Remove absolute path to infomap, improve function and doc, add info to README

README.md

@@ -176,10 +176,12 @@ To install the required packages in a conda environment, execute:
 
 Note that NEST needs to be installed separately, see <http://www.nest-simulator.org/installation/>.
 
-In addition, reproducing the figures of Schmidt et al. (2017) requires python-igraph and networkx. To install these additional packages, execute:
+In addition, reproducing the figures of [1] requires python-igraph and networkx. To install these additional packages, execute:
 
 `pip install -r figures/Schmidt2017/additional_requirements.txt`
 
+In addition, Figure 7 of [1] requires installing the `infomap` package to perform the map equation clustering. See <http://www.mapequation.org/code.html> for all necessary information.
+
 The SLN fit in `multiarea_model/data_multiarea/VisualCortex_Data.py` and `figures/Schmidt2017/Fig5_cc_laminar_pattern.py` requires an installation of R and the R library `aod` (<http://cran.r-project.org/package=aod>). Without R installation, both scripts will directly use the resulting values of the fit (see Fig. 5 of [1]).
 
 ## Contributors

figures/Schmidt2017/graph_helpers.py

@@ -5,7 +5,7 @@ import numpy as np
 import os
 
 
-def perform_map_equation(graph_matrix, node_list, filename=''):
+def perform_map_equation(graph_matrix, node_list, filename='', infomap_path=None):
     """
     Perform the map equation of
     Rosvall M, Axelsson D, Bergstrom CT (2009) The map equation.
@@ -21,6 +21,9 @@ def perform_map_equation(graph_matrix, node_list, filename=''):
         the graph_matrix and node_list.
     filename : str
         Output file name without ending.
+    infomap_path : str
+        Path to installation of infomap. If None, the
+        infomap executable has to be in the system path.
 
     Returns
     -------
@@ -58,7 +61,8 @@ def perform_map_equation(graph_matrix, node_list, filename=''):
     """
     2. Execute map equation algorithm
     """
-    os.chdir('/home/schmidt/opt/infomap')
+    if infomap_path:
+        os.chdir(infomap_path)
     os.system('./Infomap --directed --clu --map --verbose ' +
               base_dir + '/' + net_fn + ' ' + base_dir)