Initial doc changes - #102
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cliulucien wants to merge 12 commits into
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cliulucien wants to merge 12 commits into
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cliulucien
marked this pull request as draft
September 23, 2026 09:58
…tyLab.py into initial_doc_changes
…ot faimliar with FPM.
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|
HI @cliulucien, looks like some serious bugs. If you see them, please report it separately under issues and if you fix those, please do so with a separate PR tagging those issues. |
added 2 commits
September 25, 2026 16:56
- implement dtype matching used by convert2single() - return linear and area overlap metrics from getOverlap() - use normalized probe-amplitude autocorrelation for area-overlap estimation
| The method requires JAX, which is imported when the function is | ||
| called. | ||
| """ | ||
| import jax |
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How did jax get here? If this requires some AD stuff, we need to rethink how to place this function correctly. Looking at the code below, we can use existing dependencies for this. Maybe if you could add this as an issue along with other issues/bugs you found, that would be great.
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Follow-up issues noticed during documentation review
ExperimentalData.py
binData()updates the ptychogram but does not refresh derived detector/data quantities via_setData(). It may also need to update the effective detector pixel sizedxdafter binning, depending on the intended convention.relative_intensity()is documented as comparing a frame to the brightest one, but the implementation normalizes bymean + 2 * stdinstead of the maximum intensity.Reconstruction.py
initializeObject()andinitializeProbe()and may deserve cleanup.expand_npsminload_probe()is currently unused. Determine whether this is legacy API or an unfinished feature._center_probe_angle(): np.squeeze(self.probe)[0]becomes 1D for single-mode probes but 2D for multi-mode probes.saveResults(): Use context managers consistently for FPM and probe-stack output to ensure HDF5 files are closed.I objectandI probestore amplitudes (abs) rather than intensities (abs**2).