allevitan
05bdee3861
Update the docs so it doesn't always think it's v0.2.0
2026-04-03 15:24:50 +02:00
allevitan and Claude Sonnet 4.6
7de8448319
Add .readthedocs.yaml for ReadTheDocs hosting
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Enables versioned documentation on ReadTheDocs. Installs the package
with its docs extras (sphinx, sphinx-rtd-theme, sphinx-argparse) so
autodoc can import cdtools during the build.
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com >
2026-04-03 14:28:01 +02:00
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
levita_a
3c8de5dc19
Update the example codes
2025-10-16 14:16:12 +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
allevitan
levita_a