%'civ': function associated with the interface 'civ.fig' for PIV, spline interpolation and stereo PIV (patch) %------------------------------------------------------------------------ % provides an interface for the software menucivx % function varargout = civ(varargin) % provides an interface for the software menucivx % %AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA % Copyright Joel Sommeria, 2011, LEGI / CNRS-UJF-INPG, sommeria@legi.grenoble-inp.fr %AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA % 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 (file UVMAT/COPYING.txt) for more details. %AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA function varargout = civ(varargin) %TODO: search range % Last Modified by GUIDE v2.5 08-May-2012 22:14:39 % Begin initialization code - DO NOT EDIT gui_Singleton = 1; gui_State = struct('gui_Name', mfilename, ... 'gui_Singleton', gui_Singleton, ... 'gui_OpeningFcn', @civ_OpeningFcn, ... 'gui_OutputFcn', @civ_OutputFcn, ... 'gui_LayoutFcn', [] , ... 'gui_Callback', []); if nargin && ischar(varargin{1}) && ~isempty(regexp(varargin{1},'_Callback$','once')) gui_State.gui_Callback = str2func(varargin{1}); end if nargout [varargout{1:nargout}] = gui_mainfcn(gui_State, varargin{:}); else gui_mainfcn(gui_State, varargin{:}); end % End initialization code - DO NOT EDIT %------------------------------------------------------------------------ % --- Executes just before civ is made visible. function civ_OpeningFcn(hObject, eventdata, handles, fileinput) %------------------------------------------------------------------------ % This function has no output args, see OutputFcn. %% General settings handles.output = hObject; guidata(hObject, handles); % Update handles structure set(hObject,'WindowButtonDownFcn',{'mouse_down'}) % allows mouse action with right button (zoom for uicontrol display) %% Adjust the GUI according to the binaries available in PARAM.xml path_civ=fileparts(which('civ')); %path to civ addpath (path_civ) ; %add the path to civ, (useful in case of change of working directory after civ has been s opened in the working directory) errormsg=[];%default error message xmlfile='PARAM.xml'; if exist(xmlfile,'file') try t=xmltree(xmlfile); sparam=convert(t); catch errormsg={' Unable to read the file PARAM.xml defining the civx binaries:'; lasterr}; end else errormsg=[xmlfile ' not found: path to civx binaries undefined']; end if ~isempty(errormsg) msgbox_uvmat('WARNING',errormsg); end test_batch=0;%default: ,no batch mode available if isfield(sparam,'BatchParam') && isfield(sparam.BatchParam,'BatchMode') test_batch=strcmp(sparam.BatchParam.BatchMode,'sge'); %sge is currently the only implemented batch mod end if test_batch==0 set(handles.BATCH,'Enable','off')% put the BATCH button in grey (unactivated) set(handles.BATCH,'BackgroundColor',[0.831 0.816 0.784])% put the BATCH button in grey (unactivated) end if isfield(sparam.RunParam,'CivBin') if ~exist(sparam.RunParam.CivBin,'file') sparam.RunParam.CivBin=fullfile(path_civ,sparam.RunParam.CivBin); end else sparam.RunParam.CivBin=''; end %% load the list of previously browsed files in the upper bar menu Open/ dir_perso=prefdir; % path to the directory .matlab for personal data profil_perso=fullfile(dir_perso,'uvmat_perso.mat');% personal data file uvmauvmat_perso.mat' in .matlab if exist(profil_perso,'file') h=load (profil_perso); if isfield(h,'MenuFile') for ifile=1:min(length(h.MenuFile),5) eval(['set(handles.MenuFile_' num2str(ifile) ',''Label'',h.MenuFile{ifile});']) end end end %% prepare the GUI with parameters from the input file if opened from uvmat if exist('fileinput','var')% && isfield(param,'RootName') && ~isempty(param.RootName) set(handles.RootPath,'BackgroundColor',[1 1 0])%paint RootName edit box in yellow to indicate that the file input is proceeding errormsg=display_file_name(handles,fileinput); if ~isempty(errormsg) msgbox_uvmat('ERROR',errormsg) end set(handles.RootPath,'BackgroundColor',[1 1 1])%paint RootName back to white to indicate that the file input is finished end %------------------------------------------------------------------------ % --- Outputs from this function are returned to the command line. function varargout = civ_OutputFcn(hObject, eventdata, handles) %------------------------------------------------------------------------ % Get default command line output from handles structure varargout{1} = handles.output; %------------------------------------------------------------------------ % --- Function activated by the Open/Browse... option in the upper menu bar. function MenuBrowse_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ %% get the current input root file name to initiate the browser filebase=get(handles.RootPath,'String'); oldfile=''; %default if isempty(filebase)|| isequal(filebase,'')%loads the previously stored root file name dir_perso=prefdir; profil_perso=fullfile(dir_perso,'uvmat_perso.mat'); if exist(profil_perso,'file') h=load (profil_perso); if isfield(h,'filebase')&& ischar(h.filebase) oldfile=h.filebase; end if isfield(h,'RootPath') && ischar(h.RootPath) oldfile=h.RootPath; end end else oldfile=filebase; end %% get the new input file with the browser menu={'*.xml;*.civ;*.png;*.jpg;*.tif;*.avi;*.AVI;*.nc;', ' (*.xml,*.civ,*.png,*.jpg ,.tif, *.avi,*.nc)'; '*.xml', '.xml files '; ... '*.civ', '.civ files '; ... '*.png','.png image files'; ... '*.jpg',' jpeg image files'; ... '*.tif','.tif image files'; ... '*.avi;*.AVI','.avi movie files'; ... '*.nc','.netcdf files'; ... '*.*', 'All Files (*.*)'}; [FileName, PathName, filtindex] = uigetfile( menu, 'Pick a file',oldfile); fileinput=[PathName FileName];%complete file name sizf=size(fileinput); if (~ischar(fileinput)||~isequal(sizf(1),1)),return;end %stop if fileinput not a character string %% case of the xml file opened as input (TODO: check and see whether it is useful) [path,name,ext]=fileparts(fileinput); testeditxml=0; % if isequal(ext,'.xml') % testeditxml=1; % t_browse=xmltree(fileinput); % head_element=get(t_browse,1); % if isfield(head_element,'name')&& isequal(head_element.name,'ImaDoc') % testeditxml=0; % end % end % if testeditxml==1 || isequal(ext,'.xls') % heditxml=editxml({fileinput}); % set(heditxml,'Tag','browser') % waitfor(heditxml,'Tag','idle') % if ~ishandle(heditxml) % return % end % attr=findobj(get(heditxml,'children'),'Tag','CurrentAttributes'); % set(handles.browse,'UserData',fileinput)% store for future opening with browser % fileinput=get(attr,'UserData'); % if ~exist(fileinput,'file') % return % end % end [tild,tild,tild,i1,i2,j1,j2,FileExt,NomType]=fileparts_uvmat(fileinput); %% prepare the GUI with parameters from the input file set(handles.RootPath,'BackgroundColor',[1 1 0])%paint RootName edit box in yellow to indicate that the file input is proceeding errormsg=display_file_name(handles,fileinput); if ~isempty(errormsg) msgbox_uvmat('ERROR',erromsg) end set(handles.RootPath,'BackgroundColor',[1 1 1])%paint RootName back to white to indicate that the file input is finished %------------------------------------------------------------------------ % --- Open again the file whose name has been recorded in MenuFile_1 function MenuFile_1_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ set(handles.RootPath,'BackgroundColor',[1 1 0])%paint RootName edit box in yellow to indicate that the file input is proceeding fileinput=get(handles.MenuFile_1,'Label'); errormsg=display_file_name(handles,fileinput); if ~isempty(errormsg) msgbox_uvmat('ERROR',errormsg) end set(handles.RootPath,'BackgroundColor',[1 1 1])%paint RootName back to white to indicate that the file input is finished % ----------------------------------------------------------------------- % --- Open again the file whose name has been recorded in MenuFile_2 function MenuFile_2_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ set(handles.RootPath,'BackgroundColor',[1 1 0])%paint RootName edit box in yellow to indicate that the file input is proceeding fileinput=get(handles.MenuFile_2,'Label'); errormsg=display_file_name(handles,fileinput); if ~isempty(errormsg) msgbox_uvmat('ERROR',errormsg) end set(handles.RootPath,'BackgroundColor',[1 1 1])%paint RootName back to white to indicate that the file input is finished % ----------------------------------------------------------------------- % --- Open again the file whose name has been recorded in MenuFile_3 function MenuFile_3_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ set(handles.RootPath,'BackgroundColor',[1 1 0])%paint RootName edit box in yellow to indicate that the file input is proceeding fileinput=get(handles.MenuFile_3,'Label'); errormsg=display_file_name(handles,fileinput); if ~isempty(errormsg) msgbox_uvmat('ERROR',errormsg) end set(handles.RootPath,'BackgroundColor',[1 1 1])%paint RootName back to white to indicate that the file input is finished % ----------------------------------------------------------------------- % --- Open again the file whose name has been recorded in MenuFile_4 function MenuFile_4_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ set(handles.RootPath,'BackgroundColor',[1 1 0])%paint RootName edit box in yellow to indicate that the file input is proceeding fileinput=get(handles.MenuFile_4,'Label'); errormsg=display_file_name(handles,fileinput); if ~isempty(errormsg) msgbox_uvmat('ERROR',errormsg) end set(handles.RootPath,'BackgroundColor',[1 1 1])%paint RootName back to white to indicate that the file input is finished % ----------------------------------------------------------------------- % --- Open again the file whose name has been recorded in MenuFile_5 function MenuFile_5_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ set(handles.RootPath,'BackgroundColor',[1 1 0])%paint RootName edit box in yellow to indicate that the file input is proceeding fileinput=get(handles.MenuFile_5,'Label'); errormsg=display_file_name(handles,fileinput); if ~isempty(errormsg) msgbox_uvmat('ERROR',errormsg) end set(handles.RootPath,'BackgroundColor',[1 1 1])%paint RootName back to white to indicate that the file input is finished % ----------------------------------------------------------------------- % ----------------------------------------------------------------------- % --- Open the help html file function MenuHelp_Callback(hObject, eventdata, handles) % ----------------------------------------------------------------------- path_civ=fileparts(which ('civ')); helpfile=fullfile(path_civ,'uvmat_doc','uvmat_doc.html'); if isempty(dir(helpfile)) msgbox_uvmat('ERROR','Please put the help file uvmat_doc.html in the sub-directory /uvmat_doc of the UVMAT package') else addpath (fullfile(path_civ,'uvmat_doc')) web([helpfile '#civ']) end %------------------------------------------------------------------------ % --- Function activated when a new filebase (image series) is introduced function RootPath_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ set(handles.RootPath,'BackgroundColor',[1 1 0])%paint RootName edit box in yellow to indicate that the file input is proceeding RootPath=get(handles.RootPath,'String'); RootFile=get(handles.RootFile,'String'); ref_i=str2num(get(handles.ref_i,'String')); ref_j=str2num(get(handles.ref_j,'String')); NomType=get(handles.NomType,'String'); ImaExt=get(handles.ImaExt,'String'); fileinput=fullfile_uvmat(RootPath,'',RootFile,ImaExt,NomType,ref_i,[],ref_j); errormsg=display_file_name(handles,fileinput); if ~isempty(errormsg) msgbox_uvmat('ERROR',errormsg) end set(handles.RootPath,'BackgroundColor',[1 1 1])%paint RootName back to white to indicate that the file input is finished %------------------------------------------------------------------------ % --- general function activated for an input file series function errormsg=display_file_name(handles,fileinput) %------------------------------------------------------------------------ set(handles.ListCompareMode,'Visible','on') errormsg='';%default empty error message drawnow %% enable RUN, BATCH button and 'status' display set(handles.RUN, 'Enable','On') set(handles.RUN,'BackgroundColor',[1 0 0])%set RUN button to red color set(handles.BATCH,'Enable','On') set(handles.BATCH,'BackgroundColor',[1 0 0])%set BATCH button to red color if isfield(handles,'status') set(handles.status,'Value',0); %suppress the 'status' display status_Callback([], [], handles) end %% determine nomenclature types and extension of the input files [RootPath,SubDir,RootFile,i1,i2,j1,j2,ExtInput,NomTypeInput]=fileparts_uvmat(fileinput); NomTypeNc='';%default %% case of netcdf file as input, look for a coresponding image ind_opening=0;%default if strcmp(ExtInput,'.xml') Param=xml2struct(fileinput); fill_GUI(Param,handles);%fill the GUI with the parameters retrieved from the xml file return end if strcmp(ExtInput,'.nc') NomTypeNc=NomTypeInput; if isempty(regexp(NomTypeInput,'[ab|AB|-]')) set(handles.ListCompareMode,'Value',2) %mode displacement advised if the nomencalture does not involve index pairs [RootPath,SubDir]=fileparts(RootPath); set(handles.RootFile_1,'Visible','On'); else set(handles.ListCompareMode,'Value',1) set(handles.RootFile_1,'Visible','Off'); end Data=nc2struct(fileinput,'ListGlobalAttribute','Conventions','absolut_time_T0','CivStage','Civ2_ImageA','Civ1_ImageA','Civ2_ImageB','Civ1_ImageB','fix','patch','civ2','fix2'); if isfield(Data,'Txt') errormsg=Data.Txt; return end if strcmp(Data.Conventions,'uvmat/civdata')% case of new civ data, set(handles.ListProgram,'Value',2) %select civ/Matlab by default ListProgram_Callback([],[], handles) if ~isempty(Data.CivStage)%test for civ files ind_opening=Data.CivStage; end if ~isempty(Data.Civ2_ImageB)%get the corresponding input image in the netcdf file imageinput=Data.Civ2_ImageB; [tild,ImaName,ImaExt]=fileparts(Data.Civ2_ImageA); set(handles.RootFile_1,'String',[ImaName ImaExt]) elseif ~isempty(Data.Civ1_ImageB) imageinput=Data.Civ1_ImageB; [tild,ImaName,ImaExt]=fileparts(Data.Civ1_ImageA); set(handles.RootFile_1,'String',[ImaName ImaExt]) end elseif ~isempty(Data.absolut_time_T0')% case of civx data, set(handles.ListProgram,'Value',1) %select Cix by default ListProgram_Callback([],[], handles) if ~isempty(Data.fix2) ind_opening=5; elseif ~isempty(Data.civ2) ind_opening=4; elseif ~isempty(Data.patch) ind_opening=3; elseif ~isempty(Data.fix) ind_opening=2; end % look for the corresponding input images check_letter=~isempty(regexp(NomTypeInput,'[ab|AB]$'));%detect pair label by letter NomTypeIma=NomTypeInput; if check_letter NomTypeIma=NomTypeInput(1:end-1); else r=regexp(NomTypeIma,'.-(?\d+)$','names'); if ~isempty(r) NomTypeIma=regexprep(NomTypeIma,['-' r.num2],''); end r=regexp(NomTypeIma,'.-(?\d+)','names'); if ~isempty(r) NomTypeIma=regexprep(NomTypeIma,['-' r.num2],''); end end imageinput=fullfile_uvmat(RootPath,'',RootFile,'.png',NomTypeIma,i1,[],j1); else errormsg='the input netcdf file is not civ data'; return end end %no corresponding image found, select manually with the browser ImaExt=ExtInput; if ~isempty(NomTypeNc) %no corresponding image found, select manually with the browser if ~exist(imageinput,'file') menu={'*.png;*.jpg;*.tif;*.avi;*.AVI', '(*.png,*.jpg ,*.tif, *.avi,*.AVI)'; '*.png','.png image files'; ... '*.jpg',' jpeg image files'; ... '*.tif','.tif image files'; ... '*.avi;*.AVI','.avi movie files'; ... '*.*', 'All Files (*.