I am a bit confused in the Poisson distribution. Actually I am fitting a Poisson type distribution and the I need to extract its mean and error on mean. So as we know the Poisson distribution is
In root (C/c++ based analysis framework) I defined this function like below
function = ( [0] * Power( [1] / [2] , x/[2] ) * exp (-[1]/[2]) ) / Gamma(x/[2] + 1)
Where : [0] = Normalizing parameter
[1] / [2] -> mean (mu)
x / [2] -> x
Gamma( x / [2] + 1 ) = factorial (x / [2])
So, In principle then mean of Poisson distribution is mu = 1/2 and error will be the standard deviation which is square root of mean.
But, If I am using this value then my mean is coming around 10 and hence error is ~3.
While the mean of distribution is around 2 (as we can see) so I am confused. Because the parameter 1 's value is coming out to around 2 or 3. So, should I use parameter 1 as mean value or what??
Please suggest what should I use and why?
My Full code is below:
TH1F *hClusterSize = new TH1F("hClusterSize","Cluster size for GE1/1", 10,0.,10.);
tmpTree->Draw("g1ycl.ngeoch>>hClusterSize","g1ycl#.GetEntries()==1 && g1xcl#.GetEntries()==1");
hClusterSize->GetXaxis()->SetTitle("Cluster Size");
hClusterSize->GetYaxis()->SetTitle("#Entries");
TF1 *f1 = new TF1("f1","[0]*TMath::Power(([1]/[2]),(x/[2]))*(TMath::Exp(-([1]/[2])))/TMath::Gamma((x/[2])+1)", 0, 10);
f1->SetParameters(hClusterSize->GetMaximum(), hClusterSize->GetMean(), 1);
hClusterSize->Fit("f1"); // Use option "R" = fit between "xmin" and "xmax" of the "f1"
On the root command line fitting a poisson distribution can be done like this:
TF1* func = new TF1("mypoi","[0]*TMath::Poisson(x,[1])",0,20)
func->SetParameter(0,5000) // set starting values
func->SetParameter(1,2.) // set starting values
func->SetParName(0,"Normalisation")
func->SetParName(1,"#mu")
TH1F* hist = new TH1F("hist","hist",20,-0.5,19.5)
for (int i = 0 ; i < 5000 ; i++) { hist->Fill(gRandom->Poisson(3.5)); }
hist->Draw()
hist->Fit(func)
Note that that bin centers are shifted wrt your initial post, such that the bin
center of 0 counts is at 0 and not at 0.5 (and the same for all the other bins).
Related
I have a custom (discrete) probability distribution defined somewhat in the form: f(x)/(sum(f(x')) for x' in a given discrete set X). Also, 0<=x<=1.
So I have been trying to implement it in python 3.8.2, and the problem is that the numerator and denominator both come out to be really small and python's floating point representation just takes them as 0.0.
After calculating these probabilities, I need to sample a random element from an array, whose each index may be selected with the corresponding probability in the distribution. So if my distribution is [p1,p2,p3,p4], and my array is [a1,a2,a3,a4], then probability of selecting a2 is p2 and so on.
So how can I implement this in an elegant and efficient way?
Is there any way I could use the np.random.beta() in this case? Since the difference between the beta distribution and my actual distribution is only that the normalization constant differs and the domain is restricted to a few points.
Note: The Probability Mass function defined above is actually in the form given by the Bayes theorem and f(x)=x^s*(1-x)^f, where s and f are fixed numbers for a given iteration. So the exact problem is that, when s or f become really large, this thing goes to 0.
You could well compute things by working with logs. The point is that while both the numerator and denominator might underflow to 0, their logs won't unless your numbers are really astonishingly small.
You say
f(x) = x^s*(1-x)^t
so
logf (x) = s*log(x) + t*log(1-x)
and you want to compute, say
p = f(x) / Sum{ y in X | f(y)}
so
p = exp( logf(x) - log sum { y in X | f(y)}
= exp( logf(x) - log sum { y in X | exp( logf( y))}
The only difficulty is in computing the second term, but this is a common problem, for example here
On the other hand computing logsumexp is easy enough to to by hand.
We want
S = log( sum{ i | exp(l[i])})
if L is the maximum of the l[i] then
S = log( exp(L)*sum{ i | exp(l[i]-L)})
= L + log( sum{ i | exp( l[i]-L)})
The last sum can be computed as written, because each term is now between 0 and 1 so there is no danger of overflow, and one of the terms (the one for which l[i]==L) is 1, and so if other terms underflow, that is harmless.
