mirror of
https://github.com/echemdata/galvani.git
synced 2025-12-14 01:15:34 +00:00
Merge branch 'master' into test-and-fix-Arbin
This commit is contained in:
2
.flake8
Normal file
2
.flake8
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@@ -0,0 +1,2 @@
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# This file will be ignored - see http://flake8.pycqa.org/en/2.6.0/config.html#per-project
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# Edit the [flake8] section in tox.ini instead
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@@ -10,6 +10,7 @@ from os import SEEK_SET
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import time
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from datetime import date, datetime, timedelta
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from collections import defaultdict, OrderedDict
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import functools
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import numpy as np
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@@ -18,7 +19,7 @@ if sys.version_info.major <= 2:
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str3 = str
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from string import maketrans
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else:
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str3 = lambda b: str(b, encoding='ascii')
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str3 = functools.partial(str, encoding='ascii')
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maketrans = bytes.maketrans
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@@ -71,19 +72,20 @@ def MPTfile(file_or_path):
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raise ValueError("Bad first line for EC-Lab file: '%s'" % magic)
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# TODO use rb'string' here once Python 2 is no longer supported
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nb_headers_match = re.match(b'Nb header lines : (\\d+)\\s*$', next(mpt_file))
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nb_headers_match = re.match(b'Nb header lines : (\\d+)\\s*$',
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next(mpt_file))
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nb_headers = int(nb_headers_match.group(1))
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if nb_headers < 3:
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raise ValueError("Too few header lines: %d" % nb_headers)
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## The 'magic number' line, the 'Nb headers' line and the column headers
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## make three lines. Every additional line is a comment line.
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# The 'magic number' line, the 'Nb headers' line and the column headers
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# make three lines. Every additional line is a comment line.
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comments = [next(mpt_file) for i in range(nb_headers - 3)]
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fieldnames = str3(next(mpt_file)).strip().split('\t')
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record_type = np.dtype(list(map(fieldname_to_dtype, fieldnames)))
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## Must be able to parse files where commas are used for decimal points
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# Must be able to parse files where commas are used for decimal points
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converter_dict = dict(((i, comma_converter)
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for i in range(len(fieldnames))))
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mpt_array = np.loadtxt(mpt_file, dtype=record_type,
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@@ -113,8 +115,8 @@ def MPTfileCSV(file_or_path):
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if nb_headers < 3:
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raise ValueError("Too few header lines: %d" % nb_headers)
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## The 'magic number' line, the 'Nb headers' line and the column headers
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## make three lines. Every additional line is a comment line.
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# The 'magic number' line, the 'Nb headers' line and the column headers
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# make three lines. Every additional line is a comment line.
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comments = [next(mpt_file) for i in range(nb_headers - 3)]
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mpt_csv = csv.DictReader(mpt_file, dialect='excel-tab')
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@@ -256,7 +258,8 @@ def read_VMP_modules(fileobj, read_module_data=True):
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if len(module_magic) == 0: # end of file
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break
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elif module_magic != b'MODULE':
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raise ValueError("Found %r, expecting start of new VMP MODULE" % module_magic)
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raise ValueError("Found %r, expecting start of new VMP MODULE"
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% module_magic)
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hdr_bytes = fileobj.read(VMPmodule_hdr.itemsize)
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if len(hdr_bytes) < VMPmodule_hdr.itemsize:
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@@ -280,6 +283,9 @@ def read_VMP_modules(fileobj, read_module_data=True):
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fileobj.seek(hdr_dict['offset'] + hdr_dict['length'], SEEK_SET)
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MPR_MAGIC = b'BIO-LOGIC MODULAR FILE\x1a'.ljust(48) + b'\x00\x00\x00\x00'
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class MPRfile:
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"""Bio-Logic .mpr file
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@@ -302,10 +308,8 @@ class MPRfile:
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mpr_file = open(file_or_path, 'rb')
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else:
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mpr_file = file_or_path
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mpr_magic = b'BIO-LOGIC MODULAR FILE\x1a \x00\x00\x00\x00'
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magic = mpr_file.read(len(mpr_magic))
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if magic != mpr_magic:
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magic = mpr_file.read(len(MPR_MAGIC))
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if magic != MPR_MAGIC:
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raise ValueError('Invalid magic for .mpr file: %s' % magic)
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modules = list(read_VMP_modules(mpr_file))
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@@ -326,7 +330,7 @@ class MPRfile:
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elif data_module['version'] == 2:
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column_types = np.frombuffer(data_module['data'][5:], dtype='<u2',
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count=n_columns)
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## There is 405 bytes of data before the main array starts
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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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@@ -342,8 +346,8 @@ class MPRfile:
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self.data = np.frombuffer(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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# 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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@@ -372,9 +376,9 @@ class MPRfile:
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tm = time.strptime(str3(log_module['date']), '%m-%d-%y')
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self.enddate = date(tm.tm_year, tm.tm_mon, tm.tm_mday)
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## There is a timestamp at either 465 or 469 bytes
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## I can't find any reason why it is one or the other in any
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## given file
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# There is a timestamp at either 465 or 469 bytes
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# I can't find any reason why it is one or the other in any
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# given file
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ole_timestamp1 = np.frombuffer(log_module['data'][465:],
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dtype='<f8', count=1)
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ole_timestamp2 = np.frombuffer(log_module['data'][469:],
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@@ -400,10 +404,10 @@ class MPRfile:
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ole_timedelta = timedelta(days=ole_timestamp[0])
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self.timestamp = ole_base + ole_timedelta
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if self.startdate != self.timestamp.date():
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raise ValueError("""Date mismatch:
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Start date: %s
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End date: %s
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Timestamp: %s""" % (self.startdate, self.enddate, self.timestamp))
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raise ValueError("Date mismatch:\n"
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+ " Start date: %s\n" % self.startdate
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+ " End date: %s\n" % self.enddate
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+ " Timestamp: %s\n" % self.timestamp)
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def get_flag(self, flagname):
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if flagname in self.flags_dict:
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@@ -1 +1,3 @@
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from .BioLogic import MPTfile, MPRfile
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from .BioLogic import MPRfile, MPTfile
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__all__ = ['MPRfile', 'MPTfile']
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@@ -7,8 +7,8 @@ import csv
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import argparse
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## The following scripts are adapted from the result of running
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## $ mdb-schema <result.res> oracle
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# The following scripts are adapted from the result of running
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# $ mdb-schema <result.res> oracle
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mdb_tables = ["Version_Table", "Global_Table", "Resume_Table",
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"Channel_Normal_Table", "Channel_Statistic_Table",
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@@ -126,7 +126,8 @@ CREATE TABLE Channel_Statistic_Table
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-- Version 1.14 ends here, version 5.23 continues
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Charge_Time REAL DEFAULT NULL,
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Discharge_Time REAL DEFAULT NULL,
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FOREIGN KEY (Test_ID, Data_Point) REFERENCES Channel_Normal_Table (Test_ID, Data_Point)
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FOREIGN KEY (Test_ID, Data_Point)
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REFERENCES Channel_Normal_Table (Test_ID, Data_Point)
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); """,
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"Auxiliary_Table": """
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CREATE TABLE Auxiliary_Table
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@@ -137,7 +138,8 @@ CREATE TABLE Auxiliary_Table
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Data_Type INTEGER,
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X REAL,
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"dX/dt" REAL,
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FOREIGN KEY (Test_ID, Data_Point) REFERENCES Channel_Normal_Table (Test_ID, Data_Point)
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FOREIGN KEY (Test_ID, Data_Point)
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REFERENCES Channel_Normal_Table (Test_ID, Data_Point)
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); """,
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"Event_Table": """
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CREATE TABLE Event_Table
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@@ -220,9 +222,10 @@ CREATE TABLE Smart_Battery_Data_Table
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ChargingCurrent REAL DEFAULT NULL,
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ChargingVoltage REAL DEFAULT NULL,
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ManufacturerData REAL DEFAULT NULL,
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FOREIGN KEY (Test_ID, Data_Point) REFERENCES Channel_Normal_Table (Test_ID, Data_Point)
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FOREIGN KEY (Test_ID, Data_Point)
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REFERENCES Channel_Normal_Table (Test_ID, Data_Point)
