Added a class to read in .mpt files as numpy record arrays

Realised that comparing numpy arrays read in from the binary .mpr
files to a csv.DictReader would be more work than just writing a
new function to read in a record array.

BioLogic.py

@@ -1,11 +1,84 @@
 # -*- coding: utf-8 -*-
 """Code to read in data files from Bio-Logic instruments"""
 
+__all__ = ['MPTfileCSV', 'MPTfile']
+
 import re
 import csv
 
+import numpy as np
+
+
+def fieldname_to_dtype(fieldname):
+    """Converts a column header from the MPT file into a tuple of
+    canonical name and appropriate numpy dtype"""
+
+    if fieldname == 'mode':
+        return ('mode', np.uint8)
+    elif fieldname in ("ox/red", "error", "control changes", "Ns changes",
+                       "counter inc."):
+        return (fieldname, np.bool_)
+    elif fieldname in ("time/s", "Ewe/V", "P/W", "(Q-Qo)/mA.h", "x"):
+        return (fieldname, np.float_)
+    elif fieldname in ("dq/mA.h", "dQ/mA.h"):
+        return ("dQ/mA.h", np.float_)
+    elif fieldname in ("I/mA", "<I>/mA"):
+        return ("I/mA", np.float_)
+    elif fieldname in ("control/V", "control/V/mA"):
+        return ("control/V/mA", np.float_)
+    else:
+        raise ValueError("Invalid column header: %s" % fieldname)
+
 
 def MPTfile(file_or_path):
+    """Opens .mpt files as numpy record arrays
+
+    Checks for the correct headings, skips any comments and returns a
+    numpy record array object and a list of comments
+    """
+
+    if isinstance(file_or_path, str):
+        mpt_file = open(file_or_path, 'rb')
+    else:
+        mpt_file = file_or_path
+
+    magic = next(mpt_file)
+    if magic != b'EC-Lab ASCII FILE\r\n':
+        raise ValueError("Bad first line for EC-Lab file: '%s'" % magic)
+
+    nb_headers_match = re.match(b'Nb header lines : (\d+)\s*$', next(mpt_file))
+    nb_headers = int(nb_headers_match.group(1))
+    if nb_headers < 3:
+        raise ValueError("Too few header lines: %d" % nb_headers)
+
+    ## The 'magic number' line, the 'Nb headers' line and the column headers
+    ## make three lines. Every additional line is a comment line.
+    comments = [next(mpt_file) for i in range(nb_headers - 3)]
+
+    fieldnames = next(mpt_file).decode('ascii').strip().split('\t')
+
+    expected_fieldnames = (
+        ["mode", "ox/red", "error", "control changes", "Ns changes",
+         "counter inc.", "time/s", "control/V/mA", "Ewe/V", "dq/mA.h",
+         "P/W", "<I>/mA", "(Q-Qo)/mA.h", "x"],
+        ["mode", "ox/red", "error", "control changes", "Ns changes",
+         "counter inc.", "time/s", "control/V", "Ewe/V", "I/mA",
+         "dQ/mA.h", "P/W"],
+        ["mode", "ox/red", "error", "control changes", "Ns changes",
+         "counter inc.", "time/s", "control/V", "Ewe/V", "<I>/mA",
+         "dQ/mA.h", "P/W"])
+    if fieldnames not in expected_fieldnames:
+        raise ValueError("Unrecognised headers for MPT file format %s" %
+                         fieldnames)
+
+    record_type = np.dtype(list(map(fieldname_to_dtype, fieldnames)))
+
+    mpt_array = np.loadtxt(mpt_file, dtype=record_type)
+
+    return mpt_array, comments
+
+
+def MPTfileCSV(file_or_path):
     """Simple function to open MPT files as csv.DictReader objects
 
     Checks for the correct headings, skips any comments and returns a
@@ -21,7 +94,7 @@ def MPTfile(file_or_path):
     if magic != 'EC-Lab ASCII FILE\n':
         raise ValueError("Bad first line for EC-Lab file: '%s'" % magic)
 
-    nb_headers_match = re.match('Nb header lines : (\d+)', next(mpt_file))
+    nb_headers_match = re.match('Nb header lines : (\d+)\s*$', next(mpt_file))
     nb_headers = int(nb_headers_match.group(1))
     if nb_headers < 3:
         raise ValueError("Too few header lines: %d" % nb_headers)

tests/test_BioLogic.py

@@ -4,7 +4,7 @@ import os.path
 
 from nose.tools import ok_, eq_, raises
 
-from .. import MPTfile
+from ..BioLogic import MPTfile, MPTfileCSV
 
 testdata_dir = os.path.join(os.path.dirname(__file__), 'testdata')
 
@@ -12,6 +12,20 @@ testdata_dir = os.path.join(os.path.dirname(__file__), 'testdata')
 def test_open_MPT():
     mpt1, comments = MPTfile(os.path.join(testdata_dir, 'bio-logic1.mpt'))
     eq_(comments, [])
+    eq_(mpt1.dtype.names, ("mode", "ox/red", "error", "control changes",
+                           "Ns changes", "counter inc.", "time/s",
+                           "control/V/mA", "Ewe/V", "dQ/mA.h", "P/W",
+                           "I/mA", "(Q-Qo)/mA.h", "x"))
+
+
+@raises(ValueError)
+def test_open_MPT_fails_for_bad_file():
+    mpt1 = MPTfile(os.path.join(testdata_dir, 'bio-logic1.mpr'))
+
+
+def test_open_MPT_csv():
+    mpt1, comments = MPTfileCSV(os.path.join(testdata_dir, 'bio-logic1.mpt'))
+    eq_(comments, [])
     eq_(mpt1.fieldnames, ["mode", "ox/red", "error", "control changes",
                           "Ns changes", "counter inc.", "time/s",
                           "control/V/mA", "Ewe/V", "dq/mA.h", "P/W",
@@ -19,5 +33,5 @@ def test_open_MPT():
 
 
 @raises(ValueError)
-def test_open_MPT_fails_for_bad_file():
-    mpt1 = MPTfile(os.path.join(testdata_dir, 'bio-logic1.mpr'))
+def test_open_MPT_csv_fails_for_bad_file():
+    mpt1 = MPTfileCSV(os.path.join(testdata_dir, 'bio-logic1.mpr'))