def process_s(s):
s.values[s.values == 0] = np.nan
s.values[np.logical_or(np.isinf(s.values), np.isnan(s.values))] = np.nan
s, had_outlier = _setnull_s_outliers(s)
while had_outlier:
s, had_outlier = _setnull_s_outliers(s)
has_null = s.isnull().any()
if has_null:
try:
r, c = np.nonzero(np.isfinite(s.values))
y = s.lat[r].values
x = s.lon[c].values
points = (x, y)
values = s.values[r, c]
grid_x, grid_y = np.meshgrid(s.lon.values, s.lat.values)
try:
sgrid = griddata(points,
values, (grid_x, grid_y),
method='cubic')
except QhullError:
sgrid = np.zeros(s.shape)
try:
sgrid_l = griddata(points,
values, (grid_x, grid_y),
method='linear')
except QhullError:
sgrid_l = np.empty(s.shape)
sgrid_l.fill(np.nan)
sgrid_n = griddata(points,
values, (grid_x, grid_y),
method='nearest')
mask_zero = sgrid <= 0
sgrid[mask_zero] = sgrid_l[mask_zero]
mask_nan = np.isnan(sgrid)
sgrid[mask_nan] = sgrid_n[mask_nan]
s = xr.DataArray(sgrid, coords=[s.lat, s.lon])
except ValueError as e:
if e.args[0] == 'No points given':
# No valid scaler factors
s.values[:] = 1
else:
raise
return s
def inv_dense_corres(dense_corres_a2b, pre_cache_x2d=None):
H, W = dense_corres_a2b.shape[:2]
if pre_cache_x2d is None:
x_a = x_2d_coords(H, W).reshape((H, W, 2))
else:
x_a = pre_cache_x2d.reshape((H, W, 2))
dense_corres_b2a = griddata(dense_corres_a2b.reshape((H * W, 2)),
x_a.reshape((H * W, 2)),
x_a.reshape((H * W, 2)),
method='linear',
fill_value=-1)
return dense_corres_b2a.reshape((H, W, 2))
def _extract_h5(self, dm):
# cells = []
tab = dm.get_table('power_map', '/')
metadata = dict()
try:
b = tab._v_attrs['bounds']
except Exception as e:
print('exception', e)
b = 1
metadata['bounds'] = -float(b), float(b)
try:
bd = tab._v_attrs['beam_diameter']
except Exception as e:
print('exception', e)
bd = 0
try:
po = tab._v_attrs['power']
except Exception as e:
print('exception', e)
po = 0
metadata['beam_diameter'] = bd
metadata['power'] = po
xs, ys, power = array([(r['x'], r['y'], r['power'])
for r in tab.iterrows()]).T
# xs, ys, power = array(xs), array(ys), array(power)
# n = power.shape[0]
# print n
xi = linspace(min(xs), max(xs), 50)
yi = linspace(min(ys), max(ys), 50)
X = xi[None, :]
Y = yi[:, None]
power = griddata(
(xs, ys),
power,
(X, Y),
fill_value=0,
# method='cubic'
)
return rot90(power, k=2), metadata
def _extract_h5(self, dm):
# cells = []
tab = dm.get_table('power_map', '/')
metadata = dict()
try:
b = tab._v_attrs['bounds']
except Exception as e:
print('exception', e)
b = 1
metadata['bounds'] = -float(b), float(b)
try:
bd = tab._v_attrs['beam_diameter']
except Exception as e:
print('exception', e)
bd = 0
try:
po = tab._v_attrs['power']
except Exception as e:
print('exception', e)
po = 0
metadata['beam_diameter'] = bd
metadata['power'] = po
