OpenCMISS Zinc/Iron libraries for python v2.7

[Marco Marra]

Hello,

Marco Marra from University of Twente (The Netherlands) here. I'm very interested in the MAP project.

I managed to get the MAP client to run in an anaconda Python 2.7 environment. When it comes to plugins, many of them require Zinc and Iron modules from the OpenCMISS library. However, I could only find the OpenCMISS SDK for Python 3.6 on their website, which is incompatible with my Python 2.7 environment.

How should a typical environment for running the MAP client look like then? I followed the instructions quite neatly, although not exactly since I use anaconda Python. But is Python v2.7 ok to run the MAP client with plugins? How do I get the OpenCMISS libraries to work? Are there OpenCMISS libraries for Python v2.x out there?

Best regards,
Marco

[Bryce Killen]

Hi Marco,

A lot of questions so let me try to unpack them.

How should a typical environment for running the MAP client look like then?

I have run the mapclient through the generic anaconda environment and also a dedicated mapclient environment and probably much to your disgust I have had no issues.

But is Python v2.7 ok to run the MAP client

Yes in fact python 2.7 is the recommended version of python

To get back to your original question, you said :

When it comes to plugins, many of them require Zinc and Iron modules from the OpenCMISS library

Is there any plugin in particular you are trying to use ? When are you actually have the issue? When trying to load the plugins or trying to run them ?

If you are getting an errors , it would be helpful to screenshot them and post them in the reply so we know exactly the issue.

Thanks

Bryce

[Marco Marra]

Hi Bryce,

Thank you for your answers.

Meanwhile, I installed the MAP client on linux with Python 2.7 and that went smooth. I also found the FAI workshop page, where there are specific instructions for Windows with Anaconda environment. I will give it another try by following those.

Is there any plugin in particular you are trying to use ? When are you actually have the issue? When trying to load the plugins or trying to run them ?

The issues were at loading time. What I did was: I downloaded the entire plugins collection from github, and I added the root plugins directory to the MAP client plugins manager. This was not very smart I suppose. I will try with one plugin at a time, so I can see better what the issues are.

What I'm particularly interested in is the workflow for generating patient-specific musculoskeletal models from partial medical images. It is also not immediately clear to me, by just looking at the plugins names, who does what and which plugins to install (that's why I downloaded them all in the first place). I assume that the plugins used in the FAI workshop at section 'Bone Mesh Generation Workflow' http://map-client-fai-workshop.readthed ... shgen.html are the ones?

Thanks

Marco

[Bryce Killen]

Hi Marco,

Upon inspection of my own instance of the mapclient when launching it from Anaconda I also get the following error which is I think your original question

OpenCM.PNG (7.6 KiB) Viewed 738 times

This is nothing to be alarmed at as all my plugins work fine.

You are looking in the right place, the FAI workshop (https://readthedocs.org/projects/map-cl ... -workshop/) is based on doing exactly you are wanting to do. As you said, the best way to operate is to only download the plugins which you actually want to use because if you have too many it will make it hard to find the ones you are looking for.

What I would suggest to do is, delete all the plugins you have previously downloaded and only download those you need. If there is an issue with the plugins , it will be displayed in the anaconda prompt once you launch MAP and will not be displayed in the available plugins in the left hand side. You may need to scroll up to through your anaconda prompt a little to see this error.

Also if you open the workshop-workflows and try to open any workflow, if you are missing any plugins this will be displayed in the mapclient workspace.

Cheers
Bryce

[Karen Fitzgerald]

Hi Marco,

I see that you managed to successfully install MAP Client on Linux. Could you please provide install instructions or point me to what instructions you used in this successful install, as my install following the instructions here failed: http://map-client.readthedocs.io/en/lat ... stallation

Thanks

Karen

[Bryce Killen]

Hi Karen,

I am not sure if this is related to your previous post. If you are still wanting to install MAP on Linux, if you are able to send me the exact errors you are getting I can follow up to try and find and provide some specific instruction for Linux.

Thanks