workshop: explicit rotation pass to DirectPtychography

notebooks/berk_workshop_v1.ipynb

@@ -376,9 +376,11 @@
     "# Fit origin (needed by estimate_detector_rotation) + run estimate.\n",
     "com_model.fit_origin_background()\n",
     "com_model.estimate_detector_rotation()\n",
-    "print(f\"detector rotation = {com_model.detector_rotation_deg:.2f}°\")\n",
+    "best_rotation_deg = com_model.detector_rotation_deg\n",
+    "best_rotation_rad = np.deg2rad(best_rotation_deg)\n",
+    "print(f\"detector rotation = {best_rotation_deg:.2f}°  ({best_rotation_rad:.4f} rad)\")\n",
     "\n",
-    "# Recompute the curl-vs-angle curve to plot it.\n",
+    "# Recompute curl-vs-angle for the plot.\n",
     "angles_deg = torch.arange(-89, 90, 1, device=com_model.device, dtype=torch.float32)\n",
     "com_t = com_model.origin_measured.view(*dset.shape[:2], 2)\n",
     "com_n = com_t - com_t.mean(dim=(0, 1))\n",
@@ -392,7 +394,7 @@
     "\n",
     "fig, ax = plt.subplots(figsize=(6, 3.5))\n",
     "ax.plot(angles, curl, lw=1.5)\n",
-    "ax.axvline(com_model.detector_rotation_deg, color=\"red\", lw=1, label=f\"{com_model.detector_rotation_deg:.1f}°\")\n",
+    "ax.axvline(best_rotation_deg, color=\"red\", lw=1, label=f\"{best_rotation_deg:.1f}°\")\n",
     "ax.set_xlabel(\"rotation angle (deg)\")\n",
     "ax.set_ylabel(\"mean |curl(CoM)|\")\n",
     "ax.set_title(\"Scan-detector rotation from CoM curl\")\n",
@@ -407,13 +409,13 @@
    "source": [
     "## Step 5 — Phase retrieval: `DirectPtychography` + optuna aberration fit\n",
     "\n",
-    "Build `DirectPtychography` once, then **fit the C10, C12, phi12 aberrations\n",
-    "from the data itself** with a small optuna loop (30 trials, ~5 s on T4). The\n",
-    "fitted coefs go into the final reconstructions.\n",
+    "Build `DirectPtychography` with the **rotation found in Step 4b** (`best_rotation_rad`),\n",
+    "then **fit C10, C12, phi12 from the data** with a 30-trial optuna loop (~5 s on T4).\n",
+    "The fitted aberration coefs go into the final reconstructions.\n",
     "\n",
-    "Why fit per-dataset: SSB silently returns zeros when the aberrations are\n",
-    "wrong — it needs the probe phase profile to deconvolve. Fitting on each\n",
-    "dataset means the workshop works on YOUR data, no prior calibration assumed."
+    "Why fit per-dataset: SSB silently returns zeros when the aberrations are wrong —\n",
+    "it needs the probe phase profile to deconvolve. Fitting on each dataset means the\n",
+    "workshop works on YOUR data, no prior calibration assumed."
    ]
   },
   {
@@ -437,11 +439,11 @@
     "    dset,\n",
     "    energy=meta[\"voltage_kV\"] * 1e3,                          # 300 kV -> 300000 eV\n",
     "    semiangle_cutoff=meta[\"probe_semiangle_mrad\"] * 1e-3,     # 30 mrad -> 0.030 rad\n",
-    "    rotation_angle=None,                                       # auto-estimate\n",
+    "    rotation_angle=best_rotation_rad,                          # from Step 4b CoM curl\n",
     "    device=\"cuda\" if torch.cuda.is_available() else \"cpu\",\n",
     "    verbose=True,\n",
     ")\n",
-    "print(\"DirectPtychography built\")"
+    "print(f\"DirectPtychography built with rotation = {np.rad2deg(best_rotation_rad):.2f}°\")"
    ]
   },
   {