source: trunk/src/series/aver_stat.m @ 598

Last change on this file since 598 was 598, checked in by sommeria, 8 years ago

various bugs repaired . civ_series further developed

File size: 13.4 KB
Line 
1%'aver_stat': calculate field average over a time series
2%------------------------------------------------------------------------
3% function ParamOut=aver_stat(Param)
4%
5%%%%%%%%%%% GENERAL TO ALL SERIES ACTION FCTS %%%%%%%%%%%%%%%%%%%%%%%%%%%
6%
7%OUTPUT
8% ParamOut: sets options in the GUI series.fig needed for the function
9%
10%INPUT:
11% In run mode, the input parameters are given as a Matlab structure Param copied from the GUI series.
12% In batch mode, Param is the name of the corresponding xml file containing the same information
13% when Param.Action.RUN=0 (as activated when the current Action is selected
14% in series), the function ouput paramOut set the activation of the needed GUI elements
15%
16% Param contains the elements:(use the menu bar command 'export/GUI config' in series to
17% see the current structure Param)
18%    .InputTable: cell of input file names, (several lines for multiple input)
19%                      each line decomposed as {RootPath,SubDir,Rootfile,NomType,Extension}
20%    .OutputSubDir: name of the subdirectory for data outputs
21%    .OutputDirExt: directory extension for data outputs
22%    .Action: .ActionName: name of the current activated function
23%             .ActionPath:   path of the current activated function
24%             .ActionExt: fct extension ('.m', Matlab fct, '.sh', compiled   Matlab fct
25%             .RUN =0 for GUI input, =1 for function activation
26%             .RunMode='local','background', 'cluster': type of function  use
27%             
28%    .IndexRange: set the file or frame indices on which the action must be performed
29%    .FieldTransform: .TransformName: name of the selected transform function
30%                     .TransformPath:   path  of the selected transform function
31%    .InputFields: sub structure describing the input fields withfields
32%              .FieldName: name(s) of the field
33%              .VelType: velocity type
34%              .FieldName_1: name of the second field in case of two input series
35%              .VelType_1: velocity type of the second field in case of two input series
36%              .Coord_y: name of y coordinate variable
37%              .Coord_x: name of x coordinate variable
38%    .ProjObject: %sub structure describing a projection object (read from ancillary GUI set_object)
39%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
40
41function ParamOut=aver_stat(Param)
42
43%% set the input elements needed on the GUI series when the action is selected in the menu ActionName
44if isstruct(Param) && isequal(Param.Action.RUN,0)
45    ParamOut.AllowInputSort='off';...% allow alphabetic sorting of the list of input file SubDir (options 'off'/'on', 'off' by default)
46    ParamOut.WholeIndexRange='off';...% prescribes the file index ranges from min to max (options 'off'/'on', 'off' by default)
47    ParamOut.NbSlice='on'; ...%nbre of slices ('off' by default)
48    ParamOut.VelType='two';...% menu for selecting the velocity type (options 'off'/'one'/'two',  'off' by default)
49    ParamOut.FieldName='two';...% menu for selecting the field (s) in the input file(options 'off'/'one'/'two', 'off' by default)
50    ParamOut.FieldTransform = 'on';...%can use a transform function
51    ParamOut.ProjObject='on';...%can use projection object(option 'off'/'on',
52    ParamOut.Mask='off';...%can use mask option   (option 'off'/'on', 'off' by default)
53    ParamOut.OutputDirExt='.stat';%set the output dir extension
