0001 function [clist, out] = gateTool(varargin)
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0137
0138 data = intProcessInput( varargin );
0139
0140
0141
0142 if data.merge_flag
0143 data.clist = intDoMerge( data.clist, [], data.skip3D_flag );
0144 end
0145
0146
0147
0148
0149
0150 if data.make_flag
0151 data = intMakeGate( data, data.ind );
0152 end
0153
0154
0155 if data.show_all_flag
0156 data.clist = intShowAll( data.clist, 1, data );
0157 elseif data.show_flag
0158 data = intShow( data );
0159 end
0160
0161
0162 if data.strip_flag
0163 data = intDoStrip( data );
0164 end
0165
0166
0167
0168 if data.export_flag
0169 intcsv( data.clist, data );
0170 end
0171
0172
0173
0174 if data.get_flag
0175 if data.time_flag
0176 out = squeeze(intGet3D( data.clist, data.g_ind ));
0177 else
0178 out = intGet( data.clist, data.g_ind );
0179 end
0180 elseif data.stat_flag
0181
0182
0183
0184
0185 intShowKS( data );
0186 elseif data.get_gate_flag
0187
0188 if ~data.time_flag
0189 if data.which_gate <= numel( data.clist.gate )
0190 out = data.clist.gate(data.which_gate);
0191 else
0192 error( ['There are only ', num2str( numel( data.clist.gate ) ), ' gates.'] );
0193 end
0194 else
0195 if ~isfield( data.clist, 'gate3D' )
0196 error( 'There is not gate3D field.' );
0197 else
0198 if data.which_gate <= numel( data.clist.gate3D )
0199 out = data.clist.gate3D(data.which_gate);
0200 else
0201 error( ['There are only ', num2str( numel( data.clist.gate3D ) ), ' gates.'] );
0202 end
0203 end
0204
0205 end
0206 end
0207
0208
0209 clist = data.clist;
0210
0211 if data.save_flag
0212 intSaveClist( data );
0213 end
0214
0215 end
0216
0217
0218 function data = intProcessInput( varargin )
0219
0220 varargin = varargin{1};
0221 nargin = numel( varargin );
0222
0223 data.make_flag = false;
0224
0225 data.strip_flag = false;
0226 data.log_flag = false([1,3]);
0227 data.merge_flag = false;
0228 data.bin_flag = false;
0229 data.hist_flag = false;
0230 data.kde_flag = false;
0231 data.time_flag = false;
0232 data.dot_flag = false;
0233 data.dothist_flag = false;
0234 data.inv_flag = false;
0235 data.get_flag = false;
0236 data.stat_flag = false;
0237 data.skip3D_flag = false;
0238 data.export_flag = false;
0239 data.drill_flag = false;
0240 data.error_flag = false;
0241 data.newfig_flag = false;
0242 data.line_flag = false;
0243 data.save_flag = false;
0244 data.noshow_flag = false;
0245
0246 data.trace_flag = false;
0247
0248 data.get_gate_flag = false;
0249 data.name_flag = false;
0250 data.den_flag = false;
0251 data.noclear_flag = false;
0252
0253 data.show_flag = false;
0254 data.show_all_flag = false;
0255 data.array_flag = false;
0256
0257 data.clist = [];
0258 data.h = [];
0259 data.legend = {};
0260
0261 data.ind = [];
0262 data.bin = [];
0263 data.color = [];
0264 data.rk = [];
0265 data.rm = [];
0266 data.g_ind = [];
0267
0268 data.units = [1,1];
0269 data.fig_ptr = [];
0270 data.minBinNum = 5;
0271 data.multi = 500;
0272
0273 data.im = {};
0274
0275
0276 data.cond_flag = false;
0277
0278 load_flag = false;
0279
0280 if nargin == 0
0281 error( 'gate must have at least one argument (a clist)' );
0282 else
0283 next_arg = varargin{1};
0284
0285 if any(strcmp( 'time',varargin )) || ...
0286 any(strcmp( '3d',varargin )) || ...
0287 any(strcmp( '3D',varargin ))
0288 data.time_flag = true;
0289 end
0290
0291 if any(strcmp( 'noshow',varargin ))
0292 data.noshow_flag = true;
0293 end
0294
0295 if ischar( next_arg )
0296
0297 if any(strcmp( 'drill',varargin ))
0298 data.drill_flag = true;
0299 end
0300
0301
0302
0303 next_arg = intLoadClist( next_arg, data );
0304 load_flag = true;
0305 end
0306
0307 if (~iscell( next_arg )) && (~isstruct( next_arg ))
0308 error( 'First argument must be a clist' );
0309 end
0310
0311
0312 clist = next_arg;
0313 clist = intFixDef3D( clist );
0314
0315 data.clist = clist;
0316
0317
0318 if iscell( next_arg );
0319 data.array_flag = true;
0320 end
0321
0322 counter = 1;
0323
0324
0325 if nargin == 1 && ~load_flag
0326 data.strip_flag = true;
0327 end
0328
0329
0330 while counter < nargin
0331
0332 counter = counter + 1;
0333 next_arg = varargin{counter};
0334
0335 if ~ischar( next_arg )
0336 disp( next_arg );
0337 error( 'is not a command string' );
0338 end
0339
0340 switcher = lower(next_arg);
0341 switch switcher
0342 case 'log'
0343
0344 counter = counter + 1;
0345
0346 if counter > nargin
0347 error( 'You need to specify which axes to log scale' );
0348 end
0349 next_arg = varargin{counter};
0350
0351 if isnumeric( next_arg )
0352 ind = next_arg;
0353 data.log_flag( ind ) = true;
0354 else
0355 data.log_flag( [1,2] ) = true;
0356 counter = counter-1;
0357 end
0358 case 'skip3d'
0359 data.skip3D_flag = true;
0360
0361 case 'drill'
0362 data.drill_flag = true;
0363
0364 case 'err'
0365 data.error_flag = true;
0366
0367
0368 case 'line'
0369 data.line_flag = true;
0370 data.dot_flag = true;
0371 case 'save'
0372 data.save_flag = true;
0373
0374 counter = counter + 1;
0375 next_arg = varargin{counter};
0376
0377 if counter > nargin
0378 error( 'Not enough arguments for add' )
0379 end
0380 next_arg = varargin{counter};
0381 if ~ischar( next_arg )
0382 error( '2nd argument of add must be a str name for the field' );
0383 end
0384
0385 data.save_name = next_arg;
0386
0387 case 'noshow'
0388
0389 data.noshow_flag = true;
0390
0391 case 'mult'
0392 counter = counter + 1;
0393 if counter > nargin
0394 error( 'Not enough arguments for MULT.' )
0395 end
0396 next_arg = varargin{counter};
0397
0398 if isnumeric( next_arg )
0399 data.mult = next_arg;
0400 end
0401
0402
0403
0404
0405
0406
0407
0408
0409
0410
0411
0412
0413
0414
0415
0416
0417 case 'newfig'
0418 data.newfig_flag = true;
0419
0420 case 'getgate'
0421
0422
0423 counter = counter + 1;
0424 if counter > nargin
0425 error( 'Need to specify which clist.' );
0426 end
0427
0428 next_arg = varargin{counter};
0429 if isnumeric( next_arg )
0430 data.which_gate = next_arg;
0431
0432 if numel(data.clist) ~= 1 || ~isstruct(data.clist)
0433 error('Get gate only works with a single clist');
0434 end
0435
0436 data.get_gate_flag = true;
0437 else
0438 error( 'getGate needs a numeric argument .' );
0439 end
0440
0441
0442 case 'clear'
0443
0444 counter = counter + 1;
0445 if counter > nargin
0446 cind = [];
0447 else
0448 cind = [];
0449 next_arg = varargin{counter};
0450 if isnumeric( next_arg )
0451 cind = next_arg;
0452
0453 else
0454 counter = counter - 1;
0455 end
0456 end
0457
0458 data.clist = intClear( data.clist, cind );
0459
0460 case {'xls','csv'}
0461 counter = counter + 1;
0462 if counter > nargin
0463 error( 'Not enough arguments for xls/csv. Must provide filename.' )
0464 end
0465 next_arg = varargin{counter};
0466 if ~ischar( next_arg )
0467 error( 'You must include a filename.' );
0468 end
0469 data.export_filename = next_arg;
0470
0471 data.export_index = [];
0472
0473 counter = counter + 1;
0474 if counter > nargin || ischar( varargin{counter} )
0475 counter = counter - 1;
0476 else
0477 data.export_index = varargin{counter};
0478 end
0479
0480 switch switcher
0481 case 'xls'
0482 data.which_export_flag = 2;
0483 case 'csv'
0484 data.which_export_flag = 1;
0485 end
0486
0487 data.export_flag = true;
0488
0489 case 'save'
0490 counter = counter + 1;
0491 if counter > nargin
0492 error( 'Not enough arguments for save. Must provide filename.' )
0493 end
0494 next_arg = varargin{counter};
0495 if ~ischar( next_arg )
0496 error( 'You must include a filename.' );
0497 end
0498 filename = next_arg;
0499
0500 clist = data.clist;
0501
0502 if isstruct( data.clist )
0503 save( filename,'-struct','clist' );
0504 else
0505 save( filename,'-v7.3','clist' );
0506 end
0507
0508
0509
0510
0511 case 'units'
0512 counter = counter + 1;
0513 if counter > nargin
0514 error( 'Not enough arguments for units. Must provide a scalar or vector.' )
0515 end
0516 next_arg = varargin{counter};
0517 if ~isnumeric( next_arg )
0518 error( 'units must be scalar or vector.' );
0519 else
0520 data.units = next_arg;
0521 end
0522
0523
0524 case 'add'
0525
0526 if numel( data.clist ) ~= 1
0527 error( 'You can only add a field to a clist structure, not a cell array' );
0528 end
0529
0530 counter = counter + 1;
0531 if counter > nargin
0532 error( 'Not enough arguments for add' )
0533 end
0534 next_arg = varargin{counter};
0535 if ~isnumeric( next_arg )
0536 error( '1st argument of add must be the data' );
0537 end
0538
0539 if numel( next_arg ) ~= size( data.clist.data, 1)
0540 error( 'added data size must match the clist data dimension' );
0541 end
0542
0543 ss = size(data.clist.data);
