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 |
|
---|
41 | %=======================================================================
|
---|
42 | % Copyright 2008-2014, LEGI UMR 5519 / CNRS UJF G-INP, Grenoble, France
|
---|
43 | % http://www.legi.grenoble-inp.fr
|
---|
44 | % Joel.Sommeria - Joel.Sommeria (A) legi.cnrs.fr
|
---|
45 | %
|
---|
46 | % This file is part of the toolbox UVMAT.
|
---|
47 | %
|
---|
48 | % UVMAT is free software; you can redistribute it and/or modify
|
---|
49 | % it under the terms of the GNU General Public License as published
|
---|
50 | % by the Free Software Foundation; either version 2 of the license,
|
---|
51 | % or (at your option) any later version.
|
---|
52 | %
|
---|
53 | % UVMAT is distributed in the hope that it will be useful,
|
---|
54 | % but WITHOUT ANY WARRANTY; without even the implied warranty of
|
---|
55 | % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
|
---|
56 | % GNU General Public License (see LICENSE.txt) for more details.
|
---|
57 | %=======================================================================
|
---|
58 |
|
---|
59 | function ParamOut=aver_stat(Param)
|
---|
60 |
|
---|
61 | %% set the input elements needed on the GUI series when the action is selected in the menu ActionName
|
---|
62 | if isstruct(Param) && isequal(Param.Action.RUN,0)% function activated from the GUI series but not RUN
|
---|
63 | ParamOut.AllowInputSort='off';% allow alphabetic sorting of the list of input file SubDir (options 'off'/'on', 'off' by default)
|
---|
64 | ParamOut.WholeIndexRange='off';% prescribes the file index ranges from min to max (options 'off'/'on', 'off' by default)
|
---|
65 | ParamOut.NbSlice='on'; %nbre of slices ('off' by default)
|
---|
66 | ParamOut.VelType='two';% menu for selecting the velocity type (options 'off'/'one'/'two', 'off' by default)
|
---|
67 | ParamOut.FieldName='two';% menu for selecting the field (s) in the input file(options 'off'/'one'/'two', 'off' by default)
|
---|
68 | ParamOut.FieldTransform = 'on';%can use a transform function
|
---|
69 | ParamOut.ProjObject='on';%can use projection object(option 'off'/'on',
|
---|
70 | ParamOut.Mask='off';%can use mask option (option 'off'/'on', 'off' by default)
|
---|
71 | ParamOut.OutputDirExt='.stat';%set the output dir extension
|
---|
72 | 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
|
---|
73 | % check for selection of a projection object
|
---|
74 | hseries=findobj(allchild(0),'Tag','series');% handles of the GUI series
|
---|
75 | if ~isfield(Param,'ProjObject')
|
---|
76 | answer=msgbox_uvmat('INPUT_Y-N','use a projection object?');
|
---|
77 | if strcmp(answer,'Yes')
|
---|
78 | hhseries=guidata(hseries);
|
---|
79 | set(hhseries.CheckObject,'Visible','on')
|
---|
80 | set(hhseries.CheckObject,'Value',1)
|
---|
81 | Param.CheckObject=1;
|
---|
82 | series('CheckObject_Callback',hseries,[],hhseries); %file input with xml reading in uvmat, show the image in phys coordinates
|
---|
83 | end
|
---|
84 | end
|
---|
85 | % introduce bin size for histograms
|
---|
86 | if isfield(Param,'CheckObject') && Param.CheckObject
|
---|
87 | SeriesData=get(hseries,'UserData');
|
---|
88 | if ismember(SeriesData.ProjObject.ProjMode,{'inside','outside'})
|
---|
89 | answer=msgbox_uvmat('INPUT_TXT','set bin size for histograms (or keep ''auto'' by default)?','auto');
|
---|
90 | ParamOut.ActionInput.VarMesh=str2num(answer);
|
---|
91 | end
|
---|
92 | end
|
---|
93 | % check the existence of the first and last file in the series
|
---|
94 | first_j=[];
|
---|
95 | if isfield(Param.IndexRange,'first_j'); first_j=Param.IndexRange.first_j; end
|
---|
96 | last_j=[];
|
---|
97 | if isfield(Param.IndexRange,'last_j'); last_j=Param.IndexRange.last_j; end
|
---|
98 | PairString='';
|
---|
99 | if isfield(Param.IndexRange,'PairString'); PairString=Param.IndexRange.PairString; end
|
---|
100 | [i1,i2,j1,j2] = get_file_index(Param.IndexRange.first_i,first_j,PairString);
|
---|
101 | FirstFileName=fullfile_uvmat(Param.InputTable{1,1},Param.InputTable{1,2},Param.InputTable{1,3},...
