-
Notifications
You must be signed in to change notification settings - Fork 21
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
Use MorphIO as the IO layer #18
Conversation
I had to change the format of |
I'm afraid we still have data in this "unsupported" format (2015 Cell paper morphology release). Have they been updated or is there a way to update them? |
Lol, ok. It's not in the spec. I'll talk with @mgeplf tomorrow to see if it's best to update the spec and make morphio support it or to update the morphologies. |
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
Can we ensure that this change will not have an impact on the loaded data? A "functional" test would be useful in this case. For instance could we test that the 2 actual bio neurons (in test_data/valid, C010398B-P2.CNG.swc, C010398B-P2.h5) are loaded the same way as before?
@@ -17,7 +17,7 @@ | |||
|
|||
neu_test = Neuron.Neuron() | |||
neu_test.set_soma(soma_test) | |||
neu_test.append_tree(apical_test, td) |
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
This is actually crucial for supporting "weird" cell types. Removing it will block the analysis of the microglia datasets, BigNeuron data and possible other "unsupported" data. Do you have a plan to include arbitrary tree types that the user can customize?
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
Yes, I was just looking at it. I'll re-add the tree_type argument and test it. I'll remove you from the PR, polish it and re-add you.
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
Thanks a lot! That will be useful.
@lidakanari which files in the 2015 release have |
I think it is from the 2012 release (which is used for the 2015 Cell paper). They are the unraveled cells. Are the new unraveled cells in the updated structure? If that's the case, the issue will only relate to previous releases. |
From what I can see, the |
Yeah, the Which isn't part of the spec, and therefore isn't handled by MorphIO. An example of this h5v2 file would be interesting to see, as I don't believe I have ever seen it before. |
Hi. I'm cleaning my opened PR list so I'm closing this one. And it is probably no longer relevant. Feel free to ping me the day you want it to be re-opened. |
No description provided.