Merge pull request #246 from pycroscopy/plotly-support

Plotly support

Author: gduscher

.github/workflows/actions.yml

@@ -21,7 +21,7 @@ jobs:
       max-parallel: 5
       matrix:
 
-        python-version: ['3.10', '3.11', '3.12', '3.13']
+        python-version: ['3.10', '3.11', '3.12', '3.13', '3.14']
 
     steps:
     - uses: actions/checkout@v3

pyTEMlib/eds_tools/eds_tools.py

@@ -29,7 +29,7 @@
 
 import pyTEMlib
 import pyTEMlib.file_reader
-from .utilities import elements as elements_list
+from ..utilities import elements as elements_list
 from .eds_xsections import quantify_cross_section, quantification_k_factors
 
 
@@ -294,7 +294,7 @@ def get_x_ray_lines(spectrum, element_list):
     x_sections = pyTEMlib.xrpa_x_sections.x_sections
     energy_scale = spectrum.get_spectral_dims(return_axis=True)[0].values
     for element in element_list:
-        atomic_number = pyTEMlib.eds_tools.elements_list.index(element)
+        atomic_number = elements_list.index(element)
         out_tags[element] ={'Z': atomic_number}
         lines = pyTEMlib.xrpa_x_sections.x_sections.get(str(atomic_number), {}).get('lines', {})
         if not lines:

pyTEMlib/eds_tools/eds_xsections.py

@@ -1,32 +1,24 @@
 """
-Module for calculating electron ionization cross sections for EDS quantification.
-Based on the Bote & Salvat (2008, 2009) cross sections for inner shell ionization
-by electron impact.
-Also includes cascade corrections for Coster-Kronig, Auger, and fluorescence
-emission.
-Values from xraylib package are used for fluorescence yields, radiative rates,
-Coster-Kronig probabilities, and Auger yields/rates.
-References:
-- D. Bote and F. Salvat, "Calculations of inner-shell ionization by electron 
-  impact with the distorted-wave and plane-wave Born approximations","
-- Bote, David, et al. "Cross sections for ionization of K, L and M shells of 
-  atoms by impact of electrons and positrons with energies up to 1 GeV: 
-  Analytical formulas." 
-  Atomic Data and Nuclear Data Tables 95.6 (2009): 871-909. 
-- Browning, N. D., et al. "A model for calculating cross sections for electron
-  impact ionization of atoms from threshold to 10 MeV." 
-    Journal of Applied Physics 83.11 (1998): 5736-5744.
+Cross-Sections and k-factor file reading and writing
+Use em_tables or manufactorers k-factor data for quantification.
+
+part of pyTEMlib
+
+Author: Gerd Duscher
+
+collected in directory 12/2025
 """
+
 import os
 import json
 import numpy as np
 import scipy
 import csv
 import xml
 
-from .config_dir import config_path
-from .utilities import elements as elements_list
-from .utilities import get_z
+from ..config_dir import config_path
+from ..utilities import elements as elements_list
+from ..utilities import get_z
 
 import pyTEMlib
 

pyTEMlib/eels_tools/low_loss_tools.py

@@ -426,7 +426,7 @@ def kroeger_core(e_data, a_data, eps_data, acceleration_voltage_kev, thickness,
        return P, P*scale*1e2,p_vol*1e2, p_simple*1e2
     
 
-    $d^2P/(dEd\\Omega) = \\frac{1}{\\pi^2 a_0 m_0 v^2} \\Im \left[ \\frac{t\\mu^2}{\\varepsilon \\phi^2 } \right]
+    $d^2P/(dEd\\Omega) = \\frac{1}{\\pi^2 a_0 m_0 v^2} \\Im \\left[ \\frac{t\\mu^2}{\\varepsilon \\phi^2 } \\right]
     
     # Internally everything is calculated in SI units
     # acceleration_voltage_kev = 200 #keV

tests/test_utilities.py

@@ -35,14 +35,14 @@ def test_lorentz_peak_normalization():
 def test_gauss_zero_width_returns_zeros():
     x = np.linspace(-5, 5, 11)
     p = [0.0, 1.0, 0.0]  # p[2] == 0 should yield zeros
-    y = utilities.gauss(x, p)
+    y = utilities.gauss(x, np.array(p))
     assert np.allclose(y, 0.0)
 
 
 def test_gauss_peak_at_center():
     x = np.linspace(-5, 5, 101)
     p = [0.0, 3.0, 1.2]  # mean=0, amplitude=3
-    y = utilities.gauss(x, p)
+    y = utilities.gauss(x,np.array(p))
     # maximum value should be close to amplitude
     assert pytest.approx(3.0, rel=1e-5) == float(np.max(y))
     # center value equals maximum