0544
0545 tmp_data = next_arg;
0546 tmp_data = reshape( tmp_data, [numel(tmp_data),1]);
0547
0548 counter = counter + 1;
0549 if counter > nargin
0550 error( 'Not enough arguments for add' )
0551 end
0552 next_arg = varargin{counter};
0553 if ~ischar( next_arg )
0554 error( '2nd argument of add must be a str name for the field' );
0555 end
0556 field_name = next_arg;
0557
0558 data.clist.data = [data.clist.data,tmp_data];
0559
0560 field_name_ = [num2str( size(data.clist.data,2) ),': ',field_name];
0561
0562 data.clist.def{ss(2)+1} = field_name;
0563
0564 disp( ['Adding field ',field_name_] );
0565
0566
0567 case 'add3d'
0568
0569
0570 if numel( data.clist ) ~= 1
0571 error( 'You can only add a field to a clist structure, not a cell array' );
0572 end
0573
0574 counter = counter + 1;
0575 if counter > nargin
0576 error( 'Not enough arguments for add' )
0577 end
0578 next_arg = squeeze(varargin{counter});
0579 if ~isnumeric( next_arg )
0580 error( '1st argument of add must be the data' );
0581 end
0582
0583 if ~all(size( next_arg ) == [size( data.clist.data3D,1),size( data.clist.data3D,3)] )
0584 error( 'added data size must match the clist data3D dimension' );
0585 end
0586
0587 tmp_data = next_arg;
0588
0589 ss = size(data.clist.data3D);
0590
0591 counter = counter + 1;
0592 if counter > nargin
0593 error( 'Not enough arguments for add' )
0594 end
0595 next_arg = varargin{counter};
0596 if ~ischar( next_arg )
0597 error( '2nd argument of add must be a str name for the field' );
0598 end
0599 field_name = next_arg;
0600
0601 if numel(ss) == 2
0602 ss(3) = 1;
0603 end
0604
0605 data.clist.data3D = cat(2,data.clist.data3D,reshape(tmp_data,[ss(1),1,ss(3)]));
0606
0607 field_name_ = [num2str( ss(2)+1 ),': ',field_name];
0608
0609 data.clist.def3D{ss(2)+1} = field_name;
0610
0611 disp( ['Adding field ',field_name_] );
0612
0613
0614 case 'add3dt'
0615 data.clist = intDoAddT( data.clist );
0616 case 'trace'
0617 data.trace_flag = true;
0618
0619 case 'get'
0620 data.get_flag = true;
0621
0622 counter = counter + 1;
0623 if counter > nargin
0624 error( 'Not enough arguments for get' )
0625 end
0626 next_arg = varargin{counter};
0627 if ~isnumeric( next_arg )
0628 error( 'indices must be numeric' );
0629 end
0630
0631 data.g_ind = next_arg;
0632
0633
0634 case 'def'
0635 def = intGetDef( data.clist );
0636 def = intFixDef( def )';
0637 disp( def );
0638 case 'def3d'
0639 def = intGetDef3D( data.clist );
0640 def = intFixDef( def )';
0641 disp( def );
0642 case 'merge'
0643 data.merge_flag = true;
0644 case 'den'
0645 data.den_flag = true;
0646 case 'no clear'
0647 data.noclear_flag = true;
0648 case 'kde'
0649 data.kde_flag = true;
0650
0651 case 'rk'
0652 counter = counter + 1;
0653 next_arg = varargin{counter};
0654
0655 if isnumeric( next_arg )
0656 data.rk = next_arg;
0657 else
0658 error( 'KDE kernal radius must be a double' );
0659 end
0660 case 'rm'
0661 counter = counter + 1;
0662 next_arg = varargin{counter};
0663
0664 if isnumeric( next_arg )
0665 data.rm = next_arg;
0666 else
0667 error( 'KDE kernal radius must be a double' );
0668 end
0669 case 'cond'
0670 data.cond_flag = true;
0671 case 'inv'
0672 data.inv_flag = true;
0673 case 'res'
0674 counter = counter + 1;
0675 next_arg = varargin{counter};
0676
0677 if isnumeric( next_arg )
0678 data.mult = next_arg;
0679
0680 else
0681 error( 'Resolution must be a double.' );
0682 end
0683
0684 case 'squeeze'
0685
0686 data.clist = intSqueeze( data.clist );
0687
0688 case 'expand'
0689
0690 data.clist = intExpand( data.clist );
0691
0692 case 'name'
0693
0694
0695 counter = counter + 1;
0696 next_arg = varargin{counter};
0697
0698 if ~isstr( next_arg )
0699 error( 'name is not a string' );
0700 else
0701 name = next_arg;
0702 if ~data.array_flag
0703 data.clist.name = name;
0704 else
0705 data.clist = intDoAll( data.clist, 'name', name, data.time_flag);
0706 end
0707 end
0708
0709 case 'bin'
0710 data.bin_flag = true;
0711
0712 counter = counter + 1;
0713 bin = varargin{counter};
0714
0715 if iscell( bin ) || isnumeric( bin )
0716 data.bin = bin;
0717 else
0718 error( 'Bin must be numeric ar a cell.' );
0719 end
0720
0721 case {'make','gate'}
0722 counter = counter + 1;
0723 if counter > nargin
0724 error( 'Not enough arguments for add' )
0725 end
0726 next_arg = varargin{counter};
0727
0728 if isnumeric( next_arg )
0729
0730 data.ind = next_arg;
0731
0732 counter = counter + 1;
0733 if ~(counter > nargin)
0734 next_arg = varargin{counter};
0735 if isnumeric( next_arg )
0736
0737 tmp_gate.ind = data.ind;
0738
0739 if numel( data.ind ) == 1
0740 tmp_gate.x = next_arg;
0741 elseif numel( data.ind ) == 2
0742 tmp_gate.xx = next_arg;
0743 end
0744
0745 data = intMakeGate( data, tmp_gate );
0746
0747 else
0748 data.make_flag = true;
0749 counter = counter - 1;
0750 end
0751 else
0752 data.make_flag = true;
0753 end
0754 elseif isstruct( next_arg )
0755 data = intMakeGate( data, next_arg );
0756 else
0757 error( 'gate must be numeric ind list or struct' );
0758 end
0759
0760 case {'make3d','gate3d'}
0761
0762 counter = counter + 1;
0763 next_arg = varargin{counter};
0764
0765 data.time_flag = true;
0766
0767 if isnumeric( next_arg )
0768 data.make_flag = true;
0769 data.ind = next_arg;
0770
0771 elseif isstruct( next_arg )
0772 data = intMakeGate( data, next_arg );
0773 else
0774 error( 'gate must be numeric ind list or struct' );
0775 end
0776
0777 case {'time','3d' }
0778
0779 data.time_flag = true;
0780
0781 case 'show'
0782 data.show_flag = true;
0783
0784 counter = counter + 1;
0785
0786 if (counter <= nargin) && isnumeric( varargin{counter} )
0787 data.ind = varargin{counter};
0788 else
0789 data.show_all_flag = true;
0790 counter = counter - 1;
0791 end
0792
0793 case 'hist'
0794
0795 data.hist_flag = true;
0796
0797 case 'stat'
0798 data.stat_flag = true;
0799
0800 case 'dothist'
0801
0802 data.dothist_flag = true;
0803
0804 case 'dot'
0805
0806 data.dot_flag = true;
0807
0808 case 'strip'
0809
0810 data.strip_flag = true;
0811
0812 case 'color'
0813
0814 counter = counter + 1;
0815 color = varargin{counter};
0816
0817 if ~data.array_flag
0818 data.clist.color = color;
0819 else
0820 data.clist = intDoAll( data.clist, 'color', color, data.time_flag);
0821 end
0822 case ''
0823
0824 otherwise
0825 disp( [next_arg, ' is not a command'] );
0826
0827 end
0828
0829 end
0830
0831
0832 end
0833
0834 if numel( data.ind ) == 2
0835 data.stat_flag = false;
0836 end
0837
0838
0839 if ~data.hist_flag && ~data.kde_flag && ~data.dot_flag
0840
0841 if (numel( data.ind ) == 2)
0842 if data.time_flag
0843 data.kde_flag = true;
0844 else
0845 data.dot_flag = true;
0846 end
0847 if numel( data.ind ) == 1
0848 data.hist_flag = true;
0849 end
0850
0851 end
0852
0853
0854 end
0855
0856 if numel( data.bin ) == 1 && numel( data.ind ) == 2
0857 error( 'Dimension of bin must match ind.' );
0858 end
0859
0860 end
0861
0862
0863 function clist = intDoAll( clist, comm_, arg_, time_flag )
0864
0865 if ~exist( 'arg_', 'var' )
0866 arg_ = '';
0867 end
0868
0869 if iscell( clist )
0870 nc = numel( clist );
0871 for ii = 1:nc
0872 if time_flag
0873 clist{ii} = gateTool( clist{ii}, comm_, arg_, 'noshow', '3d' );
0874 else
0875 clist{ii} = gateTool( clist{ii}, comm_, arg_, 'noshow' );
0876 end
0877 end
0878 elseif isstruct( clist )
0879 if time_flag
0880 clist = gateTool( clist, comm_, arg_, 'noshow', '3d' );
0881 else
0882 clist = gateTool( clist, comm_, arg_, 'noshow' );
0883 end
0884 end
0885
0886 end
0887
0888
0889
0890
0891 function data = intDoStrip( data )
0892
0893 if data.array_flag
0894 data.clist = intDoAll( data.clist, 'strip', '', data.time_flag );
0895 else
0896 clist = data.clist;
0897 clist0 = clist;
0898
0899
0900 if isfield( clist0, 'gate' );
0901 clist0 = rmfield( clist0, {'gate'} );
0902 end
0903 if isfield( clist0, 'idExclude' );
0904 clist0 = rmfield( clist0, {'idExclude'} );
0905 end
0906 if isfield( clist0, 'idExclude' );
0907 clist0 = rmfield( clist0, {'idExclude'} );
0908 end
0909
0910
0911 ss = size(clist.data);
0912 inflag = true(ss(1),1);
0913
0914 if isfield( clist, 'idExclude' ) && ~isempty(clist.idExclude)
0915 inflag = ~ismember(clist.data(:,1), clist.idExclude);
0916 end
0917
0918 if isfield( clist, 'idInclude' ) && ~isempty(clist.idInclude)
0919 inflag = ismember(clist.data(:,1), clist.idInclude);
0920 end
0921
0922 if isfield( clist, 'gate' ) && ~isempty ('gate.clist')
0923 for ii = 1:numel(clist.gate)
0924 if numel(clist.gate(ii).ind) == 2
0925 inflag = and(inflag, inpolygon( clist.data(:,clist.gate(ii).ind(1)), ...
0926 clist.data(:,clist.gate(ii).ind(2)), ...