|
---|
102 | Param.InputTable{1,5},Param.InputTable{1,4},i1,i2,j1,j2);
|
---|
103 | if ~exist(FirstFileName,'file')
|
---|
104 | msgbox_uvmat('WARNING',['the first input file ' FirstFileName ' does not exist'])
|
---|
105 | else
|
---|
106 | [i1,i2,j1,j2] = get_file_index(Param.IndexRange.last_i,last_j,PairString);
|
---|
107 | LastFileName=fullfile_uvmat(Param.InputTable{1,1},Param.InputTable{1,2},Param.InputTable{1,3},...
|
---|
108 | Param.InputTable{1,5},Param.InputTable{1,4},i1,i2,j1,j2);
|
---|
109 | if ~exist(LastFileName,'file')
|
---|
110 | msgbox_uvmat('WARNING',['the last input file ' LastFileName ' does not exist'])
|
---|
111 | end
|
---|
112 | end
|
---|
113 | return
|
---|
114 | end
|
---|
115 |
|
---|
116 | %%%%%%%%%%%% STANDARD PART %%%%%%%%%%%%
|
---|
117 | ParamOut=[];%default output
|
---|
118 | %% read input parameters from an xml file if input is a file name (batch mode)
|
---|
119 | checkrun=1;
|
---|
120 | if ischar(Param)
|
---|
121 | Param=xml2struct(Param);% read Param as input file (batch case)
|
---|
122 | checkrun=0;
|
---|
123 | end
|
---|
124 | hseries=findobj(allchild(0),'Tag','series');
|
---|
125 | RUNHandle=findobj(hseries,'Tag','RUN');%handle of RUN button in GUI series
|
---|
126 | WaitbarHandle=findobj(hseries,'Tag','Waitbar');%handle of waitbar in GUI series
|
---|
127 |
|
---|
128 | %% define the directory for result file (with path=RootPath{1})
|
---|
129 | OutputDir=[Param.OutputSubDir Param.OutputDirExt];
|
---|
130 |
|
---|
131 | %% root input file(s) name, type and index series
|
---|
132 | RootPath=Param.InputTable(:,1);
|
---|
133 | RootFile=Param.InputTable(:,3);
|
---|
134 | SubDir=Param.InputTable(:,2);
|
---|
135 | NomType=Param.InputTable(:,4);
|
---|
136 | FileExt=Param.InputTable(:,5);
|
---|
137 | hdisp=disp_uvmat('WAITING...','checking the file series',checkrun);
|
---|
138 | [filecell,i1_series,i2_series,j1_series,j2_series]=get_file_series(Param);
|
---|
139 | if ~isempty(hdisp),delete(hdisp),end;
|
---|
140 | %%%%%%%%%%%%
|
---|
141 | % The cell array filecell is the list of input file names, while
|
---|
142 | % filecell{iview,fileindex}:
|
---|
143 | % iview: line in the table corresponding to a given file series
|
---|
144 | % fileindex: file index within the file series,
|
---|
145 | % 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
|
---|
146 | % i1_series(iview,fileindex) expresses the same indices as a 1D array in file indices
|
---|
147 | %%%%%%%%%%%%
|
---|
148 | NbView=numel(i1_series);%number of input file series (lines in InputTable)
|
---|
149 | NbField_j=size(i1_series{1},1); %nb of fields for the j index (bursts or volume slices)
|
---|
150 | NbField_i=size(i1_series{1},2); %nb of fields for the i index
|
---|
151 | NbField=NbField_j*NbField_i; %total number of fields
|
---|
152 |
|
---|
153 | %% determine the file type on each line from the first input file
|
---|