*)'}; [FileName, PathName] = uigetfile( menu, 'Pick an input image file',fileparts(fileparts(fileinput))); imageinput=[PathName FileName];%complete file name end fileinput=imageinput; end %% scan the image file series [FilePath,FileName,ImaExt]=fileparts(fileinput); % detect the file type, get the movie object if relevant, and look for the corresponding file series: % the root name and indices may be corrected by including the first index i1 if a corresponding xml file exists [RootPath,SubDir,RootFile,i1_series,i2_series,j1_series,j2_series,NomTypeIma,FileType,Object,i1,i2,j1,j2]=find_file_series(FilePath,[FileName ImaExt]); % [RootPath,FileName,ImaExt]=fileparts(fileinput); % [RootFile,i1_series,tild,j1_series,tild,NomTypeIma,FileType,Object]=find_file_series(RootPath,[FileName ImaExt]); % if strcmp(NomTypeInput,'*')% movies will be opened at the first frame % i1=1; % i2=[]; % j1=[]; % j2=[]; % end switch FileType case {'image','multimage','video'} otherwise errormsg='invalid input file: enter an image, a movie or civ .nc file'; return end % RootName=fullfile(RootPath,RootFile); set(handles.RootPath,'String',RootPath) set(handles.RootFile,'String',RootFile) browse=get(handles.RootPath,'UserData'); % browse.nom_type_nc=NomTypeNc; browse.incr_pair=[0 0];%default %% fill reference indices from the input file indices num_ref_i=i1;%efaulmt ref index if ~isempty(i2) num_ref_i=floor((num_ref_i+i2)/2); end num_ref_j=j1; if ~isempty(j2) num_ref_j=floor((num_ref_j+j2)/2); end %% scan the images if a civ file has been opened MinIndex_i=min(i1_series(i1_series>0)); MinIndex_j=min(j1_series(j1_series>0)); MaxIndex_i=max(i1_series(i1_series>0)); MaxIndex_j=max(j1_series(j1_series>0)); %% look for an image documentation file ext_imadoc='';%default RootName=fullfile(RootPath,RootFile); if exist([RootName '.xml'],'file') ext_imadoc='.xml'; elseif exist([RootName '.civxml'],'file') ext_imadoc='.civxml'; elseif exist([RootName '.civ'],'file') ext_imadoc='.civ'; elseif exist([RootName '.avi'],'file') ext_imadoc='.avi'; elseif exist([RootName '.AVI'],'file') ext_imadoc='.AVI'; end set(handles.ImaDoc,'String',ext_imadoc)% display the extension name for the image documentation file used %% read the time in the image documentation file time=[]; TimeUnit=''; %default CoordUnit='';%default pxcm_search=1; if ~isempty(ext_imadoc) set(handles.ImaDoc,'BackgroundColor',[1 1 0]) % set edit box to yellow cloro to indicate that the file reading is beginning drawnow switch ext_imadoc case '.civxml'%OBSOLETE [tild,tild,time]=read_civxml([RootName '.civxml']); mode='pair j1-j2'; if isempty(nom_type_ima)% dtermine types by default if not already selected by browser or uvmat nom_type_ima='_i_j'; end case '.xml' [XmlData,warntext]=imadoc2struct([RootName '.xml']); ext_ima_read=[]; nom_type_read=[]; if isfield(XmlData,'Heading')&&isfield(XmlData.Heading','ImageName')&&ischar(XmlData.Heading.ImageName)% get image nom type and extension from the xml file %[PP,FF,fc,str2,str_a,str_b,ext_ima_read,nom_type_read]=name2display(XmlData.Heading.ImageName); [tild,tild,tild,tild,tild,tild,tild,tild,nom_type_read]=fileparts_uvmat(XmlData.Heading.ImageName); fullname=fullfile(fileparts(RootName),XmlData.Heading.ImageName); %full name (including path) of the first image defined by the xmle file, if ~exist(fullname,'file') msgbox_uvmat('WARNING',['FirstImage ' fullname ' defined in the xml file does not exist']) end end if isfield(XmlData,'Time') time=XmlData.Time; %transform .Time to a column vector if it is a line vector thenomenclature uses a single index: correct possible bug in xml if isequal(MaxIndex_i,1) && ~isequal(MaxIndex_j,1)% .Time is a line vector if numel(nom_type_read)>=2 && isempty(regexp(nom_type_read(2:end),'\D','once')) time=time'; MaxIndex_i=MaxIndex_j; MaxIndex_j=1; end end end if isfield(XmlData,'TimeUnit') TimeUnit=XmlData.TimeUnit; end if isfield(XmlData,'GeometryCalib') tsai=XmlData.GeometryCalib; if isfield(tsai,'fx_fy') pxcm_search=max(tsai.fx_fy(1),tsai.fx_fy(2));%pixels:cm estimated for the search range end if isfield(tsai,'CoordUnit') CoordUnit=tsai.CoordUnit; end end case '.civ'% OBSOLETE: case of .civ image documentation file [error,time,TimeUnit,mode,npx,npy]=read_imatext([RootName '.civ']); if error==2, msgbox_uvmat('WARNING',['no file ' RootName '.civ']); elseif error==1, msgbox_uvmat('WARNING','inconsistent number of fields in the .civ file'); end nom_type_ima='001a'; case {'.avi','.AVI'} nom_type_ima='*'; ImaExt=ext_imadoc; set(handles.ListPairMode,'Value',1); set(handles.ListPairMode,'String',{'series(Di)'}) dt=0.04;%default if exist([RootName ext_imadoc],'file')==2 hhh=which('videoreader'); if isempty(hhh)%use old video function of matlab imainfo=aviinfo([RootName ext_imadoc]);%read infos on the avi movie dt=1/imainfo.FramesPerSecond;%time interval between successive frames MaxIndex_i=imainfo.NumFrames;%number of frames % XmlData.Time=(0:1/imainfo.FramesPerSecond:(imainfo.NumFrames-1)/imainfo.FramesPerSecond)'; % nbfield=imainfo.NumFrames; % set(handles.Dt_txt,'String',['Dt=' num2str(1000/imainfo.FramesPerSecond) 'ms']);%display the elementary time interval in millisec % ColorType=imainfo.ImageType;%='truecolor' for color images else %use video function videoreader of matlab imainfo=get(videoreader([RootName ext_imadoc]));%read infos on the avi movie dt=1/imainfo.FrameRate;%time interval between successive frames MaxIndex_i=imainfo.NumberOfFrames;%number of frames % XmlData.Time=(0:1/imainfo.FrameRate:(imainfo.NumberOfFrames-1)/imainfo.FrameRate)'; % nbfield=imainfo.NumberOfFrames; % set(handles.Dt_txt,'String',['Dt=' num2str(1000/imainfo.FrameRate) 'ms']);%display the elementary time interval in millisec % ColorType='truecolor'; end time=(dt*(0:MaxIndex_i-1))';%list of image times TimeUnit='s'; end set(handles.ImaDoc,'BackgroundColor',[1 1 1])% set display box back to whiter end end %% timing display %show the reference image edit box if relevant (not needed for movies or in the absence of time information if numel(time)>=2 % if there are at least two time values to define dt MaxIndex_i=min(size(time,1),MaxIndex_i); MaxIndex_j=min(size(time,2),MaxIndex_j); time=[zeros(size(time,1),1) time]; %insert a vertical line of zeros (to deal with zero file indices) time=[zeros(1,size(time,2)); time]; %insert a horizontal line of zeros set(handles.ImaDoc,'UserData',time); %store the matrix of times set(handles.dt_unit,'String',['dt in m' TimeUnit]); set(handles.TimeUnit,'String',TimeUnit); else set(handles.ImaDoc,'String',''); %xml file not used for timing time=(i1_series(:,1)+0:size(i1_series,1)-1);% time=index i time=time'*ones(1,size(i1_series,2),1); %makes a time matrix with the same time for all j indices TimeUnit='frame'; end set(handles.ImaDoc,'UserData',time); %store the matrix of times set(handles.dt_unit,'String',['dt in m' TimeUnit]);%display dt in unit 10-3 of the time (e.g ms) set(handles.TimeUnit,'String',TimeUnit); set(handles.nb_field,'String',num2str(MaxIndex_i)); set(handles.nb_field2,'String',num2str(MaxIndex_j)); set(handles.CoordUnit,'String',CoordUnit) set(handles.SearchRange,'UserData', pxcm_search); set(handles.ImaExt,'String',ImaExt) set(handles.NomType,'String',NomTypeIma) set(handles.ref_i,'String',num2str(num_ref_i)) set(handles.ref_j,'String',num2str(num_ref_j)) %% update i and j index range if a nc file has been opened or pb withmin max image indices: % then set first and last to the inputfile index by default first_i=str2num(get(handles.first_i,'String')); last_i=str2num(get(handles.last_i,'String')); if isempty(first_i) || isempty(last_i)||isempty(MinIndex_i)||isempty(MaxIndex_i) set(handles.first_i,'String',num2str(num_ref_i)); set(handles.last_i,'String',num2str(num_ref_i));% end if ind_opening~=0 || isempty(first_i) || isempty(last_i)|| first_iMaxIndex_i set(handles.first_i,'String',num2str(num_ref_i)); set(handles.last_i,'String',num2str(num_ref_i));% end %j index range first_j=str2num(get(handles.first_j,'String')); last_j=str2num(get(handles.last_i,'String')); if isempty(first_j) || isempty(last_j)||isempty(MinIndex_j)||isempty(MaxIndex_j) set(handles.first_j,'String',num2str(num_ref_j)); set(handles.last_j,'String',num2str(num_ref_j));% elseif ind_opening~=0 || first_jMaxIndex_j set(handles.first_j,'String',num2str(num_ref_j)); set(handles.last_j,'String',num2str(num_ref_j));% end %% set the civ options depending on the input file content when a nc file has been opened ListOptions={'CheckCiv1', 'CheckFix1' 'CheckPatch1', 'CheckCiv2', 'CheckFix2', 'CheckPatch2'}; if ind_opening~=0 for index = 1:ind_opening set(handles.(ListOptions{index}),'value',0) end end for index = ind_opening+2:6 set(handles.(ListOptions{index}),'value',0) end set(handles.(ListOptions{min(ind_opening+1,6)}),'value',1) update_CivOptions(handles,1) %% set the menus of image pairs and default selection for civ %%%%%%%%%%%%%%%%%%% %check_letter=~isempty(regexp(NomTypeIma,'[ab|AB]$'));%detect pair label by letter if isequal(NomTypeNc,'_1-2')||isempty(MaxIndex_j)|| (MaxIndex_j==1) set(handles.ListPairMode,'Value',1) set(handles.ListPairMode,'String',{'series(Di)'}) elseif MaxIndex_i==1 && MaxIndex_j>1% simple series in j set(handles.ListPairMode,'String',{'pair j1-j2';'series(Dj)'}) if MaxIndex_j <= 10 set(handles.ListPairMode,'Value',1)% advice 'pair j1-j2' except in MaxIndex_j is large end else set(handles.ListPairMode,'String',{'pair j1-j2';'series(Dj)';'series(Di)'})%multiple choice if strcmp(NomTypeNc,'_1-2_1') set(handles.ListPairMode,'Value',3)% advise 'series(Di)' elseif MaxIndex_j <= 10 set(handles.ListPairMode,'Value',1)% advice 'pair j1-j2' except in MaxIndex_j is large end end %% scan files to update the subdirectory list display listot=dir(RootPath);%directory of RootPath idir=0; listdir={''};%default % get the list of existing civ subdirectories in the path of theinput root file for ilist=1:length(listot) if listot(ilist).isdir name=listot(ilist).name; if ~isequal(name,'.') && ~isequal(name,'..') idir=idir+1; listdir{idir,1}=listot(ilist).name; end end end %% update the selection for civ1 and civ2 if ~isempty(SubDir)% subdir for civ1 and civ2 initiated by the input SubdirCiv1=SubDir; SubdirCiv2=SubDir; set(handles.SubdirCiv1,'String',SubDir) set(handles.SubdirCiv2,'String',SubDir) else% currently selected subdir preserved SubdirCiv1=get(handles.SubdirCiv1,'String'); SubdirCiv2=get(handles.SubdirCiv2,'String'); if isempty(SubdirCiv1)% default subdir name='CIV' set(handles.SubdirCiv1,'String','CIV'); SubdirCiv1='CIV'; end if isempty(SubdirCiv2)% default subdir name='CIV' set(handles.SubdirCiv2,'String','CIV'); SubdirCiv2='CIV'; end end %% update the subdirectory menus ValueCiv1=find(strcmp(SubdirCiv1,listdir));%search the index of subdir in the cell listdir if isempty(ValueCiv1)% if the input subdir is not found ValueCiv1=numel(listdir)+1;%new subdirectory requested for civ1 end ValueCiv2=find(strcmp(SubdirCiv2,listdir));%search the index of subdir in the cell listdir if isempty(ValueCiv2)% if the input subdir is not found ValueCiv2=numel(listdir)+1;%new subdirectory requested for civ2 end set(handles.ListSubdirCiv1,'String',[listdir;'new...']) set(handles.ListSubdirCiv2,'String',[listdir;'new...']) set(handles.ListSubdirCiv1,'Value',ValueCiv1) set(handles.ListSubdirCiv2,'Value',ValueCiv2) if isempty(listdir) set(handles.SubdirCiv1,'String','CIV') set(handles.SubdirCiv2,'String','CIV') end %% store info set(handles.RootPath,'UserData',browse)% store the nomenclature type %% list the possible index pairs, depending on the option set in ListPairMode ListPairMode_Callback([], [], handles) %% store the root input filename for future opening profil_perso=fullfile(prefdir,'uvmat_perso.mat'); if exist(profil_perso,'file') save (profil_perso,'RootPath','-append'); %store the root name for future opening of uvmat else txt=ver('MATLAB'); Release=txt.Release; relnumb=str2double(Release(3:4)); if relnumb >= 14 save (profil_perso,'RootPath','-V6'); %store the root name for future opening of uvmat else save (profil_perso,'RootPath'); %store the root name for future opening of uvmat end end set(handles.RootPath,'BackgroundColor',[1 1 1]) %------------------------------------------------------------------------ % --- Executes on carriage return on the subdir checkciv1 edit window function SubdirCiv1_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ SubDir=get(handles.SubdirCiv1,'String'); menu_str=get(handles.ListSubdirCiv1,'String');% read the list of subdirectories for update ichoice=find(strcmp(SubDir,menu_str),1); if isempty(ichoice) ilist=numel(menu_str); %select 'new...' in the menu else ilist=ichoice; end set(handles.ListSubdirCiv1,'Value',ilist)% select the selected subdir in the menu if get(handles.CheckCiv1,'Value')% if Civ1 is performed set(handles.SubdirCiv2,'String',SubDir);% set by default civ2 directory the same as civ1 set(handles.ListSubdirCiv2,'Value',ilist) else % if Civ1 data already exist errormsg=find_netcpair_civ(handles,1); %update the list of available pairs from netcdf files in the new directory if ~isempty(errormsg) msgbox_uvmat('ERROR',errormsg) end end %------------------------------------------------------------------------ % --- Executes on carriage return on the SubDir checkciv1 edit window function SubdirCiv2_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ SubDir=get(handles.SubdirCiv1,'String'); menu_str=get(handles.ListSubdirCiv2,'String');% read the list of subdirectories for update ichoice=find(strcmp(SubDir,menu_str),1); if isempty(ichoice) ilist=numel(menu_str); %select 'new...' in the menu else ilist=ichoice; end set(handles.ListSubdirCiv2,'Value',ilist)% select the selected subdir in the menu %update the list of available pairs from netcdf files in the new directory if ~get(handles.CheckCiv2,'Value') && ~get(handles.CheckCiv1,'Value') && ~get(handles.CheckFix1,'Value') && ~get(handles.CheckPatch1,'Value') errormsg=find_netcpair_civ(handles,2); if ~isempty(errormsg) msgbox_uvmat('ERROR',errormsg) end end %------------------------------------------------------------------------ % --- Executes on button press in CheckCiv1. function CheckCiv1_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ update_CivOptions(handles,0) %------------------------------------------------------------------------ % --- Executes on button press in CheckFix1. function CheckFix1_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ update_CivOptions(handles,0) %------------------------------------------------------------------------ % --- Executes on button press in CheckPatch1. function CheckPatch1_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ update_CivOptions(handles,0) %------------------------------------------------------------------------ % --- Executes on button press in CheckCiv2. function CheckCiv2_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ update_CivOptions(handles,0) %------------------------------------------------------------------------ % --- Executes on button press in CheckFix2. function CheckFix2_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ update_CivOptions(handles,0) %------------------------------------------------------------------------ % --- Executes on button press in CheckPatch2. function CheckPatch2_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ update_CivOptions(handles,0) %------------------------------------------------------------------------ % --- activated by any checkbox controling the selection of Civ1,Fix1,Patch1,Civ2,Fix2,Patch2 function update_CivOptions(handles,opening) %------------------------------------------------------------------------ checkbox=zeros(1,6); checkbox(1)=get(handles.CheckCiv1,'Value'); checkbox(2)=get(handles.CheckFix1,'Value'); checkbox(3)=get(handles.CheckPatch1,'Value'); checkbox(4)=get(handles.CheckCiv2,'Value'); checkbox(5)=get(handles.CheckFix2,'Value'); checkbox(6)=get(handles.CheckPatch2,'Value'); ind_selected=find(checkbox,1); if ~isempty(ind_selected) RootPath=get(handles.RootPath,'String'); if isempty(RootPath) msgbox_uvmat('ERROR','Please open an image or PIV .nc file with the upper bar menu Open/Browse...') return end end set(handles.PairIndices,'Visible','on') set(handles.SubdirCiv1,'Visible','on') set(handles.ListSubdirCiv1,'Visible','on') set(handles.TitleSubdirCiv1,'Visible','on') if ~opening errormsg=find_netcpair_civ(handles,1); % select the available netcdf files if ~isempty(errormsg) msgbox_uvmat('ERROR',errormsg) end end if max(checkbox(4:6))% case of civ2 pair choice needed set(handles.TitlePairCiv2,'Visible','on') set(handles.TitleSubdirCiv2,'Visible','on') set(handles.SubdirCiv2,'Visible','on') set(handles.ListSubdirCiv2,'Visible','on') set(handles.ListPairCiv2,'Visible','on') if ~opening errormsg=find_netcpair_civ(handles,2); % select the available netcdf files if ~isempty(errormsg) msgbox_uvmat('ERROR',errormsg) end end else set(handles.TitleSubdirCiv2,'Visible','off') set(handles.SubdirCiv2,'Visible','off') set(handles.ListSubdirCiv2,'Visible','off') set(handles.ListPairCiv2,'Visible','off') end options={'Civ1','Fix1','Patch1','Civ2','Fix2','Patch2'}; for ilist=1:length(options) if checkbox(ilist) set(handles.(options{ilist}),'Visible','on') else set(handles.(options{ilist}),'Visible','off') end end %------------------------------------------------------------------------ % --- Executes on button press in RUN: processing on local computer function RUN_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ set(handles.RUN, 'Enable','Off') set(handles.RUN,'BackgroundColor',[0.831 0.816 0.784]) batch=0; errormsg=launch_jobs(hObject, eventdata, handles,batch); set(handles.RUN, 'Enable','On') set(handles.RUN,'BackgroundColor',[1 0 0]) % display errors or start status callback to visualise results if ~isempty(errormsg) display(errormsg) msgbox_uvmat('ERROR',errormsg) elseif isfield(handles,'status') %&& ~isequal(get(handles.ListPairMode,'Value'),3) set(handles.status,'Value',1);%suppress status display status_Callback(hObject, eventdata, handles) end %------------------------------------------------------------------------ % --- Executes on button press in BATCH: remote processing function BATCH_Callback(hObject, eventdata, handles) % ----------------------------------------------------------------------- set(handles.BATCH, 'Enable','Off') set(handles.BATCH,'BackgroundColor',[0.831 0.816 0.784]) batch=1; errormsg=launch_jobs(hObject, eventdata, handles, batch); set(handles.BATCH, 'Enable','On') set(handles.BATCH,'BackgroundColor',[1 0 0]) % display errors or start status callback to visualise results if ~isempty(errormsg) display(errormsg) msgbox_uvmat('ERROR',errormsg) elseif isfield(handles,'status') set(handles.status,'Value',1);%suppress status display status_Callback(hObject, eventdata, handles) end %------------------------------------------------------------------- % --- Executes on button press in status. function status_Callback(hObject, eventdata, handles) %------------------------------------------------------------------- val=get(handles.status,'Value'); if val==0 set(handles.status,'BackgroundColor',[0 1 0]) hfig=findobj(allchild(0),'name','civ_status'); if ~isempty(hfig) delete(hfig) end return end set(handles.status,'BackgroundColor',[1 1 0]) drawnow listtype={'civ1','fix1','patch1','civ2','fix2','patch2'}; Param.CheckCiv1=get(handles.CheckCiv1,'Value'); Param.CheckFix1=get(handles.CheckFix1,'Value'); Param.CheckPatch1=get(handles.CheckPatch1,'Value'); Param.CheckCiv2=get(handles.CheckCiv2,'Value'); Param.CheckFix2=get(handles.CheckFix2,'Value'); Param.CheckPatch2=get(handles.CheckPatch2,'Value'); box_test=[Param.CheckCiv1 Param.CheckFix1 Param.CheckPatch1 Param.CheckCiv2 Param.CheckFix2 Param.CheckPatch2]; option_civ=find(box_test,1,'last');%last selected option (non-zero index of box_test) filecell=get(handles.civ,'UserData');%retrieve the list of output files expected for PIV test_new=0; if ~isfield(filecell,'nc') test_new=1; [ref_i,ref_j,errormsg]=find_ref_indices(handles); if ~isempty(errormsg) msgbox_uvmat('ERROR',errormsg) return end filecell=set_civ_filenames(handles,ref_i,ref_j,box_test);%determine the output file expected from the GUI status end if ~isequal(box_test(4:6),[0 0 0]) civ_files=filecell.nc.civ2;%case of civ2 operations else civ_files=filecell.nc.civ1; end [root,filename,ext]=fileparts(civ_files{1}); [rootroot,SubDir,extdir]=fileparts(root); hfig=findobj(allchild(0),'name','civ_status'); if