Description of superSeggerViewer

0001 function superSeggerViewer(dirname)
0002 % superSeggerViewer : interactive visulization of the segmented data.
0003 % It displays a menu from which the user can make choices and vizualize or
0004 % analyze the segmented data.
0005 %
0006 % important notes :
0007 % - it saves a file in the directory named .trackOptiView.mat where it
0008 % saves the flags from the previous launch
0009 % - it uses the clist which can be gated to only show cells that pass specific
0010 % criteria. it outlines and analyzes only cells that pass the gate, to display
0011 % the full dataset the gate needs to be deleted.
0012 %
0013 %
0014 %
0015 % INPUT :
0016 %       dirname : main directory that contains files segemented by supeSegger
0017 %       it must be the directory that has raw_im and xy1 etc folders.
0018 %       It can be run from the seg file directly but some functions that require
0019 %       cell files will not work.
0020 %
0021 %
0022 % Copyright (C) 2016 Wiggins Lab
0023 % Written by Stella Stylianidou, Paul Wiggins, Connor Brennan.
0024 % University of Washington, 2016
0025 % This file is part of SuperSegger.
0026 %
0027 % SuperSegger is free software: you can redistribute it and/or modify
0028 % it under the terms of the GNU General Public License as published by
0029 % the Free Software Foundation, either version 3 of the License, or
0030 % (at your option) any later version.
0031 %
0032 % SuperSegger is distributed in the hope that it will be useful,
0033 % but WITHOUT ANY WARRANTY; without even the implied warranty of
0034 % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
0035 % GNU General Public License for more details.
0036 %
0037 % You should have received a copy of the GNU General Public License
0038 % along with SuperSegger.  If not, see <http://www.gnu.org/licenses/>.
0039 
0040 %% Load Constants and Initialize Flags
0041 
0042 global canUseErr;
0043 hf = figure(1);
0044 clf;
0045 mov = struct;
0046 CONST = [];
0047 touch_list = [];
0048 setHeader =[];
0049 
0050 % Add slash to the file name if it doesn't exist
0051 if(nargin<1 || isempty(dirname))
0052     dirname=uigetdir();
0053 end
0054 
0055 dirname = fixDir(dirname);
0056 dirname0 = dirname;
0057 
0058 % load flags if they already exist to maintain state between launches
0059 filename_flags = [dirname0,'.superSeggerViewer.mat'];
0060 FLAGS = [];
0061 if exist( filename_flags, 'file' )
0062     load(filename_flags);
0063     FLAGS = fixFlags(FLAGS);
0064 else
0065     FLAGS = fixFlags(FLAGS);
0066     error_list = [];
0067     nn = 1;
0068     dirnum = 1;
0069 end
0070 
0071 % Load info from one of the xy directories. dirnum tells you which one. If
0072 % you quit the program in an xy dir, it goes to that xy dir.
0073 clist = [];
0074 contents_xy =dir([dirname, 'xy*']);
0075 num_xy = numel(contents_xy);
0076 direct_contents = dir([dirname, '*seg.mat']);
0077 
0078 
0079 if num_xy~=0
0080     if isdir([dirname0,contents_xy(dirnum).name,filesep,'seg_full'])
0081         dirname_seg = [dirname0,contents_xy(dirnum).name,filesep,'seg_full',filesep];
0082     else
0083         dirname_seg = [dirname0,contents_xy(dirnum).name,filesep,'seg',filesep];
0084     end
0085     
0086     dirname_cell = [dirname0,contents_xy(dirnum).name,filesep,'cell',filesep];
0087     dirname_xy = [dirname0,contents_xy(dirnum).name,filesep];
0088     
0089     % Open clist if it exists
0090     clist_name = [dirname0,contents_xy(dirnum).name,filesep,'clist.mat'];
0091     if exist( clist_name, 'file' )
0092         clist = load([dirname0,contents_xy(dirnum).name,filesep,'clist.mat']);
0093     else
0094         clist = [];
0095     end
0096     
0097     ixy = intGetNum( contents_xy(dirnum).name );
0098     header = ['xy',num2str(ixy),': '];
0099 else
0100     if numel(direct_contents) == 0
0101         disp('There are no xy dirs. Choose a different directory.');
0102         return;
0103     else % loading from the seg directory directly
0104         dirname_cell = dirname;
0105         dirname_xy = dirname;
0106         dirname_seg = dirname;
0107         ixy = 1;
0108         header = ['seg',num2str(ixy),': '];
0109     end
0110 end
0111 
0112 if exist([dirname0,'CONST.mat'],'file')
0113     CONST = load([dirname0,'CONST.mat']);
0114     if isfield( CONST, 'CONST' )
0115         CONST = CONST.CONST;
0116     end
0117 else
0118     disp(['Exiting. There is a CONST.mat file at the root', ...
0119         'level of the data directory. Loading default 60XEcLB']);
0120     CONST = loadConstants(60,0);
0121 end
0122 
0123 contents=dir([dirname_seg, '*seg.mat']);
0124 num_im = length(contents);
0125 
0126 if (num_im == 0)
0127     error('No files found in the seg directory');
0128 end
0129 
0130 % for calculations that take time like the consensus array
0131 % you can save the array in a folder so that it is loaded from there
0132 % instead of calculated repeatedly.