154 | ImageTypeOptions={'image','multimage','mmreader','video'};
|
---|
155 | NcTypeOptions={'netcdf','civx','civdata'};
|
---|
156 | for iview=1:NbView
|
---|
157 | if ~exist(filecell{iview,1}','file')
|
---|
158 | disp_uvmat('ERROR',['the first input file ' filecell{iview,1} ' does not exist'],checkrun)
|
---|
159 | return
|
---|
160 | end
|
---|
161 | [FileInfo{iview},MovieObject{iview}]=get_file_info(filecell{iview,1});
|
---|
162 | FileType{iview}=FileInfo{iview}.FileType;
|
---|
163 | CheckImage{iview}=~isempty(find(strcmp(FileType{iview},ImageTypeOptions)));% =1 for images
|
---|
164 | CheckNc{iview}=~isempty(find(strcmp(FileType{iview},NcTypeOptions)));% =1 for netcdf files
|
---|
165 | if ~isempty(j1_series{iview})
|
---|
166 | frame_index{iview}=j1_series{iview};
|
---|
167 | else
|
---|
168 | frame_index{iview}=i1_series{iview};
|
---|
169 | end
|
---|
170 | end
|
---|
171 |
|
---|
172 | %% calibration data and timing: read the ImaDoc files
|
---|
173 | [XmlData,NbSlice_calib,time,errormsg]=read_multimadoc(RootPath,SubDir,RootFile,FileExt,i1_series,i2_series,j1_series,j2_series);
|
---|
174 | if size(time,1)>1
|
---|
175 | diff_time=max(max(diff(time)));
|
---|
176 | if diff_time>0
|
---|
177 | disp_uvmat('WARNING',['times of series differ by (max) ' num2str(diff_time)],checkrun)
|
---|
178 | end
|
---|
179 | end
|
---|
180 |
|
---|
181 | %% coordinate transform or other user defined transform
|
---|
182 | transform_fct='';%default
|
---|
183 | if isfield(Param,'FieldTransform')&&~isempty(Param.FieldTransform.TransformName)
|
---|
184 | addpath(Param.FieldTransform.TransformPath)
|
---|
185 | transform_fct=str2func(Param.FieldTransform.TransformName);
|
---|
186 | rmpath(Param.FieldTransform.TransformPath)
|
---|
187 | if isfield(Param,'TransformInput')
|
---|
188 | XmlData{1}.TransformInput=Param.TransformInput;
|
---|
189 | end
|
---|
190 | end
|
---|
191 |
|
---|
192 | %%%%%%%%%%%% END STANDARD PART %%%%%%%%%%%%
|
---|
193 | % EDIT FROM HERE
|
---|
194 |
|
---|
195 | %% check the validity of input file types and set the output file type
|
---|
196 | if CheckImage{1}
|
---|
197 | FileExtOut='.png'; % write result as .png images for image inputs
|
---|
198 | elseif CheckNc{1}
|
---|
199 | FileExtOut='.nc';% write result as .nc files for netcdf inputs
|
---|
200 | else
|
---|
201 | disp_uvmat('ERROR',['invalid file type input ' FileType{1}],checkrun)
|
---|
202 | return
|
---|
203 | end
|
---|
204 | if NbView==2 && ~isequal(CheckImage{1},CheckImage{2})
|
---|
205 | disp_uvmat('ERROR','input must be two image series or two netcdf file series',checkrun)
|
---|
206 | return
|
---|
207 | end
|
---|
208 | if isfield(Param,'ProjObject') && ~strcmp(Param.ProjObject.Type,'plane')
|
---|
209 | FileExtOut='.nc';% write result as .nc files (even for image input)
|
---|
210 | end
|
---|
211 |
|
---|
212 | %% settings for the output file
|
---|
