source: trunk/src/series/check_data_files.m @ 619

Last change on this file since 619 was 616, checked in by sommeria, 11 years ago

particle_tracking added, cleaning for other functions in 'series'

File size: 8.7 KB
1%%'check_data_files': check the existence, type and status of the files selected by series.fig
3% function GUI_input=check_data_files(Param)
5%%%%%%%%%%% GENERAL TO ALL SERIES ACTION FCTS %%%%%%%%%%%%%%%%%%%%%%%%%%%
7% GUI_input=list of options in the GUI series.fig needed for the function
10% In run mode, the input parameters are given as a Matlab structure Param copied from the GUI series.
11% In batch mode, Param is the name of the corresponding xml file containing the same information
12% In the absence of input (as activated when the current Action is selected
13% in series), the function ouput GUI_input set the activation of the needed GUI elements
15% Param contains the elements:(use the menu bar command 'export/GUI config' in series to see the current structure Param)
16%    .InputTable: cell of input file names, (several lines for multiple input)
17%                      each line decomposed as {RootPath,SubDir,Rootfile,NomType,Extension}
18%    .OutputSubDir: name of the subdirectory for data outputs
19%    .OutputDir: directory for data outputs, including path
20%    .Action: .ActionName: name of the current activated function
21%             .ActionPath:   path of the current activated function
22%    .IndexRange: set the file or frame indices on which the action must be performed
23%    .FieldTransform: .TransformName: name of the selected transform function
24%                     .TransformPath:   path  of the selected transform function
25%                     .TransformHandle: corresponding function handle
26%    .InputFields: sub structure describing the input fields withfields
27%              .FieldName: name of the field
28%              .VelType: velocity type
29%              .FieldName_1: name of the second field in case of two input series
30%              .VelType_1: velocity type of the second field in case of two input series
31%    .ProjObject: %sub structure describing a projection object (read from ancillary GUI set_object)
34function ParamOut=check_data_files(Param)
36%% input preparation mode (no RUN)
37if isstruct(Param) && isequal(Param.Action.RUN,0)
38    ParamOut.AllowInputSort='off';% allow alphabetic sorting of the list of input file SubDir (options 'off'/'on', 'off' by default)
39    ParamOut.WholeIndexRange='off';% prescribes the file index ranges from min to max (options 'off'/'on', 'off' by default)
40    ParamOut.NbSlice='on';%nbre of slices ('off' by default)
41    ParamOut.VelType='off';% menu for selecting the velocity type (options 'off'/'one'/'two',  'off' by default)
42    ParamOut.FieldName='off';% menu for selecting the field (s) in the input file(options 'off'/'one'/'two', 'off' by default)
43    ParamOut.FieldTransform = 'off';%can use a transform function
44    ParamOut.ProjObject='off';%can use projection object(option 'off'/'on',
45    ParamOut.Mask='off';%can use mask option   (option 'off'/'on', 'off' by default)
46    ParamOut.OutputDirExt='';%set the output dir extension (blank=no output dir)
49%%%%%%%%%%%%  STANDARD PART  %%%%%%%%%%%%
51%% read input parameters from an xml file if input is a file name (batch mode)
53if ischar(Param)
54    Param=xml2struct(Param);% read Param as input file (batch case)
55    checkrun=0;
58%% root input file(s) and type
65if isempty(i1_series)
66    return
69% The cell array filecell is the list of input file names, while
70% filecell{iview,fileindex}:
71%        iview: line in the table corresponding to a given file series
72%        fileindex: file index within  the file series,
73% i1_series(iview,ref_j,ref_i)... are the corresponding arrays of indices i1,i2,j1,j2, depending on the input line iview and the two reference indices ref_i,ref_j
74% i1_series(iview,fileindex) expresses the same indices as a 1D array in file indices
77if isfield(Param.IndexRange,'NbSlice')&&~isempty(Param.IndexRange.NbSlice)
78    NbSlice=Param.IndexRange.NbSlice;
80nbview=numel(i1_series);%number of input file series (lines in InputTable)
81nbfield_j=size(i1_series{1},1); %nb of fields for the j index (bursts or volume slices)
82nbfield_i=size(i1_series{1},2); %nb of fields for the i index
83nbfield=nbfield_j*nbfield_i; %total number of fields
