diff --git a/SiEPIC_EBeam_PDK_Verification_Check.gds b/SiEPIC_EBeam_PDK_Verification_Check.gds
index 67c61a03..45e6afd3 100644
Binary files a/SiEPIC_EBeam_PDK_Verification_Check.gds and b/SiEPIC_EBeam_PDK_Verification_Check.gds differ
diff --git a/klayout_dot_config/libraries/SiEPIC-EBeam.gds b/klayout_dot_config/libraries/SiEPIC-EBeam.gds
index 55862933..baf74a6a 100644
Binary files a/klayout_dot_config/libraries/SiEPIC-EBeam.gds and b/klayout_dot_config/libraries/SiEPIC-EBeam.gds differ
diff --git a/klayout_dot_config/pymacros/INTERCONNECT.lym b/klayout_dot_config/pymacros/INTERCONNECT.lym
index d12ecadb..8c0ca355 100644
--- a/klayout_dot_config/pymacros/INTERCONNECT.lym
+++ b/klayout_dot_config/pymacros/INTERCONNECT.lym
@@ -44,7 +44,7 @@ version = sys.version
 
 import string
 
-
+"""
 def netlist_extraction(topcell):
   # Collection of functions to extract the circuit netlist from the physical layout
   
@@ -66,7 +66,7 @@ def netlist_extraction(topcell):
   identify_all_nets(optical_pins, optical_waveguides, optical_components)
 
   return optical_waveguides, optical_components
-  
+"""  
 
 
 
@@ -94,10 +94,10 @@ LayerINTERCONNECTN = layout.layer(LayerINTERCONNECT)
 
 
 # extract the circuit netlist from the physical layout:
-optical_waveguides, optical_components = netlist_extraction(topcell)
+optical_waveguides, optical_components = netlist_extraction(topcell)[:2]
   
 # Output the Spice netlist:
-text_Spice = generate_Spice_file(topcell, optical_waveguides, optical_components)
+text_Spice, num_detectors = generate_Spice_file(topcell, optical_waveguides, optical_components)
 print text_Spice
 
 filename = '/tmp/%s.spi' % topcell.name
@@ -112,11 +112,17 @@ text_lsf = 'switchtolayout;\n'
 text_lsf += 'deleteall;\n'
 text_lsf += 'importnetlist("%s");\n' % filename
 text_lsf += 'run;\n'
-text_lsf += 't1 = getresult("ONA_1", "input 1/mode 1/gain");\n'
-text_lsf += 'visualize(t1);\n'
+for i in range(0, num_detectors):
+  text_lsf += 't%s = getresult("ONA_1", "input %s/mode 1/gain");\n' % (i+1, i+1)
+text_lsf += 'visualize(t1'
+for i in range(1, num_detectors):
+  text_lsf += ', t%s' % (i+1)
+text_lsf += ');\n'
+
 file.write (text_lsf)
 file.close()
 
+print(text_lsf)
 
 if sys.platform.startswith('freebsd'):
     # FreeBSD-specific code here...
diff --git a/klayout_dot_config/pymacros/ResultsMarker_tests.lym b/klayout_dot_config/pymacros/ResultsMarker_tests.lym
new file mode 100644
index 00000000..5cc587c2
--- /dev/null
+++ b/klayout_dot_config/pymacros/ResultsMarker_tests.lym
@@ -0,0 +1,63 @@
+<?xml version="1.0" encoding="utf-8"?>
+<klayout-macro>
+ <description/>
+ <version/>
+ <category>pymacros</category>
+ <prolog/>
+ <epilog/>
+ <doc/>
+ <autorun>false</autorun>
+ <autorun-early>false</autorun-early>
+ <shortcut/>
+ <show-in-menu>false</show-in-menu>
+ <group-name/>
+ <menu-path/>
+ <interpreter>python</interpreter>
+ <dsl-interpreter-name/>
+ <text>import pya
+
+# Experimenting with the Results database Rdb.
+
+
+
+# Configure variables to draw structures in the presently selected cell:
+lv = pya.Application.instance().main_window().current_view()
+if lv == None:
+  raise Exception("No view selected")
+# Find the currently selected layout.
+ly = pya.Application.instance().main_window().current_view().active_cellview().layout() 
+if ly == None:
+  raise Exception("No layout")
+cv = pya.Application.instance().main_window().current_view().active_cellview()
+# find the currently selected cell:
+cell = pya.Application.instance().main_window().current_view().active_cellview().cell
+if cell == None:
+  raise Exception("No cell")
+# fetch the database parameters
+dbu = ly.dbu
+
+
+rdb_i = lv.create_rdb("SiEPIC_Verification")
+rdb = lv.rdb(rdb_i)
+
+rdb_cat_id_wg = rdb.create_category("Waveguide errors")
+rdb_cat_id_wg_disc = rdb.create_category(rdb_cat_id_wg, "Disconnected Waveguides")
+rdb_cat_id_wg_disc.description = "Disconnected waveguides"
+
+rdb.top_cell_name = cell.name
+rdb_cell = rdb.create_cell(cell.name)
+
+rdb_item = rdb.create_item(rdb_cell.rdb_id(),rdb_cat_id_wg_disc.rdb_id())
+rdb_item.add_value(pya.RdbItemValue(pya.DBox.new(0.0, 0.0, 100.0, 200.0)))
+
+#rdb_item.add_value(pya.RdbItemValue(DPath))
+
+
+
+#marker = pya.Marker.new(lv)
+#marker.set(pya.DBox.new(0.0, 0.0, 100.0, 200.0))
+# to hide the marker:
+
+
+lv.show_rdb(rdb_i, cv.cell_index)</text>
+</klayout-macro>
diff --git a/klayout_dot_config/pymacros/SiEPIC_EBeam_Path_to_Waveguide.lym b/klayout_dot_config/pymacros/SiEPIC_EBeam_Path_to_Waveguide.lym
index c567fd01..e1732c6a 100644
--- a/klayout_dot_config/pymacros/SiEPIC_EBeam_Path_to_Waveguide.lym
+++ b/klayout_dot_config/pymacros/SiEPIC_EBeam_Path_to_Waveguide.lym
@@ -119,7 +119,8 @@ for o in object_selection:
     print ("Selected object is a shape")
     if o.shape.is_path():
       c = o.shape.cell
-      if c.name == "ROUND_PATH" and c.is_pcell_variant() and c.pcell_parameters_by_name()['layer'] == LayerSi:
+      print (c.basic_name())
+      if c.basic_name() == "ROUND_PATH" and c.is_pcell_variant() and c.pcell_parameters_by_name()['layer'] == LayerSi:
         # we have a waveguide GUIDING_LAYER selected
         print ("GUIDING_LAYER in ROUND_PATH on LayerSi. We will not convert this to waveguide!")
       else:
diff --git a/klayout_dot_config/pymacros/SiEPIC_EBeam_Verification.lym b/klayout_dot_config/pymacros/SiEPIC_EBeam_Verification.lym
index 89fbd992..4bdbc7d5 100644
--- a/klayout_dot_config/pymacros/SiEPIC_EBeam_Verification.lym
+++ b/klayout_dot_config/pymacros/SiEPIC_EBeam_Verification.lym
@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="utf-8"?>
 <klayout-macro>
- <description>SiEPIC: Verification and Netlist generation</description>
+ <description>SiEPIC: Verification (rdb)</description>
  <version>0.1.2</version>
  <category>pymacros</category>
  <prolog/>
@@ -22,7 +22,7 @@ This file is part of the SiEPIC_EBeam_PDK
 by Lukas Chrostowski (c) 2015
 