213 | NomTypeOut=nomtype2pair(NomType{1});% determine the index nomenclature type for the output file
|
---|
214 | first_i=i1_series{1}(1);
|
---|
215 | last_i=i1_series{1}(end);
|
---|
216 | if isempty(j1_series{1})% if there is no second index j
|
---|
217 | first_j=1;last_j=1;
|
---|
218 | else
|
---|
219 | first_j=j1_series{1}(1);
|
---|
220 | last_j=j1_series{1}(end);
|
---|
221 | end
|
---|
222 |
|
---|
223 | %% Set field names and velocity types
|
---|
224 | InputFields{1}=[];%default (case of images)
|
---|
225 | if NbView==2
|
---|
226 | InputFields{2}=[];%default (case of images)
|
---|
227 | end
|
---|
228 | if isfield(Param,'InputFields')
|
---|
229 | InputFields{1}=Param.InputFields;
|
---|
230 | if NbView==2
|
---|
231 | InputFields{2}=Param.InputFields;%default
|
---|
232 | if isfield(Param.InputFields,'FieldName_1')
|
---|
233 | InputFields{2}.FieldName=Param.InputFields.FieldName_1;
|
---|
234 | if isfield(Param.InputFields,'VelType_1')
|
---|
235 | InputFields{2}.VelType=Param.InputFields.VelType_1;
|
---|
236 | end
|
---|
237 | end
|
---|
238 | end
|
---|
239 | end
|
---|
240 | nbfiles=0;%counter of the successfully read files (bad files are skipped)
|
---|
241 | VarMesh=[];
|
---|
242 | if isfield(Param,'ProjObject') && ismember(Param.ProjObject.ProjMode,{'inside','outside'})
|
---|
243 | if isfield(Param,'ActionInput') && isfield(Param.ActionInput,'VarMesh')%case of histograms
|
---|
244 | VarMesh=Param.ActionInput.VarMesh;
|
---|
245 | else
|
---|
246 | VarMesh=[];
|
---|
247 | disp_uvmat('WARNING','automatic bin size for histograms, select aver_stat again to set the value',checkrun)
|
---|
248 | end
|
---|
249 | end
|
---|
250 | %%%%%%%%%%%%%%%% loop on field indices %%%%%%%%%%%%%%%%
|
---|
251 | for index=1:NbField
|
---|
252 | update_waitbar(WaitbarHandle,index/NbField)
|
---|
253 | if ~isempty(RUNHandle)&& ~strcmp(get(RUNHandle,'BusyAction'),'queue')
|
---|
254 | disp('program stopped by user')
|
---|
255 | break
|
---|
256 | end
|
---|
257 |
|
---|
258 | %%%%%%%%%%%%%%%% loop on views (input lines) %%%%%%%%%%%%%%%%
|
---|
259 | for iview=1:NbView
|
---|
260 | % reading input file(s)
|
---|
261 | [Data{iview},tild,errormsg] = read_field(filecell{iview,index},FileType{iview},InputFields{iview},frame_index{iview}(index));
|
---|
262 | if ~isempty(errormsg)
|
---|
263 | errormsg=['error of input reading: ' errormsg];
|
---|
264 | break
|
---|
265 | end
|
---|
266 | if ~isempty(NbSlice_calib)
|
---|
267 | Data{iview}.ZIndex=mod(i1_series{iview}(index)-1,NbSlice_calib{iview})+1;%Zindex for phys transform
|
---|
268 | end
|
---|
269 | end
|
---|
270 | %%%%%%%%%%%%%%%% end loop on views (input lines) %%%%%%%%%%%%%%%%
|
---|
271 | %%%%%%%%%%%% END STANDARD PART %%%%%%%%%%%%
|
---|
272 | % EDIT FROM HERE
|
---|
273 |
|
---|
274 | if isempty(errormsg)
|
---|
275 | Field=Data{1}; % default input field structure
|
---|
276 | nbfiles=nbfiles+1; %increment the file counter
