Pass different files as parameters - circos

I have a few queries with regards to Circos plots.
I want to include a legend within the plot to indicate what does the different circles within the plot represent.
I want to rename the plot sub-routines in a way that when I run circos I can use param properties to pass the files and not hardcore them completely.
Mentioned below is my conf file for the plot generation.
And the code that I am using is this:
perl circos-0.66/bin/circos --conf circos-tutorials-0.66/tutorials/6/6/c1.conf -outputdir . -outputfile image.png
CONF:
<<include etc/colors_fonts_patterns.conf>>
<<include ideogram.conf>>
<<include t1.conf>>
show_ticks* = no
karyotype = karyotype/karyotype.human.txt
<image>
<<include etc/image.conf>>
</image>
chromosomes_units = 1000000
chromosomes_display_default = yes
chromosome_scale = 1
<plots>
type = text
color = black
label_font = bold
label_size = 24p
<plot>
file = text.Coordinates.txt
r1 = 1r
r0 = 1r
show_links = yes
link_dims = 0p,0p,70p,0p,10p
link_thickness = 2p
link_color = black
</plot>
<plot>
file = SNP_INDEL.txt
r1 = 0.9r
r0 = 0.8r
type = text
color = red
show_links = yes
link_dims = 4p,4p,8p,4p,4p
link_thickness = 2p
link_color = red
</plot>
<plot2>
file = Var_Class.txt
r1 = 0.7r
r0 = 0.6r
type = text
color = blue
show_links = yes
link_dims = 4p,4p,8p,4p,4p
link_thickness = 2p
link_color = blue
</plot>
<plot>
file = 1000G.txt
r1 = 0.5r
r0 = 0.4r
type = text
color = orange
show_links = yes
link_dims = 4p,4p,8p,4p,4p
link_thickness = 2p
link_color = orange
</plot>
<plot>
file = OMIM.txt
r1 = 0.3r
r0 = 0.2r
type = text
color = green
show_links = yes
link_dims = 4p,4p,8p,4p,4p
link_thickness = 2p
link_color = green
</plot>
</plots>

Related

Convert RGB Image to CMY

How to Convert RGB color Image or simply image to CMY color Image and Extract Each Component cyan (C) magenta (M) and yellow (Y) ?
My approach :-
I=imread('Capture2.PNG');
I3 = I;
I2 =I;
I1 = I;
I1(:,:,2:3)=0;
RED = I1;
I2(:,:,1:2) = 0;
BLUE = I2;
I3(:,:,1:3)=0;
GREEN=I3;
tic;
figure;imshow(RED);
figure;imshow(BLUE);
figure;imshow(GREEN);
c = 1.0-RED;
m = 1.0-GREEN;
y = 1.0-BLUE;
figure;imshow(c);
figure;imshow(m);
figure;imshow(y);
You can use makecform to create color-space transformation:
I=imread('Capture2.PNG');
cform = makecform('srgb2cmyk');
cmykI = applycform(I,cform);
BTW, in your question it seems like I is of type uint8 and therefore in range [0..255], to get the complement of each component, you need to subtract them from 255 and not 1.0:
c = 255-RED;
m = 255-GREEN;
y = 255-BLUE;