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); """,
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## The following tables are not present in version 1.14
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# The following tables are not present in version 1.14
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'MCell_Aci_Data_Table': """
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CREATE TABLE MCell_Aci_Data_Table
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(
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@@ -233,7 +236,8 @@ CREATE TABLE MCell_Aci_Data_Table
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Phase_Shift REAL,
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Voltage REAL,
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Current REAL,
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FOREIGN KEY (Test_ID, Data_Point) REFERENCES Channel_Normal_Table (Test_ID, Data_Point)
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FOREIGN KEY (Test_ID, Data_Point)
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REFERENCES Channel_Normal_Table (Test_ID, Data_Point)
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);""",
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'Aux_Global_Data_Table': """
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CREATE TABLE Aux_Global_Data_Table
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@@ -288,7 +292,8 @@ CREATE TABLE Smart_Battery_Clock_Stretch_Table
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VCELL3 INTEGER,
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VCELL2 INTEGER,
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VCELL1 INTEGER,
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FOREIGN KEY (Test_ID, Data_Point) REFERENCES Channel_Normal_Table (Test_ID, Data_Point)
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FOREIGN KEY (Test_ID, Data_Point)
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REFERENCES Channel_Normal_Table (Test_ID, Data_Point)
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);"""}
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mdb_create_indices = {
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@@ -306,11 +311,14 @@ CREATE TEMPORARY TABLE capacity_helper(
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Discharge_Capacity REAL NOT NULL,
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Charge_Energy REAL NOT NULL,
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Discharge_Energy REAL NOT NULL,
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FOREIGN KEY (Test_ID, Cycle_Index) REFERENCES Channel_Normal_Table (Test_ID, Cycle_Index)
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FOREIGN KEY (Test_ID, Cycle_Index)
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REFERENCES Channel_Normal_Table (Test_ID, Cycle_Index)
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);
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INSERT INTO capacity_helper
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SELECT Test_ID, Cycle_Index, max(Charge_Capacity), max(Discharge_Capacity), max(Charge_Energy), max(Discharge_Energy)
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SELECT Test_ID, Cycle_Index,
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max(Charge_Capacity), max(Discharge_Capacity),
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max(Charge_Energy), max(Discharge_Energy)
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FROM Channel_Normal_Table
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GROUP BY Test_ID, Cycle_Index;
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@@ -328,11 +336,14 @@ CREATE TABLE Capacity_Sum_Table(
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Discharge_Capacity_Sum REAL NOT NULL,
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Charge_Energy_Sum REAL NOT NULL,
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Discharge_Energy_Sum REAL NOT NULL,
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FOREIGN KEY (Test_ID, Cycle_Index) REFERENCES Channel_Normal_Table (Test_ID, Cycle_Index)
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FOREIGN KEY (Test_ID, Cycle_Index)
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REFERENCES Channel_Normal_Table (Test_ID, Cycle_Index)
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);
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INSERT INTO Capacity_Sum_Table
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SELECT a.Test_ID, a.Cycle_Index, total(b.Charge_Capacity), total(b.Discharge_Capacity), total(b.Charge_Energy), total(b.Discharge_Energy)
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SELECT a.Test_ID, a.Cycle_Index,
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total(b.Charge_Capacity), total(b.Discharge_Capacity),
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total(b.Charge_Energy), total(b.Discharge_Energy)
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FROM capacity_helper AS a LEFT JOIN capacity_helper AS b
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ON (a.Test_ID = b.Test_ID AND a.Cycle_Index > b.Cycle_Index)
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GROUP BY a.Test_ID, a.Cycle_Index;
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@@ -342,16 +353,24 @@ DROP TABLE capacity_helper;
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CREATE VIEW IF NOT EXISTS Capacity_View
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AS SELECT Test_ID, Data_Point, Test_Time, Step_Time, DateTime,
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Step_Index, Cycle_Index, Current, Voltage, "dV/dt",
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Discharge_Capacity + Discharge_Capacity_Sum - Charge_Capacity - Charge_Capacity_Sum AS Net_Capacity,
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Discharge_Capacity + Discharge_Capacity_Sum + Charge_Capacity + Charge_Capacity_Sum AS Gross_Capacity,
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Discharge_Energy + Discharge_Energy_Sum - Charge_Energy - Charge_Energy_Sum AS Net_Energy,
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Discharge_Energy + Discharge_Energy_Sum + Charge_Energy + Charge_Energy_Sum AS Gross_Energy
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( (Discharge_Capacity + Discharge_Capacity_Sum)
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- (Charge_Capacity + Charge_Capacity_Sum) ) AS Net_Capacity,
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( (Discharge_Capacity + Discharge_Capacity_Sum)
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+ (Charge_Capacity + Charge_Capacity_Sum) ) AS Gross_Capacity,
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( (Discharge_Energy + Discharge_Energy_Sum)
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- (Charge_Energy + Charge_Energy_Sum) ) AS Net_Energy,
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( (Discharge_Energy + Discharge_Energy_Sum)
