bml_coding2annot

 BML_CODING2ANNOT creates annot table from CodingMatrix 

 Use as
   annot = bml_codingmatrix2annot(cfg)

 cfg.CodingMatPath    - path to mat file with coding info
 cfg.EventsPerTrial   - double, defaults depends on CodingAppVersion
 cfg.roi              - roi table with sessions audio sync information
 cfg.audio_chanel     - string indicating audio channel (optinal)
 cfg.CodingAppVersion - char, defines format expected for CodingMatrix
                      - accepted values are 'U01_v1' (default), 'pilot'

 returns annot table with one row per trial (syllable triplet)

0001 function annot = bml_coding2annot(cfg)
0002 
0003 % BML_CODING2ANNOT creates annot table from CodingMatrix
0004 %
0005 % Use as
0006 %   annot = bml_codingmatrix2annot(cfg)
0007 %
0008 % cfg.CodingMatPath    - path to mat file with coding info
0009 % cfg.EventsPerTrial   - double, defaults depends on CodingAppVersion
0010 % cfg.roi              - roi table with sessions audio sync information
0011 % cfg.audio_chanel     - string indicating audio channel (optinal)
0012 % cfg.CodingAppVersion - char, defines format expected for CodingMatrix
0013 %                      - accepted values are 'U01_v1' (default), 'pilot'
0014 %
0015 % returns annot table with one row per trial (syllable triplet)
0016 
0017 % Todo: take sync table as input, read audio files, use them to sync the
0018 % Audio variable of the mat and, with that, get the times in master
0019 % coordinates.
0020 %
0021 
0022 if nargin ~= 1
0023   error('Use as bml_coding2annot(cfg)');
0024 end
0025 
0026 CodingMatPath = bml_getopt_single(cfg,'CodingMatPath');
0027 assert(~isempty(CodingMatPath),'cfg.CodingMatPath required in single argument call');
0028 load(CodingMatPath,'CodingMatrix');
0029 load(CodingMatPath,'EventTimes');
0030 load(CodingMatPath,'SkipEvents');
0031 load(CodingMatPath,'WordList');
0032 load(CodingMatPath,'Afs');
0033 
0034 roi              = bml_getopt(cfg,'roi');
0035 CodingAppVersion = bml_getopt(cfg,'CodingAppVersion','U01_v1');
0036 AudioCoord       = bml_getopt(cfg,'warpcoords');
0037 praat            = bml_getopt(cfg,'praat');
0038 audio_channel    = bml_getopt(cfg,'audio_channel');
0039 
0040 if isempty(AudioCoord) || praat
0041   %loading sychronized audio to get the time-mapping
0042   roi = bml_sync_consolidate(roi);
0043   sync_audio = bml_load_continuous(roi);
0044   
0045   if ~isempty(audio_channel)
0046     cfg1=[];
0047     cfg1.channel = audio_channel;
0048     sync_audio = ft_selectdata(cfg1,sync_audio);
0049   end
0050   
0051   % unwarping to facilitate correlation with coding_audio
0052   loadedAudioCoord = bml_raw2coord(sync_audio);
0053   sync_audio_time = sync_audio.time;
0054   sync_audio.time{1} = (1:length(sync_audio.time{1}))./sync_audio.fsample;
0055   
0056   %loading coding audio
0057   cfg1=[]; cfg1.CodingMatPath = CodingMatPath;
0058   coding_audio = bml_coding2raw(cfg1);
0059 
0060   if isempty(AudioCoord)
0061     AudioCoord = loadedAudioCoord;
0062     
0063     fprintf('Calculating alignment between coding and roi audios');
0064     cfg1=[]; cfg1.method='lpf';
0065     assert(sync_audio.fsample == Afs, 'roi''s Fs should be equivalent to Coding Audio Afs');      
0066     [coding_audio_dt, max_corr] = bml_timealign(cfg1, sync_audio, coding_audio);
0067     
0068     AudioCoord.s1 = AudioCoord.s1 - round(coding_audio_dt*Afs);
0069     AudioCoord.s2 = AudioCoord.s2 - round(coding_audio_dt*Afs);
0070     
0071     if max_corr < 0.95
0072       warning('max_cor = %f should be near 1', max_corr)
0073     end    
0074   end
0075   if praat
0076     sync_audio.time = sync_audio_time; %setting sync time
0077     coding_audio.time{1} = bml_idx2time(AudioCoord, 1:length(coding_audio.time{1}));    
