update docs

Author: chyumin

hdsort-compiled/README.md

@@ -1,12 +1,14 @@
-# HDsort Compiled Docker Images
+# HDsort Compiled Docker Image
 
 This documentation is intended to show how to create a Docker image with Matlab compiled HDsort 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 the sorter
 
 There are three main steps for generating a functional HDsort docker image:
 1. Compile HDsort as Matlab's Standalone Application
-2. Create a (base) docker image with Matlab Runtime and the compiled application from step 1
+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
 
+Steps 1 and 2 are done by `compile.sh` script, while step 3 is done by `build.sh` script
+
 ## Requirements
 - Packaging a MATLAB Docker image is supported on Linux only
 - Docker
@@ -17,45 +19,19 @@ There are three main steps for generating a functional HDsort docker image:
 - Fuzzy_Logic Toolbox
 - More requirements to be checked and listed...
 
-## Compiling HDsort as Matlab's Standalone Application
+## Cloning repositories
 - Git clone or Download HDsort [source code](https://git.bsse.ethz.ch/hima_public/HDsort)
-- Open Matlab
-- Set Matlab's workspace folder to `/path/to/spikeinterface-dockerfiles/hdsort-compiled`
-- Run `mcc` command with `hdsort_compiled.m` as base and adding path to git cloned HDSort:
-```matlab
->> mcc -m hdsort_compiled.m -a <git-cloned-path>/HDsort
-```
+- Git clone or Download spikeinterface [source code](https://github.com/SpikeInterface/spikeinterface)
 
 ## Generating Base Docker Image
-- To generate the base docker image (called `hdsort-matlab-base`) with the compiled application, run the following command in Matlab console:
-```matlab
->> compiler.package.docker('hdsort_compiled', 'requiredMCRProducts.txt', 'ImageName', 'hdsort-matlab-base')
+`compile.sh` script generates the base docker image (called `hdsort-matlab-base`) with the matlab compiled HDSort application
+- Run compile script:
+```bash
+$ source compile.sh /path/to/HDSort /path/to/spikeinterface
 ```
 
-
-- [Optional] Files generated by Matlab Compiler can be deleted:
-  - In your terminal, go to the `hdsort-compiled` folder in this project:
-  ```bash
-  $ cd /path/to/spikeinterface-dockerfiles/hdsort-compiled
-  ```
-
-  - Run `rm` command:
-  ```bash
-  $ rm -r \
-    hdsort-matlab-basedocker \
-    hdsort_compiled \
-    includedSupportPackages.txt \
-    mccExcludedFiles.log \
-    readme.txt \
-    requiredMCRProducts.txt \
-    run_hdsort_compiled.sh \
-    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 waveclus:
-
+The Dockerfile in this folder applies some fixes and updates to the base image in order to properly run HDSort:
 
 - In your terminal, go to the  folder for this project:
 ```

ironclust-compiled/README.md

@@ -4,7 +4,7 @@ This documentation is intended to show how to create a Docker image with Matlab
 
 There are three main steps for generating a functional ironclust docker image:
 1. Compile Ironclust as Matlab's Standalone Application
-2. Create a (base) docker image with Matlab Runtime and the compiled application from step 1
+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
 
 ## Requirements
@@ -21,42 +21,20 @@ There are three main steps for generating a functional ironclust docker image:
 
 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 Ironclust as Matlab's Standalone Application
+## Cloning repositories
 - Git clone or Download ironclust [source code](https://github.com/flatironinstitute/ironclust.git)
-- Open Matlab
-- Set Matlab's workspace folder to: `<git-cloned-path>/ironclust/matlab`
-- In Matlab console run:
-```
->> mcc -m p_ironclust.m -a <git-cloned-path>/ironclust/matlab/*.* -a <git-cloned-path>/ironclust/matlab/prb -a <git-cloned-path>/ironclust/matlab/prb_json
-```
+- Git clone or Download spikeinterface [source code](https://github.com/SpikeInterface/spikeinterface)
+
 
 ## Generating Base Docker Image
-- To generate the base docker image (called `ironclust-matlab-base`) with the compiled application, run the following command in Matlab console:
-```
->> compiler.package.docker('p_ironclust', 'requiredMCRProducts.txt', 'ImageName', 'ironclust-matlab-base')
+`compile.sh` script generates the base docker image (called `ironclust-matlab-base`) with the matlab compiled ironclust application
+- Run compile script:
+```bash
+$ source compile.sh /path/to/ironclust /path/to/spikeinterface
 ```
 