|
---|
277 | %% coordinate transform (or other user defined transform)
|
---|
278 | if ~isempty(transform_fct)
|
---|
279 | switch nargin(transform_fct)
|
---|
280 | case 4
|
---|
281 | if length(Data)==2
|
---|
282 | Field=transform_fct(Data{1},XmlData{1},Data{2},XmlData{2});
|
---|
283 | else
|
---|
284 | Field=transform_fct(Data{1},XmlData{1});
|
---|
285 | end
|
---|
286 | case 3
|
---|
287 | if length(Data)==2
|
---|
288 | Field=transform_fct(Data{1},XmlData{1},Data{2});
|
---|
289 | else
|
---|
290 | Field=transform_fct(Data{1},XmlData{1});
|
---|
291 | end
|
---|
292 | case 2
|
---|
293 | Field=transform_fct(Data{1},XmlData{1});
|
---|
294 | case 1
|
---|
295 | Field=transform_fct(Data{1});
|
---|
296 | end
|
---|
297 | end
|
---|
298 |
|
---|
299 | %% field projection on an object
|
---|
300 | if Param.CheckObject
|
---|
301 | if strcmp(Param.ProjObject.ProjMode,'interp_tps')
|
---|
302 | Field=tps_coeff_field(Field,check_proj_tps);% calculate tps coefficients if needed
|
---|
303 | end
|
---|
304 | [Field,errormsg]=proj_field(Field,Param.ProjObject,VarMesh);
|
---|
305 | if ~isempty(errormsg)
|
---|
306 | disp_uvmat('ERROR',['error in aver_stat/proj_field:' errormsg],checkrun)
|
---|
307 | return
|
---|
308 | end
|
---|
309 | end
|
---|
310 |
|
---|
311 | %%%%%%%%%%%% MAIN RUNNING OPERATIONS %%%%%%%%%%%%
|
---|
312 | if nbfiles==1 %first field
|
---|
313 | time_1=[];
|
---|
314 | if isfield(Field,'Time')
|
---|
315 | time_1=Field.Time(1);
|
---|
316 | end
|
---|
317 | DataOut=Field;%outcome reproduces the first (projected) field by default
|
---|
318 | DataOut.Conventions='uvmat'; %suppress Conventions='uvmat/civdata' for civ input files
|
---|
319 | if isfield(Param,'ProjObject')&& ismember(Param.ProjObject.ProjMode,{'inside','outside'})%case of histograms
|
---|
320 | for ivar=1:numel(Field.ListVarName)% list of variable names before projection (histogram)
|
---|
321 | VarName=Field.ListVarName{ivar};
|
---|
322 | if isfield(Data{1},VarName)
|
---|
323 | DataOut.(VarName)=Field.(VarName);
|
---|
324 | DataOut.([VarName 'Histo'])=zeros(size(DataOut.(VarName)));
|
---|
325 | VarMesh=DataOut.(VarName)(2)-DataOut.(VarName)(1);
|
---|
326 | end
|
---|
327 | end
|
---|
328 | disp(['mesh for histogram = ' num2str(VarMesh)])
|
---|
329 | else
|
---|
330 | errorvar=zeros(numel(Field.ListVarName));%index of errorflag associated to each variable
|
---|
331 | if isfield(Field,'VarAttribute')
|
---|
332 | for ivar=1:numel(Field.ListVarName)
|
---|
333 | VarName=Field.ListVarName{ivar};
|
---|
334 | DataOut.(VarName)=zeros(size(DataOut.(VarName)));% initiate each field to zero
|
---|
335 | NbData.(VarName)=zeros(size(DataOut.(VarName)));% initiate the nbre of good data to zero
|
---|
336 |
|
---|
337 | for iivar=1:length(Field.VarAttribute)
|
---|
338 | if isequal(Field.VarDimName{iivar},Field.VarDimName{ivar})&& isfield(Field.VarAttribute{iivar},'Role')...
