Added new section, languages improvements

README.md

@@ -7,31 +7,32 @@ Implementation of the Game of Life with rule switching.
 This repo contains model and scripts used to run numerical experiments for Game
 of Life with rule switching mechanisms. 
 
-## Reproducing data
+# Reproducing data
 
-Scripts in this repo can be used to reproduce data ilustrattgin the behaviur of
+Scripts in this repo can be used to reproduce data illustrating the behaviour of
 the Game of Live cellular automata extended with the mechanisms for rule
-switching. Additionally, the model can be used in asynchronouse and synhronouse
+switching. Additionally, the model can be used in asynchronous and synchronous
 mode.
 
-Compilation and code runing is controlled by file `Makefile` in the main
-directory. This file should be modified to suit our NetLogo installation.
-In the provided `Makefile` it is assumes that NetLogo is installed in
+Code compilation and runing is controlled by file `Makefile` in the main
+directory. This file should be modified to suit our NetLogo installation.  In
+the provided `Makefile` it is assumes that NetLogo is installed in
 
     ~/Local/NetLogo/3.0.0
 
-directory. It is also assumed that `java` and `javac` are in you PATH.
+directory. It is also assumed that `java` and `javac` are in you `PATH`
+environment variable.
 
 `Makefile` also uses GNU pararell for running Java programmes. 
 
-### Fianl configurations
+## Final configurations
 
 Sample configurations are produced using `GenerateExample.java` script. To
 compile this file run
 
     make
 
-in the main directory. This will also compile `CalculateMeanLiving.java`.
+in the main directory. This will also compile `CalculateMeanLiving.java` and `GenerateConfigurations.java`.
 
 Examples are generated by issuing
 
@@ -53,7 +54,7 @@ To plot all data from the generated examples run
 
 **Note:** Plots are saved in `plots` subdirectory.
 
-### Realizations
+## Realizations
 
 Exlemplary realizations can be obtained by using `run.sh` script and
 `experiments.xml` file. For each experiment defined in `experiments.xml` file,
@@ -79,17 +80,56 @@ To plot data from the realizations run
 
 **Note:** Configure name of the data files in the plotting script.  
 
-### Average growth
+## Average growth
+
+Data for the average number of living cells are calculate by
+`CalculateMeanLiving.java` and can be obtained by running
 
-Date for the average number of living cells are calculate by `CalculateMeanLiving.java` and can be obtained by running
-
     make calcmean
 
 You need to compile `CalculateMeanLiving.java` first
 
 **Note:** BY default, 200 realizations are used fo averaging. This value can be
 modified in `CalculateMeanLiving.java` file by altering `steps` variable. 
 
-Ploting of the data is handled by `plot_living_average.py`, which accepts one argument with name of the data file.
+Ploting of the data is handled by `plot_living_average.py`, which accepts one
+argument with name of the data file.
+
+**Note:** Data from this experiment are saved in
+*`living_data_250steps_200runs.csv` file. This file is included in the
+*repository. The name of the file used to save data should be configured in
+*`Makefile` and in the plotting script `plot_living_average.py`.
+
+## Mutual entropy
+
+For the purposa of analysing the mutula entropy of the generated patters it is
+necessary to generate a number of final configurations. This data are generate
+using `genfc` target in the Makefile,
+
+    make gencf
+
+You nee to compile `GenerateConfigurations.java` prior to running this command.
+
+Resultsing `csv` files in `configurations` subdirectory. For each combination of
+parameters 1000 files representing final configuraitons are generated. The names
+of the resulting configurations can be saved in a shhell variable using
+
+    golTypes=$(for i in *_0001.csv ; do echo `echo $i | sed s/_0001.csv//g` ; done)
+
+in the `configurations` directory. 
+
+The calculation of the average mutula entropy is implemented in
+`analyze_mutent.py` script. Using GNU parallel the analysis rsults can be
+obtained by running
+
+    parallel ./analyze.py {} ::: $golTypes
+
+in `configurations` subdirectory.
+
+This will result in one `*.dat` file for each combination of parameters. To
+obtain the file with all data run 
+
+    bash postprocess_dat.sh 
 
-**Note:** Data from this experiment are saved in `living_data_250steps_200runs.csv` file. This should be configures in `Makefile` and in the plotting script `plot_living_average.py`.
+script. This will produce `anayze_mutent.csv`, used by the plotting script
+`plot_mutual_entropy.py` located in the main directory.