0133 dirSave = [dirname,'superSeggerViewer',filesep];
0134 if ~exist(dirSave,'dir')
0135     mkdir(dirSave);
0136 else
0137     if exist([dirSave,'dataImArray.mat'],'file')
0138         load ([dirSave,'dataImArray'],'dataImArray');
0139     end
0140 end
0141 
0142 runFlag = (nn<=num_im);
0143 
0144 % This flag controls whether you reload from file
0145 first_flag = true;
0146 resetFlag = true;
0147 FLAGS.e_flag = 0 ;
0148 
0149 %% Run the main loop... and run it while the runFlag is true.
0150 while runFlag
0151     figure(1);
0152     
0153     contents=dir([dirname_seg, '*seg.mat']);
0154     num_segs = length(contents);
0155     
0156     contents=dir([dirname_seg, '*err.mat']);
0157     num_errs = length(contents);
0158     
0159     num_im = max(num_segs, num_errs);
0160     
0161     %Use region IDs if cells IDs unavailable
0162     if nn > num_errs || FLAGS.useSegs
0163         canUseErr = 0;
0164         contents=dir([dirname_seg, '*seg.mat']);
0165     else
0166         canUseErr = 1;
0167         contents=dir([dirname_seg, '*err.mat']);
0168     end
0169     
0170     % load current frame
0171     if resetFlag
0172         resetFlag = false;
0173         [data_r, data_c, data_f] = intLoadDataViewer( dirname_seg, ...
0174             contents, nn, num_im, clist, FLAGS);
0175     end
0176     
0177     clean_axis = [0 , 1 , 0  ,1];
0178     
0179     if ~first_flag && all(axis~=clean_axis)
0180         tmp_axis = axis;
0181     else % if first time - load image to get the axis
0182         clf;
0183         imshow(data_c.phase);
0184         tmp_axis = axis;
0185         first_flag = false;
0186     end
0187     
0188     %Force flags to required values when data is unavailable
0189     forcedFlags = FLAGS;
0190     forcedFlags.cell_flag = forcedFlags.cell_flag & shouldUseErrorFiles(FLAGS);
0191     %Force cell flag to 0 when err files not present
0192     
0193     showSeggerImage( data_c, data_r, data_f, forcedFlags, clist, CONST, []);
0194     flagsStates = intSetStateStrings(FLAGS,CONST);
0195     
0196     axis(tmp_axis);
0197     
0198     
0199     % Main Menu
0200     disp('------------------------------SuperSegger Data Viewer-------------------------------------');
0201     disp('-------------------------------------Main Menu--------------------------------------------');
0202     disp(['q  : To quit                                  reset : Reset axis to default   ']);
0203     disp(['x# : Switch xy directory from ', num2str(ixy), '               #  : Go to Frame Number #']);
0204     disp('----------------------------------Display Options-----------------------------------------');
0205     disp(['    Region info: ', num2str(num_segs), ' frames.   Cell info: ', num2str(num_errs), ' frames.   Current frame: ', num2str(nn)]);
0206     if ~FLAGS.cell_flag
0207         fprintf(2, 'Displaying region data.\n');
0208     end
0209     if FLAGS.useSegs
0210         fprintf(2, 'Using seg files. Displaying region IDs instead of cell IDs.\n');
0211     elseif ~canUseErr
0212         fprintf(2, 'No cell info for this frame. Displaying region IDs instead.\n');
0213     end
0214     disp(' ');
0215     disp(['id  : Show/Hide Cell Numbers ', [flagsStates.idState],'            seg : Use seg files ', flagsStates.useSegs]);
0216     disp(['r  : Show/Hide Region Outlines ', [flagsStates.rState],'          rs  : Show/Hide Region scores ', [flagsStates.regionScores]]);
0217     disp(['p  : Show/Hide Cell Poles ', flagsStates.pState,'               outline  : Outline cells ', flagsStates.vState]);
0218     disp(['f#  : Change channel ', [flagsStates.fState],'                  s  : Show Fluor Foci Scores ', [flagsStates.sState]]);
0219     disp(['filter : Filtered fluorescence ',flagsStates.filtState,'          CC : Use Complete Cell Cycles ', flagsStates.CCState] );
0220     disp(['falseCol : False Color ', flagsStates.falseColState,'                  log : Log View ', flagsStates.logState ]);
0221     disp(['find# : Find Cell Number #']);
0222     disp('-------------------------------------Link Options-----------------------------------------');
0223     if ~canUseErr || FLAGS.useSegs
0224         fprintf(2, 'Cell information must be availble to use this feature.\n');
0225     end
0226     if ~canUseErr
0227         fprintf(2, 'Please complete the linking phase of superSegger\n');
0228     end
0229     if FLAGS.useSegs
0230         fprintf(2, 'Please enable use of err files (seg command)\n');
0231     end
0232     disp(['link  : Show Linking Information               mother : Show mothers ', flagsStates.showMothers]);
0233     disp(['daughter  : Show daughters ', flagsStates.showDaughters]);
0234     disp('-----------------------------------Output Options-----------------------------------------');
0235     disp(['con  : Show Consensus                         cKym : Show consensus kymograph']);
0236     disp(['kymAll : Mosaic Kymograph of all cells        kym# : Show Kymograph for Cell #']);