isempty(hfig) hfig=figure('DeleteFcn',@stop_status); set(hfig,'MenuBar','none')% suppress the menu bar set(hfig,'NumberTitle','off')%suppress the fig number in the title set(hfig,'name','civ_status') set(hfig,'tag','civ_status') set(hfig,'UserData',civ_files) hlist= uicontrol('Style','listbox','Units','normalized', 'Position',[0.05 0.09 0.9 0.71], 'Callback', {'open_uvmat'},'tag','list'); uicontrol('Style','edit','Units','normalized', 'Position', [0.05 0.87 0.9 0.1],'tag','msgbox','Max',2,'String','checking files...'); uicontrol('Style','frame','Units','normalized', 'Position', [0.05 0.81 0.9 0.05]); uicontrol('Style','pushbutton','Units','normalized', 'Position', [0.7 0.01 0.2 0.07],'String','Close','FontWeight','bold','FontUnits','normalized','FontSize',0.9,'Callback',@close_GUI); hrefresh=uicontrol('Style','pushbutton','Units','normalized', 'Position', [0.1 0.01 0.2 0.07],'String','Refresh','FontWeight','bold','FontUnits','normalized','FontSize',0.9,'Callback',@refresh_GUI); BarPosition=[0.05 0.81 0.01 0.05]; uicontrol('Style','frame','Units','normalized', 'Position',BarPosition ,'BackgroundColor',[1 0 0],'tag','waitbar'); drawnow end set(hrefresh,'UserData',option_civ) filepath=fileparts(civ_files{1}); set(hlist,'UserData',fileparts(filepath)) refresh_GUI(hrefresh,[]) %------------------------------------------------------------------------ % launched by refreshing the status figure function refresh_GUI(hObject, eventdata) %------------------------------------------------------------------------ Tabchar={}; BarPosition=[0.05 0.81 0.01 0.05]; hfig=get(hObject,'parent'); civ_files=get(hfig,'UserData'); [filepath,filename,ext]=fileparts(civ_files{1}); [tild,SubDir,extdir]=fileparts(filepath); SubDir=[SubDir extdir]; option_civ=get(hObject,'UserData'); nbfiles=numel(civ_files); count=0; testrecent=0; % while count= option_civ count=count+1; end [filepath,filename,ext]=fileparts(civ_files{ifile}); Tabchar{ifile,1}=[fullfile(SubDir,filename) ext '...' option_str]; end datnum=datnum(datnum~=0);%keep the non zero values corresponding to existing files if isempty(datnum) if testrecent message='no civ result created yet'; else message=''; end else datnum=datnum(datnum~=0);%keep the non zero values corresponding to existing files [first,ind]=min(datnum); [last,indlast]=max(datnum); % if test_new % message='existing file status, no processing launched yet'; % else message={[num2str(count) ' file(s) done over ' num2str(nbfiles)] ;['oldest modification: ' cell2mat(filefound(ind)) ' : ' datestr(first)];... ['latest modification: ' cell2mat(filefound(indlast)) ' : ' datestr(last)]}; % end end %hfig=findobj(allchild(0),'name','civ_status'); % if isempty(hfig)% the status list has been deleted % return % else hlist=findobj(hfig,'tag','list'); hmsgbox=findobj(hfig,'tag','msgbox'); hwaitbar=findobj(hfig,'tag','waitbar'); set(hlist,'String',Tabchar) set(hmsgbox,'String', message) if count>0 %&& ~test_new BarPosition(3)=0.9*count/nbfiles; set(hwaitbar,'Position',BarPosition) end % end % [root,filename,ext]=fileparts(civ_files{1}); % [rootroot,SubDir,extdir]=fileparts(root); % % set(hlist,'UserData',rootroot) % if count<10||(nbfiles-count)<10 % pause(.5)% wait 0.5 seconds for next check % else % pause(10)% wait 10 seconds for next check % end % end %------------------------------------------------------------------------ % launched by deleting the status figure function stop_status(hObject, eventdata) %------------------------------------------------------------------------ hciv=findobj(allchild(0),'tag','civ'); hhciv=guidata(hciv); set(hhciv.status,'value',0) %reset the status uicontrol in the GUI civ set(hhciv.status,'BackgroundColor',[0 1 0]) %------------------------------------------------------------------------ % launched by pressing OK on the status figure function close_GUI(hObject, eventdata) %------------------------------------------------------------------------ delete(gcbf) %------------------------------------------------------------------------ % --- Main lauch command, called by RUN and BATCH function errormsg=launch_jobs(hObject, eventdata, handles, batch) %----------------------------------------------------------------------- errormsg='';%default %% read the input parameters from the GUI civ Param=read_GUI(handles.civ); %% check the selected list of operations: operations={'Civ1','Fix1','Patch1','Civ2','Fix2','Patch2'}; box_test=[Param.CheckCiv1 Param.CheckFix1 Param.CheckPatch1 Param.CheckCiv2 Param.CheckFix2 Param.CheckPatch2]; index_first=find(box_test==1,1); if isempty(index_first) errormsg='no selected operation'; return end index_last=find(box_test==1,1,'last'); box_used=box_test(index_first : index_last); [box_missing,ind_missing]=min(box_used); if isequal(box_missing,0); %there is a missing step in the sequence of operations errormsg=['missing' cell2mat(operations(ind_missing))]; return end %% check mask if selecetd %could be included in get_mask callback ? if isequal(get(handles.CheckMask,'Value'),1) maskname=get(handles.Mask,'String'); if ~exist(maskname,'file') get_mask_civ1_Callback(hObject, eventdata, handles); end end if isequal(get(handles.CheckMask,'Value'),1) maskname=get(handles.Mask,'String'); if ~exist(maskname,'file') get_mask_fix1_Callback(hObject, eventdata, handles); end end if isequal(get(handles.CheckMask,'Value'),1) maskname=get(handles.Mask,'String'); if ~exist(maskname,'file') get_mask_civ2_Callback(hObject, eventdata, handles); end end if isequal(get(handles.CheckMask,'Value'),1) maskname=get(handles.Mask,'String'); if ~exist(maskname,'file') get_mask_fix2_Callback(hObject, eventdata, handles); end end %% reinitialise status callback if isfield(handles,'status') set(handles.status,'Value',0);%suppress status display status_Callback(hObject, eventdata, handles) end %% read the PARAM.xml file to get the binaries (and batch_mode if batch) path_civ=fileparts(which('civ')); %path to the source directory of uvmat xmlfile='PARAM.xml'; if exist(xmlfile,'file')% search parameter xml file in the whole matlab path t=xmltree(xmlfile); s=convert(t); else errormsg=['no file ' xmlfile]; return end test_interp=0; %eviter les variables test_ (LG) if batch if isfield(s,'BatchParam') Param.xml=s.BatchParam; if isfield(Param.xml,'BatchMode') batch_mode=Param.xml.BatchMode; if ~ismember(batch_mode,{'sge','oar'}) errormsg=['batch mode ' batch_mode ' not supported by UVMAT']; return end end else errormsg='no batch civ binaries defined in PARAM.xml'; return end else % run if isfield(s,'RunParam') Param.xml=s.RunParam; else errormsg='no run civ binaries defined in PARAM.xml'; return end end %% check batch mode supported if batch switch batch_mode case 'sge' test_command='qstat'; case 'oar' test_command='oarstat'; end [s,w]=system(test_command); if ~isequal(s,0) errormsg=[batch_mode ' batch system not available']; return end end %% check if the binaries exist ListProgram=get(handles.ListProgram,'String'); CivMode=ListProgram{get(handles.ListProgram,'Value')}; binary_list={}; switch CivMode case 'CivX' binary_list={'Civ1Bin','Civ2Bin','PatchBin','FixBin'}; case 'CivAll'% desactivated option binary_list={'Civ'}; case 'Matlab' if batch binary_list={'CivmBin'}; % verifier MenuMatlab installe sur le cluster % difficile a faire a priori end end for bin_name=binary_list %loop on the list of binaries if isfield(Param.xml,bin_name{1})% bin_name{1} =current name in the list if exist(Param.xml.(bin_name{1}),'file') [path,name,ext]=fileparts(Param.xml.(bin_name{1})); currentdir=pwd; if exist(path,'dir') cd(path); binpath=pwd;%path of the binary Param.xml.(bin_name{1})=fullfile(binpath,[name ext]); cd(currentdir) else errormsg=['path ' path ' for binaries defined in PARAM.xml does not exist']; return end else %look for the full path if the file name has been defined with a relative path in PARAM.xm fullname=fullfile(path_civ,Param.xml.(bin_name{1})); if exist(fullname,'file') Param.xml.(bin_name{1})=fullname; else errormsg=['Binary ' Param.xml.(bin_name{1}) ' defined in PARAM.xml does not exist']; return end end end end display('files OK, processing...') %% set the list of files and check them display('checking the files...') [ref_i,ref_j,errormsg]=find_ref_indices(handles); if ~isempty(errormsg) return end [filecell,i1_civ1,i2_civ1,j1_civ1,j2_civ1,i1_civ2,i2_civ2,j1_civ2,j2_civ2,nom_type_nc,xx,yy,compare]=... set_civ_filenames(handles,ref_i,ref_j,box_test); Rootbat=fileparts(filecell.nc.civ1{1,1});%output netcdf file (without extention) set(handles.civ,'UserData',filecell);%store for futur use of status callback if isempty(filecell)% (error message displayed in fct set_civ_filenames) return end nbfield=numel(i1_civ1); nbslice=numel(j1_civ1); if ~strcmp(CivMode,'CivX') if Param.CheckCiv1 [Param.Civ1.FileTypeA,FileInfo,Param.Civ1.ImageA]=get_file_type(filecell.ima1.civ1{1}); [Param.Civ1.FileTypeB,FileInfo,Param.Civ1.ImageB]=get_file_type(filecell.ima2.civ1{1}); end if Param.CheckCiv2 [Param.Civ2.FileTypeA,FileInfo,Param.Civ2.ImageA]=get_file_type(filecell.ima1.civ2{1}); [Param.Civ2.FileTypeB,FileInfo,Param.Civ2.ImageB]=get_file_type(filecell.ima2.civ2{1}); end end %% MAIN LOOP time=get(handles.ImaDoc,'UserData'); %get the set of times TimeUnit=get(handles.TimeUnit,'String'); checkframe=strcmp(TimeUnit,'frame'); batch_file_list=[];%should be renamed file_list, can be used for xml or bash files for ifile=1:nbfield for j=1:nbslice % initiate system command switch CivMode case 'CivX' if isunix % check: necessaire aussi en RUN? cmd=['#!/bin/bash \n '... '#$ -cwd \n '... 'hostname && date \n '... 'umask 002 \n'];%allow writting access to created files for user group else cmd=[]; end case 'CivAll' CivAllxml=xmltree;% xml contents, all parameters CivAllCmd=''; CivAllxml=set(CivAllxml,1,'name','CivDoc'); end % define output file name if Param.CheckCiv2==1 || Param.CheckFix2==1 || Param.CheckPatch2==1 OutputFile=filecell.nc.civ2{ifile,j}; else OutputFile=filecell.nc.civ1{ifile,j}; end OutputFile=regexprep(OutputFile,'.nc',''); if Param.CheckCiv1 % read image-dependent parameters Param.Civ1.ImageA=filecell.ima1.civ1{ifile,j}; Param.Civ1.ImageB=filecell.ima2.civ1{ifile,j}; if ~checkframe% && size(time,1)>=i2_civ1(ifile) && size(time,2)>=j2_civ1(j) Param.Civ1.Dt=(time(i2_civ1(ifile)+1,j2_civ1(j)+1)-time(i1_civ1(ifile)+1,j1_civ1(j)+1)); else Param.Civ1.Dt=1; end Param.Civ1.Time=((time(i2_civ1(ifile)+1,j2_civ1(j)+1)+time(i1_civ1(ifile)+1,j1_civ1(j)+1))/2); if strcmp(CivMode,'CivX') Param.Civ1.term_a=num2stra(j1_civ1(j),nom_type_nc);%UTILITE? Param.Civ1.term_b=num2stra(j2_civ1(j),nom_type_nc);% end form=imformats(regexprep(get(handles.ImaExt,'String'),'^.',''));%look for image formats if isempty(form) ImageInfo=get(VideoReader(filecell.ima1.civ1{1,1})); Param.Civ1.ImageBitDepth=ImageInfo.BitsPerPixel/3; else ImageInfo=imfinfo(filecell.ima1.civ1{1,1});%read the first image to get the size Param.Civ1.ImageBitDepth=ImageInfo.BitDepth; end Param.Civ1.ImageWidth=ImageInfo.Width; Param.Civ1.ImageHeight=ImageInfo.Height; Param.Civ1.i1=i1_civ1(ifile); Param.Civ1.i2=i2_civ1(ifile); % read mask parameters if Param.Civ1.CheckMask % the lines below should be changed with the new gui if ~exist(Param.Civ1.Mask,'file') maskbase=[filecell.filebase '_' Param.Civ1.Mask]; % nbslice_mask=str2double(Param.Civ1.Mask(1:end-4)); % i1_mask=mod(i1_civ1(ifile)-1,nbslice_mask)+1; [RootPathMask,RootFileMask]=fileparts(maskbase); Param.Civ1.Mask=fullfile_uvmat(RootPathMask,[],RootFileMask,'.png','_1',i1_mask); end end % read grid parameters if Param.Civ1.CheckGrid if numel(Param.Civ1.Grid)>=4 && isequal(Param.Civ1.Grid(end-3:end),'grid') nbslice_grid=str2double(Param.Civ1.Grid(1:end-4)); % if ~isnan(nbslice_grid) i1_grid=mod(i1_civ1(ifile)-1,nbslice_grid)+1; Param.Civ1.Grid=[filecell.filebase '_' fullfile_uvmat('','',Param.Civ1.Grid,'.grid','_1',i1_grid)]; % Param.Civ1.Grid=[filecell.filebase '_' name_generator(Param.Civ1.Grid,i1_grid,1,'.grid','_i')]; if ~exist(Param.Civ1.GridName,'file') errormsg='grid file absent for civ1'; return end elseif ~exist(Param.Civ1.Grid,'file') errormsg='grid file absent for civ1'; return end end end % send command switch CivMode case 'CivX' [cmd_civ,errormsg]=cmd_civ1(filecell.nc.civ1{ifile,j},Param); cmd=[cmd cmd_civ '\n']; if ~isempty(errormsg) return end case 'CivAll' CivAllCmd=[CivAllCmd ' civ1 ']; str=CIV1_CMD_Unified(filecell.nc.civ1{ifile,j},'',Param.Civ1); fieldnames=fields(str); [CivAllxml,uid_civ1]=add(CivAllxml,1,'element','civ1'); for ilist=1:length(fieldnames) val=eval(['str.' fieldnames{ilist}]); if ischar(val) [CivAllxml,uid_t]=add(CivAllxml,uid_civ1,'element',fieldnames{ilist}); [CivAllxml,uid_t2]=add(CivAllxml,uid_t,'chardata',val); end end end end if Param.CheckFix1 switch CivMode case 'CivX' cmd=[cmd... cmd_fix(filecell.nc.civ1{ifile,j},Param,'Fix1') '\n']; case 'CivAll'%to abandon fix1.inputFileName=filecell.nc.civ1{ifile,j} ; fix1.fi1=num2str(param.fix1.flagindex1(1)); fix1.fi2=num2str(param.fix1.flagindex1(2)); fix1.fi3=num2str(param.fix1.flagindex1(3)); fix1.threshC=num2str(param.fix1.thresh_vecC1); fix1.threshV=num2str(param.fix1.thresh_vel1); fieldnames=fields(fix1); [CivAllxml,uid_fix1]=add(CivAllxml,1,'element','fix1'); for ilist=1:length(fieldnames) val=eval(['fix1.' fieldnames{ilist}]); if ischar(val) [CivAllxml,uid_t]=add(CivAllxml,uid_fix1,'element',fieldnames{ilist}); [CivAllxml,uid_t2]=add(CivAllxml,uid_t,'chardata',val); end end CivAllCmd=[CivAllCmd ' fix1 ']; end end %CheckPatch1 if Param.CheckPatch1==1 switch CivMode case 'CivX' cmd=[cmd... cmd_patch(filecell.nc.civ1{ifile,j},Param,'Patch1') '\n']; case 'CivAll' patch1.inputFileName=filecell.nc.civ1{ifile,j} ; patch1.nopt=subdomain_patch1; patch1.maxdiff=thresh_patch1; patch1.ro=rho_patch1; test_grid=get(handles.get_gridpatch1,'Value'); if test_grid patch1.gridflag='y'; gridname=get(handles.grid_patch1,'String'); if isequal(gridname(end-3:end),'grid') nbslice_grid=str2double(gridname(1:end-4)); % if ~isnan(nbslice_grid) i1_grid=mod(i1_civ1(ifile)-1,nbslice_grid)+1; patch1.gridPatch=[filecell.filebase '_' fullfile_uvmat('','',gridname,'.grid','_1',i1_grid)]; % patch1.gridPatch=[filecell.filebase '_' name_generator(gridname,i1_grid,1,'.grid','_i')]; if ~exist(patch1.gridPatch,'file') errormsg='grid file absent for patch1'; return end elseif exist(gridname,'file') patch1.gridPatch=gridname; else errormsg='grid file absent for patch1'; return end end else patch1.gridPatch='none'; patch1.gridflag='n'; patch1.m=nx_patch1; patch1.n=ny_patch1; end patch1.convectFlow='n'; fieldnames=fields(patch1); [CivAllxml,uid_patch1]=add(CivAllxml,1,'element','patch1'); for ilist=1:length(fieldnames) val=eval(['patch1.' fieldnames{ilist}]); if ischar(val) [CivAllxml,uid_t]=add(CivAllxml,uid_patch1,'element',fieldnames{ilist}); [CivAllxml,uid_t2]=add(CivAllxml,uid_t,'chardata',val); end end CivAllCmd=[CivAllCmd ' patch1 ']; end end if Param.CheckCiv2==1 Param.Civ2.ImageA=filecell.ima1.civ2{ifile,j}; Param.Civ2.ImageB=filecell.ima2.civ2{ifile,j}; if ~checkframe %&& size(time,1)>=i2_civ2(ifile) && size(time,2)>=j2_civ2(j) Param.Civ2.Dt=time(i2_civ2(ifile)+1,j2_civ2(j)+1)-time(i1_civ2(ifile)+1,j1_civ2(j)+1); else Param.Civ2.Dt=1; end Param.Civ2.Time=(time(i2_civ2(ifile)+1,j2_civ2(j)+1)+time(i1_civ2(ifile)+1,j1_civ2(j)+1))/2; if strcmp(CivMode,'CivX') Param.Civ2.term_a=num2stra(j1_civ2(j),nom_type_nc); Param.Civ2.term_b=num2stra(j2_civ2(j),nom_type_nc); end Param.Civ2.filename_nc1=filecell.nc.civ1{ifile,j}; Param.Civ2.filename_nc1(end-2:end)=[]; % remove '.nc' % mask if Param.Civ2.CheckMask if ~exist(Param.Civ2.Mask,'file') maskbase=[filecell.filebase '_' Param.Civ2.Mask]; % nbslice_mask=str2double(Param.Civ2.Mask(1:end-4)); % i1_mask=mod(i1_civ2(ifile)-1,nbslice_mask)+1; [RootPathMask,RootFileMask]=fileparts(maskbase); Param.Civ2.Mask=fullfile_uvmat(RootPathMask,[],RootFileMask,'.png','_1',i1_mask); % Param.Civ2.Mask=name_generator(maskbase,i1_mask,1,'.png','_i'); end end %grid if Param.Civ2.CheckGrid if numel(Param.Civ2.Grid)>=4 && isequal(Param.Civ2.Grid(end-3:end),'grid') nbslice_grid=str2double(Param.Civ2.Grid(1:end-4)); % if ~isnan(nbslice_grid) i1_grid=mod(i1_civ2(ifile)-1,nbslice_grid)+1; Param.Civ2.Grid=[filecell.filebase '_' fullfile_uvmat('','',gridname,'.grid','_1',i1_grid)]; % Param.Civ2.Grid=[filecell.filebase '_' name_generator(gridname,i1_grid,1,'.grid','_i')]; end end end form=imformats(regexprep(get(handles.ImaExt,'String'),'^.',''));%look for image formats if isempty(form) ImageInfo=get(VideoReader(filecell.ima1.civ2{1,1})); Param.Civ2.ImageBitDepth=ImageInfo.BitsPerPixel/3; else ImageInfo=imfinfo(filecell.ima1.civ2{1,1});%read the first image to get the size Param.Civ2.ImageBitDepth=ImageInfo.BitDepth; end Param.Civ2.ImageWidth=ImageInfo.Width; Param.Civ2.ImageHeight=ImageInfo.Height; Param.Civ2.i1=i1_civ2(ifile); Param.Civ2.i2=i2_civ2(ifile); switch CivMode case 'CivX' cmd=[cmd... cmd_civ2(filecell.nc.civ2{ifile,j},Param) '\n']; case 'CivAll' CivAllCmd=[CivAllCmd ' civ2 ']; str=CIV2_CMD_Unified(filecell.nc.civ2{ifile,j},'',Param.Civ2); fieldnames=fields(str); [CivAllxml,uid_civ2]=add(CivAllxml,1,'element','civ2'); for ilist=1:length(fieldnames) val=eval(['str.' fieldnames{ilist}]); if ischar(val) [CivAllxml,uid_t]=add(CivAllxml,uid_civ2,'element',fieldnames{ilist}); [CivAllxml,uid_t2]=add(CivAllxml,uid_t,'chardata',val); end end end end % CheckFix2 if Param.CheckFix2==1 switch CivMode case 'CivX' cmd=[cmd... cmd_fix(filecell.nc.civ2{ifile,j},Param,'Fix2') '\n']; case 'CivAll' fix2.inputFileName=filecell.nc.civ2{ifile,j} ; fix2.fi1=num2str(flagindex2(1)); fix2.fi2=num2str(flagindex2(2)); fix2.fi3=num2str(flagindex2(3)); fix2.threshC=num2str(thresh_vec2C); fix2.threshV=num2str(thresh_vel2); fieldnames=fields(fix2); [CivAllxml,uid_fix2]=add(CivAllxml,1,'element','fix2'); for ilist=1:length(fieldnames) val=eval(['fix2.' fieldnames{ilist}]); if ischar(val) [CivAllxml,uid_t]=add(CivAllxml,uid_fix2,'element',fieldnames{ilist}); [CivAllxml,uid_t2]=add(CivAllxml,uid_t,'chardata',val); end end CivAllCmd=[CivAllCmd ' fix2 ']; end end %CheckPatch2 if Param.CheckPatch2==1 switch CivMode case 'CivX' cmd=[cmd... cmd_patch(filecell.nc.civ1{ifile,j},Param,'Patch2') '\n']; case 'CivAll' patch2.inputFileName=filecell.nc.civ1{ifile,j} ; patch2.nopt=subdomain_patch2; patch2.maxdiff=thresh_patch2; patch2.ro=rho_patch2; test_grid=get(handles.get_gridpatch2,'Value'); if test_grid patch2.gridflag='y'; gridname=get(handles.grid_patch2,'String'); if isequal(gridname(end-3:end),'grid') nbslice_grid=str2double(gridname(1:end-4)); % if ~isnan(nbslice_grid) i1_grid=mod(i1_civ2(ifile)-1,nbslice_grid)+1; patch2.gridPatch=[filecell.filebase '_' fullfile_uvmat('','',gridname,'.grid','_1',i1_grid)]; % patch2.gridPatch=[filecell.filebase '_' name_generator(gridname,i1_grid,1,'.grid','_i')]; if ~exist(patch2.gridPatch,'file') errormsg='grid file absent for patch2'; return end elseif exist(gridname,'file') patch2.gridPatch=gridname; else errormsg='grid file absent for patch2'; return end end else patch2.gridPatch='none'; patch2.gridflag='n'; patch2.m=nx_patch2; patch2.n=ny_patch2; end patch2.convectFlow='n'; fieldnames=fields(patch2); [CivAllxml,uid_patch2]=add(CivAllxml,1,'element','patch2'); for ilist=1:length(fieldnames) val=eval(['patch2.' fieldnames{ilist}]); if ischar(val) [CivAllxml,uid_t]=add(CivAllxml,uid_patch2,'element',fieldnames{ilist}); [CivAllxml,uid_t2]=add(CivAllxml,uid_t,'chardata',val); end end CivAllCmd=[CivAllCmd ' patch2 ']; end end switch CivMode case {'CivX','CivAll'} if isequal(CivMode,'CivAll') save(CivAllxml,[OutputFile '.xml']); cmd=[cmd sparam.CivBin ' -f ' OutputFile '.xml ' CivAllCmd ' >' OutputFile '.log' '\n']; end % create the .bat file used in run or batch filename_bat=[OutputFile '.bat']; [fid,message]=fopen(filename_bat,'w'); if isequal(fid,-1) errormsg=['creation of .bat file: ' message]; return end fprintf(fid,cmd); fclose(fid); if isunix system(['chmod +x ' filename_bat]); end batch_file_list{length(batch_file_list)+1}=filename_bat; case 'Matlab' drawnow if ~strcmp(compare,'stereo PIV') filename_xml=[OutputFile '.civ.xml']; t=struct2xml(Param); save(t,filename_xml) if batch path_civ=fileparts(which('civ')); filename_bat=[OutputFile '.bat']; [fid,message]=fopen(filename_bat,'w'); if isequal(fid,-1) errormsg= ['creation of .bat file: ' message]; return end % text_matlabscript=[... % '#!