diff --git a/scripts/dynamics/plot_renewal_events_displ_hist.py b/scripts/dynamics/plot_renewal_events_displ_hist.py
index e15bf975..bfea78ce 100644
--- a/scripts/dynamics/plot_renewal_events_displ_hist.py
+++ b/scripts/dynamics/plot_renewal_events_displ_hist.py
@@ -1,8 +1,8 @@
#!/usr/bin/env python3
-
# This file is part of MDTools.
-# Copyright (C) 2020 Andreas Thum
+# Copyright (C) 2021 The MDTools Development Team and all contributors
+# listed in the file AUTHORS.rst
#
# MDTools is free software: you can redistribute it and/or modify it
# under the terms of the GNU General Public License as published by the
@@ -18,6 +18,9 @@
# along with MDTools. If not, see .
+__author__ = "Andreas Thum"
+
+
import sys
import os
from datetime import datetime
@@ -28,6 +31,8 @@
import matplotlib.pyplot as plt
from matplotlib.backends.backend_pdf import PdfPages
import mdtools as mdt
+import mdtools.plot as mdtplt # TODO: Replace deprecated functions
+plt.style.use("default") # TODO: Use MDTools plotting style
if __name__ == '__main__':
@@ -227,18 +232,20 @@
frameon=False,
clear=True,
tight_layout=True)
- mdt.plot.hist(ax=axis,
- x=data,
- xmin=args.XMIN,
- xmax=args.XMAX,
- ymin=args.YMIN,
- ymax=args.YMAX,
- xlabel=r'$' + xlabel[i] + r'$ / ' + args.LUNIT,
- ylabel=r'$p(' + xlabel[i] + r')$',
- bins=bins[i],
- range=(args.START, args.STOP),
- density=True)
- mdt.plot.plot(
+ mdtplt.hist(
+ ax=axis,
+ x=data,
+ xmin=args.XMIN,
+ xmax=args.XMAX,
+ ymin=args.YMIN,
+ ymax=args.YMAX,
+ xlabel=r'$' + xlabel[i] + r'$ / ' + args.LUNIT,
+ ylabel=r'$p(' + xlabel[i] + r')$',
+ bins=bins[i],
+ range=(args.START, args.STOP),
+ density=True,
+ )
+ mdtplt.plot(
ax=axis,
x=x[i],
y=mdt.stats.gaussian(x=x[i],
@@ -251,7 +258,8 @@
xlabel=r'$' + xlabel[i] + r'$ / ' + args.LUNIT,
ylabel=r'$p(' + xlabel[i] + r')$',
label="Fit",
- color='black')
+ color='black',
+ )
plt.tight_layout()
pdf.savefig()
plt.close()
diff --git a/scripts/dynamics/plot_renewal_events_displ_vs_post0.py b/scripts/dynamics/plot_renewal_events_displ_vs_post0.py
index 51cdec5a..c1a3ee78 100644
--- a/scripts/dynamics/plot_renewal_events_displ_vs_post0.py
+++ b/scripts/dynamics/plot_renewal_events_displ_vs_post0.py
@@ -1,8 +1,8 @@
#!/usr/bin/env python3
-
# This file is part of MDTools.
-# Copyright (C) 2020 Andreas Thum
+# Copyright (C) 2021 The MDTools Development Team and all contributors
+# listed in the file AUTHORS.rst
#
# MDTools is free software: you can redistribute it and/or modify it
# under the terms of the GNU General Public License as published by the
@@ -18,6 +18,9 @@
# along with MDTools. If not, see .
+__author__ = "Andreas Thum"
+
+
import sys
import os
from datetime import datetime
@@ -27,6 +30,8 @@
import matplotlib.pyplot as plt
from matplotlib.backends.backend_pdf import PdfPages
import mdtools as mdt
+import mdtools.plot as mdtplt # TODO: Replace deprecated functions
+plt.style.use("default") # TODO: Use MDTools plotting style
if __name__ == '__main__':
@@ -319,7 +324,7 @@
axis = axes[1]
axis.axhline(y=0, color='black')
- img = mdt.plot.scatter(
+ img = mdtplt.scatter(
ax=axis,
x=pos_t0,
y=displ.T[i],
@@ -331,7 +336,8 @@
xlabel=r'${}(t_0)$ / {}'.format(args.DIRECTION, args.LUNIT),
ylabel=r'$\Delta ' + ylabel[i] + r'(\tau_{renew})$ / ' + args.LUNIT,
marker='x',
- cmap='plasma')
+ cmap='plasma',
+ )
cbar = plt.colorbar(img, ax=axis)
cbar.set_label(label=r'$\tau_{renew}$ / ' + args.TUNIT,
fontsize=fontsize_labels)
@@ -346,18 +352,20 @@
length=0.5 * tick_length,
labelsize=0.8 * fontsize_ticks)
- mdt.plot.vlines(ax=axis,
- x=bins,
- start=axis.get_ylim()[0],
- stop=axis.get_ylim()[1],
- xmin=args.XMIN,
- xmax=args.XMAX,
- ymin=args.YMIN,
- ymax=args.YMAX,
- color='black',
- linestyle='dotted')
-
- mdt.plot.plot(
+ mdtplt.vlines(
+ ax=axis,
+ x=bins,
+ start=axis.get_ylim()[0],
+ stop=axis.get_ylim()[1],
+ xmin=args.XMIN,
+ xmax=args.XMAX,
+ ymin=args.YMIN,
+ ymax=args.YMAX,
+ color='black',
+ linestyle='dotted',
+ )
+
+ mdtplt.plot(
ax=axis,
x=bins[1:] - np.diff(bins) / 2,
y=displ_means.T[i][1:],
@@ -369,9 +377,10 @@
ylabel=r'$\Delta ' + ylabel[i] + r'(\tau_{renew})$ / ' + args.LUNIT,
label=r'$\langle \Delta ' + ylabel[i] + r' \rangle$',
color='red',
- marker='o')
+ marker='o',
+ )
- mdt.plot.plot(
+ mdtplt.plot(
ax=axis,
x=bins[1:] - np.diff(bins) / 2,
y=msd_means.T[i][1:],
@@ -383,9 +392,10 @@
ylabel=r'$\Delta ' + ylabel[i] + r'(\tau_{renew})$ / ' + args.LUNIT,
label=r'$\langle \Delta ' + ylabel[i] + r'^2 \rangle$',
color='blue',
- marker='^')
+ marker='^',
+ )
- mdt.plot.plot(
+ mdtplt.plot(
ax=axis,
x=bins[1:] - np.diff(bins) / 2,
y=displ_vars.T[i][1:],
@@ -397,7 +407,8 @@
ylabel=r'$\Delta ' + ylabel[i] + r'(\tau_{renew})$ / ' + args.LUNIT,
label=r'$\langle \Delta ' + ylabel[i] + r'^2 \rangle - \langle \Delta ' + ylabel[i] + r' \rangle ^2$',
color='green',
- marker='s')
+ marker='s',
+ )
axis.legend(loc='lower left',
numpoints=1,
@@ -405,14 +416,16 @@
fontsize=fontsize_legend)
if args.INFILE2 is not None:
- mdt.plot.plot(ax=axes[0],
- x=data[:, 0],
- y=data[:, 1],
- xmin=args.XMIN,
- xmax=args.XMAX,
- ymin=np.min(data[:, 1]),
- ymax=np.max(data[:, 1]),
- color='black')
+ mdtplt.plot(
+ ax=axes[0],
+ x=data[:, 0],
+ y=data[:, 1],
+ xmin=args.XMIN,
+ xmax=args.XMAX,
+ ymin=np.min(data[:, 1]),
+ ymax=np.max(data[:, 1]),
+ color='black',
+ )
axes[0].xaxis.set_visible(False)
axes[0].yaxis.set_visible(False)
axes[0].spines['bottom'].set_visible(False)
diff --git a/scripts/dynamics/plot_renewal_events_displ_vs_trenew_binned.py b/scripts/dynamics/plot_renewal_events_displ_vs_trenew_binned.py
index cd51c56e..59b30281 100644
--- a/scripts/dynamics/plot_renewal_events_displ_vs_trenew_binned.py
+++ b/scripts/dynamics/plot_renewal_events_displ_vs_trenew_binned.py
@@ -1,8 +1,8 @@
#!/usr/bin/env python3
-
# This file is part of MDTools.
-# Copyright (C) 2020 Andreas Thum
+# Copyright (C) 2021 The MDTools Development Team and all contributors
+# listed in the file AUTHORS.rst
#
# MDTools is free software: you can redistribute it and/or modify it
# under the terms of the GNU General Public License as published by the
@@ -18,6 +18,9 @@
# along with MDTools. If not, see .
+__author__ = "Andreas Thum"
+
+
import sys
import os
from datetime import datetime
@@ -28,6 +31,8 @@
import matplotlib.pyplot as plt
from matplotlib.backends.backend_pdf import PdfPages
import mdtools as mdt
+import mdtools.plot as mdtplt # TODO: Replace deprecated functions
+plt.style.use("default") # TODO: Use MDTools plotting style
if __name__ == '__main__':
@@ -380,23 +385,27 @@
frameon=False,
clear=True,
tight_layout=True)
- mdt.plot.plot(ax=axis,
- x=t,
- y=nevents[1:],
- xmin=args.XMIN,
- xmax=args.XMAX,
- xlabel=r'$\tau_{renew}$ / ' + args.TUNIT,
- ylabel=r'$N_{renew}$',
- color='black',
- marker='o')
- mdt.plot.vlines(ax=axis,
- x=tbins,
- start=axis.get_ylim()[0],
- stop=axis.get_ylim()[1],
- xmin=args.XMIN,
- xmax=args.XMAX,
- color='black',
- linestyle='dotted')
+ mdtplt.plot(
+ ax=axis,
+ x=t,
+ y=nevents[1:],
+ xmin=args.XMIN,
+ xmax=args.XMAX,
+ xlabel=r'$\tau_{renew}$ / ' + args.TUNIT,
+ ylabel=r'$N_{renew}$',
+ color='black',
+ marker='o',
+ )
+ mdtplt.vlines(
+ ax=axis,
+ x=tbins,
+ start=axis.get_ylim()[0],
+ stop=axis.get_ylim()[1],
+ xmin=args.XMIN,
+ xmax=args.XMAX,
+ color='black',
+ linestyle='dotted',
+ )
plt.tight_layout()
pdf.savefig()
plt.close()
@@ -410,7 +419,7 @@
tight_layout=True)
axis.axhline(y=0, color='black')
if args.DCOLOR is None:
- mdt.plot.scatter(
+ mdtplt.scatter(
ax=axis,
x=trenew,
y=displ.T[i],
@@ -420,9 +429,10 @@
ymax=args.YMAX,
xlabel=r'$\tau_{renew}$ / ' + args.TUNIT,
ylabel=r'$\Delta ' + ylabel[i] + r'(\tau_{renew})$ / ' + args.LUNIT,
- marker='x')
+ marker='x',
+ )
else:
- img = mdt.plot.scatter(
+ img = mdtplt.scatter(
ax=axis,
x=trenew,
y=displ.T[i],
@@ -434,7 +444,8 @@
xlabel=r'$\tau_{renew}$ / ' + args.TUNIT,
ylabel=r'$\Delta ' + ylabel[i] + r'(\tau_{renew})$ / ' + args.LUNIT,
marker='x',
- cmap='plasma')
+ cmap='plasma',
+ )
cbar = plt.colorbar(img, ax=axis)
cbar.set_label(label=r'${}(t_0)$ / {}'.format(args.DCOLOR, args.LUNIT),
fontsize=fontsize_labels)
@@ -448,17 +459,19 @@
direction='out',
length=0.5 * tick_length,
labelsize=0.8 * fontsize_ticks)
- mdt.plot.vlines(ax=axis,
- x=tbins,
- start=axis.get_ylim()[0],
- stop=axis.get_ylim()[1],
- xmin=args.XMIN,
- xmax=args.XMAX,
- ymin=args.YMIN,
- ymax=args.YMAX,
- color='black',
- linestyle='dotted')
- mdt.plot.plot(
+ mdtplt.vlines(
+ ax=axis,
+ x=tbins,
+ start=axis.get_ylim()[0],
+ stop=axis.get_ylim()[1],
+ xmin=args.XMIN,
+ xmax=args.XMAX,
+ ymin=args.YMIN,
+ ymax=args.YMAX,
+ color='black',
+ linestyle='dotted',
+ )
+ mdtplt.plot(
ax=axis,
x=t,
y=displ_mean.T[i][1:],
@@ -470,8 +483,9 @@
ylabel=r'$\Delta ' + ylabel[i] + r'(\tau_{renew})$ / ' + args.LUNIT,
label=r'$\langle \Delta ' + ylabel[i] + r' \rangle$',
color='red',
- marker='o')
- mdt.plot.plot(
+ marker='o',
+ )
+ mdtplt.plot(
ax=axis,
x=t,
y=np.sqrt(msd_mean.T[i][1:]),
@@ -483,8 +497,9 @@
ylabel=r'$\Delta ' + ylabel[i] + r'(\tau_{renew})$ / ' + args.LUNIT,
label=r'$\sqrt{\langle \Delta ' + ylabel[i] + r'^2 \rangle}$',
color='blue',
- marker='^')
- mdt.plot.plot(
+ marker='^',
+ )
+ mdtplt.plot(
ax=axis,
x=t,
y=displ_std.T[i][1:],
@@ -496,7 +511,8 @@
ylabel=r'$\Delta ' + ylabel[i] + r'(\tau_{renew})$ / ' + args.LUNIT,
label=r'$\sqrt{\langle \Delta ' + ylabel[i] + r'^2 \rangle - \langle \Delta ' + ylabel[i] + r' \rangle ^2}$',
color='green',
- marker='s')
+ marker='s',
+ )
axis.legend(loc='upper center',
bbox_to_anchor=(0.5, 1.32),
ncol=2,
@@ -626,7 +642,7 @@
tight_layout=True)
axis.axhline(y=0, color='black')
if args.DCOLOR is None:
- img = mdt.plot.scatter(
+ img = mdtplt.scatter(
ax=axis,
x=trenew,
y=displ.T[i],
@@ -636,9 +652,10 @@
ymax=args.YMAX,
xlabel=r'$\tau_{renew}$ / ' + args.TUNIT,
ylabel=r'$\Delta ' + ylabel[i] + r'(\tau_{renew})$ / ' + args.LUNIT,
- marker='x')
+ marker='x',
+ )
else:
- img = mdt.plot.scatter(
+ img = mdtplt.scatter(
ax=axis,
x=trenew,
y=displ.T[i],
@@ -650,7 +667,8 @@
xlabel=r'$\tau_{renew}$ / ' + args.TUNIT,
ylabel=r'$\Delta ' + ylabel[i] + r'(\tau_{renew})$ / ' + args.LUNIT,
marker='x',
- cmap='plasma')
+ cmap='plasma',
+ )
cbar = plt.colorbar(img, ax=axis)
cbar.set_label(label=r'${}(t_0)$ / {}'.format(args.DCOLOR, args.LUNIT),
fontsize=fontsize_labels)
@@ -664,17 +682,19 @@
direction='out',
length=0.5 * tick_length,
labelsize=0.8 * fontsize_ticks)
- mdt.plot.vlines(ax=axis,
- x=tbins,
- start=axis.get_ylim()[0],
- stop=axis.get_ylim()[1],
- xmin=args.XMIN,
- xmax=args.XMAX,
- ymin=args.YMIN,
- ymax=args.YMAX,
- color='black',
- linestyle='dotted')
- mdt.plot.plot(
+ mdtplt.vlines(
+ ax=axis,
+ x=tbins,
+ start=axis.get_ylim()[0],
+ stop=axis.get_ylim()[1],
+ xmin=args.XMIN,
+ xmax=args.XMAX,
+ ymin=args.YMIN,
+ ymax=args.YMAX,
+ color='black',
+ linestyle='dotted',
+ )
+ mdtplt.plot(
ax=axis,
x=t,
y=popt_displ.T[0][i][1:],
@@ -686,8 +706,9 @@
ylabel=r'$\Delta ' + ylabel[i] + r'(\tau_{renew})$ / ' + args.LUNIT,
label=r'$\mu$',
color='red',
- marker='o')
- mdt.plot.plot(
+ marker='o',
+ )
+ mdtplt.plot(
ax=axis,
x=t,
y=popt_displ.T[1][i][1:],
@@ -699,8 +720,9 @@
ylabel=r'$\Delta ' + ylabel[i] + r'(\tau_{renew})$ / ' + args.LUNIT,
label=r'$\sigma$',
color='blue',
- marker='^')
- mdt.plot.plot(
+ marker='^',
+ )
+ mdtplt.plot(
ax=axis,
x=t,
y=non_gaus.T[i][1:],
@@ -712,7 +734,8 @@
ylabel=r'$\Delta ' + ylabel[i] + r'(\tau_{renew})$ / ' + args.LUNIT,
label=r'$A$',
color='green',
- marker='s')
+ marker='s',
+ )
plt.tight_layout()
pdf.savefig()
plt.close()
diff --git a/scripts/dynamics/plot_renewal_events_displa_vs_displb.py b/scripts/dynamics/plot_renewal_events_displa_vs_displb.py
index cf1dfdb0..544ddf48 100644
--- a/scripts/dynamics/plot_renewal_events_displa_vs_displb.py
+++ b/scripts/dynamics/plot_renewal_events_displa_vs_displb.py
@@ -1,8 +1,8 @@
#!/usr/bin/env python3
-
# This file is part of MDTools.
-# Copyright (C) 2020 Andreas Thum
+# Copyright (C) 2021 The MDTools Development Team and all contributors
+# listed in the file AUTHORS.rst
#
# MDTools is free software: you can redistribute it and/or modify it
# under the terms of the GNU General Public License as published by the
@@ -18,6 +18,9 @@
# along with MDTools. If not, see .
+__author__ = "Andreas Thum"
+
+
import sys
import os
from datetime import datetime
@@ -28,6 +31,8 @@
import matplotlib.pyplot as plt
from matplotlib.backends.backend_pdf import PdfPages
import mdtools as mdt
+import mdtools.plot as mdtplt # TODO: Replace deprecated functions
+plt.style.use("default") # TODO: Use MDTools plotting style
if __name__ == '__main__':
@@ -277,7 +282,7 @@
axis.axhline(y=0, color='black')
axis.axvline(x=0, color='black')
- img = mdt.plot.scatter(
+ img = mdtplt.scatter(
ax=axis,
x=displ1,
y=displ2,
@@ -289,7 +294,8 @@
xlabel=r'$\Delta ' + args.DIRECTION1 + r'(\tau_{renew})$ / ' + args.LUNIT,
ylabel=r'$\Delta ' + args.DIRECTION2 + r'(\tau_{renew})$ / ' + args.LUNIT,
marker='x',
- cmap='plasma')
+ cmap='plasma',
+ )
cbar = plt.colorbar(img, ax=axis)
cbar.set_label(label=r'$\tau_{renew}$ / ' + args.TUNIT,
fontsize=fontsize_labels)
@@ -305,7 +311,7 @@
labelsize=0.8 * fontsize_ticks)
diagonal = np.linspace(*axis.get_xlim())
- mdt.plot.plot(
+ mdtplt.plot(
ax=axis,
x=diagonal,
y=diagonal,
@@ -317,7 +323,8 @@
ylabel=r'$\Delta ' + args.DIRECTION2 + r'(\tau_{renew})$ / ' + args.LUNIT,
label="Diagonal",
color='black',
- linestyle='--')
+ linestyle='--',
+ )
axis.axvline(x=np.mean(displ1),
color='red',
diff --git a/scripts/dynamics/plot_renewal_events_msd_vs_post0.py b/scripts/dynamics/plot_renewal_events_msd_vs_post0.py
index 37c7fa13..1d4f86cb 100644
--- a/scripts/dynamics/plot_renewal_events_msd_vs_post0.py
+++ b/scripts/dynamics/plot_renewal_events_msd_vs_post0.py
@@ -1,8 +1,8 @@
#!/usr/bin/env python3
-
# This file is part of MDTools.
-# Copyright (C) 2020 Andreas Thum
+# Copyright (C) 2021 The MDTools Development Team and all contributors
+# listed in the file AUTHORS.rst
#
# MDTools is free software: you can redistribute it and/or modify it
# under the terms of the GNU General Public License as published by the
@@ -18,6 +18,9 @@
# along with MDTools. If not, see .
+__author__ = "Andreas Thum"
+
+
import sys
import os
from datetime import datetime
@@ -27,6 +30,8 @@
import matplotlib.pyplot as plt
from matplotlib.backends.backend_pdf import PdfPages
import mdtools as mdt
+import mdtools.plot as mdtplt # TODO: Replace deprecated functions
+plt.style.use("default") # TODO: Use MDTools plotting style
if __name__ == '__main__':
@@ -333,7 +338,7 @@
mask = (msd_tot > 0)
else:
mask = slice(0, len(msd_tot))
- img = mdt.plot.scatter(
+ img = mdtplt.scatter(
ax=axis,
x=pos_t0[mask],
y=msd_tot[mask],
@@ -346,7 +351,8 @@
xlabel=r'${}(t_0)$ / {}'.format(args.DIRECTION, args.LUNIT),
ylabel=r'$\Delta r^2(\tau_{renew})$ / ' + args.LUNIT + r'$^2$',
marker='x',
- cmap='plasma')
+ cmap='plasma',
+ )
cbar = plt.colorbar(img, ax=axis)
cbar.set_label(label=r'$\tau_{renew}$ / ' + args.TUNIT,
fontsize=fontsize_labels)
@@ -361,22 +367,24 @@
length=0.5 * tick_length,
labelsize=0.8 * fontsize_ticks)
- mdt.plot.vlines(ax=axis,
- x=bins,
- start=axis.get_ylim()[0],
- stop=axis.get_ylim()[1],
- xmin=args.XMIN,
- xmax=args.XMAX,
- ymin=ymin[l],
- ymax=args.YMAX,
- color='black',
- linestyle='dotted')
+ mdtplt.vlines(
+ ax=axis,
+ x=bins,
+ start=axis.get_ylim()[0],
+ stop=axis.get_ylim()[1],
+ xmin=args.XMIN,
+ xmax=args.XMAX,
+ ymin=ymin[l],
+ ymax=args.YMAX,
+ color='black',
+ linestyle='dotted',
+ )
if logy[l]:
mask = (msd_tot_mean[1:] > 0)
else:
mask = slice(0, len(msd_tot_mean))
- mdt.plot.errorbar(
+ mdtplt.errorbar(
ax=axis,
x=(bins[1:] - np.diff(bins) / 2)[mask],
y=msd_tot_mean[1:][mask],
@@ -389,17 +397,20 @@
xlabel=r'${}(t_0)$ / {}'.format(args.DIRECTION, args.LUNIT),
ylabel=r'$\Delta r^2(\tau_{renew})$ / ' + args.LUNIT + r'$^2$',
color='red',
- marker='o')
+ marker='o',
+ )
if args.INFILE2 is not None:
- mdt.plot.plot(ax=axes[0],
- x=data[:, 0],
- y=data[:, 1],
- xmin=args.XMIN,
- xmax=args.XMAX,
- ymin=np.min(data[:, 1]),
- ymax=np.max(data[:, 1]),
- color='black')
+ mdtplt.plot(
+ ax=axes[0],
+ x=data[:, 0],
+ y=data[:, 1],
+ xmin=args.XMIN,
+ xmax=args.XMAX,
+ ymin=np.min(data[:, 1]),
+ ymax=np.max(data[:, 1]),
+ color='black',
+ )
axes[0].xaxis.set_visible(False)
axes[0].yaxis.set_visible(False)
axes[0].spines['bottom'].set_visible(False)
@@ -435,7 +446,7 @@
mask = (msd.T[i] > 0)
else:
mask = slice(0, len(msd.T[i]))
- img = mdt.plot.scatter(
+ img = mdtplt.scatter(
ax=axis,
x=pos_t0[mask],
y=msd.T[i][mask],
@@ -448,7 +459,8 @@
xlabel=r'${}(t_0)$ / {}'.format(args.DIRECTION, args.LUNIT),
ylabel=ylabel[i] + args.LUNIT + r'$^2$',
marker='x',
- cmap='plasma')
+ cmap='plasma',
+ )
cbar = plt.colorbar(img, ax=axis)
cbar.set_label(label=r'$\tau_{renew}$ / ' + args.TUNIT,
fontsize=fontsize_labels)
@@ -463,22 +475,24 @@
length=0.5 * tick_length,
labelsize=0.8 * fontsize_ticks)
- mdt.plot.vlines(ax=axis,
- x=bins,
- start=axis.get_ylim()[0],
- stop=axis.get_ylim()[1],
- xmin=args.XMIN,
- xmax=args.XMAX,
- ymin=ymin[l],
- ymax=args.YMAX,
- color='black',
- linestyle='dotted')
+ mdtplt.vlines(
+ ax=axis,
+ x=bins,
+ start=axis.get_ylim()[0],
+ stop=axis.get_ylim()[1],
+ xmin=args.XMIN,
+ xmax=args.XMAX,
+ ymin=ymin[l],
+ ymax=args.YMAX,
+ color='black',
+ linestyle='dotted',
+ )
if logy[l]:
mask = (msd_mean.T[i][1:] > 0)
else:
mask = slice(0, len(msd_mean.T[i]))
- mdt.plot.errorbar(
+ mdtplt.errorbar(
ax=axis,
x=(bins[1:] - np.diff(bins) / 2)[mask],
y=msd_mean.T[i][1:][mask],
@@ -491,17 +505,20 @@
xlabel=r'${}(t_0)$ / {}'.format(args.DIRECTION, args.LUNIT),
ylabel=ylabel[i] + args.LUNIT + r'$^2$',
color='red',
- marker='o')
+ marker='o',
+ )
if args.INFILE2 is not None:
- mdt.plot.plot(ax=axes[0],
- x=data[:, 0],
- y=data[:, 1],
- xmin=args.XMIN,
- xmax=args.XMAX,
- ymin=np.min(data[:, 1]),
- ymax=np.max(data[:, 1]),
- color='black')
+ mdtplt.plot(
+ ax=axes[0],
+ x=data[:, 0],
+ y=data[:, 1],
+ xmin=args.XMIN,
+ xmax=args.XMAX,
+ ymin=np.min(data[:, 1]),
+ ymax=np.max(data[:, 1]),
+ color='black',
+ )
axes[0].xaxis.set_visible(False)
axes[0].yaxis.set_visible(False)
axes[0].spines['bottom'].set_visible(False)
diff --git a/scripts/dynamics/plot_renewal_events_msd_vs_trenew.py b/scripts/dynamics/plot_renewal_events_msd_vs_trenew.py
index bcbb82a1..d4fb256e 100644
--- a/scripts/dynamics/plot_renewal_events_msd_vs_trenew.py
+++ b/scripts/dynamics/plot_renewal_events_msd_vs_trenew.py
@@ -1,8 +1,8 @@
#!/usr/bin/env python3
-
# This file is part of MDTools.
-# Copyright (C) 2020 Andreas Thum
+# Copyright (C) 2021 The MDTools Development Team and all contributors
+# listed in the file AUTHORS.rst
#
# MDTools is free software: you can redistribute it and/or modify it
# under the terms of the GNU General Public License as published by the
@@ -18,6 +18,9 @@
# along with MDTools. If not, see .
+__author__ = "Andreas Thum"
+
+
import sys
import os
from datetime import datetime
@@ -28,6 +31,8 @@
import matplotlib.pyplot as plt
from matplotlib.backends.backend_pdf import PdfPages
import mdtools as mdt
+import mdtools.plot as mdtplt # TODO: Replace deprecated functions
+plt.style.use("default") # TODO: Use MDTools plotting style
if __name__ == '__main__':
@@ -239,7 +244,7 @@
displ0[-1] = np.count_nonzero(msd_tot == 0)
mask = (msd_tot > 0)
if args.DCOLOR is None:
- mdt.plot.scatter(
+ mdtplt.scatter(
ax=axis,
x=trenew[mask],
y=msd_tot[mask],
@@ -251,9 +256,10 @@
logy=True,
xlabel=r'$\tau_{renew}$ / ' + args.TUNIT,
ylabel=r'$\Delta r^2(\tau_{renew})$ / ' + args.LUNIT + r'$^2$',
- marker='x')
+ marker='x',
+ )
else:
- img = mdt.plot.scatter(
+ img = mdtplt.scatter(
ax=axis,
x=trenew[mask],
y=msd_tot[mask],
@@ -267,7 +273,8 @@
xlabel=r'$\tau_{renew}$ / ' + args.TUNIT,
ylabel=r'$\Delta r^2(\tau_{renew})$ / ' + args.LUNIT + r'$^2$',
marker='x',
- cmap='plasma')
+ cmap='plasma',
+ )
cbar = plt.colorbar(img, ax=axis)
cbar.set_label(label=r'${}(t_0)$ / {}'.format(args.DCOLOR, args.LUNIT),
fontsize=fontsize_labels)
@@ -282,7 +289,7 @@
length=0.5 * tick_length,
labelsize=0.8 * fontsize_ticks)
mask = (running_average_tot > 0)
- mdt.plot.plot(
+ mdtplt.plot(
ax=axis,
x=trenew[mask][sort_ix[mask]],
y=running_average_tot[mask],
@@ -295,10 +302,11 @@
xlabel=r'$\tau_{renew}$ / ' + args.TUNIT,
ylabel=r'$\Delta r^2(\tau_{renew})$ / ' + args.LUNIT + r'$^2$',
label="Running average",
- color='red')
+ color='red',
+ )
fit = mdt.dyn.msd(t=trenew, D=popt[-1], d=3)
mask = (fit > 0)
- mdt.plot.plot(
+ mdtplt.plot(
ax=axis,
x=trenew[mask],
y=fit[mask],
@@ -311,7 +319,8 @@
xlabel=r'$\tau_{renew}$ / ' + args.TUNIT,
ylabel=r'$\Delta r^2(\tau_{renew})$ / ' + args.LUNIT + r'$^2$',
label="Fit",
- color='black')
+ color='black',
+ )
plt.tight_layout()
pdf.savefig()
plt.close()
@@ -325,7 +334,7 @@
displ0[i] = np.count_nonzero(data == 0)
mask = (data > 0)
if args.DCOLOR is None:
- mdt.plot.scatter(
+ mdtplt.scatter(
ax=axis,
x=trenew[mask],
y=data[mask],
@@ -337,9 +346,10 @@
logy=True,
xlabel=r'$\tau_{renew}$ / ' + args.TUNIT,
ylabel=r'$\Delta ' + ylabel[i] + r'^2(\tau_{renew})$ / ' + args.LUNIT + r'$^2$',
- marker='x')
+ marker='x',
+ )
else:
- img = mdt.plot.scatter(
+ img = mdtplt.scatter(
ax=axis,
x=trenew[mask],
y=data[mask],
@@ -353,7 +363,8 @@
xlabel=r'$\tau_{renew}$ / ' + args.TUNIT,
ylabel=r'$\Delta ' + ylabel[i] + r'^2(\tau_{renew})$ / ' + args.LUNIT + r'$^2$',
marker='x',
- cmap='plasma')
+ cmap='plasma',
+ )
cbar = plt.colorbar(img, ax=axis)
cbar.set_label(label=r'${}(t_0)$ / {}'.format(args.DCOLOR, args.LUNIT),
fontsize=fontsize_labels)
@@ -368,7 +379,7 @@
length=0.5 * tick_length,
labelsize=0.8 * fontsize_ticks)
mask = (running_average.T[i] > 0)
- mdt.plot.plot(
+ mdtplt.plot(
ax=axis,
x=trenew[mask][sort_ix[mask]],
y=running_average.T[i][mask],
@@ -381,10 +392,11 @@
xlabel=r'$\tau_{renew}$ / ' + args.TUNIT,
ylabel=r'$\Delta ' + ylabel[i] + r'^2(\tau_{renew})$ / ' + args.LUNIT + r'$^2$',
label="Running average",
- color='red')
+ color='red',
+ )
fit = mdt.dyn.msd(t=trenew, D=popt[i], d=1)
mask = (fit > 0)
- mdt.plot.plot(
+ mdtplt.plot(
ax=axis,
x=trenew[mask],
y=fit[mask],
@@ -397,7 +409,8 @@
xlabel=r'$\tau_{renew}$ / ' + args.TUNIT,
ylabel=r'$\Delta ' + ylabel[i] + r'^2(\tau_{renew})$ / ' + args.LUNIT + r'$^2$',
label="Fit",
- color='black')
+ color='black',
+ )
plt.tight_layout()
pdf.savefig()
plt.close()
diff --git a/scripts/dynamics/plot_renewal_events_msd_vs_trenew_binned.py b/scripts/dynamics/plot_renewal_events_msd_vs_trenew_binned.py
index 186b0016..8f97ab59 100644
--- a/scripts/dynamics/plot_renewal_events_msd_vs_trenew_binned.py
+++ b/scripts/dynamics/plot_renewal_events_msd_vs_trenew_binned.py
@@ -1,8 +1,8 @@
#!/usr/bin/env python3
-
# This file is part of MDTools.
-# Copyright (C) 2020 Andreas Thum
+# Copyright (C) 2021 The MDTools Development Team and all contributors
+# listed in the file AUTHORS.rst
#
# MDTools is free software: you can redistribute it and/or modify it
# under the terms of the GNU General Public License as published by the
@@ -18,6 +18,9 @@
# along with MDTools. If not, see .
+__author__ = "Andreas Thum"
+
+
import sys
import os
from datetime import datetime
@@ -28,6 +31,8 @@
import matplotlib.pyplot as plt
from matplotlib.backends.backend_pdf import PdfPages
import mdtools as mdt
+import mdtools.plot as mdtplt # TODO: Replace deprecated functions
+plt.style.use("default") # TODO: Use MDTools plotting style
if __name__ == '__main__':
@@ -338,23 +343,27 @@
frameon=False,
clear=True,
tight_layout=True)
- mdt.plot.plot(ax=axis,
- x=tbins[1:] - np.diff(tbins) / 2,
- y=nevents[1:],
- xmin=0,
- xmax=args.XMAX,
- xlabel=r'$\tau_{renew}$ / ' + args.TUNIT,
- ylabel=r'$N_{renew}$',
- color='black',
- marker='o')
- mdt.plot.vlines(ax=axis,
- x=tbins,
- start=axis.get_ylim()[0],
- stop=axis.get_ylim()[1],
- xmin=args.XMIN,
- xmax=args.XMAX,
- color='black',
- linestyle='dotted')
+ mdtplt.plot(
+ ax=axis,
+ x=tbins[1:] - np.diff(tbins) / 2,
+ y=nevents[1:],
+ xmin=0,
+ xmax=args.XMAX,
+ xlabel=r'$\tau_{renew}$ / ' + args.TUNIT,
+ ylabel=r'$N_{renew}$',
+ color='black',
+ marker='o',
+ )
+ mdtplt.vlines(
+ ax=axis,
+ x=tbins,
+ start=axis.get_ylim()[0],
+ stop=axis.get_ylim()[1],
+ xmin=args.XMIN,
+ xmax=args.XMAX,
+ color='black',
+ linestyle='dotted',
+ )
plt.tight_layout()
pdf.savefig()
plt.close()
@@ -367,7 +376,7 @@
displ0[-1] = np.count_nonzero(msd_tot == 0)
mask = (msd_tot > 0)
if args.DCOLOR is None:
- mdt.plot.scatter(
+ mdtplt.scatter(
ax=axis,
x=trenew[mask],
y=msd_tot[mask],
@@ -379,9 +388,10 @@
logy=True,
xlabel=r'$\tau_{renew}$ / ' + args.TUNIT,
ylabel=r'$\Delta r^2(\tau_{renew})$ / ' + args.LUNIT + r'$^2$',
- marker='x')
+ marker='x',
+ )
else:
- img = mdt.plot.scatter(
+ img = mdtplt.scatter(
ax=axis,
x=trenew[mask],
y=msd_tot[mask],
@@ -395,7 +405,8 @@
xlabel=r'$\tau_{renew}$ / ' + args.TUNIT,
ylabel=r'$\Delta r^2(\tau_{renew})$ / ' + args.LUNIT + r'$^2$',
marker='x',
- cmap='plasma')
+ cmap='plasma',
+ )
cbar = plt.colorbar(img, ax=axis)
cbar.set_label(label=r'${}(t_0)$ / {}'.format(args.DCOLOR, args.LUNIT),
fontsize=fontsize_labels)
@@ -409,18 +420,20 @@
direction='out',
length=0.5 * tick_length,
labelsize=0.8 * fontsize_ticks)
- mdt.plot.vlines(ax=axis,
- x=tbins,
- start=axis.get_ylim()[0],
- stop=axis.get_ylim()[1],
- xmin=args.XMIN,
- xmax=args.XMAX,
- ymin=args.YMIN,
- ymax=args.YMAX,
- color='black',
- linestyle='dotted')
+ mdtplt.vlines(
+ ax=axis,
+ x=tbins,
+ start=axis.get_ylim()[0],
+ stop=axis.get_ylim()[1],
+ xmin=args.XMIN,
+ xmax=args.XMAX,
+ ymin=args.YMIN,
+ ymax=args.YMAX,
+ color='black',
+ linestyle='dotted',
+ )
mask = ~(msd_tot_mean[1:] < 0)
- mdt.plot.errorbar(
+ mdtplt.errorbar(
ax=axis,
x=t[mask],
y=msd_tot_mean[1:][mask],
@@ -435,10 +448,11 @@
ylabel=r'$\Delta r^2(\tau_{renew})$ / ' + args.LUNIT + r'$^2$',
label=r'$\langle \Delta r^2 \rangle$',
color='red',
- marker='o')
+ marker='o',
+ )
fit = mdt.dyn.msd(t=trenew, D=popt_msd[-1], d=3)
mask = (fit > 0)
- mdt.plot.plot(
+ mdtplt.plot(
ax=axis,
x=trenew[mask],
y=fit[mask],
@@ -451,7 +465,8 @@
xlabel=r'$\tau_{renew}$ / ' + args.TUNIT,
ylabel=r'$\Delta r^2(\tau_{renew})$ / ' + args.LUNIT + r'$^2$',
label="Fit",
- color='black')
+ color='black',
+ )
plt.tight_layout()
pdf.savefig()
plt.close()
@@ -465,7 +480,7 @@
displ0[i] = np.count_nonzero(data == 0)
mask = (data > 0)
if args.DCOLOR is None:
- mdt.plot.scatter(
+ mdtplt.scatter(
ax=axis,
x=trenew[mask],
y=data[mask],
@@ -477,9 +492,10 @@
logy=True,
xlabel=r'$\tau_{renew}$ / ' + args.TUNIT,
ylabel=r'$\Delta ' + ylabel[i] + r'^2(\tau_{renew})$ / ' + args.LUNIT + r'$^2$',
- marker='x')
+ marker='x',
+ )
else:
- img = mdt.plot.scatter(
+ img = mdtplt.scatter(
ax=axis,
x=trenew[mask],
y=data[mask],
@@ -493,7 +509,8 @@
xlabel=r'$\tau_{renew}$ / ' + args.TUNIT,
ylabel=r'$\Delta ' + ylabel[i] + r'^2(\tau_{renew})$ / ' + args.LUNIT + r'$^2$',
marker='x',
- cmap='plasma')
+ cmap='plasma',
+ )
cbar = plt.colorbar(img, ax=axis)
cbar.set_label(label=r'${}(t_0)$ / {}'.format(args.DCOLOR, args.LUNIT),
fontsize=fontsize_labels)
@@ -507,18 +524,20 @@
direction='out',
length=0.5 * tick_length,
labelsize=0.8 * fontsize_ticks)
- mdt.plot.vlines(ax=axis,
- x=tbins,
- start=axis.get_ylim()[0],
- stop=axis.get_ylim()[1],
- xmin=args.XMIN,
- xmax=args.XMAX,
- ymin=args.YMIN,
- ymax=args.YMAX,
- color='black',
- linestyle='dotted')
+ mdtplt.vlines(
+ ax=axis,
+ x=tbins,
+ start=axis.get_ylim()[0],
+ stop=axis.get_ylim()[1],
+ xmin=args.XMIN,
+ xmax=args.XMAX,
+ ymin=args.YMIN,
+ ymax=args.YMAX,
+ color='black',
+ linestyle='dotted',
+ )
mask = ~(msd_mean.T[i][1:] < 0)
- mdt.plot.errorbar(
+ mdtplt.errorbar(
ax=axis,
x=t[mask],
y=msd_mean.T[i][1:][mask],
@@ -533,10 +552,11 @@
ylabel=r'$\Delta ' + ylabel[i] + r'^2(\tau_{renew})$ / ' + args.LUNIT + r'$^2$',
label=r'$\langle \Delta ' + ylabel[i] + r'^2 \rangle$',
color='red',
- marker='o')
+ marker='o',
+ )
fit = mdt.dyn.msd(t=trenew, D=popt_msd[i], d=1)
mask = (fit > 0)
- mdt.plot.plot(
+ mdtplt.plot(
ax=axis,
x=trenew[mask],
y=fit[mask],
@@ -549,7 +569,8 @@
xlabel=r'$\tau_{renew}$ / ' + args.TUNIT,
ylabel=r'$\Delta ' + ylabel[i] + r'^2(\tau_{renew})$ / ' + args.LUNIT + r'$^2$',
label="Fit",
- color='black')
+ color='black',
+ )
plt.tight_layout()
pdf.savefig()
plt.close()
@@ -724,7 +745,7 @@
tight_layout=True)
axis.axhline(y=0, color='black')
- mdt.plot.plot(
+ mdtplt.plot(
ax=axis,
x=t,
y=msd_tot_non_gaus[1:],
@@ -735,23 +756,26 @@
xlabel=r'$\tau_{renew}$ / ' + args.TUNIT,
ylabel=r'$A(\tau_{renew})$',
label=r'$\Delta r^2$',
- marker='o')
-
- mdt.plot.vlines(ax=axis,
- x=tbins,
- start=axis.get_ylim()[0],
- stop=axis.get_ylim()[1],
- xmin=args.XMIN,
- xmax=args.XMAX,
- ymin=args.YMIN,
- ymax=args.YMAX,
- color='black',
- linestyle='dotted')
+ marker='o',
+ )
+
+ mdtplt.vlines(
+ ax=axis,
+ x=tbins,
+ start=axis.get_ylim()[0],
+ stop=axis.get_ylim()[1],
+ xmin=args.XMIN,
+ xmax=args.XMAX,
+ ymin=args.YMIN,
+ ymax=args.YMAX,
+ color='black',
+ linestyle='dotted',
+ )
label = (r'$\Delta x^2$', r'$\Delta y^2$', r'$\Delta z^2$')
marker = ('^', 's', 'D')
for i, data in enumerate(msd_non_gaus.T):
- mdt.plot.plot(
+ mdtplt.plot(
ax=axis,
x=t,
y=data[1:],
@@ -762,7 +786,8 @@
xlabel=r'$\tau_{renew}$ / ' + args.TUNIT,
ylabel=r'$A(\tau_{renew})$',
label=label[i],
- marker=marker[i])
+ marker=marker[i],
+ )
plt.tight_layout()
pdf.savefig()
diff --git a/scripts/dynamics/plot_renewal_events_msda_vs_msdb.py b/scripts/dynamics/plot_renewal_events_msda_vs_msdb.py
index 642fbfac..f1cdfe16 100644
--- a/scripts/dynamics/plot_renewal_events_msda_vs_msdb.py
+++ b/scripts/dynamics/plot_renewal_events_msda_vs_msdb.py
@@ -1,8 +1,8 @@
#!/usr/bin/env python3
-
# This file is part of MDTools.
-# Copyright (C) 2020 Andreas Thum
+# Copyright (C) 2021 The MDTools Development Team and all contributors
+# listed in the file AUTHORS.rst
#
# MDTools is free software: you can redistribute it and/or modify it
# under the terms of the GNU General Public License as published by the
@@ -18,6 +18,9 @@
# along with MDTools. If not, see .
+__author__ = "Andreas Thum"
+
+
import sys
import os
from datetime import datetime
@@ -28,6 +31,8 @@
import matplotlib.pyplot as plt
from matplotlib.backends.backend_pdf import PdfPages
import mdtools as mdt
+import mdtools.plot as mdtplt # TODO: Replace deprecated functions
+plt.style.use("default") # TODO: Use MDTools plotting style
if __name__ == '__main__':
@@ -281,7 +286,7 @@
tight_layout=True)
mask = (msd1 > 0) & (msd2 > 0)
- img = mdt.plot.scatter(
+ img = mdtplt.scatter(
ax=axis,
x=msd1[mask],
y=msd2[mask],
@@ -295,7 +300,8 @@
xlabel=r'$\Delta ' + args.DIRECTION1 + r'^2(\tau_{renew})$ / ' + args.LUNIT + r'$^2$',
ylabel=r'$\Delta ' + args.DIRECTION2 + r'^2(\tau_{renew})$ / ' + args.LUNIT + r'$^2$',
marker='x',
- cmap='plasma')
+ cmap='plasma',
+ )
cbar = plt.colorbar(img, ax=axis)
cbar.set_label(label=r'$\tau_{renew}$ / ' + args.TUNIT,
fontsize=fontsize_labels)
@@ -311,7 +317,7 @@
labelsize=0.8 * fontsize_ticks)
diagonal = np.linspace(*axis.get_xlim())
- mdt.plot.plot(
+ mdtplt.plot(
ax=axis,
x=diagonal,
y=diagonal,
@@ -324,7 +330,8 @@
xlabel=r'$\Delta ' + args.DIRECTION1 + r'^2(\tau_{renew})$ / ' + args.LUNIT + r'$^2$',
ylabel=r'$\Delta ' + args.DIRECTION2 + r'^2(\tau_{renew})$ / ' + args.LUNIT + r'$^2$',
color='black',
- linestyle='--')
+ linestyle='--',
+ )
axis.axvline(x=np.mean(msd1),
color='blue',
diff --git a/scripts/dynamics/plot_renewal_events_nevents_vs_post0.py b/scripts/dynamics/plot_renewal_events_nevents_vs_post0.py
index 8bc4e0af..6936647c 100644
--- a/scripts/dynamics/plot_renewal_events_nevents_vs_post0.py
+++ b/scripts/dynamics/plot_renewal_events_nevents_vs_post0.py
@@ -1,8 +1,8 @@
#!/usr/bin/env python3
-
# This file is part of MDTools.
-# Copyright (C) 2020 Andreas Thum
+# Copyright (C) 2021 The MDTools Development Team and all contributors
+# listed in the file AUTHORS.rst
#
# MDTools is free software: you can redistribute it and/or modify it
# under the terms of the GNU General Public License as published by the
@@ -18,6 +18,9 @@
# along with MDTools. If not, see .
+__author__ = "Andreas Thum"
+
+
import sys
import os
from datetime import datetime
@@ -27,6 +30,8 @@
import matplotlib.pyplot as plt
from matplotlib.backends.backend_pdf import PdfPages
import mdtools as mdt
+import mdtools.plot as mdtplt # TODO: Replace deprecated functions
+plt.style.use("default") # TODO: Use MDTools plotting style
if __name__ == '__main__':
@@ -324,7 +329,7 @@
gridspec_kw={'height_ratios': [1 / 5, 1]})
axis = axes[1]
- mdt.plot.errorbar(
+ mdtplt.errorbar(
ax=axis,
x=bins[1:] - np.diff(bins) / 2,
y=nevents[1:],
@@ -337,28 +342,33 @@
xlabel=r'${}(t_0)$ / {}'.format(args.DIRECTION, args.LUNIT),
ylabel=r'$N_{renew}$',
color='black',
- marker='o')
-
- mdt.plot.vlines(ax=axis,
- x=bins,
- start=axis.get_ylim()[0],
- stop=axis.get_ylim()[1],
- xmin=args.XMIN,
- xmax=args.XMAX,
- ymin=ymin[i],
- ymax=args.YMAX,
- color='black',
- linestyle='dotted')
+ marker='o',
+ )
+
+ mdtplt.vlines(
+ ax=axis,
+ x=bins,
+ start=axis.get_ylim()[0],
+ stop=axis.get_ylim()[1],
+ xmin=args.XMIN,
+ xmax=args.XMAX,
+ ymin=ymin[i],
+ ymax=args.YMAX,
+ color='black',
+ linestyle='dotted',
+ )
if args.INFILE2 is not None:
- mdt.plot.plot(ax=axes[0],
- x=xdata,
- y=ydata,
- xmin=args.XMIN,
- xmax=args.XMAX,
- ymin=np.min(ydata),
- ymax=np.max(ydata),
- color='black')
+ mdtplt.plot(
+ ax=axes[0],
+ x=xdata,
+ y=ydata,
+ xmin=args.XMIN,
+ xmax=args.XMAX,
+ ymin=np.min(ydata),
+ ymax=np.max(ydata),
+ color='black',
+ )
axes[0].xaxis.set_visible(False)
axes[0].yaxis.set_visible(False)
axes[0].spines['bottom'].set_visible(False)
@@ -381,7 +391,7 @@
constrained_layout=True,
gridspec_kw={'height_ratios': [1 / 5, 1]})
- mdt.plot.plot(
+ mdtplt.plot(
ax=axes[1],
x=bins[1:] - np.diff(bins) / 2,
y=n_compounds_per_bin[1:],
@@ -393,27 +403,32 @@
xlabel=r'${}(t_0)$ / {}'.format(args.DIRECTION, args.LUNIT),
ylabel=r'$\langle N_{' + args.NAME + r'} \rangle$',
color='black',
- marker='o')
-
- mdt.plot.vlines(ax=axes[1],
- x=bins,
- start=axes[1].get_ylim()[0],
- stop=axes[1].get_ylim()[1],
- xmin=args.XMIN,
- xmax=args.XMAX,
- ymin=ymin[i],
- ymax=args.YMAX,
- color='black',
- linestyle='dotted')
-
- mdt.plot.plot(ax=axes[0],
- x=xdata,
- y=ydata,
- xmin=args.XMIN,
- xmax=args.XMAX,
- ymin=np.min(ydata),
- ymax=np.max(ydata),
- color='black')
+ marker='o',
+ )
+
+ mdtplt.vlines(
+ ax=axes[1],
+ x=bins,
+ start=axes[1].get_ylim()[0],
+ stop=axes[1].get_ylim()[1],
+ xmin=args.XMIN,
+ xmax=args.XMAX,
+ ymin=ymin[i],
+ ymax=args.YMAX,
+ color='black',
+ linestyle='dotted',
+ )
+
+ mdtplt.plot(
+ ax=axes[0],
+ x=xdata,
+ y=ydata,
+ xmin=args.XMIN,
+ xmax=args.XMAX,
+ ymin=np.min(ydata),
+ ymax=np.max(ydata),
+ color='black',
+ )
axes[0].xaxis.set_visible(False)
axes[0].yaxis.set_visible(False)
axes[0].spines['bottom'].set_visible(False)
@@ -433,7 +448,7 @@
constrained_layout=True,
gridspec_kw={'height_ratios': [1 / 5, 1]})
- mdt.plot.errorbar(
+ mdtplt.errorbar(
ax=axes[1],
x=bins[1:] - np.diff(bins) / 2,
y=nevents[1:] / n_compounds_per_bin[1:],
@@ -446,27 +461,32 @@
xlabel=r'${}(t_0)$ / {}'.format(args.DIRECTION, args.LUNIT),
ylabel=r'$N_{renew}$ / $\langle N_{' + args.NAME + r'} \rangle$',
color='black',
- marker='o')
-
- mdt.plot.vlines(ax=axes[1],
- x=bins,
- start=axes[1].get_ylim()[0],
- stop=axes[1].get_ylim()[1],
- xmin=args.XMIN,
- xmax=args.XMAX,
- ymin=ymin[i],
- ymax=args.YMAX,
- color='black',
- linestyle='dotted')
-
- mdt.plot.plot(ax=axes[0],
- x=xdata,
- y=ydata,
- xmin=args.XMIN,
- xmax=args.XMAX,
- ymin=np.min(ydata),
- ymax=np.max(ydata),
- color='black')
+ marker='o',
+ )
+
+ mdtplt.vlines(
+ ax=axes[1],
+ x=bins,
+ start=axes[1].get_ylim()[0],
+ stop=axes[1].get_ylim()[1],
+ xmin=args.XMIN,
+ xmax=args.XMAX,
+ ymin=ymin[i],
+ ymax=args.YMAX,
+ color='black',
+ linestyle='dotted',
+ )
+
+ mdtplt.plot(
+ ax=axes[0],
+ x=xdata,
+ y=ydata,
+ xmin=args.XMIN,
+ xmax=args.XMAX,
+ ymin=np.min(ydata),
+ ymax=np.max(ydata),
+ color='black',
+ )
axes[0].xaxis.set_visible(False)
axes[0].yaxis.set_visible(False)
axes[0].spines['bottom'].set_visible(False)
diff --git a/scripts/dynamics/plot_renewal_events_post0_vs_postrenew.py b/scripts/dynamics/plot_renewal_events_post0_vs_postrenew.py
index a3030427..3d491d85 100644
--- a/scripts/dynamics/plot_renewal_events_post0_vs_postrenew.py
+++ b/scripts/dynamics/plot_renewal_events_post0_vs_postrenew.py
@@ -1,8 +1,8 @@
#!/usr/bin/env python3
-
# This file is part of MDTools.
-# Copyright (C) 2020 Andreas Thum
+# Copyright (C) 2021 The MDTools Development Team and all contributors
+# listed in the file AUTHORS.rst
#
# MDTools is free software: you can redistribute it and/or modify it
# under the terms of the GNU General Public License as published by the
@@ -18,6 +18,9 @@
# along with MDTools. If not, see .
+__author__ = "Andreas Thum"
+
+
import sys
import os
from datetime import datetime
@@ -27,6 +30,8 @@
import matplotlib.pyplot as plt
from matplotlib.backends.backend_pdf import PdfPages
import mdtools as mdt
+import mdtools.plot as mdtplt # TODO: Replace deprecated functions
+plt.style.use("default") # TODO: Use MDTools plotting style
if __name__ == '__main__':
@@ -317,7 +322,7 @@
gridspec_kw={'height_ratios': [1 / 5, 1]})
axis = axes[1]
- img = mdt.plot.scatter(
+ img = mdtplt.scatter(
ax=axis,
x=pos_t0_new_event,
y=pos_tend_preceding_event,
@@ -329,7 +334,8 @@
xlabel=r'$' + args.DIRECTION + r'(t_0 + \tau_{renew})$ / ' + args.LUNIT,
ylabel=r'$' + args.DIRECTION + r'(t_0^\prime)$ / ' + args.LUNIT,
marker='x',
- cmap='plasma')
+ cmap='plasma',
+ )
cbar = plt.colorbar(img, ax=axis)
cbar.set_label(label=r'$\tau_{renew}$ / ' + args.TUNIT,
fontsize=fontsize_labels)
@@ -345,29 +351,33 @@
labelsize=0.8 * fontsize_ticks)
if i > 0:
- mdt.plot.vlines(ax=axis,
- x=bins,
- start=axis.get_ylim()[0],
- stop=axis.get_ylim()[1],
- xmin=args.XMIN,
- xmax=args.XMAX,
- ymin=args.YMIN,
- ymax=args.YMAX,
- color='black',
- linestyle='dotted')
+ mdtplt.vlines(
+ ax=axis,
+ x=bins,
+ start=axis.get_ylim()[0],
+ stop=axis.get_ylim()[1],
+ xmin=args.XMIN,
+ xmax=args.XMAX,
+ ymin=args.YMIN,
+ ymax=args.YMAX,
+ color='black',
+ linestyle='dotted',
+ )
if i > 1:
- mdt.plot.hlines(ax=axis,
- y=bins,
- start=axis.get_xlim()[0],
- stop=axis.get_xlim()[1],
- xmin=args.XMIN,
- xmax=args.XMAX,
- ymin=args.YMIN,
- ymax=args.YMAX,
- color='black',
- linestyle='dotted')
+ mdtplt.hlines(
+ ax=axis,
+ y=bins,
+ start=axis.get_xlim()[0],
+ stop=axis.get_xlim()[1],
+ xmin=args.XMIN,
+ xmax=args.XMAX,
+ ymin=args.YMIN,
+ ymax=args.YMAX,
+ color='black',
+ linestyle='dotted',
+ )
diagonal = np.linspace(*axis.get_xlim())
- mdt.plot.plot(
+ mdtplt.plot(
ax=axis,
x=diagonal,
y=diagonal,
@@ -377,17 +387,20 @@
ymax=args.YMAX,
xlabel=r'$' + args.DIRECTION + r'(t_0 + \tau_{renew})$ / ' + args.LUNIT,
ylabel=r'$' + args.DIRECTION + r'(t_0^\prime)$ / ' + args.LUNIT,
- color='black')
+ color='black',
+ )
if args.INFILE2 is not None:
- mdt.plot.plot(ax=axes[0],
- x=data[:, 0],
- y=data[:, 1],
- xmin=args.XMIN,
- xmax=args.XMAX,
- ymin=np.min(data[:, 1]),
- ymax=np.max(data[:, 1]),
- color='black')
+ mdtplt.plot(
+ ax=axes[0],
+ x=data[:, 0],
+ y=data[:, 1],
+ xmin=args.XMIN,
+ xmax=args.XMAX,
+ ymin=np.min(data[:, 1]),
+ ymax=np.max(data[:, 1]),
+ color='black',
+ )
axes[0].xaxis.set_visible(False)
axes[0].yaxis.set_visible(False)
axes[0].spines['bottom'].set_visible(False)
diff --git a/scripts/dynamics/plot_renewal_events_postrenew_vs_post0.py b/scripts/dynamics/plot_renewal_events_postrenew_vs_post0.py
index af86343a..30cdfa9f 100644
--- a/scripts/dynamics/plot_renewal_events_postrenew_vs_post0.py
+++ b/scripts/dynamics/plot_renewal_events_postrenew_vs_post0.py
@@ -1,8 +1,8 @@
#!/usr/bin/env python3
-
# This file is part of MDTools.
-# Copyright (C) 2020 Andreas Thum
+# Copyright (C) 2021 The MDTools Development Team and all contributors
+# listed in the file AUTHORS.rst
#
# MDTools is free software: you can redistribute it and/or modify it
# under the terms of the GNU General Public License as published by the
@@ -18,6 +18,9 @@
# along with MDTools. If not, see .
+__author__ = "Andreas Thum"
+
+
import sys
import os
from datetime import datetime
@@ -27,6 +30,8 @@
import matplotlib.pyplot as plt
from matplotlib.backends.backend_pdf import PdfPages
import mdtools as mdt
+import mdtools.plot as mdtplt # TODO: Replace deprecated functions
+plt.style.use("default") # TODO: Use MDTools plotting style
if __name__ == '__main__':
@@ -311,7 +316,7 @@
gridspec_kw={'height_ratios': [1 / 5, 1]})
axis = axes[1]
- img = mdt.plot.scatter(
+ img = mdtplt.scatter(
ax=axis,
x=pos_t0,
y=pos_trenew,
@@ -323,7 +328,8 @@
xlabel=r'${}(t_0)$ / {}'.format(args.DIRECTION, args.LUNIT),
ylabel=r'$' + args.DIRECTION + r'(t_0 + \tau_{renew})$ / ' + args.LUNIT,
marker='x',
- cmap='plasma')
+ cmap='plasma',
+ )
cbar = plt.colorbar(img, ax=axis)
cbar.set_label(label=r'$\tau_{renew}$ / ' + args.TUNIT,
fontsize=fontsize_labels)
@@ -338,29 +344,33 @@
length=0.5 * tick_length,
labelsize=0.8 * fontsize_ticks)
- mdt.plot.vlines(ax=axis,
- x=bins,
- start=axis.get_ylim()[0],
- stop=axis.get_ylim()[1],
- xmin=args.XMIN,
- xmax=args.XMAX,
- ymin=args.YMIN,
- ymax=args.YMAX,
- color='black',
- linestyle='dotted')
+ mdtplt.vlines(
+ ax=axis,
+ x=bins,
+ start=axis.get_ylim()[0],
+ stop=axis.get_ylim()[1],
+ xmin=args.XMIN,
+ xmax=args.XMAX,
+ ymin=args.YMIN,
+ ymax=args.YMAX,
+ color='black',
+ linestyle='dotted',
+ )
if i == 1:
- mdt.plot.hlines(ax=axis,
- y=bins,
- start=axis.get_xlim()[0],
- stop=axis.get_xlim()[1],
- xmin=args.XMIN,
- xmax=args.XMAX,
- ymin=args.YMIN,
- ymax=args.YMAX,
- color='black',
- linestyle='dotted')
+ mdtplt.hlines(
+ ax=axis,
+ y=bins,
+ start=axis.get_xlim()[0],
+ stop=axis.get_xlim()[1],
+ xmin=args.XMIN,
+ xmax=args.XMAX,
+ ymin=args.YMIN,
+ ymax=args.YMAX,
+ color='black',
+ linestyle='dotted',
+ )
diagonal = np.linspace(*axis.get_xlim())
- mdt.plot.plot(
+ mdtplt.plot(
ax=axis,
x=diagonal,
y=diagonal,
@@ -370,9 +380,10 @@
ymax=args.YMAX,
xlabel=r'${}(t_0)$ / {}'.format(args.DIRECTION, args.LUNIT),
ylabel=r'$' + args.DIRECTION + r'(t_0 + \tau_{renew})$ / ' + args.LUNIT,
- color='black')
+ color='black',
+ )
- mdt.plot.errorbar(
+ mdtplt.errorbar(
ax=axis,
x=bins[1:] - np.diff(bins) / 2,
y=pos_trenew_mean[1:],
@@ -384,17 +395,20 @@
xlabel=r'${}(t_0)$ / {}'.format(args.DIRECTION, args.LUNIT),
ylabel=r'$' + args.DIRECTION + r'(t_0 + \tau_{renew})$ / ' + args.LUNIT,
color='red',
- marker='o')
+ marker='o',
+ )
if args.INFILE2 is not None:
- mdt.plot.plot(ax=axes[0],
- x=data[:, 0],
- y=data[:, 1],
- xmin=args.XMIN,
- xmax=args.XMAX,
- ymin=np.min(data[:, 1]),
- ymax=np.max(data[:, 1]),
- color='black')
+ mdtplt.plot(
+ ax=axes[0],
+ x=data[:, 0],
+ y=data[:, 1],
+ xmin=args.XMIN,
+ xmax=args.XMAX,
+ ymin=np.min(data[:, 1]),
+ ymax=np.max(data[:, 1]),
+ color='black',
+ )
axes[0].xaxis.set_visible(False)
axes[0].yaxis.set_visible(False)
axes[0].spines['bottom'].set_visible(False)
diff --git a/scripts/dynamics/plot_renewal_events_ref_dist.py b/scripts/dynamics/plot_renewal_events_ref_dist.py
index 74bba6fc..b7feb9a9 100644
--- a/scripts/dynamics/plot_renewal_events_ref_dist.py
+++ b/scripts/dynamics/plot_renewal_events_ref_dist.py
@@ -1,8 +1,8 @@
#!/usr/bin/env python3
-
# This file is part of MDTools.
-# Copyright (C) 2020 Andreas Thum
+# Copyright (C) 2021 The MDTools Development Team and all contributors
+# listed in the file AUTHORS.rst
#
# MDTools is free software: you can redistribute it and/or modify it
# under the terms of the GNU General Public License as published by the
@@ -18,6 +18,9 @@
# along with MDTools. If not, see .
+__author__ = "Andreas Thum"
+
+
import sys
import os
from datetime import datetime
@@ -26,6 +29,8 @@
import numpy as np
import matplotlib.pyplot as plt
import mdtools as mdt
+import mdtools.plot as mdtplt # TODO: Replace deprecated functions
+plt.style.use("default") # TODO: Use MDTools plotting style
if __name__ == '__main__':
@@ -268,7 +273,7 @@
gridspec_kw={'height_ratios': [1 / 5, 1]})
axis = axes[1]
- mdt.plot.plot(
+ mdtplt.plot(
ax=axis,
x=bins[1:] - np.diff(bins) / 2,
y=distribution[1:],
@@ -279,28 +284,33 @@
xlabel=r'${}(t_0)$ / {}'.format(args.DIRECTION, args.LUNIT),
ylabel=r'$p$',
color='black',
- marker='o')
+ marker='o',
+ )
- mdt.plot.vlines(ax=axis,
- x=bins,
- start=axis.get_ylim()[0],
- stop=axis.get_ylim()[1],
- xmin=args.XMIN,
- xmax=args.XMAX,
- ymin=args.YMIN,
- ymax=args.YMAX,
- color='black',
- linestyle='dotted')
+ mdtplt.vlines(
+ ax=axis,
+ x=bins,
+ start=axis.get_ylim()[0],
+ stop=axis.get_ylim()[1],
+ xmin=args.XMIN,
+ xmax=args.XMAX,
+ ymin=args.YMIN,
+ ymax=args.YMAX,
+ color='black',
+ linestyle='dotted',
+ )
if args.INFILE2 is not None:
- mdt.plot.plot(ax=axes[0],
- x=xdata,
- y=ydata,
- xmin=args.XMIN,
- xmax=args.XMAX,
- ymin=np.min(ydata),
- ymax=np.max(ydata),
- color='black')
+ mdtplt.plot(
+ ax=axes[0],
+ x=xdata,
+ y=ydata,
+ xmin=args.XMIN,
+ xmax=args.XMAX,
+ ymin=np.min(ydata),
+ ymax=np.max(ydata),
+ color='black',
+ )
axes[0].xaxis.set_visible(False)
axes[0].yaxis.set_visible(False)
axes[0].spines['bottom'].set_visible(False)
diff --git a/scripts/dynamics/plot_renewal_events_t0_vs_trenew.py b/scripts/dynamics/plot_renewal_events_t0_vs_trenew.py
index 4089a818..6e2554de 100644
--- a/scripts/dynamics/plot_renewal_events_t0_vs_trenew.py
+++ b/scripts/dynamics/plot_renewal_events_t0_vs_trenew.py
@@ -1,8 +1,8 @@
#!/usr/bin/env python3
-
# This file is part of MDTools.
-# Copyright (C) 2020 Andreas Thum
+# Copyright (C) 2021 The MDTools Development Team and all contributors
+# listed in the file AUTHORS.rst
#
# MDTools is free software: you can redistribute it and/or modify it
# under the terms of the GNU General Public License as published by the
@@ -18,6 +18,9 @@
# along with MDTools. If not, see .
+__author__ = "Andreas Thum"
+
+
import sys
import os
from datetime import datetime
@@ -26,6 +29,8 @@
import numpy as np
import matplotlib.pyplot as plt
import mdtools as mdt
+import mdtools.plot as mdtplt # TODO: Replace deprecated functions
+plt.style.use("default") # TODO: Use MDTools plotting style
if __name__ == '__main__':
@@ -170,7 +175,7 @@
clear=True,
tight_layout=True)
- img = mdt.plot.scatter(
+ img = mdtplt.scatter(
ax=axis,
x=t0_new_event,
y=tend_preceding_event,
@@ -180,10 +185,11 @@
ymax=args.YMAX,
xlabel=r'$t_0 + \tau_{renew}$ / ' + args.TUNIT,
ylabel=r'$t_0^\prime$ / ' + args.TUNIT,
- marker='x')
+ marker='x',
+ )
diagonal = np.linspace(*axis.get_xlim())
- mdt.plot.plot(
+ mdtplt.plot(
ax=axis,
x=diagonal,
y=diagonal,
@@ -193,7 +199,8 @@
ymax=args.YMAX,
xlabel=r'$t_0 + \tau_{renew}$ / ' + args.TUNIT,
ylabel=r'$t_0^\prime$ / ' + args.TUNIT,
- color='black')
+ color='black',
+ )
mdt.fh.backup(args.OUTFILE)
plt.tight_layout()
diff --git a/scripts/dynamics/plot_renewal_events_transition_matrix.py b/scripts/dynamics/plot_renewal_events_transition_matrix.py
index 9083ddd9..2ccc182c 100644
--- a/scripts/dynamics/plot_renewal_events_transition_matrix.py
+++ b/scripts/dynamics/plot_renewal_events_transition_matrix.py
@@ -1,8 +1,8 @@
#!/usr/bin/env python3
-
# This file is part of MDTools.
-# Copyright (C) 2020 Andreas Thum
+# Copyright (C) 2021 The MDTools Development Team and all contributors
+# listed in the file AUTHORS.rst
#
# MDTools is free software: you can redistribute it and/or modify it
# under the terms of the GNU General Public License as published by the
@@ -18,6 +18,9 @@
# along with MDTools. If not, see .
+__author__ = "Andreas Thum"
+
+
import sys
import os
from datetime import datetime
@@ -29,6 +32,8 @@
from matplotlib.backends.backend_pdf import PdfPages
from matplotlib.ticker import MaxNLocator
import mdtools as mdt
+import mdtools.plot as mdtplt # TODO: Replace deprecated functions
+plt.style.use("default") # TODO: Use MDTools plotting style
if __name__ == '__main__':
@@ -409,7 +414,7 @@
axis.yaxis.set_major_locator(MaxNLocator(integer=True))
xy = np.append(active_set, active_set[-1] + 1) - 0.5
- mdt.plot.pcolormesh(
+ mdtplt.pcolormesh(
ax=axis,
x=xy,
y=xy,
@@ -421,7 +426,8 @@
xlabel=r'Bin $j$',
ylabel=r'Bin $i$',
cbarlabel=cbarlabel[i],
- cmap=cmap[i])
+ cmap=cmap[i],
+ )
axis.invert_yaxis()
axis.xaxis.set_label_position('top')
@@ -440,16 +446,18 @@
tight_layout=True)
axis.xaxis.set_major_locator(MaxNLocator(integer=True))
axis.yaxis.set_major_locator(MaxNLocator(integer=True))
- mdt.plot.plot(ax=axis,
- x=active_set,
- y=eigvecs,
- xmin=0.5,
- xmax=len(bins) - 0.5,
- ymin=0,
- xlabel=r'Bin $i$',
- ylabel="Stationary distribution",
- color='black',
- marker='o')
+ mdtplt.plot(
+ ax=axis,
+ x=active_set,
+ y=eigvecs,
+ xmin=0.5,
+ xmax=len(bins) - 0.5,
+ ymin=0,
+ xlabel=r'Bin $i$',
+ ylabel="Stationary distribution",
+ color='black',
+ marker='o',
+ )
plt.tight_layout()
pdf.savefig()
plt.close()
@@ -470,7 +478,7 @@
inactive,
np.nan,
axis=1)
- mdt.plot.pcolormesh(
+ mdtplt.pcolormesh(
ax=axis,
x=bins,
y=bins,
@@ -482,7 +490,8 @@
xlabel=r'$' + args.DIRECTION + r'(t_0 + \tau_{renew})$ / ' + args.LUNIT,
ylabel=r'${}(t_0)$ / {}'.format(args.DIRECTION, args.LUNIT),
cbarlabel=cbarlabel[i],
- cmap=cmap[i])
+ cmap=cmap[i],
+ )
yticks = np.array(axis.get_yticks())
mask = ((yticks >= axis.get_xlim()[0]) &
@@ -517,7 +526,7 @@
axis = axes[1]
eigvecs = np.insert(eigvecs, inactive, np.nan, axis=0)
- mdt.plot.plot(
+ mdtplt.plot(
ax=axis,
x=bins[1:] - np.diff(bins) / 2,
y=eigvecs,
@@ -527,26 +536,31 @@
xlabel=r'${}(t_0)$ / {}'.format(args.DIRECTION, args.LUNIT),
ylabel="Stationary distribution",
color='black',
- marker='o')
- mdt.plot.vlines(ax=axis,
- x=bins,
- start=axis.get_ylim()[0],
- stop=axis.get_ylim()[1],
- xmin=args.MIN,
- xmax=args.MAX,
- ymin=0,
- color='black',
- linestyle='dotted')
+ marker='o',
+ )
+ mdtplt.vlines(
+ ax=axis,
+ x=bins,
+ start=axis.get_ylim()[0],
+ stop=axis.get_ylim()[1],
+ xmin=args.MIN,
+ xmax=args.MAX,
+ ymin=0,
+ color='black',
+ linestyle='dotted',
+ )
if args.INFILE2 is not None:
- mdt.plot.plot(ax=axes[0],
- x=xdata,
- y=ydata,
- xmin=args.MIN,
- xmax=args.MAX,
- ymin=np.min(ydata),
- ymax=np.max(ydata),
- color='black')
+ mdtplt.plot(
+ ax=axes[0],
+ x=xdata,
+ y=ydata,
+ xmin=args.MIN,
+ xmax=args.MAX,
+ ymin=np.min(ydata),
+ ymax=np.max(ydata),
+ color='black',
+ )
axes[0].xaxis.set_visible(False)
axes[0].yaxis.set_visible(False)
axes[0].spines['bottom'].set_visible(False)
@@ -580,7 +594,7 @@
gridspec_kw={'height_ratios': [1 / 5, 1]})
axis = axes[1]
- mdt.plot.errorbar(
+ mdtplt.errorbar(
ax=axis,
x=bins[1:] - np.diff(bins) / 2,
y=nevents,
@@ -592,17 +606,20 @@
xlabel=r'${}(t_0)$ / {}'.format(args.DIRECTION, args.LUNIT),
ylabel=r'$N_{renew}$',
label="Simulation",
- marker='o')
- mdt.plot.vlines(ax=axis,
- x=bins,
- start=axis.get_ylim()[0],
- stop=axis.get_ylim()[1],
- xmin=args.MIN,
- xmax=args.MAX,
- ymin=ymin[i],
- color='black',
- linestyle='dotted')
- mdt.plot.plot(
+ marker='o',
+ )
+ mdtplt.vlines(
+ ax=axis,
+ x=bins,
+ start=axis.get_ylim()[0],
+ stop=axis.get_ylim()[1],
+ xmin=args.MIN,
+ xmax=args.MAX,
+ ymin=ymin[i],
+ color='black',
+ linestyle='dotted',
+ )
+ mdtplt.plot(
ax=axis,
x=bins[1:] - np.diff(bins) / 2,
y=eigvecs * np.sum(nevents),
@@ -613,17 +630,20 @@
xlabel=r'${}(t_0)$ / {}'.format(args.DIRECTION, args.LUNIT),
ylabel=r'$N_{renew}$',
label="Model",
- marker='s')
+ marker='s',
+ )
if args.INFILE2 is not None:
- mdt.plot.plot(ax=axes[0],
- x=xdata,
- y=ydata,
- xmin=args.MIN,
- xmax=args.MAX,
- ymin=np.min(ydata),
- ymax=np.max(ydata),
- color='black')
+ mdtplt.plot(
+ ax=axes[0],
+ x=xdata,
+ y=ydata,
+ xmin=args.MIN,
+ xmax=args.MAX,
+ ymin=np.min(ydata),
+ ymax=np.max(ydata),
+ color='black',
+ )
axes[0].xaxis.set_visible(False)
axes[0].yaxis.set_visible(False)
axes[0].spines['bottom'].set_visible(False)
@@ -647,7 +667,7 @@
clear=True,
constrained_layout=True,
gridspec_kw={'height_ratios': [1 / 5, 1]})
- mdt.plot.errorbar(
+ mdtplt.errorbar(
ax=axes[1],
x=bins[1:] - np.diff(bins) / 2,
y=nevents / n_compounds_per_bin[1:],
@@ -659,17 +679,20 @@
xlabel=r'${}(t_0)$ / {}'.format(args.DIRECTION, args.LUNIT),
ylabel=r'$N_{renew}$ / $\langle N_{' + args.NAME + r'} \rangle$',
label="Simulation",
- marker='o')
- mdt.plot.vlines(ax=axes[1],
- x=bins,
- start=axes[1].get_ylim()[0],
- stop=axes[1].get_ylim()[1],
- xmin=args.MIN,
- xmax=args.MAX,
- ymin=ymin[i],
- color='black',
- linestyle='dotted')
- mdt.plot.plot(
+ marker='o',
+ )
+ mdtplt.vlines(
+ ax=axes[1],
+ x=bins,
+ start=axes[1].get_ylim()[0],
+ stop=axes[1].get_ylim()[1],
+ xmin=args.MIN,
+ xmax=args.MAX,
+ ymin=ymin[i],
+ color='black',
+ linestyle='dotted',
+ )
+ mdtplt.plot(
ax=axes[1],
x=bins[1:] - np.diff(bins) / 2,
y=eigvecs * np.sum(nevents) / n_compounds_per_bin[1:][:, None],
@@ -680,15 +703,18 @@
xlabel=r'${}(t_0)$ / {}'.format(args.DIRECTION, args.LUNIT),
ylabel=r'$N_{renew}$ / $\langle N_{' + args.NAME + r'} \rangle$',
label="Model",
- marker='s')
- mdt.plot.plot(ax=axes[0],
- x=xdata,
- y=ydata,
- xmin=args.MIN,
- xmax=args.MAX,
- ymin=np.min(ydata),
- ymax=np.max(ydata),
- color='black')
+ marker='s',
+ )
+ mdtplt.plot(
+ ax=axes[0],
+ x=xdata,
+ y=ydata,
+ xmin=args.MIN,
+ xmax=args.MAX,
+ ymin=np.min(ydata),
+ ymax=np.max(ydata),
+ color='black',
+ )
axes[0].xaxis.set_visible(False)
axes[0].yaxis.set_visible(False)
axes[0].spines['bottom'].set_visible(False)
diff --git a/scripts/dynamics/plot_renewal_events_trenew_hist.py b/scripts/dynamics/plot_renewal_events_trenew_hist.py
index a8280389..2dac289f 100644
--- a/scripts/dynamics/plot_renewal_events_trenew_hist.py
+++ b/scripts/dynamics/plot_renewal_events_trenew_hist.py
@@ -1,8 +1,8 @@
#!/usr/bin/env python3
-
# This file is part of MDTools.
-# Copyright (C) 2020 Andreas Thum
+# Copyright (C) 2021 The MDTools Development Team and all contributors
+# listed in the file AUTHORS.rst
#
# MDTools is free software: you can redistribute it and/or modify it
# under the terms of the GNU General Public License as published by the
@@ -18,6 +18,9 @@
# along with MDTools. If not, see .
+__author__ = "Andreas Thum"
+
+
import sys
import os
from datetime import datetime
@@ -28,6 +31,8 @@
import matplotlib.pyplot as plt
from matplotlib.backends.backend_pdf import PdfPages
import mdtools as mdt
+import mdtools.plot as mdtplt # TODO: Replace deprecated functions
+plt.style.use("default") # TODO: Use MDTools plotting style
if __name__ == '__main__':
@@ -198,17 +203,19 @@
frameon=False,
clear=True,
tight_layout=True)
- mdt.plot.hist(ax=axis,
- x=trenew,
- xmin=args.XMIN,
- xmax=args.XMAX,
- ymin=args.YMIN,
- ymax=args.YMAX,
- xlabel=r'$\tau_{renew}$ / ' + args.TUNIT,
- ylabel="Counts",
- bins=bins,
- range=(args.START, args.STOP),
- density=False)
+ mdtplt.hist(
+ ax=axis,
+ x=trenew,
+ xmin=args.XMIN,
+ xmax=args.XMAX,
+ ymin=args.YMIN,
+ ymax=args.YMAX,
+ xlabel=r'$\tau_{renew}$ / ' + args.TUNIT,
+ ylabel="Counts",
+ bins=bins,
+ range=(args.START, args.STOP),
+ density=False,
+ )
plt.tight_layout()
pdf.savefig()
plt.close()
@@ -218,28 +225,32 @@
frameon=False,
clear=True,
tight_layout=True)
- mdt.plot.hist(ax=axis,
- x=trenew,
- xmin=args.XMIN,
- xmax=args.XMAX,
- ymin=args.YMIN,
- ymax=args.YMAX,
- xlabel=r'$\tau_{renew}$ / ' + args.TUNIT,
- ylabel=r'$p(\tau_{renew})$',
- bins=bins,
- range=(args.START, args.STOP),
- density=True)
- mdt.plot.plot(ax=axis,
- x=x,
- y=mdt.stats.exp_dist(x=x, rate=popt),
- xmin=args.XMIN,
- xmax=args.XMAX,
- ymin=args.YMIN,
- ymax=args.YMAX,
- xlabel=r'$\tau_{renew}$ / ' + args.TUNIT,
- ylabel=r'$p(\tau_{renew})$',
- label="Fit",
- color='black')
+ mdtplt.hist(
+ ax=axis,
+ x=trenew,
+ xmin=args.XMIN,
+ xmax=args.XMAX,
+ ymin=args.YMIN,
+ ymax=args.YMAX,
+ xlabel=r'$\tau_{renew}$ / ' + args.TUNIT,
+ ylabel=r'$p(\tau_{renew})$',
+ bins=bins,
+ range=(args.START, args.STOP),
+ density=True,
+ )
+ mdtplt.plot(
+ ax=axis,
+ x=x,
+ y=mdt.stats.exp_dist(x=x, rate=popt),
+ xmin=args.XMIN,
+ xmax=args.XMAX,
+ ymin=args.YMIN,
+ ymax=args.YMAX,
+ xlabel=r'$\tau_{renew}$ / ' + args.TUNIT,
+ ylabel=r'$p(\tau_{renew})$',
+ label="Fit",
+ color='black',
+ )
plt.tight_layout()
pdf.savefig()
plt.close()
diff --git a/scripts/dynamics/plot_renewal_events_trenew_vs_post0.py b/scripts/dynamics/plot_renewal_events_trenew_vs_post0.py
index 654e9f14..12b39507 100644
--- a/scripts/dynamics/plot_renewal_events_trenew_vs_post0.py
+++ b/scripts/dynamics/plot_renewal_events_trenew_vs_post0.py
@@ -1,8 +1,8 @@
#!/usr/bin/env python3
-
# This file is part of MDTools.
-# Copyright (C) 2020 Andreas Thum
+# Copyright (C) 2021 The MDTools Development Team and all contributors
+# listed in the file AUTHORS.rst
#
# MDTools is free software: you can redistribute it and/or modify it
# under the terms of the GNU General Public License as published by the
@@ -18,6 +18,9 @@
# along with MDTools. If not, see .
+__author__ = "Andreas Thum"
+
+
import sys
import os
from datetime import datetime
@@ -27,6 +30,8 @@
import matplotlib.pyplot as plt
import matplotlib.colors as colors
import mdtools as mdt
+import mdtools.plot as mdtplt # TODO: Replace deprecated functions
+plt.style.use("default") # TODO: Use MDTools plotting style
if __name__ == '__main__':
@@ -306,7 +311,7 @@
gridspec_kw={'height_ratios': [1 / 5, 1]})
axis = axes[1]
- img = mdt.plot.scatter(
+ img = mdtplt.scatter(
ax=axis,
x=pos_t0,
y=trenew,
@@ -319,9 +324,12 @@
ylabel=r'$\tau_{renew}$ / ' + args.TUNIT,
marker='x',
cmap='coolwarm',
- norm=colors.TwoSlopeNorm(vmin=np.min(displ),
- vcenter=0,
- vmax=np.max(displ)))
+ norm=colors.TwoSlopeNorm(
+ vmin=np.min(displ),
+ vcenter=0,
+ vmax=np.max(displ),
+ ),
+ )
cbar = fig.colorbar(img, ax=axis)
cbar.set_label(label=r'$\Delta ' + args.DIRECTION + r'$ / ' + args.LUNIT,
fontsize=fontsize_labels)
@@ -336,18 +344,20 @@
length=0.5 * tick_length,
labelsize=0.8 * fontsize_ticks)
- mdt.plot.vlines(ax=axis,
- x=bins,
- start=axis.get_ylim()[0],
- stop=axis.get_ylim()[1],
- xmin=args.XMIN,
- xmax=args.XMAX,
- ymin=args.YMIN,
- ymax=args.YMAX,
- color='black',
- linestyle='dotted')
-
- mdt.plot.errorbar(
+ mdtplt.vlines(
+ ax=axis,
+ x=bins,
+ start=axis.get_ylim()[0],
+ stop=axis.get_ylim()[1],
+ xmin=args.XMIN,
+ xmax=args.XMAX,
+ ymin=args.YMIN,
+ ymax=args.YMAX,
+ color='black',
+ linestyle='dotted',
+ )
+
+ mdtplt.errorbar(
ax=axis,
x=bins[1:] - np.diff(bins) / 2,
y=trenew_mean[1:],
@@ -359,17 +369,20 @@
xlabel=r'${}(t_0)$ / {}'.format(args.DIRECTION, args.LUNIT),
ylabel=r'$\tau_{renew}$ / ' + args.TUNIT,
color='black',
- marker='o')
+ marker='o',
+ )
if args.INFILE2 is not None:
- mdt.plot.plot(ax=axes[0],
- x=data[:, 0],
- y=data[:, 1],
- xmin=args.XMIN,
- xmax=args.XMAX,
- ymin=np.min(data[:, 1]),
- ymax=np.max(data[:, 1]),
- color='black')
+ mdtplt.plot(
+ ax=axes[0],
+ x=data[:, 0],
+ y=data[:, 1],
+ xmin=args.XMIN,
+ xmax=args.XMAX,
+ ymin=np.min(data[:, 1]),
+ ymax=np.max(data[:, 1]),
+ color='black',
+ )
axes[0].xaxis.set_visible(False)
axes[0].yaxis.set_visible(False)
axes[0].spines['bottom'].set_visible(False)
diff --git a/scripts/structure/plot_topological_map.py b/scripts/structure/plot_topological_map.py
index 212a302e..447b237a 100644
--- a/scripts/structure/plot_topological_map.py
+++ b/scripts/structure/plot_topological_map.py
@@ -1,8 +1,8 @@
#!/usr/bin/env python3
-
# This file is part of MDTools.
-# Copyright (C) 2020 Andreas Thum
+# Copyright (C) 2021 The MDTools Development Team and all contributors
+# listed in the file AUTHORS.rst
#
# MDTools is free software: you can redistribute it and/or modify it
# under the terms of the GNU General Public License as published by the
@@ -18,6 +18,9 @@
# along with MDTools. If not, see .
+__author__ = "Andreas Thum"
+
+
# This python script is inspired by the work of Florian Müller-Plathe
# and Wilfred F. van Gunsteren which was adapted by Oleg Borodin and
# Grant D. Smith
@@ -39,6 +42,8 @@
from matplotlib.backends.backend_pdf import PdfPages
from matplotlib.ticker import MaxNLocator
import mdtools as mdt
+import mdtools.plot as mdtplt # TODO: Replace deprecated functions
+plt.style.use("default") # TODO: Use MDTools plotting style
# Matplotlib: Nested Gridspecs
@@ -556,7 +561,7 @@
linestyles='--')
for a_ix in ab_ix.T:
- mdt.plot.scatter(
+ mdtplt.scatter(
ax=axis,
x=times[::effective_plotevery],
y=a_ix[::effective_plotevery],
@@ -573,7 +578,8 @@
cmap=cmap,
vmin=vmin,
vmax=vmax,
- norm=norm)
+ norm=norm,
+ )
if rb < len(res_blocks) - 2:
axis.tick_params(labelbottom=False)
axis.set_xlabel('')
@@ -607,14 +613,16 @@
if vmin_ix == vmax_ix:
vmin_ix = 0
vmax_ix = len(data[:, 1])
- mdt.plot.plot(ax=axis,
- x=data[:, 0],
- y=data[:, 1],
- xmin=vmin,
- xmax=vmax,
- ymin=np.min(data[vmin_ix:vmax_ix, 1]),
- ymax=np.max(data[vmin_ix:vmax_ix, 1]),
- color='black')
+ mdtplt.plot(
+ ax=axis,
+ x=data[:, 0],
+ y=data[:, 1],
+ xmin=vmin,
+ xmax=vmax,
+ ymin=np.min(data[vmin_ix:vmax_ix, 1]),
+ ymax=np.max(data[vmin_ix:vmax_ix, 1]),
+ color='black',
+ )
axis.xaxis.set_visible(False)
axis.yaxis.set_visible(False)
axis.spines['bottom'].set_visible(False)