Index: /trunk/src/mouse_motion.m =================================================================== --- /trunk/src/mouse_motion.m (revision 971) +++ /trunk/src/mouse_motion.m (revision 972) @@ -224,7 +224,13 @@ sin_om=sin(pi*om/180); pos=[xy(1,1) xy(1,2) 0]; - pos=cos_om*pos+sin_om*cross(OmAxis,pos)+(1-cos_om)*(OmAxis*pos')*OmAxis; - end - pos=pos+Field.ProjObjectCoord; + %pos=cos_om*pos+sin_om*cross(OmAxis,pos)+(1-cos_om)*(OmAxis*pos')*OmAxis; + coeff=OmAxis(3)*(1-cos_om); + norm_plane(1)=OmAxis(1)*coeff+OmAxis(2)*sin_om; + norm_plane(2)=OmAxis(2)*coeff-OmAxis(1)*sin_om; + norm_plane(3)=OmAxis(3)*coeff+cos_om; + %Z0=norm_plane*Field.ProjObjectCoord'/norm_plane(3); + pos(3)=-(norm_plane(1)*pos(1)-norm_plane(2)*pos(2))/norm_plane(3); + end + pos=pos+Field.ProjObjectCoord; text_displ_3=[text_displ_3 'x,y,z=' num2str(pos,4)]; end Index: /trunk/src/phys_XYZ.m =================================================================== --- /trunk/src/phys_XYZ.m (revision 971) +++ /trunk/src/phys_XYZ.m (revision 972) @@ -41,8 +41,8 @@ norm_plane(2)=OmAxis(2)*coeff-OmAxis(1)*sin_om; norm_plane(3)=OmAxis(3)*coeff+cos_om; - Z0=norm_plane*Calib.SliceCoord(Zindex,:)'/norm_plane(3); - else +% Z0=norm_plane*Calib.SliceCoord(Zindex,:)'/norm_plane(3); + end Z0=Calib.SliceCoord(Zindex,3);%horizontal plane z=cte - end +% end Z0virt=Z0; if isfield(Calib,'InterfaceCoord') && isfield(Calib,'RefractionIndex') Index: /trunk/src/phys_ima.m =================================================================== --- /trunk/src/phys_ima.m (revision 971) +++ /trunk/src/phys_ima.m (revision 972) @@ -61,27 +61,30 @@ [Rangx]=phys_XYZ(Calib,Rangx,[0.5 0.5],ZIndex);%case of translations without rotation and quadratic deformation [xx,Rangy]=phys_XYZ(Calib,[0.5 0.5],Rangy,ZIndex); - else + else % the image needs to be interpolated to the new coordinates zphys=0; %default if isfield(Calib,'SliceCoord') %.Z= index of plane - SliceCoord=Calib.SliceCoord(ZIndex,:); - zphys=SliceCoord(3); %to generalize for non-parallel planes - -% if isfield(Calib,'SliceAngle')&&~isequal(Calib.SliceAngle,[0 0 0]) -% om=norm(Calib.SliceAngle);%norm of rotation angle in radians -% OmAxis=Calib.SliceAngle/om; %unit vector marking the rotation axis -% cos_om=cos(pi*om/180); -% sin_om=sin(pi*om/180); -% pos=[xy(1,1) xy(1,2) 0]; -% pos=cos_om*pos+sin_om*cross(OmAxis,pos)+(1-cos_om)*(OmAxis*pos')*OmAxis; -% end - - -% if isfield(Calib,'InterfaceCoord') && isfield(Calib,'RefractionIndex') + SliceCoord=Calib.SliceCoord(ZIndex,:); + zphys=SliceCoord(3); %to generalize for non-parallel planes + if isfield(Calib, 'SliceAngle') && ~isequal(Calib.SliceAngle,[0 0 0]) && ~isequal(Calib.SliceAngle(ZIndex,:),[0 0 0]) + testangle=1; + om=norm(Calib.SliceAngle(ZIndex,:));%norm of rotation angle in radians + OmAxis=Calib.SliceAngle(ZIndex,:)/om; %unit vector marking the rotation axis + cos_om=cos(pi*om/180); + sin_om=sin(pi*om/180); + coeff=OmAxis(3)*(1-cos_om); + norm_plane(1)=OmAxis(1)*coeff+OmAxis(2)*sin_om; + norm_plane(2)=OmAxis(2)*coeff-OmAxis(1)*sin_om; + norm_plane(3)=OmAxis(3)*coeff+cos_om; + %Z0=norm_plane*Calib.SliceCoord(ZIndex,:)'/norm_plane(3); + Z0=Calib.SliceCoord(ZIndex,3); + zphys=Z0-(norm_plane(1)*X-norm_plane(2)*Y)/norm_plane(3); + end +% if isfield(Calib,'InterfaceCoord') && isfield(Calib,'RefractionIndex') % H=Calib.InterfaceCoord(3); % if H>zphys % zphys=H-(H-zphys)/Calib.RefractionIndex; %corrected z (virtual object) % end -% end +% end end xima=0.5:npx(icell)-0.5;%image coordinates