%'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 %======================================================================= % Copyright 2008-2016, LEGI UMR 5519 / CNRS UGA G-INP, Grenoble, France % http://www.legi.grenoble-inp.fr % Joel.Sommeria - Joel.Sommeria (A) legi.cnrs.fr % % This file is part of the toolbox UVMAT. % % UVMAT is free software; you can redistribute it and/or modify % it under the terms of the GNU General Public License as published % by the Free Software Foundation; either version 2 of the license, % or (at your option) any later version. % % UVMAT is distributed in the hope that it will be useful, % but WITHOUT ANY WARRANTY; without even the implied warranty of % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the % GNU General Public License (see LICENSE.txt) for more details. %======================================================================= function varargout = civ(varargin) %TODO: search range % Last Modified by GUIDE v2.5 09-Mar-2013 22:50:23 % 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=fullfile(path_civ,'PARAM.xml'); test_batch=0;%default: ,no batch mode available sparam=[]; if ~exist(xmlfile,'file') [success,message]=copyfile(fullfile(path_civ,'PARAM.xml.default'),xmlfile); end if exist(xmlfile,'file') try t=xmltree(xmlfile); sparam=convert(t); catch ME errormsg={' Unable to read the file PARAM.xml defining the civx binaries:';ME.message}; msgbox_uvmat('WARNING',errormsg); end else [s,w]=system('oarstat'); if ~isequal(s,0) [s,w]=system('qstat'); end if isequal(s,0) test_batch=1; end end if isfield(sparam,'BatchParam') && isfield(sparam.BatchParam,'BatchMode') batch_mode=sparam.BatchParam.BatchMode; test_command=''; switch batch_mode case 'sge' test_command='qstat'; case 'oar' test_command='oarstat'; end if ~isempty(test_command) [s,w]=system(test_command); if isequal(s,0) test_batch=1; end end end RUNVal=get(handles.RunMode,'Value'); if test_batch==0 if RUNVal>2 set(handles.RunMode,'Value',1) end set(handles.RunMode,'String',{'local';'background'}) else set(handles.RunMode,'String',{'local';'background';'cluster'}) 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 Program_Callback([],[], handles) %------------------------------------------------------------------------ % --- 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'); SubDirImages=get(handles.SubDirImages,'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,SubDirImages,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 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 xml file as input, read the civ parameters ind_opening=0;%default if strcmp(ExtInput,'.xml') %reinitialise menus set(handles.ListPairMode,'Value',1) set(handles.ListPairMode,'String',{''}) set(handles.ListPairCiv1,'Value',1) set(handles.ListPairCiv1,'String',{''}) set(handles.ListPairCiv2,'Value',1) set(handles.ListPairCiv2,'String',{''}) Param=xml2struct(fileinput); %read parameters from the xml input file fill_GUI(Param,handles.civ);%fill the GUI with the parameters retrieved from the xml file return end %% case of netcdf file as input, get the civ processing stage and look for a coresponding image imageinput=fileinput;%default if strcmp(ExtInput,'.nc') NomTypeNc=NomTypeInput; if isempty(regexp(NomTypeInput,'[ab|AB|-]', 'once')) set(handles.ListCompareMode,'Value',2) %mode displacement advised if the nomencalture does not involve index pairs set(handles.RootFile_1,'Visible','On'); else set(handles.ListCompareMode,'Value',1) set(handles.RootFile_1,'Visible','Off'); end imageinput=''; 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 % settings for new civ data, if strcmp(Data.Conventions,'uvmat/civdata')% case of new civ data, set(handles.Program,'Value',1) %select civ/Matlab by default Program_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 % settings for civx data, elseif ~isempty(Data.absolut_time_T0')% case of civx data, set(handles.Program,'Value',3) %select Cix by default Program_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 else errormsg='the input netcdf file is not civ data'; return end % look for the corresponding input images check_letter=~isempty(regexp(NomTypeInput,'[ab|AB]$','once'));%detect pair label by letter NomTypeIma=NomTypeInput; if check_letter NomTypeIma=NomTypeInput(1:end-1); else r=regexp(NomTypeIma,'.-(?\d+)$','names'); if ~isempty(r) NomTypeIma=regexprep(NomTypeIma,['-' r.num2],''); end r=regexp(NomTypeIma,'.-(?\d+)','names'); if ~isempty(r) NomTypeIma=regexprep(NomTypeIma,['-' r.num2],''); end end if ~exist(imageinput,'file') imageinput=fullfile_uvmat(RootPath,regexprep(SubDir,'.civ(_?)