source: trunk/src/series/extract_rdvision_new.m @ 889

Last change on this file since 889 was 889, checked in by sommeria, 8 years ago

extract_rdvision_new for the new image acquisition system

File size: 34.7 KB
Line 
1%'extract_rdvision': relabel an image series with two indices, and correct errors from the RDvision transfer program
2%------------------------------------------------------------------------
3% function ParamOut=extract_rdvision(Param)
4%------------------------------------------------------------------------
5%
6%%%%%%%%%%% GENERAL TO ALL SERIES ACTION FCTS %%%%%%%%%%%%%%%%%%%%%%%%%%%
7%
8%OUTPUT
9% ParamOut: sets options in the GUI series.fig needed for the function
10%
11%INPUT:
12% In run mode, the input parameters are given as a Matlab structure Param copied from the GUI series.
13% In batch mode, Param is the name of the corresponding xml file containing the same information
14% when Param.Action.RUN=0 (as activated when the current Action is selected
15% in series), the function ouput paramOut set the activation of the needed GUI elements
16%
17% Param contains the elements:(use the menu bar command 'export/GUI config' in series to
18% see the current structure Param)
19%    .InputTable: cell of input file names, (several lines for multiple input)
20%                      each line decomposed as {RootPath,SubDir,Rootfile,NomType,Extension}
21%    .OutputSubDir: name of the subdirectory for data outputs
22%    .OutputDirExt: directory extension for data outputs
23%    .Action: .ActionName: name of the current activated function
24%             .ActionPath:   path of the current activated function
25%             .ActionExt: fct extension ('.m', Matlab fct, '.sh', compiled   Matlab fct
26%             .RUN =0 for GUI input, =1 for function activation
27%             .RunMode='local','background', 'cluster': type of function  use
28%             
29%    .IndexRange: set the file or frame indices on which the action must be performed
30%    .FieldTransform: .TransformName: name of the selected transform function
31%                     .TransformPath:   path  of the selected transform function
32%    .InputFields: sub structure describing the input fields withfields
33%              .FieldName: name(s) of the field
34%              .VelType: velocity type
35%              .FieldName_1: name of the second field in case of two input series
36%              .VelType_1: velocity type of the second field in case of two input series
37%              .Coord_y: name of y coordinate variable
38%              .Coord_x: name of x coordinate variable
39%    .ProjObject: %sub structure describing a projection object (read from ancillary GUI set_object)
40%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
41
42%=======================================================================
43% Copyright 2008-2014, LEGI UMR 5519 / CNRS UJF G-INP, Grenoble, France
44%   http://www.legi.grenoble-inp.fr
45%   Joel.Sommeria - Joel.Sommeria (A) legi.cnrs.fr
46%
47%     This file is part of the toolbox UVMAT.
48%
49%     UVMAT is free software; you can redistribute it and/or modify
50%     it under the terms of the GNU General Public License as published
51%     by the Free Software Foundation; either version 2 of the license,
52%     or (at your option) any later version.
53%
54%     UVMAT is distributed in the hope that it will be useful,
55%     but WITHOUT ANY WARRANTY; without even the implied warranty of
56%     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
57%     GNU General Public License (see LICENSE.txt) for more details.
58%=======================================================================
59
60function ParamOut=extract_rdvision(Param) %default output=relabel_i_j(Param)
61
62%% set the input elements needed on the GUI series when the action is selected in the menu ActionName
63if isstruct(Param) && isequal(Param.Action.RUN,0)
64    ParamOut.AllowInputSort='off';...% allow alphabetic sorting of the list of input file SubDir (options 'off'/'on', 'off' by default)
65    ParamOut.WholeIndexRange='on';...% prescribes the file index ranges from min to max (options 'off'/'on', 'off' by default)
66    ParamOut.NbSlice='one'; ...%nbre of slices, 'one' prevents splitting in several processes, ('off' by default)
67    ParamOut.VelType='off';...% menu for selecting the velocity type (options 'off'/'one'/'two',  'off' by default)
68    ParamOut.FieldName='off';...% menu for selecting the field (s) in the input file(options 'off'/'one'/'two', 'off' by default)
69    ParamOut.FieldTransform = 'off';...%can use a transform function
70    ParamOut.ProjObject='off';...%can use projection object(option 'off'/'on',
71    ParamOut.Mask='off';...%can use mask option   (option 'off'/'on', 'off' by default)
72    ParamOut.OutputSubDirMode='custom'; %output folder given by the program, not by the GUI series
73     % detect the set of image folder
74    RootPath=Param.InputTable{1,1};
75    ListStruct=dir(RootPath);   
76    ListCells=struct2cell(ListStruct);% transform dir struct to a cell arrray
77    check_bad=strcmp('.',ListCells(1,:))|strcmp('..',ListCells(1,:));%detect the dir '.' to exclude it
78    check_dir=cell2mat(ListCells(4,:));% =1 for directories, =0 for files
79    ListDir=ListCells(1,find(check_dir & ~check_bad));
80%     InputTable=cell(numel(ListDir),5);
81%     InputTable(:,2)=ListDir';
82    isel=0;
83    InputTable=Param.InputTable;
84    for ilist=1:numel(ListDir)
85        ListStructSub=dir(fullfile(RootPath,ListDir{ilist}));
86        ListCellSub=struct2cell(ListStructSub);% transform dir struct to a cell arrray
87        detect_seq=regexp(ListCellSub(1,:),'.seq$');
88        seq_index=find(~cellfun('isempty',detect_seq),1);
89        if ~isempty(seq_index)
90%             msgbox_uvmat('ERROR',['not seq file in ' ListDir{ilist} ': please check the input folders'])
91%         else
92           isel=isel+1;
93           InputTable{isel,1}=RootPath;
94           InputTable{isel,2}=ListDir{ilist};
95            RootFile=regexprep(ListCellSub{1,seq_index},'.seq$','');
96            InputTable{isel,3}=RootFile;
97        InputTable{isel,4}='*';
98        InputTable{isel,5}='.seq';
99    end
100    end
101    hseries=findobj(allchild(0),'Tag','series');% find the parent GUI 'series'
102    hhseries=guidata(hseries); %handles of the elements in 'series'
103    set(hhseries.InputTable,'Data',InputTable)
