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
gnzng
be28903be7
refactor: CI installation process to use 'uv' for faster dependency management
2025-11-10 12:23:09 -08:00
Abe Levitan
5d43b05822
Merge pull request #54 from gnzng/versiontests
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Add tests for version existence and semantic format
2025-10-31 11:47:25 +01:00
gnzng
f79836bfc2
Add tests for version existence and semantic format
2025-10-29 21:40:12 -07:00
Damian Guenzing
14e4c99ec7
Merge pull request #53 from cdtools-developers/version_source_of_truth
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Add cdtools.__version__ and set it up so that there is a single source of truth for the version number
2025-10-29 21:34:33 -07:00
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
Dayne Yoshiki Sasaki
1fa9a75806
Merge pull request #52 from cdtools-developers/bugfix/masking
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Fix a high priority bug with the masking system which was introduced in the switch to reconstructors classes
2025-10-24 07:14:41 -07:00
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
Dayne Yoshiki Sasaki
fbfbf4fa87
Merge pull request #49 from cdtools-developers/show_original_pos
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Add the original positions to the fancy_ptycho position plotting
2025-10-19 12:05:48 -07:00
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
d9c4ebfdf3
Merge pull request #47 from yoshikisd/refactor/reconstructors
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Separate optimization methods from CDIModel into separate class Reconstructors
2025-10-17 20:15:43 -03:00
Dayne Yoshiki Sasaki
6443b16f5c
Merge pull request #1 from cdtools-developers/refactor/reconstructors
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Various suggested changes for the reconstructors branch
2025-10-17 15:58:47 -07:00
levita_a
7d39015719
response to dayne's review
2025-10-17 23:41:08 +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
f022b5e2c4
Get the tests passing again after the change of the optimization functions in the model classes
2025-10-16 15:58:28 +02:00
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
allevitan
levita_a