From 7412fd377133d0d62c09d2e05a153ace04bc124d Mon Sep 17 00:00:00 2001
From: Maximilian Schmidt <max.schmidt@fz-juelich.de>
Date: Thu, 29 Mar 2018 10:00:21 +0900
Subject: [PATCH] Add requirements file for add. requirements for figures of
Schmidt2017, make Fig5 script independent of R installation, update README
file with information on requirements
---
README.md | 8 +++++++-
figures/Schmidt2017/Fig5_cc_laminar_pattern.py | 17 +++++++++++------
figures/Schmidt2017/additional_requirements.txt | 2 ++
3 files changed, 20 insertions(+), 7 deletions(-)
create mode 100644 figures/Schmidt2017/additional_requirements.txt
diff --git a/README.md b/README.md
index 9966533..c6a31fb 100644
--- a/README.md
+++ b/README.md
@@ -176,6 +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:
+
+`pip install -r figures/Schmidt2017/additional_requirements.txt`
+
+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
All authors of the publications [1-3] made contributions to the scientific content.
@@ -183,6 +189,6 @@ The code base was written by Maximilian Schmidt, Jannis Schuecker, and Sacha van
## Citation
-If you use this code, we ask you to cite the appropriate papers in your publication. For the multi-area model itself, please [1] and [3]. If you use the mean-field theory or the stabilization method, please cite [2] in addition. We provide bibtex entries in `CITATION`.
+If you use this code, we ask you to cite the appropriate papers in your publication. For the multi-area model itself, please cite [1] and [3]. If you use the mean-field theory or the stabilization method, please cite [2] in addition. We provide bibtex entries in `CITATION`.
<img src="https://raw.githubusercontent.com/nest/nest-simulator/master/extras/logos/nest-simulated.png" alt="NEST simulated" width="200"/>
diff --git a/figures/Schmidt2017/Fig5_cc_laminar_pattern.py b/figures/Schmidt2017/Fig5_cc_laminar_pattern.py
index 40f1ad1..f46a51c 100644
--- a/figures/Schmidt2017/Fig5_cc_laminar_pattern.py
+++ b/figures/Schmidt2017/Fig5_cc_laminar_pattern.py
@@ -147,12 +147,17 @@ Fit of SLN vs. architectural type differences
SLN_array = np.array(data[:, 10], dtype=np.float)
densities = np.array(data[:, 7], dtype=np.float)
-proc = subprocess.Popen(
- ["Rscript", os.path.join(datapath, 'SLN_logdensities.R')],
- stdout=subprocess.PIPE)
-out = proc.communicate()[0].decode('utf-8')
-R_fit = [float(out.split('\n')[1].split(' ')[1]),
- float(out.split('\n')[1].split(' ')[3])]
+# Call R script to perform SLN fit
+try:
+ proc = subprocess.Popen(["Rscript",
+ os.path.join(datapath, 'SLN_logdensities.R')],
+ stdout=subprocess.PIPE)
+ out = proc.communicate()[0].decode('utf-8')
+ R_fit = [float(out.split('\n')[1].split(' ')[1]),
+ float(out.split('\n')[1].split(' ')[3])]
+except OSError:
+ print("No R installation, taking hard-coded fit parameters.")
+ R_fit = [-0.1516142, -1.5343200]
print(R_fit)
ax = axes['A']
diff --git a/figures/Schmidt2017/additional_requirements.txt b/figures/Schmidt2017/additional_requirements.txt
new file mode 100644
index 0000000..d607158
--- /dev/null
+++ b/figures/Schmidt2017/additional_requirements.txt
@@ -0,0 +1,2 @@
+python-igraph
+networkx
--
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