Add ShowDiffraction detection denoise

CHANGELOG.md

@@ -6,6 +6,18 @@ new `rcN` heading when that rc is published to TestPyPI.
 
 ## Unreleased
 
+- ShowDiffraction detection denoise: center refinement and spot/ring detection
+  now run on a denoised view of the frame (`detect_denoise`, default `"auto"`:
+  Anscombe for sparse counting data, light Gaussian for moderate-SNR data,
+  identity when clean). All fits and measurements keep using the raw frame, so
+  positions and radii are never biased by the smoothing.
+- ShowDiffraction `detect_spots` exposes its shot-noise contrast floor as
+  `noise_sigma`; lower it on frames whose diffuse scattering or detector
+  shadows inflate the robust noise estimate past real peak contrast.
+- ShowDiffraction display denoise: a view-only `denoise` trait (including the
+  new Poisson non-local means `nlm` filter, which keeps spots sharp where the
+  detection blur softens them) and a `show_detection_view` toggle that
+  displays what detection saw; both leave stored data and measurements raw.
 - Add `ChooseLattice`, an interactive 2D selector for choosing an ordered
   origin, a1, and a2 and exposing their `(row, col)` coordinates and derived
   lattice vectors for downstream analysis.

docs/api/showdiffraction.md

@@ -58,11 +58,11 @@ no console error, no NaN frame).
 | 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 every isolated peak with contrast at least 10% of the strongest (`min_relative`); no count cap |
+| Detect spots | `_detect_spots_request`, `spots` | Auto-finds every isolated peak with contrast at least 10% of the strongest (`min_relative`); candidates come from the `detect_denoise` view, positions are refined on raw data; no count cap |
 | Add / remove spot (click) | `_spot_add_request`, `_spot_remove_request`, `spots` | Marker placed/removed; d-spacing updates |
 | 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 |
+| Detect rings | `_detect_rings_request`, `rings` | Auto-finds all Debye–Scherrer rings above the profile prominence threshold, on the `detect_denoise` view; ring fits stay on the raw profile; 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 |

