Scripts to display resting and task BOLD of TVB nodes

Author: Antonio Ulloa

.DS_Store

@@ -36,14 +36,16 @@
 #   This file (plot_neural_tvb.py) was created on September 13, 2015.
 #
 #
-#   Author: Antonio Ulloa. Last updated by Antonio Ulloa on September 13, 2015  
+#   Author: Antonio Ulloa. Last updated by Antonio Ulloa on August 29, 2016  
 # **************************************************************************/
 
 # plot_neural_tvb.py
 #
-# Plot output data files of Hagmann's brain simulation using TVB
+# Plot output data files of Hagmann's brain simulation using TVB and Hybrid TVB/LSNM
+# simulation (side to side)
 
 # what are the locations of relevant TVB nodes within TVB array?
+# the following are the so-called 'host nodes'
 v1_loc = 345
 v4_loc = 393
 it_loc = 413
@@ -75,6 +77,8 @@
 hybrid_tvb_lsnm = np.load('output.36trials.with_feedback/tvb_neuronal.npy')
 
 
+# the following nodes have the strongest connections with host nodes
+# ... as determined by script "display_hagmann_brain_connectivity"
 tvb_v1 = tvb[:, 0, 346, 0]
 tvb_v4 = tvb[:, 0, 391, 0]
 tvb_it = tvb[:, 0, 412, 0]
@@ -114,7 +118,7 @@
 ax.plot(real_time, hybrid_v1, color='k', linewidth=2)
 ax.set_yticks([])
 ax.set_xlim([0, 5])
-ax.set_ylim([0, 1])
+#ax.set_ylim([0, 1])
 #ax.set_title('SIMULATED ELECTRICAL ACTIVITY, HAGMANNS BRAIN')
 plt.ylabel('V1', rotation='horizontal', horizontalalignment='right')
 
@@ -124,7 +128,7 @@
 ax.set_yticks([])
 ax.set_xticks([])
 ax.set_xlim(0, 5)
-ax.set_ylim([0, 1])
+#ax.set_ylim([0, 1])
 plt.ylabel('V4', rotation='horizontal', horizontalalignment='right')
 
 ax = plt.subplot(7,1,5)
@@ -133,7 +137,7 @@
 ax.set_yticks([])
 ax.set_xticks([])
 ax.set_xlim(0, 5)
-ax.set_ylim([0, 1])
+#ax.set_ylim([0, 1])
 plt.ylabel('IT', rotation='horizontal', horizontalalignment='right')
 
 ax = plt.subplot(7,1,4)
@@ -142,7 +146,7 @@
 ax.set_yticks([])
 ax.set_xticks([])
 ax.set_xlim(0, 5)
-ax.set_ylim([0, 1])
+#ax.set_ylim([0, 1])
 plt.ylabel('FS', rotation='horizontal', horizontalalignment='right')
 
 ax = plt.subplot(7,1,3)
@@ -151,7 +155,7 @@
 ax.set_yticks([])
 ax.set_xticks([])
 ax.set_xlim(0, 5)
-ax.set_ylim([0, 1])
+#ax.set_ylim([0, 1])
 plt.ylabel('D1', rotation='horizontal', horizontalalignment='right')
 
 ax = plt.subplot(7,1,2)
@@ -160,7 +164,7 @@
 ax.set_yticks([])
 ax.set_xticks([])
 ax.set_xlim(0, 5)
-ax.set_ylim([0, 1])
+#ax.set_ylim([0, 1])
 plt.ylabel('D2', rotation='horizontal', horizontalalignment='right')
 
 ax = plt.subplot(7,1,1)
@@ -169,7 +173,7 @@
 ax.set_yticks([])
 ax.set_xticks([])
 ax.set_xlim(0, 5)
-ax.set_ylim([0, 1])
+#ax.set_ylim([0, 1])
 plt.ylabel('FR', rotation='horizontal', horizontalalignment='right')
 
 #plt.tight_layout()

analysis/.DS_Store

@@ -38,7 +38,7 @@
 #
 #   Author: Antonio Ulloa
 #
-#   Last updated by Antonio Ulloa on December 6 2015
+#   Last updated by Antonio Ulloa on August 30 2016
 #
 # **************************************************************************/
 
@@ -112,115 +112,65 @@
 
 #plt.suptitle('SYNAPTIC ACTIVITIES')
 
-# plot V1 BOLD time-series in yellow
+# plot V1 syn time-series in yellow
 ax = plt.subplot(7,1,1)
 ax.set_yticks([])
 ax.set_xticks([])
-ax.set_xlim(0,200)
 ax.plot(lsnm_syn[0,1:], linewidth=3.0, color='yellow')
 
-# display gray bands in figure area to show where control blocks are located
-ax.axvspan(17.5, 34.0, facecolor='gray', alpha=0.6)
-ax.axvspan(50.5, 67.0, facecolor='gray', alpha=0.6)
-ax.axvspan(83.5, 100.0, facecolor='gray', alpha=0.6)
-ax.axvspan(116.5, 133.0, facecolor='gray', alpha=0.6)
-ax.axvspan(149.5, 166.0, facecolor='gray', alpha=0.6)
-ax.axvspan(182.5, 199.0, facecolor='gray', alpha=0.6)
 plt.ylabel('V1/V2', rotation='horizontal', horizontalalignment='right')
 plt.gca().set_axis_bgcolor('black')
 
-# plot V4 BOLD time-series in green
+# plot V4 syn time-series in green
 ax = plt.subplot(7,1,2)
 ax.plot(lsnm_syn[1,1:], linewidth=3.0, color='lime')
 ax.set_yticks([])
 ax.set_xticks([])
 
