Merge pull request #72 from zezhong-zhang/dev

support Dirac GOS

doc/user_guide/eels.rst

@@ -274,6 +274,12 @@ The model for the GOS can be specified with the ``GOS`` argument
 By default, a freely usable tabulated dataset, in `gosh <https://gitlab.com/gguzzina/gosh>`__
 format, is downloaded from Zenodo:
 `doi:10.5281/zenodo.7645765 <https://zenodo.org/record/7645765>`_.
+As an alternative, one can use the `Dirac GOS <https://arxiv.org/abs/2405.10151>`_ to include the relativistic effects using the Dirac solution, which can be downloaded from Zenodo: `doi:10.5281/zenodo.12800856 <https://zenodo.org/record/12800856>`_. The Dirac GOS can be used as follows:
+
+.. code-block:: python
+
+    >>> m = s.create_model(ll=ll, GOS="Dirac")
+
 
 Custom GOS saved in the `gosh <https://gitlab.com/gguzzina/gosh>`__ format can be used,
 the following example download a previous version (1.0) of the GOS file from Zenodo

examples/model_fitting/EELS_curve_fitting.py

@@ -1,3 +1,4 @@
+# %%
 """
 EELS curve fitting
 ==================
@@ -21,3 +22,11 @@
 m.enable_fine_structure()
 m.multifit(kind="smart")
 m.plot()
+
+# one can also use the Dirac GOS by specifying the GOS parameter
+m = s.create_model(low_loss=ll, GOS="dirac")
+m.enable_fine_structure()
+m.multifit(kind="smart")
+m.plot()
+
+# %%

exspy/components/eels_cl_edge.py

@@ -19,18 +19,19 @@
 
 import functools
 import logging
+import warnings
 import math
 
 import numpy as np
 from scipy.interpolate import splev
 
 from hyperspy.component import Component
-from exspy.misc.eels.gosh_gos import GoshGOS, _GOSH_DOI
+from exspy.misc.eels.gosh_gos import GoshGOS, GOSH_SOURCES
 from exspy.misc.eels.hartree_slater_gos import HartreeSlaterGOS
 from exspy.misc.eels.hydrogenic_gos import HydrogenicGOS
 from exspy.misc.eels.effective_angle import effective_angle
 from hyperspy.ui_registry import add_gui_method
-
+from hyperspy.exceptions import VisibleDeprecationWarning
 
 _logger = logging.getLogger(__name__)
 
@@ -75,8 +76,9 @@ class EELSCLEdge(Component):
 
     The preferred option is to use a database of cross sections in GOSH
     format. One such database can be freely downloaded from Zenodo at:
-    https://doi.org/%s while information on the GOSH format
-    are available at: https://gitlab.com/gguzzina/gosh .
+    https://doi.org/%s while information on the GOSH format are available at: https://gitlab.com/gguzzina/gosh. Alternatively,
+    one can use the Dirac GOSH database to include relativistic effects,
+    available at: https://doi.org/%s.
 
     eXSpy also supports Peter Rez's Hartree Slater cross sections
     parametrised as distributed by Gatan in their Digital Micrograph (DM)
@@ -92,11 +94,11 @@ class EELSCLEdge(Component):
         Usually a string, for example, ``'Ti_L3'`` for the GOS of the titanium L3
         subshell. If a dictionary is passed, it is assumed that Hartree Slater
         GOS was exported using `GOS.as_dictionary`, and will be reconstructed.
-    GOS : ``'gosh'``, ``'hydrogenic'``, ``'Hartree-Slater'`` or str
-        The GOS to use. Default is ``'gosh'``. If str, it must the path to gosh
-        GOS file.
+    GOS : ``'dft'``,``'dirac'``, ``'hydrogenic'``, ``'Hartree-Slater'`` or str
+        The GOS to use. Default is ``'dft'``. If str, it must the path to gosh GOS file.
+        The ``'dft'`` and ``'dirac'`` databases are in the ``'gosh'`` format.
     gos_file_path : str, None
-        Only with ``GOS='gosh'``. Specify the file path of the gosh file
+        Only with ``GOS='dft' or 'dirac'``. Specify the file path of the gosh file
         to use. If None, use the file from  https://doi.org/%s
 
     Attributes
@@ -146,7 +148,7 @@ class EELSCLEdge(Component):
     _fine_structure_coeff_free = True
     _fine_structure_spline_active = True
 
