I am trying to implement code for the light speed labeling technique described in this article (I cannot use the Image Processing Toolbox): https://pdfs.semanticscholar.org/ef31/7c257603004d818ca1e2a2aa67d36d40147e.pdf (see section 2, page 7).
Here is my Matlab code for LSL equivalence construction (algorithm 14, step 2).
function [EQ,ERAi,nea] = LSL_equivalence(EQ,ERim1,RLCi,ERAim1,ERAi,NERi,nea,lImg)
% LSL_EQUIVALENCE build the associative table between er and ea
% GOAL: to create a Look Up Table to be applied to ERi to create EAi.
for er = 1:2:NERi % check segments one by one
% read the boundaries of each segment to obtain de relative labels of every agacent segment in the prev line
j0 = RLCi(er);
j1 = RLCi(er+1);
er0 = ERim1(j0+1); % label of the first segment
er1 = ERim1(j1+1); % the label of the last segment
% check label parity: segments are odd, background is even
% bitand([1 2 3 4 5],1) == [1 0 1 0 1]
if bitand(er0,1) == 0 % if er0 is even
er0 = er0 + 1;
end
if bitand(er1,1) == 0 % if er1 is even
er1 = er1 -1;
end
if er1 >= er0 % if there is an adjacency
ea = ERAim1(er0+1); % absolute label of the first segment
a = EQ(ea+1); % a is the ancestor (smallest label of the equivalence class)
for erk = (er0+2):2:er1
eak = ERAim1(erk+1);
ak = EQ(eak+1);
% min extraction and propagation
if a < ak
EQ(eak+1) = a;
else
a = ak;
EQ(ea+1) = a;
ea = eak;
end
end
ERAi(er+1) = a; % the global min of all ak ancestors
else % if there are no adjacent labels make a new label
nea = nea + 1;
ERAi(er+1) = nea;
end
end
end
I am having some trouble with indexes, as the pseudo code described in the article has indexes starting with 0 and Matlab works with 1. I have already found some C++ code in this Stack Overflow post Implementing LSL for Connected Component Labeling/Blob Extraction (I applied suggested changes) and also in this git repo https://github.com/prittt/YACCLAB/blob/master/include/labeling_lacassagne_2016_code.inc. I fail to see the differences.
Also, I'm having some trouble understanding what an equivalence class is (which is what goes in matrix EQ). Thanks ahead of time!
I realize this is coming a bit late, but I just put up a piece of code that is similar to what the light speed labeling algorithm does. I'll give a brief description of how I solved the index problem.
The first step of LSL is take each column of pixels and finds the start and stop positions of consecutively labeled pixels. You can do that in Matlab like this:
I = imread('text.png');
[rows,cols] = find(xor(I(2:end,:),I(1:end-1,:)));
What this gives you is the row and column of the start and stop position of each run of pixels in a column, except its non-inclusive indexing. By non-inclusive indexing I mean the indices of pixels runs from I(r(2*n-1),c(2*n-1)) to I(r(2*n)-1,c(2*n)) for each pixel run (n). You should note that the paper operates along rows where the above code operates along columns, but the same principle applies. You should also note that the above code does not cover the circumstance of labeled pixels on the edge of the image.
If you want to see a complete implementation, I posted my code on the Matlab File Exchange. I don't claim that it copies LSL exactly, but it works on many of the same principles.
