Minor notebook bugfixes

jadball · Dec 13, 2024 · bfcd7d2 · bfcd7d2
1 parent 6ee83cf
commit bfcd7d2
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Showing 3 changed files with 10 additions and 20 deletions.
diff --git a/ImageD11/nbGui/S3DXRD/4_visualise.ipynb b/ImageD11/nbGui/S3DXRD/4_visualise.ipynb
@@ -290,10 +290,10 @@
    },
    "outputs": [],
    "source": [
-    "# look at unit cells\n",
+    "# look at unit cells - mean of a, b, c for cubic for now\n",
     "\n",
     "fig, ax = plt.subplots()\n",
-    "ax.hist(tmap.unitcell[0, :, :, :3].ravel(), bins=1000)\n",
+    "ax.hist(tmap.unitcell[0, :, :, :3].mean(axis=-1).ravel(), bins=1000)\n",
     "ax.set_xlabel('unitcell of pixel')\n",
     "plt.show()"
    ]

diff --git a/ImageD11/nbGui/S3DXRD/tomo_3_refinement_minor_phase.ipynb b/ImageD11/nbGui/S3DXRD/tomo_3_refinement_minor_phase.ipynb
@@ -564,6 +564,11 @@
     "\n",
     "        refine = PBPRefine(dset=ds, y0=y0, fpks=fpks, hkl_tol_origins=hkl_tol_origins, hkl_tol_refine=hkl_tol_refine, hkl_tol_refine_merged=hkl_tol_refine_merged, ds_tol=ds_tol, ifrac=ifrac, phase_name=minor_phase_str, forref=forref)\n",
     "        \n",
+    "        refine.own_filename = os.path.splitext(refine.own_filename)[0] + f'_{phase_str}.h5'\n",
+    "        refine.icolf_filename = os.path.splitext(refine.icolf_filename)[0] + f'_{phase_str}.h5'\n",
+    "        refine.pbpmap_filename = os.path.splitext(refine.pbpmap_filename)[0] + f'_{phase_str}.h5'\n",
+    "        refine.refinedmap_filename = os.path.splitext(refine.refinedmap_filename)[0] + f'_{phase_str}.h5'\n",
+    "        \n",
     "        refine.setmap(pmap)\n",
     "        refine.setpeaks(cf_2d)\n",
     "        refine.mask = pmap.best_npks > 0\n",

diff --git a/ImageD11/nbGui/calibration/silicon_calib.ipynb b/ImageD11/nbGui/calibration/silicon_calib.ipynb
@@ -39,7 +39,8 @@
     "import ImageD11.columnfile\n",
     "import ImageD11.indexing\n",
     "import ImageD11.grain\n",
-    "import ImageD11.nbGui.fit_geometry"
+    "import ImageD11.nbGui.fit_geometry\n",
+    "import silx.io"
    ]
   },
   {
@@ -154,7 +155,7 @@
    "source": [
     "# guess the detector distance in um\n",
     "# you can also manually specify\n",
-    "distance_guess = auto_guess_distance(ds.masterfile, ds.scans[-1])  # detector distance in um\n",
+    "distance_guess = auto_guess_distance(dset.masterfile, dset.scans[-1])  # detector distance in um\n",
     "# distance_guess = 140000  # 140 mm"
    ]
   },
@@ -220,22 +221,6 @@
     "ui.fitGui()"
    ]
   },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {
-    "tags": []
-   },
-   "outputs": [],
-   "source": [
-    "ui.valuewidgets['fit_tolerance'].value = 0.5\n",
-    "ui.fit(2,9)\n",
-    "ui.valuewidgets['fit_tolerance'].value = 0.05\n",
-    "ui.fit(3,21)\n",
-    "ui.fit(0,180)\n",
-    "ui.updateGui()"
-   ]
-  },
   {
    "cell_type": "code",
    "execution_count": null,