(\d*)$',''),RootFile,'.png',NomTypeIma,i1,[],j1); 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 if ~exist(imageinput,'file') return %abandon of the browser is cancelled end end %fileinput=imageinput; end %% scan the image file series [FilePath,FileName,ImaExt]=fileparts(imageinput); % 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,SubDirImages,RootFile,i1_series,tild,j1_series,tild,NomTypeIma,FileInfo,MovieObject]=find_file_series(FilePath,[FileName ImaExt]); FileType=FileInfo.FileType; switch FileType case {'image','multimage','video','mmreader'} otherwise errormsg='invalid input file: enter an image, a movie or civ .nc file'; return end set(handles.RootPath,'String',RootPath) set(handles.SubDirImages,'String',SubDirImages) set(handles.RootFile,'String',RootFile) if strcmp(ExtInput,'.nc') SubDirCiv=regexprep(SubDir,['^' SubDirImages],'');%suppress the root SuddirImages; else SubDirCiv= '.civ'; end set(handles.SubdirCiv1,'String',SubDirCiv) set(handles.SubdirCiv2,'String',SubDirCiv) browse=get(handles.RootPath,'UserData'); browse.incr_pair=[0 0];%default %% 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 XmlFileName=find_imadoc(RootPath,SubDir,RootFile,ImaExt); if isempty(XmlFileName) if (strcmp(FileType,'video') || strcmp(FileType,'mmreader')) ext_imadoc=ImaExt;% the timing from the video movie is used else ext_imadoc=''; end else [tild,tild,ext_imadoc]=fileparts(XmlFileName); 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(XmlFileName) set(handles.ImaDoc,'BackgroundColor',[1 1 0]) % set edit box to yellow cloro to indicate that the file reading is beginning drawnow [XmlData,warntext]=imadoc2struct(XmlFileName); nom_type_read=[]; if isfield(XmlData,'Time') && ~isempty(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,'Camera') && isfield(XmlData.Camera,'TimeUnit') TimeUnit=XmlData.Camera.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 end if isempty(time) && (strcmp(FileType,'video') || strcmp(FileType,'mmreader')) set(handles.ListPairMode,'Value',1); dt=1/get(MovieObject,'FrameRate');%time interval between successive frames if strcmp(NomTypeIma,'*') set(handles.ListPairMode,'String',{'series(Di)'}) MaxIndex_i=get(MovieObject,'NumberOfFrames'); %time=(dt*(0:MaxIndex_i-1))';%list of image times time=zeros(MaxIndex_i+1,2); time(:,2)=dt*(0:MaxIndex_i)'; else set(handles.ListPairMode,'String',[{'series(Dj)'};{'series(Di)'}]) MaxIndex_i=max(i1_series(i1_series>0)); MaxIndex_j=get(MovieObject,'NumberOfFrames'); %time=ones(MaxIndex_i,1)*(dt*(0:MaxIndex_j-1));%list of image times time=[0;dt*ones(MaxIndex_j,1)]*(0:MaxIndex_j); enable_j(handles,'on') end TimeUnit='s'; set(handles.ImaDoc,'BackgroundColor',[1 1 1])% set display box back to whiter 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 if size(time,1)MaxIndex_i||num_ref_iMaxIndex_j||num_ref_jMaxIndex_i first_i=num_ref_i; last_i=num_ref_i; set(handles.first_i,'String',num2str(first_i)); set(handles.last_i,'String',num2str(last_i));% end %j index range first_j=str2num(get(handles.first_j,'String')); last_j=str2num(get(handles.last_j,'String')); if isempty(first_j) || isempty(last_j)||isempty(MinIndex_j)||isempty(MaxIndex_j)||ind_opening~=0 || first_jMaxIndex_j first_j=num_ref_j; last_j=num_ref_j; set(handles.first_j,'String',num2str(first_j)); set(handles.last_j,'String',num2str(last_j));% end if num_ref_i>last_i || num_ref_ilast_j || num_ref_j1% 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 elseif ~(strcmp(FileType,'video') || strcmp(FileType,'mmreader')) 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 %% 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.TitleSubdirCiv1,'Visible','on') if opening==0 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.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]) set(handles.RUN,'UserData',now)% record the time of launch errormsg=launch_jobs(hObject, eventdata, handles); 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 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); uicontrol('Style','pushbutton','Units','normalized', 'Position', [0.7 0.01 0.2 0.07],'String','Close','FontWeight','bold','FontUnits','normalized','FontSize',0.9,'Callback',@stop_status); 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 StatusData.time_ref=get(handles.RUN,'UserData');% get the time of launch StatusData.option_civ=option_civ; set(hrefresh,'UserData',StatusData) 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'); StatusData=get(hObject,'UserData'); civ_files=get(hfig,'UserData'); [filepath,filename,ext]=fileparts(civ_files{1}); [tild,SubDir,extdir]=fileparts(filepath); SubDir=[SubDir extdir]; option_civ=StatusData.option_civ; nbfiles=numel(civ_files); testrecent=0; count=0; datnum=zeros(1,nbfiles); filefound=cell(1,nbfiles); for ifile=1:nbfiles detect=exist(civ_files{ifile},'file'); % check the existence of the file option=0; if detect==0 option_str='not created'; else datfile=dir(civ_files{ifile}); if isfield(datfile,'datenum') datnum(ifile)=datfile.datenum;%only available in recent matlab versions testrecent=1; end filefound(ifile)={datfile.name}; % check the content netcdf file Data=nc2struct(civ_files{ifile},'ListGlobalAttribute','CivStage','patch2','fix2','civ2','patch','fix'); option_list={'civ1','fix1','patch1','civ2','fix2','patch2'}; if ~isempty(Data.CivStage) option=Data.CivStage;%case of Matlab civ else if ~isempty(Data.patch2) && isequal(Data.patch2,1) option=6; elseif ~isempty(Data.fix2) && isequal(Data.fix2,1) option=5; elseif ~isempty(Data.civ2) && isequal(Data.civ2,1); option=4; elseif ~isempty(Data.patch) && isequal(Data.patch,1); option=3; elseif ~isempty(Data.fix) && isequal(Data.fix,1); option=2; else option=1; end end option_str=option_list{option}; if datnum(ifile)= 