I used below code to create two movies of histographs in Matlab:
h1 = figure
hold on
vid = VideoWriter('graph.avi');open(vid);
for t=1:time
figure(h1);
cla
hist(eighsum(t,:),40)
currFrame = getframe(h1);
writeVideo(vid,currFrame);
end
close(vid);
and
h2 = figure
hold on
video = VideoWriter('graphh.avi');open(video);
sizeclu = cell(1,size(clustersize,2));
for i = 1:numel(sizeclu)
sizeclu{i} = [clustersize{:,i}];
figure(h2);
cla
hist(sizeclu{i})
currFrame = getframe(h2); % gets only figure 2
writeVideo(video,currFrame);
end
close(video);
I want numbers below 1 don't be shown in the histogram. How can I do that?
do:
[counts,centers] = hist(eighsum(t,:),40);
centers(counts < 1) = [];
counts(counts < 1) = [];
bar(centers,counts);
Related
I have 30 heatmap subplots. How could I present these subplots as an animation or a movie (i.e. one heatmap each 0.5 seconds)?
The subplots are obtained with the following code:
var = {'GeneX','GeneY','GeneZ'};
syms x y z S
alpha_x = 3.9e-2;
beta_x = 6.1;
z_x = 1.3e-5;
n_zx = 2.32;
alpha_y= 4.3e-2;
beta_y = 5.7;
x_y = 7.9e-4;
n_xy = n_zx;
delta_y = 1.05;
x_z = 12e-2;
n_xz = n_zx;
y_z = 11e-3;
n_yz = n_zx;
delta_z = 0.2;
ACDC_X = (alpha_x+beta_x*S)/(1+S+(z/z_x)^n_zx)-x;
ACDC_Y = (alpha_y+beta_y*S)/(1+S+(x/x_y)^n_xy)-delta_y*y;
ACDC_Z = 1/(1+(x/x_z)^n_xz+(y/y_z)^n_yz)-delta_z*z;
ACDCsys_div = [ ACDC_X, ACDC_Y, ACDC_Z ];
J = jacobian(ACDCsys_div,[x;y;z]);
Jsolnew(x,y,z,S) = [J];
%%Construction of the coordinates as a matrix
A = load('matlab.mat','unnamed');% import data from directory
a2 = struct2array(A);% coordinates of the equilibrium point.
numofGraphs = 80;
bx = length(a2(1,1:numofGraphs));
%% Construction of the heatmaps
figure;
hmapax = ceil(sqrt(bx));
for kk = 1:bx %bnx %All bin windows = iteration
JacACDCnew(:,:,kk) = Jsolnew(a2(1,kk),a2(2,kk),a2(3,kk),a2(4,kk));
ACDC_HmapJnew = double(JacACDCnew(:,:,kk));
subplot(hmapax,hmapax,kk);%
heatmap(var,var,ACDC_HmapJnew,'ColorScaling','log');
S = a2(4,kk);
title(['Jac','s=',num2str(S)]);
end
Consider the following example:
function q56130816
% Load some data:
frames = imread('https://i.stack.imgur.com/03kN8.gif');
frames(frames > 1) = 2;
% Create subplots:
figure('WindowState','maximized'); subplot(2,4,1);
for ind1 = 1:8
subplot(2,4,ind1);
imagesc(frames(:,:,1,ind1)); axis image; axis off;
end
colormap([255 255 255; 188 188 188; 244 128 36]./255);
% Capture subplots as frames:
for ind1 = 8:-1:1
frameHolder(ind1) = getframe( subplot(2, 4 ,ind1) );
end
% Play as movie:
hF = figure(); movie(hF, frameHolder, 20, 2);
Which will turn:
Into:
As you can see, in the example above I used getframe, but frames can also be captured using print, as mentioned in the getframe docs. Frames can also be exported to a video file, as explained here.
Animation credit: frames were screen-captured from Johan Lindell's Codepen example.
I'm planning to plot a graph of velocity against time using matlab. The change of time is 0.05 and total time 15. When time change, the graph will change and save a figure of that. I had mat file which contained all the data for time and velocity.
E.g, t=0, v=0, plot and save, t=0.05, v=1, plot and save until t=15.
I tried to use v=v+1 (which acts like i++) but failed to read the value of v in 2nd row. Any other method to do so?
Thank You.
