function [port_bonds, status] = abg2cbg(system_name, system_type, full_name,
					port_bonds,
					port_bond_direction,
					port_status,
					derivative_causality,
					typefile, infofile, errorfile)

  ## abg2cbg - acausal to causal bg conversion
  ##
  ##     ###################################### 
  ##     ##### Model Transformation Tools #####
  ##     ######################################
  ## 
  ## Matlab function  abg2cbg.m
  ## Acausal bond graph to causal bond graph: mfile format
  ## [bonds,status] = abg2cbg(system_name, system_type, full_name, port_bonds, infofile)

  ## ###############################################################
  ## ## Version control history
  ## ###############################################################
  ## ## $Id$
  ## ## $Log$
  ## ## Revision 1.53  2009/11/02 16:54:03  geraint
  ## ## Replaced deprecated functions from Octave 2.1 for Octave 3.0: is_struct -> isstruct, struct_contains -> isfield, struct_elements -> fieldnames, is_complex -> iscomplex, setstr -> char
  ## ##
  ## ## Revision 1.52  2004/09/07 18:22:53  geraint
  ## ## Issues a more helpful error message than the cryptic Octave stuff
  ## ## if there are unconnected ports.
  ## ##
  ## ## Revision 1.51  2004/02/20 20:42:40  geraint
  ## ## Initialize Flipped.cons with [] instead of "".
  ## ##
  ## ## Revision 1.50  2003/03/13 15:18:39  gawthrop
  ## ## Now uses __ to delimit subsystems in names.
  ## ##
  ## ## Revision 1.49  2001/07/26 05:02:53  geraint
  ## ## Now writes cbg.fig when under-causal (again).
  ## ##
  ## ## Revision 1.48  2001/07/23 23:20:27  gawthrop
  ## ## Now only writes to type.sh and cbg.m when causality is completed.
  ## ##
  ## ## Revision 1.47  2000/03/20 16:45:26  peterg
  ## ## *** empty log message ***
  ## ##
  ## ## Revision 1.46  2000/02/17 16:14:49  peterg
  ## ## *** empty log message ***
  ## ##
  ## ## Revision 1.45  1999/11/01 03:17:45  peterg
  ## ## Added extra info - current subsystem
  ## ##
  ## ## Revision 1.44  1999/03/11 23:54:11  peterg
  ## ## Include possibility of vector SS when finding port_bond_index
  ## ##
  ## ## Revision 1.43  1998/12/14 15:19:36  peterg
  ## ## Added missing "derivative_causality," argument to recursive call of
  ## ## this function
  ## ##
  ## ## Revision 1.42  1998/12/03 14:55:40  peterg
  ## ## Now uses number of components with complete causality to measure
  ## ## progress of algorithm -- Done.
  ## ## This replaces bond count -- done.
  ## ##
  ## ## Revision 1.41  1998/11/20 10:52:28  peterg
  ## ## Copies port bonds if the port bonds ARE set
  ## ## -- replaces Copies port bonds if the component bonds are NOT set
  ## ##
  ## ## Revision 1.40  1998/09/02 11:47:09  peterg
  ## ## Now uses explicit ordered list of ports instead of port.index.
  ## ## Note that subsystems are still treated in arbitrary order.
  ## ##
  ## ## Revision 1.39  1998/08/25 20:06:16  peterg
  ## ## Writes flipped port info
  ## ##
  ## ## Revision 1.38  1998/08/25 09:15:28  peterg
  ## ## Fixed couple of problems with using two copies of the one data
  ## ## stucture:
  ## ##
  ## ## ABG_field and ABG.field
  ## ##
  ## ## Maybe this is conceptually wrong?
  ## ##
  ## ## Revision 1.37  1998/08/25 08:33:29  peterg
  ## ## Now does ports as well - fixed string prob by using deblank
  ## ##
  ## ## Revision 1.36  1998/08/25 06:44:40  peterg
  ## ## Furhter revisions
  ## ##
  ## ## Revision 1.35  1998/08/24 10:16:32  peterg
  ## ## Coverted to new structure - still needs status sorting.
  ## ##
  ## ## Revision 1.34  1998/08/24 07:35:03  peterg
  ## ## About to go to new abg format.
  ## ##
  ## ## Revision 1.33  1998/07/29 13:36:37  peterg
  ## ## Don't set port status if there aren't any ports.
  ## ##
  ## ## Revision 1.32  1998/07/28 19:06:11  peterg
  ## ## *** empty log message ***
  ## ##
  ## ## Revision 1.31  1998/07/28 13:15:10  peterg
  ## ## Vector SS ports included.
  ## ##
  ## ## Revision 1.30  1998/07/27 20:29:49  peterg
  ## ## Had another go at causality ....
  ## ##   1. Impose external causality onto all port bonds
  ## ##   2. Set C_cause.m so that it DOESN'T set causality
  ## ##       -- I_cause is already ok !
  ## ##
  ## ## Revision 1.29  1998/07/10 09:01:42  peterg
  ## ## Added error + info file in new form
  ## ##
  ## ## Revision 1.28  1998/07/08 09:23:42  peterg
  ## ## Undid the previous change -- needs more thought.
  ## ##
  ## ## Revision 1.27  1998/07/03 19:03:31  peterg
  ## ## Always override the causality of port bonds!
  ## ##
  ## ## Revision 1.26  1998/06/27 13:24:04  peterg
  ## ## Causality now set correctly for:
  ## ## 	multi-port C and I
  ## ## 	C and I with arrows pointing in
  ## ##
  ## ## Revision 1.25  1998/06/25 18:53:30  peterg
  ## ## Actually, the previous comment was optimistic.
  ## ## The port causalities on a compound are now forced to be the same as
  ## ## that specified by a a _cuase.m file (if it exists)
  ## ##
  ## ## Revision 1.24  1998/06/25 17:45:03  peterg
  ## ## No change -- but checked that explicit causality works!
  ## ##
  ## ## Revision 1.23  1998/04/04 10:46:37  peterg
  ## ## Coerces port bonds to have smae direction as the imposing bonds
  ## ## _cbg now generates the (coerced) components as welll as the (coerced)
  ## ## causality.
  ## ##
  ## ## Revision 1.22  1997/08/19 10:21:09  peterg
  ## ## Only copy port cuaslity info if not already set within the
  ## ## subsystem. I thought I'd done this already ....
  ## ##
  ## ## Revision 1.21  1997/08/18 16:25:25  peterg
  ## ## Minor bug fixes
  ## ##
  ## ## Revision 1.20  1997/08/18 12:45:24  peterg
  ## ## Replaced: comp_bonds = bonds(bond_list,:)
  ## ## by: 	for kk = 1:n_comp
  ## ## 	  comp_bonds(kk,:) = bonds(comp(kk),:);
  ## ## 	end;
  ## ##
  ## ## to avoid an octave bug in 1.92.
  ## ##
  ## ## Revision 1.19  1997/08/18 11:23:59  peterg
  ## ## Main component loop now misses out the ports (SS:[]) -- the causality
  ## ## is merely passed through these components.
  ## ##
  ## ## Revision 1.18  1997/08/08 08:11:04  peterg
  ## ## Suppress compoment trace.
  ## ##
  ## ## Revision 1.17  1997/08/07 16:10:13  peterg
  ## ## Move the if status ..  to the beginning of the main loop.
  ## ##
  ## ## Revision 1.16  1997/08/04 13:11:19  peterg
  ## ## Only change to component-orientated causality for simple components
  ## ## NOT for compound components.
  ## ##
  ## ## Revision 1.15  1997/01/05 12:25:59  peterg
  ## ## More informative message about port bonds incompatible with  ports
  ## ##
  ## ## Revision 1.14  1996/12/31 16:20:42  peterg
  ## ## Just write causality information at top level -- it gets a bit
  ## ## voluminous if written at deeper levels.
  ## ##
  ## ## Revision 1.13  1996/12/31 11:49:09  peterg
  ## ## Don't copy port bond causality if already set -- allows subsystem
  ## ## causality to be preset directely on named SS.
  ## ##
  ## ## Revision 1.12  1996/12/31 11:42:36  peterg
  ## ## *** empty log message ***
  ## ##
  ## ## Revision 1.11  1996/12/07  17:10:48  peterg
  ## ## Allows port SS at top level - ie takes it to be an ardianry SS at top
  ## ## level.
  ## ##
  ## ## Revision 1.10  1996/12/04 21:48:55  peterg
  ## ## Compares full-name with empty string (instead of testing for zero
  ## ## length.
  ## ##
  ## ## Revision 1.9  1996/08/30  12:55:40  peter
  ## ## More heirachical stuff added.
  ## ##
  ## ## Revision 1.8  1996/08/26  10:04:25  peterg
  ## ## Fixed error due to a line wrap.
  ## ##
  ## ##Revision 1.7  1996/08/16  12:58:58  peter
  ## ## Now does preferred causality of I and C.
  ## ## Revision 1.6  1996/08/09 08:27:29  peter
  ## ## Added a few deguging lines
  ## ##
  ## ## Revision 1.5  1996/08/08 18:06:18  peter
  ## ## Unified file naming scheme
  ## ##
  ## ## Revision 1.4  1996/08/08 08:30:06  peter
  ## ## The cbg filename contains the system name - this makes things easier
  ## ## when setting up the m to fig translation and m to ese translation
  ## ##
  ## ## Revision 1.3  1996/08/05 18:53:21  peter
  ## ## Fixed bug passing causality from subsystems.
  ## ##
  ## ## Revision 1.2  1996/08/05 15:41:41  peter
  ## ## Now recursively does causality on subsystems.
  ## ##
  ## ## Revision 1.1  1996/08/04 17:55:55  peter
  ## ## Initial revision
  ## ##
  ## ###############################################################


