Index: /trunk/src/browse_data.m =================================================================== --- /trunk/src/browse_data.m (revision 1067) +++ /trunk/src/browse_data.m (revision 1068) @@ -1,3 +1,4 @@ -%'browse_data': function for scanning directories in a campaign + +%'browse_data': function for scanning directories in a campaign %------------------------------------------------------------------------ % function varargout = series(varargin) @@ -24,15 +25,15 @@ function varargout = browse_data(varargin) -% Last Modified by GUIDE v2.5 17-Apr-2019 18:15:24 +% Last Modified by GUIDE v2.5 08-Jul-2019 23:32:39 % Begin initialization code - DO NOT EDIT gui_Singleton = 1; gui_State = struct('gui_Name', mfilename, ... - 'gui_Singleton', gui_Singleton, ... - 'gui_OpeningFcn', @browse_data_OpeningFcn, ... - 'gui_OutputFcn', @browse_data_OutputFcn, ... - 'gui_LayoutFcn', [] , ... - 'gui_Callback', []); -if nargin && ischar(varargin{1}) && ~isempty(regexp(varargin{1},'_Callback','once')) + 'gui_Singleton', gui_Singleton, ... + 'gui_OpeningFcn', @browse_data_OpeningFcn, ... + 'gui_OutputFcn', @browse_data_OutputFcn, ... + 'gui_LayoutFcn', [] , ... + 'gui_Callback', []); +if nargin && ischar(varargin{1}) && ~isempty(regexp(varargin{1},'_Callback','once')) gui_State.gui_Callback = str2func(varargin{1}); end @@ -74,9 +75,9 @@ set(hObject, 'Position', FigPos); set(hObject, 'Units', OldUnits); -if exist('MultiDevices','var') && strcmp(MultiDevices,'on') - set(handles.DataSeries,'Max',2) -else - set(handles.DataSeries,'Max',1) -end +% if exist('MultiDevices','var') && strcmp(MultiDevices,'on') +% set(handles.DataSeries,'Max',2) +% else +% set(handles.DataSeries,'Max',1) +% end if exist('EnableMirror','var') && strcmp(EnableMirror,'on') set(handles.CreateMirror,'Visible','on') @@ -91,45 +92,38 @@ InputDir=pwd;% current dir is the starting data series by default end -% [Experiment,DataSeries,Ext]=fileparts(DataSeries); -% DataSeries=[DataSeries Ext]; -% [Campaign,Experiment,Ext]=fileparts(Experiment); -% Experiment=[Experiment Ext]; + [ExpWithPath,DataSeries]=fileparts(InputDir); -[Campaign,Experiment,Ext]=fileparts(ExpWithPath); -[tild,CampaignName]=fileparts(Campaign); -RootXml=fullfile(Campaign,[CampaignName '.xml']); +[Experiment,Device,Ext]=fileparts(ExpWithPath); +Device=[Device Ext]; +[SourceDir,Experiment,Ext]=fileparts(Experiment); +Experiment=[Experiment Ext]; +% [tild,CampaignName]=fileparts(Campaign); +% RootXml=fullfile(Campaign,[CampaignName '.xml']); s=[]; -if exist(RootXml,'file') - [s,Heading]=xml2struct(RootXml);%read the xml file - if isfield(s,'SourceDir') - set(handles.SourceDir,'String',s.SourceDir);%display the source dir if a mirror has been opened - set(handles.MirrorDir,'Visible','on');% mirror dir display - set(handles.MirrorDir,'String',Campaign);%display the opened mirror dir - set(handles.CreateMirror,'String','update_mirror') - end -end +% if exist(RootXml,'file') +% [s,Heading]=xml2struct(RootXml);%read the xml file +% if isfield(s,'SourceDir') +% set(handles.SourceDir,'String',s.SourceDir);%display the source dir if a mirror has been opened +% set(handles.MirrorDir,'Visible','on');% mirror dir display +% set(handles.MirrorDir,'String',Campaign);%display the opened mirror dir +% set(handles.CreateMirror,'String','update_mirror') +% end +% end if isempty(s) %a source dir has been opened - set(handles.SourceDir,'String',Campaign); + set(handles.SourceDir,'String',SourceDir); set(handles.MirrorDir,'Visible','off');% no mirror dir display set(handles.CreateMirror,'String','create_mirror') end -errormsg=scan_campaign(handles,Campaign,Experiment,ExpWithPath); +set(handles.DataSeries,'String',{['+/' DataSeries]}); +set(handles.ListDevices,'String',{['+/' Device]}); +errormsg=scan_campaign(handles,SourceDir,['+/' Experiment]); if ~isempty(errormsg) msgbox_uvmat('ERROR',errormsg) return end -% set(handles.OK,'Visible','on') -% set(handles.Cancel,'Visible','on') - -%set(handles.browse_data,'WindowStyle','modal')% Make the GUI -%modal%%%%%%%%%%%%%%%%%%%%%%% + set(hObject,'Visible','on') -drawnow -% UIWAIT makes GUI wait for user response (see UIRESUME)%%%%%%%%%%%%%%%%TO -% CHECK -%uiwait(handles.browse_data); - - - +drawnow + %------------------------------------------------------------------------ % --- Outputs from this function are returned to the command line. @@ -149,32 +143,32 @@ [SourcePath,ProjectName]=fileparts(SourceDir); if strcmp(get(handles.MirrorDir,'Visible'),'on') - MirrorDir=get(handles.MirrorDir,'String');% name of the mirror folder +MirrorDir=get(handles.MirrorDir,'String');% name of the mirror folder else% create the mirror folder if it does not exist - MirrorRoot=uigetfile_uvmat('select the folder which must contain the mirror directory:',SourcePath,'uigetdir'); - if isempty(MirrorRoot) - return - elseif strcmp(MirrorRoot,SourcePath) - msgbox_uvmat('ERROR','The mirror folder must be different from the source') - return - else - MirrorDir=fullfile(MirrorRoot,ProjectName); - end - if exist(MirrorDir,'dir') - msgbox_uvmat('ERROR',['The folder ' MirrorDir ' chosen as new mirror campaign already exists']) - return - else - [s,errormsg]=mkdir(MirrorDir)% create the mirror dir - if s~=1 - msgbox_uvmat('ERROR',['error in creating ' MirrorDir ': ' errormsg]) - return - end - end - MirrorDoc.SourceDir=SourceDir; - t=struct2xml(MirrorDoc); - set(t,1,'name','DataTree'); - save(t,fullfile(MirrorDir,[ProjectName '.xml']))% create an xml file in the mirror folder to indicate its source folder - set(handles.MirrorDir,'String',MirrorDir) - set(handles.MirrorDir,'Visible','on') - set(handles.CreateMirror,'String','update_mirror') +MirrorRoot=uigetfile_uvmat('select the folder which must contain the mirror directory:',SourcePath,'uigetdir'); +if isempty(MirrorRoot) +return +elseif strcmp(MirrorRoot,SourcePath) +msgbox_uvmat('ERROR','The mirror folder must be different from the source') +return +else +MirrorDir=fullfile(MirrorRoot,ProjectName); +end +if exist(MirrorDir,'dir') +msgbox_uvmat('ERROR',['The folder ' MirrorDir ' chosen as new mirror campaign already exists']) +return +else +[s,errormsg]=mkdir(MirrorDir)% create the mirror dir +if s~=1 +msgbox_uvmat('ERROR',['error in creating ' MirrorDir ': ' errormsg]) +return +end +end +MirrorDoc.SourceDir=SourceDir; +t=struct2xml(MirrorDoc); +set(t,1,'name','DataTree'); +save(t,fullfile(MirrorDir,[ProjectName '.xml']))% create an xml file in the mirror folder to indicate its source folder +set(handles.MirrorDir,'String',MirrorDir) +set(handles.MirrorDir,'Visible','on') +set(handles.CreateMirror,'String','update_mirror') end ExpName={''}; @@ -182,28 +176,28 @@ %% update the mirror from the source dir if exist(SourceDir,'dir') - hdir=dir(SourceDir); %list files and dirs - idir=0; - for ilist=1:length(hdir) - if hdir(ilist).isdir% scan all subfolders - dirname=hdir(ilist).name;% - if ~isequal(dirname(1),'.')