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source: trunk/src/series/extract_multitif.m @ 932

Last change on this file since 932 was 931, checked in by sommeria, 8 years ago

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1%'ima2netcdf': read image series and transform to netcdf
2%------------------------------------------------------------------------
3
4   
5% function ParamOut=ima2netcdf(Param)
6%
7%%%%%%%%%%% GENERAL TO ALL SERIES ACTION FCTS %%%%%%%%%%%%%%%%%%%%%%%%%%%
8%
9%OUTPUT
10% ParamOut: sets options in the GUI series.fig needed for the function
11%
12%INPUT:
13% In run mode, the input parameters are given as a Matlab structure Param copied from the GUI series.
14% In batch mode, Param is the name of the corresponding xml file containing the same information
15% when Param.Action.RUN=0 (as activated when the current Action is selected
16% in series), the function ouput paramOut set the activation of the needed GUI elements
17%
18% Param contains the elements:(use the menu bar command 'export/GUI config' in series to
19% see the current structure Param)
20%    .InputTable: cell of input file names, (several lines for multiple input)
21%                      each line decomposed as {RootPath,SubDir,Rootfile,NomType,Extension}
22%    .OutputSubDir: name of the subdirectory for data outputs
23%    .OutputDirExt: directory extension for data outputs
24%    .Action: .ActionName: name of the current activated function
25%             .ActionPath:   path of the current activated function
26%             .ActionExt: fct extension ('.m', Matlab fct, '.sh', compiled   Matlab fct
27%             .RUN =0 for GUI input, =1 for function activation
28%             .RunMode='local','background', 'cluster': type of function  use
29%             
30%    .IndexRange: set the file or frame indices on which the action must be performed
31%    .FieldTransform: .TransformName: name of the selected transform function
32%                     .TransformPath:   path  of the selected transform function
33%    .InputFields: sub structure describing the input fields withfields
34%              .FieldName: name(s) of the field
35%              .VelType: velocity type
36%              .FieldName_1: name of the second field in case of two input series
37%              .VelType_1: velocity type of the second field in case of two input series
38%              .Coord_y: name of y coordinate variable
39%              .Coord_x: name of x coordinate variable
40%    .ProjObject: %sub structure describing a projection object (read from ancillary GUI set_object)
41%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
42
43%=======================================================================
44% Copyright 2008-2016, LEGI UMR 5519 / CNRS UGA G-INP, Grenoble, France
45%   http://www.legi.grenoble-inp.fr
46%   Joel.Sommeria - Joel.Sommeria (A) legi.cnrs.fr
47%
48%     This file is part of the toolbox UVMAT.
49%
50%     UVMAT is free software; you can redistribute it and/or modify
51%     it under the terms of the GNU General Public License as published
52%     by the Free Software Foundation; either version 2 of the license,
53%     or (at your option) any later version.
54%
55%     UVMAT is distributed in the hope that it will be useful,
56%     but WITHOUT ANY WARRANTY; without even the implied warranty of
57%     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
58%     GNU General Public License (see LICENSE.txt) for more details.
59%=======================================================================
60
61function ParamOut=ima2netcdf(Param)
62
63%%%%%%%%%%%%%%%%%    INPUT PREPARATION MODE (no RUN)    %%%%%%%%%%%%%%%%%
64if isstruct(Param) && isequal(Param.Action.RUN,0)
65    ParamOut.AllowInputSort='off';% allow alphabetic sorting of the list of input file SubDir (options 'off'/'on', 'off' by default)
66    ParamOut.WholeIndexRange='on';% prescribes the file index ranges from min to max (options 'off'/'on', 'off' by default)
67    ParamOut.NbSlice='on'; % edit box nbre of slices made active
68    ParamOut.VelType='off';% menu for selecting the velocity type (options 'off'/'one'/'two',  'off' by default)
69    ParamOut.FieldName='off';% menu for selecting the field (s) in the input file(options 'off'/'one'/'two', 'off' by default)
70    ParamOut.FieldTransform = 'off';%can use a transform function
71    ParamOut.ProjObject='off';%can use projection object(option 'off'/'on',
72    ParamOut.Mask='off';%can use mask option   (option 'off'/'on', 'off' by default)
73    ParamOut.OutputDirExt='.png';%set the output dir extension
74    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
75   
76    %% root input file(s) and type
77    % check the existence of the first file in the series
78        first_j=[];% note that the function will propose to cover the whole range of indices
79    if isfield(Param.IndexRange,'MinIndex_j'); first_j=Param.IndexRange.MinIndex_j; end
80    last_j=[];
81    if isfield(Param.IndexRange,'MaxIndex_j'); last_j=Param.IndexRange.MaxIndex_j; end
82    PairString='';
83    if isfield(Param.IndexRange,'PairString'); PairString=Param.IndexRange.PairString; end
84    [i1,i2,j1,j2] = get_file_index(Param.IndexRange.first_i,first_j,PairString);
