More data formats supported about impedance.py HOT 40 CLOSED

PowerSuite support added in lktsui@cf47664 over at my repository

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Awesome! I'm finishing up the testing for Versastudio and Zplot. Will push to my repository by EoD.

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BioLogic data support added based off of the example that @BGerwe provided

lktsui@cd00b6a

Note: user runedevros is me. I can't figure out how to not get it to attribute to that handle I use for my personal stuff when I push on my home PC.

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There are raw data files for autolab impedance experiments in the supplemental files from @mdmurbach @vwhu paper. Search on the paper osf DOI 10.17605/OSF.IO/TDNWA

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Definitely @vwhu and @linnetteteo have a sample file.

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Thx, Matt. Didn't really think about fact we are weirdos who do our own signal processing on the time domain data.

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Interesting. In my limited experience with Biologic I found it necessary to export each data file to .txt with their EC-Lab software. Otherwise, the data is in a format unreadable by text editors like Notepad++ but, again, my experience with Biologic is limited.

I realize this isn't helpful for your situation, but I just wrote support for Solartron .z files, and VersaStudio .par files.

Example VersaStudio file

It sounds like you're using a Princeton Applied Research potentiostat-- do you mind sharing what model? It seems like multiple control software can be used on the same potentiostat, so we may want to consider identifier data formats by the software rather than hardware.

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@all-contributors please add @lktsui for code and test
@all-contributors please add @BGerwe for code and test

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Sorry for all the spam on this one... I thought adding this contributors bot would make things easier... (maybe it will now that it's setup haha).

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I would like to keep it open so that people can submit requests here for us to support their data formats.

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I propose we close this issue and direct new data format requests use to the new "Data File Support" issue template!

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Do you have particular data formats in mind? I can help with including Versastat .par files and Solartron .z file types.

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Biologic's would be nice. I was told there was a text version of the data format.

I also have some data that came out of a PAR potentiostat controlled with PowerSuite that I would like to support.

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Example for PowerSuite EIS datafile

It's almost an TSV except they have an extra space between each line for some unknown reason.

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That was my understanding for Biologics as well. May be easiest to take whatever their EC-Lab exports in text format.

The data in my example comes from an old PAR 2273 on loan from another group running PowerSuite on Windows XP. Don't have access to the instrument any more unfortunately.

I agree that grouping data reading ability by software makes more sense. Especially for a manufacturer as old as PAR, they have gone through a number of control software which use different data formats, not to mention 3rd party control software like Scribner's Z-plot.

I would suggest something like: readVersaStudio, readPowerSuite, readZplot

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Agreed. As for the PowerSuite data, is the example you provided unaltered? I was expecting some experiment settings to precede the data.

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Yes. I got it straight from the export to text option.

PowerSuite has their own binary blob format for storing settings and results for a set of experiments and each experiment has to be individually exported to text in a format where experimental options aren't preserved.

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Ok, everything has passed local checks. BGerwe@ 40b87a9

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These both look awesome! Great job of also including tests for each 🚀

I think you both have the ability to merge PRs, but I'd be happy to review them as well. Let me know if there's anything else I can help with!

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@all-contributors please add @lktsui for code and test

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@mdmurbach

I've put up a pull request to add @lktsui! 🎉

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@all-contributors please add @BGerwe for code and test

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@mdmurbach

I've put up a pull request to add @BGerwe! 🎉

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@all-contributors please add @BGerwe for code and test

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@mdmurbach

I've put up a pull request to add @BGerwe! 🎉

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I also added a tip pointing to these new features in the getting started page in 7babd5a. Might eventually be worth adding some more documentation around how to use these functions, how to request a new addition, etc. on the preprocessing page as well.

For now 2 questions:

• Should we leave this open for any more data types?
• I'm thinking we can do a release of v0.5 with these updates or do you think there are more to add right now?

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I think we should leave it open a little while longer. BioLogic is an easy target right now (even if it requires a tedious exporting step).

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👍 Sounds good to me! Do you have access to a biologic instrument or are we still looking for someone with some data?

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I added a BioLogic example data file to my fork, if you're eager for it, but didn't get around to writing the support today.

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@mdmurbach I can't find the thread where you mentioned this, but go ahead an release as v0.5 if you want. I haven't had enough time to work on Bode plot functionality, and probably won't for a other couple of weeks.

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👍 awesome, sounds good @BGerwe

@lktsui do you want to submit the PR for adding the biologic function?

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Is there a way to revert the changes that @BGerwe made to plotting.py only for this PR? The pull request I sent is failing the tests since the biologic data file got pulled in Commit 827d47b along with some changes to plotting.py which were in progress.

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Released as a part of v0.5! aa37038

I’ll leave up to y’all if it makes sense to close this issue now or keep it open

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In working to improve the test coverage of preprocessing I found we don't have any data for Autolab or Parstat. If anyone has access to those file types, please include them in the data directory. Thanks in advance!

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Maybe @linnetteteo or @vwhu have some example data? 😄

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The impedance files for the paper above are custom .csvs of time domain data that are written by autolab, but I think the files that make sense to add would be for the typical impedance output of the autolab instrument (i.e. you were to just do a typical EIS experiment).

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I do have data files from the parstat, although that uses the Versastudio software and I see that there is already an example versastudio .par file

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@linnetteteo Would you mind sending me the parstat file so I can check if the formatting is the same as versastat?

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Here's a CHInstruments 660E data file. I don't think we have a way of reading this format yet.

The instrument saves it as a binary blob which we can't read by default but it is also possible to export it as text.

data_chinstruments.txt

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