xs, ys, power = array([(r['x'], r['y'], r['power'])
for r in tab.iterrows()]).T
# xs, ys, power = array(xs), array(ys), array(power)
# n = power.shape[0]
# print n
xi = linspace(min(xs), max(xs), 50)
yi = linspace(min(ys), max(ys), 50)
X = xi[None, :]
Y = yi[:, None]
power = griddata((xs, ys), power, (X, Y),
fill_value=0,
# method='cubic'
)
return rot90(power, k=2), metadata
def _add_data(self, data):
# def _refresh_data(v):
tab, x, y, col, row, mag, sid = data
# self.debug('{} {} {} {} {}'.format(*v[1:]))
self._write_datum(tab, x, y, col, row, mag)
self.graph.add_datum((x, mag), series=sid)
self._xs = hstack((self._xs, x))
self._ys = hstack((self._ys, y))
self._zs = hstack((self._zs, mag))
# xl, xh = self._bounds[:2]
# yl, yh = self._bounds[2:]
if col % 10 == 0 and row:
cg = self.contour_graph
xx = self._xs
yy = self._ys
z = self._zs
# print 'xx-----', xx
# print 'yy-----', yy
zd = griddata(
(xx, yy),
z,
self.area,
# method='cubic',
fill_value=0)
zd = rot90(zd, k=2)
# zd = zd.T
# print zd
if not cg.plots[0].plots.keys():
cg.new_series(
z=zd,
xbounds=(-self._padding, self._padding),
ybounds=(-self._padding, self._padding),
# xbounds=(xl, xh),
# ybounds=(yl, yh),
style='contour')
else:
cg.plots[0].data.set_data('z0', zd)
def _add_data(self, data):
# def _refresh_data(v):
tab, x, y, col, row, mag, sid = data
# self.debug('{} {} {} {} {}'.format(*v[1:]))
self._write_datum(tab, x, y, col, row, mag)
self.graph.add_datum((x, mag), series=sid)
self._xs = hstack((self._xs, x))
self._ys = hstack((self._ys, y))
self._zs = hstack((self._zs, mag))
# xl, xh = self._bounds[:2]
# yl, yh = self._bounds[2:]
if col % 10 == 0 and row:
cg = self.contour_graph
xx = self._xs
yy = self._ys
z = self._zs
# print 'xx-----', xx
# print 'yy-----', yy
zd = griddata((xx, yy), z, self.area,
# method='cubic',
fill_value=0)
zd = rot90(zd, k=2)
# zd = zd.T
# print zd
if not cg.plots[0].plots.keys():
cg.new_series(z=zd,
xbounds=(-self._padding, self._padding),
ybounds=(-self._padding, self._padding),
# xbounds=(xl, xh),
# ybounds=(yl, yh),
style='contour')
else:
cg.plots[0].data.set_data('z0', zd)
def min(self, source_depths, receiver_depths, distances, method='linear'):
'''
Returns the minimum (minima) travel time(s) for the point(s) identified by
(source_depths, receiver_depths, distances) by building a grid and
interpolating on the points identified by each
```
P[i] = (source_depths[i], receiver_depths[i], distances[i])
```
if the source file has been built with
receiver depths == [0]. It uses a 2d linear interpolation on a grid. It uses
scipy griddata
:param source_depths: numeric or numpy array of length n: the source depth(s), in km
:param receiver_depths: numeric or numpy array of length n: the receiver depth(s), in km.
