electronmicroscopy · henryhng · Jul 4, 2026 · Jul 5, 2026 · Jul 5, 2026 · Jul 5, 2026
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -71,6 +71,12 @@ new `rcN` heading when that rc is published to TestPyPI.
 - 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.
 - 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.
+- 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.
+- Add `quantem showdiffraction`: one command from a diffraction pattern (or the real Fe3O4 SAED via `--demo`) to an analyzed standalone HTML through the Auto pipeline, with `--phase` library calibration and indexing.
+- Add the `showdiffraction_fe3o4` tutorial dataset loader (public dataset hub download with packaged fallback) and rework the ShowDiffraction tutorial around a quickstart and what the widget solves.
+- 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).
 - 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.
 - Add a Show2D HAADF underlay: `underlay=True` on a `(haadf, map)` pair adds a third panel blending the map onto the HAADF lattice, with a `magenta` colormap so bright atomic columns render magenta instead of clipping to white. Tune with `underlay_alpha` and `underlay_haadf_gain`.

diff --git a/README.md b/README.md
@@ -29,9 +29,9 @@ python -c "import quantem.widget; print(quantem.widget.__version__)"
 | `Show2D` | 2D image or stack | image + contrast, FFT, line profiles, scale bar, display-side denoise, view-only low/high/band-pass frequency filters |
 | `Show3D` | 3D stack | scrub / play through frames |
 | `Show3DSlices` | 3D volume | orthogonal-slice viewer |
+| `ShowDiffraction` | 2D diffraction pattern or 3D stack | spot/ring d-spacings, center refinement, calibration, phase indexing |
 | `Show4DSTEM` | 4D-STEM array, or 5D stack | live virtual detectors (BF / ABF / ADF), CoM / iCoM / DPC, dataset slider + compare grid, offline WebGPU export |
 | `ShowPtycho` | 4D-STEM master / SSB result | interactive SSB phase review: C10/C12/phi12/rotation sliders re-reconstruct in ~5-18 ms on-GPU; kernel-less WebGPU folder export for laptops |
-| `ShowDiffraction` | 2D pattern or 3D stack | d-spacing, g-vector, and angle measurement on Bragg spots and rings |
 | `ChooseLattice` | 2D image | ordered origin, a1, and a2 point selection for lattice-vector measurements |
 | `ShowEDS` | EDS/EELS spectrum image | linked element map, spectrum, energy band, real-space ROI, and automatic element identification |
 | `ShowFolder` | microscopy session folder | fast thumbnail browser, grouping, and file selection |
@@ -47,6 +47,7 @@ ChooseLattice(np.random.rand(512, 512))
 Show1D(np.random.rand(100), x_label="frame", y_label="defocus", y_unit="nm")
 Show2D(np.random.rand(512, 512))
 Show4DSTEM(np.random.rand(64, 64, 128, 128))
+ShowDiffraction(np.random.rand(512, 512))
 ShowEDS(np.random.poisson(2, (64, 64, 256)).astype("uint16"))
 ShowFolder("/data/session")
 ```
@@ -95,6 +96,7 @@ quantem show4dstem ./masters/ --html         # 4D-STEM             -> shareable
 quantem showptycho scan_master.h5            # raw 4D-STEM master  -> user-owned review project
 quantem showptycho ./ptycho-export/          # existing project    -> WebGPU browser review
 quantem showfolder ./session/                # microscopy folder   -> ShowFolder notebook/HTML
+quantem showdiffraction pattern.npy          # diffraction         -> analyzed ShowDiffraction HTML
 quantem html tutorial.ipynb                  # a notebook          -> standalone offline HTML
 ```
 
