From 1a48167203d61c8c550a6574aad3a2e5fd17ee77 Mon Sep 17 00:00:00 2001
From: Maximilian Schmidt <max.schmidt@fz-juelich.de>
Date: Thu, 29 Mar 2018 17:07:55 +0900
Subject: [PATCH] Update reference to anatomy paper, fix references in all
scripts and files, rename figures folder
---
CITATION | 21 +-
README.md | 10 +-
figures/Schmidt2017/cmap.py | 263 ------------------
.../Fig1_model_overview.eps | 0
.../Fig2_anatomy.eps | 0
.../Fig2_anatomy.py | 0
.../Fig3_construction.py | 0
.../Fig3_syntypes.eps | 0
.../Fig4_connectivity.eps | 0
.../Fig4_connectivity.py | 0
.../Fig5_cc_laminar_pattern.eps | 0
.../Fig5_cc_laminar_pattern.py | 0
.../Fig5_syn_illustration.eps | 0
.../Fig6_conn_indegree.eps | 0
.../Fig6_conn_prob.eps | 0
.../Fig6_connectivity_measures.eps | 0
.../Fig6_connectivity_measures.py | 0
.../Fig7_community_structure.eps | 0
.../Fig7_community_structure.py | 0
.../Fig8_laminar_paths.eps | 0
.../Fig8_laminar_paths.py | 0
.../{Schmidt2017 => Schmidt2018}/README.md | 2 +-
.../{Schmidt2017 => Schmidt2018}/Snakefile | 0
.../additional_requirements.txt | 0
.../graph_helpers.py | 4 +-
.../{Schmidt2017 => Schmidt2018}/helpers.py | 2 +-
.../plotcolors.py | 0
.../{Schmidt2017 => Schmidt2018}/plotfuncs.py | 0
.../{Schmidt2017 => Schmidt2018}/plotstyle.rc | 0
.../tex/FB_paths.tex | 0
.../tex/FF_paths.tex | 0
.../tex/HL_paths.tex | 0
.../tex/HZ_paths.tex | 0
.../tex/LH_paths.tex | 0
.../tex/compile_tex.sh | 0
.../tex/define_bools.tex | 0
.../{Schmidt2017 => Schmidt2018}/tex/defs.tex | 0
.../tex/draw_paths.tex | 0
.../tex/draw_pops.tex | 0
.../tex/indirect_23E.eps | 0
.../tex/indirect_4E23E.eps | 0
.../tex/indirect_4E5E.eps | 0
.../tex/indirect_5E.eps | 0
.../tex/indirect_6E.eps | 0
.../tex/lateral_paths.tex | 0
.../tex/texcolors.tex | 0
multiarea_model/data_multiarea/Model.py | 6 +-
.../data_multiarea/VisualCortex_Data.py | 4 +-
multiarea_model/multiarea_model.py | 4 +-
multiarea_model/theory.py | 2 +-
50 files changed, 29 insertions(+), 289 deletions(-)
delete mode 100644 figures/Schmidt2017/cmap.py
rename figures/{Schmidt2017 => Schmidt2018}/Fig1_model_overview.eps (100%)
rename figures/{Schmidt2017 => Schmidt2018}/Fig2_anatomy.eps (100%)
rename figures/{Schmidt2017 => Schmidt2018}/Fig2_anatomy.py (100%)
rename figures/{Schmidt2017 => Schmidt2018}/Fig3_construction.py (100%)
rename figures/{Schmidt2017 => Schmidt2018}/Fig3_syntypes.eps (100%)
rename figures/{Schmidt2017 => Schmidt2018}/Fig4_connectivity.eps (100%)
rename figures/{Schmidt2017 => Schmidt2018}/Fig4_connectivity.py (100%)
rename figures/{Schmidt2017 => Schmidt2018}/Fig5_cc_laminar_pattern.eps (100%)
rename figures/{Schmidt2017 => Schmidt2018}/Fig5_cc_laminar_pattern.py (100%)
rename figures/{Schmidt2017 => Schmidt2018}/Fig5_syn_illustration.eps (100%)
rename figures/{Schmidt2017 => Schmidt2018}/Fig6_conn_indegree.eps (100%)
rename figures/{Schmidt2017 => Schmidt2018}/Fig6_conn_prob.eps (100%)
rename figures/{Schmidt2017 => Schmidt2018}/Fig6_connectivity_measures.eps (100%)
rename figures/{Schmidt2017 => Schmidt2018}/Fig6_connectivity_measures.py (100%)
rename figures/{Schmidt2017 => Schmidt2018}/Fig7_community_structure.eps (100%)
rename figures/{Schmidt2017 => Schmidt2018}/Fig7_community_structure.py (100%)
rename figures/{Schmidt2017 => Schmidt2018}/Fig8_laminar_paths.eps (100%)
rename figures/{Schmidt2017 => Schmidt2018}/Fig8_laminar_paths.py (100%)
rename figures/{Schmidt2017 => Schmidt2018}/README.md (90%)
rename figures/{Schmidt2017 => Schmidt2018}/Snakefile (100%)
rename figures/{Schmidt2017 => Schmidt2018}/additional_requirements.txt (100%)
rename figures/{Schmidt2017 => Schmidt2018}/graph_helpers.py (99%)
rename figures/{Schmidt2017 => Schmidt2018}/helpers.py (99%)
rename figures/{Schmidt2017 => Schmidt2018}/plotcolors.py (100%)
rename figures/{Schmidt2017 => Schmidt2018}/plotfuncs.py (100%)
