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StatsClass.py
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StatsClass.py
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# -*- coding: utf-8 -*-
"""
Created on Wed Jul 15 15:34:40 2015
@author: Fuller
"""
import numpy as np
import cv2
class Stats:
def __init__(self, name=None, fullName=None, ylabel=None, style='b.', defaultVal=0, color=(0,0,1)):
self.name = name
self.fullName = fullName
self.ylabel = ylabel
self.style = style
self.defaultVal = defaultVal
def set_name(self, name):
self.name = name
def get_name(self):
return self.name
def set_full_name(self, fullName):
self.fullName = fullName
def get_full_name(self):
return self.fullName
def set_ylabel(self, ylabel):
self.ylabel = ylabel
def get_ylabel(self):
return self.ylabel
def set_style(self, style):
self.style = style
def get_style(self):
return self.style
def set_defaultVal(self, defaultVal):
self.defaultVal = defaultVal
def get_defaultVal(self):
return self.defaultVal
def set_color(self, color):
self.color = color
def get_color(self):
return self.color
def generate_circle(self,R,center,N=100):
"""
Generate an array of x and y values that lie evenly spaced on a circle
with the specified center and radius.
"""
theta = np.linspace(0.0,2.0*np.pi,N)
y = R*np.sin(theta) + center[1]
x = R*np.cos(theta) + center[0]
return x,y
def generate_periodic_circle(self,R, var, xCenter, yCenter, freq, fn):
"""
Generates points that map out a circle with a given periodic function
overlayed.
fn can be the following:
Fun.sine -> overlays sine wave with amplitude "var"
Fun.sawtooth -> overlays the increasing sawtooth that begins at (R-var) and
increases up to (R+var) in each period
Fun.triangle -> overlays the increasing-decreasing triangle, which begins at
(R-var), reaches (R+var) halfway through the period, and then decreases
back to (R-var) by the end of the period.
"""
# The perimeter for a triangle wave is about sqrt((circum)^2+(2*var*freq)^2),
# A little bit is added to get the formula used below, just in case.
nPts = int(2*np.sqrt((2*np.pi*R)**2.0 + (2*var*freq)**2.0)) # ensure sufficient points to fill perimeter
theta = np.linspace(0,2*np.pi, nPts)
# Initalize xy, array of tuples of x- and y-values
xy = np.array([[0,0]])
if freq == 0:
period = 0
else:
period = 2*np.pi/freq
for i in range(len(theta)):
pert = fn(theta[i], period, var)
r = R + pert
# Convert from polar to Cartesian coordinates
x = r*np.cos(theta[i]) + xCenter
y = r*np.sin(theta[i]) + yCenter
xy = np.concatenate((xy,np.array([[x,y]])))
return xy[1:len(xy)]
def sawtooth(self,x, period, var):
"""
Calculates y-value for an increasing sawtooth with amplitude "var" above
and below y = 0, i.e. it begins at (0,-var), passes through (period/2,0),
and ends at (period,+var) in each period.
"""
if period == 0:
return x
else:
x = x % period
frac = x/period
y = (2*frac-1)*var
return y
def sine(self,x, period, var):
"""
Calculates y-value for a sine wave starting at the origin.
"""
return var*np.sin((2*np.pi/period)*x)
def triangle(self,x, period, var):
"""
Calculates y-value for an increasing-decreasing triangle function with
amplitude "var" above and below y = 0, i.e. it begins at (0,-var),
increases to (period/2,+var), and decreases to (period,-var).
"""
if period == 0:
return x
else:
x = x % period
frac = 2*abs(0.5 - (x/period))
y = (1-2*frac)*var
return y
def get_corrected_arclength(self,pts,closed=False):
"""
Smooths the digital curve defined by the row-column tuples in the numpy
array "pts" using a 5-point average, i.e., it replaces each tuple with an
average of the two previous points, the two succeeding points, and the
point itself. The arc-length is then calculated by scaling up the image
to 3-decimal-place precision, applying the OpenCV arcLength function, and
scaling back down.