This may however lose a little accuracy. A refinement would be to recognize the set A of indices where
l[i]>=L-eps (eps a user set parameter, eg 1)
And then compute
N = Sum{ i in A | exp(l[i]-L)}
B = log1p( Sum{ i not in A | exp(l[i]-L)}/N)
S = L + log( N) + B
I want to calculate the Maximised value of the particular user based on his Interest | Popularity | both Interest and Popularity using following Linear Programming Problem(LPP) equation
using pulp package in python3.7.
I have 4 lists
INTEREST = [5,10,15,20,25]
POPULARITY = [4,8,12,16,20]
USER = [1,2,3,4,5]
cost = [2,4,6,8,10]
and 2 variable values as
e=0.5 ; e may take (0 or 1 or 0.5)
budget=20
and
i=0 to n ; n is length of the list
means, the summation want to perform for all list values.
Here, if e==0 means Interest will 0 ; if e==1 means Popularity will 0 ; if e==0.5 means Interest and Popularity will be consider for Max Value
Also xi takes 0 or 1; if xi==1 then the user will be consider else if xi==0 then the user will not be consider.
and my pulp code as below
from pulp import *
INTEREST = [5,10,15,20,25]
POPULARITY = [4,8,12,16,20]
USER = [1,2,3,4,5]
cost = [2,4,6,8,10]
e=0.5
budget=10
#PROBLEM VARIABLE
prob = LpProblem("MaxValue", LpMaximize)
# DECISION VARIABLE
int_vars = LpVariable.dicts("Interest", INTEREST,0,4,LpContinuous)
pop_vars = LpVariable.dicts("Popularity",
POPULARITY,0,4,LpContinuous)
user_vars = LpVariable.dicts("User",
USER,0,4,LpBinary)
#OBJECTIVE fUNCTION
prob += lpSum(USER(i)((INTEREST[i]*e for i in INTEREST) +
(POPULARITY[i]*(1-e) for i in POPULARITY)))
# CONSTRAINTS
prob += USER(i)cost(i) <= budget
#SOLVE
prob.solve()
print("Status : ",LpStatus[prob.status])
# PRINT OPTIMAL SOLUTION
print("The Max Value = ",value(prob.objective))
Now I am getting 2 errors as
1) line 714, in addInPlace for e in other:
2) line 23, in
prob += lpSum(INTEREST[i]e for i in INTEREST) +
lpSum(POPULARITY[i](1-e) for i in POPULARITY)
IndexError: list index out of range
What I did wrong in my code. Guide me to resolve this problem. Thanks in advance.
I think I finally understand what you are trying to achieve. I think the problem with your description is to do with terminology. In a linear program we reserve the term variable for those variables which we want to be selected or chosen as part of the optimisation.
If I understand your needs correctly your python variables e and budget would be considered parameters or constants of the linear program.
I believe this does what you want:
from pulp import *
import numpy as np
INTEREST = [5,10,15,20,25]
POPULARITY = [4,8,12,16,20]
COST = [2,4,6,8,10]
N = len(COST)
set_user = range(N)
e=0.5
budget=10
#PROBLEM VARIABLE
prob = LpProblem("MaxValue", LpMaximize)
# DECISION VARIABLE
x = LpVariable.dicts("user_selected", set_user, 0, 1, LpBinary)
# OBJECTIVE fUNCTION
prob += lpSum([x[i]*(INTEREST[i]*e + POPULARITY[i]*(1-e)) for i in set_user])
# CONSTRAINTS
prob += lpSum([x[i]*COST[i] for i in set_user]) <= budget
#SOLVE
prob.solve()
print("Status : ",LpStatus[prob.status])
# PRINT OPTIMAL SOLUTION
print("The Max Value = ",value(prob.objective))
# Show which users selected
x_soln = np.array([x[i].varValue for i in set_user])
print("user_vars: ")
print(x_soln)
Which should return the following, i.e. with these particular parameters only the last user is selected for inclusion - but this decision will change - for example if you increase the budget to 100 all users will be selected.
Status : Optimal
The Max Value = 22.5
user_vars:
[0. 0. 0. 0. 1.]
I must solve the Euler Bernoulli differential beam equation which is:
w’’’’(x) = q(x)
and boundary conditions:
w(0) = w(l) = 0
and
w′′(0) = w′′(l) = 0
The beam is as shown on the picture below:
beam
The continious force q is 2N/mm.
I have to use shooting method and scipy.integrate.odeint() func.
I can't even manage to start as i do not understand how to write the differential equation as a system of equation
Can someone who understands solving of differential equations with boundary conditions in python please help!