 This Python file implements layout verification and netlist extraction
-
+displays results in Marker Database Browser, using Results Database (rdb)
 
 Version history:
 
@@ -60,235 +60,12 @@ Lukas Chrostowski           2015/11/18
 Lukas Chrostowski           2015/11/19
  - moved some functions to SiEPIC_EBeam_functions
 
- 
-"""
-
-
-import pya
-import math
-#import numpy
-MODULE_NUMPY = False
-import math
-import string
-
-
-  
-def flag_waveguide_error(dpoints, text, optical_waveguide, topcell):
-  # global variable "layout_errors" of class "Layout_error" used for storing all the errors.
-  a1 = []
-  for p in dpoints:
-    a1.append (pya.Point(int(p[0]), int(p[1])))
-  path = pya.Path(a1, optical_waveguide.wg_width*4/dbu)
-  topcell.shapes(LayerErrorN).insert(path)
-  x,y = xy_mean_mult(dpoints, dbu)
-  layout_errors.append(Layout_error(text, x, y) )
-  print (text)
-  wtext.insertHtml('%s&lt;br&gt;' %text)
-
+Lukas Chrostowski           2015/11/21
+ - adding Results Database (rdb) and Marker Database Browser, for error viewing
 
-def check_waveguides(optical_waveguides, topcell, error_layer):
-  # check waveguides for basic errors.
-  num_errors=0
 
-  for o in optical_waveguides:
-    found_error = False
-
-    # Check for paths with &gt; 2 vertices
-    if (o.wg_type == 0 and o.num_points &gt; 2):
-      text = "  *** Layout error.  Waveguide path (%s, %s): Only 2 points allowed in a path. Convert to a waveguide (ROUND_PATH) if necessary. " \
-            % ( o.points[0][0]*dbu, o.points[0][1]*dbu) 
-      dpoints = o.points
-      found_error = True
-      flag_waveguide_error(dpoints, text, o, topcell)
-
-    # find the minimum segment to make sure that the bends have large enough radius
-    if (o.wg_type == 1):
-      # first segment:
-      segment = distance_xy ( o.points[0], o.points[1] ) 
-      if segment &lt; o.radius:
-        text =  "  *** Layout warning.  Not enough space (%s) to accommodate the desired bend radius (%s) for waveguide end." % (segment, o.radius)
-        dpoints=[ o.points[0], o.points[1] ] 
-        found_error = True 
-        flag_waveguide_error(dpoints, text, o, topcell)
-      # last segment:
-      segment = distance_xy ( o.points[len(o.points)-2], o.points[len(o.points)-1] ) 
-      if segment &lt; o.radius:
-        text =  "  *** Layout warning.  Not enough space (%s) to accommodate the desired bend radius (%s) for waveguide end." % (segment, o.radius)
-        dpoints=[ o.points[len(o.points)-2], o.points[len(o.points)-1] ]
-        flag_waveguide_error(dpoints, text, o, topcell)
-        found_error = True
-      # go through each of the middle segments:
-      for j in range(1, len(o.points)-2):
-        segment = distance_xy ( o.points[j], o.points[j+1] ) 
-        if segment &lt; 2*o.radius and segment != 0:
-          text =  "  *** Layout warning.  Not enough space (%s) to accommodate the desired bend radius (%s) for a mid-segment." % (segment, o.radius)
-          dpoints=[ o.points[j], o.points[j+1] ] 
-          flag_waveguide_error(dpoints, text, o, topcell)
-          found_error = True
-
-      # Check for waveguides with too few bend points
-      recommended_points = points_per_circle(o.radius)
-      if o.bend_pts &lt; 0.75 * recommended_points:
-        text =  "  *** Layout warning.  Waveguide bends should have at least %s points per circle for a %s micron radius." \
-                     % (int(recommended_points), o.radius)
-        dpoints=o.points
-        found_error = True
-        flag_waveguide_error(dpoints, text, o, topcell)
-              
-
-
-
-
-def check_components(cell, LayerDevRecN):
-  # function to go through all the cells
-  # check that the cell has at most ONE DevRec shape.  
-  return False
  
