def gaussianArrND(shape=(256, 256), sigma=2., peakVal=None, orig=None, rot=0):
try:
ndim = len(shape)
except TypeError:
shape = [shape]
ndim = 1
sidx = ndim + 2
slices = [Ellipsis] + [slice(0, m) for m in shape]
inds, LD = imgFit.rotateIndicesND(slices, N.float32, rot)
#inds = N.indices(shape, N.float32)
try:
if len(sigma) != ndim:
raise ValueError, 'len(sigma) must be the same as len(shape)'
except TypeError:
sigma = [sigma] * ndim
if orig is None:
c = N.asarray(shape, N.float32) / 2.
else:
c = N.asarray(orig, N.float32)
if peakVal:
k0 = peakVal
else:
k0 = 1. / (N.average(sigma) * ((2 * N.pi)**0.5))
param = [0, k0] + list(c) + list(sigma)
param = N.asarray(param, N.float32)
return imgFit.yGaussianND(param, inds, sidx)
def arr_histStretch(img, imgMin=None, imgMax=None, scaleMax=None):
"""
scaleMax = None: use maximum possible for the dtype
"""
if imgMin is None:
imgMin = img.min()
if imgMax is None:
imgMax = img.max()
if scaleMax is None:
img = N.asarray(img)
scaleMax = 1 << (img.nbytes // img.size) * 8
scaleMax -= 1
img = img - imgMin #img.min()
ratio = float(scaleMax) / imgMax #img.max()
return N.asarray(ratio * img, img.dtype.type)
def paddingFourier(arr, shape, value=0, interpolate=True):
"""
arr: assuming origin at 0, rfft product (half x size), up to 3D
shape: target shape
value: the value to fill in empty part
interpolate: shift by interpolation if necessary
return array with target shape
"""
# prepare buffer
dtype = arr.dtype.type
canvas = N.empty(shape, dtype)
canvas[:] = value
# calc and shift
shapeS = N.array(arr.shape)
shapeL = N.asarray(shape)
halfS = shapeS / 2.
subpx_shift = halfS % 1
if interpolate and N.sometrue(subpx_shift):
arr = U.nd.shift(arr, subpx_shift)
# create empty list for slices
nds = arr.ndim - 1
choices = ['slice(halfS[%i])', 'slice(-halfS[%i], None)']
nchoices = len(choices)
nds2 = nds**2
slcs = []
for ns in range(nds2):
slcs.append([])
for n in range(nchoices * nds):
slcs[ns].append(
[Ellipsis]) # Ellipsis help to make arbitray number of list
# fill the empty list by slice (here I don't know how to use 4D..)
for i in range(nds2):
for d in range(nds):
for x in range(nds):
for c, choice in enumerate(choices):
if d == 0 and x == 0:
idx = x * (nchoices) + c
else: # how can I use 4D??
idx = x * (nchoices) + (nchoices - 1) - c
exec('content=' + choice % d)
slcs[i][idx] += [content]
# cutout and paste
for slc in slcs:
for s in slc:
s.append(slice(shapeS[-1]))
#print s
canvas[s] = arr[s]
return canvas
def mask_gaussianND(arr, zyx, v, sigma=2., ret=None, rot=0, clipZero=True):
'''
subtract elliptical gaussian at y,x with peakVal v
if ret, return arr, else, arr itself is edited
'''
import imgGeo
zyx = N.asarray(zyx)
ndim = arr.ndim
shape = N.array(arr.shape)
try:
if len(sigma) != ndim:
raise ValueError, 'len(sigma) must be the same as len(shape)'
else:
sigma = N.asarray(sigma)
except TypeError: #(TypeError, ValueError):
sigma = N.asarray([sigma] * ndim)
# prepare small window
slc = imgGeo.nearbyRegion(shape, N.floor(zyx), sigma * 10)
inds, LD = imgFit.rotateIndicesND(slc, dtype=N.float32, rot=rot)
param = (
0,
v,
) + tuple(zyx) + tuple(sigma)
sidx = 2 + ndim
g = imgFit.yGaussianND(N.asarray(param), inds, sidx).astype(arr.dtype.type)
roi = arr[slc]
if clipZero:
g = N.where(g > roi, roi, g)
if ret:
e = N.zeros_like(arr)
e[slc] = g # this may be faster than copy()
return arr - e
else:
arr[slc] -= g
def gaussianArr2D(
