update

Update of EELS

Author: gduscher

.gitattributes

@@ -0,0 +1,2 @@
+# SCM syntax highlighting & preventing 3-way merges
+pixi.lock merge=binary linguist-language=YAML linguist-generated=true -diff

.gitignore

@@ -300,3 +300,6 @@ pyTEMlib/eds_tools/get_bote_salvat.py
 pyTEMlib/diffraction_tools/kinematic copy.py
 example_data/01-EELS Acquire_STO.hf5
 example_data/01-EELS Acquire_STO-1.hf5
+# pixi environments
+.pixi/*
+!.pixi/config.toml

README.md

@@ -107,7 +107,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 13,
+   "execution_count": 3,
    "metadata": {
     "slideshow": {
      "slide_type": "-"
@@ -118,9 +118,7 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "The autoreload extension is already loaded. To reload it, use:\n",
-      "  %reload_ext autoreload\n",
-      "pyTEM version:  0.2025.12.1\n",
+      "pyTEM version:  0.2026.3.0\n",
       "notebook version:  2025.12.06\n"
      ]
     }
@@ -129,7 +127,6 @@
     "%matplotlib  widget\n",
     "import os\n",
     "import sys\n",
-    "single\n",
     "\n",
     "import matplotlib\n",
     "import matplotlib.pyplot as plt\n",
@@ -527,58 +524,24 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 8,
+   "execution_count": 2,
    "metadata": {},
    "outputs": [
     {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "Of the 3374 possible reflection 854 are allowed.\n",
-      "here\n",
-      "Of the 854 allowed reflection 33  have unique distances.\n",
-      "\n",
-      "\n",
-      " [hkl]  \t 1/d [1/nm] \t d [nm] \t F^2 \n",
-      "[1. 1. 1.] \t 4.25 \t         0.2355 \t 729.11 \n",
-      "[0. 0. 2.] \t 4.90 \t         0.2039 \t 599.47 \n",
-      "[2. 0. 2.] \t 6.94 \t         0.1442 \t 333.71 \n",
-      "[1. 1. 3.] \t 8.13 \t         0.1230 \t 241.36 \n",
-      "[2. 2. 2.] \t 8.49 \t         0.1177 \t 219.62 \n",
-      "[0. 0. 4.] \t 9.81 \t         0.1020 \t 158.02 \n",
-      "[3. 3. 1.] \t 10.69 \t         0.0936 \t 128.30 \n",
-      "[2. 0. 4.] \t 10.97 \t         0.0912 \t 120.38 \n",
-      "[4. 2. 2.] \t 12.01 \t         0.0832 \t 95.48 \n",
-      "[3. 3. 3.] \t 12.74 \t         0.0785 \t 81.88 \n",
-      "[4. 0. 4.] \t 13.87 \t         0.0721 \t 65.29 \n",
-      "[5. 1. 3.] \t 14.51 \t         0.0689 \t 57.83 \n",
-      "[4. 4. 2.] \t 14.71 \t         0.0680 \t 55.65 \n",
-      "[0. 2. 6.] \t 15.51 \t         0.0645 \t 48.14 \n",
-      "[5. 3. 3.] \t 16.08 \t         0.0622 \t 43.55 \n",
-      "[2. 2. 6.] \t 16.27 \t         0.0615 \t 42.17 \n",
-      "[4. 4. 4.] \t 16.99 \t         0.0589 \t 37.33 \n",
-      "[5. 1. 5.] \t 17.51 \t         0.0571 \t 34.26 \n",
-      "[0. 4. 6.] \t 17.68 \t         0.0566 \t 33.33 \n",
-      "[2. 4. 6.] \t 18.35 \t         0.0545 \t 29.98 \n",
-      "[5. 3. 5.] \t 18.83 \t         0.0531 \t 27.81 \n",
-      "[7. 3. 3.] \t 20.07 \t         0.0498 \t 23.11 \n",
-      "[6. 4. 4.] \t 20.22 \t         0.0495 \t 22.62 \n",
-      "[0. 6. 6.] \t 20.81 \t         0.0481 \t 20.78 \n",
-      "[5. 5. 5.] \t 21.24 \t         0.0471 \t 19.56 \n",
-      "[6. 6. 2.] \t 21.38 \t         0.0468 \t 19.18 \n",
-      "[7. 5. 3.] \t 22.34 \t         0.0448 \t 16.79 \n",
-      "[6. 6. 4.] \t 23.00 \t         0.0435 \t 15.36 \n",
-      "[5. 5. 7.] \t 24.40 \t         0.0410 \t 12.80 \n",
-      "[7. 3. 7.] \t 25.36 \t         0.0394 \t 11.32 \n",
-      "[6. 6. 6.] \t 25.48 \t         0.0392 \t 11.16 \n",
-      "[7. 7. 5.] \t 27.19 \t         0.0368 \t 9.05 \n",
-      "[7. 7. 7.] \t 29.73 \t         0.0336 \t 6.73 \n"
+     "ename": "NameError",
+     "evalue": "name 'pyTEMlib' is not defined",
+     "output_type": "error",
+     "traceback": [
+      "\u001b[31m---------------------------------------------------------------------------\u001b[39m",
+      "\u001b[31mNameError\u001b[39m                                 Traceback (most recent call last)",
+      "\u001b[36mCell\u001b[39m\u001b[36m \u001b[39m\u001b[32mIn[2]\u001b[39m\u001b[32m, line 7\u001b[39m\n\u001b[32m      4\u001b[39m verbose = \u001b[38;5;28;01mTrue\u001b[39;00m\n\u001b[32m      5\u001b[39m \u001b[38;5;66;03m# --------------------------------------------\u001b[39;00m\n\u001b[32m----> \u001b[39m\u001b[32m7\u001b[39m atoms = \u001b[43mpyTEMlib\u001b[49m.crystal_tools.structure_by_name(structure)\n\u001b[32m      8\u001b[39m main_dataset.structures[\u001b[33m'\u001b[39m\u001b[33mStructure_000\u001b[39m\u001b[33m'\u001b[39m] = atoms\n\u001b[32m      9\u001b[39m main_dataset.metadata[\u001b[33m'\u001b[39m\u001b[33mexperiment\u001b[39m\u001b[33m'\u001b[39m][\u001b[33m'\u001b[39m\u001b[33mhkl_max\u001b[39m\u001b[33m'\u001b[39m]  = hkl_max\n",
+      "\u001b[31mNameError\u001b[39m: name 'pyTEMlib' is not defined"
      ]
     }
    ],
    "source": [
     "# -----Input for ring pattern calculation ----\n",
-    "structure = 'gold'\n",
+    "structure = 'aluminum'\n",
     "hkl_max = 7\n",
     "verbose = True\n",
     "# --------------------------------------------\n",