source: trunk/src/series/aver_stat.m @ 544

Last change on this file since 544 was 526, checked in by sommeria, 12 years ago

bugs corrected; Posiibility of usual 1D plots introduced with the new way of using get_field. time_series and aver_stat updated

File size: 15.0 KB
Line 
1%'aver_stat': calculate field average, used with series.fig
2% this function can be used as a template for applying a global operation (here averaging) on a series of input fields
3%------------------------------------------------------------------------
4% function ParamOut=aver_stat(Param)
5%
6%%%%%%%%%%% GENERAL TO ALL SERIES ACTION FCTS %%%%%%%%%%%%%%%%%%%%%%%%%%%
7%
8% This function is used in four modes by the GUI series:
9%           1) config GUI: with no input argument, the function determine the suitable GUI configuration
10%           2) interactive input: the function is used to interactively introduce input parameters, and then stops
11%           3) RUN: the function itself runs, when an appropriate input  structure Param has been introduced.
12%           4) BATCH: the function itself proceeds in BATCH mode, using an xml file 'Param' as input.
13%
14% This function is used in four modes by the GUI series:
15%           1) config GUI: with no input argument, the function determine the suitable GUI configuration
16%           2) interactive input: the function is used to interactively introduce input parameters, and then stops
17%           3) RUN: the function itself runs, when an appropriate input  structure Param has been introduced.
18%           4) BATCH: the function itself proceeds in BATCH mode, using an xml file 'Param' as input.
19%
20%OUTPUT
21% GUI_input=list of options in the GUI series.fig needed for the function
22%
23%INPUT:
24% In run mode, the input parameters are given as a Matlab structure Param copied from the GUI series.
25% In batch mode, Param is the name of the corresponding xml file containing the same information
26% In the absence of input (as activated when the current Action is selected
27% in series), the function ouput GUI_input set the activation of the needed GUI elements
28%
29% Param contains the elements:(use the menu bar command 'export/GUI config' in series to see the current structure Param)
30%    .InputTable: cell of input file names, (several lines for multiple input)
31%                      each line decomposed as {RootPath,SubDir,Rootfile,NomType,Extension}
32%    .OutputSubDir: name of the subdirectory for data outputs
33%    .OutputDirExt: directory extension for data outputs
34%    .Action: .ActionName: name of the current activated function
35%             .ActionPath:   path of the current activated function
36%    .IndexRange: set the file or frame indices on which the action must be performed
37%    .FieldTransform: .TransformName: name of the selected transform function
38%                     .TransformPath:   path  of the selected transform function
39%                     .TransformHandle: corresponding function handle
40%    .InputFields: sub structure describing the input fields withfields
41%              .FieldName: name of the field
42%              .VelType: velocity type
43%              .FieldName_1: name of the second field in case of two input series
44%              .VelType_1: velocity type of the second field in case of two input series
45%    .ProjObject: %sub structure describing a projection object (read from ancillary GUI set_object)
46%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
47
48function ParamOut=aver_stat(Param)
49
50%% set the input elements needed on the GUI series when the action is selected in the menu ActionName
51if ~exist('Param','var') % case with no input parameter
52    ParamOut={'AllowInputSort';'off';...% allow alphabetic sorting of the list of input files (options 'off'/'on', 'off' by default)
53        'WholeIndexRange';'off';...% prescribes the file index ranges from min to max (options 'off'/'on', 'off' by default)
54        'NbSlice';'on'; ...%nbre of slices ('off' by default)
55        'VelType';'two';...% menu for selecting the velocity type (options 'off'/'one'/'two',  'off' by default)
56        'FieldName';'two';...% menu for selecting the field (s) in the input file(options 'off'/'one'/'two', 'off' by default)
57        'FieldTransform'; 'on';...%can use a transform function
58        'ProjObject';'on';...%can use projection object(option 'off'/'on',
59        'Mask';'off';...%can use mask option   (option 'off'/'on', 'off' by default)
60        'OutputDirExt';'.stat';...%set the output dir extension
61               ''};
62        return
63end
64
65%%%%%%%%%%%%  STANDARD PART  %%%%%%%%%%%%
66%% select different modes,  RUN, parameter input, BATCH
67% BATCH  case: read the xml file for batch case
68if ischar(Param)
69        Param=xml2struct(Param);
70        checkrun=0;
71% RUN case: parameters introduced as the input structure Param
72else
73    if isfield(Param,'Specific')&& strcmp(Param.Specific,'?')
