Index: /issm/trunk-jpl/src/m/classes/numberedcostfunction.m
===================================================================
--- /issm/trunk-jpl/src/m/classes/numberedcostfunction.m	(revision 22387)
+++ /issm/trunk-jpl/src/m/classes/numberedcostfunction.m	(revision 22387)
@@ -0,0 +1,119 @@
+%M1QN3INVERSION class definition
+%
+%   Usage:
+%      numberedcostfunction=numberedcostfunction();
+
+classdef numberedcostfunction
+	properties (SetAccess=public) 
+		cost_functions              = NaN
+		cost_functions_coefficients = NaN
+		vx_obs                      = NaN
+		vy_obs                      = NaN
+		vz_obs                      = NaN
+		vel_obs                     = NaN
+		thickness_obs               = NaN
+		surface_obs                 = NaN
+	end
+	methods
+		function self = numberedcostfunction(varargin) % {{{
+			switch nargin
+				case 0
+					self=setdefaultparameters(self);
+				case 1
+					self=structtoobj(numberedcostfunction(),varargin{1});
+				otherwise
+					error('constructor not supported');
+			end
+		end % }}}
+		function self = extrude(self,md) % {{{
+			self.vx_obs=project3d(md,'vector',self.vx_obs,'type','node');
+			self.vy_obs=project3d(md,'vector',self.vy_obs,'type','node');
+			self.vel_obs=project3d(md,'vector',self.vel_obs,'type','node');
+			self.thickness_obs=project3d(md,'vector',self.thickness_obs,'type','node');
+			if numel(self.cost_functions_coefficients)>1,self.cost_functions_coefficients=project3d(md,'vector',self.cost_functions_coefficients,'type','node');end;
+			if numel(self.min_parameters)>1,self.min_parameters=project3d(md,'vector',self.min_parameters,'type','node');end;
+			if numel(self.max_parameters)>1,self.max_parameters=project3d(md,'vector',self.max_parameters,'type','node');end;
+		end % }}}
+		function self = setdefaultparameters(self) % {{{
+
+			%several responses can be used:
+			self.cost_functions=101;
+
+		end % }}}
+		function md = checkconsistency(self,md,solution,analyses) % {{{
+
+			num_costfunc=size(md.inversion.cost_functions,2);
+
+			md = checkfield(md,'fieldname','inversion.cost_functions','size',[1 num_costfunc],'values',supportedcostfunctions());
+			md = checkfield(md,'fieldname','inversion.cost_functions_coefficients','size',[md.mesh.numberofvertices num_costfunc],'>=',0);
+
+			if strcmp(solution,'BalancethicknessSolution')
+				md = checkfield(md,'fieldname','inversion.thickness_obs','size',[md.mesh.numberofvertices 1],'NaN',1,'Inf',1);
+				md = checkfield(md,'fieldname','inversion.surface_obs','size',[md.mesh.numberofvertices 1],'NaN',1,'Inf',1);
+			elseif strcmp(solution,'BalancethicknessSoftSolution')
+				md = checkfield(md,'fieldname','inversion.thickness_obs','size',[md.mesh.numberofvertices 1],'NaN',1,'Inf',1);
+			else
+				md = checkfield(md,'fieldname','inversion.vx_obs','size',[md.mesh.numberofvertices 1],'NaN',1,'Inf',1);
+				if ~strcmp(domaintype(md.mesh),'2Dvertical'),
+					md = checkfield(md,'fieldname','inversion.vy_obs','size',[md.mesh.numberofvertices 1],'NaN',1,'Inf',1);
+				end
+			end
+		end % }}}
+		function disp(self) % {{{
+			disp(sprintf('   numberedcostfunction parameters:'));
+			fielddisplay(self,'cost_functions','indicate the type of response for each optimization step');
+			fielddisplay(self,'cost_functions_coefficients','cost_functions_coefficients applied to the misfit of each vertex and for each control_parameter');
+			fielddisplay(self,'vx_obs','observed velocity x component [m/yr]');
+			fielddisplay(self,'vy_obs','observed velocity y component [m/yr]');
+			fielddisplay(self,'vel_obs','observed velocity magnitude [m/yr]');
+			fielddisplay(self,'thickness_obs','observed thickness [m]');
+			fielddisplay(self,'surface_obs','observed surface elevation [m]');
+			disp('Available cost functions:');
+			disp('   101: SurfaceAbsVelMisfit');
+			disp('   102: SurfaceRelVelMisfit');
+			disp('   103: SurfaceLogVelMisfit');
+			disp('   104: SurfaceLogVxVyMisfit');
+			disp('   105: SurfaceAverageVelMisfit');
+			disp('   201: ThicknessAbsMisfit');
+			disp('   501: DragCoefficientAbsGradient');
+			disp('   502: RheologyBbarAbsGradient');
+			disp('   503: ThicknessAbsGradient');
+		end % }}}
+		function marshall(self,prefix,md,fid) % {{{
+
+			yts=md.constants.yts;
+
+			WriteData(fid,prefix,'name','md.inversion.type','data',2,'format','Integer');
+			WriteData(fid,prefix,'object',self,'class','inversion','fieldname','cost_functions_coefficients','format','DoubleMat','mattype',1);
+			WriteData(fid,prefix,'object',self,'class','inversion','fieldname','vx_obs','format','DoubleMat','mattype',1,'scale',1./yts);
+			WriteData(fid,prefix,'object',self,'class','inversion','fieldname','vy_obs','format','DoubleMat','mattype',1,'scale',1./yts);
+			WriteData(fid,prefix,'object',self,'class','inversion','fieldname','vz_obs','format','DoubleMat','mattype',1,'scale',1./yts);
+			WriteData(fid,prefix,'object',self,'class','inversion','fieldname','vel_obs','format','DoubleMat','mattype',1,'scale',1./yts);
+			if(numel(self.thickness_obs)==md.mesh.numberofelements),
+				mattype=2;
+			else
+				mattype=1;
+			end
+			WriteData(fid,prefix,'object',self,'class','inversion','fieldname','thickness_obs','format','DoubleMat','mattype',mattype);
+			WriteData(fid,prefix,'object',self,'class','inversion','fieldname','surface_obs','format','DoubleMat','mattype',mattype);
+
+			%process cost functions
+			num_cost_functions=size(self.cost_functions,2);
+			data=marshallcostfunctions(self.cost_functions);
+			WriteData(fid,prefix,'data',data,'name','md.inversion.cost_functions','format','StringArray');
+			WriteData(fid,prefix,'data',num_cost_functions,'name','md.inversion.num_cost_functions','format','Integer');
+		end % }}}
+		function savemodeljs(self,fid,modelname) % {{{
+		
+			writejs2Darray(fid,[modelname '.inversion.cost_functions'],self.cost_functions);
+			writejs2Darray(fid,[modelname '.inversion.cost_functions_coefficients'],self.cost_functions_coefficients);
+			writejs1Darray(fid,[modelname '.inversion.vx_obs'],self.vx_obs);
+			writejs1Darray(fid,[modelname '.inversion.vy_obs'],self.vy_obs);
+			writejs1Darray(fid,[modelname '.inversion.vz_obs'],self.vz_obs);
+			writejs1Darray(fid,[modelname '.inversion.vel_obs'],self.vel_obs);
+			writejs1Darray(fid,[modelname '.inversion.thickness_obs'],self.thickness_obs);
+			writejs1Darray(fid,[modelname '.inversion.surface_obs'],self.surface_obs);
+
+		end % }}}
+	end
+end