/bin/bash \n'... % '. /etc/sysprofile \n'... % 'matlab -nodisplay -nosplash -nojvm <','.stderr') ' '... '-O ' regexprep(filename_joblist,'\.txt\>','.stdout') ' '... extra_oar ' '... '"oar-parexec -s -f ' filename_joblist ' '... '-l ' filename_joblist '.log"']; filename_oarcommand=fullfile(Rootbat,'oar_command'); fid=fopen(filename_oarcommand,'w'); fprintf(fid,[oar_command '\n']); fclose(fid); display(oar_command); eval(['! . ' filename_oarcommand]) case 'oar-dispatch' %oar-dispatch.pl ncores=str2double(... inputdlg('Number of cores (max 36)','oarsub parameter',1,{'6'})... ); walltime_onejob=600;%seconds filename_joblist=fullfile(Rootbat,'job_list.txt'); fid=fopen(filename_joblist,'w'); for p=1:length(batch_file_list) oar_command=['oarsub -n CIVX '... '-E ' regexprep(batch_file_list{p},'\.bat\>','.stderr') ' -O ' regexprep(batch_file_list{p},'\.bat\>','.stdout ')... '-l "/core=1,walltime=' datestr(walltime_onejob/86400,13) '" ' batch_file_list{p}]; fprintf(fid,[oar_command '\n']); end fclose(fid); oar_command=['oarsub -t container -n civx-container '... '-l /core=' num2str(ncores)... ',walltime=' datestr(1.05*walltime_onejob/86400*max(length(batch_file_list),ncores)/ncores,13) ' '... '-E ' regexprep(filename_joblist,'\.txt\>','.stderr') ' '... '-O ' regexprep(filename_joblist,'\.txt\>','.stdout') ' '... '"oar-dispatch -f ' filename_joblist '"']; filename_oarcommand=fullfile(Rootbat,'oar_command'); fid=fopen(filename_oarcommand,'w'); fprintf(fid,[oar_command '\n']); fclose(fid); display(oar_command); eval(['! . ' filename_oarcommand]) case 'mpilauncher' filename_joblist=fullfile(Rootbat,'job_list.txt'); fid=fopen(filename_joblist,'w'); for p=1:length(batch_file_list) fprintf(fid,[batch_file_list{p} '\n']); end fclose(fid) text_oarscript=[... '#!/bin/bash \n'... '#OAR -n Mylauncher \n'... '#OAR -l node=4/core=5,walltime=0:15:00 \n'... '#OAR -E ' fullfile(Rootbat,'stderrfile.log') ' \n'... '#OAR -O ' fullfile(Rootbat,'stdoutfile.log') ' \n'... '# ========================================================= \n'... '# This simple program launch a multinode parallel OpenMPI mpilauncher \n'... '# application for coriolis PIV post-processing. \n'... '# OAR uses oarshmost wrapper to propagate the user environement. \n'... '# This wrapper assert that the user has the same environment on all the \n'... '# allocated nodes (basic behavior needed by most MPI applications). \n'... '# \n'... '# REQUIREMENT: \n'... '# the oarshmost wrapper should be installed in $HOME/bin directory. \n'... '# If a different location is used, change the line following the comment "Bidouille" \n'... '# ========================================================= \n'... '# USER should only modify these 2 lines \n'... 'WORKDIR=' pwd ' \n'... 'COMMANDE="mpilauncher -f ' filename_joblist '" \n'... '# ========================================================= \n'... '# DO NOT MODIFY the FOLOWING LINES. (or be carefull) \n'... 'echo "job starting on: "`hostname` \n'... 'MPINODES="-host `tr [\\\\\\n] [,] <$OAR_NODEFILE |sed -e "s/,$/ /"`" \n'... 'NCPUS=`cat $OAR_NODEFILE |wc -l` \n'... '#========== Bidouille ============== \n'... 'export OMPI_MCA_plm_rsh_agent=oar-envsh \n'...% 'cd $WORKDIR \n'... 'CMD="mpirun -np $NCPUS -wdir $WORKDIR $MPINODES $COMMANDE" \n'... 'echo "I run: $CMD" \n'... '$CMD \n'... 'echo "job ending" \n'... ]; % oarsub -S ./oar.sub filename_oarscript=fullfile(Rootbat,'oar_command'); fid=fopen(filename_oarscript,'w'); fprintf(fid,[text_oarscript]); fclose(fid); eval(['!chmod +x ' filename_oarscript]); eval(['!oarsub -S ' filename_oarscript]); end end else if ~isequal(CivMode,'Matlab') filename_superbat=fullfile(Rootbat,'job_list.bat'); fid=fopen(filename_superbat,'w'); if fid==-1 msgbox_uvmat('ERROR',['cannot create the command file ' filename_superbat]) return end for p=1:length(batch_file_list) if isunix fprintf(fid,['sh ' batch_file_list{p} '\n']); else fprintf(fid,['@call "' regexprep(batch_file_list{p},'\\','\\\\') '"' '\n']); end end fclose(fid); if(isunix) system(['chmod +x ' filename_superbat]); end system([filename_superbat ' &']);% execute main commmand end end %% save interface state if isfield(filecell,'nc') if isfield(filecell.nc,'civ2') fileresu=filecell.nc.civ2{1,1}; else fileresu=filecell.nc.civ1{1,1}; end end [RootPath,SubDir,RootFile]=fileparts_uvmat(fileresu); namedoc=fullfile(RootPath,SubDir,RootFile); detect=1; while detect==1 namefigfull=[namedoc '.fig']; hh=dir(namefigfull); if ~isempty(hh) detect=1; namedoc=[namedoc '.0']; else detect=0; end end Param=rmfield(Param,'status'); Param=rmfield(Param,'xml'); t=struct2xml(Param); t=set(t,1,'Name','CivDoc');% set the head label save(t,[namedoc '.CivDoc.xml']); %save GUI parameters as xml file saveas(gcbf,namefigfull);%save the interface with name namefigfull (A CHANGER EN FICHIER .xml) %Save info in personal profile (initiate browser next time) TODO MenuFile={}; dir_perso=prefdir; profil_perso=fullfile(dir_perso,'uvmat_perso.mat'); if exist(profil_perso,'file') hh=load (profil_perso); if isfield(hh,'MenuFile') MenuFile=hh.MenuFile; end if isfield(filecell.nc,'civ2') MenuFile=[filecell.nc.civ2{1,1}; MenuFile]; else MenuFile=[filecell.nc.civ1{1,1}; MenuFile]; end save (profil_perso,'MenuFile','-append'); %store the file names for future opening of uvmat else MenuFile=filecell.ima1.civ1(1,1); save (profil_perso,'MenuFile') end %------------------------------------------------------------------------ % --- determine the list of reference indices of processing file function [ref_i,ref_j,errormsg]=find_ref_indices(handles) %------------------------------------------------------------------------ errormsg=''; %default error message first_i=str2double(get(handles.first_i,'String'));%first index i last_i=str2double(get(handles.last_i,'String'));%last index i incr_i=str2double(get(handles.incr_i,'String'));% increment if isequal(get(handles.first_j,'Visible'),'on') first_j=str2double(get(handles.first_j,'String'));%first index j last_j=str2double(get(handles.last_j,'String'));%last index j incr_j=str2double(get(handles.incr_j,'String'));% increment else first_j=1; last_j=1; incr_j=1; end ref_i=first_i:incr_i:last_i;% list of i indices (reference values for each pair) ref_j=first_j:incr_j:last_j;% list of j indices (reference values for each pair) if isnan(first_i)||isnan(first_j) errormsg='first field number not defined'; elseif isnan(last_i)||isnan(last_j) errormsg='last field number not defined'; elseif isnan(incr_i)||isnan(incr_j) errormsg='increment in field number not defined'; elseif last_i < first_i || last_j < first_j errormsg='last field number must be larger than the first one'; end %------------------------------------------------------------------------ % --- determine the list of filenames and indices needed for launch_job %------------------------------------------------------------------------ % OUTPUT: % filecell: structure of cell arrays {ref_i,ref_j} containing all the filenames involved in the civ process % the indices ref_i and ref_j correspond to the list of reference indices % .filebase=fullfile(RootPath,RootFile) used to construct mask names, grid names, CivDoc xml file % .ima1.civ1,.ima1.civ2: first image for civ1 and civ2 respectively (possibly different) % .ima2.civ1,.ima2.civ2: second image for civ1 and civ2 respectively (possibly different) % .nc.civ1,.nc.civ2: netcdf files containing civ1 and civ2 data respectively (possibly different) % i1_civ1,i2_civ1,j1_civ1,j2_civ1,i1_civ2,i2_civ2,j1_civ2,j2_civ2: arrays of files indices, needed for timing records function [filecell,i1_civ1,i2_civ1,j1_civ1,j2_civ1,i1_civ2,i2_civ2,j1_civ2,j2_civ2,NomType_nc,file_ref_fix1,file_ref_fix2,compare]=... set_civ_filenames(handles,ref_i,ref_j,checkbox) %------------------------------------------------------------------------ filecell=[];%default ListProgram=get(handles.ListProgram,'String'); CivMode=ListProgram{get(handles.ListProgram,'Value')};%Program to use , CivX or Matlab %% get the root name and check dir RootPath=get(handles.RootPath,'String'); RootFile=get(handles.RootFile,'String'); filecell.filebase=fullfile(RootPath,RootFile); if isempty(filecell.filebase) msgbox_uvmat('ERROR','please open an image with the upper menu option Open/Browse...') return end if ~exist(RootPath,'dir') msgbox_uvmat('ERROR',['path to images ' RootPath ' not found']) return end [tild,message]=fileattrib(RootPath); if ~isempty(message) && ~isequal(message.UserWrite,1) msgbox_uvmat('ERROR',['No writting access to ' RootPath]) return end %check result directory subdir_civ1=get(handles.SubdirCiv1,'String');%subdirectory subdir_civ1 for the netcdf output data subdir_civ2=get(handles.SubdirCiv2,'String'); if isequal(subdir_civ1,''),subdir_civ1='CIV'; end% put default subdir if isequal(subdir_civ2,''),subdir_civ2=subdir_civ1; end% put default subdir %% choose root names depending on ListCompareMode =displacement, shift, PIV or stereo PIV ListCompareMode=get(handles.ListCompareMode,'String'); compare=ListCompareMode{get(handles.ListCompareMode,'Value')}; % set the nomenclature type of the nc files depending on the pair mode if strcmp(compare,'displacement')||strcmp(compare,'shift') mode='displacement'; else mode_list=get(handles.ListPairMode,'String'); mode_value=get(handles.ListPairMode,'Value'); mode=mode_list{mode_value}; end NomType_ima2=get(handles.NomType,'String'); NomType_nc=nomtype2pair(NomType_ima2,mode); % set the rootfile and image indexing RootFile_ima2=get(handles.RootFile,'String');%root file for the second image series ext_ima=get(handles.ImaExt,'String'); % image extension (the same for all images) switch compare case 'PIV' RootFile_ima1=RootFile_ima2;% root name of the two image series is the same NomType_ima1=NomType_ima2;% the index of the first image follows the index of the second one RootFile_nc=RootFile_ima2; case 'displacement' RootFile_ima1=get(handles.RootFile_1,'String');% root name of the first image series set by handles.RootFile_1 NomType_ima1='';% no indexing of the first image, a fixed reference for the whole series RootFile_nc=RootFile_ima2; case 'shift' RootFile_ima1=get(handles.RootFile_1,'String');% root name of the first image series set by handles.RootFile_1 NomType_ima1=NomType_ima2;% the index of the first image follows the index of the second one RootFile_nc=[RootFile_ima1 '-' RootFile_ima2]; end %determine the list of file indices involved [i1_civ1,i2_civ1,j1_civ1,j2_civ1,i1_civ2,i2_civ2,j1_civ2,j2_civ2]=... find_pair_indices(handles,ref_i,ref_j,mode); %determine the new filebase for 'displacement' ListPairMode (comparison of two series) %filebase_B=filebase;% root name of the second field series for stereo % filebase_A=filebase;%default % if strcmp(compare,'PIV') % filebase_AB=filebase; % else % [Path2,Name2]=fileparts(filebase_B); % Name1=RootFile_ima1; % filebase_AB=fullfile(Path2,[Name2 '-' Name1]); % end % [RootPath_AB,RootFile_AB]=fileparts(filebase_AB); % % [RootPath_ima1,RootFile_ima1]=fileparts(filebase_B); % [RootPath_ima2,RootFile_ima2]=fileparts(filebase_B); % [RootPath_nc,RootFile_nc]=fileparts(filebase_B);%default % if strcmp(compare,'displacement') % % [RootPath_ima1,RootFile_ima1]=fileparts(filebase_B); % % [RootPath_ima2,RootFile_ima2]=fileparts(filebase_B); % [RootPath_nc,RootFile_nc]=fileparts(filebase_B); % elseif strcmp(compare,'shift') % RootPath_nc=RootPath_AB; % RootFile_nc=RootFile_AB; % end % else % filebase_ima1=filebase_B; % filebase_ima2=filebase_B; % filebase_nc=filebase_B; % [RootPath_ima1,RootFile_ima1]=fileparts(filebase_ima1); % [RootPath_ima2,RootFile_ima2]=fileparts(filebase_ima2); % [RootPath_nc,RootFile_nc]=fileparts(filebase_nc); % [RootPath_A,RootFile_A]=fileparts(filebase_A); %% determine reference files for fix: file_ref_fix1={};%default file_ref_fix2={}; nbfield=length(i1_civ1); nbslice=length(j1_civ1); if checkbox(2)==1% fix1 performed ref=get(handles.ref_fix1,'UserData');%read data on the ref file stored by get_ref_fix1_Callback if ~isempty(ref) first_i=str2double(get(handles.first_i,'String')); last_i=str2double(get(handles.last_i,'String')); incr_i=str2double(get(handles.incr_i,'String')); first_j=str2double(get(handles.first_j,'String')); last_j=str2double(get(handles.last_j,'String')); incr_j=str2double(get(handles.incr_j,'String')); num_i_ref=first_i:incr_i:last_i; num_j_ref=first_j:incr_j:last_j; if isequal(mode,'displacement') num_i1=num_i_ref; num_i2=num_i_ref; num_j1=num_j_ref; num_j2=num_j_ref; elseif isequal(mode,'pair j1-j2')% isequal(mode,'st_pair j1-j2') num_i1=num_i_ref; num_i2=num_i1; num_j1=ref.num_a*ones(size(num_i_ref)); num_j2=ref.num_b*ones(size(num_i_ref)); elseif isequal(mode,'series(Di)') % isequal(mode,'st_series(Di)') delta1=floor((ref.num2-ref.num1)/2); delta2=ceil((ref.num2-ref.num1)/2); num_i1=num_i_ref-delta1*ones(size(num_i_ref)); num_i2=num_i_ref+delta2*ones(size(num_i_ref)); if isempty(ref.num_a) ref.num_a=1; end num_j1=ref.num_a*ones(size(num_i1)); num_j2=num_j1; elseif isequal(mode,'series(Dj)')%| isequal(mode,'st_series(Dj)') delta1=floor((ref.num_b-ref.num_a)/2); delta2=ceil((ref.num_b-ref.num_a)/2); num_i1=ref.num1*ones(size(num_i_ref)); num_i2=num_i1; num_j1=num_j_ref-delta1*ones(size(num_j_ref)); num_j2=num_j_ref+delta2*ones(size(num_j_ref)); end for ifile=1:nbfield for j=1:nbslice [RootPathRef,RootFile]=fileparts(ref.filebase); file_ref=fullfile_uvmat(RootPathRef,ref.subdir,RootFile,'.nc',ref.NomType,num_i1(ifile),num_i2(ifile),num_j1(j),num_j2(j)); file_ref_fix1(ifile,j)={file_ref}; if ~exist(file_ref,'file') msgbox_uvmat('ERROR',['reference file ' file_ref ' not found for fix1']) filecell=[]; return end end end end end %% determine reference files for fix2: if checkbox(5)==1% fix2 performed ref=get(handles.ref_fix2,'UserData'); if ~isempty(ref) first_i=str2double(get(handles.first_i,'String')); last_i=str2double(get(handles.last_i,'String')); incr_i=str2double(get(handles.incr_i,'String')); first_j=str2double(get(handles.first_j,'String')); last_j=str2double(get(handles.last_j,'String')); incr_j=str2double(get(handles.incr_j,'String')); num_i_ref=first_i:incr_i:last_i; num_j_ref=first_j:incr_j:last_j; if isequal(mode,'displacement') num_i1=num_i_ref; num_i2=num_i_ref; num_j1=num_j_ref; num_j2=num_j_ref; elseif isequal(mode,'pair j1-j2') num_i1=num_i_ref; num_i2=num_i1; num_j1=ref.num_a; num_j2=ref.num_b; elseif isequal(mode,'series(Di)') delta1=floor((ref.num2-ref.num1)/2); delta2=ceil((ref.num2-ref.num1)/2); num_i1=num_i_ref-delta1*ones(size(num_i_ref)); num_i2=num_i_ref+delta2*ones(size(num_i_ref)); num_j1=ref.num_a*ones(size(num_i1)); num_j2=num_j1; elseif isequal(mode,'series(Dj)') delta1=floor((ref.num_b-ref.num_a)/2); delta2=ceil((ref.num_b-ref.num_a)/2); num_i1=ref.num1*ones(size(num_i_ref)); num_i2=num_i1; num_j1=num_j_ref-delta1*ones(size(num_j_ref)); num_j2=num_j_ref+delta2*ones(size(num_j_ref)); end for ifile=1:nbfield for j=1:nbslice [RootPathRef,RootFile]=fileparts(ref.filebase); file_ref=fullfile_uvmat(RootPathRef,ref.subdir,RootFile,'.nc',ref.NomType,num_i1(ifile),num_i2(ifile),num_j1(j),num_j2(j)); file_ref_fix2(ifile,j)={file_ref}; if ~exist(file_ref,'file') msgbox_uvmat('ERROR',['reference file ' file_ref ' not found for fix2']) filecell={}; return end end end end end %% check the existence of the netcdf and image files involved % %%%%%%%%%%%% case CheckCiv1 activated %%%%%%%%%%%%% if