- 
-
-def flag_component_error(box, text, x, y):
-  # global variable "layout_errors" of class "Layout_error" used for storing all the errors.
-  topcell.shapes(LayerErrorN).insert(box)
-  layout_errors.append(Layout_error(text, x, y) )
-  print text
-  wtext.insertHtml('%s&lt;br&gt;' %text)
-
-
-def check_connectivity(optical_components, topcell, LayerErrorN):
-  # Make sure that all pins/waveguides are connected, i.e., dangling pins/waveguides.
-  # Flag disconnected pins
-  # Flag disconnected waveguides
-  # Make sure that waveguides / pins are connected in the correct direction
-
-  for k in range(0,len(optical_components)):
-    if optical_components[k].npins != len(optical_components[k].nets):
-      text = "  *** Connectivity error.  Mismatch between the number of pins (%s) on the component (%s, %s) at (%s, %s), and the number of nets (%s)." \
-            % ( optical_components[k].npins, optical_components[k].component, optical_components[k].index, \
-                optical_components[k].x, optical_components[k].y, len(optical_components[k].nets) )
-      bbox = layout.cell(optical_components[k].instance).bbox()
-      box = bbox.transformed(pya.Trans(optical_components[k].rotate, optical_components[k].flip, \
-                optical_components[k].x/dbu,optical_components[k].y/dbu))
-#      flag_component_error(box, text, optical_components[k].x, optical_components[k].y)
-
-      # go through all the pins in the component, and check if they aren't assigned to a net
-      for m in range(0,optical_components[k].npins):
-        pin = optical_pins[optical_components[k].pins[m]]
-        if pin.net == 0 and pin.pin_type == 1:  # disconnected pin on a pin_type = 1 (component)
-          text = "  *** Found disconnected pin #%s at (%s, %s)." % (pin.index, pin.x*dbu, pin.y*dbu)
-          box = pya.Box(pin.x-3000, pin.y-3000, pin.x+3000, pin.y+3000)
-#          flag_component_error(box, text, pin.x*dbu, pin.y*dbu)
-
-  for pin in optical_pins:
-    if pin.net == -1 and pin.pin_type != 2:  # disconnected pin not on a pin_type = 2 (optical IO)
-      text = "  *** Found disconnected pin #%s, type %s, at (%s, %s), component #%s {%s}" \
-          % (pin.index, pin.pin_type, pin.x*dbu, pin.y*dbu, \
-             pin.component_n, optical_components[pin.component_n].component)
-      box = pya.Box(pin.x-3000, pin.y-3000, pin.x+3000, pin.y+3000)
-      flag_component_error(box, text, pin.x*dbu, pin.y*dbu)
-
-  for w1 in optical_waveguides:
-    # examine the beginning of the waveguide:
-    if w1.net1 == -1:
-      text = "  *** Found disconnected waveguide at (%s, %s), net1" \
-          % (w1.points[0][0]*dbu, w1.points[0][1]*dbu)
-      flag_waveguide_error( [w1.points[0], w1.points[1]], text, optical_waveguides[w1.index], topcell)
-    # examine the end of the waveguide:
-    if w1.net2 == -1:
-      text = "  *** Found disconnected waveguide at (%s, %s), net2" \
-          % (w1.points[len(w1.points)-1][0]*dbu, w1.points[len(w1.points)-1][1]*dbu)
-      flag_waveguide_error([w1.points[len(w1.points)-1], w1.points[len(w1.points)-2]], \
-               text, optical_waveguides[w1.index], topcell)
-
-  # Make sure that waveguides / pins are connected in the correct direction (colinear check)
-    
-
-
-def list_optical_components(optical_components):
-  # list all Optical_component objects from an array
-  # input array, optical_components
-  # example output:         
-  # X_grating_coupler_1 N$7 N$6 grating_coupler library="custom/genericcml" sch_x=-1.42 sch_y=-0.265 sch_r=0 sch_f=false
-
-  for o in optical_components:
-    nets_str = ""
-    for n in o.nets:
-      nets_str += " N$" + str(n)
-    flip = ' sch_f=true' if o.flip else ''
-    if o.rotate &gt; 0:
-      rotate = ' sch_r=%s' % str(o.rotate)
-    else:
-      rotate = ''
-#    t = '%s %s %s library="%s" lay_x=%s lay_y=%s sch_x=%s sch_y=%s %s%s'  % \
-#         ( "X"+o.component+"_"+str(o.index), nets_str, o.component, o.library, str (o.x * 1e-6), o.y * 1e-6, o.x, o.y, rotate, flip)
-    t = '  %s %s %s library="%s" sch_x=%s sch_y=%s %s%s'  % \
-         ( "X"+o.component+"_"+str(o.index), nets_str, o.component, o.library, eng_str(o.x * 5e-2), eng_str(o.y * 5e-2), rotate, flip)
-    print (t)
-    wtext.insertHtml('%s&lt;br&gt;' %t)
-
-def list_optical_waveguides(list_optical_waveguides):
-  # list all Optical_waveguides objects from an array
-  # input array, optical_waveguides
-  # example output:         
-  # X5 9 10 ebeam_wg_strip_1550 library="Design kits/ebeam_v1.0" wg_length=7.86299e-06 wg_width=5.085e-07 sch_x=-1.42 sch_y=-0.265
-
-  for o in list_optical_waveguides:
-    nets_str = "N$%s N$%s" %(o.net1, o.net2)
-    x,y = xy_mean_mult(o.points, dbu)
-#    t = '%s %s %s library="%s" wg_length=%s wg_width=%s lay_x=%s lay_y=%s sch_x=%5.3f sch_y=%5.3f'  % \
-#           ( "Xwg" + str(o.index), nets_str, o.component, o.library, eng_str(o.length*1e-6), eng_str(o.wg_width*1e-6), \
-#             eng_str(x * 1e-6), eng_str(y * 1e-6), x, y)
-    t = '  %s %s %s library="%s" wg_length=%s wg_width=%s sch_x=%s sch_y=%s'  % \
-           ( "Xwg" + str(o.index), nets_str, o.component, o.library, \
-             eng_str(o.length*1e-6), eng_str(o.wg_width*1e-6), eng_str(x * 5e-2), eng_str(y * 5e-2))
-    print (t)
-    wtext.insertHtml('%s&lt;br&gt;' %t)
-    
-
-def gen_ui():
-  global wdg
-  
-  # If the window is already here, destroy it and start over again.
-  if 'wdg' in globals():
-    if wdg is not None and not wdg.destroyed():
-      wdg.destroy()
-  global wtext
-
-  def button_clicked(checked):
-    """ Event handler: "OK" button clicked """
-    wdg.destroy()
-
-  wdg = pya.QDialog(pya.Application.instance().main_window())
-
-  wdg.setAttribute(pya.Qt.WA_DeleteOnClose)
-  wdg.setWindowTitle("SiEPIC-EBeam-PDK Verification and Netlist Generation")
-
-  wdg.resize(1200, 2500)
-  wdg.move(1, 1)
-
-  grid = pya.QGridLayout(wdg)
-
-  windowlabel1 = pya.QLabel(wdg)
-  windowlabel1.setText("Verification output:")
-  wtext = pya.QTextEdit(wdg)
-  wtext.enabled = True
-  wtext.setText('')
-  wtext.LineWrapMode = pya.QTextEdit.NoWrap
-
-  ok = pya.QPushButton("OK", wdg)
-  ok.clicked(button_clicked)   # attach the event handler
-  netlist = pya.QPushButton("Netlist Export", wdg) # not implemented
-
-  grid.addWidget(windowlabel1, 0, 0, 1, 3)
-  grid.addWidget(wtext, 1, 1, 3, 3)
-  grid.addWidget(netlist, 4, 2)
-  grid.addWidget(ok, 4, 3)
-
-  grid.setRowStretch(3, 1)
-  grid.setColumnStretch(1, 1)
-
-  wdg.show()
-
-
+"""
 
 # ************************************************************************
 # ************************************************************************
@@ -296,16 +73,6 @@ def gen_ui():
 # ************************************************************************
 # ************************************************************************
 
-#from time import strftime, clock
-import time
-
-# Create a GUI for the output:
-gen_ui()
-print(wdg)
-wtext.insertHtml('Running SiEPIC-EBeam-PDK Verification and Netlist Generation.&lt;br&gt;')
-wtext.insertHtml('* KLayout SiEPIC_EBeam_PDK v%s, %s.&lt;br&gt;' % (SiEPIC_Version, time.strftime("%Y-%m-%d %H:%M:%S") ) )
-clock_start = time.clock()
-
 
 # Configure variables to draw structures in the presently selected cell:
 lv = pya.Application.instance().main_window().current_view()
@@ -315,6 +82,7 @@ if lv == None:
 layout = pya.Application.instance().main_window().current_view().active_cellview().layout() 
 if layout == None:
   raise Exception("No layout")
+cv = pya.Application.instance().main_window().current_view().active_cellview()
 # find the currently selected cell:
 topcell = pya.Application.instance().main_window().current_view().active_cellview().cell
 if topcell == None:
@@ -322,7 +90,6 @@ if topcell == None:
 # fetch the database parameters
 dbu = layout.dbu
 
-
 # Define layers based on PDK_functions:
 LayerSiN = layout.layer(LayerSi)
 LayerTextN = layout.layer(LayerText)
@@ -332,8 +99,6 @@ LayerFbrTgtN = layout.layer(LayerFbrTgt)
 LayerErrorN = layout.layer(LayerError)
 LayerINTERCONNECTN = layout.layer(LayerINTERCONNECT)
 
-# Clear the previous errors:
-clear_ErrorLayer(topcell, LayerErrorN)
 
 # initialize the arrays to keep track of layout objects
 reset_Optical_classes()
@@ -342,91 +107,49 @@ optical_waveguides = []
 optical_pins = []
 optical_nets = []
 
+# Create a Results Database
+rdb_i = lv.create_rdb("SiEPIC_Verification")
+rdb = lv.rdb(rdb_i)
+rdb.top_cell_name = topcell.name
+rdb_cell = rdb.create_cell(topcell.name)
 