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); message={[num2str(count) ' file(s) done over ' num2str(nbfiles)] ;['oldest modification: ' cell2mat(filefound(ind)) ' : ' datestr(first)];... ['latest modification: ' cell2mat(filefound(indlast)) ' : ' datestr(last)]}; end 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 %------------------------------------------------------------------------ % 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) %------------------------------------------------------------------------ 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([], [], 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=fullfile(path_civ,'PARAM.xml'); s=[]; if exist(xmlfile,'file')% search parameter xml file in the whole matlab path t=xmltree(xmlfile); s=convert(t); end% default configuration if ~isfield(s,'RunParam') Param.xml.Civ1Bin=fullfile('bin','civ1'); Param.xml.Civ2Bin=fullfile('bin','civ2'); Param.xml.FixBin=fullfile('bin','fix_flag'); Param.xml.PatchBin=fullfile('bin','patch_up'); end if strcmp(Param.RunMode,'cluster') %computation dispatched on a cluster 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 %default configuration Param.xml.Civ1Bin=fullfile('bin','civ1'); Param.xml.Civ2Bin=fullfile('bin','civ2'); Param.xml.FixBin=fullfile('bin','fix_flag'); Param.xml.PatchBin=fullfile('bin','patch_up'); % Param.xml.CivmBin=fullfile('bin','civ_matlab'); Param.xml.BatchMode='oar';% TODO : allow choice for sge end else % run if isfield(s,'RunParam') Param.xml=s.RunParam; else %default configuration Param.xml.Civ1Bin=fullfile('bin','civ1'); Param.xml.Civ2Bin=fullfile('bin','civ2'); Param.xml.FixBin=fullfile('bin','fix_flag'); Param.xml.PatchBin=fullfile('bin','patch_up'); end end %Param.xml.CivmBin=fullfile('bin','civ_matlab'); %% check if the binaries exist : to move in civ_opening binary_list={}; switch Param.Program case 'CivX' binary_list={'Civ1Bin','Civ2Bin','PatchBin','FixBin'}; case 'CivAll'% desactivated option binary_list={'Civ'}; % case 'civ_matlab.sh'% compiled version of civ_matlab % binary_list={'CivmBin'}; 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 ~isunix Param.xml.(bin_name{1})=[regexprep(Param.xml.(bin_name{1}),'/','\') '.exe']; end if exist(Param.xml.(bin_name{1}),'file') [path,name,ext]=fileparts(Param.xml.(bin_name{1})); currentdir=pwd; if isempty(path) path=fileparts(which('civ.m')); end 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 specified 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}) ' specified in PARAM.xml does not exist']; return end end end end if strcmp(Param.Program,'civ_matlab.sh') if ~exist(fullfile(path_civ,'civ_matlab.sh'),'file') errormsg=[{'no file civ_matlab.sh found'}; {'run compile_functions.m to create it by compiling civ_matlab.m'}]; return end end %% 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,tild,tild,compare,errormsg]=... set_civ_filenames(handles,ref_i,ref_j,box_test); if ~isempty(errormsg) return end set(handles.civ,'UserData',filecell);%store for futur use of status callback display('files OK, processing...') %% create subfolders for log, cmx, nml, xml, bat RootBat=fileparts(filecell.nc.civ1{1,1}); switch(Param.Program) case {'CivX','CivAll'} dir_list={'0_BAT','0_CMX','0_LOG'}; case {'civ_matlab','civ_matlab.sh'} dir_list={'0_BAT','0_XML'}; end for k=1:length(dir_list) if ~exist(fullfile(RootBat,dir_list{k}),'dir') mkdir(fullfile(RootBat,dir_list{k})); end end %% get information on input images or movies nbfield=numel(i1_civ1); nbslice=numel(j1_civ1); % if strcmp(Param.Program,'civ_matlab') if Param.CheckCiv1 [ImageInfoA_civ1,Param.Civ1.ImageA]=get_file_info(filecell.ima1.civ1{1}); Param.Civ1.FileTypeA=ImageInfoA_civ1.FileType; [ImageInfoB_civ1,Param.Civ1.ImageB]=get_file_info(filecell.ima2.civ1{1}); Param.Civ1.FileTypeB=ImageInfoB_civ1.FileType; end if Param.CheckCiv2 [ImageInfoA_civ2,Param.Civ2.ImageA]=get_file_info(filecell.ima1.civ2{1}); Param.Civ2.FileTypeA=ImageInfoA_civ2.FileType; [ImageInfoB_civ2,Param.Civ2.ImageB]=get_file_info(filecell.ima2.civ2{1}); Param.Civ2.FileTypeB=ImageInfoB_civ2.FileType; 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 NomTypeIma=get(handles.NomType,'String'); for ifile=1:nbfield for j=1:nbslice % define output file name if Param.CheckCiv2==1 || Param.CheckFix2==1 || Param.CheckPatch2==1 Param.OutputFile=filecell.nc.civ2{ifile,j}; else Param.OutputFile=filecell.nc.civ1{ifile,j}; end Param.OutputFile=regexprep(Param.OutputFile,'.nc',''); if Param.CheckCiv1 % read image-dependent parameters 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(Param.Program,'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 Param.Civ1.ImageA=filecell.ima1.civ1{ifile,j}; Param.Civ1.ImageB=filecell.ima2.civ1{ifile,j}; Param.Civ1.ImageBitDepth=ImageInfoA_civ1.BitDepth; Param.Civ1.ImageWidth=ImageInfoA_civ1.Width; Param.Civ1.ImageHeight=ImageInfoA_civ1.Height; if strcmp(NomTypeIma,'*') Param.Civ1.FrameIndexA=i1_civ1(ifile); Param.Civ1.FrameIndexB=i2_civ1(ifile); else% case of movies indexed with i, the frame index is then in j Param.Civ1.FrameIndexA=j1_civ1(j); Param.Civ1.FrameIndexB=j2_civ1(j); end % 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)]; 