-- [Optional] Files generated by Matlab Compiler can be deleted:
-  - In your terminal, go to the folder for this project:
-  ```
-  $ cd <git-cloned-path>/ironclust/
-  ```
-  - Run `rm` command:
-  ```
-  $ rm -r \
-    matlab/includedSupportPackages.txt \
-	matlab/ironclust-matlab-basedocker \
-	matlab/mccExcludedFiles.log \
-	matlab/p_ironclust \
-	matlab/readme.txt \
-	matlab/requiredMCRProducts.txt \
-	matlab/run_p_ironclust.sh \
-	matlab/unresolvedSymbols.txt
-  ```
-
-
 ## Extending Base Image/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 ironclust:
+The Dockerfile in this folder applies some fixes and updates to the base image in order to properly run ironclust:
 
 - In your terminal, go to the  folder for this project:
 ```
@@ -68,7 +46,6 @@ $ cd /path/to/spikeinterface-dockerfiles/ironclust-compiled
 $ 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

kilosort_no_license/README.md

@@ -18,12 +18,14 @@ This documentation is intended to show how to create a Docker image with Matlab
 
 There are four main steps to generate a functional kilosort-compiled docker image:
 
-1. Kilosort Setup
+1. Compile Kilosort CUDA files
 2. Compile Kilosort 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
 
-Detailed descriptions for each step are documented in `README.md` for each supported kilosort version folder (`kilosort-compiled`, `kilosort2-compiled` and so on)
+Steps 1 to 3 are done by `compile.sh` script, while step 4 is done by `build.sh` script.
+
+Steps to run scripts and create the images are documented in `README.md` for each supported kilosort version folder (`kilosort-compiled`, `kilosort2-compiled` and so on)
 
 Licenses for Matlab and toolboxes are needed only for compiling kilosort 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.
 

kilosort_no_license/kilosort-compiled/README.md

@@ -2,48 +2,18 @@
 
 ## 1. Kilosort Setup
 - Git clone or Download Kilosort [source code](https://github.com/cortex-lab/KiloSort)
-- Open Matlab
-- Compile Kilosort mexfiles:
-  - Set Matlab's workspace folder to `<git-cloned-path>/KiloSort/CUDA`
-  - In Matlab console run:
-    ```matlab
-    >> mexGPUall
-    ```
+- Git clone or Download spikeinterface [source code](https://github.com/SpikeInterface/spikeinterface)
 
-## 2. Compiling Kilosort as Matlab's Standalone Application
-- Set Matlab's workspace folder to `/path/to/spikeinterface-dockerfiles/kilosort_no_license`
-- Run `mcc` command with `utils` folder and kilosort path:
-```matlab
->> mcc -m kilosort-compiled/ks_compiled.m -a utils -a <git-cloned-path>/KiloSort
-```
-
-## 3. Generating Base Docker Image
-- To generate the base docker image (called `ks-matlab-base`) with the compiled application, run the following command in Matlab console:
-```matlab
->> compiler.package.docker('ks_compiled', 'requiredMCRProducts.txt', 'ImageName', 'ks-matlab-base')
+## 2. Create base image
+`compile.sh` script generates the base docker image (called `ks2-matlab-base`) with the matlab compiled Kilosort application
+- Run compile script:
+```bash
+$ source compile.sh /path/to/KiloSort /path/to/spikeinterface
 ```
 
-- [Optional] Files generated by Matlab Compiler can be deleted:
-  - In your terminal, go to the `kilosort_no_license` folder in this project:
-  ```bash
-  $ cd /path/to/spikeinterface-dockerfiles/kilosort_no_license
-  ```
-  - Run `rm` command:
-  ```bash
-  $ rm -r \
-    includedSupportPackages.txt \
-    ks-matlab-basedocker/ \
-    ks_compiled \
-    mccExcludedFiles.log \
-    readme.txt \
-    requiredMCRProducts.txt \
-    run_ks_compiled.sh \
-    unresolvedSymbols.txt
-  ```
-
-## 4. Extending Base Image and creating final image
+## 3. 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 kilosort:
+The Dockerfile in this folder applies some fixes and updates to the base image in order to properly run kilosort:
 
