jnkather

% (c) Jakob Nikolas Kather 2015
% contact: http://www.kather.me

% aim is to create a 1D-stairstep array, i.e. transform 
% 1 2 3 4 to 
% 1 1 1 2 2 2 3 3 3 4 4 4

matrix = 1:4
newSize = 3
step_matrix = reshape(repmat(matrix,newSize,1),1,[])

jnkather

% (c) Jakob Nikolas Kather 2015
% contact: http://www.kather.me

function rgb = hex2rgb(hexString)
	if size(hexString,2) ~= 6
		error('invalid input: not 6 characters');
	else
		r = double(hex2dec(hexString(1:2)))/255;
		g = double(hex2dec(hexString(3:4)))/255;
		b = double(hex2dec(hexString(5:6)))/255;

jnkather

% (c) Jakob Nikolas Kather 2015
% contact: http://www.kather.me

% this code uses a histological image and performs the following steps
% - convert to optical density (OD) space (ref: Ruifrok et al. http://www.ncbi.nlm.nih.gov/pubmed/11531144)
% - plot image pixels in OD space
% - color pixels according to their original color
% this script can be used to visualize the color distribution of a given histological image

% get source image

jnkather

% (c) Jakob Nikolas Kather 2015
% contact: http://www.kather.me

% this function plots a plane through the points x,y,z in a 3D plot

function normal = plotPlane(x,y,z)

    % plot triangle through x y z, optional
    % fill3([x(1),y(1),z(1)],[x(2),y(2),z(2)],[x(3),y(3),z(3)],'b') 

jnkather

#!/bin/bash
cd ~/BitBucket/master-thesis/
pdflatex main.tex
bibtex main
pdflatex main.tex
echo '######### last run #########'
pdflatex main.tex
open main.pdf
open main.log
exit

jnkather

pandoc --filter pandoc-citeproc -s main.md -o main.pdf --bibliography=library.bib

jnkather

% JN Kather, 2015
% Show the RGB gamut in CIELAB space
figure();
[X,Y,Z] = meshgrid(linspace(0,1,25)); 
colors = ([X(:),Y(:),Z(:)]);
colorsLAB = rgb2lab(colors);
scatter3(colorsLAB(:,1),colorsLAB(:,2),colorsLAB(:,3),100,colors,'filled');

jnkather

% JN Kather, 2015
% Show a CIELAB color cube composed of 25^3 balls
% note: Matlab CIELAB colorspace goes approx. from -108 to +100 as measured
% with: colors = rgb2lab(jet(100)); min(colors(:)), max(colors(:))
figure();
[X,Y,Z] = meshgrid(linspace(-108,100,15)); 
colors = lab2rgb([double(X(:)),double(Y(:)),double(Z(:))]);
scatter3(X(:),Y(:),Z(:),100,colors,'filled');
xlabel('L'); ylabel('a'); zlabel('b');
axis equal tight

jnkather

% JN Kather 2015
% calculate distance from a given point for a cloud of points, 2D

% cloud of points
Pts = rand(500,2); 

% calculate distance from P(px|py)
px = 0.5; py = 0.5
distance = sqrt((Pts(:,1)-px).^2 + (Pts(:,2)-py).^2);

jnkather

% JN Kather 2015
% calculate distance from a given point for a cloud of points, 3D

% cloud of points
Pts = rand(10000,3); 

% calculate distance from P(px|py|pz)
px = 0.5; py = 0.5; pz = 0.5;
distance = sqrt( (Pts(:,1)-px).^2 + ...
                 (Pts(:,2)-py).^2 + ...