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 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(Param.Program,'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 Param.Civ2.ImageBitDepth=ImageInfoA_civ2.BitDepth; Param.Civ2.ImageWidth=ImageInfoA_civ2.Width; Param.Civ2.ImageHeight=ImageInfoA_civ2.Height; if strcmp(NomTypeIma,'*') Param.Civ2.FrameIndexA=i1_civ2(ifile); Param.Civ2.FrameIndexB=i2_civ2(ifile); else% case of movies indexed with i, the frame index is then in j Param.Civ2.FrameIndexA=j1_civ2(j); Param.Civ2.FrameIndexB=j2_civ2(j); end end % write the command and eventually the cmx, xml or nml files cmd=write_cmd(Param); write_param(Param); % create the command file name .m, .bat or .sh depending on the run option switch Param.Program case {'civ_matlab'} filename_bat=regexprep(Param.OutputFile,'(.+)([/\\])(.+$)','$1$20_BAT$2$3.m'); [BatRoot,BatFile]=fileparts(filename_bat); BatFile=regexprep(BatFile,'-','__');%transform name to suppress'-' (not valid for .m files) filename_bat=[fullfile(BatRoot,BatFile) '.m']; case {'CivX','CivAll','civ_matlab.sh'} switch computer case {'PCWIN','PCWIN64'} filename_bat=regexprep(Param.OutputFile,'(.+)([/\\])(.+$)','$1$20_BAT$2$3.bat'); case {'GLNX86','GLNXA64','MACI64'} filename_bat=regexprep(Param.OutputFile,'(.+)([/\\])(.+$)','$1$20_BAT$2$3.sh'); end end % print the command in the bat file [fid,message]=fopen(filename_bat,'w'); if isequal(fid,-1) errormsg=['creation of .bat file: ' message]; return end fprintf(fid,cmd); fclose(fid); % special case for civ_matlab on cluster if strcmp(Param.Program,'civ_matlab') && strcmp(Param.RunMode,'cluster') filename_bat2=regexprep(Param.OutputFile,'(.+)([/\\])(.+$)','$1$20_BAT$2$3.sh'); [fid,message]=fopen(filename_bat2,'w'); if isequal(fid,-1) errormsg=['creation of .bat file: ' message]; return end fprintf(fid,['#!/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"\n']; filename_oarcommand=fullfile(RootBat,'oar_command'); fid=fopen(filename_oarcommand,'w'); fprintf(fid,oar_command); fclose(fid); fprintf(oar_command);% display in command line system(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=1800; % 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 case {'background','local'} switch Param.Program case {'civ_matlab'} switch Param.RunMode case 'background' switch computer case {'PCWIN','PCWIN64'} 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 fprintf(fid,['matlab -automation '... '-r "addpath(''' regexprep(path_civ,'\\','\\\\') ''');']); for p=1:length(batch_file_list) fprintf(fid,['run ' regexprep(batch_file_list{p},'\\','\\\\') ';']); end fprintf(fid, 'exit"'); fclose(fid); dos([filename_superbat ' &']); case {'GLNX86','GLNXA64','MACI64'} filename_superbat=fullfile(RootBat,'job_list.sh'); fid=fopen(filename_superbat,'w'); if fid==-1 msgbox_uvmat('ERROR',['cannot create the command file ' filename_superbat]) return end fprintf(fid,['#!/bin/bash \n' ... '/etc/sysprofile \n'... 'matlab -nodisplay -nosplash -nojvm -logfile <.*\D)(?\d+)$','names');%detect whether name ends by a number if isempty(r) r(1).root=[subdir_civ1_new '_']; r(1).num1='0'; end subdir_civ1_new=[r(1).root num2str(str2num(r(1).num1)+1)];%increment the index by 1 or put 1 subdir_civ2=subdir_civ1_new; end break end filecell.nc.civ1(ifile,j)={filename}; end if detect% if a netcdf file already exists break end end %create the new SubdirCiv1 if ~exist(fullfile(RootPath,subdir_civ1_new),'dir') [xx,msg1]=mkdir(fullfile(RootPath,subdir_civ1_new)); if ~strcmp(msg1,'') errormsg=['cannot create ' subdir_civ1_new ': ' msg1];%error message for directory creation return elseif isunix [xx,msg2] = fileattrib(fullfile(RootPath,subdir_civ1_new),'+w','g'); %yield writing access (+w) to user group (g) if ~strcmp(msg2,'') errormsg=['pb of permission for ' fullfile(RootPath,subdir_civ1_new) ': ' msg2];%error message for directory creation return end end end if strcmp(compare,'stereo PIV')&&(strcmp(mode,'pair j1-j2')||strcmp(mode,'series(Dj)')||strcmp(mode,'series(Di)'))%check second nc series for ifile=1:nbfield for j=1:nbslice filename=fullfile_uvmat(RootPath,subdir_civ1_new,RootFile_A,'.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)1 check_j=1; NomType_imanew1='_1_1'; else NomType_imanew1='_1'; end end h = waitbar(0,'copy images to the .png format for civ1');% display a wait bar for ifile=1:nbfield waitbar(ifile/nbfield); for j=1:nbslice filename=fullfile_uvmat(RootPath,SubDirImages,RootFile_ima1,'.png',NomType_imanew1,i1_civ1(ifile),[],j1_civ1(j)); if ~exist(filename,'file') if check_j A=read_image(filecell.ima1.civ1{ifile,j},FileType,MovieObject,j1_civ1(j)); else A=read_image(filecell.ima1.civ1{ifile,j},FileType,MovieObject,i1_civ1(ifile)); end imwrite(uint16(sum(A,3)),filename,'BitDepth',16); end filecell.ima1.civ1(ifile,j)={filename}; filename=fullfile_uvmat(RootPath,SubDirImages,RootFile_ima2,'.png',NomType_imanew1,i2_civ1(ifile),[],j2_civ1(j)); if ~exist(filename,'file') if check_j A=read_image(filecell.ima1.civ1{ifile,j},FileType,MovieObject,j2_civ1(j)); else A=read_image(filecell.ima1.civ1{ifile,j},FileType,MovieObject,i2_civ1(ifile)); end imwrite(uint16(sum(A,3)),filename,'BitDepth',16); end