We Keep Coding

Final code problem in finding the nearest neighbour

I need help for this code in finding the nearest neighbor distance between point locations. I think the problem is that instead of adding 'nearestdistance' to 'Sumdistance' only if it is smaller than the previous 'newdistance' it adds the nearest distance no matter what. Though I might be wrong. Code shown below:
q = loadPoints(f)
n = 1416
Sumdistance = 0
for i in q:
iID = int(i.getID())
x1 = float(i.getX())
y1 = float(i.getY())
nearestdistance = 999999999999999999999999999
for j in range(0, n):
if j != iID:
jID = (q[j].getID())
x2 = float(q[j].getX())
y2 = float(q[j].getY())
dx = x1 - x2
dy = y1 - y2
newdistance = math.sqrt(math.pow(dx,2) + (math.pow(dy,2)))
if newdistance < nearestdistance:
nearestdistance = newdistance
else nearestdistance =
Sumdistance = Sumdistance + nearestdistance
area = 10000000000
Do = Sumdistance/n
De = 0.5/(math.sqrt(n/area))
ANN = Do/De
print(ANN)
Thank you!

You are correct - you should always add nearestdistance to Sumdistance after iterating the neighbors.
for i in q:
......
for j in range(0, n):
if j != iID:
........
if newdistance < nearestdistance:
nearestdistance = newdistance
Sumdistance += nearestdistance
Note that the final sum will include reverse neighbors, ie a -> b and b -> a

making poisson spheres distribution on python but cannot figure out where is the bug

I am new to programming, so I hope my stupid questions do not bug you.
I am now trying to calculate the poisson sphere distribution(a 3D version of the poisson disk) using python and then plug in the result to POV-RAY so that I can generate some random distributed packing rocks.
I am following these two links:
[https://github.com/CodingTrain/Rainbow-Code/blob/master/CodingChallenges/CC_33_poisson_disc/sketch.js#L13]
[https://www.cs.ubc.ca/~rbridson/docs/bridson-siggraph07-poissondisk.pdf]
tl;dr
0.Create an n-dimensional grid array and cell size = r/sqrt(n) where r is the minimum distance between each sphere. All arrays are set to be default -1 which stands for 'without point'
1.Create an initial sample. (it should be placed randomly but I choose to put it in the middle). Put it in the grid array. Also, intialize an active array. Put the initial sample in the active array.
2.While the active list is not empty, pick a random index. Generate points near it and make sure the points are not overlapping with nearby points(only test with the nearby arrays). If no sample can be created near the 'random index', kick the 'random index' out. Loop the process.
And here is my code:
import math
from random import uniform
import numpy
import random
radius = 1 #you can change the size of each sphere
mindis = 2 * radius
maxx = 10 #you can change the size of the container
maxy = 10
maxz = 10
k = 30
cellsize = mindis / math.sqrt(3)
nrofx = math.floor(maxx / cellsize)
nrofy = math.floor(maxy / cellsize)
nrofz = math.floor(maxz / cellsize)
grid = []
active = []
default = numpy.array((-1, -1, -1))
for fillindex in range(nrofx * nrofy * nrofz):
grid.append(default)
x = uniform(0, maxx)
y = uniform(0, maxy)
z = uniform(0, maxz)
firstpos = numpy.array((x, y, z))
firsti = maxx // 2
firstj = maxy // 2
firstk = maxz // 2
grid[firsti + nrofx * (firstj + nrofy * firstk)] = firstpos
active.append(firstpos)
while (len(active) > 0) :
randindex = math.floor(uniform(0,len(active)))
pos = active[randindex]
found = False
for attempt in range(k):
offsetx = uniform(mindis, 2 * mindis)
offsety = uniform(mindis, 2 * mindis)
offsetz = uniform(mindis, 2 * mindis)
samplex = offsetx * random.choice([1,-1])
sampley = offsety * random.choice([1,-1])
samplez = offsetz * random.choice([1,-1])
sample = numpy.array((samplex, sampley, samplez))
sample = numpy.add(sample, pos)
xcoor = math.floor(sample.item(0) / cellsize)
ycoor = math.floor(sample.item(1) / cellsize)
zcoor = math.floor(sample.item(2) / cellsize)
attemptindex = xcoor + nrofx * (ycoor + nrofy * zcoor)
if attemptindex >= 0 and attemptindex < nrofx * nrofy * nrofz and numpy.all([sample, default]) == True and xcoor > 0 and ycoor > 0 and zcoor > 0 :
test = True
for testx in range(-1,2):
for testy in range(-1, 2):
for testz in range(-1, 2):
testindex = (xcoor + testx) + nrofx * ((ycoor + testy) + nrofy * (zcoor + testz))
if testindex >=0 and testindex < nrofx * nrofy * nrofz :
neighbour = grid[testindex]
if numpy.all([neighbour, sample]) == False:
if numpy.all([neighbour, default]) == False:
distance = numpy.linalg.norm(sample - neighbour)
if distance > mindis:
test = False
if test == True and len(active)<len(grid):
found = True
grid[attemptindex] = sample
active.append(sample)
if found == False:
del active[randindex]
for printout in range(len(grid)):
print("<" + str(active[printout][0]) + "," + str(active[printout][1]) + "," + str(active[printout][2]) + ">")
print(len(grid))
My code seems to run forever.
Therefore I tried to add a print(len(active)) in the last of the while loop.
Surprisingly, I think I discovered the bug as the length of the active list just keep increasing! (It is supposed to be the same length as the grid) I think the problem is caused by the active.append(), but I can't figure out where is the problem as the code is literally the 90% the same as the one made by Mr.Shiffman.
I don't want to free ride this but I have already checked again and again while correcting again and again for this code :(. Still, I don't know where the bug is. (why do the active[] keep appending!?)
Thank you for the precious time.