0237     disp(['twrAll : Towers of all cells                  twr# : Tower for Cell #']);
0238     disp(['movie : Movie of this xy position             movie#  : Movie of # cell']);
0239     disp(['save : Save Figure #']);
0240     disp('-------------------------------------Gate Options-----------------------------------------');
0241     if ~isempty(clist)
0242         disp(['    Clist: ', [dirname0,contents_xy(dirnum).name,filesep,'clist.mat']]);
0243     else
0244         fprintf(2, 'No clist loaded, these commands will not work.\n');
0245     end
0246     disp(' ');
0247     disp(['g  : Make Gate                                G  : Create xy-combined clist, gated.']);
0248     disp(['moveG  : Move gated cells                     clear : Clear all Gates ']);
0249     disp(['hist : Histogram of clist quantity            hist2 : Plotting two clist quantities ']);
0250     disp('-------------------------------------Debug Options----------------------------------------');
0251     disp('k : Enter debugging mode');
0252     disp('------------------------------------------------------------------------------------------');
0253     disp(' ');
0254     if FLAGS.e_flag
0255         intDispError( data_c, FLAGS );
0256     end
0257     if ~isempty( touch_list );
0258         disp('Warning! Frames touched. Run re-link.');
0259         touch_list;
0260     end
0261     
0262     disp([header, 'Frame num [1...',num2str(num_im),']: ',num2str(nn)]);
0263     
0264     %pause;
0265     c = input(':','s');
0266     
0267     % LIST OF COMMANDS
0268     if isempty(c)
0269         % do nothing
0270         
0271     elseif strcmpi (c,'falseCol') % false color view
0272         if ~isfield( CONST,'view') || ...
0273                 ~isfield( CONST.view,'falseColorFlag')|| isempty( CONST.view.falseColorFlag )
0274             CONST.view.falseColorFlag = true;
0275         else
0276             CONST.view.falseColorFlag = ~CONST.view.falseColorFlag;
0277         end
0278         
0279     elseif  strcmpi(c,'log') % log view
0280         if ~isfield( CONST, 'view' ) || ~isfield( CONST.view, 'LogView' ) || ...
0281                 isempty( CONST.view.LogView )
0282             CONST.view.LogView = true;
0283         else
0284             CONST.view.LogView = ~CONST.view.LogView;
0285         end
0286         
0287     elseif strcmpi(c,'q') % Quit Command
0288         if exist('clist','var') && ~isempty(clist)
0289             save( [dirname0,contents_xy(dirnum).name,filesep,'clist.mat'],'-STRUCT','clist');
0290         else
0291             disp('Error saving clist file.');
0292         end
0293         runFlag = 0  ;
0294         
0295     elseif strcmpi(c,'CC') % Toggle Between Full Cell Cycles
0296         CONST.view.showFullCellCycleOnly = ~CONST.view.showFullCellCycleOnly ;
0297         
0298         if CONST.view.showFullCellCycleOnly
0299             figure(2);
0300             clist = gateMake( clist, 9, [1.1 inf] ); % stat0 above 1
0301             close(2);
0302             disp('Only showing complete Cell Cycles')
0303             resetFlag = 1;
0304         else
0305             figure(2);
0306             clist = gateStrip ( clist, 9 ); % clear stat0 gate
0307             close(2);
0308             disp('Showing incomplete Cell Cycles')
0309             resetFlag = 1;
0310         end
0311     elseif strcmpi(c,'hist') % choose characteristics and values to gate cells
0312         disp('Choose histogram characteristic')
0313         disp(clist.def')
0314         cc = str2double(input('Characteristic [ ] :','s')) ;
0315         figure(2);
0316         clf;
0317         gateHist(clist,cc);
0318         
0319     elseif strcmpi(c,'hist2') % choose characteristics and values to gate cells
0320         disp('Choose histogram characteristic')
0321         cc1 = str2double(input('Characteristic 1 [ ] :','s')) ;
0322         cc2 = str2double(input('Characteristic 2 [ ] :','s')) ;
0323         figure(2);
0324         clf;
0325         gateHistDot(clist, [cc1 cc2]);
0326         
0327     elseif strcmpi(c,'save') % choose characteristics and values to gate cells
0328         figNum = str2double(input('Figure number :','s')) ;
0329         filename = input('Filename :','s') ;
0330         savename = sprintf('%s/%s',dirSave,filename);
0331         saveas(figNum,(savename),'fig');
0332         print(figNum,'-depsc',[(savename),'.eps'])
0333         saveas(figNum,(savename),'png');
0334         disp (['Figure ', num2str(figNum) ,' is saved in eps, fig and png format at ',savename]);
0335         
0336     elseif numel(c) >= 4 && strcmpi(c(1:4), 'find') % Find Single Cells as F(number), an X appears on the iamge wehre the cell is
0337         if numel(c) > 4
0338             find_num = floor(str2double(c(5:end)));
0339             if FLAGS.cell_flag && shouldUseErrorFiles(FLAGS)
0340                 regnum = find( data_c.regs.ID == find_num);
0341                 
0342                 if ~isempty( regnum )
0343                     plot(data_c.regs.props(regnum).Centroid(1),...
