echemdata/galvani

Read proprietary file formats from electrochemical test stations

galvani

Read proprietary file formats from electrochemical test stations.

Usage

Bio-Logic .mpr files

Use the MPRfile class from BioLogic.py (exported in the main package)

from galvani import BioLogic
import pandas as pd

mpr_file = BioLogic.MPRfile('test.mpr')
df = pd.DataFrame(mpr_file.data)

Arbin .res files

Use the ./galvani/res2sqlite.py script to convert the .res file to a sqlite3 database with the same schema, which can then be interrogated with external tools or directly in Python. For example, to extract the data into a pandas DataFrame (will need to be installed separately):

import sqlite3
import pandas as pd
from galvani.res2sqlite import convert_arbin_to_sqlite
convert_arbin_to_sqlite("input.res", "output.sqlite")
with sqlite3.connect("output.sqlite") as db:
    df = pd.read_sql(sql="select * from Channel_Normal_Table", con=db)

This functionality requires MDBTools to be installed on the local system.

Installation

The latest galvani releases can be installed from PyPI via

pip install galvani

The latest development version can be installed with pip directly from GitHub:

pip install git+https://github.com/echemdata/galvani

Development installation and contributing

If you wish to contribute to galvani, please clone the repository and install the testing dependencies:

git clone [email protected]:echemdata/galvani
cd galvani
pip install -e .\[tests\]

Code can be contributed back via GitHub pull requests and new features or bugs can be discussed in the issue tracker.

galvani's Issues

Output a pandas DataFrame rather than a numpy record array

Pandas is significantly easier to use. On the other hand, an end user can easily convert the numpy array to pandas after receiving it as a result.

NotImplementedError: Column ID 174 after column control/mA is unknown (similar to #64)

I was trying to read one .mpr file and it was continuously generating the following errors:

1)'NotImplementedError: Column ID 174 after column control/mA is unknown'
BioLogic.py script modified and it is now reading the .mpr file correctly:
Here below the change:
(line 186) 174: ('Ewe/V', '<f4'), added.

At the moment I am reading properly also all the other files.

Please double-check if this change can be pushed
Test_error.zip
?

I started analyzing ECLab.exe, here are my first results

I started looking at the installed EClab.exe (version 11.36) and found some interesting data. Apparently, all column names are stored in a sorted array at 0x143E56D and continuing:

# Maps from colID to a tuple defining a numpy dtype
# names can be read from installed EClab.exe (version 11.36 from 0x143E56D)
VMPdata_colID_dtype_map = {
    #TODO: ('ox/red', TODO),
    #TODO: ('error', TODO),
    4: ('time/s', '<f8'),
    5: ('control/V/mA', '<f4'),
    6: ('Ewe/V', '<f4'),
    7: ('dQ/mA.h', '<f8'),
    8: ('I/mA', '<f4'),  # 8 is either I or <I> ??  --> it is I/mA
    9: ('Ece/V', '<f4'),
    # 10: ('Aux/V', TODO),
    11: ('I/mA', '<f8'),
    # 12: ('log(|<I>/A|)', TODO),
    13: ('(Q-Qo)/mA.h', '<f8'),
    # 14: does not exist?
    # 15: does not exist?
    16: ('Analog IN 1/V', '<f4'),
    # 17: ('Analog IN 2/V', '<f4'),
    # 18: ('Analog IN 3/V', '<f4'),
    19: ('control/V', '<f4'),
    20: ('control/mA', '<f4'),
    # 21: ('control changes', TODO),
    # 22: ('log(|I/A|)', TODO),
    23: ('dQ/mA.h', '<f8'),  # Same as 7?
    24: ('cycle number', '<f8'),
    # 25: ('DQ/mA.h', TODO),
# ...
}

There are some bytes of variable length between the column names and it looks like they might contain type information. Anyways, I will work on this with low priority but I will share my findings as soon as I have more.

