Add missing files for dynamics_manuscript figures, fix bugs in Fig2_bistability.py

figures/Schmidt2018_dyn/Fig2_bistability.eps

@@ -2,7 +2,7 @@
 %%BoundingBox: 13 13 515 374
 %%HiResBoundingBox: 13.1732 13.1732 514.071 373.415
 %%Creator: PyX 0.14.1
-%%CreationDate: Wed May 16 12:18:47 2018
+%%CreationDate: Thu Jun  7 09:15:20 2018
 %%EndComments
 %%BeginProlog
 %%BeginResource: BeginEPSF
@@ -42,7 +42,7 @@ BeginEPSF
 %%HiResBoundingBox: 0.000000 0.000000 510.235200 315.342696
 %%Creator: GPL Ghostscript 922 (ps2write)
 %%LanguageLevel: 2
-%%CreationDate: D:20180516121846+09'00'
+%%CreationDate: D:20180607091517+09'00'
 %%EndComments
 %%BeginProlog
 save
@@ -19320,7 +19320,7 @@ EndEPSF
 BeginEPSF
 113.386 240.945 283.465 131.47 rectclip
 [0.554725 0.000000 0.000000 0.554725 113.385827 241.499607] concat
-%%BeginDocument: phasespace_sketch.eps
+%%BeginDocument: Fig2_bistability_phasespace_sketch.eps
 %!PS-Adobe-3.0 EPSF-3.0
 %%Creator: cairo 1.14.6 (http://cairographics.org)
 %%CreationDate: Thu Jul 27 11:53:48 2017

figures/Schmidt2018_dyn/Fig2_bistability.py

@@ -55,9 +55,9 @@ for key, label in zip(keys, data_labels):
 
 labels = ['A', 'B', 'C']
 
-for i, k in enumerate(['LA', 'HA', 'LA_post']):
-    ax = axes[labels[i]]
-    ax2 = axes[labels[i] + '2']
+for k, key in enumerate(['LA', 'HA', 'LA_post']):
+    ax = axes[labels[k]]
+    ax2 = axes[labels[k] + '2']
     print(k)
     matrix = np.zeros((len(M.area_list), 8))
 
@@ -66,7 +66,7 @@ for i, k in enumerate(['LA', 'HA', 'LA_post']):
             if pop not in M.structure[area]:
                 rate = np.nan
             else:
-                rate = data[k][area][pop][0]
+                rate = data[key][area][pop][0]
 
             if rate == 0.0:
                 rate = 1e-5
@@ -74,11 +74,11 @@ for i, k in enumerate(['LA', 'HA', 'LA_post']):
 
     matrix = np.transpose(matrix)
 
-    if i == 0:
+    if k == 0:
         matrix_plot(panel_factory.figure, ax, matrix, position='left')
         rate_histogram_plot(panel_factory.figure, ax2,
                             matrix, position='left')
-    elif i == 1:
+    elif k == 1:
         matrix_plot(panel_factory.figure, ax, matrix, position='center')
         rate_histogram_plot(panel_factory.figure, ax2,
                             matrix, position='center')
@@ -98,7 +98,7 @@ pyx.text.preamble(r"\usepackage{helvet}")
 c = pyx.canvas.canvas()
 c.insert(pyx.epsfile.epsfile(0.5, 0.5, "Fig2_bistability_mpl.eps", width=17.6))
 c.insert(pyx.epsfile.epsfile(
-    4., 8.5, "phasespace_sketch.eps", width=10.))
+    4., 8.5, "Fig2_bistability_phasespace_sketch.eps", width=10.))
 c.insert(pyx.epsfile.epsfile(1., 3.1, "Epop.eps", width=0.75))
 c.insert(pyx.epsfile.epsfile(1., 2., "Ipop.eps", width=0.75))
 

figures/Schmidt2018_dyn/plotstyle.rc

+# set default backend
+backend : GTK3Agg
+
+# resolution of figures in dpi
+# does not influence eps output
+figure.dpi : 150
+savefig.dpi : 300
+
+# set default figuresize
+figure.figsize : 12.0, 7.42
+
+# font
+font.size : 8
+legend.fontsize : 8
+font.family : sans-serif
+
+# size of lines
+lines.linewidth : 1.5
+lines.antialiased : True
+
+# size of markers (points in point plots)
+lines.markersize : 3.0
+patch.linewidth : 1.0
+axes.linewidth : 1.0 # edge linewidth
+
+# ticks distances
+xtick.major.size : 4 # major tick size in points
+xtick.minor.size : 2 # minor tick size in points
+lines.markeredgewidth : 0.5 # line width of ticks
+xtick.major.pad : 4 # distance to major tick label in points
+xtick.minor.pad : 4 # distance to the minor tick label in points
+ytick.major.size : 4  # major tick size in points
+ytick.minor.size : 2 # minor tick size in points
+ytick.major.pad : 4 # distance to major tick label in points
+ytick.minor.pad : 4 # distance to the minor tick label in points
+
+# ticks textsize
+ytick.labelsize : 8
+xtick.labelsize : 8
+
+# axes labelsize
+axes.labelsize : 8
+
+# use latex to generate the labels in plots
+# not needed anymore in newer versions
+# using this, font detection fails on adobe illustrator 2010-07-20
+text.usetex : True
+text.latex.preamble : \usepackage{amsmath}
+ps.useafm : False # use of afm fonts, results in small files
+ps.fonttype : 3 # Output Type 3 (Type3) or Type 42 (TrueType)
+
+# set different default color cycle
+axes.color_cycle : 4c72b0, 55a868, c44e52, 8172b2, ccb974, 64b5cd
\ No newline at end of file