Merge pull request #155 from pycroscopy/use_dict3

include API in jupyter book

.gitignore

@@ -221,3 +221,9 @@ notebooks/Imaging/EMDReader_Spectrum_FEI (1).emd
 notebooks/Imaging/NionReader_ImageStack_STO_HAADF.h5
 example_data/p1-3-hr3-1.hf5
 notebooks/Spectroscopy/EDS-Copy1.ipynb
+_autosummary/pyTEMlib.atom_tools.rst
+_autosummary/pyTEMlib.eels_tools.rst
+_autosummary/pyTEMlib.file_tools.rst
+_autosummary/pyTEMlib.image_tools.rst
+_autosummary/pyTEMlib.info_widget.rst
+_autosummary/pyTEMlib.kinematic_scattering.rst

_config.yml

@@ -15,6 +15,18 @@ logo                        : logo.png  # A path to the book logo
 execute:
   execute_notebooks: force
 
+sphinx:
+  extra_extensions:
+  - 'sphinx.ext.autodoc'
+  - 'sphinx.ext.doctest'
+  - 'sphinx.ext.intersphinx'
+  - 'sphinx.ext.todo'
+  - 'sphinx.ext.mathjax'
+  - 'sphinx.ext.napoleon'
+  - 'sphinx.ext.viewcode'
+  - 'sphinx.ext.autosummary'
+
+
 # Define the name of the latex output file for PDF builds
 latex:
   latex_documents:

_toc.yml

@@ -9,4 +9,9 @@ chapters:
 - file: notebooks/2_Image_Tools
   sections:
     - file: notebooks/Imaging/Adaptive_Fourier_Filter
-- file: notebooks/3_Spectroscopy_Tools
+- file: notebooks/3_Spectroscopy_Tools
+  sections:
+    - file: notebooks/Spectroscopy/Analyse_Low_Loss
+    - file: notebooks/Spectroscopy/EDS
+
+- file: api

api.rst

@@ -0,0 +1,17 @@
+API Reference
+=============
+
+Package Structure
+-----------------
+The package structure is simple, with 5 main modules: `diffraction`: , `imaging`:, and `spectroscopy`.
+
+.. autosummary::
+   :toctree: _autosummary
+   :recursive:
+
+   pyTEMlib.file_tools
+   pyTEMlib.kinematic_scattering
+   pyTEMlib.eels_tools
+   pyTEMlib.image_tools
+   pyTEMlib.atom_tools
+   pyTEMlib.info_widget