-# Search the layout for the components and waveguides:
-print ("")
-print ("* calling find_all_components() – DevRec:")
-find_all_components(topcell, LayerDevRecN, LayerPinRecN, LayerFbrTgtN)
-clock_find_all_components = time.clock()
-print ("")
-print ("* calling find_all_waveguides():")
-find_all_waveguides(topcell, LayerSiN)
-clock_find_all_waveguides = time.clock()
-print ("")
-print ("* print_Optical_all, after find_all_{components, waveguides}:")
-print_Optical_all(optical_components, optical_waveguides, optical_pins, optical_nets)
 
+if 'wtext' in globals():
+  # don't use the text window for output.
+  del(wtext)
 
+# Search the layout for the components and waveguides:
 # Search the arrays to identify all the nets:
-print ("")
-print ("* calling identify_all_nets():")
-clock_identify_all_nets0 = time.clock()
-identify_all_nets(optical_pins, optical_waveguides, optical_components)
-clock_identify_all_nets = time.clock()
-print ("")
-print ("print_Optical_all, after identify_all_nets:")
-print_Optical_all(optical_components, optical_waveguides, optical_pins, optical_nets)
-clock_identify_layout = time.clock()
+optical_waveguides, optical_components = netlist_extraction(topcell)[:2]
 
 
+# ********* Verification ********* 
 # Check the layout for errors, using the above arrays:
 print ("")
 print ("Checking layout for errors: ")
-wtext.insertHtml('&lt;br&gt;* Checking layout for errors:&lt;br&gt;&lt;br&gt;')
 layout_errors=[]
 # Check components - overlapping
-check_components(topcell, LayerDevRecN)
-clock_check_components = time.clock()
+number_errors = check_components(rdb, topcell, LayerDevRecN)
 # Check waveguides for waveguide-specific problems:
-check_waveguides(optical_waveguides, topcell, LayerErrorN)
-clock_check_waveguides = time.clock()
+number_errors += check_waveguides(rdb, optical_waveguides, topcell, LayerErrorN)
 # Check connectivity between components and waveguides:
-check_connectivity(optical_components, topcell, LayerErrorN)
-clock_check_connectivity = time.clock()
+number_errors += check_connectivity(rdb, optical_components, topcell, LayerErrorN)
 lv.add_missing_layers()
 print ("*** Number of errors found: %s." % len(layout_errors) )
-wtext.insertHtml('&lt;br&gt;*** Number of errors found: %s.&lt;br&gt;' % len(layout_errors) )
-clock_verify_layout = time.clock()
-
-
-# Output the Spice netlist:
-text_Spice = generate_Spice_file(topcell, optical_waveguides, optical_components)
-wtext.insertPlainText(text_Spice)
-clock_netlist = time.clock()
-
-
-# Find the automated measurement coordinates:
-wtext.insertHtml('&lt;br&gt;* Automated measurement coordinates:&lt;br&gt;&lt;br&gt;')
-print ("")
-print ("Automated measurement coordinates: ")
-print ("")
-t = find_automated_measurement_labels(topcell, LayerTextN)
-wtext.insertHtml (t)
-clock_automated_measurements = time.clock()
+print ("*** Number of errors found: %s." % number_errors )
 
-
-wtext.insertHtml('&lt;br&gt;CPU time for searching layout: find_all_components %s, find_all_waveguides %s&lt;br&gt;' \
-% (clock_find_all_components-clock_start, clock_find_all_waveguides-clock_find_all_components) )
-
-wtext.insertHtml('&lt;br&gt;CPU time for identify_all_nets %s&lt;br&gt;' \
-% (clock_identify_all_nets-clock_identify_all_nets0) )
-
-wtext.insertHtml('&lt;br&gt;CPU time for verification: check_components %s, check_waveguides %s, check_connectivity %s&lt;br&gt;' \
-% (clock_check_components-clock_identify_all_nets, clock_check_waveguides-clock_check_components, clock_check_connectivity-clock_check_waveguides) )
-
-wtext.insertHtml('&lt;br&gt;CPU time for Spice netlist %s, automated measurements %s&lt;br&gt;' \
-% (clock_netlist-clock_verify_layout, clock_automated_measurements-clock_netlist) )
-
-wtext.insertHtml('&lt;br&gt;total CPU time: %s. &lt;br&gt;' % (time.clock() - clock_start) )
-
-
-# Done
-wtext.insertHtml('&lt;br&gt;Done.&lt;br&gt;')
+  
 print ("")
 print ("Done. ")
 print ("")
 
 
+#displays results in Marker Database Browser, using Results Database (rdb)
+if number_errors&gt;0:
+  v = pya.MessageBox.warning("Errors", "%s layout errors detected.  \nPlease review errors using the 'Marker Database Browser'." % number_errors, pya.MessageBox.Ok)
+  lv.show_rdb(rdb_i, cv.cell_index)
+else:
+  v = pya.MessageBox.warning("Errors", "No layout errors detected.", pya.MessageBox.Ok)
 
