allevitan
91db5b3c64
Update remaining models to new plot registration system
2026-03-20 19:01:22 +01:00
allevitan
e7f943e254
Made a few more updates to some example scripts, to show the panel plot mode
2026-03-20 17:35:25 +01:00
allevitan and Claude Sonnet 4.6
f4260837bc
Add title option to plot_image and wrappers; misc fixes
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- Add title parameter to plot_image, plot_real, plot_imag, plot_amplitude,
plot_phase, and plot_colorized
- Various fixes to base.py and fancy_ptycho.py
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com >
2026-03-20 17:20:52 +01:00
allevitan and Claude Sonnet 4.6
dd744a00a4
Improve plotting infrastructure and fix various bugs
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- Switch panel plots to use subfigures with constrained_layout for better layout management
- Add plot_loss_history method to CDIModel base class
- Fix matplotlib compatibility for older versions (interactive backend detection)
- Make CUDA usage conditional in examples
- Add panel_plot_mode and plot_level params to FancyPtycho constructor
- Default plot_level filtering to 1 instead of 0
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com >
2026-03-20 15:33:49 +01:00
levita_a
44fe36d24f
Kill a bunch of bugs and make the flow more sensible by hand
2026-03-20 11:09:13 +01:00
allevitan
f3581b88db
A first prototype from claude to test on Ra
2026-03-20 09:47:38 +01:00
levita_a
1dd116d277
Add the additional factor of R^2
2026-02-11 11:06:29 +01:00
levita_a
e52c6e38aa
Remove the spurious 'probe_shape' parameter
2026-02-10 11:46:14 +01:00
levita_a
65e4882fdd
Merge remote-tracking branch 'origin/master' into near_field_ptycho
2026-01-14 17:09:17 +01:00
yoshikisd
69a94f0fe8
Bragg2DPtycho scattering_mode string values only inspected if scattering_mode is a string
2025-12-18 18:15:19 +00:00
Dayne Yoshiki Sasaki
126bfaa92c
Merge pull request #62 from cdtools-developers/fix-divzero-error
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Stop Ptycho2DDataset.inspec() from raising a divzero error in many situations
2025-12-08 10:08:13 -08:00
levita_a
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
2025-12-02 15:27:20 +01:00
yoshikisd
7286bad264
Added heirarchy of surface_normal definition in Bragg2DPtycho from_dataset
2025-12-01 22:20:28 +00:00
yoshikisd
bac95b7636
Make it easier to change surface normal in Bragg2DPtycho.from_dataset
2025-11-20 21:42:19 +00:00
levita_a
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
2025-11-19 10:46:01 +01:00
levita_a
ab7048e375
merge updates to master
2025-11-19 10:29:33 +01:00
levita_a
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)
2025-10-28 16:06:21 +01:00
levita_a
e38ebd7372
Fix a high priority bug with the masking system which was introduced in the switch to reconstructors classes
2025-10-24 15:11:46 +02:00
levita_a
86e85e1853
Fix a bug where the x-axis was double flipped
2025-10-19 13:08:16 +02:00
levita_a
3eec9c0cec
Add the original positions to the fancy_ptycho position plotting
2025-10-19 12:45:19 +02:00
Abe Levitan and Dayne Yoshiki Sasaki
9d633074d8
Apply suggestions from code review
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Co-authored-by: Dayne Yoshiki Sasaki <37006268+yoshikisd@users.noreply.github.com >
2025-10-17 18:37:38 -03:00
levita_a
8328b852d3
Update the docs to include the reconstructors class and discuss their use in the examples
2025-10-16 14:43:04 +02:00
levita_a
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
2025-10-13 19:20:42 +02:00
levita_a
a089dc3b72
Switch to a simpler pattern for the CDIModel.<algorithm>_optimize functions that preserves the old behavior when the old pattern is used
2025-10-13 14:26:07 +02:00
levita_a
766a7d1adf
Move to better supported strategy for avoiding circular imports
2025-10-13 14:20:38 +02:00
yoshikisd
82ce845385
Changed the names of the reconstructors and updated the old optimizer class documentation
2025-08-04 16:51:24 +00:00
yoshikisd
404d03bbd3
Rebased CDIModel to use Reconstructors for reconstructions.
