Index: /issm/trunk-jpl/src/m/classes/cfsurfacelogvel.m
===================================================================
--- /issm/trunk-jpl/src/m/classes/cfsurfacelogvel.m	(revision 22508)
+++ /issm/trunk-jpl/src/m/classes/cfsurfacelogvel.m	(revision 22508)
@@ -0,0 +1,104 @@
+%MISFIT class definition
+%
+%   Usage:
+%      cfsurfacelogvel=cfsurfacelogvel();
+%      cfsurfacelogvel=cfsurfacelogvel('name','SurfaceAltimetry',...
+%                    'definitionstring','Outputdefinition1',... 
+%                    'observation_string','SurfaceObservations',...
+%                    'observation',md.geometry.surface,...
+%                    'weights',ones(md.mesh.numberofvertices,1),...
+%                    'weights_string','WeightsSurfaceObservations',...
+%							'datatime',time);
+%
+%
+
+classdef cfsurfacelogvel
+	properties (SetAccess=public)
+		%cfsurfacelogvel
+		name               = '';
+		definitionstring   = ''; %string that identifies this output definition uniquely, from 'Outputdefinition[1-100]'
+		vxobs					 = NaN; %observed field that we compare the model against
+		vxobs_string		 = ''; %string for observed field.
+		vyobs			       = NaN; %observed field that we compare the model against
+		vyobs_string		 = ''; %string for observed field.
+		weights            = NaN; %weight coefficients for every vertex
+		weights_string     = ''; %string to identify this particular set of weights
+		datatime				 = 0; %time in years from start that the data is from 
+		cumulated          = NaN; %do we cumulate cfsurfacelogvel through time?
+	end
+	
+	methods
+		function self = extrude(self,md) % {{{
+			if ~isnan(self.weights)
+				self.weights=project3d(md,'vector',self.weights,'type','node');
+			end
+			if ~isnan(self.vxobs)
+				self.vxobs=project3d(md,'vector',self.vxobs,'type','node');
+			end
+		end % }}}
+		function self = cfsurfacelogvel(varargin) % {{{
+			if nargin==0,
+				self=setdefaultparameters(self);
+			else
+				%use provided options to change fields
+				options=pairoptions(varargin{:});
+
+				%get name
+				self.name=getfieldvalue(options,'name','');
+				self.definitionstring=getfieldvalue(options,'definitionstring');
+				self.vxobs=getfieldvalue(options,'vxobs',NaN);
+				self.vyobs=getfieldvalue(options,'vyobs',NaN);
+				self.vxobs_string=getfieldvalue(options,'vxobs_string');			
+				self.vyobs_string=getfieldvalue(options,'vyobs_string');
+				self.weights=getfieldvalue(options,'weights',NaN);
+				self.weights_string=getfieldvalue(options,'weights_string','');
+				self.datatime = getfieldvalue(options, 'datatime');
+
+			end
+		end % }}}
+		function self = setdefaultparameters(self) % {{{
+			self.datatime = 0;
+		end % }}}
+		function md = checkconsistency(self,md,solution,analyses) % {{{
+
+			if ~ischar(self.name),
+				error('cfsurfacelogvel error message: ''name'' field should be a string!');
+			end
+			OutputdefinitionStringArray={};
+			for i=1:100
+				OutputdefinitionStringArray{i}=strcat('Outputdefinition',num2str(i));
+			end
+			md = checkfield(md,'fieldname','self.definitionstring','field',self.definitionstring,'values',OutputdefinitionStringArray);
+
+			md = checkfield(md,'fieldname','self.vxobs','field',self.vxobs,'timeseries',1,'NaN',1,'Inf',1);
+			md = checkfield(md,'fieldname','self.weights','field',self.weights,'timeseries',1,'NaN',1,'Inf',1);
+			md = checkfield(md,'fieldname','self.datatime','field',self.datatime,'<=',md.timestepping.final_time);
+
+		end % }}}
+		function md = disp(self) % {{{
+		