 </text>
 </klayout-macro>
diff --git a/klayout_dot_config/pymacros/SiEPIC_EBeam_Verification_text.lym b/klayout_dot_config/pymacros/SiEPIC_EBeam_Verification_text.lym
new file mode 100644
index 00000000..3832264d
--- /dev/null
+++ b/klayout_dot_config/pymacros/SiEPIC_EBeam_Verification_text.lym
@@ -0,0 +1,258 @@
+<?xml version="1.0" encoding="utf-8"?>
+<klayout-macro>
+ <description>SiEPIC: Verification and Netlist generation</description>
+ <version/>
+ <category>pymacros</category>
+ <prolog/>
+ <epilog/>
+ <doc/>
+ <autorun>false</autorun>
+ <autorun-early>false</autorun-early>
+ <shortcut/>
+ <show-in-menu>true</show-in-menu>
+ <group-name/>
+ <menu-path/>
+ <interpreter>python</interpreter>
+ <dsl-interpreter-name/>
+ <text># Python script
+# SiEPIC_EBeam_Verification
+
+"""
+This file is part of the SiEPIC_EBeam_PDK
+by Lukas Chrostowski (c) 2015
+
+This Python file implements layout verification and netlist extraction
+displays results in a text window
+
+
+Version history:
+
+Lukas Chrostowski 2015/11/11
+ - Optical_net class
+ - find all LayerSi paths and waveguides, and save optical net vertices 
+ - find all PinRec paths
+ - find all DevRec polygons and boxes
+ - check_waveguides
+   - waveguide bend minimum
+   - paths with corners (more than 2 points)
+   - bend radius less than specified
+ - error marker layer and class; clear errors
+
+Lukas Chrostowski 2015/11/12
+ - determining where pins/waveguides overlap to generate a netlist
+ - initial Spice output for components including waveguides and nets.
+ - check nets &amp; components
+   - incorrect number of nets connected to a component (disconnected, or too many)
+ 
+Lukas Chrostowski           2015/11/15
+ - fix for Python 3.4: print ("xxx")
+ - moved some functions from here, to the common "SiEPIC_EBeam_functions file, so they are accessible elsewhere.
+ - added pin# text label on PinRec layer; sort pins in Spice output using these names.
+
+Lukas Chrostowski           2015/11/16
+ - fixes for component pin_type = Optical IO / FbrTgt being incorrectly handled; added Optical_pin.pin_type
+
+Lukas Chrostowski           2015/11/17
+ - debugging &amp; fixing Verification problems
+
+Lukas Chrostowski           2015/11/18
+ - removed need for numpy.array
+
+Lukas Chrostowski           2015/11/19
+ - moved some functions to SiEPIC_EBeam_functions
+
+Lukas Chrostowski           2015/11/21
+ - adding Results Database (rdb) and Marker Database Browser, for error viewing
+
+
+ 
+"""
+
+
+def gen_ui():
+  global wdg
+  
+  # If the window is already here, destroy it and start over again.
+  if 'wdg' in globals():
+    if wdg is not None and not wdg.destroyed():
+      wdg.destroy()
+  global wtext
+
+  def button_clicked(checked):
+    """ Event handler: "OK" button clicked """
+    wdg.destroy()
+
+  wdg = pya.QDialog(pya.Application.instance().main_window())
+
+  wdg.setAttribute(pya.Qt.WA_DeleteOnClose)
+  wdg.setWindowTitle("SiEPIC-EBeam-PDK Verification and Netlist Generation")
+
+  wdg.resize(1200, 2500)
+  wdg.move(1, 1)
+
+  grid = pya.QGridLayout(wdg)
+
+  windowlabel1 = pya.QLabel(wdg)
+  windowlabel1.setText("Verification output:")
+  wtext = pya.QTextEdit(wdg)
+  wtext.enabled = True
+  wtext.setText('')
+  wtext.LineWrapMode = pya.QTextEdit.NoWrap
+
+  ok = pya.QPushButton("OK", wdg)
+  ok.clicked(button_clicked)   # attach the event handler
+  netlist = pya.QPushButton("Netlist Export", wdg) # not implemented
+
+  grid.addWidget(windowlabel1, 0, 0, 1, 3)
+  grid.addWidget(wtext, 1, 1, 3, 3)
+  grid.addWidget(netlist, 4, 2)
+  grid.addWidget(ok, 4, 3)
+
+  grid.setRowStretch(3, 1)
+  grid.setColumnStretch(1, 1)
+
+  wdg.show()
+
+
+
+# ************************************************************************
+# ************************************************************************
+#  Main script:
+# ************************************************************************
+# ************************************************************************
+
+#from time import strftime, clock
+import time
+
+# Create a GUI for the output:
+gen_ui()
+
+if 'wtext' in globals():
+  wtext.insertHtml('Running SiEPIC-EBeam-PDK Verification and Netlist Generation.&lt;br&gt;')
+  wtext.insertHtml('* KLayout SiEPIC_EBeam_PDK v%s, %s.&lt;br&gt;' % (SiEPIC_Version, time.strftime("%Y-%m-%d %H:%M:%S") ) )
+clock_start = time.clock()
+
+
+# Configure variables to draw structures in the presently selected cell:
+lv = pya.Application.instance().main_window().current_view()
+if lv == None:
+  raise Exception("No view selected")
+# Find the currently selected layout.
+layout = pya.Application.instance().main_window().current_view().active_cellview().layout() 
+if layout == None:
+  raise Exception("No layout")
+cv = pya.Application.instance().main_window().current_view().active_cellview()
+# find the currently selected cell:
+topcell = pya.Application.instance().main_window().current_view().active_cellview().cell
+if topcell == None:
+  raise Exception("No cell")
+# fetch the database parameters
+dbu = layout.dbu
+
+
+# Define layers based on PDK_functions:
+LayerSiN = layout.layer(LayerSi)
+LayerTextN = layout.layer(LayerText)
+LayerPinRecN = layout.layer(LayerPinRec)
+LayerDevRecN = layout.layer(LayerDevRec)
+LayerFbrTgtN = layout.layer(LayerFbrTgt)
+LayerErrorN = layout.layer(LayerError)
+LayerINTERCONNECTN = layout.layer(LayerINTERCONNECT)
+
+# Clear the previous errors:
+clear_ErrorLayer(topcell, LayerErrorN)
+
+# initialize the arrays to keep track of layout objects
+reset_Optical_classes()
+optical_components = []
+optical_waveguides = []
+optical_pins = []
+optical_nets = []
+
+# Create a Results Database
+rdb_i = lv.create_rdb("SiEPIC_Verification")
+rdb = lv.rdb(rdb_i)
+rdb.top_cell_name = topcell.name
+rdb_cell = rdb.create_cell(topcell.name)
+
+
+# Search the layout for the components and waveguides:
+# Search the arrays to identify all the nets:
+optical_waveguides, optical_components, clock_find_all_components, clock_find_all_waveguides, clock_identify_all_nets \
+  = netlist_extraction(topcell)
+
+clock_identify_layout = time.clock()
+
+
+# ********* Verification ********* 
+# Check the layout for errors, using the above arrays:
+print ("")
+print ("Checking layout for errors: ")
+if 'wtext' in globals():
+  wtext.insertHtml('&lt;br&gt;* Checking layout for errors:&lt;br&gt;&lt;br&gt;')
+layout_errors=[]
+# Check components - overlapping
+check_components(rdb, topcell, LayerDevRecN)
+clock_check_components = time.clock()
+# Check waveguides for waveguide-specific problems:
+check_waveguides(rdb, optical_waveguides, topcell, LayerErrorN)
+clock_check_waveguides = time.clock()
+# Check connectivity between components and waveguides:
+check_connectivity(rdb, optical_components, topcell, LayerErrorN)
+clock_check_connectivity = time.clock()
+lv.add_missing_layers()
+print ("*** Number of errors found: %s." % len(layout_errors) )
+if 'wtext' in globals():
+  wtext.insertHtml('&lt;br&gt;*** Number of errors found: %s.&lt;br&gt;' % len(layout_errors) )
+clock_verify_layout = time.clock()
+
+
+# Output the Spice netlist:
+text_Spice = generate_Spice_file(topcell, optical_waveguides, optical_components)
+if 'wtext' in globals():
+  wtext.insertPlainText(text_Spice)
+clock_netlist = time.clock()
+
+
+# Find the automated measurement coordinates:
+if 'wtext' in globals():
+  wtext.insertHtml('&lt;br&gt;* Automated measurement coordinates:&lt;br&gt;&lt;br&gt;')
+print ("")
+print ("Automated measurement coordinates: ")
+print ("")
+t = find_automated_measurement_labels(topcell, LayerTextN)
+if 'wtext' in globals():
+  wtext.insertHtml (t)
+clock_automated_measurements = time.clock()
+
+if 'wtext' in globals():
+
+  wtext.insertHtml('&lt;br&gt;CPU time for searching layout: find_all_components %s, find_all_waveguides %s&lt;br&gt;' \
+  % (clock_find_all_components-clock_start, clock_find_all_waveguides-clock_find_all_components) )
+
+  wtext.insertHtml('&lt;br&gt;CPU time for identify_all_nets %s&lt;br&gt;' \
+  % (clock_identify_all_nets-clock_find_all_components) )
+
+  wtext.insertHtml('&lt;br&gt;CPU time for verification: check_components %s, check_waveguides %s, check_connectivity %s&lt;br&gt;' \
+  % (clock_check_components-clock_identify_all_nets, clock_check_waveguides-clock_check_components, clock_check_connectivity-clock_check_waveguides) )
+
+  wtext.insertHtml('&lt;br&gt;CPU time for Spice netlist %s, automated measurements %s&lt;br&gt;' \
+  % (clock_netlist-clock_verify_layout, clock_automated_measurements-clock_netlist) )
+
+  wtext.insertHtml('&lt;br&gt;total CPU time: %s. &lt;br&gt;' % (time.clock() - clock_start) )
+
+
+# Done
+if 'wtext' in globals():
+  wtext.insertHtml('&lt;br&gt;Done.&lt;br&gt;')
+  
+print ("")
+print ("Done. ")
+print ("")
+
+
+#lv.show_rdb(rdb_i, cv.cell_index)
+
+
+</text>
+</klayout-macro>
diff --git a/klayout_dot_config/pymacros/SiEPIC_EBeam_Waveguide_to_Path.lym b/klayout_dot_config/pymacros/SiEPIC_EBeam_Waveguide_to_Path.lym
index 1120d630..6bf781ef 100644
--- a/klayout_dot_config/pymacros/SiEPIC_EBeam_Waveguide_to_Path.lym
+++ b/klayout_dot_config/pymacros/SiEPIC_EBeam_Waveguide_to_Path.lym
@@ -102,7 +102,7 @@ for o in object_selection:
   elif o.shape:
     print ("Selected object is a shape.")
     c = o.shape.cell
-    if c.name == "ROUND_PATH" and c.is_pcell_variant() and c.pcell_parameters_by_name()['layer'] == LayerSi:
+    if c.basic_name() == "ROUND_PATH" and c.is_pcell_variant() and c.pcell_parameters_by_name()['layer'] == LayerSi:
       # we have a waveguide GUIDING_LAYER selected
       print ("Selected object is a GUIDING_LAYER in ROUND_PATH on LayerSi.")
       trans = o.source_trans().s_trans()
diff --git a/klayout_dot_config/pymacros/SiEPIC_EBeam_functions.lym b/klayout_dot_config/pymacros/SiEPIC_EBeam_functions.lym
index a2320047..2bb8d00d 100644
--- a/klayout_dot_config/pymacros/SiEPIC_EBeam_functions.lym
+++ b/klayout_dot_config/pymacros/SiEPIC_EBeam_functions.lym
@@ -65,6 +65,10 @@ Lukas Chrostowski           2015/11/19
  - finding the laser and detectors in the layout
  - generating a Spice netlist including Optical Network Analyzer; ready for Lumerical INTERCONNECT
  - Added Python 2 &amp; 3 compatibility for iter.next() vs. next(iter)
+
+Lukas Chrostowski           2015/11/21
+ - bug fix in points_mult, that argument in the function was being modified. needed to copy it.
+ 
  
