Direct ptychography: real-space montage, empirical probes, non-electron units - #281

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gvarnavi wants to merge 33 commits into

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diffractive_imaging

Commits on Aug 14, 2026

fix(serialize): round-trip tuple and list subclasses

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bb3fa39
refactor(direct-ptycho): extract DirectPtychographyBase, and fix three bugs

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b0dff8f
feat(direct-ptycho): add ShadowMontagePtychography, with tests for both classes

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f3482a1
refactor(direct-ptycho): derive object sampling from the field of view

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c8b12c1
feat(direct-ptycho): default the montage to nearest-neighbour deposition

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bab7926

Commits on Aug 15, 2026

feat(direct-ptycho): position-dependent defocus for tilted samples

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b5a877b
feat(direct-ptycho): real-space SSB/OBF/MF via a truncated stencil

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60fe1a3
feat(direct-ptycho): DirectPtychography.from_dataset3d for ungridded scans

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073fa37
fix(direct-ptycho): fill regridding holes with the occupied mean, not zero

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d3407d8
feat(direct-ptycho): expose regridding diagnostics on from_dataset3d

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5739d2f
fix(direct-ptycho): warn that regridded ungridded scans cannot be upsampled

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2881b87
feat(direct-ptycho): upsample_positions, so ungridded scans can unfold

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345bfbd
refactor(direct-ptycho): a finer scan_sampling is the whole story

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5e60d42
fix(direct-ptycho): make the ungridded and montage paths work on MPS

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3294590

Commits on Aug 16, 2026

fix(imaging): correct the sub-pixel cross-correlation refinement

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e57c81c
feat(direct-ptycho): pin the canvas to a window of the specimen

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a888ca8
fix(direct-ptycho): score the whole patch, not its densest spots

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bd935c8
feat(direct-ptycho): let the hyperparameter searches take a loss

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1cfe888
feat(direct-ptycho): expose the map behind a defocus-gradient fit

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772f5f7

Commits on Aug 20, 2026

feat(direct-ptycho): take a wavelength, not only an electron energy

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0d435d0
feat(direct-ptycho): reconstruct from an empirical complex probe

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271e854
perf(direct-ptycho): evaluate the montage convolutions by FFT

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529055d
fix(direct-ptycho): sample an empirical probe without interpolating

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6d3c56c
fix(direct-ptycho): support rotation with an empirical probe

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67ce1e9
feat(direct-ptycho): state the bright-field mask, and pin a wrapped canvas

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67b474f
feat(direct-ptycho): run iCoM on the montage, and with any probe

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28cf4a8
fix(direct-ptycho): warn when a wrapped canvas is smaller than the scan

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f285ae1
feat(direct-ptycho): a truncated iCoM stencil is riCOM

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a905cdf
perf(direct-ptycho): sum the detector before convolving for riCOM

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bcab3f6

Commits on Aug 21, 2026

refactor(direct-ptycho): rename ShadowMontagePtychography to DirectPtychographyMontage

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6504fcd
docs(direct-ptycho): describe the class that exists now, not the one that did

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921a100

Commits on Aug 30, 2026

cleaning up docstrings
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9f6bfb3
Merge remote-tracking branch 'origin/dev' into diffractive_imaging
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e908a24