Pure-Python inverse error function

Are there any pure-python implementations of the inverse error function?
I know that SciPy has scipy.special.erfinv(), but that relies on some C extensions. I'd like a pure python implementation.
I've tried writing my own using the Wikipedia and Wolfram references, but it always seems to diverge from the true value when the arg is > 0.9.
I've also attempted to port the underlying C code that Scipy uses (ndtri.c and the cephes polevl.c functions) but that's also not passing my unit tests.
Edit: As requested, I've added the ported code.
Docstrings (and doctests) have been removed because they're longer than the functions. I haven't yet put much effort into making the port more pythonic - I'll worry about that once I get something that passes unit tests.
Supporting functions from cephes polevl.c
def polevl(x, coefs, N):
ans = 0
power = len(coefs) - 1
for coef in coefs[:N]:
ans += coef * x**power
power -= 1
return ans
def p1evl(x, coefs, N):
return polevl(x, [1] + coefs, N)
Main Inverse Error Function
def inv_erf(z):
if z < -1 or z > 1:
raise ValueError("`z` must be between -1 and 1 inclusive")
if z == 0:
return 0
if z == 1:
return math.inf
if z == -1:
return -math.inf
# From scipy special/cephes/ndrti.c
def ndtri(y):
# approximation for 0 <= abs(z - 0.5) <= 3/8
P0 = [
-5.99633501014107895267E1,
9.80010754185999661536E1,
-5.66762857469070293439E1,
1.39312609387279679503E1,
-1.23916583867381258016E0,
]
Q0 = [
1.95448858338141759834E0,
4.67627912898881538453E0,
8.63602421390890590575E1,
-2.25462687854119370527E2,
2.00260212380060660359E2,
-8.20372256168333339912E1,
1.59056225126211695515E1,
-1.18331621121330003142E0,
]
# Approximation for interval z = sqrt(-2 log y ) between 2 and 8
# i.e., y between exp(-2) = .135 and exp(-32) = 1.27e-14.
P1 = [
4.05544892305962419923E0,
3.15251094599893866154E1,
5.71628192246421288162E1,
4.40805073893200834700E1,
1.46849561928858024014E1,
2.18663306850790267539E0,
-1.40256079171354495875E-1,
-3.50424626827848203418E-2,
-8.57456785154685413611E-4,
]
Q1 = [
1.57799883256466749731E1,
4.53907635128879210584E1,
4.13172038254672030440E1,
1.50425385692907503408E1,
2.50464946208309415979E0,
-1.42182922854787788574E-1,
-3.80806407691578277194E-2,
-9.33259480895457427372E-4,
]
# Approximation for interval z = sqrt(-2 log y ) between 8 and 64
# i.e., y between exp(-32) = 1.27e-14 and exp(-2048) = 3.67e-890.
P2 = [
3.23774891776946035970E0,
6.91522889068984211695E0,
3.93881025292474443415E0,
1.33303460815807542389E0,
2.01485389549179081538E-1,
1.23716634817820021358E-2,
3.01581553508235416007E-4,
2.65806974686737550832E-6,
6.23974539184983293730E-9,
]
Q2 = [
6.02427039364742014255E0,
3.67983563856160859403E0,
1.37702099489081330271E0,
2.16236993594496635890E-1,
1.34204006088543189037E-2,
3.28014464682127739104E-4,
2.89247864745380683936E-6,
6.79019408009981274425E-9,
]
s2pi = 2.50662827463100050242
code = 1
if y > (1.0 - 0.13533528323661269189): # 0.135... = exp(-2)
y = 1.0 - y
code = 0
if y > 0.13533528323661269189:
y = y - 0.5
y2 = y * y
x = y + y * (y2 * polevl(y2, P0, 4) / p1evl(y2, Q0, 8))
x = x * s2pi
return x
x = math.sqrt(-2.0 * math.log(y))
x0 = x - math.log(x) / x
z = 1.0 / x
if x < 8.0: # y > exp(-32) = 1.2664165549e-14
x1 = z * polevl(z, P1, 8) / p1evl(z, Q1, 8)
else:
x1 = z * polevl(z, P2, 8) / p1evl(z, Q2, 8)
x = x0 - x1
if code != 0:
x = -x
return x
result = ndtri((z + 1) / 2.0) / math.sqrt(2)
return result