0344                         data_c.regs.props(regnum).Centroid(2), ...
0345                         'yx','MarkerSize',50);
0346                 else
0347                     disp('couldn''t find that cell');
0348                 end
0349             else
0350                 if (find_num <= data_c.regs.num_regs) && (find_num >0)
0351                     plot(data_c.regs.props(find_num).Centroid(1),...
0352                         data_c.regs.props(find_num).Centroid(2), ...
0353                         'yx','MarkerSize',50);
0354                 else
0355                     disp( 'Out of range' );
0356                 end
0357             end
0358             input('Press any key','s');
0359         else
0360             disp ('Please provide cell number');
0361         end
0362         
0363     elseif strcmpi(c(1),'x')   % Change xy positions
0364         
0365         if numel(c)>1
0366             c = c(2:end);
0367             ll_ = floor(str2num(c));
0368             
0369             if ~isempty(ll_) && (ll_>=1) && (ll_<=num_xy)
0370                 try
0371                     save( [dirname0,contents_xy(dirnum).name,filesep,'clist.mat'],'-STRUCT','clist');
0372                 catch ME
0373                     printError(ME);
0374                     disp( 'Error writing clist file.');
0375                 end
0376                 
0377                 dirnum = ll_;
0378                 dirname_seg = [dirname0,contents_xy(ll_).name,filesep,'seg',filesep];
0379                 dirname_cell = [dirname0,contents_xy(ll_).name,filesep,'cell',filesep];
0380                 dirname_xy = [dirname0,contents_xy(ll_).name,filesep];
0381                 ixy = intGetNum( contents_xy(dirnum).name );
0382                 header = ['xy',num2str(ixy),': '];
0383                 contents=dir([dirname_seg, '*seg.mat']);
0384                 error_list = [];
0385                 clist = load([dirname0,contents_xy(ll_).name,filesep,'clist.mat']);
0386                 resetFlag = true;
0387             else
0388                 disp ('Incorrect number for xy position');
0389             end
0390             
0391         else
0392             disp ('Number of xy position missing');
0393             
0394         end
0395         
0396     elseif strcmpi(c,'r')  % Show/Hide Region Outlines
0397         FLAGS.P_flag = ~FLAGS.P_flag;
0398         FLAGS.Outline_flag = 0;
0399         
0400     elseif strcmpi(c,'outline') % Show/Hide Region Outlines
0401         FLAGS.Outline_flag = ~FLAGS.Outline_flag;
0402         
0403     elseif strcmpi(c,'reset') % Reset axis to default
0404         first_flag = true;
0405         resetFlag = 1;
0406         
0407     elseif numel(c) == 2 && c(1) == 'f' && isnum(c(2)) % Toggle Between Fluorescence and Phase Images
0408         disp('toggling between phase and fluorescence');
0409         f = 0;
0410         while true
0411             if isfield(data_c, ['fluor' num2str(f+1)] )
0412                 f = f+1;
0413             else
0414                 break
0415             end
0416         end
0417         c = round(str2double(c(2)));
0418         if isnan(c) || c < 0 || c > f
0419             FLAGS.f_flag = 0;
0420         else
0421             FLAGS.f_flag = c;
0422         end
0423         
0424     elseif strcmpi(c, 'filter') % Toggle Between filtered and unfiltered
0425         disp('filtering');
0426         FLAGS.filt = ~ FLAGS.filt;
0427         
0428     elseif strcmpi(c,'g') % choose characteristics and values to gate cells
0429         disp('Choose gating characteristic')
0430         disp(clist.def')
0431         cc = input('Gate Number(s) [ ] :','s') ;
0432         figure(2)
0433         clist = gateMake(clist,str2num(cc)) ;
0434         resetFlag = 1;
0435         
0436     elseif strcmpi(c,'Clear')  % Clear All Gates
0437         tmp_axis = axis;
0438         clist.gate = [] ;
0439         clf;
0440         resetFlag = 1;
0441         axis( tmp_axis );
0442         
0443     elseif strcmpi(c,'MoveG')   % moves gated cell files to a different directory
0444         header = 'trackOptiView: ';
0445         trackOptiGateCellFiles( dirname_cell, clist);
0446         
0447     elseif strcmpi(c, 'Gtot')
0448         % creates a clist for all xy positions, gated from loaded clist.
