def assign_interpol_controller(self):
""" controller from optimal actions """
# Compute grid of u
self.u_policy_grid = []
# for all inputs
for k in range(self.sys.m):
self.u_policy_grid.append(
np.zeros(self.grid_sys.xgriddim, dtype=float))
# For all state nodes
for node in range(self.grid_sys.nodes_n):
# use tuple to get dynamic list of indices
indices = tuple(self.grid_sys.nodes_index[node, i]
for i in range(self.n_dim))
# If no action is good
if (self.action_policy[indices] == -1):
# for all inputs
for k in range(self.sys.m):
self.u_policy_grid[k][indices] = 0
else:
# for all inputs
for k in range(self.sys.m):
self.u_policy_grid[k][
indices] = self.grid_sys.actions_input[
self.action_policy[indices], k]
# Compute Interpol function
self.interpol_functions = []
# for all inputs
for k in range(self.sys.m):
if self.n_dim == 2:
self.interpol_functions.append(
interpol2D(
self.grid_sys.xd[0],
self.grid_sys.xd[1],
self.u_policy_grid[k],
bbox=[None, None, None, None],
kx=1,
ky=1,
))
elif self.n_dim == 3:
self.interpol_functions.append(
rgi([
self.grid_sys.xd[0], self.grid_sys.xd[1],
self.grid_sys.xd[2]
], self.u_policy_grid[k]))
else:
points = tuple(self.grid_sys.xd[i] for i in range(self.n_dim))
self.interpol_functions.append(
rgi(points, self.u_policy_grid[k], method='linear'))
# Asign Controller
self.ctl.vi_law = self.vi_law
def Interpolators(self):
""" Add the u and v `Interpolator <https://docs.scipy.org/doc/scipy-0.16.1/reference/generated/scipy.interpolate.RegularGridInterpolator.html>`_ objects to the weather object (two new attributes :
self.uInterpolator and self.vInterpolator).
::
u = self.uInterpolator([t,lat,lon])
#with u in m/s, t in days, lat and lon in degrees.
"""
self.uInterpolator = rgi((self.time, self.lat, self.lon), self.u)
self.vInterpolator = rgi((self.time, self.lat, self.lon), self.v)
def interp_VQ(self, dset, qT=False, V_label= 'Voltage', q_label='mAh/g', num_pts = 100):
'''Interpolates exp data to get eos'''
if qT != False:
#theoretical cap supplied; otherwise use self.theor_Q
self.theor_Q = qT
dset['Qf']=dset[q_label]/self.theor_Q
self.q_grid=dset['Qf']
self.V_grid=dset[V_label]
self.V = rgi((self.q_grid.values,), self.V_grid.values)
self.q = rgi((self.V_grid.values,), self.q_grid.values)
return()
def interpfungen(x, y, z, data0, data1, data2):
fn0 = rgi((x, y, z), data0)
fn1 = rgi((x, y, z), data1)
fn2 = rgi((x, y, z), data2)
def fun(pos, guess):
postuple = (pos[0], pos[1], pos[2])
theta = [fn0(postuple), fn1(postuple), fn2(postuple)]
err = False
return theta, err
return fun
def interp3(xx, yy, zz, V, points, shape):
interp = rgi((xx, yy, zz), V, bounds_error=False, fill_value=0)
values = interp(points)
values = values.reshape((int(shape[1]), int(shape[0]), int(shape[2])))
values = rotate(values, -90)
values = np.fliplr(values)
return values
def crustal_model_files(alt = [200, 1000], anomaly = 'Global', lim = [0., 360. -90., 90.], binsize = 0.1):
""""
Reads the .bin IDL files of the crustal magnetic field model (Langlais) for a range of altitudes and creates a function based on a linear interpolation.
Parameters:
alt: 2-elements array, optional
The array containing the altitude range. Default is [200, 1000] km.
anomaly: string, optional
The anomaly index, e. g., A1, A2, A6, etc. This string is used to find the directory where the model matrices are located. Default is 'Global'.
lim: 4-elements array, optional
An array cointaining the limits for latitude and longitude data, in which: [lon_min, lon_max, lat_min, lat_max]. Default is the whole range of Mars.
binsize: double, optional
The size of the lon and lat bins (must be the same size). Default is 0.1 degrees.
Returns:
A function and a matrix containing the data.
"""
longitude = np.linspace(lim[0], lim[1], int((lim[1] - lim[0]) / binsize + 1))
latitude = np.linspace(lim[2], lim[3], int((lim[3] - lim[2]) / binsize + 1))
altitude = np.linspace(alt[0], alt[1], int(alt[1] - alt[0] + 1))
br = np.empty((len(longitude), len(latitude), len(altitude)))
for i in range(len(altitude)):
h = int(i + alt[0])
data = sp.io.readsav('/home/oliveira/ccati_mexuser/LANGLAIS_Matrices/'+anomaly+'/LANGLAIS_BR_ALT_' + \
str(h) + '_RES_01.bin')
br[:, :, i] = data['zbins'].T
fn = rgi((longitude, latitude, altitude), br)
return fn, br
def GetInterpolater(hdulist, E,species):
"Returns a regulargridinterpolator object which can be called as interp((r,z),method='linear')."
# Returns Ebin nor nuclei output file assuming E=10*1.2^i in Kin. Energy in MeV
EBin = int(np.round(np.log(E/10.)/np.log(1.2)))
if species == 'proton':
"Primary + Secondary Protons."
vals = np.sum(hdulist[0].data[5:7,EBin],axis=0)
if species == 'antiproton':
"Secondary + Tertiary Antiproton"
vals = np.sum(hdulist[0].data[3:5,EBin],axis=0)
if species == 'electron':
"Primary + Secondary Electrons."
vals = hdulist[0].data[0,EBin]
if species == 'positron':
"Secondary + Tertiary Positron"
vals = np.sum(hdulist[0].data[1:3,EBin],axis=0)
# Build Grid for interpolator based on FITS header
height = -hdulist[0].header['CRVAL2']
radius = hdulist[0].header['CDELT1']*hdulist[0].header['NAXIS1']
grid_r = np.linspace(0,radius,hdulist[0].header['NAXIS1'])
grid_z = np.linspace(-height, height,hdulist[0].header['NAXIS2'])
interp = rgi((grid_r,grid_z),np.transpose(vals),fill_value=np.float32(0), method='linear',bounds_error=False)
return interp
def bp_smear(im_r):
im_hat, R = im_r
'''
# only necessary on windows
import numpy as np
N = im_hat.shape[0]
from scipy.interpolate import RegularGridInterpolator as rgi
# set the frequency range
if (N % 2 == 0):
freq_range = np.arange(-N/2, N/2)
else:
freq_range = np.arange(-(N-1)/2, (N+1)/2)
# creating the sample grid
sample_grid = np.array(np.meshgrid(freq_range, freq_range, freq_range)).T
'''
'''rotating the sample_grid by multiplying by rotation matrix transpose
Since R is orthonormal, this is the same as inverting
Multiplying by R transpose gives us the coordinates in the local basis
'''
local_x, local_y, local_z = np.tensordot(R.T, sample_grid, axes=(1, 3))
# smearing on the local_z coordinates
local_smear = np.sinc(local_z / N)
# #interpolator for the local_x and local_y coordinates. Interpolates on the FT
local_interpolator = rgi((freq_range, freq_range), im_hat, bounds_error=False, fill_value=0)
# local back projection
local_backproj_hat = local_interpolator(np.stack((local_x, local_y), axis=3)) * local_smear
print('completed smear')
return local_backproj_hat, local_smear
def run_sample(self, filepath):
"""
Run sampling.