84nbfield_i=floor(nbfield/NbSlice);%total number of  indexes in a slice (adjusted to an integer number of slices)
85nbfield=nbfield_i*NbSlice; %total number of fields after adjustement
87%determine the file type on each line from the first input file
90for iview=1:nbview
91    [FileType{iview},FileInfo{iview},Object{iview}]=get_file_type(filecell{iview,1});
92    CheckImage{iview}=~isempty(find(strcmp(FileType{iview},ImageTypeOptions)));% =1 for images
93    CheckNc{iview}=~isempty(find(strcmp(FileType{iview},NcTypeOptions)));% =1 for netcdf files
97for iview=1:nbview
98    if isequal(FileType{iview},'mmreader')||isequal(FileType{iview},'video')||isequal(FileType{iview},'multimage')
99        [tild,FileInfo]=get_file_type(filecell{iview,1});
100        Tabchar{1}=filecell{iview,1};%info.Filename;
101        Tabchar{2}='';
102        Tabchar{3}=[num2str(FileInfo.FrameRate) ' frames/s '];
103%         Tabchar{4}='';
104%         Tabchar{5}=['  compression' FileInfo.VideoCompression];
105%         Tabchar{6}=[ 'quality ' num2str(FileInfo.Quality)];
106    else
107        Tabchar={};
108        %LOOP ON SLICES
109        for i_slice=1:NbSlice
110            index_slice=i_slice:NbSlice:nbfield;
111            filefound={};
112            datnum=zeros(1,nbfield_j);
113            for ifile=1:nbfield_i
114                if checkrun
115                    stopstate=get(Param.RUNHandle,'BusyAction');
116                    update_waitbar(Param.WaitbarHandle,ifile/nbfield_i)
117                else
118                    stopstate='queue';
119                end
120                if isequal(stopstate,'queue')% enable STOP command
121                    file=filecell{iview,index_slice(ifile)};
122                    [Path,Name,ext]=fileparts(file);
123                    detect=exist(file,'file'); % check the existence of the file
124                    if detect==0
125                        lastfield='not found';
126                    else
127                        datfile=dir(file);
128                        if isfield(datfile,'datenum')
129                            datnum(ifile)=datfile.datenum;
130                            filefound(ifile)={};
131                        end
132                        lastfield='';
133                        [FileType{iview},FileInfo,Object]=get_file_type(file);
134                        if strcmp(FileType{iview},'civx')||strcmp(FileType{iview},'civdata')
135                            if isfield(FileInfo,'CivStage')
136                                liststage={'civ1','fix1','patch1','civ2','fix2','patch2'};
137                                lastfield=liststage{FileInfo.CivStage};
138                            end
139                        end
140                        lastfield=[FileType{iview} ', ' lastfield];
141                    end
142                    Tabchar(1,i_slice)={['slice #' num2str(i_slice)]};
143                    Tabchar(ifile+1,i_slice)={[file '...' lastfield]};
144                end
145            end
146        end
147        if isempty(filefound)
148            if NbSlice>1
149                message=['no set of ' num2str(NbSlice) ' (NbSlices) files found'];
150            else
151                message='no file found';
152            end
153        else
154            datnum=datnum(find(datnum));%keep the non zero values corresponding to existing files
155            filefound=filefound(find(datnum));
156            [first,ind]=min(datnum);
157            [last,indlast]=max(datnum);
158            message={['oldest modification:  ' filefound{ind} ' : ' datestr(first)];...
159                ['latest modification:  ' filefound{indlast} ' : ' datestr(last)]};
160        end
161        if ~isempty(Tabchar)
162            Tabchar=reshape(Tabchar,NbSlice*(nbfield_i+1),1);
163        end
164    end
165    hfig=figure(iview);
166    clf
167    if iview>1
168        pos=get(iview-1,'Position');
169        pos(1)=pos(1)+(iview-1)*pos(1)/nbview;
170        set(hfig,'Position',pos)
171    end
172    set(hfig,'name',['check_data_files:view= ' num2str(iview)])
173    set(hfig,'MenuBar','none')% suppress the menu bar
174    set(hfig,'NumberTitle','off')%suppress the fig number in the title
175    h=uicontrol('Style','listbox', 'Position', [20 20 500 300], 'String', Tabchar, 'Callback', {'open_uvmat'});
176    hh=uicontrol('Style','listbox', 'Position', [20 340 500 40], 'String', message);
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