https://www.mathworks.com/matlabcentral/fileexchange/70323-ftllabel?s_tid=prof_contriblnk
Related
Apologies for the long post but this takes a bit to explain. I'm trying to make a script that finds the longest linear portion of a plot. Sample data is in a csv file here, it is stress and strain data for calculating the shear modulus of 3D printed samples. The code I have so far is the following:
x_data = [];
y_data = [];
x_data = Data(:,1);
y_data = Data(:,2);
plot(x_data,y_data);
grid on;
answer1 = questdlg('Would you like to load last attempt''s numbers?');
switch answer1
case 'Yes'
[sim_slopes,reg_data] = regr_and_longest_part(new_x_data,new_y_data,str2num(answer2{3}),str2num(answer2{2}),K);
case 'No'
disp('Take a look at the plot, find a range estimate, and press any button to continue');
pause;
prompt = {'Eliminate values ABOVE this x-value:','Eliminate values BELOW this x-value:','Size of divisions on x-axis:','Factor for similarity of slopes:'};
dlg_title = 'Point elimination';
num_lines = 1;
defaultans = {'0','0','0','0.1'};
if isempty(answer2) < 1
defaultans = {answer2{1},answer2{2},answer2{3},answer2{4}};
end
answer2 = inputdlg(prompt,dlg_title,num_lines,defaultans);
uv_of_x_range = str2num(answer2{1});
lv_of_x_range = str2num(answer2{2});
x_div_size = str2num(answer2{3});
K = str2num(answer2{4});
close all;
iB = find(x_data > str2num(answer2{1}),1,'first');
iS = find(x_data > str2num(answer2{2}),1,'first');
new_x_data = x_data(iS:iB);
new_y_data = y_data(iS:iB);
[sim_slopes, reg_data] = regr_and_longest_part(new_x_data,new_y_data,str2num(answer2{3}),str2num(answer2{2}),K);
end
[longest_section0, Midx]= max(sim_slopes(:,4)-sim_slopes(:,3));
longest_section=1+longest_section0;
long_sec_x_data_start = x_div_size*(sim_slopes(Midx,3)-1)+lv_of_x_range;
long_sec_x_data_end = x_div_size*(sim_slopes(Midx,4)-1)+lv_of_x_range;
long_sec_x_data_start_idx=find(new_x_data >= long_sec_x_data_start,1,'first');
long_sec_x_data_end_idx=find(new_x_data >= long_sec_x_data_end,1,'first');
long_sec_x_data = new_x_data(long_sec_x_data_start_idx:long_sec_x_data_end_idx);
long_sec_y_data = new_y_data(long_sec_x_data_start_idx:long_sec_x_data_end_idx);
[b_long_sec, longes_section_reg_data] = robustfit(long_sec_x_data,long_sec_y_data);
plot(long_sec_x_data,b_long_sec(1)+b_long_sec(2)*long_sec_x_data,'LineWidth',3,'LineStyle',':','Color','k');
function [sim_slopes,reg_data] = regr_and_longest_part(x_points,y_points,x_div,lv,K)
reg_data = cell(1,3);
scatter(x_points,y_points,'.');
grid on;
hold on;
uv = lv+x_div;
ii=0;
while lv <= x_points(end)
if uv > x_points(end)
uv = x_points(end);
end
ii=ii+1;
indices = find(x_points>lv & x_points<uv);
temp_x_points = x_points((indices));
temp_y_points = y_points((indices));
if length(temp_x_points) <= 2
break;
end
[b,stats] = robustfit(temp_x_points,temp_y_points);
reg_data{ii,1} = b(1);
reg_data{ii,2} = b(2);
reg_data{ii,3} = length(indices);
plot(temp_x_points,b(1)+b(2)*temp_x_points,'LineWidth',2);
lv = lv+x_div;
uv = lv+x_div;
end
sim_slopes = NaN(length(reg_data),4);
sim_slopes(1,:) = [reg_data{1,1},0,1,1];
idx=1;
for ii=2:length(reg_data)
coff =sim_slopes(idx,1);
if abs(reg_data{ii,1}-coff) <= K*coff
C=zeros(ii-sim_slopes(idx,3)+1,1);
for kk=sim_slopes(idx,3):ii
C(kk)=reg_data{kk,1};
end
sim_slopes(idx,1)=mean(C);
sim_slopes(idx,2)=std(C);
sim_slopes(idx,4)=ii;
else
idx = idx + 1;
sim_slopes(idx,1)=reg_data{ii,1};
sim_slopes(idx,2)=0;
sim_slopes(idx,3)=ii;
sim_slopes(idx,4)=ii;
end
end
end
Apologies for the code not being well optimized, I'm still relatively new to MATLAB. I did not use derivatives because my data is relatively noisy and derivation might have made it worse.