Thanks :)
The shooting method
To solve the fourth order ODE BVP with scipy.integrate.odeint() using the shooting method you need to:
1.) Separate the 4th order ODE into 4 first order ODEs by substituting:
u = w
u1 = u' = w' # 1
u2 = u1' = w'' # 2
u3 = u2' = w''' # 3
u4 = u3' = w'''' = q # 4
2.) Create a function to carry out the derivation logic and connect that function to the integrate.odeint() like this:
function calc(u, x , q)
{
return [u[1], u[2], u[3] , q]
}
w = integrate.odeint(calc, [w(0), guess, w''(0), guess], xList, args=(q,))
Explanation:
We are sending the boundary value conditions to odeint() for x=0 ([w(0), w'(0) ,w''(0), w'''(0)]) which calls the function calc which returns the derivatives to be added to the current state of w. Note that we are guessing the initial boundary conditions for w'(0) and w'''(0) while entering the known w(0)=0 and w''(0)=0.
Addition of derivatives to the current state of w occurs like this:
# the current w(x) value is the previous value plus the current change of w in dx.
w(x) = w(x-dx) + dw/dx
# others are calculated the same
dw(x)/dx = dw(x-dx)/dx + d^2w(x)/dx^2
# etc.
This is why we are returning values [u[1], u[2], u[3] , q] instead of [u[0], u[1], u[2] , u[3]] from the calc function, because u[1] is the first derivative so we add it to w, etc.
3.) Now we are able to set up our shooting method. We will be sending different initial boundary values for w'(0) and w'''(0) to odeint() and then check the end result of the returned w(x) profile to determine how close w(L) and w''(L) got to 0 (the known boundary conditions).
The program for the shooting method:
# a function to return the derivatives of w
def returnDerivatives(u, x, q):
return [u[1], u[2], u[3], q]
# a shooting funtion which takes in two variables and returns a w(x) profile for x=[0,L]
def shoot(u2, u4):
# the number of x points to calculate integration -> determines the size of dx
# bigger number means more x's -> better precision -> longer execution time
xSteps = 1001
# length of the beam
L= 1.0 # 1m
xSpace = np.linspace(0, L, xSteps)
q = 0.02 # constant [N/m]
# integrate and return the profile of w(x) and it's derivatives, from x=0 to x=L
return odeint(returnDerivatives, [ 0, u2, 0, u4] , xSpace, args=(q,))
# the tolerance for our results.
tolerance = 0.01
# how many numbers to consider for u2 and u4 (the guess boundary conditions)
u2_u4_maxNumbers = 1327 # bigger number, better precision, slower program
# you can also divide into separate variables like u2_maxNum and u4_maxNum
# these are already tested numbers (the best results are somewhere in here)
u2Numbers = np.linspace(-0.1, 0.1, u2_u4_maxNumbers)
# the same as above
u4Numbers = np.linspace(-0.5, 0.5, u2_u4_maxNumbers)
# result list for extracted values of each w(x) profile => [u2Best, u4Best, w(L), w''(L)]
# which will help us determine if the w(x) profile is inside tolerance
resultList = []
# result list for each U (or w(x) profile) => [w(x), w'(x), w''(x), w'''(x)]
resultW = []
# start generating numbers for u2 and u4 and send them to odeint()
for u2 in u2Numbers:
for u4 in u4Numbers:
U = []
U = shoot(u2,u4)
# get only the last row of the profile to determine if it passes tolerance check
result = U[len(U)-1]
# only check w(L) == 0 and w''(L) == 0, as those are the known boundary cond.
if (abs(result[0]) < tolerance) and (abs(result[2]) < tolerance):
# if the result passed the tolerance check, extract some values from the
# last row of the w(x) profile which we will need later for comaprisons
resultList.append([u2, u4, result[0], result[2]])
# add the w(x) profile to the list of profiles that passed the tolerance
# Note: the order of resultList is the same as the order of resultW
resultW.append(U)
# go through the resultList (list of extracted values from last row of each w(x) profile)
for i in range(len(resultList)):
x = resultList[i]
# both boundary conditions are 0 for both w(L) and w''(L) so we will simply add
# the two absolute values to determine how much the sum differs from 0
y = abs(x[2]) + abs(x[3])
# if we've just started set the least difference to the current
if i == 0:
minNum = y # remember the smallest difference to 0
index = 0 # remember index of best profile
elif y < minNum:
# current sum of absolute values is smaller
minNum = y
index = i
# print out the integral for w(x) over the beam
sum = 0
for i in resultW[index]:
sum = sum + i[0]
print("The integral of w(x) over the beam is:")
print(sum/1001) # sum/xSteps
This outputs:
The integral of w(x) over the beam is:
0.000135085272117
To print out the best profile for w(x) that we found:
print(resultW[index])
which outputs something like:
# w(x) w'(x) w''(x) w'''(x)
[[ 0.00000000e+00 7.54147813e-04 0.00000000e+00 -9.80392157e-03]
[ 7.54144825e-07 7.54142917e-04 -9.79392157e-06 -9.78392157e-03]
[ 1.50828005e-06 7.54128237e-04 -1.95678431e-05 -9.76392157e-03]
...,
[ -4.48774290e-05 -8.14851572e-04 1.75726275e-04 1.01560784e-02]
[ -4.56921910e-05 -8.14670764e-04 1.85892353e-04 1.01760784e-02]
[ -4.65067671e-05 -8.14479780e-04 1.96078431e-04 1.01960784e-02]]
To double check the results from above we will also solve the ODE using the numerical method.
