fixFlags

 fixFlags : fixes and initializes flags for superSeggerViewer.

   INPUT :
       FLAGS : previous flags
   OUTPUT : 
       FLAGS : fixed flags
 
 Copyright (C) 2016 Wiggins Lab 
 Written by Paul Wiggins, Stella Stylianidou, Connor Brennan.
 University of Washington, 2016
 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/>.

0001 function FLAGS = fixFlags(FLAGS)
0002 % fixFlags : fixes and initializes flags for superSeggerViewer.
0003 %
0004 %   INPUT :
0005 %       FLAGS : previous flags
0006 %   OUTPUT :
0007 %       FLAGS : fixed flags
0008 %
0009 % Copyright (C) 2016 Wiggins Lab
0010 % Written by Paul Wiggins, Stella Stylianidou, Connor Brennan.
0011 % University of Washington, 2016
0012 % This file is part of SuperSegger.
0013 %
0014 % SuperSegger is free software: you can redistribute it and/or modify
0015 % it under the terms of the GNU General Public License as published by
0016 % the Free Software Foundation, either version 3 of the License, or
0017 % (at your option) any later version.
0018 %
0019 % SuperSegger is distributed in the hope that it will be useful,
0020 % but WITHOUT ANY WARRANTY; without even the implied warranty of
0021 % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
0022 % GNU General Public License for more details.
0023 %
0024 % You should have received a copy of the GNU General Public License
0025 % along with SuperSegger.  If not, see <http://www.gnu.org/licenses/>.
0026 
0027 
0028 % displays legend for regions/ poles
0029 if ~isfield(FLAGS,'legend')
0030     FLAGS.legend = 1;
0031 end
0032 
0033 
0034 % displays cell numbers instead of region numbers
0035 if ~isfield(FLAGS,'cell_flag')
0036     FLAGS.cell_flag  = 1;
0037 end
0038 
0039 if ~isfield(FLAGS,'m_flag')
0040     FLAGS.m_flag  = 0;
0041 end
0042 
0043 % displays cell ids/regions ids
0044 if ~isfield(FLAGS,'ID_flag')
0045     FLAGS.ID_flag  = 0;
0046 end
0047 
0048 % tight - does not allow modification of segments
0049 if ~isfield(FLAGS,'T_flag')
0050     FLAGS.T_flag  = 0;
0051 end
0052 
0053 % shows region fills
0054 if ~isfield(FLAGS,'P_flag')
0055     FLAGS.P_flag  = 1;
0056 end
0057 
0058 % shows region outlines
0059 if ~isfield(FLAGS,'Outline_flag')
0060     FLAGS.Outline_flag  = 0;
0061 end
0062 
0063 % shows errors
0064 if ~isfield(FLAGS,'e_flag')
0065     FLAGS.e_flag  = 0;
0066 end
0067 
0068 % shows fluorescence channel given in f_flag
0069 if ~isfield(FLAGS,'f_flag')
0070     FLAGS.f_flag  = 0;
0071 end
0072 
0073 % shows composite image of all fluor channels found
0074 if ~isfield(FLAGS,'composite')
0075     FLAGS.composite  = 0;
0076 end
0077 
0078 % shows poles
0079 if ~isfield(FLAGS,'p_flag')
0080     FLAGS.p_flag  = 0;
0081 end
0082 
0083 % shows foci scores
0084 if ~isfield(FLAGS,'s_flag')
0085     FLAGS.s_flag  = 1;
0086 end
0087 
0088 
0089 if ~isfield(FLAGS,'c_flag')
0090     FLAGS.c_flag  = 1;
0091 end
0092 
0093 
0094 % shows filtered fluorescence
0095 if ~isfield(FLAGS,'filt')
0096     FLAGS.filt = 1;
0097 end
0098 
0099 % shows phase image or mask if it is 0
0100 if ~isfield(FLAGS, 'phase_flag');
0101     FLAGS.phase_flag = 1;
0102 end
0103 
0104 % modifies the transparency of the phase/mask - use as double from 0 - 1
0105 if ~isfield(FLAGS, 'phase_level');
0106     FLAGS.phase_level = 1;
0107 end
0108 
0109 % not used
0110 if ~isfield(FLAGS,'lyse_flag')
0111     FLAGS.lyse_flag = 0;
0112 end
0113 
0114 % shows regions scores
0115 if ~isfield(FLAGS,'regionScores')
0116     FLAGS.regionScores = 0;
0117 end
0118 
0119 % uses seg files
0120 if ~isfield(FLAGS,'useSegs')
0121     FLAGS.useSegs = 0;
0122 end
0123 
0124 % shows linking from frame to frame
0125 if ~isfield(FLAGS,'showLinks')
0126     FLAGS.showLinks = 0;
0127 end
0128 
0129 % shows linking with mothers
0130 if ~isfield(FLAGS,'showMothers')
0131     FLAGS.showMothers = 0;
0132 end
0133 
0134 % shows linking with daughters
0135 if ~isfield(FLAGS,'showDaughters')
0136     FLAGS.showDaughters = 0;
0137 end
0138 
0139 end