&&~isequal(dirname(1),'0')%skip subfolder beginning by '0' - idir=idir+1; - mirror=fullfile(MirrorDir,hdir(ilist).name);% corresponding name in the mirror - if ~exist(mirror,'dir') - mkdir(mirror)% create the mirror folder if it does not exist - end - ExpName{idir}=['+/' hdir(ilist).name];% insert '+/' in the list to show that it is a folder - end - % look for the list of 'devices' - else - %warning for isolated files - end - end - set(handles.ListExperiments,'String',[{'*'};ExpName']) - set(handles.ListExperiments,'Value',1) - update_experiments(handles,[{'*'};ExpName'],SourceDir,MirrorDir) - % ListExperiments_Callback(hObject, eventdata, handles) % list the content of the experiment -else - msgbox_uvmat('ERROR',['The input ' SourceDir ' is not a directory']) +hdir=dir(SourceDir); %list files and dirs +idir=0; +for ilist=1:length(hdir) +if hdir(ilist).isdir% scan all subfolders +dirname=hdir(ilist).name;% +if ~isequal(dirname(1),'.')&&~isequal(dirname(1),'0')%skip subfolder beginning by '0' +idir=idir+1; +mirror=fullfile(MirrorDir,hdir(ilist).name);% corresponding name in the mirror +if ~exist(mirror,'dir') +mkdir(mirror)% create the mirror folder if it does not exist +end +ExpName{idir}=['+/' hdir(ilist).name];% insert '+/' in the list to show that it is a folder +end +% look for the list of 'devices' +else +%warning for isolated files +end +end +set(handles.ListExperiments,'String',[{'*'};ExpName']) +set(handles.ListExperiments,'Value',1) +update_experiments(handles,[{'*'};ExpName'],SourceDir,MirrorDir) +% ListExperiments_Callback(hObject, eventdata, handles) % list the content of the experiment +else +msgbox_uvmat('ERROR',['The input ' SourceDir ' is not a directory']) end set(handles.SourceDir,'BackgroundColor',[1 1 1]) @@ -212,15 +206,124 @@ % List the experiments in a campaign, filling the menu ListExperiments %------------------------------------------------------------------------ -function errormsg=scan_campaign(handles,Campaign,Experiment,DataInput) +function errormsg=scan_campaign(handles,SourceDir,Experiment) %------------------------------------------------------------------------ errormsg=''; -if ~isempty(regexp(Campaign,'^http'))|| exist(Campaign,'dir') - ListStruct=dir_uvmat(Campaign); %list files and dirs +if ~isempty(regexp(SourceDir,'^http'))|| exist(SourceDir,'dir') + ListStruct=dir_uvmat(SourceDir); %list files and dirs, extende to OpenDAP case if numel(ListStruct)>1000% A campaign folder must contain maily a list of 'experiment' sub-folders - errormsg=[Campaign ' contains too many items (>1000) to be a Project folder']; + errormsg=[SourceDir ' contains too many items (>1000) to be a Project folder']; return end + [ListFiles,index]=list_dir_1(SourceDir,Experiment); + set(handles.ListExperiments,'String',ListFiles) + set(handles.ListExperiments,'Value',index)% initialise the menu selection with the folder defined by the input + ListExperiments_Callback([],[], handles) +else + msgbox_uvmat('ERROR',['The input ' Campaign ' is not a directory']) +end + +%------------------------------------------------------------------------ +% --- Executes on selection change in ListExperiments. +%------------------------------------------------------------------------ +function ListExperiments_Callback(hObject, eventdata, handles) + +if strcmp(get(handles.MirrorDir,'Visible'),'on') + SourceDir=get(handles.MirrorDir,'String'); +else + SourceDir=get(handles.SourceDir,'String'); +end +ListExperiments=get(handles.ListExperiments,'String'); +list_val=get(handles.ListExperiments,'Value'); +ListExperiments=ListExperiments(list_val);%choose the selected experiments +ListDevices=get(handles.ListDevices,'String');% list of devices +list_val=get(handles.ListDevices,'Value');% currently selected devices +Device=''; +if numel(ListDevices)>=list_val +Device=ListDevices(list_val);%choose selected devices +end +[ListFiles,indices]=list_dir_2(SourceDir,ListExperiments,Device); +set(handles.ListDevices,'String',ListFiles) +set(handles.ListDevices,'Value',indices)% initialise the menu selection with the folder defined by the input +ListDevices_Callback([],[], handles) + +%------------------------------------------------------------------------ +% --- Executes on selection change in ListExperiments. +%------------------------------------------------------------------------ +function ListDevices_Callback(hObject, eventdata, handles) + +ListDevices=get(handles.ListDevices,'String');% list of devices +list_val=get(handles.ListDevices,'Value');% currently selected devices +ListDevices=ListDevices(list_val);%choose selected devices +if strcmp(get(handles.MirrorDir,'Visible'),'on') + SourceDir=get(handles.MirrorDir,'String'); +else + SourceDir=get(handles.SourceDir,'String'); +end +ListExperiments=get(handles.ListExperiments,'String'); +list_val=get(handles.ListExperiments,'Value'); +ListExperiments=ListExperiments(list_val);%choose the selected experiments + +DataSeries=get(handles.DataSeries,'String'); +list_val=get(handles.DataSeries,'Value'); +if numel(DataSeries)>=list_val + DataSeries=DataSeries(list_val); +else + DataSeries=[]; +end +[ListFiles,indices]=list_dir_3(SourceDir,ListExperiments,ListDevices,DataSeries); +set(handles.DataSeries,'String',ListFiles) +set(handles.DataSeries,'Value',indices)% initialise the menu selection with the folder defined by the input + +%------------------------------------------------------------------------ +% --- List the DataSeries when a set of experiments is selected +%------------------------------------------------------------------------ +% function list_dataseries(handles,ListExperiments,MirrorPath) +% +% DataSeries={}; +% for iexp=1:numel(ListExperiments) +% if strcmp(ListExperiments{iexp}(1),'+')% if the item is a directory +% ListExperiments{iexp}(1)=[];%remove the first char '+' used to mark folders +% ListStruct=dir(fullfile(MirrorPath,ListExperiments{iexp})); %list files and dir in the source experiment directory +% ListCells=struct2cell(ListStruct);%transform dir struct to a cell arrray +% ListFiles=ListCells(1,:);%list of dir and file names +% cell_remove=regexp(ListFiles,'^(-|\.|\+/\.)');% detect strings beginning by '-' ,'.' or '+/.'