Lab Notebook: Estimating body height in ant locomotion

Contents

TODO

Changelog

Initialize

clear all; close all; clc
version

ans =

9.1.0.441655 (R2016b)

Import meta data

p.meta.filename  = ['G:/dropbox/todo/ant_impulse/dat/ant_metadata.xlsx'];
p.meta.sheetname  = 'Protokoll';

a = exist('exl');
if a == 0
    exl = dataset('XLSFile',p.meta.filename,...
        'Sheet','Protokoll','range','A5:DZ2425');
end

Subsetting

select tracked data (criteria: no stopping, no starting, gait cycle within capture window)

fil = (exl.W2014force ==  1 ) ;
% fil = (exl.W2014force ==  1 & (char(exl.ant)       == 'C') ) ;
sub1 = exl(fil,exl.Properties.VarNames);
n_sub1 = length(sub1);

Import data and calculate

% Kinematic data root
p.raw.kin    = 'G:/archive/dat/120901_digitalization/'; % data
einheit.kin = 10.^(-3); % units

% Error handling
err = [];

% results dataset
d = [];

for k = 1:n_sub1

    % display progress
    % disp([num2str(k),'/',num2str(n_sub1),'/',num2str(sum(err))]);

    % error handling
    try
        % Import kinematic data

        id = char(sub1.id(k));
        datadir = [p.raw.kin,id];

        % import center of origin
        clear xy0 xz0 n
        xy0   = impHedrickLab(datadir,id,'x0','txt');
        xz0   = impHedrickLab(datadir,id,'z0','txt');

        % number of data points
        n.kin = length(xy0);

        % only first row cotains relevant data
        xy0 = repmat(xy0(1,:),n.kin,1);
        xz0 = repmat(xz0(1,:),n.kin,1);

        % import petiolous marker
        b3  = impHedrickLab(datadir,id,'b3','txt') - xy0;
        b3z = impHedrickLab(datadir,id,'b3z','txt')- xz0;
        % average for x value, x in two planes
        b3(:,1) = mean([b3(:,1) b3z(:,1)],2);

        % import neck marker
        b2  = impHedrickLab(datadir,id,'b2','txt') - xy0;
        b2z = impHedrickLab(datadir,id,'b2z','txt')- xz0;
        % average for x value, x in two planes
        b2(:,1) = mean([b2(:,1) b2z(:,1)],2);


        % select data for one gait cycle (touchdown leg 2)
        cut.Gait = [sub1.td12(k):1:sub1.td22(k)];

        b3      = b3(cut.Gait,:);
        b3(:,3) = b3z(cut.Gait,2);

        b2      = b2(cut.Gait,:);
        b2(:,3) = b2z(cut.Gait,2);

        % estimate center of mass location
        b2b3(k,1)  = mean(norm_t(b2-b3));
        if strcmp(sub1.ant(k),'C')

for Cataglyphis: "This distance represents 5% (20%) of the length of the thorax." McMeeking, R. M.; Arzt, E. & Wehner, R. Cataglyphis desert ants improve their mobility by raising the gaster J. Theoret. Biol., 2012, 297, 17-25

        COM = b3 + (b2-b3)./repmat(norm_t(b2-b3),1,3).*b2b3(k,1).*0.2;

        elseif strcmp(sub1.ant(k),'F')

for Formica: "Marker B3 was located on average less than 0.3 mm away from the CoM." Reinhardt, L. & Blickhan, R. Level locomotion in wood ants: evidence for grounded running J. Exp. Biol., 2014, 217, 2358-2370 COM = b3;

        COM = b3 + (b2-b3)./repmat(norm_t(b2-b3),1,3).*0.3;

        end


        % allocate data
        d.COMheight(k,1)       = mean(COM(:,3)).*einheit.kin;
        d.Petiolousheight(k,1) = mean(b3(:,3)).*einheit.kin ;
        d.Neckheight(k,1)      = mean(b2(:,3)).*einheit.kin;
        d.FramesKin(k,1)       = n.kin;
        d.ant(k,1)             = sub1.ant(k);
        d.m(k,1)               = sub1.m(k);
        d.deg(k,1)             = sub1.deg(k);
        d.id{k,1}              = id;
        d.err(k,1)             = 0;

    catch me
        err(k) = 1;
        d.err(k,1) = 1;
    end
end

Errors

sub1.id(logical(err));
d.ant(isnan(d.COMheight));

Table summary

grpstats(dataset(d),{'ant','deg'},{'nanmean','nanmedian','nanstd'},...
    'DataVars','COMheight')

ans = 

             ant        deg    GroupCount    nanmean_COMheight
    C_-60    'C'        -60    45            0.0025814        
    C_-30    'C'        -30    45            0.0036085        
    C_0      'C'          0    45            0.0038155        
    C_30     'C'         30    45            0.0030433        
    C_60     'C'         60    45            0.0025091        
    F_-90    'F'        -90    42            0.0025737        
    F_-60    'F'        -60    45            0.0022442        
    F_-30    'F'        -30    45            0.0024738        
    F_0      'F'          0    45            0.0025671        
    F_30     'F'         30    45            0.0021281        
    F_60     'F'         60    45            0.0024673        
    F_90     'F'         90    15            0.0022549        


             nanmedian_COMheight    nanstd_COMheight
    C_-60    0.0023784              0.00065322      
    C_-30     0.003518              0.00043904      
    C_0      0.0038414              0.00068379      
    C_30     0.0030213              0.00043018      
    C_60     0.0024237              0.00047596      
    F_-90    0.0025883              0.00031913      
    F_-60    0.0021919              0.00024084      
    F_-30    0.0024724              0.00028236      
    F_0      0.0025029              0.00054191      
    F_30     0.0020584              0.00031102      
    F_60     0.0025194              0.00030705      
    F_90     0.0023294              0.00028427      

Plot boxplot

bh = boxplot(d.COMheight./einheit.kin,{d.ant,d.deg},'factorseparator',[1 1],...
    'labelverbosity','majorminor','medianstyle','line','notch','on',...
    'colorgroup',{d.ant},'boxstyle',...
    'outline','factordirection','list','boxstyle','outline',...
    'symbol','+k','jitter',0.5);
title('Draft for: Slope-dependent body height adjustments in ant locomotion')
xlabel({'Species';'Slope in deg'})
ylabel('COMheight in mm')
shg

From: Reinhardt, L. & Blickhan, R. Level locomotion in wood ants: evidence for grounded running J. Exp. Biol., 2014, 217, 2358-2370

From: Weihmann, T. & Blickhan, R. Comparing inclined locomotion in a ground-living and a climbing ant species: sagittal plane kinematics. J. Comp. Physiol. A Neuroethol. Sens. Neural. Behav. Physiol., 2009, 195, 1011-1020

Published with MATLAB® R2016b