levita_a
f55b35f0dd
Stop stopping at each plot to show it
2026-03-24 16:56:44 +01:00
allevitan
603486e824
Change the default colormap for exponentiated objects to match that for un-exponentiated objects, and also update test_fancy_ptycho to show all the plots (not just plot level 2)
2026-03-24 16:55:56 +01:00
allevitan
ad2b09f2f0
Update the tests to work better when checking the model plotting, and make sure to cover panel_plot_mode=False
2026-03-24 16:19:26 +01:00
allevitan and Claude Sonnet 4.6
29e9fddd72
Add test coverage for plot_translations, plot_nanomap, and plot_nanomap_with_images
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Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com >
2026-03-24 16:01:45 +01:00
allevitan
25c7b66c7c
Do a final review of all the examples to ensure they work and are well structured
2026-03-24 11:10:23 +01:00
allevitan and Claude Sonnet 4.6
5c5c0be7c6
Reformat plotting function signatures to one-parameter-per-line style
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All public functions in plotting.py now use the expanded multi-line
signature format with trailing commas for consistency and readability.
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com >
2026-03-24 11:00:43 +01:00
levita_a
4201b41573
Made more adjustments to the plotting system to avoid using constained_layout, which was causing hangups during live plotting and didn't look as nice
2026-03-24 09:13:51 +01:00
levita_a
f979388280
Fix an annoying warning coming from double-setting the figsize
2026-03-21 21:42:16 +01:00
allevitan
29656fd78e
Improve the colorized plotting further, and add a colorbar which will be useful for publishing figures now that it's not just a simple hsv lookup. Also fix a bug with nonresponsive windows when all model plots are closed, but the dataset plots are still showing.
2026-03-21 21:27:16 +01:00
allevitan
f04ac9f0ec
Make the colorized plot look nicer, with a more perceptually uniform mapping and a colorbar for accurate reading of phases
2026-03-21 17:35:14 +01:00
allevitan
a4a38530d1
Update the plot_image functions to show sliders
2026-03-21 14:57:16 +01:00
allevitan
f8ff525722
Add example patterns for jupyter notebooks
2026-03-21 08:41:18 +01:00
levita_a
dafb204aa0
Fix a bug where closed windows wouldn't reopen at the original size
2026-03-20 20:18:32 +01:00
allevitan
bef907c032
Added a minimum plotting interval to model.inspect(dataset) to make it easier to not plot so much without manual intervention
2026-03-20 20:01:40 +01:00
levita_a
f35141dcc8
Check that all the models work (all but Multislice2DPtycho, which was already broken, and make necessary tweaks
2026-03-20 19:39:47 +01:00
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
Dayne Yoshiki Sasaki
ca3c48e83d
Merge pull request #67 from cdtools-developers/new_high_NA_intensity
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A small fix to the high NA propagator
2026-02-11 09:41:05 -08:00
levita_a
1dd116d277
Add the additional factor of R^2
2026-02-11 11:06:29 +01:00
Dayne Yoshiki Sasaki
e56f3c959f
Merge pull request #31 from cdtools-developers/near_field_ptycho
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Adding near field ptychography
2026-02-10 09:52:52 -08:00
levita_a
e52c6e38aa
Remove the spurious 'probe_shape' parameter
2026-02-10 11:46:14 +01:00
levita_a
1d57005b33
Add the example data
2026-02-06 13:28:00 +01:00
levita_a
65e4882fdd
Merge remote-tracking branch 'origin/master' into near_field_ptycho
2026-01-14 17:09:17 +01:00
levita_a
a97e4cdf39
Add licensed near-field ptycho data to enable testing
2026-01-14 17:01:11 +01:00
Abe Levitan
98d2acf032
Merge pull request #66 from cdtools-developers/bugfix/surface_normal_strip
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Fix a bug preventing the default surface normal of [0 0 1] from ever being defined in Bragg2DPtycho
2025-12-19 14:55:59 +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
Abe Levitan
9402939e40
Merge pull request #63 from cdtools-developers/surface_normal
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Make it easier to change the surface normal in Bragg2DPtycho.from_dataset
2025-12-04 09:08:46 +01:00
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
Dayne Yoshiki Sasaki
4a94ea13c9
Merge pull request #61 from gnzng/customdocs
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[docs] Adding instruction to build custom documentation based on version or commit hashes
2025-11-18 13:12:38 -08:00
gnzng
444b56b829
docs: update installation instructions for dependencies to include pip
2025-11-16 11:21:36 -06:00
gnzng
4d18171e59
docs: add instructions for building custom documentation
2025-11-16 11:00:33 -06:00
Dayne Yoshiki Sasaki
36055d04be
Merge pull request #59 from gnzng/quickfixdocs
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fix: documentation build step to use Sphinx directly
2025-11-12 14:54:57 -08:00
gnzng
f0f44e3c83
fix: documentation build step to use Sphinx directly
2025-11-12 11:54:17 -06:00
Abe Levitan
562bcab171
Merge pull request #57 from gnzng/pyprojecttoml
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Change to Pyproject.toml installation and uv, remove python 3.8 support, add python 3.13 and 3.14 support
2025-11-12 16:41:21 +01:00
gnzng
3f46caf757
update authors list in pyproject.toml and move further doc link
2025-11-12 09:04:53 -06:00
gnzng
3c9e9eb1c7
adding pure pip install pipeline to CI
2025-11-12 08:59:37 -06:00
gnzng
11ed3df35e
ending python 3.8 support, adding python 3.14 to automatic test
2025-11-11 14:33:55 -06:00
gnzng
5a3e154e8d
add Python 3.13 to the CI workflow matrix
2025-11-10 12:50:59 -08:00
gnzng
e94499a6a4
fix: update pytest command to use 'uv' for consistency in CI workflow
2025-11-10 12:42:32 -08:00
gnzng
18c794b5db
fix: add virtual environment creation step in CI github workflows
2025-11-10 12:37:44 -08:00
gnzng
728cf9d590
update readme and installation docs
2025-11-10 12:23:25 -08:00
levita_a
allevitan