rename figures/{Schmidt2017 => Schmidt2018}/plotstyle.rc (100%)
rename figures/{Schmidt2017 => Schmidt2018}/tex/FB_paths.tex (100%)
rename figures/{Schmidt2017 => Schmidt2018}/tex/FF_paths.tex (100%)
rename figures/{Schmidt2017 => Schmidt2018}/tex/HL_paths.tex (100%)
rename figures/{Schmidt2017 => Schmidt2018}/tex/HZ_paths.tex (100%)
rename figures/{Schmidt2017 => Schmidt2018}/tex/LH_paths.tex (100%)
rename figures/{Schmidt2017 => Schmidt2018}/tex/compile_tex.sh (100%)
rename figures/{Schmidt2017 => Schmidt2018}/tex/define_bools.tex (100%)
rename figures/{Schmidt2017 => Schmidt2018}/tex/defs.tex (100%)
rename figures/{Schmidt2017 => Schmidt2018}/tex/draw_paths.tex (100%)
rename figures/{Schmidt2017 => Schmidt2018}/tex/draw_pops.tex (100%)
rename figures/{Schmidt2017 => Schmidt2018}/tex/indirect_23E.eps (100%)
rename figures/{Schmidt2017 => Schmidt2018}/tex/indirect_4E23E.eps (100%)
rename figures/{Schmidt2017 => Schmidt2018}/tex/indirect_4E5E.eps (100%)
rename figures/{Schmidt2017 => Schmidt2018}/tex/indirect_5E.eps (100%)
rename figures/{Schmidt2017 => Schmidt2018}/tex/indirect_6E.eps (100%)
rename figures/{Schmidt2017 => Schmidt2018}/tex/lateral_paths.tex (100%)
rename figures/{Schmidt2017 => Schmidt2018}/tex/texcolors.tex (100%)
diff --git a/CITATION b/CITATION
index 5bbbc25..89bd848 100644
--- a/CITATION
+++ b/CITATION
@@ -1,6 +1,6 @@
@article{Schuecker17,
author = {Schuecker, Jannis and Schmidt, Maximilian and van Albada, Sacha J. and Diesmann, Markus and Helias, Moritz},
- journal = ploscb,
+ journal = {PLOS Computational Biology},
publisher = {Public Library of Science},
title = {Fundamental Activity Constraints Lead to Specific Interpretations of the Connectome},
year = {2017},
@@ -8,18 +8,21 @@
volume = {13},
pages = {1-25},
number = {2},
- doi = {10.1371/journal.pcbi.1005179}
+ doi = {10.1371/jour.pcbi.1005179}
}
-@article{Schmidt17,
- title={Multi-scale account of the network structure of macaque visual cortex},
- author={Schmidt, Maximilian and Bakker, Rembrandt and Hilgetag, Claus Christian and Diesmann, Markus and van Albada, Sacha Jennifer},
- journal=bsf,
- year={2017},
- doi={https://doi.org/10.1007/s00429-017-1554-4}
+@article{Schmidt18_1,
+ title={Multi-scale account of the network structure of macaque visual cortex},
+ author={Schmidt, Maximilian and Bakker, Rembrandt and Hilgetag, Claus Christian and Diesmann, Markus and van Albada, Sacha Jennifer},
+ journal={Brain Structure and Function},
+ year={2018},
+ volume={223},
+ number={3},
+ pages={1409--1435},
+ doi={https://doi.org/10.1007/s00429-017-1554-4}
}
-@article{Schmidt18,
+@article{Schmidt18_2,
title={A multi-scale layer-resolved spiking network model of resting-state dynamics in macaque visual cortical areas}
author={Schmidt, Maximilian and Bakker, Rembrandt and Shen, Kelly and Bezgin, Gleb and Diesmann, Markus and Sacha Jennifer van Albada},
year={2018},
diff --git a/README.md b/README.md
index 89bf812..9fb1219 100644
--- a/README.md
+++ b/README.md
@@ -5,9 +5,9 @@ This code implements the spiking network model of macaque visual cortex develope
at the Institute of Neuroscience and Medicine (INM-6), Research Center Jülich.
The model has been documented in the following publications:
-1. Schmidt M, Bakker R, Hilgetag CC, Diesmann M & van Albada SJ (2017)
+1. Schmidt M, Bakker R, Hilgetag CC, Diesmann M & van Albada SJ
Multi-scale account of the network structure of macaque visual cortex
- Brain Structure and Function (2017) [https://doi.org/10.1007/s00429-017-1554-4](https://doi.org/10.1007/s00429-017-1554-4)
+ Brain Structure and Function (2018), 223:1409 [https://doi.org/10.1007/s00429-017-1554-4](https://doi.org/10.1007/s00429-017-1554-4)
2. Schuecker J, Schmidt M, van Albada SJ, Diesmann M & Helias M (2017)
Fundamental Activity Constraints Lead to Specific Interpretations of the Connectome.
