def _set_arrays(self):
imarr, darr = equalize_array_masks(self._unequal_image_subset,
self._unequal_depth_subset)
fullim = self.img_rds.band_array
if self.surf_refraction:
imarr = surface_refraction_correction(imarr)
fullim = surface_refraction_correction(fullim)
if self.surf_reflectance:
acceptable = ['ndarray', 'list', 'tuple']
if type(self.surf_reflectance).__name__ in acceptable:
imarr = surface_reflectance_correction(imarr,
self.surf_reflectance)
fullim = surface_reflectance_correction(
fullim, self.surf_reflectance)
elif self.surf_reflectance == True:
imarr = surface_reflectance_correction(imarr)
fullim = surface_reflectance_correction(fullim)
else:
raise TypeError("If self.surf_reflectance doesn't evaluate to \
False, then it should be an ndarray, a list, or a \
tuple.")
self.image_subset_array = imarr
self.full_image_array = fullim
self.depth_subset_array = darr.squeeze()
return True
def regression_plot(Z,X,band_names=None,visible_only=True,figsize=(12,7)):
"""
Produce a figure with a plot for each image band that displays the
relationship between depth and radiance and gives a visual representation
of the regression carried out in the `slopes` and `regressions` methods.
Notes
-----
This method doesn't come directly from Lyzenga 1978 but the author of this
code found it helpful.
Parameters
----------
Z : np.ma.MaskedArray
Array of depth values repeated for each band so that Z.shape==X.shape.
The mask needs to be the same too so that Z.mask==X.mask for all the
bands.
X : np.ma.MaskedArray
The array of log transformed radiance values from equation B1 of
Lyzenga 1978.
Returns
-------
figure
A matplotlib figure.
"""
if band_names is None:
band_names = ['Band'+str(i+1) for i in range(X.shape[-1])]
nbands = X.shape[-1]
if np.atleast_3d(Z).shape[-1] == 1:
Z = np.repeat(np.atleast_3d(Z), nbands, 2)
if visible_only:
fig, axs = plt.subplots( 2, 3, figsize=figsize)
else:
fig, axs = plt.subplots( 2, 4, figsize=figsize )
regs = regressions(Z,X)
for i, ax in enumerate(axs.flatten()):
if i > nbands-1:
continue
slp, incpt, rval = regs[:,i]
# print X.shape, Z.shape
x, y = equalize_array_masks(Z[...,i], X[...,i])
if x.count() < 2:
continue
x, y = x.compressed(), y.compressed()
# print "i = {}, x.shape = {}, y.shape = {}".format(i, x.shape, y.shape)
ax.scatter( x, y, alpha=0.1, edgecolor='none', c='gold' )
smth = lowess(y,x,frac=0.2)
# ax.plot(smth.T[0],smth.T[1],c='black',alpha=0.5)
ax.plot(smth.T[0],smth.T[1],c='black',alpha=0.5,linestyle='--')
reglabel = "m=%.2f, r=%.2f" % (slp,rval)
f = lambda x: incpt + slp * x
ax.plot( x, f(x), c='brown', label=reglabel, alpha=1.0 )
ax.set_title( band_names[i] )
ax.set_xlabel( r'Depth (m)' )
ax.set_ylabel( r'$X_i$' )
ax.legend(fancybox=True, framealpha=0.5)
plt.tight_layout()
return fig
def regression_plot(Z, X, band_names=None, visible_only=True, figsize=(12, 7)):
"""
Produce a figure with a plot for each image band that displays the
relationship between depth and radiance and gives a visual representation
of the regression carried out in the `slopes` and `regressions` methods.
Notes
-----
This method doesn't come directly from Lyzenga 1978 but the author of this
code found it helpful.
Parameters
----------
Z : np.ma.MaskedArray
Array of depth values repeated for each band so that Z.shape==X.shape.
The mask needs to be the same too so that Z.mask==X.mask for all the
bands.
X : np.ma.MaskedArray
The array of log transformed radiance values from equation B1 of
Lyzenga 1978.
Returns
-------
figure
A matplotlib figure.
"""
if band_names is None:
band_names = ['Band' + str(i + 1) for i in range(X.shape[-1])]
nbands = X.shape[-1]
if np.atleast_3d(Z).shape[-1] == 1:
Z = np.repeat(np.atleast_3d(Z), nbands, 2)
if visible_only:
fig, axs = plt.subplots(2, 3, figsize=figsize)
else:
fig, axs = plt.subplots(2, 4, figsize=figsize)
regs = regressions(Z, X)
for i, ax in enumerate(axs.flatten()):
if i > nbands - 1:
continue
slp, incpt, rval = regs[:, i]
# print X.shape, Z.shape
x, y = equalize_array_masks(Z[..., i], X[..., i])
if x.count() < 2:
continue
x, y = x.compressed(), y.compressed()
# print "i = {}, x.shape = {}, y.shape = {}".format(i, x.shape, y.shape)
ax.scatter(x, y, alpha=0.1, edgecolor='none', c='gold')
smth = lowess(y, x, frac=0.2)
# ax.plot(smth.T[0],smth.T[1],c='black',alpha=0.5)
ax.plot(smth.T[0], smth.T[1], c='black', alpha=0.5, linestyle='--')
reglabel = "m=%.2f, r=%.2f" % (slp, rval)
f = lambda x: incpt + slp * x
ax.plot(x, f(x), c='brown', label=reglabel, alpha=1.0)
ax.set_title(band_names[i])
ax.set_xlabel(r'Depth (m)')
ax.set_ylabel(r'$X_i$')
ax.legend(fancybox=True, framealpha=0.5)
plt.tight_layout()
return fig
def _set_arrays(self):
# get prediction and true arrays
parr, tarr = self.pred_rds.band_array.squeeze(), self.true_rds.band_array.squeeze()
if type(self.pred_range).__name__ != 'NoneType':
parr = np.ma.masked_outside(parr, *self.pred_range)
if type(self.true_range).__name__ != 'NoneType':
tarr = np.ma.masked_outside(tarr, *self.true_range)
parr, tarr = equalize_array_masks(parr, tarr)
self.pred_arr = parr
self.true_arr = tarr
return True
def _set_arrays(self):
# get prediction and true arrays
parr, tarr = self.pred_rds.band_array.squeeze(
), self.true_rds.band_array.squeeze()
if type(self.pred_range).__name__ != 'NoneType':
parr = np.ma.masked_outside(parr, *self.pred_range)
if type(self.true_range).__name__ != 'NoneType':
tarr = np.ma.masked_outside(tarr, *self.true_range)
parr, tarr = equalize_array_masks(parr, tarr)
self.pred_arr = parr
self.true_arr = tarr
return True
def lyzenga_depth_estimation(self, Rinf=None, bands=None, n_std=0,
n_jobs=4):
"""
This will implement the linear depth estimation method described in
Lyzenga et al. 2006. This doc string needs a bit more detail but I don't
have time right now. Check `OpticalRS.Lyzenga2006` for more detail. This
method just wraps some of the code from that module to make it easier to
run.
