Kinetic Theory Model - physics

Edit: I've now fixed the problem I asked about. The spheres were leaving the box in the corners, where the if statements (in the while loop shown below) got confused. In the bits of code that reverse the individual components of velocity on contact with walls, some elif statements were used. When elif is used (as far as I can tell) if the sphere exceeds more than one position limit at a time, the program only reverses the velocity component for one of them. This is rectified when replacing elif with simply if. I'm not sure if I quite understand the reason behind this, so hopefully someone cleverer than I will comment such information, but for now, if anyone has the same problem, I hope my limited input helps!
Some context first:
I'm trying to build a model of the kinetic theory of gases in VPython, as a revision exercise for my (Physics) degree. This involves me building a hollow box and putting a bunch of spheres in it, randomly positioned throughout the box. I then need to assign each of the spheres its own random velocity and then use a loop to adjust the position of each sphere with reference to its velocity vector and a time step.
The spheres should also undergo elastic collisions with each wall and all other spheres.
When a sphere meets a wall in the x-direction, its x-velocity component is reversed and similarly in the y and z directions.
When a sphere meets another sphere, they swap velocities.
Currently, my code works so far as creating the right number of spheres and distributing them randomly and giving each sphere its own random velocity. The spheres also move as they should, except for collisions. The spheres should all stay inside the box as they should bounce off all the walls. They appear to be bouncing off each other, however, occasionally a sphere or two will go straight through the box.
I am extremely new to programming and I don't quite understand what's going on here or why it's happening but I'd be very grateful if someone could help me.
Below is the code I have so far (I've tried to comment what I'm doing at each step):
##########################################################
# This code is meant to create an empty box and then create
# a certain number of spheres (num_spheres) that will sit inside
# the box. Each sphere will then be assigned a random velocity vector.
# A loop will then adjust the position of each sphere to make them
# move. The spheres will undergo elastic collisions with the box walls
# and also with the other spheres in the box.
##########################################################
from visual import *
import random as random
import numpy as np
num_spheres = 15
fps = 24 #fps of while loop (later)
dt = 1.0/fps #time step
l = 40 #length of box
w = 2 #width of box
radius = 0.5 #radius of spheres
##########################################################
# Creating an empty box with sides length/height l, width w
wallR = box(pos = (l/2.0,0,0), size=(w,l,l), color=color.white, opacity=0.25)
wallL = box(pos = (-l/2.0,0,0), size=(w,l,l), color=color.white, opacity=0.25)
wallU = box(pos = (0,l/2.0,0), size=(l,w,l), color=color.white, opacity=0.25)
wallD = box(pos = (0,-l/2.0,0), size=(l,w,l), color=color.white, opacity=0.25)
wallF = box(pos = (0,0,l/2.0), size=(l,l,w), color=color.white, opacity=0.25)
wallB = box(pos = (0,0,-l/2.0), size=(l,l,w), color=color.white, opacity=0.25)
#defining a function that creates a list of 'num_spheres' randomly positioned spheres
def create_spheres(num):
global l, radius
particles = [] # Create an empty list
for i in range(0,num): # Loop i from 0 to num-1
v = np.random.rand(3)
particles.append(sphere(pos= (3.0/4.0*l) * (v - 0.5), #pos such that spheres are inside box
radius = radius, color=color.red, index=i))
# each sphere is given an index for ease of referral later
return particles
#defining a global variable = the array of velocities for the spheres
velarray = []
#defining a function that gives each sphere a random velocity
def velocity_spheres(sphere_list):
global velarray
for sphere in spheres:
#making the sign of each velocity component random
rand = random.randint(0,1)
if rand == 1:
sign = 1
else:
sign = -1
mu = 10 #defining an average for normal distribution
sigma = 0.1 #defining standard deviation of normal distribution
# 3 random numbers form the velocity vector
vel = vector(sign*random.normalvariate(mu, sigma),sign*random.normalvariate(mu, sigma),
sign*random.normalvariate(mu, sigma))
velarray.append(vel)
spheres = create_spheres(num_spheres) #creating some spheres
velocity_spheres(spheres) # invoking the velocity function
while True:
rate(fps)
for sphere in spheres:
sphere.pos += velarray[sphere.index]*dt
#incrementing sphere position by reference to its own velocity vector
if abs(sphere.pos.x) > (l/2.0)-w-radius:
(velarray[sphere.index])[0] = -(velarray[sphere.index])[0]
#reversing x-velocity on contact with a side wall
elif abs(sphere.pos.y) > (l/2.0)-w-radius:
(velarray[sphere.index])[1] = -(velarray[sphere.index])[1]
#reversing y-velocity on contact with a side wall
elif abs(sphere.pos.z) > (l/2.0)-w-radius:
(velarray[sphere.index])[2] = -(velarray[sphere.index])[2]
#reversing z-velocity on contact with a side wall
for sphere2 in spheres: #checking other spheres
if sphere2 != sphere:
#making sure we aren't checking the sphere against itself
if abs(sphere2.pos-sphere.pos) < (sphere.radius+sphere2.radius):
#if the other spheres are touching the sphere we are looking at
v1 = velarray[sphere.index]
#noting the velocity of the first sphere before the collision
velarray[sphere.index] = velarray[sphere2.index]
#giving the first sphere the velocity of the second before the collision
velarray[sphere2.index] = v1
#giving the second sphere the velocity of the first before the collision
Thanks again for any help!

