Changeset 867 for trunk/src/series

Timestamp:

Feb 12, 2015, 9:31:47 PM (9 years ago)

Author:

sommeria

Message:

python option added in series and bug corrections

Location:

trunk/src/series

Files:

• aver_stat.m (modified) (7 diffs)
• histo_diff.m (added)
• merge_proj.m (modified) (5 diffs)
• time_series.m (modified) (1 diff)

trunk/src/series/aver_stat.m

@@ -136 +136 @@
 for iview=1:NbView
     if ~exist(filecell{iview,1}','file')
-        msgbox_uvmat('ERROR',['the first input file ' filecell{iview,1} ' does not exist'])
+        disp_uvmat('ERROR',['the first input file ' filecell{iview,1} ' does not exist'],checkrun)
         return
     end
@@ -155 +155 @@
     diff_time=max(max(diff(time)));
     if diff_time>0
-        msgbox_uvmat('WARNING',['times of series differ by (max) ' num2str(diff_time)])
+        disp_uvmat('WARNING',['times of series differ by (max) ' num2str(diff_time)],checkrun)
     end   
 end
@@ -176 +176 @@
     FileExtOut='.nc';% write result as .nc files for netcdf inputs
 else
-    msgbox_uvmat('ERROR',['invalid file type input ' FileType{1}])
+    disp_uvmat('ERROR',['invalid file type input ' FileType{1}],checkrun)
     return
 end
 if NbView==2 && ~isequal(CheckImage{1},CheckImage{2})
-    msgbox_uvmat('ERROR','input must be two image series or two netcdf file series')
+    disp_uvmat('ERROR','input must be two image series or two netcdf file series',checkrun)
     return
 end
@@ -216 +216 @@
 % index_slice=i_slice:NbSlice:nbfield;% select file indices of the slice
 nbfiles=0;
-nbmissing=0;
+% nbmissing=0;
 
 %%%%%%%%%%%%%%%% loop on field indices %%%%%%%%%%%%%%%%
@@ -275 +275 @@
             [Field,errormsg]=proj_field(Field,Param.ProjObject);
             if ~isempty(errormsg)
-                msgbox_uvmat('ERROR',['error in aver_stat/proj_field:' errormsg])
+                disp_uvmat('ERROR',['error in aver_stat/proj_field:' errormsg],checkrun)
                 return
             end
@@ -289 +289 @@
             DataOut=Field;%default
             DataOut.Conventions='uvmat'; %suppress Conventions='uvmat/civdata' for civ input files
-            for ivar=1:length(Field.ListVarName)
+            errorvar=zeros(numel(Field.ListVarName));%index of errorflag associated to each variable
+            for ivar=1:numel(Field.ListVarName)
                 VarName=Field.ListVarName{ivar};
-                DataOut.(VarName)=double(DataOut.(VarName));
-            end
-        else   %current field
-            for ivar=1:length(Field.ListVarName)
-                VarName=Field.ListVarName{ivar};
-                sizmean=size(DataOut.(VarName));
-                siz=size(Field.(VarName));
-                if ~isequal(DataOut.(VarName),0)&& ~isequal(siz,sizmean)
-                    disp_uvmat('ERROR',['unequal size of input field ' VarName ', need to project  on a grid'],checkrun)
-                    return
+                DataOut.(VarName)=zeros(size(DataOut.(VarName)));% initiate each field to zero
+                NbData.(VarName)=zeros(size(DataOut.(VarName)));% initiate the nbre of good data to zero
+                for iivar=1:length(Field.VarAttribute)
+                    if isequal(Field.VarDimName{iivar},Field.VarDimName{ivar})&& isfield(Field.VarAttribute{iivar},'Role')...
+                            && strcmp(Field.VarAttribute{iivar}.Role,'errorflag')
+                        errorvar(ivar)=iivar; % index of the errorflag variable corresponding to ivar
+                    end
+                end
+            end
+            DataOut.ListVarName(errorvar(errorvar~=0))=[]; %remove errorflag from result
+            DataOut.VarDimName(errorvar(errorvar~=0))=[]; %remove errorflag from result
+            DataOut.VarAttribute(errorvar(errorvar~=0))=[]; %remove errorflag from result
+        end   %current field
+        for ivar=1:length(DataOut.ListVarName)
+            VarName=Field.ListVarName{ivar};
+            sizmean=size(DataOut.(VarName));
+            siz=size(Field.(VarName));
+            if ~isequal(DataOut.(VarName),0)&& ~isequal(siz,sizmean)
+                disp_uvmat('ERROR',['unequal size of input field ' VarName ', need to project  on a grid'],checkrun)
+                return
+            else
+                if errorvar(ivar)==0
+                    check_bad=isnan(Field.(VarName));%=0 for NaN data values, 1 else
                 else
-                    DataOut.(VarName)=DataOut.(VarName)+ double(Field.(VarName)); % update the sum
+                    check_bad=isnan(Field.(VarName)) | Field.(Field.ListVarName{errorvar(ivar)})~=0;%=0 for NaN or error flagged data values, 1 else
                 end
+                Field.(VarName)(check_bad)=0; %set to zero NaN or data marked by error flag
+                DataOut.(VarName)=DataOut.(VarName)+ double(Field.(VarName)); % update the sum
+                NbData.(VarName)=NbData.(VarName)+ ~check_bad;% records the number of data for each point
             end
         end
@@ -315 +332 @@
 for ivar=1:length(Field.ListVarName)
     VarName=Field.ListVarName{ivar};
-    DataOut.(VarName)=DataOut.(VarName)/nbfiles; % normalize the mean
-end
+    DataOut.(VarName)=DataOut.(VarName)./NbData.(VarName); % normalize the mean
+end
+nbmissing=NbField-nbfiles;
 if nbmissing~=0
-    msgbox_uvmat('WARNING',[num2str(nbmissing) ' input files are missing or skipted'])
+    disp_uvmat('WARNING',[num2str(nbmissing) ' input files are missing or skipted'],checkrun)
 end
 if isempty(time) % time is read from files