104    ParamOut.ActionInput.LogPath=RootPath;% indicate the path for the output info: 0_LOG ....
105return
106end
107
108ParamOut=[];
109%%%%%%%%%%%% STANDARD PART  %%%%%%%%%%%%
110%% read input parameters from an xml file if input is a file name (batch mode)
111checkrun=1;
112if ischar(Param)
113    Param=xml2struct(Param);% read Param as input file (batch case)
114    checkrun=0;
115end
116hseries=findobj(allchild(0),'Tag','series');
117RUNHandle=findobj(hseries,'Tag','RUN');%handle of RUN button in GUI series
118WaitbarHandle=findobj(hseries,'Tag','Waitbar');%handle of waitbar in GUI series
119
120%% root input file(s) and type
121RootPath=Param.InputTable{1,1};
122if ~isempty(find(~strcmp(RootPath,Param.InputTable(:,1))))% if the Rootpath for each camera are not identical
123    disp_uvmat('ERROR','Rootpath for all cameras must be identical',checkrun)
124    return
125end
126
127% get the set of input file names (cell array filecell), and the lists of
128% input file or frame indices i1_series,i2_series,j1_series,j2_series
129[filecell,i1_series,i2_series,j1_series,j2_series]=get_file_series(Param);
130
131%OutputDir=[Param.OutputSubDir Param.OutputDirExt];
132 
133% numbers of slices and file indices
134nbfield_j=size(i1_series{1},1); %nb of fields for the j index (bursts or volume slices)
135nbfield_i=size(i1_series{1},2); %nb of fields for the i index
136nbfield=nbfield_j*nbfield_i; %total number of fields
137
138%determine the file type on each line from the first input file
139
140FileInfo=get_file_info(filecell{1,1});
141if strcmp(FileInfo.FileType,'rdvision')
142    if ~isequal(FileInfo.NumberOfFrames,nbfield)
143        msgbox_uvmat('ERROR',['the whole series of ' num2str(FileInfo.NumberOfFrames) ' images must be extracted at once'])
144        %rmfield(OutputDir)
145        return
146    end
147    %% interactive input of specific parameters (for RDvision system)
148    display('converting images from RDvision system...')
149else
150    msgbox_uvmat('ERROR','the input is not from rdvision: a .seq or .sqb file must be opened')
151    return
152end
153t=xmltree;
154%%% A REMETTREE %%%%%%%%%%%%%%%%%%%%%
155save(t,fullfile(RootPath,'Running.xml'))%create an xml file to indicate that processing takes place
156
157%% calibration data and timing: read the ImaDoc files
158mode=''; %default
159timecell={};
160itime=0;
161NbSlice_calib={};
162
163%SubDirBase=regexprep(SubDir{1},'\..*','');%take the root part of SubDir, before the first dot '.'