of corners Index: /trunk/src/series.m =================================================================== --- /trunk/src/series.m (revision 971) +++ /trunk/src/series.m (revision 972) @@ -2714,4 +2714,5 @@ end + function [TimeValue,DtValue]=get_time(ref_i,ref_j,PairString,InputTable,FileInfo,TimeName,DtName) [i1,i2,j1,j2] = get_file_index(ref_i,ref_j,PairString); @@ -3486,5 +3487,5 @@ % --- Executes on button press in SetPairs. -function SetPairs_Callback(hObject, iview, handles) +function SetPairs_Callback(hObject, eventdata, handles) %% delete previous occurrence of 'set_pairs' @@ -3510,4 +3511,5 @@ ListViewLines=find(cellfun('isempty',PairString)==0);%find list of non empty pairs ListViewMenu=cell(numel(ListViewLines),1); +iview=get(handles.PairString,'Value'); for ilist=1:numel(ListViewLines) ListViewMenu{ilist}=num2str(ListViewLines(ilist)); Index: /trunk/src/series/extract_multitif.m =================================================================== --- /trunk/src/series/extract_multitif.m (revision 971) +++ /trunk/src/series/extract_multitif.m (revision 972) @@ -59,5 +59,5 @@ %======================================================================= -function ParamOut=ima2netcdf(Param) +function ParamOut=extract_multitif(Param) %%%%%%%%%%%%%%%%% INPUT PREPARATION MODE (no RUN) %%%%%%%%%%%%%%%%% @@ -73,5 +73,5 @@ ParamOut.OutputDirExt='.png';%set the output dir extension ParamOut.OutputFileMode='NbSlice';% '=NbInput': 1 output file per input file index, '=NbInput_i': 1 file per input file index i, '=NbSlice': 1 file per slice - + ParamOut.CheckOverwriteVisible='on'; % manage the overwrite of existing files (default=1) %% root input file(s) and type % check the existence of the first file in the series @@ -148,5 +148,5 @@ %count=316;%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%CORRECTION EXP08: 4684 images -> start at 316 start 67->_11_1 %count=1934%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%CORRECTION EXP07: 3066 images -%% loop on the files +%% loop on the files for ifile=1:numel(ListFile) update_waitbar(WaitbarHandle,ifile/numel(ListFile)) @@ -158,19 +158,48 @@ NbFrames=numel(imfinfo(ImageName)); % loop on the frames within the tiff file - for iframe=1:NbFrames - A=imread(ImageName,iframe); - - if isequal(ImagesPerLevel,1)% mode series + for iframe=1:NbFrames + if isequal(ImagesPerLevel,1)% mode series i_index=count+1; OutputFile=fullfile(OutputDir,['img_' num2str(count+1) '.png']); - else % indices i and j + else % indices i and j i_index=fix(count/ImagesPerLevel)+1; j_index=mod(count,ImagesPerLevel)+1; OutputFile=fullfile(OutputDir,['img_' num2str(i_index) '_' num2str(j_index) '.png']); end - imwrite(A,OutputFile,'BitDepth',16) + if Param.CheckOverwrite ||~exist(OutputFile,'file') + A=imread(ImageName,iframe); + imwrite(A,OutputFile,'BitDepth',16); + disp([OutputFile ' written']) + else + disp([OutputFile ' already exists']) + end count=count+1; end end + +% for ifile=1:numel(ListFile) +% update_waitbar(WaitbarHandle,ifile/numel(ListFile)) +% if ~isempty(RUNHandle)&& ~strcmp(get(RUNHandle,'BusyAction'),'queue') +% disp('program stopped by user') +% break +% end +% ImageName=fullfile(DirImages,ListFile{ifile}); +% NbFrames=numel(imfinfo(ImageName)); +% % loop on the frames within the tiff file +% for iframe=1:NbFrames +% A=imread(ImageName,iframe); +% +% if isequal(ImagesPerLevel,1)% mode series +% i_index=count+1; +% OutputFile=fullfile(OutputDir,['img_' num2str(count+1) '.png']); +% else % indices i and j +% i_index=fix(count/ImagesPerLevel)+1; +% j_index=mod(count,ImagesPerLevel)+1; +% OutputFile=fullfile(OutputDir,['img_' num2str(i_index) '_' num2str(j_index) '.png']); +% end +% imwrite(A,OutputFile,'BitDepth',16) +% count=count+1; +% end +% end %% create the xml file of PCO camera @@ -181,7 +210,7 @@ %% remove initial files if transfer OK - if i_index== (size(XmlInput.Time,1)-1) - - [SUCCESS,MESSAGE]=rmdir(DirImages,'s') - - end +% if i_index== (size(XmlInput.Time,1)-1) +% +% [SUCCESS,MESSAGE]=rmdir(DirImages,'s') +% +% end Index: /trunk/src/series/extract_multitif_parallel.m =================================================================== --- /trunk/src/series/extract_multitif_parallel.m (revision 972) +++ /trunk/src/series/extract_multitif_parallel.m (revision 972) @@ -0,0 +1,234 @@ +%'ima2netcdf': read image series and transform to netcdf +%------------------------------------------------------------------------ + + +% function ParamOut=ima2netcdf(Param) +% +%%%%%%%%%%% GENERAL TO ALL SERIES ACTION FCTS %%%%%%%%%%%%%%%%%%%%%%%%%%% +% +%OUTPUT +% ParamOut: sets options in the GUI series.fig needed for the function +% +%INPUT: +% In run mode, the input parameters are given as a Matlab structure Param copied from the GUI series. +% In batch mode, Param is the name of the corresponding xml file containing the same information +% when Param.Action.RUN=0 (as activated when the current Action is selected +% in series), the function ouput paramOut set the activation of the needed GUI elements +% +% Param contains the elements:(use the menu bar command 'export/GUI config' in series to +% see the current structure Param) +% .InputTable: cell of input file names, (several lines for multiple input) +% each line decomposed as {RootPath,SubDir,Rootfile,NomType,Extension} +% .OutputSubDir: name of the subdirectory for data outputs +% .OutputDirExt: directory extension for data outputs +% .Action: .ActionName: name of the current activated function +% .ActionPath: path of the current activated function +% .ActionExt: fct extension ('.m', Matlab fct, '.sh', compiled Matlab fct +% .RUN =0 for GUI input, =1 for function activation +% .RunMode='local','background', 'cluster': type of function use +% +% .IndexRange: set the file or frame indices on which the action must be performed +% .FieldTransform: .TransformName: name of the selected transform function +% .TransformPath: path of the selected transform function +% .InputFields: sub structure describing the input fields withfields +% .FieldName: name(s) of the field +% .VelType: velocity type +% .FieldName_1: name of the second field in case of two input series +% .VelType_1: velocity type of the second field in case of two input series +% .Coord_y: name of y coordinate variable +% .Coord_x: name of x coordinate variable +% .ProjObject: %sub structure describing a projection object (read from ancillary GUI set_object) +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% + +%======================================================================= +% Copyright 2008-2016, LEGI UMR 5519 / CNRS UGA G-INP, Grenoble, France +% http://www.legi.grenoble-inp.fr +% Joel.Sommeria - Joel.Sommeria (A) legi.cnrs.fr +% +% This file is part of the toolbox UVMAT. +% +% UVMAT is free software; you can redistribute it and/or modify +% it under the terms of the GNU General Public License as published +% by the Free Software Foundation; either version 2 of the