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Author	SHA1	Message	Date
gnzng	aff8dd43d6	add tv_loss to __all__	2024-11-05 16:54:37 -08:00
gnzng	af626b37f6	Introduce HoloDataset class to include loading data from .h5 and .tif files for holography reconstructions	2024-10-30 11:17:07 -07:00
gnzng	155dda9060	Refactor amplitude_mse function to include normalization option ... The amplitude_mse function in losses.py has been modified to include a new optional parameter, normalization. When set to True, the loss is normalized by the sum of the simulated intensities. This change improves the flexibility and usability of the function. Add total_variation_loss for images	2024-10-25 17:08:13 -07:00
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	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	2f16c43a11	Add an MIT license to the repo to prep for open release	2024-10-10 17:26:28 +02:00
allevitan	7fba211b5d	Merge pull request #1 from cdtools-developers/signal_estimate ... Add the tools to quickly estimate the signal level from raw data	2024-09-20 13:44:51 +02:00
levita_a	30593c9c5c	Get the mean pattern to show up by default with dataset.inspect()	2024-09-20 13:42:12 +02:00
levita_a	6b2358df36	Add a fourier translation to fancy ptycho	2024-09-19 18:09:37 +02:00
levita_a	ad9420c3f2	random things	2024-09-17 14:46:56 +02:00
levita_a	1052d5bcb6	Move documentation to the new organization	2024-09-02 14:23:59 +02:00
allevitan	3b6b0534af	Merge pull request #1 from allevitan/organization ... Organization	2024-09-02 11:20:37 +02:00
Abe Levitan	13a2ba86df	Make big changes to docs to update the tutorial section, and also to finally autoload the documentation of the models and datasets	2024-09-01 13:04:28 +02:00
levita_a	30a989fe3e	Add first tests for models, and replace t.tensor with t.as_tensor in models	2024-08-30 16:10:26 +02:00
levita_a	21b618d2e0	Remove the vestigges of the polarization-dependent code. It belongs in it's own repo	2024-08-30 14:13:36 +02:00
levita_a	47aa3c41e2	Remove a bunch of models that really didn't belong in the main repo, and fix an issue with the RPI interaction conventions	2024-08-30 11:53:20 +02:00
levita_a	b3b19554d0	Add a phase only constraint to RPI and fancy_ptycho, misc small changes	2024-08-30 11:29:51 +02:00
levita_a	35f140d348	Fully replace orthogonalize_probes and update most models	2024-07-25 17:35:48 +02:00
levita_a	943dde13e6	Fix a remaining bug in orthogonalize_probes and also fix some lingering issues with the liveplotting for unified mode fancy ptycho	2024-07-25 16:32:10 +02:00
levita_a	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	2024-07-25 15:46:53 +02:00
levita_a	a02a0466ae	fix a stupid bug I introduced at the last minute in the last commit	2024-07-02 10:58:17 +02:00
levita_a	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	2024-07-01 17:16:07 +02:00
levita_a	ee0d483f26	excise some old code from the RPI model that was making it fail, re: the old way of cropping out a detector slice	2024-06-26 11:09:43 +02:00
levita_a	29d14c9537	Get a basic version of checkpointing working	2024-04-18 14:22:14 +02:00
levita_a	edc94ec09b	Introducing new multislice model	2024-04-18 09:28:03 +02:00
levita_a	7b2509cfe1	remove useless old examples, and update the examples and docs to be useful for the current version	2024-02-26 17:56:19 +01:00
levita_a	46b00807c8	Fix a bug that I introduced in fancy_ptycho's oversampling, and also update some example scripts	2024-02-26 13:44:46 +01:00
levita_a	d7c7e8f396	start getting the docs back up to date	2024-02-23 16:54:48 +01:00
levita_a	2e6db5517d	get the projected views for bragg_2d_Ptycho working	2024-02-22 15:57:35 +01:00
levita_a	30f9b142b6	Fix up bragg_2d_ptycho a bit and add model.save_on_exception	2024-02-22 14:41:07 +01:00
Abe Levitan	5925ee74ab	Checked and fixed the tests, got them all running	2024-02-12 14:55:26 -05:00
Abe Levitan	1502d567bf	honestly, not sure	2024-02-12 09:49:26 -05:00
Abe Levitan	dd30f58d2d	Start to make the lab bragg ptycho code sane, and fix the bug with probe bases when using probe fourier crop	2024-02-11 17:32:41 -05:00
Abe Levitan	44a6fac37a	Add a tool to split ptycho datasets and a context manager to save .mat files, and slightly adjust the save format	2024-02-11 10:29:07 -05:00
Abraham Levitan	e48970f7a9	Add an option for probe fourier crop to Bragg 2D Ptycho	2024-02-10 13:42:22 -05:00
levita_a	d0a0d12521	Add a normalize reconstruction set function	2024-01-04 16:50:10 +01:00
levita_a	7c269cff47	remove an errant print statement	2023-12-04 15:35:05 +01:00
levita_a	f3b6ac9056	fix the numerical stability issue in the angular spectrum propagator code, but remove the ability to choose whether or not to include an explicit z dependence	2023-12-04 15:29:40 +01:00
levita_a	a9e0157707	Get tests to past and removeopt_for_fft	2023-12-01 15:58:18 +01:00
Abe Levitan	8ef3411604	Whoops I forgot some files in the last commit	2023-11-08 13:09:54 +01:00
Abe Levitan	1f44fdd57c	Some misc work toward the no analyzer jones matrix model (polarization swept)	2023-11-08 13:09:10 +01:00
Abe Levitan	e8023703a0	Start documenting the models, and change the default FOV on fancy_ptycho reconstruction inspections	2023-10-17 15:38:48 +02:00
Abe Levitan	88aedcc448	Update the poisson loss function to use xlogy and start work on the poisson + detector loss function	2023-08-15 10:47:50 -07:00
Abe Levitan	a5699ed508	fix the oversampling + finite pixel issue	2023-03-15 12:05:54 -07:00
Abe Levitan	10cffb62c3	Add wavelength info to the data saved by fancy_ptycho	2023-02-16 17:26:56 -08:00
Abe Levitan	9f341fb4bd	update the requirements files and fix a bug that prevented install when not in developer mode	2023-01-13 11:59:07 -08:00