Significant rewrite of superSeggerViewerGui and underlying code to wo…

…rk with multiple channels

Internal/intGetChannelNum.m

@@ -0,0 +1,17 @@
+function nnc = intGetChannelNum( data )
+%% comp number of fluor channels
+
+nc = numel(find(~cellfun('isempty',strfind(fieldnames(data),'fluor'))));
+nnc = 0;
+
+for jj = 1:nc
+
+    fluorName =  ['fluor',num2str(jj)];
+
+    if isfield( data, fluorName )
+        nnc = nnc + 1;
+    end
+
+end
+
+end

Internal/intMakeMinMax.m

@@ -0,0 +1,6 @@
+    function minmax = intMakeMinMax( im )
+        minner = medfilt2( im, [2,2], 'symmetric' );
+        maxxer = max( minner(:));
+        minner = min( minner(:));
+        minmax = [minner,maxxer];
+    end

Internal/intRange.m

@@ -0,0 +1,6 @@
+function ranger = intRange( im, CDFr )
+% put max and min in range
+
+ranger = [min( im ),max( im )];
+
+end

viz/doDrawCellOutlinePAW.m

@@ -0,0 +1,109 @@
+function doDrawCellOutlinePAW( data, channel, ids1, ids2)
+% Description : 
+%
+% Opens fig with outlines of cells drawn. The script currently allows
+% you to input two sets of cell IDs to be colored in blue (ids1) and red
+% (ids2). Currently any cells with IDs not listed in ids1 or ids2 will be
+% outlined in yellow. This is all customizable. If you wish to
+% change the colors, replace 'b' etc with the color of your choice. If you
+% do not want cells whose IDs are missing from the ID lists to be outlined, 
+% remove code in 'else' block. If you wish to send in additional id lists,
+% add ids3, etc to the line above, and ammend the if/else block.
+%
+% List of inputs:
+%
+% data: A loaded err.mat file for the image you want outlines drawn on
+% channel: The channel to draw outline on (1-phase, 2-fluor1)
+% ids1: IDs of cells you want outlined in one color (default: blue)
+% ids2: IDs of cells you want outlined in a second color (default: red)
+% 
+%
+% Copyright (C) 2016 Wiggins Lab
+% Written by Silas Boye Nissen, Connor Brennan, Stella Stylianidou.
+% University of Washington, 2016. Modified in 2018 by S Mangiameli and 
+% P. Wiggins.
+% This file is part of SuperSegger.
+%
+% SuperSegger is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% SuperSegger is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with SuperSegger.  If not, see <http://www.gnu.org/licenses/>.
+
+% Fill unset inputs
+if ~exist('ids1','var') || isempty( ids1 )
+    ids1 = [];
+end
+
+if ~exist('ids2','var') || isempty( ids2 )
+    ids2 = [];
+end
+
+
+
+
+
+
+
+% Draw outlines
+
+rl = data.regs.regs_label;
+ids = data.regs.ID;
+nc = max( rl(:) );
+
+props = regionprops( rl, 'PixelList' );
+
+% Sets color depending on cell ID
+for ii = 1:nc
+
+    id = ids(ii);
+
+    if ismember(id,ids1)
+        cc = 'b';
+    elseif ismember(id, ids2)
+        cc = 'r';
+    else
+        cc = 'y';
+    end
+
+    % Mask for current region
+    tmp = rl;
+    tmp(tmp ~= ii) = 0;
+
+    % Increase size of mask by 1 px and find boundary
+    se = strel('disk',1);
+    tmp2 = logical(imdilate(tmp,se));
+    [y,x] = find(tmp2 == 1);
+    k = boundary(x,y,1);
+
+
+    hold on;
+    skip = 1;
+    kk = k([1:skip:end]);
+    kk = kk([end-3:end,1:end,1:4]);
+
+    n = 1:numel(kk);
+    nn = 5:1:(numel(kk)-1);
+
+    % Interprets from pixel outline to smooth drawn outline
+    % xx = interp1( n, x(kk), nn,'spline' );
+    % yy = interp1( n, y(kk), nn,'spline' );
+
+    p = 0.1; %smaller value of p gives more smoothing
+    xx = fnval(csaps( n, x(kk),p), nn);
+    yy = fnval(csaps( n, y(kk),p), nn);
+
+
+    % Plots outline on phase image
+    plot( xx, yy, 'LineStyle','-','Color',cc,'LineWidth', .5 );
+
+end
+
+end

