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Neural-Systems-at-UIO / nutil

https://nutil.readthedocs.io/en/latest/
GNU General Public License v3.0
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Python files empty #315

Closed Noy987 closed 10 months ago

Noy987 commented 10 months ago

Seeking assistance in understanding why my python files are empty. Added the logs below from Nutil. I'd appreciate any insights or guidance, thanks!

"LOG: Type of operation: Quantifier" "MESSAGE: Required memory: 0.0149727 GB. Free memory : 15931 GB from a total of 15931 GB installed (0 %) usage" "LOG: Executing..." QFile::copy: Empty or null file name "LOG: Generating summary report"

"LOG: Creating summary " "LOG: Generating sheets " "LOG: Saving report to C:/Users/Noy/Desktop/Project/test_3/Output/\Reports\test_3_CustomRegions.xlsx" "LOG: Releasing C:/Users/Noy/Desktop/Project/test_3/Output/\Reports\test_3_CustomRegions.xlsx"

"MESSAGE: ** Count of pixels 9078" "MESSAGE: WARNING: The JSON/XML file contains info about sections that are not included in the analysis. Make sure that you are using the correct anchor XML or JSON file."

"MESSAGE: ** Count of pixels 9078" QIODevice::read (QFile, "\..\plot\plot_reference_atlas_regions.py"): device not open QIODevice::read (QFile, "\..\plot\plot_custom_regions.py"): device not open QIODevice::read (QFile, "\..\plot\plot_lib.py"): device not open ""

sharoncy commented 10 months ago

Sorry to hear it's not working for you. For the plotting feature to work, Python has to be installed on your computer (including Numpy, Pandas and Matplotlib packages), and the location of the Python.exe specified in the Nutil settings. I'd install everything locally (on the C:drive). See the tip here: https://nutil.readthedocs.io/en/latest/Technical.html.

The plotting feature can be useful for obtaining a quick preview of your results. However, it doesn't usually format the plots optimally, so you will probably have to remake them anyway. If it proves difficult to set up, probably better to create your own plots.

Noy987 commented 10 months ago

Thank you for the great advice, I localized my python files and it worked!

The plots are PNG files, is there a way for me to edit/adjust them by myself in python or another program or app?

Are the plots' code supposed to be in the scripts folder? Unfortunately, that folder has empty files too right now (shown in the screenshots). They also appear empty in PyCharm (shown in the screenshots).

Any advice on this matter would be very helpful, thanks!

plots folder scrips folder pycharm

sharoncy commented 10 months ago

Great you got it to work. The scripts are meant to be published in the output folder, so yes that's a bug. You can find the Python scripts on Github which should allow you to recreate plots according to your own requirements. https://github.com/Neural-Systems-at-UIO/nutil/tree/master/Publish/source/plot. My colleague has also published various Python scripts for working with and plotting Nutil results, you might find something useful there. https://github.com/ingvildeb/nutil_scripts

Noy987 commented 10 months ago

I will look at the links, thank you so much!

Noy987 commented 10 months ago

Hey,

Would very appreciate some help on understanding how to use the plots' code. I copied them to PyCharm and this is what i get:

C:\Users\PycharmProjects\test\venv\Scripts\python.exe C:\Users\PycharmProjects\test\main.py Usage: python plot_reference_atlas_regions [nutil directory] [type] [parameters]

Process finished with exit code 1

how do I continue here?

sharoncy commented 10 months ago

Hi. I haven't tried running the code myself so I can't really advise, sorry. The plotting code shared with the Nutil software is set up to run automatically with Nutil and looks complicated to edit, so I suspect the code shared by my colleague is easier to adopt. (https://github.com/ingvildeb/nutil_scripts). However, if you have trouble, it is also possible to make these plots directly with Excel, R or another statistical package. Use the RefAtlasRegion and CustomRgion reports as the starting point.