(dir beginning by . ) +% cell_remove_tild=regexp(ListFiles,'~$');% detect tild the end of file nqme (do not list) +% check_keep=cellfun('isempty', cell_remove) & cellfun('isempty', cell_remove_tild); +% check_dir=cell2mat(ListCells(4,:));% =1 for directories, =0 for files +% for ilist=1:numel(ListFiles) +% if check_keep(ilist)% loop on eligible DataSeries folders +% mirror=fullfile(MirrorPath,ListExperiments{iexp},ListFiles{ilist});%source folder +% if ~exist(mirror,'file') && ~exist(mirror,'dir')% if the name is a broken link +% delete(mirror)% delete broken link +% else %update the list of dataSeries +% [tild,msg]=fileattrib(mirror); +% if check_dir(ilist) +% ListFiles{ilist}=['+/' ListFiles{ilist}];%mark dir by '+' in the list +% end +% if isempty(find(strcmp(ListFiles{ilist},DataSeries), 1))% if the item is not already in DataSeries +% DataSeries=[DataSeries;ListFiles{ilist}]; %append the item to the list +% end +% end +% end +% end +% end +% end +% if get(handles.CheckDevices,'Value') +% set(handles.ListDevices,'Value',1) +% set(handles.ListDevices,'String',sort(DataSeries)) +% CheckDevices_Callback([],[], handles) +% else +% set(handles.DataSeries,'Value',1) +% set(handles.DataSeries,'String',sort(DataSeries)) +% end + +%------------------------------------------------------------------------ +% Provide a list to display +%------------------------------------------------------------------------ +function [ListFiles,indices]=list_dir_1(SourceDir,ListSub) + + ListStruct=dir_uvmat(SourceDir); %list files and dirs, extende to OpenDAP case ListCells=struct2cell(ListStruct);% transform dir struct to a cell arrray - ListFiles=ListCells(1,:);%list of dir and file names + ListFiles=ListCells(1,:); check_dir=cell2mat(ListCells(4,:));% =1 for directories, =0 for files ListFiles(check_dir)=regexprep(ListFiles(check_dir),'^.+','+/$0');% put '+/' in front of dir name display @@ -228,87 +331,87 @@ check_keep=cellfun('isempty', cell_remove); ListFiles=sort((ListFiles(check_keep))'); - index=find(strcmp(['+/' Experiment],ListFiles)); - if isempty(index), index=1; end - set(handles.ListExperiments,'String',ListFiles) - set(handles.ListExperiments,'Value',index)% initialise the menu selection with the folder defined by the input - ListExperiments_Callback([],[], handles) - DataSeries=get(handles.DataSeries,'String'); - index=find(strcmp(['+/' DataInput],DataSeries)); - if isempty(index) - index=find(strcmp(['~/' DataInput],DataSeries)); + +if ischar(ListSub) + indices=find(strcmp(ListSub,ListFiles)); +else + indices=[]; + for ilist=1:numel(ListSub) + index=find(strcmp(ListSub{ilist},ListFiles)); + indices=[indices index]; end - if ~isempty(index) - set(handles.DataSeries,'Value',index) +end +if isempty(indices), indices=1; end + +%------------------------------------------------------------------------ +% Provide a list to display +%------------------------------------------------------------------------ +function [ListFilesTot,indices]=list_dir_2(SourceDir,ListDir,ListSub) +ListFilesTot={}; +for ilist=1:numel(ListDir) + if ~isempty(regexp(ListDir{ilist},'^\+/')) + ListDir{ilist}=regexprep(ListDir{ilist},'^\+/',''); + ListStruct=dir_uvmat(fullfile(SourceDir,ListDir{ilist})); %list files and dirs, extende to OpenDAP case + ListCells=struct2cell(ListStruct);% transform dir struct to a cell arrray + ListFiles=ListCells(1,:); + check_dir=cell2mat(ListCells(4,:));% =1 for directories, =0 for files + ListFiles(check_dir)=regexprep(ListFiles(check_dir),'^.+','+/$0');% put '+/' in front of dir name display + cell_remove=regexp(ListFiles,'^(-|\.|\+/\.)');% detect strings beginning by '-' ,'.' or '+/.'(dir beginning by . ) + check_keep=cellfun('isempty', cell_remove); + ListFilesTot=[ListFilesTot;(ListFiles(check_keep))']; end -else - msgbox_uvmat('ERROR',['The input ' Campaign ' is not a directory']) -end - -%------------------------------------------------------------------------ -% --- Executes on selection change in ListExperiments. -%------------------------------------------------------------------------ - function ListExperiments_Callback(hObject, eventdata, handles) - -if strcmp(get(handles.MirrorDir,'Visible'),'on') - MirrorPath=get(handles.MirrorDir,'String'); -else - MirrorPath=get(handles.SourceDir,'String'); -end -ListExperiments=get(handles.ListExperiments,'String'); -list_val=get(handles.ListExperiments,'Value'); -ListExperiments=ListExperiments(list_val);%choose selected experiments -list_dataseries(handles,ListExperiments,MirrorPath) - -%------------------------------------------------------------------------ -% --- List the DataSeries when a set of experiments is selected -%------------------------------------------------------------------------ - function list_dataseries(handles,ListExperiments,MirrorPath) - -DataSeries={}; -for iexp=1:numel(ListExperiments) - if strcmp(ListExperiments{iexp}(1),'+')% if the item is a directory - ListExperiments{iexp}(1)=[];%remove the first char '+' used to mark folders - ListStruct=dir(fullfile(MirrorPath,ListExperiments{iexp})); %list files and dir in the source experiment directory - ListCells=struct2cell(ListStruct);%transform dir struct to a cell arrray - ListFiles=ListCells(1,:);%list of dir and file names - cell_remove=regexp(ListFiles,'^(-|\.|\+/\.)');% detect strings beginning by '-' ,'.' or '+/.'(dir beginning by . ) - cell_remove_tild=regexp(ListFiles,'~$');% detect tild the end of file nqme (do not list) - check_keep=cellfun('isempty', cell_remove) & cellfun('isempty', cell_remove_tild); - check_dir=cell2mat(ListCells(4,:));% =1 for directories, =0 for files - for ilist=1:numel(ListFiles) - if check_keep(ilist)% loop on eligible DataSeries folders - mirror=fullfile(MirrorPath,ListExperiments{iexp},ListFiles{ilist});%source folder - if ~exist(mirror,'file') && ~exist(mirror,'dir')% if the name is a broken link - delete(mirror)% delete broken link - else %update the list of dataSeries - [tild,msg]=fileattrib(mirror); -% msg.Name=regexprep(msg.Name,'^/.','/');%remove the dot in /. at the beginning of the name -% if ~strcmp(msg.Name,mirror)% if it is a link -% ListFiles{ilist}=['~' ListFiles{ilist}];%mark link by '@' in the list -% end - if check_dir(ilist) - ListFiles{ilist}=['+/' ListFiles{ilist}];%mark dir by '+' in the list - end - if isempty(find(strcmp(ListFiles{ilist},DataSeries), 1))% if the item is not already in DataSeries - DataSeries=[DataSeries;ListFiles{ilist}]; %append the item to the list - end - end +end +ListFilesTot=unique(ListFilesTot); +if ischar(ListSub) + indices=find(strcmp(ListSub,ListFilesTot)); +else + indices=[]; + for ilist=1:numel(ListSub) + index=find(strcmp(ListSub{ilist},ListFilesTot)); + indices=[indices index]; + end +end +if isempty(indices), indices=1; end + + +%------------------------------------------------------------------------ +% Provide a list to display +%------------------------------------------------------------------------ +function [ListFilesTot,indices]=list_dir_3(SourceDir,ListDir,ListSub,ListSubSub) +ListFilesTot={}; +for ilist=1:numel(ListDir) + if ~isempty(regexp(ListDir{ilist},'^\+/')) + ListDir{ilist}=regexprep(ListDir{ilist},'^\+/',''); + for isub=1:numel(ListSub) + if ~isempty(regexp(ListSub{isub},'^\+/')) + ListSub{isub}=regexprep(ListSub{isub},'^\+/',''); + ListStruct=dir_uvmat(fullfile(SourceDir,ListDir{ilist},ListSub{isub})); %list files and dirs, extende to OpenDAP case + ListCells=struct2cell(ListStruct);% transform dir struct to a cell arrray + ListFiles=ListCells(1,:); + check_dir=cell2mat(ListCells(4,:));% =1 for directories, =0 for files + ListFiles(check_dir)=regexprep(ListFiles(check_dir),'^.