 """
 
@@ -72,6 +76,14 @@ SiEPIC_Version = '0.1.6'
 
 import pya
 import math
+import string
+
+try:
+  import numpy
+except ImportError:
+  #import numpy
+  print ("no numpy")
+  MODULE_NUMPY = False
 
 
 # SiEPIC-EBeam-PDK Layers:
@@ -85,8 +97,6 @@ LayerINTERCONNECT = pya.LayerInfo(733,0)
 
 
 
-#import numpy
-MODULE_NUMPY = False
 
 # Determine whether we have Python 2 or Python 3
 import sys
@@ -216,14 +226,17 @@ def reset_Optical_classes():
   Layout_error.n = 0
 
 # multiply an array of points by a constant
-def points_mult(dpoints, mult):
+def points_mult(dpoints1, mult):
+  # create a new empty list.  Otherwise, this function would modify the original list
+  # http://stackoverflow.com/questions/240178/python-list-of-lists-changes-reflected-across-sublists-unexpectedly
+  newlist = [[0]*2 for n in range(len(dpoints1))] 
   if MODULE_NUMPY:
-    return numpy.array(dpoints)*mult
+    return numpy.array(dpoints1)*mult
   else:
     for i in range(0,2):
-      for j in range(0,len(points)):
-        dpoints[j][i] *= mult
-    return dpoints
+      for j in range(0,len(dpoints1)):
+        newlist[j][i] = dpoints1[j][i]*mult
+    return newlist
 
 # calculate the mean in (x,y) for an array of points
 def xy_mean_mult(dpoints,dbu):
@@ -355,8 +368,6 @@ def find_all_components(cell, LayerDevRecN, LayerPinRecN, LayerFbrTgtN):
           path= iter2.shape().path.transformed(iter2.itrans())
           path= path.transformed(iter1.itrans())
           points = path_to_points(path)  
-          x = points[0][0]
-          y = points[0][1]
           #print ( "%s: PinRec in cell {%s}, path -- %s"   % (i, iter2.cell().name, path) )
           path_points.append(points)
           path_shape.append(iter2.shape())
@@ -373,8 +384,8 @@ def find_all_components(cell, LayerDevRecN, LayerPinRecN, LayerFbrTgtN):
             pya.Point( pin_info2[p1].pin_x, pin_info2[p1].pin_y ) )
           if check_text_in_pin:
             points = path_points[p2]  
-            x = points[0][0]
-            y = points[0][1]
+            x = (points[0][0]+points[1][0])/2   # midpoint of pin path
+            y = (points[0][1]+points[1][1])/2
             pin_index = len(optical_pins)
             optical_pins.append (Optical_pin (pin_index, points, component_index, x, y, 1) )
             optical_components[component_index].npins += 1
@@ -469,8 +480,8 @@ def points_to_Dpath(points, w):
   a1 = []
   for p in points:
     a1.append (pya.DPoint(p[0], p[1]))
-  wg_path = pya.DPath(a1, w)
-  return wg_path
+  wg_path1 = pya.DPath(a1, w)
+  return wg_path1
 
 
 def points_to_path(points, w):
@@ -482,7 +493,7 @@ def points_to_path(points, w):
   
   
 def polygon_to_points(polygon):
-  # for some reason, you assign points to a polygon, but not read them!
+  # for some reason, you can assign points to a polygon, but not read them!
   # http://www.klayout.de/doc/code/class_SimplePolygon.html
   # This function reads the points one by one and returns an array of points
   npts = polygon.to_simple_polygon().points
@@ -959,7 +970,7 @@ def generate_Spice_file(topcell, optical_waveguides, optical_components):
   # main circuit
   text += '%s%s %s sch_x=-1 sch_y=-1\n\n' % (topcell.name, opticalIO_pins, topcell.name)
 