164
165%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
166%%%  loop on the cameras ( #iview)
167%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
168% RootPath=Param.InputTable(:,1);
169% RootFile=Param.InputTable(:,3);
170% SubDir=Param.InputTable(:,2);
171% NomType=Param.InputTable(:,4);
172% FileExt=Param.InputTable(:,5);
173
174% [XmlData,NbSlice_calib,time,errormsg]=read_multimadoc(RootPath,SubDir,RootFile,FileExt,i1_series,i2_series,j1_series,j2_series);
175% if size(time,1)>1
176%     diff_time=max(max(diff(time)));
177%     if diff_time>0
178%         disp_uvmat('WARNING',['times of series differ by (max) ' num2str(diff_time)],checkrun)
179%     end   
180% end
181%
182%      nbfield2=size(time,1);
183
184
185
186for iview=1:size(Param.InputTable,1)
187     filexml=[fullfile(RootPath,Param.InputTable{iview,3}) '.xml'];%new convention: xml at the level of the image folder
188    if ~exist(filexml,'file')
189        disp_uvmat('ERROR',[filexml ' missing'],checkrun)
190        return
191    end
192%     %[XmlData,error]=imadoc2struct_special(filexml);
193     [XmlData,error]=imadoc2struct(filexml);
194%     if ~isempty(error)
195%         disp(error)
196%     end
197%     if isfield(XmlData,'Time')
198%         itime=itime+1;
199%         timecell{itime}=XmlData.Time;
200%     end
201%     if isfield(XmlData,'GeometryCalib') && isfield(XmlData.GeometryCalib,'SliceCoord')
202%         NbSlice_calib{1}=size(XmlData.GeometryCalib.SliceCoord,1);%nbre of slices for Zindex in phys transform
203%         if ~isequal(NbSlice_calib{1},NbSlice_calib{1})
204%             msgbox_uvmat('WARNING','inconsistent number of Z indices for the two field series');
205%         end
206%     end
207   
208   
209%     % correction to RDvision xml file
210%   t=xmltree(filexml);
211%     
212%     % correct Dtj and Dtk
213 %    NomTypeNew='_1_1';% new file nomencalture by default
214%     ImageName='img_1_1.png';% first image name
215%      if isfield(XmlData,'NbDtj')
216%          uid_NbDtj=find(t,'ImaDoc/Camera/BurstTiming/NbDtj');
217%          uid_value=children(t,uid_NbDtj);
218%         if ~isempty(uid_value)
219%             t=set(t,uid_value(1),'value',num2str(XmlData.NbDtj));
220%         end
221%     end
222%     if isfield(XmlData,'NbDtk')
223%         uid_NbDtk=find(t,'ImaDoc/Camera/BurstTiming/NbDtk');
224%         uid_value=children(t,uid_NbDtk);
225%         if ~isempty(uid_value)
226%             t=set(t,uid_value(1),'value',num2str(XmlData.NbDtk));
227%         end
228%     end
229%     if isempty(j1_series{1}) && isfield(XmlData,'NbDti')
230%         uid_Dti=find(t,'ImaDoc/Camera/BurstTiming/Dti');
231%         t=add(t,uid_Dti,'chardata',num2str(XmlData.Dti));
232%         uid_NbDti=find(t,'ImaDoc/Camera/BurstTiming/NbDti');
233%         t=add(t,uid_NbDti,'chardata',num2str(XmlData.NbDti));
234%         uid_NbDtj=find(t,'ImaDoc/Camera/BurstTiming/NbDtj');
235%         uid_NbDtk=find(t,'ImaDoc/Camera/BurstTiming/NbDtk');
236%         t=delete(t,uid_NbDtj);
237%         t=delete(t,uid_NbDtk);
238%         uid_Dtj=find(t,'ImaDoc/Camera/BurstTiming/Dtj');
239%         uid_Dtk=find(t,'ImaDoc/Camera/BurstTiming/Dtk');
240%         t=delete(t,uid_Dtj);
241%         t=delete(t,uid_Dtk);
242%         NomTypeNew='_1';
243%         ImageName='img_1.png';
244%     end
245%     
246%     %update information of 'Heading'
247%     uid_Heading=find(t,'ImaDoc/Heading');
248%     if isempty(uid_Heading)
249%         [t,uid_Heading]=add(t,1,'element','Heading');
250%     end
251%     uid_SubCampaign=find(t,'ImaDoc/Heading/SubCampaign');
252%     if ~isempty(uid_SubCampaign), t=delete(t,uid_SubCampaign); end
253%     uid_Experiment=find(t,'ImaDoc/Heading/Experiment');
254%     if ~isempty(uid_Experiment), t=delete(t,uid_Experiment); end
255%     uid_Device=find(t,'ImaDoc/Heading/Device');
256%     if ~isempty(uid_Device), t=delete(t,uid_Device); end
257%     uid_Record=find(t,'ImaDoc/Heading/Record');
258%     if ~isempty(uid_Record), t=delete(t,uid_Record); end
259%     uid_DateExp=find(t,'ImaDoc/Heading/DateExp');
260%     if ~isempty(uid_DateExp), t=delete(t,uid_DateExp); end
261%     
262%     %indicate the name of the first image (as a check that the xml file is not moved)
263%     uid_ImageName=find(t,'ImaDoc/Heading/ImageName');
264%     if isempty(uid_ImageName)
265%         [t,uid_ImageName]=add(t,uid_Heading,'element','ImageName');
266%     end
267%     uid_value=children(t,uid_ImageName);
268%     if isempty(uid_value)
269%         t=add(t,uid_ImageName,'chardata',ImageName);%indicate  name of the first image, with ;png extension
270%     else
271%         t=set(t,uid_value(1),'value',ImageName);%indicate  name of the first image, with ;png extension
272%     end
273%     
274%     %indicate the date and time of the image acquisition start