0449         if ~isfield( clist, 'gate' )
0450             clist.gate = [];
0451         end
0452         
0453         for ll_ = 1:num_xy
0454             filename = [dirname0,contents_xy(ll_).name,filesep,'clist.mat'];
0455             clist_tmp = gate(load(filename ));
0456             if  ll_ == 1
0457                 clist_comp =clist_tmp;
0458             else
0459                 clist_comp.data = [clist_comp.data; clist_tmp.data];
0460             end
0461         end
0462         
0463         save( [dirname0,'clist_comp.mat'], '-STRUCT', 'clist_comp' );
0464         
0465         
0466     elseif strcmpi(c,'id') % Show Cell Numbers
0467         FLAGS.ID_flag = ~FLAGS.ID_flag;
0468         if FLAGS.ID_flag
0469             FLAGS.regionScores = 0;
0470         end
0471         
0472     elseif strcmpi(c,'s') % Show Fluorescent Foci score values
0473         FLAGS.s_flag = ~FLAGS.s_flag;
0474         
0475     elseif numel(c) > 1 && c(1) == 's' && all(isnum(c(2:end))) % Toggle Between Fluorescence and Phase Images
0476         disp(['showing foci with scores higher than  ', c(2:end)]);
0477         FLAGS.s_flag = 1;
0478         CONST.getLocusTracks.FLUOR1_MIN_SCORE = str2double(c(2:end));
0479         
0480     elseif strcmpi(c,'p')  % Show Cell Poles
0481         FLAGS.p_flag = ~FLAGS.p_flag;
0482         
0483     elseif strcmpi(c,'k') % Enter Debugging Mode
0484         tmp_axis = axis;
0485         disp('Press "continue" on the editor tab to exit debugging mode')
0486         keyboard
0487         clf;
0488         axis( tmp_axis );
0489         
0490     elseif strcmpi(c,'KymAll') % Make Kymograph Mosaic for All Cells
0491         tmp_axis = axis;
0492         clf;
0493         makeKymoMosaic( dirname_cell, CONST );
0494         disp('press enter to continue.');
0495         pause;
0496         axis(tmp_axis);
0497         
0498     elseif strcmpi(c,'twrAll') %  Show Cell Towers for All Cells
0499         tmp_axis = axis;
0500         clf;
0501         
0502         if numel(c) > 1
0503             ll_ = floor(str2num(c(2:end)));
0504         else
0505             ll_ = [];
0506         end
0507         
0508         makeFrameStripeMosaic([dirname_cell], CONST, ll_,true );
0509         axis equal
0510         
0511         disp('press enter to continue.');
0512         pause;
0513         axis(tmp_axis);
0514         
0515     elseif strcmpi(c,'con') % Show existant consensus for this XY or calculate new one
0516         % it uses the current clist if datImArray has not been recalculated
0517         % before
0518         skip = 5;
0519         mag = 4;
0520         fnum = 1;
0521         alreadyExistsImArray = exist('dataImArray','var') && ~isempty(dataImArray);
0522         if alreadyExistsImArray
0523             answer = input(' dataImArray already calculated - recalculate? [y/n]:','s');
0524         end
0525         
0526         if ~alreadyExistsImArray || strcmpi(answer,'y')
0527             [dataImArray] = makeConsensusArray( dirname_cell, CONST, skip,mag,fnum);
0528             save ([dirSave,'dataImArray'],'dataImArray');
0529         end
0530         
0531         [imMosaic, imColor, imBW, imInv, imMosaic10 ] = makeConsensusImage( dataImArray,CONST,skip,mag,0);
0532         figure(2)
0533         clf
0534         imshow(imColor)
0535         disp('press enter to continue.');
0536         pause;
0537         
0538     elseif strcmpi(c,'cKym') % Show existant consensus for this XY or calculate new one
0539         skip = 5;
0540         mag = 4;
0541         fnum = 1;
0542         alreadyExistsImArray = exist('dataImArray','var') && ~isempty(dataImArray);
0543         if alreadyExistsImArray
0544             answer = input(' dataImArray already calculated - recalculate? [y/n]:','s');
0545         end
0546         
0547         if ~alreadyExistsImArray || strcmpi(answer,'y')
0548             [dataImArray] = makeConsensusArray( dirname_cell, CONST, skip,mag,fnum);
0549             save ([dirSave,'dataImArray'],'dataImArray');
0550         end
0551         
0552         
0553         [kymo,kymoMask] = makeConsensusKymo(dataImArray.imCellNorm, dataImArray.maskCell , 1);
0554         disp('press enter to continue.');
0555         pause;
0556     elseif numel(c)>2 && strcmpi(c(1:3),'twr') % Cell Tower for Single Cell
0557         
0558         if numel(c) > 3
0559             comma_pos = findstr(c,',');
0560             
0561             if isempty(comma_pos)
0562                 ll_ = floor(str2num(c(4:end)));
0563                 xdim__ = [];
0564             else
0565                 ll_ = floor(str2num(c(4:comma_pos(1))));
0566                 xdim__ = floor(str2num(c(comma_pos(1):end)));
0567             end
0568             
0569             padStr = getPadSize( dirname_cell, [] );
0570             
0571             if ~isempty( padStr )
0572                 data_cell = [];
0573                 filename_cell_C = [dirname_cell,'Cell',num2str(ll_,padStr),'.mat'];
0574                 filename_cell_c = [dirname_cell,'cell',num2str(ll_,padStr),'.mat'];
0575                 
0576                 if exist(filename_cell_C, 'file' )
0577                     filename_cell = filename_cell_C;
0578                 elseif exist(filename_cell_c, 'file' )
