Commit Graph

Select branches

Hide Pull Requests

FRC

check_analysis_tools

fix_multi_object

gh-pages

high_NA

holo-reconstructions

master

multigpu

multilayer_reflection

#1

#12

#13

#16

#17

#18

#19

#2

#21

#22

#24

#25

#26

#27

#28

#29

#3

#30

#31

#32

#34

#34

#35

#36

#39

#4

#40

#41

#43

#44

#45

#45

#46

#46

#47

#49

#5

#52

#53

#54

#55

#55

#57

#58

#58

#59

#6

#61

#62

#63

#66

#67

#7

#70

#71

#72

#73

#74

#75

#76

#77

#79

#80

#80

#81

#82

#86

#87

#88

#89

#90

#91

#93

#94

#95

v0.3.0

v0.3.0docs

v0.3.0pypi

v0.3.0pypi1

v0.3.1

v0.3.2

Mono Color

• 65e4882fdd Merge remote-tracking branch 'origin/master' into near_field_ptycho levita_a 2026-01-14 17:09:17 +01:00
• a97e4cdf39 Add licensed near-field ptycho data to enable testing levita_a 2026-01-14 17:01:11 +01:00
• 98d2acf032 Merge pull request #66 from cdtools-developers/bugfix/surface_normal_strip Abe Levitan 2025-12-19 14:55:59 +01:00
• e059c18402 Make the timeout default 30 seconds and enforce timeout in units of seconds yoshikisd 2025-12-18 21:46:01 +00:00
• 69a94f0fe8 Bragg2DPtycho scattering_mode string values only inspected if scattering_mode is a string yoshikisd 2025-12-18 18:15:19 +00:00
• 83ebbf8de4 Merge branch 'master' into FRC FRC gnzng 2025-12-12 16:39:50 -08:00
• 1e5d1d777b merge master into branch gnzng 2025-12-12 16:39:17 -08:00
• 9792b141ef Merge remote-tracking branch 'origin/master' into multigpu yoshikisd 2025-12-12 00:34:51 +00:00
• ebe5b54bea Merge remote-tracking branch 'origin/master' into multigpu yoshikisd 2025-12-12 00:33:59 +00:00
• 126bfaa92c Merge pull request #62 from cdtools-developers/fix-divzero-error Dayne Yoshiki Sasaki 2025-12-08 10:08:13 -08:00
• 9402939e40 Merge pull request #63 from cdtools-developers/surface_normal Abe Levitan 2025-12-04 09:08:46 +01:00
• 8f3ad59c6d Suggested changes: Make surface_normal work with anything castable to an array with np.asarray, change the check for length-3 to cover all cases, and add a check to explicitly fail if the scattering_mode argument is improperly set, instead of silently falling back to default levita_a 2025-12-02 15:27:20 +01:00
• 7286bad264 Added heirarchy of surface_normal definition in Bragg2DPtycho from_dataset yoshikisd 2025-12-01 22:20:28 +00:00
• bac95b7636 Make it easier to change surface normal in Bragg2DPtycho.from_dataset yoshikisd 2025-11-20 21:42:19 +00:00
• c78b528930 Change how the dataset mask is calculated, so that it only raises a divide by zero error if unmasked pixels have an issue. Add an option to ptycho_2d_dataset to plot the mask levita_a 2025-11-19 10:46:01 +01:00
• ab7048e375 merge updates to master levita_a 2025-11-19 10:29:33 +01:00
• 4a94ea13c9 Merge pull request #61 from gnzng/customdocs Dayne Yoshiki Sasaki 2025-11-18 13:12:38 -08:00
• 444b56b829 docs: update installation instructions for dependencies to include pip gnzng 2025-11-16 11:21:36 -06:00
• 4d18171e59 docs: add instructions for building custom documentation gnzng 2025-11-16 11:00:33 -06:00
• 36055d04be Merge pull request #59 from gnzng/quickfixdocs Dayne Yoshiki Sasaki 2025-11-12 14:54:57 -08:00
• f0f44e3c83 fix: documentation build step to use Sphinx directly gnzng 2025-11-12 11:54:17 -06:00
• 562bcab171 Merge pull request #57 from gnzng/pyprojecttoml Abe Levitan 2025-11-12 16:41:21 +01:00
• 3f46caf757 update authors list in pyproject.toml and move further doc link gnzng 2025-11-12 09:04:53 -06:00
• 3c9e9eb1c7 adding pure pip install pipeline to CI gnzng 2025-11-12 08:59:37 -06:00
• 11ed3df35e ending python 3.8 support, adding python 3.14 to automatic test gnzng 2025-11-11 14:33:55 -06:00
• 5a3e154e8d add Python 3.13 to the CI workflow matrix gnzng 2025-11-10 12:50:59 -08:00
• e94499a6a4 fix: update pytest command to use 'uv' for consistency in CI workflow gnzng 2025-11-10 12:42:32 -08:00
• 18c794b5db fix: add virtual environment creation step in CI github workflows gnzng 2025-11-10 12:37:44 -08:00