-    def __init__(self, element_subshell, GOS="gosh", gos_file_path=None):
+    def __init__(self, element_subshell, GOS="dft", gos_file_path=None):
         # Declare the parameters
         self.fine_structure_components = FSet(component=self)
         Component.__init__(
@@ -168,14 +170,28 @@ def __init__(self, element_subshell, GOS="gosh", gos_file_path=None):
         self.GOS = None
 
         if GOS == "gosh":
-            self.GOS = GoshGOS(element_subshell, gos_file_path=gos_file_path)
+            warnings.warn(
+                "The value 'gosh' of the `GOS` parameter has been renamed to 'dft' in "
+                "eXSpy 0.3.0, use `GOS='dft'` instead. "
+                "Using `GOS='gosh'` will stop working in eXSpy 1.0.",
+                VisibleDeprecationWarning,
+            )
+            GOS = "dft"
+        if GOS == "dft":
+            self.GOS = GoshGOS(
+                element_subshell, gos_file_path=gos_file_path, source="dft"
+            )
+        elif GOS == "dirac":
+            self.GOS = GoshGOS(
+                element_subshell, gos_file_path=gos_file_path, source="dirac"
+            )
         elif GOS == "Hartree-Slater":  # pragma: no cover
             self.GOS = HartreeSlaterGOS(element_subshell)
         elif GOS == "hydrogenic":
             self.GOS = HydrogenicGOS(element_subshell)
         else:
             raise ValueError(
-                "GOS must be one of 'gosh', 'hydrogenic' or 'Hartree-Slater'."
+                "GOS must be one of 'dft', 'dirac','hydrogenic' or 'Hartree-Slater'."
             )
         self.onset_energy.value = self.GOS.onset_energy
         self.onset_energy.free = False
@@ -187,7 +203,9 @@ def __init__(self, element_subshell, GOS="gosh", gos_file_path=None):
         self.intensity.bmax = None
 
         self._whitelist["GOS"] = ("init", GOS)
-        if GOS == "gosh":
+        if GOS == "dft":
+            self._whitelist["element_subshell"] = ("init", self.GOS.as_dictionary(True))
+        elif GOS == "dirac":
             self._whitelist["element_subshell"] = ("init", self.GOS.as_dictionary(True))
         elif GOS == "Hartree-Slater":  # pragma: no cover
             self._whitelist["element_subshell"] = ("init", self.GOS.as_dictionary(True))
@@ -535,4 +553,8 @@ def as_dictionary(self, fullcopy=True):
         return dic
 
 
-EELSCLEdge.__doc__ %= (_GOSH_DOI, _GOSH_DOI)
+EELSCLEdge.__doc__ %= (
+    GOSH_SOURCES["dft"]["DOI"],
+    GOSH_SOURCES["dirac"]["DOI"],
+    GOSH_SOURCES["dft"]["DOI"],
+)

exspy/docstrings/model.py

@@ -19,14 +19,16 @@
 
 """Common docstring snippets for model."""
 
-from exspy.misc.eels.gosh_gos import _GOSH_DOI
+from exspy.misc.eels.gosh_gos import GOSH_SOURCES
 
-GOS_PARAMETER = """GOS : 'hydrogenic', 'gosh', 'Hartree-Slater'.
-            The GOS to use. Default is ``'gosh'``.
+GOS_PARAMETER = """GOS : 'hydrogenic', 'dft', 'dirac', 'Hartree-Slater'.
+            The GOS to use. Default is ``'dft'``.
 
         gos_file_path : str, None
-            Only with GOS='gosh'. Specify the file path of the gosh file
-            to use. If None, use the file from doi:{}""".format(_GOSH_DOI)
+            Only with GOS='dft' or 'dirac'. Specify the file path of the gosh file
+            to use. If None, use the file from doi:{}""".format(
+    GOSH_SOURCES["dft"]["DOI"]
+)
 
 EELSMODEL_PARAMETERS = """ll : None or EELSSpectrum
             If an EELSSpectrum is provided, it will be assumed that it is

exspy/misc/eels/gosh_gos.py

@@ -32,9 +32,17 @@
 R = constants.value("Rydberg constant times hc in eV")
 a0 = constants.value("Bohr radius")
 
-_GOSH_DOI = "10.5281/zenodo.7645765"
-_GOSH_URL = f"doi:{_GOSH_DOI}/Segger_Guzzinati_Kohl_1.5.0.gosh"
-_GOSH_KNOWN_HASH = "md5:7fee8891c147a4f769668403b54c529b"
+DFT_GOSH = {
+    "DOI": "10.5281/zenodo.7645765",
+    "URL": "doi:10.5281/zenodo.7645765/Segger_Guzzinati_Kohl_1.5.0.gosh",
+    "KNOWN_HASH": "md5:7fee8891c147a4f769668403b54c529b",
+}
+DIRAC_GOSH = {
+    "DOI": "10.5281/zenodo.12800856",
+    "URL": "doi:10.5281/zenodo.12800856/Dirac_GOS_compact.gosh",
+    "KNOWN_HASH": "md5:01a855d3750d2c063955248358dbee8d",
+}
+GOSH_SOURCES = {"dft": DFT_GOSH, "dirac": DIRAC_GOSH}
 
 
 class GoshGOS(TabulatedGOS):
@@ -79,20 +87,25 @@ class GoshGOS(TabulatedGOS):
         "subshell_factor": None,
     }
 