0579                     filename_cell = filename_cell_c;
0580                 else
0581                     filename_cell = [];
0582                 end
0583                 
0584                 if isempty( filename_cell )
0585                     disp( ['Files: ',filename_cell_C,' and ',filename_cell_c,' do not exist.']);
0586                 else
0587                     try
0588                         data_cell = load( filename_cell );
0589                     catch ME
0590                         printError(ME);
0591                         disp(['Error loading: ', filename_cell] );
0592                     end
0593                     
0594                     if ~isempty( data_cell )
0595                         figure(2);
0596                         clf;
0597                         im_tmp = makeFrameMosaic(data_cell, CONST, xdim__);
0598                     end
0599                     
0600                 end
0601             end
0602         else
0603             disp ('Please enter a number next to twr');
0604         end
0605         
0606     elseif numel(c)>2 && strcmpi(c(1:3),'kym') % Show Kymograph for Single Cell
0607         
0608         if numel(c) > 3
0609             num = floor(str2num(c(4:end)));
0610             data_cell = loadCellData(num,dirname_cell, []);
0611             
0612             if ~isempty( data_cell )
0613                 figure(2);
0614                 clf;
0615                 makeKymographC(data_cell, 1, CONST,[],FLAGS.filt);
0616                 ylabel('Long Axis (pixels)');
0617                 xlabel('Time (frames)' );
0618                 disp('Press enter to continue');
0619             end
0620         else
0621             disp ('Please enter a number next to kym');
0622         end
0623         
0624     elseif numel(c)>5 && strcmpi(c(1:5),'movie') % movie for single Cell
0625         if numel(c) > 5
0626             num = floor(str2double(c(6:end)));
0627             [data_cell,cell_name] = loadCellData(num,dirname_cell, []);
0628             if ~isempty(data_cell)
0629                 mov = makeCellMovie(data_cell);
0630                 disp('Save movie?')
0631                 d = input('[y/n]:','s');
0632                 if strcmpi(d,'y')
0633                     saveFilename = [dirSave,cell_name(1:end-4),'.avi'];
0634                     disp (['Saving movie at ',saveFilename]);
0635                     v = VideoWriter(saveFilename);
0636                     open(v)
0637                     writeVideo(v,mov)
0638                     close(v)
0639                 end
0640             end
0641         end
0642         
0643     elseif strcmpi(c,'movie')  % Make Time-Lapse Images for Movies
0644         
0645         tmp_axis = axis;
0646         
0647         clear mov;
0648         mov.cdata = [];
0649         mov.colormap = [];
0650         
0651         for ii = 1:num_im
0652             [data_r, data_c, data_f] = intLoadDataViewer( dirname_seg, ...
0653                 contents, ii, num_im, clist, FLAGS);
0654             tmp_im =  showSeggerImage( data_c, data_r, data_f, FLAGS, clist, CONST, []);
0655             axis(tmp_axis);
0656             drawnow;
0657             mov(ii) = getframe;
0658             disp( ['Frame number: ', num2str(ii)] );
0659         end
0660         
0661         
0662         disp('Save movie?')
0663         d = input('[y/n]:','s');
0664         if strcmpi(d,'y')
0665             name = input('filename:','s');
0666             saveFilename = [dirSave,name,'.avi'];
0667             disp (['Saving movie at ',saveFilename]);
0668             v = VideoWriter(saveFilename);
0669             v.FrameRate = 2; % frames per second
0670             open(v)
0671             writeVideo(v,mov)
0672             close(v)
0673         end
0674         
0675         resetFlag = true;
0676         
0677     elseif strcmpi(c,'e')
0678         % Show Error List
0679         FLAGS.e_flag = ~FLAGS.e_flag;
0680         
0681     elseif strcmpi(c,'rs') % Toggle display of region scores
0682         FLAGS.regionScores = ~FLAGS.regionScores;
0683         if FLAGS.regionScores
0684             FLAGS.ID_flag = 0;
0685         end
0686         
0687     elseif strcmpi(c,'seg') % Toggle display of region scores
0688         FLAGS.useSegs = ~FLAGS.useSegs;
0689         resetFlag = true;
0690         
0691         %% DEVELOPER FUNCTIONS : Use at your own risk
0692     elseif strcmpi(c,'link')  % Show links
0693         FLAGS.showLinks = ~FLAGS.showLinks;
0694         resetFlag = true;
0695         
0696     elseif strcmpi(c,'mother')  % Show links
0697         FLAGS.showMothers = ~FLAGS.showMothers;
0698         
0699     elseif strcmpi(c,'daughter')  % Show links
0700         FLAGS.showDaughters = ~FLAGS.showDaughters;
0701         
0702     elseif strcmpi(c,'editSegs')  % Edit Segments, allows to turn on and off segments
0703         disp('Are you sure you want to edit the segments?')
0704         d = input('[y/n]:','s');
0705         if strcmpi(d,'y')
0706             segsTLEdit(dirname_seg, nn, CONST);
0707         end
0708         
0709     elseif strcmpi(c, 'relink') % Re-Link - relinks the cells after modifications in segments
0710         disp('Are you sure you want to relink and remake the cell files?')