@@ -84,7 +84,7 @@ the figures from [1]. The scripts for [2] and [3] will follow soon.
If snakemake is installed, the figures can be produced by executing
`snakemake` in the respective folder:
- cd figures/Schmidt2017/
+ cd figures/Schmidt2018/
snakemake
@@ -181,11 +181,11 @@ Note that NEST needs to be installed separately, see <http://www.nest-simulator.
In addition, reproducing the figures of [1] requires networkx, python-igraph and pyx. To install these additional packages, execute:
-`pip install -r figures/Schmidt2017/additional_requirements.txt`
+`pip install -r figures/Schmidt2018/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]).
+The SLN fit in `multiarea_model/data_multiarea/VisualCortex_Data.py` and `figures/Schmidt2018/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/cmap.py b/figures/Schmidt2017/cmap.py
deleted file mode 100644
index 62d9c23..0000000
--- a/figures/Schmidt2017/cmap.py
+++ /dev/null
@@ -1,263 +0,0 @@
-from matplotlib.colors import LinearSegmentedColormap
-"""
-Manual implementation of the inferno colormap
-which is part of matplotlib since version 1.5
-"""
-cm_data = [[1.46159096e-03, 4.66127766e-04, 1.38655200e-02],
- [2.26726368e-03, 1.26992553e-03, 1.85703520e-02],
- [3.29899092e-03, 2.24934863e-03, 2.42390508e-02],
- [4.54690615e-03, 3.39180156e-03, 3.09092475e-02],
- [6.00552565e-03, 4.69194561e-03, 3.85578980e-02],
- [7.67578856e-03, 6.13611626e-03, 4.68360336e-02],
- [9.56051094e-03, 7.71344131e-03, 5.51430756e-02],
- [1.16634769e-02, 9.41675403e-03, 6.34598080e-02],
- [1.39950388e-02, 1.12247138e-02, 7.18616890e-02],
- [1.65605595e-02, 1.31362262e-02, 8.02817951e-02],
- [1.93732295e-02, 1.51325789e-02, 8.87668094e-02],
- [2.24468865e-02, 1.71991484e-02, 9.73274383e-02],
- [2.57927373e-02, 1.93306298e-02, 1.05929835e-01],
- [2.94324251e-02, 2.15030771e-02, 1.14621328e-01],
- [3.33852235e-02, 2.37024271e-02, 1.23397286e-01],
- [3.76684211e-02, 2.59207864e-02, 1.32232108e-01],
- [4.22525554e-02, 2.81385015e-02, 1.41140519e-01],
- [4.69146287e-02, 3.03236129e-02, 1.50163867e-01],
- [5.16437624e-02, 3.24736172e-02, 1.59254277e-01],
- [5.64491009e-02, 3.45691867e-02, 1.68413539e-01],
- [6.13397200e-02, 3.65900213e-02, 1.77642172e-01],
- [6.63312620e-02, 3.85036268e-02, 1.86961588e-01],
- [7.14289181e-02, 4.02939095e-02, 1.96353558e-01],
- [7.66367560e-02, 4.19053329e-02, 2.05798788e-01],
- [8.19620773e-02, 4.33278666e-02, 2.15289113e-01],
- [8.74113897e-02, 4.45561662e-02, 2.24813479e-01],
- [9.29901526e-02, 4.55829503e-02, 2.34357604e-01],
- [9.87024972e-02, 4.64018731e-02, 2.43903700e-01],
- [1.04550936e-01, 4.70080541e-02, 2.53430300e-01],
- [1.10536084e-01, 4.73986708e-02, 2.62912235e-01],
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- [8.37165425e-01, 2.88384647e-01, 2.52987700e-01],
- [8.41968959e-01, 2.92933312e-01, 2.48563825e-01],
- [8.46708768e-01, 2.97558528e-01, 2.44112767e-01],
- [8.51383572e-01, 3.02260213e-01, 2.39635512e-01],
- [8.55992130e-01, 3.07038188e-01, 2.35132978e-01],
- [8.60533241e-01, 3.11892183e-01, 2.30606009e-01],
- [8.65005747e-01, 3.16821833e-01, 2.26055368e-01],
- [8.69408534e-01, 3.21826685e-01, 2.21481734e-01],
- [8.73740530e-01, 3.26906201e-01, 2.16885699e-01],
- [8.78000715e-01, 3.32059760e-01, 2.12267762e-01],
- [8.82188112e-01, 3.37286663e-01, 2.07628326e-01],
- [8.86301795e-01, 3.42586137e-01, 2.02967696e-01],
- [8.90340885e-01, 3.47957340e-01, 1.98286080e-01],
- [8.94304553e-01, 3.53399363e-01, 1.93583583e-01],
- [8.98192017e-01, 3.58911240e-01, 1.88860212e-01],
- [9.02002544e-01, 3.64491949e-01, 1.84115876e-01],
- [9.05735448e-01, 3.70140419e-01, 1.79350388e-01],
- [9.09390090e-01, 3.75855533e-01, 1.74563472e-01],
- [9.12965874e-01, 3.81636138e-01, 1.69754764e-01],
- [9.16462251e-01, 3.87481044e-01, 1.64923826e-01],