notebooks/Spectroscopy/Analyse_Low_Loss.ipynb

@@ -163,7 +163,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": 1,
    "metadata": {
     "ExecuteTime": {
      "start_time": "2024-01-15T14:40:42.347318700Z"
@@ -175,13 +175,23 @@
    },
    "outputs": [
     {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "The autoreload extension is already loaded. To reload it, use:\n",
-      "  %reload_ext autoreload\n",
-      "Using kinematic_scattering library version {_version_ }  by G.Duscher\n",
-      "pyTEM version:  0.2024.01.1\n"
+     "ename": "ImportError",
+     "evalue": "DLL load failed while importing _imaging: The specified module could not be found.",
+     "output_type": "error",
+     "traceback": [
+      "\u001b[1;31m---------------------------------------------------------------------------\u001b[0m",
+      "\u001b[1;31mImportError\u001b[0m                               Traceback (most recent call last)",
+      "Cell \u001b[1;32mIn[1], line 1\u001b[0m\n\u001b[1;32m----> 1\u001b[0m \u001b[43mget_ipython\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mrun_line_magic\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[38;5;124;43mmatplotlib\u001b[39;49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[38;5;124;43mwidget\u001b[39;49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[43m)\u001b[49m\n\u001b[0;32m      2\u001b[0m \u001b[38;5;28;01mimport\u001b[39;00m \u001b[38;5;21;01mmatplotlib\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mpylab\u001b[39;00m \u001b[38;5;28;01mas\u001b[39;00m \u001b[38;5;21;01mplt\u001b[39;00m\n\u001b[0;32m      3\u001b[0m \u001b[38;5;28;01mimport\u001b[39;00m \u001b[38;5;21;01mnumpy\u001b[39;00m \u001b[38;5;28;01mas\u001b[39;00m \u001b[38;5;21;01mnp\u001b[39;00m\n",
+      "File \u001b[1;32m~\\AppData\\Local\\anaconda3\\lib\\site-packages\\IPython\\core\\interactiveshell.py:2456\u001b[0m, in \u001b[0;36mInteractiveShell.run_line_magic\u001b[1;34m(self, magic_name, line, _stack_depth)\u001b[0m\n\u001b[0;32m   2454\u001b[0m     kwargs[\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mlocal_ns\u001b[39m\u001b[38;5;124m'\u001b[39m] \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mget_local_scope(stack_depth)\n\u001b[0;32m   2455\u001b[0m \u001b[38;5;28;01mwith\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mbuiltin_trap:\n\u001b[1;32m-> 2456\u001b[0m     result \u001b[38;5;241m=\u001b[39m fn(\u001b[38;5;241m*\u001b[39margs, \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mkwargs)\n\u001b[0;32m   2458\u001b[0m \u001b[38;5;66;03m# The code below prevents the output from being displayed\u001b[39;00m\n\u001b[0;32m   2459\u001b[0m \u001b[38;5;66;03m# when using magics with decorator @output_can_be_silenced\u001b[39;00m\n\u001b[0;32m   2460\u001b[0m \u001b[38;5;66;03m# when the last Python token in the expression is a ';'.\u001b[39;00m\n\u001b[0;32m   2461\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28mgetattr\u001b[39m(fn, magic\u001b[38;5;241m.\u001b[39mMAGIC_OUTPUT_CAN_BE_SILENCED, \u001b[38;5;28;01mFalse\u001b[39;00m):\n",
+      "File \u001b[1;32m~\\AppData\\Local\\anaconda3\\lib\\site-packages\\IPython\\core\\magics\\pylab.py:99\u001b[0m, in \u001b[0;36mPylabMagics.matplotlib\u001b[1;34m(self, line)\u001b[0m\n\u001b[0;32m     97\u001b[0m     \u001b[38;5;28mprint\u001b[39m(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mAvailable matplotlib backends: \u001b[39m\u001b[38;5;132;01m%s\u001b[39;00m\u001b[38;5;124m\"\u001b[39m \u001b[38;5;241m%\u001b[39m backends_list)\n\u001b[0;32m     98\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[1;32m---> 99\u001b[0m     gui, backend \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mshell\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43menable_matplotlib\u001b[49m\u001b[43m(\u001b[49m\u001b[43margs\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mgui\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mlower\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;28;43;01mif\u001b[39;49;00m\u001b[43m \u001b[49m\u001b[38;5;28;43misinstance\u001b[39;49m\u001b[43m(\u001b[49m\u001b[43margs\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mgui\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;28;43mstr\u001b[39;49m\u001b[43m)\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;28;43;01melse\u001b[39;49;00m\u001b[43m \u001b[49m\u001b[43margs\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mgui\u001b[49m\u001b[43m)\u001b[49m\n\u001b[0;32m    100\u001b[0m     \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_show_matplotlib_backend(args\u001b[38;5;241m.\u001b[39mgui, backend)\n",