0711         d = input('[y/n]:','s');
0712         if strcmpi(d,'y')
0713             delete([dirname_cell,'*.mat']);
0714             delete([dirname,'*trk.mat*']);
0715             delete([dirname,'*err.mat*']);
0716             delete([dirname,'.trackOpti*']);
0717             delete([dirname_xy,'clist.mat']);
0718             % Re-Run trackOpti
0719             skip = 1;
0720             CLEAN_FLAG = false;
0721             header = 'trackOptiView: ';
0722             trackOpti(dirname_xy,skip,CONST, CLEAN_FLAG, header);
0723         end
0724     else % we assume that it is a number for a frame change.
0725         tmp_nn = str2num(c);
0726         if ~isempty(tmp_nn)
0727             nn = tmp_nn;
0728             if nn > num_im;
0729                 nn = num_im;
0730             elseif nn< 1
0731                 nn = 1;
0732             end
0733             resetFlag = true;
0734         else % not a number - command not found
0735             disp ('Command not found');
0736         end
0737     end
0738 end
0739 
0740 try
0741     save(filename_flags, 'FLAGS', 'nn', 'dirnum', 'error_list' );
0742 catch
0743     disp('Error saving flag preferences.');
0744 end
0745 
0746 end
0747 
0748 
0749 % END OF MAIN FUNCTION (superSeggerViewer)
0750 
0751 % INTERNAL FUNCTIONS
0752 function [nameInfo] = getDirStruct( dirname )
0753 
0754 contents = dir( [dirname,filesep,'*.tif'] );
0755 
0756 nt  = [];
0757 nc  = [];
0758 nxy = [];
0759 nz  = [];
0760 
0761 num_im = numel(contents);
0762 
0763 for i = 1:num_im;
0764     nameInfo = ReadFileName( contents(i).name );
0765     
0766     nt  = [nt,  nameInfo.npos(1,1)];
0767     nc  = [nc,  nameInfo.npos(2,1)];
0768     nxy = [nxy, nameInfo.npos(3,1)];
0769     nz  = [nz,  nameInfo.npos(4,1)];
0770 end
0771 
0772 nt  = sort(unique(nt));
0773 nc  = sort(unique(nc));
0774 nxy = sort(unique(nxy));
0775 nz  = sort(unique(nz));
0776 
0777 xyPadSize = floor(log(max(nxy))/log(10))+1;
0778 padString = ['%0',num2str(xyPadSize),'d'];
0779 
0780 num_xy = numel(nxy);
0781 num_c  = numel(nc);
0782 num_z  = numel(nz);
0783 num_t  = numel(nt);
0784 
0785 nameInfo.nt  = nt;
0786 nameInfo.nc  = nc;
0787 nameInfo.nxy = nxy;
0788 nameInfo.nz  = nz;
0789 end
0790 
0791 function ixy = intGetNum( str_xy )
0792 ixy = str2num(str_xy(ismember(str_xy, '0123456789' )));
0793 end
0794 
0795 function intDispError( data_c, FLAGS )
0796 % intDispError
0797 for kk = 1:data_c.regs.num_regs
0798     if isfield(data_c,'regs') &&...
0799             isfield(data_c.regs, 'error') && ...
0800             isfield(data_c.regs.error,'label') && ...
0801             ~isempty( data_c.regs.error.label{kk} )
0802         if FLAGS.cell_flag && shouldUseErrorFiles(FLAGS) && isfield( data_c.regs, 'ID' )
0803             disp(  ['Cell: ', num2str(data_c.regs.ID(kk)), ', ', ...
0804                 data_c.regs.error.label{kk}] );
0805         else
0806             disp(  [ data_c.regs.error.label{kk}] );
0807         end
0808     end
0809 end
0810 end
0811 
0812 
0813 function flagsStates = intSetStateStrings(FLAGS,CONST)
0814 % intSetStateStrings : sets default flags for when the program begins
0815 flagsStates.vState = '(on) ';
0816 flagsStates.mState = '(on) ';
0817 flagsStates.idState = '(on) ';
0818 flagsStates.TState = '(on) ';
0819 flagsStates.PState ='(on) ';
0820 flagsStates.pState ='(off) ';
0821 flagsStates.rState = '(on) ';
0822 flagsStates.eState = '(on) ';
0823 flagsStates.fState = '(Fluor)';
0824 flagsStates.CCState ='(on) ';
0825 flagsStates.PValState = '';
0826 flagsStates.lyseState = '';
0827 flagsStates.sState = '(on) ';
0828 
0829 if ~FLAGS.cell_flag
0830     flagsStates.vState = '(off)';
0831 end
0832 
0833 if ~FLAGS.Outline_flag
0834     flagsStates.vState = '(off)';
0835 end
0836 
0837 if ~FLAGS.m_flag
0838     flagsStates.mState = '(off)';
0839 end
0840 
0841 if ~FLAGS.ID_flag
0842     flagsStates.idState = '(off)';
0843 end
0844 
0845 if ~FLAGS.T_flag
0846     flagsStates.TState = '(off)';
0847 end
0848 
0849 if ~FLAGS.P_flag % regions
0850     flagsStates.rState = '(off)';
0851 end
0852 if ~FLAGS.e_flag