license, +% or (at your option) any later version. +% +% UVMAT is distributed in the hope that it will be useful, +% but WITHOUT ANY WARRANTY; without even the implied warranty of +% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +% GNU General Public License (see LICENSE.txt) for more details. +%======================================================================= + +function ParamOut=ima2netcdf(Param) + +%%%%%%%%%%%%%%%%% INPUT PREPARATION MODE (no RUN) %%%%%%%%%%%%%%%%% +if isstruct(Param) && isequal(Param.Action.RUN,0) + ParamOut.AllowInputSort='off';% allow alphabetic sorting of the list of input file SubDir (options 'off'/'on', 'off' by default) + ParamOut.WholeIndexRange='on';% prescribes the file index ranges from min to max (options 'off'/'on', 'off' by default) + ParamOut.NbSlice='off'; % impose calculation in a single process (no parallel processing to avoid 'holes')) + ParamOut.VelType='off';% menu for selecting the velocity type (options 'off'/'one'/'two', 'off' by default) + ParamOut.FieldName='off';% menu for selecting the field (s) in the input file(options 'off'/'one'/'two', 'off' by default) + ParamOut.FieldTransform = 'off';%can use a transform function + ParamOut.ProjObject='off';%can use projection object(option 'off'/'on', + ParamOut.Mask='off';%can use mask option (option 'off'/'on', 'off' by default) + ParamOut.OutputDirExt='.png';%set the output dir extension + ParamOut.OutputFileMode='NbSlice';% '=NbInput': 1 output file per input file index, '=NbInput_i': 1 file per input file index i, '=NbSlice': 1 file per slice + ParamOut.CheckOverwriteVisible='on'; % manage the overwrite of existing files (default=1) + %% root input file(s) and type + % check the existence of the first file in the series + first_j=[];% note that the function will propose to cover the whole range of indices + if isfield(Param.IndexRange,'MinIndex_j'); first_j=Param.IndexRange.MinIndex_j; end + last_j=[]; + if isfield(Param.IndexRange,'MaxIndex_j'); last_j=Param.IndexRange.MaxIndex_j; end + PairString=''; + if isfield(Param.IndexRange,'PairString'); PairString=Param.IndexRange.PairString; end + [i1,i2,j1,j2] = get_file_index(Param.IndexRange.first_i,first_j,PairString); + FirstFileName=fullfile_uvmat(Param.InputTable{1,1},Param.InputTable{1,2},Param.InputTable{1,3},... + Param.InputTable{1,5},Param.InputTable{1,4},i1,i2,j1,j2); + if ~exist(FirstFileName,'file') + msgbox_uvmat('WARNING',['the first input file ' FirstFileName ' does not exist']) + end + + %% check the validity of input file types + FileInfo=get_file_info(FirstFileName); + if ~strcmp(FileInfo.FileType,'multimage') + msgbox_uvmat('ERROR',['invalid file type input: ' FileInfo.FileType ' not an image']) + return + end + xmlinput=uigetfile_uvmat('pick xml file for timing',fileparts(fileparts(FirstFileName)),'.xml'); + [tild,ParamOut.ActionInput.XmlFile]=fileparts(xmlinput); + ParamOut.ActionInput.XmlFile + + return +end +%%%%%%%%%%%%%%%%% STOP HERE FOR PAMETER INPUT MODE %%%%%%%%%%%%%%%%% + +%% read input parameters from an xml file if input is a file name (batch mode) +checkrun=1; +RUNHandle=[]; +WaitbarHandle=[]; +if ischar(Param) + Param=xml2struct(Param);% read Param as input file (batch case) + checkrun=0; +else + hseries=findobj(allchild(0),'Tag','series'); + RUNHandle=findobj(hseries,'Tag','RUN');%handle of RUN button in GUI series + WaitbarHandle=findobj(hseries,'Tag','Waitbar');%handle of waitbar in GUI series +end + +%% list of input images +% DirImages=fullfile(Param.InputTable{1,1},Param.InputTable{1,2}); +% ListStruct=dir(DirImages); +% ListCells=struct2cell(ListStruct);% transform dir struct to a cell arrray +% check_bad=strcmp('.',ListCells(1,:))|strcmp('..',ListCells(1,:));%detect the dir '.' to exclude it +% check_dir=cell2mat(ListCells(4,:));% =1 for directories, =0 for files +% ListFile=ListCells(1,find(~check_dir & ~check_bad)); + +%% check file names +% RootName=regexprep(ListFile{1},'.tif$','') +% rank(1)=1; +% for ilist=2:numel(ListFile) +% rank_str=regexprep(ListFile{ilist},'.tif$',''); +% rank(ilist)=regexprep(rank_str,['^' RootName '@'],''); +% % if ~isequal(str2num(rank),ilist-1) +% % disp(['error in the list of input file # ' num2str(ilist-1)]) +% % return +% % end +% end + +%% output directory +OutputDir=fullfile(Param.InputTable{1,1},[Param.OutputSubDir Param.OutputDirExt]); + +%% Timing +XmlInputFile=fullfile(Param.InputTable{1,1},[Param.ActionInput.XmlFile '.xml']) +XmlInput=imadoc2struct(XmlInputFile,'Camera'); + +%% Main loop + +ImagesPerLevel=size(XmlInput.Time,2)-1;%100; +% count=0; +%count=316;%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%CORRECTION EXP08: 4684 images -> start at 316 start 67->_11_1 +%count=1934%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%CORRECTION EXP07: 3066 images +%% loop on the files +%for ifile=1:numel(ListFile) +% update_waitbar(WaitbarHandle,ifile/numel(ListFile)) +% if ~isempty(RUNHandle)&& ~strcmp(get(RUNHandle,'BusyAction'),'queue') +% disp('program stopped by user') +% break +% end +% ImageName=fullfile(DirImages,ListFile{ifile}); +% NbFrames=numel(imfinfo(ImageName)); +% loop on the frames within the tiff file +if Param.IndexRange.first_i==1% first slice of processing + firstindex=0; + count=0; +else + firstindex=Param.IndexRange.first_i; + ImageName=fullfile(Param.InputTable{1,1},Param.InputTable{1,2},'im.tif'); + NbFrames=numel(imfinfo(ImageName)); + count=Param.IndexRange.first_i*NbFrames; +end +for ifile=firstindex:Param.IndexRange.last_i + if firstindex==0 && ifile==0% first slice of processing + ImageName=fullfile(Param.InputTable{1,1},Param.InputTable{1,2},'im.tif') + else + ImageName=fullfile(Param.InputTable{1,1},Param.InputTable{1,2},['im@' num2str(ifile,'%04d') '.tif']) + end + NbFrames=numel(imfinfo(ImageName)); + for iframe=1:NbFrames + iframe + if isequal(ImagesPerLevel,1)% mode series + OutputFile=fullfile(OutputDir,['img_' num2str(count+1) '.png']); + else % indices i and j + i_index=fix(count/ImagesPerLevel)+1; + j_index=mod(count,ImagesPerLevel)+1; + OutputFile=fullfile(OutputDir,['img_' num2str(i_index) '_' num2str(j_index) '.png']); + end + if Param.CheckOverwrite ||~exist(OutputFile,'file') + A=imread(ImageName,iframe); + imwrite(A,OutputFile,'BitDepth',16); + disp([OutputFile ' written']) + else + disp([OutputFile ' already exists']) + end + count=count+1; + end +end + %end + +% for ifile=1:numel(ListFile) +% update_waitbar(WaitbarHandle,ifile/numel(ListFile)) +% if ~isempty(RUNHandle)&& ~strcmp(get(RUNHandle,'BusyAction'),'queue') +% disp('program stopped by user') +% break +% end +% ImageName=fullfile(DirImages,ListFile{ifile}); +% NbFrames=numel(imfinfo(ImageName)); +% % loop on the frames within the tiff file +% for iframe=1:NbFrames +% A=imread(ImageName,iframe); +% +% if isequal(ImagesPerLevel,1)% mode series +% i_index=count+1; +% OutputFile=fullfile(OutputDir,['img_' num2str(count+1) '.png']); +% else % indices i and j +% i_index=fix(count/ImagesPerLevel)+1; +% j_index=mod(count,ImagesPerLevel)+1; +% OutputFile=fullfile(OutputDir,['img_' num2str(i_index) '_' num2str(j_index) '.png']); +% end +% imwrite(A,OutputFile,'BitDepth',16) +% count=count+1; +% end +% end + +%% create the xml file of PCO camera +% XmlInput.Camera.CameraName='PCO'; +% t=struct2xml(XmlInput.Camera); +% t=set(t,1,'name','ImaDoc'); +% save(t,fullfile(Param.InputTable{1,1},'PCO.xml')) + +%% remove initial files if transfer OK +% if i_index== (size(XmlInput.Time,1)-1) +% +% [SUCCESS,MESSAGE]=rmdir(DirImages,'s') +% +% end Index: /trunk/src/transform_field/ima_color2BW.m =================================================================== --- /trunk/src/transform_field/ima_color2BW.m (revision 971) +++ /trunk/src/transform_field/ima_color2BW.m (revision 972) @@ -30,5 +30,5 @@ DataOut=DataIn; %default if ndims(DataOut.A)==3 - DataOut.A=uint16(sum(double(DataOut.A,3)));%sum on color components, transform in 16 bit BW images + DataOut.A=uint16(sum(double(DataOut.A),3));%sum on color components, transform in 16 bit BW images end Index: /trunk/src/uvmat.m =================================================================== --- /trunk/src/uvmat.m (revision 971) +++ /trunk/src/uvmat.m (revision 972) @@ -1177,7 +1177,7 @@ 'String',num2str(SliceAngle(1)),'FontUnits','points','FontSize',12,'FontWeight','bold','TooltipString','''num_SliceAngle_1_1'':first slice angle of inclination around the x axis');%edit box uicontrol('Style','edit','Units','normalized', 'Position', [4*ii+3*ww 0.95-5*ii-4.2*hh ww hh],'tag','num_SliceAngle_1_2','BackgroundColor',[1 1 1],... - 'String',num2str(SliceAngle(2)),'FontUnits','points','FontSize',12,'FontWeight','bold','TooltipString','''num_SliceAngle_1_2'':last slice angle of inclination around the x axis');%edit box + 'String',num2str(SliceAngle(1)),'FontUnits','points','FontSize',12,'FontWeight','bold','TooltipString','''num_SliceAngle_1_2'':last slice angle of inclination around the x axis');%edit box uicontrol('Style','edit','Units','normalized', 'Position', [3*ii+2*ww 0.95-6*ii-5.2*hh ww hh],'tag','num_SliceAngle_2_1','BackgroundColor',[1 1 1],... - 'String',num2str(SliceAngle(1)),'FontUnits','points','FontSize',12,'FontWeight','bold','TooltipString','''num_SliceAngle_2_1'':first slice angle of inclination around the y axis');%edit box + 'String',num2str(SliceAngle(2)),'FontUnits','points','FontSize',12,'FontWeight','bold','TooltipString','''num_SliceAngle_2_1'':first slice angle of inclination around the y axis');%edit box uicontrol('Style','edit','Units','normalized', 'Position', [4*ii+3*ww 0.95-6*ii-5.2*hh ww hh],'tag','num_SliceAngle_2_2','BackgroundColor',[1 1 1],... 'String',num2str(SliceAngle(2)),'FontUnits','points','FontSize',12,'FontWeight','bold','TooltipString','''num_SliceAngle_2_2'':last slice angle of inclination around the y axis');%edit box @@ -1269,4 +1269,6 @@ uvmat('InputFileREFRESH_Callback',huvmat,[],hhuvmat); %file input with xml reading in uvmat, show the image in phys coordinates set(hObject,'BackgroundColor',[1 0 0]);% paint button back to red + +delete(hset_slice) %------------------------------------------------------------------------ @@ -1338,6 +1340,6 @@ function set_slice_Cancel_Callback(hObject,eventdata) %------------------------------------------------------------------------ -hfig=get(hObject,'parent'); -delete(hfig) +hset_slice=get(hObject,'parent'); +delete(hset_slice) %-----------------------------------------------------------------------