I've managed to get the get the code to find the longest straight part of the plot by splitting the data up into sections called x_div_size then performing a robustfit on each section, the results of which are written into reg_data. The code then runs through reg_data and finds which lines have the most similar slopes, determined by the K factor, by calculating the average of the slopes in a section of the plot and makes a note of it in sim_slopes. It then finds the longest interval with max(sim_slopes(:,4)-sim_slopes(:,3)) and performs a regression on it to give the final answer.
The problem is that it will only consider the first straight portion that it comes across. When the data is plotted, it has a few parts where it seems straightest:
As an example, when I run the script with answer2 = {'0.2','0','0.0038','0.3'} I get the following, where the black line is the straightest part found by the code:
I have the following questions:
It's clear that from about x = 0.04 to x = 0.2 there is a long straight part and I'm not sure why the script is not finding it. Playing around with different values the script always seems to pick the first longest straight part, ignoring subsequent ones.
MATLAB complains that Warning: Iteration limit reached. because there are more than 50 regressions to perform. Is there a way to bypass this limit on robustfit?
When generating sim_slopes there might be section of the plot whose slope is too different from the average of the previous slopes so it gets marked as the end of a long section. But that section sometimes is sandwiched between several other sections on either side which instead have similar slopes. How would it be possible to tell the script to ignore one wayward section and to continue as if it falls within the tolerance allowed by the K value?
Take a look at the Douglas-Peucker algorithm. If you think of your (x,y) values as the vertices of an (open) polygon, this algorithm will simplify it for you, such that the largest distance from the simplified polygon to the original is smaller than some threshold you can choose. The simplified polygon will be the set of straight lines. Find the two vertices that are furthest apart, and you're done.
MATLAB has an implementation in the Mapping Toolbox called reducem. You might also find an implementation on the File Exchange (but be careful, there is also really bad code on there). Or, you can roll your own, it's quite a simple algorithm.
You can also try using the ischange function to detect changes in the intercept and slope of the data, and then extract the longest portion from that.
Using the sample data you provided, here is what I see from a basic attempt:
>> T = readtable('Data.csv');
>> T = rmmissing(T); % Remove rows with NaN
>> T = groupsummary(T,'Var1','mean'); % Average duplicate timestamps
>> [tf,slopes,intercepts] = ischange(T.mean_Var2, 'linear', 'SamplePoints', T.Var1); % find changes
>> plot(T.Var1, T.mean_Var2, T.Var1, slopes.*T.Var1 + intercepts)
which generates the plot
You should be able to extract the longest segment based on the indices given by find(tf).
You can also tune the parameters of ischange to get fewer or more segments. Adding the name-value pair 'MaxNumChanges' with a value of 4 or 5 produces more linear segments with a tighter fit to the curve, for example, which effectively removes the kink in the plot that you see.
I have a mathematical equation that describes a dynamical system as
The parameters are defined as follows
k1=1; S=1; Kd=1; p=2; tau=10; k2=1; ET=1; Km=1;
I coded the system as
y(1) = 1; % based on the y-axes starting point in the last figure
y(2) = y(1) + k1*S*Kd^p/(Kd^p + y(1)^p) - k2*ET*y(1)/(Km + y(1)); % to avoid errors
for t=1:100
y(t+1) = y(t+1) + (k1*S*Kd^p/(Kd^p + y(t)^p) - k2*ET*y(t+1)/(Km + y(t+1)));
end
plot(y);
Note that I did not use tau=10 for simplicity and instead used a delayed version by 1 instead of 10 (because I am not sure how to insert a delay of 10)
And obtained the following result
However, I need to obtain this
Can anyone help me rectify the mistake in my code?
Thanking you in advance.
If we assume that for Y(t) = 0 for t < 0 then you're code could be modified to produce a similar plot. However, it looks like the plot you are looking to generate uses different initial conditions. If you're just looking to measure Tc then it appears that the signal stabilizes with the period you're looking for.
k1=1; S=1; Kd=1; p=2; tau=10; k2=1; ET=1; Km=1;
% time step size (tau MUST be divisible by dt to ensure proper array indexing)
dt = 0.01;
% time series
t = -10:dt:100;
% initialize y to all zeros so that y(t)=0 for all t<0 (initial condition)
y = zeros(size(t));
% Find starting and ending indexes to iterate from t=0 to t=100-dt
idx0 = find(t == 0);
idx1 = numel(t)-1;
% initial condition y(0) = 1
y(idx0) = 1;
for n = idx0:idx1
% The indexing used here ensures the following equivalences.
