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• 40d53222ba Merge pull request #95 from cdtools-developers/bump_to_0.3.3.dev0 master Abe Levitan 2026-08-16 09:24:15 -06:00
• 790857817d bump to next dev version levita_a 2026-08-16 17:19:46 +02:00
• 408bdc1265 Merge pull request #94 from cdtools-developers/bump_to_0.3.2 v0.3.2 Abe Levitan 2026-08-16 09:01:44 -06:00
• 623da99959 bump version to 0.3.2 levita_a 2026-08-16 01:11:00 +02:00
• f8cc9bd7d0 Merge pull request #93 from cdtools-developers/bugfix/dataset_inspect_gpu Abe Levitan 2026-08-15 16:58:55 -06:00
• d740e0484e Add test coverage for dataset.inspect on GPU and fix the relevant bug levita_a 2026-08-04 02:24:11 +02:00
• b3c452f16f Merge pull request #91 from cdtools-developers/alternate_lr_proposal sheng_p1 2026-07-24 14:20:03 +02:00
• 289182f3f3 Update the documentation to include the example for adjusting learning rates per-parameter levita_a 2026-07-23 15:05:23 +02:00
• 3252a0dd8f Update SGD to allow per-parameter learning rates and add test coverage levita_a 2026-07-23 15:00:33 +02:00
• f6e0654445 Update model.Adam_optimize() levita_a 2026-07-23 14:18:24 +02:00
• a6dca51e3e First working version levita_a 2026-07-23 14:11:03 +02:00
• d0122b1161 adjust lr sheng_p1 2026-07-23 11:54:14 +02:00
• 8cf217f5d8 Add feature adjust learning rate sheng_p1 2026-07-23 11:50:01 +02:00
• 3e63ca2bcd Merge pull request #87 from cdtools-developers/fix_plotting_memory_leak Abe Levitan 2026-07-23 09:36:59 +02:00
• f499f5460b Merge pull request #88 from cdtools-developers/move_to_rtd Abe Levitan 2026-07-23 09:29:41 +02:00
• ebe4e79b20 Remove the custom docs build callout Abe Levitan 2026-07-23 09:11:56 +02:00
• f16624ecd6 Redirect the old GitHub Pages docs to Read the Docs gh-pages allevitan 2026-07-23 09:04:28 +02:00
• 310f78e362 Update the docs to point to readthedocs allevitan 2026-07-23 09:03:41 +02:00
• d5f898a3fd Fix a memory leak in the plotting which was causing issues over long reconstructions levita_a 2026-07-22 10:54:42 +02:00
• 49cafdb177 Merge pull request #86 from cdtools-developers/fix_near_field_pr Abe Levitan 2026-07-15 13:11:59 +02:00
• 211f0ac533 Apply a fix to the subpixel shifting for near-field ptycho to enable good position refinement levita_a 2026-07-11 07:14:48 +02:00
• a00085ba0a Merge pull request #82 from cdtools-developers/bump032dev1 Abe Levitan 2026-06-18 09:33:06 +02:00
• f94ca02b20 bump the dev version to help referencing the latest batch of changes allevitan 2026-06-18 09:26:58 +02:00
• 6faade0ac1 Merge pull request #77 from cdtools-developers/savenload Abe Levitan 2026-06-17 15:23:30 +02:00
• 57a0c34229 Merge pull request #81 from cdtools-developers/fix_oversampling_pix_size Abe Levitan 2026-06-17 15:22:48 +02:00
• 30da2ceeda Merge branch 'fix_oversampling_pix_size' into savenload allevitan 2026-06-17 00:56:48 +02:00
• 5caad890b8 Fix a high priority issue with the probe pixel size when probe_fourier_crop and oversampling are both used allevitan 2026-06-17 00:56:13 +02:00
• 8bb70748da Add the new save and load style to all other models except for Multislice2DPtycho, which is depricated anyway allevitan 2026-06-16 17:15:57 +02:00
• 6af72e1ce0 Update the docs to include the new example for loading and viewing a ptychography reconstruction allevitan 2026-06-16 16:13:51 +02:00
• 4d360f1361 Update all referencs in the examples documentation to follow the new pattern allevitan 2026-06-16 16:08:17 +02:00
• dd31c39dc4 Add info on loading datasets to the tutorial allevitan 2026-06-16 16:03:09 +02:00
• ed268a2c9c Update the saved gold ball ptycho treconstruction so it works with the new saving and loading levita_a 2026-06-16 15:48:14 +02:00
• 4eb3a9879c Make the loading code for fancyptycho a bit more robust allevitan 2026-06-16 15:26:06 +02:00
• 45949534f8 Remove the datset arg from all remaining examples of model.inspect() in the example code allevitan 2026-06-16 14:24:18 +02:00
• 8ced842a58 Merge in master allevitan 2026-06-16 14:19:17 +02:00
• b6c96557a0 Fix the object display and also update the interactions so that multi-mode objects work as intended fix_multi_object levita_a 2026-04-28 14:36:46 +02:00
• 29f0036248 Merge pull request #79 from cdtools-developers/bugfix/saving_loss_metrics Abe Levitan 2026-04-20 16:06:44 +02:00