The code is
i = 001
dt = t(2,1) - t(1,1);
k = dt*(i-1);
filename1 = 'front_data';
matFileName = sprintf('%s.mat', filename1);
matData = load(matFileName);
t = matData.time;
fv = matData.front_velocity;
fig = figure%('visible', 'off');
s = t(1,1);
fv = fv(1,1);
lot (s,fv,'*')
pic_filename = sprintf('front_data%02d.jpeg', k);
print(fig,pic_filename,'-djpeg')
istart = 002
iend = 301
for i = istart:iend
k = dt*(i-1);
t = t+dt
filename1 = 'front_data';
matFileName = sprintf('%s.mat', filename1);
matData = load(matFileName);
t = matData.time;
fv = matData.front_velocity;
v = fv(1,1);
v = v+1;
h = figure
axis([0 15 0 0.6])
plot(t,v,'*')
pic_filename = sprintf('front_data%02d.jpeg', k);
print(h,pic_filename,'-djpeg')
end
And the example I refer is the [https://www.mathworks.com/matlabcentral/answers/110632-how-to-increment-a-variable]
I reduced your example to the essential parts.
istart = 2;
iend = 301;
counter=istart;
%load data
% filename1 = 'front_data';
% matFileName = sprintf('%s.mat', filename1);
% matData = load(matFileName);
% t = matData.time;
% fv = matData.front_velocity;
%for demonstaration
t=0:.05:15;
fv=rand(size(t));
for i = istart:iend
%update
time = t(istart:counter);
values = fv(istart:counter);
%plot
plot(time,values,'*')
%increase index
counter=counter+1;
end
As you are loading always the same data in the loop you can do it once outside the loop, and for plotting you just update the length of your vector to be plotted. You could also just append the new value to the actual list.
I am trying to reconstruct an image using the projections from the Neutron image scanner. I am using the following code. I am not able to obtain a meaningful reconstructed image.
Can anybody advise me on where I am going wrong.
much appreciated,
Vani
filename = strcat(' Z:\NIST_Data\2016\SEPT\example reconstructed\carboxylic\carboxylic reconstructed part 3\Coral\',srcFiles(i).name);
I=imread(filename);
P = im2double(I);
if i == 1
array3d = P;
else
array3d = cat(3, array3d, P);
end
end
num = size(array3d,3);
for p = 1:num
PR = double(squeeze(array3d(p,:,:)));
[L,C]=size(PR);
w = [-pi : (2*pi)/L : pi-(2*pi)/L];
Filt = abs(sin(w));
Filt = Filt(1:463);
for i = 1:C,
IMG = fft(PR(:,i));
end
FiltIMG = IMG*Filt; %FiltIMG = filter (b, a, IMG);
% Remove any remaining imaginary parts
FIL = real(FiltIMG);
% filter the projections
%filtPR = projfilter(PR);
%filtPR = filterplus(PR);
filtPR = FIL;
THETA=0:180;
% figure out how big our picture is going to be.
n = size(filtPR,1);
sideSize = n;
% convert THETA to radians
th = (pi/180)*THETA;
% set up the image
m = length(THETA);
BPI = zeros(sideSize,sideSize);
% find the middle index of the projections
midindex = (n+1)/2;
% set up x and y matrices
x = 1:sideSize;
y = 1:sideSize;
[X,Y] = meshgrid(x,y);
xpr = X - (sideSize+1)/2;
ypr = Y - (sideSize+1)/2;
% loop over each projection
%figure
%colormap(jet)
%M = moviein(m);
for i = 1:m
tic
disp(['On angle ', num2str(THETA(i))]);
% figure out which projections to add to which spots
filtIndex = round(midindex + xpr*sin(th(i)) - ypr*cos(th(i)));
% if we are "in bounds" then add the point
BPIa = zeros(sideSize,sideSize);
spota = find((filtIndex > 0) & (filtIndex <= n));
newfiltIndex = filtIndex(spota);
BPIa(spota) = filtPR(newfiltIndex(:),i);
%keyboard
BPI = BPI + BPIa;
toc
%imagesc(BPI)
%M(:,i) = getframe;
%figure(2)
%plot(filtPR(:,i));
%keyboard
end
BPI = BPI./m;
h=figure
imagesc(BPI)
