add Dirac GOS for EELS quantification

hyperspy · Aug 23, 2024 · 31edc79 · 31edc79
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diff --git a/EELS/EELS_analysis.ipynb b/EELS/EELS_analysis.ipynb
@@ -22,6 +22,7 @@
     "* 20/7/2019 Katherine MacArthur - Checked for Hyperspy 1.5.1 and commented out sections requiring Gatan GOS files.\n",
     "* 30/7/2019 Magnus Nord - Minor text improvements for M&M19 short course\n",
     "* 9/3/2024 Magnus Nord - Updated to work with HyperSpy 2.0.0\n",
+    "* 23/8/2024 Zezhong Zhang - Add Dirac GOS example in curve fitting quantification\n",
     "\n",
     "## Table of contents\n",
     "\n",
@@ -753,6 +754,76 @@
     "hs.plot.plot_spectra([m[edge].intensity.as_signal() for edge in edges], legend=edges)"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "By default, exspy uses the [DFT GOS](https://zenodo.org/records/7645765) based on the Schrödinger equation. As alternative, we can also use the [Dirac GOS](https://zenodo.org/records/12800856) to include the relativistic effects, as described in this [arxiv paper](https://arxiv.org/pdf/2405.10151). The switch of the GOS is simply done by assigning the `GOS` parameter when creating the model."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "m_dirac = s.create_model(low_loss=s_ll, GOS='dirac')"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "We can plot the difference between the two GOS models for each edge, where the solid lines are Dirac results and dashed lines are DFT results. "
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import matplotlib.pyplot as plt\n",
+    "plt.figure()\n",
+    "edges = (\"Ti_L3\", \"Mn_L3\", \"O_K\", \"La_M5\")\n",
+    "color_list = [\"r\", \"g\", \"b\", \"k\"]\n",
+    "for edge in edges:\n",
+    "    color = color_list.pop()\n",
+    "    plt.plot(m_dirac[edge].GOS.energy_axis, m_dirac[edge].GOS.qint, label=edge + \" (Dirac)\", color=color)\n",
+    "    plt.plot(m[edge].GOS.energy_axis, m[edge].GOS.qint, label=edge + \" (DFT)\", color=color, linestyle=\"--\")\n",
+    "plt.xlim(400, 1000)\n",
+    "plt.legend()\n",
+    "plt.show()\n",
+    "plt.xlabel(\"Energy loss (eV)\")\n",
+    "plt.ylabel(\"Scattering cross-section (barn/eV)\")"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "We can also compare the quantification line profiles:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "m_dirac.components.O_K.onset_energy.value = 528\n",
+    "m_dirac.components.O_K.onset_energy.assign_current_value_to_all()\n",
+    "m_dirac.components.Mn_L3.onset_energy.value\n",
+    "m_dirac.components.Mn_L3.onset_energy.value = 638.5\n",
+    "m_dirac.components.Mn_L3.onset_energy.assign_current_value_to_all()\n",
+    "m_dirac.enable_fine_structure()\n",
+    "m_dirac.multifit(kind='smart')\n",
+    "edges = (\"Ti_L3\", \"Mn_L3\", \"O_K\", \"La_M5\")\n",
+    "linestyle_list = ['-']* len(edges) + ['--']* len(edges)\n",
+    "color_list = ['r', 'g', 'b', 'k']*2\n",
+    "hs.plot.plot_spectra([m_dirac[edge].intensity.as_signal() for edge in edges] + [m[edge].intensity.as_signal() for edge in edges], legend=edges, linestyle=linestyle_list, color=color_list)"
+   ]
+  },
   {
    "cell_type": "markdown",
    "metadata": {},
@@ -1024,7 +1095,7 @@
    },
    "outputs": [],
    "source": [
-    "m = s.create_model(low_loss=s_ll, auto_background=False)"
+    "m = s.create_model(low_loss=s_ll, auto_background=False, GOS='dirac')"
    ]
   },
   {
@@ -1506,7 +1577,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.8"
+   "version": "3.11.9"
   },
   "widgets": {
    "application/vnd.jupyter.widget-state+json": {

diff --git a/EELS/EELS_elemental_mapping.ipynb b/EELS/EELS_elemental_mapping.ipynb
@@ -25,7 +25,8 @@
     "\n",
     "* 2017/09/27: Initial version by Ida Hjorth\n",
     "* 2019/11/14: Update to HyperSpy 1.5, and minor improvements to text by Magnus Nord\n",
-    "* 2024/3/16: Update to work with HyperSpy 2.0, by Magnus Nord"
+    "* 2024/3/16: Update to work with HyperSpy 2.0, by Magnus Nord\n",
+    "* 23/8/2024 Zezhong Zhang - Add Dirac GOS example in mapping"
    ]
   },
   {
@@ -438,6 +439,33 @@
     "Cu_map.save(\"Cu_map.jpg\", scalebar=True, output_size=500)"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "By default, exspy utilizes the [DFT GOS](https://zenodo.org/records/7645765), which is based on the Schrödinger equation. However, if you need to account for relativistic effects, you can switch to the [Dirac GOS](https://zenodo.org/records/12800856), as detailed in this [arxiv paper](https://arxiv.org/pdf/2405.10151). Changing the GOS is straightforward; you can do this by setting the GOS parameter when creating the model."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "m_dirac = s_eels.create_model(GOS='dirac')\n",
+    "m.fit_component(m.components.PowerLaw, signal_range=(700, 900), only_current=False)\n",
+    "m_dirac.fit_component(m_dirac.components.Cu_L3, signal_range=(950, 1000), only_current=False)\n",
+    "m_dirac.fit_component(m_dirac.components.Zn_L3, signal_range=(1050, 1150), only_current=False)\n",
+    "m_dirac.set_all_edges_intensities_positive()\n",
+    "m_dirac.multifit()\n",
+    "Zn_map_dirac = m_dirac.components.Zn_L3.intensity.as_signal()\n",
+    "Cu_map_dirac = m_dirac.components.Cu_L3.intensity.as_signal()\n",
+    "hs.plot.plot_images([Zn_map_dirac, Cu_map_dirac])\n",
+    "plt.savefig(\"Zn_Cu_elemental_maps_dirac.png\")\n",
+    "hs.plot.plot_images([Zn_map_dirac, Cu_map_dirac], overlay=True, label=[\"Zn\", \"Cu\"], axes_decor=\"off\")\n",
+    "plt.savefig(\"Zn_Cu_elemental_maps_overlay_dirac.png\")"
+   ]
+  },
   {
    "cell_type": "markdown",
    "metadata": {},
@@ -518,7 +546,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.8"
+   "version": "3.11.9"
   }
  },
  "nbformat": 4,