- [9.19878710e-01, 3.93389034e-01, 1.60070152e-01],
- [9.23214783e-01, 3.99358867e-01, 1.55193185e-01],
- [9.26470039e-01, 4.05389282e-01, 1.50292329e-01],
- [9.29644083e-01, 4.11479007e-01, 1.45366973e-01],
- [9.32736555e-01, 4.17626756e-01, 1.40416519e-01],
- [9.35747126e-01, 4.23831237e-01, 1.35440416e-01],
- [9.38675494e-01, 4.30091162e-01, 1.30438175e-01],
- [9.41521384e-01, 4.36405243e-01, 1.25409440e-01],
- [9.44284543e-01, 4.42772199e-01, 1.20354038e-01],
- [9.46964741e-01, 4.49190757e-01, 1.15272059e-01],
- [9.49561766e-01, 4.55659658e-01, 1.10163947e-01],
- [9.52075421e-01, 4.62177656e-01, 1.05030614e-01],
- [9.54505523e-01, 4.68743522e-01, 9.98735931e-02],
- [9.56851903e-01, 4.75356048e-01, 9.46952268e-02],
- [9.59114397e-01, 4.82014044e-01, 8.94989073e-02],
- [9.61292850e-01, 4.88716345e-01, 8.42893891e-02],
- [9.63387110e-01, 4.95461806e-01, 7.90731907e-02],
- [9.65397031e-01, 5.02249309e-01, 7.38591143e-02],
- [9.67322465e-01, 5.09077761e-01, 6.86589199e-02],
- [9.69163264e-01, 5.15946092e-01, 6.34881971e-02],
- [9.70919277e-01, 5.22853259e-01, 5.83674890e-02],
- [9.72590351e-01, 5.29798246e-01, 5.33237243e-02],
- [9.74176327e-01, 5.36780059e-01, 4.83920090e-02],
- [9.75677038e-01, 5.43797733e-01, 4.36177922e-02],
- [9.77092313e-01, 5.50850323e-01, 3.90500131e-02],
- [9.78421971e-01, 5.57936911e-01, 3.49306227e-02],
- [9.79665824e-01, 5.65056600e-01, 3.14091591e-02],
- [9.80823673e-01, 5.72208516e-01, 2.85075931e-02],
- [9.81895311e-01, 5.79391803e-01, 2.62497353e-02],
- [9.82880522e-01, 5.86605627e-01, 2.46613416e-02],
- [9.83779081e-01, 5.93849168e-01, 2.37702263e-02],
- [9.84590755e-01, 6.01121626e-01, 2.36063833e-02],
- [9.85315301e-01, 6.08422211e-01, 2.42021174e-02],
- [9.85952471e-01, 6.15750147e-01, 2.55921853e-02],
- [9.86502013e-01, 6.23104667e-01, 2.78139496e-02],
- [9.86963670e-01, 6.30485011e-01, 3.09075459e-02],
- [9.87337182e-01, 6.37890424e-01, 3.49160639e-02],
- [9.87622296e-01, 6.45320152e-01, 3.98857472e-02],
- [9.87818759e-01, 6.52773439e-01, 4.55808037e-02],
- [9.87926330e-01, 6.60249526e-01, 5.17503867e-02],
- [9.87944783e-01, 6.67747641e-01, 5.83286889e-02],
- [9.87873910e-01, 6.75267000e-01, 6.52570167e-02],
- [9.87713535e-01, 6.82806802e-01, 7.24892330e-02],
- [9.87463516e-01, 6.90366218e-01, 7.99897176e-02],
- [9.87123759e-01, 6.97944391e-01, 8.77314215e-02],
- [9.86694229e-01, 7.05540424e-01, 9.56941797e-02],
- [9.86174970e-01, 7.13153375e-01, 1.03863324e-01],
- [9.85565739e-01, 7.20782460e-01, 1.12228756e-01],
- [9.84865203e-01, 7.28427497e-01, 1.20784651e-01],
- [9.84075129e-01, 7.36086521e-01, 1.29526579e-01],
- [9.83195992e-01, 7.43758326e-01, 1.38453063e-01],
- [9.82228463e-01, 7.51441596e-01, 1.47564573e-01],
- [9.81173457e-01, 7.59134892e-01, 1.56863224e-01],
- [9.80032178e-01, 7.66836624e-01, 1.66352544e-01],
- [9.78806183e-01, 7.74545028e-01, 1.76037298e-01],
- [9.77497453e-01, 7.82258138e-01, 1.85923357e-01],
- [9.76108474e-01, 7.89973753e-01, 1.96017589e-01],
- [9.74637842e-01, 7.97691563e-01, 2.06331925e-01],
- [9.73087939e-01, 8.05409333e-01, 2.16876839e-01],
- [9.71467822e-01, 8.13121725e-01, 2.27658046e-01],
- [9.69783146e-01, 8.20825143e-01, 2.38685942e-01],
- [9.68040817e-01, 8.28515491e-01, 2.49971582e-01],
- [9.66242589e-01, 8.36190976e-01, 2.61533898e-01],
- [9.64393924e-01, 8.43848069e-01, 2.73391112e-01],
- [9.62516656e-01, 8.51476340e-01, 2.85545675e-01],
- [9.60625545e-01, 8.59068716e-01, 2.98010219e-01],
- [9.58720088e-01, 8.66624355e-01, 3.10820466e-01],
- [9.56834075e-01, 8.74128569e-01, 3.23973947e-01],
- [9.54997177e-01, 8.81568926e-01, 3.37475479e-01],
- [9.53215092e-01, 8.88942277e-01, 3.51368713e-01],
- [9.51546225e-01, 8.96225909e-01, 3.65627005e-01],
- [9.50018481e-01, 9.03409063e-01, 3.80271225e-01],