-    def __init__(self, element_subshell, gos_file_path=None):
+    def __init__(self, element_subshell, gos_file_path=None, source="dft"):
         """
         Parameters
         ----------
         element_subshell : str
             For example, 'Ti_L3' for the GOS of the titanium L3 subshell
         gos_file_path : str
             The path of the gosh file to use.
+        source : str
+            The source of the GOS data. Options are 'dft' or 'dirac'.
         """
 
         if gos_file_path is None:
+            source = source.lower()
+            assert source in GOSH_SOURCES.keys(), f"Invalid source: {source}"
+            self._name = source
             gos_file_path = pooch.retrieve(
-                url=_GOSH_URL,
-                known_hash=_GOSH_KNOWN_HASH,
+                url=GOSH_SOURCES[source]["URL"],
+                known_hash=GOSH_SOURCES[source]["KNOWN_HASH"],
                 progressbar=preferences.General.show_progressbar,
             )
         self.gos_file_path = gos_file_path

exspy/models/eelsmodel.py

@@ -67,14 +67,16 @@ def __init__(
         auto_background=True,
         auto_add_edges=True,
         low_loss=None,
-        GOS="gosh",
+        GOS="dft",
         dictionary=None,
+        gos_file_path=None,
     ):
         """
         Build an EELS model.
 
         Parameters
         ----------
+        GOS : Generalized Oscillator Strength, availiable option in ['hydrogenic', 'dft', 'dirac', 'Hartree-Slater'], default is 'dft'.
         spectrum : a EELSSpectrum instance
         %s
 
@@ -94,6 +96,7 @@ def __init__(
         self.convolution_axis = None
         self.low_loss = low_loss
         self.GOS = GOS
+        self.gos_file_path = gos_file_path
         self.edges = []
         self._background_components = []
         self._whitelist.update(
@@ -410,10 +413,9 @@ def _add_edges_from_subshells_names(self, e_shells=None):
         if e_shells is None:
             e_shells = list(self.signal.subshells)
         e_shells.sort()
-        master_edge = EELSCLEdge(e_shells.pop(), self.GOS)
-        # If self.GOS was None, the GOS is set by eels_cl_edge so
-        # we reassing the value of self.GOS
-        self.GOS = master_edge.GOS._name
+        master_edge = EELSCLEdge(
+            e_shells.pop(), self.GOS, gos_file_path=self.gos_file_path
+        )
         self.append(master_edge)
         element = master_edge.element
         while len(e_shells) > 0:
@@ -429,7 +431,9 @@ def _add_edges_from_subshells_names(self, e_shells=None):
                 # Add the other subshells of the same element
                 # and couple their intensity and onset_energy to that of the
                 # master edge
-                edge = EELSCLEdge(e_shells.pop(), GOS=self.GOS)
+                edge = EELSCLEdge(
+                    e_shells.pop(), GOS=self.GOS, gos_file_path=self.gos_file_path
+                )
 
                 edge.intensity.twin = master_edge.intensity
                 edge.onset_energy.twin = master_edge.onset_energy

exspy/signals/eels.py

@@ -1626,7 +1626,7 @@ def create_model(
         low_loss=None,
         auto_background=True,
         auto_add_edges=True,
-        GOS="gosh",
+        GOS="dft",
         gos_file_path=None,
         dictionary=None,
     ):
@@ -1635,6 +1635,7 @@ def create_model(
         Parameters
         ----------
         %s
+        GOS: Generalized Oscillator Strength, availiable option in ['hydrogenic', 'dft', 'dirac', 'Hartree-Slater'], default is 'dft'
 
