Description of segInfoCurv

0001 function seg_info = segsInfoCurv(segs_props, segs_props_tmp, regs_prop, regs_label,disk1)
0002 % segsInfoCurv : Calculates the properties of the segments used for segment scoring.
0003 % Uses the image curvature to calculate some of the properties.
0004 %
0005 % INPUT :
0006 %   segs_props : calculated segment properties
0007 %   segs_props_tmp : calculated segment properties tmp
0008 %   regs_prop : region properties
0009 %   regs_label : region labels
0010 %   disk1 : disk for dilating/eroding
0011 % OUTPUT :
0012 %   seg_info : array with parameters used for segment scoring
0013 %
0014 % Copyright (C) 2016 Wiggins Lab
0015 % Written by Paul Wiggins & Stella Stylianidou.
0016 % University of Washington, 2016
0017 % This file is part of SuperSegger.
0018 %
0019 % SuperSegger is free software: you can redistribute it and/or modify
0020 % it under the terms of the GNU General Public License as published by
0021 % the Free Software Foundation, either version 3 of the License, or
0022 % (at your option) any later version.
0023 %
0024 % SuperSegger is distributed in the hope that it will be useful,
0025 % but WITHOUT ANY WARRANTY; without even the implied warranty of
0026 % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
0027 % GNU General Public License for more details.
0028 %
0029 % You should have received a copy of the GNU General Public License
0030 % along with SuperSegger.  If not, see <http://www.gnu.org/licenses/>.
0031 
0032 
0033 nn = segs_props.Area;
0034 sim_ii = size(segs_props_tmp.phase);
0035 % mask_ii_out are the pixels around the segment so that a second d over
0036 % the segment can be computed.
0037 if nn>2
0038     mask_ii_end  = (compConn(segs_props_tmp.mask,4)==1);
0039     mask_ii_out  = xor(bwmorph( xor(segs_props_tmp.mask,mask_ii_end), 'dilate' ),segs_props_tmp.mask);
0040 elseif nn == 1
0041     mask_ii_out  = xor(bwmorph( segs_props_tmp.mask, 'dilate'),segs_props_tmp.mask);
0042 else
0043     mask_ii_out  = imdilate( segs_props_tmp.mask, disk1)-segs_props_tmp.mask;
0044     mask_ii_out  = and(mask_ii_out,(compConn(mask_ii_out,4)>0));
0045 end
0046 
0047 % seg_info(:,1) is the minimum phase intensity on the seg
0048 [seg_info(1),ind] = min(segs_props_tmp.phase(:).*double(segs_props_tmp.mask(:))+1e6*double(~segs_props_tmp.mask(:)));
0049 
0050 % seg_info(:,2) is the mean phase intensity on the seg
0051 seg_info(2) = mean(segs_props_tmp.phase(segs_props_tmp.mask));
0052 
0053 % seg_info(:,3) is area of the seg
0054 seg_info(3) = nn;
0055 
0056 % seg_info(:,4) is the mean second d of the phase normal to the seg
0057 seg_info(4) = mean(segs_props_tmp.phase(mask_ii_out)) - seg_info(2);
0058 
0059 % next we want to do some more calculation around the minimum phase
0060 % pixel. sub1 and sub2 are the indicies in the cropped image
0061 [sub1,sub2] = ind2sub(sim_ii,ind);
0062 % sub1_ and sub2_ are the indices in the whole image.
0063 %     sub1_ = sub1-1+yymin;
0064 %     sub2_ = sub2-1+xxmin;
0065 
0066 % calculate the local second d of the phase at the min pixel
0067 % normal to the seg and parallel to it.
0068 % min_pixel is the mask of the min pixel
0069 min_pixel = false(sim_ii);
0070 min_pixel(sub1,sub2) = true;
0071 % outline the min pixel
0072 min_pixel_out = bwmorph( min_pixel, 'dilate');
0073 % and mask/anti-mask it
0074 ii_min_para   = and(min_pixel_out,segs_props_tmp.mask);
0075 ii_min_norm   = xor(min_pixel_out,ii_min_para);
0076 
0077 % seg_info(:,5) is the second d of the phase normal to the seg at the
0078 % min pixel
0079 seg_info(5) = mean(segs_props_tmp.phase(ii_min_norm))-mean(segs_props_tmp.phase(ii_min_para));
0080 
0081 % seg_info(:,6) is the second d of the phase parallel to the seg at the
0082 % min pixel
0083 tmp_mask = xor(ii_min_para,min_pixel);
0084 seg_info(6) = mean(segs_props_tmp.phase(tmp_mask))-seg_info(1);
0085 
0086 if isnan(seg_info(6))
