50 Commits

Include renames

Author	SHA1	Message	Date
allevitan	25224d4d44	deal with the string_ related issues	2024-10-13 13:08:17 -04:00
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
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
Abe Levitan	a260168d9d	Honestly I don't know, I must have forgotten to commit something	2023-01-10 16:30:35 -08:00
abe	e13b519e22	some horrible state but I need to stop developing on perlmutter	2022-10-17 16:32:59 -07:00
abe	cb954a6067	Fix the annoying warning printing from interactions and get a minimum usable script going for simpleptycho and distributeddataparallel	2022-10-16 17:06:44 -07:00
Abe Levitan	1a34aaef60	Start making changes to enable multi-GPU, beginning with simple_ptycho	2022-10-16 12:01:55 -07:00
Abe Levitan	978c9d3206	Add an option to simulate finite pixel sizes	2022-09-29 14:14:43 -07:00
Abe Levitan	036fa8ea2c	remove dependency on fftpack completely	2022-08-19 10:02:11 -07:00
Abe Levitan	b8b508ce2c	remove a dependency on scipy fftpack	2022-08-19 09:30:41 -07:00
Abe Levitan	858d8f3b2a	Make edits to the docs to handle the lowercaseness of cdtools now	2022-06-08 13:30:49 -07:00
Abe Levitan	672096085b	renamed to lowercase	2022-06-08 13:13:13 -07:00
Abe Levitan	b8500bd5a8	renaming	2022-06-08 13:12:50 -07:00
Abe Levitan	883ac0175a	Changed module name no lowercase because that's really how it should be	2022-06-08 12:52:33 -07:00
Abe Levitan	442fa2c71f	move to a src directory layout	2022-06-08 12:09:03 -07:00