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Tweaks to make things work on Python 2

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This commit is contained in:
Chris Kerr
2013-12-12 13:46:03 +00:00
parent 34440068a7
commit 5c747fe404
1 changed files with 15 additions and 8 deletions
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23
BioLogic.py
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@@ -3,6 +3,7 @@
__all__ = ['MPTfileCSV', 'MPTfile'] __all__ = ['MPTfileCSV', 'MPTfile']
import sys
import re import re
import csv import csv
from os import SEEK_SET, SEEK_CUR from os import SEEK_SET, SEEK_CUR
@@ -14,6 +15,12 @@ from warnings import warn
import numpy as np import numpy as np
if sys.version_info.major <= 2:
str3 = str
else:
str3 = lambda b: str(b, encoding='ascii')
def fieldname_to_dtype(fieldname): def fieldname_to_dtype(fieldname):
"""Converts a column header from the MPT file into a tuple of """Converts a column header from the MPT file into a tuple of
canonical name and appropriate numpy dtype""" canonical name and appropriate numpy dtype"""
@@ -34,7 +41,7 @@ def fieldname_to_dtype(fieldname):
return ("I/mA", np.float_) return ("I/mA", np.float_)
else: else:
raise ValueError("Invalid column header: %s" % fieldname) raise ValueError("Invalid column header: %s" % fieldname)
def MPTfile(file_or_path): def MPTfile(file_or_path):
"""Opens .mpt files as numpy record arrays """Opens .mpt files as numpy record arrays
@@ -152,7 +159,7 @@ def VMPdata_dtype_from_colIDs(colIDs):
dtype_dict['(Q-Qo)/C'] = '<f4' dtype_dict['(Q-Qo)/C'] = '<f4'
else: else:
raise NotImplementedError("column type %d not implemented" % colID) raise NotImplementedError("column type %d not implemented" % colID)
return np.dtype(list(dtype_dict.items())) return np.dtype(list(dtype_dict.items()))
def read_VMP_modules(fileobj, read_module_data=True): def read_VMP_modules(fileobj, read_module_data=True):
@@ -224,7 +231,7 @@ class MPRfile:
maybe_log_module = [m for m in modules if m['shortname'] == b'VMP LOG '] maybe_log_module = [m for m in modules if m['shortname'] == b'VMP LOG ']
n_data_points = np.fromstring(data_module['data'][:4], dtype='<u4') n_data_points = np.fromstring(data_module['data'][:4], dtype='<u4')
n_columns = int(data_module['data'][4]) n_columns = np.fromstring(data_module['data'][4:5], dtype='u1')
if data_module['version'] == 0: if data_module['version'] == 0:
column_types = np.fromstring(data_module['data'][5:], dtype='u1', column_types = np.fromstring(data_module['data'][5:], dtype='u1',
@@ -241,7 +248,9 @@ class MPRfile:
raise ValueError("Unrecognised version for data module: %d" % raise ValueError("Unrecognised version for data module: %d" %
data_module['version']) data_module['version'])
assert(not any(remaining_headers)) for empty_byte in remaining_headers:
assert(empty_byte == b'\x00')
self.dtype = VMPdata_dtype_from_colIDs(column_types) self.dtype = VMPdata_dtype_from_colIDs(column_types)
self.data = np.fromstring(main_data, dtype=self.dtype) self.data = np.fromstring(main_data, dtype=self.dtype)
assert(self.data.shape[0] == n_data_points) assert(self.data.shape[0] == n_data_points)
@@ -252,14 +261,12 @@ class MPRfile:
self.cols = column_types self.cols = column_types
self.npts = n_data_points self.npts = n_data_points
tm = time.strptime(str(settings_mod['date'], encoding='ascii'), tm = time.strptime(str3(settings_mod['date']), '%m/%d/%y')
'%m/%d/%y')
self.startdate = date(tm.tm_year, tm.tm_mon, tm.tm_mday) self.startdate = date(tm.tm_year, tm.tm_mon, tm.tm_mday)
if maybe_log_module: if maybe_log_module:
log_module, = maybe_log_module log_module, = maybe_log_module
tm = time.strptime(str(log_module['date'], encoding='ascii'), tm = time.strptime(str3(log_module['date']), '%m/%d/%y')
'%m/%d/%y')
self.enddate = date(tm.tm_year, tm.tm_mon, tm.tm_mday) self.enddate = date(tm.tm_year, tm.tm_mon, tm.tm_mday)
## There is a timestamp at either 465 or 469 bytes ## There is a timestamp at either 465 or 469 bytes