Compiling via mcc command, updates in readme

Author: chyumin

kilosort3-compiled/README.md

@@ -2,18 +2,18 @@
 
 This documentation is intended to show how to create a Docker image with Matlab compiled implementation of Kilosort3 sorter. The main goal of this project is to avoid the requirement of Matlab Licenses and also abstract the installation and setup steps to run kilosort
 
-There are three main steps for generating a functional kilosort3-compiled docker image:
+There are four main steps to generate a functional kilosort3-compiled docker image:
 
-1. Compile kilosort3 as Standalone Application
-2. Create a (base) docker image with Matlab Runtime and the compiled application from step 1
-3. Extend the docker image from step 2 for improvements and fixes
+1. Kilosort Setup
+2. Compile Kilosort3 as Standalone Application
+3. Create a (base) docker image with Matlab Runtime and the compiled application from step 2
+4. Extend the docker image from step 3 for improvements and fixes
 
 ## Requirements
 - Packaging a MATLAB Docker image is supported on Linux only
 - Docker
 - Matlab
 - NVIDIA GPU and CUDA capabilities
-- [nvidia-container-toolkit](https://docs.nvidia.com/datacenter/cloud-native/container-toolkit/install-guide.html#setting-up-nvidia-container-toolkit): required to run a docker with GPU capabilities
 
 ### Matlab Requirements
 - MATLAB Compiler
@@ -23,7 +23,7 @@ There are three main steps for generating a functional kilosort3-compiled docker
 
 Licenses for Matlab and toolboxes are needed only for compiling ironclust as Standalone Application and to generate the base Docker image. After this process, no license will be required, either to extend the base image or to run the sorter.
 
-## Compiling Kilosort as Matlab's Standalone Application
+## Kilosort Setup 
 - Git clone or Download kilosort [source code](https://github.com/MouseLand/Kilosort)
 - Open Matlab
 - Compile Kilosort mexfiles:
@@ -32,27 +32,42 @@ Licenses for Matlab and toolboxes are needed only for compiling ironclust as Sta
     ```
     >> mexGPUall
     ```
+
+## Compiling Kilosort as Matlab's Standalone Application
 - Set Matlab's workspace folder to `/path/to/spikeinterface-dockerfiles/kilosort3-compiled/matlab_files`
-- Open Matlab's `Application Compiler` (located in `APPS` Tab)
-- Click on `+` sign in Add Main File, Select `ks3_compiled.m` and Click `Open`
-- In the section `Files required for your application to run`:
-	- Click on `+` sign button, Select `utils` folder and click `Open`
-	- Click on `+` sign button again, Select the folder of the cloned `Kilosort` project and click `Open`
-- On Application Compiler window, Click on `Package`, Save the `ks3_compiled.prj` file and wait for Matlab to Compile the project. A folder (named `ks3_compiled` by default) with compiled files will be generated.
-- Close `Package` and `Application Compiler` windows
+- Run `mcc` command with `utils` folder and kilosort path:
+```
+>> mcc -m ks3_compiled.m -a utils -a  <git-cloned-path>/Kilosort
+```
 
 ## Generating Base Docker Image
-- In Matlab console run:
+- To generate the base docker image (called `ks3-matlab-base`) with compiled application, run the following command in Matlab console:
 ```
->> compiler.package.docker('ks3_compiled/for_testing/ks3_compiled', 'ks3_compiled/for_testing/requiredMCRProducts.txt', 'ImageName', 'ks3-matlab-base')
+>> compiler.package.docker('ks3_compiled', 'requiredMCRProducts.txt', 'ImageName', 'ks3-matlab-base')
 ```
 
-This command will create an image called `ks3-matlab-base` to be used in the next step
-
-## Extending Base Image/Creating final image
+- [Optional] Files generated by Matlab Compiler can be deleted:
+  - In your terminal, go to the folder for this project:
+  ```
+  $ cd /path/to/spikeinterface-dockerfiles/kilosort3-compiled
+  ```
+  - Run `rm` command:
+  ```
+  $ rm -r \
+    matlab_files/includedSupportPackages.txt \
+    matlab_files/ks3-matlab-basedocker/ \
+    matlab_files/ks3_compiled \
+    matlab_files/mccExcludedFiles.log \
+    matlab_files/readme.txt \
+    matlab_files/requiredMCRProducts.txt \
+    matlab_files/run_ks3_compiled.sh \
+    matlab_files/unresolvedSymbols.txt \
+  ```
+
+## Extending Base Image and creating final image
 The Dockerfile in this folder applies some fixes and updates to the base image generated automatically by Matlab in order to properly run kilosort3:
 
-- In your terminal, go to the current folder:
+- In your terminal, go to the folder for this project:
 ```
 $ cd /path/to/spikeinterface-dockerfiles/kilosort3-compiled
 ```
@@ -65,6 +80,8 @@ $ source build.sh
 
 ## Running a container
 
+- [nvidia-container-toolkit](https://docs.nvidia.com/datacenter/cloud-native/container-toolkit/install-guide.html#setting-up-nvidia-container-toolkit) is required to run a docker with GPU capabilities
+
 The base syntax to run dockerized kilosort is:
 
 ```