0078     bml_praat(sync_audio, bml_conform_to(sync_audio,coding_audio));
0079   end
0080 end
0081 
0082 annot=table();
0083 if ismember(CodingAppVersion,{'U01_v1'})
0084   EventsPerTrial   = bml_getopt(cfg,'EventsPerTrial',3);
0085   N_trials = size(CodingMatrix,2);
0086     if SkipEvents + N_trials * EventsPerTrial > length(EventTimes)
0087     warning("Less EventTimes than expected based on CodingMatrix.");
0088     N_trials = floor((length(EventTimes) - SkipEvents)/EventsPerTrial);
0089   end
0090   for i=1:N_trials
0091     id=i;
0092     
0093     %initial trial time in Audio seconds
0094     ti = EventTimes(SkipEvents + i * EventsPerTrial);  
0095 
0096     %CodingMatrix row 1: Phonetic code in latex
0097     phoneticCode=CodingMatrix(1,i);
0098 
0099     %CodingMatrix row 2: Syllable errors
0100     err_syl1=CodingMatrix{2,i}(1);
0101     err_syl2=CodingMatrix{2,i}(2);
0102     err_syl3=CodingMatrix{2,i}(3);
0103 
0104     %CodingMatrix row 3: Syl onset time
0105     onset_syl=bml_strnumcell2ordvec(CodingMatrix{3,i}); %in Audio seconds
0106     if size(onset_syl,2) < 3
0107       onset_syl = [onset_syl, nan(1,3-size(onset_syl,2))];
0108     end    
0109     onset_syl1=bml_idx2time(AudioCoord,(onset_syl(1)+ti)*Afs); %in sfm
0110     onset_syl2=bml_idx2time(AudioCoord,(onset_syl(2)+ti)*Afs); %in sfm
0111     onset_syl3=bml_idx2time(AudioCoord,(onset_syl(3)+ti)*Afs); %in sfm
0112     
0113     %CodingMatrix row 4: Syl offset time
0114     offset_syl = bml_strnumcell2ordvec(CodingMatrix{4,i}); %in Audio seconds
0115     if isempty(offset_syl)
0116       offset_syl = nan;
0117     end
0118     %completing missing offsets
0119     if length(offset_syl)==length(onset_syl)
0120       offset_syl_complete = offset_syl;
0121       offset_syl_coded = ones(1,length(offset_syl_complete));
0122     else
0123       offset_syl_complete = zeros(1,length(onset_syl));
0124       offset_syl_coded = zeros(1,length(onset_syl));
0125       onset_syl_inf = [onset_syl inf];
0126       j=1; %offset_syl counter
0127       for k=1:(length(onset_syl))
0128         if j <= length(offset_syl) 
0129           if offset_syl(j) <= onset_syl_inf(k+1)
0130             offset_syl_complete(k) = offset_syl(j);
0131             offset_syl_coded(k) = 1;
0132             j = j + 1;
0133           else
0134             offset_syl_complete(k) = onset_syl_inf(k+1);
0135             offset_syl_coded(k) = 0;
0136           end
0137         else
0138             offset_syl_complete(k) = NaN;
0139             offset_syl_coded(k) = 0;          
0140           warning('Inconsistent syl offset times in trial %i',i)
0141         end
0142       end
0143     end
0144     offset_syl1=bml_idx2time(AudioCoord,(offset_syl_complete(1)+ti) * Afs);%in sfm
0145     offset_syl2=bml_idx2time(AudioCoord,(offset_syl_complete(2)+ti) * Afs);%in sfm
0146     offset_syl3=bml_idx2time(AudioCoord,(offset_syl_complete(3)+ti) * Afs);%in sfm
0147     offset_coded_syl1=offset_syl_coded(1);
0148     offset_coded_syl2=offset_syl_coded(2);
0149     offset_coded_syl3=offset_syl_coded(3); 
0150 
0151     %CodingMatrix row 5: Vowel onset time
0152     onset_vowel=bml_strnumcell2ordvec(CodingMatrix{5,i}); %in Audio seconds
0153     if size(onset_vowel,2) < 3
0154       onset_vowel = [onset_vowel, nan(1,3-size(onset_vowel,2))];
0155     end  
0156     onset_vowel1=bml_idx2time(AudioCoord,(onset_vowel(1)+ti) * Afs);
0157     onset_vowel2=bml_idx2time(AudioCoord,(onset_vowel(2)+ti) * Afs);
0158     onset_vowel3=bml_idx2time(AudioCoord,(onset_vowel(3)+ti) * Afs);
0159 
0160     %CodingMatrix row 6: Vowel offsets, not coded
0161     %CodingMatrix row 7: Preword onset times
0162     %CodingMatrix row 8: Preword offset times
