source: trunk/src/series/aver_stat.m @ 673

Last change on this file since 673 was 673, checked in by sommeria, 11 years ago

various bugs corrected

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
54    ParamOut.OutputFileMode='NbSlice';% '=NbInput': 1 output file per input file index, '=NbInput_i': 1 file per input file index i, '=NbSlice': 1 file per slice
55    filecell=get_file_series(Param);%check existence of the first input file
56    if ~exist(filecell{1,1},'file')
57        msgbox_uvmat('WARNING','the first input file does not exist')
58    end
59    return
60end
61
62%%%%%%%%%%%%  STANDARD PART  %%%%%%%%%%%%
63ParamOut=[];%default output
64%% read input parameters from an xml file if input is a file name (batch mode)
65checkrun=1;
66if ischar(Param)
67    Param=xml2struct(Param);% read Param as input file (batch case)
68    checkrun=0;
69end
70hseries=findobj(allchild(0),'Tag','series');
71RUNHandle=findobj(hseries,'Tag','RUN');%handle of RUN button in GUI series
72WaitbarHandle=findobj(hseries,'Tag','Waitbar');%handle of waitbar in GUI series
73
74%% define the directory for result file (with path=RootPath{1})
75OutputDir=[Param.OutputSubDir Param.OutputDirExt];
76   
77%% root input file(s) name, type and index series
78RootPath=Param.InputTable(:,1);
79RootFile=Param.InputTable(:,3);
80SubDir=Param.InputTable(:,2);
81NomType=Param.InputTable(:,4);
82FileExt=Param.InputTable(:,5);
83[filecell,i1_series,i2_series,j1_series,j2_series]=get_file_series(Param);
84%%%%%%%%%%%%
85% The cell array filecell is the list of input file names, while
86% filecell{iview,fileindex}:
87%        iview: line in the table corresponding to a given file series
88%        fileindex: file index within  the file series,
89% 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
90% i1_series(iview,fileindex) expresses the same indices as a 1D array in file indices
91%%%%%%%%%%%%
92NbView=numel(i1_series);%number of input file series (lines in InputTable)
93NbField_j=size(i1_series{1},1); %nb of fields for the j index (bursts or volume slices)
94NbField_i=size(i1_series{1},2); %nb of fields for the i index
95NbField=NbField_j*NbField_i; %total number of fields
96
97%% determine the file type on each line from the first input file
98ImageTypeOptions={'image','multimage','mmreader','video'};
99NcTypeOptions={'netcdf','civx','civdata'};
100for iview=1:NbView
101    if ~exist(filecell{iview,1}','file')
102        msgbox_uvmat('ERROR',['the first input file ' filecell{iview,1} ' does not exist'])
103        return
104    end
105    [FileType{iview},FileInfo{iview},MovieObject{iview}]=get_file_type(filecell{iview,1});
106    CheckImage{iview}=~isempty(find(strcmp(FileType{iview},ImageTypeOptions)));% =1 for images
107    CheckNc{iview}=~isempty(find(strcmp(FileType{iview},NcTypeOptions)));% =1 for netcdf files
108    if ~isempty(j1_series{iview})
109        frame_index{iview}=j1_series{iview};
110    else
111        frame_index{iview}=i1_series{iview};
112    end
113end
114
115%% calibration data and timing: read the ImaDoc files
116[XmlData,NbSlice_calib,time,errormsg]=read_multimadoc(RootPath,SubDir,RootFile,FileExt,i1_series,i2_series,j1_series,j2_series);
117if size(time,1)>1
118    diff_time=max(max(diff(time)));
119    if diff_time>0
120        msgbox_uvmat('WARNING',['times of series differ by (max) ' num2str(diff_time)])
121    end   
122end
123
124%% coordinate transform or other user defined transform
125transform_fct='';%default
126if isfield(Param,'FieldTransform')&&~isempty(Param.FieldTransform.TransformName)
127    addpath(Param.FieldTransform.TransformPath)
128    transform_fct=str2func(Param.FieldTransform.TransformName);
129    rmpath(Param.FieldTransform.TransformPath)
130end
131
