Changeset 1181 for trunk/src/series

Timestamp:

May 21, 2025, 6:14:05 PM (9 months ago)

Author:

sommeria

Message:

image rescale included in civ_series input

Location:

trunk/src/series

Files:

• check_data_files.m (modified) (1 diff)
• civ_input.fig (modified) (previous)
• civ_input.m (modified) (6 diffs)
• civ_series.m (modified) (4 diffs)
• filter_time_singlefile.m (modified) (3 diffs)

trunk/src/series/check_data_files.m

@@ -176 +176 @@
             end
         else
-            datnum=datnum(datnum);%keep the non zero values corresponding to existing files
-            filefound=filefound(datnum);
+            datnum=datnum(datnum~=0);%keep the non zero values corresponding to existing files
+            filefound=filefound(datnum~=0);
             [first,ind]=min(datnum);
             [last,indlast]=max(datnum);

trunk/src/series/civ_input.m

@@ -91 +91 @@
 if isfield(SeriesData,'FileInfo')
     FileType=SeriesData.FileInfo{1}.FileType;% info on the first input file series
-    FieldType=SeriesData.FileInfo{1}.FieldType;% info on the first input file series
+    %FieldType=SeriesData.FileInfo{1}.FieldType;% info on the first input file series
 else
     set(hhseries.REFRESH,'BackgroundColor',[1 0 1])% indicate that the file input in series needs to be refreshed 
@@ -207 +207 @@
     set(handles.TimeSource,'String',Param.IndexRange.TimeSource);
 else
+    msgbox_uvmat('WARNING','timing not defined (check xml file), default values used')
     set(handles.TimeSource,'String',''); %xml file not used for timing
     TimeUnit='frame';
@@ -377 +378 @@
 %% list the possible index pairs, depending on the option set in ListPairMode
 ListPairMode_Callback([], [], handles)
-
+if isfield(Param,'ActionInput')&& isfield(Param.ActionInput,'PairIndices')
+    if isfield(Param.ActionInput.PairIndices,'ListPairCiv1')
+        PairChoiceCiv1=find(strcmp(Param.ActionInput.PairIndices.ListPairCiv1,get(handles.ListPairCiv1,'String')));
+        if ~isempty(PairChoiceCiv1)
+            set(handles.ListPairCiv1,'Value',PairChoiceCiv1)
+        end
+    end
+    if isfield(Param.ActionInput.PairIndices,'ListPairCiv2')
+        PairChoiceCiv2=find(strcmp(Param.ActionInput.PairIndices.ListPairCiv2,get(handles.ListPairCiv2,'String')));
+        if ~isempty(PairChoiceCiv2)
+            set(handles.ListPairCiv2,'Value',PairChoiceCiv2)
+        end
+    end
+end
+  
 %% set the GUI to modal: wait for OK to close
 set(handles.civ_input,'WindowStyle','modal')% Make the GUI modal
@@ -810 +825 @@
 %reproduce by default the chosen pair in the checkciv2 menu
 set(handles.ListPairCiv2,'Value',get(handles.ListPairCiv1,'Value'))%civ2 selection the same as civ1 by default
-ListPairCiv2_Callback(hObject, eventdata, handles)
-
-%------------------------------------------------------------------------
-% --- Executes on selection change in ListPairCiv2.
-function ListPairCiv2_Callback(hObject, eventdata, handles)
-%------------------------------------------------------------------------
+%ListPairCiv2_Callback(hObject, eventdata, handles)
+
+% %------------------------------------------------------------------------
+% % --- Executes on selection change in ListPairCiv2.
+% function ListPairCiv2_Callback(hObject, eventdata, handles)
+% %------------------------------------------------------------------------
 