0087     disp([header,'NaN in seg_info!']);
0088 end
0089 
0090 % We also wish to add information about the neighboring regions. First we
0091 % have to determine what these regions are... ie the regs_label number
0092 % By construction, each seg touches two regions. Ind_reg is the vector
0093 % of the region indexes--after we eliminate '0'.
0094 uu = segs_props_tmp.regs_label(imdilate( segs_props_tmp.mask, disk1));
0095 ind_reg = unique(uu(logical(uu)));
0096 
0097 % seg_info(:,7) and seg_info(:,8) are the min and max area of the
0098 % neighboring regions
0099 seg_info(7)  = min( regs_prop(ind_reg(:)).Area);
0100 seg_info(8)  = max( regs_prop(ind_reg(:)).Area);
0101 
0102 % seg_info(:,9) and seg_info(:,10) are the min and max minor axis
0103 % length of the neighboring regions
0104 seg_info(9)  = min( regs_prop(ind_reg(:)).MinorAxisLength);
0105 seg_info(10) = max( regs_prop(ind_reg(:)).MinorAxisLength);
0106 
0107 % seg_info(:,11) and seg_info(:,12) are the min and max major axis
0108 % length of the neighboring regions
0109 seg_info(11) = min( regs_prop(ind_reg(:)).MajorAxisLength);
0110 seg_info(12) = max( regs_prop(ind_reg(:)).MajorAxisLength);
0111 
0112 % seg_info(:,11), seg_info(:,12), and seg_info(:,13) are the min
0113 % and max major axis length of the segment itself, including the
0114 % square of the major axis length... which would allow a non-
0115 % linarity in the length cutoff. No evidence that this helps...
0116 % just added it because I could.
0117 seg_info(13) = segs_props.MinorAxisLength;
0118 seg_info(14) = segs_props.MajorAxisLength;
0119 seg_info(15) = segs_props.MajorAxisLength^2;
0120 
0121 
0122 % Next we want to do some calculation looking at the size of
0123 % the regions, normal and parallel to the direction of the
0124 % segment. This is a bit computationally expensive, but worth
0125 % it I think.
0126 
0127 % Get size of the regions in local coords
0128 
0129 % This function computes the principal axes of the segment
0130 % mask. e1 is aligned with the major axis and e2 with the
0131 % minor axis and com is the center of mass.
0132 [e1,e2] = makeRegionAxisFast( segs_props.Orientation );
0133 
0134 % L1 is the length of the projection of the region on the
0135 % major axis and L2 is the lenght of the projection on the
0136 % minor axis.
0137 L1 = [0 0];
0138 L2 = [0 0];
0139 
0140 % Loop through the two regions
0141 
0142 
0143 for kk = 1:numel(ind_reg);
0144     % get a new cropping region for each region with 2 pix padding
0145     [xx_,yy_] = getBBpad(regs_prop(ind_reg(kk)).BoundingBox,segs_props_tmp.sim,2);
0146     
0147     % mask the region of interest
0148     kk_mask = (regs_label(yy_, xx_) == ind_reg(kk));
0149     
0150     % This function computes the projections lengths on e1 and e2.
0151     [L1(kk),L2(kk)] = makeRegionSize( kk_mask,e1,e2);
0152 end
0153 
0154 % seg_info(:,16) and seg_info(:,17) are the min and max Length of the
0155 % regions projected onto the major axis of the segment.
0156 seg_info(16) = max(L1); % max and min region length para to seg
0157 seg_info(17) = min(L1);
0158 % seg_info(:,16) and seg_info(:,17) are the min and max Length of the
0159 % regions projected onto the minor axis of the segment.
0160 seg_info(18) = max(L2); % max and min region length normal to seg
0161 seg_info(19) = min(L2);
0162 
0163 % put in the curvatures
0164 Cmaj = e1(1).^2.*segs_props.f_xx + 2*e1(1).*e1(2).*segs_props.f_xy + e1(2).^2.*segs_props.f_yy;
0165 Cmin = e2(1).^2.*segs_props.f_xx + 2*e2(1).*e2(2).*segs_props.f_xy + e2(2).^2.*segs_props.f_yy;
0166 
0167 seg_info(20) = segs_props.G;
0168 seg_info(21) = segs_props.G_;
0169 
0170 seg_info(22) = Cmaj;
0171 seg_info(23) = Cmin;
0172 
0173 seg_info(24) = segs_props.C1;
0174 seg_info(25) = segs_props.C2;
0175 
0176 
0177 end
segInfoCurv

PURPOSE

SYNOPSIS

DESCRIPTION

CROSS-REFERENCE INFORMATION

SOURCE CODE