- [9.48683391e-01, 9.10472964e-01, 3.95289169e-01],
- [9.47594362e-01, 9.17399053e-01, 4.10665194e-01],
- [9.46809163e-01, 9.24168246e-01, 4.26373236e-01],
- [9.46391536e-01, 9.30760752e-01, 4.42367495e-01],
- [9.46402951e-01, 9.37158971e-01, 4.58591507e-01],
- [9.46902568e-01, 9.43347775e-01, 4.74969778e-01],
- [9.47936825e-01, 9.49317522e-01, 4.91426053e-01],
- [9.49544830e-01, 9.55062900e-01, 5.07859649e-01],
- [9.51740304e-01, 9.60586693e-01, 5.24203026e-01],
- [9.54529281e-01, 9.65895868e-01, 5.40360752e-01],
- [9.57896053e-01, 9.71003330e-01, 5.56275090e-01],
- [9.61812020e-01, 9.75924241e-01, 5.71925382e-01],
- [9.66248822e-01, 9.80678193e-01, 5.87205773e-01],
- [9.71161622e-01, 9.85282161e-01, 6.02154330e-01],
- [9.76510983e-01, 9.89753437e-01, 6.16760413e-01],
- [9.82257307e-01, 9.94108844e-01, 6.31017009e-01],
- [9.88362068e-01, 9.98364143e-01, 6.44924005e-01]]
-
-cm_inferno = LinearSegmentedColormap.from_list(__file__, cm_data)
diff --git a/figures/Schmidt2017/Fig1_model_overview.eps b/figures/Schmidt2018/Fig1_model_overview.eps
similarity index 100%
rename from figures/Schmidt2017/Fig1_model_overview.eps
rename to figures/Schmidt2018/Fig1_model_overview.eps
diff --git a/figures/Schmidt2017/Fig2_anatomy.eps b/figures/Schmidt2018/Fig2_anatomy.eps
similarity index 100%
rename from figures/Schmidt2017/Fig2_anatomy.eps
rename to figures/Schmidt2018/Fig2_anatomy.eps
diff --git a/figures/Schmidt2017/Fig2_anatomy.py b/figures/Schmidt2018/Fig2_anatomy.py
similarity index 100%
rename from figures/Schmidt2017/Fig2_anatomy.py
rename to figures/Schmidt2018/Fig2_anatomy.py
diff --git a/figures/Schmidt2017/Fig3_construction.py b/figures/Schmidt2018/Fig3_construction.py
similarity index 100%
rename from figures/Schmidt2017/Fig3_construction.py
rename to figures/Schmidt2018/Fig3_construction.py
diff --git a/figures/Schmidt2017/Fig3_syntypes.eps b/figures/Schmidt2018/Fig3_syntypes.eps
similarity index 100%
rename from figures/Schmidt2017/Fig3_syntypes.eps
rename to figures/Schmidt2018/Fig3_syntypes.eps
diff --git a/figures/Schmidt2017/Fig4_connectivity.eps b/figures/Schmidt2018/Fig4_connectivity.eps
similarity index 100%
rename from figures/Schmidt2017/Fig4_connectivity.eps
rename to figures/Schmidt2018/Fig4_connectivity.eps
diff --git a/figures/Schmidt2017/Fig4_connectivity.py b/figures/Schmidt2018/Fig4_connectivity.py
similarity index 100%
rename from figures/Schmidt2017/Fig4_connectivity.py
rename to figures/Schmidt2018/Fig4_connectivity.py
diff --git a/figures/Schmidt2017/Fig5_cc_laminar_pattern.eps b/figures/Schmidt2018/Fig5_cc_laminar_pattern.eps
similarity index 100%
rename from figures/Schmidt2017/Fig5_cc_laminar_pattern.eps
rename to figures/Schmidt2018/Fig5_cc_laminar_pattern.eps
diff --git a/figures/Schmidt2017/Fig5_cc_laminar_pattern.py b/figures/Schmidt2018/Fig5_cc_laminar_pattern.py
similarity index 100%
rename from figures/Schmidt2017/Fig5_cc_laminar_pattern.py
rename to figures/Schmidt2018/Fig5_cc_laminar_pattern.py
diff --git a/figures/Schmidt2017/Fig5_syn_illustration.eps b/figures/Schmidt2018/Fig5_syn_illustration.eps
similarity index 100%
rename from figures/Schmidt2017/Fig5_syn_illustration.eps
rename to figures/Schmidt2018/Fig5_syn_illustration.eps
diff --git a/figures/Schmidt2017/Fig6_conn_indegree.eps b/figures/Schmidt2018/Fig6_conn_indegree.eps
similarity index 100%
rename from figures/Schmidt2017/Fig6_conn_indegree.eps
rename to figures/Schmidt2018/Fig6_conn_indegree.eps
diff --git a/figures/Schmidt2017/Fig6_conn_prob.eps b/figures/Schmidt2018/Fig6_conn_prob.eps
similarity index 100%
rename from figures/Schmidt2017/Fig6_conn_prob.eps
rename to figures/Schmidt2018/Fig6_conn_prob.eps
diff --git a/figures/Schmidt2017/Fig6_connectivity_measures.eps b/figures/Schmidt2018/Fig6_connectivity_measures.eps