 %------------------------------------------------------------------------
@@ -1527 +1542 @@
     set(obj,'Visible','off')
 end
+set(handles.ConfigSource,'String','NEW')
+set(handles.OK,'BackgroundColor',[1 0 1])
+
+
+%------------------------------------------------------------------------
+% --- Executes on button press in CheckRescale.
+function CheckRescale_Callback(hObject, eventdata, handles)
+%------------------------------------------------------------------------
+huipanel=get(hObject,'parent');
+obj(1)=findobj(huipanel,'Tag','num_Maxtanh');
+obj(2)=findobj(huipanel,'Tag','title_Maxtanh');
+if get(hObject,'Value')% if chck box has been selected
+    set(obj,'Visible','on')
+else
+    set(obj,'Visible','off')
+end
+set(handles.ConfigSource,'String','NEW')
+set(handles.OK,'BackgroundColor',[1 0 1])
+
+%------------------------------------------------------------------------
+% --- synchronise the image threshold for civ1 and civ2
+function num_MaxIma_Callback(hObject, eventdata, handles)
+MaxIma_string=get(hObject,'String');
+set(handles.num_MaxIma,'String',MaxIma_string);
+set(handles.num_MaxIma,'Visible','on');
+set(handles.title_Threshold,'Visible','on');
+set(handles.CheckThreshold,'Value',true);
+
+set(handles.ConfigSource,'String','NEW')
+set(handles.OK,'BackgroundColor',[1 0 1])
+
+%------------------------------------------------------------------------
+% --- synchronise the image rescaling threshold for civ1 and civ2
+function num_Maxtanh_Callback(hObject, eventdata, handles)
+Maxtanh_string=get(hObject,'String');
+set(handles.num_Maxtanh,'String',Maxtanh_string);
+set(handles.num_Maxtanh,'Visible','on');
+set(handles.title_Maxtanh,'Visible','on');
+set(handles.CheckRescale,'Value',true);
+
 set(handles.ConfigSource,'String','NEW')
 set(handles.OK,'BackgroundColor',[1 0 1])
@@ -1952 +2007 @@
 
 
-function edit108_Callback(hObject, eventdata, handles)
-% hObject    handle to edit108 (see GCBO)
-% eventdata  reserved - to be defined in a future version of MATLAB
-% handles    structure with handles and user data (see GUIDATA)
-
-% Hints: get(hObject,'String') returns contents of edit108 as text
-%        str2double(get(hObject,'String')) returns contents of edit108 as a double
-
-
 % --- Executes on button press in CheckBackground.
 function CheckBackground_Callback(hObject, eventdata, handles)

trunk/src/series/civ_series.m

@@ -69 +69 @@
     Data.VelType='off';% menu for selecting the velocity type (options 'off'/'one'/'two',  'off' by default)
     Data.FieldName='on';% menu for selecting the field (s) in the input file(options 'off'/'one'/'two', 'off' by default)
-    Data.FieldTransform = 'on';%can use a transform function
+    Data.FieldTransform = 'off';%can use a transform function
     Data.ProjObject='off';%can use projection object(option 'off'/'on',
     Data.Mask='off';%can use mask option   (option 'off'/'on', 'off' by default)
@@ -258 +258 @@
 CheckRelabel=isfield(Param,'FileSeries' );%=true for index relabeling (PCO)
 
-%% introduce input image transform
-transform_fct=[];%default, no transform
-if isfield(Param,'FieldTransform')&&~isempty(Param.FieldTransform.TransformName)
-        currentdir=pwd;
-    cd(Param.FieldTransform.TransformPath)
-    transform_fct=str2func(Param.FieldTransform.TransformName);
-    cd (currentdir)
-end
+% %% introduce input image transform
+% transform_fct=[];%default, no transform
+% if isfield(Param,'FieldTransform')&&~isempty(Param.FieldTransform.TransformName)
+%         currentdir=pwd;
+%     cd(Param.FieldTransform.TransformPath)
+%     transform_fct=str2func(Param.FieldTransform.TransformName);
+%     cd (currentdir)
+% end
 