@@ -106,6 +108,7 @@ quantem html tutorial.ipynb                  # a notebook          -> standalone
 | `quantem show4dstem <master(s) / folder>` | one or more `*_master.h5` | live Show4DSTEM notebook (or `--html`) |
 | `quantem showptycho <master(s) / folder>` | one or more `*_master.h5`, or an existing project | one index with direct ShowPtycho and Show4DSTEM browser viewers |
 | `quantem showfolder <folder>` | microscopy session folder | ShowFolder notebook (or `--html`) |
+| `quantem showdiffraction <pattern>` | a diffraction pattern, or `--demo` | analyzed ShowDiffraction HTML: rings and fits; with `--phase`, calibration and hkl |
 | `quantem html <notebook.ipynb>` | a notebook you wrote | runs it, bakes outputs into one offline HTML |
 | `quantem github <notebook.ipynb>` | a notebook copy for GitHub | strips widget state, embeds compressed pictures for GitHub's preview |
 

diff --git a/docs/api/datasets.md b/docs/api/datasets.md
@@ -11,6 +11,7 @@ from quantem.widget.datasets import (
     show2d_gold,
     show3d_gold,
     show4dstem_gold,
+    showdiffraction_fe3o4,
     showfolder_gold,
 )
 ```
@@ -65,6 +66,7 @@ widget-tutorials/show1d/ducky/small/show1d_monitor.jsonl
 widget-tutorials/show1d/ducky/small/snapshots/*.npy
 widget-tutorials/shared/gold-haadf/full/data.npy
 widget-tutorials/show4dstem/gold-128-bin8/full/data.npy
+widget-tutorials/showdiffraction/fe3o4-saed/small/data.npy
 widget-tutorials/showfolder/gold-haadf-session/small/*.emd
 ```
 

diff --git a/docs/api/html-export.md b/docs/api/html-export.md
@@ -122,7 +122,7 @@ browse-quality or count-preserving.
 |---|---|---|---|---|---|---|
 | Show1D | yes | `single` | `full` | `1`, `2`, `4`, `8` | no | preserves every trace/x sample; linked 2D snapshot and profile panels use a NaN-aware area mean, with pixel size and panel/profile coordinates rescaled |
 | Show2D | yes | `single` | `full`, `uint8` | planned | no | `uint8` stores display-scaled image data |
-| Show3D | yes | `single`; large reviews use `export_sidecar(...)` folder output | `full`, `uint8` | planned | yes, via `export_sidecar(...)` | `uint8` stores display-scaled volume data; folder output keeps the viewer HTML small and loads the stack from a nearby data file. See the [advanced tutorial](../tutorials/advanced.md) for the full-resolution folder workflow. |
+| Show3D | yes | `single` | `full`, `uint8` | `1`, `2`, `4`, `8` | no | `uint8` stores display-scaled volume data; use explicit downsampling for smaller portable reports. Legacy sidecar folders remain readable but cannot be newly created. |
 | Show3DSlices | yes | `single` | `full`, `uint8` | planned | no | `uint8` stores display-scaled volume data |
 | Show4DSTEM | yes | `single`; interactive exports may write a local launcher/folder when a companion payload must be served | `uint8`, `full`/`uint16` | detector: `1`, `2`, `4`, `8`; scan: `1`, `2`, `4`, `8` | yes, for companion-data interactive exports and HDF5 bundles | `export_kind="report"` writes static PNG virtual-image pages with no raw 4D; `export_kind="interactive"` writes browser WebGPU raw-4D payload. The CLI WebGPU folder keeps source HDF5 beside `index.html` and `Show4DSTEM.command`. `scan_bin` and `det_bin` are explicit mean-binning choices. |
 | ShowEDS | yes | `single`, `folder` | `full` | `2`, `4` | yes | count-preserving sum downsample across spatial and energy axes |
@@ -133,7 +133,7 @@ The public Python calls are:
 |---|---|
 | Show1D | `export_html(path=None, title=None, mode="single", encoding="full", downsample=None)` |
 | Show2D | `export_html(path=None, title=None, mode="single", encoding="full", downsample=None)` |
-| Show3D | `export_html(path=None, title=None, mode="single", encoding="full", downsample=None)`; multi-GB folder reviews use `export_sidecar(out_dir)` |
+| Show3D | `export_html(path=None, title=None, mode="single", encoding="full", downsample=None)` |
 | Show3DSlices | `export_html(path=None, title=None, mode="single", encoding="full", downsample=None)` |
 | Show4DSTEM | `export_html(path=None, title=None, mode="single", encoding=None, downsample=None, dtype="uint8", det_bin=1, scan_bin=1, real_space_bin=None, export_kind="interactive", dataset_scope="unhidden")`; for compact screening use `export_kind="report"` |
 | ShowPtycho | `export_webgpu_folder(out_dir)` for browser-side SSB review from compressed HDF5 source files; transient BF-indexed reducers are built in WebGPU |
@@ -149,7 +149,6 @@ Existing compatibility aliases remain supported:
 | `dtype="uint16"` | `encoding="full"` |
 | `det_bin=2` | `downsample=2` |
 | `binning=4` | `downsample=4` |
-| `mode="sidecar"` | `mode="folder"` |
 