"""
l = len(pts)
ptsDown2 = np.concatenate((pts[2:l],pts[0:2]))
ptsDown1 = np.concatenate((pts[1:l],np.array([(pts[0][0],pts[0][1])])))
ptsUp1 = np.concatenate((np.array([(pts[l-1][0],pts[l-1][1])]),pts[0:l-1]))
ptsUp2 = np.concatenate((pts[l-2:l],pts[0:l-2]))
summedPts = ptsDown2 + ptsDown1 + pts + pts + ptsUp1 + ptsUp2
avePts = summedPts/5.0
zoomAvePts = 1000.0*avePts
arcLength = cv2.arcLength(zoomAvePts.astype(int),closed)/1000.0
return arcLength
def get_value(self, statName, aveRad, diskRad,
diskCenter,r,rMin, rMax, amp,adjustedArcLength, wettedArea):
if statName == "aveRad":
nonDimRad = float(aveRad)/diskRad
return nonDimRad
if statName == "rMin":
nonDimRMin = float(rMin)/diskRad
return nonDimRMin
if statName == "rMax":
nonDimRMax = float(rMax)/diskRad
return nonDimRMax
#TODO Debug calculation of excPerim so diskMaskIm returns 1.0
if statName == "excPerim":
center = (2*aveRad,2*aveRad)
X,Y = self.generate_circle(aveRad,center)
xy = np.array([(X[l],Y[l]) for l in range(len(X))])
perfectCirc = float(self.get_corrected_arclength(xy.astype(int),closed=True))
excPerim = adjustedArcLength/perfectCirc #(2*np.pi*aveRad)/1.09#(2*np.pi*diskRad/diskCirc)
return excPerim
if statName == "fracWetArea":
return wettedArea/(np.pi*diskRad**2.0)
if statName == "sineFreq":
freq = 0
while True:
sinusoidalCnt = self.generate_periodic_circle(aveRad,amp,diskCenter,freq,self.sine)
testArcLength = cv2.arcLength(sinusoidalCnt.astype(int),True)
if testArcLength >= adjustedArcLength:
break
else:
freq += 1
return freq
if statName == "sawtoothFreq":
freq = 0
while True:
sawtoothCnt = self.generate_periodic_circle(aveRad,amp,diskCenter,freq,self.sawtooth)
testArcLength = cv2.arcLength(sawtoothCnt.astype(int),True)
if testArcLength >= adjustedArcLength:
break
else:
freq += 1
return freq
if statName == "triangleFreq":
freq = 0
while True:
triangleCnt = self.generate_periodic_circle(aveRad,amp,diskCenter,freq,self.triangle)
testArcLength = cv2.arcLength(triangleCnt.astype(int),True)
if testArcLength >= adjustedArcLength:
break
else:
freq += 1
return freq
if statName == "quarterAmplFreq":
# Calculate frequency
rQ = rMin + 1/float(4)*(rMax-rMin); freq = 0
for l in range(1,len(r)):
rQOutPrev = r[l-1] > rQ
rQOut = r[l] > rQ
if rQOutPrev and not rQOut:
freq += 1
return freq
if statName == "halfAmplFreq":
# Calculate frequency
rHalf = (rMax+rMin)/2; freq = 0
for l in range(1,len(r)):
rHalfOutPrev = r[l-1] > rHalf
rHalfOut = r[l] > rHalf
if rHalfOutPrev and not rHalfOut:
freq += 1
return freq
#TODO Fix this calculation
if statName == "fftFreq":
fft = np.fft.rfft(r)
fft = fft[1:]
maxVal = fft.max()
maxMode = fft.searchsorted(maxVal)+1 # +1 corrects for removal of 0th element
return maxMode
if statName == "stDev":
stDev = np.std(r)
scaledStDev = stDev/aveRad
return scaledStDev
def main(self, statsList, aveRad, diskRad, diskCenter,r,rMin, rMax, amp,
adjustedArcLength, wettedArea):
statsVec = np.zeros(len(statsList))
for i in range(len(statsList)):
statsVec[i] = self.get_value(statsList[i], aveRad, diskRad,
diskCenter,r,rMin, rMax, amp,adjustedArcLength, wettedArea)
return statsVec
if __name__ == '__main__':
print