shape=(256, 256), sigma=[2., 2.], peakVal=None, orig=None, rot=0):
"""
>1.5x faster implemetation than gaussianArrND
shape: (y,x)
sigma: scaler or [sigmay, sigmax]
orig: (y,x)
rot: scaler anti-clockwise
return N.float32
"""
shape = N.asarray(shape, N.uint)
try:
if len(sigma) == len(shape):
sy = 2 * (sigma[0] * sigma[0])
sx = 2 * (sigma[1] * sigma[1])
elif len(sigma) == 1:
sx = sy = 2 * (sigma[0] * sigma[0])
else:
raise ValueError, 'sigma must be scaler or [sigmay, sigmax]'
except TypeError: # sigma scaler
sx = sy = 2 * (sigma * sigma)
# print y, x
if rot:
yyi, xxi = imgFit.rotateIndices2D(shape, rot, orig, N.float32)
else:
if orig is None:
y, x = shape / 2. - 0.5 # pixel center remove
else:
y, x = N.subtract(orig, 0.5) # pixel center remove
yi, xi = N.indices(shape, dtype=N.float32)
yyi = y - yi
xxi = x - xi
k1 = -(yyi) * (yyi) / (sy) - (xxi) * (xxi) / (sx)
if peakVal:
k0 = peakVal
else:
k0 = 1. / ((sx + sy) / 2. * ((2 * N.pi)**0.5))
return k0 * N.exp(k1)
def evenShapeArr(a):
"""
return even shaped array
"""
shapeA = N.asarray(a.shape)
shapeM = shapeA.copy()
for i, s in enumerate(shapeM):
if not i and s == 1:
continue
elif s % 2:
shapeM[i] -= 1
#sy,sx = shapeA
#if sx % 2:# or sy %2:
# sx += 1
#if sy % 2:
# sy += 1
#shapeM = N.array([sy, sx])
if N.sometrue(shapeA < shapeM):
a = paddingMed(a, shapeM)
elif N.sometrue(shapeA > shapeM):
a = cutOutCenter(a, shapeM, interpolate=False)
return a
def highPassF(af, highpassSigma=2.5, wiener=0.2, cutoffFreq=3):
"""
fourie space operations
af: array after rfft
half_nyx: half shape required for highpass filter
highpassSigma: highpass filter, if 0, highpass is not done
wiener: wiener coefficient for highpass filte
cutoffFreq: band-pass around origin
return: array BEFORE irfft
WARNING: af will be changed, so use copy() if necessary
"""
global _G, _G_SHAPE
if highpassSigma:
# if half_nyx is None:
ny, nx = af.shape
sy2 = ny / 2.
sx2 = nx - 1
shape = (sy2 * 2, sx2 + 1)
if _G is not None and N.alltrue(_G_SHAPE == shape):
g = _G
else:
g = gaussianArr2D(shape, highpassSigma, peakVal=1, orig=(sy2, 0))
_G = g
_G_SHAPE = N.asarray(shape)
g += wiener
af[:sy2] /= g[sy2:]
af[sy2:] /= g[:sy2]
# kill DC
af.flat[0] = 0
# kill lowest freq
af[0:cutoffFreq] = 0
af[:, 0:cutoffFreq] = 0
return af
def Xcorr(a,
b,
highpassSigma=2.5,
wiener=0.2,
cutoffFreq=3,
forceSecondPeak=None,
acceptOrigin=True,
maskSigmaFact=1.,
removeY=None,
removeX=None,
ret=None,
normalize=True,
gFit=True,
lap=None,
win=11):
"""
returns (y,x), image
if ret is True, returns [v, yx, image]
to get yx cordinate of the image,
yx += N.divide(picture.shape, 2)
a, b: 2D array
highpassSigma: sigma value used for highpass pre-filter
wiener: wiener value used for highpass pre-filter
cutoffFreq: kill lowest frequency component from 0 to this level
forceSecondPeak: If input is n>0 (True is 1), pick up n-th peak
acceptOrigin: If None, result at origin is rejected, look for the next peak
maskSigmaFact: Modifier to remove previous peak to look for another peak
removeYX: Rremove given number of pixel high intensity lines of the Xcorr
Y: Vertical, X: Horizontal
normalize: intensity normalized
gFit: peak is fitted to 2D gaussian array, if None use center of mass
win: window for gFit
if b is a + (y,x) then, answer is (-y,-x)
"""
shapeA = N.asarray(a.shape)
shapeB = N.asarray(b.shape)
shapeM = N.max([shapeA, shapeB], axis=0)
shapeM = N.where(shapeM % 2, shapeM + 1, shapeM)
center = shapeM / 2.