checkbox(1)==1; detect=1; vers=0; subdir_civ1_new=subdir_civ1; while detect==1 %create a new subdir if the netcdf files already exist for ifile=1:nbfield for j=1:nbslice filename=fullfile_uvmat(RootPath,subdir_civ1_new,RootFile_nc,'.nc',NomType_nc,i1_civ1(ifile),i2_civ1(ifile),j1_civ1(j),j2_civ1(j)); detect=exist(filename,'file')==2; if detect% if a netcdf file already exists indstr=regexp(subdir_civ1_new,'\D'); if indstr(end)length(list_civ2) list_civ2=list_civ1; index_civ2=index_civ1; end str_civ2=list_civ2{index_civ2};%string defining the image pairs for civ2 if isequal (mode,'series(Di)') lastfield=str2double(get(handles.nb_field,'String')); num1_civ1=ref_i-floor(index_civ1/2)*ones(size(ref_i));% set of first image numbers num2_civ1=ref_i+ceil(index_civ1/2)*ones(size(ref_i)); num_a_civ1=ref_j; num_b_civ1=ref_j; num1_civ2=ref_i-floor(index_civ2/2)*ones(size(ref_i)); num2_civ2=ref_i+ceil(index_civ2/2)*ones(size(ref_i)); num_a_civ2=ref_j; num_b_civ2=ref_j; % adjust the first and last field number lastfield=str2double(get(handles.nb_field,'String')); if isnan(lastfield) indsel=find((num1_civ1 >= 1)&(num1_civ2 >= 1)); else indsel=find((num2_civ1 <= lastfield)&(num2_civ2 <= lastfield)&(num1_civ1 >= 1)&(num1_civ2 >= 1)); end if length(indsel)>=1 firstind=indsel(1); lastind=indsel(end); set(handles.first_i,'String',num2str(ref_i(firstind)))%update the display of first and last fields set(handles.last_i,'String',num2str(ref_i(lastind))) ref_i=ref_i(indsel); num1_civ1=num1_civ1(indsel); num1_civ2=num1_civ2(indsel); num2_civ1=num2_civ1(indsel); num2_civ2=num2_civ2(indsel); end elseif isequal (mode,'series(Dj)') lastfield_j=str2double(get(handles.nb_field2,'String')); num1_civ1=ref_i;% set of first image numbers num2_civ1=ref_i; num_a_civ1=ref_j-floor(index_civ1/2)*ones(size(ref_j)); num_b_civ1=ref_j+ceil(index_civ1/2)*ones(size(ref_j)); num1_civ2=ref_i; num2_civ2=ref_i; num_a_civ2=ref_j-floor(index_civ2/2)*ones(size(ref_j)); num_b_civ2=ref_j+ceil(index_civ2/2)*ones(size(ref_j)); % adjust the first and last field number if isnan(lastfield_j) indsel=find((num_a_civ1 >= 1)&(num_a_civ2 >= 1)); else indsel=find((num_b_civ1 <= lastfield_j)&(num_b_civ2 <= lastfield_j)&(num_a_civ1 >= 1)&(num_a_civ2 >= 1)); end if length(indsel)>=1 firstind=indsel(1); lastind=indsel(end); set(handles.first_j,'String',num2str(ref_j(firstind)))%update the display of first and last fields set(handles.last_j,'String',num2str(ref_j(lastind))) ref_j=ref_j(indsel); num_a_civ1=num_a_civ1(indsel); num_b_civ1=num_b_civ1(indsel); num_a_civ2=num_a_civ2(indsel); num_b_civ2=num_b_civ2(indsel); end elseif isequal(mode,'pair j1-j2') %case of bursts (png_old or png_2D) displ_num=get(handles.ListPairCiv1,'UserData'); num1_civ1=ref_i; num2_civ1=ref_i; num_a_civ1=displ_num(1,index_civ1); num_b_civ1=displ_num(2,index_civ1); num1_civ2=ref_i; num2_civ2=ref_i; num_a_civ2=displ_num(1,index_civ2); num_b_civ2=displ_num(2,index_civ2); elseif isequal(mode,'displacement') num1_civ1=ref_i; num2_civ1=ref_i; num_a_civ1=ref_j; num_b_civ1=ref_j; num1_civ2=ref_i; num2_civ2=ref_i; num_a_civ2=ref_j; num_b_civ2=ref_j; end %------------------------------------------------------------------------ % --- Executes on button press in ListCompareMode. function ListCompareMode_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ ListCompareMode=get(handles.ListCompareMode,'String'); option=ListCompareMode{get(handles.ListCompareMode,'Value')}; if ~strcmp(option,'PIV') % case 'displacement' or 'stereo PIV' filebase=get(handles.RootPath,'String'); set(handles.sub_txt,'Visible','on') set(handles.RootFile_1,'Visible','On');%mkes the second file input window visible mode_store=get(handles.ListPairMode,'String');%get the present 'mode' set(handles.ListCompareMode,'UserData',mode_store);%store the mode display set(handles.ListPairMode,'Visible','off') %% open an image file with the browser ind_opening=1;%default browse.incr_pair=[0 0]; %default oldfile=get(handles.RootPath,'String'); menu={'*.png;*.jpg;*.tif;*.avi;*.AVI;', ' (*.png,*.jpg ,.tif, *.avi,*.AVI)'; '*.png','.png image files'; ... '*.jpg',' jpeg image files'; ... '*.tif','.tif image files'; ... '*.avi;*.AVI','.avi movie files'; ... '*.*', 'All Files (*.*)'}; if strcmp(option,'displacement') comment='Pick the reference file for displacements'; else comment='Pick a file of the second series'; end [FileName, PathName] = uigetfile( menu, comment,oldfile); fileinput=[PathName FileName];%complete file name sizf=size(fileinput); if (~ischar(fileinput)||~isequal(sizf(1),1)),return;end %stop if fileinput not a character string [path,name,ext]=fileparts(fileinput); [path1]=fileparts(filebase); if isunix [status,path]=system(['readlink ' path]); [status,path1]=system(['readlink ' path1]);% look for the true path in case of symbolic paths end if ~strcmp(path1,path) msgbox_uvmat('ERROR','The second image or series must be in the same directory as the first one') return end if strcmp(option,'displacement') [tild,RootFile_1]=fileparts(name); else [FilePath,FileName,Ext]=fileparts(fileinput); % detect the file type, get the movie object if relevant, and look for the corresponding file series: % the root name and indices may be corrected by including the first index i1 if a corresponding xml file exists [RootPath,SubDir,RootFile_1,i1_series,i2_series,j1_series,j2_series,nom_type_1,FileType,Object,i1,i2,j1,j2]=find_file_series(FilePath,[FileName Ext]); % [tild,tild,RootFile_1,tild,tild,tild,tild,tild,nom_type_1]=fileparts_uvmat(fileinput); %[RootFile_1,i1_series,tild,j1_series,tild,nom_type_1,FileType,Object]=find_file_series(PathName,FileName); %check image nom type if ~strcmp(nom_type_1,get(handles.NomType,'String')) msgbox_uvmat('ERROR','The second image series must have the same indexing type as the first one, or use the option displacement for a fixed image') return end end %check image extension if ~strcmp(ext,get(handles.ImaExt,'String')) msgbox_uvmat('ERROR','The second image series must have the same extension name as the first one') return end set(handles.RootFile_1,'String',RootFile_1); else set(handles.ListPairMode,'Visible','on') set(handles.RootFile_1,'Visible','Off'); set(handles.sub_txt,'Visible','off') set(handles.RootFile_1,'String',[]); mode_store=get(handles.ListCompareMode,'UserData'); set(handles.ListPairMode,'Value',1) set(handles.ListPairMode,'String',mode_store) set(handles.CheckStereo,'Value',0) set(handles.ListPairMode,'Value',1) % mode 'civX' selected by default end % if strcmp(option,'stereo PIV') && get(handles.CheckPatch1,'Value') % set(handles.CheckStereo,'Visible','on') % else % set(handles.CheckStereo,'Visible','off') % end % if strcmp(option,'stereo PIV') && get(handles.CheckPatch2,'Value') % set(handles.CheckStereo,'Visible','on') % else % set(handles.CheckStereo,'Visible','off') % end ListPairMode_Callback(hObject, eventdata, handles) %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% % Callbacks in the uipanel Pair Indices %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %------------------------------------------------------------------------ % --- Executes on button press in ListPairMode. function ListPairMode_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ compare_list=get(handles.ListCompareMode,'String'); val=get(handles.ListCompareMode,'Value'); compare=compare_list{val}; if strcmp(compare,'displacement')||strcmp(compare,'shift') mode='displacement'; else mode_list=get(handles.ListPairMode,'String'); if ischar(mode_list) mode_list={mode_list}; end mode_value=get(handles.ListPairMode,'Value'); mode=mode_list{mode_value}; end displ_num=[];%default ref_i=str2double(get(handles.ref_i,'String')); % last_i=str2num(get(handles.last_i,'String')); time=get(handles.ImaDoc,'UserData'); %get the set of times TimeUnit=get(handles.TimeUnit,'String'); checkframe=strcmp(TimeUnit,'frame'); siztime=size(time); nbfield=siztime(1)-1; nbfield2=siztime(2)-1; indchosen=1; %%first pair selected by default %displ_num used to define the indices of the civ pairs % in mode 'pair j1-j2', j1 and j2 are the file indices, else the indices % are relative to the reference indices ref_i and ref_j respectively. if isequal(mode,'pair j1-j2')%| isequal(mode,'st_pair j1-j2') dt=1; displ=''; index=0; numlist_a=[]; numlist_B=[]; %get all the time intervals in bursts displ_dt=1;%default nbfield2=min(nbfield2,10);%limitate the number of pairs to 10x10 for numod_a=1:nbfield2-1 %nbfield2 always >=2 for 'pair j1-j2' mode for numod_b=(numod_a+1):nbfield2 index=index+1; numlist_a(index)=numod_a; numlist_b(index)=numod_b; if size(time,2)>1 && ~checkframe dt(numod_a,numod_b)=time(ref_i+1,numod_b+1)-time(ref_i+1,numod_a+1);%first time interval dt displ_dt(index)=dt(numod_a,numod_b); else displ_dt(index)=1; end end end [dtsort,indsort]=sort(displ_dt); if ~isempty(numlist_a) displ_num(1,:)=numlist_a(indsort); displ_num(2,:)=numlist_b(indsort); end displ_num(3,:)=0; displ_num(4,:)=0; enable_j(handles, 'off') elseif isequal(mode,'series(Dj)') %| isequal(mode,'st_series(Dj)') index=1:200; displ_num(1,index)=-floor(index/2); displ_num(2,index)=ceil(index/2); displ_num(3:4,index)=zeros(2,200); enable_j(handles, 'on') elseif isequal(mode,'series(Di)') %| isequal(mode,'st_series(Di)') index=1:200; displ_num(1:2,index)=zeros(2,200); displ_num(3,index)=-floor(index/2); displ_num(4,index)=ceil(index/2); enable_i(handles, 'on') if nbfield2 > 1 enable_j(handles, 'on') else enable_j(handles, 'off') end elseif isequal(mode,'displacement')%the pairs have the same indices displ_num(1,1)=0; displ_num(2,1)=0; displ_num(3,1)=0; displ_num(4,1)=0; if nbfield > 1 || nbfield==0 enable_i(handles, 'on') else enable_j(handles, 'off') end if nbfield2 > 1 enable_j(handles, 'on') else enable_j(handles, 'off') end end set(handles.ListPairCiv1,'UserData',displ_num); errormsg=find_netcpair_civ( handles,1); if ~isempty(errormsg) msgbox_uvmat('ERROR',errormsg) end % find_netcpair_civ2(handles) function enable_i(handles, state) set(handles.itext,'Visible',state) set(handles.first_i,'Visible',state) set(handles.last_i,'Visible',state) set(handles.incr_i,'Visible',state) set(handles.nb_field,'Visible',state) set(handles.ref_i,'Visible',state) function enable_j(handles, state) set(handles.jtext,'Visible',state) set(handles.first_j,'Visible',state) set(handles.last_j,'Visible',state) set(handles.incr_j,'Visible',state) set(handles.nb_field2,'Visible',state) set(handles.ref_j,'Visible',state) %------------------------------------------------------------------------ % --- Executes on selection change in ListPairCiv1. function ListPairCiv1_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ %reproduce by default the chosen pair in the checkciv2 menu list_pair=get(handles.ListPairCiv1,'String');%get the menu of image pairs index_pair=get(handles.ListPairCiv1,'Value'); displ_num=get(handles.ListPairCiv1,'UserData'); % num_a=displ_num(1,index_pair); % num_b=displ_num(2,index_pair); list_pair2=get(handles.ListPairCiv2,'String');%get the menu of image pairs if index_pair<=length(list_pair2) set(handles.ListPairCiv2,'Value',index_pair); end %update first_i and last_i according to the chosen image pairs mode_list=get(handles.ListPairMode,'String'); mode_value=get(handles.ListPairMode,'Value'); mode=mode_list{mode_value}; if isequal(mode,'series(Di)') first_i=str2double(get(handles.first_i,'String')); last_i=str2double(get(handles.last_i,'String')); incr_i=str2double(get(handles.incr_i,'String')); num1=first_i:incr_i:last_i; lastfield=str2double(get(handles.nb_field,'String')); if ~isnan(lastfield) test_find=(num1-floor(index_pair/2)*ones(size(num1))>0)& ... (num1+ceil(index_pair/2)*ones(size(num1))<=lastfield); num1=num1(test_find); end set(handles.first_i,'String',num2str(num1(1))); set(handles.last_i,'String',num2str(num1(end))); elseif isequal(mode,'series(Dj)') first_j=str2double(get(handles.first_j,'String')); last_j=str2double(get(handles.last_j,'String')); incr_j=str2double(get(handles.incr_j,'String')); num_j=first_j:incr_j:last_j; lastfield2=str2double(get(handles.nb_field2,'String')); if ~isnan(lastfield2) test_find=(num_j-floor(index_pair/2)*ones(size(num_j))>0)& ... (num_j+ceil(index_pair/2)*ones(size(num_j))<=lastfield2); num1=num_j(test_find); end set(handles.first_j,'String',num2str(num1(1))); set(handles.last_j,'String',num2str(num1(end))); end %------------------------------------------------------------------------ % --- Executes on selection change in ListPairCiv2. function ListPairCiv2_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ index_pair=get(handles.ListPairCiv2,'Value');%get the selected position index in the menu %update first_i and last_i according to the chosen image pairs mode_list=get(handles.ListPairMode,'String'); mode_value=get(handles.ListPairMode,'Value'); mode=mode_list{mode_value}; if isequal(mode,'series(Di)') first_i=str2double(get(handles.first_i,'String')); last_i=str2double(get(handles.last_i,'String')); incr_i=str2double(get(handles.incr_i,'String')); num1=first_i:incr_i:last_i; lastfield=str2double(get(handles.nb_field,'String')); if ~isnan(lastfield) test_find=(num1-floor(index_pair/2)*ones(size(num1))>0)& ... (num1+ceil(index_pair/2)*ones(size(num1))<=lastfield); num1=num1(test_find); end set(handles.first_i,'String',num2str(num1(1))); set(handles.last_i,'String',num2str(num1(end))); elseif isequal(mode,'series(Dj)') first_j=str2double(get(handles.first_j,'String')); last_j=str2double(get(handles.last_j,'String')); incr_j=str2double(get(handles.incr_j,'String')); num_j=first_j:incr_j:last_j; lastfield2=str2double(get(handles.nb_field2,'String')); if ~isnan(lastfield2) test_find=(num_j-floor(index_pair/2)*ones(size(num_j))>0)& ... (num_j+ceil(index_pair/2)*ones(size(num_j))<=lastfield2); num1=num_j(test_find); end set(handles.first_j,'String',num2str(num1(1))); set(handles.last_j,'String',num2str(num1(end))); end %------------------------------------------------------------------------ function ref_i_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ mode_list=get(handles.ListPairMode,'String'); mode_value=get(handles.ListPairMode,'Value'); mode=mode_list{mode_value}; errormsg=find_netcpair_civ(handles,1);% update the menu of pairs depending on the available netcdf files if isequal(mode,'series(Di)') || ...% we do patch2 only (get(handles.CheckCiv2,'Value')==0 && get(handles.CheckCiv1,'Value')==0 && get(handles.CheckFix1,'Value')==0 && get(handles.CheckPatch1,'Value')==0) errormsg=find_netcpair_civ( handles,2); end if ~isempty(errormsg) msgbox_uvmat('ERROR',errormsg) end %------------------------------------------------------------------------ function ref_j_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ mode_list=get(handles.ListPairMode,'String'); mode_value=get(handles.ListPairMode,'Value'); mode=mode_list{mode_value}; if isequal(get(handles.CheckCiv1,'Value'),0)|| isequal(mode,'series(Dj)') errormsg=find_netcpair_civ(handles,1);% update the menu of pairs depending on the available netcdf files end if isequal(mode,'series(Dj)') || ... (get(handles.CheckCiv2,'Value')==0 && get(handles.CheckCiv1,'Value')==0 && get(handles.CheckFix1,'Value')==0 && get(handles.CheckPatch1,'Value')==0) errormsg=find_netcpair_civ(handles,2); end if ~isempty(errormsg) msgbox_uvmat('ERROR',errormsg) end %------------------------------------------------------------------------ % determine the menu for checkciv1 pairs depending on existing netcdf file at the middle of % the field series set by first_i, incr, last_i % index=1: look for pairs for civ1 % index=2: look for pairs for civ2 function errormsg=find_netcpair_civ(handles,index) %------------------------------------------------------------------------ set(gcf,'Pointer','watch')% set the mouse pointer to 'watch' (clock) %% initialisation errormsg=''; browse=get(handles.RootPath,'UserData'); compare_list=get(handles.ListCompareMode,'String'); val=get(handles.ListCompareMode,'Value'); compare=compare_list{val}; if strcmp(compare,'displacement')||strcmp(compare,'shift') mode='displacement'; else mode_list=get(handles.ListPairMode,'String'); mode_value=get(handles.ListPairMode,'Value'); if isempty(mode_list) return end mode=mode_list{mode_value}; end nom_type_ima=get(handles.NomType,'String'); %% determine nom_type_nc, nomenclature type of the .nc files: [nom_type_nc]=nomtype2pair(nom_type_ima,mode); %% reads .nc subdirectoy and image numbers from the interface subdir_civ1=get(handles.SubdirCiv1,'String');%subdirectory subdir_civ1 for the netcdf data subdir_civ2=get(handles.SubdirCiv2,'String');%subdirectory subdir_civ2 for the netcdf data ref_i=str2double(get(handles.ref_i,'String')); if isequal(mode,'pair j1-j2')%|isequal(mode,'st_pair j1-j2') ref_j=0; else ref_j=str2double(get(handles.ref_j,'String')); if isnan(ref_j) ref_j=1; end end time=get(handles.ImaDoc,'UserData');%get the set of times TimeUnit=get(handles.TimeUnit,'String'); checkframe=strcmp(TimeUnit,'frame'); displ_num=get(handles.ListPairCiv1,'UserData'); %% eliminate the first pairs inconsistent with the position if isempty(displ_num) nbpair=0; else nbpair=length(displ_num(1,:));%nbre of displayed pairs if isequal(mode,'series(Di)') %| isequal(mode,'st_series(Di)') nbpair=min(2*ref_i-1,nbpair);%limit the number of pairs with positive first index elseif isequal(mode,'series(Dj)')% | isequal(mode,'st_series(Dj)') nbpair=min(2*ref_j-1,nbpair);%limit the number of pairs with positive first index end end nbpair=min(200,nbpair);%limit the number of displayed pairs to 200 %% case with no Civ1 operation, netcdf files need to exist for reading displ_pair={''}; select=ones(size(1:nbpair));%flag for displayed pairs =1 for display testpair=0; RootPath=get(handles.RootPath,'String'); RootFile=get(handles.RootFile,'String'); if index==1 % case civ1 if ~get(handles.CheckCiv1,'Value') % if ~exist(fullfile(RootPath,subdir_civ1),'dir') errormsg=['no civ1 file