Fail to import some columns from data

I obtain different results when exporting data from EClab into text format and when using .mpr file and galvani (before loading the data in a dataframe).

Text results

Using text file, I obtain the following columns:
mode, ox/red, error, control changes, Ns changes, counter inc., Ns, time/s, dq/mA.h, (Q-Qo)/mA.h, control/V/mA, Ecell/V, I Range, Energy charge/W.h, Energy discharge/W.h, Capacitance charge/µF, Capacitance discharge/µF, I/mA, x, Q discharge/mA.h, Q charge/mA.h, Capacity/mA.h, Efficiency/%, control/V, control/mA, cycle number, P/W.

Galvani results

Whereas with galvani from.mpr I only obtain:
'flags', 'Ns', 'time/s', 'dQ/mA.h', '(Q-Qo)/mA.h', 'control/V/mA', Ewe/V', 'I Range', 'Q charge/discharge/mA.h', 'half cycle', 'Energy charge/W.h', 'Energy discharge/W.h', 'Capacitance charge/µF', 'Capacitance discharge/µF'

Issue

I'm unfamiliar with binary files and I found this package excellent for my purposes. The .mpr file I have is not corrupted and send no error. The missing columns are not present in the VMPdata_dtype_from_colIDs function (at least the Intensity I/mA column which I was particularly interested in,as well as P/W), so the import error must be previously in the code, such as in read_VMP_modules. My skills did not allow me to go much further than that...
Hope you can fix this!

Set up continuous integration

Including the "build:passing" button

Licensing to use galvani in other projects

Since galvani is primarily designed to solve an "upstream" issue in electrochemical data analysis, I think galvani is especially powerful when combined with other electrochemical data analysis packages. Unfortunately, the GPL-3.0 copyleft license is restrictive, which limits its utility for these contexts. See this issue as an example.

Would the original authors consider releasing this code with a more permissive license such as MIT? There is some discussion of the legal issues involved on SO, see here as an example. Thanks!

dType of colIDs

Because I also have to work with Bio-Logic instruments I tried to port your source (the mpr part) to IgorPro (because I use Igor for my work on the data).

There I noticed some differences in the size of the colIDs:
4 and 6 can be both f4 (in CA scans) and f8 (in CV scans),
11 and 24 were f4 (not f8),
131 was u1 (not u2), and
435 is f4 (new?) - gives the same data as 434.

Only with these settings I got reasonable data out of the file.

Add SPDX / fsfe-reuse metadata

Add machine-readable copyright and licensing metadata.

https://reuse.software/

https://github.com/fsfe/reuse-docs/

TypeError when using numpy 1.12.0

Hi,

get a TypeError when using galvani with numpy v1.12.0.

Traceback (most recent call last):
  File "test.py", line 15, in 
    mpt1, comments = MPRfile(os.path.join(testdata_dir, 'test.mpr'))
  File "/usr/local/lib/python3.5/dist-packages/galvani-0.0.1a1-py3.5.egg/galvani/BioLogic.py", line 298, in __init__
TypeError: only integer scalar arrays can be converted to a scalar index

Tests fail with "ValueError: Invalid magic for .mpr file: b'version https://git-lfs.github.com/spec/v1\noid sha25'"

When I run pytest from the project root directory, 18 test fail, all with the same error message:

____________________________________________________________ test_MPR6_matches_MPT6 _____________________________________________________________

testdata_dir = '/home/user/galvani/tests/testdata'

    def test_MPR6_matches_MPT6(testdata_dir):
>       mpr = MPRfile(os.path.join(testdata_dir, 'bio_logic6.mpr'))

tests/test_BioLogic.py:213: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

self = <galvani.BioLogic.MPRfile object at 0x75c16c88b430>, file_or_path = '/home/user/galvani/tests/testdata/bio_logic6.mpr'

    def __init__(self, file_or_path):
        self.loop_index = None
        if isinstance(file_or_path, str):
            mpr_file = open(file_or_path, 'rb')
        else:
            mpr_file = file_or_path
        magic = mpr_file.read(len(MPR_MAGIC))
        if magic != MPR_MAGIC:
>           raise ValueError('Invalid magic for .mpr file: %s' % magic)
E           ValueError: Invalid magic for .mpr file: b'version https://git-lfs.github.com/spec/v1\noid sha25'

galvani/BioLogic.py:382: ValueError

Timezone awareness

It appears from initial inspection that .mpr files use local time for timestamps. Further investigation is needed.