"""
timer = common.Timer()
Rs = self.get_views()
# As rendering might be slower, we wait for rendering to finish.
# This allows to run rendering and fusing in parallel (more or less).
depths = common.read_hdf5(filepath)
timer.reset()
tsdf = self.fusion(depths, Rs)
xs = np.linspace(-0.5, 0.5, tsdf.shape[0])
ys = np.linspace(-0.5, 0.5, tsdf.shape[1])
zs = np.linspace(-0.5, 0.5, tsdf.shape[2])
tsdf_func = rgi((xs, ys, zs), tsdf)
modelname = os.path.splitext(os.path.splitext(os.path.basename(filepath))[0])[0]
points = self.get_random_points(tsdf)
values = tsdf_func(points)
t_loc, t_scale = self.get_transform(modelname)
occupancy = (values <= 0.)
out_file = self.get_outpath(filepath)
np.savez(out_file, points=points, occupancy=occupancy, loc=t_loc, scale=t_scale)
print('[Data] wrote %s (%f seconds)' % (out_file, timer.elapsed()))
def find_best(im_i, im_j):
im_i_f = rgi((grid_range, grid_range), im_i, bounds_error=False, fill_value=0)
im_j_f = rgi((grid_range, grid_range), im_j, bounds_error=False, fill_value=0)
# tracks angle pairs and pair quality)
best_lines = [None, -np.inf]
for theta in angles:
for psi in angles:
li = im_i_f(grid_range[:, None] * np.array([np.cos(theta), np.sin(theta)], None))
lj = im_j_f(grid_range[:, None] * np.array([np.cos(psi), np.sin(psi)], None))
forward = np.dot(li / np.linalg.norm(li), lj / np.linalg.norm(lj))
if forward > best_lines[1]:
best_lines[0] = (psi, theta)
best_lines[1] = forward
backward = np.dot(np.flipud(li), lj)
if backward > best_lines[1]:
best_lines[0] = (np.pi + psi, theta)
best_lines[1] = backward
return best_lines[0]
def get_regular_grid_interpolator(self, rgi_file):
#SRC
x, y, band_data = self.get_gsw_information(rgi_file)
interpolator = rgi(points=(y[::-1], x),
values=np.flip(band_data, 0),
method='nearest',
bounds_error=False,
fill_value=255)
del x, y, band_data
return interpolator
def reinterp_to_grid(data, old_Xgrid, new_Ns, Ls):
xg, yg, zg = old_Xgrid
xg, yg, zg = pad_grid(xg), pad_grid(yg), pad_grid(zg)
data_interp = rgi((zg, yg, xg), pad_array(data))
Zg_hires, Yg_hires, Xg_hires = reinterp_generate_grid(new_Ns,
Ls,
return_mesh=1,
pad=0)
pts = np.array([Zg_hires.ravel(), Yg_hires.ravel(), Xg_hires.ravel()]).T
return data_interp(pts).reshape(*new_Ns)
def project_fst_parallel(mol, orientations, return_hat=False, pad=0):
"""
works like project_fst but takes iterable of rotation matrices and runs in parallel
does not work on Windows
"""
# shape of data, apply desired padding and find good size for FFT
N = next_fast_len(mol.shape[0] + pad)
# set the frequency range
if N % 2 == 0:
w = np.arange(-N / 2, N / 2)
else:
w = np.arange(-(N - 1) / 2, (N + 1) / 2)
# pad roughly evenly
mol = np.pad(mol, (int(np.ceil((N - mol.shape[0]) / 2)), int(np.floor((N - mol.shape[0]) / 2))),
mode='constant')
# coordinate grid
omega = np.meshgrid(w, w, w, indexing='ij')
# Fourier transform
rho_hat = np.fft.fftshift(np.fft.fftn(mol))
rho_hat *= np.sign((1 - (np.abs(omega[0] + omega[1] + omega[2]) % 2) * 2)) / N ** 3
del mol
# create sampling grid
eta_x, eta_y = np.meshgrid(w, w, indexing='ij')
eta_x = eta_x[:, :, None]
eta_y = eta_y[:, :, None]
# interpolation function
rho_hat_f = rgi((w, w, w), rho_hat, bounds_error=False, fill_value=0)
def project_(R):
grid = eta_x * R.T[0] + eta_y * R.T[1]
# values of data's FFT interpolated to points on slice, tweak dimensions to make broadcasting work
im_hat = rho_hat_f(grid)[:, :, None]
# scaling factor
im_hat *= np.sign((1 - (np.abs(eta_x + eta_y) % 2) * 2)) * N ** 2
# returns im_hat if return_hat argument is true
if return_hat:
return im_hat
# apply inverse FFT to translate back to original space
im = np.real(np.fft.ifftn(np.fft.ifftshift(im_hat[:, :, 0])))
# memory saving stuff
return im
with Pool() as p:
images = p.map(project_, orientations)
return list(images)
def init_multigrid(proj, geo, alpha, alg):
# WARNING: This takes a lot of memory!
if alg == 'SART':
italg = tigre.algorithms.sart
if alg == 'SIRT':
italg = tigre.algorithms.sirt
finalsize = geo.nVoxel
maxval = max(proj.ravel())
minval = min(proj.ravel())
# Start with 16 (raise this for larger images)
geo.nVoxel = np.array([16, 16, 16])
geo.dVoxel = geo.sVoxel / geo.nVoxel
if (geo.nVoxel > finalsize).all():
return np.zeros(finalsize, dtype=np.float32)
niter = 100
initres = np.zeros(geo.nVoxel, dtype=np.float32)
while (geo.nVoxel != finalsize).all():
geo.dVoxel = geo.sVoxel / geo.nVoxel
initres = italg(proj, geo, alpha, niter, init=initres, verbose=False)
# get new dims(should be a way to do this more efficiently).
geo.nVoxel = geo.nVoxel * 2
geo.nVoxel[geo.nVoxel > finalsize] = finalsize[geo.nVoxel > finalsize]
geo.dVoxel = geo.sVoxel / geo.nVoxel
(x, y, z) = (np.linspace(minval,
maxval,
geo.nVoxel[0] / 2,
dtype=np.float32),
np.linspace(minval,
maxval,
geo.nVoxel[1] / 2,
dtype=np.float32),
np.linspace(minval,
maxval,
geo.nVoxel[2] / 2,
dtype=np.float32))
# evaluate the function sart at the points xv,yv,zv
xv, yv, zv = [
tile_array(tile_array(x, 2), geo.nVoxel[0]**2),
tile_array(tile_array(y, 2), geo.nVoxel[0]**2),
tile_array(tile_array(x, 2), geo.nVoxel[0]**2)
]
initres = rgi((x, y, z), initres)(np.column_stack((xv, yv, zv)))
initres = initres.reshape(geo.nVoxel)
return initres
def interp3(xrange, yrange, zrange, v, xi, yi, zi, **kwargs):
#http://stackoverflow.com/questions/21836067/interpolate-3d-volume-with-numpy-and-or-scipy
#from numpy import array
from scipy.interpolate import RegularGridInterpolator as rgi
x = np.arange(xrange[0],xrange[1])
y = np.arange(yrange[0],yrange[1])
z = np.arange(zrange[0],zrange[1])
interpolator = rgi((x,y,z), v, **kwargs)
pts = np.array([np.reshape(xi,(-1)), np.reshape(yi,(-1)), np.reshape(zi,(-1))]).T
Vi = interpolator(pts)
return np.reshape(Vi, np.shape(xi))
def init_multigrid(proj, geo, alpha,alg):
# WARNING: This takes a lot of memory!
if alg=='SART':
italg = tigre.algorithms.sart
if alg=='SIRT':
italg = tigre.algorithms.sirt
finalsize = geo.nVoxel
maxval= max(proj.ravel())
minval = min(proj.ravel())
# Start with 16 (raise this for larger images)
geo.nVoxel = np.array([16, 16, 16])
geo.dVoxel = geo.sVoxel / geo.nVoxel
if (geo.nVoxel > finalsize).all():
return np.zeros(finalsize, dtype=np.float32)
niter = 100
initres = np.zeros(geo.nVoxel, dtype=np.float32)
while (geo.nVoxel != finalsize).all():
geo.dVoxel = geo.sVoxel / geo.nVoxel
initres = italg(proj, geo, alpha, niter, init=initres,verbose=False)