|
---|
339 | && strcmp(Field.VarAttribute{iivar}.Role,'errorflag')
|
---|
340 | errorvar(ivar)=iivar; % index of the errorflag variable corresponding to ivar
|
---|
341 | end
|
---|
342 | end
|
---|
343 | end
|
---|
344 | DataOut.ListVarName(errorvar(errorvar~=0))=[]; %remove errorflag from result
|
---|
345 | DataOut.VarDimName(errorvar(errorvar~=0))=[]; %remove errorflag from result
|
---|
346 | DataOut.VarAttribute(errorvar(errorvar~=0))=[]; %remove errorflag from result
|
---|
347 | else
|
---|
348 | for ivar=1:numel(Field.ListVarName)
|
---|
349 | VarName=Field.ListVarName{ivar};
|
---|
350 | DataOut.(VarName)=zeros(size(DataOut.(VarName)));% initiate each field to zero
|
---|
351 | NbData.(VarName)=zeros(size(DataOut.(VarName)));% initiate the nbre of good data to zero
|
---|
352 | end
|
---|
353 | end
|
---|
354 |
|
---|
355 | end
|
---|
356 | end %current field
|
---|
357 | for ivar=1:length(DataOut.ListVarName)
|
---|
358 | VarName=DataOut.ListVarName{ivar};
|
---|
359 | sizmean=size(DataOut.(VarName));
|
---|
360 | siz=size(Field.(VarName));
|
---|
361 | if isfield(Param,'ProjObject') && ismember(Param.ProjObject.ProjMode,{'inside','outside'})
|
---|
362 | if isfield(Data{1},VarName)
|
---|
363 | MaxValue=max(DataOut.(VarName));% current max of histogram absissa
|
---|
364 | MinValue=min(DataOut.(VarName));% current min of histogram absissa
|
---|
365 | % VarMesh=Field.VarAttribute{ivar}.Mesh;
|
---|
366 | MaxIndex=round(MaxValue/VarMesh);
|
---|
367 | MinIndex=round(MinValue/VarMesh);
|
---|
368 | MaxIndex_new=round(max(Field.(VarName)/VarMesh));% max of the current field
|
---|
369 | MinIndex_new=round(min(Field.(VarName)/VarMesh));
|
---|
370 | if MaxIndex_new>MaxIndex% the variable max for the current field exceeds the previous one
|
---|
371 | DataOut.(VarName)=[DataOut.(VarName) VarMesh*(MaxIndex+1:MaxIndex_new)];% append the new variable values
|
---|
372 | DataOut.([VarName 'Histo'])=[DataOut.([VarName 'Histo']) zeros(1,MaxIndex_new-MaxIndex)]; % append the new histo values
|
---|
373 | end
|
---|
374 | if MinIndex_new <= MinIndex-1
|
---|
375 | DataOut.(VarName)=[VarMesh*(MinIndex_new:MinIndex-1) DataOut.(VarName)];% insert the new variable values
|
---|
376 | DataOut.([VarName 'Histo'])=[zeros(1,MinIndex-MinIndex_new) DataOut.([VarName 'Histo'])];% insert the new histo values
|
---|
377 | ind_start=1;
|
---|
378 | else
|
---|
379 | ind_start=MinIndex_new-MinIndex+1;
|
---|
380 | end
|
---|
381 | DataOut.([VarName 'Histo'])(ind_start:ind_start+MaxIndex_new-MinIndex_new)=...