[MPR File] ValueError: time data 'XX.XX.XX' does not match format '%m-%d-%y'

Hi, I tried using Galvani for the first time and when trying to load the mpr file from a BioLogic potentiostat, it raises the following exception:

ValueError: time data '11.12.20' does not match format '%m/%d/%y'
ValueError: time data '11.12.20' does not match format '%m-%d-%y'

It seems like my date format uses dots instead of "/" or "-". Don't know if it has to do with my EC-Labs settings or maybe that the date format of the OS is set to using "." (which is the standard for German date format).

I changed lines 398ff. in "BioLogic.py" to

try:
  tm = time.strptime(settings_mod['date'].decode('ascii'), '%m/%d/%y')
except ValueError:
  try:
      tm = time.strptime(settings_mod['date'].decode('ascii'), '%m-%d-%y')
  except ValueError:
      tm = time.strptime(settings_mod['date'].decode('ascii'), '%m.%d.%y')

and the same for the similar lines 418ff. which solved the problem. Maybe you want to integrate the additional date format in Galvani, @chatcannon.

BTW: Thanks a lot for this really nice python package! :)

parse file header

When converting an mpr file to an mpt file, there is a lot of header information, e.g.:

example MPT file header

EC-Lab ASCII FILE
Nb header lines : 191                         

Galvano Electrochemical Impedance Spectroscopy

Run on channel : 1 (SN 36210)
User : 
CE vs. WE compliance from -10 V to 10 V
Electrode connection : standard
Ewe ctrl range : min = -10.00 V, max = 10.00 V
Safety Limits :
	Ewe min = -0.50 V
	Ewe max = 2.80 V
	for t > 10 ms
	Do not start on E overload
Acquisition started on : 08/11/2021 16:03:59.530
Loaded Setting File :  C:\BT-Lab\Daten\PT\Gedruckte Ti PTLs\Ui-Kennlinie.mps
Saved on :
	File : 210811_N115_T80_p1_Probe11_02_GEIS_C01.mpr
	Directory : C:\EC-Lab\PT\gedruckte PTLs\
	Host : 130.75.205.160
Device : SP-150 (SN 1235)
Address : USB
EC-Lab for windows v11.36 (software)
Internet server v11.36 (firmware)
Command interpretor v11.36 (firmware)
Electrode material : 
Initial state : 
Electrolyte : 
Comments : 
Current amplifier : SP-150B-20A
Electrode surface area : 0.001 cm�
Characteristic mass : 0.001 g
Equivalent Weight : 0.000 g/eq.
Density : 0.000 g/cm3
Cycle Definition : Charge/Discharge alternance

It would be really useful if this project could read these information from mpr files. Specifically, I really need the experiment method (Galvano Electrochemical Impedance Spectroscopy in the above example`).

use pyproject.toml

This project uses setup.py which still gets legacy support. According to the documentation, modern Python projects should use pyproject.toml instead.

'R/Ohm' missing in VMPdata_colID_dtype_map

I was trying to read one .mpr file and it was continuously generating the following errors:

1)'NotImplementedError: Column ID 69 after column (Q-Qo)/mA.h is unknown'
BioLogic.py script modified and it is now reading the .mpr file correctly:
Here below the change:
(line 163) 69: ('R/Ohm', '<f4'), added.