 - In your terminal, go to the folder for this project:
 ```bash

kilosort_no_license/kilosort2-compiled/README.md

@@ -1,53 +1,19 @@
 # Generating Compiled Kilosort2 Docker Image
 
-## 1. Kilosort Setup 
-- Git clone or Download Kilosort [source code](https://github.com/MouseLand/Kilosort)
-- Git checkout to the correct version:
-```bash
-$ git checkout tags/v2.0
-```
-- Open Matlab
-- Compile Kilosort mexfiles:
-  - Set Matlab's workspace folder to `<git-cloned-path>/Kilosort/CUDA`
-  - In Matlab console run:
-    ```matlab
-    >> mexGPUall
-    ```
-
-## 2. Compiling Kilosort as Matlab's Standalone Application
-- Set Matlab's workspace folder to `/path/to/spikeinterface-dockerfiles/kilosort_no_license`
-- Run `mcc` command with `utils` folder and kilosort path:
-```matlab
->> mcc -m kilosort2-compiled/ks2_compiled.m -a utils -a <git-cloned-path>/Kilosort
-```
+## 1. Kilosort Setup
+- Git clone or Download kilosort [source code](https://github.com/MouseLand/Kilosort)
+- Git clone or Download spikeinterface [source code](https://github.com/SpikeInterface/spikeinterface)
 
-## 3. Generating Base Docker Image
-- To generate the base docker image (called `ks2-matlab-base`) with the compiled application, run the following command in Matlab console:
-```matlab
->> compiler.package.docker('ks2_compiled', 'requiredMCRProducts.txt', 'ImageName', 'ks2-matlab-base')
+## 2. Create base image
+`compile.sh` script generates the base docker image (called `ks2-matlab-base`) with the matlab compiled Kilosort2 application
+- Run compile script:
+```bash
+$ source compile.sh /path/to/Kilosort /path/to/spikeinterface
 ```
 
-- [Optional] Files generated by Matlab Compiler can be deleted:
-  - In your terminal, go to the `kilosort_no_license` folder in this project:
-  ```bash
-  $ cd /path/to/spikeinterface-dockerfiles/kilosort_no_license
-  ```
-  - Run `rm` command:
-  ```bash
-  $ rm -r \
-    includedSupportPackages.txt \
-    ks2-matlab-basedocker/ \
-    ks2_compiled \
-    mccExcludedFiles.log \
-    readme.txt \
-    requiredMCRProducts.txt \
-    run_ks2_compiled.sh \
-    unresolvedSymbols.txt
-  ```
-
-## 4. Extending Base Image and creating final image
+## 3. 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 kilosort2:
+The Dockerfile in this folder applies some fixes and updates to the base image in order to properly run kilosort2:
 
 - In your terminal, go to the folder for this project:
 ```bash

kilosort_no_license/kilosort2_5-compiled/README.md

@@ -1,53 +1,19 @@
 # Generating Compiled Kilosort2_5 Docker Image
 
-## 1. Kilosort Setup 
-- Git clone or Download Kilosort [source code](https://github.com/MouseLand/Kilosort)
-- Git checkout to the correct version:
-```bash
-$ git checkout tags/v2.5
-```
-- Open Matlab
-- Compile Kilosort mexfiles:
-  - Set Matlab's workspace folder to `<git-cloned-path>/Kilosort/CUDA`
-  - In Matlab console run:
-    ```matlab
-    >> mexGPUall
-    ```
-
-## 2. Compiling Kilosort as Matlab's Standalone Application
-- Set Matlab's workspace folder to `/path/to/spikeinterface-dockerfiles/kilosort_no_license`
-- Run `mcc` command with `utils` folder and kilosort path:
-```matlab
->> mcc -m kilosort2_5-compiled/ks2_5_compiled.m -a utils -a <git-cloned-path>/Kilosort
-```
+## 1. Setup
+- Git clone or Download kilosort [source code](https://github.com/MouseLand/Kilosort)
+- Git clone or Download spikeinterface [source code](https://github.com/SpikeInterface/spikeinterface)
 
-## 3. Generating Base Docker Image
-- To generate the base docker image (called `ks2_5-matlab-base`) with the compiled application, run the following command in Matlab console:
-```matlab
->> compiler.package.docker('ks2_5_compiled', 'requiredMCRProducts.txt', 'ImageName', 'ks2_5-matlab-base')
+## 2. Create base image
+`compile.sh` script generates the base docker image (called `ks2_5-matlab-base`) with the matlab compiled Kilosort2_5 application
+- Run compile script:
+```bash
+$ source compile.sh /path/to/Kilosort /path/to/spikeinterface
 ```
 