0853     flagsStates.eState = '(off)';
0854 end
0855 
0856 if ~FLAGS.f_flag
0857     flagsStates.fState = '(Phase)';
0858 end
0859 
0860 if ~FLAGS.s_flag
0861     flagsStates.sState = '(off)';
0862 end
0863 if ~FLAGS.p_flag
0864     flagsStates.pState = '(off)';
0865 end
0866 if ~CONST.view.showFullCellCycleOnly
0867     flagsStates.CCState= '(off)';
0868 end
0869 if ~FLAGS.lyse_flag
0870     flagsStates.lyseState = '(off)';
0871 end
0872 flagsStates.falseColState = '(on) ';
0873 if ~CONST.view.falseColorFlag
0874     flagsStates.falseColState= '(off)';
0875 end
0876 
0877 flagsStates.logState = '(on) ';
0878 if ~CONST.view.LogView
0879     flagsStates.logState = '(off)';
0880 end
0881 
0882 flagsStates.filtState = '(on) ';
0883 if ~FLAGS.filt
0884     flagsStates.filtState = '(off)';
0885 end
0886 
0887 flagsStates.regionScores = '(on) ';
0888 if ~FLAGS.regionScores
0889     flagsStates.regionScores = '(off)';
0890 end
0891 
0892 flagsStates.useSegs = '(on) ';
0893 if ~FLAGS.useSegs
0894     flagsStates.useSegs = '(off)';
0895 end
0896 
0897 
0898 flagsStates.showLinks = '(on) ';
0899 if ~FLAGS.showLinks
0900     flagsStates.showLinks = '(off)';
0901 end
0902 
0903 flagsStates.showDaughters = '(on) ';
0904 if ~FLAGS.showDaughters
0905     flagsStates.showDaughters = '(off)';
0906 end
0907 
0908 flagsStates.showMothers = '(on) ';
0909 if ~FLAGS.showMothers
0910     flagsStates.showMothers = '(off)';
0911 end
0912 
0913 end
0914 
0915 
0916 function intCons(dirname0, contents_xy, setHeader, CONST)
0917 xyDir = [dirname0,contents_xy.name,filesep];
0918 dircons = [xyDir,'/consensus/']
0919 
0920 if ~exist(dircons,'dir')
0921     mkdir(dircons);
0922 end
0923 
0924 ixy = intGetNum( contents_xy.name );
0925 header = ['xy',num2str(ixy),': '];
0926 
0927 if exist([dircons, 'consColor_', setHeader, '_', num2str(ixy,'%02d'), '.tif'],'file')
0928     disp('Consensus Already Calculated')
0929     imColor = imread([dircons, 'consColor_', setHeader, '_', num2str(ixy,'%02d'), '.tif']);
0930     figure(1)
0931     clf
0932     imshow(imColor);
0933     disp('Press any key to continue')
0934     pause;
0935 else
0936     
0937     disp('No Images Found.')
0938     disp('Calculate New Consensus?')
0939     d = input('[y/n]:','s');
0940     
0941     if strcmpi(d,'y')
0942         if isdir([dirname0,contents_xy.name,filesep,'seg_full'])
0943             dirname = [dirname0,contents_xy.name,filesep,'seg_full',filesep];
0944         end
0945         
0946         dirname_cell = [dirname0,contents_xy.name,filesep,'cell',filesep];
0947         disp( ['Doing ',num2str(ixy)] );
0948         skip = 1;
0949         mag = 4;
0950         [dataImArray] = makeConsensusArray( [dirname_cell], CONST, skip, mag, [] );
0951         [imMosaic, imColor, imBW, imInv, imMosaic10 ] = makeConsensusImage( dataImArray,CONST,skip,mag,0);
0952         
0953         figure(1)
0954         clf
0955         imshow(imColor)
0956         
0957         if ~isempty( imMosaic10 )
0958             disp('Save consensus images?')
0959             d = input('[y/n]:','s');
0960             % this just saves the consensus images.
0961             if strcmpi(d,'y')
0962                 save([dircons,'consensus'],'imMosaic', 'imColor', 'imBW', 'imInv', 'imMosaic10');
0963                 imwrite( imBW,    [dircons, 'consBW_',    setHeader, '_', num2str(ixy,'%02d'), '.tif'], 'tif' );
0964                 imwrite( imColor, [dircons, 'consColor_', setHeader, '_', num2str(ixy,'%02d'), '.tif'], 'tif' );
0965                 imwrite( imInv,   [dircons, 'consInv_',   setHeader, '_', num2str(ixy,'%02d'), '.tif'], 'tif' );
0966                 imwrite( imMosaic10,   [dircons, 'typical_',   setHeader, '_', num2str(ixy,'%02d'), '.tif'], 'tif' );
0967             end
0968         else
0969             disp( ['Found no cells in ', dirname_cell, '.'] );
0970         end
0971         
0972     else
0973         
0974         return
0975         
0976     end
0977 end
0978 end
superSeggerViewer

PURPOSE

SYNOPSIS

DESCRIPTION

CROSS-REFERENCE INFORMATION

SUBFUNCTIONS

SOURCE CODE