I think the error in your code is in the for loop over coefficients in the polevl function. If you replace what you have with the function below everything seems to work.
def polevl(x, coefs, N):
ans = 0
power = len(coefs) - 1
for coef in coefs:
ans += coef * x**power
power -= 1
return ans
I have tested it against scipy's implementation with the following code:
import numpy as np
from scipy.special import erfinv
N = 100000
x = np.random.rand(N) - 1.
# Calculate the inverse of the error function
y = np.zeros(N)
for i in range(N):
y[i] = inv_erf(x[i])
assert np.allclose(y, erfinv(x))

sympy? some digging may be needed to see how its implemented internally http://docs.sympy.org/latest/modules/functions/special.html#sympy.functions.special.error_functions.erfinv
from sympy import erfinv
erfinv(0.9).evalf(30)
1.16308715367667425688580351562

Fast Voxel Traversal 2D

I'm trying traverse all the cells that a line goes through. I've found the Fast Voxel Traversal Algorithm that seems to fit my needs, but I'm currently finding to be inaccurate. Below is a graph with a red line and points as voxel coordinates that the algorithm gives. As you can see it is almost correct except for the (4, 7) point, as it should be (5,6). I'm not sure if i'm implementing the algorithm correctly either so I've included it in Python. So i guess my question is my implementation correct or is there a better algo to this?
Thanks
def getVoxelTraversalPts(strPt, endPt, geom):
Max_Delta = 1000000.0
#origin
x0 = geom[0]
y0 = geom[3]
(sX, sY) = (strPt[0], strPt[1])
(eX, eY) = (endPt[0], endPt[1])
dx = geom[1]
dy = geom[5]
sXIndex = ((sX - x0) / dx)
sYIndex = ((sY - y0) / dy)
eXIndex = ((eX - sXIndex) / dx) + sXIndex
eYIndex = ((eY - sYIndex) / dy) + sYIndex
deltaX = float(eXIndex - sXIndex)
deltaXSign = 1 if deltaX > 0 else -1 if deltaX < 0 else 0
stepX = deltaXSign
tDeltaX = min((deltaXSign / deltaX), Max_Delta) if deltaXSign != 0 else Max_Delta
maxX = tDeltaX * (1 - sXIndex + int(sXIndex)) if deltaXSign > 0 else tDeltaX * (sXIndex - int(sXIndex))
deltaY = float(eYIndex - sYIndex)
deltaYSign = 1 if deltaY > 0 else -1 if deltaY < 0 else 0
stepY = deltaYSign
tDeltaY = min(deltaYSign / deltaY, Max_Delta) if deltaYSign != 0 else Max_Delta
maxY = tDeltaY * (1 - sYIndex + int(sYIndex)) if deltaYSign > 0 else tDeltaY * (sYIndex - int(sYIndex))
x = sXIndex
y = sYIndex
ptsIndexes = []
pt = [round(x), round(y)]
ptsIndexes.append(pt)
prevPt = pt
while True:
if maxX < maxY:
maxX += tDeltaX
x += deltaXSign
else:
maxY += tDeltaY
y += deltaYSign
pt = [round(x), round(y)]
if pt != prevPt:
#print pt
ptsIndexes.append(pt)
prevPt = pt
if maxX > 1 and maxY > 1:
break
return (ptsIndexes)

