source: trunk/src/series/aver_stat.m @ 595

Last change on this file since 595 was 595, checked in by sommeria, 11 years ago

steps further to use series with cluster. Some bsolete functions removed

File size: 14.7 KB
RevLine 
[573]1%'aver_stat': calculate field average over a time series
[169]2%------------------------------------------------------------------------
[457]3% function ParamOut=aver_stat(Param)
[169]4%
[447]5%%%%%%%%%%% GENERAL TO ALL SERIES ACTION FCTS %%%%%%%%%%%%%%%%%%%%%%%%%%%
[457]6%
7% This function is used in four modes by the GUI series:
8%           1) config GUI: with no input argument, the function determine the suitable GUI configuration
9%           2) interactive input: the function is used to interactively introduce input parameters, and then stops
10%           3) RUN: the function itself runs, when an appropriate input  structure Param has been introduced.
11%           4) BATCH: the function itself proceeds in BATCH mode, using an xml file 'Param' as input.
12%
13% This function is used in four modes by the GUI series:
14%           1) config GUI: with no input argument, the function determine the suitable GUI configuration
15%           2) interactive input: the function is used to interactively introduce input parameters, and then stops
16%           3) RUN: the function itself runs, when an appropriate input  structure Param has been introduced.
17%           4) BATCH: the function itself proceeds in BATCH mode, using an xml file 'Param' as input.
18%
[169]19%OUTPUT
20% GUI_input=list of options in the GUI series.fig needed for the function
21%
22%INPUT:
[447]23% In run mode, the input parameters are given as a Matlab structure Param copied from the GUI series.
24% In batch mode, Param is the name of the corresponding xml file containing the same information
25% In the absence of input (as activated when the current Action is selected
26% in series), the function ouput GUI_input set the activation of the needed GUI elements
[169]27%
[447]28% Param contains the elements:(use the menu bar command 'export/GUI config' in series to see the current structure Param)
29%    .InputTable: cell of input file names, (several lines for multiple input)
30%                      each line decomposed as {RootPath,SubDir,Rootfile,NomType,Extension}
31%    .OutputSubDir: name of the subdirectory for data outputs
[474]32%    .OutputDirExt: directory extension for data outputs
[447]33%    .Action: .ActionName: name of the current activated function
34%             .ActionPath:   path of the current activated function
35%    .IndexRange: set the file or frame indices on which the action must be performed
36%    .FieldTransform: .TransformName: name of the selected transform function
37%                     .TransformPath:   path  of the selected transform function
38%                     .TransformHandle: corresponding function handle
39%    .InputFields: sub structure describing the input fields withfields
40%              .FieldName: name of the field
41%              .VelType: velocity type
42%              .FieldName_1: name of the second field in case of two input series
43%              .VelType_1: velocity type of the second field in case of two input series
44%    .ProjObject: %sub structure describing a projection object (read from ancillary GUI set_object)
45%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
46
[457]47function ParamOut=aver_stat(Param)
[447]48
49%% set the input elements needed on the GUI series when the action is selected in the menu ActionName
[592]50if isstruct(Param) && isequal(Param.Action.RUN,0)
51    ParamOut.AllowInputSort='off';...% allow alphabetic sorting of the list of input file SubDir (options 'off'/'on', 'off' by default)
52    ParamOut.WholeIndexRange='off';...% prescribes the file index ranges from min to max (options 'off'/'on', 'off' by default)
53    ParamOut.NbSlice='on'; ...%nbre of slices ('off' by default)
54    ParamOut.VelType='two';...% menu for selecting the velocity type (options 'off'/'one'/'two',  'off' by default)
55    ParamOut.FieldName='two';...% menu for selecting the field (s) in the input file(options 'off'/'one'/'two', 'off' by default)
