Fixing example of validation, fixing validation.py and adding support for Kolibrik

docs/source/examples/validation_example.ipynb

@@ -192,10 +192,10 @@
     "ax2 = fig.add_subplot(gs[2,:])\n",
     "\n",
     "# plot original data\n",
-    "plot_nyquist(ax1, Z, fmt='s')\n",
+    "plot_nyquist(ax=ax1, Z=Z, fmt='s')\n",
     "\n",
     "# plot measurement model\n",
-    "plot_nyquist(ax1, meas_model.predict(f), fmt='-', scale=1e3, units='\\Omega')\n",
+    "plot_nyquist(ax=ax1, Z=meas_model.predict(f), fmt='-', scale=1e3, units='\\Omega')\n",
     "\n",
     "ax1.legend(['Data', 'Measurement model'], loc=2, fontsize=12)\n",
     "\n",
@@ -330,10 +330,10 @@
     "ax2 = fig.add_subplot(gs[2,:])\n",
     "\n",
     "# plot original data\n",
-    "plot_nyquist(ax1, Z, fmt='s')\n",
+    "plot_nyquist(ax=ax1, Z=Z, fmt='s')\n",
     "\n",
     "# plot measurement model\n",
-    "plot_nyquist(ax1, Z_linKK, fmt='-', scale=1e3, units='\\Omega')\n",
+    "plot_nyquist(ax=ax1, Z=Z_linKK, fmt='-', scale=1e3, units='\\Omega')\n",
     "\n",
     "ax1.legend(['Data', 'Lin-KK model'], loc=2, fontsize=12)\n",
     "\n",

impedance/preprocessing.py

@@ -390,6 +390,39 @@ def readCHInstruments(filename):
 
     return np.array(f), np.array(Z)
 
+def readKolibrik(filename):
+    """ function for dat files from Kolibrik Potentiostats
+
+    Parameters
+    ----------
+    filename: string
+        Filename of .dat file to extract impedance data
+
+    Returns
+    -------
+    frequencies : np.ndarray
+        Array of frequencies
+    impedance : np.ndarray of complex numbers
+        Array of complex impedances
+
+    """
+
+    with open(filename, 'r', encoding="utf8") as input_file:
+        lines = input_file.readlines()
+
+    for i, line in enumerate(lines):
+        if line.find('[Data]') != -1:
+            start_line = i
+
+    raw_data = lines[start_line+2:-1]
+    f, Z = [], []
+    for line in raw_data:
+        each = line.split('\t')
+        f.append(float(each[5]))
+        Z.append(complex(float(each[3]), float(each[4])))
+
+    return np.array(f), np.array(Z)
+
 
 def readCSV(filename):
     """ function for reading plain csv files

impedance/validation.py

@@ -277,7 +277,7 @@ def eval_linKK(elements, ts, f):
     circuit_string = circuit_string.strip(',')
     circuit_string += '])'
 
-    return eval(circuit_string, circuit_elements)
+    return eval(circuit_string, {**circuit_elements, 'np': np})
 
 
 def residuals_linKK(elements, ts, Z, f, residuals='real'):