+','+/$0');% put '+/' in front of dir name display + cell_remove=regexp(ListFiles,'^(-|\.|\+/\.)');% detect strings beginning by '-' ,'.' or '+/.'(dir beginning by . ) + check_keep=cellfun('isempty', cell_remove); + ListFilesTot=[ListFilesTot;(ListFiles(check_keep))']; end end end end -if get(handles.CheckDevices,'Value') - set(handles.ListDevices,'Value',1) -set(handles.ListDevices,'String',sort(DataSeries)) -CheckDevices_Callback([],[], handles) -else -set(handles.DataSeries,'Value',1) -set(handles.DataSeries,'String',sort(DataSeries)) -end +ListFilesTot=unique(ListFilesTot); +if ischar(ListSubSub) + indices=find(strcmp(ListSubSub,ListFilesTot)); +else + indices=[]; + for ilist=1:numel(ListSubSub) + index=find(strcmp(ListSubSub{ilist},ListFilesTot)); + indices=[indices index]; + end +end +if isempty(indices), indices=1; end + %------------------------------------------------------------------------ % --- Executes when the mirror is created or updated %------------------------------------------------------------------------ - function update_experiments(handles,ListExperiments,CampaignPath,MirrorPath) +function update_experiments(handles,ListExperiments,CampaignPath,MirrorPath) DataSeries={}; @@ -344,10 +447,10 @@ if strcmp(answer,'Yes') delete(mirror); - system(['ln -s ' DataSeries ' ' mirror]); % create the link to the source folder + system(['ln -s ' DataSeries ' ' mirror]); % create the link to the source folder end end end else% create mirror to the data series if needed - system(['ln -s ' DataSeries ' ' mirror]); % create the link to the source folder + system(['ln -s ' DataSeries ' ' mirror]); % create the link to the source folder end if isempty(find(strcmp(ListFiles{ilist},DataSeries), 1))% if the item is not already in DataSeries @@ -367,5 +470,5 @@ % --- Executes on button press in CampaignDoc. function CampaignDoc_Callback(hObject, eventdata, handles) -%------------------------------------------------------------------------ +%------------------------------------------------------------------------ answer=msgbox_uvmat('INPUT_Y-N','This function will update the global xml rpresentation of the data set and the Heading of each xml file'); if ~isequal(answer{1},'OK') @@ -397,10 +500,10 @@ ExpName=List.Experiment{iexp}.name; t = attributes(t,'add',uid_exp,'DirName',List.Experiment{iexp}.name); - + if isfield(List.Experiment{iexp},'Device') for idevice=1:length(List.Experiment{iexp}.Device) [t,uid_device]=add(t,uid_exp,'element','Device'); DeviceName=List.Experiment{iexp}.Device{idevice}.name; - t = attributes(t,'add',uid_device,'DirName',List.Experiment{iexp}.Device{idevice}.name); + t = attributes(t,'add',uid_device,'DirName',List.Experiment{iexp}.Device{idevice}.name); if isfield(List.Experiment{iexp}.Device{idevice},'xmlfile') for ixml=1:length(List.Experiment{iexp}.Device{idevice}.xmlfile) @@ -413,8 +516,8 @@ [t,uid_xml]=add(t,uid_device,'element','ImaDoc'); t = attributes(t,'add',uid_xml,'source','file'); - [t]=add(t,uid_xml,'chardata',List.Experiment{iexp}.Device{idevice}.xmlfile{ixml}); + [t]=add(t,uid_xml,'chardata',List.Experiment{iexp}.Device{idevice}.xmlfile{ixml}); end end - elseif isfield(List.Experiment{iexp}.Device{idevice},'Record') + elseif isfield(List.Experiment{iexp}.Device{idevice},'Record') for irecord=1:length(List.Experiment{iexp}.Device{idevice}.Record) RecordName=List.Experiment{iexp}.Device{idevice}.Record{irecord}.name; @@ -447,32 +550,32 @@ -%------------------------------------------------------------------------ -% --- Executes on button press in OK. -%------------------------------------------------------------------------ -function OK_Callback(hObject, eventdata, handles) - -if strcmp(get(handles.MirrorDir,'Visible'),'on') - Campaign=get(handles.MirrorDir,'String'); -else - Campaign=get(handles.SourceDir,'String'); -end -handles.output=[]; -handles.output.Campaign=Campaign; -Experiment=get(handles.ListExperiments,'String'); -IndicesExp=get(handles.ListExperiments,'Value'); -if ~isequal(IndicesExp,1)% if first element ('*') selected all the experiments are selected - Experiment=Experiment(IndicesExp);% use the selection of the list of experiments -end -Experiment=regexprep(Experiment,'^\+/','');% remove the +/ used to mark dir -Device=get(handles.DataSeries,'String'); -Value=get(handles.DataSeries,'Value'); -Device=Device(Value); -Device=regexprep(Device,'^\+/','');% remove the +/ used to mark dir -Device=regexprep(Device,'^~','');% remove the ~ used to mark symbolic link -handles.output.Experiment=Experiment; -handles.output.DataSeries=Device; -guidata(hObject, handles);% Update handles structure -uiresume(handles.browse_data); -drawnow +% %------------------------------------------------------------------------ +% % --- Executes on button press in OK. +% %------------------------------------------------------------------------ +% function OK_Callback(hObject, eventdata, handles) +% +% if strcmp(get(handles.MirrorDir,'Visible'),'on') +% Campaign=get(handles.MirrorDir,'String'); +% else +% Campaign=get(handles.SourceDir,'String'); +% end +% handles.output=[]; +% handles.output.Campaign=Campaign; +% Experiment=get(handles.ListExperiments,'String'); +% IndicesExp=get(handles.ListExperiments,'Value'); +% if ~isequal(IndicesExp,1)% if first element ('*') selected all the experiments are selected +% Experiment=Experiment(IndicesExp);% use the selection of the list of experiments +% end +% Experiment=regexprep(Experiment,'^\+/','');% remove the +/ used to mark dir +% Device=get(handles.DataSeries,'String'); +% Value=get(handles.DataSeries,'Value'); +% Device=Device(Value); +% Device=regexprep(Device,'^\+/','');% remove the +/ used to mark dir +% Device=regexprep(Device,'^~','');% remove the ~ used to mark symbolic link +% handles.output.Experiment=Experiment; +% handles.output.DataSeries=Device; +% guidata(hObject, handles);% Update handles structure +% uiresume(handles.browse_data); +% drawnow %------------------------------------------------------------------------ @@ -491,13 +594,5 @@ %------------------------------------------------------------------------ function closefcn(gcbo, eventdata) -% if isequal(get(handles.browse_data, 'waitstatus'), 'waiting') -% % The GUI is still in UIWAIT, us UIRESUME -% handles.output = get(hObject,'String'); -% guidata(hObject, handles); % Update handles structure -% uiresume(handles.browse_data); -% else -% % The GUI is no longer waiting, just close it -% delete(handles.browse_data); -% end + hseries=findobj(allchild(0),'Tag','series'); if ~isempty(hseries) @@ -511,77 +606,145 @@ end -%------------------------------------------------------------------------ -% --- Executes on key press over figure1 with no controls selected. -%------------------------------------------------------------------------ -function