Changeset 956 for trunk

Timestamp:

Jun 22, 2016, 8:10:14 PM (8 years ago)

Author:

sommeria

Message:

various

Location:

trunk/src

Files:

• series/ima2vol.m (modified) (2 diffs)
• series/merge_proj.m (modified) (3 diffs)
• transform_field/ima_filter.m (modified) (1 diff)
• uvmat.m (modified) (2 diffs)

trunk/src/series/ima2vol.m

@@ -46 +46 @@
     ParamOut.ProjObject='on';%can use projection object(option 'off'/'on',
     ParamOut.Mask='on';%can use mask option   (option 'off'/'on', 'off' by default)
-    ParamOut.OutputDirExt='.vertical_cut';%set the output dir extension
+    ParamOut.OutputDirExt='.vol';%set the output dir extension
     ParamOut.OutputFileMode='NbInput';% '=NbInput': 1 output file per input file index, '=NbInput_i': 1 file per input file index i, '=NbSlice': 1 file per slice
       %check the input files
@@ -133 +133 @@
         end
         if jfile==1
-            vol=zeros(nbfield_j,size(Data.A,1),size(Data.A,2));
-            Z=1:nbfield_j;%default Z values
+            VolData.A=zeros(nbfield_j,size(Data.A,1),size(Data.A,2));
+            VolData.Coord_z=1:nbfield_j;%default Z values
         end
-        vol(jfile,:,:)=double(Data.A);%concacene along y
-        Z(jfile)=Data.PlaneCoord(3);
+        VolData.A(jfile,:,:)=Data.A;%concacene along y
+        VolData.Coord_z(jfile)=Data.PlaneCoord(3);
     end
-    if ifile==1
-        npx=size(Data.A,2);
-        npy=size(Data.A,1);
-        npz=256;
-        ind_x=round(npx/2)-10:round(npx/2)+10;%image index at the mid x position
-        ind_y=round(npy/2)-10:round(npy/2)+10;;%image index at the mid y position
-        
-        %write xml calibration file, using the first file
-            Rangx=Data.Coord_x;
-            Rangy=Data.Coord_y;
-            Rangz=[Z(end) Z(1)];
+%         npx=size(Data.A,2);
+%         npy=size(Data.A,1);
+%         npz=256;
+%         ind_x=round(npx/2)-10:round(npx/2)+10;%image index at the mid x position
+%         ind_y=round(npy/2)-10:round(npy/2)+10;%image index at the mid y position
+%         ind_y=ind_y-100;% shift to avoid the injector
+%         %write xml calibration file, using the first file
+%             Rangx=Data.Coord_x;
+%             Rangy=Data.Coord_y;
+%             Rangz=[Z(end) Z(1)];
+%     
+%         GeometryCal.CalibrationType='rescale';
+%         GeometryCal.CoordUnit=Data.CoordUnit;
+%         GeometryCal.focal=1;
+%         %scaling along x, y and z
+%         pxcmx=(npx-1)/(Rangx(2)-Rangx(1));
+%         pxcmy=(npy-1)/(Rangy(1)-Rangy(2));
+%         pxcmz=(npz-1)/(Rangz(2)-Rangz(1));
+%         T_x=-pxcmx*Rangx(1)+0.5;
+%         T_y=-pxcmy*Rangy(2)+0.5;
+%         T_z=-pxcmz*Rangz(2)+0.5;
+%         % xml file for x cut
+%         GeometryCal.R=[pxcmx,0,0;0,pxcmz,0;0,0,1];
+%         GeometryCal.Tx_Ty_Tz=[T_x T_z 1];
+%         ImaDoc.GeometryCalib=GeometryCal;
+%         t=struct2xml(ImaDoc);
+%         t=set(t,1,'name','ImaDoc');
+%         save(t,fullfile(RootPath{1},SubdirOut,'cut_x.xml'))
+%                    % xml file for y cut
+%         GeometryCal.R=[pxcmy,0,0;0,pxcmz,0;0,0,1];
+%         GeometryCal.Tx_Ty_Tz=[T_y T_z 1];
+%         ImaDoc.GeometryCalib=GeometryCal;
+%         t=struct2xml(ImaDoc);
+%         t=set(t,1,'name','ImaDoc');
+%         save(t,fullfile(RootPath{1},SubdirOut,'cut_y.xml')) 
+%     end
     