74        checkrun=1;% will only search interactive input parameters (preparation of BATCH mode)
75    else
76        checkrun=2; % indicate the RUN option is used
77    end
78    hseries=guidata(Param.hseries);%handles of the GUI series
79end
80ParamOut=Param; %default output
81OutputDir=[Param.OutputSubDir Param.OutputDirExt];
82   
83%% root input file(s) and type
84RootPath=Param.InputTable(:,1);
85RootFile=Param.InputTable(:,3);
86SubDir=Param.InputTable(:,2);
87NomType=Param.InputTable(:,4);
88FileExt=Param.InputTable(:,5);
89[filecell,i1_series,i2_series,j1_series,j2_series]=get_file_series(Param);
90%%%%%%%%%%%%
91% The cell array filecell is the list of input file names, while
92% filecell{iview,fileindex}:
93%        iview: line in the table corresponding to a given file series
94%        fileindex: file index within  the file series,
95% 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
96% i1_series(iview,fileindex) expresses the same indices as a 1D array in file indices
97%%%%%%%%%%%%
98NbSlice=1;%default
99if isfield(Param.IndexRange,'NbSlice')&&~isempty(Param.IndexRange.NbSlice)
100    NbSlice=Param.IndexRange.NbSlice;
101end
102nbview=numel(i1_series);%number of input file series (lines in InputTable)
103nbfield_j=size(i1_series{1},1); %nb of fields for the j index (bursts or volume slices)
104nbfield_i=size(i1_series{1},2); %nb of fields for the i index
105nbfield=nbfield_j*nbfield_i; %total number of fields
106nbfield_i=floor(nbfield/NbSlice);%total number of  indexes in a slice (adjusted to an integer number of slices)
107nbfield=nbfield_i*NbSlice; %total number of fields after adjustement
108
109%determine the file type on each line from the first input file
110ImageTypeOptions={'image','multimage','mmreader','video'};
111NcTypeOptions={'netcdf','civx','civdata'};
112for iview=1:nbview
113    if ~exist(filecell{iview,1}','file')
114        msgbox_uvmat('ERROR',['the first input file ' filecell{iview,1} ' does not exist'])
115        return
116    end
117    [FileType{iview},FileInfo{iview},MovieObject{iview}]=get_file_type(filecell{iview,1});
118    CheckImage{iview}=~isempty(find(strcmp(FileType{iview},ImageTypeOptions)));% =1 for images
119    CheckNc{iview}=~isempty(find(strcmp(FileType{iview},NcTypeOptions)));% =1 for netcdf files
120    if ~isempty(j1_series{iview})
121        frame_index{iview}=j1_series{iview};
122    else
123        frame_index{iview}=i1_series{iview};
124    end
125end
126
127%% calibration data and timing: read the ImaDoc files
128[XmlData,NbSlice_calib,time,errormsg]=read_multimadoc(RootPath,SubDir,RootFile,FileExt,i1_series,i2_series,j1_series,j2_series);
129if size(time,1)>1
130    diff_time=max(max(diff(time)));
131    if diff_time>0
132        msgbox_uvmat('WARNING',['times of series differ by (max) ' num2str(diff_time)])
133    end   
134end
135
136%% coordinate transform or other user defined transform
137transform_fct='';%default
138if isfield(Param,'FieldTransform')&&~isempty(Param.FieldTransform.TransformName)
139    addpath(Param.FieldTransform.TransformPath)
140    transform_fct=str2func(Param.FieldTransform.TransformName);
141    rmpath(Param.FieldTransform.TransformPath)
142end
143
144%%%%%%%%%%%% END STANDARD PART  %%%%%%%%%%%%
145 % EDIT FROM HERE
146
147%% check the validity of  input file types
148if CheckImage{1}
149    FileExtOut='.png'; % write result as .png images for image inputs
150elseif CheckNc{1}
151    FileExtOut='.nc';% write result as .nc files for netcdf inputs
152else
153    msgbox_uvmat('ERROR',['invalid file type input ' FileType{1}])
154    return
155end
156if nbview==2 && ~isequal(CheckImage{1},CheckImage{2})
157        msgbox_uvmat('ERROR','input must be two image series or two netcdf file series')
158    return
159end
160NomTypeOut='_1-2_1';% output file index will indicate the first and last ref index in the series