-  return text
+  return text, len(detector_nets)
 
 
 def eng_str(x):
@@ -989,8 +1000,264 @@ def eng_str(x):
       #return sign+str(z)+'E'+str(engr_exponent)
 #      return sign+ '%3.3f' % z +str(str_engr_exponent)
       return sign+ str(z) +str(str_engr_exponent)
+
+
+def netlist_extraction(topcell):
+  # Collection of functions to extract the circuit netlist from the physical layout
+  
+  import time
+
+  # Search the layout for the components and waveguides:
+  print ("")
+  print ("* calling find_all_components() – DevRec:")
+  find_all_components(topcell, LayerDevRecN, LayerPinRecN, LayerFbrTgtN)
+  clock_find_all_components = time.clock()
+
+  print ("")
+  print ("* calling find_all_waveguides():")
+  find_all_waveguides(topcell, LayerSiN)
+  clock_find_all_waveguides = time.clock()
+
+#  print ("")
+#  print ("* print_Optical_all, after find_all_{components, waveguides}:")
+#  print_Optical_all(optical_components, optical_waveguides, optical_pins, optical_nets)
+
+  # Search the arrays to identify all the nets:
+  print ("")
+  print ("* calling identify_all_nets():")
+  identify_all_nets(optical_pins, optical_waveguides, optical_components)
+  clock_identify_all_nets = time.clock()
+
+  print ("")
+  print ("print_Optical_all, after identify_all_nets:")
+  print_Optical_all(optical_components, optical_waveguides, optical_pins, optical_nets)
+
+  return optical_waveguides, optical_components, \
+  clock_find_all_components, clock_find_all_waveguides, clock_identify_all_nets
+
+
+  
+def flag_waveguide_error(dpoints, text, optical_waveguide, topcell):
+  # global variable "layout_errors" of class "Layout_error" used for storing all the errors.
+  a1 = []
+  for p in dpoints:
+    a1.append (pya.Point(int(p[0]), int(p[1])))
+  path = pya.Path(a1, optical_waveguide.wg_width*4/dbu)
+  x,y = xy_mean_mult(dpoints, dbu)
+  layout_errors.append(Layout_error(text, x, y) )
+  print (text)
+  if 'wtext' in globals():
+    topcell.shapes(LayerErrorN).insert(path)
+    wtext.insertHtml('%s&lt;br&gt;' %text)
+
+
+def check_waveguides(rdb, optical_waveguides, topcell, error_layer):
+  # check waveguides for basic errors.
+  num_errors=0
+
+  rdb_cell = next(rdb.each_cell())
+
+  rdb_cat_id_wg = rdb.create_category("Waveguide errors")
+  
+  rdb_cat_id_wg_path = rdb.create_category(rdb_cat_id_wg, "Path")
+  rdb_cat_id_wg_path.description = "Waveguide path: Only 2 points allowed in a path. Convert to a waveguide (ROUND_PATH) if necessary."
+
+  rdb_cat_id_wg_radius = rdb.create_category(rdb_cat_id_wg, "Radius")
+  rdb_cat_id_wg_radius.description = "Not enough space to accommodate the desired bend radius for the waveguide end."
+
+  rdb_cat_id_wg_bendpts = rdb.create_category(rdb_cat_id_wg, "Bend points")
+  rdb_cat_id_wg_bendpts.description = "Waveguide bend should have more points per circle."
+
+
+  for o in optical_waveguides:
+
+    # Check for paths with &gt; 2 vertices
+    if (o.wg_type == 0 and o.num_points &gt; 2):
+      text = "  *** Layout error.  Waveguide path (%s, %s): Only 2 points allowed in a path. Convert to a waveguide (ROUND_PATH) if necessary. " \
+            % ( o.points[0][0]*dbu, o.points[0][1]*dbu) 
+      dpoints = o.points
+      num_errors += 1
+      flag_waveguide_error(dpoints, text, o, topcell)
+      rdb_item = rdb.create_item(rdb_cell.rdb_id(),rdb_cat_id_wg_path.rdb_id())
+      rdb_item.add_value(pya.RdbItemValue( points_to_Dpath(points_mult(dpoints, dbu),o.wg_width) ) )
+
+    # find the minimum segment to make sure that the bends have large enough radius
+    if (o.wg_type == 1):
+      # first segment:
+      segment = distance_xy ( o.points[0], o.points[1] ) 
+      if segment &lt; o.radius:
+        text =  "  *** Layout warning.  Not enough space (%s) to accommodate the desired bend radius (%s) for waveguide end." % (segment, o.radius)
+        dpoints=[ o.points[0], o.points[1] ] 
+        num_errors += 1
+        flag_waveguide_error(dpoints, text, o, topcell)
+        rdb_item = rdb.create_item(rdb_cell.rdb_id(),rdb_cat_id_wg_radius.rdb_id())
+        rdb_item.add_value(pya.RdbItemValue( points_to_Dpath(points_mult(dpoints, dbu),o.wg_width) ) )
+      # last segment:
+      segment = distance_xy ( o.points[len(o.points)-2], o.points[len(o.points)-1] ) 
+      if segment &lt; o.radius:
+        text =  "  *** Layout warning.  Not enough space (%s) to accommodate the desired bend radius (%s) for waveguide end." % (segment, o.radius)
+        dpoints=[ o.points[len(o.points)-2], o.points[len(o.points)-1] ]
+        num_errors += 1
+        flag_waveguide_error(dpoints, text, o, topcell)
+        rdb_item = rdb.create_item(rdb_cell.rdb_id(),rdb_cat_id_wg_radius.rdb_id())
+        rdb_item.add_value(pya.RdbItemValue( points_to_Dpath(points_mult(dpoints, dbu),o.wg_width) ) )
+      # go through each of the middle segments:
+      for j in range(1, len(o.points)-2):
+        segment = distance_xy ( o.points[j], o.points[j+1] ) 
+        if segment &lt; 2*o.radius and segment != 0:
+          text =  "  *** Layout warning.  Not enough space (%s) to accommodate the desired bend radius (%s) for a mid-segment." % (segment, o.radius)
+          dpoints=[ o.points[j], o.points[j+1] ] 
+          num_errors += 1
+          flag_waveguide_error(dpoints, text, o, topcell)
+          rdb_item = rdb.create_item(rdb_cell.rdb_id(),rdb_cat_id_wg_radius.rdb_id())
+          rdb_item.add_value(pya.RdbItemValue( points_to_Dpath(points_mult(dpoints, dbu),o.wg_width) ) )
+
+      # Check for waveguides with too few bend points
+      recommended_points = points_per_circle(o.radius)
+      if o.bend_pts &lt; 0.75 * recommended_points:
+        text =  "  *** Layout warning.  Waveguide bends should have at least %s points per circle for a %s micron radius." \
+                     % (int(recommended_points), o.radius)
+        dpoints=o.points
+        num_errors += 1
+        flag_waveguide_error(dpoints, text, o, topcell)
+        rdb_item = rdb.create_item(rdb_cell.rdb_id(),rdb_cat_id_wg_bendpts.rdb_id())
+        rdb_item.add_value(pya.RdbItemValue( points_to_Dpath(points_mult(dpoints, dbu),o.wg_width) ) )
+              
+  return num_errors
+
+
+def check_components(rdb, cell, LayerDevRecN):
+  # function to go through all the cells
+  # check that the cell has at most ONE DevRec shape.  
+  return False
+ 
+ 
+
+def flag_component_error(box, text, x, y):
+  # global variable "layout_errors" of class "Layout_error" used for storing all the errors.
+  layout_errors.append(Layout_error(text, x, y) )
+  print text
+  if 'wtext' in globals():
+    topcell.shapes(LayerErrorN).insert(box)
+    wtext.insertHtml('%s&lt;br&gt;' %text)
+
+
+def check_connectivity(rdb, optical_components, topcell, LayerErrorN):
+  # Make sure that all pins/waveguides are connected, i.e., dangling pins/waveguides.
+  # Flag disconnected pins
+  # Flag disconnected waveguides
+  # Make sure that waveguides / pins are connected in the correct direction (identify_nets only finds colinear pins/waveguides) 
+
+  num_errors=0
+
+  rdb_cell = next(rdb.each_cell())
+
+  rdb_cat_id = rdb.create_category("Connectivity errors")
+
+  rdb_cat_id_discwg = rdb.create_category(rdb_cat_id, "Disconnected waveguide")
+  rdb_cat_id_discwg.description = "Disconnected waveguides"
+
+  rdb_cat_id_discpin = rdb.create_category(rdb_cat_id, "Disconnected pin")
+  rdb_cat_id_discpin.description = "Disconnected pin"
+
+  if 0:
+   for k in range(0,len(optical_components)):
+    if optical_components[k].npins != len(optical_components[k].nets):
+      text = "  *** Connectivity error.  Mismatch between the number of pins (%s) on the component (%s, %s) at (%s, %s), and the number of nets (%s)." \
+            % ( optical_components[k].npins, optical_components[k].component, optical_components[k].index, \
+                optical_components[k].x, optical_components[k].y, len(optical_components[k].nets) )
+      bbox = layout.cell(optical_components[k].instance).bbox()
+      box = bbox.transformed(pya.Trans(optical_components[k].rotate, optical_components[k].flip, \
+                optical_components[k].x/dbu,optical_components[k].y/dbu))
+#      flag_component_error(box, text, optical_components[k].x, optical_components[k].y)
+
+      # go through all the pins in the component, and check if they aren't assigned to a net
+      for m in range(0,optical_components[k].npins):
+        pin = optical_pins[optical_components[k].pins[m]]
+        if pin.net == 0 and pin.pin_type == 1:  # disconnected pin on a pin_type = 1 (component)
+          text = "  *** Found disconnected pin #%s at (%s, %s)." % (pin.index, pin.x*dbu, pin.y*dbu)
+          box = pya.Box(pin.x-3000, pin.y-3000, pin.x+3000, pin.y+3000)
+#          flag_component_error(box, text, pin.x*dbu, pin.y*dbu)
+
+  for pin in optical_pins:
+    if pin.net == -1 and pin.pin_type != 2:  # disconnected pin not on a pin_type = 2 (optical IO)
+      text = "  *** Found disconnected pin #%s, type %s, at (%s, %s), component #%s {%s}" \
+          % (pin.index, pin.pin_type, pin.x*dbu, pin.y*dbu, \
+             pin.component_n, optical_components[pin.component_n].component)
+      box = pya.Box(pin.x-3000, pin.y-3000, pin.x+3000, pin.y+3000)
+      num_errors += 1
+      flag_component_error(box, text, pin.x*dbu, pin.y*dbu)
+      rdb_item = rdb.create_item(rdb_cell.rdb_id(),rdb_cat_id_discpin.rdb_id())
+      rdb_item.add_value(pya.RdbItemValue( pya.DBox(pin.x*dbu-0.3, pin.y*dbu-0.3, pin.x*dbu+0.3, pin.y*dbu+0.3) ) )
+
+  for w1 in optical_waveguides:
+    print (w1.points)
+    # examine the beginning of the waveguide:
+    if w1.net1 == -1:
+      text = "  *** Found disconnected waveguide at (%s, %s), net1" \
+          % (w1.points[0][0]*dbu, w1.points[0][1]*dbu)
+      dpoints = [w1.points[0], w1.points[1]]
+      num_errors += 1
+      flag_waveguide_error( dpoints, text, optical_waveguides[w1.index], topcell)
+      rdb_item = rdb.create_item(rdb_cell.rdb_id(),rdb_cat_id_discwg.rdb_id())
+      rdb_item.add_value(pya.RdbItemValue( points_to_Dpath(points_mult(dpoints, dbu),w1.wg_width) ) )
+    # examine the end of the waveguide:
+    if w1.net2 == -1:
+      text = "  *** Found disconnected waveguide at (%s, %s), net2" \
+          % (w1.points[len(w1.points)-1][0]*dbu, w1.points[len(w1.points)-1][1]*dbu)
+      dpoints = [w1.points[len(w1.points)-1], w1.points[len(w1.points)-2]]
+      print (dpoints)
+      num_errors += 1
+      flag_waveguide_error(dpoints, \
+               text, optical_waveguides[w1.index], topcell)
+      rdb_item = rdb.create_item(rdb_cell.rdb_id(),rdb_cat_id_discwg.rdb_id())
+      rdb_item.add_value(pya.RdbItemValue( points_to_Dpath(points_mult(dpoints, dbu),w1.wg_width) ) )
+
+  return num_errors
     