-        GeometryCal.CalibrationType='rescale';
-        GeometryCal.CoordUnit=Data.CoordUnit;
-        GeometryCal.focal=1;
-        %scaling along x, y and z
-        pxcmx=(npx-1)/(Rangx(2)-Rangx(1));
-        pxcmy=(npy-1)/(Rangy(1)-Rangy(2));
-        pxcmz=(npz-1)/(Rangz(2)-Rangz(1));
-        T_x=-pxcmx*Rangx(1)+0.5;
-        T_y=-pxcmy*Rangy(2)+0.5;
-        T_z=-pxcmz*Rangz(2)+0.5;
-        % xml file for x cut
-        GeometryCal.R=[pxcmx,0,0;0,pxcmz,0;0,0,1];
-        GeometryCal.Tx_Ty_Tz=[T_x T_z 1];
-        ImaDoc.GeometryCalib=GeometryCal;
-        t=struct2xml(ImaDoc);
-        t=set(t,1,'name','ImaDoc');
-        save(t,fullfile(RootPath{1},SubdirOut,'cut_x.xml'))
-                   % xml file for y cut
-        GeometryCal.R=[pxcmy,0,0;0,pxcmz,0;0,0,1];
-        GeometryCal.Tx_Ty_Tz=[T_y T_z 1];
-        ImaDoc.GeometryCalib=GeometryCal;
-        t=struct2xml(ImaDoc);
-        t=set(t,1,'name','ImaDoc');
-        save(t,fullfile(RootPath{1},SubdirOut,'cut_y.xml')) 
-    end
-    cut_y=squeeze(mean(vol(:,:,ind_x),3));
-    cut_y=interp1(Z,cut_y,linspace(Z(1),Z(end),npz));
-    cut_x=squeeze(mean(vol(:,ind_y,:),2));
-    cut_x=interp1(Z,cut_x,linspace(Z(1),Z(end),npz));
-    
-    filename_x=fullfile_uvmat(RootPath{1},SubdirOut,'cut_x','.png','_1',i1_series{1}(jfile,ifile),[],j1);
-    filename_y=fullfile_uvmat(RootPath{1},SubdirOut,'cut_y','.png','_1',i1_series{1}(jfile,ifile),[],j1);
-    %  filename_new=name_generator(basename_new,num_i,1,'.vol','_i');
-    imwrite(uint8(vol),filename_x,'png','BitDepth',8)%
-    display([filename_x 'written (8bits image)'])
-    imwrite(uint8(vol),filename_y,'png','BitDepth',8)%
-    display([filename_y 'written (8bits image)'])
+    filename=fullfile_uvmat(RootPath{1},SubdirOut,RootFile{1},'.nc','_1',i1_series{1}(jfile,ifile),[],j1);
+    VolData.ListVarName={'Coord_z','Coord_y','Coord_x','A'};
+    VolData.VarDimName={'Coord_z','Coord_y','Coord_x',{'Coord_z','Coord_y','Coord_x'}};
+    VolData.Coord_x=Data.Coord_x;
+    VolData.Coord_y=Data.Coord_y;
+    struct2nc(filename,VolData)
+    disp([filename ' written'])
 end
 

trunk/src/series/merge_proj.m

@@ -203 +203 @@
 if min(cell2mat(CheckImage))==1 && (~Param.CheckObject || strcmp(Param.ProjObject.Type,'plane'))
     FileExtOut='.png'; %image output (input and proj result = image)
-    for iview=1:NbView
-        BitDepth(iview)=FileInfo{iview}.BitDepth;
-    end
-    BitDepth=max(BitDepth);
 else
     FileExtOut='.nc'; %netcdf output
@@ -357 +353 @@
     %% recording the merged field
     if strcmp(FileExtOut,'.png')    %output as image
-        if BitDepth==8
-            imwrite(uint8(MergeData.A),OutputFile,'BitDepth',8)
-        else
-            imwrite(uint16(MergeData.A),OutputFile,'BitDepth',16)
-        end
         if index==1
+            if strcmp(class(MergeData.A),'uint8')
+            BitDepth=8;
+            else
+              BitDepth=16;  
+            end
             %write xml calibration file, using the first file
             siz=size(MergeData.A);
@@ -391 +387 @@
             save(t,[fileparts(OutputFile) '.xml'])
         end
-        
+        if BitDepth==8
+            imwrite(uint8(MergeData.A),OutputFile,'BitDepth',8)
+        else
+            imwrite(uint16(MergeData.A),OutputFile,'BitDepth',16)
+        end
     else   %output as netcdf files
         MergeData.ListGlobalAttribute={'Conventions','Project','InputFile_1','InputFile_end','NbCoord','NbDim'};

trunk/src/transform_field/ima_filter.m

@@ -29 +29 @@
 %=======================================================================
 
-function DataOut=ima_filter(DataIn,Param)
+function DataOut=ima_filter(DataIn)
 
-%% request input parameters
-if isfield(DataIn,'Action') && isfield(DataIn.Action,'RUN') && isequal(DataIn.Action.RUN,0)
-    prompt = {'npx';'npy'};
-    dlg_title = 'get the filter size in x and y';
-    num_lines= 2;
-    def     = { '20';'20'};
-    if isfield(Param,'TransformInput')&&isfield(Param.TransformInput,'FilterBoxSize_x')&&...
-            isfield(Param.TransformInput,'FilterBoxSize_y')
-        def={num2str(Param.TransformInput.FilterBoxSize_x);num2str(Param.TransformInput.FilterBoxSize_y)};
-    end
-    answer = inputdlg(prompt,dlg_title,num_lines,def);
-    DataOut.TransformInput.FilterBoxSize_x=str2num(answer{1}); %size of the filtering window
-    DataOut.TransformInput.FilterBoxSize_y=str2num(answer{2}); %size of the filtering window
-    return
-end
-
+Origin_x=469;
 DataOut=DataIn; %default
+DataOut.A=
 
 %definition of the cos shape matrix filter

trunk/src/uvmat.m

@@ -784 +784 @@
 end
 %create avi open
-aviobj=avifile(MovieName,'Compression','None','fps',fps);
-
+%aviobj=avifile(MovieName,'Compression','None','fps',fps);
+
+aviobj = VideoWriter(MovieName,'Uncompressed AVI');
+open(aviobj)
 %% get info from uvmat and adjust it
 huvmat=findobj(allchild(0),'Tag','uvmat');
@@ -806 +808 @@
             set(htitle,'String',regexprep(Title,'t=\d+.\d*',['t=' time_str]))
             mov=getframe(figure_movie);
-            aviobj=addframe(aviobj,mov);
-    end
-end
-aviobj=close(aviobj);
+           % aviobj=addframe(aviobj,mov);
+            writeVideo(aviobj,mov);
+    end
+end
+close(aviobj);
 msgbox_uvmat('CONFIRMATION',{['movie ' MovieName ' created '];['with ' num2str(FrameNumber) ' frames']})