• a516f418b9 Fix a high priority bug where reconstructions will crash upon saving, and add test coverage to prevent a repeat levita_a 2026-04-20 15:40:55 +02:00
• 65a75b5c7e Merge pull request #70 from cdtools-developers/newpoisson Abe Levitan 2026-04-17 15:12:03 +02:00
• 83b1ed5d27 Add a script to demonstrate loading from a saved reconstruction and add the obj_view_crop and units arguments back levita_a 2026-04-13 17:29:10 +02:00
• b9dcb03a93 Remove the need to use dataset for model.inspect() and model.save_results(), and update the examples accordingly. Docs and ipython notebooks not yet updated allevitan 2026-04-13 17:10:58 +02:00
• 6aa5df081b Add from_results_dict / from_results_h5 model loading from saved h5 files allevitanandClaude Sonnet 4.6 2026-04-13 15:47:07 +02:00
• fcd0b31b2c Fix a bug with the mask implementation for the normalizers conflicting with SimplePtycho, and update the thresholds to accomodate the new normalization with masks and for intensity_MSE levita_a 2026-04-13 15:44:52 +02:00
• d8fade9f32 Update the amplitude MSE and intensity MSE loss to act equivalently - currently, the intensity MSE loss was by default a mean, but amplitude was by default a sum. Both functions now have a flag, use_sum=False, which is False by default. This changes the default behavior of amplitude_mse. All models, including the tutorial version of simple_ptycho, are updated accordingly and test coverage was added. allevitan 2026-04-13 14:34:05 +02:00
• 3c15b19ba7 Find and fix a bug where the normalization code didn't properly include masks levita_a 2026-04-10 16:22:58 +02:00
• 3d10f36739 Fix a bug where the normalizers stopped the loss history from being saved as a numpy scalar, and added test coverage levita_a 2026-04-05 22:23:23 +02:00
• 388d1669f3 Final checks to ensure all tests pass with the new scaling levita_a 2026-04-05 21:52:14 +02:00
• 8ee8bf9237 Fix bug where fancyptycho test was not being run on GPU levita_a 2026-04-03 18:59:09 +02:00
• b6553fd522 Update the example near field ptycho code to use Poisson NLL levita_a 2026-03-19 18:35:57 +01:00
• 3ccdc24d3f Restructure loss coverage in reconstruction tests allevitanandClaude Sonnet 4.6 2026-03-19 17:53:10 +01:00
• 178e9a4e4e Add loss function coverage to slow reconstruction tests allevitanandClaude Sonnet 4.6 2026-03-19 17:40:07 +01:00
• d644782e94 Update poisson_nll test to match sum-based implementation allevitanandClaude Sonnet 4.6 2026-03-19 17:24:31 +01:00
• fd17ae30ba Update tutorial to use loss instance attribute pattern allevitanandClaude Sonnet 4.6 2026-03-19 17:14:08 +01:00
• 8c380a34a6 Add intensity_mse loss option to all models allevitanandClaude Sonnet 4.6 2026-03-19 17:07:45 +01:00
• d2c09acd44 Get all tests passing by updating the loss thresholds for the new normalizations, and add the new normalization to all models levita_a 2026-03-19 16:49:57 +01:00
• 023ab318ee Added some better documentation to the loss functions allevitan 2026-03-19 13:22:02 +01:00
• 4dbcffd67b Attempted to update the normalizations for the loss functions in a way which allows for a nice normalization of the Poisson NLL. The slow tests will now likely fail allevitan 2026-03-19 11:15:00 +01:00
• 3f028e2fbf Merge pull request #72 from cdtools-developers/feature/betterplots Abe Levitan 2026-04-03 18:23:41 +02:00
• 06105d38c7 Merge pull request #76 from cdtools-developers/v0.3.2.dev Abe Levitan 2026-04-03 18:22:19 +02:00
• 3b6e73b48c Start on 0.3.2.dev levita_a 2026-04-03 18:20:53 +02:00
• a87e3415d2 Responding to self-review comments allevitan 2026-04-03 17:54:59 +02:00
• 40f829b430 Merge pull request #71 from cdtools-developers/bugfix/intensity_loading Abe Levitan 2026-04-03 16:24:16 +02:00
• d7d5ed8401 Merge pull request #73 from cdtools-developers/v0.3.1 v0.3.1 Abe Levitan 2026-04-03 15:43:45 +02:00
• 548358771c Update docs for v0.3.0 so that they say the correct version v0.3.0docs allevitan 2026-04-03 15:37:10 +02:00
• 48a9a7f8ac Merge pull request #75 from cdtools-developers/readthedocs Abe Levitan 2026-04-03 15:29:16 +02:00
• 05bdee3861 Update the docs so it doesn't always think it's v0.2.0 allevitan 2026-04-03 15:24:50 +02:00
• 31818caabd add .readthedocs.yaml allevitan 2026-04-03 14:57:44 +02:00
• e84dc9f76e Merge pull request #74 from cdtools-developers/readthedocs Abe Levitan 2026-04-03 14:32:24 +02:00
