Add figure pdf version

CardiacModelling · Jul 18, 2019 · db838a3 · db838a3
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commit db838a3
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Showing 17 changed files with 23 additions and 15 deletions.
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
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
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
diff --git a/room-temperature-only/figs/paper/rmsd-hist.pdf b/room-temperature-only/figs/paper/rmsd-hist.pdf
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
@@ -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
@@ -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
@@ -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
@@ -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
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
diff --git a/temperature-dependency/figs/paper/fitting-and-validation-herg37oc-zoom.pdf b/temperature-dependency/figs/paper/fitting-and-validation-herg37oc-zoom.pdf
diff --git a/temperature-dependency/figs/paper/fitting-and-validation-recordings-all.pdf b/temperature-dependency/figs/paper/fitting-and-validation-recordings-all.pdf
diff --git a/temperature-dependency/figs/paper/rmsd-hist-herg37oc.pdf b/temperature-dependency/figs/paper/rmsd-hist-herg37oc.pdf
diff --git 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
@@ -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
@@ -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
@@ -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')