# get new dims(should be a way to do this more efficiently).
geo.nVoxel = geo.nVoxel * 2
geo.nVoxel[geo.nVoxel > finalsize] = finalsize[geo.nVoxel > finalsize]
geo.dVoxel = geo.sVoxel / geo.nVoxel
(x,y,z)=(
np.linspace(minval, maxval, geo.nVoxel[0]/2,dtype=np.float32),
np.linspace(minval, maxval, geo.nVoxel[1]/2,dtype=np.float32),
np.linspace(minval, maxval, geo.nVoxel[2]/2,dtype=np.float32)
)
# evaluate the function sart at the points xv,yv,zv
xv,yv,zv=[tile_array(tile_array(x,2), geo.nVoxel[0]**2),
tile_array(tile_array(y,2), geo.nVoxel[0]**2),
tile_array(tile_array(x,2), geo.nVoxel[0]**2)]
initres = rgi((x, y, z), initres)(np.column_stack((xv,yv,zv)))
initres = initres.reshape(geo.nVoxel)
return initres
def transform_by_matrix(voxel, matrix, offset):
"""
transform a voxel by matrix, then apply an offset
Note that the offset is applied after the transformation
"""
sx, sy, sz = voxel.shape
gridx, gridy, gridz = _get_centeralized_mesh_grid(sx, sy, sz) # the coordinate grid of the new voxel
mesh = np.array([gridx.reshape(-1), gridy.reshape(-1), gridz.reshape(-1)])
mesh_rot = np.dot(np.linalg.inv(matrix), mesh) + np.array([sx / 2, sy / 2, sz / 2]).reshape(3, 1)
mesh_rot = mesh_rot - np.array(offset).reshape(3, 1) # grid for new_voxel should get a negative offset
interp = rgi((np.arange(sx), np.arange(sy), np.arange(sz)), voxel,
method='linear', bounds_error=False, fill_value=0)
new_voxel = interp(mesh_rot.T).reshape(sx, sy, sz) # todo: move mesh to center
return new_voxel
def project_fst(mol, R, return_hat=False, pad=0):
"""
simulates EM results given molecule mol and rotation matrix R
if return_hat is True, returns FT of image
pad specified number of zeros to pad edges with, default is 0
"""
# shape of data
N = next_fast_len(mol.shape[0] + pad)
# set the frequency range
if N % 2 == 0:
w = np.arange(-N / 2, N / 2)
else:
w = np.arange(-(N - 1) / 2, (N + 1) / 2)
# pad as roughly evenly
mol = np.pad(mol, (int(np.ceil((N - mol.shape[0]) / 2)), int(np.floor((N - mol.shape[0]) / 2))),
mode='constant')
# coordinate grid
omega = np.meshgrid(w, w, w)
# Fourier transform
rho_hat = np.fft.fftshift(np.fft.fftn(mol))
rho_hat *= np.sign((1 - (np.abs(omega[0] + omega[1] + omega[2]) % 2) * 2)) / N ** 3
# create sampling grid
eta_x, eta_y = np.meshgrid(w, w)
eta_x = eta_x[:, :, None]
eta_y = eta_y[:, :, None]
grid = eta_x * R.T[0] + eta_y * R.T[1]
# interpolation function
rho_hat_f = rgi((w, w, w), rho_hat, bounds_error=False, fill_value=0)
# values of data's FFT interpolated to points on slice, tweak dimensions to make broadcasting work
im_hat = rho_hat_f(grid)[:, :, None]
# scaling factor
im_hat *= np.sign((1 - (np.abs(eta_x + eta_y) % 2) * 2)) * N ** 2
# returns im_hat if return_hat argument is true
if return_hat:
return im_hat
# apply inverse FFT to translate back to original space
im = np.real(np.fft.ifftn(np.fft.ifftshift(im_hat[:, :, 0])))
return im
def _interp3D(xs, ys, zs, values, shape):
'''
3-D interpolation on a non-uniform grid, where z is non-uniform but x, y are uniform
'''
from scipy.interpolate import RegularGridInterpolator as rgi
# First interpolate uniformly in the z-direction
flipflag = False
Nfac = 10
NzLevels = Nfac * shape[2]
nx, ny = shape[:2]
zmax = np.nanmax(zs)
zmin = np.nanmin(zs)
zshaped = np.reshape(zs, shape)
# if zs are upside down, flip to interpolate vertically
if np.nanmean(zshaped[..., 0]) > np.nanmean(zshaped[..., -1]):
flipflag = True
zshaped = np.flip(zshaped, axis=2)
values = np.flip(values, axis=2)
dz = (zmax - zmin) / NzLevels
# TODO: change to use mean height levels
zvalues = zmin + dz * np.arange(NzLevels)
new_zs = np.tile(zvalues, (nx, ny, 1))
values = fillna3D(values)
new_var = interp_along_axis(zshaped,
new_zs,
values,
axis=2,
method='linear',
pad=False)
# This assumes that the input data is in the correct projection; i.e.
# the native weather grid projection
xvalues = np.unique(xs)
yvalues = np.unique(ys)
# TODO: temporarily switch x, y values until can confirm
interp = rgi((yvalues, xvalues, zvalues),
new_var,
bounds_error=False,
fill_value=np.nan)
return interp
def bguSlice(gamma, IF, EIF):
ih = IF.shape[0]
iw = IF.shape[1]
gh = gamma.shape[0]
gw = gamma.shape[1]
gd = gamma.shape[2]
ao = gamma.shape[3]
ai = gamma.shape[4]
x = repmat(np.arange(0, iw), ih, 1)
y = repmat(np.arange(0, ih).T, iw, 1).T
bg_coord_x = (x + 0.5) * (gw - 1) / iw
bg_coord_y = (y + 0.5) * (gh - 1) / ih
bg_coord_z = EIF * (gd - 1)
bg_coord_xx = bg_coord_x + 1
bg_coord_yy = bg_coord_y + 1
bg_coord_zz = bg_coord_z + 1
xx = np.linspace(0, gh, gh)
yy = np.linspace(0, gw, gw)
zz = np.linspace(0, gd, gd)
affine_model = get_td_list(ai, ao)
for j in range(ai):
for i in range(ao):
my_inter_fun = rgi((xx, yy, zz),
gamma[:, :, :, i, j],
bounds_error=False)
pts = np.array([bg_coord_xx, bg_coord_yy, bg_coord_zz]).T
# print(np.max(gamma))
affine_model[i][j] = my_inter_fun(pts).T
print('[INFO]>>> affine_model[{}][{}].shape:{}'.format(
i, j, affine_model[i][j].shape))
ll = np.ones((ih, iw))
ll_ = np.array([IF[:, :, 0], IF[:, :, 1], IF[:, :, 2], ll])
input1 = ll_.swapaxes(0, 1).swapaxes(1, 2)
output = 0
for i in range(ai):
new_ = np.array(
[affine_model[0][i], affine_model[1][i], affine_model[2][i]])
affine_model2 = new_.swapaxes(0, 1).swapaxes(1, 2)
print('[INFO]>>> affine_model2.shape:{}'.format(affine_model2.shape))
output = output + (affine_model2 * input1[:, :, i][:, :, None])
return output
def InturpEle(self, matrix):
#interpolates initial elevation data to be of given size
datasize = matrix.shape
yres = (datasize[0] - 1) / self.yres
xres = (datasize[1] - 1) / self.xres
x, y = np.linspace(0, datasize[1] - 1,
datasize[1]), np.linspace(0, datasize[0] - 1,
datasize[0])
grid = rgi((y, x), matrix)
output = np.empty((self.yres, self.xres))
for i in range(self.yres):
yloc = i * yres
for j in range(self.xres):
xloc = j * xres
output[i, j] = grid([yloc, xloc])
return output
def test_regular_grid_interpolator():
points = [np.linspace(0, 1, 100) for i in range(3)]
M = np.random.normal(size=[100] * 3)
y = tuple([np.random.uniform(size=100) for i in range(3)])
r = RegularGridInterpolator(tuple([tf.constant(p) for p in points]),
tf.constant(M),
method='linear')
from scipy.interpolate import RegularGridInterpolator as rgi
r_ = rgi(points, M, method='linear', fill_value=None, bounds_error=False)
sess = tf.Session()
u = sess.run(r(y))
sess.close()
u_ = r_(y)
# import pylab as plt
# print(u-u_)
# plt.hist(u-u_,bins=100)
# plt.show()
#print(u-u_)
assert np.all(np.isclose(u, u_, atol=1e-4))
def _brgi(self):
"""
Regular grid interpolator for B.
