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ECSHackWeek / impedance.py

A Python package for working with electrochemical impedance data
MIT License
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[BUG] .mpr file related to PEIS measurment (aquisited from a VPM3 biologic potentiostat) is not supporting. error: "Column ID 17 after column Analog IN 1/V is unknown" #245

Closed Mehdisoley closed 1 year ago

Mehdisoley commented 1 year ago

I wanted to put my data (PEIS data) aquisited from a VPM3 biologic pootentiostat into a pandas library. This is my code:

from galvani import BioLogic import pandas as pd mpr_file = BioLogic.MPRfile("Cr-1-polveri_di_Grafite_01_PEIS_C01.mpr") df = pd.DataFrame(mpr_file.data)

but it return me this error:

NotImplementedError Traceback (most recent call last) Input In [11], in <cell line: 4>() 1 from galvani import BioLogic 2 import pandas as pd ----> 4 mpr_file = BioLogic.MPRfile("Cr-1-polveri_di_Grafite_01_PEIS_C01.mpr") 5 df = pd.DataFrame(mpr_file.data)

File D:\Anaconda\lib\site-packages\galvani\BioLogic.py:413, in MPRfile.init(self, file_or_path) 408 raise ValueError("Unrecognised version for data module: %d" % 409 data_module['version']) 411 assert(not any(remaining_headers)) --> 413 self.dtype, self.flags_dict = VMPdata_dtype_from_colIDs(column_types) 414 self.data = np.frombuffer(main_data, dtype=self.dtype) 415 assert(self.data.shape[0] == n_data_points)

File D:\Anaconda\lib\site-packages\galvani\BioLogic.py:310, in VMPdata_dtype_from_colIDs(colIDs) 308 type_list.append((unique_field_name, field_type)) 309 else: --> 310 raise NotImplementedError("Column ID {cid} after column {prev} " 311 "is unknown" 312 .format(cid=colID, 313 prev=type_list[-1][0])) 314 return np.dtype(type_list), flags_dict

NotImplementedError: Column ID 17 after column Analog IN 1/V is unknown

BGerwe commented 1 year ago

Hi there, thanks for opening the issue. Respectfully, it seems like this error is coming from the galvani package and not impedance. We've played with supporting the .mpr file type (#115), but got stalled with confusion over proper licensing procedure.

If you export the file to a .mpt in the BioLogic software, you'll be able to read it in with impedance.preprocessing.readBioLogic()

Mehdisoley commented 1 year ago

Thank you for your answer. yes when I convert it to txt file it is working. however as I am dealing with a lot of file it would be better to work with original data. Is there any Forum or Room about galvani so I can publish my issue there?

BGerwe commented 1 year ago

Try posting on https://github.com/echemdata/galvani that's the homepage listed on PyPI.