Add biologic data functionality (#59)

* Added example BioLogic data file. Started working on Bode plot function * Added loading of data from Biologic ECLab MPT format * Added loading of data from Biologic ECLab MPT format * Reverted plotting.py to commit ebdb855 * BioLogic Data files need latin-w specied as their encoding.
ECSHackWeek · Nov 1, 2019 · 66b389c · 66b389c
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diff --git a/data/exampleDataBioLogic.mpt b/data/exampleDataBioLogic.mpt
@@ -0,0 +1,104 @@
+EC-Lab ASCII FILE
+Nb header lines : 61                          
+
+Potentio Electrochemical Impedance Spectroscopy
+
+Run on channel : 1 (SN 30924)
+User : 
+CE vs. WE compliance from -10 V to 10 V
+Electrode connection : standard
+Ewe ctrl range : min = -2.50 V, max = 2.50 V
+Safety Limits :
+	Do not start on E overload
+Acquisition started on : 02/04/2018 10:02:46
+Technique started on : 02/04/2018 10:02:46
+Saved on :
+	File : EIS OCV after.mpr
+	Directory : C:\Users\shadd\OneDrive\Documents\EC-Lab\Data\Samples\LSC Thin Film Dynamic XAS\eis\
+	Host : 100.88.9.64
+Device : SP-150 (SN 10791079)
+Address : USB
+EC-Lab for windows v11.18 (software)
+Internet server v11.18 (firmware)
+Command interpretor v11.16 (firmware)
+Electrode material : 
+Initial state : 
+Electrolyte : 
+Comments : 
+Electrode surface area : 0.001 cm�
+Characteristic mass : 0.001 g
+Equivalent Weight : 0.000 g/eq.
+Density : 0.000 g/cm3
+Cycle Definition : Charge/Discharge alternance
+Mode                Single sine         
+E (V)               0.0000              
+vs.                 Ref                 
+tE (h:m:s)          0:00:0.0000         
+record              0                   
+dI                  0.000               
+unit dI             mA                  
+dt (s)              0.000               
+fi                  1.000               
+unit fi             kHz                 
+ff                  10.000              
+unit ff             mHz                 
+Nd                  9                   
+Points              per decade          
+spacing             Logarithmic         
+Va (mV)             20.0                
+pw                  0.10                
+Na                  1                   
+corr                0                   
+E range min (V)     -2.500              
+E range max (V)     2.500               
+I Range             Auto                
+Bandwidth           5                   
+nc cycles           0                   
+goto Ns'            0                   
+nr cycles           0                   
+inc. cycle          0                   
+
+freq/Hz	Re(Z)/Ohm	-Im(Z)/Ohm	|Z|/Ohm	Phase(Z)/deg	time/s	<Ewe>/V	<I>/mA	Cs/�F	Cp/�F	cycle number	I Range	|Ewe|/V	|I|/A	Re(Y)/Ohm-1	Im(Y)/Ohm-1	|Y|/Ohm-1	Phase(Y)/deg	
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diff --git a/impedance/preprocessing.py b/impedance/preprocessing.py
@@ -25,7 +25,7 @@ def readFile(filename, instrument=None):
     """
 
     supported_types = ['gamry', 'autolab', 'parstat', 'zplot', 'versastudio'
-                       'powersuite']
+                       'powersuite', 'biologic']
 
     if instrument is not None:
         assert instrument in supported_types,\
@@ -36,6 +36,8 @@ def readFile(filename, instrument=None):
         f, Z = readGamry(filename)
     elif instrument == 'autolab':
         f, Z = readAutolab(filename)
+    elif instrument == 'biologic':
+        f, Z = readBioLogic(filename)
     elif instrument == 'parstat':
         f, Z = readParstat(filename)
     elif instrument == 'zplot':
@@ -114,6 +116,44 @@ def readAutolab(filename):
     return np.array(f), np.array(Z)
 
 
+def readBioLogic(filename):
+    """ function for reading the .mpt file from Biologic
+        EC-lab software
+
+        Parameters
+        ----------
+        filename: string
+            Filename of .csv file to extract impedance data from
+
+        Returns
+        -------
+        frequencies : np.ndarray
+            Array of frequencies
+        impedance : np.ndarray of complex numbers
+            Array of complex impedances
+
+        """
+
+    with open(filename, 'r', encoding="latin-1") as input_file:
+        lines = input_file.readlines()
+
+    header_line = lines[1]
+
+    # MPT data format has variable number of header lines
+    number_header_lines = int(header_line.split(":")[1])
+
+    raw_data = lines[number_header_lines:]
+    f, Z = [], []
+    for line in raw_data:
+        each = line.split('\t')
+        f.append(float(each[0]))
+
+        # MPT data format saves the imaginary portion as -Im(Z) not Im(Z)
+        Z.append(complex(float(each[1]), -1*float(each[2])))
+
+    return np.array(f), np.array(Z)
+
+
 def readParstat(filename):
     """ function for reading the .txt file from Parstat