% y(n+1) = y(t+dt)
% y(n) = y(t)
% y(n - round(tau/dt)) = y(t-tau)
%
% Note that (y(t+dt)-y(t))/dt is approximately y'(t)
% Solving for y(t+dt) we get the following formula
y(n+1) = y(n) + dt*((k1*S*Kd^p/(Kd^p + y(n - round(tau/dt))^p) - k2*ET*y(n)/(Km + y(n))));
end
% plot y(t) for t > 0
plot(t(t>0),y(t>0));
Result
Seeing as things stabilize we can take the values in one of the periods and use those for the initial conditions and we get.
Edit: To elaborate, the function contains a delay of 10 which means that instead of just a single initial condition at y(0), we also need to initialize all values from t=-10 to 0. In the code posted in this answer I arbitrarily assumed that y(t) = 0 for t < 0 and y(0) = 1 because I don't know otherwise. Once we run the code and see that the signal becomes periodic we can borrow the values from one of these periods to use those as the initial conditions.
From the diagram you posted we can use our intuition to guess that, before time 0, the signal probably looks something like the region highlighted in the figure below.
If, rather than using zero to initialize y at y < 0, we copy the values in the red highlighted region, then we get a plot that is more like what you desire.
To get the plot shown above I ran the script once, then found the indices in y for the part I wanted to use as initial conditions, then copied those into a new array.
init_cond = y(7004:8004);
Then I changed script to use this array as the initial condition and changed the initial y values to
y = zeros(size(t));
y(1:1001) = init_cond;
and ran the modified script again.
Edit 2: The built-in function dde23 appears to be applicable for your problem. To see an example run the command edit ddex1 in the command window.
I have edited a code that i found online that helps me draw points somehow distributed on a graph based on the minimum distance between them
This is the code that i have so far
x(1)=rand(1)*1000; %Random coordinates of the first point
y(1)=rand(1)*1000;
minAllowableDistance = 30; %IF THIS IS TOO BIG, THE LOOP DOES NOT END
numberOfPoints = 300; % Number of points equivalent to the number of sites
keeperX = x(1); % Initialize first point
keeperY = y(1);
counter = 2;
for k = 2 : numberOfPoints %Dropping another point, and checking if it can be positioned
done=0;
trial_counter=1;
while (done~=1)
x(k)=rand(1)*1000;
y(k)=rand(1)*1000;
thisX = x(k); % Get a trial point.
thisY = y(k);
% See how far is is away from existing keeper points.
distances = sqrt((thisX-keeperX).^2 + (thisY - keeperY).^2);
minDistance = min(distances);
if minDistance >= minAllowableDistance
keeperX(k) = thisX;
keeperY(k) = thisY;
done=1;
trial_counter=trial_counter+1;
counter = counter + 1;
end
if (trial_counter>2)
done=1;
end
end
end
end
So this code is working fine, but sometimes matlab is freezing if the points are above 600. The problem is full , and no more points are added so matlab is doing the work over and over. So i need to find a way when the trial_counter is larger than 2, for the point to find a space that is empty and settle there.
The trial_counter is used to drop a point if it doesn't fit on the third time.
Thank you
Since trial_counter=trial_counter+1; is only called inside if minDistance >= minAllowableDistance, you will easily enter an infinite loop if minDistance < minAllowableDistance (e.g. if your existing points are quite closely packed).
How you do this depends on what your limitations are, but if you're looking at integer points in a set range, one possibility is to keep the points as a binary image, and use bwdist to work out the distance transform, then pick an acceptable point. So each iteration would be (where BW is your stored "image"/2D binary matrix where 1 is the selected points):
D = bwdist(BW);
maybe_points = find(D>minAllowableDistance); % list of possible locations
n = randi(length(maybe_points)); % pick one location
BW(maybe_points(n))=1; % add it to your matrix
(then add some checking such that if you can't find any allowable points the loop quits)
I have the following Markov chain:
This chain shows the states of the Spaceship, which is in the asteroid belt: S1 - is serviceable, S2 - is broken. 0.12 - the probability of destroying the Spaceship by a collision with an asteroid. 0.88 - the probability of that a collision will not be critical. Need to find the probability of a serviceable condition of the ship after the third collision.
