From de84f9dd403aa084bd0bb712253a35be79d21ad7 Mon Sep 17 00:00:00 2001
From: Chris Kerr <cjk34@cam.ac.uk>
Date: Wed, 11 Dec 2013 13:14:19 +0000
Subject: [PATCH] Added column IDs from step voltammetry

---
 BioLogic.py            | 27 +++++++++------------------
 tests/test_BioLogic.py | 33 ++++++++++++++++++++++++++-------
 2 files changed, 35 insertions(+), 25 deletions(-)

diff --git a/BioLogic.py b/BioLogic.py
index 4a402f3..16ae929 100644
--- a/BioLogic.py
+++ b/BioLogic.py
@@ -24,8 +24,10 @@ def fieldname_to_dtype(fieldname):
                        "counter inc."):
         return (fieldname, np.bool_)
     elif fieldname in ("time/s", "Ewe/V", "P/W", "(Q-Qo)/mA.h", "x",
-                       "control/V", "control/V/mA"):
+                       "control/V", "control/V/mA", "(Q-Qo)/C"):
         return (fieldname, np.float_)
+    elif fieldname in ("cycle number",):
+        return (fieldname, np.int_)
     elif fieldname in ("dq/mA.h", "dQ/mA.h"):
         return ("dQ/mA.h", np.float_)
     elif fieldname in ("I/mA", "<I>/mA"):
@@ -60,23 +62,6 @@ def MPTfile(file_or_path):
     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', 'dq/mA.h',
-         '<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:
-        warn("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)
@@ -155,10 +140,16 @@ def VMPdata_dtype_from_colIDs(colIDs):
             dtype_dict['dQ/mA.h'] = '<f8'
         elif colID == 8:
             dtype_dict['I/mA'] = '<f4'
+        elif colID == 11:
+            dtype_dict['I/mA'] = '<f8'
         elif colID == 19:
             dtype_dict['control/V'] = '<f4'
+        elif colID == 24:
+            dtype_dict['cycle number'] = '<f8'
         elif colID == 70:
             dtype_dict['P/W'] = '<f4'
+        elif colID == 434:
+            dtype_dict['(Q-Qo)/C'] = '<f4'
         else:
             raise NotImplementedError("column type %d not implemented" % colID)
     return np.dtype(list(dtype_dict.items()))    
diff --git a/tests/test_BioLogic.py b/tests/test_BioLogic.py
index 9b169f8..af71206 100644
--- a/tests/test_BioLogic.py
+++ b/tests/test_BioLogic.py
@@ -77,19 +77,30 @@ def test_open_MPR5():
     eq_(mpr.enddate, date(2013, 1, 28))
 
 
+def test_open_MPR6():
+    mpr = MPRfile(os.path.join(testdata_dir, 'bio-logic6.mpr'))
+    ## Check the dates as a basic test that it has been read properly
+    eq_(mpr.startdate, date(2012, 9, 11))
+    ## no end date because no VMP LOG module
+
+
 @raises(ValueError)
 def test_open_MPR_fails_for_bad_file():
     mpr1 = MPRfile(os.path.join(testdata_dir, 'arbin1.res'))
 
 
 def assert_MPR_matches_MPT(mpr, mpt):
-    
+
     def assert_field_matches(fieldname, decimal):
         if fieldname in mpr.dtype.fields:
             assert_array_almost_equal(mpr.data[fieldname],
                                       mpt[fieldname],
                                       decimal=decimal)
 
+    def assert_field_exact(fieldname):
+        if fieldname in mpr.dtype.fields:
+            assert_array_equal(mpr.data[fieldname], mpt[fieldname])
+
     assert_array_equal(mpr.data["flags"] & 0x03, mpt["mode"])
     assert_array_equal(np.array(mpr.data["flags"] & 0x04, dtype=np.bool_),
                        mpt["ox/red"])
@@ -97,8 +108,9 @@ def assert_MPR_matches_MPT(mpr, mpt):
                        mpt["error"])
     assert_array_equal(np.array(mpr.data["flags"] & 0x10, dtype=np.bool_),
                        mpt["control changes"])
-    assert_array_equal(np.array(mpr.data["flags"] & 0x20, dtype=np.bool_),
-                       mpt["Ns changes"])
+    if "Ns changes" in mpt.dtype.fields:                    
+        assert_array_equal(np.array(mpr.data["flags"] & 0x20, dtype=np.bool_),
+                           mpt["Ns changes"])
     ## Nothing uses the 0x40 bit of the flags
     assert_array_equal(np.array(mpr.data["flags"] & 0x80, dtype=np.bool_),
                        mpt["counter inc."])
@@ -114,12 +126,12 @@ def assert_MPR_matches_MPT(mpr, mpt):
                               mpt["Ewe/V"],
                               decimal=6)  # 32 bit float precision
 
-    assert_array_almost_equal(mpr.data["dQ/mA.h"],
-                              mpt["dQ/mA.h"],
-                              decimal=17)  # 64 bit float precision
-
+    assert_field_matches("dQ/mA.h", decimal=17)  # 64 bit float precision
     assert_field_matches("P/W", decimal=10)  # 32 bit float precision for 1.xxE-5
     assert_field_matches("I/mA", decimal=6)  # 32 bit float precision
+    
+    assert_field_exact("cycle number")
+    assert_field_matches("(Q-Qo)/C", decimal=6)  # 32 bit float precision
 
 
 def test_MPR1_matches_MPT1():
@@ -149,3 +161,10 @@ def test_MPR5_matches_MPT5():
                              open(os.path.join(testdata_dir, 'bio-logic5.mpt'),
                                   mode='rb')))
     assert_MPR_matches_MPT(mpr, mpt)
+
+
+def test_MPR6_matches_MPT6():
+    mpr = MPRfile(os.path.join(testdata_dir, 'bio-logic6.mpr'))
+    mpt, comments = MPTfile(os.path.join(testdata_dir, 'bio-logic6.mpt'))
+    mpr.data = mpr.data[:958]  # .mpt file is incomplete
+    assert_MPR_matches_MPT(mpr, mpt)