similarity index 100%
rename from figures/Schmidt2017/Fig6_connectivity_measures.eps
rename to figures/Schmidt2018/Fig6_connectivity_measures.eps
diff --git a/figures/Schmidt2017/Fig6_connectivity_measures.py b/figures/Schmidt2018/Fig6_connectivity_measures.py
similarity index 100%
rename from figures/Schmidt2017/Fig6_connectivity_measures.py
rename to figures/Schmidt2018/Fig6_connectivity_measures.py
diff --git a/figures/Schmidt2017/Fig7_community_structure.eps b/figures/Schmidt2018/Fig7_community_structure.eps
similarity index 100%
rename from figures/Schmidt2017/Fig7_community_structure.eps
rename to figures/Schmidt2018/Fig7_community_structure.eps
diff --git a/figures/Schmidt2017/Fig7_community_structure.py b/figures/Schmidt2018/Fig7_community_structure.py
similarity index 100%
rename from figures/Schmidt2017/Fig7_community_structure.py
rename to figures/Schmidt2018/Fig7_community_structure.py
diff --git a/figures/Schmidt2017/Fig8_laminar_paths.eps b/figures/Schmidt2018/Fig8_laminar_paths.eps
similarity index 100%
rename from figures/Schmidt2017/Fig8_laminar_paths.eps
rename to figures/Schmidt2018/Fig8_laminar_paths.eps
diff --git a/figures/Schmidt2017/Fig8_laminar_paths.py b/figures/Schmidt2018/Fig8_laminar_paths.py
similarity index 100%
rename from figures/Schmidt2017/Fig8_laminar_paths.py
rename to figures/Schmidt2018/Fig8_laminar_paths.py
diff --git a/figures/Schmidt2017/README.md b/figures/Schmidt2018/README.md
similarity index 90%
rename from figures/Schmidt2017/README.md
rename to figures/Schmidt2018/README.md
index 0076ca9..9a8558f 100644
--- a/figures/Schmidt2017/README.md
+++ b/figures/Schmidt2018/README.md
@@ -1,6 +1,6 @@
## Figures of Schmidt M, Bakker R, Hilgetag C-C, Diesmann M and van Albada SJ: "Multi-scale account of the network structure of macaque visual cortex"
-This folder contains the scripts to reproduce all figures of Schmidt M, Bakker R, Hilgetag C-C, Diesmann M and van Albada SJ: "Multi-scale account of the network structure of macaque visual cortex", Brain Structure and Function (2017) [https://doi.org/10.1007/s00429-017-1554-4](https://doi.org/10.1007/s00429-017-1554-4)
+This folder contains the scripts to reproduce all figures of Schmidt M, Bakker R, Hilgetag C-C, Diesmann M and van Albada SJ: "Multi-scale account of the network structure of macaque visual cortex", Brain Structure and Function (2018), 223:1409 [https://doi.org/10.1007/s00429-017-1554-4](https://doi.org/10.1007/s00429-017-1554-4)
Please note: Figures 2, 5, and 8 show slight deviations from the published figures in the paper. Published Figures 2 and 5 miss a few data points. This error slipped in during the review process. Importantly, the presented fits are identical in the (correct) figures in this repository and in the manuscript. These deviations thus do not affect the scientific conclusions.
diff --git a/figures/Schmidt2017/Snakefile b/figures/Schmidt2018/Snakefile
similarity index 100%
rename from figures/Schmidt2017/Snakefile
rename to figures/Schmidt2018/Snakefile
diff --git a/figures/Schmidt2017/additional_requirements.txt b/figures/Schmidt2018/additional_requirements.txt
similarity index 100%
rename from figures/Schmidt2017/additional_requirements.txt
rename to figures/Schmidt2018/additional_requirements.txt
diff --git a/figures/Schmidt2017/graph_helpers.py b/figures/Schmidt2018/graph_helpers.py
similarity index 99%
rename from figures/Schmidt2017/graph_helpers.py
rename to figures/Schmidt2018/graph_helpers.py
index 3e6ff88..5047f82 100644
--- a/figures/Schmidt2017/graph_helpers.py
+++ b/figures/Schmidt2018/graph_helpers.py
@@ -101,7 +101,7 @@ def modularity(g, membership):
and cluster memberships.
See Schmidt, M., Bakker, R., Hilgetag, C.C. et al.