56    ParamOut.FieldTransform = 'on';...%can use a transform function
57    ParamOut.ProjObject='on';...%can use projection object(option 'off'/'on',
58    ParamOut.Mask='off';...%can use mask option   (option 'off'/'on', 'off' by default)
59    ParamOut.OutputDirExt='.stat';%set the output dir extension
60return
[27]61end
62
[474]63%%%%%%%%%%%%  STANDARD PART  %%%%%%%%%%%%
[594]64ParamOut=[];
[592]65%% read input parameters from an xml file if input is a file name (batch mode)
66checkrun=1;
[457]67if ischar(Param)
[592]68    Param=xml2struct(Param);% read Param as input file (batch case)
69    checkrun=0;
[361]70end
[592]71
72
[462]73ParamOut=Param; %default output
[474]74OutputDir=[Param.OutputSubDir Param.OutputDirExt];
75   
[457]76%% root input file(s) and type
77RootPath=Param.InputTable(:,1);
78RootFile=Param.InputTable(:,3);
79SubDir=Param.InputTable(:,2);
80NomType=Param.InputTable(:,4);
81FileExt=Param.InputTable(:,5);
[374]82[filecell,i1_series,i2_series,j1_series,j2_series]=get_file_series(Param);
[474]83%%%%%%%%%%%%
84% The cell array filecell is the list of input file names, while
85% filecell{iview,fileindex}:
[447]86%        iview: line in the table corresponding to a given file series
87%        fileindex: file index within  the file series,
88% 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
89% i1_series(iview,fileindex) expresses the same indices as a 1D array in file indices
[474]90%%%%%%%%%%%%
[595]91% NbSlice=1;%default
92% if isfield(Param.IndexRange,'NbSlice')&&~isempty(Param.IndexRange.NbSlice)
93%     NbSlice=Param.IndexRange.NbSlice;
94% end
[454]95nbview=numel(i1_series);%number of input file series (lines in InputTable)
[457]96nbfield_j=size(i1_series{1},1); %nb of fields for the j index (bursts or volume slices)
97nbfield_i=size(i1_series{1},2); %nb of fields for the i index
98nbfield=nbfield_j*nbfield_i; %total number of fields
[595]99%nbfield_i=floor(nbfield/NbSlice);%total number of  indexes in a slice (adjusted to an integer number of slices)
100%nbfield=nbfield_i*NbSlice; %total number of fields after adjustement
[43]101
[447]102%determine the file type on each line from the first input file
103ImageTypeOptions={'image','multimage','mmreader','video'};
104NcTypeOptions={'netcdf','civx','civdata'};
[27]105for iview=1:nbview
[451]106    if ~exist(filecell{iview,1}','file')
107        msgbox_uvmat('ERROR',['the first input file ' filecell{iview,1} ' does not exist'])
108        return
109    end
110    [FileType{iview},FileInfo{iview},MovieObject{iview}]=get_file_type(filecell{iview,1});
[447]111    CheckImage{iview}=~isempty(find(strcmp(FileType{iview},ImageTypeOptions)));% =1 for images
112    CheckNc{iview}=~isempty(find(strcmp(FileType{iview},NcTypeOptions)));% =1 for netcdf files
[454]113    if ~isempty(j1_series{iview})
114        frame_index{iview}=j1_series{iview};
115    else
116        frame_index{iview}=i1_series{iview};
117    end
[27]118end
119
[451]120%% calibration data and timing: read the ImaDoc files
[470]121[XmlData,NbSlice_calib,time,errormsg]=read_multimadoc(RootPath,SubDir,RootFile,FileExt,i1_series,i2_series,j1_series,j2_series);
122if size(time,1)>1
[27]123    diff_time=max(max(diff(time)));
124    if diff_time>0
[447]125        msgbox_uvmat('WARNING',['times of series differ by (max) ' num2str(diff_time)])
[27]126    end   
127end
128
[447]129%% coordinate transform or other user defined transform
130transform_fct='';%default
[478]131if isfield(Param,'FieldTransform')&&~isempty(Param.FieldTransform.TransformName)
[474]132    addpath(Param.FieldTransform.TransformPath)
133    transform_fct=str2func(Param.FieldTransform.TransformName);
134    rmpath(Param.FieldTransform.TransformPath)
[27]135end
[474]136
[447]137%%%%%%%%%%%% END STANDARD PART  %%%%%%%%%%%%
138 % EDIT FROM HERE
139
140%% check the validity of  input file types
141if CheckImage{1}
142    FileExtOut='.png'; % write result as .png images for image inputs
143elseif CheckNc{1}
144    FileExtOut='.nc';% write result as .nc files for netcdf inputs
145else
146    msgbox_uvmat('ERROR',['invalid file type input ' FileType{1}])
147    return
