def split_matrix(parId, iterator):
x0 = -1
y0 = -1
z0 = -1
t0 = 0
for x in iterator:
x0 = x[1][0]
y0 = x[1][1]
z0 = x[1][2]
t0 += 1
vol10 = npy2vol(BC_vol1.value, 3)
vol20 = npy2vol(BC_vol2.value, 3)
boxhalf_x1 = BC_sizeX.value / 2
boxhalf_y1 = BC_sizeY.value / 2
boxhalf_z1 = BC_sizeZ.value / 2
vol1_sub = subvolume(vol10, x0 - boxhalf_x1, y0 - boxhalf_y1, z0 - boxhalf_z1, BC_sizeX.value, BC_sizeY.value, BC_sizeZ.value)
vol2_sub = subvolume(vol20, x0 - boxhalf_x1, y0 - boxhalf_y1, z0 - boxhalf_z1, BC_sizeX.value, BC_sizeY.value, BC_sizeZ.value)
avg1 = mean(vol1_sub)
vol1_sub1 = hanning_taper(vol1_sub, avg1)
avg2 = mean(vol2_sub)
vol2_sub1 = hanning_taper(vol2_sub, avg2)
res = fsc2_v(vol1_sub1, vol2_sub1, BC_fsc_criterion.value, BC_max_resolution.value, BC_pixelSize.value, x0, y0, z0)
tup = (round(res,6), x0, y0, z0)
del avg1, avg2, vol1_sub1, vol2_sub1
del vol1_sub, vol2_sub, res, vol10, vol20, boxhalf_x1, boxhalf_y1, boxhalf_z1, x0, y0, z0, t0
return tup
def add(volume, SNR=1):
"""
add Adds white noise to volume
@param volume: A volume
@param SNR: Signal to Noise ratio of result
@type SNR: int or float > 0
@return: Volume containing noise with SNR == SNR
@author: Thomas Hrabe
"""
if (SNR < 0):
return volume
from math import sqrt
from pytom_volume import vol, mean, variance, gaussianNoise
m = mean(volume)
s = sqrt(variance(volume, False) / SNR) # SNR = Var(signal) / Var(noise)
# s = sqrt(variance(volume,False)/SNR)-variance(volume,False)
#
# if s<0:
# return volume
# elif s==0:
# s =1
noise = vol(volume.sizeX(), volume.sizeY(), volume.sizeZ())
gaussianNoise(noise, m, s) # s is actually the std
result = volume + noise
return result
def mean0std1(volume, copyFlag=False):
"""
mean0std1: normalises input volume to mean 0 and std 1. Procedure is performed inplace if copyFlag is unspecified!!!
@param volume: Data containing either an image or a volume
@param copyFlag: If True a copy of volume will be returned. False unless specified otherwise.
@return: If copyFlag == True, then return a normalised copy.
@author: Thomas Hrabe
"""
import pytom_volume
from math import sqrt
from pytom.tools.maths import epsilon
if volume.__class__ == pytom_volume.vol_comp:
from pytom.basic.fourier import ifft, iftshift
volume = iftshift(ifft(volume))
if not copyFlag:
volumeMean = pytom_volume.mean(volume)
volume.shiftscale(-volumeMean, 1)
volumeStd = sqrt(pytom_volume.variance(volume, False))
if volumeStd < epsilon:
raise ValueError(
'pytom_normalise.mean0std1 : The standard deviation is too low for division! '
+ str(volumeStd))
volume.shiftscale(0, 1. / float(volumeStd))
else:
volumeCopy = pytom_volume.vol(volume.sizeX(), volume.sizeY(),
volume.sizeZ())
volumeCopy.copyVolume(volume)
volumeMean = pytom_volume.mean(volumeCopy)
volumeCopy.shiftscale(-1. * volumeMean, 1)
volumeStd = sqrt(pytom_volume.variance(volumeCopy, False))
if volumeStd < epsilon:
raise ValueError(
'pytom_normalise.mean0std1 : The standard deviation is too low for division! '
+ str(volumeStd))
#volumeCopy.shiftscale(-1.*volumeMean,1)
volumeCopy.shiftscale(0, 1 / float(volumeStd))
return volumeCopy
def mean0std1_Test(self):
import pytom_volume
from pytom.basic.normalise import mean0std1
v = pytom_volume.read('./testData/ribo.em')
m = mean0std1(v, True)
me = pytom_volume.mean(m)
var = pytom_volume.variance(m, False)
assert epsilon >= me >= -epsilon #mean value test
assert 1 + epsilon >= var >= 1 - epsilon
def rescale_to_avg_std(volume1, nuavg, nustd):
avg = mean(volume1)
std = np.sqrt(variance(volume1, False))
if (std > 1e-30):
scale = nustd/std
else:
scale = 1
shift = nuavg - avg*scale
x = volume1.sizeX()
y = volume1.sizeY()
z = volume1.sizeZ()
for zz in xrange(0,z):
for yy in xrange(0,y):
for xx in xrange(0,x):
val = volume1(xx,yy,zz)*scale + shift
volume1.setV(round(val,6),xx,yy,zz)
return volume1
def calculate_difference_map(v1,
band1,
v2,
band2,
mask=None,
focus_mask=None,
align=True,
sigma=None,
threshold=0.4):
"""mask if for alignment, while focus_mask is for difference map.
