polish intro, theory and setup with annotated figures

data/theory/mktheory.py

@@ -56,7 +56,7 @@ def gen_reticle_empty():
 
     ax.axis('off')
     ax.set_aspect("equal")
-    plt.savefig('wafer.pdf')
+    plt.savefig('wafer.pdf', transparent=True)
 
 def gen_reticle_patterns():
     plt.clf()