browse_data_KeyPressFcn(hObject, eventdata, handles) +% %------------------------------------------------------------------------ +% % --- Executes on key press over figure1 with no controls selected. +% %------------------------------------------------------------------------ +% function browse_data_KeyPressFcn(hObject, eventdata, handles) -% Check for "enter" or "escape" -if isequal(get(hObject,'CurrentKey'),'escape') - % User said no by hitting escape - handles.output = 'Cancel'; - - % Update handles structure - guidata(hObject, handles); - - uiresume(handles.browse_data); -end -if isequal(get(hObject,'CurrentKey'),'return') - uiresume(handles.browse_data); -end +% % Check for "enter" or "escape" +% if isequal(get(hObject,'CurrentKey'),'escape') +% % User said no by hitting escape +% handles.output = 'Cancel'; +% +% % Update handles structure +% guidata(hObject, handles); +% +% uiresume(handles.browse_data); +% end +% if isequal(get(hObject,'CurrentKey'),'return') +% uiresume(handles.browse_data); +% end % --- Executes on button press in Up. -function Up_Callback(hObject, eventdata, handles) -SourceDir=get(handles.SourceDir,'String'); -browse_data(SourceDir) - - -% --- Executes on button press in Down. function Down_Callback(hObject, eventdata, handles) SourceDir=get(handles.SourceDir,'String'); ListExperiments=get(handles.ListExperiments,'String'); list_val=get(handles.ListExperiments,'Value'); -SourceFolder=regexprep(ListExperiments{list_val(1)},'+',''); -set(handles.SourceDir,'String',fullfile(SourceDir,SourceFolder)) +if ischar(ListExperiments) + Exp=ListExperiments; +else + Exp=ListExperiments{list_val(1)}; +end +Exp=regexprep(Exp,'^\+/',''); +SourceDirNew=fullfile(SourceDir,Exp); +set(handles.SourceDir,'String',SourceDirNew);% New SourceDir +ListDevices=get(handles.ListDevices,'String'); +DeviceIndices=get(handles.ListDevices,'Value'); +set(handles.ListExperiments,'String',ListDevices);%replace Experiments by Devices +set(handles.ListExperiments,'Value',DeviceIndices);%replace Experiments by Devices DataSeries=get(handles.DataSeries,'String'); -ValueDevice=get(handles.DataSeries,'Value'); -set(handles.ListExperiments,'String',DataSeries) -set(handles.ListExperiments,'Value',ValueDevice) -ListExperiments_Callback(hObject, [], handles) - - -% --- Executes on selection change in DataSeries. -function DataSeries_Callback(hObject, eventdata, handles) - - -% --- Executes on button press in CheckDevices. -function CheckDevices_Callback(hObject, eventdata, handles) -if get(handles.CheckDevices,'Value') - set(handles.ListDevices,'Visible','on') - ListDevices=get(handles.DataSeries,'String'); - Index=get(handles.DataSeries,'Value'); - set(handles.ListDevices,'String',ListDevices) - set(handles.ListDevices,'Value',Index) - set(handles.DataSeries,'Value',1) - if strcmp(get(handles.MirrorDir,'Visible'),'on') - MirrorPath=get(handles.MirrorDir,'String'); - else - MirrorPath=get(handles.SourceDir,'String'); - end - IndexExperiment=get(handles.ListExperiments,'Value'); - ListExperiment=get(handles.ListExperiments,'String'); - Experiment=ListExperiment{get(handles.ListExperiments,'Value')}; - Experiment=regexprep(Experiment,'^\+/','');% remove the +/ used to mark dir - Experiment=regexprep(Experiment,'^~','');% remove the ~ used to mark symbolic link - Device=regexprep(ListDevices{Index},'^\+/','');% remove the +/ used to mark dir - Device=regexprep(Device,'^~','');% remove the ~ used to mark symbolic link - DataSeries=dir(fullfile(MirrorPath,Experiment,Device)); - DataSeriesCell=struct2cell(DataSeries); - set(handles.DataSeries,'String',DataSeriesCell(1,:)') -else - ListDevices=get(handles.ListDevices,'String'); - Index=get(handles.ListDevices,'Value'); - set(handles.ListDevices,'Visible','off') - set(handles.DataSeries,'String',ListDevices) - set(handles.DataSeries,'Value',Index) -end +list_val=get(handles.DataSeries,'Value'); +set(handles.ListDevices,'String',DataSeries);%replace Devices by DataSeries +set(handles.ListDevices,'Value',list_val);%replace Devices by DataSeries + +[ListFiles,indices]=list_dir_3(SourceDirNew,ListDevices(DeviceIndices),DataSeries(list_val),[]); +set(handles.DataSeries,'String',ListFiles) +set(handles.DataSeries,'Value',indices)% initialise the menu selection with the folder defined by the input + + +% --- Executes on button press in Down. +function Up_Callback(hObject, eventdata, handles) +SourceDir=get(handles.SourceDir,'String'); +[SourceDir,Exp]=fileparts(SourceDir); +set(handles.SourceDir,'String',SourceDir) + +% set(handles.ListExperiments,'Value',indices) +%[ListFiles,indices]=list_dir_1(SourceDir,Exp); +% set(handles.ListExperiments,'String',ListFiles) +% set(handles.ListExperiments,'Value',indices) +ListDevices=get(handles.ListDevices,'String'); +DeviceIndices=get(handles.ListDevices,'Value'); +set(handles.DataSeries,'String',ListDevices); +set(handles.DataSeries,'Value',DeviceIndices); + +ListExperiments=get(handles.ListExperiments,'String'); +ExpIndices=get(handles.ListExperiments,'Value'); +set(handles.ListDevices,'String',ListExperiments); +set(handles.ListDevices,'Value',ExpIndices); + +set(handles.ListExperiments,'String',{['+/' Exp]}) +set(handles.ListExperiments,'Value',1) + +% ListExperiments=get(handles.ListExperiments,'String'); +% list_val=get(handles.ListExperiments,'Value'); +% SourceFolder=regexprep(ListExperiments{list_val(1)},'+',''); +% set(handles.SourceDir,'String',fullfile(SourceDir,SourceFolder)) +% DataSeries=get(handles.DataSeries,'String'); +% ValueDevice=get(handles.DataSeries,'Value'); +% set(handles.ListExperiments,'String',DataSeries) +% set(handles.ListExperiments,'Value',ValueDevice) +% ListExperiments_Callback(hObject, [], handles) + + +% % --- Executes on selection change in DataSeries. +% function DataSeries_Callback(hObject, eventdata, handles) +% SourceDir=get(handles.SourceDir,'String'); +% ListData=get(handles.DataSeries,'String'); +% Folder=ListData{get(handles.DataSeries,'Value')}; +% if ~isempty(regexp(Folder,'^\+/'))% if a folder is selected +% Folder=regexprep(Folder,'\+/',''); +% ListExperiments=get(handles.ListExperiments,'String'); +% list_val=get(handles.ListExperiments,'Value'); +% for iexp=1:numel(list_val) +% ExpName=regexprep(ListExperiments{list_val(iexp)},'\+/',''); +% FullName=fullfile(SourceDir,ExpName,Folder); +% dd=dir(FullName); +% check_sub=1; +% for idir=1:numel(dd) +% ListData{ilist}=dd(ilist).name; +% if dd(ilist).isdir && ~strcmp(dd(ilist).name,'.')&& ~strcmp(dd(ilist).name,'..')