de-twin

A digital twin of a Direct Electron camera on a TEM: the column, the specimen, the in-situ holder and the detector, advancing on one clock. Develop and test automated microscope control without a microscope, a camera or DE-Server, and plug the same twin into the real software when you have it.

Documentation: https://cssfrancis.github.io/de-twin/

pip install de-twin            # numpy, scipy, diffsims, orix
pip install "de-twin[deapi]"   # + a deapi-compatible DE-Server stand-in

Quick start

from de_twin import DigitalTwin

twin = DigitalTwin("Dense Au on holey C", camera="DE16", holder="sim-heating")
twin.column.set("Magnification", 50_000)
twin.column.move_stage(x=12.5, y=-3.0)        # um, waits for the stage
twin.column.set_defocus_um(-1.5)

img = twin.snap(1.0)                          # dark/gain-corrected electrons, like DE-Server
raw = twin.raw_frame(0.025)                   # one raw uint16 frame: offset, noise, defects
truth = twin.flux(twin.request())             # noiseless e-/px/s, for scoring automation

What is simulated

• Column: JEOL/TFS-style modes, magnification and camera-length ladders, stage motion, beam current and illumination, defocus, astigmatism, shifts and tilts, axial aberrations (C1 to C5), and an optional CEOS-like probe/image corrector with drift and tuning.
• Specimen: seeded grids, thin films, proteins in ice, FIB lamellae and an in-situ heating chip; every grain is a real crystal (diffsims + orix) that responds to tilt.
• Image formation: wave-optical TEM with a CTF, kinematic SAED/NBD/CBED, coherent 4D-STEM for ptychography and tcBF, and physical dose.
• Detector: every DE camera model, with dark, gain, noise, defects, saturation, binning and counting, so references are needed and work.
• Holder: a simulated DENS-style heating chip, or a real DENS Impulse holder.

Plug it into real software

de-twin serve --soap 5002 --deapi 13240 --shm

Each part can also follow real hardware instead of simulating it: --mirror-temchannel HOST for a real (or Dummy) DE-TEM-Channel, --holder impulse for a DENS Impulse holder.

DE-Server's side of the shared-memory frame source is two small files in cpp/.

Contributing and releases

See CONTRIBUTING.md. Changes are recorded as towncrier fragments in upcoming_changes/, and releases follow the procedure in the development docs.

MIT licensed.