275%     % if isfield(FileInfo,'binrepertoire') && isfield(FileInfo,'starttime')
276%     %     sep_pos=regexp(FileInfo.binrepertoire,'T');
277%     %     DateTime=FileInfo.starttime;
278%     %     if ~isempty(sep_pos)
279%     %         DateTime=[FileInfo.binrepertoire(1:sep_pos-1) ' ' DateTime];
280%     %     end
281%     %     uid_DateTime=find(t,'ImaDoc/Heading/DateTime');
282%     %     if isempty(uid_DateTime)
283%     %         [t,uid_DateTime]=add(t,uid_Heading,'element','DateTime');
284%     %     end
285%     %     uid_value=children(t,uid_DateTime);
286%     %     if isempty(uid_value)
287%     %         t=add(t,uid_DateTime,'chardata',DateTime);%indicate  name of the first image, with ;png extension
288%     %     else
289%     %         t=set(t,uid_value(1),'value',DateTime);%indicate  name of the first image, with ;png extension
290%     %     end
291%     % end
292%     
293%     %% backup the previous xml file and save the corrected one
294% %    [success,message]=copyfile(filexml,[filexml '~']);%make backup
295% %     if success~=1
296% %         disp(['errror in xml file backup: ' message]);
297% %         return
298% %     end
299%     save(t,filexml)
300
301    nbfield2=size(XmlData.Time,2)-1;
302    if nbfield2>1
303        NomTypeNew='_1_1';
304    else
305         NomTypeNew='_1';
306    end
307    %% get the names of .seq and .sqb files
308    switch Param.InputTable{iview,5}
309        case {'.seq','.sqb'}
310            filename_seq=fullfile(RootPath,Param.InputTable{iview,2},[Param.InputTable{iview,3} '.seq']);
311            filename_sqb=fullfile(RootPath,Param.InputTable{iview,2},[Param.InputTable{iview,3} '.sqb']);
312        otherwise
313            errormsg='input file extension must be .seq or .sqb';
314    end
315    if ~exist(filename_seq,'file')
316        errormsg=[filename_seq ' does not exist'];
317        return
318    end
319   
320    %% get data from .seq file
321    s=ini2struct(filename_seq);
322    SeqData=s.sequenceSettings;
323    SeqData.width=str2double(SeqData.width);
324    SeqData.height=str2double(SeqData.height);
325    SeqData.bytesperpixel=str2double(SeqData.bytesperpixel);
326    SeqData.nb_frames=str2double(s.sequenceSettings.numberoffiles);
327    if isempty(SeqData.binrepertoire)%used when binrepertoire empty, strange feature of rdvision
328        SeqData.binrepertoire=regexprep(s.sequenceSettings.bindirectory,'\\$','');%tranform Windows notation to Linux
329        SeqData.binrepertoire=regexprep(SeqData.binrepertoire,'\','/');
330        [tild,binrepertoire,DirExt]=fileparts(SeqData.binrepertoire);
331        SeqData.binrepertoire=[SeqData.binrepertoire DirExt];
332    end
333%     PathDir=fileparts(PathDir);
334   
335    %% reading the .sqb file
336    m = memmapfile(filename_sqb,'Format', { 'uint32' [1 1] 'offset'; ...
337        'uint32' [1 1] 'garbage1';...
338        'double' [1 1] 'timestamp';...
339        'uint32' [1 1] 'file_idx';...
340        'uint32' [1 1] 'garbage2' },'Repeat',SeqData.nb_frames);
341   
342    %%%%%%%BRICOLAGE in case of unreadable .sqb file: remplace lecture du fichier
343%         ind=[111 114:211];%indices of bin files
344%         w=1024;%w=width of images in pixels
345%         h=1024;%h=height of images in pixels
346%         bpp=2;% nbre of bytes per pixel
347%         lengthimage=w*h*bpp;% lengthof an image record on the binary file
348%         nbimages=32; %nbre of images of each camera in a bin file
349%         for ii=1:32*numel(ind)
350%             data(ii).offset=mod(ii-1,32)*2*lengthimage+lengthimage;%Dalsa_2
351%             %data(ii).offset=mod(ii-1,32)*2*lengthimage;%Dalsa_1
352%             data(ii).file_idx=ind(ceil(ii/32));
353%             data(ii).timestamp=0.2*(ii-1);
354%         end
355%         m.Data=data;
356    %%%%%%%
357   
358    for ii=1: numel(m.Data)
359        timestamp(ii)=m.Data(ii).timestamp;
360    end
361    %timestamp %todo: check withDt from the xml file
362    [BinSize,errormsg]=binread_rdv_series(RootPath,SeqData,m.Data,nbfield2,NomTypeNew)
363    if ~isempty(errormsg)
364        disp_uvmat('ERROR',errormsg,checkrun)
365        return
366    end
367end
368delete(fullfile(RootPath,'Running.xml'))%delete the  xml file to indicate that processing is finished
369
370%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
371%--------- reads a series of bin files
372%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
373function [BinSize,errormsg]=binread_rdv_series(PathDir,SeqData,SqbData,nbfield2,NomTypeNew)
374% BINREAD_RDV Permet de lire les fichiers bin gᅵnᅵrᅵs par Hiris ᅵ partir du
375% fichier seq associᅵ.
376%   [IMGS,TIMESTAMPS,NB_FRAMES] = BINREAD_RDV(FILENAME,FRAME_IDX) lit
377%   l'image d'indice FRAME_IDX de la sï¿œquence FILENAME.
378%
379%   Entrï¿œes
380%   -------
381%   FILENAME  : Nom du fichier sï¿œquence (.seq).