161if checkrun==1
162    return % stop here for input checks
163end
164
165%% Set field names and velocity types
166InputFields{1}=[];%default (case of images)
167if isfield(Param,'InputFields')
168    InputFields{1}=Param.InputFields;
169end
170if nbview==2
171    InputFields{2}=[];%default (case of images)
172    if isfield(Param,'InputFields')
173        InputFields{2}=Param.InputFields{1};%default
174        if isfield(Param.InputFields,'FieldName_1')
175            InputFields{2}.FieldName=Param.InputFields.FieldName_1;
176            if isfield(Param.InputFields,'VelType_1')
177                InputFields{2}.VelType=Param.InputFields.VelType_1;
178            end
179        end
180    end
181end
182
183%% MAIN LOOP ON SLICES
184for i_slice=1:NbSlice
185    index_slice=i_slice:NbSlice:nbfield;% select file indices of the slice
186    nbfiles=0;
187    nbmissing=0;
188
189    %%%%%%%%%%%%%%%% loop on field indices %%%%%%%%%%%%%%%%
190    for index=index_slice
191        if checkrun
192            update_waitbar(hseries.Waitbar,index/(nbfield))
193            stopstate=get(hseries.RUN,'BusyAction');
194        else
195            stopstate='queue';
196        end
197        if isequal(stopstate,'queue')% enable STOP command
198           
199        %%%%%%%%%%%%%%%% loop on views (input lines) %%%%%%%%%%%%%%%%
200        for iview=1:nbview
201            % reading input file(s)
202            [Data{iview},tild,errormsg] = read_field(filecell{iview,index},FileType{iview},InputFields{iview},frame_index{iview}(index));
203            if ~isempty(errormsg)
204                errormsg=['error of input reading: ' errormsg];
205                break
206            end
207            if ~isempty(NbSlice_calib)
208                Data{iview}.ZIndex=mod(i1_series{iview}(index)-1,NbSlice_calib{iview})+1;%Zindex for phys transform
209            end
210        end
211        else
212            errormsg='stop';
213        end
214        %%%%%%%%%%%%%%%% end loop on views (input lines) %%%%%%%%%%%%%%%%
215        %%%%%%%%%%%% END STANDARD PART  %%%%%%%%%%%%
216        % EDIT FROM HERE
217   
218        if isempty(errormsg)
219            Field=Data{1}; % default input field structure
220            %% coordinate transform (or other user defined transform)
221            if ~isempty(transform_fct)
222                switch nargin(transform_fct)
223                    case 4
224                        if length(Data)==2
225                            Field=transform_fct(Data{1},XmlData{1},Data{2},XmlData{2});
226                        else
227                            Field=transform_fct(Data{1},XmlData{1});
228                        end
229                    case 3
230                        if length(Data)==2
231                            Field=transform_fct(Data{1},XmlData{1},Data{2});
232                        else
233                            Field=transform_fct(Data{1},XmlData{1});
234                        end
235                    case 2
236                        Field=transform_fct(Data{1},XmlData{1});
237                    case 1
238                        Field=transform_fct(Data{1});
239                end
240            end
241           
242            %% calculate tps coefficients if needed
243            if isfield(Param.ProjObject,'ProjMode')&& strcmp(Param.ProjObject.ProjMode,'filter')
244                Field=calc_tps(Field,check_proj_tps);
245            end
246
247            %field projection on an object
248            if Param.CheckObject
249                [Field,errormsg]=proj_field(Field,Param.ProjObject);
250                if ~isempty(errormsg)
251                    msgbox_uvmat('ERROR',['error in aver_stat/proj_field:' errormsg])
252                    return
253                end