The elif statements within the while loop in the code given in the original question are/were the cause of the problem. The conditional statement, elif, is only applicable if the original, if, condition is not satisfied. The circumstance wherein a sphere meets the corner of the box satisfies at least two of the conditions for reversing velocity components. This means that, while one would expect (at least) two velocity components to be reversed, only one is. That is, the direction specified by the if statement is reversed, whereas the component(s) mentioned in the elif statement(s) are not, as the first condition has been satisfied and, hence, the elif statements are ignored.
If each elif is changed to be a separate if statement, the code works as intended.

Related

Freefalling objects fly through a center of gravity in VPython, the moment they hit the center though they speed up and shoot out to the side

I have this function here
def gravitationalForce(p1,p2):
G = 1=
rVector = p1.pos - p2.pos
# if vp.mag(rVector) <.01:
# planet1.pos =- planet1.pos
# star.pos = - star.pos
rMagnitude = vp.mag(rVector)
rHat = rVector / rMagnitude
F = - rHat * G * p1.mass * p2.mass /rMagnitude**2
return F
and what I'm trying to do is make a single object/sphere that starts with a momentum of zero, some distance from a massive object. Over time the object pulls it in, and then it flies through to the other side, slowing down, and osculating back and forth. My issue is that while I am accurately simulating gravity between the two points, the moment the magnitude of the radius hits 0, the force seems to go to infinity, shooting the particle out at very high speeds in the following time steps, before it has a chance to be slowed down my the force of gravity on the other side. I tried to skip over the center when it was some small radius by implementing the conditional
# if vp.mag(rVector) <.01:
# planet1.pos =- planet1.pos
# star.pos = - star.pos
but this made no change and the object still shoots out.
Here are the given objects I generate
star = vp.sphere(pos=vp.vector(0,0,0), radius=0.2, color=vp.color.yellow,
mass = 2.0*10000, momentum=vp.vector(0,0,0), make_trail=True)
planet1 = vp.sphere(pos=vp.vector(-1,0,0), radius=0.05, color=vp.color.green,
mass = 1, momentum=vp.vector(10,0,0), make_trail=True)
You need to check to see whether the next step would, if carried out, put the planet inside the star. If so, you might move to the near side of the star, then move at (say) a constant speed to the other side of the star and turn on gravity again. The alternative would be to take very short steps while inside the star. This isn't quite physical, because you really need to use Gauss's law to calculate (in the approximation of a constant density for the star) the actual gravitational force.