+      "File \u001b[1;32m~\\AppData\\Local\\anaconda3\\lib\\site-packages\\IPython\\core\\interactiveshell.py:3633\u001b[0m, in \u001b[0;36mInteractiveShell.enable_matplotlib\u001b[1;34m(self, gui)\u001b[0m\n\u001b[0;32m   3612\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21menable_matplotlib\u001b[39m(\u001b[38;5;28mself\u001b[39m, gui\u001b[38;5;241m=\u001b[39m\u001b[38;5;28;01mNone\u001b[39;00m):\n\u001b[0;32m   3613\u001b[0m \u001b[38;5;250m    \u001b[39m\u001b[38;5;124;03m\"\"\"Enable interactive matplotlib and inline figure support.\u001b[39;00m\n\u001b[0;32m   3614\u001b[0m \n\u001b[0;32m   3615\u001b[0m \u001b[38;5;124;03m    This takes the following steps:\u001b[39;00m\n\u001b[1;32m   (...)\u001b[0m\n\u001b[0;32m   3631\u001b[0m \u001b[38;5;124;03m        display figures inline.\u001b[39;00m\n\u001b[0;32m   3632\u001b[0m \u001b[38;5;124;03m    \"\"\"\u001b[39;00m\n\u001b[1;32m-> 3633\u001b[0m     \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01mmatplotlib_inline\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mbackend_inline\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m configure_inline_support\n\u001b[0;32m   3635\u001b[0m     \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01mIPython\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mcore\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m pylabtools \u001b[38;5;28;01mas\u001b[39;00m pt\n\u001b[0;32m   3636\u001b[0m     gui, backend \u001b[38;5;241m=\u001b[39m pt\u001b[38;5;241m.\u001b[39mfind_gui_and_backend(gui, \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mpylab_gui_select)\n",
+      "File \u001b[1;32m~\\AppData\\Local\\anaconda3\\lib\\site-packages\\matplotlib_inline\\__init__.py:1\u001b[0m\n\u001b[1;32m----> 1\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01m.\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m backend_inline, config  \u001b[38;5;66;03m# noqa\u001b[39;00m\n\u001b[0;32m      2\u001b[0m __version__ \u001b[38;5;241m=\u001b[39m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124m0.1.6\u001b[39m\u001b[38;5;124m\"\u001b[39m  \u001b[38;5;66;03m# noqa\u001b[39;00m\n",
+      "File \u001b[1;32m~\\AppData\\Local\\anaconda3\\lib\\site-packages\\matplotlib_inline\\backend_inline.py:6\u001b[0m\n\u001b[0;32m      1\u001b[0m \u001b[38;5;124;03m\"\"\"A matplotlib backend for publishing figures via display_data\"\"\"\u001b[39;00m\n\u001b[0;32m      3\u001b[0m \u001b[38;5;66;03m# Copyright (c) IPython Development Team.\u001b[39;00m\n\u001b[0;32m      4\u001b[0m \u001b[38;5;66;03m# Distributed under the terms of the BSD 3-Clause License.\u001b[39;00m\n\u001b[1;32m----> 6\u001b[0m \u001b[38;5;28;01mimport\u001b[39;00m \u001b[38;5;21;01mmatplotlib\u001b[39;00m\n\u001b[0;32m      7\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01mmatplotlib\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m colors\n\u001b[0;32m      8\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01mmatplotlib\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mbackends\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m backend_agg\n",
+      "File \u001b[1;32m~\\AppData\\Local\\anaconda3\\lib\\site-packages\\matplotlib\\__init__.py:161\u001b[0m\n\u001b[0;32m    157\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01mpackaging\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mversion\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m parse \u001b[38;5;28;01mas\u001b[39;00m parse_version\n\u001b[0;32m    159\u001b[0m \u001b[38;5;66;03m# cbook must import matplotlib only within function\u001b[39;00m\n\u001b[0;32m    160\u001b[0m \u001b[38;5;66;03m# definitions, so it is safe to import from it here.\u001b[39;00m\n\u001b[1;32m--> 161\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01m.\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m _api, _version, cbook, _docstring, rcsetup\n\u001b[0;32m    162\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01mmatplotlib\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mcbook\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m sanitize_sequence\n\u001b[0;32m    163\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01mmatplotlib\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01m_api\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m MatplotlibDeprecationWarning\n",