2)'NotImplementedError: Column ID 26 after column Energy/W.h is unknown'
BioLogic.py script modified and it is now reading the .mpr file correctly:
Here below the change:
(line 155) 26: ('Rapp/Ohm', '<f4'), added.
[see attached file

Rapp_Error.zip]

At the moment I am reading properly also all the other files.

Please double-check if this change can be pushed?

Column type 168 not implemented

Hi, sorry to bother you again, but I think I may have found another unimplemented feature which is now causing an error.

When I try to load in the attached file, I get "NotImplementedError: column type 168 not implemented".

I am having this same problem with all the data I have recorded today. I didn't update EC-lab or change the parameters of the technique so I find it really odd that the data from today cannot be loaded when all the older data files can.

files.zip

Arbin MDB loading without an external program

e.g. using a C extension

Add debug logging

Use the logging module to write some debug output on what is happening during file loading.

This can also be used for warnings etc.

Only run the linting tools once during testing

Currently the tox tests run flake8 and reuse lint multiple times - once for every python version tested. Instead, the linting tools should only run once, in a separate tox environment.

Code style checking

Checking tools to consider:

• bandit - https://bandit.readthedocs.io/en/latest/
• flake8 - http://flake8.pycqa.org/en/latest/
• mypy - http://www.mypy-lang.org/
• pylint - http://pylint.pycqa.org/en/latest/

flake8 plugins:

• flake8-docstrings
• flake8-import-order
• flake8-quotes
• flake8-bandit
• flake8-mypy

Receiving NotImplementedError: column type 471 not implemented

Hi! I'm trying to open .mpr files using the following code

from galvani import BioLogic as BL
import pandas as pd

mpr = BL.MPRfile(path)
df = pd.DataFrame(mpr.data)
df.head()

however, I always get the error

NotImplementedError: column type 471 not implemented

Am I doing something wrong?

Similar issue to #27 and #48

In the Biologic.MPRfile class this error seems to arise on certain files:

ValueError: Invalid magic for .mpr file: b'<?xml version="1.0" encoding="UTF-8"?>\r\n<Configurati'

This is generated from BT-Lab version 1.65.

Similar problem as #27

I ran into a similar bug as #27, while doing Biologic.MPRfile('path/to/mpr.mpr')

ValueError: Invalid magic for .mpr file: b'\r\n<Configurati'

from

File "/Users/suweiguo/anaconda3/envs/eclab2/lib/python3.6/site-packages/galvani-0.1.0-py3.6.egg/galvani/BioLogic.py", line 314, in init

which is probably due to the very old Biologic VMP

less-strict parsing mode

Currently the MPR parsing code raises Exceptions in any case where it gets data it does not understand. In many cases the user might prefer parsing to continue with possibly incorrect metadata rather than failing altogether.

Refactor `fieldname_to_dtype` function

The "if name in (long list) elif name in (other long list)" block is unwieldy. It should be refactored to use sets or mappings.

Consider using git-lfs to store test data

Currently the test data files are stored on figshare.com and retrieved with wget in get_testdata.sh

Now that github supports storing data files with git-lfs, this could be an attractive alternative.

ValueError: time data '03-14-19' does not match format '%m/%d/%y'

Hello,
I'm getting a ValueError from the date pulled by BioLogic.py. The weird thing is it worked on files generated yesterday but not today, and we haven't changed anything. I believe the data file was generated by version 11.02 of EC-labs. The full error is below. Thanks!

