From 9d06fabde0413419e0c27b854ce126a94eb81082 Mon Sep 17 00:00:00 2001
From: Eric Prestat <eric.prestat@gmail.com>
Date: Sun, 17 Mar 2024 19:33:58 +0000
Subject: [PATCH] Fix restoring Gosh and Hartree Slater GOS: `subshell_factor`
 was missing from the `whitelist` and therefore its value wasn't restored

---
 exspy/misc/eels/gosh_gos.py                  |    1 +
 exspy/misc/eels/hartree_slater_gos.py        |    1 +
 exspy/tests/components/coreloss_spectrum.msa | 2062 +++++++++++++++++
 exspy/tests/components/lowloss_spectrum.msa  | 2064 ++++++++++++++++++
 exspy/tests/components/test_ceels_cl_edge.py |   21 -
 exspy/tests/components/test_eels_cl_edge.py  |   51 +
 pyproject.toml                               |    3 +-
 7 files changed, 4181 insertions(+), 22 deletions(-)
 create mode 100644 exspy/tests/components/coreloss_spectrum.msa
 create mode 100644 exspy/tests/components/lowloss_spectrum.msa
 delete mode 100644 exspy/tests/components/test_ceels_cl_edge.py
 create mode 100644 exspy/tests/components/test_eels_cl_edge.py

diff --git a/exspy/misc/eels/gosh_gos.py b/exspy/misc/eels/gosh_gos.py
index 122d2e794..74f355df6 100644
--- a/exspy/misc/eels/gosh_gos.py
+++ b/exspy/misc/eels/gosh_gos.py
@@ -76,6 +76,7 @@ class GoshGOS(TabulatedGOS):
         "qaxis": None,
         "element": None,
         "subshell": None,
+        "subshell_factor": None,
     }
 
     def __init__(self, element_subshell, gos_file_path=None):
diff --git a/exspy/misc/eels/hartree_slater_gos.py b/exspy/misc/eels/hartree_slater_gos.py
index 8c891afd7..8439136fa 100644
--- a/exspy/misc/eels/hartree_slater_gos.py
+++ b/exspy/misc/eels/hartree_slater_gos.py
@@ -107,6 +107,7 @@ class HartreeSlaterGOS(TabulatedGOS):
         "qaxis": None,
         "element": None,
         "subshell": None,
+        "subshell_factor": None,
     }
 
     def read_elements(self):
diff --git a/exspy/tests/components/coreloss_spectrum.msa b/exspy/tests/components/coreloss_spectrum.msa
new file mode 100644
index 000000000..7ed567b70
--- /dev/null
+++ b/exspy/tests/components/coreloss_spectrum.msa
@@ -0,0 +1,2062 @@
+#FORMAT      : EMSA/MAS Spectral Data File
+#VERSION     : 1.0
+#TITLE       : 
+#OWNER       : 
+#NPOINTS     : 2048.00
+#NCOLUMNS    : 1.00000
+#XUNITS      : eV
+#YUNITS      : Counts
+#DATATYPE    : Y
+#XPERCHAN    : 0.200000
+#OFFSET      : 360.000
+#SIGNALTYPE  : ELS
+#SPECTRUM    : 
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+#ENDOFDATA   : 
diff --git a/exspy/tests/components/lowloss_spectrum.msa b/exspy/tests/components/lowloss_spectrum.msa
new file mode 100644
index 000000000..99bb19e7e
--- /dev/null
+++ b/exspy/tests/components/lowloss_spectrum.msa
@@ -0,0 +1,2064 @@
+#FORMAT      : EMSA/MAS Spectral Data File
+#VERSION     : 1.0
+#TITLE       : 
+#DATE        : 04-SEP-2012
+#TIME        : 23:14
+#OWNER       : 
+#NPOINTS     : 2048.00
+#NCOLUMNS    : 1.00000
+#XUNITS      : eV
+#YUNITS      : Counts
+#DATATYPE    : Y
+#XPERCHAN    : 0.200000
+#OFFSET      : -40.0000
+#SIGNALTYPE  : ELS
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+#ENDOFDATA   : 
diff --git a/exspy/tests/components/test_ceels_cl_edge.py b/exspy/tests/components/test_ceels_cl_edge.py
deleted file mode 100644
index dccad8723..000000000
--- a/exspy/tests/components/test_ceels_cl_edge.py
+++ /dev/null
@@ -1,21 +0,0 @@
-# -*- coding: utf-8 -*-
-# Copyright 2007-2024 The eXSpy developers
-#
-# This file is part of eXSpy.
-#
-# eXSpy is free software: you can redistribute it and/or modify
-# it under the terms of the GNU General Public License as published by
-# the Free Software Foundation, either version 3 of the License, or
-# (at your option) any later version.
-#
-# eXSpy is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-# GNU General Public License for more details.
-#
-# You should have received a copy of the GNU General Public License
-# along with eXSpy. If not, see <https://www.gnu.org/licenses/#GPL>.
-
-
-def test_eels_cl_edge():
-    pass
diff --git a/exspy/tests/components/test_eels_cl_edge.py b/exspy/tests/components/test_eels_cl_edge.py
new file mode 100644
index 000000000..88eb9e111
--- /dev/null
+++ b/exspy/tests/components/test_eels_cl_edge.py
@@ -0,0 +1,51 @@
+# -*- coding: utf-8 -*-
+# Copyright 2007-2024 The eXSpy developers
+#
+# This file is part of eXSpy.
+#
+# eXSpy is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# eXSpy is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with eXSpy. If not, see <https://www.gnu.org/licenses/#GPL>.
+
+from pathlib import Path
+
+import hyperspy.api as hs
+import numpy as np
+
+
+TEST_DATA_DIR = Path(__file__).parent
+
+
+def test_restore_EELS_model(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)
+    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())
diff --git a/pyproject.toml b/pyproject.toml
index f57cff804..7ac9c9dcf 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -120,7 +120,8 @@ include = ["exspy*"]
 [tool.setuptools.package-data]
 "*" = [
   "*hspy",
-  "*.yaml"
+  "*.yaml",
+  "*.msa",
   ]
 
 [tool.setuptools_scm]