Update README.md

README.md

@@ -4,34 +4,26 @@ This repository contains my work on the multiworm tracker for the [MRC-CSC](http
 
 # Installation
 
-## Requirements.
-- Python 3 + numpy matplotlib pytables pandas h5py scipy scikit-learn scikit-image seaborn xlrd pyqt cython
-- ffmpeg
-- openCV3
-- hdf5
-- Cython including a compatible C/C++ compiler.
-- Additionally it requires to clone the [open-worm-analysis-toolbox](https://github.com/openworm/open-worm-analysis-toolbox) from OpenWorm for the feature extraction.
-
-## Installation using python homebrew (OS X)
+## Installation using Homebrew (OS X)
 Run `bash installation_script.sh brew`. If it is not a clean installation, I cannot warranty this script will work since I have encountered conflict with previous versions of the libraries installed by homebrew. In the future I might develop a script that allow to remove previous installations.
 
-## Installation using anaconda (OS X/Linux).
+## Installation using Anaconda (OS X/Linux).
 Run `bash installation_script.sh`.
 On linux there might be some problems with dependencies. It might be requiered to install from scratch ffmpeg and pyqt5.
 
-## Windows installation.
+## Installation for Windows.
 - Download and install [git tools for windows](https://git-scm.com/download/win). Make sure to select "Select Windows' default window". Otherwise you will have to use MinTTY as command line.
 - Clone this repository and  [OpenWorm analysis toolbox](https://github.com/openworm/open-worm-analysis-toolbox):
 ```
 git clone https://github.com/ver228/Multiworm_Tracking
 git clone https://github.com/openworm/open-worm-analysis-toolbox
 ```
 - Install [ffmpeg](https://ffmpeg.org/download.html). [Here](http://adaptivesamples.com/how-to-install-ffmpeg-on-windows/) are friendly installation instructions.
-- Download [anaconda](https://www.continuum.io/downloads) or [miniconda](http://conda.pydata.org/miniconda.html) with python 3.5.
+- Download [miniconda](http://conda.pydata.org/miniconda.html) with python 3.5.
 - Run `installation_script.bat` inside the Multiworm_Tracking root directory.
 
-##Issues
-- If you recieve an error related with a module in segWormPython you will need to compile the cython files. It will require the same C compiler used to compile python. On OS X you need to install xcode using the app store. On Windows using python 3.5 you have to install [visual studio community 2015](https://www.visualstudio.com/en-us/products/visual-studio-community-vs.aspx) (use custom installation and select Visual C++). Then run `python3 setup.py build_ext --inplace` in the directory `Multiworm_Tracking/MWTracker/trackWorms/segWormPython/cythonFile`, and try to check again if it was a succesful installation.
-
 ## Test installation and examples.
-The installation can be checked running the script [./Tests/run_test.py](https://github.com/ver228/Multiworm_Tracking/blob/master/Tests/run_tests.py). The example files used in the tests are donwloaded in the [installation script](https://github.com/ver228/Multiworm_Tracking/blob/master/installation_script.sh) using the [link](https://imperiallondon-my.sharepoint.com/personal/ajaver_ic_ac_uk/_layouts/15/guestaccess.aspx?guestaccesstoken=ldZ18fLY%2bzlu7XuO9mbKVdyiKoH4naiesqiLXWU4vGQ%3d&docid=0cec4e52f4ccf4d5b8bb3a737020fc12f&rev=1) stored in the variable EXAMPLES_LINK.
+The installation can be checked running the script [./Tests/run_test.py](https://github.com/ver228/Multiworm_Tracking/blob/master/Tests/run_tests.py). The example data used by the tests is downloaded by [installation_script.sh](https://github.com/ver228/Multiworm_Tracking/blob/master/installation_script.sh), see the variable EXAMPLES_LINK. The data can be downloaded manually using the following [link](https://imperiallondon-my.sharepoint.com/personal/ajaver_ic_ac_uk/_layouts/15/guestaccess.aspx?guestaccesstoken=ldZ18fLY%2bzlu7XuO9mbKVdyiKoH4naiesqiLXWU4vGQ%3d&docid=0cec4e52f4ccf4d5b8bb3a737020fc12f&rev=1).
+
+## Possible issues.
+- If you recieve an error related with a module in segWormPython you will need to re-compile the cython files. Cython requires the same C compiler used to compile python. On OS X you need to install xcode using the app store. On Windows using python 3.5 you have to install [visual studio community 2015](https://www.visualstudio.com/en-us/products/visual-studio-community-vs.aspx) (use custom installation and select Visual C++). Finally to compile it go to the directory `Multiworm_Tracking/MWTracker/trackWorms/segWormPython/cythonFile` and run  `python3 setup.py build_ext --inplace`.