54return
55end
56
57%%%%%%%%%%%%  STANDARD PART  %%%%%%%%%%%%
58ParamOut=[];
59%% read input parameters from an xml file if input is a file name (batch mode)
60checkrun=1;
61if ischar(Param)
62    Param=xml2struct(Param);% read Param as input file (batch case)
63    checkrun=0;
64end
65
66
67ParamOut=Param; %default output
68OutputDir=[Param.OutputSubDir Param.OutputDirExt];
69   
70%% root input file(s) and type
71RootPath=Param.InputTable(:,1);
72RootFile=Param.InputTable(:,3);
73SubDir=Param.InputTable(:,2);
74NomType=Param.InputTable(:,4);
75FileExt=Param.InputTable(:,5);
76[filecell,i1_series,i2_series,j1_series,j2_series]=get_file_series(Param);
77%%%%%%%%%%%%
78% The cell array filecell is the list of input file names, while
79% filecell{iview,fileindex}:
80%        iview: line in the table corresponding to a given file series
81%        fileindex: file index within  the file series,
82% 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
83% i1_series(iview,fileindex) expresses the same indices as a 1D array in file indices
84%%%%%%%%%%%%
85% NbSlice=1;%default
86% if isfield(Param.IndexRange,'NbSlice')&&~isempty(Param.IndexRange.NbSlice)
87%     NbSlice=Param.IndexRange.NbSlice;
88% end
89nbview=numel(i1_series);%number of input file series (lines in InputTable)
90nbfield_j=size(i1_series{1},1); %nb of fields for the j index (bursts or volume slices)
91nbfield_i=size(i1_series{1},2); %nb of fields for the i index
92nbfield=nbfield_j*nbfield_i; %total number of fields
93%nbfield_i=floor(nbfield/NbSlice);%total number of  indexes in a slice (adjusted to an integer number of slices)
94%nbfield=nbfield_i*NbSlice; %total number of fields after adjustement
95
96%determine the file type on each line from the first input file
97ImageTypeOptions={'image','multimage','mmreader','video'};
98NcTypeOptions={'netcdf','civx','civdata'};
99for iview=1:nbview
100    if ~exist(filecell{iview,1}','file')
101        msgbox_uvmat('ERROR',['the first input file ' filecell{iview,1} ' does not exist'])
102        return
103    end
104    [FileType{iview},FileInfo{iview},MovieObject{iview}]=get_file_type(filecell{iview,1});
105    CheckImage{iview}=~isempty(find(strcmp(FileType{iview},ImageTypeOptions)));% =1 for images
106    CheckNc{iview}=~isempty(find(strcmp(FileType{iview},NcTypeOptions)));% =1 for netcdf files
107    if ~isempty(j1_series{iview})
108        frame_index{iview}=j1_series{iview};
109    else
110        frame_index{iview}=i1_series{iview};
111    end
112end
113
114%% calibration data and timing: read the ImaDoc files
115[XmlData,NbSlice_calib,time,errormsg]=read_multimadoc(RootPath,SubDir,RootFile,FileExt,i1_series,i2_series,j1_series,j2_series);
116if size(time,1)>1
117    diff_time=max(max(diff(time)));
118    if diff_time>0
119        msgbox_uvmat('WARNING',['times of series differ by (max) ' num2str(diff_time)])
120    end   
121end
122
123%% coordinate transform or other user defined transform
124transform_fct='';%default
125if isfield(Param,'FieldTransform')&&~isempty(Param.FieldTransform.TransformName)
126    addpath(Param.FieldTransform.TransformPath)
127    transform_fct=str2func(Param.FieldTransform.TransformName);
128    rmpath(Param.FieldTransform.TransformPath)
129end
130
131%%%%%%%%%%%% END STANDARD PART  %%%%%%%%%%%%
132 % EDIT FROM HERE
133
134%% check the validity of  input file types
135if CheckImage{1}
136    FileExtOut='.png'; % write result as .png images for image inputs
137elseif CheckNc{1}
138    FileExtOut='.nc';% write result as .nc files for netcdf inputs
139else
140    msgbox_uvmat('ERROR',['invalid file type input ' FileType{1}])
141    return
142end