The numerical method
To solve the problem using the numerical method we first need to solve the differential equations. We will get four constants which we need to find with the help of the boundary conditions. The boundary conditions will be used to form a system of equations to help find the necessary constants.
For example:
w’’’’(x) = q(x);
means that we have this:
d^4(w(x))/dx^4 = q(x)
Since q(x) is constant after integrating we have:
d^3(w(x))/dx^3 = q(x)*x + C
After integrating again:
d^2(w(x))/dx^2 = q(x)*0.5*x^2 + C*x + D
After another integration:
dw(x)/dx = q(x)/6*x^3 + C*0.5*x^2 + D*x + E
And finally the last integration yields:
w(x) = q(x)/24*x^4 + C/6*x^3 + D*0.5*x^2 + E*x + F
Then we take a look at the boundary conditions (now we have expressions from above for w''(x) and w(x)) with which we make a system of equations to solve the constants.
w''(0) => 0 = q(x)*0.5*0^2 + C*0 + D
w''(L) => 0 = q(x)*0.5*L^2 + C*L + D
This gives us the constants:
D = 0 # from the first equation
C = - 0.01 * L # from the second (after inserting D=0)
After repeating the same for w(0)=0 and w(L)=0 we obtain:
F = 0 # from first
E = 0.01/12.0 * L^3 # from second
Now, after we have solved the equation and found all of the integration constants we can make the program for the numerical method.
The program for the numerical method
We will make a FOR loop to go through the entire beam for every dx at a time and sum up (integrate) w(x).
L = 1.0 # in meters
step = 1001.0 # how many steps to take (dx)
q = 0.02 # constant [N/m]
integralOfW = 0.0; # instead of w(0) enter the boundary condition value for w(0)
result = []
for i in range(int(L*step)):
x= i/step
w = (q/24.0*pow(x,4) - 0.02/12.0*pow(x,3) + 0.01/12*pow(L,3)*x)/step # current w fragment
# add up fragments of w for integral calculation
integralOfW += w
# add current value of w(x) to result list for plotting
result.append(w*step);
print("The integral of w(x) over the beam is:")
print(integralOfW)
which outputs:
The integral of w(x) over the beam is:
0.00016666652805511192
Now to compare the two methods
Result comparison between the shooting method and the numerical method
The integral of w(x) over the beam:
Shooting method -> 0.000135085272117
Numerical method -> 0.00016666652805511192
That's a pretty good match, now lets see check the plots:
From the plots it's even more obvious that we have a good match and that the results of the shooting method are correct.
To get even better results for the shooting method increase xSteps and u2_u4_maxNumbers to bigger numbers and you can also narrow down the u2Numbers and u4Numbers to the same set size but a smaller interval (around the best results from previous program runs). Keep in mind that setting xSteps and u2_u4_maxNumbers too high will cause your program to run for a very long time.
You need to transform the ODE into a first order system, setting u0=w one possible and usually used system is
u0'=u1,
u1'=u2,
u2'=u3,
u3'=q(x)
This can be implemented as
def ODEfunc(u,x): return [ u[1], u[2], u[3], q(x) ]
Then make a function that shoots with experimental initial conditions and returns the components of the second boundary condition
def shoot(u01, u03): return odeint(ODEfunc, [0, u01, 0, u03], [0, l])[-1,[0,2]]
Now you have a function of two variables with two components and you need to solve this 2x2 system with the usual methods. As the system is linear, the shooting function is linear as well and you only need to find the coefficients and solve the resulting linear system.