254            end
255            nbfiles=nbfiles+1;
256           
257            %%%%%%%%%%%% MAIN RUNNING OPERATIONS  %%%%%%%%%%%%
258            %update sum
259            if nbfiles==1 %first field
260                time_1=[];
261                if isfield(Field,'Time')
262                    time_1=Field.Time(1);
263                end
264                DataOut=Field;%default
265                for ivar=1:length(Field.ListVarName)
266                    VarName=Field.ListVarName{ivar};
267                    DataOut.(VarName)=double(DataOut.(VarName));
268                end
269            else   %current field
270                for ivar=1:length(Field.ListVarName)
271                    VarName=Field.ListVarName{ivar};
272                    sizmean=size(DataOut.(VarName));
273                    siz=size(Field.(VarName));
274                    if ~isequal(DataOut.(VarName),0)&& ~isequal(siz,sizmean)
275                        msgbox_uvmat('ERROR',['unequal size of input field ' VarName ', need to project  on a grid'])
276                        return
277                    else
278                        DataOut.(VarName)=DataOut.(VarName)+ double(Field.(VarName)); % update the sum
279                    end
280                end
281            end
282            %%%%%%%%%%%%   END MAIN RUNNING OPERATIONS  %%%%%%%%%%%%
283        else
284            display(errormsg)
285        end
286    end
287    %%%%%%%%%%%%%%%% end loop on field indices %%%%%%%%%%%%%%%%
288   
289    for ivar=1:length(Field.ListVarName)
290        VarName=Field.ListVarName{ivar};
291        DataOut.(VarName)=DataOut.(VarName)/nbfiles; % normalize the mean
292    end
293    if nbmissing~=0
294        msgbox_uvmat('WARNING',[num2str(nbmissing) ' input files are missing or skipted'])
295    end
296    if isempty(time) % time is read from files
297        if isfield(Field,'Time')
298            time_end=Field.Time(1);%last time read
299            if ~isempty(time_1)
300                DataOut.Time=time_1;
301                DataOut.Time_end=time_end;
302            end
303        end
304    else  % time from ImaDoc prevails if it exists
305        j1=1;%default
306        if ~isempty(j1_series{1})
307            j1=j1_series{1};
308        end
309        DataOut.Time=time(1,i1_series{1}(1),j1filexml);
310        DataOut.Time_end=time(end,i1_series{end}(end),j1_series{end}(end));
311    end
312   
313    %writting the result file
314    OutputFile=fullfile_uvmat(RootPath{1},OutputDir,RootFile{1},FileExtOut,NomTypeOut,i1_series{1}(1),i1_series{1}(end),i_slice,[]);
315    if CheckImage{1} %case of images
316        if isequal(FileInfo{1}.BitDepth,16)||(numel(FileInfo)==2 &&isequal(FileInfo{2}.BitDepth,16))
317            DataOut.A=uint16(DataOut.A);
318            imwrite(DataOut.A,OutputFile,'BitDepth',16); % case of 16 bit images
319        else
320            DataOut.A=uint8(DataOut.A);
321            imwrite(DataOut.A,OutputFile,'BitDepth',8); % case of 16 bit images
322        end
323        display([OutputFile ' written']);
324    else %case of netcdf input file , determine global attributes
325        errormsg=struct2nc(OutputFile,DataOut); %save result file
326        if isempty(errormsg)
327            display([OutputFile ' written']);
328        else
329            msgbox_uvmat('ERROR',['error in writting result file: ' errormsg])
330            display(errormsg)
331        end
332    end  % end averaging  loop
333end
334%%%%%%%%%%%%%%%% end loop on slices %%%%%%%%%%%%%%%%
335
336%% open the result file with uvmat (in RUN mode)
337if checkrun
338%     hget_field=findobj(allchild(0),'name','get_field');%find the get_field... GUI
339%     delete(hget_field)
340    uvmat(OutputFile)% open the last result file with uvmat
341end
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