 %%%%% MAIN LOOP %%%%%%
@@ -445 +445 @@
         end
 
-
-        %% user defined image transform
-        if ~isempty(transform_fct)
-               par_civ1 =transform_fct(par_civ1,Param);
+ % case of image luminosity rescaling 
+      if par_civ1.CheckRescale &&~isempty(par_civ1.Maxtanh)
+               par_civ1.ImageA =par_civ1.Maxtanh*tanh(double(par_civ1.ImageA)/par_civ1.Maxtanh);
+               par_civ1.ImageB=par_civ1.Maxtanh*tanh(double(par_civ1.ImageB)/par_civ1.Maxtanh);
         end
         
@@ -672 +672 @@
         end
         
-                %% user defined image transform
-        if ~isempty(transform_fct)
-               par_civ2 =transform_fct(par_civ2,Param);
-        end
-        
+%                 %% user defined image transform
+%         if ~isempty(transform_fct)
+%                par_civ2 =transform_fct(par_civ2,Param);
+%         end
+         %% case of image luminosity rescaling 
+      if par_civ2.CheckRescale &&~isempty(par_civ2.Maxtanh)
+               par_civ2.ImageA =par_civ2.Maxtanh*tanh(double(par_civ2.ImageA)/par_civ2.Maxtanh);
+               par_civ2.ImageB=par_civ2.Maxtanh*tanh(double(par_civ2.ImageB)/par_civ2.Maxtanh);
+        end
         
         % get the guess from patch1 or patch2 (case 'CheckCiv3')

trunk/src/series/filter_time_singlefile.m

@@ -1 @@
-%'filter_time_single': apply a a sliding filter in a time series, put the time series in a single netcdf file (problematic...) 
-%------------------------------------------------------------------------
+%'filter_time_single': apply a a sliding filter to a time series and concatene the result in a single netcdf file
 % function ParamOut=filter_time(Param)
 %
@@ -149 +148 @@
 
