diff --git a/README.md b/README.md index c6a31fbc4829087433fe29bf21d8b8d46a5a8b11..ef40a296dd68658f38724fca51a933bb9c0494cb 100644 --- a/README.md +++ b/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 diff --git a/figures/Schmidt2017/graph_helpers.py b/figures/Schmidt2017/graph_helpers.py index 76c3038782302b99e88588805f6ff53d26a3b1b4..953e5c4d71ce115bb13c5e282a9677aa725a34d8 100644 --- a/figures/Schmidt2017/graph_helpers.py +++ b/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)