available: subdirectory ' subdir_civ1 ' does not exist']; set(handles.ListPairCiv1,'String',{}); return end for ipair=1:nbpair filename=fullfile_uvmat(RootPath,subdir_civ1,RootFile,'.nc',nom_type_nc,... ref_i+displ_num(3,ipair),ref_i+displ_num(4,ipair),ref_j+displ_num(1,ipair),ref_j+displ_num(2,ipair)); select(ipair)=exist(filename,'file')==2;% put flag to 0 if the file does not exist end % case of no displayed pair if isequal(select,zeros(size(1:nbpair))) if isfield(browse,'incr_pair') && ~isequal(browse.incr_pair,[0 0]) num_i1=ref_i-floor(browse.incr_pair(1)/2); num_i2=ref_i+ceil(browse.incr_pair(1)/2); num_j1=ref_j-floor(browse.incr_pair(2)/2); num_j2=ref_j+ceil(browse.incr_pair(2)/2); filename=fullfile_uvmat(RootPath,subdir_civ1,RootFile,'.nc',nom_type_nc,num_i1,num_i2,num_j1,num_j2); select(1)=exist(filename,'file')==2; testpair=1; else if isequal(mode,'series(Dj)')% | isequal(mode,'st_series(Dj)') errormsg=['no civ1 file available for the selected reference index j=' num2str(ref_j) ' and subdirectory ' subdir_civ1]; else errormsg=['no civ1 file available for the selected reference indices (i,j)= ' num2str(ref_i) ', ' num2str(ref_j) ' and subdirectory ' subdir_civ1]; end set(handles.ListPairCiv1,'String',{''}); %COMPLETER CAS STEREO return end end end else %case civ2 alone if ~get(handles.CheckCiv2,'Value') && ~get(handles.CheckCiv1,'Value') && ~get(handles.CheckFix1,'Value') && ~get(handles.CheckPatch1,'Value') if ~exist(fullfile(RootPath,subdir_civ2,ext_dir),'dir') errordlg(['no civ2 file available: subdirectory ' subdir_civ2 ' does not exist']) set(handles.ListPairCiv2,'Value',1); set(handles.ListPairCiv2,'String',{''}); return end for ipair=1:nbpair filename=fullfile_uvmat(RootPath,subdir_civ1,RootFile,'.nc',nom_type_nc,... ref_i+displ_num(3,ipair),ref_i+displ_num(4,ipair),ref_j+displ_num(1,ipair),ref_j+displ_num(2,ipair)); select(ipair)=exist(filename,'file')==2; end if isequal(select,zeros(size(1:nbpair))) if isfield(browse,'incr_pair') num_i1=ref_i-floor(browse.incr_pair(1)/2); num_i2=ref_i+floor((browse.incr_pair(1)+1)/2); num_j1=ref_j-floor(browse.incr_pair(2)/2); num_j2=ref_j+floor((browse.incr_pair(2)+1)/2); filename=fullfile_uvmat(RootPath,subdir_civ2,RootFile,'.nc',nom_type_nc,num_i1,num_i2,num_j1,num_j2); select(1)=exist(filename,'file')==2; else if isequal(mode,'series(Dj)')% | isequal(mode,'st_series(Dj)') errormsg=['no civ2 file available for the selected reference index j=' num2str(ref_j) ' and subdirectory ' subdir_civ2]; else errormsg=['no civ2 file available for the selected reference index i=' num2str(ref_i) ' and subdirectory ' subdir_civ2]; end set(handles.ListPairCiv2,'Value',1); set(handles.ListPairCiv2,'String',{''}); return end end end end %% determine the menu display in .ListPairCiv1 % the menu depends on the mode defined in ListPairMode_callback through the array displ_num: % displ_num(1,:)=indices j1 % displ_num(2,:)=indices j2 % displ_num(3,:)=indices i1 % displ_num(4,:)=indices i2 % in mode 'pair j1-j2', j1 and j2 are the file indices, else the indices % are relative to the reference indices ref_i and ref_j respectively. if isequal(mode,'series(Di)') if testpair displ_pair{1}=['Di= ' num2str(-floor(browse.incr_pair(1)/2)) '|' num2str(ceil(browse.incr_pair(1)/2))]; else for ipair=1:nbpair if select(ipair) displ_pair{ipair}=['Di= ' num2str(-floor(ipair/2)) '|' num2str(ceil(ipair/2))]; %if ~checkframe && size(time,1)>=ref_i+1+displ_num(4,ipair) && size(time,2)>=ref_j+1+displ_num(2,ipair)&&displ_num(2,ipair)>=1 &&displ_num(1,ipair)>=1 % dt=time(ref_i+1+displ_num(4,ipair),ref_j+1+displ_num(2,ipair))-time(ref_i+1+displ_num(3,ipair),ref_j+1+displ_num(1,ipair));%time interval dt if ~checkframe && size(time,1)>=ref_i+1+ceil(ipair/2) && size(time,2)>=ref_j+1&& ref_i-floor(ipair/2)>=0 && ref_j>=0 dt=time(ref_i+1+ceil(ipair/2),ref_j+1)-time(ref_i+1-floor(ipair/2),ref_j+1);%time interval dtref_j+1 else dt=1; end displ_pair{ipair}=[displ_pair{ipair} ' :dt= ' num2str(dt*1000)]; else displ_pair{ipair}='...'; %pair not displayed in the menu end end end elseif isequal(mode,'series(Dj)') if testpair displ_pair{1}=['Dj= ' num2str(-floor(browse.incr_pair(1)/2)) '|' num2str(ceil(browse.incr_pair(1)/2))]; else for ipair=1:nbpair if select(ipair) displ_pair{ipair}=['Dj= ' num2str(-floor(ipair/2)) '|' num2str(ceil(ipair/2))]; if ~checkframe && size(time,1)>=ref_i+1+displ_num(4,ipair) && size(time,2)>=ref_j+1+displ_num(2,ipair) dt=time(ref_i+1+displ_num(4,ipair),ref_j+1+displ_num(2,ipair))-time(ref_i+1+displ_num(3,ipair),ref_j+1+displ_num(1,ipair));%time interval dt displ_pair{ipair}=[displ_pair{ipair} ' :dt= ' num2str(dt*1000)]; end else displ_pair{ipair}='...'; %pair not displayed in the menu end end end elseif isequal(mode,'pair j1-j2')%case of pairs for ipair=1:nbpair if select(ipair) if ~checkframe && size(time,2)>1 dt=time(ref_i+1+displ_num(4,ipair),displ_num(2,ipair)+1)-time(ref_i+1+displ_num(3,ipair),displ_num(1,ipair)+1);%time interval dt else % time set by default to i index dt=1; end displ_pair{ipair}=['j= ' num2stra(displ_num(1,ipair),nom_type_ima) '-' num2stra(displ_num(2,ipair),nom_type_ima) ... ' :dt= ' num2str(dt*1000)]; else displ_pair{ipair}='...'; %pair not displayed in the menu end end elseif isequal(mode,'displacement') displ_pair={'Di=Dj=0'}; end if index==1 set(handles.ListPairCiv1,'String',displ_pair'); end %% determine the default selection in the pair menu ichoice=find(select,1);% index of selected pair if (isempty(ichoice) || ichoice < 1); ichoice=1; end; initial=get(handles.ListPairCiv1,'Value');%initial choice of pair if initial>nbpair || (numel(select)>=initial && ~isequal(select(initial),1)) set(handles.ListPairCiv1,'Value',ichoice);% first valid pair proposed by default in the menu end initial=get(handles.ListPairCiv2,'Value'); if initial>length(displ_pair')%|~isequal(select(initial),1) if ichoice <= length(displ_pair') set(handles.ListPairCiv2,'Value',ichoice);% same pair proposed by default for civ2 else set(handles.ListPairCiv2,'Value',1);% same pair proposed by default for civ2 end end set(handles.ListPairCiv2,'String',displ_pair'); set(gcf,'Pointer','arrow') % %------------------------------------------------------------------------ % % call 'view_field.fig' to display the field selected in the list of 'status' % function open_view_field(hObject, eventdata) % %------------------------------------------------------------------------ % list=get(hObject,'String'); % index=get(hObject,'Value'); % rootroot=get(hObject,'UserData'); % filename=list{index}; % ind_dot=strfind(filename,'...'); % filename=filename(1:ind_dot-1); % filename=fullfile(rootroot,filename); % delete(get(hObject,'parent'))%delete the display figure to stop the check process % if exist(filename,'file')%visualise the vel field if it exists % uvmat(filename) % set(gcbo,'Value',1) % end %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% % Callbacks in the uipanel Reference Indices %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %------------------------------------------------------------------------ function first_i_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ first_i=str2double(get(handles.first_i,'String')); set(handles.ref_i,'String', num2str(first_i))% reference index for pair dt = first index ref_i_Callback(hObject, eventdata, handles)%refresh dispaly of dt for pairs (in case of non constant dt) %------------------------------------------------------------------------ function first_j_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ first_j=str2num(get(handles.first_j,'String')); set(handles.ref_j,'String', num2str(first_j))% reference index for pair dt = first index ref_j_Callback(hObject, eventdata, handles)%refresh dispaly of dt for pairs (in case of non constant dt) %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% % Callbacks in the uipanel Civ1 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %------------------------------------------------------------------------ % --- Executes on button press in SearchRange: determine the search range num_Searchx,num_Searchy function SearchRange_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ %determine pair numbers if strcmp(get(handles.num_UMin,'Visible'),'off') set(handles.u_title,'Visible','on') set(handles.v_title,'Visible','on') set(handles.num_UMin,'Visible','on') set(handles.num_UMax,'Visible','on') set(handles.num_VMin,'Visible','on') set(handles.num_VMax,'Visible','on') set(handles.CoordUnit,'Visible','on') set(handles.TimeUnit,'Visible','on') set(handles.slash_title,'Visible','on') set(handles.min_title,'Visible','on') set(handles.max_title,'Visible','on') set(handles.unit_title,'Visible','on') else get_search_range(hObject, eventdata, handles) end %------------------------------------------------------------------------ % --- determine the search range num_Searchx,num_Searchy and shift function get_search_range(hObject, eventdata, handles) %------------------------------------------------------------------------ param_civ1=read_GUI(handles.Civ1); umin=param_civ1.UMin; umax=param_civ1.UMax; vmin=param_civ1.VMin; vmax=param_civ1.VMax; %switch min_title and max_title in case of error if umax<=umin umin_old=umin; umin=umax; umax=umin_old; set(handles.num_UMin,'String', num2str(umin)) set(handles.num_UMax,'String', num2str(umax)) end if vmax<=vmin vmin_old=vmin; vmin=vmax; vmax=vmin_old; set(handles.num_VMin,'String', num2str(vmin)) set(handles.num_VMax,'String', num2str(vmax)) end if ~(isempty(umin)||isempty(umax)||isempty(vmin)||isempty(vmax)) list_pair=get(handles.ListPairCiv1,'String');%get the menu of image pairs index=get(handles.ListPairCiv1,'Value'); pair_string=list_pair{index}; time=get(handles.ImaDoc,'UserData'); %get the set of times pxcm=get(handles.SearchRange,'UserData'); mode_list=get(handles.ListPairMode,'String'); mode_value=get(handles.ListPairMode,'Value'); mode=mode_list{mode_value}; if isequal (mode, 'series(Di)' ) ref_i=str2double(get(handles.ref_i,'String')); num1=ref_i-floor(index/2);% first image numbers num2=ref_i+ceil(index/2); num_a=1; num_b=1; elseif isequal (mode, 'series(Dj)') num1=1; num2=1; ref_j=str2double(get(handles.ref_j,'String')); num_a=ref_j-floor(index/2);% first image numbers num_b=ref_j+ceil(index/2); elseif isequal(mode,'pair j1-j2') %case of bursts (png_old or png_2D) ref_i=str2double(get(handles.ref_i,'String')); num1=ref_i; num2=ref_i; r=regexp(pair_string,'(?(Di=)|(Dj=)) -*(?\d+)\|(?\d+)','names'); if isempty(r) r=regexp(pair_string,'(?\d+)(?-)(?\d+)','names'); end num_a=str2num(r.num1); num_b=str2num(r.num2); end dt=time(num2+1,num_b+1)-time(num1+1,num_a+1); ibx=str2double(get(handles.num_Bx,'String')); iby=str2double(get(handles.num_By,'String')); umin=dt*pxcm*umin; umax=dt*pxcm*umax; vmin=dt*pxcm*vmin; vmax=dt*pxcm*vmax; shiftx=round((umin+umax)/2); shifty=round((vmin+vmax)/2); isx=(umax+2-shiftx)*2+param_civ1.Bx; isx=2*ceil(isx/2)+1; isy=(vmax+2-shifty)*2+param_civ1.Bx; isy=2*ceil(isy/2)+1; set(handles.num_Shiftx,'String',num2str(shiftx)); set(handles.num_Shifty,'String',num2str(shifty)); set(handles.num_Searchx,'String',num2str(isx)); set(handles.num_Searchy,'String',num2str(isy)); end %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% % Callbacks in the uipanel Fix1 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %------------------------------------------------------------------------ % --- Executes on button press in CheckMask. function get_mask_fix1_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ maskval=get(handles.CheckMask,'Value'); if isequal(maskval,0) set(handles.Mask,'String','') else mask_displ='no mask'; %default filebase=get(handles.RootPath,'String'); [nbslice, flag_mask]=get_mask(filebase,handles); if isequal(flag_mask,1) mask_displ=[num2str(nbslice) 'mask']; elseif get(handles.ListCompareMode,'Value')>1 & ~isequal(mask_displ,'no mask')% look for the second mask series filebase_a=get(handles.RootFile_1,'String'); [nbslice_a, flag_mask_a]=get_mask(filebase_a,handles); if isequal(flag_mask_a,0) || ~isequal(nbslice_a,nbslice) mask_displ='no mask'; end end if isequal(mask_displ,'no mask') [FileName, PathName, filterindex] = uigetfile( ... {'*.png', ' (*.png)'; '*.png', '.png files '; ... '*.*', 'All Files (*.*)'}, ... 'Pick a mask file *.png',filebase); mask_displ=fullfile(PathName,FileName); if ~exist(mask_displ,'file') mask_displ='no mask'; end end if isequal(mask_displ,'no mask') set(handles.CheckMask,'Value',0) set(handles.CheckMask,'Value',0) set(handles.CheckMask,'Value',0) else %set(handles.CheckMask,'Value',1) set(handles.CheckMask,'Value',1) end set(handles.Mask,'String',mask_displ) set(handles.Mask,'String',mask_displ) set(handles.Mask,'String',mask_displ) end %------------------------------------------------------------------------ % --- Executes on button press in CheckMask: select box for mask option function get_mask_civ2_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ maskval=get(handles.CheckMask,'Value'); if isequal(maskval,0) set(handles.Mask,'String','') else mask_displ='no mask'; %default filebase=get(handles.RootPath,'String'); [nbslice, flag_mask]=get_mask(filebase,handles); if isequal(flag_mask,1) mask_displ=[num2str(nbslice) 'mask']; elseif get(handles.ListCompareMode,'Value')>1 & ~isequal(mask_displ,'no mask')% look for the second mask series filebase_a=get(handles.RootFile_1,'String'); [nbslice_a, flag_mask_a]=get_mask(filebase_a,handles); if isequal(flag_mask_a,0) || ~isequal(nbslice_a,nbslice) mask_displ='no mask'; end end if isequal(mask_displ,'no mask') [FileName, PathName, filterindex] = uigetfile( ... {'*.png', ' (*.png)'; '*.png', '.png files '; ... '*.*', 'All Files (*.*)'}, ... 'Pick a mask file *.png',filebase); mask_displ=fullfile(PathName,FileName); if ~exist(mask_displ,'file') mask_displ='no mask'; end end if isequal(mask_displ,'no mask') set(handles.CheckMask,'Value',0) set(handles.CheckMask,'Value',0) else set(handles.CheckMask,'Value',1) end set(handles.Mask,'String',mask_displ) set(handles.Mask,'String',mask_displ) end %------------------------------------------------------------------------ % --- Executes on button press in CheckMask. function get_mask_fix2_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ maskval=get(handles.CheckMask,'Value'); if isequal(maskval,0) set(handles.Mask,'String','') else mask_displ='no mask'; %default filebase=get(handles.RootPath,'String'); [nbslice, flag_mask]=get_mask(filebase,handles); if isequal(flag_mask,1) mask_displ=[num2str(nbslice) 'mask']; elseif get(handles.ListCompareMode,'Value')>1 & ~isequal(mask_displ,'no mask')% look for the second mask series filebase_a=get(handles.RootFile_1,'String'); [nbslice_a, flag_mask_a]=get_mask(filebase_a,handles); if isequal(flag_mask_a,0) || ~isequal(nbslice_a,nbslice) mask_displ='no mask'; end end if isequal(mask_displ,'no mask') [FileName, PathName, filterindex] = uigetfile( ... {'*.png', ' (*.png)'; '*.png', '.png files '; ... '*.*', 'All Files (*.*)'}, ... 'Pick a mask file *.png',filebase); mask_displ=fullfile(PathName,FileName); if ~exist(mask_displ,'file') mask_displ='no mask'; end end if isequal(mask_displ,'no mask') set(handles.CheckMask,'Value',0) end set(handles.Mask,'String',mask_displ) end %------------------------------------------------------------------------ % --- function called to look for mask files function [nbslice, flag_mask]=get_mask(filebase,handles) %------------------------------------------------------------------------ %detect mask files, images with appropriate file base %[filebase '_' xx 'mask'], xx=nbslice %flag_mask=1 indicates detection flag_mask=0;%default nbslice=1; % subdir=get(handles.SubdirCiv1,'String'); [Path,Name]=fileparts(filebase); if ~isdir(Path) msgbox_uvmat('ERROR','no path for input files') return end % currentdir=pwd; % cd(Path);%move in the dir of the root name filebase maskfiles=dir(fullfile(Path,[Name '_*mask_*.png']));%look for mask files % cd(currentdir);%come back to the current working directory if ~isempty(maskfiles) % msgbox_uvmat('ERROR','no mask available, to create it use Tools/Make mask in the upper menu bar of uvmat') % else flag_mask=1; maskname=maskfiles(1).name;% take the first mask file in the list [Path2,Name,ext]=fileparts(maskname); Namedouble=double(Name); val=(48>Namedouble)|(Namedouble>57);% select the non-numerical characters ind_mask=findstr('mask',Name); i=ind_mask-1; while val(i)==0 && i>0 i=i-1; end nbslice=str2double(Name(i+1:ind_mask-1)); if ~isnan(nbslice) && Name(i)=='_' flag_mask=1; else msgbox_uvmat('ERROR',['bad mask file ' Name ext ' found in ' Path2]) return nbslice=1; end end %------------------------------------------------------------------------ % --- function called to look for grid files function [nbslice, flag_mask]=get_grid(filebase,handles) %------------------------------------------------------------------------ flag_mask=0;%default nbslice=1; [Path,Name]=fileparts(filebase); currentdir=pwd; cd(Path);%move in the dir of the root name filebase maskfiles=dir([Name '_*grid_*.grid']);%look for mask files cd(currentdir);%come back to the current working directory if ~isempty(maskfiles) flag_mask=1; maskname=maskfiles(1).name;% take the first mask file in the list [Path2,Name,ext]=fileparts(maskname); Namedouble=double(Name); val=(48>Namedouble)|(Namedouble>57);% select the non-numerical characters ind_mask=findstr('grid',Name); i=ind_mask-1; while val(i)==0 && i>0 i=i-1; end nbslice=str2double(Name(i+1:ind_mask-1)); if ~isnan(nbslice) && Name(i)=='_' flag_mask=1; else msgbox_uvmat('ERROR',['bad grid file ' Name ext ' found in ' Path2]) return nbslice=1; end end %------------------------------------------------------------------------ % --- transform numbers to letters function str=num2stra(num,nom_type) %------------------------------------------------------------------------ if isempty(nom_type) str=''; elseif strcmp(nom_type(end),'a') str=char(96+num); elseif strcmp(nom_type(end),'A') str=char(96+num); elseif isempty(nom_type(2:end))%a single index str=''; else str=num2str(num); end %------------------------------------------------------------------------ % --- Executes on button press in ListSubdirCiv1. function ListSubdirCiv1_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ list_subdir_civ1=get(handles.ListSubdirCiv1,'String'); val=get(handles.ListSubdirCiv1,'Value'); SubDir=list_subdir_civ1{val}; if strcmp(SubDir,'new...') if get(handles.CheckCiv1,'Value') SubDir='CIV'; %default subdirectory else msgbox_uvmat('ERROR','select CheckCiv1 to perform a new Civ operation') return end end set(handles.SubdirCiv1,'String',SubDir); errormsg=find_netcpair_civ(handles,1); if ~isempty(errormsg) msgbox_uvmat('ERROR',errormsg) end %------------------------------------------------------------------------ % --- Executes on button press in ListSubdirCiv2. function ListSubdirCiv2_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ list_subdir_civ2=get(handles.ListSubdirCiv2,'String'); val=get(handles.ListSubdirCiv2,'Value'); SubDir=list_subdir_civ2{val}; if strcmp(SubDir,'new...') if get(handles.CheckCiv2,'Value') SubDir='CIV'; %default subdirectory else msgbox_uvmat('ERROR','select CheckCiv2 to perform a new Civ operation') return end end set(handles.SubdirCiv2,'String',SubDir); %------------------------------------------------------------------------ % --- Executes on button press in CheckGrid. function CheckGrid_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ value=get(hObject,'Value'); hparent=get(hObject,'parent'); hchildren=get(hparent,'children'); handle_txtbox=findobj(hchildren,'tag','txt_Grid'); handle_dx=findobj(hchildren,'tag','num_Dx'); handle_dy=findobj(hchildren,'tag','num_Dy'); handle_title_dx=findobj(hchildren,'tag','title_Dx'); handle_title_dy=findobj(hchildren,'tag','title_Dy'); testgrid=0; filegrid=''; if value filebase=get(handles.RootPath,'String'); [nbslice, flag_grid]=get_grid(filebase,handles);% look for a grid with appropriate name if isequal(flag_grid,1) filegrid=[num2str(nbslice) 'grid']; testgrid=1; else % browse for a grid filegrid=get(hObject,'UserData');%look for previous grid name stored as UserData if exist(filegrid,'file') filebase=filegrid; end [FileName, PathName, filterindex] = uigetfile( ... {'*.grid', ' (*.grid)'; '*.grid', '.grid files '; ... '*.