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Created function to process the list of column types and return a numpy dtype
This commit is contained in:
Chris Kerr
96
BioLogic.py
96
BioLogic.py
@@ -8,6 +8,7 @@ import csv
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from os import SEEK_SET, SEEK_CUR
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import time
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from datetime import date
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from collections import OrderedDict
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import numpy as np
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@@ -129,19 +130,28 @@ VMPmodule_hdr = np.dtype([('shortname', 'S10'),
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('length', '<u4'),
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('version', '<u4'),
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('date', 'S8')])
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VMPdata_dtype = np.dtype([('flags', 'u1'),
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("time/s", '<f8'),
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("control/V/mA", '<f4'),
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("Ewe/V", '<f4'),
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("dQ/mA.h", '<f8'),
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("P/W", '<f4')])
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VMPdata_dtype_extra = np.dtype([('flags', '<u2'),
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('blank', 'a1'),
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("time/s", '<f8'),
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("control/V/mA", '<f4'),
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("Ewe/V", '<f4'),
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("dQ/mA.h", '<f8'),
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("P/W", '<f4')])
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def VMPdata_dtype_from_colIDs(colIDs):
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dtype_dict = OrderedDict()
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for colID in colIDs:
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if colID in (1, 2, 3, 21, 31, 65):
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dtype_dict['flags'] = 'u1'
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elif colID in (131,):
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dtype_dict['flags2'] = '<u2'
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elif colID == 4:
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dtype_dict['time/s'] = '<f8'
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elif colID == 5:
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dtype_dict['control/V/mA'] = '<f4'
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elif colID == 6:
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dtype_dict['Ewe/V'] = '<f4'
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elif colID == 7:
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dtype_dict['dQ/mA.h'] = '<f8'
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elif colID == 70:
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dtype_dict['P/W'] = '<f4'
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else:
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raise NotImplementedError("column type %d not implemented" % colID)
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return np.dtype(list(dtype_dict.items()))
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def read_VMP_modules(fileobj, read_module_data=True):
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@@ -210,59 +220,43 @@ class MPRfile:
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self.modules = modules
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settings_mod, = (m for m in modules if m['shortname'] == b'VMP Set ')
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data_module, = (m for m in modules if m['shortname'] == b'VMP data ')
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log_module, = (m for m in modules if m['shortname'] == b'VMP LOG ')
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maybe_log_module = [m for m in modules if m['shortname'] == b'VMP LOG ']
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n_data_points = np.fromstring(data_module['data'][:4], dtype='<u4')
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## not actually sure if this is the number of columns or if it means
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## something else:
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n_columns = int(data_module['data'][4])
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if data_module['version'] == 0:
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## There is 100 bytes of data before the main array starts
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assert(n_columns == 11)
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column_types = np.fromstring(data_module['data'][5:], dtype='u1',
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count=n_columns)
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np.testing.assert_array_equal(column_types,
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[1, 2, 3, 21, 31, 65,
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4, 5, 6, 7, 70])
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assert(data_module['length'] - 100 ==
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VMPdata_dtype.itemsize * n_data_points)
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self.data = np.frombuffer(data_module['data'],
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dtype=VMPdata_dtype,
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offset=100)
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remaining_headers = data_module['data'][5 + n_columns:100]
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main_data = data_module['data'][100:]
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elif data_module['version'] == 2:
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## There is 405 bytes of data before the main array starts
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column_types = np.fromstring(data_module['data'][5:], dtype='<u2',
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count=n_columns)
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if n_columns == 11:
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np.testing.assert_array_equal(column_types,
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[1, 2, 3, 21, 31, 65,
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4, 5, 6, 7, 70])
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assert(data_module['length'] - 405 ==
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VMPdata_dtype.itemsize * n_data_points)
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self.data = np.frombuffer(data_module['data'],
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dtype=VMPdata_dtype,
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offset=405)
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elif n_columns == 12:
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np.testing.assert_array_equal(column_types,
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[1, 2, 3, 21, 31, 65,
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131, 4, 5, 6, 7, 70])
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assert(data_module['length'] - 405 ==
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VMPdata_dtype_extra.itemsize * n_data_points)
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self.data = np.frombuffer(data_module['data'],
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dtype=VMPdata_dtype_extra,
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offset=405)
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assert(np.all(self.data['blank'] == b'\x00'))
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else:
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raise ValueError("Cannot deal with n_columns = %d" % n_columns)
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## There is 405 bytes of data before the main array starts
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remaining_headers = data_module['data'][5 + 2 * n_columns:405]
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main_data = data_module['data'][405:]
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else:
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raise ValueError("Unrecognised version for data module: %d" %
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data_module['version'])
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assert(not any(remaining_headers))
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self.dtype = VMPdata_dtype_from_colIDs(column_types)
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self.data = np.fromstring(main_data, dtype=self.dtype)
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assert(self.data.shape[0] == n_data_points)
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## No idea what these 'column types' mean or even if they are actually
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## column types at all
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self.version = int(data_module['version'])
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self.cols = column_types
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self.npts = n_data_points
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tm = time.strptime(str(settings_mod['date'], encoding='ascii'),
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'%m/%d/%y')
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self.startdate = date(tm.tm_year, tm.tm_mon, tm.tm_mday)
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tm = time.strptime(str(log_module['date'], encoding='ascii'),
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'%m/%d/%y')
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self.enddate = date(tm.tm_year, tm.tm_mon, tm.tm_mday)
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if maybe_log_module:
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log_module, = maybe_log_module
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tm = time.strptime(str(log_module['date'], encoding='ascii'),
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'%m/%d/%y')
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self.enddate = date(tm.tm_year, tm.tm_mon, tm.tm_mday)
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