def l2norm(self, delta, array0):
num = 0
den = 0
for k in list(delta.keys()):
num += afnumpy.sum((delta[k] * delta[k].conj()).real)
den += afnumpy.sum((array0[k] * array0[k].conj()).real)
return np.sqrt(num / den)
def l2norm(self, delta, array0):
num = 0
den = 0
for k in delta.keys():
num += afnumpy.sum( (delta[k] * delta[k].conj()).real )
den += afnumpy.sum( (array0[k] * array0[k].conj()).real )
return np.sqrt(num / den)
def test_sum():
b = numpy.random.random(3)
a = afnumpy.array(b)
fassert(afnumpy.sum(a), numpy.sum(b))
fassert(afnumpy.sum(a,axis=0), numpy.sum(b,axis=0))
fassert(afnumpy.sum(a,keepdims=True), numpy.sum(b,keepdims=True))
b = numpy.random.random((2,3))
a = afnumpy.array(b)
fassert(afnumpy.sum(a), numpy.sum(b))
fassert(afnumpy.sum(a,axis=0), numpy.sum(b,axis=0))
def test_sum():
b = numpy.random.random(3)
a = afnumpy.array(b)
fassert(afnumpy.sum(a), numpy.sum(b))
fassert(afnumpy.sum(a, axis=0), numpy.sum(b, axis=0))
fassert(afnumpy.sum(a, keepdims=True), numpy.sum(b, keepdims=True))
b = numpy.random.random((2, 3))
a = afnumpy.array(b)
fassert(afnumpy.sum(a), numpy.sum(b))
fassert(afnumpy.sum(a, axis=0), numpy.sum(b, axis=0))
def radial_symetry_af2(background, inds=None, tots=None, is_fft_shifted=True):
if (inds is None) or (tots is None):
print('initialising...')
i = np.fft.fftfreq(background.shape[0]) * background.shape[0]
j = np.fft.fftfreq(background.shape[1]) * background.shape[1]
k = np.fft.fftfreq(background.shape[2]) * background.shape[2]
i, j, k = np.meshgrid(i, j, k, indexing='ij')
rs = np.rint(np.sqrt(i**2 + j**2 + k**2)).astype(np.int)
if is_fft_shifted is False:
rs = np.fft.fftshift(rs)
rs = afnumpy.array(rs.ravel())
# store a list of indexes and totals
inds = []
tots = []
for i in range(0, afnumpy.max(rs) + 1):
m = (rs == i)
j = afnumpy.where(m)
inds.append(j)
tots.append(afnumpy.float(afnumpy.sum(m)))
out = background.ravel()
for ind, tot in zip(inds[:5], tots[:5]):
out[ind] = 2.
#a = afnumpy.sum(background[ind])
#out[ind] = afnumpy.sum(background[ind]) #/ tot
return out, inds, tots
def radial_symetry_af2(background, inds = None, tots = None, is_fft_shifted = True):
if (inds is None) or (tots is None) :
print 'initialising...'
i = np.fft.fftfreq(background.shape[0]) * background.shape[0]
j = np.fft.fftfreq(background.shape[1]) * background.shape[1]
k = np.fft.fftfreq(background.shape[2]) * background.shape[2]
i, j, k = np.meshgrid(i, j, k, indexing='ij')
rs = np.rint(np.sqrt(i**2 + j**2 + k**2)).astype(np.int)
if is_fft_shifted is False :
rs = np.fft.fftshift(rs)
rs = afnumpy.array(rs.ravel())
# store a list of indexes and totals
inds = []
tots = []
for i in range(0, afnumpy.max(rs)+1):
m = (rs == i)
j = afnumpy.where(m)
inds.append(j)
tots.append(afnumpy.float(afnumpy.sum(m)))
out = background.ravel()
for ind, tot in zip(inds[:5], tots[:5]) :
out[ind] = 2.
#a = afnumpy.sum(background[ind])
#out[ind] = afnumpy.sum(background[ind]) #/ tot
return out, inds, tots
def radial_symetry_af(background, rs=None, is_fft_shifted=True):
if rs is None:
i = np.fft.fftfreq(background.shape[0]) * background.shape[0]
j = np.fft.fftfreq(background.shape[1]) * background.shape[1]
k = np.fft.fftfreq(background.shape[2]) * background.shape[2]
i, j, k = np.meshgrid(i, j, k, indexing='ij')
rs = np.rint(np.sqrt(i**2 + j**2 + k**2)).astype(np.int)
if is_fft_shifted is False:
rs = np.fft.fftshift(rs)
rs = afnumpy.array(rs)
out = background
for i in range(0, afnumpy.max(rs) + 1):
m = (rs == i)
msum = afnumpy.sum(m)
if msum > 1:
out[m] = afnumpy.sum(background[m]) / float(msum)
return out, rs, None
def radial_symetry_af(background, rs = None, is_fft_shifted = True):
if rs is None :
i = np.fft.fftfreq(background.shape[0]) * background.shape[0]
j = np.fft.fftfreq(background.shape[1]) * background.shape[1]
k = np.fft.fftfreq(background.shape[2]) * background.shape[2]
i, j, k = np.meshgrid(i, j, k, indexing='ij')
rs = np.rint(np.sqrt(i**2 + j**2 + k**2)).astype(np.int)
if is_fft_shifted is False :
rs = np.fft.fftshift(rs)
rs = afnumpy.array(rs)
out = background
for i in range(0, afnumpy.max(rs)+1):
m = (rs == i)
msum = afnumpy.sum(m)
if msum > 1 :
out[m] = afnumpy.sum(background[m]) / float(msum)
return out, rs, None
def choose_N_highest_pixels(array, N, tol=1.0e-5, maxIters=1000, support=None):
"""
Use bisection to find the root of
e(x) = \sum_i (array_i > x) - N
then return (array_i > x) a boolean mask
This is faster than using percentile (surprising)
If support0 is not None then values outside the support
are ignored.