0927 clist.gate(ii).xx(:,1), clist.gate(ii).xx(:,2) ));
0928 else
0929 x = clist.data(:,clist.gate(ii).ind);
0930 xg = clist.gate(ii).x;
0931
0932 if numel(xg)==1
0933 inflag = and( inflag, xg==x );
0934 else
0935 inflag = and( inflag, and( x > min(xg), x < max(xg)));
0936 end
0937 end
0938 end
0939 end
0940
0941
0942 clist0.data = clist.data(inflag,:);
0943 if isfield(clist,'data3D') && isfield(clist,'def3D') && ~data.skip3D_flag
0944 clist0.def3D = clist.def3D;
0945 clist0.data3D = clist.data3D(inflag,:,:);
0946 end
0947
0948 data.clist = clist0;
0949
0950 if numel(clist0.data) == 0
0951 disp( 'Warning: At least one clist is empty after gating.' );
0952 end
0953 end
0954
0955 end
0956
0957
0958 function data = intMakeGate( data, arg_ )
0959
0960 clist0 = data.clist;
0961
0962
0963 if isstruct(arg_)
0964
0965 ind = arg_.ind;
0966
0967 if iscell( data.clist )
0968 data.clist = intDoAll( data.clist, 'make', arg_, data.time_flag );
0969 else
0970 if ~data.time_flag
0971 if isfield( data.clist, 'gate' ) && ~isempty( data.clist.gate )
0972 data.clist.gate = intMergeStruct(data.clist.gate,arg_);
0973 else
0974 data.clist.gate = arg_;
0975 end
0976 else
0977 if isfield( data.clist, 'gate3D' ) && ~isempty( data.clist.gate3D )
0978 data.clist.gate3D = intMergeStruct(data.clist.gate3D,arg_);
0979 else
0980 data.clist.gate3D = arg_;
0981 end
0982 end
0983 end
0984 elseif isnumeric( arg_ )
0985 intShow( data );
0986 hold on;
0987
0988 ylim_ = ylim;
0989
0990
0991 if numel( data.ind ) == 1
0992 disp( 'Click on the max and min value to make a gate.');
0993 for i = 1:2
0994 try
0995 tmp = ginput(1);
0996 catch
0997
0998 return;
0999 end
1000 if ~isempty(tmp)
1001 gxx(i,:) = tmp;
1002 plot( gxx(i,1)+[0,0], ylim_, 'r--' );
1003 end
1004 end
1005
1006 ind = data.ind;
1007 tmp_gate.x = gxx(:,1);
1008 tmp_gate.ind = data.ind;
1009 tmp_gate.xx = [];
1010
1011
1012 if data.time_flag
1013 def = intGetDef3D( data.clist );
1014 disp( ['Gate selected for ', def{data.ind}] );
1015 else
1016 def = intGetDef( data.clist );
1017 disp( ['Gate selected for ', def{data.ind}] );
1018 end
1019
1020 disp(tmp_gate.x);
1021
1022 hold on;
1023 plot( gxx(1)+[0,0], ylim_, 'r--' );
1024 hold on;
1025 plot( gxx(2)+[0,0], ylim_, 'r--' );
1026
1027 elseif numel( data.ind ) == 2
1028
1029
1030 c_flag = 1;
1031 disp('Draw polygon. Finish by pressing return' );
1032 i = 0;
1033 xx = zeros( 100, 2 );
1034
1035 while c_flag;
1036 dvar = 0;
1037
1038 i = i+1;
1039 tmp = ginput(1);
1040 if isempty(tmp)
1041 if i ~= 1
1042 plot( xx([i-1,1],1), xx([i-1,1],2), 'r-' );
1043 end
1044
1045 c_flag = false;
1046 numvert = i-1;
1047 else
1048 dr = (xx(1,:)-tmp );
1049 if (i>1) && (sum((dr.^2)) < dvar*0.001 )
1050 numvert = i-1;
1051 c_flag = false;
1052 plot( xx([1,numvert],1), xx([1,numvert],2), 'r-' );
1053 else
1054 xx(i,:) = tmp;
1055
1056 if i == 1
1057 plot( xx(1,1), xx(1,2), 'r-' );
1058 else
1059 plot( xx([i,i-1],1), xx([i,i-1],2), 'r-' );
1060 end
1061 end
1062 end
1063 end
1064
1065 xx = xx(1:numvert,:);
1066
1067 tmp_gate.ind = data.ind;
1068 tmp_gate.xx = xx;
1069 tmp_gate.x = [];
1070
1071
1072 if data.time_flag
1073 def = intGetDef3D( data.clist );
1074 disp( ['Gate selected for ', def{data.ind(1)},', ',def{data.ind(2)}] );
1075 else
1076 def = intGetDef( data.clist );
1077 disp( ['Gate selected for ', def{data.ind(1)},', ',def{data.ind(2)}] );
1078 end
1079 disp( tmp_gate.xx );
1080
1081 else
1082 error( 'Too many ind to gate. Must be either 1 or 2.' );
1083 end
1084
1085
1086 if ~data.time_flag
1087 data.clist = gateTool( data.clist, 'make', tmp_gate, 'noshow' );
1088
1089 else
1090 data.clist = gateTool( data.clist, 'make', tmp_gate, 'noshow', '3d' );
1091
1092 end
1093
1094
1095
1096 else
1097 error( 'Make gate in must be gate structure of indices' );
1098 end
1099
1100
1101 if ~data.noshow_flag
1102 tmp_clist = data.clist;
1103
1104 if data.time_flag
1105 gates = intDrillForGate3D(tmp_clist);
1106 intShowGate( clist0, gates(end), numel(gates), data.time_flag );
1107 else
1108 gates = intDrillForGate(tmp_clist);
1109 intShowGate( clist0, gates(end), numel(gates), data.time_flag );
1110 end
1111 end
1112
1113 end
1114
1115
1116 function gate_ = intDrillForGate( clist )
1117 if iscell( clist )
1118 gate_ = intDrillForGate( clist{1} );
1119 elseif isstruct( clist )
1120 gate_ = clist(1).gate;
1121 else
1122 error( 'clist type not expected' );
1123 end
1124 end
1125
1126 function gate_ = intDrillForGate3D( clist )
1127 if iscell( clist )
1128 gate_ = intDrillForGate( clist{1} );
1129 elseif isstruct( clist )
1130 gate_ = clist(1).gate3D;
1131 else
1132 error( 'clist type not expected' );
1133 end
1134 end
1135
1136
1137 function [clist, fignum] = intShowAll( clist, fignum, data )
1138
1139 if ~exist( 'fignum', 'var' )
1140 fignum = 1;
1141 end
1142
1143
1144
1145 clist0 = clist;
1146
1147 clist0 = gateTool( clist, 'clear' );
1148 gates = intDrillForGate( clist );
1149 ng = numel( gates );
1150
1151 for ii = 1:ng
1152
1153 fignum = fignum + 1;
1154
1155 figure(fignum);
1156 clf;
1157
1158
1159 [N,N0] = intShowGate( clist0, gates(ii), ii, data.time_flag );
1160
1161
1162 data.N(ii) = N;
1163 data.N0(ii) = N0;
1164
1165
1166
1167 clist0 = gateTool( clist0, 'gate', gates(ii), 'noshow' );
1168 end
1169
1170 end
1171
1172
1173 function [out] = intGetCellNum( clist )
1174 clist = gateTool( clist, 'merge', 'skip3D' );
1175
1176 num = size( clist.data, 1 );
1177
1178 clist = gateTool( clist, 'strip', 'skip3D' );
1179
1180 numG = size( clist.data, 1 );
1181
1182 out = [numG,num];
1183 end
1184
1185
1186
1187 function [N,N0] = intShowGate( clist, gate_var, gate_num, time_flag )
1188
1189 if ~exist( 'gate_num', 'var' )
1190 gate_num = 0;
1191 end
1192
1193
1194 if time_flag
1195 tmp = gateTool( clist, 'strip', 'merge' );
1196 N0 = size( tmp.data3D, 1);
1197 tmp = gateTool( tmp, 'gate', gate_var, 'noshow', '3d','strip' );
1198 N = size( tmp.data3D, 1);
1199
1200 gateTool( clist, 'show', gate_var.ind, '3d' );
1201 else
1202 tmp = gateTool( clist, 'strip', 'merge', 'skip3d' );
1203 N0 = size( tmp.data, 1);
1204 tmp = gateTool( tmp, 'gate', gate_var, 'noshow', 'skip3d','strip' );
1205 N = size( tmp.data, 1);
1206
1207 gateTool( clist, 'show', gate_var.ind );
1208 end
1209
1210
1211
1212
1213
1214 hold on;
1215 if numel(gate_var.ind)==1
1216 ylim_ = ylim;
1217
1218 plot( gate_var.x(1)+0*ylim_,ylim_, '.--', 'color','r' );
1219 if numel( gate_var.x )>1
1220 plot( gate_var.x(2)+0*ylim_,ylim_, '.--', 'color','r' );
1221 end
1222 else
1223 plot( gate_var.xx([1:end,1],1), gate_var.xx([1:end,1],2), '.--', 'color', 'r' );
1224 end
1225
1226 name = '';
1227
1228 if isfield( clist, 'name' )
1229 name = clist.name;
1230 end
1231
1232 title( [name,' Gate: ',num2str(gate_num), ' Cell count: ',num2str(N), ' / ', num2str( N0 )] );
1233
1234
1235 end
1236
1237
1238 function data0 = intShow( data0 )
1239
1240 data0.stat = [];
1241
1242 if ~data0.noclear_flag
1243 clf;
1244 end
1245
1246 data = data0;
1247
1248 if data.time_flag
1249 data.clist = gateTool( data.clist, 'strip', 'time' );
1250 else
1251 data.clist = gateTool( data.clist, 'strip', 'skip3D' );
1252 end
1253
1254
1255
1256 if data0.hist_flag || (numel( data0.ind )==1) || data0.kde_flag
1257 data1 = data;
1258 data1.clist = intDoMerge( data1.clist, [], ~data.time_flag );
1259
1260 data.binS = intMakeBins( data1.clist, data1 );
1261 end
1262
1263
1264 data = intIntShow( data.clist, data );
1265
1266 nf = max( [1, numel( data.fig_ptr )] );
1267
1268 for jj = 1:nf
1269
1270 if ~isempty( data.fig_ptr )
1271 figure( data.fig_ptr(jj) );
1272 end
1273
1274 if (numel( data.ind ) == 2) && ...
1275 (~data.dot_flag)
1276
1277
1278 xx1 = data.xx{1};
1279 xx2 = data.xx{2};
1280
1281 if data.log_flag(2)
1282 xx1 = exp(xx1);
1283 end
1284 if data.log_flag(1)
1285 xx2 = exp(xx2);
1286 end
1287
1288 if size(data.clist,2)>1 && ~data.newfig_flag
1289 if ~data.log_flag(3)
1290 data.im = data.im/max(data.im(:));
1291 end
1292 if data.inv_flag
1293 data.im = 1-data.im;
1294 end
1295 end
1296
1297 if data.log_flag(1)
1298 xx2 = log10(xx2);
1299 end
1300
1301 if data.log_flag(2)
1302 xx1 = log10(xx1);
1303 end
1304
1305 if iscell( data.im )
1306 im = data.im{jj};
1307 else
1308 im = data.im;
1309 end
1310
1311 imagesc( xx2, xx1, im );
1312
1313
1314
1315 hold on;
1316
1317 if size(data.clist,2)==1 || data.newfig_flag
1318 intFixColorBar(im);
1319 end
1320
1321
1322 axis( [xx2(1),xx2(end),xx1(1),xx1(end)] );
1323 set(gca,'layer','top')
1324 end
1325
1326
1327
1328 if data.log_flag(1)
1329 if (numel(data.ind)==1) || ~( data.kde_flag || data.hist_flag )
1330 set(gca,'XScale','log' );
1331 end
1332 end
1333
1334 if data.log_flag(2)
1335 if (numel(data.ind)==1) || ~( data.kde_flag || data.hist_flag )
1336 set(gca,'YScale','log' );
1337 end
1338 end
1339
1340
1341 def = intGetDef( data.clist );
1342 def3D = intGetDef3D( data.clist );
1343
1344 if data.time_flag
1345 labs = def3D(data.ind);
1346 else
1347 labs = def(data.ind);
1348 end
1349
1350