Matplotlib.odeint giving wrong solution for simple formula of acc = Gm/r**2

I made a program to calculate the motion of any object (in this case moon) by earth's pull, with zero initial velocity, the moon should just oscillate in a straight line back and forth the earth until it stops at earth exactly right on top of the Earth, so plotting time versus distance I should get a graph similar to a damping signal, instead, I am getting an infinitely decrementing plot.
I have tried :-
giving different initial speeds to the moon, but got the same result, it seems like the way I am using odeint to solve the differential equation is wrong? Not sure. Very new to coding.
Assuming 1000 seconds in not enough for this to happen, so I increased the time to 1e+5,1e+10,1e+20, it seems like odeint couldn't handle that because it gave a different solution every time I run the program for the exact same parameters, received the follow warning:
ODEintWarning: Excess work done on this call (perhaps wrong Dfun type). Run with full_output = 1 to get quantitative information. warnings.warn(warning_msg, ODEintWarning)
Is there some other function I should use to solve this differential equation?
Reduced the masses to 10,20 and G and r to 10,10, and received the same warning as in case (2)
Any feed back helps
from scipy.integrate import odeint
import matplotlib.pyplot as plt
G=6.67408e-11 #N-m2/kg2 #N-m2/kg2
m1 = 5.972e+24 # kg , mass of earth
m2 = 7.348e+22 # kg , mass of moon
def dvdt(S, t):
# v = dr./dt, so a = dv/dt
r,v = S
return [v,
-G*m1 / r**2]
# initial values
r10 = 0 # position of earth in meters
r20 = 4e+8 # position of moon from earth in meters
v10 = 0 # velocity of earth m/s
v20 = 0 # velocity of moon relative to earth m/s
S0 = [r20, v20]
t = np.linspace(0,1000,100)
# solving the differential eqn
acc = odeint(dvdt,S0, t)
r,v = acc.T
# plotting
plt.plot(t,r)
plt.xlabel('Time')
plt.ylabel('Distance between earth and moon')
plt.show()
The scenario assumes that the two bodies are "shifted out of phase", so that they behave like dark matter to each other, no electro-weak or strong nuclear forces.
The effective gravity below the radius of Earth is determined by the mass inside the current radius, the influences of the outer shell add to zero.
The force vector always points to the center, for the one-dimensional motion the sign of the force has always to be opposite to the sign of the coordinate.
In total thus
R1 = 6.7e+6 # m
acc = -sign(r) * G*(m1*min(1,abs(r)/R1)**3) / abs(r)**2
= -G*m1 * r/max(R1,abs(r))**3
If this is implemented, one gets the expected oscillating plot