trunk/src/series/merge_proj.m

@@ -196 +196 @@
     FileExtOut='.nc'; %netcdf output
 end
-NomTypeOut=NomType;% output file index will indicate the first and last ref index in the series
+%NomTypeOut=NomType;% output file index will indicate the first and last ref index in the series
 RootFileOut=RootFile{1};
 for iview=2:NbView
@@ -403 +403 @@
 end
 errormsg='';
-MergeData=Data{1};% merged field= first field by default, reproduces the glabal attributes of the first field
+MergeData=Data{1};% merged field= first field by default, reproduces the global attributes of the first field
 NbView=length(Data);
-if NbView==1
-    return
+if NbView==1% if there is only one field, just reproduce it in MergeData
+    return 
 end
 
@@ -419 +419 @@
     if NbDim(icell)~=1 % skip field cells which are of dim 1
         switch CellInfo{icell}.CoordType
-            case 'scattered'  %case of input fields with unstructured coordinates: just concacene data
+            case 'scattered'  %case of input fields with unstructured coordinates: just concatene data
                 for ivar=CellInfo{icell}.VarIndex %  indices of the selected variables in the list FieldData.ListVarName
                     VarName=Data{1}.ListVarName{ivar};
-                    %MergeData=Data{1};% merged field= first field by default, reproduces the glabal attributes of the first field
                     for iview=2:NbView
                         MergeData.(VarName)=[MergeData.(VarName); Data{iview}.(VarName)];
@@ -431 +430 @@
                 if isfield(CellInfo{icell},'VarIndex_errorflag') && ~isempty(CellInfo{icell}.VarIndex_errorflag)
                     FFName=Data{1}.ListVarName{CellInfo{icell}.VarIndex_errorflag};% name of errorflag variable
+                    MergeData.ListVarName(CellInfo{icell}.VarIndex_errorflag)=[];%remove error flag variable in MergeData (will use NaN instead)
+                    MergeData.VarDimName(CellInfo{icell}.VarIndex_errorflag)=[];
+                    MergeData.VarAttribute(CellInfo{icell}.VarIndex_errorflag)=[];
                 end
                 % select good data on each view
@@ -441 +443 @@
                             check_bad=isnan(Data{iview}.(VarName)) | Data{iview}.(FFName)~=0;%=0 for NaN or error flagged data values, 1 else
                         end
-                        Data{iview}.(VarName)(check_bad)=0; %set to zero NaN or masked data
+                        Data{iview}.(VarName)(check_bad)=0; %set to zero NaN or data marked by error flag
                         if iview==1
-                            MergeData.(VarName)=Data{1}.(VarName);% correct the field of MergeData
+                            %MergeData.(VarName)=Data{1}.(VarName);% initiate MergeData with the first field
                             NbAver=~check_bad;% initiate NbAver: the nbre of good data for each point
                         elseif size(Data{iview}.(VarName))~=size(MergeData.(VarName))
                             errormsg='sizes of the input matrices do not agree, need to interpolate on a common grid using a projection object';
                             return
-                        else      
-                         
-                            MergeData.(VarName)=MergeData.(VarName) + Data{iview}.(VarName);%add data
+                        else                             
+                            MergeData.(VarName)=MergeData.(VarName) +double(Data{iview}.(VarName));%add data
                             NbAver=NbAver + ~check_bad;% add 1 for good data, 0 else
                         end
                     end
                     MergeData.(VarName)(NbAver~=0)=MergeData.(VarName)(NbAver~=0)./NbAver(NbAver~=0);% take average of defined data at each point
+                    MergeData.(VarName)(NbAver==0)=NaN;% set to NaN the points with no good data
                 end
         end
-        if isempty(FFName)
-            FFName='FF';
-        end
-        MergeData.(FFName)(NbAver~=0)=0;% flag to 1 undefined summed data
-        MergeData.(FFName)(NbAver==0)=1;% flag to 1 undefined summed data
+%         if isempty(FFName)
+%             FFName='FF';
+%         end
+%         MergeData.(FFName)(NbAver~=0)=0;% flag to 1 undefined summed data
+%         MergeData.(FFName)(NbAver==0)=1;% flag to 1 undefined summed data
     end
 end

trunk/src/series/time_series.m

@@ -207 +207 @@
 %% Set field names and velocity types
 InputFields{1}=[];%default (case of images)
+if nbview==2
+    InputFields{2}=[];%default (case of images)
+end
 if isfield(Param,'InputFields')
     InputFields{1}=Param.InputFields;
-end
-if nbview==2
-    InputFields{2}=[];%default (case of images)
-    if isfield(Param,'InputFields')
-        InputFields{2}=Param.InputFields{1};%default
+    if nbview==2
+        InputFields{2}=Param.InputFields;%default
         if isfield(Param.InputFields,'FieldName_1')
             InputFields{2}.FieldName=Param.InputFields.FieldName_1;