Dividing the image into equal number of parts in Matlab

I have lena image in Matlab. First I need to find the centroid C, and then divide the image into equal number of parts. I can calculate the centroid of the image but from that how can I divide the image into equal number of parts as shown below. Please anyone help me.
Thanks
Using poly2mask to create binary sectors and using the resulting sectors for indexing
Code:
im = imread('peppers.png');
r = 300;
out1 = ones(max(size(im,1),r*2)+2,max(size(im,2),r*2)+2,3).*255;
xoffset = floor((size(out1,2)-size(im,2))/2);
yoffset = floor((size(out1,1)-size(im,1))/2);
out1(yoffset:yoffset+size(im,1)-1,xoffset:xoffset+size(im,2)-1,:) = im(:,:,:);
im = out1;
cy = floor(size(im,1)/2);
cx = floor(size(im,2)/2);
figure;
imshow(uint8(im));
hold on
pos = [cx-r+1 cy-r+1 r*2 r*2];
rectangle('Position',pos,'Curvature',[1 1]);
x1 = [-r, 0, -r*cosd(45), -r*cosd(45); r, 0, r*cosd(45), r*cosd(45)]+cx+1;
y1 = [0, -r, -r*sind(45), r*sind(45); 0, r, r*sind(45), -r*sind(45)]+cy+1;
plot(x1,y1);
hold off
figure;
for i = 0:45:315
t = linspace(-i,-i-45,128);
x = [cx, cx+r*cosd(t), cx];
y = [cy, cy+r*sind(t), cy];
bw = poly2mask( x, y, size(im,1),size(im,2));
bw = repmat(bw,1,1,3);
out = ones(size(im,1),size(im,2),size(im,3)).*155;
out(bw) = im(bw);
subplot(2,4,(i/45)+1); imshow(uint8(out));
end;
Results:
Original Image
Partitions drawn over Original Image
Segments of the image
Update
for getting pixel values of the lines, by using Bresenham function from here
figure;
bw1 = zeros(size(im,1),size(im,2));
outmat = zeros(size(bw1));
[X,Y] = bresenham(cx+1-r,cy+1,cx+1+r,cy+1);
ind = sub2ind(size(outmat), Y, X);
outmat(ind) = 1;
[X,Y] = bresenham(cx+1,cy+1-r,cx+1,cy+1+r);
ind = sub2ind(size(outmat), Y, X);
outmat(ind) = 1;
[X,Y] = bresenham(cx+1-r*cosd(45),cy+1-r*sind(45),cx+1+r*cosd(45),cy+1+r*sind(45));
ind = sub2ind(size(outmat), Y, X);
outmat(ind) = 1;
[X,Y] = bresenham(cx+1-r*cosd(45),cy+1+r*sind(45),cx+1+r*cosd(45),cy+1-r*sind(45));
ind = sub2ind(size(outmat), Y, X);
outmat(ind) = 1;
se = strel('disk',5); %// change the '5' value to affect thickness of the line
outmat = imdilate(outmat,se);
outmat = repmat(boolean(outmat),1,1,3);
outmat1 = zeros(size(outmat));
outmat1(outmat) = im(outmat);
imshow(uint8(outmat1));
Pixel values under each lines
Check the following code. I just did it for a grayscale image. You can now change it to a color image as well. Check and pls confirm this is what you wanted.
clear all;
i = rgb2gray(imread('hestain.png'));
imshow(i);
cr = floor(size(i,1)/2);
cl = floor(size(i,2)/2);
r = min(cr, cl);
a = 90;
r1 = cr;
c1 = size(i,2);
v1=[c1 r1]-[cl cr];
i2 = zeros(size(i,1),size(i,2),ceil(360/a));
for ri = 1:size(i,1)
for ci = 1:size(i,2)
v2=[ci ri]-[cl cr];
a2 = mod(-atan2(v1(1)*v2(2)-v1(2)*v2(1), v1*v2'), 2*pi) * 180/pi;
d2 = pdist([ci ri; cl cr],'euclidean');
if d2<=r
if ceil(a2/a)==0
a2 =1;
end
i2(ri,ci,ceil(a2/a)) = i(ri,ci);
end
end
end
figure;
for i=1:360/a
subplot(2,180/a,i);
imshow(mat2gray(i2(:,:,i)));
end
Sample output:

LPR with MATLAB: how to find only one rectangle?

I am using the following code in MATLAB to find the rectangle containing a car's license plate:
clc
clear
close all
%Open Image
I = imread('plate_1.jpg');
figure, imshow(I);
%Gray Image
Ib = rgb2gray(I);
figure,
subplot(1,2,1), imshow(Ib);
%Enhancement
Ih = histeq(Ib);
subplot(1,2,2), imshow(Ih);
figure,
subplot(1,2,1), imhist(Ib);
subplot(1,2,2), imhist(Ih);
%Edge Detection
Ie = edge(Ih, 'sobel');
figure,
subplot(1,2,1), imshow(Ie);
%Dilation
Id = imdilate(Ie, strel('diamond', 1));
subplot(1,2,2), imshow(Id);
%Fill
If = imfill(Id, 'holes');
figure, imshow(If);
%Find Plate
[lab, n] = bwlabel(If);
regions = regionprops(lab, 'All');
regionsCount = size(regions, 1) ;
for i = 1:regionsCount
region = regions(i);
RectangleOfChoice = region.BoundingBox;
PlateExtent = region.Extent;
PlateStartX = fix(RectangleOfChoice(1));
PlateStartY = fix(RectangleOfChoice(2));
PlateWidth = fix(RectangleOfChoice(3));
PlateHeight = fix(RectangleOfChoice(4));
if PlateWidth >= PlateHeight*3 && PlateExtent >= 0.7
im2 = imcrop(I, RectangleOfChoice);
figure, imshow(im2);
end
end
Plates all have white backgrounds. Currently,I use the rectangles' ratio of width to height to select candidate regions for output. This gives the plate rectangle in addition to several other irrelevant ones in the case of a white car. What method can I use to get only one output: the license plate?
Also, I don't find a plate at all when I run the code on a black car. Maybe that's because the car's color is the same as the plate edge.
Are there any alternatives to edge detection to avoid this problem?
Try this !!!
I = imread('http://8pic.ir/images/88146564605446812704.jpg');
im=rgb2gray(I);
sigma=1;
f=zeros(128,128);
f(32:96,32:96)=255;
[g3, t3]=edge(im, 'canny', [0.04 0.10], sigma);
se=strel('rectangle', [1 1]);
BWimage=imerode(g3,se);
gg = imclearborder(BWimage,8);
bw = bwareaopen(gg,200);
gg1 = imclearborder(bw,26);
imshow(gg1);
%Dilation
Id = imdilate(gg1, strel('diamond', 1));
imshow(Id);
%Fill
If = imfill(Id, 'holes');
imshow(If);
%Find Plate
[lab, n] = bwlabel(If);
regions = regionprops(lab, 'All');
regionsCount = size(regions, 1) ;
for i = 1:regionsCount
region = regions(i);
RectangleOfChoice = region.BoundingBox;
PlateExtent = region.Extent;
PlateStartX = fix(RectangleOfChoice(1));
PlateStartY = fix(RectangleOfChoice(2));
PlateWidth = fix(RectangleOfChoice(3));
PlateHeight = fix(RectangleOfChoice(4));
if PlateWidth >= PlateHeight*1 && PlateExtent >= 0.7
im2 = imcrop(I, RectangleOfChoice);
%figure, imshow(I);
figure, imshow(im2);
end
end