"""
from scipy.interpolate import RegularGridInterpolator as rgi
if self._rgi is not None:
return self._rgi
# - (rho,s,phi) coordinates:
rho = self.grid.rg
s = self.grid.sg
phi = self.grid.pg
br, bth, bph = self.bg
# Because we need the cartesian grid to stretch just beyond r=rss,
# add an extra dummy layer of magnetic field pointing radially outwards
rho = np.append(rho, rho[-1] + 0.01)
extras = np.ones(br.shape[0:2] + (1, ))
br = np.concatenate((br, extras), axis=2)
bth = np.concatenate((bth, 0 * extras), axis=2)
bph = np.concatenate((bph, 0 * extras), axis=2)
# - convert to Cartesian components and make interpolator on
# (rho,s,phi) grid:
ph3, s3, rh3 = np.meshgrid(phi, s, rho, indexing='ij')
sin_th = np.sqrt(1 - s3**2)
cos_th = s3
sin_ph = np.sin(ph3)
cos_ph = np.cos(ph3)
# Directly stack the expressions below, to save a bit of memory
# bx = (sin_th * cos_ph * br) + (cos_th * cos_ph * bth) - (sin_ph * bph)
# by = (sin_th * sin_ph * br) + (cos_th * sin_ph * bth) + (cos_ph * bph)
# bz = (cos_th * br) - (sin_th * bth)
bstack = np.stack(
((sin_th * cos_ph * br) + (cos_th * cos_ph * bth) - (sin_ph * bph),
(sin_th * sin_ph * br) + (cos_th * sin_ph * bth) + (cos_ph * bph),
(cos_th * br) - (sin_th * bth)),
axis=-1)
self._rgi = rgi((phi, s, rho), bstack, bounds_error=False)
return self._rgi
def radar2model_grid(radar_map, radar_lat, radar_lon, radar_height, model_lats,
model_lons, vertical_levels):
my_interpolating_function = rgi((radar_lat, radar_lon, radar_height),
radar_map,
fill_value=-999.0)
radar_at_model_space = numpy.empty(
(len(model_lats), len(model_lons), len(vertical_levels)))
for i, cmlats in enumerate(model_lats):
for j, cmlons in enumerate(model_lons):
for k, cl in enumerate(vertical_levels):
if cmlats < radar_lat.max() and cmlats > radar_lat.min(
) and cmlons < radar_lon.max() and cmlons > radar_lon.min():
pts = numpy.array([[cmlats, cmlons, cl]])
vi = my_interpolating_function(pts)
else:
vi = -999.0
radar_at_model_space[i, j, k] = vi
return radar_at_model_space
def mask_seafloor(D):
"""
Use known bathymetry to mask Sv and power
Bit too chunky without more work
"""
# Load in gridded bathymetry
bathy_file = '/home/hugke729/PhD/Data/Penny_Strait/Penny_strait.mat'
Dz = loadmat(bathy_file)
lon, lat, z = [Dz['topo' + key] for key in ['lon', 'lat', 'depth']]
z_interp = rgi((lon[:, 0], lat[0, :]), z)
z_along_line = z_interp(np.c_[D['lon'], D['lat']])
Z = D['z'][:, np.newaxis]*np.ones_like(D['Sv'])
z_below_bot = Z > z_along_line
D['power'] = ma.masked_where(z_below_bot, D['power'])
D['Sv'] = ma.masked_where(z_below_bot, D['Sv'])
return D
def remap_data_on_query_points(data1,xyz2):
# this function queries the dataset stored in the data1 dictionary at the
# locations specified by the grid points xyz2 and stores the data in the
# variable dataq
print "interpolating data to a uniform grid\n"
x1 = np.array(data1['x'])
y1 = np.array(data1['y'])
z1 = np.array(data1['z'])
x2 = np.array(xyz2['x'])
y2 = np.array(xyz2['y'])
z2 = np.array(xyz2['z'])
dataq = {}
# construct a new structured volume with uniform and equal spacing along
# all the three axes
xq,yq,zq = np.meshgrid(x2,y2,z2,indexing = 'ij')
# create array of string to query the data dictionary
# var = ['rho', 'u', 'v', 'w', 'p', 'T']
# query data for various flow parameters and store in dataq
# for current_var in var:
current_var = 'rho'
my_interpolating_function = rgi((x1,y1,z1), np.array(data1[current_var]))
dataq[current_var] = my_interpolating_function(np.array([xq,yq,zq]).T)
# perform tranpose to maintain shape
dataq[current_var] = np.transpose(dataq[current_var])
# store the grid points
dataq['x'] = x2
dataq['y'] = y2
dataq['z'] = z2
return dataq
def grid_align(V,
T,
V_scale=None,
V_origin=None,
bounds_error=False,
fill_value=np.nan):
assert (len(V.shape) == len(T.shape))
if V_scale is None:
V_scale = np.array(T.shape) / np.array(V.shape)
if V_origin is None:
V_origin = np.zeros(len(V.shape))
assert (not np.any(V_scale == 0))
V_axes = [
np.linspace(V_origin[ax],
V_origin[ax] + (V.shape[ax] - 1) * V_scale[ax],
num=V.shape[ax]) for ax in range(len(V.shape))
]
interp_func = rgi(V_axes,
V,
bounds_error=bounds_error,
fill_value=fill_value)
points = np.argwhere(np.ones_like(T))
return interp_func(points).reshape(T.shape)
xs = np.load(
'UNSW4_1st withBG TEST ephiQWM UNSW4_1st structure 2nm 800x800 - 10-4-12-4.npz'
)['xs']
ys = np.load(
'UNSW4_1st withBG TEST ephiQWM UNSW4_1st structure 2nm 800x800 - 10-4-12-4.npz'
)['ys']
zs = np.load(
'UNSW4_1st withBG TEST ephiQWM UNSW4_1st structure 2nm 800x800 - 10-4-12-4.npz'
)['zs']
ephi = 10**6 * np.load(
'UNSW4_1st withBG TEST ephiQWM UNSW4_1st structure 2nm 800x800 - 10-4-12-4.npz'
)['ephi']
interpolate = rgi(points=(xs, ys, zs), values=ephi, bounds_error=False)
def V_hrl(point):
return interpolate(point)[0] + V_step(point[2])
def V_doubledot(point):
return double_HO(point[0]) + V_HO1d(point[1]) + V_step(point[2])
def dV_doubledot(point):
return np.add(np.add(dV_double_HO(point[0]), dV_HO1d(point[1])),
dV_step(point[2]))
def find_reduced_dim(datadir, imgdir):
print('making figure 3 ...')