382%   FRAME_IDX : Indice de l'image ï¿œ lire. Si FRAME_IDX vaut -1 alors la
383%   sï¿œquence est entiï¿œrement lue. Si FRAME_IDX est un tableau d'indices
384%   alors toutes les images d'incides correspondant sont lues. Si FRAME_IDX
385%   est un tableau vide alors aucune image n'est lue mais le nombre
386%   d'images et tous les timestamps sont renvoyï¿œs. Les indices commencent ï¿œ
387%   1 et se termines ï¿œ NB_FRAMES.
388%
389%   Sorties
390%   -------
391%   IMGS        : Images de sortie.
392%   TIMESTAMPS  : Timestaps des images lues.
393%   NB_FRAMES   : Nombres d'images dans la sï¿œquence.
394NbBinFile=0;
395BinSize=0;
396fid=0;
397errormsg='';
398classname=sprintf('uint%d',SeqData.bytesperpixel*8);
399
400classname=['*' classname];
401BitDepth=8*SeqData.bytesperpixel;%needed to write images (8 or 16 bits)
402binrepertoire=fullfile(PathDir,SeqData.binrepertoire);
403OutputDir=fullfile(PathDir,SeqData.sequencename);
404if ~exist(OutputDir,'dir')
405    %     errormsg=[OutputDir ' already exist, delete it first'];
406    %     return
407    % end
408    [s,errormsg]=mkdir(OutputDir);
409   
410    if s==0
411        disp(errormsg)
412        return%not able to create new image dir
413    end
414end
415for ii=1:SeqData.nb_frames
416    j1=[];
417    if ~isequal(nbfield2,1)
418        j1=mod(ii-1,nbfield2)+1;
419    end
420    i1=floor((ii-1)/nbfield2)+1;
421    OutputFile=fullfile_uvmat(PathDir,SeqData.sequencename,'img','.png',NomTypeNew,i1,[],j1);% TODO: set NomTypeNew from SeqData.mode
422    fname=fullfile(binrepertoire,sprintf('%s%.5d.bin',SeqData.binfile,SqbData(ii).file_idx));
423    if exist(OutputFile,'file')
424        fid=0;
425    else
426        if fid==0 || ~strcmp(fname,fname_prev) % open the bin file if not in use
427            if fid~=0
428                fclose(fid);%close the previous bin file if relevant
429            end
430            [fid,msg]=fopen(fname,'rb');
431            if isequal(fid,-1)
432                disp(['error in opening ' fname ': ' msg])
433            else
434                disp([fname ' opened for reading'])
435            end
436            fseek(fid,SqbData(ii).offset,-1);%look at the right starting place in the bin file
437            NbBinFile=NbBinFile+1;%counter of binary files (for checking purpose)
438            BinSize(NbBinFile)=0;% strat counter for new bin file
439        else
440            %             fclose(fid);%close the previous bin file
441            %             fid=fopen(fname,'rb');% open the new bin file
442            fseek(fid,SqbData(ii).offset,-1);%look at the right starting place in the bin file
443        end
444        fname_prev=fname;
445        A=reshape(fread(fid,SeqData.width*SeqData.height,classname),SeqData.width,SeqData.height);%read the current image
446        A=A';
447        BinSize(NbBinFile)=BinSize(NbBinFile)+SeqData.width*SeqData.height*SeqData.bytesperpixel*8; %record bits read
448        try
449            imwrite(A,OutputFile,'BitDepth',BitDepth) % case of 16 bit images
450            disp([OutputFile ' written']);
451            % [s,errormsg] = fileattrib(OutputFile,'-w','a'); %set images to read only '-w' for all users ('a')
452            %         if ~s
453            % %             disp_uvmat('ERROR',errormsg,checkrun);
454            %             return
455            %         end
456        catch ME
457            errormsg=ME.message;
458            return
459        end
460    end
461end
462if fid~=0
463fclose(fid)
464end
465
466
467
468
469% for ifile=1:nbfield
470%             update_waitbar(WaitbarHandle,ifile/nbfield)
471%     if ~isempty(RUNHandle) && ~strcmp(get(RUNHandle,'BusyAction'),'queue')
472%         disp('program stopped by user')
473%         break
474%     end
475%     [A,FileInfo,timestamps]=read_rdvision(filename,ifile);
476%     if ifile==1
477%         classA=class(A);
478%         if strcmp(classA,'uint8')
479%             BitDepth=8;
480%         else
481%         BitDepth=16;
482%         end
483%     end
484%     j1=[];
485%     if ~isequal(nbfield2,1)
486%     j1=mod(ifile-1+first_label,nbfield2)+1;
487%     end
488%     i1=floor((ifile-1+first_label)/nbfield2)+1;
489%     OutputFile=fullfile_uvmat(RootPath{1},OutputDir,'img','.png',NomTypeNew,i1,[],j1);
490%     try
491%         imwrite(A,OutputFile,'BitDepth',BitDepth) % case of 16 bit images
492%     disp([OutputFile ' written']);
493%         [s,errormsg] = fileattrib(OutputFile,'-w','a'); %set images to read only '-w' for all users ('a')
494%         if ~s
495%             disp_uvmat('ERROR',errormsg,checkrun);
496%             return
497%         end
498%     catch ME
