def descriptor(seq, median_len):
ns = list(map(numMappingPP, seq)) # here we map the nucleotides to numbers
## we ensure that all the sequences have the same size
I = median_len - len(
ns
) # change "median_len" to other length stat for length normalization
if I > 0: # when the seq size is smaller than the median
ns_temp = pywt.pad(ns, I, 'antisymmetric') #wextend('1','asym',ns,I);
ns_temp = np.array(ns_temp)
#print(len(ns_temp), len(ns))
ns_new = ns_temp[
I:ns_temp.shape[0]] #nsNew = nsTemp((I+1):length(nsTemp));
elif I < 0: # when the seq size is bigger than the median
ns = np.array(ns)
ns_new = ns[0:median_len]
else:
ns_new = np.array(ns)
#print(ns_new.shape)
#print("processing FFT...")
fourier_transform = fft(ns_new)
#print("getting magnitude spectra...")
magnitud_spectra = np.abs(fourier_transform) # %magnitude spectra
return ns_new, fourier_transform, magnitud_spectra
def pad_to_mult(self, support, mult):
if len(support) % mult == 0:
return support
else:
self.swt_buffer_length = mult - (len(support) % mult)
return pywt.pad(support, (0, self.swt_buffer_length),
mode='smooth')
def test_pad_nd():
for ndim in [2, 3]:
x = np.arange(4**ndim).reshape((4, ) * ndim)
if ndim == 2:
pad_widths = [(2, 1), (2, 3)]
else:
pad_widths = [(2, 1), ] * ndim
for mode in pywt.Modes.modes:
xp = pywt.pad(x, pad_widths, mode)
# expected result is the same as applying along axes separably
xp_expected = x.copy()
for ax in range(ndim):
xp_expected = np.apply_along_axis(pywt.pad,
ax,
xp_expected,
pad_widths=[pad_widths[ax]],
mode=mode)
assert_array_equal(xp, xp_expected)
def metric(self, field, cm, verify=False):
"""
Compute metric(s) for a single field
Parameters
----------
field : numpy array of shape (npx,npx) - npx is number of pixels
Cloud water path field.
cm : numpy array of shape (npx,npx)
Cloud mask field.
Returns
-------
woi1 : float
First wavelet organisation index (scale distribution).
woi2 : float
Second wavelet organisation index (total amount of stuff).
woi3 : float
Third wavelet organisation index (directional alignment).
"""
# STATIONARY/UNDECIMATED Direct Wavelet Transform
field = pywt.pad(field, self.pad, "periodic")
scaleMax = int(np.log(field.shape[0]) / np.log(2))
coeffs = pywt.swt2(field, "haar", scaleMax, norm=True, trim_approx=True)
# Bug in pywt -> trim_approx=False does opposite of its intention
# Structure of coeffs:
# - coeffs -> list with nScales indices. Each scale is a 2-power of
# the image resolution. For 512x512 images we have
# 512 = 2^9 -> 10 scales
# - coeffs[i] -> Contains three directions:
# [0] - Horizontal
# [1] - Vertical
# [2] - Diagonal
specs = np.zeros((len(coeffs), 3)) # Shape (nScales,3)
k = np.arange(0, len(specs))
for i in range(len(coeffs)):
if i == 0:
ec = coeffs[i] ** 2
specs[i, 0] = np.mean(ec)
else:
for j in range(len(coeffs[i])):
ec = coeffs[i][j] ** 2 # Energy -> squared wavelet coeffs
specs[i, j] = np.mean(ec) # Domain-averaging at each scale
# Decompose into ''large scale'' energy and ''small scale'' energy
# Large scales are defined as 0 < k < 5
specs = specs[1:]
specL = specs[:5, :]
specS = specs[5:, :]
Ebar = np.sum(np.mean(specs, axis=1))
Elbar = np.sum(np.mean(specL, axis=1))
Esbar = np.sum(np.mean(specS, axis=1))
Eld = np.sum(specL, axis=0)
Esd = np.sum(specS, axis=0)
# Compute wavelet organisation index
woi1 = Elbar / Ebar
woi2 = (Elbar + Esbar) / np.sum(cm)
woi3 = (
1.0
/ 3
* np.sqrt(
np.sum(((Esd - Esbar) / Esbar) ** 2 + ((Eld - Elbar) / Elbar) ** 2)
)
)
woi = np.log(woi1) + np.log(woi2) + np.log(woi3)
if self.plot:
labs = ["Horizontal", "Vertical", "Diagonal"]
fig, axs = plt.subplots(ncols=2, figsize=(8, 4))
axs[0].imshow(field, "gist_ncar")
axs[0].set_xticks([])
axs[0].set_yticks([])
axs[0].set_title("CWP")
for i in range(3):
axs[1].plot(k[1:], specs[:, i], label=labs[i])
axs[1].set_xscale("log")
axs[1].set_xlabel(r"Scale number $k$")
axs[1].set_ylabel("Energy")
axs[1].set_title("Wavelet energy spectrum")
axs[1].legend()
plt.tight_layout()
plt.show()
if verify:
return specs
else:
return woi1, woi2, woi3, woi
def test_pad_1d():
x = [1, 2, 3]
assert_array_equal(pywt.pad(x, (4, 6), 'periodization'),
[1, 2, 3, 3, 1, 2, 3, 3, 1, 2, 3, 3, 1, 2])
assert_array_equal(pywt.pad(x, (4, 6), 'periodic'),
[3, 1, 2, 3, 1, 2, 3, 1, 2, 3, 1, 2, 3])
assert_array_equal(pywt.pad(x, (4, 6), 'constant'),
[1, 1, 1, 1, 1, 2, 3, 3, 3, 3, 3, 3, 3])
assert_array_equal(pywt.pad(x, (4, 6), 'zero'),
[0, 0, 0, 0, 1, 2, 3, 0, 0, 0, 0, 0, 0])
assert_array_equal(pywt.pad(x, (4, 6), 'smooth'),
[-3, -2, -1, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9])
assert_array_equal(pywt.pad(x, (4, 6), 'symmetric'),
[3, 3, 2, 1, 1, 2, 3, 3, 2, 1, 1, 2, 3])
assert_array_equal(pywt.pad(x, (4, 6), 'antisymmetric'),
[3, -3, -2, -1, 1, 2, 3, -3, -2, -1, 1, 2, 3])
assert_array_equal(pywt.pad(x, (4, 6), 'reflect'),
[1, 2, 3, 2, 1, 2, 3, 2, 1, 2, 3, 2, 1])
assert_array_equal(pywt.pad(x, (4, 6), 'antireflect'),
[-3, -2, -1, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9])
# equivalence of various pad_width formats
assert_array_equal(pywt.pad(x, 4, 'periodic'),
pywt.pad(x, (4, 4), 'periodic'))
assert_array_equal(pywt.pad(x, (4, ), 'periodic'),
pywt.pad(x, (4, 4), 'periodic'))
assert_array_equal(pywt.pad(x, [(4, 4)], 'periodic'),
pywt.pad(x, (4, 4), 'periodic'))
def apply_pad_x(self):
self.x = pywt.pad(self.x, self.PAD_WIDTH, 'antireflect')