Compatibility issue Python 2.7 vs Python 3.x for the code

[SparshJ]

Sir,

I am a graduate student at Virginia Tech trying to implement your IELU pipeline. The problem I keep running into is that your code is written in Python 2.7 (forgive me if I'm grossly mistaken) whereas the few dependencies like PyMCubes which come with your package are all in Python 3.x. The main error I keep getting for now is that the super function needs at least 1 argument whereas the code passes 0 arguments (conforming to the python 3.x syntax standards). I believe that this is only one of the numerous problems I face while trying the implementation. I have spent two weeks trying to find a way around this. I request you to help me with a possible solution soon.

Thank you

[aestrivex]

Someday the code will get ported to py3 but in the meantime you can force your python distribution to use the 2.7 version of the dependencies. When ielu was released the dependencies were also in 2.7. Does anaconda not just do this for you?

On Tue, Oct 23, 2018, 8:07 PM SparshJ notifications@github.com wrote:

Sir,

I am a graduate student at Virginia Tech trying to implement your IELU pipeline. The problem I keep running into is that your code is written in Python 2.7 (forgive me if I'm grossly mistaken) whereas the few dependencies like PyMCubes which come with your package are all in Python 3.x. The main error I keep getting for now is that the super function needs at least 1 argument whereas the code passes 0 arguments (conforming to the python 3.x syntax standards). I believe that this is only one of the numerous problems I face while trying the implementation. I have spent two weeks trying to find a way around this. I request you to help me with a possible solution soon.

Thank you

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[SparshJ]

Sir, Thank you for the response. I'm not sure whether Anaconda can do that for me. I tried a few times, but I eventually managed to create a Pyconda environment. I then installed all the dependencies from inside that environment, and then executed the ielu/setup.py script. After that, executing the ielu file inside bin launched the IELU GUI.

I hope there is a simpler way to implement this as I want to install the pipeline on a second computer as well. I passed the input data for a patient. For the MRI, I pointed the GUI to the freesurfer subjects directory with that particular patient's folder, and for the CT I converted the DICOM images to nii.gz using MRICRON software. It generated two output files, and I used the last generated file (o232443.nii.gz). The output I got is attached below:

[image: Screenshot from 2018-10-29 17-14-34.png] This doesn't quite look right to me. Maybe the execution isn't running fully. Please note that most of out patients have only the depth electrodes, and no grid electrodes at all. How would you suggest we use the pipeline in our case then? Is there a way to 'tell' it that there are only depth electrodes? I am also facing trouble while getting the 3D visualization image on the left part of the screen. I get the error "TypeError: init() got an unexpected keyword argument 'curv' " . Also, when I try to press 'Examine CT Scan' , I get the error " ImportError: No module named enable.component_editor " on the terminal screen. When I try automatic electrode sorting, I get "No good angles found". I may be missing something very simple here, but I'm unable to get this running properly. I would appreciate any help I can get. I have attached part of the terminal output as a text file with this mail.

Thank you Sparsh Jain

On Tue, Oct 23, 2018 at 8:11 PM Roan LaPlante notifications@github.com wrote:

Someday the code will get ported to py3 but in the meantime you can force your python distribution to use the 2.7 version of the dependencies. When ielu was released the dependencies were also in 2.7. Does anaconda not just do this for you?

On Tue, Oct 23, 2018, 8:07 PM SparshJ notifications@github.com wrote:

Sir,

I am a graduate student at Virginia Tech trying to implement your IELU pipeline. The problem I keep running into is that your code is written in Python 2.7 (forgive me if I'm grossly mistaken) whereas the few dependencies like PyMCubes which come with your package are all in Python 3.x. The main error I keep getting for now is that the super function needs at least 1 argument whereas the code passes 0 arguments (conforming to the python 3.x syntax standards). I believe that this is only one of the numerous problems I face while trying the implementation. I have spent two weeks trying to find a way around this. I request you to help me with a possible solution soon.

Thank you

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.

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