|
---|
382 | DataOut.([VarName 'Histo'])(ind_start:ind_start+MaxIndex_new-MinIndex_new)+Field.([VarName 'Histo']);
|
---|
383 | end
|
---|
384 | elseif ~isequal(DataOut.(VarName),0)&& ~isequal(siz,sizmean)
|
---|
385 | disp_uvmat('ERROR',['unequal size of input field ' VarName ', need to project on a grid'],checkrun)
|
---|
386 | return
|
---|
387 | else
|
---|
388 | if errorvar(ivar)==0
|
---|
389 | check_bad=isnan(Field.(VarName));%=0 for NaN data values, 1 else
|
---|
390 | else
|
---|
391 | check_bad=isnan(Field.(VarName)) | Field.(Field.ListVarName{errorvar(ivar)})~=0;%=0 for NaN or error flagged data values, 1 else
|
---|
392 | end
|
---|
393 | Field.(VarName)(check_bad)=0; %set to zero NaN or data marked by error flag
|
---|
394 | DataOut.(VarName)=DataOut.(VarName)+ double(Field.(VarName)); % update the sum
|
---|
395 | NbData.(VarName)=NbData.(VarName)+ ~check_bad;% records the number of data for each point
|
---|
396 | end
|
---|
397 | end
|
---|
398 | %%%%%%%%%%%% END MAIN RUNNING OPERATIONS %%%%%%%%%%%%
|
---|
399 | else
|
---|
400 | disp(errormsg)
|
---|
401 | end
|
---|
402 | end
|
---|
403 | %%%%%%%%%%%%%%%% end loop on field indices %%%%%%%%%%%%%%%%
|
---|
404 | if ~(isfield(Param,'ProjObject') && ismember(Param.ProjObject.ProjMode,{'inside','outside'}))
|
---|
405 | for ivar=1:length(Field.ListVarName)
|
---|
406 | VarName=Field.ListVarName{ivar};
|
---|
407 | DataOut.(VarName)=DataOut.(VarName)./NbData.(VarName); % normalize the mean
|
---|
408 | end
|
---|
409 | end
|
---|
410 | nbmissing=NbField-nbfiles;
|
---|
411 | if nbmissing~=0
|
---|
412 | disp_uvmat('WARNING',[num2str(nbmissing) ' input files are missing or skipped'],checkrun)
|
---|
413 | end
|
---|
414 | if isempty(time) % time is read from files
|
---|
415 | if isfield(Field,'Time')
|
---|
416 | time_end=Field.Time(1);%last time read
|
---|
417 | if ~isempty(time_1)
|
---|
418 | DataOut.Time=time_1;
|
---|
419 | DataOut.Time_end=time_end;
|
---|
420 | end
|
---|
421 | end
|
---|
422 | else % time from ImaDoc prevails if it exists
|
---|
423 | DataOut.Time=time(1);
|
---|
424 | DataOut.Time_end=time(end);
|
---|
425 | end
|
---|
426 |
|
---|
427 | %% writing the result file
|
---|
428 | OutputFile=fullfile_uvmat(RootPath{1},OutputDir,RootFile{1},FileExtOut,NomTypeOut,first_i,last_i,first_j,last_j);
|
---|
429 | if strcmp(FileExtOut,'.png') %case of images
|
---|
430 | if isequal(FileInfo{1}.BitDepth,16)||(numel(FileInfo)==2 &&isequal(FileInfo{2}.BitDepth,16))
|
---|
431 | DataOut.A=uint16(DataOut.A);
|
---|
432 | imwrite(DataOut.A,OutputFile,'BitDepth',16); % case of 16 bit images
|
---|
433 | else
|
---|
434 | DataOut.A=uint8(DataOut.A);
|
---|
435 | imwrite(DataOut.A,OutputFile,'BitDepth',8); % case of 16 bit images
|
---|
436 | end
|
---|
437 | disp([OutputFile ' written']);
|
---|
438 | else %case of netcdf file , determine global attributes
|
---|
439 | errormsg=struct2nc(OutputFile,DataOut); %save result file
|
---|
440 | if isempty(errormsg)
|
---|
441 | disp([OutputFile ' written']);
|
---|
442 | else
|
---|
443 | disp(['error in writting result file: ' errormsg])
|
---|
444 | end
|
---|
445 | end % end averaging loop
|
---|
446 |
|
---|
447 | %% open the result file with uvmat (in RUN mode)
|
---|
448 | if checkrun
|
---|
449 | uvmat(OutputFile)% open the last result file with uvmat
|
---|
450 | end
|
---|