1351 if (numel(data.ind)==2) && ( data.kde_flag || data.hist_flag )
1352 if data.log_flag(1)
1353 labs{1} = [labs{1},' (log10)'];
1354 end
1355
1356 if data.log_flag(2)
1357 labs{2} = [labs{2},' (log10)'];
1358 end
1359
1360 end
1361
1362
1363 if data.trace_flag
1364 xlabel( 'Time (Frames)', 'Interpreter','none' );
1365
1366
1367 ylabel( labs{1}, 'Interpreter','none' );
1368 else
1369 if numel( data.ind )
1370 xlabel( labs{1}, 'Interpreter','none' );
1371 end
1372
1373 if numel( data.ind ) == 2
1374 ylabel( labs{2} , 'Interpreter','none');
1375 elseif data.den_flag
1376 ylabel( 'Density', 'Interpreter','none' );
1377 else
1378 ylabel( 'Number' , 'Interpreter','none');
1379 end
1380 end
1381
1382 set( gca, 'Box', 'on' );
1383
1384 if ~data.newfig_flag
1385 legend( data.h, data.legend );
1386 end
1387
1388 set( gca, 'YDir', 'normal' );
1389
1390 end
1391
1392 if data.dot_flag || (numel(data.ind)==1)
1393 xlim_ = xlim;
1394 XM = mean(xlim_);
1395 xlim( XM+1.05*(xlim_-XM) );
1396 end
1397
1398
1399 if data.stat_flag
1400 figure;
1401 intDoBoxIt( data );
1402 end
1403
1404 data0.stat = data.stat;
1405
1406 end
1407
1408 function intFixColorBar( im )
1409 try
1410 colorbar
1411
1412 cc = colormap;
1413 cc(1,:) = [0.5,0.5,0.5];
1414 colormap(cc);
1415
1416 tmp = im;
1417 tmp(tmp==0) = nan;
1418 min_caxis = min(tmp(:));
1419 max_caxis = max(tmp(:));
1420
1421 N = size(cc,1);
1422 c = (N*min_caxis-max_caxis)/(N-1);
1423 if ~isnan( max_caxis )
1424 caxis( [c,max_caxis] );
1425 end
1426
1427 end
1428 end
1429
1430
1431
1432
1433
1434
1435
1436
1437
1438
1439
1440
1441
1442
1443
1444
1445
1446
1447
1448 function intDoBoxIt( data )
1449
1450 sort_flag = true;
1451 cc = 'k';
1452
1453 stat = data.stat;
1454 ns = numel( stat );
1455
1456 if sort_flag
1457 mean_data = [data.stat(:).mean];
1458 [~,ord] = sort( mean_data );
1459 else
1460 ord = 1:ns;
1461 end
1462
1463 zz = [0,0];
1464
1465 px = [];
1466 for jj = 1:ns
1467
1468 ii = ord(jj);
1469 px = [px,data.stat(ii).px'];
1470 end
1471 xx = data.stat(1).xx;
1472
1473
1474
1475
1476
1477
1478 bin = 1:ns;
1479
1480
1481
1482
1483
1484
1485 if data.log_flag(1)
1486 imagesc( bin, log10(xx), px );
1487 else
1488 imagesc( bin, xx, px );
1489 end
1490
1491 hold on;
1492
1493 names = {};
1494
1495 for jj = 1:ns
1496
1497 ii = ord(jj);
1498
1499 yy1 = [stat(ii).min,stat(ii).max];
1500 yy2 = stat(ii).mean+stat(ii).std*[-1,1];
1501 yy3 = stat(ii).mean+stat(ii).err*[-1,1];
1502 yy4 = stat(ii).mean;
1503
1504
1505
1506
1507
1508
1509
1510 if data.log_flag(1)
1511 plot( jj + zz, log10(yy1), ':', 'color', cc ),
1512 plot( jj + zz, log10(yy2), '-', 'color', cc ),
1513 plot( jj + zz, log10(yy3), '-', 'color', cc, 'LineWidth', 2 ),
1514 plot( jj , log10(yy4), '.', 'color', cc, 'MarkerSize', 10 ),
1515 else
1516 plot( jj + zz, yy1, ':', 'color', cc ),
1517 plot( jj + zz, yy2, '-', 'color', cc ),
1518 plot( jj + zz, yy3, '-', 'color', cc, 'LineWidth', 2 ),
1519 plot( jj , yy4, '.', 'color', cc, 'MarkerSize', 10 ),
1520 end
1521 name_tmp = stat(ii).name;
1522 ind = find(name_tmp == '(',1,'last');
1523 names{jj} = name_tmp(1:ind-2);
1524
1525 end
1526
1527
1528 intFixColorBar(px)
1529
1530
1531 set( gca, 'Xtick', [1:ns],'XTickLabels',names );
1532 set( gca, 'XTickLabelRotation', 45 )
1533 set( gca, 'YDir', 'normal' );
1534
1535
1536
1537
1538
1539
1540 def = intGetDef( data.clist );
1541 def3D = intGetDef3D( data.clist );
1542
1543
1544 if data.time_flag
1545 labs = def3D(data.ind);
1546 else
1547 labs = def(data.ind);
1548 end
1549
1550 if (numel(data.ind)==2) && ( data.kde_flag || data.hist_flag )
1551 if data.log_flag(1)
1552 labs{1} = [labs{1},' (log10)'];
1553 end
1554 end
1555
1556 tmp = labs{1};
1557 if data.log_flag(1)
1558 tmp = ['log ', tmp ];
1559 end
1560 ylabel(tmp, 'Interpreter','none' );
1561
1562
1563
1564
1565 end
1566
1567
1568
1569 function data = intIntShow( clist, data )
1570
1571
1572 if iscell(clist)
1573
1574 nc = size( clist,2 );
1575 nr = size( clist,1 );
1576
1577 if (nr~=1) && (nc~=1)
1578 error( 'At least one dimension of the clist cell array should be unitary' );
1579 else
1580 if nr > 1
1581 if data.time_flag
1582 clist = gateTool( clist, 'merge', 'time' );
1583 else
1584 clist = gateTool( clist, 'merge', 'skip3D' );
1585 end
1586 data = intIntShow( clist, data );
1587 else
1588 for ii = 1:nc
1589 data = intIntShow( clist{ii}, data );
1590 end
1591 end
1592 end
1593
1594 else
1595
1596 [data] = intIntIntShow( clist, data );
1597 hold on;
1598 end
1599
1600 end
1601
1602
1603
1604 function [data] = intIntIntShow( clist, data )
1605
1606 stat = [];
1607
1608 if isfield( clist, 'name' );
1609 name = clist.name;
1610 else
1611 name = ['data ', num2str(numel( data.h )) ];
1612 end
1613
1614 if data.newfig_flag
1615 data.fig_ptr = [data.fig_ptr, figure()];
1616 end
1617
1618 switch numel( data.ind )
1619
1620 case 0
1621 error( 'No indices to show' );
1622 case 1
1623 if data.kde_flag
1624 [data,h,stat] = intShowKDE1D( clist, data, name );
1625
1626
1627 else
1628 [data,h,stat] = intShowHist1D( clist, data, name );
1629 end
1630 case 2
1631 if data.hist_flag
1632 [data,h] = intShowHist2D( clist, data, name );
1633 elseif data.dot_flag
1634 [data,h] = intShowDot( clist, data, name );
1635 elseif data.kde_flag
1636 [data,h] = intShowKDE2D( clist, data, name );
1637 else
1638 [data,h] = intShowDot( clist, data, name );
1639 end
1640 end
1641
1642 data.h = [data.h,h];
1643
1644
1645
1646 nc = size( clist.data, 1 );
1647
1648 stat.name0 = name;
1649
1650 if data.time_flag
1651 name = [name,' (',num2str( data.n, '%1.2g' ),' points)'];
1652 else
1653 name = [name,' (',num2str( nc ),' cells)'];
1654 end
1655
1656 stat.name = name;
1657
1658 if data.newfig_flag
1659 legend( h, name );
1660 else
1661 data.legend = {data.legend{:},name};
1662 end
1663
1664 if isfield( data, 'stat' ) && ~isempty( data.stat )
1665 data.stat = [data.stat,stat];
1666 else
1667 data.stat = [stat];
1668 end
1669
1670 end
1671
1672
1673 function [data,h,stat] = intShowHist1D( clist, data, name )
1674
1675 stat = [];
1676
1677 [x1,x0,flagger,n] = intGetDataC( clist, data,1 );
1678 data.n = n;
1679
1680 [y,x] = hist( x1, data.binS.xx );
1681 dy = intDoError(y);
1682
1683 if data.den_flag
1684 dx = diff(x(1:2));
1685
1686
1687 normer = 1./(dx*sum(y(:)));
1688 y = y*normer;
1689 dy = dy*normer;
1690 end
1691
1692
1693 if data.log_flag(1)
1694 x_plot = exp(x);
1695 else
1696 x_plot = x;
1697 end
1698
1699 if isfield( clist, 'color' )
1700 cc = clist.color;
1701 h = plot( x_plot,y, '.-', 'color', cc );
1702 else
1703 h = plot( x_plot,y, '.-' );
1704 cc = h.Color;
1705 end
1706
1707 if data.error_flag
1708 hold on;
1709 plot( x_plot,intFixError(y-dy), ':', 'color', cc );
1710 plot( x_plot,intFixError(y+dy), ':', 'color', cc );
1711 end
1712
1713
1714 if ~data.bin_flag
1715 data.bin = x;
1716 end
1717
1718 if data.stat_flag
1719 stat = intDoStatAn( x0, x_plot, y, n, data, cc, name );
1720 end
1721
1722 end
1723
1724
1725 function stat = intDoStatAn( x1, x, y, n, data, cc, name )
1726
1727 hold on;
1728
1729 styl = '%1.3e';
1730
1731
1732 x1_mean = mean( x1 );
1733 x1_std = std( x1 );
1734 x1_max = max( x1 );
1735 x1_min = min( x1 );
1736 x1_p1 = x1_mean+x1_std;
1737 x1_p1m = x1_mean+x1_std/sqrt(n);
1738 x1_m1 = x1_mean-x1_std;
1739 x1_m1m = x1_mean-x1_std/sqrt(n);
1740
1741 all_out_text = [name,' -- stats: n = ',num2str( n, styl ),', '];
1742
1743 y1_mean = interp1( x,y, x1_mean );
1744 y1_p1 = interp1( x,y, x1_p1 );
1745 y1_p1m = interp1( x,y, x1_p1m );
1746 y1_m1 = interp1( x,y, x1_m1 );
1747 y1_m1m = interp1( x,y, x1_m1m );
1748 y1_max = interp1( x,y, x1_max ,'linear','extrap');
1749 y1_min = interp1( x,y, x1_min,'linear','extrap' );
1750
1751
1752 stat = [];
1753 stat.mean = x1_mean;
1754 stat.std = x1_std;
1755 stat.err = x1_std/sqrt(n);
1756 stat.px = y;
1757 stat.xx = x;
1758 stat.max = x1_max;
1759 stat.min = x1_min;
1760 stat.n = n;
1761 stat.x = x1;
1762
1763 if data.log_flag(2)
1764 del = [1e-1,1];
1765 else
1766 del = [0,1];
1767 end
1768
1769
1770 plot( x1_mean+[0,0], del*y1_mean, 'x:', 'color', cc, 'MarkerSize', 10 );
1771
1772 out_text = [' mean: ',num2str( x1_mean, styl )];
1773 text( x1_mean, y1_mean/2, out_text, 'color', cc );
1774 all_out_text = [ all_out_text, out_text,','];
1775
1776 plot( x1_p1+[0,0], del*y1_p1, 'x:', 'color', cc, 'MarkerSize', 10 );
1777
1778 out_text = [' std: ',num2str( x1_std, styl )];
1779 text( x1_p1, y1_p1*.75, out_text, 'color', cc );
1780 all_out_text = [ all_out_text, out_text,','];
1781
1782 plot( x1_m1+[0,0], del*y1_m1, 'x:', 'color', cc, 'MarkerSize', 10 );
1783
1784
1785
1786
1787
1788 plot( x1_p1m+[0,0], del*y1_p1m, 'x:', 'color', cc, 'MarkerSize', 10 );
1789 plot( x1_m1m+[0,0], del*y1_m1m, 'x:', 'color', cc, 'MarkerSize', 10 );
1790
1791
1792
1793 out_text = [' error: ',num2str( x1_std/sqrt(n), styl )];
1794 text( x1_p1m, y1_p1m*.25, out_text, 'color', cc );
1795 all_out_text = [ all_out_text, out_text,','];
1796
1797 out_text = [' max: ',num2str( x1_std/sqrt(n), styl )];