 
+
+def list_optical_components(optical_components):
+  # list all Optical_component objects from an array
+  # input array, optical_components
+  # example output:         
+  # X_grating_coupler_1 N$7 N$6 grating_coupler library="custom/genericcml" sch_x=-1.42 sch_y=-0.265 sch_r=0 sch_f=false
+
+  for o in optical_components:
+    nets_str = ""
+    for n in o.nets:
+      nets_str += " N$" + str(n)
+    flip = ' sch_f=true' if o.flip else ''
+    if o.rotate &gt; 0:
+      rotate = ' sch_r=%s' % str(o.rotate)
+    else:
+      rotate = ''
+#    t = '%s %s %s library="%s" lay_x=%s lay_y=%s sch_x=%s sch_y=%s %s%s'  % \
+#         ( "X"+o.component+"_"+str(o.index), nets_str, o.component, o.library, str (o.x * 1e-6), o.y * 1e-6, o.x, o.y, rotate, flip)
+    t = '  %s %s %s library="%s" sch_x=%s sch_y=%s %s%s'  % \
+         ( "X"+o.component+"_"+str(o.index), nets_str, o.component, o.library, eng_str(o.x * 5e-2), eng_str(o.y * 5e-2), rotate, flip)
+    print (t)
+    wtext.insertHtml('%s&lt;br&gt;' %t)
+
+def list_optical_waveguides(list_optical_waveguides):
+  # list all Optical_waveguides objects from an array
+  # input array, optical_waveguides
+  # example output:         
+  # X5 9 10 ebeam_wg_strip_1550 library="Design kits/ebeam_v1.0" wg_length=7.86299e-06 wg_width=5.085e-07 sch_x=-1.42 sch_y=-0.265
+
+  for o in list_optical_waveguides:
+    nets_str = "N$%s N$%s" %(o.net1, o.net2)
+    x,y = xy_mean_mult(o.points, dbu)
+#    t = '%s %s %s library="%s" wg_length=%s wg_width=%s lay_x=%s lay_y=%s sch_x=%5.3f sch_y=%5.3f'  % \
+#           ( "Xwg" + str(o.index), nets_str, o.component, o.library, eng_str(o.length*1e-6), eng_str(o.wg_width*1e-6), \
+#             eng_str(x * 1e-6), eng_str(y * 1e-6), x, y)
+    t = '  %s %s %s library="%s" wg_length=%s wg_width=%s sch_x=%s sch_y=%s'  % \
+           ( "Xwg" + str(o.index), nets_str, o.component, o.library, \
+             eng_str(o.length*1e-6), eng_str(o.wg_width*1e-6), eng_str(x * 5e-2), eng_str(y * 5e-2))
+    print (t)
+    wtext.insertHtml('%s&lt;br&gt;' %t)
+
+
 def waveguide_set_target_length():
   # Function to move the edges of a waveguide to obtain a target length
   # - Dialog prompts user for a target length, and to click on an edge to select shape and edge to move