-# display gray bands in figure area to show where control blocks are located
-ax.axvspan(17.5, 34.0, facecolor='gray', alpha=0.6)
-ax.axvspan(50.5, 67.0, facecolor='gray', alpha=0.6)
-ax.axvspan(83.5, 100.0, facecolor='gray', alpha=0.6)
-ax.axvspan(116.5, 133.0, facecolor='gray', alpha=0.6)
-ax.axvspan(149.5, 166.0, facecolor='gray', alpha=0.6)
-ax.axvspan(182.5, 199.0, facecolor='gray', alpha=0.6)
 plt.ylabel('V4', rotation='horizontal', horizontalalignment='right')
 plt.gca().set_axis_bgcolor('black')
 
-# plot IT BOLD time-series in blue
+# plot IT syn time-series in blue
 ax = plt.subplot(7,1,3)
 ax.plot(lsnm_syn[2,1:], linewidth=3.0, color='blue')
 ax.set_yticks([])
 ax.set_xticks([])
 
-# display gray bands in figure area to show where control blocks are located
-ax.axvspan(17.5, 34.0, facecolor='gray', alpha=0.6)
-ax.axvspan(50.5, 67.0, facecolor='gray', alpha=0.6)
-ax.axvspan(83.5, 100.0, facecolor='gray', alpha=0.6)
-ax.axvspan(116.5, 133.0, facecolor='gray', alpha=0.6)
-ax.axvspan(149.5, 166.0, facecolor='gray', alpha=0.6)
-ax.axvspan(182.5, 199.0, facecolor='gray', alpha=0.6)
 plt.ylabel('IT', rotation='horizontal', horizontalalignment='right')
 plt.gca().set_axis_bgcolor('black')
 
-# plot FS BOLD time-series in orange
+# plot FS syn time-series in orange
 ax = plt.subplot(7,1,4)
 ax.plot(lsnm_syn[3,1:], linewidth=3.0, color='orange')
 ax.set_yticks([])
 ax.set_xticks([])
 
-# display gray bands in figure area to show where control blocks are located
-ax.axvspan(17.5, 34.0, facecolor='gray', alpha=0.6)
-ax.axvspan(50.5, 67.0, facecolor='gray', alpha=0.6)
-ax.axvspan(83.5, 100.0, facecolor='gray', alpha=0.6)
-ax.axvspan(116.5, 133.0, facecolor='gray', alpha=0.6)
-ax.axvspan(149.5, 166.0, facecolor='gray', alpha=0.6)
-ax.axvspan(182.5, 199.0, facecolor='gray', alpha=0.6)
 plt.ylabel('FS', rotation='horizontal', horizontalalignment='right')
 plt.gca().set_axis_bgcolor('black')
 
-# plot D1 BOLD time-series in red
+# plot D1 syn time-series in red
 ax = plt.subplot(7,1,5)
 ax.plot(lsnm_syn[4,1:], linewidth=3.0, color='red')
 ax.set_yticks([])
 ax.set_xticks([])
 
-# display gray bands in figure area to show where control blocks are located
-ax.axvspan(17.5, 34.0, facecolor='gray', alpha=0.6)
-ax.axvspan(50.5, 67.0, facecolor='gray', alpha=0.6)
-ax.axvspan(83.5, 100.0, facecolor='gray', alpha=0.6)
-ax.axvspan(116.5, 133.0, facecolor='gray', alpha=0.6)
-ax.axvspan(149.5, 166.0, facecolor='gray', alpha=0.6)
-ax.axvspan(182.5, 199.0, facecolor='gray', alpha=0.6)
 plt.ylabel('D1', rotation='horizontal', horizontalalignment='right')
 plt.gca().set_axis_bgcolor('black')
 
-# plot D2 BOLD time-series in pink
+# plot D2 syn time-series in pink
 ax = plt.subplot(7,1,6)
 ax.plot(lsnm_syn[5,1:], linewidth=3.0, color='pink')
 ax.set_yticks([])
 ax.set_xticks([])
 
-# display gray bands in figure area to show where control blocks are located
-ax.axvspan(17.5, 34.0, facecolor='gray', alpha=0.6)
-ax.axvspan(50.5, 67.0, facecolor='gray', alpha=0.6)
-ax.axvspan(83.5, 100.0, facecolor='gray', alpha=0.6)
-ax.axvspan(116.5, 133.0, facecolor='gray', alpha=0.6)
-ax.axvspan(149.5, 166.0, facecolor='gray', alpha=0.6)
-ax.axvspan(182.5, 199.0, facecolor='gray', alpha=0.6)
 plt.ylabel('D2', rotation='horizontal', horizontalalignment='right')
 plt.gca().set_axis_bgcolor('black')
 
-# plot FR BOLD time-series in purple
+# plot FR syn time-series in purple
 ax = plt.subplot(7,1,7)
 ax.plot(lsnm_syn[6,1:], linewidth=3.0, color='darkorchid')
 ax.set_yticks([])
 
-# display gray bands in figure area to show where control blocks are located
-ax.axvspan(17.5, 34.0, facecolor='gray', alpha=0.6)
-ax.axvspan(50.5, 67.0, facecolor='gray', alpha=0.6)
-ax.axvspan(83.5, 100.0, facecolor='gray', alpha=0.6)
-ax.axvspan(116.5, 133.0, facecolor='gray', alpha=0.6)
-ax.axvspan(149.5, 166.0, facecolor='gray', alpha=0.6)
-ax.axvspan(182.5, 199.0, facecolor='gray', alpha=0.6)
 plt.ylabel('FR', rotation='horizontal', horizontalalignment='right')
 plt.gca().set_axis_bgcolor('black')