  mtt_info(sprintf("Completing causality for subsystem %s", system_name), infofile);

  pc = '%';
  sub_delim = "__";		# Subsystem delimiter

  if nargin<1
    system_name = 'no_name';
  end;

  if nargin<4
    port_bonds = [];
  end;

  if nargin<5
    infofile = 'stdout';
  end;

  ## Are we at the top level of the heirarchy?
  at_top_level = strcmp(full_name, '');

  ## Create a file to contain shell commands which map subsystem types 
  ## onto components
#   if at_top_level # Then at top level
#     fprintf(typefile, "# Commands to map types onto subsystems\n");
#     fprintf(typefile, "# File %s_type.sh\n", system_name);
#     fprintf(typefile, "# Generated by MTT at %s\n\n", ctime(time));
#   end;

  ## Create the (full) system name
  if at_top_level
    full_name = system_name;
    system_type = system_name;
  else
    full_name = [full_name, sub_delim, system_name];
  end;
  
  fun_name = [system_type, "_abg"];

  disp("====================================");
  disp(["BEGIN: ", full_name, " (", fun_name, ")"]);
  disp("====================================");

  ## If no such function - then there is nothing to be done.
  if exist(fun_name)~=2
    mtt_error(["m-file ", fun_name, " does not exist"], errorfile);
    bonds = [];
    status = [];
    return
  end;

  ## Evaluate the system function to get the bonds and number of ports
  ##eval(["[bonds,components,n_ports,N_ports]=", fun_name, ";"]);
  eval(["[ABG]=", fun_name, ";"]);
  !isfield(ABG,"subsystems")
  if !isfield(ABG,"subsystems")# Are there any subsystems?
    return;			# Nothing to do
  else
    [n_subsystems,junk] = size(fieldnames(ABG.subsystems))
  endif
  
  if isfield(ABG,"portlist")# Are there any ports?
    [n_ports,junk] = size(ABG.portlist);
    ##     port_bond_index=zeros(n_ports,1);
    i_port = 0;
    for i=1:n_ports		# Find indices of the internal ports
      name = deblank(ABG.portlist(i,:)); # Name of this port
      eval(["port = ABG.ports.",name,";"]); # Extract port info
      for j=1:length(port.connections) # Maybe vector SS
	port_bond_index(++i_port) = abs(port.connections(j));
      endfor;
    endfor
  else
    n_ports = 0;
  endif				   

  
  [n_bonds,columns] = size(ABG.bonds);# Find number of bonds
  if (columns ~= 2)&(n_bonds>0)
    error("Incorrect bonds matrix: must have 2 columns");
  end;

  
  ## Find number of components
  ##  [n_components,m_components] = size(components);
  ##  if n_components==0 # there is nothing to be done
  ##    return
  ##  end;


  
  ## Coerce the port (SS:[]) component bonds to have the same direction as
  ## of the bonds in the encapsulating system -- but not at top level
  Flipped.ports="";Flipped.subs="";Flipped.cons=[];
  
  if (n_ports>0)&&(!at_top_level) # Coerce directions
    for i=1:n_ports
      name = deblank(ABG.portlist(i,:)); # Name of this port
      eval(["port = ABG.ports.",name,";"]); # Extract port info
      disp ("----");
      i
      name
      port
      port_bond_direction
      port.connections