The voxels that you are walking start at 0.0, i.e. the first voxel spans space from 0.0 to 1.0, a not from -0.5 to 0.5 as you seem to be assuming. In other words, they are the ones marked with dashed line, and not the solid one.
If you want voxels to be your way, you will have to fix initial maxX and maxY calculations.

Ain't nobody got time to read the paper you posted and figure out if you've implemented it correctly.
Here's a question, though. Is the algorithm you've used (a) actually meant to determine all the cells that a line passes through or (b) form a decent voxel approximation of a straight line between two points?
I'm more familiar with Bresenham's line algorithm which performs (b). Here's a picture of it in action:
Note that the choice of cells is "aesthetic", but omits certain cells the line passes through. Including these would make the line "uglier".
I suspect a similar thing is going on with your voxel line algorithm. However, looking at your data and the Bresenham image suggests a simple solution. Walk along the line of discovered cells, but, whenever you have to make a diagonal step, consider the two intermediate cells. You can then use a line-rectangle intersection algorithm (see here) to determine which of the candidate cells should have, but wasn't, included.

I guess just to be complete, I decided to use a different algo. the one referenced here dtb's answer on another question.
here's the implementation
def getIntersectPts(strPt, endPt, geom=[0,1,0,0,0,1]):
'''
Find intersections pts for every half cell size
** cell size has only been tested with 1
Returns cell coordinates that the line passes through
'''
x0 = geom[0]
y0 = geom[3]
(sX, sY) = (strPt[0], strPt[1])
(eX, eY) = (endPt[0], endPt[1])
xSpace = geom[1]
ySpace = geom[5]
sXIndex = ((sX - x0) / xSpace)
sYIndex = ((sY - y0) / ySpace)
eXIndex = ((eX - sXIndex) / xSpace) + sXIndex
eYIndex = ((eY - sYIndex) / ySpace) + sYIndex
dx = (eXIndex - sXIndex)
dy = (eYIndex - sYIndex)
xHeading = 1.0 if dx > 0 else -1.0 if dx < 0 else 0.0
yHeading = 1.0 if dy > 0 else -1.0 if dy < 0 else 0.0
xOffset = (1 - (math.modf(sXIndex)[0]))
yOffset = (1 - (math.modf(sYIndex)[0]))
ptsIndexes = []
x = sXIndex
y = sYIndex
pt = (x, y) #1st pt
if dx != 0:
m = (float(dy) / float(dx))
b = float(sY - sX * m )
dx = abs(int(dx))
dy = abs(int(dy))
if dx == 0:
for h in range(0, dy + 1):
pt = (x, y + (yHeading *h))
ptsIndexes.append(pt)
return ptsIndexes
#print("m {}, dx {}, dy {}, b {}, xdir {}, ydir {}".format(m, dx, dy, b, xHeading, yHeading))
#print("x {}, y {}, {} {}".format(sXIndex, sYIndex, eXIndex, eYIndex))
#snap to half a cell size so we can find intersections on cell boundaries
sXIdxSp = round(2.0 * sXIndex) / 2.0
sYIdxSp = round(2.0 * sYIndex) / 2.0
eXIdxSp = round(2.0 * eXIndex) / 2.0
eYIdxSp = round(2.0 * eYIndex) / 2.0
# ptsIndexes.append(pt)
prevPt = False
#advance half grid size
for w in range(0, dx * 4):
x = xHeading * (w / 2.0) + sXIdxSp
y = (x * m + b)
if xHeading < 0:
if x < eXIdxSp:
break
else:
if x > eXIdxSp:
break
pt = (round(x), round(y)) #snapToGrid
# print(w, x, y)
if prevPt != pt:
ptsIndexes.append(pt)
prevPt = pt
#advance half grid size
for h in range(0, dy * 4):
y = yHeading * (h / 2.0) + sYIdxSp
x = ((y - b) / m)
if yHeading < 0:
if y < eYIdxSp:
break
else:
if y > eYIdxSp:
break
pt = (round(x), round(y)) # snapToGrid
# print(h, x, y)
if prevPt != pt:
ptsIndexes.append(pt)
prevPt = pt
return set(ptsIndexes) #elminate duplicates