-- [Optional] Files generated by Matlab Compiler can be deleted:
-  - In your terminal, go to the `kilosort_no_license` folder in this project:
-  ```bash
-  $ cd /path/to/spikeinterface-dockerfiles/kilosort_no_license
-  ```
-  - Run `rm` command:
-  ```bash
-  $ rm -r \
-    includedSupportPackages.txt \
-    ks2_5-matlab-basedocker/ \
-    ks2_5_compiled \
-    mccExcludedFiles.log \
-    readme.txt \
-    requiredMCRProducts.txt \
-    run_ks2_5_compiled.sh \
-    unresolvedSymbols.txt
-  ```
-
-## 4. Extending Base Image and creating final image
+## 3. 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 kilosort2_5:
+The Dockerfile in this folder applies some fixes and updates to the base image in order to properly run kilosort2_5:
 
 - In your terminal, go to the folder for this project:
 ```bash

kilosort_no_license/kilosort3-compiled/README.md

@@ -1,49 +1,19 @@
 # Generating Compiled Kilosort3 Docker Image
 
-## 1. Kilosort Setup 
-- Git clone or Download Kilosort [source code](https://github.com/MouseLand/Kilosort)
-- Open Matlab
-- Compile Kilosort mexfiles:
-  - Set Matlab's workspace folder to `<git-cloned-path>/Kilosort/CUDA`
-  - In Matlab console run:
-    ```matlab
-    >> mexGPUall
-    ```
+## 1. Kilosort Setup
+- Git clone or Download kilosort [source code](https://github.com/MouseLand/Kilosort)
+- Git clone or Download spikeinterface [source code](https://github.com/SpikeInterface/spikeinterface)
 
-## 2. Compiling Kilosort as Matlab's Standalone Application
-- Set Matlab's workspace folder to `/path/to/spikeinterface-dockerfiles/kilosort_no_license`
-- Run `mcc` command with `utils` folder and kilosort path:
-```matlab
->> mcc -m kilosort3-compiled/ks3_compiled.m -a utils -a <git-cloned-path>/Kilosort
-```
-
-## 3. Generating Base Docker Image
-- To generate the base docker image (called `ks3-matlab-base`) with the compiled application, run the following command in Matlab console:
-```matlab
->> compiler.package.docker('ks3_compiled', 'requiredMCRProducts.txt', 'ImageName', 'ks3-matlab-base')
+## 2. Create base image
+`compile.sh` script generates the base docker image (called `ks3-matlab-base`) with the matlab compiled Kilosort3 application
+- Run compile script:
+```bash
+$ source compile.sh /path/to/Kilosort /path/to/spikeinterface
 ```
 
-- [Optional] Files generated by Matlab Compiler can be deleted:
-  - In your terminal, go to the `kilosort_no_license` folder in this project:
-  ```bash
-  $ cd /path/to/spikeinterface-dockerfiles/kilosort_no_license
-  ```
-  - Run `rm` command:
-  ```bash
-  $ rm -r \
-    includedSupportPackages.txt \
-    ks3-matlab-basedocker/ \
-    ks3_compiled \
-    mccExcludedFiles.log \
-    readme.txt \
-    requiredMCRProducts.txt \
-    run_ks3_compiled.sh \
-    unresolvedSymbols.txt
-  ```
-
-## 4. Extending Base Image and creating final image
+## 3. 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:
+The Dockerfile in this folder applies some fixes and updates to the base image in order to properly run kilosort3:
 
 - In your terminal, go to the folder for this project:
 ```bash