docs/tutorials/showdiffraction.ipynb

@@ -27,7 +27,7 @@
     "quantem showdiffraction --demo                   # no data needed: real Fe3O4 SAED\n",
     "```\n",
     "\n",
-    "The same analysis is a few lines in a notebook. `showdiffraction_fe3o4` fetches the tutorial pattern (a packaged copy is used offline): Fe3O4 nanoparticles on an amorphous carbon support. The broad support halo near d = 3.6 Å is skipped with `exclude_radius`; Auto refines the center, detects rings, calibrates from the Fe3O4 phase, fits ring profiles, and indexes hkl."
+    "The same analysis is a few lines in a notebook. `showdiffraction_fe3o4` fetches the tutorial pattern (a packaged copy is used offline): Fe3O4 nanoparticles on an amorphous carbon support. The broad support halo near d = 3.6 \u00c5 is skipped with `exclude_radius`; Auto refines the center, detects rings, calibrates from the Fe3O4 phase, fits ring profiles, and indexes hkl."
    ]
   },
   {
@@ -51,7 +51,7 @@
        "version_minor": 1
       },
       "text/plain": [
-       "ShowDiffraction(shape=(1, 512, 512), sampling=(1.0 Å, 0.004992728220367598 1/Å), frame=0/1, title='Fe3O4 SAED (real)')"
+       "ShowDiffraction(shape=(1, 512, 512), sampling=(1.0 \u00c5, 0.004992728220367598 1/\u00c5), frame=0/1, title='Fe3O4 SAED (real)')"
       ]
      },
      "execution_count": 1,
@@ -96,7 +96,7 @@
     "\n",
     "- One-click pipeline: Auto chains center refinement, ring detection, phase calibration, profile fitting, and hkl indexing; every step is also a plain Python call.\n",
     "- Exact crystallography: d-spacings and interplanar angles from the full metric tensor for any crystal system, systematic absences for the common structure types, and a phase library of 100+ standards with cited lattice constants.\n",
-    "- Honest identification: candidates are ranked by plain facts (matched lines, mean Δd, missing strong lines), and ranking stays a verification aid; nothing is applied silently.\n",
+    "- Honest identification: candidates are ranked by plain facts (matched lines, mean \u0394d, missing strong lines), and ranking stays a verification aid; nothing is applied silently.\n",
     "- Distortion-aware: a fitted elliptical distortion corrects every radius, profile, and calibration rather than being a separate pass.\n",
     "- Reproducible: JSON state save/load, CSV/JSON measurement tables, and the same analysis from the notebook, the exported HTML, or the `quantem` CLI."
    ]
@@ -190,7 +190,7 @@
        "version_minor": 1
       },
       "text/plain": [
-       "ShowDiffraction(shape=(1, 256, 256), sampling=(1.0 Å, 0.018 1/Å), frame=0/1, spots=12, title='Single-crystal SAED')"
+       "ShowDiffraction(shape=(1, 256, 256), sampling=(1.0 \u00c5, 0.018 1/\u00c5), frame=0/1, spots=12, title='Single-crystal SAED')"
       ]
      },
      "execution_count": 3,
@@ -246,7 +246,7 @@
        "version_minor": 1
       },
       "text/plain": [
-       "ShowDiffraction(shape=(1, 512, 512), sampling=(1.0 Å, 0.003988000818768712 1/Å), frame=0/1, title='Magnetite-like rings')"
+       "ShowDiffraction(shape=(1, 512, 512), sampling=(1.0 \u00c5, 0.003988000818768712 1/\u00c5), frame=0/1, title='Magnetite-like rings')"
       ]
      },
      "execution_count": 4,
@@ -294,18 +294,18 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Fe3O4: 5/5 lines, mean Δd 0.82%, missing strong n/a\n",
-      "γ-Fe2O3: 5/5 lines, mean Δd 0.87%, missing strong n/a\n",
-      "α-Fe2O3 (hematite): 5/5 lines, mean Δd 1.26%, missing strong n/a\n",
-      "α-Fe: 1/5 lines, mean Δd 2.78%, missing strong n/a\n",
+      "Fe3O4: 5/5 lines, mean \u0394d 0.82%, missing strong n/a\n",
+      "\u03b3-Fe2O3: 5/5 lines, mean \u0394d 0.87%, missing strong n/a\n",
+      "\u03b1-Fe2O3 (hematite): 5/5 lines, mean \u0394d 1.26%, missing strong n/a\n",
+      "\u03b1-Fe: 1/5 lines, mean \u0394d 2.78%, missing strong n/a\n",
       "Fe3O4\n"
      ]
     }
    ],
    "source": [
     "from quantem.widget import library_phase\n",
     "\n",
-    "expected = [library_phase(n) for n in (\"Fe3O4\", \"γ-Fe2O3\", \"α-Fe2O3 (hematite)\", \"α-Fe\")]\n",
+    "expected = [library_phase(n) for n in (\"Fe3O4\", \"\u03b3-Fe2O3\", \"\u03b1-Fe2O3 (hematite)\", \"\u03b1-Fe\")]\n",
     "verified = real.identify_phase(expected)\n",
     "\n",
     "for candidate in verified:\n",
@@ -314,7 +314,7 @@
     "    missing = candidate[\"n_missing_strong\"]\n",
     "    print(\n",
     "        f\"{candidate['name']}: {candidate['matched']}/{candidate['n_obs']} lines, \"\n",
-    "        f\"mean Δd {error_text}, \"\n",
+    "        f\"mean \u0394d {error_text}, \"\n",
     "        f\"missing strong {'n/a' if missing is None else missing}\"\n",
     "    )\n",
     "\n",
@@ -323,6 +323,20 @@
     "print(candidates[0][\"name\"])"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "id": "29b98a84",
+   "metadata": {},
+   "source": "## Detection denoise\n\nThe real Fe3O4 SAED thinned to a median of 0.5 counts per pixel, analyzed twice side by side. Detection and Auto run on a matched-filter denoised view (`detect_denoise`, default `auto`; Anscombe on counting data) while ring fits and measurements stay on the raw counts. The right panel also sets the display-only `denoise = \"nlm\"` so the pattern itself is readable; `show_detection_view` shows what detection saw instead."
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "8edfbcc8",
+   "metadata": {},
+   "outputs": [],
+   "source": "from ipywidgets import HBox, Layout\n\nfrom quantem.widget.data import showdiffraction_fe3o4\n\nfe3o4_saed = showdiffraction_fe3o4(verbose=False)\nscale = 0.5 / np.median(fe3o4_saed[fe3o4_saed > 0])\nsparse_saed = np.random.default_rng(2).poisson(np.clip(fe3o4_saed, 0, None) * scale).astype(np.float32)\n\n\ndef low_dose_auto(mode, title):\n    w = ShowDiffraction(sparse_saed, title=title, offline=True, verbose=False, panel_width_px=430)\n    w.detect_denoise = mode\n    if mode != \"none\":\n        w.denoise = \"nlm\"\n    w.phase_name = \"Fe3O4\"\n    w.run_auto()\n    indexed = sum(1 for r in w.rings if r.get(\"hkl\"))\n    print(f\"{title}: calibration rms {w.calibration_rms_px:.2f} px, {indexed}/{len(w.rings)} rings indexed\")\n    return w\n\n\nraw = low_dose_auto(\"none\", \"raw\")\ndenoised = low_dose_auto(\"auto\", \"denoised\")\nHBox([raw, denoised], layout=Layout(overflow=\"auto\"))"
+  },
   {
    "cell_type": "markdown",
    "id": "sddsave01",
@@ -351,9 +365,9 @@
      "output_type": "stream",
      "text": [
       "Magnetite-like rings\n",
-      "════════════════════════════════\n",
+      "\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\n",
       "Frames:   1 (showing #0)\n",
-      "Detector: 512×512 (0.0040 1/Å/px)\n",
+      "Detector: 512\u00d7512 (0.0040 1/\u00c5/px)\n",
       "Calibration: phase (rms 0.62 px)\n",
       "Center:   (255.5, 255.5)  BF r=13.1 px\n",
       "Spots:    0\n",
@@ -406,4 +420,4 @@
  },
  "nbformat": 4,
  "nbformat_minor": 5
-}
+}