def longAxisOrthDist(self):
from PYME.Analysis.binAvg import binAvg
xvs = np.linspace(-1, 1, self.nsteps)
bms = []
mc = self.chans[self.masterChan]
for c in self.chans:
bn, bm, bs = binAvg(mc.A0 / mc.geom_length, c.data, xvs)
bss = bm * bn
bn, bm, bs = binAvg(mc.A0 / mc.geom_length, c.data * mc.SA, xvs)
bb = bm * bn
bms.append(bb / bss)
return xvs, bms
def imageDensityAtDistance(A, mask, voxelsize = None, bins=100):
'''Calculates the distribution of a label at varying distances from a mask.
Negative distances are on the inside of the mask.
Parameters:
A - intensity image
mask - binary mask
voxelsize - size of the pixels/voxels - should be either a constant, or an iterable
with a length equal to the number of dimensions in the data
bins - either a number of bins, or an array of bin edges
Returns:
bn - integrated intensity in distance bin
bm - mean intensity in distance bin
bins - the bin edges
'''
if voxelsize == None:
voxelsize = numpy.ones(len(A.shape))
dt = -ndimage.distance_transform_edt(mask, sampling=voxelsize)
dt = dt + ndimage.distance_transform_edt(1- ndimage.binary_dilation(mask), sampling=voxelsize)
if numpy.isscalar(bins):
bins = numpy.linspace(dt.min(), dt.max(), bins+1)
#print bins
bn, bm, bs = binAvg.binAvg(dt, A, bins)
return bn, bm, bins
def OnColoc(self, event):
from PYME.Analysis import binAvg
voxelsize = self.image.voxelsize
#assume we have exactly 2 channels #FIXME - add a selector
#grab image data
imA = self.image.data[:,:,:,0].squeeze()
imB = self.image.data[:,:,:,1].squeeze()
X, Y = np.mgrid[0:float(imA.shape[0]), 0:float(imA.shape[1])]
X = X/X.shape[0]
Y = Y/X.shape[1]
X = X - .5
Y = Y - .5
R = np.sqrt(X**2 + Y**2)
H1 = pylab.fftn(imA)
H2 = pylab.fftn(imB)
rB = np.linspace(0,R.max())
bn, bm, bs = binAvg.binAvg(R, pylab.fftshift(abs(H1*H2)), rB)
bn1, bm1, bs1 = binAvg.binAvg(R, pylab.fftshift(abs(H1*H1)), rB)
bn2, bm2, bs2 = binAvg.binAvg(R, pylab.fftshift(abs(H2*H2)), rB)
pylab.figure()
ax = pylab.gca()
ax.plot(rB[:-1], bm/np.sqrt(bm1*bm2))
ax.plot(rB[:-1], 2./np.sqrt(bn/2))
xt = np.array([10., 15, 20, 30, 50, 80, 100, 150])
rt = voxelsize[0]/xt
pylab.xticks(rt[::-1],['%d' % xi for xi in xt[::-1]])
pylab.show()
def angularDist(self):
from PYME.Analysis.binAvg import binAvg
xvs = np.linspace(-np.pi, np.pi, self.nsteps)
bms = []
mc = self.chans[self.masterChan]
for c in self.chans:
bn, bm, bs = binAvg(mc.Theta, c.data, xvs)
bb = bm * bn
bms.append(bb / bb.sum())
return xvs, bms
def shortAxisDist(self):
from PYME.Analysis.binAvg import binAvg
xvs = np.linspace(-500, 500, self.nsteps)
bms = []
mc = self.chans[self.masterChan]
for c in self.chans:
bn, bm, bs = binAvg(mc.SA, c.data, xvs)
bb = bm * bn
bms.append(bb / bb.sum())
return xvs, bms
def RadialDistN(self):
from PYME.Analysis.binAvg import binAvg
xvs = np.linspace(0, 1, self.nsteps)
bms = []
mc = self.chans[self.masterChan]
R = mc.R / (mc.geom_length / 2)
for c in self.chans:
bn, bm, bs = binAvg(R, c.data, xvs)
bb = bm * bn
bms.append(bb / bb.sum())
return xvs, bms
def radialDistN(self):
from PYME.Analysis.binAvg import binAvg
xvs = np.linspace(0, 2, self.nsteps)
bms = []
mc = self.chans[self.masterChan]
r = mc.r / (mc.geom_length / 2)
for c in self.chans:
bn, bm, bs = binAvg(r, c.data, xvs)
bb = bm * bn
bms.append(bb / bb.sum())
return xvs, bms
def OnColoc(self, event):
import matplotlib.pyplot as plt
from PYME.Analysis import binAvg
voxelsize = self.image.voxelsize
#assume we have exactly 2 channels #FIXME - add a selector
#grab image data
imA = self.image.data[:,:,:,0].squeeze()
imB = self.image.data[:,:,:,1].squeeze()
X, Y = np.mgrid[0:float(imA.shape[0]), 0:float(imA.shape[1])]
X = X/X.shape[0]
Y = Y/X.shape[1]
X = (X - .5)
Y = Y - .5
R = np.sqrt(X**2 + Y**2)
H1 = np.fft.fftn(imA)
H2 = np.fft.fftn(imB)
#rB = np.linspace(0,R.max())
rB = np.linspace(0, 0.5, 100)
bn, bm, bs = binAvg.binAvg(R, np.fft.fftshift(H1*H2.conjugate()).real, rB)
bn1, bm1, bs1 = binAvg.binAvg(R, np.fft.fftshift((H1*H1.conjugate()).real), rB)
bn2, bm2, bs2 = binAvg.binAvg(R, np.fft.fftshift((H2*H2.conjugate()).real), rB)
plt.figure()
ax = plt.gca()
#FRC
FRC = bm/np.sqrt(bm1*bm2)
ax.plot(rB[:-1], FRC)
#noise envelope???????????