OpenCV detect blobs on the image

I need to find (and draw rect around)/get max and min radius blobs on the image. (samples below)
the problem is to find correct filters for the image that will allow Canny or Threshold transformation to highlight the blobs. then I going to use findContours to find the rectangles.
I've tryed:
Threshold - with different level
blur->erode->erode->grayscale->canny
change image tone with variety of "lines"
and ect. the better result was to detect piece (20-30%) of blob. and this info not allowed to draw rect around blob. also, thanks for shadows, not related to blob dots were detected, so that also prevents to detect the area.
as I understand I need to find counter that has hard contrast (not smooth like in shadow). Is there any way to do that with openCV?
Update
cases separately: image 1, image 2, image 3, image 4, image 5, image 6, image 7, image 8, image 9, image 10, image 11, image 12
One more Update
I believe that the blob have the contrast area at the edge. So, I've tried to make edge stronger: I've created 2 gray scale Mat: A and B, apply Gaussian blur for the second one - B (to reduce noise a bit), then I've made some calculations: goes around every pixel and find max difference between Xi,Yi of 'A' and nearby dots from 'B':
and apply max difference to Xi,Yi. so I get smth like this:
is i'm on the right way? btw, can I reach smth like this via OpenCV methods?
Update Image Denoising helps to reduce noize, Sobel - to highlight the contours, then threshold + findContours and custome convexHull gets smth similar I'm looking for but it not good for some blobs.
Since there are big differences between the input images, the algorithm should be able to adapt to the situation. Since Canny is based on detecting high frequencies, my algorithm treats the sharpness of the image as the parameter used for preprocessing adaptation. I didn't want to spend a week figuring out the functions for all the data, so I applied a simple, linear function based on 2 images and then tested with a third one. Here are my results:
Have in mind that this is a very basic approach and is only proving a point. It will need experiments, tests, and refining. The idea is to use Sobel and sum over all the pixels acquired. That, divided by the size of the image, should give you a basic estimation of high freq. response of the image. Now, experimentally, I found values of clipLimit for CLAHE filter that work in 2 test cases and found a linear function connecting the high freq. response of the input with a CLAHE filter, yielding good results.
sobel = get_sobel(img)
clip_limit = (-2.556) * np.sum(sobel)/(img.shape[0] * img.shape[1]) + 26.557
That's the adaptive part. Now for the contours. It took me a while to figure out a correct way of filtering out the noise. I settled for a simple trick: using contours finding twice. First I use it to filter out the unnecessary, noisy contours. Then I continue with some morphological magic to end up with correct blobs for the objects being detected (more details in the code). The final step is to filter bounding rectangles based on the calculated mean, since, on all of the samples, the blobs are of relatively similar size.
import cv2
import numpy as np
def unsharp_mask(img, blur_size = (5,5), imgWeight = 1.5, gaussianWeight = -0.5):
gaussian = cv2.GaussianBlur(img, (5,5), 0)
return cv2.addWeighted(img, imgWeight, gaussian, gaussianWeight, 0)
def smoother_edges(img, first_blur_size, second_blur_size = (5,5), imgWeight = 1.5, gaussianWeight = -0.5):
img = cv2.GaussianBlur(img, first_blur_size, 0)
return unsharp_mask(img, second_blur_size, imgWeight, gaussianWeight)
def close_image(img, size = (5,5)):
kernel = np.ones(size, np.uint8)
return cv2.morphologyEx(img, cv2.MORPH_CLOSE, kernel)
def open_image(img, size = (5,5)):
kernel = np.ones(size, np.uint8)
return cv2.morphologyEx(img, cv2.MORPH_OPEN, kernel)
def shrink_rect(rect, scale = 0.8):
center, (width, height), angle = rect
width = width * scale
height = height * scale
rect = center, (width, height), angle
return rect
def clahe(img, clip_limit = 2.0):
clahe = cv2.createCLAHE(clipLimit=clip_limit, tileGridSize=(5,5))
return clahe.apply(img)
def get_sobel(img, size = -1):
sobelx64f = cv2.Sobel(img,cv2.CV_64F,2,0,size)
abs_sobel64f = np.absolute(sobelx64f)
return np.uint8(abs_sobel64f)
img = cv2.imread("blobs4.jpg")
# save color copy for visualizing
imgc = img.copy()
# resize image to make the analytics easier (a form of filtering)
resize_times = 5
img = cv2.resize(img, None, img, fx = 1 / resize_times, fy = 1 / resize_times)
img = cv2.cvtColor(img, cv2.COLOR_BGR2GRAY)
# use sobel operator to evaluate high frequencies
sobel = get_sobel(img)
# experimentally calculated function - needs refining
clip_limit = (-2.556) * np.sum(sobel)/(img.shape[0] * img.shape[1]) + 26.557
# don't apply clahe if there is enough high freq to find blobs
if(clip_limit < 1.0):
clip_limit = 0.1
# limit clahe if there's not enough details - needs more tests
if(clip_limit > 8.0):
clip_limit = 8
# apply clahe and unsharp mask to improve high frequencies as much as possible
img = clahe(img, clip_limit)
img = unsharp_mask(img)
# filter the image to ensure edge continuity and perform Canny
# (values selected experimentally, using trackbars)
img_blurred = (cv2.GaussianBlur(img.copy(), (2*2+1,2*2+1), 0))
canny = cv2.Canny(img_blurred, 35, 95)
# find first contours
_, cnts, _ = cv2.findContours(canny.copy(), cv2.RETR_LIST, cv2.CHAIN_APPROX_SIMPLE)
