def lineProfile2(self, slice):
""" one slice
Returns:
x: ndarray, one point for each point in the profile (NOT images/slice in stack)
"""
if slice % 300 == 0:
print(' worker lineProfile2() slice:', slice, 'of',
self.numImages)
try:
intensityProfile = profile.profile_line(self.data[slice, :, :],
self.src,
self.dst,
linewidth=self.linewidth)
x = np.asarray([
a for a in range(len(intensityProfile))
]) # make alist of x points (todo: should be um, not points!!!)
yFit, FWHM, left_idx, right_idx = self.fitGaussian(
x, intensityProfile)
except ValueError as e:
print(
'!!!!!!!!!! *********** !!!!!!!!!!!!! my exception in lineProfile2() ... too many values to unpack (expected 2)'
)
print('e:', e)
return (None, None, None, None, None, None)
return (x, intensityProfile, yFit, FWHM, left_idx, right_idx)
def lineProfile(self, slice, src, dst, linewidth=3, doFit=True):
""" one slice
Returns:
x: ndarray, one point for each point in the profile (NOT images/slice in stack)
"""
'''
print('!!!! lineProfile() slice:', slice, 'src:', src, 'dst:', dst)
print(' slice:', slice)
print(' src:', src, type(src))
print(' dst:', dst, type(dst))
print(' self.data.shape:', self.data.shape)
print(' linewidth:', linewidth, type(linewidth))
'''
#channel = 0
#intensityProfile = profile.profile_line(self.stack.stack[channel,slice,:,:], src, dst, linewidth=linewidth)
try:
#print('self.data[slice,:,:].shape', self.data[slice,:,:].shape)
intensityProfile = profile.profile_line(self.data[slice, :, :],
src,
dst,
linewidth=linewidth)
x = np.asarray([
a for a in range(len(intensityProfile))
]) # make alist of x points (todo: should be um, not points!!!)
yFit, FWHM, left_idx, right_idx = self.fitGaussian(
x, intensityProfile)
except ValueError as e:
print(
'!!!!!!!!!! *********** !!!!!!!!!!!!! my exception in lineProfile() ... too many values to unpack (expected 2)'
)
print('e:', e)
return (None, None, None, None, None, None)
'''
print('lineProfile() slice:', slice)
print(' x.shape:', x.shape)
print(' intensityProfile.shape:', intensityProfile.shape)
print(' yFit.shape:', yFit.shape)
print(' FWHM:', FWHM, 'left_idx:', left_idx, 'right_idx:', right_idx)
'''
return (x, intensityProfile, yFit, FWHM, left_idx, right_idx)