metacell / hnn-ui Goto Github PK

Combine both setCfgFromFile and set_cfg_from_params

Given the recent renaming of attributes we need to update
canvas_keys = ["_diam", "_L", "N_pyr_x", "N_pyr_y", "gridSpacingPyr", "sizeY"]

When HNN-UI is launched, it tries to read from ./hnn_ui/metadata folder, so if the project is not launched from the project's root directory, the folder is never found and we are not able to load.

Maybe we can save in jupyter's config file the path where utilities/install.pywas launched and keep it as a reference to point in the HNN-UI direction. Or add an extra attr to the launching command

(This issue does not affect the docker image because the dockerfile ends with WORKDIR $HOME/HNN-UI)

Bring the latest hnn model configs and target https://github.com/Neurosim-lab/netpyne/tree/hnn_12Aug19/netpyne/analysis.

Change iplotRatePSD to iplotDipolePSD

Hey, right now we have the NetPyNE MI duplicated inside the HNN repo
it’s the file called netpyne_model_interpreter
we have the same inside NetPyNE UI
we should be able to do something more elegant

• Test latest release installation
• Improve readme

We have to add to install.py nrnivmodl ./hnn_ui/mod so that we have the mod files already available

• All dependencies must come from tags/releases
• Ask Salvador to prepare a release of NetPyNE with the dipole changes
• Test
• Merge to master
• Create new release and tag the repo

Possible solution:
Update save/load model with suggested methods:
MetaCell/geppetto-hnn#85
MetaCell/geppetto-hnn#84

if param file has weight of 0 for a particular input or the weight is not specified at all, or the timing of the event is outside of the simulation duration, it's not supposed to be used

Probably the second mechanism is Ca concentration decay cad.mod and the controlled parameter is time constante tau in ms.

L2Basket and L5Basket are overlapping in the 3D model

The folder name Layer 2:3 is not compatible with Windows filesystems. Propose renaming to Layer 2 consistent with variable naming, e.g.

caldw@DESKTOP-LHCRPOM ~/repos$ git clone https://github.com/MetaCell/HNN-UI.git
remote: Enumerating objects: 83, done.
remote: Counting objects: 100% (83/83), done.
remote: Compressing objects: 100% (65/65), done.
remote: Total 1204 (delta 38), reused 43 (delta 17), pack-reused 1121
Receiving objects: 100% (1204/1204), 9.60 MiB | 9.36 MiB/s, done.
Resolving deltas: 100% (579/579), done.
fatal: cannot create directory at 'hnn_ui/metadata/cellParams/Layer 2:3': Invalid argument
warning: Clone succeeded, but checkout failed.
You can inspect what was checked out with 'git status'
and retry the checkout with 'git checkout -f HEAD'

There appear to be 3 folders to rename (2 in the first link, 1 in second):
https://github.com/MetaCell/HNN-UI/tree/bd17a1dd59f12889976739869fe347df3639a6c9/hnn_ui/metadata/networkParams
https://github.com/MetaCell/HNN-UI/tree/bd17a1dd59f12889976739869fe347df3639a6c9/hnn_ui/metadata/cellParams

CellParams method missing in ui branch in netpyne is causing the docker image not being able to create the model. Either we bring dev into ui or we install hnn-ui with netpyne dev branch