Traceback (most recent call last):
File "/usr/lib/python3.7/site-packages/flask/app.py", line 2292, in wsgi_app
response = self.full_dispatch_request()
File "/usr/lib/python3.7/site-packages/flask/app.py", line 1815, in full_dispatch_request
rv = self.handle_user_exception(e)
File "/usr/lib/python3.7/site-packages/flask/app.py", line 1718, in handle_user_exception
reraise(exc_type, exc_value, tb)
File "/usr/lib/python3.7/site-packages/flask/_compat.py", line 35, in reraise
raise value
File "/usr/lib/python3.7/site-packages/flask/app.py", line 1813, in full_dispatch_request
rv = self.dispatch_request()
File "/usr/lib/python3.7/site-packages/flask/app.py", line 1799, in dispatch_request
return self.view_functionsrule.endpoint
File "/home/FREDsense/automated_analysis/WebFrontEnd.py", line 84, in ec_assay
output = runAnalysis(file_filenames, timestamp)
File "/home/FREDsense/automated_analysis/scripts/Peak_Analysis.py", line 92, in runAnalysis
mpr = MPRfile(filename)
File "/home/FREDsense/.local/lib/python3.7/site-packages/galvani/BioLogic.py", line 353, in init
tm = time.strptime(str3(settings_mod['date']), '%m/%d/%y')
File "/usr/lib/python3.7/_strptime.py", line 571, in _strptime_time
tt = _strptime(data_string, format)[0]
File "/usr/lib/python3.7/_strptime.py", line 359, in _strptime
(data_string, format))
ValueError: time data '03-14-19' does not match format '%m/%d/%y'

Release to PyPI

Release a new PyPI package including all recent changes

Once #38 is merged then we should update the pip package so that the bug fixes are available to users.

Create a GitHub organization and transfer the repo

To allow collaborative development work, see discussion on #26

Create an organization: https://github.com/organizations/new

Transfer the galvani repo there: https://help.github.com/en/articles/transferring-a-repository

Add @bcolsen as a collaborator

Add support for data module version 3

Hi!

I'm doing my Masters and will probably continue with my PhD working with EC-Lab quite a bit and I've just about had it with the .mpr file format which requires me to export the data manually every single time.

I stumbled upon this seemingly amazing module and I've been trying to import data using the BioLogic.MPRfile function, but I can't seem to get it to work as I get "ValueError: Unrecognised version for data module: 3" when I run
BioLogic.MPRfile("some_file.mpr")

I have some experience with python but mainly as a tool for data analysis, so my troubles may be a result of my very limited Python knowledge.

I was hoping that you might have an idea as to how I could get this module to work so that I may import .mpr files directly into Python.

(I wasn't really sure how to reach out for help here so I opened an issue as I could find no other way of doing so. I'm sorry if this was an inappropriate way of going about it)

Migrate from nose to pytest / tox

https://nose.readthedocs.io/en/latest/#note-to-users

DeprecationWarning for np.fromstring

When running the tests:

DeprecationWarning: The binary mode of fromstring is deprecated, as it behaves surprisingly on unicode inputs. Use frombuffer instead

NotImplementedError: Column ID 509 after column Rdc/Ohm is unknown

Trying to add 'Acir/Dcir Control', but I failed, example mpr and mpt can be found at the attached links.

https://drive.google.com/file/d/1DZ7tvy2EOntFyqlfnam-CL6AhmaJGAl1/view?usp=sharing
https://drive.google.com/file/d/1BIHCRX_ja-4tqGGLpkHK-I0ESMnbOsOQ/view?usp=sharing

ValueError: Found b'\x82\xe0zOVP', expecting start of new VMP MODULE

I got tired of EC-lab's plotting functionality, so I've been working on my own program for live data plotting using EC-lab's .mpr files.

However, the plot sometimes stops updating and the error below is printed.
ValueError: Found b'\x82\xe0zOVP', expecting start of new VMP MODULE
I have no problems otherwise plotting the data, and I can restart the live plotting program and it'll work for a while until it encounters this error again.

Do you have any idea what causes this or how I could fix it? I tried looking around in the Biologic.py file, but don't really understand in which instance the error is triggered.

Duplicate columns in the main data biologic

I have a files from a my new biologic that has duplicate columns. The columns have the same ID and data. As a result the file errors saying the dtype doesn't match the length of data.

This happens because the ordered dict only registers one of the columns.

