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9f1a5bcae9 . Anastasiia Kutakh 2021-08-02 13:46:36 -04:00
09d172c9a3 testing polarization Anastasiia Kutakh 2021-08-01 21:28:37 -04:00
709c3f398d . Anastasiia Kutakh 2021-07-31 21:33:14 -04:00
026f1c2b0b . Anastasiia Kutakh 2021-07-31 21:26:26 -04:00
070622a9e1 . Anastasiia Kutakh 2021-07-30 00:32:23 -04:00
0bfbc98922 . Anastasiia Kutakh 2021-07-29 14:03:57 -04:00
6924ce58fe changed polarization and polarized_fancy_ptycho interaction Anastasiia Kutakh 2021-07-29 02:59:37 -04:00
a4d70bc375 Update polarized_fancy_ptycho.py Abe Levitan 2021-07-28 17:14:41 -04:00
a3e9ebebf5 Some small notes in the code Abe Levitan 2021-07-28 17:05:55 -04:00
3a68fd35b2 Add the required import statements Abe Levitan 2021-07-28 15:38:33 -04:00
d067dcac9d not tested/debugged yet Anastasiia Kutakh 2021-07-28 07:04:22 -04:00
899317ae0f not tested/debugged yet Anastasiia Kutakh 2021-07-28 06:59:18 -04:00
530a7717ac . Anastasiia Kutakh 2021-07-28 00:40:15 -04:00
e7d7323e50 Added a polarization dependent ptychography dataset class so we can save and load data! Abe Levitan 2021-07-26 14:46:02 -04:00
a36c6c8893 Remove the SLM files, we should keep them somewhere else Abe Levitan 2021-07-06 14:58:40 -04:00
26b144d95a Merge branch 'complex_numbers' BBringing in complex numbers! Abe Levitan 2021-07-06 14:56:28 -04:00
3e72243a50 Update the docs a bit Abe Levitan 2021-07-06 14:55:29 -04:00
53cd966c33 Update the RPI model and clean up the examples section Abe Levitan 2021-07-06 13:58:00 -04:00
8ddcc7683f Start cleaning up the repo and tidying up the example scripts Abe Levitan 2021-06-28 11:14:41 -04:00
76e6d5efae get tests working Abe Levitan 2021-06-21 16:55:34 -04:00
8f58242efe Changed basic near field propagator to use the generalized function internally, and fixed band-limiting Abe Levitan 2021-06-18 18:06:05 -04:00
e4a521656d Changed how I implement the generalized propagator and (I believe) FIX the sign problems with propagation directiongit add --all! Abe Levitan 2021-06-18 17:41:38 -04:00
c2b8f2fe1b Bring all the tools to the point where they pass the tests Abe Levitan 2021-06-18 14:01:39 -04:00
a3765e9097 remove all reference to cmath, get code and tests to the point where they run at least. Abe Levitan 2021-06-17 16:47:24 -04:00
188a685503 Fix a bug in multislice where it doesn't work when prevent_alias is set to True Abe Levitan 2021-06-02 14:48:57 -04:00
2854a872ee Make a program to visualize the shot to shot fluctuations when using the unified mode model Abe Levitan 2021-04-08 16:28:24 -04:00
2774953c2a Fix a bug in the incoherent probe mode update Abe Levitan 2021-03-15 18:55:05 -04:00
f6f8084978 Added unified modes to multislice, added units to fancy_ptycho, and added more sane normalization option (for reconstructions) to unified mode models Abe Levitan 2021-03-11 17:01:55 -05:00
6b7a0701a6 Update plotting functions to deal better with images that have multiple layers Abe Levitan 2021-02-26 15:31:51 -05:00
cea860bdf9 Fix an issue with unified_mode_ptycho not working in model.compare, and fix colorbars for model.compare Abe Levitan 2021-02-05 12:30:29 -05:00
d664bf351b Remove the original, worse unified mode model, and update the plotting functions to handle stacks of images, very helpful for multislice and also multi-mode models Abe Levitan 2021-02-04 18:55:55 -05:00
fdca857046 make some tweaks to how the multislice works Abe Levitan 2021-01-30 09:22:15 -05:00
043751a8b6 Speed up the multislice model 5x, but probably break lots of other models doing it, so remember to clean upgit status Abe Levitan 2021-01-27 22:33:45 -05:00
0dec5aa9fd Intermediate state in optimization, improved the round interaction but not sinc yet Abe Levitan 2021-01-27 20:27:31 -05:00