# prepare black image to draw contours
canvas = np.ones(img.shape, np.uint8)
for c in cnts:
l = cv2.arcLength(c, False)
x,y,w,h = cv2.boundingRect(c)
aspect_ratio = float(w)/h
# filter "bad" contours (values selected experimentally)
if l > 500:
continue
if l < 20:
continue
if aspect_ratio < 0.2:
continue
if aspect_ratio > 5:
continue
if l > 150 and (aspect_ratio > 10 or aspect_ratio < 0.1):
continue
# draw all the other contours
cv2.drawContours(canvas, [c], -1, (255, 255, 255), 2)
# perform closing and blurring, to close the gaps
canvas = close_image(canvas, (7,7))
img_blurred = cv2.GaussianBlur(canvas, (8*2+1,8*2+1), 0)
# smooth the edges a bit to make sure canny will find continuous edges
img_blurred = smoother_edges(img_blurred, (9,9))
kernel = np.ones((3,3), np.uint8)
# erode to make sure separate blobs are not touching each other
eroded = cv2.erode(img_blurred, kernel)
# perform necessary thresholding before Canny
_, im_th = cv2.threshold(eroded, 50, 255, cv2.THRESH_BINARY)
canny = cv2.Canny(im_th, 11, 33)
# find contours again. this time mostly the right ones
_, cnts, _ = cv2.findContours(canny.copy(), cv2.RETR_EXTERNAL, cv2.CHAIN_APPROX_SIMPLE)
# calculate the mean area of the contours' bounding rectangles
sum_area = 0
rect_list = []
for i,c in enumerate(cnts):
rect = cv2.minAreaRect(c)
_, (width, height), _ = rect
area = width*height
sum_area += area
rect_list.append(rect)
mean_area = sum_area / len(cnts)
# choose only rectangles that fulfill requirement:
# area > mean_area*0.6
for rect in rect_list:
_, (width, height), _ = rect
box = cv2.boxPoints(rect)
box = np.int0(box * 5)
area = width * height
if(area > mean_area*0.6):
# shrink the rectangles, since the shadows and reflections
# make the resulting rectangle a bit bigger
# the value was guessed - might need refinig
rect = shrink_rect(rect, 0.8)
box = cv2.boxPoints(rect)
box = np.int0(box * resize_times)
cv2.drawContours(imgc, [box], 0, (0,255,0),1)
# resize for visualizing purposes
imgc = cv2.resize(imgc, None, imgc, fx = 0.5, fy = 0.5)
cv2.imshow("imgc", imgc)
cv2.imwrite("result3.png", imgc)
cv2.waitKey(0)
Overall I think that's a very interesting problem, a little bit too big to be answered here. The approach I presented is due to be treated as a road sign, not a complete solution. Tha basic idea being:
Adaptive preprocessing.
Finding contours twice: for filtering and then for the actual classification.
Filtering the blobs based on their mean size.
Thanks for the fun and good luck!
Here is the code I used:
import cv2
from sympy import Point, Ellipse
import numpy as np
x1='C:\\Users\\Desktop\\python\\stack_over_flow\\XsXs9.png'
image = cv2.imread(x1,0)
image1 = cv2.imread(x1,1)
x,y=image.shape
median = cv2.GaussianBlur(image,(9,9),0)
median1 = cv2.GaussianBlur(image,(21,21),0)
a=median1-median
c=255-a
ret,thresh1 = cv2.threshold(c,12,255,cv2.THRESH_BINARY)
kernel=np.ones((5,5),np.uint8)
dilation = cv2.dilate(thresh1,kernel,iterations = 1)
kernel=np.ones((5,5),np.uint8)
opening = cv2.morphologyEx(dilation, cv2.MORPH_OPEN, kernel)
cv2.imwrite('D:\\test12345.jpg',opening)
ret,contours,hierarchy = cv2.findContours(opening,cv2.RETR_EXTERNAL,cv2.CHAIN_APPROX_SIMPLE)
c=np.size(contours[:])
Blank_window=np.zeros([x,y,3])
Blank_window=np.uint8(Blank_window)
for u in range(0,c-1):
if (np.size(contours[u])>200):
ellipse = cv2.fitEllipse(contours[u])
(center,axes,orientation) =ellipse
majoraxis_length = max(axes)
minoraxis_length = min(axes)
eccentricity=(np.sqrt(1-(minoraxis_length/majoraxis_length)**2))
if (eccentricity<0.8):
cv2.drawContours(image1, contours, u, (255,1,255), 3)
cv2.imwrite('D:\\marked.jpg',image1)
Here problem is to find a near circular object. This simple solution is based on finding the eccentricity for each and every contour. Such objects being detected is the drop of water.
I have a partial solution in place.
FIRST
I initially converted the image to the HSV color space and tinkered with the value channel. On doing so I came across something unique. In almost every image, the droplets have a tiny reflection of light. This was highlighted distinctly in the value channel.
Upon inverting this I was able to obtain the following:
Sample 1:
Sample 2:
Sample 3:
SECOND
Now we have to extract the location of those points. To do so I performed anomaly detection on the inverted value channel obtained. By anomaly I mean the black dot present in them.
In order to do this I calculated the median of the inverted value channel. I allotted pixel value within 70% above and below the median to be treated as normal pixels. But every pixel value lying beyond this range to be anomalies. The black dots fit perfectly there.
Sample 1:
Sample 2:
Sample 3:
It did not turn out well for few images.
As you can see the black dot is due to the reflection of light which is unique to the droplets of water. Other circular edges might be present in the image but the reflection distinguishes the droplet from those edges.
THIRD
Now since we have the location of these black dots, we can perform Difference of Gaussians (DoG) (also mentioned in the update of the question) and obtain relevant edge information. If the obtained location of the black dots lie within the edges discovered it is said to be a water droplet.
Disclaimer: This method does not work for all the images. You can add your suggestions to this.
Good day , I am working on this subject and my advice to you is; First, after using many denoising filters such as Gaussian filters, process the image after that.
You can blob-detection these circles not with countors.