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+ (Charge_Energy + Charge_Energy_Sum) ) AS Gross_Energy
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FROM Channel_Normal_Table NATURAL JOIN Capacity_Sum_Table;
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"""
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def mdb_get_data_text(s3db, filename, table):
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print("Reading %s..." % table)
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insert_pattern = re.compile(
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r'INSERT INTO "\w+" \([^)]+?\) VALUES \(("[^"]*"|[^")])+?\);\n',
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re.IGNORECASE
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)
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# TODO after dropping Python 2 support - use Popen as contextmanager
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try:
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mdb_sql = sp.Popen(['mdb-export', '-I', 'postgres', filename, table],
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@@ -369,12 +388,11 @@ def mdb_get_data_text(s3db, filename, table):
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insert_match = None
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mdb_output = mdb_sql.stdout.read()
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while len(mdb_output) > 0:
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insert_match = re.match(r'INSERT INTO "\w+" \([^)]+?\) VALUES \(("[^"]*"|[^")])+?\);\n',
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mdb_output, re.IGNORECASE)
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insert_match = insert_pattern.match(mdb_output)
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s3db.execute(insert_match.group())
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mdb_output = mdb_output[insert_match.end():]
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s3db.commit()
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except:
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except BaseException:
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print("Error while importing %s" % table)
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if mdb_output:
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print("Remaining mdb-export output:", mdb_output)
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@@ -404,8 +422,11 @@ def mdb_get_data_numeric(s3db, filename, table):
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quoted_headers = ['"%s"' % h for h in mdb_headers]
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joined_headers = ', '.join(quoted_headers)
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joined_placemarks = ', '.join(['?' for h in mdb_headers])
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insert_stmt = 'INSERT INTO "{0}" ({1}) VALUES ({2});'.format(table,
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joined_headers, joined_placemarks)
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insert_stmt = 'INSERT INTO "{0}" ({1}) VALUES ({2});'.format(
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table,
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joined_headers,
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joined_placemarks,
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)
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s3db.executemany(insert_stmt, mdb_csv)
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s3db.commit()
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finally:
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@@ -428,7 +449,6 @@ def convert_arbin_to_sqlite(input_file, output_file):
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"""
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s3db = sqlite3.connect(output_file)
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for table in reversed(mdb_tables + mdb_5_23_tables):
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s3db.execute('DROP TABLE IF EXISTS "%s";' % table)
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@@ -439,7 +459,9 @@ def convert_arbin_to_sqlite(input_file, output_file):
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print("Creating indices for %s..." % table)
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s3db.executescript(mdb_create_indices[table])
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if (s3db.execute("SELECT Version_Schema_Field FROM Version_Table;").fetchone()[0] == "Results File 5.23"):
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csr = s3db.execute("SELECT Version_Schema_Field FROM Version_Table;")
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version_text, = csr.fetchone()
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if (version_text == "Results File 5.23"):
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for table in mdb_5_23_tables:
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s3db.executescript(mdb_create_scripts[table])
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mdb_get_data(input_file, table)
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@@ -454,7 +476,9 @@ def convert_arbin_to_sqlite(input_file, output_file):
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def main(argv=None):
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parser = argparse.ArgumentParser(description="Convert Arbin .res files to sqlite3 databases using mdb-export")
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parser = argparse.ArgumentParser(
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description="Convert Arbin .res files to sqlite3 databases using mdb-export",
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)
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parser.add_argument('input_file', type=str) # need file name to pass to sp.Popen
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parser.add_argument('output_file', type=str) # need file name to pass to sqlite3.connect
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@@ -127,7 +127,7 @@ def assert_MPR_matches_MPT(mpr, mpt, comments):
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assert_array_equal(mpr.get_flag("control changes"), mpt["control changes"])
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if "Ns changes" in mpt.dtype.fields:
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assert_array_equal(mpr.get_flag("Ns changes"), mpt["Ns changes"])
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## Nothing uses the 0x40 bit of the flags
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# Nothing uses the 0x40 bit of the flags
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assert_array_equal(mpr.get_flag("counter inc."), mpt["counter inc."])
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assert_array_almost_equal(mpr.data["time/s"],
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Reference in New Issue
Block a user