Add missing file, update README, fix formatting figure script, add missing requirement

README.md

@@ -184,7 +184,7 @@ 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 [1] requires networkx, python-igraph and pyx. To install these additional packages, execute:
+In addition, reproducing the figures of [1] requires networkx, python-igraph, pycairo and pyx. To install these additional packages, execute:
 
 `pip install -r figures/Schmidt2018/additional_requirements.txt`
 

figures/Schmidt2018/Fig5_cc_laminar_pattern.py

@@ -2,7 +2,6 @@ import matplotlib.pyplot as pl
 import numpy as np
 import json
 import pyx
-import subprocess
 import os
 
 from helpers import area_list, population_labels, layer_labels
@@ -31,7 +30,6 @@ if NEURON_DENSITIES_AVAILABLE:
     print(width, height)
     pl.rcParams['figure.figsize'] = (width, height)
 
-
     axes = {}
     gs1 = gridspec.GridSpec(1, 1)
     gs1.update(left=0.1, right=0.47, top=0.95, bottom=0.75, wspace=0.1, hspace=0.3)
@@ -43,7 +41,6 @@ if NEURON_DENSITIES_AVAILABLE:
     axes['B2'] = pl.subplot(gs2[1:2, :1])
     axes['B3'] = pl.subplot(gs2[2:3, :1])
 
-
     gs3 = gridspec.GridSpec(3, 1)
     gs3.update(left=0.6, right=0.95, top=0.65, bottom=0.1, wspace=0.1, hspace=0.8)
     axes['D'] = pl.subplot(gs3[:1, :1])
@@ -80,7 +77,6 @@ if NEURON_DENSITIES_AVAILABLE:
                           'horizontalalignment': 'left', 'verticalalignment':
                           'bottom'}, transform=axes[label].transAxes)
 
-
     data = np.loadtxt(os.path.join(raw_datapath, 'RData_prepared_logdensities.txt'),
                       skiprows=3, dtype='S10')
     target = np.array(data[:, 1], dtype=str)
@@ -124,11 +120,9 @@ if NEURON_DENSITIES_AVAILABLE:
                     y += overlap['visual'][area_key + '_M132'][FV91] / 100.
             neuron_densities[area] = {'overall': x / y}
 
-
     def integrand(x, mu, sigma):
         return 1 / (sigma * np.sqrt(2 * np.pi)) * np.exp(-(x - mu) ** 2 / (2. * sigma ** 2))
 
-
     def probit(x,):
         if isinstance(x, np.ndarray):
             res = [integrate.quad(integrand, -1000., ii,
@@ -137,11 +131,9 @@ if NEURON_DENSITIES_AVAILABLE:
             res = integrate.quad(integrand, -1000., x, args=(0., 1.))[0]
         return res
 
-
     def chi2(x, y, z, n):
         return 1. / (n) * np.sum(((x - y) / z) ** 2)
 
-
     """
     Fit of SLN vs. architectural type differences
     """

figures/Schmidt2018/README.md

@@ -6,7 +6,7 @@ Please note: Figures 2, 5, and 8 show slight deviations from the published figur
 
 Please note that the placement of areas in Figure 7 will deviate from the published figure, because their location depends on the force-directed algorithm implemented in `igraph` and `python-igraph` does not allow manual setting of the random seed for the algorithm. This is a mere visual issue and does not affect the scientific content.
 
-Please note that, since we currently cannot publish the data on Neuronal Densities, Figure 2 can currently not be produced and executing it throws an error.
+Please note that, since we currently cannot publish the data on Neuronal Densities, Figures 2 and 5 can currently not be produced and executing it throws an error.
 
 If snakemake is installed, the figures can be produced by executing
 

figures/Schmidt2018/additional_requirements.txt

-python-igraph
 networkx
+pycairo
+python-igraph
 pyx

figures/Schmidt2018/tex/define_pops.tex

+\pnode(1.55, 0.9){s6E}{}
+\pnode(1.55, 1.9){s5E}{}
+\pnode(1.55, 2.9){s4E}{}
+\pnode(1.55, 3.9){s23E}{}
+
+\pnode(4.75, 0.9){t6E}{}
+\pnode(4.75, 1.9){t5E}{}
+\pnode(4.75, 2.9){t4E}{}
+\pnode(4.75, 3.9){t23E}{}
+
+\pnode(5.75, 0.9){t6I}{}
+\pnode(5.75, 1.9){t5I}{}
+\pnode(5.75, 2.9){t4I}{}
+\pnode(5.75, 3.9){t23I}{}
+
+%%% Local Variables:
+%%% mode: latex
+%%% TeX-master: t
+%%% End: