diff --git a/room-temperature-only/figs/paper/fitting-and-validation-herg25oc1_D19-zoom.pdf b/room-temperature-only/figs/paper/fitting-and-validation-herg25oc1_D19-zoom.pdf new file mode 100644 index 00000000..787b85be Binary files /dev/null and b/room-temperature-only/figs/paper/fitting-and-validation-herg25oc1_D19-zoom.pdf differ diff --git a/room-temperature-only/figs/paper/fitting-and-validation-recordings-samey.pdf b/room-temperature-only/figs/paper/fitting-and-validation-recordings-samey.pdf new file mode 100644 index 00000000..8c083581 Binary files /dev/null and b/room-temperature-only/figs/paper/fitting-and-validation-recordings-samey.pdf differ diff --git a/room-temperature-only/figs/paper/fitting-and-validation-selected-cells-zoom.pdf b/room-temperature-only/figs/paper/fitting-and-validation-selected-cells-zoom.pdf new file mode 100644 index 00000000..56df239b Binary files /dev/null and b/room-temperature-only/figs/paper/fitting-and-validation-selected-cells-zoom.pdf differ diff --git a/room-temperature-only/figs/paper/rmsd-hist.pdf b/room-temperature-only/figs/paper/rmsd-hist.pdf new file mode 100644 index 00000000..48af3889 Binary files /dev/null and b/room-temperature-only/figs/paper/rmsd-hist.pdf differ diff --git a/room-temperature-only/paper-fitting-and-validation-one-cell-zoom.py b/room-temperature-only/paper-fitting-and-validation-one-cell-zoom.py index a96570a2..abb1da6c 100644 --- a/room-temperature-only/paper-fitting-and-validation-one-cell-zoom.py +++ b/room-temperature-only/paper-fitting-and-validation-one-cell-zoom.py @@ -477,7 +477,7 @@ file_name, cell), bbox_inch='tight', pad_inches=0, dpi=100) plt.savefig('%s/fitting-and-validation-%s_%s-zoom.png' % (savedir, file_name, \ cell), bbox_inch='tight', pad_inches=0, dpi=300) -# plt.savefig('%s/fitting-and-validation-%s_%s-zoom.pdf' % (savedir, \ -# file_name, cell), format='pdf', bbox_inch='tight', pad_inches=0) +plt.savefig('%s/fitting-and-validation-%s_%s-zoom.pdf' % (savedir, file_name, \ + cell), format='pdf', bbox_inch='tight', pad_inches=0) print('Done') diff --git a/room-temperature-only/paper-fitting-and-validation-recordings.py b/room-temperature-only/paper-fitting-and-validation-recordings.py index 286b5c21..025d99c1 100644 --- a/room-temperature-only/paper-fitting-and-validation-recordings.py +++ b/room-temperature-only/paper-fitting-and-validation-recordings.py @@ -423,19 +423,19 @@ if prt not in protocol_iv: axes[ai, aj].plot(times, data / norm, lw=0.2, alpha=0.1, - c=colour_list[i_CELL]) + c=colour_list[i_CELL], rasterized=True) else: iv_i = protocols.get_corrected_iv(data, times, *protocol_iv_args[prt]()) iv_v = protocol_iv_v[prt]() * 1000 # mV axes[ai, aj].plot(iv_v, iv_i / np.max(iv_i), lw=0.5, alpha=0.5, - c=colour_list[i_CELL]) + c=colour_list[i_CELL], rasterized=True) # Plot inset if prt in add_inset.keys(): # not in provtocol_iv axins[ai, aj].plot(times, data / norm, lw=0.2, alpha=0.1, - c=colour_list[i_CELL]) + c=colour_list[i_CELL], rasterized=True) # @@ -447,7 +447,7 @@ bbox_inch='tight', pad_inches=0, dpi=100) plt.savefig('%s/fitting-and-validation-recordings-samey.png' % savedir, bbox_inch='tight', pad_inches=0, dpi=300) -# plt.savefig('%s/fitting-and-validation-recordings.pdf' % savedir, -# format='pdf', bbox_inch='tight', pad_inches=0) +plt.savefig('%s/fitting-and-validation-recordings-samey.pdf' % savedir, + format='pdf', bbox_inch='tight', pad_inches=0, dpi=300) print('Done') diff --git a/room-temperature-only/paper-fitting-and-validation-selected-cells-zoom.py b/room-temperature-only/paper-fitting-and-validation-selected-cells-zoom.py index 941cb08b..389c5056 100644 --- a/room-temperature-only/paper-fitting-and-validation-selected-cells-zoom.py +++ b/room-temperature-only/paper-fitting-and-validation-selected-cells-zoom.py @@ -585,7 +585,7 @@ plt.savefig('%s/fitting-and-validation-selected-cells-zoom.png' % savedir, bbox_inch='tight', pad_inches=0, dpi=300) # This pdf version can get up to 40+MB! -# plt.savefig('%s/fitting-and-validation-selected-cells-zoom.pdf' % savedir, -# format='pdf', bbox_inch='tight', pad_inches=0) +plt.savefig('%s/fitting-and-validation-selected-cells-zoom.pdf' % savedir, + format='pdf', bbox_inch='tight', pad_inches=0) print('Done') diff --git a/room-temperature-only/paper-rmsd-hist.py b/room-temperature-only/paper-rmsd-hist.py index 8c290e7d..46582437 100644 --- a/room-temperature-only/paper-rmsd-hist.py +++ b/room-temperature-only/paper-rmsd-hist.py @@ -365,5 +365,7 @@ grid.update(wspace=0.2, hspace=0.0) plt.savefig('%s/rmsd-hist.png' % (savedir), bbox_inch='tight', pad_inches=0, dpi=300) +plt.savefig('%s/rmsd-hist.pdf' % (savedir), format='pdf', bbox_inch='tight', + pad_inches=0) print('Done') diff --git a/temperature-dependency/figs/paper/fitting-and-validation-eyring-q10-ap2hz-v2.pdf b/temperature-dependency/figs/paper/fitting-and-validation-eyring-q10-ap2hz-v2.pdf new file mode 100644 index 00000000..aad31f5e Binary files /dev/null and b/temperature-dependency/figs/paper/fitting-and-validation-eyring-q10-ap2hz-v2.pdf differ diff --git a/temperature-dependency/figs/paper/fitting-and-validation-eyring-q10-staircaseramp-v2.pdf b/temperature-dependency/figs/paper/fitting-and-validation-eyring-q10-staircaseramp-v2.pdf new file mode 100644 index 00000000..547c1e46 Binary files /dev/null and b/temperature-dependency/figs/paper/fitting-and-validation-eyring-q10-staircaseramp-v2.pdf differ diff --git a/temperature-dependency/figs/paper/fitting-and-validation-herg37oc-zoom.pdf b/temperature-dependency/figs/paper/fitting-and-validation-herg37oc-zoom.pdf new file mode 100644 index 00000000..5cca0a97 Binary files /dev/null and b/temperature-dependency/figs/paper/fitting-and-validation-herg37oc-zoom.pdf differ diff --git a/temperature-dependency/figs/paper/fitting-and-validation-recordings-all.pdf b/temperature-dependency/figs/paper/fitting-and-validation-recordings-all.pdf new file mode 100644 index 00000000..9a906548 Binary files /dev/null and b/temperature-dependency/figs/paper/fitting-and-validation-recordings-all.pdf differ diff --git a/temperature-dependency/figs/paper/rmsd-hist-herg37oc.pdf b/temperature-dependency/figs/paper/rmsd-hist-herg37oc.pdf new file mode 100644 index 00000000..ebe374ea Binary files /dev/null and b/temperature-dependency/figs/paper/rmsd-hist-herg37oc.pdf differ diff --git a/temperature-dependency/paper-fitting-and-validation-eyring-q10-v2.py