Since neither a dictionary nor a numpy recarray can have the same keys this raises a problem.

I have a PR to fix this.

Unable to parse all columns in .mpr file

I've been looking at the past couple of issues regarding unparsable columns due to not enough colIDs present in the dictionaries in the BioLogic.py source code. I followed the procedures in several of these issues and was able to retrieve some more column headers by adding new colIDs myself. When looking at my .mpt file, I notice that there are around 8-9 additional columns present in my file which aren't present in the dictionaries. I was successfully able to retrieve two columns from those because I kept getting a NotImplementedError along with a colID that I had to enter in the dictionary. However, after I got these two columns, I stopped receiving NotImplementedErrors for some reason, even though from the corresponding .mpt file I know that there are more columns I need to parse which aren't found in the BioLogic.py dictionaries. When I run mpr_object.dtype.names to print out all the columns which got parsed, I get the following tuple:

('flags', 'Ns', 'I Range', 'time/s', 'control/V/mA', 'Ewe/V', 'I/mA', 'dQ/mA.h', '(Q-Qo)/mA.h', 'Energy/W.h', 'Q charge/discharge/mA.h', 'half cycle', 'Temperature/°C', 'Energy charge/W.h', 'Energy discharge/W.h', 'Capacitance charge/µF', 'Capacitance discharge/µF')

However, when I check through my .mpt file, there are more columns past the last one which are left to be parsed but aren't being parsed for some reason. I also am not receiving any additional NotImplementedErrors for me to be able to reverse engineer the remaining columns. One thing I did notice, however, is that in the .mpt file, the next column which isn't being parsed and is located immediately after Capacitance discharge/µF called x. It seems like this is the only column name in the file which is just a char and not a string, so could there be some fundamental comparison issue in the source code that could possibly explain why all the columns past x aren't being examined/parsed by the BioLogic.py code?

Please let me know if this is an issue anyone has received before and if there are possible suggestions to fixing it. Also let me know if you want me to send an example file/output if you're still not sure what my issue is. Thank you!

column 23 has wrong label

The column with id 7 should be named dq/mA.h, not dQ/mA.h. The manual says (excerpt):

Variables Description	Variable name/unit
Common Variables
dq : charge increment between two recorded values	dq/mA.h
Additional variables
dQ: charge on a potential step	dQ/mA.h

I am asking my boss if I can add an example file to this issue.

Receiving sqlite3.OperationalError when running res2sqlite.py

I am trying to parse a .res file for a project with the convert_arbin_to_sqlite() function in res2sqlite.py; however, I keep receiving an sqlite3.OperationalError.

This is the code snippet I am trying to run:
res.convert_arbin_to_sqlite(infilepath, outfilepath) # outfilepath is a .s3db file
connection = sqlite3.connect(outfilepath)
cursor = connection.execute('SELECT * FROM Global_Table')
data = cursor.fetchall()

However, after trying to run this, I keep receiving the following error message:
sqlite3.OperationalError: table Global_Table has no column named Log_Can_BMS_Data_Flag

I checked the res2sqlite.py source code, specifically the part where the Global_Table is created (starting from Line 37), and I notice that there are several columns, the first one being Log_Can_BMS_Data_Flag, which seem to be read in by my .res file but aren't present in the res2sqlite.py source code during the Global_Table creation process.

Has anyone received this kind of error before, and if so, can I please receive some assistance on it? Thanks!

Try parsing unknown columns as '<f4' with name "Unknown"

Currently the Bio-Logic .mpr parser exits with an error if it encounters an unknown column ID. This made sense at the time of writing because I had no way of knowing the data type of the new column and thus how many bytes it would take up in the file.

Looking at the file history, it seems that all new columns added in the past three years have been '<f4' (32-bit float). https://github.com/echemdata/galvani/blame/master/galvani/BioLogic.py

This means that it is probably safe to assume that any new unknown columns will also be 32-bit floats. This will make it possible to load the file despite the presence of unknown columns.