arrs = [a, b]
arrsS = ['a', 'b']
arrsF = []
for i, arr in enumerate(arrs):
if arr.dtype not in [N.float32, N.float64]:
arr = N.asarray(arr, N.float32)
# this convolution has to be done beforehand to remove 2 pixels at the edge
if lap == 'nothing':
pass
elif lap:
arr = arr_Laplace(arr, mask=2)
else:
arr = arr_sorbel(arr, mask=1)
if N.sometrue(shapeA < shapeM):
arr = paddingMed(arr, shapeM)
if normalize:
mi, ma, me, sd = U.mmms(arr)
arr = (arr - me) / sd
if i == 1:
arr = F.shift(arr)
af = F.rfft(arr)
af = highPassF(af, highpassSigma, wiener, cutoffFreq)
arrsF.append(af)
# start cross correlation
af, bf = arrsF
bf = bf.conjugate()
cf = af * bf
# go back to space domain
c = F.irfft(cf)
# c = _changeOrigin(cr)
# removing lines
if removeX:
yi, xi = N.indices((removeX, shapeM[-1])) #sx))
yi += center[-2] - removeX / 2. #sy/2 - removeX/2
c[yi, xi] = 0
if removeY:
yi, xi = N.indices((shapeM[-2], removeY)) #sy, removeY))
xi += center[-1] - removeY / 2. #sx/2 - removeY/2
c[yi, xi] = 0
# find the first peak
if gFit:
v, yx, s = findMaxWithGFit(c, win=win) #, window=win, gFit=gFit)
if v == 0:
v, yx, s = findMaxWithGFit(c, win=win +
2) #, window=win+2, gFit=gFit)
if v == 0:
v = U.findMax(c)[0]
yx = N.add(yx, 0.5)
#yx += 0.5
else:
vzyx = U.findMax(c)
v = vzyx[0]
yx = vzyx[-2:]
s = 2.5
yx -= center
if N.alltrue(N.abs(yx) < 1.0) and not acceptOrigin:
forceSecondPeak = True
# forceSecondPeak:
if not forceSecondPeak:
forceSecondPeak = 0
for i in range(int(forceSecondPeak)):
print '%i peak was removed' % (i + 1) #, sigma: %.2f' % (i+1, s)
yx += center
g = gaussianArr2D(c.shape, sigma=s / maskSigmaFact, peakVal=v, orig=yx)
c = c - g
#c = mask_gaussian(c, yx[0], yx[1], v, s)
if gFit:
v, yx, s = findMaxWithGFit(c, win=win) #, window=win, gFit=gFit)
if v == 0:
v, yx, s = findMaxWithGFit(c, win=win +
2) #, window=win+2, gFit=gFit)
if v == 0:
v = U.findMax(c)[0]
yx -= (center - 0.5)
else:
vzyx = U.findMax(c)
v = vzyx[0]
if not gFit:
yx = centerOfMass(c, vzyx[-2:]) - center
if lap is not 'nothing':
c = paddingValue(c, shapeM + 2)
if ret == 2:
return yx, af, bf.conjugate()
elif ret:
return v, yx, c
else:
return yx, c
def mask_value(arr, zyx, r=2.5, value=0):
''' Edit the pixels around zyx to be zero '''
import imgGeo
sls = imgGeo.nearbyRegion(arr.shape, zyx, 2 * N.asarray(r) + 1)
arr[sls] = value
def pointsCutOutND(arr,
posList,
windowSize=100,
sectWise=None,
interpolate=True):
"""
array: nd array
posList: ([(z,)y,x]...)
windowSize: scalar (in pixel or as percent < 1.) or ((z,)y,x)
if arr.ndim > 2, and len(windowSize) == 2, then
cut out section-wise (higher dimensions stay the same)
sectWise: conern only XY of windowSize (higher dimensions stay the same)
interpolate: shift array by subpixel interpolation to adjust center
return: list of array centered at each pos in posList
"""
shape = N.array(arr.shape)
center = shape / 2.
# prepare N-dimensional window size
try:
len(windowSize) # seq
if sectWise:
windowSize = windowSize[-2:]
if len(windowSize) != arr.ndim:
dim = len(windowSize)
windowSize = tuple(shape[:-dim]) + tuple(windowSize)
except TypeError: # scaler
if windowSize < 1 and windowSize > 0: # percentage
w = shape * windowSize
if sectWise:
w[:-2] = shape[:-2]
windowSize = w.astype(N.uint16)
else:
windowSize = N.where(shape >= windowSize, windowSize, shape)
if sectWise:
windowSize = arr.shape[:-2] + windowSize[-2:]
windowSize = N.asarray(windowSize)
# cutout individual position
arrList = []
for pos in posList:
# prepare N-dimensional coordinate
n = len(pos)
if n != len(windowSize):
temp = center.copy()
center[-n:] = pos
pos = center
# calculate idx
ori = pos - (windowSize / 2.) # float value
oidx = N.ceil(ori) # idx
subpxl = oidx - ori # subpixel mod
if interpolate and N.sometrue(subpxl): # comit to make shift
SHIFT = 1
else:
SHIFT = 0
# prepare slice
# when comitted to make shift, first cut out window+1,
# then make subpixle shift, and then cutout 1 edge
slc = [Ellipsis] # Ellipsis is unnecessary, just in case...
slc_edge = [slice(1, -1, None)] * arr.ndim
for d in range(arr.ndim):
start = oidx[d] - SHIFT
if start < 0:
start = 0
slc_edge[d] = slice(0, slc_edge[d].stop, None)
stop = oidx[d] + windowSize[d] + SHIFT
if stop > shape[d]:
stop = shape[d]
slc_edge[d] = slice(slc_edge[d].start, shape[d], None)
slc += [slice(int(start), int(stop), None)]
# cutout, shift and cutout
try:
canvas = arr[slc]
if SHIFT:
canvas = U.nd.shift(canvas, subpxl)
canvas = canvas[slc_edge]
check = 1
except IndexError:
print 'position ', pos, ' was skipped'
check = 0
raise
if check:
arrList += [N.ascontiguousarray(canvas)]
return arrList