Merge pull request #8 from SpikeInterface/matlab_for_kilosort

move matlab_for_kilosort over from spikeforest repo

Author: alejoe91

kilosort2/Dockerfile

@@ -1,4 +1,4 @@
-FROM magland/matlab_for_kilosort:0.1.0
+FROM spikeinterface/matlab_for_kilosort:0.1.0
 
 #########################################
 ### Python                                                               

kilosort3/Dockerfile

@@ -1,4 +1,4 @@
-FROM magland/matlab_for_kilosort:0.1.0
+FROM spikeinterface/matlab_for_kilosort:0.1.0
 
 #########################################
 ### Python                                                               

matlab_for_kilosort/docker1/Dockerfile

@@ -0,0 +1,3 @@
+FROM mathworks/matlab:r2020b
+
+USER root

matlab_for_kilosort/docker1/build.sh

@@ -0,0 +1,4 @@
+#!/bin/bash
+set -e
+
+docker build -t matlab_docker1 .

matlab_for_kilosort/matlab_docker.md

@@ -0,0 +1,76 @@
+# Creating a docker image with matlab for kilosort
+
+The goal here is to get a matlab docker image that has the necessary toolboxes to run kilosort. (In order to run matlab within the container, you'll need to provide runtime license information.)
+
+First build the matlab_docker1 image (see the docker1 subdirectory)
+
+Then:
+
+```bash
+docker run -it --rm matlab_docker1
+```
+
+Enter your matlab user name and password to start matlab.
+
+Copy the credentials that are inside the container (from a new terminal):
+
+```bash
+docker cp <container-id>:/root/.matlab/MathWorks/MATLAB/LNUCredentials/LNUCreds.info $HOME/container_LNUCreds.info
+```
+
+where `<container-id>` is the ID of the docker container you are running
+
+Exit the docker image, and restart via:
+
+```bash
+xhost +
+docker run -it --rm -e DISPLAY=$DISPLAY -v /tmp/.X11-unix:/tmp/.X11-unix:ro --shm-size=512M -v $HOME/container_LNUCreds.info:/root/.matlab/MathWorks/MATLAB/LNUCredentials/LNUCreds.info matlab_docker1 bash
+```
+
+Then inside the container run
+
+```
+matlab
+```
+
+Now you shouldn't need to enter your credentials, and you should get a graphical matlab session! Importantly, however, your credentials are not actually stored in the docker image.
+
+From the GUI click Add-Ons -> Get Add-Ons
+
+Install the required toolboxes. For kilosort, that would be: parallel computing toolbox, signal processing toolbox, Statistics and Machine Learning Toolbox.
+
+I think you may need to install them one at a time.
+
+Then close matlab withing the container (but keep the container running) and commit the image:
+
+```bash
+docker commit <container-id> magland/docker_for_kilosort:0.1.0
+```
+
+Now try to create a new container with the committed image:
+
+```bash
+docker run -it magland/docker_for_kilosort:0.1.0 bash
+```
+
+Then run `matlab` inside that new container. It should ask for the user name and password. And you should have the toolboxes installed! To check this, type `ver` in matlab, and you should see something like:
+
+```
+>> ver
+-----------------------------------------------------------------------------------------------------
+MATLAB Version: 9.9.0.1592791 (R2020b) Update 5
+MATLAB License Number: 40764494
+Operating System: Linux 5.4.0-70-generic #78~18.04.1-Ubuntu SMP Sat Mar 20 14:10:07 UTC 2021 x86_64
+Java Version: Java 1.8.0_202-b08 with Oracle Corporation Java HotSpot(TM) 64-Bit Server VM mixed mode
+-----------------------------------------------------------------------------------------------------
+MATLAB                                                Version 9.9         (R2020b)
+Parallel Computing Toolbox                            Version 7.3         (R2020b)
+Signal Processing Toolbox                             Version 8.5         (R2020b)
+Statistics and Machine Learning Toolbox               Version 12.0        (R2020b)
+```
+
+Finally, push to dockerhub
+
+```bash
+docker push spikeinterface/matlab_for_kilosort:0.1.0
+```