*', 'All Files (*.*)'}, ... 'Pick a file',filebase); filegrid=fullfile(PathName,FileName); set(hObject,'UserData',filegrid);%store for future use if ~(isempty(FileName)||isempty(PathName)||isequal(FileName,0)||~exist(filegrid,'file')) testgrid=1; end end end if testgrid set(handle_dx,'Visible','off'); set(handle_dy,'Visible','off'); set(handle_title_dy,'Visible','off'); set(handle_title_dx,'Visible','off'); set(handle_txtbox,'Visible','on') set(handle_txtbox,'String',filegrid) else set(hObject,'Value',0); set(handle_dx,'Visible','on'); set(handle_dy,'Visible','on'); set(handle_title_dy,'Visible','on'); set(handle_title_dx,'Visible','on'); set(handle_txtbox,'Visible','off') end %% if hObject is on the checkciv1 frame, duplicate action for checkciv2 frame PanelName=get(hparent,'tag'); if strcmp(PanelName,'Civ1') hchildren=get(handles.Civ2,'children'); handle_checkbox=findobj(hchildren,'tag','CheckGrid'); handle_txtbox=findobj(hchildren,'tag','txt_Grid'); handle_dx=findobj(hchildren,'tag','num_Dx'); handle_dy=findobj(hchildren,'tag','num_Dy'); handle_title_dx=findobj(hchildren,'tag','title_Dx'); handle_title_dy=findobj(hchildren,'tag','title_Dy'); set(handle_checkbox,'UserData',filegrid);%store for future use if testgrid set(handle_checkbox,'Value',1); set(handle_dx,'Visible','off'); set(handle_dy,'Visible','off'); set(handle_title_dx,'Visible','off'); set(handle_title_dy,'Visible','off'); set(handle_txtbox,'Visible','on') set(handle_txtbox,'String',filegrid) % else % set(handle_checkbox,'Value',0); % set(handles.CheckGrid,'Value',0); % set(handle_dx,'Visible','on'); % set(handle_dy,'Visible','on'); % set(handle_title_dx,'Visible','on'); % set(handle_title_dy,'Visible','on'); % set(handle_txtbox,'Visible','off') end end %------------------------------------------------------------------------ % --- Executes on button press in CheckMask: common to all panels (civ1, Civ2..) function CheckMask_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ value=get(hObject,'Value'); hparent=get(hObject,'parent'); parent_tag=get(hparent,'Tag'); hchildren=get(hparent,'children'); handle_txtbox=findobj(hchildren,'tag','Mask');% look for the mask name box in the same panel testmask=0; if value filebase=get(handles.RootPath,'String'); [nbslice, flag_mask]=get_mask(filebase,handles);% look for a mask with appropriate name if isequal(flag_mask,1) filemask=[num2str(nbslice) 'mask']; testmask=1; else % browse for a mask filemask=get(hObject,'UserData');%look for previous mask name stored as UserData if exist(filemask,'file') filebase=filemask; end [FileName, PathName] = uigetfile( ... {'*.png', ' (*.png)'; '*.png', '.png files '; ... '*.*', 'All Files (*.*)'}, ... 'Pick a mask file *.png',filebase); filemask=fullfile(PathName,FileName); set(hObject,'UserData',filemask);%store for future use if ~(isempty(FileName)||isempty(PathName)||isequal(FileName,0)||~exist(filemask,'file')) testmask=1; end end end if testmask if strcmp(parent_tag,'Civ1') set(handles.Mask,'Visible','on') set(handles.Mask,'String',filemask) set(handles.CheckMask,'Value',1) end % switch parent_tag % % case 'Fix1' % % stage=2; % case 'Civ2' % stage=3; % % case 'Fix2' % % stage=4; % end % set(handles.Mask(stage:end),'Visible','on') % set(handles.Mask(stage:end),'String',filemask) % set(handles.CheckMask(stage:end),'Value',1) else set(hObject,'Value',0); set(handle_txtbox,'Visible','off') end % --- Executes on button press in get_gridpatch1. function get_gridpatch1_Callback(hObject, eventdata, handles) filebase=get(handles.RootPath,'String'); [FileName, PathName, filterindex] = uigetfile( ... {'*.grid', ' (*.grid)'; '*.grid', '.grid files '; ... '*.*', 'All Files (*.*)'}, ... 'Pick a file',filebase); filegrid=fullfile(PathName,FileName); set(handles.grid_patch1,'string',filegrid); %------------------------------------------------------------------------ % --- Executes on button press in get_gridpatch2. function get_gridpatch2_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ %------------------------------------------------------------------------ % --- STEREO Interp function cmd=RUN_STINTERP(stinterpBin,filename_A_nc,filename_B_nc,filename_nc,nx_patch,ny_patch,rho_patch,subdomain_patch,thresh_value,xmlA,xmlB) %------------------------------------------------------------------------ namelog=[filename_nc(1:end-3) '_stinterp.log']; cmd=[stinterpBin ' -f1 ' filename_A_nc ' -f2 ' filename_B_nc ' -f ' filename_nc ... ' -m ' nx_patch ' -n ' ny_patch ' -ro ' rho_patch ' -nopt ' subdomain_patch ' -c1 ' xmlA ' -c2 ' xmlB ' -xy x -Nfy 1024 > ' namelog ' 2>&1']; % redirect standard output to the log file %------------------------------------------------------------------------ %--read images and convert them to the uint16 format used for PIV function A=read_image(filename,type_ima,num,movieobject) %------------------------------------------------------------------------ %num is the view number needed for an avi movie switch type_ima case 'movie' A=read(movieobject,num); case 'avi' mov=aviread(filename,num); A=frame2im(mov(1)); case 'multimage' A=imread(filename,num); case 'image' A=imread(filename); end siz=size(A); if length(siz)==3;%color images A=sum(double(A),3); A=uint16(A); end %------------------------------------------------------------------------ % --- Executes on button press in get_ref_fix1. function get_ref_fix1_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ filebase=get(handles.RootPath,'String'); [FileName, PathName, filterindex] = uigetfile( ... {'*.nc', ' (*.nc)'; '*.nc', 'netcdf files '; ... '*.*', 'All Files (*.*)'}, ... 'Pick a file',filebase); fileinput=[PathName FileName]; sizf=size(fileinput); if (~ischar(fileinput)||~isequal(sizf(1),1)),return;end %stop if fileinput not a character string %[Path,File,field_count,str2,str_a,str_b,ref.ext,ref.nom_type,ref.subdir]=name2display(fileinput); [Path,ref.subdir,File,ref.num1,ref.num2,ref.num_a,ref.num_b,ref.ext,ref.nom_type]=fileparts_uvmat(fileinput); ref.filebase=fullfile(Path,File); % ref.num_a=stra2num(str_a); % ref.num_b=stra2num(str_b); % ref.num1=str2double(field_count); % ref.num2=str2double(str2); browse=[];%initialisation if ~isequal(ref.ext,'.nc') msgbox_uvmat('ERROR','the reference file must be in netcdf format (*.nc)') return end set(handles.ref_fix1,'String',[fullfile(ref.subdir,File) '....nc']); set(handles.ref_fix1,'UserData',ref) menu_field{1}='civ1'; Data=nc2struct(fileinput,[]); if isfield(Data,'patch') && isequal(Data.patch,1) menu_field{2}='filter1'; end if isfield(Data,'civ2') && isequal(Data.civ2,1) menu_field{3}='civ2'; end if isfield(Data,'patch2') && isequal(Data.patch2,1) menu_field{4}='filter2'; end set(handles.field_ref1,'String',menu_field); set(handles.field_ref1,'Value',length(menu_field)); set(handles.num_MinVel,'Value',2); set(handles.num_MinVel,'String','1');%default threshold set(handles.ref_fix1,'Enable','on') %------------------------------------------------------------------------ % --- Executes on button press in get_ref_fix2. function get_ref_fix2_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ if isequal(get(handles.get_ref_fix2,'Value'),1) filebase=get(handles.RootPath,'String'); [FileName, PathName, filterindex] = uigetfile( ... {'*.nc', ' (*.nc)'; '*.nc', 'netcdf files '; ... '*.*', 'All Files (*.*)'}, ... 'Pick a file',filebase); fileinput=[PathName FileName]; sizf=size(fileinput); if (~ischar(fileinput)||~isequal(sizf(1),1)),return;end %stop if fileinput not a character string %[Path,File,field_count,str2,str_a,str_b,ref.ext,ref.nom_type,ref.subdir]=name2display(fileinput); [Path,ref.subdir,File,ref.num1,ref.num2,ref.num_a,ref.num_b,ref.ext,ref.nom_type]=fileparts_uvmat(fileinput); ref.filebase=fullfile(Path,File); % ref.num_a=stra2num(str_a); % ref.num_b=stra2num(str_b); % ref.num1=str2num(field_count); % ref.num2=str2num(str2); browse=[];%initialisation if ~isequal(ref.ext,'.nc') msgbox_uvmat('ERROR','the reference file must be in netcdf format (*.nc)') return end set(handles.ref_fix2,'String',[fullfile(ref.subdir,File) '....nc']); set(handles.ref_fix2,'UserData',ref) menu_field{1}='civ1'; Data=nc2struct(fileinput,[]); if isfield(Data,'patch') && isequal(Data.patch,1) menu_field{2}='filter1'; end if isfield(Data,'civ2') && isequal(Data.civ2,1) menu_field{3}='civ2'; end if isfield(Data,'patch2') && isequal(Data.patch2,1) menu_field{4}='filter2'; end set(handles.field_ref2,'String',menu_field); set(handles.field_ref2,'Value',length(menu_field)); set(handles.num_MinVel,'Value',2); set(handles.num_MinVel,'String','1');%default threshold set(handles.ref_fix2,'Enable','on') set(handles.ref_fix2,'Visible','on') set(handles.field_ref2,'Visible','on') else set(handles.ref_fix2,'Visible','off') set(handles.field_ref2,'Visible','off') end %------------------------------------------------------------------------ function ref_fix1_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ set(handles.num_MinVel,'Value',1); set(handles.field_ref1,'Value',1) set(handles.field_ref1,'String',{' '}) set(handles.ref_fix1,'UserData',[]); set(handles.ref_fix1,'String',''); set(handles.thresh_vel1,'String','0'); %------------------------------------------------------------------------ function ref_fix2_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ set(handles.num_MinVel,'Value',1); set(handles.field_ref2,'Value',1) set(handles.field_ref2,'String',{' '}) set(handles.ref_fix2,'UserData',[]); set(handles.ref_fix2,'String',''); set(handles.num_MinVel,'String','0'); %------------------------------------------------------------------------ % --- TO ABANDON Executes on button press in test_stereo1. function CheckStereo_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ hparent=get(hObject,'parent'); parent_tag=get(hparent,'Tag'); hchildren=get(hparent,'children'); handle_txtbox=findobj(hchildren,'tag','txt_Mask'); if isequal(get(hObject,'Value'),0) set(handles.num_SubdomainSize,'Visible','on') set(handles.num_SmoothingParam,'Visible','on') else set(handles.num_SubdomainSize,'Visible','off') set(handles.num_SmoothingParam,'Visible','off') end % %------------------------------------------------------------------------ % % --- Executes on button press in CheckStereo. % function StereoCheck_Callback(hObject, eventdata, handles) % %------------------------------------------------------------------------ % if isequal(get(handles.CheckStereo,'Value'),0) % set(handles.num_SubdomainSize,'Visible','on') % set(handles.num_SmoothingParam,'Visible','on') % else % set(handles.num_SubdomainSize,'Visible','off') % set(handles.num_SmoothingParam,'Visible','off') % end %------------------------------------------------------------------------ % --- Executes on button press in TestCiv1: prepare the image correlation function % activated by mouse motion function TestCiv1_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ drawnow if get(handles.TestCiv1,'Value') set(handles.TestCiv1,'BackgroundColor',[0.7 0.7 0.7])% paint TestCiv1 button to grey to confirm civ launch ref_i=str2double(get(handles.ref_i,'String'));% read reference i index if strcmp(get(handles.ref_j,'Visible'),'on') ref_j=str2double(get(handles.ref_j,'String'));% read reference j index if relevant else ref_j=1;%default j index end [filecell,i1,i2,j1,j2,i1_civ2,i2_civ2,j1_civ2,j2_civ2,nom_type_nc,file_ref_fix1,file_ref_fix2]=... set_civ_filenames(handles,ref_i,ref_j,[1 0 0 0 0 0]);% get the corresponding file name and indices Data.ListVarName={'ny','nx','A'}; Data.VarDimName= {'ny','nx',{'ny','nx'}}; Data.A=imread(filecell.ima1.civ1{1}); % read the first image if ndims(Data.A)==3 %case of color image Data.VarDimName= {'ny','nx',{'ny','nx','rgb'}}; end Data.ny=[size(Data.A,1) 1]; Data.nx=[1 size(Data.A,2)]; Data.CoordUnit='pixel';% used to set equal scaling for x and y in image dispaly par_civ1=read_GUI(handles.Civ1); par_civ1.ImageWidth=size(Data.A,2); par_civ1.ImageHeight=size(Data.A,1); par_civ1.Mask='all';% will provide only the grid set for PIV, no image correlation par_civ1.i1=i1; par_civ1.i2=i2; Param.Civ1=par_civ1; Grid=civ_matlab(Param);% get the grid of x, y positions set for PIV hview_field=view_field(Data); %view the image in the GUI view_field set(0,'CurrentFigure',hview_field) hhview_field=guihandles(hview_field); set(hview_field,'CurrentAxes',hhview_field.axes3) ViewData=get(hview_field,'UserData'); ViewData.CivHandle=handles.civ;% indicate the handle of the civ GUI in view_field ViewData.axes3.B=imread(filecell.ima2.civ1{1});%store the second image in the UserData of the GUI view_field ViewData.axes3.X=Grid.Civ1_X; %keep the set of points in memeory ViewData.axes3.Y=Grid.Civ1_Y; set(hview_field,'UserData',ViewData) corrfig=findobj(allchild(0),'tag','corrfig');% look for a current figure for image correlation display if isempty(corrfig) corrfig=figure; set(corrfig,'tag','corrfig') set(corrfig,'name','image correlation') set(corrfig,'DeleteFcn',{@closeview_field})% end set(handles.TestCiv1,'BackgroundColor',[1 0 0]) else set(handles.TestCiv1,'BackgroundColor',[1 0 0])% paint button to red corrfig=findobj(allchild(0),'tag','corrfig');% look for a current figure for image correlation display if ~isempty(corrfig) delete(corrfig) end hview_field=findobj(allchild(0),'tag','view_field');% look for view_field if ~isempty(hview_field) delete(hview_field) end end %------------------------------------------------------------------------ %----function introduced for the correlation window figure, activated by deleting this window function closeview_field(gcbo,eventdata) %------------------------------------------------------------------------ hview_field=findobj(allchild(0),'tag','view_field');% look for view_field if ~isempty(hview_field) delete(hview_field) end %------------------------------------------------------------------------ % --- Executes on button press in CheckThreshold. function CheckThreshold_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ huipanel=get(hObject,'parent'); obj(1)=findobj(huipanel,'Tag','num_MinIma'); obj(2)=findobj(huipanel,'Tag','num_MaxIma'); obj(3)=findobj(huipanel,'Tag','title_Threshold'); if get(hObject,'Value') set(obj,'Visible','on') else set(obj,'Visible','off') end %------------------------------------------------------------------------ function [cmd,errormsg]=cmd_civ1(filename,Param) %------------------------------------------------------------------------ %pixels per cm and matrix of the image times, read from the .civ file by uvmat %changes : filename_cmx -> filename ( no extension ) cmd=''; filename=regexprep(filename,'.nc',''); %file name for the result if isequal(Param.Civ1.Dt,0) Param.Civ1.Dt=1 ;%case of 'displacement' mode end Param.Civ1.ImageA=regexprep(Param.Civ1.ImageA,'.png',''); Param.Civ1.ImageB=regexprep(Param.Civ1.ImageB,'.png',''); [fid,errormsg]=fopen([filename '.civ1.cmx'],'w'); if isequal(fid,-1) errormsg=['cmd file ' filename ' cannot be created: ' errormsg]; return end fprintf(fid,['############## CMX file' '\n' ]); fprintf(fid, ['FirstImage ' regexprep(Param.Civ1.ImageA,'\\','\\\\') '\n' ]);% for windows compatibility fprintf(fid, ['LastImage ' regexprep(Param.Civ1.ImageB,'\\','\\\\') '\n' ]);% for windows compatibility fprintf(fid, ['XX' '\n' ]); if isfield(Param.Civ1,'Mask') fprintf(fid, ['Mask ' 'y' '\n' ]); fprintf(fid, ['MaskName ' regexprep(Param.Civ1.Mask,'\\','\\\\') '\n' ]); else fprintf(fid, ['Mask ' 'n' '\n' ]); fprintf(fid, ['MaskName ' 'noFile use default' '\n' ]); end