"""
if bands is None:
bands = self.nbands
if Rinf is None:
Rinf = deep_water_means(self.imarr[...,:bands], n_std=n_std)
X = np.ma.log(self.imarr[...,:bands] - Rinf)
X = equalize_band_masks(X)
# need to re-equalize, might have lost pixels in log transform
Xtrain, deparr = equalize_array_masks(X, self.known_depth_arr)
return fit_and_predict(Xtrain, deparr, X, n_jobs=n_jobs)
def regressions(Z, X):
"""
Carry out the regression discussed in Appendix B of Lyzenga 1978. `Z` is
the depths and `X` is the log radiance values. X = a - b z is the
formula so depth is the x in the regression and radiance is the y.
Parameters
----------
Z : np.ma.MaskedArray
Array of depth values.
X : np.ma.MaskedArray
The array of log transformed radiance values from equation B1 of
Lyzenga 1978.
Returns
-------
np.array
A 3 x N-bands array containing the slopes, intercepts, and r_values
of the regressions. In terms of equation B1 from Lyzenga 1978, that
would be (b_i, a_i, r_value_i) for each band.
"""
nbands = X.shape[-1]
if np.atleast_3d(Z).shape[-1] == 1:
Z = np.repeat(np.atleast_3d(Z), nbands, 2)
slopes = []
intercepts = []
rvals = []
for band in range(nbands):
z, x = equalize_array_masks(Z[..., band], X[..., band])
# print z.count(), x.count()
try:
slope,intercept,r_value,p_value,std_err = linregress(z.compressed(),\
x.compressed())
except IndexError:
slope, intercept, r_value, p_value, std_err = np.repeat(
np.nan, 5, 0)
# eq B1 is X=a-bz
slopes.append(slope)
intercepts.append(intercept)
rvals.append(r_value)
return np.array((slopes, intercepts, rvals))
def regressions(Z,X):
"""
Carry out the regression discussed in Appendix B of Lyzenga 1978. `Z` is
the depths and `X` is the log radiance values. X = a - b z is the
formula so depth is the x in the regression and radiance is the y.
Parameters
----------
Z : np.ma.MaskedArray
Array of depth values.
X : np.ma.MaskedArray
The array of log transformed radiance values from equation B1 of
Lyzenga 1978.
Returns
-------
np.array
A 3 x N-bands array containing the slopes, intercepts, and r_values
of the regressions. In terms of equation B1 from Lyzenga 1978, that
would be (b_i, a_i, r_value_i) for each band.
"""
nbands = X.shape[-1]
if np.atleast_3d(Z).shape[-1] == 1:
Z = np.repeat(np.atleast_3d(Z), nbands, 2)
slopes = []
intercepts = []
rvals = []
for band in range(nbands):
z, x = equalize_array_masks(Z[...,band], X[...,band])
# print z.count(), x.count()
try:
slope,intercept,r_value,p_value,std_err = linregress(z.compressed(),\
x.compressed())
except IndexError:
slope,intercept,r_value,p_value,std_err = np.repeat(np.nan, 5, 0)
# eq B1 is X=a-bz
slopes.append( slope )
intercepts.append( intercept )
rvals.append( r_value )
return np.array((slopes,intercepts,rvals))
def _set_arrays(self):
imarr, darr = equalize_array_masks(self._unequal_image_subset, self._unequal_depth_subset)
fullim = self.img_rds.band_array
if self.surf_refraction:
imarr = surface_refraction_correction(imarr)
fullim = surface_refraction_correction(fullim)
if self.surf_reflectance:
acceptable = ['ndarray','list','tuple']
if type(self.surf_reflectance).__name__ in acceptable:
imarr = surface_reflectance_correction(imarr, self.surf_reflectance)
fullim = surface_reflectance_correction(fullim, self.surf_reflectance)
elif self.surf_reflectance == True:
imarr = surface_reflectance_correction(imarr)
fullim = surface_reflectance_correction(fullim)
else:
raise TypeError("If self.surf_reflectance doesn't evaluate to \
False, then it should be an ndarray, a list, or a \
tuple.")
self.image_subset_array = imarr
self.full_image_array = fullim
self.depth_subset_array = darr.squeeze()
return True