# Set up figure
fig = plt.figure()
# Load data
txtdir = datadir + 'l1_l2/txt_files/'
TC_R_avg_imp = np.loadtxt(txtdir + "/TC_R_avg_imp.txt")
TC_R_avg_unalt = np.loadtxt(txtdir + "/TC_R_avg_unalt.txt")
TC_R_rms_imp = np.loadtxt(txtdir + "/TC_R_rms_imp.txt")
TC_R_rms_unalt = np.loadtxt(txtdir + "/TC_R_rms_unalt.txt")
TC_P1_avg_imp = np.loadtxt(txtdir + "/TC_P1_avg_imp.txt")
TC_P1_avg_unalt = np.loadtxt(txtdir + "/TC_P1_avg_unalt.txt")
TC_P1_rms_imp = np.loadtxt(txtdir + "/TC_P1_rms_imp.txt")
TC_P1_rms_unalt = np.loadtxt(txtdir + "/TC_P1_rms_unalt.txt")
TC_P2_avg_imp = np.loadtxt(txtdir + "/TC_P2_avg_imp.txt")
TC_P2_avg_unalt = np.loadtxt(txtdir + "/TC_P2_avg_unalt.txt")
TC_P2_rms_imp = np.loadtxt(txtdir + "/TC_P2_rms_imp.txt")
TC_P2_rms_unalt = np.loadtxt(txtdir + "/TC_P2_rms_unalt.txt")
TC_A_avg_imp = np.loadtxt(txtdir + "/TC_A_avg_imp.txt")
TC_A_avg_unalt = np.loadtxt(txtdir + "/TC_A_avg_unalt.txt")
TC_A_rms_imp = np.loadtxt(txtdir + "/TC_A_rms_imp.txt")
TC_A_rms_unalt = np.loadtxt(txtdir + "/TC_A_rms_unalt.txt")
# Data information
l2min = 0 / 64 # x min
l2max = 32 / 64 # x max
l2inc = 1 / 64 # x increment
l1min = 0 / 64 # y min
l1max = 32 / 64 # y max
l1inc = 1 / 64 # y increment
l2 = np.arange(l2min, l2max + l2inc, l2inc)
l1 = np.arange(l1min, l1max + l1inc, l1inc)
L2, L1 = np.meshgrid(l2, l1, indexing='ij')
# Make 2D array of compression ratio
L0 = 1.0 - L1 - L2
R = 16 * L0 + 4 * L1 + L2
print(R)
# R = 16*L0**2 + 4*L1**2 + L2**2 + \
# 4*L1*L2 + L1*L2 + L0*L2
# print(R2)
grid1 = AxesGrid(fig, (0.08, 0.54, 0.80, 0.35),
nrows_ncols=(1, 4),
axes_pad=0.1,
aspect=True,
label_mode="L",
share_all=True,
cbar_location="right",
cbar_mode="single",
cbar_size="7%",
cbar_pad="3%")
grid2 = AxesGrid(fig, (0.08, 0.12, 0.80, 0.35),
nrows_ncols=(1, 4),
axes_pad=0.1,
aspect=False,
label_mode="L",
share_all=True,
cbar_location="right",
cbar_mode="none")
# Get locations on fixed compression ratio
ax = grid1[1].axes
Rim = ax.contour(L2, L1, R, [6,8,10,12], origin='lower', \
colors=('m','b','g','y'))
# Rim = ax.contour(L2, L1, L0, [0.2,0.4,0.6,0.8], origin='lower', \
# colors=('m','b','g','y'))
ax.clabel(Rim, Rim.levels, inline=True, inline_spacing=30, \
fmt=r'$r = %i$', fontsize=8, rightside_up=True, \
manual=[(0.1,0.1),(0.2,0.2),(0.3,0.3),(0.4,0.4)])
xr6 = Rim.allsegs[0][0][:, 0]
yr6 = Rim.allsegs[0][0][:, 1]
xr8 = Rim.allsegs[1][0][:, 0]
yr8 = Rim.allsegs[1][0][:, 1]
xr10 = Rim.allsegs[2][0][:, 0]
yr10 = Rim.allsegs[2][0][:, 1]
xr12 = Rim.allsegs[3][0][:, 0]
yr12 = Rim.allsegs[3][0][:, 1]
# xr6 = np.linspace(0, 0.5, 9)
# xr8 = np.linspace(0, 0.5, 9)
# xr10 = np.linspace(0, 0.5, 9)
# xr12 = np.linspace(0, 0.5, 9)
# yr6 = np.linspace(1/8, 1/8, 9)
# yr8 = np.linspace(2/8, 2/8, 9)
# yr10 = np.linspace(3/8, 3/8, 9)
# yr12 = np.linspace(4/8, 4/8, 9)
xyr6 = np.stack((xr6, yr6), axis=1)
xyr8 = np.stack((xr8, yr8), axis=1)
xyr10 = np.stack((xr10, yr10), axis=1)
xyr12 = np.stack((xr12, yr12), axis=1)
Xr6, Yr6 = np.meshgrid(xr6, yr6, indexing='ij')
Xr8, Yr8 = np.meshgrid(xr8, yr8, indexing='ij')
Xr10, Yr10 = np.meshgrid(xr10, yr10, indexing='ij')
Xr12, Yr12 = np.meshgrid(xr12, yr12, indexing='ij')
for i in range(4):
ax = grid1[i].axes
if i == 0:
num = TC_R_avg_imp
den = TC_R_avg_unalt
ax.set_title('Computing R')
elif i == 1:
num = TC_P1_avg_imp
den = TC_P1_avg_unalt
ax.set_title('Computing P1')
elif i == 2:
num = TC_P2_avg_imp
den = TC_P2_avg_unalt
ax.set_title('Computing P2')
elif i == 3:
num = TC_A_avg_imp
den = TC_A_avg_unalt
ax.set_title('Computing A')
img = num / den
# img = np.exp(num/den)
# img = np.log10(np.sqrt(num/den))
print(np.max(img))
print(np.min(img))
# line0 = ax.contour(L2, L1, img, [0.75, 0.9], origin='lower', colors=('k'), \
# linestyles=(':'))
# x075 = line0.allsegs[0][0][:,0]
# y075 = line0.allsegs[0][0][:,1]
# x09 = line0.allsegs[1][0][:,0]
# y09 = line0.allsegs[1][0][:,1]
# xy075 = np.stack((x075, y075), axis=1)
# xy09 = np.stack((x09, y09), axis=1)
# Rim = ax.contour(L2, L1, L0, [0.2,0.4,0.6,0.8], origin='lower', \
# colors=('m','b','g','y'))
# ax.clabel(line0, line0.levels, inline=True, inline_spacing=30, \
# fmt=r'$r = %i$', fontsize=8, rightside_up=True, \
# manual=[(0.1,0.1)])
# xr8 = Rim.allsegs[1][0][:,0]
# yr8 = Rim.allsegs[1][0][:,1]
# xr10 = Rim.allsegs[2][0][:,0]
# yr10 = Rim.allsegs[2][0][:,1]
# xr12 = Rim.allsegs[3][0][:,0]
# yr12 = Rim.allsegs[3][0][:,1]
# im = ax.contourf(L2, L1, img, 100, origin='lower', \
# extent=[l2min,l2max,l1min,l1max], cmap='bwr', \
# vmin=-0.8, vmax=0.2)
im = ax.contourf(L2, L1, img, 100, origin='lower', \