+			disp(sprintf('   TimeMisfit:\n'));
+
+			fielddisplay(self,'name','identifier for this cfsurfacelogvel response');
+			fielddisplay(self,'definitionstring','string that identifies this output definition uniquely, from ''Outputdefinition[1-10]''');
+			fielddisplay(self,'vxobs','observed field that we compare the model against');
+			fielddisplay(self,'vxobs_string','observation string');
+			fielddisplay(self,'weights','weights (at vertices) to apply to the cfsurfacelogvel');
+			fielddisplay(self,'weights_string','string for weights for identification purposes');
+			fielddisplay(self,'datatime','time to compare data to model for misfit');
+
+		end % }}}
+		function md = marshall(self,prefix,md,fid) % {{{
+
+		WriteData(fid,prefix,'data',self.name,'name','md.cfsurfacelogvel.name','format','String');
+		WriteData(fid,prefix,'data',self.definitionstring,'name','md.cfsurfacelogvel.definitionstring','format','String');
+		WriteData(fid,prefix,'data',self.vxobs,'name','md.cfsurfacelogvel.vxobs','format','DoubleMat','mattype',1,'timeserieslength',md.mesh.numberofvertices+1,'yts',md.constants.yts);
+		WriteData(fid,prefix,'data',self.vxobs_string,'name','md.cfsurfacelogvel.vxobs_string','format','String');
+		WriteData(fid,prefix,'data',self.vyobs,'name','md.cfsurfacelogvel.vyobs','format','DoubleMat','mattype',1,'timeserieslength',md.mesh.numberofvertices+1,'yts',md.constants.yts);
+		WriteData(fid,prefix,'data',self.vyobs_string,'name','md.cfsurfacelogvel.vyobs_string','format','String');
+		WriteData(fid,prefix,'data',self.weights,'name','md.cfsurfacelogvel.weights','format','DoubleMat','mattype',1,'timeserieslength',md.mesh.numberofvertices+1,'yts',md.constants.yts);
+		WriteData(fid,prefix,'data',self.weights_string,'name','md.cfsurfacelogvel.weights_string','format','String');
+		WriteData(fid,prefix,'data',round(self.datatime*md.constants.yts),'name','md.cfsurfacelogvel.datatime','format','Integer');
+		end % }}}
+	end
+end
Index: /issm/trunk-jpl/src/m/classes/cfsurfacesquare.m
===================================================================
--- /issm/trunk-jpl/src/m/classes/cfsurfacesquare.m	(revision 22508)
+++ /issm/trunk-jpl/src/m/classes/cfsurfacesquare.m	(revision 22508)
@@ -0,0 +1,103 @@
+%MISFIT class definition
+%
+%   Usage:
+%      cfsurfacesquare=cfsurfacesquare();
+%      cfsurfacesquare=cfsurfacesquare('name','SurfaceAltimetry',...
+%                    'definitionstring','Outputdefinition1',... 
+%							'model_string','Surface',...
+%                    'observation_string','SurfaceObservations',...
+%                    'observation',md.geometry.surface,...
+%                    'weights',ones(md.mesh.numberofvertices,1),...
+%                    'weights_string','WeightsSurfaceObservations',...
+%							'datatime',time);
+%
+%
+
+classdef cfsurfacesquare
+	properties (SetAccess=public)
+		%cfsurfacesquare
+		name               = '';
+		definitionstring   = ''; %string that identifies this output definition uniquely, from 'Outputdefinition[1-100]'
+		model_string       = ''; %string for field that is modeled
+		observation        = NaN; %observed field that we compare the model against
+		observation_string = ''; %string for observed field.
+		weights            = NaN; %weight coefficients for every vertex
+		weights_string     = ''; %string to identify this particular set of weights
+		datatime				 = 0; %time in years from start that the data is from 
+		cumulated          = NaN; %do we cumulate cfsurfacesquare through time?