efficient way to draw continuous line in psychopy

I'm looking for a more efficient way to draw continuous lines in PsychoPy. That's what I've come up with, for now...
edit: the only improvement I could think of is to add a new line only if the mouse has really moved by adding if (mspos1-mspos2).any():
ms = event.Mouse(myWin)
lines = []
mspos1 = ms.getPos()
while True:
mspos2 = ms.getPos()
if (mspos1-mspos2).any():
lines.append(visual.Line(myWin, start=mspos1, end=mspos2))
for j in lines:
j.draw()
myWin.flip()
mspos1 = mspos2
edit: I tried it with Shape.Stim (code below), hoping that it would work better, but it get's edgy even more quickly..
vertices = [ms.getPos()]
con_line = visual.ShapeStim(myWin,
lineColor='red',
closeShape=False)
myclock.reset()
i = 0
while myclock.getTime() < 15:
new_pos = ms.getPos()
if (vertices[i]-new_pos).any():
vertices.append(new_pos)
i += 1
con_line.vertices=vertices
con_line.draw()
myWin.flip()
The problem is that it becomes too ressource demanding to draw those many visual.Lines or manipulate those many vertices in the visual.ShapeStim on each iteration of the loop. So it will hang on the draw (for Lines) or vertex assignment (for ShapeStim) so long that the mouse has moved enough for the line to show discontinuities ("edgy").
So it's a performance issue. Here are two ideas:
Have a lower threshold for the minimum distance travelled by the mouse before you want to add a new coordinate to the line. In the example below I impose a the criterion that the mouse position should be at least 10 pixels away from the previous vertex to be recorded. In my testing, this compressed the number of vertices recorded per second to about a third. This strategy alone will postpone the performance issue but not prevent it, so on to...
Use the ShapeStim solution but regularly use new ShapeStims, each with fewer vertices so that the stimulus to be updated isn't too complex. In the example below I set the complexity at 500 pixels before shifting to a new stimulus. There might be a small glitch while generating the new stimulus, but nothing I've noticed.
So combining these two strategies, starting and ending mouse drawing with a press on the keyboard:
# Setting things up
from psychopy import visual, event, core
import numpy as np
# The crucial controls for performance. Adjust to your system/liking.
distance_to_record = 10 # number of pixels between coordinate recordings
screenshot_interval = 500 # number of coordinate recordings before shifting to a new ShapeStim
# Stimuli
myWin = visual.Window(units='pix')
ms = event.Mouse()
myclock = core.Clock()
# The initial ShapeStim in the "stimuli" list. We can refer to the latest
# as stimuli[-1] and will do that throughout the script. The others are
# "finished" and will only be used for draw.
stimuli = [visual.ShapeStim(myWin,
lineColor='white',
closeShape=False,
vertices=np.empty((0, 2)))]
# Wait for a key, then start with this mouse position
event.waitKeys()
stimuli[-1].vertices = np.array([ms.getPos()])
myclock.reset()
while not event.getKeys():
# Get mouse position
new_pos = ms.getPos()
# Calculating distance moved since last. Pure pythagoras.
# Index -1 is the last row.index
distance_moved = np.sqrt((stimuli[-1].vertices[-1][0]-new_pos[0])**2+(stimuli[-1].vertices[-1][1]-new_pos[1])**2)
# If mouse has moved the minimum required distance, add the new vertex to the ShapeStim.
if distance_moved > distance_to_record:
stimuli[-1].vertices = np.append(stimuli[-1].vertices, np.array([new_pos]), axis=0)
# ... and show it (along with any "full" ShapeStims
for stim in stimuli:
stim.draw()
myWin.flip()
# Add a new ShapeStim once the old one is too full
if len(stimuli[-1].vertices) > screenshot_interval:
print "new shapestim now!"
stimuli.append(visual.ShapeStim(myWin,
lineColor='white',
closeShape=False,
vertices=[stimuli[-1].vertices[-1]])) # start from the last vertex