1798
1799
1800 all_out_text = [ all_out_text, out_text,','];
1801
1802 out_text = [' min: ',num2str( x1_std/sqrt(n), styl )];
1803
1804
1805 all_out_text = [ all_out_text, out_text,'.'];
1806
1807 disp( all_out_text );
1808 end
1809
1810
1811 function dy = intDoError( y )
1812
1813 dy = sqrt( y );
1814 dy(dy<1) = 1;
1815
1816 end
1817
1818 function y = intFixError( y )
1819
1820 y(y<0) = 0;
1821
1822 end
1823
1824
1825 function [data,h,stat] = intShowKDE1D( clist, data, name )
1826
1827 stat = [];
1828
1829 [x1,x0,flagger,n] = intGetDataC( clist, data, 1 );
1830 data.n = n;
1831
1832 bin = data.binS(1).xx;
1833 dx = data.binS(1).dx;
1834 rk = data.binS(1).rk_pix;
1835
1836 [y,x] = hist( x1, bin );
1837
1838
1839 if data.log_flag(1)
1840 x_plot = exp(x);
1841 else
1842 x_plot = x;
1843 end
1844
1845
1846
1847 [yf,dyf] = intConv1Dint( y, rk );
1848
1849
1850
1851 if data.den_flag
1852 normer = 1./( sum(y(:))*dx );
1853 yf = yf*normer;
1854 dyf = dyf*normer;
1855 end
1856
1857 if isfield( clist, 'color' )
1858 cc = clist.color;
1859 h = plot( x_plot,yf, '-', 'color', cc );
1860 else
1861 h = plot( x_plot,yf, '-' );
1862 cc = h.Color;
1863 end
1864
1865 if data.error_flag
1866 hold on;
1867 plot( x_plot,intFixError(yf-dyf), ':', 'color', cc );
1868 plot( x_plot,intFixError(yf+dyf), ':', 'color', cc );
1869 end
1870
1871
1872 if ~data.bin_flag
1873 data.bin = x;
1874 end
1875
1876
1877 if data.stat_flag
1878 stat = intDoStatAn( x0, x_plot, yf, n, data, cc, name);
1879 end
1880
1881
1882 end
1883
1884
1885 function binS_vec = intMakeBins( clist, data )
1886
1887 for ii = 1:numel( data.ind )
1888 if data.kde_flag
1889 num = data.multi;
1890 else
1891 if isfield( data, 'bin' ) && ~isempty( data.bin )
1892 num = data.bin(ii);
1893 else
1894 num = intChooseBin(clist, data, ii);
1895 end
1896 end
1897
1898 binS = intMakeDX( clist, data, num, ii );
1899
1900 if ~data.kde_flag
1901 binS.rk_pix = [];
1902 binS.rm_pix = [];
1903 else
1904 if isfield( data, 'rk' ) && ~isempty( data.rk )
1905 binS.rk_pix = data.rk(ii)/binS.dx;
1906 else
1907 binS.rk_pix = intChooseRK(clist, data, ii);
1908 end
1909
1910 if isfield( data, 'rm' ) && ~isempty( data.rm )
1911 binS.rm_pix = data.rm(ii)/binS.dx;
1912 else
1913 binS.rm_pix = binS.rk_pix;
1914 end
1915 end
1916
1917 binS_vec(ii) = binS;
1918 end
1919 end
1920
1921
1922 function binS = intMakeDX( clist, data, num, ind )
1923 x = intGetData( clist, data, data.ind(ind), data.units(ind) );
1924 if data.log_flag(ind)
1925 x = log(x);
1926 end
1927 x = fixVals( x );
1928
1929 x_max = max( x(:) );
1930 x_min = min( x(:) );
1931
1932 if x_max == x_min
1933 tmp = x_max;
1934 x_max = tmp+1;
1935 x_min = tmp-1;
1936 elseif isempty( x_max )
1937 DX = 1;
1938 x_max = 0.5;
1939 x_min = -0.5;
1940 end
1941
1942 DX = x_max - x_min;
1943 xx = DX*(0:(num-1))/(num-1)+x_min;
1944 dx = xx(2)-xx(1);
1945
1946 binS.xx = xx;
1947 binS.dx = dx;
1948 binS.DX = DX;
1949 binS.x_max = x_max;
1950 binS.x_min = x_min;
1951 binS.x = x;
1952 end
1953
1954
1955
1956 function dx_min = intFindSmallest( x )
1957
1958 dx_min = min(diff(sort(unique(x(:)))));
1959
1960 if isempty( dx_min )
1961 dx_min = 1;
1962 end
1963
1964
1965 end
1966
1967
1968 function num_ = intChooseBin(clist, data, ind)
1969
1970 del = 2;
1971
1972 binS = intMakeDX( clist, data, 2, ind );
1973 x = intGetDataC( clist, data, ind );
1974
1975 dx_min = intFindSmallest( x );
1976 maxBinNum = min( [floor(binS.DX/dx_min),data.multi]);
1977
1978 ln_vec = log(data.minBinNum):log(del):log(maxBinNum);
1979 n_vec = round( exp(ln_vec) );
1980
1981 num_n = numel(n_vec);
1982
1983 if num_n == 0
1984 num_ = data.multi;
1985 else
1986 switcher = nan( [1,num_n] );
1987
1988 for ii = 1:num_n
1989 num = n_vec(ii);
1990 binS = intMakeDX( clist, data, num, ind );
1991
1992 y = hist( x, binS.xx );
1993
1994 if false
1995 delta_y = abs(diff(y));
1996 dy = sqrt( (y(2:end)+y(1:end-1))/2 );
1997 else
1998 tmp = diff(y);
1999 tmp = tmp([1,1:end,end]);
2000 delta_y = abs(tmp(2:end)+tmp(1:end-1))/2;
2001 dy = sqrt( y );
2002 end
2003
2004
2005 switcher(ii) = sum( y.*(delta_y > 2*dy))/sum(y);
2006 end
2007
2008
2009 cutt = 0.5;
2010
2011 ind_n = find( switcher < cutt, 1, 'first' ) - 1;
2012
2013 if isempty( ind_n ) || ind_n < 1 || ind_n > num_n
2014 if switcher(1) < cutt
2015 ind_n = 1;
2016 num_ = n_vec(ind_n);
2017 elseif switcher(end) > cutt
2018 num_ = maxBinNum;
2019 ind_n = num_n;
2020 end
2021 end
2022
2023 num_ = n_vec(ind_n);
2024 end
2025 end
2026
2027
2028 function rk_pix = intChooseRK(clist, data, ind)
2029
2030 binS = intMakeDX( clist, data, data.multi, ind );
2031 x = intGetDataC( clist, data, ind );
2032
2033 dx_min = intFindSmallest( x );
2034 maxBinNum = min( [(binS.DX/dx_min),data.multi]);
2035
2036
2037 ln_vec = log(data.minBinNum):log(1.5):log(maxBinNum);
2038 n_vec = round( exp(ln_vec) );
2039 rk_vec = data.multi./n_vec;
2040
2041 num_n = numel(n_vec);
2042
2043 if num_n == 0
2044 rk_pix = 1;
2045 else
2046 switcher = nan( [1,num_n] );
2047
2048 for ii = 1:num_n
2049 num = n_vec(ii);
2050
2051 y = hist( x, binS.xx );
2052 [y,dy] = intConv1Dint( y, rk_vec(ii) );
2053
2054 delta_y = rk_vec(ii)*abs(diff(y));
2055 dy = (dy(1:end-1)+dy(2:end))/2;
2056 y_ = (y(2:end)+y(1:end-1))/2;
2057
2058 switcher(ii) =sum( y_.*(delta_y > 2*dy))/sum(y_);
2059 end
2060
2061 cutt = .5;
2062
2063 ind_n = find( switcher < cutt, 1, 'first' ) - 1;
2064
2065 if isempty( ind_n ) || ind_n < 1 || ind_n > num_n
2066 if switcher(1) < cutt
2067 ind_n = 1;
2068 elseif switcher(end) > cutt
2069 ind_n = num_n;
2070 end
2071 end
2072
2073 rk_pix = rk_vec(ind_n);
2074 end
2075 end
2076
2077
2078 function [x,flagger] = fixVals( x )
2079
2080 flagger = ~( isinf( x ) + isnan( x) + imag( x ) );
2081 x = x(flagger);
2082
2083 end
2084
2085
2086 function [data,h] = intShowHist2D( clist, data, name )
2087
2088 [x_vec,x0,flagger,n] = intGetDataC( clist, data, [1,2] );
2089 data.n = n;
2090 x1 = x_vec(:,1);
2091 x2 = x_vec(:,2);
2092
2093 [y,xx] = hist3( [x2,x1], {data.binS(2).xx,data.binS(1).xx} );
2094
2095 if data.cond_flag
2096 ys = sum( y, 1 );
2097
2098 ys(ys==0) = 1;
2099
2100 y = y./(ones([size(y,1),1])*ys);
2101
2102
2103
2104 end
2105
2106 if data.log_flag(3)
2107 y = log(y);
2108 y(isinf(y)) = nan;
2109 y(isnan(y)) = min(y(:));
2110 end
2111
2112
2113 hold on;
2114 if isfield( clist, 'color' )
2115 cc = clist.color;
2116 h = plot( nan, nan, '.', 'color', cc);
2117
2118 else
2119 h = plot( nan, nan, '.');
2120 end
2121
2122 cc = h.Color;
2123
2124 if ischar( cc )
2125 cc = convert_color( cc)
2126 end
2127
2128
2129
2130 if (size( data.clist,2 ) > 1) && ~data.newfig_flag
2131 dd = y/max(y(:));
2132
2133 im = cat(3, dd*cc(1), dd*cc(2), dd*cc(3) );
2134
2135
2136 if isfield( data, 'im' ) && ~isempty( data.im )
2137 data.im = data.im + im;
2138 else
2139 data.im = im;
2140 end
2141
2142 else
2143 data.im = {data.im{:},y};
2144 end
2145
2146 data.xx = xx;
2147
2148
2149 end
2150
2151
2152 function [data,h] = intShowKDE2D( clist, data, name )
2153
2154 [x_vec,x0,flagger,n] = intGetDataC( clist, data, [1,2] );
2155 data.n = n;
2156 x1 = x_vec(:,1);
2157 x2 = x_vec(:,2);
2158
2159 bin = {data.binS(2).xx,data.binS(1).xx};
2160 dx = [data.binS(2).dx,data.binS(1).dx];
2161
2162 [y,xx] = hist3( [x2,x1], bin );
2163
2164
2165 if data.cond_flag
2166 ys = sum( y, 1 );
2167
2168 ys(ys==0) = 1;
2169
2170 y = y./(ones([size(y,1),1])*ys);
2171
2172
2173
2174 end
2175
2176
2177 y = intConv2D( y, data );
2178
2179 if data.den_flag
2180 y = y./sum(y(:));
2181 end
2182
2183 y = y/prod(dx);
2184
2185 if data.log_flag(3)
2186 y = log(y);
2187 y(isinf(y)) = nan;
2188
2189 end
2190
2191
2192 hold on;
2193
2194 if isfield( clist, 'color' )
2195 cc = clist.color;
2196 h = plot( nan, nan, '.', 'color', cc);
2197
2198 else
2199 h = plot( nan, nan, '.');
2200 end
2201
2202
2203 cc = h.Color;
2204
2205 if ischar( cc )
2206 cc = convert_color( cc);
2207 end
2208
2209 if data.inv_flag
2210 cc = 1-cc;
2211 end
2212
2213 if size( data.clist, 2 ) > 1 && ~data.newfig_flag
2214
2215
2216 dd = y/max(y(:));
2217
2218 im = cat(3, dd*cc(1), dd*cc(2), dd*cc(3) );
2219
2220
2221 if isfield( data, 'im' ) && ~isempty( data.im )
2222 data.im = data.im + im;
2223 else
2224 data.im = im;
2225 end
2226
2227 else
2228 data.im = {data.im{:},y};
2229 end
2230
2231 data.xx = xx;
2232 data.bin = bin;
2233
2234
2235 end
2236
2237
2238 function [yf] = intConv2D( y, data )
2239
2240 rk = [data.binS(1).rk_pix,data.binS(2).rk_pix];
2241 rm = [data.binS(1).rm_pix,data.binS(2).rm_pix];
2242
2243
2244
2245 xx = -ceil(1.1*rm(1)):ceil(1.1*rm(1));
2246 yy = -ceil(1.1*rm(2)):ceil(1.1*rm(2));
2247 [X,Y] = meshgrid( xx,yy);
2248 R = sqrt((X./rm(1)).^2+(Y./rm(2)).^2);
2249 fdisk = double( R<=1 );
2250
2251
2252
2253 xx = -ceil(7*rk(1)):ceil(7*rk(1));
2254 yy = -ceil(7*rk(2)):ceil(7*rk(2));
2255 [X,Y] = meshgrid( xx,yy);
2256 R = sqrt((X./rk(1)).^2+(Y./rk(2)).^2);
2257
2258 fgaus = exp( -R.^2/2 )/(2*pi*rk(1)*rk(2));
2259
2260 minner = imfilter( y, fdisk, 0 );