Adding an image to an animation in matlab

I created a 3D stick man walking in matlab and I want to add an image as the floor that he is walking on. I'm not sure how to go about doing this. I looked at an example of someone adding an image as a background. That is kinda what I want but I want it to appear as the floor. I going to give the stick man a trajectory and make him walk across the floor. Can anyone point me in the right direction.
Ok now I got it thanks to Andrey.
clear all
cyl = UnitCylinder(2);
sph = UnitSphere(2);
% Head
L1 = 2;
Head = translate(scale(sph,L1/2, L1/2, L1/2),0,0,L1+4.5);
Head.facecolor = 'yellow';
%Shoulder
r2 = 0.3;
L2 = 3;
Shoulder = translate(rotateX(scale(cyl,r2/2,r2/2,L2/2),90),0,0,5);
Shoulder.facecolor = 'red';
%Left Upper Arm
w1_s = [-20:4:20 20:-4:-20];
r3 = 0.3;
L3 = 2;
Upper_Arm_left = translate(scale(cyl,r3/2,r3/2,L3/2),0,0,-L3/2);
Upper_Arm_left.facecolor = 'red';
%Right Upper Arm
Upper_Arm_right = translate(scale(cyl,r3/2,r3/2,L3/2),0,0,-L3/2);
Upper_Arm_right.facecolor = 'red';
%Left Forearm
w2_s = [-5:1:5 5:-1:-5];
L3_f = 2.5;
Fore_Arm_left = translate(scale(cyl,r3/2,r3/2,L3_f/2),0,0,-L3_f/2);
Fore_Arm_left.facecolor = 'red';
%Right Forearm
Fore_Arm_right = translate(scale(cyl,r3/2,r3/2,L3_f/2),0,0,-L3_f/2);
Fore_Arm_right.facecolor = 'red';
%Chest
r4 = 2;
L4 = 2;
Chest = translate(scale(cyl,r4/2,r4/2,L4/2),0, 0, 5-L4/2);
Chest.facecolor = 'yellow';
%Weist
r5 = 1;
L5 = 2;
Weist = translate(scale(cyl,r5/2,r5/2,L5/2),0, 0, 5-L4-L5/2);
Weist.facecolor = 'yellow';
%Hip
L6 = 1.5;
Hip = translate(rotateX(scale(cyl,r2/2,r2/2,L6/2),90),0,0,5-L4-L5-r2/2);
Hip.facecolor = 'green';
%Left Upper Leg
r7 = 0.4;
L7 = 2.5;
L71 = (L6/2+r7/2);
L72 = 5-L7/2-L4-L5;
Upper_Leg_left = translate(scale(cyl,r7/2,r7/2,L7/2),0,0,-L7/2);
Upper_Leg_left.facecolor = 'green';
%Right Upper Leg
Upper_Leg_right = translate(scale(cyl,r7/2,r7/2,L7/2),0,0,-L7/2);
Upper_Leg_right.facecolor = 'green';
%Left Lower Leg
L7_f = 3;
Lower_Leg_left = translate(scale(cyl,r7/2,r7/2,L7_f/2),0,0,-L7_f/2);
Lower_Leg_left.facecolor = 'green';
%Right Lower Leg
Lower_Leg_right = translate(scale(cyl,r7/2,r7/2,L7_f/2),0,0,-L7_f/2);
Lower_Leg_right.facecolor = 'green';
angle1 = 0;
angle2 = 0;
for i = 1:120
angle1 = w1_s(rem(i,length(w1_s))+1);
angle2 = w2_s(rem(i,length(w1_s))+1);
Arm_left = combine(translate(rotateY(Fore_Arm_left,angle2),0,0,-L3), Upper_Arm_left);
Arm_right = combine(translate(rotateY(Fore_Arm_right,-angle2),0,0,-L3), Upper_Arm_right);
Arm_left = translate(rotateY(Arm_left,angle1),0,-L2/2,(5-L3/2)+L3/2);
Arm_right = translate(rotateY(Arm_right,-angle1),0,L2/2,(5-L3/2)+L3/2);
Leg_left = combine(translate(rotateY(Lower_Leg_left,-angle2),0,0,-L7), Upper_Leg_left);
Leg_right = combine(translate(rotateY(Lower_Leg_right,angle2),0,0,-L7), Upper_Leg_right);
Leg_left = translate(rotateY(Leg_left,-angle1),0,-L71,L72+L7/2);
Leg_right = translate(rotateY(Leg_right,angle1),0,L71,L72+L7/2);
Upper_Body = combine(Head, Shoulder, Arm_left, Arm_right, Chest, Weist);
Lower_Body = combine(Hip, Leg_left, Leg_right);
walker = combine(Upper_Body, Lower_Body);
cla
img = imread('peppers.png');
[X,Y] = ndgrid([-10 10],[-10 10]);
zImage = [-5 -5; -5 -5];
surf(X,Y,zImage,'CData',img,'FaceColor','texturemap');
% view([1 1 1]);
hold on
view(3)
set(gca,'xlim',[-10 10],'ylim',[-10 10],'zlim',[-6 6]);
renderpatch(walker);
camlight
box on
drawnow
pause(0.04)
end
I want to get something like this floor but I don't know how to do it. This person used a .fig in their code.This is a piece of what they used.
F1 = open('background1.fig');
background_gca = gca;
F2 = figure(2);
.
.
.
clf(F2)
copyobj(background_gca,F2);
view([-40,25])
set(gca,'xlim',[-5 5],'ylim',[-5 5],'zlim',[0 10]);
renderpatch(walker);
camlight
box on
% axis off
drawnow;
You had a small syntax error:
First, you reversed z and y :
surf(xImage,zImage,yImage,...)
Also, you should think about surf as a surface. Thus, all z should be 0
img = imread('peppers.png');
[X,Y] = ndgrid([-5 5],[-5 5]);
zImage = [0 0; 0 0];
surf(X,Y,zImage,'CData',img,'FaceColor','texturemap');
view([1 1 1]);
make that background image as GIF image, it feels like man walking on floor
otherwise visit here, useful video:http://www.youtube.com/watch?v=Ztb6_kIkXb8