For most applications, this value can be set to zero
:param distances: numeric or numpy array of length n: the distance(s), in degrees
:param method: forwarded to `scipy.griddata` function
:return: a numpy array of length n denoting the minimum travel time(s) of this model for
each P
'''
# Handle the case some arguments are scalars and some arrays:
source_depths, receiver_depths, distances = \
np.broadcast_arrays(source_depths, receiver_depths, distances)
# handle the case all arguments scalars. See
# https://stackoverflow.com/questions/29318459/python-function-that-handles-scalar-or-arrays
allscalars = all(_.ndim == 0
for _ in (source_depths, receiver_depths, distances))
if source_depths.ndim == 0:
source_depths = source_depths[None] # Makes x 1D
if receiver_depths.ndim == 0:
receiver_depths = receiver_depths[None] # Makes x 1D
if distances.ndim == 0:
distances = distances[None] # Makes x 1D
# correct source depths and receiver depths
source_depths[source_depths < 0] = 0
receiver_depths[receiver_depths < 0] = 0
# correct distances to be compatible with obpsy traveltimes calculations:
distances = distances % 360
# set values symmetric to 180 degrees if greater than 180:
_mask = distances > 180
if _mask.any(
): # does this speeds up (allocate mask array once)? FIXME: check
distances[_mask] = 360 - distances[_mask]
# set source depths to nan if out of bounds. This prevent method = 'nearest'
# to return non nan values and be consistent with 'linear' and 'cubic'
if self._unique_receiver_depth:
# get values without receiver depth dimension:
values = np.hstack((self._km2deg(source_depths).reshape(-1, 1),
distances.reshape(-1, 1)))
else:
values = np.hstack((self._km2deg(source_depths).reshape(-1, 1),
self._km2deg(receiver_depths).reshape(-1, 1),
distances.reshape(-1, 1)))
ret = griddata(self._gridpts,
self._gridvals,
values,
method=method,
rescale=False,
fill_value=np.nan)
# ret is almost likely a float, so we can set now nans for out of boun values
# we cannot do it before on any input array cause int arrays do not support nan assignement
ret[(source_depths > self._sourcedepth_bounds_km[1]) |
(receiver_depths > self._receiverdepth_bounds_km[1])] = np.nan
# return scalar if inputs are scalar, array oitherwise
return np.squeeze(ret) if allscalars else ret
# imports
import nmafeat
from prody import *
import numpy as np
# %%
nmafeat.computeNMDfile()
(coords, modes) = nmafeat.extractModesCoords()
print(f"Values range from {coords.min()} to {coords.max()}")
# %%
dmin = coords.min() - 2
dmax = coords.max() + 2
a = np.mgrid[dmin:dmax:101j,dmin:dmax:101j,dmin:dmax:101j]
a = a.reshape(3,1030301).transpose()
# %%
import scipy.interpolate.ndgriddata as ndgriddata
mode1_interp = ndgriddata.griddata(coords, modes[0], a) # interpolate the data onto the grid
# %%
# Eureka! Maybe it worked!:
# is not nan
mode1_interp[~np.isnan(mode1_interp)].size
# %%
# is nan
mode1_interp[np.isnan(mode1_interp)].size
# %%
δ = np.gradient(mode1_interp)
# %%
δ[0][~np.isnan(δ[0])].size
# %%
m1i_orig = mode1_interp.reshape(3,101,101,101)
# %%
m1i_grad = np.gradient(m1i_orig)
metadata['power'] = po
xs, ys, power = array([(r['x'], r['y'], r['power'])
for r in tab.iterrows()]).T
# xs, ys, power = array(xs), array(ys), array(power)
# n = power.shape[0]
# print n
xi = linspace(min(xs), max(xs), 50)
yi = linspace(min(ys), max(ys), 50)
X = xi[None, :]
Y = yi[:, None]
power = griddata((xs, ys), power, (X, Y),
fill_value=0,
# method='cubic'
)
return rot90(power, k=2), metadata
# return flipud(fliplr(power)), metadata
# for row in tab.iterrows():
# x = int(row['col'])
# try:
# nr = cells[x]
# except IndexError:
# cells.append([])
# nr = cells[x]
#
# # baseline = self._calc_baseline(table, index) if self.correct_baseline else 0.0
# baseline = 0
# pwr = row['power']
def scale_anoms(s, obs_anoms):
vals_d = obs_anoms.copy()
mask_wet = vals_d.values > 0
vals_d.values[mask_wet] = vals_d.values[mask_wet] + s.values[mask_wet]
mask_wet_invalid = np.logical_and(mask_wet, vals_d.values <= 0)
has_invalid = mask_wet_invalid.any()
try:
if has_invalid:
s.values[np.logical_or(mask_wet_invalid, ~mask_wet)] = np.nan
r, c = np.nonzero(np.isfinite(s.values))