&& isempty(regexp(dd(ilist).name,'^_LOG'))... +% && isempty(regexp(dd(ilist).name,'^_LOG'))&& isempty(regexp(dd(ilist).name,'^_XML')) +% check_sub=1; +% ListData{ilist}=['+/' dd(ilist).name]; +% end +% end +% if check_sub +% set(handles.ListDevices,'String',ListData); +% set(handles.ListDevices,'Visible','on'); +% set(handles.DataSeries,'String',ListData) +% break +% end +% end +% end + +% % --- Executes on button press in CheckDevices. +% function CheckDevices_Callback(hObject, eventdata, handles) +% if get(handles.CheckDevices,'Value') +% set(handles.ListDevices,'Visible','on') +% ListDevices=get(handles.DataSeries,'String'); +% Index=get(handles.DataSeries,'Value'); +% set(handles.ListDevices,'String',ListDevices) +% set(handles.ListDevices,'Value',Index) +% set(handles.DataSeries,'Value',1) +% if strcmp(get(handles.MirrorDir,'Visible'),'on') +% MirrorPath=get(handles.MirrorDir,'String'); +% else +% MirrorPath=get(handles.SourceDir,'String'); +% end +% IndexExperiment=get(handles.ListExperiments,'Value'); +% ListExperiment=get(handles.ListExperiments,'String'); +% Experiment=ListExperiment{get(handles.ListExperiments,'Value')}; +% Experiment=regexprep(Experiment,'^\+/','');% remove the +/ used to mark dir +% Experiment=regexprep(Experiment,'^~','');% remove the ~ used to mark symbolic link +% Device=regexprep(ListDevices{Index},'^\+/','');% remove the +/ used to mark dir +% Device=regexprep(Device,'^~','');% remove the ~ used to mark symbolic link +% DataSeries=dir(fullfile(MirrorPath,Experiment,Device)); +% DataSeriesCell=struct2cell(DataSeries); +% set(handles.DataSeries,'String',DataSeriesCell(1,:)') +% else +% ListDevices=get(handles.ListDevices,'String'); +% Index=get(handles.ListDevices,'Value'); +% set(handles.ListDevices,'Visible','off') +% set(handles.DataSeries,'String',ListDevices) +% set(handles.DataSeries,'Value',Index) +% end Index: /trunk/src/geometry_calib.m =================================================================== --- /trunk/src/geometry_calib.m (revision 1067) +++ /trunk/src/geometry_calib.m (revision 1068) @@ -273,26 +273,58 @@ hbrowse=findobj(allchild(0),'Tag','browse_data'); if ~isempty(hbrowse)% look for the GUI 'replicate' - BrowseHandles=guidata(hbrowse); - SourceDir=get(BrowseHandles.SourceDir,'String'); - ListExperiments=get(BrowseHandles.ListExperiments,'String'); - ListValues=get(BrowseHandles.ListExperiments,'Value'); - ListExperiments=ListExperiments(ListValues); - DataSeries=get(BrowseHandles.DataSeries,'String'); - Val=get(BrowseHandles.DataSeries,'Value'); - DataFolder=DataSeries{Val}; - for ilist=1:numel(ListExperiments) - SubDirBase=regexprep(DataFolder,'+/',''); - ListExperiments{ilist}=regexprep(ListExperiments{ilist},'+/',''); - XmlName=fullfile(SourceDir,ListExperiments{ilist},[SubDirBase '.xml']); + BrowseData=guidata(hbrowse); + SourceDir=get(BrowseData.SourceDir,'String'); + ListExp=get(BrowseData.ListExperiments,'String'); + ExpIndices=get(BrowseData.ListExperiments,'Value'); + ListExp=ListExp(ExpIndices); + ListDevices=get(BrowseData.ListDevices,'String'); + DeviceIndices=get(BrowseData.ListDevices,'Value'); + ListDevices=ListDevices(DeviceIndices); + ListDataSeries=get(BrowseData.DataSeries,'String'); + DataSeriesIndices=get(BrowseData.DataSeries,'Value'); + ListDataSeries=ListDataSeries(DataSeriesIndices); + NbExp=0; % counter of the number of experiments set by the GUI browse_data + for iexp=1:numel(ListExp) + if ~isempty(regexp(ListExp{iexp},'^\+/'))% if it is a folder + for idevice=1:numel(ListDevices) + if ~isempty(regexp(ListDevices{idevice},'^\+/'))% if it is a folder + for isubdir=1:numel(ListDataSeries) + if ~isempty(regexp(ListDataSeries{isubdir},'^\+/'))% if it is a folder + lpath= fullfile(SourceDir,regexprep(ListExp{iexp},'^\+/',''),... + regexprep(ListDevices{idevice},'^\+/','')); + ldir= regexprep(ListDataSeries{isubdir},'^\+/',''); + if exist(fullfile(lpath,ldir),'dir') + NbExp=NbExp+1; + ListPath{NbExp}=lpath; + ListSubdir{NbExp}=ldir; + ExpIndex{NbExp}=iexp; + end + end + end + end + end + end + end + for iexp=1:NbExp + XmlName=fullfile(ListPath{iexp},[ListSubdir{iexp} '.xml']); + if exist(XmlName,'file') + check_update=1; + else + check_update=0; + end errormsg=update_imadoc(GeometryCalib,XmlName,'GeometryCalib');% introduce the calibration data in the xml file if ~strcmp(errormsg,'') msgbox_uvmat('ERROR',errormsg); else - display([XmlName ' updated with calibration parameters']) + if check_update + display([XmlName ' updated with calibration parameters']) + else + display([XmlName ' created with calibration parameters']) + end nbcalib=nbcalib+1; end end end - msgbox_uvmat('CONFIMATION',[SubDirBase ' calibrated for ' num2str(nbcalib) ' experiments']); + msgbox_uvmat('CONFIMATION',['calibration replicated for ' num2str(NbExp) ' experiments']); else %% copy the xml file from the old location if appropriate, then update with the calibration parameters Index: /trunk/src/plot_field.m =================================================================== --- /trunk/src/plot_field.m (revision 1067) +++ /trunk/src/plot_field.m (revision 1068) @@ -1408,5 +1408,5 @@ yi=rangy(1):dxy(1):rangy(2); A=griddata(vec_X,vec_Y,vec_A,xi,yi'); - A=reshape(A,length(yi),length(xi)); + A=reshape(A,length(yi),length(xi));total else x=vec_X(1:index(1));% the set of abscissa (obtained on the first line) Index: /trunk/src/series.m =================================================================== --- /trunk/src/series.m (revision 1067) +++ /trunk/src/series.m (revision 1068) @@ -1594,26 +1594,64 @@ end -%% Look for prcessing on multiple experiments set by the GUI browse_data -NbExp=1; -ListExp=Param.InputTable(1,1); - +%% Look for processing on multiple experiments set by the GUI browse_data +NbExp=1;% initiate the number of experiments set by the GUI browse_data, =1 otherwise if get(handles.Replicate,'Value') + set(handles.Replicate,'BackgroundColor',[1 1 0])%paint Relicate button in yellow hh=findobj(allchild(0),'Tag','browse_data'); BrowseData=guidata(hh); SourceDir=get(BrowseData.SourceDir,'String'); ListExp=get(BrowseData.ListExperiments,'String'); - ListExp=ListExp(get(BrowseData.ListExperiments,'Value')); - NbExp=numel(ListExp) % number of experiments set possibly by the GUI browse_data, =1 otherwise - for ilist=1:NbExp - ListExp{ilist}=regexprep(ListExp{ilist},'+',''); - ListExp{ilist}= [SourceDir ListExp{ilist}]; - end -end - + ExpIndices=get(BrowseData.ListExperiments,'Value'); + ListExp=ListExp(ExpIndices); + ListDevices=get(BrowseData.ListDevices,'String'); + DeviceIndices=get(BrowseData.ListDevices,'Value'); + ListDevices=ListDevices(DeviceIndices); + ListDataSeries=get(BrowseData.DataSeries,'String'); + DataSeriesIndices=get(BrowseData.DataSeries,'Value'); + ListDataSeries=ListDataSeries(DataSeriesIndices); + NbExp=0; % counter of the number of experiments set by the GUI browse_data + for iexp=1:numel(ListExp) + if ~isempty(regexp(ListExp{iexp},'^\+/'))% if it is a folder + for idevice=1:numel(ListDevices) + if ~isempty(regexp(ListDevices{idevice},'^\+/'))% if it is a folder + for isubdir=1:numel(ListDataSeries) + if ~isempty(regexp(ListDataSeries{isubdir},'^\+/'))% if it is a folder + lpath= fullfile(SourceDir,regexprep(ListExp{iexp},'^\+/',''),... + regexprep(ListDevices{idevice},'^\+/','')); + ldir= regexprep(ListDataSeries{isubdir},'^\+/',''); + if