143if nbview==2 && ~isequal(CheckImage{1},CheckImage{2})
144        msgbox_uvmat('ERROR','input must be two image series or two netcdf file series')
145    return
146end
147NomTypeOut='_1-2_1';% output file index will indicate the first and last ref index in the series
148
149
150%% Set field names and velocity types
151InputFields{1}=[];%default (case of images)
152if isfield(Param,'InputFields')
153    InputFields{1}=Param.InputFields;
154end
155if nbview==2
156    InputFields{2}=[];%default (case of images)
157    if isfield(Param,'InputFields')
158        InputFields{2}=Param.InputFields{1};%default
159        if isfield(Param.InputFields,'FieldName_1')
160            InputFields{2}.FieldName=Param.InputFields.FieldName_1;
161            if isfield(Param.InputFields,'VelType_1')
162                InputFields{2}.VelType=Param.InputFields.VelType_1;
163            end
164        end
165    end
166end
167
168% for i_slice=1:NbSlice
169% index_slice=i_slice:NbSlice:nbfield;% select file indices of the slice
170nbfiles=0;
171nbmissing=0;
172
173%%%%%%%%%%%%%%%% loop on field indices %%%%%%%%%%%%%%%%
174for index=1:nbfield
175%for index=index_slice
176      if checkrun
177            stopstate=get(Param.RUNHandle,'BusyAction');
178            update_waitbar(Param.WaitbarHandle,index/nbfield)
179      else
180            stopstate='queue';
181      end
182    if isequal(stopstate,'queue')% enable STOP command
183
184    %%%%%%%%%%%%%%%% loop on views (input lines) %%%%%%%%%%%%%%%%
185    for iview=1:nbview
186        % reading input file(s)
187        [Data{iview},tild,errormsg] = read_field(filecell{iview,index},FileType{iview},InputFields{iview},frame_index{iview}(index));
188        if ~isempty(errormsg)
189            errormsg=['error of input reading: ' errormsg];
190            break
191        end
192        if ~isempty(NbSlice_calib)
193            Data{iview}.ZIndex=mod(i1_series{iview}(index)-1,NbSlice_calib{iview})+1;%Zindex for phys transform
194        end
195    end
196    else
197        errormsg='stop';
198    end
199    %%%%%%%%%%%%%%%% end loop on views (input lines) %%%%%%%%%%%%%%%%
200    %%%%%%%%%%%% END STANDARD PART  %%%%%%%%%%%%
201    % EDIT FROM HERE
202
203    if isempty(errormsg)
204        Field=Data{1}; % default input field structure
205        %% coordinate transform (or other user defined transform)
206        if ~isempty(transform_fct)
207            switch nargin(transform_fct)
208                case 4
209                    if length(Data)==2
210                        Field=transform_fct(Data{1},XmlData{1},Data{2},XmlData{2});
211                    else
212                        Field=transform_fct(Data{1},XmlData{1});
213                    end
214                case 3
215                    if length(Data)==2
216                        Field=transform_fct(Data{1},XmlData{1},Data{2});
217                    else
218                        Field=transform_fct(Data{1},XmlData{1});
219                    end
220                case 2
221                    Field=transform_fct(Data{1},XmlData{1});
222                case 1
223                    Field=transform_fct(Data{1});
224            end
225        end
226
227        %% calculate tps coefficients if needed
228        if isfield(Param,'ProjObject')&&isfield(Param.ProjObject,'ProjMode')&& strcmp(Param.ProjObject.ProjMode,'interp_tps')
229            Field=tps_coeff_field(Field,check_proj_tps);
230        end
231
232        %field projection on an object
233        if Param.CheckObject
234            [Field,errormsg]=proj_field(Field,Param.ProjObject);
235            if ~isempty(errormsg)
236                msgbox_uvmat('ERROR',['error in aver_stat/proj_field:' errormsg])