      if (i > max (size (port_bond_direction)))
	the_system = sprintf ("\"%s:%s\"", system_type, system_name);
	mtt_error (sprintf ("Please check that %s has no disconnected ports.", the_system));
	mtt_error (sprintf ("abg2cbg: port_bond_direction(%d) does not exist.", i));
	exit(1);
      end
      if (sign(port.connections)!=port_bond_direction(i)) # Direction different?
      	eval(["ABG.ports.",name,".connections = - port.connections;"]); # Flip direction at port
	Flipped.ports=[Flipped.ports;name];	# Remember which port has been flipped
        bond_index=abs(port.connections); # Index of bond on port
      	mtt_info(sprintf("Flip port %s on %s" ...
			 ,name,full_name),infofile); # And report
      	for [subsystem,name] = ABG.subsystems # and at the other end
	  for k=1:length(subsystem.connections)
	    if (abs(subsystem.connections(k))==bond_index) # Then flip the connection
	      eval(["ABG.subsystems.",name,".connections(k)   = -subsystem.connections(k);"]);
	      Flipped.subs=[Flipped.subs;name];	# Remember which subsystem has been flipped
	      Flipped.cons=[Flipped.cons;k];	# Remember which connection has been flipped
      	      mtt_info(sprintf("Flip subsystem %s on %s" ...
			       ,name,full_name),infofile); # And report
	    endif
	  endfor
      	endfor			# subsystem = ABG.subsystems

      	ABG.bonds(bond_index,:) = -ABG.bonds(bond_index,:);	# Flip the bond causalities 
	##(these are arrow-orientated)
      endif			# Is the direction different?
    endfor			# port = ABG.ports
  endif				# (n_ports>0)&&(!at_top_level)

  ## If not at top level, then copy the port bonds.
  if !at_top_level		# Find number of port bonds

    for j=1:n_ports
      jj = port_bond_index(j); # The index of the bond
      for k = 1:2
	##	if ABG.bonds(jj,k)==0 # only copy if not already set
	##	  ABG.bonds(jj,k) = port_bonds(j,k);
	##	endif
	if port_bonds(j,k)!=0	# only copy if port bonds are set
	  ABG.bonds(jj,k) = port_bonds(j,k);
	endif
      endfor
    endfor
  else
    n_port_bonds=0;
  endif
  
  ## Causality indicator
  total = 2*n_bonds;
  done = sum(sum(abs(ABG.bonds)))/total*100;

  fields=["ports";"subsystems"];	# Do for both ports and subsystems -
  ## ports first
  for i=1:2
    field=deblank(fields(i,:));
    if isfield(ABG,field);
      eval(["ABG_field = ABG.",field, ";"]);
      field,ABG_field
      
      sum_ok = 0; n_comp = 0;
      for [subsystem,name] = ABG_field# Find % status = 0 (causally complete)
    	eval(["ok = (ABG_field.",name,".status==0);"]);
	sum_ok = sum_ok + ok; n_comp ++;
      endfor;
      Done = sum_ok/n_comp*100
      
      ## Outer while loop sets preferred causality
      ci_index=1;

      ##      for [subsystem,name] = ABG_field# Set new status field to -1
      ##    	eval(["ABG_field.",name,".status=-1;"]);
      ##      endfor;
      
      while( ci_index>0)
    	old_done = inf;
    	old_Done = inf;
	
    	while Done!=old_Done	# Inner loop propagates causality
	  old_Done = Done;
	  for [subsystem,name] = ABG_field
	    name,subsystem
      	    if subsystem.status != 0 # only do this if causality not yet complete
	      comp = subsystem.connections; # Get the bonds on this component
	      bond_list = abs(comp);
	      direction = sign(comp)'*[1 1];
              n_bonds = length(bond_list);

	      if strcmp(subsystem.type,"0") # Change names
	    	subsystem.type = "zero";
	      end;
	      if strcmp(subsystem.type,"1")
	    	subsystem.type = "one";
	      end;
	      
	      cause_name = [subsystem.type, "_cause"];# Component causality procedure name
	      eqn_name = [subsystem.type, "_eqn"]; #Component equation procedure name
	      
	      comp_bonds=[];	# Bonds on this component (arrow-orientated) -- these become the
	      for kk = 1:n_bonds # port bonds on the ith component of this subsystem.
	    	comp_bonds(kk,:) = ABG.bonds(bond_list(kk),:);
	      end;

	      if exist(eqn_name)!=2 # Try a compound component
		## Port status depends on whether the corresponding bonds are
		##  fully causal at this stage.
            	one = ones(n_bonds,1);
            	port_status = (sum(abs(comp_bonds'))'==2*one) - one;
		
	    	port_bond_direction = -sign(subsystem.connections)'; # Direction of bonds

            	if exist(cause_name)==2	# If there is a predefined causality function; use it
		  comp_bonds = comp_bonds.*(port_bond_direction*[1 1]);	# Convert from arrow orientated to component orientated causality
		  eval([ "[comp_bonds] = ", cause_name, "(comp_bonds);" ]); # Evaluate the built-in causality procedure