• 728cf9d590 update readme and installation docs gnzng 2025-11-10 12:23:25 -08:00
• be28903be7 refactor: CI installation process to use 'uv' for faster dependency management gnzng 2025-11-10 12:23:09 -08:00
• e5996a49fd Merge branch 'master' into multigpu yoshikisd 2025-11-09 04:19:51 +00:00
• 32e92562eb Added multi-GPU pytests yoshikisd 2025-11-09 03:53:42 +00:00
• a8d2bfa07f Simplified the logic in MASTER_ADDR and MASTER_PORT definition in multigpu.setup yoshikisd 2025-11-09 03:37:25 +00:00
• cd584fca81 multigpu.setup now recognizes MASTER_ADDR and MASTER_PORT when setting up spawn-based jobs yoshikisd 2025-11-09 03:34:08 +00:00
• cad3d9cc33 Fixed linting issues on multigpu yoshikisd 2025-11-09 00:32:50 +00:00
• 1a3d0cd011 Modified runtime error message in multigpu.setup yoshikisd 2025-11-09 00:28:54 +00:00
• 842bb49a01 Added example script for running a multi-GPU speed test yoshikisd 2025-11-09 00:19:18 +00:00
• 6f15c362f3 Added example scripts for running multi-GPU jobs with spawn or torchrun yoshikisd 2025-11-09 00:19:00 +00:00
• b784620515 Multi-GPU compatibility added for CDIModel yoshikisd 2025-11-08 23:36:27 +00:00
• 0f1f990e10 Added a check for init_method in multigpu.setup yoshikisd 2025-11-08 23:33:05 +00:00
• b0604d4595 Prevent dataset from plotting/saving outside of Rank 0 yoshikisd 2025-11-08 06:46:23 +00:00
• 8d8da151d7 Multi-GPU compatability added for base Reconstructor and AdamReconstructor yoshikisd 2025-11-08 06:41:48 +00:00
• 10229e4e28 Renamed cdtools.tools.distributed to cdtools.tools.multigpu. Also added several functions to multigpu yoshikisd 2025-11-08 06:35:08 +00:00
• 5d43b05822 Merge pull request #54 from gnzng/versiontests Abe Levitan 2025-10-31 11:47:25 +01:00
• f79836bfc2 Add tests for version existence and semantic format gnzng 2025-10-29 21:40:12 -07:00
• 14e4c99ec7 Merge pull request #53 from cdtools-developers/version_source_of_truth Damian Guenzing 2025-10-29 21:34:33 -07:00
• 008fef6244 Add cdtools.__version__ and set it up so that there is a single source of truth for the version number. Still not done with setuptools_scm, but one step at a time) levita_a 2025-10-28 16:06:21 +01:00
• 1fa9a75806 Merge pull request #52 from cdtools-developers/bugfix/masking Dayne Yoshiki Sasaki 2025-10-24 07:14:41 -07:00
• e38ebd7372 Fix a high priority bug with the masking system which was introduced in the switch to reconstructors classes levita_a 2025-10-24 15:11:46 +02:00
• e4a713cdf1 Fix frequency calculation in line_based_frc for 2D case gnzng 2025-10-21 20:15:40 -07:00
• fded573ef8 Added additional functions to distributed yoshikisd 2025-10-20 01:07:32 +00:00
• 0268f5bc97 Created the distributed module yoshikisd 2025-10-19 21:05:16 +00:00
• fbfbf4fa87 Merge pull request #49 from cdtools-developers/show_original_pos Dayne Yoshiki Sasaki 2025-10-19 12:05:48 -07:00
• 86e85e1853 Fix a bug where the x-axis was double flipped levita_a 2025-10-19 13:08:16 +02:00
• 3eec9c0cec Add the original positions to the fancy_ptycho position plotting levita_a 2025-10-19 12:45:19 +02:00
• d9c4ebfdf3 Merge pull request #47 from yoshikisd/refactor/reconstructors Abe Levitan 2025-10-17 20:15:43 -03:00
• 6443b16f5c Merge pull request #1 from cdtools-developers/refactor/reconstructors Dayne Yoshiki Sasaki 2025-10-17 15:58:47 -07:00
• 7d39015719 response to dayne's review levita_a 2025-10-17 23:41:08 +02:00
• 9d633074d8 Apply suggestions from code review Abe LevitanandDayne Yoshiki Sasaki 2025-10-17 18:37:38 -03:00
• f022b5e2c4 Get the tests passing again after the change of the optimization functions in the model classes levita_a 2025-10-16 15:58:28 +02:00
• 8328b852d3 Update the docs to include the reconstructors class and discuss their use in the examples levita_a 2025-10-16 14:43:04 +02:00
• 3c8de5dc19 Update the example codes levita_a 2025-10-16 14:16:12 +02:00
• aa684f27eb Change the pattern for Reconstructor so that the optimizer is defined at object creation, and move the dataloader creation logic to the base optimize() function as it was reused in all subclasses levita_a 2025-10-13 19:20:42 +02:00