+	end
+	
+	methods
+		function self = extrude(self,md) % {{{
+			if ~isnan(self.weights)
+				self.weights=project3d(md,'vector',self.weights,'type','node');
+			end
+			if ~isnan(self.observation)
+				self.observation=project3d(md,'vector',self.observation,'type','node');
+			end
+		end % }}}
+		function self = cfsurfacesquare(varargin) % {{{
+			if nargin==0,
+				self=setdefaultparameters(self);
+			else
+				%use provided options to change fields
+				options=pairoptions(varargin{:});
+
+				%get name
+				self.name=getfieldvalue(options,'name','');
+				self.definitionstring=getfieldvalue(options,'definitionstring');
+				self.model_string=getfieldvalue(options,'model_string');
+				self.observation=getfieldvalue(options,'observation',NaN);
+				self.observation_string=getfieldvalue(options,'observation_string');
+				self.weights=getfieldvalue(options,'weights',NaN);
+				self.weights_string=getfieldvalue(options,'weights_string','');
+				self.datatime = getfieldvalue(options, 'datatime');
+
+			end
+		end % }}}
+		function self = setdefaultparameters(self) % {{{
+			self.datatime = 0;
+		end % }}}
+		function md = checkconsistency(self,md,solution,analyses) % {{{
+
+			if ~ischar(self.name),
+				error('cfsurfacesquare error message: ''name'' field should be a string!');
+			end
+			OutputdefinitionStringArray={};
+			for i=1:100
+				OutputdefinitionStringArray{i}=strcat('Outputdefinition',num2str(i));
+			end
+			md = checkfield(md,'fieldname','self.definitionstring','field',self.definitionstring,'values',OutputdefinitionStringArray);
+
+			md = checkfield(md,'fieldname','self.observation','field',self.observation,'timeseries',1,'NaN',1,'Inf',1);
+			md = checkfield(md,'fieldname','self.weights','field',self.weights,'timeseries',1,'NaN',1,'Inf',1);
+			md = checkfield(md,'fieldname','self.datatime','field',self.datatime,'<=',md.timestepping.final_time);
+
+		end % }}}
+		function md = disp(self) % {{{
+		
+			disp(sprintf('   TimeMisfit:\n'));
+
+			fielddisplay(self,'name','identifier for this cfsurfacesquare response');
+			fielddisplay(self,'definitionstring','string that identifies this output definition uniquely, from ''Outputdefinition[1-10]''');
+			fielddisplay(self,'model_string','string for field that is modeled');
+			fielddisplay(self,'observation','observed field that we compare the model against');
+			fielddisplay(self,'observation_string','observation string');
+			fielddisplay(self,'weights','weights (at vertices) to apply to the cfsurfacesquare');
+			fielddisplay(self,'weights_string','string for weights for identification purposes');
+			fielddisplay(self,'datatime','time to compare data to model for misfit');
+
+		end % }}}
+		function md = marshall(self,prefix,md,fid) % {{{
+
+		WriteData(fid,prefix,'data',self.name,'name','md.cfsurfacesquare.name','format','String');
+		WriteData(fid,prefix,'data',self.definitionstring,'name','md.cfsurfacesquare.definitionstring','format','String');
+		WriteData(fid,prefix,'data',self.model_string,'name','md.cfsurfacesquare.model_string','format','String');
+		WriteData(fid,prefix,'data',self.observation,'name','md.cfsurfacesquare.observation','format','DoubleMat','mattype',1,'timeserieslength',md.mesh.numberofvertices+1,'yts',md.constants.yts);
+		WriteData(fid,prefix,'data',self.observation_string,'name','md.cfsurfacesquare.observation_string','format','String');
+		WriteData(fid,prefix,'data',self.weights,'name','md.cfsurfacesquare.weights','format','DoubleMat','mattype',1,'timeserieslength',md.mesh.numberofvertices+1,'yts',md.constants.yts);
+		WriteData(fid,prefix,'data',self.weights_string,'name','md.cfsurfacesquare.weights_string','format','String');
+		WriteData(fid,prefix,'data',round(self.datatime*md.constants.yts),'name','md.cfsurfacesquare.datatime','format','Integer');
+		end % }}}
+	end
+end