developers/variable_qe Dayne Yoshiki Sasaki 2025-06-10 08:44:22 -07:00
• 4ecc782c28 Reply to Daynes comment's and slightly loosen a tolerance in one test that has been failing levita_a 2025-06-10 14:11:01 +02:00
• b6bc7d95cc Change the behavior of FancyPtycho.center_probes to center the probe in real space even when fourier_probe is set to True levita_a 2025-04-07 09:35:59 +02:00
• 2c5587cacf Fix an issue for datasets with colinear translations levita_a 2025-01-22 16:41:18 +01:00
• da695c7c06 Merge pull request #29 from cdtools-developers/center_probe_real_space Dayne Yoshiki Sasaki 2025-06-09 19:17:10 -07:00
• 1dd389d08a Update the initialization for near field to work better with oversampling levita_a 2025-05-28 10:09:02 +02:00
• 148b9f9865 Get a basic implementation of near-field ptycho working including initialization and oversampling levita_a 2025-05-26 16:58:27 +02:00
• b74aa82c32 Merge pull request #28 from cdtools-developers/bugfix/notranslationdataset Abe Levitan 2025-05-20 11:52:00 +02:00
• 2c2f2d2d93 Add a way to save and load the quantum efficiency masks, and add test coverage levita_a 2025-05-13 16:05:16 +02:00
• 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 levita_a 2025-05-13 14:06:02 +02:00
• ac1499f511 get it running in principle, but it is not good levita_a 2025-04-07 11:28:15 +02:00
• 91717b65d6 Change the behavior of FancyPtycho.center_probes to center the probe in real space even when fourier_probe is set to True levita_a 2025-04-07 09:35:59 +02:00
• cb5942c39a Fix an issue for datasets with colinear translations levita_a 2025-01-22 16:41:18 +01:00
• d853a141bf Merge pull request #26 from gnzng/update-doc-link Abe Levitan 2025-04-02 18:32:31 +02:00
• a2ec05f63b Update CITATION.cff Damian Guenzing 2025-04-01 10:45:07 -07:00
• dbd54f310b Update README.md Damian Guenzing 2025-04-01 10:43:54 -07:00
• 1c434dd277 Merge pull request #25 from cdtools-developers/bugfix/h5_strings Dayne Yoshiki Sasaki 2025-03-20 12:03:00 -07:00
• 2fd917350d response to Dayne's review levita_a 2025-03-20 10:46:24 +01:00
• 5b6fd79b28 Add tests for nested_dict_to_numpy and nested_dict_to_torch levita_a 2025-03-18 13:13:47 +01:00
• a30930b082 Fix bug with loading h5 files including strings, and add test coverage for h5_to_nested_dict and nested_dict_to_h5 levita_a 2025-03-18 11:54:06 +01:00
• fbc23af55b Rename HoloDataset to DirectCDIDataset and update related methods for clarity holo-reconstructions gnzng 2025-03-10 14:21:19 -07:00
• b4eee52aed Merge branch 'master' into holo-reconstructions gnzng 2025-03-10 14:21:19 -07:00
• ac8db438f5 very basic plotting funtion for holographic / cdi type of reconstructions gnzng 2025-03-10 14:21:19 -07:00
• fce2add124 Merge pull request #24 from gnzng/fix-doc-deployment Dayne Yoshiki Sasaki 2025-03-07 13:23:00 -08:00
• 48ca3a675a remove environment from github actions gnzng 2025-03-07 08:48:33 -08:00
• ee7f7eecd4 Merge pull request #21 from gnzng/master allevitan 2025-03-07 16:25:05 +01:00
• 54decc486a Merge pull request #22 from gnzng/fix-gaussian allevitan 2025-03-07 16:22:00 +01:00
• f8bebd0436 typo, factor -> factors gnzng 2025-03-04 14:21:51 -08:00
• efadaf807e Rename probe_size parameter to probe_shape in FancyPtycho and MultislicePtycho classes to match the gaussian_probe function gnzng 2025-03-04 14:20:09 -08:00
• e1b76f0959 DOCS: Force-Push due to rebasing unnecessary large commits to just add an extra doc publishing action gnzng 2025-03-02 13:07:30 -08:00
• a097dd50d2 Update .gitignore to include .DS_Store files gnzng 2025-03-02 13:05:39 -08:00
• db2450c5ae Merge pull request #18 from gnzng/master allevitan 2025-02-27 10:34:19 +01:00
• b39cd2b705 updated installation.rst for pip installation Damian Guenzing 2025-02-26 15:24:29 +00:00
• 165ff8aced Merge branch 'cdtools-developers:master' into master Damian Guenzing 2025-02-26 07:19:48 -08:00
• a7904491be Added a function to allow for deletion of translation positions with logical indexing (#16) 3 people 2025-02-25 21:52:04 -08:00
• 5f30990e55 Delete constraints.txt Damian Guenzing 2025-02-25 17:07:30 -08:00
• 9159afa987 add github workflow using pip installation for python 3.8 - 3.12 gnzng 2025-02-25 14:27:15 -08:00
• b217043616 Merge branch 'master' into holo-reconstructions gnzng 2025-02-08 17:25:27 -08:00
• 0020306dd5 Merge pull request #12 from cdtools-developers/bragg_oversampling Dayne Sasaki 2025-01-06 09:24:20 -08:00
• 1f573370fc Merge pull request #13 from yoshikisd/crop allevitan 2025-01-06 11:49:42 +01:00
• 1da20c8427 improvements: Implemented requested changes for PR13 yoshikisd 2024-12-30 01:36:54 +00:00
• c03d4284f2 Fix the issue with obj view padding in Bragg2DPtycho not working with a probe fourier crop levita_a 2024-12-23 10:10:40 +01:00
• 920f17bc66 Added a test for crop_2D_translations in Ptycho2DDataset. yoshikisd 2024-12-23 04:12:09 +00:00