- Brain Structure and Function (2017),
+ Brain Structure and Function (2018), 223:1409,
for a derivation.
Parameters
@@ -138,7 +138,7 @@ def all_pairs_bellman_ford_path(g, weight='distance'):
Compute the shorted paths between nodes of a graph
using the Bellman-Ford algorithm.
See Schmidt, M., Bakker, R., Hilgetag, C.C. et al.
- Brain Structure and Function (2017),
+ Brain Structure and Function (2018), 223:1409,
for details.
Parameters
diff --git a/figures/Schmidt2017/helpers.py b/figures/Schmidt2018/helpers.py
similarity index 99%
rename from figures/Schmidt2017/helpers.py
rename to figures/Schmidt2018/helpers.py
index c716a17..53f46ec 100644
--- a/figures/Schmidt2017/helpers.py
+++ b/figures/Schmidt2018/helpers.py
@@ -61,7 +61,7 @@ def structural_gradient(target_area, source_area, structure):
"""
Returns the structural gradient between two areas
See Schmidt, M., Bakker, R., Hilgetag, C.C. et al.
- Brain Structure and Function (2017),
+ Brain Structure and Function (2018), 223:1409,
for a definition.
Parameters
diff --git a/figures/Schmidt2017/plotcolors.py b/figures/Schmidt2018/plotcolors.py
similarity index 100%
rename from figures/Schmidt2017/plotcolors.py
rename to figures/Schmidt2018/plotcolors.py
diff --git a/figures/Schmidt2017/plotfuncs.py b/figures/Schmidt2018/plotfuncs.py
similarity index 100%
rename from figures/Schmidt2017/plotfuncs.py
rename to figures/Schmidt2018/plotfuncs.py
diff --git a/figures/Schmidt2017/plotstyle.rc b/figures/Schmidt2018/plotstyle.rc
similarity index 100%
rename from figures/Schmidt2017/plotstyle.rc
rename to figures/Schmidt2018/plotstyle.rc
diff --git a/figures/Schmidt2017/tex/FB_paths.tex b/figures/Schmidt2018/tex/FB_paths.tex
similarity index 100%
rename from figures/Schmidt2017/tex/FB_paths.tex
rename to figures/Schmidt2018/tex/FB_paths.tex
diff --git a/figures/Schmidt2017/tex/FF_paths.tex b/figures/Schmidt2018/tex/FF_paths.tex
similarity index 100%
rename from figures/Schmidt2017/tex/FF_paths.tex
rename to figures/Schmidt2018/tex/FF_paths.tex
diff --git a/figures/Schmidt2017/tex/HL_paths.tex b/figures/Schmidt2018/tex/HL_paths.tex
similarity index 100%
rename from figures/Schmidt2017/tex/HL_paths.tex
rename to figures/Schmidt2018/tex/HL_paths.tex
diff --git a/figures/Schmidt2017/tex/HZ_paths.tex b/figures/Schmidt2018/tex/HZ_paths.tex
similarity index 100%
rename from figures/Schmidt2017/tex/HZ_paths.tex
rename to figures/Schmidt2018/tex/HZ_paths.tex
diff --git a/figures/Schmidt2017/tex/LH_paths.tex b/figures/Schmidt2018/tex/LH_paths.tex
similarity index 100%
rename from figures/Schmidt2017/tex/LH_paths.tex
rename to figures/Schmidt2018/tex/LH_paths.tex
diff --git a/figures/Schmidt2017/tex/compile_tex.sh b/figures/Schmidt2018/tex/compile_tex.sh
similarity index 100%
rename from figures/Schmidt2017/tex/compile_tex.sh
rename to figures/Schmidt2018/tex/compile_tex.sh
diff --git a/figures/Schmidt2017/tex/define_bools.tex b/figures/Schmidt2018/tex/define_bools.tex
similarity index 100%
rename from figures/Schmidt2017/tex/define_bools.tex
rename to figures/Schmidt2018/tex/define_bools.tex
diff --git a/figures/Schmidt2017/tex/defs.tex b/figures/Schmidt2018/tex/defs.tex
similarity index 100%
rename from figures/Schmidt2017/tex/defs.tex
rename to figures/Schmidt2018/tex/defs.tex
diff --git a/figures/Schmidt2017/tex/draw_paths.tex b/figures/Schmidt2018/tex/draw_paths.tex
similarity index 100%
rename from figures/Schmidt2017/tex/draw_paths.tex
rename to figures/Schmidt2018/tex/draw_paths.tex
diff --git a/figures/Schmidt2017/tex/draw_pops.tex b/figures/Schmidt2018/tex/draw_pops.tex
similarity index 100%
rename from figures/Schmidt2017/tex/draw_pops.tex
rename to figures/Schmidt2018/tex/draw_pops.tex
diff --git a/figures/Schmidt2017/tex/indirect_23E.eps b/figures/Schmidt2018/tex/indirect_23E.eps
similarity index 100%
rename from figures/Schmidt2017/tex/indirect_23E.eps
rename to figures/Schmidt2018/tex/indirect_23E.eps
diff --git a/figures/Schmidt2017/tex/indirect_4E23E.eps b/figures/Schmidt2018/tex/indirect_4E23E.eps
similarity index 100%
rename from figures/Schmidt2017/tex/indirect_4E23E.eps
rename to figures/Schmidt2018/tex/indirect_4E23E.eps
diff --git a/figures/Schmidt2017/tex/indirect_4E5E.eps b/figures/Schmidt2018/tex/indirect_4E5E.eps
similarity index 100%
rename from figures/Schmidt2017/tex/indirect_4E5E.eps
rename to figures/Schmidt2018/tex/indirect_4E5E.eps
diff --git a/figures/Schmidt2017/tex/indirect_5E.eps b/figures/Schmidt2018/tex/indirect_5E.eps
similarity index 100%
rename from figures/Schmidt2017/tex/indirect_5E.eps
rename to figures/Schmidt2018/tex/indirect_5E.eps
diff --git a/figures/Schmidt2017/tex/indirect_6E.eps b/figures/Schmidt2018/tex/indirect_6E.eps
similarity index 100%
rename from figures/Schmidt2017/tex/indirect_6E.eps
rename to figures/Schmidt2018/tex/indirect_6E.eps
diff --git a/figures/Schmidt2017/tex/lateral_paths.tex b/figures/Schmidt2018/tex/lateral_paths.tex
similarity index 100%
rename from figures/Schmidt2017/tex/lateral_paths.tex
rename to figures/Schmidt2018/tex/lateral_paths.tex
diff --git a/figures/Schmidt2017/tex/texcolors.tex b/figures/Schmidt2018/tex/texcolors.tex
similarity index 100%
rename from figures/Schmidt2017/tex/texcolors.tex
rename to figures/Schmidt2018/tex/texcolors.tex
diff --git a/multiarea_model/data_multiarea/Model.py b/multiarea_model/data_multiarea/Model.py
index 0d14ab4..19eef02 100644
--- a/multiarea_model/data_multiarea/Model.py
+++ b/multiarea_model/data_multiarea/Model.py
@@ -2,9 +2,9 @@
Model
================
-This script defines the model described in Schmidt et al. (2017).
+This script defines the model described in Schmidt et al. (2018).
The procedures are described in detail in the Methods section of
-Schmidt et al. (2017).
+Schmidt et al. (2018).
It loads the data prepared by VisualCortexData.py and computes
neuronal numbers for each population, the external inputs
to each population and the number of synapses of each connection
@@ -491,7 +491,7 @@ def compute_Model_params(out_label='', mode='default'):
"""
2. Process Binzegger data
The notation follows Eqs. (11-12 and following) in
- Schmidt et al. (2017):
+ Schmidt et al. (2018):
v : layer of cortico-cortical synapse
cb : cell type
cell_layer : layer of the cell
diff --git a/multiarea_model/data_multiarea/VisualCortex_Data.py b/multiarea_model/data_multiarea/VisualCortex_Data.py
index 8aa2938..9b1deda 100644
--- a/multiarea_model/data_multiarea/VisualCortex_Data.py
+++ b/multiarea_model/data_multiarea/VisualCortex_Data.py
@@ -12,9 +12,9 @@ tasks:
viscortex_processed_data.json.
All details of the procedures in this scripts are described in
-Schmidt M, Bakker R, Hilgetag CC, Diesmann M & van Albada SJ (2017)
+Schmidt M, Bakker R, Hilgetag CC, Diesmann M & van Albada SJ
"Multi-scale account of the network structure of macaque visual cortex"
-Brain Structure and Function (2017)
+Brain Structure and Function (2018), 223:1409
Experimental Data
diff --git a/multiarea_model/multiarea_model.py b/multiarea_model/multiarea_model.py
index d678fe7..54cd8da 100644
--- a/multiarea_model/multiarea_model.py
+++ b/multiarea_model/multiarea_model.py
@@ -3,7 +3,7 @@ multiarea_model
==============
Network class to instantiate and administer instances of the
-multi-area model of macaque visual cortex by Schmidt el. (2016).
+multi-area model of macaque visual cortex by Schmidt el. (2018).
Classes
-------
@@ -17,7 +17,7 @@ label. As members, it may contain three classes:
- theory : theory class that serves to estimate the stationary state
of the network using mean-field theory
- Schuecker J, Schmidt M, van Albada SJ, Diesmann M, HeliasM(2017)
+ Schuecker J, Schmidt M, van Albada SJ, Diesmann M, Helias M (2017)
Fundamental Activity Constraints Lead to Specific Interpretations of
the Connectome. PLoS Comput Biol 13(2): e1005179.
doi:10.1371/journal.pcbi.1005179
diff --git a/multiarea_model/theory.py b/multiarea_model/theory.py
index f653505..23e17b0 100644
--- a/multiarea_model/theory.py
+++ b/multiarea_model/theory.py
@@ -3,7 +3,7 @@ theory
============
Theory package to predict the stable fixed points of the multi-area
-model of macaque visual cortex (Schmidt et al. 2015), perform further
+model of macaque visual cortex (Schmidt et al. 2018), perform further
analysis on them and to apply the stabilization procedure (Schuecker,
Schmidt et al., 2017) to the network connectivity.
--
GitLab