From e4a6c52deae587488e2448ac2d096b33996722ef Mon Sep 17 00:00:00 2001
From: Maximilian Schmidt <max.schmidt@fz-juelich.de>
Date: Thu, 29 Mar 2018 10:11:52 +0900
Subject: [PATCH] Remove absolute path to infomap, improve function and doc,
add info to README
---
README.md | 4 +++-
figures/Schmidt2017/graph_helpers.py | 8 ++++++--
2 files changed, 9 insertions(+), 3 deletions(-)
diff --git a/README.md b/README.md
index c6a31fb..ef40a29 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 76c3038..953e5c4 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)
--
GitLab