overlaping binary image on the RGB image MATLAB

i am able to overlap the binary image with the original RGB image. Through the following code.
inImage = imresize(imread('1.jpg'),0.25);
%imwrite(inImage,'original.jpg');
inImage = skyremoval(inImage);
greyImage = rgb2gray(inImage);
thresh1 = 200;
whiteLayer = greyImage > thresh1;
thresh2 = 125;
lightgreyLayer = greyImage > thresh2 & greyImage <= thresh1;
layer1 = whiteLayer*200;
layer2 = lightgreyLayer*125;
G = layer1 + layer2;
% figure,imshow(G);
se = strel('disk', 15);
Io = imopen(G, se);
figure,imshow(Io);
f = find(Io==0);
mask(:,:,1) = f; % For the red plane
% mask(:,:,2) = f; % For the green plane
% mask(:,:,3) = f; % For the blue plane
inImage(mask)=0;
I = inImage;
figure,imshow(I);
The following are the images.
Here.The first is the binary image derived from the original, second is the original and the third is the result after overlaping both binary and rgb images, by the code given above. As you can see the problem i am facing is that the part except road is cyan all i want is the part which is not road to be black. How can i do that?
Please alter my code if you can help. Thank you.
You don't need the find command, since you can index with a binary image.
Instead of
f = find(Io==0);
mask(:,:,1) = f; % For the red plane
% mask(:,:,2) = f; % For the green plane
% mask(:,:,3) = f; % For the blue plane
inImage(mask)=0;
I = inImage;
figure,imshow(I);
you can write
mask = repmat(Io==0,1,1,3); %# 1 wherever mask is false
I = inImage;
I(mask) = 0;
figure,imshow(I);

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