85    FirstFileName=fullfile_uvmat(Param.InputTable{1,1},Param.InputTable{1,2},Param.InputTable{1,3},...
86        Param.InputTable{1,5},Param.InputTable{1,4},i1,i2,j1,j2);
87    if ~exist(FirstFileName,'file')
88        msgbox_uvmat('WARNING',['the first input file ' FirstFileName ' does not exist'])
89    else
90        [i1,i2,j1,j2] = get_file_index(Param.IndexRange.last_i,last_j,PairString);
91        LastFileName=fullfile_uvmat(Param.InputTable{1,1},Param.InputTable{1,2},Param.InputTable{1,3},...
92        Param.InputTable{1,5},Param.InputTable{1,4},i1,i2,j1,j2);
93        if ~exist(FirstFileName,'file')
94             msgbox_uvmat('WARNING',['the last input file ' LastFileName ' does not exist'])
95        end
96    end
97
98    %% check the validity of  input file types
99    ImageTypeOptions={'image','multimage','mmreader','video'};%allowed input file types(images)
100    FileInfo=get_file_info(FirstFileName);
101    FileType=FileInfo.FileType;
102    CheckImage=~isempty(find(strcmp(FileType,ImageTypeOptions), 1));% =1 for images
103    if ~CheckImage
104        msgbox_uvmat('ERROR',['invalid file type input: ' FileType ' not an image'])
105        return
106    end
107   
108    return
109end
110%%%%%%%%%%%%%%%%%    STOP HERE FOR PAMETER INPUT MODE   %%%%%%%%%%%%%%%%%
111
112%% read input parameters from an xml file if input is a file name (batch mode)
113checkrun=1;
114RUNHandle=[];
115WaitbarHandle=[];
116if ischar(Param)
117    Param=xml2struct(Param);% read Param as input file (batch case)
118    checkrun=0;
119else
120hseries=findobj(allchild(0),'Tag','series');
121RUNHandle=findobj(hseries,'Tag','RUN');%handle of RUN button in GUI series
122WaitbarHandle=findobj(hseries,'Tag','Waitbar');%handle of waitbar in GUI series
123end
124
125%% list of input images
126DirImages=fullfile(Param.InputTable{1,1},Param.InputTable{1,2});
127ListStruct=dir(DirImages);   
128ListCells=struct2cell(ListStruct);% transform dir struct to a cell arrray
129check_bad=strcmp('.',ListCells(1,:))|strcmp('..',ListCells(1,:));%detect the dir '.' to exclude it
130check_dir=cell2mat(ListCells(4,:));% =1 for directories, =0 for files
131ListFile=ListCells(1,find(~check_dir & ~check_bad));
132
133% %% create the netcdf file with name flname in format NETCDF4
134 OutputDir=fullfile(Param.InputTable{1,1},[Param.OutputSubDir Param.OutputDirExt]);
135 
136% cmode = netcdf.getConstant('NETCDF4');
137% cmode = bitor(cmode, netcdf.getConstant('CLASSIC_MODEL'));
138% cmode = bitor(cmode, netcdf.getConstant('CLOBBER'));
139% nc = netcdf.create(fullfile(OutputDir,'images.nc'), cmode);
140
141%% Main loop
142ImagesPerLevel=100;%100;
143count=0;
144%count=316;%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%CORRECTION EXP08: 4684 images -> start at 316 start 67->_11_1
145%count=1934%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%CORRECTION EXP07: 3066 images
146%% loop on the files
147for ifile=1:numel(ListFile)
148    update_waitbar(WaitbarHandle,ifile/numel(ListFile))
149    if ~isempty(RUNHandle)&& ~strcmp(get(RUNHandle,'BusyAction'),'queue')
150        disp('program stopped by user')
151        break
152    end
153    ImageName=fullfile(DirImages,ListFile{ifile});
154    NbFrames=numel(imfinfo(ImageName));
155    % loop on the frames within the tiff file
156    for iframe=1:NbFrames     
157        A=imread(ImageName,iframe);
158
159        if isequal(ImagesPerLevel,1)% mode series
160           
161            OutputFile=fullfile(OutputDir,['img_' num2str(count+1) '.png']);
162        else % mode multilevel or volume (indices i and j)
163            i_index=fix(count/ImagesPerLevel)+1;
164            j_index=mod(count,ImagesPerLevel)+1;
165            OutputFile=fullfile(OutputDir,['img_' num2str(i_index) '_' num2str(j_index) '.png']);
166        end
167        imwrite(A,OutputFile,'BitDepth',16)
168        count=count+1;
169    end
170end
171
172
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