148end
149if nbview==2 && ~isequal(CheckImage{1},CheckImage{2})
150        msgbox_uvmat('ERROR','input must be two image series or two netcdf file series')
151    return
152end
153NomTypeOut='_1-2_1';% output file index will indicate the first and last ref index in the series
[442]154
[592]155
[447]156%% Set field names and velocity types
157InputFields{1}=[];%default (case of images)
158if isfield(Param,'InputFields')
159    InputFields{1}=Param.InputFields;
160end
161if nbview==2
162    InputFields{2}=[];%default (case of images)
163    if isfield(Param,'InputFields')
164        InputFields{2}=Param.InputFields{1};%default
165        if isfield(Param.InputFields,'FieldName_1')
166            InputFields{2}.FieldName=Param.InputFields.FieldName_1;
167            if isfield(Param.InputFields,'VelType_1')
168                InputFields{2}.VelType=Param.InputFields.VelType_1;
169            end
170        end
[255]171    end
172end
[447]173
174%% MAIN LOOP ON SLICES
[595]175% for i_slice=1:NbSlice
176   % index_slice=i_slice:NbSlice:nbfield;% select file indices of the slice
[255]177    nbfiles=0;
178    nbmissing=0;
[474]179
[447]180    %%%%%%%%%%%%%%%% loop on field indices %%%%%%%%%%%%%%%%
[595]181    for index=1:nbfield
182    %for index=index_slice
[592]183          if checkrun
184                stopstate=get(Param.RUNHandle,'BusyAction');
185                update_waitbar(Param.WaitbarHandle,index/nbfield)
186          else
187                stopstate='queue';
188          end
[526]189        if isequal(stopstate,'queue')% enable STOP command
190           
[447]191        %%%%%%%%%%%%%%%% loop on views (input lines) %%%%%%%%%%%%%%%%
192        for iview=1:nbview
[255]193            % reading input file(s)
[464]194            [Data{iview},tild,errormsg] = read_field(filecell{iview,index},FileType{iview},InputFields{iview},frame_index{iview}(index));
[447]195            if ~isempty(errormsg)
196                errormsg=['error of input reading: ' errormsg];
197                break
[255]198            end
[447]199            if ~isempty(NbSlice_calib)
[454]200                Data{iview}.ZIndex=mod(i1_series{iview}(index)-1,NbSlice_calib{iview})+1;%Zindex for phys transform
[447]201            end
202        end
[526]203        else
204            errormsg='stop';
205        end
[447]206        %%%%%%%%%%%%%%%% end loop on views (input lines) %%%%%%%%%%%%%%%%
207        %%%%%%%%%%%% END STANDARD PART  %%%%%%%%%%%%
208        % EDIT FROM HERE
[526]209   
[462]210        if isempty(errormsg)
[526]211            Field=Data{1}; % default input field structure
212            %% coordinate transform (or other user defined transform)
[255]213            if ~isempty(transform_fct)
[526]214                switch nargin(transform_fct)
215                    case 4
216                        if length(Data)==2
217                            Field=transform_fct(Data{1},XmlData{1},Data{2},XmlData{2});
218                        else
219                            Field=transform_fct(Data{1},XmlData{1});
220                        end
221                    case 3
222                        if length(Data)==2
223                            Field=transform_fct(Data{1},XmlData{1},Data{2});
224                        else
225                            Field=transform_fct(Data{1},XmlData{1});
226                        end
227                    case 2
228                        Field=transform_fct(Data{1},XmlData{1});
229                    case 1
230                        Field=transform_fct(Data{1});
[27]231                end
[255]232            end
233           
[526]234            %% calculate tps coefficients if needed
[592]235            if isfield(Param,'ProjObject')&&isfield(Param.ProjObject,'ProjMode')&& strcmp(Param.ProjObject.ProjMode,'interp_tps')
[585]236                Field=tps_coeff_field(Field,check_proj_tps);
[494]237            end
[526]238
[451]239            %field projection on an object
[447]240            if Param.CheckObject
[462]241                [Field,errormsg]=proj_field(Field,Param.ProjObject);
[255]242                if ~isempty(errormsg)