2261
2262 yf = imfilter( y, fgaus, 0 );
2263
2264
2265
2266 yf( minner==0) = 0;
2267 yf = yf;
2268
2269 end
2270
2271
2272 function [yf,dyf] = intConv1Dint( y, rk )
2273
2274 xx = -ceil(7*rk(1)):ceil(7*rk(1));
2275 R = sqrt((xx./rk(1)).^2);
2276
2277 fgaus = exp( -R.^2/2 )/sqrt(2*pi*rk(1)^2);
2278
2279 yf = imfilter( y, fgaus, 0 );
2280 dyf = sqrt(imfilter( y, fgaus.^2, 0 ));
2281
2282 end
2283
2284 function [yf,dyf] = intConv1D( y, data, dx )
2285
2286 if isempty( data.rk )
2287 [yf,dyf,rk] = intConv1Dadd( y, data, dx );
2288 else
2289 rk = data.rk./dx;
2290
2291
2292
2293 xx = -ceil(7*rk(1)):ceil(7*rk(1));
2294 R = sqrt((xx./rk(1)).^2);
2295
2296 fgaus = exp( -R.^2/2 )/sqrt(2*pi*rk(1)^2);
2297
2298 yf = imfilter( y, fgaus, 0 );
2299 dyf = sqrt(imfilter( y, fgaus.^2, 0 ));
2300
2301
2302
2303 end
2304
2305 end
2306
2307
2308 function [data,h] = intShowDot( clist, data, name )
2309
2310 hold on;
2311
2312
2313 if ~data.time_flag
2314 x1 = intGetData( clist, data, data.ind(1), data.units(1) );
2315 x2 = intGetData( clist, data, data.ind(2), data.units(2) );
2316
2317
2318 if isfield( clist, 'color' )
2319 h = scatter( x1, x2, [], clist.color, '.' );
2320 else
2321 h = scatter( x1, x2, '.' );
2322 end
2323 else
2324 x1 = squeeze(clist.data3D(:,data.ind(1),:));
2325 x2 = squeeze(clist.data3D(:,data.ind(2),:));
2326
2327 [~,flagger] = fixVals( x1 + x2 );
2328 data.n = sum( flagger(:) );
2329 n = data.n;
2330
2331 if isfield( clist, 'color' )
2332 cc = clist.color;
2333 h = plot( nan,nan, '.', 'color', cc );
2334 else
2335 h = plot( nan,nan, '.' );
2336 cc = h.Color;
2337 end
2338
2339 if ischar( cc )
2340 cc = convert_color(cc);
2341 end
2342
2343 nc = size( x1, 1 );
2344
2345 for ii = 1:nc
2346
2347 hh = plot( nan, nan, '.' );
2348 cc_ii = hh.Color;
2349 cc_ii = (cc_ii+cc)/2;
2350
2351 if data.line_flag
2352 plot( x1(ii,:), x2(ii,:), 'color', cc_ii );
2353
2354 start_ind = find( ~isnan( x1(ii,:)+x2(ii,:) ), 1, 'first' );
2355 end_ind = find( ~isnan( x1(ii,:)+x2(ii,:) ), 1, 'last' );
2356
2357 plot( x1(ii,start_ind), x2(ii,start_ind), '.','MarkerSize', 10, 'color', cc_ii );
2358 plot( x1(ii,end_ind), x2(ii,end_ind ), '.','MarkerSize', 10, 'color', cc_ii );
2359 else
2360 plot( x1(ii,:), x2(ii,:), '.', 'color', cc_ii );
2361 end
2362 end
2363
2364 end
2365
2366
2367 end
2368
2369
2370 function def = intGetDef( clist )
2371
2372 if isstruct( clist )
2373 def = clist.def;
2374 elseif iscell( clist )
2375 def = intGetDef( clist{1} );
2376
2377 else
2378 error( 'empty clist in intGetDef' );
2379 end
2380
2381
2382 end
2383
2384 function def = intFixDef( def )
2385
2386 if ~isempty( def )
2387
2388 nd = numel( def );
2389 for ii = 1:nd
2390 def{ii} = [num2str(ii),' : ',def{ii}];
2391 end
2392
2393 def = {'Index : Descriptor', def{:} };
2394
2395 end
2396
2397 end
2398
2399
2400 function def = intGetDef3D( clist );
2401
2402 if isstruct( clist )
2403 if isfield( clist, 'def3D' )
2404 def = clist.def3D;
2405 elseif isfield( clist, 'def3d' )
2406 def = clist.def3d;
2407
2408 else
2409 def = {};
2410 end
2411 elseif iscell( clist )
2412 def = intGetDef3D( clist{1} );
2413 else
2414 error( 'empty clist in intGetDef' );
2415 end
2416
2417
2418 end
2419
2420
2421 function outColor = convert_color(inColor)
2422
2423 charValues = 'rgbcmywk'.';
2424 rgbValues = [eye(3); 1-eye(3); 1 1 1; 0 0 0];
2425 assert(~isempty(inColor),'convert_color:badInputSize',...
2426 'Input argument must not be empty.');
2427
2428 if ischar(inColor)
2429
2430 [isColor,colorIndex] = ismember(inColor(:),charValues);
2431 assert(all(isColor),'convert_color:badInputContents',...
2432 'String input can only contain the characters ''rgbcmywk''.');
2433 outColor = rgbValues(colorIndex,:);
2434
2435 elseif isnumeric(inColor) || islogical(inColor)
2436
2437 assert(size(inColor,2) == 3,'convert_color:badInputSize',...
2438 'Numeric input must be an N-by-3 matrix');
2439 inColor = double(inColor);
2440 scaleIndex = max(inColor,[],2) > 1;
2441 inColor(scaleIndex,:) = inColor(scaleIndex,:)./255;
2442 [isColor,colorIndex] = ismember(inColor,rgbValues,'rows');
2443 assert(all(isColor),'convert_color:badInputContents',...
2444 'RGB input must define one of the colors ''rgbcmywk''.');
2445 outColor = charValues(colorIndex(:));
2446
2447 else
2448
2449 error('convert_color:badInputType',...
2450 'Input must be a character or numeric array.');
2451
2452 end
2453 end
2454
2455
2456
2457 function clistM = intDoMerge( clist, ID_ind, skip3D )
2458
2459 if ~exist( 'skip3D', 'var' )
2460 skip3D = false;
2461 end
2462
2463 if ~exist( 'ID_ind', 'var' )
2464 def = intGetDef( clist );
2465 ID_ind = find(cellfun(@(IDX) ~isempty(IDX), strfind(def, 'ID')));
2466 end
2467
2468
2469 if isstruct( clist )
2470 clistM = clist;
2471 else
2472 nc = numel( clist );
2473
2474 data = [];
2475 clistM = [];
2476
2477
2478 for ii = 1:nc
2479 if iscell( clist{ii} )
2480 clist_ = intDoMerge( clist{ii}, [], skip3D );
2481 else
2482 clist_ = clist{ii};
2483 end
2484
2485 if isempty( clistM )
2486 clistM = clist_;
2487 else
2488
2489 maxID = max( clistM.data(:,1) );
2490
2491 tmp = clist_.data(:,ID_ind);
2492 tmp = tmp + maxID;
2493 tmp(tmp==maxID) = 0;
2494
2495 clist_.data(:,ID_ind) = tmp;
2496
2497 ss1 = size( clistM.data );
2498 ss2 = size( clist_.data );
2499
2500 if ss1(2) ~= ss2(2)
2501 error( 'Clists with a different number of data descriptors are being compared. Descriptor number must match.' );
2502 end
2503
2504 clistM.data = [clistM.data;...
2505 clist_.data];
2506
2507
2508
2509 if isfield( clist_, 'data3D' ) && ~skip3D
2510 clist_.data3D(:,1,:) = clist_.data3D(:,1,:) +maxID;
2511
2512 ss1 = size(clistM.data3D);
2513 ss2 = size(clist_.data3D);
2514
2515 if ss1(2) ~= ss2(2)
2516 error( 'Clists with a different number of data3D descriptors are being compared. Descriptor number must match.' );
2517 end
2518
2519 if numel(ss1) == 2
2520 ss1(3) = 1;
2521 end
2522
2523 if numel(ss2) == 2
2524 ss2(3) = 1;
2525 end
2526
2527 if ss1(3) > ss2(3)
2528 clist_.data3D = cat(3,clist_.data3D,nan( [ss2(1:2),ss1(3)-ss2(3)] ) );
2529 elseif ss1(3) < ss2(3)
2530 clistM.data3D = cat(3,clistM.data3D,nan( [ss1(1:2),ss2(3)-ss1(3)] ) );
2531 end
2532
2533 clistM.data3D = [clistM.data3D;...
2534 clist_.data3D];
2535 end
2536 end
2537 end
2538
2539 end
2540 end
2541
2542
2543
2544 function g12 = intMergeStruct( g1, g2)
2545
2546 ng1 = numel(g1);
2547 ng2 = numel(g2);
2548
2549 tmp1 = fieldnames( g1 );
2550 tmp2 = fieldnames( g2 );
2551
2552 names = unique({tmp1{:},tmp2{:}});
2553 nnames = numel(names);
2554
2555 for ii = (ng1+ng2):-1:1
2556
2557 tmp_gate = [];
2558
2559 for jj = 1:nnames
2560
2561 if ii <= ng1
2562 tmps = g1(ii);
2563 else
2564 tmps = g2(ii-ng1);
2565 end
2566
2567 if isfield( tmps, names{jj} )
2568 tmp = getfield( tmps, names{jj} );
2569 else
2570 tmp = [];
2571 end
2572
2573 tmp_gate = setfield( tmp_gate, names{jj}, tmp );
2574 end
2575
2576 g12(ii) = tmp_gate;
2577
2578 end
2579 end
2580
2581
2582 function clist = intLoadClist( dirname, data )
2583
2584 drill_flag = data.drill_flag;
2585
2586 clist = {};
2587
2588
2589 if exist( dirname, 'file' ) == 2
2590
2591
2592 [dir_,file_,ext_] = fileparts( dirname );
2593
2594 if strcmp( ext_, '.mat' )
2595 tmp = load( dirname );
2596
2597
2598 if isstruct( tmp ) && isfield( tmp, 'clist' );
2599 clist = tmp.clist;
2600 else
2601 clist = tmp;
2602 end
2603 elseif strcmp( ext_, '.csv' )
2604 clist = intLoadCSV( dirname );
2605 else
2606 error( 'Loading files must be either .mat or .csv' );
2607 end
2608
2609 else
2610 dirname = fixDir( dirname );
2611
2612 if ~exist( dirname, 'dir' )
2613 error( ['Directory ', dirname, 'does not exist.' ] );
2614 else
2615 if drill_flag
2616 clist = intRecLoad( {}, dirname, 0 );
2617 else
2618 contentsD = dir( [dirname, 'xy*'] );
2619
2620 nc = numel( contentsD );
2621
2622 if nc == 0
2623
2624 filename = [dirname,'clist.mat'];
2625 if exist( filename, 'file' );
2626 clist = load( filename );
2627 clist.filename = GetFullPath(filename);
2628 else
2629 error([ 'Can''t find file ', filename] );
2630 end
2631
2632 else
2633
2634 filename = [dirname,'header.mat'];
2635 if exist(filename ) == 2
2636 header = load( filename );
2637 else
2638 header = [];
2639 end
2640
2641 counter = 0;
2642 for ii = 1:nc
2643 dirname_xy = fixDir( [dirname,contentsD(ii).name] );
2644
2645 filename = [dirname_xy,'clist.mat' ];
2646
2647 if exist( filename, 'file' )
2648 counter = counter+1;
2649 tmp = load( filename );
2650
2651 tmp.filename = GetFullPath(filename);
2652
2653 clist{counter} = tmp;
2654
2655 if ~isempty(header)
2656 clist{counter}.name = header.xydata(ii).geneName;
2657 end
2658 end
2659 end
2660 end
2661 end
2662 end
2663 end
2664 end
2665
2666
2667 function [clist,count] = intRecLoad( clist, dirname, count )
2668
2669 dirname = fixDir( dirname );
2670
2671 contents = dir( dirname );
2672
2673 nc = numel( contents );
2674
2675 for ii = 1:nc
2676
2677 if contents( ii).isdir && contents(ii).name(1) ~= '.'