0163     %CodingMatrix row 9: Post word onset times
0164     %CodingMatrix row 10: Post word offset times
0165     %CodingMatrix row 11: Other onset times
0166     %CodingMatrix row 12: Other offset times
0167 
0168     %CodingMatrix row 13: Note for current trial
0169     comment=CodingMatrix(13,i);
0170 
0171     %CodingMatrix row 14: Stressors binary
0172 
0173     word_triplet = WordList(i);
0174 
0175     starts = bml_idx2time(AudioCoord,(min(onset_syl)+ti) * Afs);
0176     ends = bml_idx2time(AudioCoord,(max(offset_syl)+ti) * Afs);
0177 
0178     annot = [annot; table(id, starts, ends, phoneticCode, err_syl1, err_syl2, err_syl3,...
0179       onset_syl1, offset_syl1, onset_syl2, offset_syl2, onset_syl3, offset_syl3,...
0180       onset_vowel1, onset_vowel2, onset_vowel3,...
0181       offset_coded_syl1, offset_coded_syl2, offset_coded_syl3, word_triplet, comment)];
0182 
0183   end
0184   
0185 elseif ismember(CodingAppVersion,{'pilot'})  
0186   EventsPerTrial   = bml_getopt(cfg,'EventsPerTrial',4);
0187   N_trials = size(CodingMatrix,2);
0188   if SkipEvents + N_trials * EventsPerTrial > length(EventTimes)
0189     warning("Less EventTimes than expected based on CodingMatrix.");
0190     N_trials = floor((length(EventTimes) - SkipEvents)/EventsPerTrial);
0191   end
0192   for i=1:N_trials
0193     id=i;
0194     ti = EventTimes(SkipEvents + i * EventsPerTrial);
0195     
0196     %CodingMatrix row 1. phonetic code in LaTex separated by '/'.
0197     phoneticCode = default_str(CodingMatrix(1,i));
0198 
0199     %CodingMatrix row 2. 1st Consonant errors
0200     err_cons1 = CodingMatrix(2,i);
0201 
0202     %CodingMatrix row 3. Vowel errors
0203     err_vowel = CodingMatrix(3,i);
0204 
0205     %CodingMatrix row 4. 2nd Consonant error
0206     err_cons2 = CodingMatrix(4,i);
0207     
0208     %CodingMatrix row 5. Word onset time
0209     onset_word=bml_idx2time(AudioCoord,(default_nan(CodingMatrix{5,i}) + ti) * Afs);
0210 
0211     %CodingMatrix row 6. Word offset time
0212     offset_word=bml_idx2time(AudioCoord,(default_nan(CodingMatrix{6,i}) + ti) * Afs);
0213     
0214     %CodingMatrix row 7. 1 if actual task presentation was revealed
0215     unveil=default_int(CodingMatrix{7,i});
0216     
0217     %CodingMatrix row 8. Notes for current trial
0218     comment=CodingMatrix(8,i);    
0219     
0220     %CodingMatrix row 9. Onset of vowel
0221     onset_vowel=bml_idx2time(AudioCoord,(default_nan(CodingMatrix{9,i}) + ti) * Afs);    
0222     
0223     %CodingMatrix row 10. Offset of vowel
0224     offset_vowel=bml_idx2time(AudioCoord,(default_nan(CodingMatrix{10,i}) + ti) * Afs);        
0225  
0226     word = WordList(i);
0227 
0228     starts = onset_word;
0229     ends = offset_word;
0230 
0231     annot = [annot; table(id, starts, ends, phoneticCode,...
0232       err_cons1, err_vowel, err_cons2, onset_word, offset_word, ...
0233       unveil, comment, onset_vowel, offset_vowel, word)];
0234     
0235   end
0236 else
0237   error('unknown CodingAppVersion')
0238 end
0239   
0240 annot = bml_annot_table(annot);
0241 annot.trial_id = annot.id;
0242 end
0243 
0244 
0245 
0246 %%%%%%%%%%%%%%%%%%%%%%%%%
0247 %%% Private functions %%%
0248 %%%%%%%%%%%%%%%%%%%%%%%%%
0249 
0250 function default = default_str(input)
0251   if isempty(input)
0252     default = {''};
0253   else
0254     default = input;
0255   end
0256 end
0257 
0258 function default = default_int(input)
0259   if isempty(input)
0260     default = 0;
0261   else
0262     default = input;
0263   end
0264 end
0265 
0266 function default = default_nan(input)
0267   if isempty(input)
0268     default = nan;
0269   else
0270     default = input;
0271   end
0272 end