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Crystalline_ImgAnlys_ObjPara.m
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Crystalline_ImgAnlys_ObjPara.m
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function[R,CrystAnlys_R] = Crystalline_ImgAnlys_ObjPara(bw,bw_ch,I,img_name,Opt_ObjPara)
%Image object paramertisation.
% [R,CrystAnlys_R] = Crystalline_ImgAnlys_ObjPara(bw,bw_ch,img_name,Opt_ObjPara)
% function to extract object features related to size and shape. bw is a
% binary mask of all objects. bw_ch is a binary convex hull of all objects.
% I is the original 8bit image. Returns R with extracted mean size/shape
% descriptors and CrystAnlys_R containing size/shape descriptors of all
% objects.
% Initialise using Opt.T_init = true and Opt.numImg to create empty data
% table.
%
% Dependencies on FileExchange packages/functions:
% > CrystAnlys
% > Crystalline_PSD_Calc
%
% OPTIONS:
% 'PSD_calc_numThres' Minimum number of object for PSD calculations.
% 'T_init' Initialise empty table creation (requires
% numImg)
% 'numImg' Total number of images in dataset.
%
% additional OPTIONS related to CrystAnlys and Crystalline_PSD_Calc!
%
% Author
% --------
% Frederik Doerr, Aug 2020 (MATLAB R2020b)
% frederik.doerr(at)strath.ac.uk | CMAC (http://www.cmac.ac.uk/)
% Github: https://github.com/FrederikDoerr
R = table();
stats_bw = regionprops(bw,'Area','Perimeter');
bw_area = sum([stats_bw(:).Area]);
bw_perimeter = sum([stats_bw(:).Perimeter]);
stats_bw_ch = regionprops(bw_ch,'Area','Perimeter');
bw_ch_Area = sum([stats_bw_ch(:).Area]);
bw_ch_Perimeter = sum([stats_bw_ch(:).Perimeter]);
bw_siPa_Anlys_Area = nan;
bw_siPa_Anlys_Perimeter = nan;
%% Single Particle Analysis
R.area = sum(bw(:));
[~,numObj] = bwlabel(bw);
R.numObj = numObj;
R.x_Dim = size(bw,2);
R.y_Dim = size(bw,1);
R.bw_area = bw_area;
R.bw_perimeter = bw_perimeter;
R.bw_ch_Area = bw_ch_Area;
R.bw_ch_Perimeter = bw_ch_Perimeter;
R.bw_siPa_Anlys_Area = bw_siPa_Anlys_Area;
R.bw_siPa_Anlys_Perimeter = bw_siPa_Anlys_Perimeter;
CrystAnlys_Opts = struct();
CrystAnlys_Opts.path_MatFolder = Opt_ObjPara.path_FileExchange;
CrystAnlys_Opts.path_FileExchange = Opt_ObjPara.path_FileExchange;
CrystAnlys_Opts.path_ExportFolder = Opt_ObjPara.path_ExportFolder;
CrystAnlys_Opts.ID = img_name;
CrystAnlys_Opts.I = I;
CrystAnlys_Opts.Imagepixelsize = Opt_ObjPara.imagepixelsize;
CrystAnlys_Opts.CryFit_On = false;
CrystAnlys_Opts.PgFit_On = false;
CrystAnlys_Opts.Print_Control_On = Opt_ObjPara.Fig_Print_On;
CrystAnlys_Opts.Print_imwrite_On = false;
CrystAnlys_Opts.Obj_Print_Control_On = Opt_ObjPara.BW_Obj_Print_On;
addpath(Opt_ObjPara.path_FileExchange)
[CrystAnlys_R] = CrystAnlys(bw,CrystAnlys_Opts);
% Post calculation
R.d_eqSph_Mean = mean(CrystAnlys_R.d_eqSph);
R.d_eqSph_Std = std(CrystAnlys_R.d_eqSph);
R.d_eqSqu_Mean = mean(CrystAnlys_R.d_eqSqu);
R.d_eqSqu_Std = std(CrystAnlys_R.d_eqSqu);
RectFit_length = CrystAnlys_R.RectFit_length;
RectFit_width = CrystAnlys_R.RectFit_width;
R.d_RectFit_max_Mean = mean(RectFit_length);
R.d_RectFit_max_Std = std(RectFit_length);
R.d_RectFit_min_Mean = mean(RectFit_width);
R.d_RectFit_min_Std = std(RectFit_width);
R.area_Mean = mean(CrystAnlys_R.area).*(Opt_ObjPara.imagepixelsize)^2;
R.area_Std = std(CrystAnlys_R.area).*(Opt_ObjPara.imagepixelsize)^2;
R.area_Min = min(CrystAnlys_R.area).*(Opt_ObjPara.imagepixelsize)^2;
R.area_Max = max(CrystAnlys_R.area).*(Opt_ObjPara.imagepixelsize)^2;
R.areaCov_Mean = mean(CrystAnlys_R.area)/(R.x_Dim*R.y_Dim);
R.shapeFact_Mean = mean(CrystAnlys_R.AspectRatio_RectFit);
R.shapeFact_Std = std(CrystAnlys_R.AspectRatio_RectFit);
R.convexFact_Mean = mean(CrystAnlys_R.convexity_area_frac);
R.convexFact_Std = std(CrystAnlys_R.convexity_area_frac);
% % % % % % % % % % % % % % % % % % % % % % % % % % % % % % % % % % % %
%% Calculate PSD
if numObj > Opt_ObjPara.PSD_calc_numThres
addpath(Opt_ObjPara.path_FileExchange)
Opt_PSD_Calc = Opt_ObjPara;
Opt_PSD_Calc.Graph_name = sprintf('%s_PSD_Calc',img_name);
[~,~,~,~,R_PSD_Calc] = Crystalline_PSD_Calc(CrystAnlys_R.d_eqSph,Opt_PSD_Calc);
R.PSD_10 = R_PSD_Calc.PSD_0_d10;
R.PSD_50 = R_PSD_Calc.PSD_0_d50;
R.PSD_90 = R_PSD_Calc.PSD_0_d90;
R.PSD_span = R_PSD_Calc.PSD_0_Span;
else
R.PSD_10 = nan;
R.PSD_50 = nan;
R.PSD_90 = nan;
R.PSD_span = nan;
end
% Create empty table
if Opt_ObjPara.T_init
R = array2table(nan(Opt_ObjPara.numImg,length(R.Properties.VariableNames)),'VariableNames',R.Properties.VariableNames);
end