"""
s0 = array.max()
s1 = array.min()
if support is not None:
a = array[support > 0]
else:
a = array
support = 1
for i in range(maxIters):
s = (s0 + s1) / 2.
e = afnumpy.sum(a > s) - N
if np.abs(e) < tol:
break
if e < 0:
s0 = s
else:
s1 = s
S = (array > s) * support
#print 'number of pixels in support:', afnumpy.sum(support), i, s, e, type(support)
return S
def choose_N_highest_pixels(array, N, tol = 1.0e-5, maxIters=1000, support=None):
"""
Use bisection to find the root of
e(x) = \sum_i (array_i > x) - N
then return (array_i > x) a boolean mask
This is faster than using percentile (surprising)
If support0 is not None then values outside the support
are ignored.
"""
s0 = array.max()
s1 = array.min()
if support is not None :
a = array[support > 0]
else :
a = array
support = 1
for i in range(maxIters):
s = (s0 + s1) / 2.
e = afnumpy.sum(a > s) - N
if np.abs(e) < tol :
break
if e < 0 :
s0 = s
else :
s1 = s
S = (array > s) * support
#print 'number of pixels in support:', afnumpy.sum(support), i, s, e, type(support)
return S
def Emod(self, modes):
M = self.Imap(modes)
eMod = afnumpy.sum(self.mask * (afnumpy.sqrt(M) - self.amp)**2)
eMod = afnumpy.sqrt(eMod / self.I_norm)
return eMod
def norm(x, ord=None, axis=None, keepdims=False):
x = asarray(x)
# Check the default case first and handle it immediately.
if ord is None and axis is None:
ndim = x.ndim
x = x.ravel(order='K')
if isComplexType(x.dtype.type):
sqnorm = dot(x.real, x.real) + dot(x.imag, x.imag)
else:
sqnorm = dot(x, x)
ret = sqrt(sqnorm)
if keepdims:
ret = ret.reshape(ndim*[1])
return ret
# Normalize the `axis` argument to a tuple.
nd = x.ndim
if axis is None:
axis = tuple(range(nd))
elif not isinstance(axis, tuple):
try:
axis = int(axis)
except:
raise TypeError("'axis' must be None, an integer or a tuple of integers")
axis = (axis,)
if len(axis) == 1:
if ord == Inf:
return abs(x).max(axis=axis, keepdims=keepdims)
elif ord == -Inf:
return abs(x).min(axis=axis, keepdims=keepdims)
elif ord == 0:
# Zero norm
return (x != 0).sum(axis=axis, keepdims=keepdims)
elif ord == 1:
# special case for speedup
return afnumpy.sum(abs(x), axis=axis, keepdims=keepdims)
elif ord is None or ord == 2:
# special case for speedup
s = (x.conj() * x).real
return sqrt(afnumpy.sum(s, axis=axis, keepdims=keepdims))
else:
try:
ord + 1
except TypeError:
raise ValueError("Invalid norm order for vectors.")
if x.dtype.type is longdouble:
# Convert to a float type, so integer arrays give
# float results. Don't apply asfarray to longdouble arrays,
# because it will downcast to float64.
absx = abs(x)
else:
absx = x if isComplexType(x.dtype.type) else asfarray(x)
if absx.dtype is x.dtype:
absx = abs(absx)
else:
# if the type changed, we can safely overwrite absx
abs(absx, out=absx)
absx **= ord
return afnumpy.sum(absx, axis=axis, keepdims=keepdims) ** (1.0 / ord)
elif len(axis) == 2:
row_axis, col_axis = axis
if not (-nd <= row_axis < nd and -nd <= col_axis < nd):
raise ValueError('Invalid axis %r for an array with shape %r' %
(axis, x.shape))
if row_axis % nd == col_axis % nd:
raise ValueError('Duplicate axes given.')