extent=[l2min,l2max,l1min,l1max], cmap='bwr', \
vmin=0, vmax=2)
# im.set_clim(-0.8, 0.8)
im.set_clim(0, 2)
cbar = ax.cax.colorbar(im)
# ax.cax.set_ylabel('$\log(TC_{im}/TC_{un})$')
ax.cax.set_ylabel('$TC_{im}/TC_{un}$')
# ax.set_xticks([ntmin,(ntmax+ntmin)/2,ntmax])
# ax.set_yticks([l1min,(l1max+l1min)/2,l1max])
ax.set_xticks(np.linspace(1 / 8, 3 / 8, 3))
ax.set_yticks(np.linspace(1 / 8, 3 / 8, 3))
ax.set_xticklabels([])
ax.set_yticklabels(['1/8', '2/8', '3/8'])
ax.set_ylabel('$\ell_1$')
ax = grid2[i].axes
# Get data along each compression ratio line
f_l0 = rgi((l2, l1), L0, method='linear')
f_l1 = rgi((l2, l1), L1, method='linear')
f_l2 = rgi((l2, l1), L2, method='linear')
# f075_l0 = f_l0(xy075)
# f075_l1 = f_l1(xy075)
# f075_l2 = f_l2(xy075)
# print(f075_l0)
# print(f075_l1)
# print(f075_l2)
# f09_l0 = f_l0(xy09)
# f09_l1 = f_l1(xy09)
# f09_l2 = f_l2(xy09)
# best_vals, covar = curve_fit(fit_equation, (f075_l0,f075_l1,f075_l2), \
# np.linspace(0.75,0.75,len(f075_l0)) )
# print('best_vals: {}'.format(best_vals))
l0_1D = np.reshape(L0, (-1))
l1_1D = np.reshape(L1, (-1))
l2_1D = np.reshape(L2, (-1))
img_1D = np.reshape(img, (-1))
# print(len(l0_1D))
# l0_1D = l0_1D[0::2]
# l1_1D = l1_1D[0::2]
# l2_1D = l2_1D[0::2]
# img_1D = img_1D[0::2]
best_vals, covar = curve_fit(fit_equation, (l0_1D, l1_1D, l2_1D),
img_1D)
print('best_vals: {}'.format(best_vals))
print('error: {}'.format(np.sqrt(np.diag(covar))))
print('covar: {}'.format(covar))
best_vals, covar = curve_fit(fit_equation2, (l0_1D, l1_1D, l2_1D),
img_1D)
print('best_vals: {}'.format(best_vals))
print('error: {}'.format(np.sqrt(np.diag(covar))))
print('covar: {}'.format(covar))
best_vals, covar = curve_fit(fit_equation3, (l0_1D, l1_1D, l2_1D),
img_1D)
print('best_vals: {}'.format(best_vals))
print('error: {}'.format(np.sqrt(np.diag(covar))))
print('covar: {}'.format(covar))
# f09 = f(xyr8)
# fr10 = f(xyr10)
# fr12 = f(xyr12)
# ax.plot(f075_l2, f075_l0, 'm-')
# ax.plot(f075_l2, f075_l1, 'b')
# ax.plot(f09_l2, f09_l0, 'm--')
# ax.plot(f09_l2, f09_l1, 'b--')
ax.grid('on')
# ax.set_xticks([ntmin,(ntmax+ntmin)/2,ntmax])
# ax.set_yticks([l1min,(l1max+l1min)/2,l1max])
ax.set_xticks(np.linspace(1 / 8, 3 / 8, 3))
# ax.set_yticks(np.linspace(1/8,3/8,3))
ax.set_xticklabels(['1/8', '2/8', '3/8'])
# ax.set_yticklabels(['1/8','2/8','3/8'])
ax.set_xlabel('$\ell_2$')
# ax.set_ylabel('$\ell_1$')
ax.set_xlim(0, 0.5)
# print('saving image ...')
fig.set_size_inches(6.5, 3.25,
forward=True) # figure size must be set here
# plt.savefig(imgdir + 'fig3.png', dpi=300)
# img = np.transpose(np.divide(num, den))
# img = np.divide(num, den)
# Xaxis, Yaxis = np.meshgrid(xaxis, yaxis, copy=False, indexing='ij')
# cont_levs = 100
# xmin = np.min(xaxis)
# xmax = np.max(xaxis)
# ymin = np.min(yaxis)
# ymax = np.max(yaxis)
# fig = plt.figure(clear=True)
# ax = fig.add_subplot(1,1,1)
print('\tdone with reduced dim')
def __LOS_Gas_Grid(tNum, n_thread, l_max,b_max,res,H2,HI,H2_mult,r_min,r_max,z_step=0.02,H2_map='PEB'):
"""
LOS Integration Kernel for Pohl, Englmaier, Bissantz 2008 (arXiv: 0712.4264)
Grid_points are linearly interpolated in 3-dimensions.
"""
#==============================================
# Integration Parameters
#==============================================
import tmp
reload(tmp)
func = tmp.func
R_solar = 8.5 # Sun at 8.5 kpc
kpc2cm = 3.08568e21
z_start,z_stop,z_step = max(R_solar-r_max,0),R_solar+r_max,z_step # los start,stop,step-size in kpc
# distances along the LOS
zz = np.linspace(start=z_start,stop=z_stop,num=int(np.ceil((z_stop-z_start)/z_step)))
deg2rad = np.pi/180.
pi = np.pi
# List of lat/long to loop over.
bb = np.linspace(-b_max+res/2.,b_max+res/2.,int(np.ceil(2*b_max/res)))*deg2rad
# divide according to thread
stride = len(bb)/n_thread
if tNum == n_thread-1: bb = bb[tNum*(stride):]
else: bb = bb[tNum*stride:(tNum+1)*stride]
ll = np.linspace(-l_max+res/2.,l_max+res/2.,np.ceil(int(2*l_max/res)))*deg2rad
# Master projected skymap
proj_skymap = np.zeros(shape=(len(bb),len(ll)))
#Prepare the interpolator based on the image info
grid_x = np.linspace(-14.95, 14.95,300)
grid_z = np.linspace(-.4875, .4875,40)
H2_PEB_Interp = rgi((grid_z,grid_x,grid_x),H2_PEB,fill_value=np.float32(0), method='linear',bounds_error=False)
grid_x = np.linspace(-50, 50,501)
grid_z = np.linspace(-2, 2,51)
HI_NS_Interp = rgi((grid_z,grid_x,grid_x),HI_NS,fill_value=np.float32(0), method='linear',bounds_error=False)
X_CO_MAX = 100*np.ones(len(zz))
# Loop latitudes
for bi in range(len(bb)):
# loop longitude
for lj in range(len(ll)):
los_sum=0.