Analytical solution showed the response - 0.681. But it is necessary to solve this problem by simulation method using any modeling tool (MATLAB Simulink, AnyLogic, Scilab, etc.).
Do you know what components should be used to simulate this process in Simulink or any other simulation environment? Any examples or links.
First, we know the three step probability transition matrix contains the answer (0.6815).
% MATLAB R2019a
P = [0.88 0.12;
0 1];
P3 = P*P*P
P(1,1) % 0.6815
Approach 1: Requires Econometrics Toolbox
This approach uses the dtmc() and simulate() functions.
First, create the Discrete Time Markov Chain (DTMC) with the probability transition matrix, P, and using dtmc().
mc = dtmc(P); % Create the DTMC
numSteps = 3; % Number of collisions
You can get one sample path easily using simulate(). Pay attention to how you specify the initial conditions.
% One Sample Path
rng(8675309) % for reproducibility
X = simulate(mc,numSteps,'X0',[1 0])
% Multiple Sample Paths
numSamplePaths = 3;
X = simulate(mc,numSteps,'X0',[numSamplePaths 0]) % returns a 4 x 3 matrix
The first row is the X0 row for the starting state (initial condition) of the DTMC. The second row is the state after 1 transition (X1). Thus, the fourth row is the state after 3 transitions (collisions).
% 50000 Sample Paths
rng(8675309) % for reproducibility
k = 50000;
X = simulate(mc,numSteps,'X0',[k 0]); % returns a 4 x 50000 matrix
prob_survive_3collisions = sum(X(end,:)==1)/k % 0.6800
We can bootstrap a 95% Confidence Interval on the mean probability to survive 3 collisions to get 0.6814 ± 0.00069221, or rather, [0.6807 0.6821], which contains the result.
numTrials = 40;
ProbSurvive_3collisions = zeros(numTrials,1);
for trial = 1:numTrials
Xtrial = simulate(mc,numSteps,'X0',[k 0]);
ProbSurvive_3collisions(trial) = sum(Xtrial(end,:)==1)/k;
end
% Mean +/- Halfwidth
alpha = 0.05;
mean_prob_survive_3collisions = mean(ProbSurvive_3collisions)
hw = tinv(1-(0.5*alpha), numTrials-1)*(std(ProbSurvive_3collisions)/sqrt(numTrials))
ci95 = [mean_prob_survive_3collisions-hw mean_prob_survive_3collisions+hw]
maxNumCollisions = 10;
numSamplePaths = 50000;
ProbSurvive = zeros(maxNumCollisions,1);
for numCollisions = 1:maxNumCollisions
Xc = simulate(mc,numCollisions,'X0',[numSamplePaths 0]);
ProbSurvive(numCollisions) = sum(Xc(end,:)==1)/numSamplePaths;
end
For a more complex system you'll want to use Stateflow or SimEvents, but for this simple example all you need is a single Unit Delay block (output = 0 => S1, output = 1 => S2), with a Switch block, a Random block, and some comparison blocks to construct the logic determining the next value of the state.
Presumably you must execute the simulation a (very) large number of times and average the results to get a statistically significant output.
You'll need to change the "seed" of the random generator each time you run the simulation.
This can be done by setting the seed to be "now" (or something similar to that).
Alternatively you could quite easily vectorize the model so that you only need to execute it once.
If you want to simulate this, it is fairly easy in matlab:
servicable = 1;
t = 0;
while servicable =1
t = t+1;
servicable = rand()<=0.88
end
Now t represents the amount of steps before the ship is broken.
Wrap this in a for loop and you can do as many simulations as you like.
Note that this can actually give you the distribution, if you want to know it after 3 times, simply add && t<3 to the while condition.
Suppose I have a vector J of jump sizes and an initial starting point X_0. Also I have boundaries 0, B (assume 0 < X_0 < B). I want to do a random walk where X_i = [min(X_{i-1} + J_i,B)]^+. (positive part). Basically if it goes over a boundary, it is made equal to the boundary. Anyone know a vectorized way to do this? The current way I am doing it consists of doing cumsums and then finding places where it violates a condition, and then starting from there and repeating the cumsum calculation, etc until I find that I stop violating the boundaries. It works when the boundaries are rarely hit, but if they are hit all the time, it basically becomes a for loop.
