Bug fixes (#25)

* Improve the handling of parameter normalization in simul_fit
* Improve the handling of constant parsing
* boost test coverage

Author: yuefan98

nleis/nleis.py

@@ -94,7 +94,10 @@ def __init__(self, circuit_1='', circuit_2='', initial_guess=[],
                     'Either circuit_1 or circuit_2 cannot be empty')
             edited_circuit = ''
             for elem in elements_1:
-                nl_elem = elem[0:-1]+'n'+elem[-1]
+                raw_elem = get_element_from_name(elem)
+                len_raw_elem = len(raw_elem)
+                nl_elem = elem[0:len_raw_elem] + 'n' + elem[len_raw_elem:]
+                # elem[0:-1]+'n'+elem[-1]
                 if nl_elem in elements_2:
                     edited_circuit += '-' + nl_elem
                 else:
@@ -160,9 +163,12 @@ def __init__(self, circuit_1='', circuit_2='', initial_guess=[],
                         len_elem = len(raw_elem)
                         nl_elem = elem[0:len_elem]+'n'+elem[len_elem:]
                         raw_nl_elem = get_element_from_name(nl_elem)
-                        if raw_nl_elem in circuit_elements.keys():
+                        allowed_elems = circuit_elements.keys()
+                        if raw_nl_elem in allowed_elems:
                             self.constants_2[nl_elem] = self.constants[elem]
                         else:
+                            # this code is kept here to ignore
+                            # EIS only constants in constnats_2
                             self.constants_2[elem] = self.constants[elem]
 
                     if raw_elem[-1] == 'n':
@@ -174,11 +180,9 @@ def __init__(self, circuit_1='', circuit_2='', initial_guess=[],
                                 + f'number of parameters ({raw_num_params})')
 
                         num_params = check_and_eval(raw_elem[0:-1]).num_params
-                        len_elem = len(raw_elem[0:-1])
                         if param_num < num_params:
-                            self.constants_1[
-                                elem[0:len_elem] +
-                                elem[len_elem+1:]] = self.constants[elem]
+                            self.constants_1[elem.replace(
+                                'n', '')] = self.constants[elem]
                         self.constants_2[elem] = self.constants[elem]
 
         else:

nleis/nleis_fitting.py

@@ -187,15 +187,17 @@ def simul_fit(frequencies, Z1, Z2, circuit_1, circuit_2, edited_circuit,
             inf_in_bounds = np.any(np.isinf(bounds[0])) \
                 or np.any(np.isinf(bounds[1]))
             if inf_in_bounds:
-                lb = np.where(bounds[0] == -np.inf, -1e10, bounds[0])
-                ub = np.where(bounds[1] == np.inf, 1e10, bounds[1])
+                lb = np.where(np.array(bounds[0]) == -np.inf, -1e10, bounds[0])
+                ub = np.where(np.array(bounds[1]) == np.inf, 1e10, bounds[1])
                 bounds = (lb, ub)
                 warnings.warn("inf is detected in the bounds, "
                               "to enable parameter normalization, "
                               "the bounds has been capped at 1e10. "
                               "You can disable parameter normalization "
                               "by set param_norm to False .")
-            # ub = bounds[1]
+            else:
+                ub = bounds[1]
+
             bounds = bounds/ub
         else:
             ub = np.ones(len(bounds[1]))

nleis/nleis_tests/test_nleis.py

@@ -87,11 +87,20 @@ def test_EISandNLEIS():
                      1e-3, 1e-3, 1e-3, 1e-2, 1000, 0,
                      # TDS1 + additioal nonlinear parameters
                      ]
+    # check correct assignment of constants
+    # when EIS element is supplied
+    NLEIS_circuit = EISandNLEIS(
+        circ_str_1, circ_str_2, initial_guess=initial_guess,
+        constants={'L0': 1e-7, 'TDS1_3': 1})
+
+    assert {'L0': 1e-7, 'TDS1_3': 1} == NLEIS_circuit.constants_1
+    assert {'TDSn1_3': 1} == NLEIS_circuit.constants_2
 
+    # check correct assignment of constants
+    # when 2nd-NLEIS element is supplied
     NLEIS_circuit = EISandNLEIS(
         circ_str_1, circ_str_2, initial_guess=initial_guess,
         constants={'L0': 1e-7, 'TDSn1_6': 0})
-
     assert {'L0': 1e-7} == NLEIS_circuit.constants_1
     assert {'TDSn1_6': 0} == NLEIS_circuit.constants_2
 
@@ -161,9 +170,17 @@ def test_EISandNLEIS():
 
     with pytest.raises(ValueError):
         NLEIS_circuit = EISandNLEIS(
-            circ_str_1, circ_str_2='', initial_guess=[1],
+            circ_str_1, circ_str_2, initial_guess=[1],
             constants={'L0': 1e-7, 'TDSn1_6': 0})
 
+    # check that wrong constants input raise ValueError
+    # when the wrong constants is applied for EIS_circuit
+
+    with pytest.raises(ValueError):
+        NLEIS_circuit = EISandNLEIS(
+            circ_str_1, circ_str_2, initial_guess=initial_guess,
+            constants={'L0': 1e-7, 'TDS1_10': 0})
+
 
 def test_eq():
     NLEIS_circuit = NLEISCustomCircuit()

nleis/nleis_tests/test_nleis_fitting.py

@@ -288,6 +288,16 @@ def test_buildCircuit():
                         constants={})[0].replace(' ', '') == \
         'R([100],[1000.0,5.0,0.01])'
 
+    # Test two elements circuit with constants for one elements
+    circuit = 'R1-R2'
+    params = [100]
+    frequencies = [1000.0, 5.0, 0.01]
+
+    assert buildCircuit(circuit, frequencies, *params,
+                        constants={'R2': 1})[0].replace(' ', '') == \
+        's([R([100],[1000.0,5.0,0.01]),' +\
+        'R([1],[1000.0,5.0,0.01])])'
+
 
 def test_mae():
     a = np.array([2 + 4*1j, 3 + 2*1j])
@@ -365,10 +375,19 @@ def test_simul_fit():
                           edited_circuit, initial_guess, constants_1={},
                           constants_2={},
                           bounds=None, opt='max', cost=0.5, max_f=10,
-                          param_norm=True, positive=True)
+                          param_norm=False, positive=False)
 
     assert np.allclose(p, results, rtol=1e-3, atol=1e-3)
 
+    # test the option of parameter normalization
+    with pytest.warns(UserWarning, match="inf is detected in the bounds"):
+        bounds = set_default_bounds(edited_circuit)
+        p, perror = simul_fit(f, Z1, Z2, circ_str_1, circ_str_2,
+                              edited_circuit, initial_guess, constants_1={},
+                              constants_2={},
+                              bounds=bounds, opt='max', cost=0.5, max_f=10,
+                              param_norm=True, positive=True)
+
 
 def test_individual_parameters():
 
@@ -446,8 +465,6 @@ def test_individual_parameters():
         constants_1={'TDS1_0': 0}, constants_2={'TDSn0_6': 0.1})
     assert np.allclose(p1, [1e-7, 1e-3, 5e-3, 1e-3, 10.0,
                        1e-02, 100.0, 1e-3, 1e-03, 1e-02, 1000.0])
-    print(p1)
-    print(p2)
     assert np.allclose(p2, [5e-3, 1e-3, 10, 1e-2, 100, 10])
 
     # test the case when only one electrode is contributing to the 2nd-NLEIS