Changeset 1203

Timestamp:

Mar 24, 2026, 5:38:30 PM (2 days ago)

Author:

sommeria

Message:

civ repaired

Location:

trunk/src

Files:

• series.m (modified) (1 diff)
• series/civ_series.m (modified) (2 diffs)
• series/usr_fct/check_field_series.m (added)

trunk/src/series.m

@@ -756 +756 @@
 XmlData=[];
 if ~isempty(XmlFileName)
-    XmlData=read_imadoct(XmlFileName);%read the imadoc file through the local fct read_imadoc
+    XmlData=read_imadoc(XmlFileName);%read the imadoc file through the local fct read_imadoc
     if isfield(XmlData,'FileSeries') && Rank==0
         set(handles.Relabel,'Visible','on')

trunk/src/series/civ_series.m

@@ -390 +390 @@
             [par_civ1.ImageB,VideoObject_B] = read_image(ImageName_B,FileType_B,VideoObject_B,FrameIndex_B);
             
-        
-        % case of background image to subtract
-        if par_civ1.CheckBackground &&~isempty(par_civ1.Background)
-            [RootPath_background,SubDir_background,RootFile_background,~,~,~,~,Ext_background]=fileparts_uvmat(Param.ActionInput.Civ1.Background);
-            if strcmp(NomTypeNc,'_1-2_1')% case of volume,backgrounds act on different j levels
-                backgroundname=fullfile_uvmat(RootPath_background,SubDir_background,RootFile_background,Ext_background,'_1',j1_series_Civ1(ifield));
-            elseif isfield(par_civ1,'NbSlice')
-                i1_background=mod(i1-1,par_civ1.NbSlice)+1;
-                backgroundname=fullfile_uvmat(RootPath_background,SubDir_background,RootFile_background,Ext_background,'_1',i1_background);
-                if strcmp(Param.ActionInput.PairIndices.ListPairMode,'series(Di)')% case of volume, background index refers to j index
-                    par_civ1.NbSlice_j=par_civ1.NbSlice;
-                end
-            else
-                backgroundname=Param.ActionInput.Civ1.Background;
-            end
-            if strcmp(backgroundoldname,backgroundname)% background exist, not already read in civ1
-                par_civ1.Background=background; %use background already opened
-            else
-                if ~isempty(regexp(backgroundname,'(^http://)|(^https://)', 'once'))|| exist(backgroundname,'file')
-                    try
-                        par_civ1.Background=uint16(imread(backgroundname));%update the background, an store it for future use
-                    catch ME
-                        if ~isempty(ME.message)
-                            errormsg=['error reading input image: ' ME.message];
-                            disp_uvmat('ERROR',errormsg,checkrun)
-                            return
-                        end
-                    end
-                else
-                    par_civ1.Background=[];
-                end
-                background=par_civ1.Background;
-                backgroundoldname=backgroundname;
-            end
-            par_civ1.ImageA=uint16(par_civ1.ImageA)-par_civ1.Background;
-            par_civ1.ImageB=uint16(par_civ1.ImageB)-par_civ1.Background;
-        end
-        
-        % 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
-        
         % par_civ1.ImageWidth=size(par_civ1.ImageA,2);
         % par_civ1.ImageHeight=size(par_civ1.ImageA,1);
@@ -467 +423 @@
         Data.ListGlobalAttribute=[ListGlobalAttribute Civ1_param];
         Data.CivStage=1;
+            
+            
+            
+        % case of background image to subtract
+        if par_civ1.CheckBackground &&~isempty(par_civ1.Background)
+            [RootPath_background,SubDir_background,RootFile_background,~,~,~,~,Ext_background]=fileparts_uvmat(Param.ActionInput.Civ1.Background);
+            if strcmp(NomTypeNc,'_1-2_1')% case of volume,backgrounds act on different j levels
+                backgroundname=fullfile_uvmat(RootPath_background,SubDir_background,RootFile_background,Ext_background,'_1',j1_series_Civ1(ifield));
+            elseif isfield(par_civ1,'NbSlice')
+                i1_background=mod(i1-1,par_civ1.NbSlice)+1;
+                backgroundname=fullfile_uvmat(RootPath_background,SubDir_background,RootFile_background,Ext_background,'_1',i1_background);
+                if strcmp(Param.ActionInput.PairIndices.ListPairMode,'series(Di)')% case of volume, background index refers to j index
+                    par_civ1.NbSlice_j=par_civ1.NbSlice;
+                end
+            else
+                backgroundname=Param.ActionInput.Civ1.Background;
+            end
+            if strcmp(backgroundoldname,backgroundname)% background exist, not already read in civ1
+                par_civ1.Background=background; %use background already opened
+            else
+                if ~isempty(regexp(backgroundname,'(^http://)|(^https://)', 'once'))|| exist(backgroundname,'file')
+                    try
+                        par_civ1.Background=uint16(imread(backgroundname));%update the background, an store it for future use
+                    catch ME
+                        if ~isempty(ME.message)
+                            errormsg=['error reading input image: ' ME.message];
+                            disp_uvmat('ERROR',errormsg,checkrun)
+                            return
+                        end
+                    end
+                else
+                    par_civ1.Background=[];
+                end
+                background=par_civ1.Background;
+                backgroundoldname=backgroundname;
+            end
+            par_civ1.ImageA=uint16(par_civ1.ImageA)-par_civ1.Background;
+            par_civ1.ImageB=uint16(par_civ1.ImageB)-par_civ1.Background;
+        end
+        
+        % 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
+        
+        
         
         % set the list of variables