update

Author: gduscher

notebooks/Spectroscopy/EDS.ipynb

@@ -468,7 +468,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 10,
+   "execution_count": 12,
    "id": "7f9e23cc-bbb2-47d1-ae3b-7ec78532aeec",
    "metadata": {
     "scrolled": true
@@ -478,17 +478,17 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Element: Nb, Corrected Atom%: 0.25, Corrected Weight%: 0.65\n",
-      "Element: Sr, Corrected Atom%: 19.56, Corrected Weight%: 46.75\n",
-      "Element: Ti, Corrected Atom%: 20.25, Corrected Weight%: 26.45\n",
-      "Element: O, Corrected Atom%: 59.93, Corrected Weight%: 26.16\n",
-      "Element: Cu, Corrected Atom%: 0.00, Corrected Weight%: 0.00\n"
+      "Element: O, Corrected Atom%: 58.60, Corrected Weight%: 25.10\n",
+      "Element: Sr, Corrected Atom%: 20.22, Corrected Weight%: 47.43\n",
+      "Element: Cu, Corrected Atom%: 0.00, Corrected Weight%: 0.00\n",
+      "Element: Ti, Corrected Atom%: 20.92, Corrected Weight%: 26.81\n",
+      "Element: Nb, Corrected Atom%: 0.26, Corrected Weight%: 0.66\n"
      ]
     }
    ],
    "source": [
     "# ------ Input ----------\n",
-    "thickness_in_nm = 250\n",
+    "thickness_in_nm = 210\n",
     "# -----------------------\n",
     "pyTEMlib.eds_tools.apply_absorption_correction(spectrum, thickness_in_nm)\n",
     "for key, value in spectrum.metadata['EDS']['GUI'].items():\n",

pyTEMlib/eds_tools/eds_tools.py

@@ -473,6 +473,7 @@ def fit_model(spectrum, use_detector_efficiency=False):
     def residuals(pp, yy):
         """ residuals for fit"""
         model = np.zeros(len(yy))
+        pp = np.abs(pp)
         for i in range(len(pp)-4):
             model += peaks[i]*pp[i]
         if use_detector_efficiency:
@@ -486,8 +487,8 @@ def residuals(pp, yy):
     y = np.array(spectrum)  # .compute()
     [p, _] = scipy.optimize.leastsq(residuals, pin, args=(y,), maxfev=10000)
 
-    update_fit_values(spectrum.metadata['EDS'], peaks, p)
-    return np.array(peaks), np.array(p)
+    update_fit_values(spectrum.metadata['EDS'], peaks, np,abs(p)
+    return np.array(peaks), np.abs(p)
 
 
 def update_fit_values(out_tags, peaks, p):

pyTEMlib/version.py

@@ -1,5 +1,5 @@
 """
 version
 """
-__version__ = '0.2026.1.3'
+__version__ = '0.2026.3.0'
 __time__ = '2026-01-28 20:58:26'