 For Show4DSTEM, prefer the newer explicit names instead of the generic
 compatibility aliases: `dtype="uint8"` or `"uint16"`, `det_bin=...`,

diff --git a/docs/api/show3d.md b/docs/api/show3d.md
@@ -578,49 +578,26 @@ For pages containing several panels, pass `panel_slot=` to
 specific numerical profile. The interactive kymograph intentionally remains a
 single-panel-page tool so its line and depth axes are unambiguous.
 
-## Full-resolution folder export (advanced)
+## Portable HTML export
 
-Use the folder export when a microscopist needs to scrub a large stack at the
-native detector/reconstruction size instead of opening a reduced one-file HTML.
-This writes a small `index.html` beside an `offline_stack.u8` data file and a
-`manifest.json`:
+Show3D writes one portable HTML file. Use `encoding="uint8"` for visual review
+and choose `downsample=1`, `2`, `4`, or `8` explicitly based on the required
+spatial detail:
 
 ```python
 from quantem.widget import Show3D
 
-w = Show3D(stack, title="800C 1.3Mx full-resolution review", debug=True)
-w.export_sidecar("/data/reports/800C_1.3Mx_fullres")
-```
-
-Serve the folder over Range-capable local HTTP; do not open the HTML with
-`file://` because the browser must fetch the data file:
-
-```bash
-# Use your project or lab helper that supports HTTP Range requests.
-python scripts/serve_sidecar_range.py \
-  --dir /data/reports/800C_1.3Mx_fullres \
-  --port 8803 --bind 127.0.0.1
+w = Show3D(stack, title="800C 1.3Mx review", debug=True)
+w.export_html(
+    "/data/reports/800C_1.3Mx_review.html",
+    encoding="uint8",
+    downsample=1,
+)
 ```
 
-Then open `http://127.0.0.1:8803/index.html`. The viewer shell should appear
-immediately. The browser then loads the full stack into memory, shows the load
-status banner, and swaps to the cached playback path when the stack is ready.
-Changing Color or the histogram range repaints the current microscope view
-immediately, marks the playback cache as updating, and rebuilds the remaining
-frames in the background. Scrubbing during that rebuild should still advance
-the current frame; once the banner clears, playback uses the cached full-stack
-path again.
-
-This workflow preserves the source spatial shape used to construct the widget.
-If you intentionally want a smaller browse artifact, make that explicit with a
-separate downsampled/single-file export rather than treating it as the
-full-resolution review copy. For the end-to-end browser checklist and example
-timing report, see the [advanced tutorial](../tutorials/advanced.md).
-
-When sharing this export, send or copy the whole folder. `index.html` is not a
-standalone result for this mode; it needs `offline_stack.u8` and `manifest.json`
-beside it. The colleague should serve the received folder with the same Range
-helper and open the local URL.
+For exact multi-gigabyte analysis, keep the live Jupyter widget connected to
+the source arrays. Show3D no longer creates companion sidecar folders. Existing
+legacy sidecar reports remain readable for compatibility.
 
 ## Animation exports