y = s.lat[r].values
x = s.lon[c].values
points = (x, y)
values = s.values[r, c]
grid_x, grid_y = np.meshgrid(s.lon.values, s.lat.values)
try:
sgrid = griddata(points,
values, (grid_x, grid_y),
method='cubic')
except QhullError:
sgrid = np.empty(s.shape)
sgrid.fill(np.nan)
sgrid_n = griddata(points,
values, (grid_x, grid_y),
method='nearest')
mask_nan = np.isnan(sgrid)
sgrid[mask_nan] = sgrid_n[mask_nan]
s = xr.DataArray(sgrid, coords=[s.lat, s.lon])
vals_d = obs_anoms.copy()
mask_wet = vals_d.values > 0
vals_d.values[
mask_wet] = vals_d.values[mask_wet] + s.values[mask_wet]
mask_wet_invalid = np.logical_and(mask_wet, vals_d.values <= 0)
has_invalid = mask_wet_invalid.any()
if has_invalid:
vals_d.values[mask_wet_invalid] = np.nan
r, c = np.nonzero(vals_d.values > 0)
y = vals_d.lat[r].values
x = vals_d.lon[c].values
points = (x, y)
values = vals_d.values[r, c]
grid_x, grid_y = np.meshgrid(vals_d.lon.values,
vals_d.lat.values)
try:
vals_d_grid = griddata(points,
values, (grid_x, grid_y),
method='cubic')
except QhullError:
vals_d_grid = np.zeros(vals_d.shape)
try:
vals_d_grid_l = griddata(points,
values, (grid_x, grid_y),
method='linear')
except QhullError:
vals_d_grid_l = np.empty(vals_d.shape)
vals_d_grid_l.fill(np.nan)
vals_d_grid_n = griddata(points,
values, (grid_x, grid_y),
method='nearest')
mask_zero = vals_d_grid <= 0
vals_d_grid[mask_zero] = vals_d_grid_l[mask_zero]
mask_nan = np.isnan(vals_d_grid)
vals_d_grid[mask_nan] = vals_d_grid_n[mask_nan]
vals_d = xr.DataArray(vals_d_grid,
coords=[vals_d.lat, vals_d.lon])
vals_d.values[obs_anoms.values == 0] = 0
except ValueError as e:
if e.args[0] == 'No points given':
# No valid scaler factors
vals_d = obs_anoms.copy()
else:
raise
return vals_d
metadata['power'] = po
xs, ys, power = array([(r['x'], r['y'], r['power'])
for r in tab.iterrows()]).T
# xs, ys, power = array(xs), array(ys), array(power)
# n = power.shape[0]
# print n
xi = linspace(min(xs), max(xs), 50)
yi = linspace(min(ys), max(ys), 50)
X = xi[None, :]
Y = yi[:, None]
power = griddata((xs, ys), power, (X, Y),
fill_value=0,
# method='cubic'
)
return rot90(power, k=2), metadata
# return flipud(fliplr(power)), metadata
# for row in tab.iterrows():
# x = int(row['col'])
# try:
# nr = cells[x]
# except IndexError:
# cells.append([])
# nr = cells[x]
#
# # baseline = self._calc_baseline(table, index) if self.correct_baseline else 0.0
# baseline = 0
# pwr = row['power']
def plot_images(self, figure, centroid, labels, density=200, smooth=0.5):
"""
Generate the parameter space plots
"""
try:
def extraxt_points_from_grid(grid2D, parx=None, pary=None):
""" Helper function that extract x,y(,z) points from all the data """
grid2D = grid2D.flatten()
if parx is not None and pary is not None:
points_x = np.array([
item["point"][parx] for item in grid2D
if item["point"] is not None
])
points_y = np.array([
item["point"][pary] for item in grid2D
if item["point"] is not None
])
points_z = np.array([
item["value"] for item in grid2D
if item["point"] is not None
])
return points_x, points_y, points_z
else:
points_x = np.array([
item["point"] for item in grid2D
if item["point"] is not None
])
points_y = np.array([
item["value"] for item in grid2D
if item["point"] is not None
])
points_x = points_x.flatten()
points_y = points_y.flatten()
xy = np.array(list(zip(points_x, points_y)),
dtype=[('x', float), ('y', float)])
xy.sort(order=['x'], axis=0)
points_x = xy['x']
points_y = xy['y']
return points_x, points_y
if self.num_params == 1:
# Only one parameter refined:
points_x, points_y = extraxt_points_from_grid(self.grid)
ax = figure.add_subplot(1, 1, 1)
ax.plot(points_x, points_y)
ax.set_ylabel("Residual error")
ax.set_xlabel(get_plot_safe(labels[0]))
else:
# Multi-parameter space:
image_grid, divider, get_grid = self._setup_image_grid(
figure, self.num_params)
# Keep a reference to the images created,
# so we can add a scale bar for all images (and they have the same range)
ims = []
tvmin, tvmax = None, None
for index, (parx, pary) in enumerate(
itertools.combinations(list(range(self.num_params)),
2)):
# Get the data for this cross section:
grid2D = self.grid[index, ...]