• a089dc3b72 Switch to a simpler pattern for the CDIModel.<algorithm>_optimize functions that preserves the old behavior when the old pattern is used levita_a 2025-10-13 14:26:07 +02:00
• 766a7d1adf Move to better supported strategy for avoiding circular imports levita_a 2025-10-13 14:20:38 +02:00
• 82ce845385 Changed the names of the reconstructors and updated the old optimizer class documentation yoshikisd 2025-08-04 16:51:24 +00:00
• 1e7fe2eb5f Added pytests for reconstructors yoshikisd 2025-08-01 22:31:40 +00:00
• 404d03bbd3 Rebased CDIModel to use Reconstructors for reconstructions. yoshikisd 2025-08-01 21:51:52 +00:00
• 76bc2fa75b Got rid of world_size attribute yoshikisd 2025-08-01 21:50:35 +00:00
• 0785eae552 Created Reconstructors class to replace optimization methods in CDIModel yoshikisd 2025-08-01 21:37:05 +00:00
• 368a2c616c remove alignment and assume aligned images as input gnzng 2025-07-29 16:35:52 -07:00
• 4c021148f0 Enhance line_based_frc function to align images using hann window and subpixel shifting gnzng 2025-07-29 16:10:45 -07:00
• 3a71d742d2 Enhance split method in Ptycho2DDataset to allow non-random dataset splitting gnzng 2025-07-29 14:28:07 -07:00
• 2a00ba9c21 Fix the initialization issue with nonuniform intensities high_NA levita_a 2025-07-21 17:00:43 +02:00
• 22a28f4043 First pass of high NA ptycho and RPI levita_a 2025-07-21 11:26:59 +02:00
• 4e19e1c108 reduce code redundancy gnzng 2025-07-15 14:58:13 -07:00
• 505466b067 add to line_based_frc function to support standard 2D FRC computation for comparison gnzng 2025-07-15 14:43:58 -07:00
• 9264228c89 Merge branch 'master' into FRC Damian Guenzing 2025-07-14 11:58:07 -07:00
• 25ca3a9317 Merge pull request #44 from cdtools-developers/flake8 Abe Levitan 2025-07-14 11:55:34 +02:00
• 027831d3a8 Add citation for FRC computation in line_based_frc function gnzng 2025-07-10 14:46:29 -07:00
• e0cf3ea2e1 Enhance line_based_frc function with detailed docstring and input validation checks gnzng 2025-07-10 14:33:47 -07:00
• 6de3491928 Add line-based FRC function and corresponding tests, and example file gnzng 2025-07-10 14:24:24 -07:00
• b6c4dbac4a modification remove amplitude exponent, there was dimension mismatch check_analysis_tools maelclemence 2025-07-08 17:24:33 +02:00
• b47216312d adding a different window for FRC than for phase ramp maelclemence 2025-07-08 16:49:22 +02:00
• fc5a76ad61 linting test_plotting.py and test_propagators.py gnzng 2025-07-07 15:13:11 -07:00
• 65e83753a8 linting test_interactions.py, test_losses.py, and test_measurements.py gnzng 2025-07-07 14:58:11 -07:00
• 88df4c0794 linting test_image_processing.py and test_initializers.py gnzng 2025-07-07 14:40:17 -07:00
• b00f39e1fe linting test_analysis.py and test_data.py gnzng 2025-07-07 14:28:23 -07:00
• 58246966f4 Add W503 to flake8 ignore list, line break before binary operator gnzng 2025-07-07 14:21:17 -07:00
• 96d8b10792 linting test_fancy_ptycho.py gnzng 2025-07-07 14:11:50 -07:00
• ecb8ee4864 linting test_simple_ptycho.py gnzng 2025-07-07 13:59:35 -07:00
• 745f7b73e6 Fix background calculation in test_Ptycho2DDataset_downsample gnzng 2025-07-07 13:55:54 -07:00
• f463144347 linting test_datasets.py gnzng 2025-07-07 13:49:46 -07:00
• 4d812db68a restructured conftest.py imports gnzng 2025-07-07 13:39:44 -07:00
• 38be347a18 lint conftest.py gnzng 2025-07-07 13:38:52 -07:00
• 93f5d1969d Add .flake8 configuration to ignore line length errors (E501) gnzng 2025-07-07 12:53:06 -07:00
• 603d47417b Merge pull request #43 from yoshikisd/bugfix/pytest_reconstruct Damian Guenzing 2025-07-07 11:55:38 -07:00
• 36de44565b Set fixed RNG seed for reconstruction pytests yoshikisd 2025-07-07 15:16:12 +00:00
• 41e6f68a19 Small modifications of phase ramp correciton and standarize set maelclemence 2025-07-07 15:04:57 +02:00
• 3516405954 Merge pull request #41 from cdtools-developers/pipdocs Damian Guenzing 2025-07-02 10:00:50 -07:00