l,b = ll[lj], bb[bi]
# z in cylindrical coords
z = zz*sin(b)
x,y = -zz*cos(l)*cos(b)+R_solar, +zz*sin(l)*cos(b)
r_2d = sqrt(x**2+y**2)
if H2==True:
# Call the interpolator on the current set of points
if H2_map=='PEB':
X_CO = 3e19*np.minimum( exp(r_2d/5.3),X_CO_MAX)
los_sum += H2_mult*sum(func(x,y,z)*H2_PEB_Interp((z,-y,x)))*z_step*kpc2cm
elif H2_map=='NS':
pass
else: raise Exception("Invalid H2 map chosen")
if HI==True:
los_sum += sum(func(x,y,z)*HI_NS_Interp((z,y,x)))*z_step*kpc2cm
proj_skymap[bi,lj] = los_sum
return proj_skymap
def ext_calc(l, b, d, npoints=100):
t = np.linspace(0, 1, npoints)
star_pos = d * np.array([
np.cos(b * np.pi / 180) * np.cos(l * np.pi / 180),
np.cos(b * np.pi / 180) * np.sin(l * np.pi / 180),
np.sin(b * np.pi / 180)
])
if star_pos[0] > 1997.5:
d = 1997.49 / (np.cos(b * np.pi / 180) * np.cos(l * np.pi / 180))
star_pos = d * np.array([
np.cos(b * np.pi / 180) * np.cos(l * np.pi / 180),
np.cos(b * np.pi / 180) * np.sin(l * np.pi / 180),
np.sin(b * np.pi / 180)
])
if star_pos[0] < -1997.5:
d = -1997.49 / (np.cos(b * np.pi / 180) * np.cos(l * np.pi / 180))
star_pos = d * np.array([
np.cos(b * np.pi / 180) * np.cos(l * np.pi / 180),
np.cos(b * np.pi / 180) * np.sin(l * np.pi / 180),
np.sin(b * np.pi / 180)
])
if star_pos[1] > 1997.5:
d = 1997.49 / np.cos(b * np.pi / 180) * np.sin(l * np.pi / 180)
star_pos = d * np.array([
np.cos(b * np.pi / 180) * np.cos(l * np.pi / 180),
np.cos(b * np.pi / 180) * np.sin(l * np.pi / 180),
np.sin(b * np.pi / 180)
])
if star_pos[1] < -1997.5:
d = -1997.49 / np.cos(b * np.pi / 180) * np.sin(l * np.pi / 180)
star_pos = d * np.array([
np.cos(b * np.pi / 180) * np.cos(l * np.pi / 180),
np.cos(b * np.pi / 180) * np.sin(l * np.pi / 180),
np.sin(b * np.pi / 180)
])
if star_pos[2] > 297.5:
d = 297.49 / np.sin(b * np.pi / 180)
star_pos = d * np.array([
np.cos(b * np.pi / 180) * np.cos(l * np.pi / 180),
np.cos(b * np.pi / 180) * np.sin(l * np.pi / 180),
np.sin(b * np.pi / 180)
])
if star_pos[2] < -297.5:
d = -297.49 / np.sin(b * np.pi / 180)
star_pos = d * np.array([
np.cos(b * np.pi / 180) * np.cos(l * np.pi / 180),
np.cos(b * np.pi / 180) * np.sin(l * np.pi / 180),
np.sin(b * np.pi / 180)
])
interpolation_points = np.array(
[star_pos[0] * t, star_pos[1] * t, star_pos[2] * t]).transpose()
interpolator = rgi((x, y, z), extmap)
interpolated_vals = interpolator(interpolation_points)
extout = sum(interpolated_vals) * (d / npoints)
return extout
import numpy as np
import pyfits
import matplotlib.pyplot as plt
from scipy.interpolate import RegularGridInterpolator as rgi
H2_hdulist = pyfits.open('./mod-total-rev2int.fit')
H2 = H2_hdulist[0].data
grid_x = np.linspace(-14.95, 14.95, 300)
grid_z = np.linspace(-.4875, .4875, 40)
H2_Interp = rgi((grid_z, grid_x, grid_x),
H2,
fill_value=np.float32(0),
method='linear',
bounds_error=False)
x = np.linspace(-1, 1, 100)
y = []
for i in x:
y.append(H2_Interp((i, 8, 0)))
plt.yscale('log')
plt.plot(x, y)
plt.show()
def flyby(output_dir,
flyby_a,
flyby_n,
do_rand_start=1,
l_start=None,
l_dir=np.array([np.pi / 8, np.sqrt(0.5), 1.]),
norm_B0=1,
method='matt',
output_plot=1):
# Loading data with the correct method scales the data to the physical variables
data = diag.load_data(output_dir,
flyby_n,
prob='from_array',
method=method)
Ns, Ls = get_grid_info(data)
Ls[:2] *= flyby_a # stretch perpendicular lengths
zg, yg, xg = reinterp_generate_grid(Ns, Ls)
# Zg, Yg, Xg = np.meshgrid(zg, yg, xg, indexing='ij') # only needed if defining a function on grid
# extending to general mean fields
rho_data = data['rho']
B = np.array((data['Bcc1'], data['Bcc2'], data['Bcc3']))
B_0 = diag.get_mag(diag.box_avg(B), axis=0) # single time entry
v_A = diag.alfven_speed(rho_data, B)
scale_B_mean = 1 / B_0 if norm_B0 else 1 # 1 / <Bx> = a^2
scale_v_A = 1 / v_A if norm_B0 else 1 # rho^1/2 / <Bx> = rho^1/2 * a^2
scale_rho = flyby_a**2 if norm_B0 else 1
Bx = pad_array(data['Bcc1'] * scale_B_mean)
By = pad_array(data['Bcc2'] * scale_B_mean)
Bz = pad_array(data['Bcc3'] * scale_B_mean)
ux = pad_array(data['vel1'] * scale_v_A)
uy = pad_array(data['vel2'] * scale_v_A)
uz = pad_array(data['vel3'] * scale_v_A)
rho = pad_array(rho_data * scale_rho)
Bmag = np.sqrt(Bx**2 + By**2 + Bz**2)
# interpolaters
Bx_i = rgi((zg, yg, xg), Bx)
By_i = rgi((zg, yg, xg), By)
Bz_i = rgi((zg, yg, xg), Bz)
ux_i = rgi((zg, yg, xg), ux)
uy_i = rgi((zg, yg, xg), uy)
uz_i = rgi((zg, yg, xg), uz)
Bmag_i = rgi((zg, yg, xg), Bmag)
rho_i = rgi((zg, yg, xg), rho)
# if plotting, do a short flyby to cut down on space
# otherwise fly through either 1/10 of the box
# or 5 million points (for large resolutions) for analysis
N_points = Ns.prod()
N_dl = 50000 if output_plot else min(int(5e6), N_points // 10)
dl = yg[1] - yg[0] # walk in steps of dy = a*Ly / Ny
total_length = N_dl * dl
lvec = np.linspace(0, total_length, N_dl, endpoint=False).reshape(N_dl, 1)
if do_rand_start:
# start at random point in box
l_start = uniform(high=Ls)
else:
assert l_start is not None, 'l_start must be a valid numpy array!'
# direction biased in x direction (z, y, x)
l_dir /= np.sqrt(np.sum(l_dir**2))
pts = np.mod(l_start + lvec * l_dir, Ls)
# Interpolate data along line running through box
FB = {}
FB['Bx'], FB['By'], FB['Bz'] = Bx_i(pts), By_i(pts), Bz_i(pts)
FB['ux'], FB['uy'], FB['uz'] = ux_i(pts), uy_i(pts), uz_i(pts)
FB['Bmag'], FB['rho'] = Bmag_i(pts), rho_i(pts)
FB['start_point'], FB['direction'] = l_start, l_dir
FB['l_param'], FB['points'] = lvec[:, 0], pts
FB['a'], FB['snapshot_number'] = flyby_a, flyby_n
FB['normed_to_Bx'] = 'true' if norm_B0 else 'false'
FB['norms'] = {'B': scale_B_mean, 'u': scale_v_A, 'rho': scale_rho}
return FB
plt.colorbar()
fig.add_subplot(1, 2, 2)
totmap = Map(np.log10(np.nansum((10.0**model)**2.0, axis=2) * dz), EMmap.meta.copy())
print np.nanmin(totmap.data), np.nanmax(totmap.data)
totmap.plot(cmap=emcm, vmin=20, vmax=30)
plt.colorbar()
plt.savefig('comparison')
plt.close()"""
# Convert cartesian density data into spherical so it can be plotted
x1 = np.linspace(xrange[0], xrange[1], side)
y1 = np.linspace(yrange[0], yrange[1], side)
z1 = np.linspace(zrange[0], zrange[1], side)
intf = rgi((x1, y1, z1), 10.0**model[:].copy())
rad = np.linspace(1.0, 1.25, 21)
lat = np.linspace(-np.pi/2, np.pi/2, 180)
lon = np.linspace(-np.pi, np.pi, 360)
print lon.shape, lat.shape, rad.shape
radi, lati, loni = np.array([i for i in product(rad, lat, lon)]).T
print loni.shape, lati.shape, radi.shape
yi = radi * np.cos(lati) * np.sin(loni)
xi = np.sin(lati)
zi = -radi * np.cos(lati) * np.cos(loni)
print xi.shape, yi.shape, zi.shape
print np.array([xi, yi, zi]).shape
modelsph = intf(np.array([xi, yi, zi]).T)
print modelsph.shape, np.nanmin(modelsph), np.nanmax(modelsph)
modelsph = modelsph.reshape(21, 180, 360)
def interpolate_output_to_new_grid(run_dir, last_iter, new_grid,
get_grid_args=dict()):
"""
Takes outputs U, V, T, S, Eta and interpolates them onto new grid
Assumes both grids are 3D and Cartesian.
