Merge pull request #230 from pycroscopy/plotly-support

Plotly support

Author: gduscher

notebooks/Imaging/Adaptive_Fourier_Filter.ipynb

@@ -101,7 +101,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": null,
    "metadata": {
     "ExecuteTime": {
      "end_time": "2024-01-28T17:26:31.896075100Z",
@@ -135,15 +135,9 @@
     "\n",
     "import sys\n",
     "sys.path.insert(0, '../../')\n",
-    "sys.path.insert(0, '../../../sipdy/')\n",
-    "sys.path.insert(0, '../../../SciFiReaders/')\n",
-    "\n",
     "\n",
     "%load_ext autoreload\n",
     "%autoreload 2\n",
-    "import SciFiReaders\n",
-    "import sidpy\n",
-    "\n",
     "import pyTEMlib\n",
     "\n",
     "\n",

notebooks/Imaging/D1-Diffraction_Rings.ipynb

@@ -893,7 +893,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "base",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },

notebooks/Imaging/D2-Diffraction_Spots.ipynb

@@ -32,25 +32,10 @@
    "id": "b468443b",
    "metadata": {},
    "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "using config dir\n",
-      "c:\\Users\\gduscher\\AppData\\Local\\anaconda3\\Lib\\site-packages\\pyTEMlib\\data fluorescent_yield.csv\n",
-      "c:\\Users\\gduscher\\AppData\\Local\\anaconda3\\Lib\\site-packages\\pyTEMlib\\data fluorescent_yield.xlsx\n",
-      "c:\\Users\\gduscher\\AppData\\Local\\anaconda3\\Lib\\site-packages\\pyTEMlib\\data k_factors_Bruker_15keV.json\n",
-      "c:\\Users\\gduscher\\AppData\\Local\\anaconda3\\Lib\\site-packages\\pyTEMlib\\data k_factors_Thermo_200keV.json\n",
-      "c:\\Users\\gduscher\\AppData\\Local\\anaconda3\\Lib\\site-packages\\pyTEMlib\\data xrays_X_section_100kV.json\n",
-      "c:\\Users\\gduscher\\AppData\\Local\\anaconda3\\Lib\\site-packages\\pyTEMlib\\data xrays_X_section_200kV.json\n",
-      "c:\\Users\\gduscher\\AppData\\Local\\anaconda3\\Lib\\site-packages\\pyTEMlib\\data xrays_X_section_300kV.json\n",
-      "c:\\Users\\gduscher\\AppData\\Local\\anaconda3\\Lib\\site-packages\\pyTEMlib\\data xrays_X_section_60kV.json\n"
-     ]
-    },
     {
      "data": {
       "text/plain": [
-       "'0.2025.11.3'"
+       "'0.2025.12.0'"
       ]
      },
      "execution_count": 1,
@@ -65,7 +50,7 @@
     "import scipy \n",
     "\n",
     "import pyTEMlib\n",
-    "pyTEMlib.__version__\n"
+    "pyTEMlib.__version__"
    ]
   },
   {
@@ -85,15 +70,15 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 2,
    "id": "35a6b103",
    "metadata": {},
    "outputs": [
     {
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "wavelength is 1.97 pm for  300 keV\n"
+      "wavelength is 4.87 pm for  60 keV\n"
      ]
     }
    ],
@@ -127,7 +112,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 13,
+   "execution_count": 3,
    "id": "e8dfa007",
    "metadata": {},
    "outputs": [
@@ -138,7 +123,8 @@
       "Help on function get_wavelength in module __main__:\n",
       "\n",
       "get_wavelength(e0: float) -> float\n",
-      "    get deBroglie wavelength of electron accelerated by energy (in eV) e0\n",
+      "    get deBroglie wavelength of electron accelerated by energy e0 (in eV)\n",
+      "\n",
       "    Parameters\n",
       "    ----------\n",
       "    e0 : float\n",

notebooks/Imaging/Zuo-HOLZ-experiment.jpg

@@ -23,14 +23,13 @@
 from . import eels_tools
 from . import eds_tools
 from . import crystal_tools
-from . import kinematic_scattering
-from . import dynamic_scattering
+from . import diffraction_tools
 from .config_dir import config_path
 from . import utilities
 from . import xrpa_x_sections
 
 __all__ = ['__version__', 'file_tools', 'image_tools', 'atom_tools',
            'graph_tools', 'probe_tools', 'eels_tools', 'eds_tools',
-           'crystal_tools', 'kinematic_scattering', 'dynamic_scattering', 
-           'config_path', 'utilities', 'xrpa_x_sections']
+           'crystal_tools', 'diffraction_tools', 'xrpa_x_sections',
+           'config_path', 'utilities']
 __author__ = 'Gerd Duscher'

notebooks/Spectroscopy/EDS-SI.ipynb

@@ -0,0 +1,38 @@
+""" diffraction tools subpackage 
+A collection of tools to analyze diffraction data
+part of pyTEMlib
+author: Gerd Duscher, UTK"""
+
+from .basic import read_poscar, example, zone_mistilt, check_sanity
+from .basic import make_pretty_labels, get_all_miller_indices
+from .basic import get_wavelength, get_metric_tensor, get_structure_factors
+from .basic import find_nearest_zone_axis, find_angles, stage_rotation_matrix
+from .basic import get_zone_rotation, scattering_matrix, gaussian, get_unit_cell
+from .basic import output_verbose, feq, form_factor
+
+from .kinematic import kinematic_scattering
+from .kinematic import calculate_kikuchi, calculate_holz
+from .kinematic import calculate_laue_zones, center_of_laue_circle
+from .kinematic import get_bragg_reflections, get_incident_wave_vector
+from .kinematic import get_dynamically_activated, ring_pattern_calculation, get_reflection_families
+from .kinematic import get_allowed_reflections, get_all_reflections
+
+from .diffraction_plot import plot_diffraction_pattern, plot_ring_pattern, warp
+from .diffraction_plot import plot_saed_parameter, plot_cbed_parameter, plot_holz_parameter
+from .diffraction_plot import plot_kikuchi, plot_reciprocal_unit_cell_2d
+from .diffraction_plot import scattering_profiles, set_center
+
+
+__all__ = ['read_poscar', 'example', 'zone_mistilt', 'check_sanity',
+           'make_pretty_labels', 'get_all_miller_indices', 'get_wavelength',
+           'get_metric_tensor', 'get_structure_factors', 'find_nearest_zone_axis', 
+           'find_angles', 'stage_rotation_matrix', 'get_zone_rotation',  'scattering_matrix',
+           'gaussian', 'get_unit_cell', 'output_verbose', 'feq', 'form_factor',
+           'kinematic_scattering', 'calculate_kikuchi', 'calculate_holz', 'get_dynamically_activated',
+           'calculate_laue_zones', 'center_of_laue_circle', 'get_bragg_reflections',
+           'get_incident_wave_vector', 'ring_pattern_calculation', get_all_reflections,
+           'get_reflection_families', 'get_allowed_reflections',
+           'plot_diffraction_pattern', 'plot_ring_pattern', 'warp',
+           'plot_saed_parameter', 'plot_cbed_parameter', 'plot_holz_parameter',
+           'plot_kikuchi', 'plot_reciprocal_unit_cell_2d', 'scattering_profiles',
+           'set_center']