incompatibility output ROI statistics with python

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    deborakeller0@gmail.com October 15, 2019 at 6:24 pm

    Hi,

    I am trying to handle the output from ROI statistics with python but there is an issue with the micron special symbol that is in the header for perimeter, area, surface area which prevents import.

    Is it possible to replace it with “um” as in fiji as this will greatly increase the compatibility with downstream handling!!

    Thanks in advance, Stephane 🙂

    Cheers

     

    Debbi

    Stephane Dallongeville October 17, 2019 at 10:29 am

    Hi Debbi,

    Definitely possible but i have to admit it’s a change that we could regret as “u” is not the correct character and also because we could eventually break compatibility with specify scripts relying on “µ” presence.
    Still we will do the change for the sake of compatibility with others tools and if nobody complains about it we may keep “um” then 🙂

    – Stephane
    deborakeller0@gmail.com November 6, 2019 at 2:19 pm

    ok – I found a libary we can import to deal with special characters (though I am still in favor of removing them coz it also causes problems when saving in txt).

    speaking of .txt …

    is it possible to add an export to a legit CSV format and ideally WITHOUT the additional first line (that specifies ==ROI inclusion == or == ROI stats== ?

    don’t know how much work it is but I am running into the excel limitations for numbers but the .txt format is a bit xombersome as well.

    cheers

    Debbi

    Stephane Dallongeville November 6, 2019 at 4:44 pm

    You’ll see that we changed ‘µ’ yo ‘u’ in Icy 2.0.3.0, that shouldn’t hurt hopefully.
    About the CSV export, what you mean by legit ? And it’s up to the plugin to implement that or not and there is no CSV export helper methods in Icy by itself. Here for instance you’re speaking about 2 different plugins (ROI Statistics and ROI Inclusion Analysis).

    You said you’re limited with the number of rows with excel, normally XLSX format should be able to handle lot of them.

    Best,

    – Stephane
    deborakeller0@gmail.com November 7, 2019 at 3:18 pm

    well, i am running into the excel xlsx limit quite often (and get empty excel file at the end for spot statistics, not roi inclusion)… hence switching over to .txt (where I think there should be no limit on file size / line numbers)

    The text export in ROI statistics is tab delimited and has a header on top. I found a work-around now, but if it were possible to have the CSV format as an option to export ROI stats or ROI inclusion stats ( or any measurements), it would be great (if easily doable).

     

    Thanks for the micron sign!

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