		  comp_bonds = comp_bonds.*(port_bond_direction*[1 1]);	# and convert from component orientated to arrow orientated causality
            	end;
		
		port_bond_direction,comp_bonds
	    	[comp_bonds,subsystem.status] = abg2cbg(name, subsystem.type, full_name, 
							comp_bonds, port_bond_direction, port_status, ...
							derivative_causality, ...
						    	typefile, infofile, errorfile);

		
	      else # its a simple component -- or explicit causality defined
		mtt_info(sprintf("Completing causality for component %s (%s)",
				 name, subsystem.type), infofile);
	    	disp(["---", name, " (", cause_name, ") ---"]);
	    	comp_bonds_in = comp_bonds
	    	
		## Convert from arrow orientated to component orientated causality
	    	comp_bonds = comp_bonds.*direction;
	    	
		## Evaluate the built-in causality procedure
		##eval([ "[comp_bonds,status(i)] = ", cause_name, "(comp_bonds);" ]);
	    	eval([ "[comp_bonds,subsystem.status] = ", cause_name, "(comp_bonds)" ]);
		## and convert from component orientated to arrow orientated causality
            	comp_bonds = comp_bonds.*direction; 
		
	    	comp_bonds_out = comp_bonds
	      end;
	      
	      ABG.bonds(bond_list,:) = comp_bonds;# Update the full bonds list
	      eval(["ABG_field.",name,".status = subsystem.status;"]);
    	    end;
	  end;

	  sum_ok = 0; n_comp = 0;
	  for [subsystem,name] = ABG_field# Find % status = 0 (causally complete)
    	    eval(["ok = (ABG_field.",name,".status==0);"]);
	    sum_ok = sum_ok + ok; n_comp ++;
	  endfor;

	  Done = sum_ok/n_comp*100
	  done = sum(sum(abs(ABG.bonds)))/total*100
	  ##disp(sprintf("Causality is #3.0f#s complete.", done, pc), infofile));
	  
    	endwhile			# done!=old_done
  	
    	[name,prefered] = getdynamic(ABG_field) # Set causality of a C or I which is not already set
    	if prefered==0
	  ci_index=0;
    	else
	  disp("Set causality of a C or I which is not already set")
	  eval(["ci_bond_index = ABG.",field,".",name,".connections;"]); # Get bonds
	  ci_direction = sign(ci_bond_index);
	  ci_bond_index = abs(ci_bond_index);
	  if derivative_causality
	    prefered = -prefered;
	  end;
	  ABG.bonds(ci_bond_index,1:2) = prefered*ci_direction'*[1 1]
	  eval(["ABG.subsystems.",name,".status=0"]); #set status of the C or I
    	endif
      endwhile			# ( ci_index>0)
      eval(["ABG.",field," = ABG_field;"]); # Copy back to actual structure
    endif			# isfield(CBG,field(i,:));
  endfor
  ##  if n_ports>0
  ##    status(1:n_ports) = zeros(n_ports,1); # Port status not relevant
  ##  endif;
  
  ## Print final causality
  ##  final_done =  (sum(status==zeros(n_components,1))/n_components)*100;
  
  if at_top_level
    mtt_info(sprintf("Final causality of %s is %3.0f%s complete.", ...
		     full_name, Done, pc), infofile);
    
    if Done<100
      mtt_error(sprintf("Unable to complete causality"),errorfile);
    end;
  endif				# at_top_level
  


  
  ## Return the port bonds - arrow orientated causality - and the direction 
  status=0;
  if !at_top_level # Not at top level
    port_bonds = ABG.bonds(port_bond_index,:); # Return port bonds
  endif;				# at top level

  for [subsystem,name] = ABG.subsystems
    if subsystem.status==-1	# Under causal
      status=-1;
      mtt_info(sprintf("Component %s (%s) is undercausal", name, subsystem.type), ...
	       infofile);
    elseif subsystem.status==1;	# Over causal
      status=-1;
      mtt_info(sprintf("Component %s (%s) is overcausal", name, subsystem.type), ...
	       infofile);
    endif;
  endfor;			# [subsystem,name] = ABG.subsystems

  ## write out the component .cbg file
    disp(["Writing ", full_name]);
    write_cbg(full_name,system_type,ABG,Flipped);
    fprintf(typefile, "$1%s$2%s$3\n", system_type, full_name);
  


  status, port_bonds
  disp("====================================");
  disp(["END: ", full_name, " (", fun_name, ")"]);
  disp("====================================");


endfunction;