• 7de8448319 Add .readthedocs.yaml for ReadTheDocs hosting allevitanandClaude Sonnet 4.6 2026-04-03 14:28:01 +02:00
• 4030218fa4 Change version to 0.3.1 allevitan 2026-03-26 15:11:55 +01:00
• 0bd8df498c Updated the documentation to reflect the changes to the plotting system allevitan 2026-03-24 21:39:04 +01:00
• 4172a9a11a A few small changes to revert unimportant edits and fix linting issues allevitan 2026-03-24 19:30:14 +01:00
• f55b35f0dd Stop stopping at each plot to show it levita_a 2026-03-24 16:56:41 +01:00
• 603486e824 Change the default colormap for exponentiated objects to match that for un-exponentiated objects, and also update test_fancy_ptycho to show all the plots (not just plot level 2) allevitan 2026-03-24 16:55:56 +01:00
• ad2b09f2f0 Update the tests to work better when checking the model plotting, and make sure to cover panel_plot_mode=False allevitan 2026-03-24 16:19:26 +01:00
• 29e9fddd72 Add test coverage for plot_translations, plot_nanomap, and plot_nanomap_with_images allevitanandClaude Sonnet 4.6 2026-03-24 16:01:45 +01:00
• 25c7b66c7c Do a final review of all the examples to ensure they work and are well structured allevitan 2026-03-24 11:10:23 +01:00
• 5c5c0be7c6 Reformat plotting function signatures to one-parameter-per-line style allevitanandClaude Sonnet 4.6 2026-03-24 11:00:43 +01:00
• 4201b41573 Made more adjustments to the plotting system to avoid using constained_layout, which was causing hangups during live plotting and didn't look as nice levita_a 2026-03-24 09:13:51 +01:00
• f979388280 Fix an annoying warning coming from double-setting the figsize levita_a 2026-03-21 21:42:16 +01:00
• 29656fd78e Improve the colorized plotting further, and add a colorbar which will be useful for publishing figures now that it's not just a simple hsv lookup. Also fix a bug with nonresponsive windows when all model plots are closed, but the dataset plots are still showing. allevitan 2026-03-21 21:27:16 +01:00
• f04ac9f0ec Make the colorized plot look nicer, with a more perceptually uniform mapping and a colorbar for accurate reading of phases allevitan 2026-03-21 17:35:14 +01:00
• a4a38530d1 Update the plot_image functions to show sliders allevitan 2026-03-21 14:57:16 +01:00
• f8ff525722 Add example patterns for jupyter notebooks allevitan 2026-03-21 08:41:18 +01:00
• dafb204aa0 Fix a bug where closed windows wouldn't reopen at the original size levita_a 2026-03-20 20:18:32 +01:00
• bef907c032 Added a minimum plotting interval to model.inspect(dataset) to make it easier to not plot so much without manual intervention allevitan 2026-03-20 20:01:40 +01:00
• f35141dcc8 Check that all the models work (all but Multislice2DPtycho, which was already broken, and make necessary tweaks levita_a 2026-03-20 19:39:47 +01:00
• 91db5b3c64 Update remaining models to new plot registration system allevitan 2026-03-20 19:01:22 +01:00
• e7f943e254 Made a few more updates to some example scripts, to show the panel plot mode allevitan 2026-03-20 17:35:25 +01:00
• f4260837bc Add title option to plot_image and wrappers; misc fixes allevitanandClaude Sonnet 4.6 2026-03-20 17:20:52 +01:00
• dd744a00a4 Improve plotting infrastructure and fix various bugs allevitanandClaude Sonnet 4.6 2026-03-20 15:33:49 +01:00
• 44fe36d24f Kill a bunch of bugs and make the flow more sensible by hand levita_a 2026-03-20 11:09:13 +01:00
• f3581b88db A first prototype from claude to test on Ra allevitan 2026-03-20 09:47:38 +01:00
• 4c89b3e46b Fix the bug with loading from datasets with intensity info when OPRP is on and add test coverage allevitan 2026-03-19 22:45:57 +01:00
• 9795f80718 Merge remote-tracking branch 'origin/master' into multigpu multigpu yoshikisd 2026-02-21 16:31:32 -08:00
• ca3c48e83d Merge pull request #67 from cdtools-developers/new_high_NA_intensity Dayne Yoshiki Sasaki 2026-02-11 09:41:05 -08:00
• 1dd116d277 Add the additional factor of R^2 levita_a 2026-02-06 13:27:10 +01:00
• e56f3c959f Merge pull request #31 from cdtools-developers/near_field_ptycho Dayne Yoshiki Sasaki 2026-02-10 09:52:52 -08:00
• e52c6e38aa Remove the spurious 'probe_shape' parameter levita_a 2026-02-10 11:46:14 +01:00
• 1d57005b33 Add the example data levita_a 2026-02-06 13:28:00 +01:00