2025-08-01 21:51:52 +00:00
yoshikisd
76bc2fa75b
Got rid of world_size attribute
2025-08-01 21:50:35 +00:00
yoshikisd
0785eae552
Created Reconstructors class to replace optimization methods in CDIModel
2025-08-01 21:37:05 +00:00
gnzng
d7a1ea82c9
adjusted warn msg based on Daynes suggestion
2025-06-17 15:50:51 -07:00
gnzng
b189c3c2af
Add warning for 64-bit float conversion in Ptycho2DDataset and added to tests
2025-06-17 11:01:30 -07:00
Dayne Yoshiki Sasaki
31318819d0
Merge branch 'cdtools-developers:master' into bugfix/rpi_compare
2025-06-11 17:03:06 -07:00
yoshikisd
4c784de922
Fixed sim_data shape change in CDIModel.compare for RPI measurements
2025-06-12 00:02:32 +00:00
levita_a
4ecc782c28
Reply to Daynes comment's and slightly loosen a tolerance in one test that has been failing
2025-06-10 14:11:01 +02:00
levita_a
b6bc7d95cc
Change the behavior of FancyPtycho.center_probes to center the probe in real space even when fourier_probe is set to True
2025-06-10 13:57:03 +02:00
levita_a
2c5587cacf
Fix an issue for datasets with colinear translations
2025-06-10 13:57:03 +02:00
levita_a
1dd389d08a
Update the initialization for near field to work better with oversampling
2025-05-28 10:09:02 +02:00
levita_a
148b9f9865
Get a basic implementation of near-field ptycho working including initialization and oversampling
2025-05-26 16:58:27 +02:00
levita_a
2c2f2d2d93
Add a way to save and load the quantum efficiency masks, and add test coverage
2025-05-13 16:05:16 +02:00
levita_a
c86e505ae5
Make it possible to add a quantum efficiency mask to a dataset, allow fancy_ptycho to load that and use it in the forward model
2025-05-13 14:06:02 +02:00
levita_a
ac1499f511
get it running in principle, but it is not good
2025-05-12 16:55:26 +02:00
levita_a
2fd917350d
response to Dayne's review
2025-03-20 10:46:24 +01:00
levita_a
5b6fd79b28
Add tests for nested_dict_to_numpy and nested_dict_to_torch
2025-03-18 13:13:47 +01:00
levita_a
a30930b082
Fix bug with loading h5 files including strings, and add test coverage for h5_to_nested_dict and nested_dict_to_h5
2025-03-18 11:54:06 +01:00
gnzng
f8bebd0436
typo, factor -> factors
2025-03-04 14:21:51 -08:00
gnzng
efadaf807e
Rename probe_size parameter to probe_shape in FancyPtycho and MultislicePtycho classes to match the gaussian_probe function
2025-03-04 14:20:09 -08:00
a7904491be
Added a function to allow for deletion of translation positions with logical indexing ( #16 )
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* Added a function to allow for deletion of translation positions via logical indexing
In ptycho_2d_dataset.py
- Created remove_translations_mask. This handles logical-indexing-based deletion of translation points
- Refactored crop_translations to be dependent on remove_translations_mask
* Add validation and tests for remove_translations_mask method in Ptycho2DDataset
* Switch mask to mask_remove
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Co-authored-by: gnzng <damian@guenzing.de >
Co-authored-by: Clemens Schmid <clemisch@tuta.io >
2025-02-26 06:52:04 +01:00
Dayne Sasaki
0020306dd5
Merge pull request #12 from cdtools-developers/bragg_oversampling
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Fixing oversampling in Bragg2DPtycho
2025-01-06 09:24:20 -08:00
yoshikisd
1da20c8427
improvements: Implemented requested changes for PR13
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For crop_translations in ptycho_2d_dataset.py
- crop_2d_translations is now crop_translations
- roi is now order-insensitive within the first and last pairs of elements.
- the definition of top, bottom, left, and right, are now consistent with figures generated by matplotlib.pyplot.imshow
- self.intensities is now updated
For tests_datasets.py
- the order-insensitivity of roi in crop_translation is tested, and tests for specific ordering of values in roi are removed.
2024-12-30 01:36:54 +00:00
levita_a
c03d4284f2
Fix the issue with obj view padding in Bragg2DPtycho not working with a probe fourier crop
2024-12-23 10:10:40 +01:00
allevitan
levita_a