2678 dirname_ii = [dirname,contents(ii).name];
2679
2680 [clist,count] = intRecLoad( clist, dirname_ii, count );
2681 elseif strcmp( contents(ii).name, 'clist.mat' )
2682 count = count+1;
2683 name = [dirname,'clist.mat'];
2684 disp( ['Loading ',name] );
2685 tmp = load( name );
2686
2687 if isstruct( tmp ) && isfield( tmp, 'clist' );
2688 clist{1,count} = tmp.clist;
2689 else
2690 clist{1,count} = tmp;
2691 end
2692
2693 end
2694 end
2695
2696
2697 end
2698
2699
2700 function clistS = intSqueeze( varargin )
2701
2702 if nargin == 1
2703 clistS = {};
2704 clistS = intSqueeze( clistS, varargin{1} );
2705 elseif nargin == 2
2706 clistS = varargin{1};
2707 clist = varargin{2};
2708
2709 nc = numel( clist );
2710
2711 for ii = 1:nc
2712
2713 if iscell( clist{ii} )
2714 clistS = intSqueeze( clistS, clist{ii} );
2715 elseif isstruct( clist{ii} )
2716 clistS = { clistS{:}, clist{ii} }';
2717 else
2718 error( 'Not a clist' );
2719 end
2720 end
2721 end
2722 end
2723
2724
2725 function clistS = intExpand( varargin )
2726
2727 if nargin == 1
2728 clistS = {};
2729 clistS = intExpand( clistS, varargin{1} );
2730 elseif nargin == 2
2731 clistS = varargin{1};
2732 clist = varargin{2};
2733
2734 nc = numel( clist );
2735
2736 for ii = 1:nc
2737
2738 if iscell( clist{ii} )
2739 clistS = intExpand( clistS, clist{ii} );
2740 elseif isstruct( clist{ii} )
2741 clistS = { clistS{:}, clist{ii} };
2742 else
2743 error( 'Not a clist' );
2744 end
2745 end
2746 end
2747 end
2748
2749
2750 function output = intGet( clist, g_ind )
2751
2752 output = [];
2753 if iscell( clist )
2754 nc = numel(clist);
2755
2756 for ii = 1:nc
2757 output = [output; intGet( clist{ii}, g_ind )];
2758 end
2759 else
2760 output = clist.data(:,g_ind);
2761 end
2762
2763 end
2764
2765
2766 function output = intGet3D( clist, g3D_ind )
2767
2768 output = [];
2769 if iscell( clist )
2770 nc = numel(clist);
2771
2772 for ii = 1:nc
2773 output = cat(1, output, intGet3D( clist{ii}, g3D_ind ));
2774 end
2775 else
2776 output = clist.data3D(:,g3D_ind,:);
2777 end
2778
2779 end
2780
2781
2782 function x = intGetData( clist, data, ind, units )
2783
2784 if ~exist( 'units', 'var' )
2785 units = 1;
2786 end
2787
2788 if data.time_flag
2789 x = clist.data3D(:,ind,:);
2790 x = x(:);
2791
2792 x = intApplyGate3D( x, clist );
2793 else
2794 x = clist.data(:,ind);
2795 end
2796
2797 x = units*x;
2798
2799 end
2800
2801
2802 function [x,x0,flagger,n] = intGetDataC( clist, data, wind )
2803
2804 tmp = intGetData( clist, data, data.ind(wind(1)), data.units(wind(1)) );
2805
2806 n_ind = numel( wind );
2807
2808 x = nan( [numel(tmp),n_ind] );
2809 x0 = nan( [numel(tmp),n_ind] );
2810
2811 for ii = 1:n_ind
2812 tmp = intGetData( clist, data, data.ind(wind(ii)), data.units(wind(ii)) );
2813
2814 x0(:,ii) = tmp;
2815
2816 if data.log_flag(wind(ii))
2817 tmp = log(tmp);
2818 end
2819
2820 x(:,ii) = tmp;
2821 end
2822
2823 [~,flagger] = fixVals( sum(x,2) );
2824
2825 x = x(flagger,:);
2826 x0 = x0(flagger,:);
2827
2828 n= sum(flagger);
2829 end
2830
2831
2832
2833 function x = intApplyGate3D( x, clist )
2834
2835 ss = size(clist.data3D);
2836 inflag = true(ss(1)*ss(3),1);
2837
2838 if isfield( clist, 'gate3D' ) && ~isempty ('gate3D.clist')
2839 for ii = 1:numel(clist.gate3D)
2840 if numel(clist.gate3D(ii).ind) == 2
2841
2842 tmp1 = clist.data3D(:,clist.gate3D(ii).ind(1),:);
2843 tmp2 = clist.data3D(:,clist.gate3D(ii).ind(2),:);
2844
2845 inflag = and(inflag, inpolygon( tmp1(:), tmp2(:), ...
2846 clist.gate3D(ii).xx(:,1), clist.gate3D(ii).xx(:,2) ));
2847 else
2848 tmp = clist.data3D(:,clist.gate3D(ii).ind,:);
2849 inflag = and( inflag, and( tmp(:) > min(clist.gate3D(ii).x), tmp(:) < max(clist.gate3D(ii).x)));
2850 end
2851 end
2852 end
2853
2854 x = x(inflag);
2855
2856 end
2857
2858
2859 function clist = intDoAddT( clist )
2860
2861 if iscell( clist )
2862 nc = numel(clist);
2863
2864 for ii = 1:nc
2865 clist{ii} = intDoAddT( clist{ii} );
2866 end
2867 elseif isstruct( clist )
2868 ss = size( clist.data3D );
2869
2870 [~,tmp] = gateTool( clist, 'get', 2, 'time' );
2871
2872 if numel(ss) == 2
2873 ss(3) = 1;
2874 end
2875 len = reshape( ~isnan(squeeze(tmp)),[ss(1),ss(3)]);
2876 age = cumsum( len, 2 );
2877 age(~len) = nan;
2878
2879 age_rel = age;
2880 age_rel = age./(max(age,[],2)*ones([1,size(age,2)]));
2881
2882 time = ones([ss(1),1])*(1:ss(3));
2883
2884 clist = gateTool( clist, 'add3D', time, 'Time (Frames)' );
2885 clist = gateTool( clist, 'add3D', age, 'Age (Frames)' );
2886 clist = gateTool( clist, 'add3D', age_rel, 'Relative Age' );
2887 else
2888 error( 'Internal error. not clist' );
2889 end
2890
2891 end
2892
2893
2894 function clist = intClear( clist, ind )
2895
2896 if iscell( clist )
2897 nc = numel(clist);
2898
2899 for ii = 1:nc
2900 clist{ii} = intClear( clist{ii}, ind );
2901 end
2902 elseif isstruct( clist )
2903 clist = gateStrip( clist, ind );
2904 end
2905
2906 end
2907
2908
2909 function intcsv( clist, data );
2910
2911
2912 filename = data.export_filename;
2913
2914 disp( 'Warning: All lists contained in clist will be stripped (ungated data removed) and merged (multiple lists combined) before xls export.');
2915
2916
2917 if ~data.time_flag
2918 clist = gateTool( clist, 'strip', 'skip3D' );
2919 clist = gateTool( clist, 'merge', 'skip3D' );
2920
2921 tmp1 = num2cell( clist.data );
2922 tmp2 = reshape( clist.def, [1,numel(clist.def)] );
2923
2924 tmp = cat(1,tmp2,tmp1);
2925 else
2926 clist = gateTool( clist, 'strip');
2927 clist = gateTool( clist, 'merge');
2928
2929 if isfield( clist, 'data3D' )
2930 if ~isfield( data, 'export_index' ) || isempty( clist.data3D ) || isempty( data.export_index )
2931 error( 'Need an export index to export data3D' );
2932 elseif ~(0<data.export_index) && data.export_index<=size(clist.data3D,2)
2933 error( 'Index outside the range of allowed indices for data3D' );
2934 else
2935 tmp = squeeze( clist.data3D(:,data.export_index,:) );
2936 end
2937 else
2938 error( 'No data3D field.' );
2939 end
2940 end
2941
2942 if data.which_export_flag == 1
2943 csvwrite2( filename, tmp );
2944 else
2945 disp( 'Warning: This function only works if excel is installed. Complain to matlab (ie mathworks) not me.' );
2946
2947 xlswrite( filename, tmp );
2948 end
2949
2950 end
2951
2952
2953 function csvwrite2( filename, data )
2954
2955
2956 cellflag = iscell( data );
2957
2958 nn = size( data );
2959
2960 fid = fopen(filename, 'w') ;
2961
2962 if fid
2963 for ii = 1:nn(1)
2964 for jj = 1:nn(2)
2965
2966 if cellflag
2967 tmp = data{ii,jj};
2968 else
2969 tmp = data(ii,jj);
2970 end
2971
2972 if ischar( tmp )
2973 fprintf(fid, '%s', tmp);
2974 elseif isnumeric( tmp )
2975 if numel( tmp ) == 1
2976 fprintf(fid, '%e', tmp);
2977 else
2978 error( 'No nonscalar allowed in csv.' );
2979 end
2980 else
2981 error( 'un recognized type in csv.' );
2982 end
2983
2984 if jj ~= nn(2);
2985 fprintf(fid, '%c', ',' );
2986 end
2987 end
2988 fprintf(fid, '\n');
2989 end
2990 fclose(fid) ;
2991 end
2992 end
2993
2994
2995
2996 function clist = intFixDef3D( clist );
2997
2998
2999 if isstruct( clist )
3000
3001 if ~isfield( clist, 'data' ) || ~isfield( clist, 'def' )
3002 disp( 'Trying to convert structure to clist.' )
3003
3004 fieldnames_ = fieldnames( clist )';
3005 tmp = { 'Cell ID',fieldnames_{:}};
3006
3007 ntmp = numel( tmp );
3008
3009
3010
3011
3012
3013
3014 def = tmp;
3015 clist_conv.def = def;
3016
3017 nc = numel( clist );
3018
3019 if nc == 1
3020 ncc = numel( getfield( clist, fieldnames_{1} ) );
3021 else
3022 ncc = nc;
3023 end
3024
3025 clist_conv.data = nan( [ncc,ntmp] );
3026 clist_conv.data(:,1) = 1:ncc;
3027
3028 for ii = 2:ntmp
3029 if nc ~= 1
3030 tmp_ = drill( clist, fieldnames_{ii-1} );
3031 else
3032 tmp_ = getfield( clist, fieldnames_{ii-1} );
3033 end
3034
3035 if isnumeric( tmp_ )
3036 clist_conv.data(:,ii) = tmp_;
3037 end
3038
3039 end
3040
3041 clist = clist_conv;
3042 end
3043
3044 if isfield( clist, 'def3d' )
3045 clist.def3D = clist.def3d;
3046 clist = rmfield( clist, 'def3d' );
3047 end