np.fft.fft off by a factor of 1000 (fitting an powerspectrum)

I'm trying to make a powerspectrum from an experimental dataset which I am reading in, and then to fit it to an theoretical curve. Now everything is working fine and I'm not getting errors, except for the fact that my curve keeps differing by a factor of 1000 from the data and I have absolutely no idea what the problem could be. I've asked a few people, but to no avail. (I hope that you guys will be able to help)
Anyways, I'm pretty sure that its not the units, as they were tripple checked by me and 2 others. Basically, I need to fit a powerspectrum to an equation by using the least squares method.
I can't post the whole code, as its rather long and a bit messy, but this is the fourier part, I added comments to all arrays and vars which have not been declared in the code)
#Calculate stuff
Nm = 10**-6 #micro to meter
KbT = 4.10E-21 #Joule
T = 297. #K
l = zvalue*Nm #meter
meany = np.mean(cleandatay*Nm) #meter (cleandata is the array that I read in from a cvs at the start.)
SDy = sum((cleandatay*Nm - meany)**2)/len(cleandatay) #meter^2
FmArray[0][i] = ((KbT*l)/SDy) #N
#print FmArray[0][i]
print float((i*100/len(filelist)))#how many % done?
#fourier
dt = cleant[1]-cleant[0] #timestep
N = len(cleandatay) #Same for cleant, its the corresponding time to cleandatay
Here is where the fourier part starts, I take the fft and turn it into a powerspectrum. Then I calculate the corresponding freq steps with the array freqs
fouriery = np.fft.fft((cleandatay*(10**-6)))
fourierpower = (np.abs(fouriery))**2
fourierpower = fourierpower[1:N/2] #remove 0th datapoint and /2 (remove negative freqs)
fourierpower = fourierpower*dt #*dt to account for steps
freqs = (1.+np.arange((N/2)-1.))/50.
#Least squares method
eta = 8.9E-4 #pa*s
Rbead = 0.5E-6#meter
constant = 2*KbT/(3*eta*pi*Rbead)
omega = 2*pi*freqs #rad/s
Wcarray = 2.*pi*np.arange(0,30, 0.02003) #0.02 = 30/len(freqs)
ChiSq = np.zeros(len(Wcarray))
for k in range(0, len(Wcarray)):
Py = (constant / (Wcarray[k]**2 + omega**2))
ChiSq[k] = sum((fourierpower - Py)**2)
pylab.loglog(omega, Py)
print k*100/len(Wcarray)
index = np.where(ChiSq == min(ChiSq))
cutoffw = Wcarray[index]
Pygoed = (constant / (Wcarray[index]**2 + omega**2))
print cutoffw
print constant
print min(ChiSq)
pylab.loglog(omega,ChiSq)
So I have no idea what could be going wrong, I think its the fft, as nothing else can really go wrong.
Below is the pic I get when I plot all the fit lines against the spectrum, as you can see it is off by about 1000 (actually exactly 1000, as this leaves a least square residue of 10^-22, but I can't just randomly multiply without knowing why)
Just to elaborate on the picture. The green dots are the fft spectrum, the lines are the fits, the red dot is where it thinks the cutoff frequency is, and the blue line is the chi-squared fit, looking for the lowest value.
Take a look at the documentation for the FFT that you are using. Many FFTs introduce a scaling factor that is usually N * result (number of samples). Multiplying by 1/N will scale the results back in line. (You said that the result is 1000 too high....could it be that you are using a 1024 size FFT?)
Your library FFT routine might include a scale factor of 1/sqrt(n).
Check the documentation for the fft you used, as the proportion of the scale factor allocated between the fft and the ifft is arbitrary.