points_x, points_y, points_z = extraxt_points_from_grid(
grid2D, parx, pary)
# Setup axis:
ax = get_grid(parx, pary)
extent = (self.minima[parx], self.maxima[parx],
self.minima[pary], self.maxima[pary])
aspect = 'auto'
# Try to interpolate the data:
xi = np.linspace(self.minima[parx], self.maxima[parx],
density)
yi = np.linspace(self.minima[pary], self.maxima[pary],
density)
zi = griddata((points_x, points_y),
points_z, (xi[None, :], yi[:, None]),
method='cubic')
# Plot it:
im = ax.imshow(zi,
origin='lower',
aspect=aspect,
extent=extent,
alpha=0.75)
ims.append(im)
im.set_cmap('gray_r')
# Get visual limits:
vmin, vmax = im.get_clim()
if index == 0:
tvmin, tvmax = vmin, vmax
else:
tvmin, tvmax = min(tvmin, vmin), max(tvmax, vmax)
# Try to add a contour & labels:
try:
ct = ax.contour(xi,
yi,
zi,
colors='k',
aspect=aspect,
extent=extent,
origin='lower')
ax.clabel(ct, colors='k', fontsize=10, format="%1.2f")
except ValueError:
pass #ignore the "zero-size array" error for now.
# Add a red cross where the 'best' solution is:
ax.plot((centroid[parx], ), (centroid[pary], ), 'r+')
# Rotate x labels
for lbl in ax.get_xticklabels():
lbl.set_rotation(90)
# Reduce number of ticks:
ax.locator_params(axis='both', nbins=5)
# Set limits:
ax.set_xlim(extent[0:2])
ax.set_ylim(extent[2:4])
# Add labels to the axes so the user knows which is which:
# TODO add some flags/color/... indicating which phase & component each parameter belongs to...
if parx == 0:
ax.set_ylabel(
str("#%d " % (pary + 1)) +
get_plot_safe(labels[pary]))
if pary == (self.num_params - 1):
ax.set_xlabel(
str("#%d " % (parx + 1)) +
get_plot_safe(labels[parx]))
# Set the data limits:
for im in ims:
im.set_clim(tvmin, tvmax)
# Make it look PRO:
if im is not None:
cbar_ax = image_grid.cbar_axes[0]
nx = 1 + (self.num_params - 1) * 2
ny1 = (self.num_params - 1) * 2
cbar_ax.set_axes_locator(
divider.new_locator(nx=nx, ny=1, ny1=ny1))
cb = cbar_ax.colorbar(im) # @UnusedVariable
except:
print(
"Unhandled exception while generating parameter space images:")
print(format_exc())
# ignore error, tell the user via the plot and return
self.clear_image(figure)
return
def plot_images(self, figure, centroid, labels, density=200, smooth=0.5):
"""
Generate the parameter space plots
"""
try:
def extraxt_points_from_grid(grid2D, parx=None, pary=None):
""" Helper function that extract x,y(,z) points from all the data """
grid2D = grid2D.flatten()
if parx is not None and pary is not None:
points_x = np.array([item["point"][parx] for item in grid2D if item["point"] is not None])
points_y = np.array([item["point"][pary] for item in grid2D if item["point"] is not None])
points_z = np.array([item["value"] for item in grid2D if item["point"] is not None])
return points_x, points_y, points_z
else:
points_x = np.array([item["point"] for item in grid2D if item["point"] is not None])
points_y = np.array([item["value"] for item in grid2D if item["point"] is not None])
points_x = points_x.flatten()
points_y = points_y.flatten()