"""
from pytom_volume import vol, power, abs, limit, transformSpline, variance, mean, max, min
from pytom.basic.normalise import mean0std1
from pytom.basic.filter import lowpassFilter
# do lowpass filtering first
lv1 = lowpassFilter(v1, band1, band1 / 10.)[0]
lv2 = lowpassFilter(v2, band2, band2 / 10.)[0]
# do alignment of two volumes, if required. v1 is used as reference.
if align:
from sh_alignment.frm import frm_align
band = int(band1 if band1 < band2 else band2)
pos, angle, score = frm_align(lv2, None, lv1, None, [4, 64], band,
lv1.sizeX() // 4, mask)
shift = [
pos[0] - v1.sizeX() // 2, pos[1] - v1.sizeY() // 2,
pos[2] - v1.sizeZ() // 2
]
# transform v2
lvv2 = vol(lv2)
transformSpline(lv2, lvv2, -angle[1], -angle[0], -angle[2],
lv2.sizeX() // 2,
lv2.sizeY() // 2,
lv2.sizeZ() // 2, -shift[0], -shift[1], -shift[2], 0,
0, 0)
else:
lvv2 = lv2
# do normalization
mean0std1(lv1)
mean0std1(lvv2)
# only consider the density beyond certain sigma
if sigma is None or sigma == 0:
pass
elif sigma < 0: # negative density counts
assert min(lv1) < sigma
assert min(lvv2) < sigma
limit(lv1, 0, 0, sigma, 0, False, True)
limit(lvv2, 0, 0, sigma, 0, False, True)
else: # positive density counts
assert max(lv1) > sigma
assert max(lvv2) > sigma
limit(lv1, sigma, 0, 0, 0, True, False)
limit(lvv2, sigma, 0, 0, 0, True, False)
# if we want to focus on specific area only
if focus_mask:
lv1 *= focus_mask
lvv2 *= focus_mask
# calculate the STD map
avg = (lv1 + lvv2) / 2
var1 = avg - lv1
power(var1, 2)
var2 = avg - lvv2
power(var2, 2)
std_map = var1 + var2
power(std_map, 0.5)
# calculate the coefficient of variance map
# std_map = std_map/abs(avg)
if focus_mask:
std_map *= focus_mask
# threshold the STD map
mv = mean(std_map)
threshold = mv + (max(std_map) - mv) * threshold
limit(std_map, threshold, 0, threshold, 1, True, True)
# do a lowpass filtering
std_map1 = lowpassFilter(std_map, v1.sizeX() // 4, v1.sizeX() / 40.)[0]
if align:
std_map2 = vol(std_map)
transformSpline(std_map1, std_map2, angle[0], angle[1], angle[2],
v1.sizeX() // 2,
v1.sizeY() // 2,
v1.sizeZ() // 2, 0, 0, 0, shift[0], shift[1], shift[2])
else:
std_map2 = std_map1
limit(std_map1, 0.5, 0, 1, 1, True, True)
limit(std_map2, 0.5, 0, 1, 1, True, True)
# return the respective difference maps
return (std_map1, std_map2)
fsc_criterion=0.143
window_size = L
increment= 4
step = increment
numberBands = int(window_size/8)
sizeX = sizeY = sizeZ = window_size
conf = SparkConf().setAppName("parallel local FSC").setMaster("local[*]")
sc = SparkContext(conf=conf)
vol1File = "./emd_3802_half_map_1.map"
vol2File = "./emd_3802_half_map_2.map"
hm1 = read(vol1File)
hm2 = read(vol2File)
avg1 = mean(hm1)
std1 = np.sqrt(variance(hm1, False))
hm20 = rescale_to_avg_std(hm2, avg1, std1)
nz = hm1.sizeZ()
ny = hm1.sizeY()
nx = hm1.sizeX()
mask_level = -1
vz = vy = vx = window_size/2
