Add method to sort integrals (#23)

* Add a method to sort integrals and a test

* Add sorting of integrals (packaged and regular), if in existence

* Add a way to only sort the names -> required for GUI

rimseval/processor.py

@@ -741,6 +741,39 @@ def run_macro(self, fname: Path) -> None:
 
         sys.path.remove(str(file_path))
 
+    def sort_integrals(self, sort_vals: bool = True) -> None:
+        """Sort all the integrals that are defined by mass.
+
+        Takes the integrals and the names and sorts them by mass. The starting mass
+        of each integral is used for sorting.
+        If no integrals are defined, this routine does nothing.
+
+        :param sort_vals: Sort the integrals and integral packages? Default: True
+
+        Example:
+            >>> crd.def_integrals
+            ["Fe-56", "Ti-46"], array([[55.8, 56.2], [45.8, 46.2]])
+            >>> crd.sort_integrals()
+            >>> crd.def_integrals
+            ["Ti-46", "Fe-56"], array([[45.8, 46.2], [55.8, 56.2]])
+        """
+        if self.def_integrals is None:
+            return
+
+        names, values = self.def_integrals
+        sort_ind = values[:, 0].argsort()
+
+        if (sort_ind == np.arange(len(names))).all():  # already sorted
+            return
+
+        names_sorted = list(np.array(names)[sort_ind])
+        self.def_integrals = names_sorted, values[sort_ind]
+
+        if self.integrals is not None and sort_vals:
+            self.integrals = self.integrals[sort_ind]
+        if self.integrals_pkg is not None and sort_vals:
+            self.integrals_pkg = self.integrals_pkg[:, sort_ind]
+
     def spectrum_full(self) -> None:
         """Create ToF and summed ion count array for the full spectrum.
 

tests/func/test_processor.py

@@ -214,6 +214,29 @@ def test_packages(crd_file):
     assert crd.nof_shots_pkg.sum() == crd.nof_shots
 
 
+def test_sort_integrals(crd_file):
+    """Sort integrals by first mass."""
+    _, _, _, fname = crd_file
+    crd = CRDFileProcessor(Path(fname))
+    crd.sort_integrals()  # does nothing, since None
+    crd.def_integrals = ["Fe-56", "Ti-46"], np.array([[55.8, 56.2], [45.8, 46.2]])
+
+    crd.integrals = np.array([[2, 2], [1, 1]])
+    crd.integrals_pkg = np.array([crd.integrals, crd.integrals - 1])
+
+    names_exp = ["Ti-46", "Fe-56"]
+    values_exp = np.array([[45.8, 46.2], [55.8, 56.2]])
+    integrals_exp = np.array([[1, 1], [2, 2]])
+    integrals_pkg_exp = np.array([[[1, 1], [2, 2]], [[0, 0], [1, 1]]])
+
+    crd.sort_integrals()
+    names_rec, values_rec = crd.def_integrals
+    assert names_rec == names_exp
+    np.testing.assert_equal(values_rec, values_exp)
+    np.testing.assert_equal(crd.integrals, integrals_exp)
+    np.testing.assert_equal(crd.integrals_pkg, integrals_pkg_exp)
+
+
 def test_spectrum_part(crd_file):
     """Cut spectrum by two shots."""
     _, ions_per_shot, _, fname = crd_file