[27]243                    msgbox_uvmat('ERROR',['error in aver_stat/proj_field:' errormsg])
244                    return
245                end
[255]246            end
247            nbfiles=nbfiles+1;
[447]248           
249            %%%%%%%%%%%% MAIN RUNNING OPERATIONS  %%%%%%%%%%%%
250            %update sum
[462]251            if nbfiles==1 %first field
252                time_1=[];
253                if isfield(Field,'Time')
254                    time_1=Field.Time(1);
[255]255                end
[462]256                DataOut=Field;%default
257                for ivar=1:length(Field.ListVarName)
258                    VarName=Field.ListVarName{ivar};
259                    DataOut.(VarName)=double(DataOut.(VarName));
260                end
261            else   %current field
262                for ivar=1:length(Field.ListVarName)
263                    VarName=Field.ListVarName{ivar};
264                    sizmean=size(DataOut.(VarName));
265                    siz=size(Field.(VarName));
266                    if ~isequal(DataOut.(VarName),0)&& ~isequal(siz,sizmean)
267                        msgbox_uvmat('ERROR',['unequal size of input field ' VarName ', need to project  on a grid'])
268                        return
269                    else
270                        DataOut.(VarName)=DataOut.(VarName)+ double(Field.(VarName)); % update the sum
271                    end
272                end
[255]273            end
[447]274            %%%%%%%%%%%%   END MAIN RUNNING OPERATIONS  %%%%%%%%%%%%
275        else
[462]276            display(errormsg)
[447]277        end
[255]278    end
[447]279    %%%%%%%%%%%%%%%% end loop on field indices %%%%%%%%%%%%%%%%
280   
[27]281    for ivar=1:length(Field.ListVarName)
282        VarName=Field.ListVarName{ivar};
[447]283        DataOut.(VarName)=DataOut.(VarName)/nbfiles; % normalize the mean
[27]284    end
285    if nbmissing~=0
286        msgbox_uvmat('WARNING',[num2str(nbmissing) ' input files are missing or skipted'])
287    end
[462]288    if isempty(time) % time is read from files
[27]289        if isfield(Field,'Time')
290            time_end=Field.Time(1);%last time read
291            if ~isempty(time_1)
[447]292                DataOut.Time=time_1;
293                DataOut.Time_end=time_end;
[27]294            end
295        end
[457]296    else  % time from ImaDoc prevails if it exists
[565]297%         j1=1;%default
298%         if ~isempty(j1_series{1})
299%             j1=j1_series{1};
300%         end
301        %DataOut.Time=time(1,i1_series{1}(1),j1);
302        %DataOut.Time_end=time(end,i1_series{end}(end),j1_series{end}(end));
303        DataOut.Time=time(1);
304        DataOut.Time_end=time(end);
[27]305    end
[255]306   
[526]307    %writting the result file
[595]308    OutputFile=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));
[447]309    if CheckImage{1} %case of images
310        if isequal(FileInfo{1}.BitDepth,16)||(numel(FileInfo)==2 &&isequal(FileInfo{2}.BitDepth,16))
311            DataOut.A=uint16(DataOut.A);
312            imwrite(DataOut.A,OutputFile,'BitDepth',16); % case of 16 bit images
[27]313        else
[447]314            DataOut.A=uint8(DataOut.A);
315            imwrite(DataOut.A,OutputFile,'BitDepth',8); % case of 16 bit images
[27]316        end
[447]317        display([OutputFile ' written']);
[55]318    else %case of netcdf input file , determine global attributes
[447]319        errormsg=struct2nc(OutputFile,DataOut); %save result file
[27]320        if isempty(errormsg)
[447]321            display([OutputFile ' written']);
[27]322        else
323            msgbox_uvmat('ERROR',['error in writting result file: ' errormsg])
324            display(errormsg)
325        end
[255]326    end  % end averaging  loop
[595]327% end
[447]328%%%%%%%%%%%%%%%% end loop on slices %%%%%%%%%%%%%%%%
[255]329
[451]330%% open the result file with uvmat (in RUN mode)
331if checkrun
[526]332%     hget_field=findobj(allchild(0),'name','get_field');%find the get_field... GUI
333%     delete(hget_field)
[451]334    uvmat(OutputFile)% open the last result file with uvmat
335end
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