PlanPtycho Storyboard

PlanPtycho Storyboard#

Use with Storyboard.

Stories#

PP-01: See Whether A Thick Crystal Fits The Settings#

User story: As a microscopist planning multislice ptychography of a thick crystal, I want to give the crystal and my usual settings and see at a glance what fits and what to change, before I spend microscope time.

Primary widgets: PlanPtycho.

Data to use: SrTiO3 built in the tutorial (cubic, a = 3.905 A), [001], 110 nm, focus 17 nm, 48 x 48 scan at 0.495 A.

Acceptance checks:

  • First paint shows four panels (Top, Side, Probe, Detector), the controls and twelve check rows.

  • Untilted, focus 17 nm: window and margin caution; overlap, reach, lean and focus split pass; each caution carries its evidence note.

  • plan.report() in Python gives the same grades as the widget.

PP-02: Drag The View Depth Through The Specimen#

User story: As a microscopist, I want to drag down the side view and watch the beam widen, so I can see where it outgrows the reconstruction window.

Acceptance checks:

  • Dragging in Side moves the white depth line; the Top overlay depth and beam width update on every move.

  • Near the exit surface the yellow beam circle in Top is larger than the dashed window square, and the Probe panel shows the wrapped beam with a red wraps note.

  • Each update lands within one display frame (measure with two chained requestAnimationFrame calls: 33 ms at 60 Hz).

PP-03: Move The Probe To The Scan Edge#

User story: As a microscopist, I want to put the probe at the edge of the scan and see how much of its beam leaves the scanned field deep in the specimen.

Acceptance checks:

  • Dragging in Top moves the probe; the Side cone follows the same position.

  • The probe starts at the scan centre; Reset Probe returns it there.

PP-04: Change Camera, Camera Length And Binning#

User story: As a microscopist, I want to switch between my cameras and camera lengths and see the model window and checks change.

Acceptance checks:

  • Camera Arina / EMPAD sets 192 / 128 px; Length 91 / 115 / 185 mm sets 0.554 / 0.461 / 0.269 mrad per Arina pixel.

  • Binning 2x gives 96 px at twice the mrad per pixel (same edge angle, half the model window); Sampling is a read-out, labelled custom calibration only when Python overrides it.

  • A 256 px scan grades margin pass; Camera custom shows editable Pixels and Sampling.

PP-05: Change The Zone Axis#

User story: As a microscopist, I want to switch the zone axis and see the projection and Bragg disks for it.

Acceptance checks (needs a live kernel):

  • Zone [011] rebuilds the Top projection with a 3.905 x 5.523 A cell and new Bragg disks within about a second.

PP-06: Tilt The Specimen#

User story: As a microscopist whose crystal is a few mrad off the zone axis, I want to see how far the columns lean through the thickness and whether that matters at my object pixel.

Acceptance checks:

  • Tilt row 3.2, Tilt col -2.4 mrad at 110 nm: Top streaks along the tilt, Side columns lean, the Detector shows the zone axis (red cross) and HOLZ ring moved off the beam axis, and the lean check reads caution, 4.4 A at 4.0 mrad.

PP-08: Move The Focus Through A Stationary Specimen, Zoom#

User story: As a microscopist, I want to drag the focus through the specimen and look closely at any panel.

Acceptance checks:

  • Dragging the dashed line in Side moves the focus (the slab does not move); the labels and the Focus splits the specimen check show the thickness above and below it, and a focus outside the slab gives caution.

  • The wheel zooms each panel about the cursor without scrolling the page; the zoom factor shows by the scale bar; double-click resets.

  • The Sample switch on Probe draws the crystal at the view depth under the probe.

PP-09: Check A Collaborator’s Acquisition#

User story: As a microscopist sent someone else’s acquisition settings, I want to type them in and see whether the data can work for ptychography.

Acceptance checks:

  • PlanPtycho(..., voltage_kV=200, semiangle_mrad=24.5, detector_px=128, detector_mrad_per_px=0.9, scan_step_A=0.4, scan_size_px=256, c10_nm=-15) shows Camera custom and every graded check pass at 40 nm.

  • Clicking a number (thickness, C10, semiangle, pixels, sampling) and typing a value updates the panels and checks on Enter.