filecell.ima2.civ1(ifile,j)={filename}; end end close(h) end if checkbox(4) %if civ2 is performed [FileInfo,MovieObject]=get_file_info(filecell.ima1.civ2{1}); FileType=FileInfo.FileType; check_j=0; if strcmp(FileType,'mmreader')||strcmp(FileType,'VideoReader')||strcmp(FileType,'multimage') if max(j1_civ2)>1 check_j=1; NomType_imanew1='_1_1'; else NomType_imanew1='_1'; end end h = waitbar(0,'copy images to the .png format for civ2');% display a wait bar for ifile=1:nbfield waitbar(ifile/nbfield); for j=1:nbslice filename=fullfile_uvmat(RootPath,SubDirImages,RootFile_ima1,'.png',NomType_imanew1,i1_civ2(ifile),[],j1_civ2(j)); if ~exist(filename,'file') if check_j A=read_image(filecell.ima1.civ1{ifile,j},FileType,MovieObject,j1_civ2(j)); else A=read_image(filecell.ima1.civ1{ifile,j},FileType,MovieObject,i1_civ2(ifile)); end imwrite(uint16(sum(A,3)),filename,'BitDepth',16); end filecell.ima1.civ2(ifile,j)={filename}; filename=fullfile_uvmat(RootPath,SubDirImages,RootFile_ima2,'.png',NomType_imanew2,i2_civ2(ifile),[],j2_civ2(j)); if ~exist(filename,'file') if check_j A=read_image(filecell.ima1.civ1{ifile,j},FileType,MovieObject,j1_civ2(j)); else A=read_image(filecell.ima1.civ1{ifile,j},FileType,MovieObject,i1_civ2(ifile)); end imwrite(uint16(sum(A,3)),filename,'BitDepth',16); end filecell.ima2.civ2(ifile,j)={filename}; end end close(h); end end end %------------------------------------------------------------------------ % --- determine the list of index pairs of processing file function [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) %------------------------------------------------------------------------ list_civ1=get(handles.ListPairCiv1,'String'); index_civ1=get(handles.ListPairCiv1,'Value'); str_civ1=list_civ1{index_civ1};%string defining the image pairs for civ1 if isempty(str_civ1)||isequal(str_civ1,'') msgbox_uvmat('ERROR','no image pair selected for civ1') return end list_civ2=get(handles.ListPairCiv2,'String'); index_civ2=get(handles.ListPairCiv2,'Value'); if index_civ2>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')); i1_civ1=ref_i-floor(index_civ1/2)*ones(size(ref_i));% set of first image numbers i2_civ1=ref_i+ceil(index_civ1/2)*ones(size(ref_i)); j1_civ1=ref_j; j2_civ1=ref_j; i1_civ2=ref_i-floor(index_civ2/2)*ones(size(ref_i)); i2_civ2=ref_i+ceil(index_civ2/2)*ones(size(ref_i)); j1_civ2=ref_j; j2_civ2=ref_j; % adjust the first and last field number lastfield=str2double(get(handles.nb_field,'String')); if isnan(lastfield) indsel=find((i1_civ1 >= 1)&(i1_civ2 >= 1)); else indsel=find((i2_civ1 <= lastfield)&(i2_civ2 <= lastfield)&(i1_civ1 >= 1)&(i1_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); i1_civ1=i1_civ1(indsel); i1_civ2=i1_civ2(indsel); i2_civ1=i2_civ1(indsel); i2_civ2=i2_civ2(indsel); end elseif isequal (mode,'series(Dj)') lastfield_j=str2double(get(handles.nb_field2,'String')); i1_civ1=ref_i;% set of first image numbers i2_civ1=ref_i; j1_civ1=ref_j-floor(index_civ1/2)*ones(size(ref_j)); j2_civ1=ref_j+ceil(index_civ1/2)*ones(size(ref_j)); i1_civ2=ref_i; i2_civ2=ref_i; j1_civ2=ref_j-floor(index_civ2/2)*ones(size(ref_j)); j2_civ2=ref_j+ceil(index_civ2/2)*ones(size(ref_j)); % adjust the first and last field number if isnan(lastfield_j) indsel=find((j1_civ1 >= 1)&(j1_civ2 >= 1)); else indsel=find((j2_civ1 <= lastfield_j)&(j2_civ2 <= lastfield_j)&(j1_civ1 >= 1)&(j1_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); j1_civ1=j1_civ1(indsel); j2_civ1=j2_civ1(indsel); j1_civ2=j1_civ2(indsel); j2_civ2=j2_civ2(indsel); end elseif isequal(mode,'pair j1-j2') %case of bursts (png_old or png_2D) displ_num=get(handles.ListPairCiv1,'UserData'); i1_civ1=ref_i; i2_civ1=ref_i; j1_civ1=displ_num(1,index_civ1); j2_civ1=displ_num(2,index_civ1); i1_civ2=ref_i; i2_civ2=ref_i; j1_civ2=displ_num(1,index_civ2); j2_civ2=displ_num(2,index_civ2); elseif isequal(mode,'displacement') i1_civ1=ref_i; i2_civ1=ref_i; j1_civ1=ref_j; j2_civ1=ref_j; i1_civ2=ref_i; i2_civ2=ref_i; j1_civ2=ref_j; j2_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')}; switch option case 'PIV' 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,'Visible','on') set(handles.ListPairMode,'Value',1) set(handles.ListPairMode,'String',mode_store) set(handles.CheckStereo,'Value',0) case 'PIV volume' 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,'Visible','on') set(handles.ListPairMode,'Value',1) set(handles.ListPairMode,'String',{'series(Di)'}) set(handles.CheckStereo,'Value',0) set(handles.last_j,'String',get(handles.nb_field2,'String'))% select the whole volume scan by default set(handles.incr_i,'String',num2str(2))% otherwise 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,FileInfo,Object,i1,i2,j1,j2]=find_file_series(FilePath,[FileName Ext]); FileType=FileInfo.FileType; %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); 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'); 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')); num_i=first_i:incr_i:last_i; lastfield=str2double(get(handles.nb_field,'String')); if ~isnan(lastfield) test_find=(num_i-floor(index_pair/2)*ones(size(num_i))>0)& ... (num_i+ceil(index_pair/2)*ones(size(num_i))<=lastfield); num_i=num_i(test_find); end