+      "File \u001b[1;32m~\\AppData\\Local\\anaconda3\\lib\\site-packages\\matplotlib\\rcsetup.py:27\u001b[0m\n\u001b[0;32m     25\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01mmatplotlib\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m _api, cbook\n\u001b[0;32m     26\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01mmatplotlib\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mcbook\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m ls_mapper\n\u001b[1;32m---> 27\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01mmatplotlib\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mcolors\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m Colormap, is_color_like\n\u001b[0;32m     28\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01mmatplotlib\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01m_fontconfig_pattern\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m parse_fontconfig_pattern\n\u001b[0;32m     29\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01mmatplotlib\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01m_enums\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m JoinStyle, CapStyle\n",
+      "File \u001b[1;32m~\\AppData\\Local\\anaconda3\\lib\\site-packages\\matplotlib\\colors.py:52\u001b[0m\n\u001b[0;32m     49\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01mnumbers\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m Real\n\u001b[0;32m     50\u001b[0m \u001b[38;5;28;01mimport\u001b[39;00m \u001b[38;5;21;01mre\u001b[39;00m\n\u001b[1;32m---> 52\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01mPIL\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m Image\n\u001b[0;32m     53\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01mPIL\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mPngImagePlugin\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m PngInfo\n\u001b[0;32m     55\u001b[0m \u001b[38;5;28;01mimport\u001b[39;00m \u001b[38;5;21;01mmatplotlib\u001b[39;00m \u001b[38;5;28;01mas\u001b[39;00m \u001b[38;5;21;01mmpl\u001b[39;00m\n",
+      "File \u001b[1;32m~\\AppData\\Local\\anaconda3\\lib\\site-packages\\PIL\\Image.py:82\u001b[0m\n\u001b[0;32m     73\u001b[0m MAX_IMAGE_PIXELS \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mint\u001b[39m(\u001b[38;5;241m1024\u001b[39m \u001b[38;5;241m*\u001b[39m \u001b[38;5;241m1024\u001b[39m \u001b[38;5;241m*\u001b[39m \u001b[38;5;241m1024\u001b[39m \u001b[38;5;241m/\u001b[39m\u001b[38;5;241m/\u001b[39m \u001b[38;5;241m4\u001b[39m \u001b[38;5;241m/\u001b[39m\u001b[38;5;241m/\u001b[39m \u001b[38;5;241m3\u001b[39m)\n\u001b[0;32m     76\u001b[0m \u001b[38;5;28;01mtry\u001b[39;00m:\n\u001b[0;32m     77\u001b[0m     \u001b[38;5;66;03m# If the _imaging C module is not present, Pillow will not load.\u001b[39;00m\n\u001b[0;32m     78\u001b[0m     \u001b[38;5;66;03m# Note that other modules should not refer to _imaging directly;\u001b[39;00m\n\u001b[0;32m     79\u001b[0m     \u001b[38;5;66;03m# import Image and use the Image.core variable instead.\u001b[39;00m\n\u001b[0;32m     80\u001b[0m     \u001b[38;5;66;03m# Also note that Image.core is not a publicly documented interface,\u001b[39;00m\n\u001b[0;32m     81\u001b[0m     \u001b[38;5;66;03m# and should be considered private and subject to change.\u001b[39;00m\n\u001b[1;32m---> 82\u001b[0m     \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01m.\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m _imaging \u001b[38;5;28;01mas\u001b[39;00m core\n\u001b[0;32m     84\u001b[0m     \u001b[38;5;28;01mif\u001b[39;00m __version__ \u001b[38;5;241m!=\u001b[39m \u001b[38;5;28mgetattr\u001b[39m(core, \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mPILLOW_VERSION\u001b[39m\u001b[38;5;124m\"\u001b[39m, \u001b[38;5;28;01mNone\u001b[39;00m):\n\u001b[0;32m     85\u001b[0m         msg \u001b[38;5;241m=\u001b[39m (\n\u001b[0;32m     86\u001b[0m             \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mThe _imaging extension was built for another version of Pillow or PIL:\u001b[39m\u001b[38;5;130;01m\\n\u001b[39;00m\u001b[38;5;124m\"\u001b[39m\n\u001b[0;32m     87\u001b[0m             \u001b[38;5;124mf\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mCore version: \u001b[39m\u001b[38;5;132;01m{\u001b[39;00m\u001b[38;5;28mgetattr\u001b[39m(core,\u001b[38;5;250m \u001b[39m\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mPILLOW_VERSION\u001b[39m\u001b[38;5;124m'\u001b[39m,\u001b[38;5;250m \u001b[39m\u001b[38;5;28;01mNone\u001b[39;00m)\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;130;01m\\n\u001b[39;00m\u001b[38;5;124m\"\u001b[39m\n\u001b[0;32m     88\u001b[0m             \u001b[38;5;124mf\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mPillow version: \u001b[39m\u001b[38;5;132;01m{\u001b[39;00m__version__\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m\"\u001b[39m\n\u001b[0;32m     89\u001b[0m         )\n",
+      "\u001b[1;31mImportError\u001b[0m: DLL load failed while importing _imaging: The specified module could not be found."
      ]
     }
    ],