e265c85d6b Touching in before I shred everything to improve efficiency Abe Levitan 2021-01-27 19:27:21 -05:00
3acd1ece3c Make it so it doesn't require a crazy amount of memory Abe Levitan 2021-01-26 22:46:15 -05:00
5fdfa969cd Add the SLM display scripts from Karo Abe Levitan 2021-01-25 21:11:37 -05:00
a536e3bdb4 Maybe last time it didn't actually commit? Abe Levitan 2021-01-25 13:38:38 -05:00
936b203aac Fix the issue with odd-sized probes & objs in RPI functions, still not fully tested Abe Levitan 2020-12-28 22:09:20 -05:00
32a8a8179d Fix an issue with the test for the poisson NLL function Abe Levitan 2020-12-28 21:45:01 -05:00
6b735a431f Clean up namespaces and also add a test of RPI with incoherent probes Abe Levitan 2020-12-28 21:32:18 -05:00
4be2af8609 Finally finally finally add an RPI model. Makes it soooo much easier... Abe Levitan 2020-12-22 14:12:51 -05:00
75011eaccf Make tweaks to the tilt correction to work with the grazing reflection data, add basic atom-modeling for electron ptychography, and update the multislice ptycho to include a bandlimit to avoid aliasing Abe Levitan 2020-12-21 12:22:04 -05:00
38345da454 Update S matrix ptychography and also update the S matrix interaction function to use a more interpretable definition of the S matrix Abe Levitan 2020-10-30 14:52:17 -04:00
aea0ff9bf8 Write a multislice and s_matrix ptychography program Abe Levitan 2020-10-28 13:55:04 -04:00
0d484c0ac3 Fix sign error in generalized near field and associated test Abe Levitan 2020-05-07 12:13:36 -04:00
31cc45da70 One more try to fix the off axis near field propagation Abe Levitan 2020-05-04 16:53:50 -04:00
9771634551 Implement test for separate propagation and offset vectors Abe Levitan 2020-04-29 20:11:03 -04:00
39cb345ccb update docs Abe Levitan 2020-04-29 17:56:48 -04:00
19f61ab946 Add option for propagation vector separate from offset vector Abe Levitan 2020-04-29 17:55:00 -04:00
a5b2337293 Further develop the 2D Bragg ptychography code and edit some tests to work with a newer version of h5py Abe Levitan 2020-04-29 13:50:13 -04:00
d586ed914e Debug and test the off-axis propagation code Abe Levitan 2020-04-24 14:16:44 -04:00
071eebd37b Finish first pass of off-axis propagation, still needs to be tested off-axis Abe Levitan 2020-04-23 20:37:13 -04:00
ad1a2e77b7 Update the exit_wave_geometry to handle paralellogram detectors Abe Levitan 2020-04-23 17:39:16 -04:00
0dc2145ee0 Merge branch 'master' of github.mit.edu:Scattering/CDTools Abe Levitan 2020-04-23 14:32:29 -04:00
fbbecbd04c First work on the off-axis propagator Abe Levitan 2020-04-23 14:32:19 -04:00
59f6d58ea6 Fix typo in tutorial Abraham Levitan 2020-04-07 10:08:27 -04:00
d8486306f7 Fix a bug with oversampling in the measurement functions Abe Levitan 2020-02-11 15:20:55 -05:00
5cac96ff24 Merge branch 'master' of github.mit.edu:Scattering/CDTools Abe Levitan 2020-02-11 15:00:48 -05:00
7cbc3f2c53 Add a TITAN STEM converter and add units to the inspect function for fancy_ptycho Abe Levitan 2020-02-11 15:00:42 -05:00
8d89a86445 Fixing strings to avoid invalid escape sequence warning David Rower 2020-02-03 12:00:56 -05:00
8d589eef86 Merge branch 'master' of github.mit.edu:Scattering/CDTools Abe Levitan 2020-01-25 19:01:11 -05:00
a1cca0dcea misc updates Abe Levitan 2020-01-25 19:01:03 -05:00
7a243842b9 Fixing wrong theta convention in converter; fixing simple_ptycho bug in dictionary syntax David Rower 2020-01-23 17:20:25 -05:00
d659f6cca1 Taking unecessary printing out of conversion function David Rower 2020-01-23 16:35:29 -05:00
7f93bdcfd3 Putting start_time in right format David Rower 2020-01-23 16:13:49 -05:00