set(handles.first_i,'String',num2str(num_i(1))); set(handles.last_i,'String',num2str(num_i(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); num_j=num_j(test_find); end set(handles.first_j,'String',num2str(num_j(1))); set(handles.last_j,'String',num2str(num_j(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')); num_i=first_i:incr_i:last_i; lastfield=str2double(get(handles.nb_field,'String')); if ~isnan(lastfield) test_find=(num_i-floor(index_pair/2)*ones(size(num_i))>0)& ... (num_i+ceil(index_pair/2)*ones(size(num_i))<=lastfield); num_i=num_i(test_find); end set(handles.first_i,'String',num2str(num_i(1))); set(handles.last_i,'String',num2str(num_i(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); num_j=num_j(test_find); end set(handles.first_j,'String',num2str(num_j(1))); set(handles.last_j,'String',num2str(num_j(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 SubDirImages=get(handles.SubDirImages,'String'); subdir_civ1=[SubDirImages get(handles.SubdirCiv1,'String')];%subdirectory subdir_civ1 for the netcdf data subdir_civ2=[SubDirImages get(handles.SubdirCiv2,'String')];%subdirectory subdir_civ2 for the netcdf data ref_i=str2double(get(handles.ref_i,'String')); ref_j=[]; if isequal(mode,'pair j1-j2')%|isequal(mode,'st_pair j1-j2') ref_j=0; elseif strcmp(get(handles.ref_j,'Visible'),'on') ref_j=str2double(get(handles.ref_j,'String')); end if isempty(ref_j) ref_j=1; 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),'dir') msgbox_uvmat('ERROR',['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_SearchBoxSize_1,num_SearchBoxSize_2 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_SearchBoxSize_1,num_SearchBoxSize_2 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_CorrBoxSize_1,'String')); iby=str2double(get(handles.num_CorrBoxSize_2,'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_SearchBoxShift_1,'String',num2str(shiftx)); set(handles.num_SearchBoxShift_2,'String',num2str(shifty)); set(handles.num_SearchBoxSize_1,'String',num2str(isx)); set(handles.num_SearchBoxSize_2,'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_grid]=get_grid(filebase,handles) %------------------------------------------------------------------------ flag_grid=0;%default nbslice=1; [Path,Name]=fileparts(filebase); currentdir=pwd; cd(Path);%move in the dir of the root name filebase gridfiles=dir([Name '_*grid_*.grid']);%look for grid files cd(currentdir);%come back to the current working directory if ~isempty(gridfiles) flag_grid=1; gridname=gridfiles(1).name;% take the first grid file in the list [Path2,Name,ext]=fileparts(gridname); Namedouble=double(Name); val=(48>Namedouble)|(Namedouble>57);% select the non-numerical characters ind_grid=findstr('grid',Name); i=ind_grid-1; while val(i)==0 && i>0 i=i-1; end nbslice=str2double(Name(i+1:ind_grid-1)); if ~isnan(nbslice) && Name(i)=='_' flag_grid=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');%handles of the parent panel hchildren=get(hparent,'children'); handle_txtbox=findobj(hchildren,'tag','Grid');% look for the grid name box in the same panel 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] = 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','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) 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 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_FieldSmooth,'Visible','on') else set(handles.num_SubDomainSize,'Visible','off') set(handles.num_FieldSmooth,'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_FieldSmooth,'Visible','on') % else % set(handles.num_subdomainsize,'Visible','off') % set(handles.num_FieldSmooth,'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]=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); FileInfo=get_file_info(filecell.ima1.civ1{1}); par_civ1.FileTypeA=FileInfo.FileType; 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.FrameIndexA=num2str(i1); par_civ1.FrameIndexB=num2str(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.PlotAxes) ViewData=get(hview_field,'UserData'); ViewData.CivHandle=handles.civ;% indicate the handle of the civ GUI in view_field ViewData.PlotAxes.B=imread(filecell.ima2.civ1{1});%store the second image in the UserData of the GUI view_field ViewData.PlotAxes.X=Grid.Civ1_X; %keep the set of points in memeory ViewData.PlotAxes.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 %'nomtype2pair': creates nomencalture for index pairs knowing the image nomenclature %--------------------------------------------------------------------- function NomTypeNc=nomtype2pair(NomTypeIma,mode) %--------------------------------------------------------------------- % OUTPUT: % NomTypeNc %--------------------------------------------------------------------- % INPUT: % 'NomTypeIma': string defining the kind of nomenclature used for images 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'); SubDirImages=get(handles.SubDirImages,'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,SubDirImages,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 Program. function