Add ShowDiffraction notebook, analysis modules, UI update, phase ID

CHANGELOG.md

@@ -70,6 +70,12 @@ new `rcN` heading when that rc is published to TestPyPI.
 - Save inside the review persists to the folder: Save writes the phase JPEG plus the aberration state into `saves/` (and downloads the JPEG), so saved states reappear with Load / download / delete on any relaunch - double-click or CLI. The bundled range server accepts writes only under `saves/`.
 - SSB reconstruction in the browser is 5.6x faster at full bright field: slider drags use a Fourier-domain BF sum with a single inverse FFT (the same `angle(mean(object))` estimator as the Python reference, corr 0.997), reaching ~50 FPS on a real 512x512x192x192 dataset at all 13137 BF pixels on an Apple-silicon laptop. Release commits keep the exact per-BF path for the loss readout.
 - Resident G(q,k) stores the Hermitian half-plane by default (bit-exact, 2x less GPU memory, faster) with an opt-in snorm16 quantized mode (4x), a GPU-memory clamp on the BF count so big scans cannot crash small GPUs, and acceptance of rfft half-plane calibrations from the CUDA backend.
+- Fix ShowEDS spectrum line markers so major lines (Fe Ka, Cu Ka, Au La) keep markers across the full energy range.
+- Harden ShowDiffraction analysis: calibration assignment and exactness, ring/ellipse/texture fit guards, zone-axis variants, stack frame provenance, per-axis canvas overlays, and hostile-input handling.
+- Fix ShowDiffraction systematic absences for spinel, bixbyite, cuprite, rutile-type, and I41/amd phases: new structure-verified rules remove symmetry-forbidden lines (for example Fe3O4 200 and anatase 002) from predicted reflection lists.
+- Improve ShowDiffraction phase matching: optimal line assignment replaces the greedy pass, missing-strong counts read n/a when a phase carries no intensities, full-circle radial wedges no longer collapse to zero width, and the ellipse fit's sector weighting is de-biased on noisy patterns.
+- ShowDiffraction mobile/touch support: fluid layout at phone widths, pointer-event canvas interactions (tap, drag, two-finger pinch/pan, double-tap reset), and a dual-thumb contrast histogram slider that syncs traits once per gesture.
+- ShowDiffraction phase library: pymatgen removed entirely (no more `phaseid` extra or CIF/Structure loaders); built-in lattice constants now carry per-entry source citations (NIST SRM / COD / primary literature).
 - Depend on `quantem.gpu[movie]>=0.0.1rc5` for the CUDA/MPS/CPU movie backend, keep migrated HDF5 and movie shims patch-compatible during the transition, and accept 3-axis `Show3DSlices(pixel_size=...)` tuples in release notebooks.
 - Keep display filtering consistent throughout review: Show3D reapplies denoise when a user scrubs to another frame, standalone Show2D/Show3D HTML paints denoised and frequency-filtered pixels on first load, and unlinked Show2D galleries show and edit each selected panel's own denoise mode, sigma, and bin without changing neighboring panels.
 - Add display-side denoise for sparse maps (EDS, low dose) to Show2D and Show3D: a Denoise menu (`none` / `gaussian` / `anscombe`, the count-respecting Anscombe smoother) with `denoise_sigma` and `denoise_bin` knobs, a `show_denoise` gate that keeps the controls row hidden until needed, and an always-on banner whenever a reduction is active. It is purely a view transform: the stored array, the stats row, and every export of raw data keep the original counts, and `none` is the lossless default. Show2D adds per-panel lists for raw-vs-denoised A/B galleries and runs the filter through a browser-side WebGPU pipeline, so exported HTML denoises without a kernel. Replaces the earlier `display_filter` / `display_sigma` / `spatial_bin` kwargs, which stay accepted as aliases for one release.

docs/api/showdiffraction.md

@@ -2,10 +2,32 @@
 
 Interactive d-spacing analysis for a single 2D diffraction pattern or a 3D
 stack (tilt/time series). Find the beam center, pick Bragg spots and rings,
-read calibrated d-spacings, and calibrate k-space from a known reflection. For
-full 4D-STEM datasets, use [Show4DSTEM](show4dstem). See the
+read calibrated d-spacings, and calibrate k-space from a known reflection. See the
 [ShowDiffraction tutorial](../tutorials/showdiffraction) for a worked example.
 
+The primary phase workflow is candidate verification: you usually know which
+phases to expect, so build them (`library_phase`, `Phase.from_cubic`,
+`Phase.from_dspacings`, or custom phases in the Phase menu) and rank only
+those with `identify_phase(database)` or the *candidates only* switch.
+`search_phases()` against the built-in library is the fallback for when you
+have no candidates in mind; narrow it with an element filter.
+
+Reference data sources: every lattice parameter in the built-in phase library
+(`PHASE_LIBRARY` in `showdiffraction.py`) is a room-temperature value taken from a
+license-clean source cited next to the entry — NIST SRM certificates and NBS
+circulars/monographs (US public domain), the Crystallography Open Database
+(CC0), or the primary literature. No values come from proprietary compilations
+such as the ICDD PDF or Pearson's Handbook.
+
+The lattice-based phase model enumerates d-spacings and geometric systematic
+absences. It does not calculate structure-factor intensities, thermal effects,
+or dynamical diffraction; use `Phase.from_dspacings` when matching against a
+measured or literature line table with intensities.
+
+Calibrated radial axes are reported as `g = 1/d` in `1/Å`; the legacy
+`radial_profile(units="q")` spelling is an alias for `units="g"`, not a
+`2πg` scattering-vector axis.
+
 ## Viewer UI
 