 %%%%%%%%%%%%%%%% loop on field indices %%%%%%%%%%%%%%%%
-disp('loop for filtering started')
-tstart = tic;
- telapsed(zeros,1,NbField)       
+disp('loop for filtering started')  
+ ncid=[];
 for index=1:NbField
     index
-    
-    Field= read_field(filecell{1,index},'netcdf',Param.InputFields);
-    
+   
+    [Field,~,errormsg]= read_field(filecell{1,index},'netcdf',Param.InputFields);
+    if ~isempty(errormsg)
+        disp(errormsg)
+        if ~isempty(ncid)
+        netcdf.close(ncid)
+        end
+        return
+    end
     %%%%%%%%%%% MAIN RUNNING OPERATIONS  %%%%%%%%%%%%
     if index==1 %first field, initialisation output data
         DataOut.ListGlobalAttribute= {'Conventions'};
         DataOut.Conventions='uvmat';
-        DataOut.ListVarName={'Time','coord_y','coord_x','Ufilter','Vfilter'};
-        DataOut.VarDimName={'Time','coord_y','coord_x',{'Time','coord_y','coord_x'},{'Time','coord_y','coord_x'}};
         npy=numel(Field.coord_y);
         npx=numel(Field.coord_x);
         ListDimName={'Time','coord_y','coord_x'};
         DimValue=[NbField npy npx];
-        VarDimIndex={1,2,3,[1 2 3],[1 2 3]};
+        ListFields=Param.InputFields.FieldName;
+        DataOut.ListVarName=[{'Time','coord_y','coord_x'} ListFields'];
+        %DataOut.VarDimName={'Time','coord_y','coord_x',{'Time','coord_y','coord_x'},{'Time','coord_y','coord_x'}};
+        DataOut.VarDimName={'Time','coord_y','coord_x'};
+        VarDimIndex={1,2,3};
+        for ifield=1:numel(ListFields)
+            DataOut.VarDimName{ifield+3}={'coord_y','coord_x','Time'};
+            Field_varid(ifield)=ifield+2;
+            VarDimIndex{ifield+3}=[2 3 1];
+        end
+
+%         VarDimIndex={1,2,3,[1 2 3],[1 2 3]};
+
         DataOut.coord_x=Field.coord_x;
         DataOut.coord_y=Field.coord_y;
         DataOut.Time=0;
-        DataOut.Ufilter=0;
-        DataOut.Vfilter=0;
+        for ifield=1:numel(ListFields)
+            DataOut.(ListFields{ifield})=0;
+        end
         [errormsg,ncid]=struct2nc(ncfile_out,DataOut,'keep_open',ListDimName,DimValue,VarDimIndex);
         netcdf.putVar(ncid,0,0,1,0)
         netcdf.putVar(ncid,1,0,npy,Field.coord_y)
         netcdf.putVar(ncid,2,0,npx,Field.coord_x)
-        Uvarid=3;
-        Vvarid=4;
+%         Uvarid=3;
+%         Vvarid=4;
         TimeBlock=zeros(Param.ActionInput.WindowLength,1);
-        Ublock=zeros(Param.ActionInput.WindowLength,npy,npx);
-        Vblock=zeros(Param.ActionInput.WindowLength,npy,npx);
-    end
+        Fieldblock=zeros(numel(ListFields),Param.ActionInput.WindowLength,npy,npx);
+        %Vblock=zeros(Param.ActionInput.WindowLength,npy,npx);
+    end
+
     TimeBlock=circshift(TimeBlock,[-1 0 ]);
-    Ublock=circshift(Ublock,[-1 0 0]); %shift U by ishift along the first index
-    Vblock=circshift(Vblock,[-1 0 0]); %shift U by ishift along the first index
     TimeBlock(end)=Field.Time;
-    Ublock(end,:,:)=Field.U;
-    Vblock(end,:,:)=Field.V;
     sumindex=min(index,Param.ActionInput.WindowLength)-1;
     Timefilter=mean(TimeBlock(end-sumindex:end,:,:));%mid time
-    Ufilter=squeeze(mean(Ublock(end-sumindex:end,:,:),1,'omitnan'));
-    Vfilter=squeeze(mean(Vblock(end-sumindex:end,:,:),1,'omitnan'));
+    Fieldblock=circshift(Fieldblock,[0 -1 0 0]); %shift U by ishift along the first index
+   % Vblock=circshift(Vblock,[-1 0 0]); %shift U by ishift along the first index
+    for ifield=1:numel(ListFields)
+    Fieldblock(ifield,end,:,:)=Field.(ListFields{ifield});
+    end
+    %Vblock(end,:,:)=Field.V;
+    Fieldfilter=squeeze(mean(Fieldblock(:,end-sumindex:end,:,:),2,'omitnan'));
+%     Ufilter=squeeze(mean(Ublock(end-sumindex:end,:,:),1,'omitnan'));
+%     Vfilter=squeeze(mean(Vblock(end-sumindex:end,:,:),1,'omitnan'));
+%     Uerror=Ufilter-Ublock(end-floor(sumindex/2),:,:);
+%     Verror=Ufilter-Vblock(end-floor(sumindex/2),:,:);
     %updating output the netcdf file
+     tstart = tic;
     netcdf.putVar(ncid,0,(index-1),Timefilter)
-    netcdf.putVar(ncid,Uvarid,[(index-1) 0 0],[1 npy npx],Ufilter)
-    netcdf.putVar(ncid,Vvarid,[(index-1) 0 0],[1 npy npx],Vfilter)
-
- telapsed(index) = toc(tstart);
+    for ifield=1:numel(ListFields)
+        netcdf.putVar(ncid,Field_varid(ifield),[ 0 0 (index-1)],[npy npx 1],squeeze(Fieldfilter(ifield,:,:)))
+    end
+%     netcdf.putVar(ncid,Uvarid,[ 0 0 (index-1)],[npy npx 1],Ufilter)
+%      netcdf.putVar(ncid,Vvarid,[0 0 (index-1)],[npy npx 1],Vfilter)
+
+ telapsed = toc(tstart)% time for writting the field
     % writing the result file as netcdf file
     %     i1=i1_series{1}(index)-ceil(NpTime/2);
@@ -212 +237 @@
 figure
 plot(telapsed)
+ylabel('time lapsed computation')
 'END'