Program_Callback(hObject, eventdata, handles) ListProgram=get(handles.Program,'String'); Program=ListProgram{get(handles.Program,'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_CorrSmooth,'Style','edit') set(handles.num_CorrSmooth,'String','1') set(handles.BATCH,'Enable','on') set(handles.CheckThreshold,'Visible','off') set(handles.CheckDeformation,'Value',1) set(handles.CheckDecimal,'Value',1) case {'civ_matlab','civ_matlab.sh'} 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_CorrSmooth,'Style','popupmenu') set(handles.num_CorrSmooth,'Value',1) set(handles.num_CorrSmooth,'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 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=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.FieldSmooth; 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.FieldSmooth; 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 % --- Executes on button press in TestCiv2. function TestCiv2_Callback(hObject, eventdata, handles) function RootFile_Callback(hObject, eventdata, handles) function SubDirImages_Callback(hObject, eventdata, handles) function errormsg=write_param(Param) %------------------------------------------------------------------------ %pixels per cm and matrix of the image times, read from the .civ file by uvmat %changes : filename_cmx -> filename ( no extension ) errormsg=''; switch Param.Program case 'CivX' if Param.CheckCiv1 filename=regexprep(Param.OutputFile,'(.+)([/\\])(.+$)','$1$20_CMX$2$3.civ1.cmx'); 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,'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.CorrBoxSize(1)) ' ' num2str(Param.Civ1.CorrBoxSize(2)) '\n' ]); fprintf(fid, ['SearchBoxeSize ' num2str(Param.Civ1.SearchBoxSize(1)) ' ' num2str(Param.Civ1.SearchBoxSize(2)) '\n' ]); fprintf(fid, ['RO ' num2str(Param.Civ1.CorrSmooth) '\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.SearchBoxShift(1)) ' ' num2str(Param.Civ1.SearchBoxShift(2)) '\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); end if Param.CheckCiv2 filename=regexprep(Param.OutputFile,'(.+)([/\\])(.+$)','$1$20_CMX$2$3.civ2.cmx'); 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,'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.CorrBoxSize(1)) ' ' num2str(Param.Civ2.CorrBoxSize(2)) '\n' ]); fprintf(fid, ['SearchBoxeSize ' num2str(Param.Civ2.CorrBoxSize(1)) ' ' num2str(Param.Civ2.CorrBoxSize(2)) '\n']); fprintf(fid, ['RO ' num2str(Param.Civ2.CorrSmooth) '\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); end case {'civ_matlab','civ_matlab.sh'} filename=regexprep(Param.OutputFile,'(.+)([/\\])(.+$)','$1$20_XML$2$3.xml'); if isunix fileattrib(fileparts(filename),'+w +x','o g');% set writting access end save(struct2xml(Param),filename); end function cmd=write_cmd(Param) % initiate system command cmd=[]; switch Param.Program case 'CivX' if isunix % check: necessaire aussi en RUN? cmd=[cmd '#!/bin/bash \n'... '#$ -cwd \n'... 'hostname && date \n'... 'umask 002 \n'];%allow writting access to created files for user group end case 'CivAll' if isunix % check: necessaire aussi en RUN? cmd=[cmd '#!/bin/bash \n'... '#$ -cwd \n'... 'hostname && date \n'... 'umask 002 \n'];%allow writting access to created files for user group end end filename=regexprep(Param.OutputFile,'.nc',''); if Param.CheckCiv1 switch Param.Program case 'CivX' if(isunix) %unix (or Mac) system cmd=[cmd 'cp -f ' regexprep(filename,'(.+)/(.+$)','$1/0_CMX/$2.civ1.cmx ') regexprep(filename,'(.+)/(.+$)','$1/$2.cmx \n')...% the cmx file gives the name to the nc file Param.xml.Civ1Bin ' -f ' regexprep(filename,'(.+)/(.+$)','$1/$2.cmx >') regexprep(filename,'(.+)/(.+$)','$1/0_LOG/$2.civ1.log \n')... % redirect standard output to the log file, the result file is named [filename '.nc'] by CIVx 'rm ' regexprep(filename,'(.+)/(.+$)','$1/$2.cmx \n')]; else %Windows system filename=regexprep(filename,'\\','\\\\'); cmd=['copy /Y ' regexprep(filename,'(.+)\\\\(.+$)','"$1\\\\0_CMX\\\\$2.civ1.cmx" ') regexprep(filename,'(.+)\\\\(.+$)','"$1\\\\$2.cmx" \n')... '"' regexprep(Param.xml.Civ1Bin,'\\','\\\\') '" -f ' regexprep(filename,'(.+)\\\\(.+$)','"$1\\\\$2.cmx" > ')... regexprep(filename,'(.+)\\\\(.+$)','"$1\\\\0_LOG\\\\$2.civ1.log" \n')... % redirect standard output to the log file 'del ' regexprep(filename,'(.+)\\\\(.+$)','"$1\\\\$2.cmx" \n')]; 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 Param.Program case 'CivX' cmd=[cmd... cmd_fix(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 switch Param.Program case 'CivX' cmd=[cmd... cmd_patch(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 switch Param.Program case 'CivX' if(isunix) cmd=[cmd 'cp -f ' regexprep(filename,'(.+)/(.+$)','$1/0_CMX/$2.civ2.cmx ') regexprep(filename,'(.+)/(.+$)','$1/$2.cmx \n')... Param.xml.Civ2Bin ' -f ' regexprep(filename,'(.+)/(.+$)','$1/$2.cmx >') regexprep(filename,'(.+)/(.+$)','$1/0_LOG/$2.civ2.log \n')...% redirect standard output to the log file, the result file is named [filename '.nc'] by CIVx 'rm ' regexprep(filename,'(.+)/(.+$)','$1/$2.cmx \n')];%rename .cmx as .checkciv2.cmx, the result file is named [filename '.nc'] by CIVx else filename=regexprep(Param.OutputFile,'.nc',''); filename=regexprep(filename,'\\','\\\\'); cmd=[cmd 'copy /Y ' regexprep(filename,'(.+)\\\\(.