In the code below, I am doing this across many samples. To 'fix' the ones that go out of the boundary, I have to loop through the samples to check...(don't think there is a vectorized 'find')
% X_init is a row vector describing initial resource values to use for
% each sample
% J is matrix where each col is a sequence of Jumps (columns = sample #)
% In this code the jumps are subtracted, but same thing
X_intvl = repmat(X_init,NumJumps,1) - cumsum(J);
X = [X_init; X_intvl];
for sample = 1:NumSamples
k = find(or(X_intvl(:,sample) > B, X_intvl(:,sample) < 0),1);
while(~isempty(k))
change = X_intvl(k-1,sample) - X_intvl(k,sample);
X_intvl(k:end,sample) = X_intvl(k:end,sample)+change;
k = find(or(X_intvl(:,sample) > B, X_intvl(:,sample) < 0),1);
end
end
Interesting question (+1).
I faced a similar problem a while back, although slightly more complex as my lower and upper bound depended on t. I never did work out a fully-vectorized solution. In the end, the fastest solution I found was a single loop which incorporates the constraints at each step. Adapting the code to your situation yields the following:
%# Set the parameters
LB = 0; %# Lower bound
UB = 5; %# Upper bound
T = 100; %# Number of observations
N = 3; %# Number of samples
X0 = (1/2) * (LB + UB); %# Arbitrary start point halfway between LB and UB
%# Generate the jumps
Jump = randn(N, T-1);
%# Build the constrained random walk
X = X0 * ones(N, T);
for t = 2:T
X(:, t) = max(min(X(:, t-1) + Jump(:, t-1), UB), 0);
end
X = X';
I would be interested in hearing if this method proves faster than what you are currently doing. I suspect it will be for cases where the constraint is binding in more than one or two places. I can't test it myself as the code you provided is not a "working" example, ie I can't just copy and paste it into Matlab and run it, as it depends on several variables for which example (or simulated) values are not provided. I tried adapting it myself, but couldn't get it to work properly?
UPDATE: I just switched the code around so that observations are indexed on columns and samples are indexed on rows, and then I transpose X in the last step. This will make the routine more efficient, since Matlab allocates memory for numeric arrays column-wise - hence it is faster when performing operations down the columns of an array (as opposed to across the rows). Note, you will only notice the speed-up for large N.
FINAL THOUGHT: These days, the JIT accelerator is very good at making single loops in Matlab efficient (double loops are still pretty slow). Therefore personally I'm of the opinion that every time you try and obtain a fully-vectorized solution in Matlab, ie no loops, you should weigh up whether the effort involved in finding a clever solution is worth the slight gains in efficiency to be made over an easier-to-obtain method that utilizes a single loop. And it is important to remember that fully-vectorized solutions are sometimes slower than solutions involving single loops when T and N are small!
I'd like to propose another vectorized solution.
So, first we should set the parameters and generate random Jumpls. I used the same set of parameters as Colin T Bowers:
% Set the parameters
LB = 0; % Lower bound
UB = 20; % Upper bound
T = 1000; % Number of observations
N = 3; % Number of samples
X0 = (1/2) * (UB + LB); % Arbitrary start point halfway between LB and UB
% Generate the jumps
Jump = randn(N, T-1);
But I changed generation code:
% Generate initial data without bounds
X = cumsum(Jump, 2);
% Apply bounds
Amplitude = UB - LB;
nsteps = ceil( max(abs(X(:))) / Amplitude - 0.5 );
for ii = 1:nsteps
ind = abs(X) > (1/2) * Amplitude;
X(ind) = Amplitude * sign(X(ind)) - X(ind);
end
% Shifting X
X = X0 + X;
So, instead of for loop I'm using cumsum function with smart post-processing.
N.B. This solution works significantly slower than Colin T Bowers's one for tight bounds (Amplitude < 5), but for loose bounds (Amplitude > 20) it works much faster.