Still a troublesome Linux issues raw_file.instrument_methods_count about fisher_py

[keesh-elucid]

We are wondering if there has been any progress on "Still a troublesome Linux issues raw_file.instrument_methods_count" ?
thx
[email protected]

[dowerner]

Dear @keesh-elucid

Sorry for the very late reply. Github still does not forward notifications to me. It seems to me that the problems you are experiencing are related to the raw file you are trying to access. I was unable to reproduce those issues with the raw files I use for testing.
If you send me a similar raw file without critical data I may be able to debug the issue in detail. As an alternative I can implement a fallback that just ignores the instrument_methods_count that cannot be read from your files.

Let me know how you want to proceed,

Cheers Dominik

[dpsmca]

Hi @dowerner,

In the fisher_py fork I created for our project, I created a bug/instrument_methods_count branch and created a test_data directory inside the examples directory -- it should be accessible here. It contains two small raw files. Both of those files cause the InstrumentMethodsCount crash when I run raw_file_reader_example.py on them, using Mac or Linux.

[dowerner]

Finally, I had the chance to test your files using a Linux system (WSL - Ubuntu 20.04 on Windows 10). It turns out that the problem occurs for all .raw files on Linux but not on Windows. Sadly, the issue is situated within the .NET binaries (provided to us by ThermoFisher) and not within the Python code. What I can offer is to implement a fallback that just returns "None" if the count cannot be extracted, obviously this won't do you much good if you need this parameter. Hopefully, we can replace the DLLs in the future so it works properly on all platforms.

[dowerner]

The fix is now implemented in version 19, feel free to open a new issue if anythin else pops up (meanwhile I fixed the github notification issue on my side 👍 )

[keesh0]

So does your fix address the following?
So, I created a C# only version of my small method.
It ran fine on Linux.
rawFile.InstrumentMethodsCount // OK
rawFile.GetInstrumentMethod(i) // OK
But, the Python wrapper crashed.

[dowerner]

To be honest I did not run a C# example. I assumed pythonnet would invoke the offending properties and methods similar to the .NET runtime in C#. If you have an idea how to fix this I'll gladly have a look. As it stands I don't know how to fix it in fisher_py.

[keesh0]

Sure, let me check with my colleague.
thx e.-