exist(fullfile(lpath,ldir),'dir') + NbExp=NbExp+1; + ListPath{NbExp}=lpath; + ListSubdir{NbExp}=ldir; + ExpIndex{NbExp}=iexp; + end + end + end + end + end + end + end + answer=msgbox_uvmat('INPUT_Y-N-Cancel',['replicate the processing on ' num2str(NbExp) ' data series']); + if strcmp(answer,'Cancel')||strcmp(answer,'No') + return + end +end +% set(handles.OutputSubDir,'String',SubDir) +% Param.OutputSubDir=SubDir; %%%%%%%%%%%%%%%%%%% LOOP ON EXPERIMENTS POSSIBLY SET BY THE GUI browse_data, NbExp=1 otherwise %%%%%%%%% for iexp=1:NbExp - Param.InputTable{1,1}=ListExp{iexp}; - set(handles.InputTable,'Data',Param.InputTable) - [xx,ExpName]=fileparts(ListExp{iexp}); + if get(handles.Replicate,'Value') + if ~strcmp(get(handles.RUN,'BusyAction'),'queue')% allow for STOP action + disp('program stopped by user') + return + end + set(BrowseData.ListExperiments,'Value',ExpIndex{iexp}) + Param.InputTable{1,1}=ListPath{iexp}; + Param.InputTable{1,2}=ListSubdir{iexp}; + Param.OutputSubDir=ListSubdir{iexp}; + set(handles.InputTable,'Data',Param.InputTable) +% set(handles.OutputSubDir,'String',ListSubdir{iexp}) + end + [xx,ExpName]=fileparts(Param.InputTable{1,1}); Param.IndexRange.first_i=str2num(get(handles.num_first_i,'String'));%reset the firrst_i and last_i for multiple experiments, modified by the splitting into NbProcess Param.IndexRange.last_i=str2num(get(handles.num_last_i,'String')); @@ -1621,5 +1659,5 @@ OutputDir=''; answer=''; - if isfield(Param,'OutputSubDir') + if isfield(Param,'OutputSubDir')% possibly update the output dir if it already exists SubDirOut=[get(handles.OutputSubDir,'String') Param.OutputDirExt]; SubDirOutNew=SubDirOut; @@ -1659,5 +1697,5 @@ Param.OutputRootFile=Param.InputTable{1,3}; % the first sorted RootFile taken for output set(handles.OutputDirExt,'String',Param.OutputDirExt) - OutputDir=fullfile(Param.InputTable{1,1},[Param.OutputSubDir Param.OutputDirExt]); % full name (with path) of output directory + OutputDir=fullfile(Param.InputTable{1,1},[Param.OutputSubDir Param.OutputDirExt]) % full name (with path) of output directory if check_create % create output directory if it does not exist [tild,msg1]=mkdir(OutputDir); @@ -1677,4 +1715,8 @@ errormsg=['cannot create ' DirXml ': ' msg1]; % error message for directory creation return + end + [success,msg] = fileattrib(DirXml,'+w','g','s'); % allow writing access for the group of users, recursively in the folder + if success==0 + msgbox_uvmat('WARNING',{['unable to set group write access to ' DirXml ':']; msg}); % error message for directory creation end end @@ -1861,4 +1903,8 @@ return end + [success,msg] = fileattrib(DirExe,'+w','g','s'); % allow writing access for the group of users, recursively in the folder + if success==0 + msgbox_uvmat('WARNING',{['unable to set group write access to ' DirExe ':']; msg}); % error message for directory creation + end end %create subdirectory for log files @@ -1869,4 +1915,8 @@ errormsg=['cannot create ' DirLog ': ' msg1]; % error message for directory creation return + end + [success,msg] = fileattrib(DirLog,'+w','g','s'); % allow writing access for the group of users, recursively in the folder + if success==0 + msgbox_uvmat('WARNING',{['unable to set group write access to ' DirLog ':']; msg}); % error message for directory creation end end @@ -2024,7 +2074,7 @@ fclose(fid); if status==0 - msgbox_uvmat('CONFIRMATION',[ActionFullName ' launched for ' ExpName ' as ' num2str(NbProcess) ' processes in cluster: press STATUS to see results']) + msgbox_uvmat('CONFIRMATION',[ActionFullName ' launched for ' ExpName ' as ' num2str(NbProcess) ' processes in cluster: press STATUS to see results']) else - msgbox_uvmat('ERROR',result) + msgbox_uvmat('ERROR',result) end % case 'cluster_pbs' % for LMFA Kepler machine: trqnsferred to fct @@ -2144,4 +2194,8 @@ end end +set(handles.Replicate,'BackgroundColor',[0 1 0]) +if NbExp>1 + set(handles.REFRESH,'BackgroundColor',[1 0 1])% set REFRESH button to magenta (input file features need to be updated) +end %------------------------------------------------------------------------ function STOP_Callback(hObject, eventdata, handles) @@ -2160,5 +2214,5 @@ Param=read_GUI(handles.series); -%% clean the output structure by removing unused information +%% clean the output structure by removing unused information if isfield(Param,'Pairs') Param=rmfield(Param,'Pairs'); % info Pairs not needed for output @@ -2203,5 +2257,5 @@ ActionList=get(handles.ActionName,'String'); % list menu fields ActionIndex=get(handles.ActionName,'Value'); -if ~isequal(ActionIndex,1)% if we are not just opening series +if ~isequal(ActionIndex,1)% if we are not just opening series InputTable=get(handles.InputTable,'Data'); if isempty(InputTable{1,4}) @@ -2301,4 +2355,5 @@ set(handles.ActionInput,'BackgroundColor',[1 1 0]) +SeriesData=get(handles.series,'UserData'); % info on the input file series %% create the function handle for Action @@ -2308,5 +2363,4 @@ if ~exist(ActionPath,'dir') ActionName_Callback(handles.ActionName, ActionPath, handles)% update the function -% msgbox_uvmat('ERROR',['The prescribed function path ' ActionPath ' does not exist']); return end @@ -2319,4 +2373,5 @@ Param=read_GUI_series(handles); % read the parameters from the GUI series Param.Action.RUN=0; +Param.SeriesData=SeriesData; ParamOut=h_fun(Param); % run the selected Action function to get the relevant input @@ -2337,5 +2392,4 @@ %% Detect the types of input files and set menus and default options in 'VelType' -SeriesData=get(handles.series,'UserData'); % info on the input file series iview_civ=find(strcmp('civx',SeriesData.FileType)|strcmp('civdata',SeriesData.FileType)); iview_netcdf=find(strcmp('netcdf',SeriesData.FileType)|strcmp('civx',SeriesData.FileType)|strcmp('civdata',SeriesData.FileType)); % all nc files, icluding civ @@ -2469,7 +2523,12 @@ set(handles.MinIndex_j,'Data',MinIndex_j(iview,:)); set(handles.MaxIndex_i,'Data',MaxIndex_i(iview,:)); - set(handles.MaxIndex_j,'Data',MaxIndex_j(iview,:)); + set(handles.MaxIndex_j,'Data',MaxIndex_j(iview,:));; TimeTable=get(handles.TimeTable,'Data'); - set(handles.TimeTable,'Data',TimeTable(iview,:)); + if size(TimeTable,1) start at 316 start 67->_11_1 -%count=1934%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%CORRECTION EXP07: 3066 images %% loop on the files % include the first tiff file with no index in the first iteration @@ -174,4 +149,5 @@ end for ifile=firstindex:Param.IndexRange.last_i + tic if firstindex==0 && ifile==0% first slice of processing ImageName=fullfile(Param.InputTable{1,1},Param.InputTable{1,2},'im.tif') @@ -181,5 +157,4 @@ NbFrames=numel(imfinfo(ImageName)); for iframe=1:NbFrames - iframe if isequal(ImagesPerLevel,1)% mode series OutputFile=fullfile(OutputDir,['img_' num2str(count+1) '.png']); @@ -198,4 +173,7 @@ count=count+1; end + tt=toc; + disp(['elapsed time (in min.) for the file im@' num2str(ifile,'%04d')]) + disp(num2str(tt/60)) end Index: /trunk/src/series/extract_rdvision.m =================================================================== --- /trunk/src/series/extract_rdvision.m (revision 1067) +++ /trunk/src/series/extract_rdvision.m (revision 1068) @@ -489,12 +489,12 @@ %% correct NbDtj and NbDti (error from RDvision) -if NbDtj==numel(Dtj)% case of bursts - NbDtj=1; - uid_motor_nbslice=find(t,'ImaDoc/TranslationMotor/Nbslice'); - if ~isempty(uid_motor_nbslice)&& ~isempty(uid_Dtk)% case of multilevel - NbSlice=str2num(get(t,get(t,uid_motor_nbslice,'contents'),'value')); - NbDti=NbSlice-1; - end -end +% if NbDtj==numel(Dtj)% case of bursts +% NbDtj=1; +% uid_motor_nbslice=find(t,'ImaDoc/TranslationMotor/Nbslice'); +% if ~isempty(uid_motor_nbslice)&& ~isempty(uid_Dtk)% case of multilevel +% NbSlice=str2num(get(t,get(t,uid_motor_nbslice,'contents'),'value')); +% NbDti=NbSlice-1; +% end +% end if isempty(Dtj)% case of simple series @@ -509,40 +509,40 @@ nbfield2=NbDtj*numel(Dtj)+1; NbFrames_xml=nbfield1*nbfield2; - if NbFrames_xmlnumel(timestamp) - nbfield1=floor(numel(timestamp)/nbfield2); - nbfieldk=floor(nbfield1/nbfieldi); - nbfield1=nbfieldi*nbfieldk; - NbDtk=nbfieldk-1; - t=set(t,uid_content_NbDtk,'value',num2str(NbDtk));% correct NbDtk in the xml file (in practice numel(Dtk)=1; - timestamp=timestamp(1:nbfield1*nbfield2); - disp(['image record stopped before end: max index i= ' num2str(nbfield1)]); - timestamp=reshape(timestamp,nbfield2,nbfield1); - end - % check Dtj with respect to timestamp - timestamp=(reshape(timestamp,nbfield2,[]))'; - diff_Dtj=diff(timestamp(1,:))-Dtj; - if max(abs(diff_Dtj))>min(Dtj)/1000 - disp(['Dtj from xml file differs from time stamp by ' num2str(max(abs(diff_Dtj))) ', '])%' - else - disp('Dtj OK'); - end +% if NbFrames_xmlnumel(timestamp) +% nbfield1=floor(numel(timestamp)/nbfield2); +% nbfieldk=floor(nbfield1/nbfieldi); +% nbfield1=nbfieldi*nbfieldk; +% NbDtk=nbfieldk-1; +% t=set(t,uid_content_NbDtk,'value',num2str(NbDtk));% correct NbDtk in the xml file (in practice numel(Dtk)=1; +% timestamp=timestamp(1:nbfield1*nbfield2); +% disp(['image record stopped before end: max index i= ' num2str(nbfield1)]); +% timestamp=reshape(timestamp,nbfield2,nbfield1); +% end +% % check Dtj with respect to timestamp +% timestamp=(reshape(timestamp,nbfield2,[]))'; +% diff_Dtj=diff(timestamp(1,:))-Dtj; +% if max(abs(diff_Dtj))>min(Dtj)/1000 +% disp(['Dtj from xml file differs from time stamp by ' num2str(max(abs(diff_Dtj))) ', '])%' +% else +% disp('Dtj OK'); +% end end %% adjust Dti -if NbDti+1>size(timestamp,1) - NbDti=size(timestamp,1)-1; -end -Dti_stamp=(timestamp(1+NbDti,1)-timestamp(1,1))/NbDti; -Dti_stamp=(timestamp(1+NbDti,1)-timestamp(2,1))/(NbDti-1); -t=set(t,uid_content_Dti,'value',num2str(Dti_stamp));%corret Dti -if abs(Dti_stamp-Dti)>Dti/1000 - disp([msg 'Dti from xml file corrected by ' num2str(Dti_stamp-Dti) ', ']);%' -else - disp('Dti OK') -end +% if NbDti+1>size(timestamp,1) +% NbDti=size(timestamp,1)-1; +% end +% Dti_stamp=(timestamp(1+NbDti,1)-timestamp(1,1))/NbDti; +% Dti_stamp=(timestamp(1+NbDti,1)-timestamp(2,1))/(NbDti-1); +% t=set(t,uid_content_Dti,'value',num2str(Dti_stamp));%corret Dti +% if abs(Dti_stamp-Dti)>Dti/1000 +% disp([msg 'Dti from xml file corrected by ' num2str(Dti_stamp-Dti) ', ']);%' +% else +% disp('Dti OK') +% end %% adjust Dtk Index: /trunk/src/series/merge_proj_polar.m =================================================================== --- /trunk/src/series/merge_proj_polar.m (revision 1067) +++ /trunk/src/series/merge_proj_polar.m (revision 1068) @@ -63,5 +63,5 @@ ParamOut.AllowInputSort='on';% allow alphabetic sorting of the list of input file SubDir (options 'off'/'on', 'off' by default) ParamOut.WholeIndexRange='off';% prescribes the file index ranges from min to max (options 'off'/'on', 'off' by default) - ParamOut.NbSlice='on'; %nbre of slices ('off' by default) + ParamOut.NbSlice='off'; %nbre of slices ('off' by default) ParamOut.VelType='one';% menu for selecting the velocity type (options 'off'/'one'/'two', 'off' by default) ParamOut.FieldName='off';% menu for selecting the field (s) in the input file(options 'off'/'one'/'two', 'off' by default) @@ -268,8 +268,6 @@ CheckOverwrite=Param.CheckOverwrite; end - +NbField for index=1:NbField - disp(['index=' num2str(index)]) - disp(['ellapsed time ' num2str(toc(tstart)/60,4) ' minutes']) update_waitbar(WaitbarHandle,index/NbField) if ~isempty(RUNHandle) && ~strcmp(get(RUNHandle,'BusyAction'),'queue') @@ -352,8 +350,12 @@ %% calculate tps coefficients Data{iview}=tps_coeff_field(Data{iview},1); - + 'tps_coeff done' %% projection on the polar grid [DataOut,VarAttribute,errormsg]=calc_field_tps(Data{iview}.Coord_tps,Data{iview}.NbCentre,Data{iview}.SubRange,... cat(3,Data{iview}.U_tps,Data{iview}.V_tps),FieldNames,cat(3,XI,YI)); + if ~isempty(errormsg) + disp(errormsg) + end + % set to NaN interpolation points which are too far from any initial data (more than 2 CoordMesh) Coord=permute(Data{iview}.Coord_tps,[1 3 2]); @@ -366,4 +368,5 @@ G=TriScatteredInterp(Coord,Coord(:,2),'nearest'); end + 'Interp done' Distx=F(XI,YI)-XI;% diff of x coordinates with the nearest measurement point Disty=G(XI,YI)-YI;% diff of y coordinates with the nearest measurement point @@ -390,4 +393,5 @@ %% merge the NbView fields + ProjData [MergeData,errormsg]=merge_field(ProjData); if ~isempty(errormsg) @@ -446,5 +450,5 @@ TimeData.div=MergeData.div; - [error,ncid]=struct2nc(OutputFile,TimeData);%save result file + error=struct2nc(OutputFile,TimeData);%save result file if isempty(error) disp(['output file ' OutputFile ' written']) @@ -453,9 +457,7 @@ end ellapsed_time=toc(tstart); - disp(['total ellapsed time ' num2str(ellapsed_time/60,2) ' minutes']) -end - -ellapsed_time=toc(tstart); -disp(['total ellapsed time ' num2str(ellapsed_time/60,2) ' minutes']) + disp(['ellapsed time since start ' num2str(ellapsed_time/60,2) ' minutes']) +end + disp([ num2str(ellapsed_time/(60*NbField),3) ' minutes per iteration']) Index: /trunk/src/uvmat.m =================================================================== --- /trunk/src/uvmat.m (revision 1067) +++ /trunk/src/uvmat.m (revision 1068) @@ -254,7 +254,7 @@ %% case of an input argument for uvmat -testinputfield=0; +%testinputfield=0; inputfile=[]; -Field=[]; +%Field=[]; if exist('input','var') if ishandle(handles.UVMAT_title) @@ -790,5 +790,5 @@ %aviobj=avifile(MovieName,'Compression','None','fps',fps); -aviobj = VideoWriter(MovieName,'Uncompressed AVI'); +aviobj = VideoWriter(MovieName,'Motion JPEG AVI'); open(aviobj) %% get info from uvmat and adjust it @@ -812,5 +812,4 @@ set(htitle,'String',regexprep(Title,'t=\d+.\d*',['t=' time_str])) mov=getframe(figure_movie); - % aviobj=addframe(aviobj,mov); writeVideo(aviobj,mov); end