fprintf(fid, ['ImageSize ' num2str(Param.Civ1.ImageWidth) ' ' num2str(Param.Civ1.ImageHeight) '\n' ]); %VERIFIER CAS GENERAL ? fprintf(fid, ['CorrelationBoxesSize ' num2str(Param.Civ1.Bx) ' ' num2str(Param.Civ1.By) '\n' ]); fprintf(fid, ['SearchBoxeSize ' num2str(Param.Civ1.Searchx) ' ' num2str(Param.Civ1.Searchy) '\n' ]); fprintf(fid, ['RO ' num2str(Param.Civ1.Rho) '\n' ]); if isfield(Param.Civ1,'Grid') fprintf(fid, ['GridSpacing ' '25' ' ' '25' '\n' ]); else fprintf(fid, ['GridSpacing ' num2str(Param.Civ1.Dx) ' ' num2str(Param.Civ1.Dy) '\n' ]); end fprintf(fid, ['XX 1.0' '\n' ]); fprintf(fid, ['Dt_TO ' num2str(Param.Civ1.Dt) ' ' num2str(Param.Civ1.Time) '\n' ]); fprintf(fid, ['PixCmXY ' '1' ' ' '1' '\n' ]); fprintf(fid, ['XX 1' '\n' ]); fprintf(fid, ['ShiftXY ' num2str(Param.Civ1.Shiftx) ' ' num2str(Param.Civ1.Shifty) '\n' ]); if isfield(Param.Civ1,'Grid') fprintf(fid, ['Grid ' 'y' '\n' ]); fprintf(fid, ['GridName ' regexprep(Param.Civ1.Grid,'\\','\\\\') '\n' ]); else fprintf(fid, ['Grid ' 'n' '\n' ]); fprintf(fid, ['GridName ' 'noFile use default' '\n' ]); end fprintf(fid, ['XX 85' '\n' ]); fprintf(fid, ['XX 1.0' '\n' ]); fprintf(fid, ['XX 1.0' '\n' ]); fprintf(fid, ['Hart 1' '\n' ]); fprintf(fid, [ 'DecimalShift 0' '\n' ]); fprintf(fid, ['Deformation 0' '\n' ]); fprintf(fid, ['CorrelationMin 0' '\n' ]); fprintf(fid, ['IntensityMin 0' '\n' ]); if ~isfield(Param.Civ1,'MinIma')% Image threshold not activated fprintf(fid, ['SeuilImage n' '\n' ]); fprintf(fid, ['SeuilImageValues 0 4096' '\n' ]);%not used in principle else% Image threshold activated if isempty(Param.Civ1.MaxIma)||isnan(Param.Civ1.MaxIma) Param.Civ1.MaxIma=2^Param.Civ1.ImageBitDepth;%take the max image value as upper bound by default end fprintf(fid, ['SeuilImage y' '\n' ]); fprintf(fid, ['SeuilImageValues ' num2str(Param.Civ1.MinIma) ' ' num2str(Param.Civ1.MaxIma) '\n' ]); end fprintf(fid, ['ImageToUse ' Param.Civ1.term_a ' ' Param.Civ1.term_b '\n' ]); % VERIFIER ? fprintf(fid, ['ImageUsedBefore null null' '\n' ]); fclose(fid); if(isunix) %unix (or Mac) system cmd=['cp -f ' filename '.civ1.cmx ' filename '.cmx \n '];% the cmx file gives the name to the nc file cmd=[cmd Param.xml.Civ1Bin ' -f ' filename '.cmx >' filename '.civ1.log \n ' ]; % redirect standard output to the log file, the result file is named [filename '.nc'] by CIVx cmd=[cmd 'rm ' filename '.cmx']; else %Windows system filename=regexprep(filename,'\\','\\\\'); cmd=['copy /Y "' filename '.civ1.cmx" "' filename '.cmx" \n ']; cmd=[cmd '"' regexprep(Param.xml.Civ1Bin,'\\','\\\\')... '" -f "' filename '.cmx" >"' filename '.civ1.log" \n ' ]; % redirect standard output to the log file cmd=[cmd 'del "' filename '.cmx"']; end function cmd=cmd_fix(filename,Param,fixname) %% switch fixname case 'Fix1' fi2_value=num2str(Param.(fixname).CheckF2); case 'Fix2' fi2_value=num2str(Param.(fixname).CheckF4);%need to understand why... end filename=regexprep(filename,'.nc',''); MaskName_string='';%default MaxVel_string='';%default if ~isempty(Param.(fixname).MinVel) MaxVel_string=[' -threshV ' num2str(Param.(fixname).MinVel)]; end if isunix cmd=[Param.xml.FixBin ' -f ' filename '.nc -fi1 ' num2str(Param.(fixname).CheckFmin2) ... ' -fi2 ' fi2_value ' -fi3 ' num2str(Param.(fixname).CheckF3) ... ' -threshC ' num2str(Param.(fixname).MinCorr) MaxVel_string MaskName_string... ' >' filename '.' lower(fixname) '.log 2>&1']; else cmd=['"' Param.xml.FixBin '" -f "' filename '.nc" -fi1 ' num2str(Param.(fixname).CheckFmin2)... ' -fi2 ' fi2_value ' -fi3 ' num2str(Param.(fixname).CheckF3) ... ' -threshC ' num2str(Param.(fixname).MinCorr) MaxVel_string MaskName_string... ' > "' filename '.' lower(fixname) '.log"']; cmd=regexprep(cmd,'\\','\\\\'); end function cmd=cmd_patch(filename,Param,patchname) %% ------------------------------------------------------------------------ filename=regexprep(filename,'.nc',''); if isunix cmd=[Param.xml.PatchBin... ' -f ' filename '.nc -m ' num2str(Param.(patchname).Nx)... ' -n ' num2str(Param.(patchname).Ny) ' -ro ' num2str(Param.(patchname).SmoothingParam)... ' -nopt ' num2str(Param.(patchname).SubdomainSize) ... ' > ' filename '.' lower(patchname) '.log 2>&1']; % redirect standard output to the log file else cmd=['"' Param.xml.PatchBin... '" -f "' filename '.nc" -m ' num2str(Param.(patchname).Nx)... ' -n ' num2str(Param.(patchname).Ny) ' -ro ' num2str(Param.(patchname).SmoothingParam)... ' -nopt ' num2str(Param.(patchname).SubdomainSize)... ' > "' filename '.' lower(patchname) '.log" 2>&1']; % redirect standard output to the log file cmd=regexprep(cmd,'\\','\\\\'); end %------------------------------------------------------------------------ % --- CheckCiv2 CheckCiv2 CheckCiv2 CheckCiv2 function [cmd,errormsg]=cmd_civ2(filename,Param) %------------------------------------------------------------------------ %pixels per cm and matrix of the image times, read from the .civ file by uvmat % global civ2Bin sge%name of the executable for checkciv1 calculation cmd=''; filename=regexprep(filename,'.nc',''); if isequal(Param.Civ2.Dt,'0') Param.Civ2.Dt='1' ;%case of 'displacement' mode end Param.Civ2.ImageA=regexprep(Param.Civ2.ImageA,'.png',''); Param.Civ2.ImageB=regexprep(Param.Civ2.ImageB,'.png','');% bug : .png appears two times ? [fid,errormsg]=fopen([filename '.civ2.cmx'],'w'); if isequal(fid,-1) return end fprintf(fid,['############## CMX file' '\n' ]); fprintf(fid, ['FirstImage ' regexprep(Param.Civ2.ImageA,'\\','\\\\') '\n' ]);% for windows compatibility fprintf(fid, ['LastImage ' regexprep(Param.Civ2.ImageB,'\\','\\\\') '\n' ]);% for windows compatibility fprintf(fid, ['XX' '\n' ]); if isfield(Param.Civ2,'Mask') fprintf(fid, ['Mask ' 'y' '\n' ]); fprintf(fid, ['MaskName ' regexprep(Param.Civ2.Mask,'\\','\\\\') '\n' ]); else fprintf(fid, ['Mask ' 'n' '\n' ]); fprintf(fid, ['MaskName ' 'noFile use default' '\n' ]); end % fprintf(fid, ['Mask ' Param.Civ2.MaskFlag '\n' ]); % fprintf(fid, ['MaskName ' regexprep(Param.Civ2.MaskName,'\\','\\\\') '\n' ]);% for windows compatibility fprintf(fid, ['ImageSize ' num2str(Param.Civ2.ImageWidth) ' ' num2str(Param.Civ2.ImageHeight) '\n' ]); % fprintf(fid, ['ImageSize ' num2str(Param.Civ2.npx) ' ' num2str(Param.Civ2.npy) '\n' ]); %VERIFIER CAS GENERAL ? fprintf(fid, ['CorrelationBoxesSize ' num2str(Param.Civ2.Bx) ' ' num2str(Param.Civ2.By) '\n' ]); fprintf(fid, ['SearchBoxeSize ' num2str(Param.Civ2.Bx) ' ' num2str(Param.Civ2.By) '\n']); fprintf(fid, ['RO ' num2str(Param.Civ2.Rho) '\n']); if isfield(Param.Civ2,'Grid') fprintf(fid, ['GridSpacing ' '25' ' ' '25' '\n' ]); else fprintf(fid, ['GridSpacing ' num2str(Param.Civ2.Dx) ' ' num2str(Param.Civ2.Dy) '\n' ]); end % fprintf(fid, ['GridSpacing ' num2str(Param.Civ2.Dx) ' ' num2str(Param.Civ2.Dy) '\n']); fprintf(fid, ['XX 1.0' '\n' ]); fprintf(fid, ['Dt_TO ' num2str(Param.Civ2.Dt) ' ' num2str(Param.Civ2.Time) '\n' ]); fprintf(fid, ['PixCmXY ' '1' ' ' '1' '\n' ]); fprintf(fid, ['XX 1' '\n' ]); fprintf(fid, 'ShiftXY 0 0\n'); if isfield(Param.Civ2,'Grid') fprintf(fid, ['Grid ' 'y' '\n' ]); fprintf(fid, ['GridName ' regexprep(Param.Civ2.Grid,'\\','\\\\') '\n' ]); else fprintf(fid, ['Grid ' 'n' '\n' ]); fprintf(fid, ['GridName ' 'noFile use default' '\n' ]); end % fprintf(fid, ['Grid ' Param.Civ2.GridFlag '\n' ]); % fprintf(fid, ['GridName ' regexprep(Param.Civ2.GridName,'\\','\\\\') '\n']); fprintf(fid, ['XX 85' '\n' ]); fprintf(fid, ['XX 1.0' '\n' ]); fprintf(fid, ['XX 1.0' '\n' ]); fprintf(fid, ['Hart 1' '\n' ]); fprintf(fid, ['DecimalShift ' num2str(Param.Civ2.CheckDecimal) '\n']); fprintf(fid, ['Deformation ' num2str(Param.Civ2.CheckDeformation) '\n']); fprintf(fid, ['CorrelationMin 0' '\n' ]); fprintf(fid, ['IntensityMin 0' '\n' ]); if ~isfield(Param.Civ2,'MinIma')% Image threshold not activated fprintf(fid, ['SeuilImage n' '\n' ]); fprintf(fid, ['SeuilImageValues 0 4096' '\n' ]);%not used in principle else% Image threshold activated if isempty(Param.Civ2.MaxIma)||isnan(Param.Civ2.MaxIma) Param.Civ2.MaxIma=2^Param.Civ2.ImageBitDepth;%take the max image value as upper bound by default end fprintf(fid, ['SeuilImage y' '\n' ]); fprintf(fid, ['SeuilImageValues ' num2str(Param.Civ2.MinIma) ' ' num2str(Param.Civ2.MaxIma) '\n' ]); end fprintf(fid, ['ImageToUse ' Param.Civ2.term_a ' ' Param.Civ2.term_b '\n' ]); % VERIFIER ? fprintf(fid, ['ImageUsedBefore ' regexprep(Param.Civ2.filename_nc1,'\\','\\\\') '\n']); fclose(fid); if(isunix) cmd=['cp -f ' filename '.civ2.cmx ' filename '.cmx\n'... Param.xml.Civ2Bin ' -f ' filename '.cmx >' filename '.civ2.log \n '... % redirect standard output to the log file, the result file is named [filename '.nc'] by CIVx 'rm ' filename '.cmx \n'];%rename .cmx as .checkciv2.cmx, the result file is named [filename '.nc'] by CIVx else filename=regexprep(filename,'\\','\\\\'); cmd=['copy /Y "' filename '.civ2.cmx" "' filename '.cmx" \n'... '"' regexprep(Param.xml.Civ2Bin,'\\','\\\\') '" -f "' filename '.cmx" >"' filename '.civ2.log" \n'... 'del "' filename '.cmx" \n']; end %------------------------------------------------------------------------ % --- CheckCiv1 Unified: TO ABADON function xml_civ1_parameters=CIV1_CMD_Unified(filename,namelog,par) %------------------------------------------------------------------------ %pixels per cm and matrix of the image times, read from the .civ file by uvmat %global CivBin%name of the executable for checkciv1 calculation civ1.image1=par.ImageA; civ1.image2=par.ImageB; civ1.imageSize_X=par.npx; civ1.imageSize_Y=par.npy; civ1.outputFileName=[filename '.nc']; civ1.correlationBoxesSize_X=par.ibx; civ1.correlationBoxesSize_Y=par.iby; civ1.searchBoxesSize_X=par.isx; civ1.searchBoxesSize_Y=par.isy; civ1.globalShift_X=par.shiftx; civ1.globalShift_Y=par.shifty; civ1.ro=par.rho; civ1.hart='y'; if isequal(par.gridflag,'y') civ1.grid=par.gridname; else civ1.grid='n'; civ1.gridSpacing_X=par.dx; civ1.gridSpacing_Y=par.dy; end if isequal(par.maskflag,'y') civ1.mask=par.maskname; end civ1.dt=par.Dt; civ1.unit='pixel'; civ1.absolut_time_T0=par.Time; civ1.pixcmx='1'; civ1.pixcmy='1'; civ1.convectFlow='n'; xml_civ1_parameters=civ1; %------------------------------------------------------------------------ % --- CheckCiv2 Unified: TO ABADON function civ2=CIV2_CMD_Unified(filename,namelog,par) %------------------------------------------------------------------------ %pixels per cm and matrix of the image times, read from the .civ file by uvmat %global CivBin%name of the executable for checkciv1 calculation filename=regexprep(filename,'.nc',''); civ2.image1=par.ImageA; civ2.image2=par.ImageB; civ2.imageSize_X=par.npx; civ2.imageSize_Y=par.npy; civ2.inputFileName=[par.filename_nc1 '.nc']; civ2.outputFileName=[filename '.nc']; civ2.correlationBoxesSize_X=par.ibx; civ2.correlationBoxesSize_Y=par.iby; civ2.ro=par.rho; %checkciv2.decimalShift=par.CheckDecimal; %checkciv2.CheckDeformation=par.CheckDeformation; if isequal(par.decimal,'1') civ2.decimalShift='y'; else civ2.decimalShift='n'; end if isequal(par.deformation,'1') civ2.deformation='y'; else civ2.deformation='n'; end if isequal(par.gridflag,'y') civ2.grid=par.gridname; else civ2.grid='n'; civ2.gridSpacing_X=par.dx; civ2.gridSpacing_Y=par.dy; end civ2.gridSpacing_X='10'; civ2.gridSpacing_Y='10';%NOTE: faut mettre gridSpacing pourque ca tourne, meme si c'est la grille qui est utilisee if isequal(par.maskflag,'y') civ2.mask=par.maskname; else civ2.mask='n'; end civ2.dt=par.Dt; civ2.unit='pixel'; civ2.absolut_time_T0=par.Time; civ2.pixcmx='1'; civ2.pixcmy='1'; civ2.convectFlow='n'; % --- Executes on button press in TestPatch1. function TestPatch1_Callback(hObject, eventdata, handles) set(handles.TestPatch1,'BackgroundColor',[1 1 0]) drawnow if get(handles.TestPatch1,'Value') ref_i=str2double(get(handles.ref_i,'String')); if strcmp(get(handles.ref_j,'Visible'),'on') ref_j=str2double(get(handles.ref_j,'String')); else ref_j=1;%default end [filecell,i1,i21,j1,j2,i1_civ2,i2_civ2,j1_civ2,j2_civ2,nom_type_nc,file_ref_fix1,file_ref_fix2]=... set_civ_filenames(handles,ref_i,ref_j,[0 0 1 0 0 0]); Data.ListVarName={'ny','nx','A'}; Data.VarDimName= {'ny','nx',{'ny','nx'}}; param_patch1=read_GUI(handles.Patch1); param_patch1.CivFile=filecell.nc.civ1{1}; Param.Patch1=param_patch1; for irho=1:7 [Data,errormsg]=civ_matlab(Param);% get the grid of x, y positions set for PIV if ~isempty(errormsg) msgbox_uvmat('ERROR',errormsg) return end SmoothingParam(irho)=Param.Patch1.SmoothingParam; Data.Civ1_U_Diff=Data.Civ1_U_Diff(Data.Civ1_FF==0); Data.Civ1_V_Diff=Data.Civ1_V_Diff(Data.Civ1_FF==0); DiffVel(irho)=sqrt(mean(Data.Civ1_U_Diff.*Data.Civ1_U_Diff+Data.Civ1_V_Diff.*Data.Civ1_V_Diff)) NbSites(irho,:)=Data.Civ1_NbSites*numel(Data.Civ1_NbSites)/numel(Data.Civ1_U_Diff); Param.Patch1.SmoothingParam=2*Param.Patch1.SmoothingParam; end figure plot(SmoothingParam,DiffVel,'b',SmoothingParam,NbSites,'r') set(handles.TestPatch1,'BackgroundColor',[1 0 0]) else corrfig=findobj(allchild(0),'tag','corrfig');% look for a current figure for image correlation display if ~isempty(corrfig) delete(corrfig) end hview_field=findobj(allchild(0),'tag','view_field');% look for view_field if ~isempty(hview_field) delete(hview_field) end end %'nomtype2pair': creates nomencalture for index pairs knowing the image nomenclature %--------------------------------------------------------------------- % [nom_type_pair]=nomtype2pair(nom_type,Dti,Dtj); %--------------------------------------------------------------------- % OUTPUT: %nom_type_nc %--------------------------------------------------------------------- % INPUT: % 'nom_type': string defining the kind of nomenclature used: %nom_type='': constant name [filebase ext] (default output if 'nom_type' is undefined) %nom_type='*': the same file [filebase ext] contains successive fields (ex avi movies) %nom_type='_i': series of files with a single index i preceded by '_'(e.g. 'aa_45.png'). %nom_type='#' series of indexed images wich is not series_i [filebase index ext], e.g. 'aa045.jpg' or 'aa45.tif' %nom_type='_i_j' matrix of files with two indices i and j separated by '_'(e.g. 'aa_45_2.png') %nom_type='_i1-i2' from pairs from a single index (e.g. 'aa_45-47.nc') %nom_type='_i_j1-j2'pairs of j indices (e.g. 'aa_45_2-3.nc') %nom_type='_i1-i2_j' pairs of i indices (e.g. 'aa_45-46_2.nc') %nom_type='#a','#A', with a numerical index and an index letter(e.g.'aa045b.png'), OBSOLETE (replaced by 'series_i_j') %nom_type='%03d' or '%04d', series of indexed images with numbers completed with zeros to 3 or 4 digits, e.g.'aa045.tif' %nom_type='_%03d', '_%04d', or '_%05d', series of indexed images with _ and numbers completed with zeros to 3, 4 or 5 digits, e.g.'aa_045.tif' %nom_type='raw_SMD', same as '#a' but with no extension ext='', OBSOLETE %nom_type='#_ab' from pairs of '#a' images (e.g. 'aa045bc.nc'), ext='.nc', OBSOLETE (replaced by 'netc_2D') %nom_type='%3dab' from pairs of '%3da' images (e.g. 'aa045bc.nc'), ext='.nc', OBSOLETE (replaced by 'netc_2D') % Dti: ~=0 if i index pairs are used % Dtj: ~=0 if i index pairs are used function NomTypeNc=nomtype2pair(NomTypeIma,mode) %determine nom_type_nc: NomTypeNc=NomTypeIma;%default switch mode case 'pair j1-j2' if ~isempty(regexp(NomTypeIma,'a$')) NomTypeNc=[NomTypeIma 'b']; elseif ~isempty(regexp(NomTypeIma,'A$')) NomTypeNc=[NomTypeIma 'B']; else r=regexp(NomTypeIma,'(?\d+)_(?\d+)$','names'); if ~isempty(r) NomTypeNc='_1_1-2'; end end case 'series(Dj)' r=regexp(NomTypeIma,'(?\d+)_(?\d+)$','names'); if ~isempty(r) NomTypeNc='_1_1-2'; end case 'series(Di)' r=regexp(NomTypeIma,'(?\d+)_(?\d+)$','names'); if ~isempty(r) NomTypeNc='_1-2_1'; else NomTypeNc='_1-2'; end end function NomType_Callback(hObject, eventdata, handles) set(handles.RootPath,'BackgroundColor',[1 1 0])%paint RootName edit box in yellow to indicate that the file input is proceeding RootPath=get(handles.RootPath,'String'); RootFile=get(handles.RootFile,'String'); ref_i=str2num(get(handles.ref_i,'String')); ref_j=str2num(get(handles.ref_j,'String')); NomType=get(handles.NomType,'String'); ImaExt=get(handles.ImaExt,'String'); fileinput=fullfile_uvmat(RootPath,'',RootFile,ImaExt,NomType,ref_i,[],ref_j); errormsg=display_file_name(handles,fileinput); if ~isempty(errormsg) msgbox_uvmat('ERROR',errormsg) end set(handles.RootPath,'BackgroundColor',[1 1 1])%paint RootName back to white to indicate that the file input is finished % --- Executes on selection change in ListProgram. function ListProgram_Callback(hObject, eventdata, handles) ListProgram=get(handles.ListProgram,'String'); Program=ListProgram{get(handles.ListProgram,'value')}; switch Program case 'CivX' set(handles.num_MaxDiff,'Visible','off') set(handles.num_MaxVel,'Visible','off') set(handles.title_MaxVel,'Visible','off') set(handles.num_Nx,'Visible','on') set(handles.num_Ny,'Visible','on') set(handles.title_Nx,'Visible','on') set(handles.title_Ny,'Visible','on') set(handles.title_MaxDiff,'Visible','off') set(handles.num_Rho,'Style','edit') set(handles.num_Rho,'String','1') set(handles.BATCH,'Enable','on') set(handles.CheckThreshold,'Visible','off') set(handles.CheckDeformation,'Value',1) set(handles.CheckDecimal,'Value',1) case 'Matlab' set(handles.num_MaxDiff,'Visible','on') set(handles.num_MaxVel,'Visible','on') set(handles.title_MaxVel,'Visible','on') set(handles.title_MaxDiff,'Visible','on') set(handles.num_Nx,'Visible','off') set(handles.num_Ny,'Visible','off') set(handles.title_Nx,'Visible','off') set(handles.title_Ny,'Visible','off') set(handles.num_Rho,'Style','popupmenu') set(handles.num_Rho,'Value',1) set(handles.num_Rho,'String',{'1';'2'}) set(handles.CheckThreshold,'Visible','on') set(handles.CheckDeformation,'Value',0)% desactivate (work in progress) set(handles.CheckDecimal,'Value',0)% desactivate (work in progress) end % --- Executes on button press in TestCiv2. function TestCiv2_Callback(hObject, eventdata, handles) function RootFile_Callback(hObject, eventdata, handles)