xy = np.array(list(zip(points_x, points_y)), dtype=[('x', float), ('y', float)])
xy.sort(order=['x'], axis=0)
points_x = xy['x']
points_y = xy['y']
return points_x, points_y
if self.num_params == 1:
# Only one parameter refined:
points_x, points_y = extraxt_points_from_grid(self.grid)
ax = figure.add_subplot(1, 1, 1)
ax.plot(points_x, points_y)
ax.set_ylabel("Residual error")
ax.set_xlabel(get_plot_safe(labels[0]))
else:
# Multi-parameter space:
image_grid, divider, get_grid = self._setup_image_grid(figure, self.num_params)
# Keep a reference to the images created,
# so we can add a scale bar for all images (and they have the same range)
ims = []
tvmin, tvmax = None, None
for index, (parx, pary) in enumerate(itertools.combinations(list(range(self.num_params)), 2)):
# Get the data for this cross section:
grid2D = self.grid[index, ...]
points_x, points_y, points_z = extraxt_points_from_grid(grid2D, parx, pary)
# Setup axis:
ax = get_grid(parx, pary)
extent = (
self.minima[parx], self.maxima[parx],
self.minima[pary], self.maxima[pary]
)
aspect = 'auto'
# Try to interpolate the data:
xi = np.linspace(self.minima[parx], self.maxima[parx], density)
yi = np.linspace(self.minima[pary], self.maxima[pary], density)
zi = griddata((points_x, points_y), points_z, (xi[None, :], yi[:, None]), method='cubic')
# Plot it:
im = ax.imshow(zi, origin='lower', aspect=aspect, extent=extent, alpha=0.75)
ims.append(im)
im.set_cmap('gray_r')
# Get visual limits:
vmin, vmax = im.get_clim()
if index == 0:
tvmin, tvmax = vmin, vmax
else:
tvmin, tvmax = min(tvmin, vmin), max(tvmax, vmax)
# Try to add a contour & labels:
try:
ct = ax.contour(xi, yi, zi, colors='k', aspect=aspect, extent=extent, origin='lower')
ax.clabel(ct, colors='k', fontsize=10, format="%1.2f")
except ValueError:
pass #ignore the "zero-size array" error for now.
# Add a red cross where the 'best' solution is:
ax.plot((centroid[parx],), (centroid[pary],), 'r+')
# Rotate x labels
for lbl in ax.get_xticklabels():
lbl.set_rotation(90)
# Reduce number of ticks:
ax.locator_params(axis='both', nbins=5)
# Set limits:
ax.set_xlim(extent[0:2])
ax.set_ylim(extent[2:4])
# Add labels to the axes so the user knows which is which:
# TODO add some flags/color/... indicating which phase & component each parameter belongs to...
if parx == 0:
ax.set_ylabel(str("#%d " % (pary + 1)) + get_plot_safe(labels[pary]))
if pary == (self.num_params - 1):
ax.set_xlabel(str("#%d " % (parx + 1)) + get_plot_safe(labels[parx]))
# Set the data limits:
for im in ims:
im.set_clim(tvmin, tvmax)
# Make it look PRO:
if im is not None:
cbar_ax = image_grid.cbar_axes[0]
nx = 1 + (self.num_params - 1) * 2
ny1 = (self.num_params - 1) * 2
cbar_ax.set_axes_locator(divider.new_locator(nx=nx, ny=1, ny1=ny1))
cb = cbar_ax.colorbar(im) # @UnusedVariable
except:
print("Unhandled exception while generating parameter space images:")
print(format_exc())
# ignore error, tell the user via the plot and return
self.clear_image(figure)
return