ShowPtycho in Jupyter

ShowPtycho in Jupyter#

ShowPtycho is an interactive SSB (single-sideband) aberration explorer for 4D-STEM data. You tune defocus (C10), astigmatism (C12 / phi12), and scan-detector rotation and watch the reconstructed phase and its FFT update live in the notebook.

SSB is a direct (non-iterative) phase retrieval: fast and interactive, but lower quality than iterative multislice ptychography. Use ShowPtycho for quick aberration tuning and review, not as a substitute for a full iterative reconstruction.

To export a standalone HTML viewer you can open without a kernel — the folder ships a double-click ShowPtycho.command launcher, or open index.html in Chrome and grant it the data folder — see Export and run ShowPtycho.

The one rule: always fit before you view#

from quantem.gpu import SSB
from quantem.widget import ShowPtycho

# 1. Open the native source with your microscope calibration.
ssb = SSB.open(
    "scan_master.h5",
    backend="auto",
    semiangle_mrad=30.0,        # convergence semiangle, mrad
    scan_sampling_A=0.264,      # real-space scan step, Angstrom
    voltage_kV=300.0,
    rotation_angle_deg=158.9,   # scan-detector rotation (run find_rotation if unknown)
)

# 2. Fit and refine the aberrations. THIS STEP IS REQUIRED.
result = ssb.fit(trials=200, refinement="nelder-mead")

# 3. Open the interactive widget — it reuses the prepared GPU session.
ShowPtycho(ssb)

Do NOT skip step 2#

# WRONG — this NEVER fits. It uses whatever aberrations you pass verbatim,
# so the phase and FFT are junk unless your numbers were already perfect.
ShowPtycho(data, semiangle_mrad=30.0, scan_sampling_A=0.264,
           voltage_kV=300.0,
           aberrations={"C10": 78.0, "C12": 17.0, "phi12": 0.5})

ShowPtycho(data, aberrations=...) is a convenience constructor that trusts the aberrations you hand it. It does not fit them. If you want the solver to find the aberrations, build an SSB, call fit(trials=200, refinement="nelder-mead"), and pass that same prepared ssb object to ShowPtycho(ssb). The returned SSBResult is also available as result for non-interactive analysis through result.phase, result.amplitude, and result.object_wave.

You can confirm the solve ran: the stats bar shows a non-null loss, and the Optuna trials + Nelder-Mead panel at the bottom is populated.

No detector binning#

Build the reconstruction at the native detector size (det_bin=1, the default). Native (e.g. 192x192) is what resolves light columns such as oxygen in a perovskite; binning throws that away. Binning also breaks the HTML export (the browser cannot bin), so keep the whole workflow un-binned.

Region-specific refit (crop)#

A smaller crop often converges more physically than the full field of view: a single global aberration and rotation hold better over a small region, so a crop can resolve oxygen the full FOV cannot.

Two ways to crop:

  • Interactively. Construct the widget with the raw master path so the Crop action appears next to Export/Reset. Enable Crop, drag a rectangle on the phase, then Refit SSB — the widget reloads only that scan region from the HDF5 source, runs 200 optimization trials plus refinement, and replaces the phase/FFT and calibration.

  • In code. Load only the region, then fit as usual:

    from quantem.gpu.io import load

data = load("scan_master.h5", dtype=None,
            scan_region=(128, 384, 128, 384)).data   # 256x256 center crop
ssb = SSB.from_array(
    data,
    semiangle_mrad=30.0,
    scan_sampling_A=0.264,
    voltage_kV=300.0,
    rotation_angle_deg=158.9,
)
result = ssb.fit(trials=200, refinement="nelder-mead")
ShowPtycho(ssb)

    256x256 is a good crop size: small enough for region-specific aberrations, big enough that the phase is not blocky. 128x128 works but displays coarse.

Checklist#

  1. Leave SSB.open(..., dtype=None) at its default for native detector precision.

  2. Native detector, det_bin=1 — do not bin.

  3. ssb.fit(trials=200, refinement="nelder-mead") — the fit is not optional.

  4. Pass the ssb object to ShowPtycho, not data + hand-typed aberrations.

  5. Confirm: stats bar loss is non-null and the trials panel is populated.