237                return
238            end
239        end
240        nbfiles=nbfiles+1;
241
242        %%%%%%%%%%%% MAIN RUNNING OPERATIONS  %%%%%%%%%%%%
243        %update sum
244        if nbfiles==1 %first field
245            time_1=[];
246            if isfield(Field,'Time')
247                time_1=Field.Time(1);
248            end
249            DataOut=Field;%default
250            for ivar=1:length(Field.ListVarName)
251                VarName=Field.ListVarName{ivar};
252                DataOut.(VarName)=double(DataOut.(VarName));
253            end
254        else   %current field
255            for ivar=1:length(Field.ListVarName)
256                VarName=Field.ListVarName{ivar};
257                sizmean=size(DataOut.(VarName));
258                siz=size(Field.(VarName));
259                if ~isequal(DataOut.(VarName),0)&& ~isequal(siz,sizmean)
260                    msgbox_uvmat('ERROR',['unequal size of input field ' VarName ', need to project  on a grid'])
261                    return
262                else
263                    DataOut.(VarName)=DataOut.(VarName)+ double(Field.(VarName)); % update the sum
264                end
265            end
266        end
267        %%%%%%%%%%%%   END MAIN RUNNING OPERATIONS  %%%%%%%%%%%%
268    else
269        display(errormsg)
270    end
271end
272%%%%%%%%%%%%%%%% end loop on field indices %%%%%%%%%%%%%%%%
273
274for ivar=1:length(Field.ListVarName)
275    VarName=Field.ListVarName{ivar};
276    DataOut.(VarName)=DataOut.(VarName)/nbfiles; % normalize the mean
277end
278if nbmissing~=0
279    msgbox_uvmat('WARNING',[num2str(nbmissing) ' input files are missing or skipted'])
280end
281if isempty(time) % time is read from files
282    if isfield(Field,'Time')
283        time_end=Field.Time(1);%last time read
284        if ~isempty(time_1)
285            DataOut.Time=time_1;
286            DataOut.Time_end=time_end;
287        end
288    end
289else  % time from ImaDoc prevails if it exists
290%         j1=1;%default
291%         if ~isempty(j1_series{1})
292%             j1=j1_series{1};
293%         end
294    %DataOut.Time=time(1,i1_series{1}(1),j1);
295    %DataOut.Time_end=time(end,i1_series{end}(end),j1_series{end}(end));
296    DataOut.Time=time(1);
297    DataOut.Time_end=time(end);
298end
299
300%writting the result file
301OutputFile=fullfile_uvmat(RootPath{1},OutputDir,RootFile{1},FileExtOut,NomTypeOut,i1_series{1}(1),i1_series{1}(end),j1_series{1}(1),j1_series{1}(end));
302if CheckImage{1} %case of images
303    if isequal(FileInfo{1}.BitDepth,16)||(numel(FileInfo)==2 &&isequal(FileInfo{2}.BitDepth,16))
304        DataOut.A=uint16(DataOut.A);
305        imwrite(DataOut.A,OutputFile,'BitDepth',16); % case of 16 bit images
306    else
307        DataOut.A=uint8(DataOut.A);
308        imwrite(DataOut.A,OutputFile,'BitDepth',8); % case of 16 bit images
309    end
310    display([OutputFile ' written']);
311else %case of netcdf input file , determine global attributes
312    errormsg=struct2nc(OutputFile,DataOut); %save result file
313    if isempty(errormsg)
314        display([OutputFile ' written']);
315    else
316        msgbox_uvmat('ERROR',['error in writting result file: ' errormsg])
317        display(errormsg)
318    end
319end  % end averaging  loop
320% end
321%%%%%%%%%%%%%%%% end loop on slices %%%%%%%%%%%%%%%%
322
323%% open the result file with uvmat (in RUN mode)
324if checkrun
325%     hget_field=findobj(allchild(0),'name','get_field');%find the get_field... GUI
326%     delete(hget_field)
327    uvmat(OutputFile)% open the last result file with uvmat
328end
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