499%         disp_uvmat('ERROR',ME.message,checkrun);
500%         return
501%     end
502%
503% end
504
505%'imadoc2struct_special': reads the xml file for image documentation
506%------------------------------------------------------------------------
507% function [s,errormsg]=imadoc2struct_special(ImaDoc,option)
508%
509% OUTPUT:
510% s: structure representing ImaDoc
511%   s.Heading: information about the data hierarchical structure
512%   s.Time: matrix of times
513%   s.TimeUnit
514%  s.GeometryCalib: substructure containing the parameters for geometric calibration
515% errormsg: error message
516%
517% INPUT:
518% ImaDoc: full name of the xml input file with head key ImaDoc
519% option: ='GeometryCalib': read  the data of GeometryCalib, including source point coordinates
520
521function [s,errormsg]=imadoc2struct_special(ImaDoc,option)
522
523%% default input and output
524if ~exist('option','var')
525    option='*';
526end
527errormsg=[];%default
528s.Heading=[];%default
529s.Time=[]; %default
530s.TimeUnit=[]; %default
531s.GeometryCalib=[];
532tsai=[];%default
533
534%% opening the xml file
535if exist(ImaDoc,'file')~=2, errormsg=[ ImaDoc ' does not exist']; return;end;%input file does not exist
536try
537    t=xmltree(ImaDoc);
538catch
539    errormsg={[ImaDoc ' is not a valid xml file']; lasterr};
540    display(errormsg);
541    return
542end
543uid_root=find(t,'/ImaDoc');
544if isempty(uid_root), errormsg=[ImaDoc ' is not an image documentation file ImaDoc']; return; end;%not an ImaDoc .xml file
545
546
547%% Heading
548uid_Heading=find(t,'/ImaDoc/Heading');
549if ~isempty(uid_Heading),
550    uid_Campaign=find(t,'/ImaDoc/Heading/Campaign');
551    uid_Exp=find(t,'/ImaDoc/Heading/Experiment');
552    uid_Device=find(t,'/ImaDoc/Heading/Device');
553    uid_Record=find(t,'/ImaDoc/Heading/Record');
554    uid_FirstImage=find(t,'/ImaDoc/Heading/ImageName');
555    s.Heading.Campaign=get(t,children(t,uid_Campaign),'value');
556    s.Heading.Experiment=get(t,children(t,uid_Exp),'value');
557    s.Heading.Device=get(t,children(t,uid_Device),'value');
558    if ~isempty(uid_Record)
559        s.Heading.Record=get(t,children(t,uid_Record),'value');
560    end
561    s.Heading.ImageName=get(t,children(t,uid_FirstImage),'value');
562end
563
564%% Camera  and timing
565if strcmp(option,'*') || strcmp(option,'Camera')
566    uid_Camera=find(t,'/ImaDoc/Camera');
567    if ~isempty(uid_Camera)
568        uid_ImageSize=find(t,'/ImaDoc/Camera/ImageSize');
569        if ~isempty(uid_ImageSize);
570            ImageSize=get(t,children(t,uid_ImageSize),'value');
571            xindex=findstr(ImageSize,'x');
572            if length(xindex)>=2
573                s.Npx=str2double(ImageSize(1:xindex(1)-1));
574                s.Npy=str2double(ImageSize(xindex(1)+1:xindex(2)-1));
575            end
576        end
577        uid_TimeUnit=find(t,'/ImaDoc/Camera/TimeUnit');
578        if ~isempty(uid_TimeUnit)
579            s.TimeUnit=get(t,children(t,uid_TimeUnit),'value');
580        end
581        uid_BurstTiming=find(t,'/ImaDoc/Camera/BurstTiming');
582        if ~isempty(uid_BurstTiming)
583            for k=1:length(uid_BurstTiming)
584                subt=branch(t,uid_BurstTiming(k));%subtree under BurstTiming
585                % reading Dtk
586                Frequency=get_value(subt,'/BurstTiming/FrameFrequency',1);
587                Dtj=get_value(subt,'/BurstTiming/Dtj',[]);
588                Dtj=Dtj/Frequency;%Dtj converted from frame unit to TimeUnit (e.g. 's')
589                NbDtj=get_value(subt,'/BurstTiming/NbDtj',[]);
590                %%%% correction RDvision %%%%
591%                 NbDtj=NbDtj/numel(Dtj);
592%                 s.NbDtj=NbDtj;
593%                 %%%%
594                Dti=get_value(subt,'/BurstTiming/Dti',[]);
595                NbDti=get_value(subt,'/BurstTiming/NbDti',1);
596                 %%%% correction RDvision %%%%
597                if isempty(Dti)% series
598                     Dti=Dtj;
599                      NbDti=NbDtj;
600                     Dtj=[];
601                     s.Dti=Dti;
602                     s.NbDti=NbDti;
603                else
604                    % NbDtj=NbDtj/numel(Dtj);%bursts
605                    if ~isempty(NbDtj)
606                    s.NbDtj=NbDtj/numel(Dtj);%bursts;
607                    else
608                        s.NbDtj=1;
609                    end
610                end
611                %%%% %%%%
612                Dti=Dti/Frequency;%Dtj converted from frame unit to TimeUnit (e.g. 's')
613
614                Time_val=get_value(subt,'/BurstTiming/Time',0);%time in TimeUnit