         Returns
         -------
@@ -1660,6 +1661,7 @@ def create_model(
             auto_add_edges=auto_add_edges,
             GOS=GOS,
             dictionary=dictionary,
+            gos_file_path=gos_file_path,
         )
         return model
 

exspy/tests/components/test_eels_cl_edge.py

@@ -49,3 +49,29 @@ def test_restore_EELS_model(tmp_path):
     s2 = hs.load(fname)
     m3 = s2.models.restore(model_name)
     np.testing.assert_allclose(m.as_signal(), m3.as_signal())
+
+
+def test_restore_EELS_model_dirac(tmp_path):
+    s = hs.load(TEST_DATA_DIR / "coreloss_spectrum.msa", signal_type="EELS")
+    ll = hs.load(TEST_DATA_DIR / "lowloss_spectrum.msa", signal_type="EELS")
+
+    s.add_elements(("Mn", "O"))
+    s.set_microscope_parameters(
+        beam_energy=300, convergence_angle=24.6, collection_angle=13.6
+    )
+
+    m = s.create_model(low_loss=ll, GOS="dirac")
+    m.enable_fine_structure()
+    m.multifit(kind="smart")
+
+    model_name = "fit1"
+    m.store(model_name)
+    fname = tmp_path / "test_save_eelsmodel.hspy"
+    s.save(tmp_path / fname)
+    m2 = s.models.restore(model_name)
+
+    np.testing.assert_allclose(m.as_signal(), m2.as_signal())
+
+    s2 = hs.load(fname)
+    m3 = s2.models.restore(model_name)
+    np.testing.assert_allclose(m.as_signal(), m3.as_signal())

exspy/tests/misc/test_gos.py

@@ -80,3 +80,16 @@ def test_binding_energy_database():
         # These elements are not in the database
         if element not in ["Bk", "Cf", "Cm", "metadata"]:
             assert "Binding_energies" in elements[element]["Atomic_properties"].keys()
+
+
+def test_dirac_gosh_not_in_conventions():
+    gos = GoshGOS("Ti_L2", source="dirac")
+    gos.subshell = "L234"
+    with pytest.raises(ValueError):
+        gos.read_gos_data()
+
+
+def test_dirac_gosh_not_in_file():
+    # Dirac GOS which doesn't have the Uue element
+    with pytest.raises(ValueError):
+        _ = GoshGOS("Uue_L3", source="dirac")

exspy/tests/models/test_eelsmodel.py

@@ -27,8 +27,9 @@
 import hyperspy.api as hs
 from exspy.misc.elements import elements_db as elements
 from hyperspy.decorators import lazifyTestClass
-from exspy.misc.eels.gosh_gos import _GOSH_URL, _GOSH_KNOWN_HASH
+from exspy.misc.eels.gosh_gos import DFT_GOSH, DIRAC_GOSH
 from exspy.signals import EELSSpectrum
+from hyperspy.exceptions import VisibleDeprecationWarning
 
 
 # Dask does not always work nicely with np.errstate,
@@ -72,20 +73,46 @@ def test_gos_hydrogenic(self):
         m.fit()
 
     def test_gos_gosh(self):
-        m = self.s.create_model(auto_add_edges=True, GOS="gosh")
-        assert m["B_K"].GOS._name == "gosh"
+        with pytest.warns(VisibleDeprecationWarning):
+            m = self.s.create_model(auto_add_edges=True, GOS="gosh")
+        assert m["B_K"].GOS._name == "dft"
+        m.fit()
+
+        with pytest.raises(ValueError):
+            self.s.create_model(auto_add_edges=True, GOS="not_a_GOS")
+
+    def test_gos_gosh_dft(self):
+        m = self.s.create_model(auto_add_edges=True, GOS="dft")
+        assert m["B_K"].GOS._name == "dft"
+        m.fit()
+
+        with pytest.raises(ValueError):
+            self.s.create_model(auto_add_edges=True, GOS="not_a_GOS")
+
+    def test_gos_gosh_dirac(self):
+        m = self.s.create_model(auto_add_edges=True, GOS="dirac")
+        assert m["B_K"].GOS._name == "dirac"
         m.fit()
 
         with pytest.raises(ValueError):
             self.s.create_model(auto_add_edges=True, GOS="not_a_GOS")
 
     def test_gos_file(self):
         gos_file_path = pooch.retrieve(
-            url=_GOSH_URL,
-            known_hash=_GOSH_KNOWN_HASH,
+            url=DFT_GOSH["URL"],
+            known_hash=DFT_GOSH["KNOWN_HASH"],
         )
         self.s.create_model(auto_add_edges=True, gos_file_path=gos_file_path)
 
+    def test_gos_file_dirac(self):
+        gos_file_path = pooch.retrieve(
+            url=DIRAC_GOSH["URL"],
+            known_hash=DIRAC_GOSH["KNOWN_HASH"],
+        )
+        self.s.create_model(
+            auto_add_edges=True, gos_file_path=gos_file_path, GOS="dirac"
+        )
+
     def test_auto_add_background_true(self):
         m = self.s.create_model(auto_background=True)
         from hyperspy.components1d import PowerLaw