if ord == 2:
ret = _multi_svd_norm(x, row_axis, col_axis, amax)
elif ord == -2:
ret = _multi_svd_norm(x, row_axis, col_axis, amin)
elif ord == 1:
if col_axis > row_axis:
col_axis -= 1
ret = afnumpy.sum(abs(x), axis=row_axis).max(axis=col_axis)
elif ord == Inf:
if row_axis > col_axis:
row_axis -= 1
ret = afnumpy.sum(abs(x), axis=col_axis).max(axis=row_axis)
elif ord == -1:
if col_axis > row_axis:
col_axis -= 1
ret = afnumpy.sum(abs(x), axis=row_axis).min(axis=col_axis)
elif ord == -Inf:
if row_axis > col_axis:
row_axis -= 1
ret = afnumpy.sum(abs(x), axis=col_axis).min(axis=row_axis)
elif ord in [None, 'fro', 'f']:
ret = sqrt(afnumpy.sum((x.conj() * x).real, axis=axis))
else:
raise ValueError("Invalid norm order for matrices.")
if keepdims:
ret_shape = list(x.shape)
ret_shape[axis[0]] = 1
ret_shape[axis[1]] = 1
ret = ret.reshape(ret_shape)
return ret
else:
raise ValueError("Improper number of dimensions to norm.")
def norm(x, ord=None, axis=None, keepdims=False):
x = asarray(x)
# Check the default case first and handle it immediately.
if ord is None and axis is None:
ndim = x.ndim
x = x.ravel(order='K')
if isComplexType(x.dtype.type):
sqnorm = dot(x.real, x.real) + dot(x.imag, x.imag)
else:
sqnorm = dot(x, x)
ret = sqrt(sqnorm)
if keepdims:
ret = ret.reshape(ndim * [1])
return ret
# Normalize the `axis` argument to a tuple.
nd = x.ndim
if axis is None:
axis = tuple(range(nd))
elif not isinstance(axis, tuple):
try:
axis = int(axis)
except:
raise TypeError(
"'axis' must be None, an integer or a tuple of integers")
axis = (axis, )
if len(axis) == 1:
if ord == Inf:
return abs(x).max(axis=axis, keepdims=keepdims)
elif ord == -Inf:
return abs(x).min(axis=axis, keepdims=keepdims)
elif ord == 0:
# Zero norm
return (x != 0).sum(axis=axis, keepdims=keepdims)
elif ord == 1:
# special case for speedup
return afnumpy.sum(abs(x), axis=axis, keepdims=keepdims)
elif ord is None or ord == 2:
# special case for speedup
s = (x.conj() * x).real
return sqrt(afnumpy.sum(s, axis=axis, keepdims=keepdims))
else:
try:
ord + 1
except TypeError:
raise ValueError("Invalid norm order for vectors.")
if x.dtype.type is longdouble:
# Convert to a float type, so integer arrays give
# float results. Don't apply asfarray to longdouble arrays,
# because it will downcast to float64.
absx = abs(x)
else:
absx = x if isComplexType(x.dtype.type) else asfarray(x)
if absx.dtype is x.dtype:
absx = abs(absx)
else:
# if the type changed, we can safely overwrite absx
abs(absx, out=absx)
absx **= ord
return afnumpy.sum(absx, axis=axis, keepdims=keepdims)**(1.0 / ord)
elif len(axis) == 2:
row_axis, col_axis = axis
if not (-nd <= row_axis < nd and -nd <= col_axis < nd):
raise ValueError('Invalid axis %r for an array with shape %r' %
(axis, x.shape))
if row_axis % nd == col_axis % nd:
raise ValueError('Duplicate axes given.')
if ord == 2:
ret = _multi_svd_norm(x, row_axis, col_axis, amax)
elif ord == -2:
ret = _multi_svd_norm(x, row_axis, col_axis, amin)
elif ord == 1:
if col_axis > row_axis:
col_axis -= 1
ret = afnumpy.sum(abs(x), axis=row_axis).max(axis=col_axis)
elif ord == Inf:
if row_axis > col_axis:
row_axis -= 1
ret = afnumpy.sum(abs(x), axis=col_axis).max(axis=row_axis)
elif ord == -1:
if col_axis > row_axis:
col_axis -= 1
ret = afnumpy.sum(abs(x), axis=row_axis).min(axis=col_axis)
elif ord == -Inf:
if row_axis > col_axis:
row_axis -= 1
ret = afnumpy.sum(abs(x), axis=col_axis).min(axis=row_axis)
elif ord in [None, 'fro', 'f']:
ret = sqrt(afnumpy.sum((x.conj() * x).real, axis=axis))
else:
raise ValueError("Invalid norm order for matrices.")
if keepdims:
ret_shape = list(x.shape)
ret_shape[axis[0]] = 1
ret_shape[axis[1]] = 1
ret = ret.reshape(ret_shape)
return ret
else:
raise ValueError("Improper number of dimensions to norm.")
def Emod(self, modes):
M = self.Imap(modes)
eMod = afnumpy.sum( self.mask * ( afnumpy.sqrt(M) - self.amp )**2 )
eMod = afnumpy.sqrt( eMod / self.I_norm )
return eMod