132%%%%%%%%%%%% END STANDARD PART  %%%%%%%%%%%%
133 % EDIT FROM HERE
134
135%% check the validity of  input file types
136if CheckImage{1}
137    FileExtOut='.png'; % write result as .png images for image inputs
138elseif CheckNc{1}
139    FileExtOut='.nc';% write result as .nc files for netcdf inputs
140else
141    msgbox_uvmat('ERROR',['invalid file type input ' FileType{1}])
142    return
143end
144if NbView==2 && ~isequal(CheckImage{1},CheckImage{2})
145    msgbox_uvmat('ERROR','input must be two image series or two netcdf file series')
146    return
147end
148
149%% settings for the output file
150NomTypeOut=nomtype2pair(NomType{1});% determine the index nomenclature type for the output file
151first_i=i1_series{1}(1);
152last_i=i1_series{1}(end);
153if isempty(j1_series{1})% if there is no second index j
154    first_j=1;last_j=1;
155else
156    first_j=j1_series{1}(1);
157    last_j=j1_series{1}(end);
158end
159
160%% Set field names and velocity types
161InputFields{1}=[];%default (case of images)
162if isfield(Param,'InputFields')
163    InputFields{1}=Param.InputFields;
164end
165if NbView==2
166    InputFields{2}=[];%default (case of images)
167    if isfield(Param,'InputFields')
168        InputFields{2}=Param.InputFields{1};%default
169        if isfield(Param.InputFields,'FieldName_1')
170            InputFields{2}.FieldName=Param.InputFields.FieldName_1;
171            if isfield(Param.InputFields,'VelType_1')
172                InputFields{2}.VelType=Param.InputFields.VelType_1;
173            end
174        end
175    end
176end
177
178% for i_slice=1:NbSlice
179% index_slice=i_slice:NbSlice:nbfield;% select file indices of the slice
180nbfiles=0;
181nbmissing=0;
182
183%%%%%%%%%%%%%%%% loop on field indices %%%%%%%%%%%%%%%%
184for index=1:NbField
185    update_waitbar(WaitbarHandle,index/NbField)
186    if ~isempty(RUNHandle)&& ~strcmp(get(RUNHandle,'BusyAction'),'queue')
187        disp('program stopped by user')
188        break
189    end
190   
191    %%%%%%%%%%%%%%%% loop on views (input lines) %%%%%%%%%%%%%%%%
192    for iview=1:NbView
193        % reading input file(s)
194        [Data{iview},tild,errormsg] = read_field(filecell{iview,index},FileType{iview},InputFields{iview},frame_index{iview}(index));
195        if ~isempty(errormsg)
196            errormsg=['error of input reading: ' errormsg];
197            break
198        end
199        if ~isempty(NbSlice_calib)
200            Data{iview}.ZIndex=mod(i1_series{iview}(index)-1,NbSlice_calib{iview})+1;%Zindex for phys transform
201        end
202    end
203    %%%%%%%%%%%%%%%% end loop on views (input lines) %%%%%%%%%%%%%%%%
204    %%%%%%%%%%%% END STANDARD PART  %%%%%%%%%%%%
205    % EDIT FROM HERE
206   
207    if isempty(errormsg)
208        Field=Data{1}; % default input field structure
209        %% coordinate transform (or other user defined transform)
210        if ~isempty(transform_fct)
211            switch nargin(transform_fct)
212                case 4
213                    if length(Data)==2
214                        Field=transform_fct(Data{1},XmlData{1},Data{2},XmlData{2});
215                    else
216                        Field=transform_fct(Data{1},XmlData{1});
217                    end
218                case 3
219                    if length(Data)==2
220                        Field=transform_fct(Data{1},XmlData{1},Data{2});
221                    else
222                        Field=transform_fct(Data{1},XmlData{1});
223                    end
224                case 2
225                    Field=transform_fct(Data{1},XmlData{1});
226                case 1
227                    Field=transform_fct(Data{1});
228            end
229        end
230       