ax.plot(rB[:-1], 2./np.sqrt(bn/2), ':')
dfrc = np.diff(FRC)
monotone = np.where(dfrc > 0)[0][0] + 1
#print FRC[:monotone], FRC[:(monotone+1)]
intercept = np.interp(1.0 - 1/7.0, 1-FRC[:monotone], rB[:monotone])
print('Intercept= %3.2f (%3.2f nm)' % (intercept, voxelsize[0]/intercept))
xt = np.array([10., 15, 20, 30, 40, 50, 70, 90, 120, 150, 200, 300, 500])
rt = voxelsize[0]/xt
plt.xticks(rt[::-1],['%d' % xi for xi in xt[::-1]], rotation='vertical')
ax.plot([0, rt[0]], np.ones(2)/7.0)
plt.grid()
plt.xlabel('Resolution [nm]')
plt.ylabel('FRC')
plt.figtext(0.5, 0.5, 'FRC intercept at %3.1f nm' % (voxelsize[0]/intercept))
plt.show()
def fourier_ring_correlation(imA, imB, voxelsize=[1.0, 1.0], window=False):
import matplotlib.pyplot as plt
from PYME.Analysis import binAvg
imA = imA.squeeze()
imB = imB.squeeze()
X, Y = np.mgrid[0:float(imA.shape[0]), 0:float(imA.shape[1])]
X = X / X.shape[0]
Y = Y / X.shape[1]
X = (X - .5)
Y = Y - .5
R = np.sqrt(X**2 + Y**2)
if window:
W = np.hanning(X.shape[0])[:, None] * np.hanning(X.shape[1])[None, :]
imA = imA * W
imB = imB * W
H1 = np.fft.fftn(imA)
H2 = np.fft.fftn(imB)
#rB = np.linspace(0,R.max())
rB = np.linspace(0, 0.5, 100)
bn, bm, bs = binAvg.binAvg(R,
np.fft.fftshift(H1 * H2.conjugate()).real, rB)
bn1, bm1, bs1 = binAvg.binAvg(R, np.fft.fftshift(
(H1 * H1.conjugate()).real), rB)
bn2, bm2, bs2 = binAvg.binAvg(R, np.fft.fftshift(
(H2 * H2.conjugate()).real), rB)
plt.figure()
ax = plt.gca()
#FRC
FRC = bm / np.sqrt(bm1 * bm2)
ax.plot(rB[:-1], FRC)
#noise envelope???????????
ax.plot(rB[:-1], 2. / np.sqrt(bn / 2), ':')
dfrc = np.diff(FRC)
#print FRC
monotone = np.where(dfrc > 0)[0][0] + 1
#print FRC[:monotone], FRC[:(monotone+1)]
intercept_m = np.interp(1.0 - 1 / 7.0, 1 - FRC[:monotone], rB[:monotone])
print('Intercept_m= %3.2f (%3.2f nm)' %
(intercept_m, voxelsize[0] / intercept_m))
from scipy import ndimage
f_s = np.sign(FRC - 1. / 7.)
fss = ndimage.gaussian_filter(f_s, 10, mode='nearest')
intercept = np.interp(0.0, -fss, rB[:-1])
print('Intercept= %3.2f (%3.2f nm)' %
(intercept, voxelsize[0] / intercept))
xt = np.array([10., 15, 20, 30, 40, 50, 70, 90, 120, 150, 200, 300, 500])
rt = voxelsize[0] / xt
plt.xticks(rt[::-1], ['%d' % xi for xi in xt[::-1]], rotation='vertical')
ax.plot([0, rt[0]], np.ones(2) / 7.0)
plt.grid()
plt.xlabel('Resolution [nm]')
plt.ylabel('FRC')
plt.ylim(0, 1.1)
plt.plot([intercept, intercept], [0, 1], '--')
plt.figtext(0.5, 0.5,
'FRC intercept at %3.1f nm' % (voxelsize[0] / intercept))
plt.figure()
plt.plot(rB[:-1], f_s)
plt.plot(rB[:-1], fss)
plt.show()