 `ShowDiffraction` supports the shared `ui_mode`, `show_title`,
@@ -31,19 +53,44 @@ no console error, no NaN frame).
 | Colormap dropdown | `dp_colormap` | Pattern recolors to the chosen map |
 | Scale mode dropdown | `dp_scale_mode` | Intensity mapped linear / log / sqrt |
 | Invert toggle | `dp_invert` | Colormap reversed |
-| Contrast min / max sliders | `dp_vmin_pct`, `dp_vmax_pct` | Display clamp changes; histogram markers move |
+| Contrast histogram (dual-thumb slider) | `dp_vmin_pct`, `dp_vmax_pct` | Drag either thumb (mouse or touch) for a live preview; traits update once on release |
 | Center mode dropdown | `center_mode` | `auto` re-detects the BF disk; `manual` enables click-to-set |
 | Click to set center (manual) | `center_row`, `center_col` | Crosshair moves; spot d-spacings recompute |
-| Detect spots | `_detect_spots_request`, `spots` | Auto-finds Bragg peaks; d-spacing table fills |
+| Detect spots | `_detect_spots_request`, `spots` | Auto-finds every isolated peak with contrast at least 10% of the strongest (`min_relative`); no count cap |
 | Add / remove spot (click) | `_spot_add_request`, `_spot_remove_request`, `spots` | Marker placed/removed; d-spacing updates |
-| Snap toggle | `snap_enabled`, `snap_radius` | New spots snap to the nearest local maximum |
-| Refine toggle | `spot_refine` | Sub-pixel Gaussian fit on/off |
-| Detect rings | `_detect_rings_request`, `rings` | Auto-finds Debye–Scherrer rings |
+| Move spot (Move + drag) | `_spot_move_request`, `spots` | Re-picks the spot at the drop position; stale hkl clears |
+| Spot pick dropdown | `spot_refine`, `snap_enabled`, `snap_radius` | Clicked spots are Gaussian-fitted, snapped to the local maximum, or kept exactly as clicked |
+| Detect rings | `_detect_rings_request`, `rings` | Auto-finds all Debye–Scherrer rings above the profile prominence threshold; no count cap |
 | Add / remove ring | `_ring_add_request`, `_ring_remove_request`, `rings` | Ring overlay; ring d-spacing updates |
 | Calibrate from spot / ring | `_calibrate_from_spot_request`, `_calibrate_from_ring_request`, `k_pixel_size` | Sets k-space pixel size from a known d |
+| Auto button | `_auto_request`, `analysis_status` | Runs center, rings, calibration, fit, and indexing in one pass; status reports failed steps only |
+| Phase menu | `phase_name`, `custom_phases` | Selects a library or custom phase for calibration and indexing; custom entries take a full lattice (a, b, c, α, β, γ) and absence rule |
+| Identify candidates only | `identify_custom_only` | Identify ranks only custom phases, skipping the library |
+| Calibrate from phase | `_calibrate_phase_request`, `calibration_rms_px` | Fits k-space sampling from ring-to-reflection assignment |
+| Index rings / spots | `_index_rings_request`, `_index_spots_request`, `zone_axis` | Fills hkl labels; spot indexing also solves the zone axis |
+| Exclude menu | `mask_regions` | Edits wedge/disk regions excluded from analysis |
+| Draw excluded disk / wedge (drag) | `mask_regions` | Drag on the pattern to add an excluded region with live preview |
+| Mask view toggle | `show_mask` | Shows or hides excluded-region overlays |
+| Fit rings | `_fit_rings_request` | Refines ring radius and width; fwhm column appears |
+| Fit ellipse / use correction | `_fit_ellipse_request`, `ellipse_corrected` | Measures distortion; the switch circularizes radii |
+| Profile panel | `show_profile`, `profile_log`, `profile_subtract_background`, `_profile_data` | Radial profile with ring markers; click adds a ring |
+| Azimuthal panel | `show_azimuthal`, `_azimuthal_data` | Intensity vs azimuth around the outermost ring |
+| hkl toggle | `show_hkl` | Shows or hides hkl labels on spots and rings |
+| Stats toggle | `show_stats` | Shows or hides the pattern-statistics readout |
+| Undo / clear spots and rings | `_spot_undo_request`, `_spot_clear_request`, `_ring_undo_request`, `_ring_clear_request` | Removes the last or all markers (Ctrl+Z also undoes) |
+| Center view | view transform | Recenters and zooms the view to the diffraction center |
+| Spot / ring CSV and JSON | measurement tables | Downloads the visible measurement table rows |
+| Refine method dropdown | `refine_method` | Picks the center-refinement algorithm (auto / symmetry / phase_corr) |
+| Refine center | `_refine_center_request`, `center_method` | Refines the center; records the method used |
+| Merge frames (3D) | `_merge_request` | Align + merge frames; appends the combined pattern |
+| Element filter box | `identify_elements` | Restricts the phase search to these elements (e.g. `Fe,O`) |
+| Identify phases | `_identify_request`, `_identify_results` | Ranked candidate phases with per-line match tables |
+| Quality panel | `_quality` | Analysis-quality snapshot: center, calibration, ellipse, ring fits, mask coverage |
+| Ring click in profile | `selected_ring_id` | Highlights the picked ring marker (0 clears) |
 | Frame slider (3D) | `frame_idx` | Scrubs to a different pattern in the stack |
 | Pan (drag) / zoom (wheel) | view transform | Pattern translates / zooms about the cursor |
-| Export → HTML | `export_request`, `export_payload` | Writes a standalone HTML viewer |
+| Touch: two-finger pinch / drag, double-tap | view transform | Pinch zooms about the fingers, two-finger drag pans, double-tap resets the view |
+| Export → PNG / HTML | `export_request`, `export_payload` | Saves the current view as a PNG image or a standalone HTML viewer |
 
 ```{seealso}
 The shared HTML-export contract is documented in [html-export](html-export).