Merge pull request #1088 from OpenChemistry/notebook-updates

Notebook updates
OpenChemistry · Apr 22, 2024 · 9587b85 · 9587b85
2 parents 0f3787a + d5545f4
commit 9587b85
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Showing 2 changed files with 4 additions and 9 deletions.
diff --git a/backend/faust/templates/vacuum_scan_prepare.ipynb.j2 b/backend/faust/templates/vacuum_scan_prepare.ipynb.j2
@@ -78,9 +78,7 @@
     "fname, scan_num, scan_id = get_scan_path(distiller_path / Path('counted') / Path(date), scan_num, scan_id=scan_id, version=1)\n",
     "\n",
     "# Load the sparse data\n",
-    "vacuum_scan = stio.load_electron_counts(fname)\n",
-    "# Remove the flyback\n",
-    "vacuum_scan = vacuum_scan[:, :-1, :, :]\n",
+    "vacuum_scan = stio.load_electron_counts(fname, keep_flyback=False) # remove flyback\n",
     "\n",
     "print('File: {}'.format(fname))\n",
     "print('Scan dimensions = {}'.format(vacuum_scan.scan_shape))\n",

diff --git a/backend/faust/templates/vacuum_scan_subtract.ipynb.j2 b/backend/faust/templates/vacuum_scan_subtract.ipynb.j2
@@ -84,10 +84,7 @@
     ")\n",
     "\n",
     "# Load the data\n",
-    "experiment = stio.load_electron_counts(fname)\n",
-    "\n",
-    "# Remove the flyback\n",
-    "experiment = experiment[:,:-1,:,:]\n",
+    "experiment = stio.load_electron_counts(fname, keep_flyback=False) # remove flyback\n",
     "\n",
     "print('File: {}'.format(fname))\n",
     "print('Scan dimensions = {}'.format(experiment.scan_shape))\n",
@@ -132,8 +129,8 @@
     "if vacuum_haadf_path.exists():\n",
     "    with ncempy.io.dm.fileDM(vacuum_haadf_path) as f0:\n",
     "        vacuum_md = f0.getMetadata(0)\n",
-    "        vacuum_camera_length = md['Microscope Info STEM Camera Length']\n",
-    "        vacuum_stem_magnification = md['Microscope Info Indicated Magnification']\n",
+    "        vacuum_camera_length = vacuum_md['Microscope Info STEM Camera Length']\n",
+    "        vacuum_stem_magnification = vacuum_md['Microscope Info Indicated Magnification']\n",
     "    if vacuum_camera_length != camera_length:\n",
     "        print(f'Vacuum camera length = {camera_length} mm')\n",
     "        raise UserWarning('camera lengths do not match')\n",