• 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 levita_a 2024-12-22 16:59:30 +01:00
• 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 levita_a 2024-12-22 15:08:23 +01:00
• 02ca31a598 Ptycho2DDataset: Add a function to shrink the range of translate positions to analyze yoshikisd 2024-12-21 00:24:53 +00:00
• 41fa25fdef Merge pull request #7 from cdtools-developers/dataset-downsample allevitan 2024-12-09 11:10:24 +01:00
• ba7c8a17c6 Add a function to downsample a dataset by an integer factor levita_a 2024-12-06 15:59:56 +01:00
• 3b7658a451 Ptycho2DDataset: Added a method for downsampling images multilayer_reflection yoshikisd 2024-12-02 15:41:55 -08:00
• 93a5083455 Merge pull request #6 from cdtools-developers/report_msg allevitan 2024-11-19 09:19:58 +01:00
• eee9ac073b Pad epoch index Clemens Schmid 2024-11-11 17:20:49 +01:00
• 4a3349bbad CDIModel: Refactor report method Clemens Schmid 2024-11-11 09:04:31 +01:00
• ce16fbcedc Merge pull request #5 from cdtools-developers/numpy2 clemisch 2024-11-08 15:17:39 +01:00
• aff8dd43d6 add tv_loss to __all__ gnzng 2024-11-05 16:54:37 -08:00
• af626b37f6 Introduce HoloDataset class to include loading data from .h5 and .tif files for holography reconstructions gnzng 2024-10-30 11:17:07 -07:00
• 155dda9060 Refactor amplitude_mse function to include normalization option gnzng 2024-10-25 17:08:13 -07:00
• 26f4eb4cd1 Merge pull request #3 from cdtools-developers/citation allevitan 2024-10-25 10:05:26 +02:00
• 6097d5549c Added a citation.cff file allevitan 2024-10-25 10:02:30 +02:00
• a86fe10e1f Merge pull request #2 from cdtools-developers/license allevitan 2024-10-25 00:42:34 +02:00
• 0cbfb556f5 Add all contributors to the license levita_a 2024-10-25 00:37:55 +02:00
• 40651eaf54 Remove the various deprication warnings related to converting h5py datasets to arrays with np.array() allevitan 2024-10-14 08:30:15 -04:00
• e9e2fd4bee Get all tests passing allevitan 2024-10-13 13:14:19 -04:00
• 25224d4d44 deal with the string_ related issues allevitan 2024-10-13 13:08:17 -04:00
• 059c253756 Added authorship and copyright info to license for data allevitan 2024-10-13 11:46:09 -04:00
• 2ed4802755 Add a CC BY license to the included datasets levita_a 2024-10-10 17:41:36 +02:00
• 2f16c43a11 Add an MIT license to the repo to prep for open release levita_a 2024-10-10 17:26:28 +02:00
• 7fba211b5d Merge pull request #1 from cdtools-developers/signal_estimate allevitan 2024-09-20 13:44:51 +02:00
• 30593c9c5c Get the mean pattern to show up by default with dataset.inspect() levita_a 2024-09-20 13:42:12 +02:00
• 6b2358df36 Add a fourier translation to fancy ptycho levita_a 2024-09-19 18:09:37 +02:00
• ad9420c3f2 random things levita_a 2024-09-17 14:46:56 +02:00
• 1052d5bcb6 Move documentation to the new organization levita_a 2024-09-02 14:23:59 +02:00
• 3b6b0534af Merge pull request #1 from allevitan/organization allevitan 2024-09-02 11:20:37 +02:00
• 13a2ba86df Make big changes to docs to update the tutorial section, and also to finally autoload the documentation of the models and datasets Abe Levitan 2024-09-01 13:04:28 +02:00
• 30a989fe3e Add first tests for models, and replace t.tensor with t.as_tensor in models levita_a 2024-08-30 16:10:26 +02:00
• 21b618d2e0 Remove the vestigges of the polarization-dependent code. It belongs in it's own repo levita_a 2024-08-30 14:13:36 +02:00
• 47aa3c41e2 Remove a bunch of models that really didn't belong in the main repo, and fix an issue with the RPI interaction conventions levita_a 2024-08-30 11:53:20 +02:00
• b3b19554d0 Add a phase only constraint to RPI and fancy_ptycho, misc small changes levita_a 2024-08-30 11:29:51 +02:00
• 35f140d348 Fully replace orthogonalize_probes and update most models levita_a 2024-07-25 17:35:48 +02:00
• 943dde13e6 Fix a remaining bug in orthogonalize_probes and also fix some lingering issues with the liveplotting for unified mode fancy ptycho levita_a 2024-07-25 16:32:10 +02:00
• 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 levita_a 2024-07-25 15:46:53 +02:00
• a02a0466ae fix a stupid bug I introduced at the last minute in the last commit levita_a 2024-07-02 10:58:17 +02:00
• 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 levita_a 2024-07-01 17:16:07 +02:00
• ee0d483f26 excise some old code from the RPI model that was making it fail, re: the old way of cropping out a detector slice levita_a 2024-06-26 11:09:43 +02:00
• 29d14c9537 Get a basic version of checkpointing working levita_a 2024-04-18 14:22:14 +02:00
• edc94ec09b Introducing new multislice model levita_a 2024-04-18 09:28:03 +02:00
• 7b2509cfe1 remove useless old examples, and update the examples and docs to be useful for the current version levita_a 2024-02-26 17:56:19 +01:00