Change pipeline parameters from outside

cellprofiler
#1

Hi!

Can you please tell me what is the easiest way to manipulate pipeline file from an other (python) program?
I would like to try out different optimizations, and to make it faster I wanted to change the parameters through the pipeline file, without using the GUI. But I fail to do this because I struggle with the encodings.

I’ve read forum topics about this, tried different versions of CP and pipeline, and even tried to find the answers in the source code, but Im not a python expert, this is too complex for me to see the connections.

If I just want to change some values of the .cppipe file (e.g. the Typical diameter of objects, in pixel units (Min,Max) ) save it, and make sure it remains readable for CP, how can I do this with using python?

Thank you in advance!

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#2

Welcome to the forum! My knowledge is a bit out of date but as I recall the pipeline file really is plain text so it shouldn’t be too much trouble.

Do you mind posting an example pipeline, what do you wish to change, and an example of an adjusted pipeline that didn’t work? You may need to upload that as a zip file. Ideally include the images you need to make the first pipeline work in the first place. It’s ok to make a super simple toy pipeline for this purpose if you prefer.

Ps. I wonder if it has to do with saving the pipeline file with a funky invisible text encoding/format, like if line endings were messed up in the process. Not all text files are identical.

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