pmask = vol(nx,ny,nz)
pmask.setAll(1)
# set up the mask for which voxels to calculate
total_num = 0
def _dspcub(volume, sigma=None, projectionAxis='z'):
"""
_dspcub: Creates a dspcub image
dspcub2PNG: display z-slices in 2D image
@param volume: The input volume
@type volume: L{pytom_volume.vol}
@parameter sigma: thresholding as multiples of standard deviation sigma
@type sigma: float
@param projectionAxis: Defines the axis. Default is z, means you look on the xy plane. (x equals to 'yz' plane, y to 'xz')
@return: Image
@rtype: Image
@@author: Pia Unverdorben
"""
if volume.sizeZ() == 1:
raise Exception('You can use ')
import Image
from pytom_volume import min, max, mean, variance, limit, subvolume
from math import sqrt, ceil, floor
sizeX = volume.sizeX()
sizeY = volume.sizeY()
sizeZ = volume.sizeZ()
if projectionAxis == 'x':
imagesPerRow = int(floor(sqrt(sizeX)))
size1 = float(sizeX)
sizeI = sizeY
sizeJ = sizeZ
elif projectionAxis == 'y':
imagesPerRow = int(floor(sqrt(sizeY)))
size1 = float(sizeY)
sizeI = sizeX
sizeJ = sizeZ
elif projectionAxis == 'z':
imagesPerRow = int(floor(sqrt(sizeZ)))
size1 = float(sizeZ)
sizeI = sizeX
sizeJ = sizeY
numberIterations = imagesPerRow * imagesPerRow
if size1 < numberIterations:
iterationSteps = float(numberIterations / size1)
else:
iterationSteps = float(size1 / numberIterations)
iterationSteps = int(iterationSteps)
if projectionAxis == 'x':
img = Image.new('L', (sizeY * imagesPerRow, sizeZ * imagesPerRow))
elif projectionAxis == 'y':
img = Image.new('L', (sizeX * imagesPerRow, sizeZ * imagesPerRow))
elif projectionAxis == 'z':
img = Image.new('L', (sizeX * imagesPerRow, sizeY * imagesPerRow))
# normalize according to standard deviation if sigma is specified
if sigma:
meanv = mean(volume)
stdv = sqrt(variance(volume, False))
minValue = meanv - float(sigma) * stdv
maxValue = meanv + float(sigma) * stdv
else:
minValue = min(volume)
maxValue = max(volume)
for sliceNumber in range(0, numberIterations, iterationSteps):
if projectionAxis == 'x':
png = Image.new('L', (sizeY, sizeZ))
elif projectionAxis == 'y':
png = Image.new('L', (sizeX, sizeZ))
elif projectionAxis == 'z':
png = Image.new('L', (sizeX, sizeY))
(yvalue, xvalue) = divmod(sliceNumber, imagesPerRow)
if projectionAxis == 'x':
vol = subvolume(volume, sliceNumber, 0, 0, 1, sizeY, sizeZ)
elif projectionAxis == 'y':
vol = subvolume(volume, 0, sliceNumber, 0, sizeX, 1, sizeZ)
elif projectionAxis == 'z':
vol = subvolume(volume, 0, 0, sliceNumber, sizeX, sizeY, 1)
vol.shiftscale(-minValue, 1)
vol.shiftscale(0, 255 / maxValue)
for i in range(sizeI):
for j in range(sizeJ):
if projectionAxis == 'x':
value = vol(0, i, j)
elif projectionAxis == 'y':
value = vol(i, 0, j)
elif projectionAxis == 'z':
value = vol(i, j, 0)
png.putpixel((i, j), int(value))
img.paste(png, (xvalue * sizeI, yvalue * sizeJ))
return img