486f58a86e Fixed special case in get_entry_info function, adding metadata to sample in converteR David Rower 2020-01-23 11:53:07 -05:00
2ad4a2a00c Merge branch 'master' of github.mit.edu:Scattering/CDTools David Rower 2020-01-23 10:54:17 -05:00
d4f9d5074c First data converter! David Rower 2020-01-23 10:54:03 -05:00
abdd0d6e1e Update docs so that they can produce a latex/pdf version as well Abraham Levitan 2019-12-16 12:40:41 -05:00
384ced5b00 Using $\mu instead of um for micrometers David Rower 2019-12-11 16:19:45 -05:00
3cf44cff9f using greek \mu instead of u for axis labels ;) David Rower 2019-12-09 19:14:08 -05:00
51eae81ee2 Fixed logical bug in get_detector_geometry, enforcing PEP 257 docstring convention of using periods David Rower 2019-12-09 13:50:36 -05:00
b5f78b47c7 add_detector now flexible for both CXI and CDTools basis conventions David Rower 2019-12-09 13:37:11 -05:00
0cf106e769 Merge branch 'master' of github.mit.edu:Scattering/CDTools David Rower 2019-12-03 15:32:22 -05:00
d330e1b84e Only adjusting colorbar when array is not a constant array (for consistency between shots), and added right/left keys for moving between shots David Rower 2019-12-03 15:32:16 -05:00
0b122b0aca Add files via upload Kiara Carloni 2019-10-21 21:38:33 +00:00
256142e2f6 Fixing typo in analysis function documentation David Rower 2019-10-10 11:53:12 -04:00
f78a39daf5 add the test for simple_ptycho_model' Abraham Levitan 2019-10-07 15:44:17 -04:00
e71c266fe4 Update the ptycho dataset with the new, more sensible, approach Abe Levitan 2019-10-05 09:30:26 -04:00
e987d40df8 Remove last of t.tensor usage from dataset loading Abe Levitan 2019-10-04 17:00:43 -04:00
120e23ef15 Write the model and dataset tutorials, update the dependencies, and various small bug fixes Abe Levitan 2019-10-04 16:53:22 -04:00
bc7caebdd9 Fix the damn dataset.inspect thing Abe Levitan 2019-10-03 17:49:10 -04:00
8197eed50e Fixed merging conflict - log scale in ptycho_2d_dataset.py David Rower 2019-10-03 15:25:27 -04:00
61f8bf733e Fixed a few bugs, 1) Title of relative displacement plot no longer dissapears, 2) slider now updates on click event, also added titles for colorbars. David Rower 2019-10-03 15:22:53 -04:00
69be77cc09 Update installation instructions for simplicity and also fix the tests to reflect new usage Abe Levitan 2019-10-02 15:56:48 -04:00
918cade834 Merge branch 'master' of github.mit.edu:Scattering/CDTools Abe Levitan 2019-10-02 13:27:41 -04:00
f58f3cc2c5 misc small changes Abe Levitan 2019-10-02 13:27:32 -04:00
6ff321eebc Typo in README David Rower 2019-09-24 17:46:03 -04:00
185fde27a0 More work on documentation Abe Levitan 2019-09-11 17:56:54 -04:00
40998908f1 refactor datasets, wrote more docs, added one more test dataset Abe Levitan 2019-09-09 14:16:42 -04:00
99d02f95cf Finish fleshing out the examples Abe Levitan 2019-09-04 18:23:34 -04:00
0377ea90be Update README to account for presence of docs Abe Levitan 2019-09-04 16:45:04 -04:00
5b521da557 Add the publishing script so we can publish the docs to github pages on the enterprise server Abe Levitan 2019-09-04 16:37:30 -04:00
e80bf05f25 Further improve docs layout and add unfinished ptycho models to repo Abe Levitan 2019-09-04 16:27:55 -04:00
de186592cb Update the docstrings on all the tools files and start laying out the docs for real Abe Levitan 2019-09-03 18:49:45 -04:00
1e3a98c599 Add and build tests for a Fourier Ring Correlation method Abe Levitan 2019-08-17 10:39:35 -04:00
d2c07bf1ac Add a tool to look at raw data Abe Levitan 2019-08-15 12:16:43 -04:00
f769806e68 Lots of small changes Abe Levitan 2019-08-15 11:14:20 -04:00
06ce14fac9 Fixed a small bug Abe Levitan 2019-07-01 15:27:57 -04:00

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