viz/doDrawCellOutlineSMM.m

@@ -0,0 +1,119 @@
+function doDrawCellOutlineSMM( data, channel, ids1, ids2)
+% Description : 
+%
+% Opens fig with outlines of cells drawn. The script currently allows
+% you to input two sets of cell IDs to be colored in blue (ids1) and red
+% (ids2). Currently any cells with IDs not listed in ids1 or ids2 will be
+% outlined in yellow. This is all customizable. If you wish to
+% change the colors, replace 'b' etc with the color of your choice. If you
+% do not want cells whose IDs are missing from the ID lists to be outlined, 
+% remove code in 'else' block. If you wish to send in additional id lists,
+% add ids3, etc to the line above, and ammend the if/else block.
+%
+% List of inputs:
+%
+% data: A loaded err.mat file for the image you want outlines drawn on
+% channel: The channel to draw outline on (1-phase, 2-fluor1)
+% ids1: IDs of cells you want outlined in one color (default: blue)
+% ids2: IDs of cells you want outlined in a second color (default: red)
+% 
+%
+% Copyright (C) 2016 Wiggins Lab
+% Written by Silas Boye Nissen, Connor Brennan, Stella Stylianidou.
+% University of Washington, 2016. Modified in 2018 by S Mangiameli and 
+% P. Wiggins.
+% This file is part of SuperSegger.
+%
+% SuperSegger is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% SuperSegger is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with SuperSegger.  If not, see <http://www.gnu.org/licenses/>.
+
+% Fill unset inputs
+if ~exist('ids1','var') || isempty( ids1 )
+    ids1 = [];
+end
+
+if ~exist('ids2','var') || isempty( ids2 )
+    ids2 = [];
+end
+
+if ~exist('channel','var') || isempty( channel )
+    channel = 1;
+end
+
+clf;
+
+% To draw outlines on the fluorescence image, replace phase with fluor
+if channel == 1
+    im = cat(3, ag(data.phase), ag(data.phase), ag(data.phase));
+elseif channel == 2
+    im = cat(3, ag(data.fluor1)*0, ag(data.fluor1), ag(data.fluor1)*0);
+elseif channel ==3
+    im = cat(3, ag(data.fluor2), ag(data.fluor2)*0, ag(data.fluor2)*0);
+end
+
+imshow( im, [] );
+hold on;
+
+rl = data.regs.regs_label;
+ids = data.regs.ID;
+nc = max( rl(:) );
+
+props = regionprops( rl, 'PixelList' );
+
+% Sets color depending on cell ID
+for ii = 1:nc
+
+    id = ids(ii);
+
+    if ismember(id,ids1)
+        cc = 'b';
+    elseif ismember(id, ids2)
+        cc = 'r';
+    else
+        cc = 'y';
+    end
+
+    % Mask for current region
+    tmp = rl;
+    tmp(tmp ~= ii) = 0;
+
+    % Increase size of mask by 1 px and find boundary
+    se = strel('disk',1);
+    tmp2 = logical(imdilate(tmp,se));
+    [y,x] = find(tmp2 == 1);
+    k = boundary(x,y,1);
+
+
+    hold on;
+    skip = 1;
+    kk = k([1:skip:end]);
+    kk = kk([end-3:end,1:end,1:4]);
+
+    n = 1:numel(kk);
+    nn = 5:1:(numel(kk)-1);
+
+    % Interprets from pixel outline to smooth drawn outline
+    % xx = interp1( n, x(kk), nn,'spline' );
+    % yy = interp1( n, y(kk), nn,'spline' );
+
+    p = 0.1; %smaller value of p gives more smoothing
+    xx = fnval(csaps( n, x(kk),p), nn);
+    yy = fnval(csaps( n, y(kk),p), nn);
+
+
+    % Plots outline on phase image
+    plot( xx, yy, 'LineStyle','-','Color',cc,'LineWidth', .5 );
+
+end
+
+end

viz/intMakeMultiChannel.m

@@ -0,0 +1,94 @@
+function im = intMakeMultiChannel( data, FLAGS, CONST, clist, nc )
+
+im = [];
+
+if (FLAGS.f_flag == 0  && ~FLAGS.composite ) || ...
+        (FLAGS.phase_flag( FLAGS.f_flag +1 ) && ~FLAGS.composite) ...
+        || (FLAGS.composite && FLAGS.include(1) );
+
+    if FLAGS.manual_lut(1) && ~isnan( FLAGS.lut_min(1) ) && ~isnan( FLAGS.lut_max(1))
+        minmax = [FLAGS.lut_min(1), FLAGS.lut_max(1)];
+    elseif FLAGS.gbl_auto(1) && isfield( clist, 'imRangeGlobal')  
+        minmax = clist.imRangeGlobal(:,1);
+    else
+        minmax = intMakeMinMax( data.phase );
+    end
+
+    im = comp( {data.phase, minmax, FLAGS.level(1)} );
+end
+
+% if you are in fluorescence mode (f_flag) draw the fluor channels
+if FLAGS.f_flag && CONST.view.falseColorFlag
+    ranger = FLAGS.f_flag;
+elseif FLAGS.composite
+   ranger = find(FLAGS.include(2:(nc+1)));
+elseif ~FLAGS.f_flag
+    ranger = [];
+else
+    ranger = FLAGS.f_flag;
+end
+
+for ii = ranger;
+
+    flName    =  ['fl',num2str(ii),'bg'];
+
+    filtName = ['fluor',num2str(ii),'_filtered'];
+
+    if FLAGS.filt(ii) && isfield( data, filtName);
+        flourName = filtName;
+    else
+        flourName = ['fluor',num2str(ii)];
+    end
+
+    im_tmp = data.(flourName);
+
+    if FLAGS.filt(ii)
+        minmax = intMakeMinMax( im_tmp );
+
+        if isfield( data, flName )     
+            minmax(1) = data.(flName);
+        end
+
+    elseif FLAGS.manual_lut(ii+1) && ~isnan( FLAGS.lut_min(ii+1) ) && ~isnan( FLAGS.lut_max(ii+1))
+        minmax = [FLAGS.lut_min(ii+1), FLAGS.lut_max(ii+1)];
+    elseif FLAGS.gbl_auto(ii+1) && isfield( clist, 'imRangeGlobal')
+        minmax = clist.imRangeGlobal(:,ii+1);
+    else
+        minmax = intMakeMinMax( im_tmp );
+
+        if isfield( data, flName )     
+            minmax(1) = data.(flName);
+        end
+
+    end
+
+    if CONST.view.falseColorFlag && FLAGS.f_flag
+        cc = jet(256);
+    else
+        cc = CONST.view.fluorColor{ii};
+    end
+
+
+    command = {im_tmp, cc, FLAGS.level(ii+1)};
+
+    if FLAGS.log_view(ii)
+        command = {command{:}, 'log'};
+    else
+        command = {command{:}, minmax };
+    end
+
+     im = comp( {im}, command );
+
+
+end
+
+
+
+
+
+
+
+
+
+
+end