+$)','"$1\\\\0_CMX\\\\$2.civ2.cmx" ') regexprep(filename,'(.+)\\\\(.+$)','"$1\\\\$2.cmx" \n')... '"' regexprep(Param.xml.Civ2Bin,'\\','\\\\') '" -f ' regexprep(filename,'(.+)\\\\(.+$)','"$1\\\\$2.cmx" > ')... regexprep(filename,'(.+)\\\\(.+$)','"$1\\\\0_LOG\\\\$2.civ2.log" \n')... % redirect standard output to the log file 'del ' regexprep(filename,'(.+)\\\\(.+$)','"$1\\\\$2.cmx" \n')]; end 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 Param.Program case 'CivX' cmd=[cmd... cmd_fix(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 Param.Program case 'CivX' cmd=[cmd... cmd_patch(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 Param.Program case 'CivAll' save(CivAllxml,[Param.OutputFile '.xml']); cmd=[cmd sparam.CivBin ' -f ' Param.OutputFile '.xml ' CivAllCmd ' >' Param.OutputFile '.log' '\n']; case 'civ_matlab' switch computer case {'PCWIN','PCWIN64'} filename=regexprep(filename,'\\','\\\\');% add '\' so that '\' are left as characters cmd=['civ_matlab(''' regexprep(filename,'(.+)([/\\])(.+$)','$1$20_XML\\$2$3.xml') ''','''... filename '.nc'');']; case {'GLNX86','GLNXA64','MACI64'} cmd=['civ_matlab(''' regexprep(filename,'(.+)([/\\])(.+$)','$1$20_XML$2$3.xml') ''','''... filename '.nc'');']; end case 'civ_matlab.sh' CivmBin=fullfile(fileparts(which('civ')),'civ_matlab.sh'); %path to the source directory of uvmat switch computer case {'PCWIN','PCWIN64'} filename=regexprep(filename,'\\','\\\\');% add '\' so that '\' are left as characters % TODO launch command in DOS case {'GLNX86','GLNXA64','MACI64'} cmd=['#!/bin/bash \n '... '#$ -cwd \n '... 'hostname && date \n '... 'umask 002 \n'... CivmBin ' ' Param.xml.RunTime ' ' regexprep(filename,'(.+)([/\\])(.+$)','$1$20_XML$2$3.xml') ' ' Param.OutputFile '.nc'];%allow writting access to created files for user group end end function cmd=cmd_fix(Param,fixname) %% switch fixname case 'Fix1' fi2_value=num2str(Param.(fixname).CheckF2); filename=regexprep(Param.OutputFile,'.nc',''); case 'Fix2' fi2_value=num2str(Param.(fixname).CheckF4);%need to understand why... filename=regexprep(Param.OutputFile,'.nc',''); end % filename=regexprep(Param.(fixname).OutFileName,'.nc',''); MaskName_string='';%default MaxVel_string='';%default if ~isempty(Param.(fixname).MinVel) MaxVel_string=[' -threshV ' num2str(Param.(fixname).MinVel)]; end if isunix cmd=[Param.xml.FixBin ' -f ' filename '.nc -fi1 ' num2str(Param.(fixname).CheckFmin2) ... ' -fi2 ' fi2_value ' -fi3 ' num2str(Param.(fixname).CheckF3) ... ' -threshC ' num2str(Param.(fixname).MinCorr) MaxVel_string MaskName_string... ' >' regexprep(filename,'(.+)/(.+$)','$1/0_LOG/$2.') lower(fixname) '.log 2>&1']; else cmd=['"' Param.xml.FixBin '" -f "' filename '.nc" -fi1 ' num2str(Param.(fixname).CheckFmin2)... ' -fi2 ' fi2_value ' -fi3 ' num2str(Param.(fixname).CheckF3) ... ' -threshC ' num2str(Param.(fixname).MinCorr) MaxVel_string MaskName_string... ' > "' regexprep(filename,'(\w+)\\(\w+$)','$1\\0_LOG\\$2.') lower(fixname) '.log"']; cmd=regexprep(cmd,'\\','\\\\'); end function cmd=cmd_patch(Param,patchname) %% ------------------------------------------------------------------------ switch patchname case 'Patch1' filename=regexprep(Param.OutputFile,'.nc',''); case 'Patch2' filename=regexprep(Param.OutputFile,'.nc',''); end % filename=regexprep(Param.(patchname).OutFileName,'.nc',''); if isunix cmd=[Param.xml.PatchBin... ' -f ' filename '.nc -m ' num2str(Param.(patchname).Nx)... ' -n ' num2str(Param.(patchname).Ny) ' -ro ' num2str(Param.(patchname).FieldSmooth)... ' -nopt ' num2str(Param.(patchname).SubDomainSize) ... ' > ' regexprep(filename,'(.+)/(.+$)','$1/0_LOG/$2.') 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).FieldSmooth)... ' -nopt ' num2str(Param.(patchname).SubDomainSize)... ' > "' filename '.' lower(patchname) '.log" 2>&1']; % redirect standard output to the log file cmd=regexprep(cmd,'\\','\\\\'); end %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% % USELESS FUNCTIONS BELOW HERE, TO CLEAN %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %------------------------------------------------------------------------ % --- 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'; % 'open_uvmat': open with uvmat the field selected in the list of 'civ/status' %------------------------------------------------------------------------ %function open_uvmat(hObject, eventdata) % % INPUT: % hObject: handle of uicontrol object containing the list % eventdata: not used function open_uvmat(hObject, eventdata) %------------------------------------------------------------------------ list=get(hObject,'String'); index=get(hObject,'Value'); rootroot=get(hObject,'UserData'); filename=list{index}; ind_dot=strfind(filename,'...'); if ~isempty(ind_dot) filename=filename(1:ind_dot-1); end filename=fullfile(rootroot,filename); if exist(filename,'file')%visualise the vel field if it exists uvmat(filename) set(gcbo,'Value',1) end % % % --- Executes on selection change in RunMode. % function RunMode_Callback(hObject, eventdata, handles) % % % function nb_field2_Callback(hObject, eventdata, handles) % % % function last_j_Callback(hObject, eventdata, handles) % % % function last_i_Callback(hObject, eventdata, handles)