231        %% calculate tps coefficients if needed
232        if isfield(Param,'ProjObject')&&isfield(Param.ProjObject,'ProjMode')&& strcmp(Param.ProjObject.ProjMode,'interp_tps')
233            Field=tps_coeff_field(Field,check_proj_tps);
234        end
235       
236        %field projection on an object
237        if Param.CheckObject
238            [Field,errormsg]=proj_field(Field,Param.ProjObject);
239            if ~isempty(errormsg)
240                msgbox_uvmat('ERROR',['error in aver_stat/proj_field:' errormsg])
241                return
242            end
243        end
244        nbfiles=nbfiles+1;
245       
246        %%%%%%%%%%%% MAIN RUNNING OPERATIONS  %%%%%%%%%%%%
247        if nbfiles==1 %first field
248            time_1=[];
249            if isfield(Field,'Time')
250                time_1=Field.Time(1);
251            end
252            DataOut=Field;%default
253            DataOut.Conventions='uvmat'; %suppress Conventions='uvmat/civdata' for civ input files
254            for ivar=1:length(Field.ListVarName)
255                VarName=Field.ListVarName{ivar};
256                DataOut.(VarName)=double(DataOut.(VarName));
257            end
258        else   %current field
259            for ivar=1:length(Field.ListVarName)
260                VarName=Field.ListVarName{ivar};
261                sizmean=size(DataOut.(VarName));
262                siz=size(Field.(VarName));
263                if ~isequal(DataOut.(VarName),0)&& ~isequal(siz,sizmean)
264                    disp_uvmat('ERROR',['unequal size of input field ' VarName ', need to project  on a grid'],checkrun)
265                    return
266                else
267                    DataOut.(VarName)=DataOut.(VarName)+ double(Field.(VarName)); % update the sum
268                end
269            end
270        end
271        %%%%%%%%%%%%   END MAIN RUNNING OPERATIONS  %%%%%%%%%%%%
272    else
273        disp(errormsg)
274    end
275end
276%%%%%%%%%%%%%%%% end loop on field indices %%%%%%%%%%%%%%%%
277
278for ivar=1:length(Field.ListVarName)
279    VarName=Field.ListVarName{ivar};
280    DataOut.(VarName)=DataOut.(VarName)/nbfiles; % normalize the mean
281end
282if nbmissing~=0
283    msgbox_uvmat('WARNING',[num2str(nbmissing) ' input files are missing or skipted'])
284end
285if isempty(time) % time is read from files
286    if isfield(Field,'Time')
287        time_end=Field.Time(1);%last time read
288        if ~isempty(time_1)
289            DataOut.Time=time_1;
290            DataOut.Time_end=time_end;
291        end
292    end
293else  % time from ImaDoc prevails if it exists
294    DataOut.Time=time(1);
295    DataOut.Time_end=time(end);
296end
297
298%% writing the result file
299OutputFile=fullfile_uvmat(RootPath{1},OutputDir,RootFile{1},FileExtOut,NomTypeOut,first_i,last_i,first_j,last_j);
300if CheckImage{1} %case of images
301    if isequal(FileInfo{1}.BitDepth,16)||(numel(FileInfo)==2 &&isequal(FileInfo{2}.BitDepth,16))
302        DataOut.A=uint16(DataOut.A);
303        imwrite(DataOut.A,OutputFile,'BitDepth',16); % case of 16 bit images
304    else
305        DataOut.A=uint8(DataOut.A);
306        imwrite(DataOut.A,OutputFile,'BitDepth',8); % case of 16 bit images
307    end
308    disp([OutputFile ' written']);
309else %case of netcdf input file , determine global attributes
310    errormsg=struct2nc(OutputFile,DataOut); %save result file
311    if isempty(errormsg)
312        disp([OutputFile ' written']);
313    else
314        disp(['error in writting result file: ' errormsg])
315    end
316end  % end averaging  loop
317
318%% open the result file with uvmat (in RUN mode)
319if checkrun
320    uvmat(OutputFile)% open the last result file with uvmat
321end
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