b/temperature-dependency/paper-fitting-and-validation-eyring-q10-v2.py index 3763a8f7..128cd2d4 100644 --- a/temperature-dependency/paper-fitting-and-validation-eyring-q10-v2.py +++ b/temperature-dependency/paper-fitting-and-validation-eyring-q10-v2.py @@ -681,5 +681,7 @@ def boolean_indexing(v, fillval=np.nan): prt), bbox_inch='tight', pad_inches=0, dpi=300) plt.savefig('%s/fitting-and-validation-eyring-q10-%s-v2.png' % (savedir, prt), bbox_inch='tight', pad_inches=0, dpi=500) +plt.savefig('%s/fitting-and-validation-eyring-q10-%s-v2.pdf' % (savedir, prt), + format='pdf', bbox_inch='tight', pad_inches=0) print('Done') diff --git a/temperature-dependency/paper-fitting-and-validation-recordings-all.py b/temperature-dependency/paper-fitting-and-validation-recordings-all.py index c9e3176e..8440bc39 100644 --- a/temperature-dependency/paper-fitting-and-validation-recordings-all.py +++ b/temperature-dependency/paper-fitting-and-validation-recordings-all.py @@ -375,7 +375,7 @@ if prt not in protocol_iv: axes[ai, aj].plot(times, data / norm_data, lw=0.2, alpha=0.1, - c=colour_list[i_CELL]) + c=colour_list[i_CELL], rasterized=True) else: iv_i = protocols.get_corrected_iv(data, times, *protocol_iv_args[prt]()) @@ -388,7 +388,7 @@ if prt in add_inset.keys(): # not in provtocol_iv axins[ai, aj].plot(times, data / norm_data, lw=0.2, alpha=0.1, - c=colour_list[i_CELL]) + c=colour_list[i_CELL], rasterized=True) # @@ -400,7 +400,7 @@ bbox_inch='tight', pad_inches=0, dpi=100) plt.savefig('%s/fitting-and-validation-recordings-all.png' % savedir, bbox_inch='tight', pad_inches=0, dpi=300) -# plt.savefig('%s/fitting-and-validation-recordings.pdf' % savedir, -# format='pdf', bbox_inch='tight', pad_inches=0) +plt.savefig('%s/fitting-and-validation-recordings-all.pdf' % savedir, + format='pdf', bbox_inch='tight', pad_inches=0, dpi=300) print('Done') diff --git a/temperature-dependency/paper-fitting-and-validation-selected-cells-zoom.py b/temperature-dependency/paper-fitting-and-validation-selected-cells-zoom.py index 455e73bf..80a5cf69 100644 --- a/temperature-dependency/paper-fitting-and-validation-selected-cells-zoom.py +++ b/temperature-dependency/paper-fitting-and-validation-selected-cells-zoom.py @@ -612,7 +612,8 @@ plt.savefig('%s/fitting-and-validation-%s-zoom.png' % (savedir, file_id), bbox_inch='tight', pad_inches=0, dpi=300) # This pdf version can get up to 40+MB! -# plt.savefig('%s/fitting-and-validation-selected-cells-zoom.pdf' % savedir, -# format='pdf', bbox_inch='tight', pad_inches=0) +if '--pdf' in sys.argv: + plt.savefig('%s/fitting-and-validation-%s-zoom.pdf' % (savedir, file_id), + format='pdf', bbox_inch='tight', pad_inches=0) print('Done') diff --git a/temperature-dependency/paper-rmsd-hist.py b/temperature-dependency/paper-rmsd-hist.py index 0e83376b..038d5e91 100644 --- a/temperature-dependency/paper-rmsd-hist.py +++ b/temperature-dependency/paper-rmsd-hist.py @@ -375,5 +375,8 @@ grid.update(wspace=0.2, hspace=0.0) plt.savefig('%s/rmsd-hist-%s.png' % (savedir, file_id), bbox_inch='tight', pad_inches=0, dpi=300) +if '--pdf' in sys.argv: + plt.savefig('%s/rmsd-hist-%s.pdf' % (savedir, file_id), format='pdf', + bbox_inch='tight', pad_inches=0) print('Done')