Deprecate Python 2

Remove python 2 compatibility code

Receiving <RuntimeError: Could not locate the 'mdb-export' executable. Check that mdbtools is properly installed.> error when trying to run convert_arbin_to_sqlite method

I'm trying to run the convert_arbin_to_sqlite method on one of my .res files and also specify the output file to be in a .s3db format. However, the code always fails on that line and provides me with this error:

RuntimeError: Could not locate the 'mdb-export' executable. Check that mdbtools is properly installed.

I then pip installed mdbtools and ran a pip freeze to see that I have version 0.3.14 installed. I also tried including an import mdbtools statement at the top of my file to see if that fixed the problem, but then I get this error:

ModuleNotFoundError: No module named 'MDButils'

I'm not sure why this is happening, so I'd appreciate any assistance or guidance from any of you. Thank you so much.

Test set-up info not available

Is there any possibility to extract the test-set up information like the ones contained in the .mps from the .mpr?
Do you know if they are hidden in the file or if they can not be retrieved from the .mpr?

Warnings about Travis CI config

https://travis-ci.org/github/echemdata/galvani/builds/704756307/config

Build config validation
root: deprecated key sudo (The key sudo has no effect anymore.)
root: missing dist, using the default xenial
root: missing os, using the default linux

Multiple measurements in one file

After solving the problems with encoding and missing column headers I end up with a single array for the EIS measurements.
galvani test.txt

Is it possible to extract the data for single measurements?
In the header meta data is present for every measurement.

UnicodeDecode Error

Hi,
Thanks for your code! I would like to use the first part to convert the MPT file into an array.
However I get the following error when calling MPTfile , and I really don't understand what to change :( Would you tell me what is going on?

error line : str3 = lambda b: str(b, encoding='ascii')
error message : UnicodeDecodeError: 'ascii' codec can't decode byte 0xb5 in position 165: ordinal not in range(128)

Thank you.
Marion

res2sqlite

Here is my code:

`from galvani import res2sqlite as r2s

Input_file = 'C012.res'
Output_file = 'new'

r2s.convert_arbin_to_sqlite(Input_file, Output_file)`

Here is the output:

Reading Version_Table...
Error while importing Version_Table

Traceback (most recent call last):
File "/pithy/code/arbin_import_test.py", line 19, in
r2s.convert_arbin_to_sqlite(Input_file, Output_file)
File "/usr/local/lib/python2.7/dist-packages/galvani/res2sqlite.py", line 417, in convert_arbin_to_sqlite
mdb_get_data(s3db, input_file, table)
File "/usr/local/lib/python2.7/dist-packages/galvani/res2sqlite.py", line 397, in mdb_get_data
mdb_get_data_text(s3db, filename, table)
File "/usr/local/lib/python2.7/dist-packages/galvani/res2sqlite.py", line 373, in mdb_get_data_text
mdb_sql.terminate()
UnboundLocalError: local variable 'mdb_sql' referenced before assignment

Can you help me with this error?

Thank you

Python 3.7 compatibility

The BioLogic parser code exits from a generator by raising StopIteration. This is no longer supported in Python 3.7 and leads to a RuntimeError.

https://docs.python.org/3/whatsnew/3.7.html#changes-in-python-behavior

https://www.python.org/dev/peps/pep-0479/

Improve README

I'm new to python, how do I run the code? Where to put the .mpt-File (from a BioLogic device) to translate? Thanks in advance!

Error when opening *mpr file: 'NotImplementedError: Column ID 27 after column control/mA is unknown'

I'm trying to open .mpr files using the galvani library.
When opening files of GCPL technique of BioLogic, everything is fine.
However, when opening files after the GCPL2 technique, I got error:

NotImplementedError: Column ID 27 after column control/mA is unknown

Looks like this file has some extra, unexpected column.
Is there a way to make this column recognizable and be able to read the file with Galvani?