saveas(h,sprintf('filtsli-FIG%d.tif',p));end
Here is my code to project Velodyne points into the images:
cam = 2;
frame = 20;
% compute projection matrix velodyne->image plane
R_cam_to_rect = eye(4);
[P, Tr_velo_to_cam, R] = readCalibration('D:/Shared/training/calib/',frame,cam)
R_cam_to_rect(1:3,1:3) = R;
P_velo_to_img = P*R_cam_to_rect*Tr_velo_to_cam;
% load and display image
img = imread(sprintf('D:/Shared/training/image_2/%06d.png',frame));
fig = figure('Position',[20 100 size(img,2) size(img,1)]); axes('Position',[0 0 1 1]);
imshow(img); hold on;
% load velodyne points
fid = fopen(sprintf('D:/Shared/training/velodyne/%06d.bin',frame),'rb');
velo = fread(fid,[4 inf],'single')';
% remove every 5th point for display speed
velo = velo(1:5:end,:);
fclose(fid);
% remove all points behind image plane (approximation
idx = velo(:,1)<5;
velo(idx,:) = [];
% project to image plane (exclude luminance)
velo_img = project(velo(:,1:3),P_velo_to_img);
% plot points
cols = jet;
for i=1:size(velo_img,1)
col_idx = round(64*5/velo(i,1));
plot(velo_img(i,1),velo_img(i,2),'o','LineWidth',4,'MarkerSize',1,'Color',cols(col_idx,:));
where readCalibration function is defined as
function [P, Tr_velo_to_cam, R_cam_to_rect] = readCalibration(calib_dir,img_idx,cam)
% load 3x4 projection matrix
P = dlmread(sprintf('%s/%06d.txt',calib_dir,img_idx),' ',0,1);
Tr_velo_to_cam = P(6,:);
R_cam_to_rect = P(5,1:9);
P = P(cam+1,:);
P = reshape(P ,[4,3])';
Tr_velo_to_cam = reshape(Tr_velo_to_cam ,[3,4])';
R_cam_to_rect = reshape(R_cam_to_rect ,[3,3])';
end
But here is the result:
what is wrong with my code? I changed the "cam" variable from 0 to 3 and none of them worked. You can find a sample of Calibration file in this link:
How to understand KITTI camera calibration files
I fixed it by myself. here is the modification in readCalibration function:
Tr_velo_to_cam = P(6,:);
Tr_velo_to_cam = reshape(Tr_velo_to_cam ,[4,3])';
Tr_velo_to_cam = [Tr_velo_to_cam;0 0 0 1];
I'm writing the code in Matlab to find interest point using DoG in the image.
Here is the main.m:
imTest1 = rgb2gray(imread('1.jpg'));
imTest1 = double(imTest1);
sigma = 0.6;
k = 5;
thresh = 3;
[x1,y1,r1] = DoG(k,sigma,thresh,imTest1);
%get the interest points and show it on the image with its scale
figure(1);
imshow(imTest1,[]), hold on, scatter(y1,x1,r1,'r');
And the function DoG is:
function [x,y,r] = DoG(k,sigma,thresh,imTest)
x = []; y = []; r = [];
%suppose 5 levels of gaussian blur
for i = 1:k
g{i} = fspecial('gaussian',size(imTest),i*sigma);
end
%so 4 levels of DoG
for i = 1:k-1
d{i} = imfilter(imTest,g{i+1}-g{i});
end
%compare the current pixel in the image to the surrounding pixels (26 points),if it is the maxima/minima, this pixel will be a interest point
for i = 2:k-2
for m = 2:size(imTest,1)-1
for n = 2:size(imTest,2)-1
id = 1;
compare = zeros(1,27);
for ii = i-1:i+1
for mm = m-1:m+1
for nn = n-1:n+1
compare(id) = d{ii}(mm,nn);
id = id+1;
end
end
end
compare_max = max(compare);
compare_min = min(compare);
if (compare_max == d{i}(m,n) || compare_min == d{i}(m,n))
if (compare_min < -thresh || compare_max > thresh)
x = [x;m];
y = [y;n];
r = [r;abs(d{i}(m,n))];
end
end
end
end
end
end
So there's a gaussian function and the sigma i set is 0.6. After running the code, I find the position is not correct and the scales looks almost the same for all interest points. I think my code should work but actually the result is not. Anybody know what's the problem?