615                if ~isempty(Dti)
616                    Dti=reshape(Dti'*ones(1,NbDti),NbDti*numel(Dti),1); %concatene Dti vector NbDti times
617                    Time_val=[Time_val;Time_val(end)+cumsum(Dti)];%append the times defined by the intervals  Dti
618                end
619                if ~isempty(Dtj)
620                    Dtj=reshape(Dtj'*ones(1,s.NbDtj),1,s.NbDtj*numel(Dtj)); %concatene Dtj vector NbDtj times
621                    Dtj=[0 Dtj];
622                    Time_val=Time_val*ones(1,numel(Dtj))+ones(numel(Time_val),1)*cumsum(Dtj);% produce a time matrix with Dtj
623                end
624                % reading Dtk
625                Dtk=get_value(subt,'/BurstTiming/Dtk',[]);
626                NbDtk=get_value(subt,'/BurstTiming/NbDtk',1);
627                %%%% correction RDvision %%%%
628                if ~isequal(NbDtk,1)
629                    NbDtk=-1+(NbDtk+1)/(NbDti+1);
630                end
631                s.NbDtk=NbDtk;
632                %%%%%
633                if isempty(Dtk)
634                    s.Time=[s.Time;Time_val];
635                else
636                    for kblock=1:NbDtk+1
637                        Time_val_k=Time_val+(kblock-1)*Dtk;
638                        s.Time=[s.Time;Time_val_k];
639                    end
640                end
641            end
642        end
643    end
644end
645
646%% motor
647if strcmp(option,'*') || strcmp(option,'GeometryCalib')
648    uid_subtree=find(t,'/ImaDoc/TranslationMotor');
649    if length(uid_subtree)==1
650        subt=branch(t,uid_subtree);%subtree under GeometryCalib
651       [s.TranslationMotor,errormsg]=read_subtree(subt,{'Nbslice','ZStart','ZEnd'},[1 1 1],[1 1 1]);
652    end
653end
654%%  geometric calibration
655if strcmp(option,'*') || strcmp(option,'GeometryCalib')
656    uid_GeometryCalib=find(t,'/ImaDoc/GeometryCalib');
657    if ~isempty(uid_GeometryCalib)
658        if length(uid_GeometryCalib)>1
659            errormsg=['More than one GeometryCalib in ' filecivxml];
660            return
661        end
662        subt=branch(t,uid_GeometryCalib);%subtree under GeometryCalib
663        cont=get(subt,1,'contents');
664        if ~isempty(cont)
665            uid_CalibrationType=find(subt,'/GeometryCalib/CalibrationType');
666            if isequal(length(uid_CalibrationType),1)
667                tsai.CalibrationType=get(subt,children(subt,uid_CalibrationType),'value');
668            end
669            uid_CoordUnit=find(subt,'/GeometryCalib/CoordUnit');
670            if isequal(length(uid_CoordUnit),1)
671                tsai.CoordUnit=get(subt,children(subt,uid_CoordUnit),'value');
672            end
673            uid_fx_fy=find(subt,'/GeometryCalib/fx_fy');
674            focal=[];%default fro old convention (Reg Wilson)
675            if isequal(length(uid_fx_fy),1)
676                tsai.fx_fy=str2num(get(subt,children(subt,uid_fx_fy),'value'));
677            else %old convention (Reg Wilson)
678                uid_focal=find(subt,'/GeometryCalib/focal');
679                uid_dpx_dpy=find(subt,'/GeometryCalib/dpx_dpy');
680                uid_sx=find(subt,'/GeometryCalib/sx');
681                if ~isempty(uid_focal) && ~isempty(uid_dpx_dpy) && ~isempty(uid_sx)
682                    dpx_dpy=str2num(get(subt,children(subt,uid_dpx_dpy),'value'));
683                    sx=str2num(get(subt,children(subt,uid_sx),'value'));
684                    focal=str2num(get(subt,children(subt,uid_focal),'value'));
685                    tsai.fx_fy(1)=sx*focal/dpx_dpy(1);
686                    tsai.fx_fy(2)=focal/dpx_dpy(2);
687                end
688            end
689            uid_Cx_Cy=find(subt,'/GeometryCalib/Cx_Cy');
690            if ~isempty(uid_Cx_Cy)
691                tsai.Cx_Cy=str2num(get(subt,children(subt,uid_Cx_Cy),'value'));
692            end
693            uid_kc=find(subt,'/GeometryCalib/kc');
694            if ~isempty(uid_kc)
695                tsai.kc=str2double(get(subt,children(subt,uid_kc),'value'));
696            else %old convention (Reg Wilson)
697                uid_kappa1=find(subt,'/GeometryCalib/kappa1');
698                if ~isempty(uid_kappa1)&& ~isempty(focal)
699                    kappa1=str2double(get(subt,children(subt,uid_kappa1),'value'));
700                    tsai.kc=-kappa1*focal*focal;
701                end
702            end
703            uid_Tx_Ty_Tz=find(subt,'/GeometryCalib/Tx_Ty_Tz');
704            if ~isempty(uid_Tx_Ty_Tz)
705                tsai.Tx_Ty_Tz=str2num(get(subt,children(subt,uid_Tx_Ty_Tz),'value'));
706            end
707            uid_R=find(subt,'/GeometryCalib/R');