3048
3049
3050 if ~isempty( clist )
3051 if isfield( clist, 'def' )
3052 clist.def = intRemoveNumDef( clist.def );
3053 end
3054 if isfield( clist, 'def3D' )
3055 clist.def3D = intRemoveNumDef( clist.def3D );
3056 end
3057 end
3058
3059 elseif iscell( clist )
3060 nc = numel( clist );
3061 for ii = 1:nc
3062 clist{ii} = intFixDef3D( clist{ii} );
3063 end
3064 end
3065
3066
3067
3068 end
3069
3070
3071 function def = intRemoveNumDef( def )
3072 nd = numel( def );
3073
3074 tmp = def{1};
3075 tmp = tmp(tmp~=' ' );
3076 if numel( tmp ) > 1 && strcmp( tmp(1:2), '1:' )
3077 for ii = 1:nd
3078 ind = find( def{ii} == ':', 1, 'last' );
3079 if ~isempty(ind)
3080 if all(ismember(def{ii}(1:ind),'0123456789 :' ))
3081 def{ii} = def{ii}(ind+1:end);
3082 ind = find( def{ii}~=' ',1, 'first');
3083 if ~isempty( ind )
3084 def{ii} = def{ii}(ind:end);
3085 end
3086 end
3087 end
3088 end
3089 end
3090 end
3091
3092
3093 function intSaveClist( data )
3094
3095 clist = data.clist;
3096
3097 if isstruct( clist )
3098 save( data.save_name, '-struct', 'clist' );
3099 else
3100 save( data.save_name, 'clist' );
3101 end
3102
3103 end
3104
3105
3106 function intShowKS( data )
3107 if isfield( data, 'stat' )
3108
3109 ns = numel( data.stat );
3110
3111 pp = nan( [ns,ns] );
3112 dd = nan( [ns,ns] );
3113 for ii = 1:ns
3114 for jj = 1:ii
3115 [dd_,pp_] = kstest2( data.stat(ii).x, data.stat(jj).x );
3116
3117 pp(ii,jj) = pp_;
3118 pp(jj,ii) = pp_;
3119
3120 dd(ii,jj) = dd_;
3121 dd(jj,ii) = dd_;
3122 end
3123 end
3124
3125 figure;
3126 subplot( 1,2,1);
3127 imagesc( pp );
3128 colormap default;
3129 set( gca, 'Ytick', 1:ns )
3130 set( gca, 'Yticklabels', {data.stat.name0} )
3131 set( gca, 'Xtick', 1:ns )
3132 set( gca, 'Xticklabels', {data.stat.name0} )
3133 set( gca, 'XTickLabelRotation', 90 )
3134 axis equal tight
3135 title( 'K-S P value' );
3136 colorbar
3137 caxis([0,1]);
3138
3139 subplot( 1,2,2);
3140 imagesc( dd );
3141 colormap default;
3142 set( gca, 'Ytick', 1:ns )
3143 set( gca, 'Yticklabels', {data.stat.name0} )
3144 set( gca, 'Xtick', 1:ns )
3145 set( gca, 'Xticklabels', {data.stat.name0} )
3146 set( gca, 'XTickLabelRotation', 90 )
3147 axis equal tight
3148 title( 'Statistically Distinct' );
3149 colorbar
3150 caxis([0,1]);
3151
3152
3153 end
3154 end
3155
3156
3157
3158 function clist = intLoadCSV( name )
3159
3160 fileptr = fopen( name );
3161
3162 if ~fileptr
3163 error( ['Can''t load file: ',name] );
3164 end
3165
3166 str = fgets( fileptr );
3167
3168 def = textscan(str,'%s','Delimiter',',');
3169 def = def{1}';
3170
3171 nd = numel( def );
3172
3173 for ii = 1:nd
3174 def{ii} = [num2str(ii),' : ',def{ii}];
3175 end
3176
3177 clist.def = def;
3178
3179 wflag = true;
3180
3181 data = [];
3182
3183 while wflag
3184
3185 str = fgets( fileptr );
3186
3187 if isnumeric( str ) && str == -1
3188 wflag = false;
3189 else
3190
3191 ent = textscan(str,'%s','Delimiter',',');
3192 ent = ent{1};
3193 ent = cellfun( @str2num,ent )';
3194
3195 data = [data;ent];
3196 end
3197
3198 end
3199
3200 clist.data = data;
3201
3202 fclose( fileptr );
3203
3204 end
3205
3206
3207 function File = GetFullPath(File, Style)
3208
3209
3210
3211
3212
3213
3214
3215
3216
3217
3218
3219
3220
3221
3222
3223
3224
3225
3226
3227
3228
3229
3230
3231
3232
3233
3234
3235
3236
3237
3238
3239
3240
3241
3242
3243
3244
3245
3246
3247
3248
3249
3250
3251
3252
3253
3254
3255
3256
3257
3258
3259
3260
3261
3262
3263
3264
3265
3266
3267
3268
3269
3270
3271
3272
3273
3274
3275
3276
3277
3278
3279
3280
3281
3282
3283
3284
3285
3286
3287
3288
3289
3290
3291
3292
3293
3294
3295
3296
3297
3298
3299
3300
3301
3302
3303
3304 if nargin < 2
3305 Style = 'auto';
3306 end
3307
3308
3309
3310
3311 if isa(File, 'cell')
3312 for iC = 1:numel(File)
3313 File{iC} = GetFullPath(File{iC}, Style);
3314 end
3315 return;
3316 end
3317
3318
3319 isWIN = strncmpi(computer, 'PC', 2);
3320 MAX_PATH = 260;
3321
3322
3323 persistent hasDataRead
3324 if isempty(hasDataRead)
3325
3326
3327
3328
3329
3330
3331
3332
3333
3334
3335
3336
3337 hasDataRead = ~isempty(which('dataread'));
3338 end
3339
3340 if isempty(File)
3341 if ischar(File) || isnumeric(File)
3342 File = cd;
3343 return;
3344 else
3345 error(['JSimon:', mfilename, ':BadTypeInput1'], ...
3346 ['*** ', mfilename, ': Input must be a string or cell string']);
3347 end
3348 end
3349
3350 if ischar(File) == 0
3351 error(['JSimon:', mfilename, ':BadTypeInput1'], ...
3352 ['*** ', mfilename, ': Input must be a string or cell string']);
3353 end
3354
3355 if isWIN
3356 FSep = '\';
3357 File = strrep(File, '/', FSep);
3358
3359
3360 if strncmp(File, '\\?\', 4)
3361 if strncmpi(File, '\\?\UNC\', 8)
3362 File = ['\', File(7:length(File))];
3363 else
3364 File = File(5:length(File));
3365 end
3366 end
3367
3368 isUNC = strncmp(File, '\\', 2);
3369 FileLen = length(File);
3370 if isUNC == 0
3371
3372 ThePath = cd;
3373 if File(1) == FSep
3374 if strncmp(ThePath, '\\', 2)
3375 sepInd = strfind(ThePath, '\');
3376 ThePath = ThePath(1:sepInd(4));
3377 else
3378 ThePath = ThePath(1:3);
3379 end
3380 end
3381
3382 if FileLen < 2 || File(2) ~= ':'
3383 if ThePath(length(ThePath)) ~= FSep
3384 if File(1) ~= FSep
3385 File = [ThePath, FSep, File];
3386 else
3387 File = [ThePath, File];
3388 end
3389 else
3390 if File(1) ~= FSep
3391 File = [ThePath, File];
3392 else
3393 ThePath(length(ThePath)) = [];
3394 File = [ThePath, File];
3395 end
3396 end
3397
3398 elseif FileLen == 2 && File(2) == ':'
3399
3400
3401
3402 if strncmpi(ThePath, File, 2)
3403 File = ThePath;
3404 else
3405 try
3406 File = cd(cd(File));
3407 catch
3408 if exist(File, 'dir')
3409 rethrow(lasterror);
3410 else
3411 File = [File, FSep];
3412 end
3413 end
3414 end
3415 end
3416 end
3417
3418 else
3419 FSep = '/';
3420 File = strrep(File, '\', FSep);
3421
3422 if strcmp(File, '~') || strncmp(File, '~/', 2)
3423 HomeDir = getenv('HOME');
3424 if ~isempty(HomeDir)
3425 File(1) = [];
3426 File = [HomeDir, File];
3427 end
3428
3429 elseif strncmpi(File, FSep, 1) == 0
3430
3431 ThePath = cd;
3432 if ThePath(length(ThePath)) == FSep
3433 File = [ThePath, File];
3434 else
3435 File = [ThePath, FSep, File];
3436 end
3437 end
3438 end
3439
3440
3441
3442 if ~isempty(strfind(File, [FSep, '.']))
3443 if isWIN
3444 if strncmp(File, '\\', 2)
3445 index = strfind(File, '\');
3446 if length(index) < 4
3447 return;
3448 end
3449 Drive = File(1:index(4));
3450 File(1:index(4)) = [];
3451 else
3452 Drive = File(1:3);
3453 File(1:3) = [];
3454 end
3455 else
3456 isUNC = false;
3457 Drive = FSep;
3458 File(1) = [];
3459 end
3460
3461 hasTrailFSep = (File(length(File)) == FSep);
3462 if hasTrailFSep
3463 File(length(File)) = [];
3464 end
3465
3466 if hasDataRead
3467 if isWIN
3468 C = dataread('string', File, '%s', 'delimiter', '\\');
3469 else
3470 C = dataread('string', File, '%s', 'delimiter', FSep);
3471 end
3472 else
3473 C = regexp(File, FSep, 'split');
3474 end
3475
3476
3477 C(strcmp(C, '.')) = [];
3478
3479
3480 R = 1:length(C);
3481 for dd = reshape(find(strcmp(C, '..')), 1, [])
3482 index = find(R == dd);
3483 R(index) = [];
3484 if index > 1
3485 R(index - 1) = [];
3486 end
3487 end
3488
3489 if isempty(R)
3490 File = Drive;
3491 if isUNC && ~hasTrailFSep
3492 File(length(File)) = [];
3493 end
3494
3495 elseif isWIN
3496
3497
3498 File = sprintf('%s\\', C{R});
3499 if hasTrailFSep
3500 File = [Drive, File];
3501 else
3502 File = [Drive, File(1:length(File) - 1)];
3503 end
3504
3505 else
3506 File = [Drive, sprintf('%s/', C{R})];
3507 if ~hasTrailFSep
3508 File(length(File)) = [];
3509 end
3510 end
3511 end
3512
3513
3514 if isWIN
3515 if ~ischar(Style)
3516 error(['JSimon:', mfilename, ':BadTypeInput2'], ...
3517 ['*** ', mfilename, ': Input must be a string or cell string']);
3518 end
3519
3520 if (strncmpi(Style, 'a', 1) && length(File) >= MAX_PATH) || ...
3521 strncmpi(Style, 'f', 1)
3522
3523
3524 if strncmp(File, '\\', 2)
3525 File = ['\\?\UNC', File(2:end)];
3526 else
3527 File = ['\\?\', File];
3528 end
3529 end
3530 end
3531 end
3532 