creating masks in an image and appending them dynamically in python using Opencv

I have this programme to discuss and I think its a challenging one.. Here I have a yml file which contains the data for an image. The image has x,y,z values and intensity data which is stored in this yml file. I have used opencv to load the data and its working fine with masking.. but I am having problems in dynamically appending the masks created.. Here is the code I made for solving the problem :
import cv
from math import floor, sqrt, ceil
from numpy import array, dot, subtract, add, linalg as lin
mask_size = 9
mask_size2 = mask_size / 2
f = open("Classified_Image1.txt", "w")
def distance(centre, point):
''' To find out the distance between centre and the point '''
dist = sqrt(
((centre[0]-point[0])**2) +
((centre[1]-point[1])**2) +
((centre[2]-point[2])**2)
)
return dist
def CalcCentre(points): # Calculates centre for a given set of points
centre = array([0,0,0])
count = 0
for p in points:
centre = add(centre, array(p[:3]))
count += 1
centre = dot(1./count, centre)
print centre
return centre
def addrow(data, points, x, y, ix , iy ):# adds row to the mask
iy = y + 1
for dx in xrange(-mask_size2 , mask_size2 + 2):
ix = x + dx
rowpoints = addpoints(data, points, iy, ix)
return rowpoints
def addcolumn(data, points, x, y, ix , iy ):# adds column to the mask
ix = x + 1
for dy in xrange(-mask_size2-1 , mask_size2 + 1):
iy = y + dy
columnpoints = addpoints(data, points, iy, ix)
return columnpoints
def addpoints (data, points, iy, ix): # adds a list of relevant points
if 0 < ix < data.width and 0 < iy < data.height:
pnt = data[iy, ix]
if pnt != (0.0, 0.0, 0.0):
print ix, iy
print pnt
points.append(pnt)
return points
def CreateMask(data, y, x):
radius = 0.3
points = []
for dy in xrange(-mask_size2, mask_size2 + 1): ''' Masking the data '''
for dx in xrange(-mask_size2, mask_size2 + 1):
ix, iy = x + dx, y + dy
points = addpoints(data, points, iy , ix )
if len(points) > 3:
centre = CalcCentre(points)
distances = []
for point in points :
dist = distance(centre, point)
distances.append(dist)
distancemax = max(distances)
print distancemax
if distancemax < radius: ''' Dynamic Part of the Programme'''
#while dist < radius: # Going into infinite loop .. why ?
p = addrow(data, points, x, y, ix , iy )
q = addcolumn(data, points, x, y, ix , iy )
dist = distance(centre, point) # While should not go in infinite
#loop as dist is changing here
print dist
print len(p), p
print len(q), q
points = p + q
points = list(set(points)) # To remove duplicate points in the list
print len(points), points
def ComputeClasses(data):
for y in range(0, data.height):
for x in range(0, data.width):
CreateMask(data, y, x)
if __name__ == "__main__":
data = cv.Load("Z:/data/xyz_00000_300.yml")
print "data loaded"
ComputeClasses(data)
Feel free to suggest alternative methods/ideas to solve this problem.
Thanks in advance.