"CVXOPT package needed to enforce constraints"

[soichih]

I've fixed some obvious issues with this app, but now I am seeing following app.

Traceback (most recent call last):
  File "/N/dc2/scratch/brlife/karst-workflows/59d4f89d6ac3590024d33731/59d4f89d6ac3590024d33734/main.py", line 44, in <module>
    positivity_constraint=True)
  File "/N/u/brlife/Karst/.local/lib/python2.7/site-packages/dipy/reconst/mapmri.py", line 235, in __init__
    'CVXOPT package needed to enforce constraints')
ValueError: CVXOPT package needed to enforce constraints

Who could help me with this issue?

[francopestilli]

Eleftherios would be best. @brain-life/dev

[soichih]

@Garyfallidis Can you take a look?

[aarya22]

Maybe I'm stating the obvious, but you could try to install CVXOPT package on brain-life.

pip install cvxopt

[soichih]

@aarya22 That fixed it.

It generated following png.

How does it look?

By the way, the submit.pbs is looks for a wrong output file and task is still failing - even though it generates the final image

https://github.com/brain-life/app-dipy-MAPMRI/blob/63f6273e871f189f5be925695f7daf153d761b47/submit.pbs#L21

[aarya22]

Great to hear. I don't know if the png is correct or not, maybe Elef or Ariel can help? I am meeting Ariel later today I can ask him about it.

As for the submit.pbs, I think the issue is that the pbs script is looking for 4 track1.tck files as output, but the application seems to be producing a png file called MAPMRI_maps_regularization.png. I can edit the pbs script to make it look for this file instead.

[Garyfallidis]

Have in mind that cvxopt is not used anymore. We use cvxpy. See later updates in master. Are you planning to use Mapmri or Mapl ? I think Mapl maybe better for clinical datasets. It's the same API - same classname for both. As we discuss before it would be much easier if first you submit a workflow on that in DIPY to make sure that all is good and have multiple reviewers looking the code that are part of the development team. Here is an example of a workflow using the ConstantSolidAngle algorithm. https://github.com/Garyfallidis/dipy/blob/det_track_workflow/bin/dipy_csa We should have something similar for mapmri.

…

On Thu, Oct 5, 2017 at 4:05 PM Aman Arya ***@***.***> wrote: Great to hear. I don't know if the png is correct or not, maybe Elef or Ariel can help? I am meeting Ariel later today I can ask him about it. As for the submit.pbs, I think the issue is that the pbs script is looking for 4 track1.tck files as output, but the application seems to be producing a png file called MAPMRI_maps_regularization.png. I can edit the pbs script to make it look for this file instead. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#1 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAIMhIHlrc-HtD9NtgBFVRNX1rMOIozmks5spTaDgaJpZM4PudNA> .

[Garyfallidis]

I can arrange a meeting with you to help with that. On Thu, Oct 5, 2017 at 4:13 PM Eleftherios Garyfallidis <elef@indiana.edu> wrote:

…

Have in mind that cvxopt is not used anymore. We use cvxpy. See later updates in master. Are you planning to use Mapmri or Mapl ? I think Mapl maybe better for clinical datasets. It's the same API - same classname for both. As we discuss before it would be much easier if first you submit a workflow on that in DIPY to make sure that all is good and have multiple reviewers looking the code that are part of the development team. Here is an example of a workflow using the ConstantSolidAngle algorithm. https://github.com/Garyfallidis/dipy/blob/det_track_workflow/bin/dipy_csa We should have something similar for mapmri. On Thu, Oct 5, 2017 at 4:05 PM Aman Arya ***@***.***> wrote: > Great to hear. I don't know if the png is correct or not, maybe Elef or > Ariel can help? I am meeting Ariel later today I can ask him about it. > > As for the submit.pbs, I think the issue is that the pbs script is > looking for 4 track1.tck files as output, but the application seems to be > producing a png file called MAPMRI_maps_regularization.png. I can edit the > pbs script to make it look for this file instead. > > — > You are receiving this because you were mentioned. > Reply to this email directly, view it on GitHub > <#1 (comment)>, > or mute the thread > <https://github.com/notifications/unsubscribe-auth/AAIMhIHlrc-HtD9NtgBFVRNX1rMOIozmks5spTaDgaJpZM4PudNA> > . >

[aarya22]

@soichih I have a pull-request to fix the pbs file, check it out.

@Garyfallidis I can't find the workflow for mapmri in the dipy workflows folder. I am pretty sure I can make the workflow myself, but I am not sure what you mean by "submit" a workflow. Do you want me to submit a pull-request with a new workflow with mapmri?

[aarya22]

@Garyfallidis I've created a workflow and a pull-request for the app. Not sure how to exactly create a workflow but check it out:

@soichih and @francopestilli Hopefully by creating workflows like this for our applications we can get more feedback from the dipy community and updates for our applications, as well make the applications far easier to make.

[francopestilli]

@aarya22 this is great thanks! I hope @Garyfallidis can let us know if this is a good way forward!