708            if ~isempty(uid_R)
709                RR=get(subt,children(subt,uid_R),'value');
710                if length(RR)==3
711                    tsai.R=[str2num(RR{1});str2num(RR{2});str2num(RR{3})];
712                end
713            end
714           
715            %look for laser plane definitions
716            uid_Angle=find(subt,'/GeometryCalib/PlaneAngle');
717            uid_Pos=find(subt,'/GeometryCalib/SliceCoord');
718            if isempty(uid_Pos)
719                uid_Pos=find(subt,'/GeometryCalib/PlanePos');%old convention
720            end
721            if ~isempty(uid_Angle)
722                tsai.PlaneAngle=str2num(get(subt,children(subt,uid_Angle),'value'));
723            end
724            if ~isempty(uid_Pos)
725                for j=1:length(uid_Pos)
726                    tsai.SliceCoord(j,:)=str2num(get(subt,children(subt,uid_Pos(j)),'value'));
727                end
728                uid_DZ=find(subt,'/GeometryCalib/SliceDZ');
729                uid_NbSlice=find(subt,'/GeometryCalib/NbSlice');
730                if ~isempty(uid_DZ) && ~isempty(uid_NbSlice)
731                    DZ=str2double(get(subt,children(subt,uid_DZ),'value'));
732                    NbSlice=get(subt,children(subt,uid_NbSlice),'value');
733                    if isequal(NbSlice,'volume')
734                        tsai.NbSlice='volume';
735                        NbSlice=NbDtj+1;
736                    else
737                        tsai.NbSlice=str2double(NbSlice);
738                    end
739                    tsai.SliceCoord=ones(NbSlice,1)*tsai.SliceCoord+DZ*(0:NbSlice-1)'*[0 0 1];
740                end
741            end   
742            tsai.SliceAngle=get_value(subt,'/GeometryCalib/SliceAngle',[0 0 0]);
743            tsai.VolumeScan=get_value(subt,'/GeometryCalib/VolumeScan','n');
744            tsai.InterfaceCoord=get_value(subt,'/GeometryCalib/InterfaceCoord',[0 0 0]);
745            tsai.RefractionIndex=get_value(subt,'/GeometryCalib/RefractionIndex',1);
746           
747            if strcmp(option,'GeometryCalib')
748                tsai.PointCoord=get_value(subt,'/GeometryCalib/SourceCalib/PointCoord',[0 0 0 0 0]);
749            end
750            s.GeometryCalib=tsai;
751        end
752    end
753end
754
755%--------------------------------------------------
756%  read a subtree
757% INPUT:
758% t: xltree
759% head_element: head elelemnt of the subtree
760% Data, structure containing
761%    .Key: element name
762%    .Type: type of element ('charg', 'float'....)
763%    .NbOccur: nbre of occurrence, NaN for un specified number
764function [s,errormsg]=read_subtree(subt,Data,NbOccur,NumTest)
765%--------------------------------------------------
766s=[];%default
767errormsg='';
768head_element=get(subt,1,'name');
769    cont=get(subt,1,'contents');
770    if ~isempty(cont)
771        for ilist=1:length(Data)
772            uid_key=find(subt,[head_element '/' Data{ilist}]);
773            if ~isequal(length(uid_key),NbOccur(ilist))
774                errormsg=['wrong number of occurence for ' Data{ilist}];
775                return
776            end
777            for ival=1:length(uid_key)
778                val=get(subt,children(subt,uid_key(ival)),'value');
779                if ~NumTest(ilist)
780                    eval(['s.' Data{ilist} '=val;']);
781                else
782                    eval(['s.' Data{ilist} '=str2double(val);'])
783                end
784            end
785        end
786    end
787
788
789%--------------------------------------------------
790%  read an xml element
791function val=get_value(t,label,default)
792%--------------------------------------------------
793val=default;
794uid=find(t,label);%find the element iud(s)
795if ~isempty(uid) %if the element named label exists
796   uid_child=children(t,uid);%find the children
797   if ~isempty(uid_child)
798       data=get(t,uid_child,'type');%get the type of child
799       if iscell(data)% case of multiple element
800           for icell=1:numel(data)
801               val_read=str2num(get(t,uid_child(icell),'value'));
802               if ~isempty(val_read)
803                   val(icell,:)=val_read;
804               end
805           end
806%           val=val';
807       else % case of unique element value
808           val_read=str2num(get(t,uid_child,'value'));
809           if ~isempty(val_read)
810               val=val_read;
811           else
812              val=get(t,uid_child,'value');%char string data
813           end
814       end
815   end
816end
817
818
819
820
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