Issue when creating a custom loss function. Sorry I am a bit new to matconvnet
So essentially the output for my Neural Network is aimed to be a vector with 2 elements (ex: [1,2]) with an error function based upon the RMSE
So I changed the cnn_train so that the labels would be instead a 2 by # of training examples. In the code below x = 1 x 1 x 2 x batchSize set and c is the labels.
function y = wf_rmse(x, c, varargin)
% Custom loss function for MSE Error
org = size(x);
x = reshape(x, size(c));
if ~isempty(varargin) && ~ischar(varargin{1}) % passed in dzdy
dzdy = varargin{1} ;
varargin(1) = [] ;
else
dzdy = [] ;
end
% Forward pass
if(nargin <= 2 || isempty(dzdy))
y = sum(sum(((x-c).^2))/2));
% Back pass
elseif(nargin == 3 && ~isempty(dzdy))
y = 2 * dzdy * (x - c);
y = reshape(y, org);
end
When I include this as part of the network, the network initializes fine, but I get an error during training of, even though the dimensions of the gradient output should match the dimensions of the others.
Error using vl_nnconv
DEROUTPUT dimensions are incompatible with X and FILTERS.
Any suggestions on resolving the issue?
I found this code snippet on raywenderlich.com, however the link to the explanation wasn't valid anymore. I "translated" the answer into Swift, I hope you can understand, it's actually quite easy even without knowing the language. Could anyone explain what exactly is going on here? Thanks for any help.
class func linesCross(#line1: Line, line2: Line) -> Bool {
let denominator = (line1.end.y - line1.start.y) * (line2.end.x - line2.start.x) -
(line1.end.x - line1.start.x) * (line2.end.y - line2.start.y)
if denominator == 0 { return false } //lines are parallel
let ua = ((line1.end.x - line1.start.x) * (line2.start.y - line1.start.y) -
(line1.end.y - line1.start.y) * (line2.start.x - line1.start.x)) / denominator
let ub = ((line2.end.x - line2.start.x) * (line2.start.y - line1.start.y) -
(line2.end.y - line2.start.y) * (line2.start.x - line1.start.x)) / denominator
//lines may touch each other - no test for equality here
return ua > 0 && ua < 1 && ub > 0 && ub < 1
}
You can find a detailed segment-intersection algorithm
in the book Computational Geometry in C, Sec. 7.7.
The SegSegInt code described there is available here.
I recommend avoiding slope calculations.
There are several "degenerate" cases that require care: collinear segments
overlapping or not, one segment endpoint in the interior of the other segments,
etc. I wrote the code to return an indication of these special cases.
This is what the code is doing.
Every point P in the segment AB can be described as:
P = A + u(B - A)
for some constant 0 <= u <= 1. In fact, when u=0 you get P=A, and you getP=B when u=1. Intermediate values of u will give you intermediate values of P in the segment. For instance, when u = 0.5 you will get the point in the middle. In general, you can think of the parameter u as the ratio between the lengths of AP and AB.
Now, if you have another segment CD you can describe the points Q on it in the same way, but with a different u, which I will call v:
Q = C + v(D - C)
Again, keep in mind that Q lies between C and D if, and only if, 0 <= v <= 1 (same as above for P).
To find the intersection between the two segments you have to equate P=Q. In other words, you need to find u and v, both between 0 and 1 such that:
A + u(B - A) = C + v(D - C)
So, you have this equation and you have to see if it is solvable within the given constraints on u and v.
Given that A, B, C and D are points with two coordinates x,y each, you can open the equation above into two equations:
ax + u(bx - ax) = cx + v(dx - cx)
ay + u(by - ay) = cy + v(dy - cy)
where ax = A.x, ay = A.y, etc., are the coordinates of the points.
Now we are left with a 2x2 linear system. In matrix form:
|bx-ax cx-dx| |u| = |cx-ax|
|by-ay cy-dy| |v| |cy-ay|
The determinant of the matrix is
det = (bx-ax)(cy-dy) - (by-ay)(cx-dx)
This quantity corresponds to the denominator of the code snippet (please check).
Now, multiplying both sides by the cofactor matrix:
|cy-dy dx-cx|
|ay-by bx-ax|
we get
det*u = (cy-dy)(cx-ax) + (dx-cx)(cy-ay)
det*v = (ay-by)(cx-ax) + (bx-ax)(cy-ay)
which correspond to the variables ua and ub defined in the code (check this too!)
Finally, once you have u and v you can check whether they are both between 0 and 1 and in that case return that there is intersection. Otherwise, there isn't.
For a given line the slope is
m=(y_end-y_start)/(x_end-x_start)
if two slopes are equal, the lines are parallel
m1=m1
(y1_end-y_start)/(x1_end-x1_start)=(y2_end-y2_start)/(x2_end-x2_start)
And this is equivalent to checking that the denominator is not zero,
Regarding the rest of the code, find the explanation on wikipedia under "Given two points on each line"