Results for 2D aren't quite right. Interpolation falls back to nearest
neighbour where it should be linear.
Inputs
------
run_dir: str
Directory containing output
last_iter: int
The number in the output filenames that are to be interpolated
For example, for T.00000360000.data, last_iter is 36000
new_grid: Grid instance
Grid from MyGrids.Grid
get_grid_args: dict
Arguments to pass to get_grid
`g_in = get_grid(run_dir, squeeze_hfacs=False, **get_grid_args)`
Returns
-------
all_outputs: dict
Contains U, V, T, S, and Eta on new grid. Shape of these arrays
are (Nz × Ny × Nx) or (Ny × Nx) for Eta
Notes
-----
Not set up to work with OBCS (hFacs are not dealt with correctly)
"""
# filterwarnings('ignore', '.*invalid value encountered in true_divide')
# filterwarnings('ignore', '.*invalid value encountered in less_equal')
# Helper function
def get_coord(grid, coord_str):
"""get_coord(g, 'xc') returns g.xc or None if g has no attribute xc
Remove extra value for xf and yf, since that's what's need in outer
function"""
try:
out = getattr(grid, coord_str)
if coord_str in ['xf', 'yf']:
out = out[:-1]
return out.copy()
except TypeError:
return None
# Input and output grids
run_dir = os.path.normpath(run_dir) + os.sep
g_in = get_grid(run_dir, squeeze_hfacs=False, **get_grid_args)
g_out = new_grid
coord_sys = dict(
U=('xf', 'yc', 'zc', 'hFacW'), V=('xc', 'yf', 'zc', 'hFacS'),
T=('xc', 'yc', 'zc', 'hFacC'), S=('xc', 'yc', 'zc', 'hFacC'),
Eta=('xc', 'yc', None, 'hFacC'))
# Preallocate dict that is returned
all_outputs = {}
for k, (x, y, z, h) in coord_sys.items():
threeD = False if k is 'Eta' else True
# Read in all grids for current quantity
xi, yi, zi, hi = [get_coord(g_in, q) for q in (x, y, z, h)]
hi = hi[0, ...] if not threeD else hi
# Read actual output
fname = run_dir + k + '*'
quantity = rdmds(fname, last_iter)
# Convert zeros to NaN for values that aren't water
# This is really important for T and S, where the average of say 35
# and 0 is unphysical. For U and V, it's not as important but still
# worthwhile
quantity[hi == 0] = np.nan
# Smooth at each depth level before interpolation. Helps reduce large
# divergences
# Update: 6/3/17. Try without smoothing
gf_opts = dict(sigma=0, keep_nans=False, gf_kwargs=dict(truncate=8))
if threeD:
for i, level in enumerate(quantity):
quantity[i, ...] = nan_gaussian_filter(level, **gf_opts)
else:
quantity = nan_gaussian_filter(quantity, **gf_opts)
# Add a border around output to avoid problems with regions between
# the centre of the first and last cells in a given dimension and the
# edge of the domain
quantity = add_border_values(quantity)
# Add in associated values to x, y, z
xp2 = np.r_[xi[0] - g_in.dx[0], xi, xi[-1] + g_in.dx[-1]]
yp2 = np.r_[yi[0] - g_in.dy[0], yi, yi[-1] + g_in.dy[-1]]
zp2 = np.r_[zi[0] - g_in.dz[0], zi, zi[-1] + g_in.dz[-1]] if threeD else None
# Grid associated with added border
pts_in = (zp2, yp2, xp2) if threeD else (yp2, xp2)
# Overall interpolation will be combo of linear and nearest neighbour
# to get the best of both
interp_input = dict(points=pts_in, values=quantity,
bounds_error=False, fill_value=None)
f_lin = rgi(method='linear', **interp_input)
f_near = rgi(method='nearest', **interp_input)
# Output grids
xo, yo, zo = [get_coord(g_out, q) for q in (x, y, z)]
if threeD:
Zo, Yo, Xo = np.meshgrid(zo, yo, xo, indexing='ij')
else:
Yo, Xo = np.meshgrid(yo, xo, indexing='ij')
pts_out = (Zo, Yo, Xo) if threeD else (Yo, Xo)
# Linear interpolate to start with, then fill in bits near boundaries
# with nearest neighbour interpolation, then fill everything else
lin_out = f_lin(pts_out)
near_out = f_near(pts_out)
lin_out_is_nan = np.isnan(lin_out)
lin_out[lin_out_is_nan] = near_out[lin_out_is_nan]
# Fill any remaining gaps
lin_out = remove_nans_laterally(lin_out, inverted_dimensions=True)
# For completely empty levels, copy the level above
if threeD:
levels_to_copy = np.where(np.all(np.isnan(lin_out), axis=(1, 2)))[0]
for level in levels_to_copy:
lin_out[level, ...] = lin_out[level - 1, ...]
all_outputs[k] = lin_out
return all_outputs
def tangent_planes_to_zone_of_interest(cropAx, parametrized_skel,
s_inx, e_inx, g_radius, g_res, shift_impose, direction, H_th):
p_inx, p_bound, p_shiftX, p_shiftY = s_inx, [], 0 , 0
sz = cropAx.shape
x, y = np.mgrid[-g_radius:g_radius:g_res, -g_radius:g_radius:g_res]
z = np.zeros_like(x)
c_mesh = (2*g_radius)/(2*g_res)
xyz = np.array([np.ravel(x), np.ravel(y), np.ravel(z)]).T
tangent_vecs = unit_tangent_vector(parametrized_skel)
interpolating_func = rgi((range(sz[0]),range(sz[1]),range(sz[2])),
cropAx,bounds_error=False,fill_value=0)
cent_ball = (x**2+y**2)<g_res*1
count = 1
while s_inx != e_inx:
#print s_inx
point = parametrized_skel[s_inx]
utv = tangent_vecs[s_inx]
if np.array_equal(utv, np.array([0, 0, 0])):
s_inx = s_inx+direction
continue
rot_axis = pr.unit_normal_vector(utv, np.array([0,0,1]))
theta = pr.angle(utv, np.array([0,0,1]))
rot_mat = pr.rotation_matrix_3D(rot_axis, theta)
rotated_plane = np.squeeze(pr.rotate_vector(xyz, rot_mat))
cross_section_plane = rotated_plane+point
cross_section = interpolating_func(cross_section_plane)
bw_cross_section = cross_section>=0.5
bw_cross_section = np.reshape(bw_cross_section, x.shape)
label_cross_section, nn = label(bw_cross_section, neighbors=4, return_num=True)
main_lbl = np.unique(label_cross_section[cent_ball])
main_lbl = main_lbl[np.nonzero(main_lbl)]
if len(main_lbl)!=1:
s_inx = s_inx+direction
continue
bw_cross_section = label_cross_section==main_lbl
nz_X = np.count_nonzero(np.sum(bw_cross_section, axis=0))
nz_Y = np.count_nonzero(np.sum(bw_cross_section, axis=1))
if (nz_X<4) | (nz_Y<4):
s_inx = s_inx+direction
continue
if shift_impose:
props = regionprops(bw_cross_section.astype(np.int))
y0, x0 = props[0].centroid
shiftX = np.round(c_mesh-x0).astype(np.int)
shiftY = np.round(c_mesh-y0).astype(np.int)
p = max(abs(shiftX), abs(shiftY))
if p != 0:
bw_cross_section = np.pad(bw_cross_section, p, mode='constant')
bw_cross_section = np.roll(bw_cross_section,shiftY,axis=0)
bw_cross_section = np.roll(bw_cross_section,shiftX,axis=1)
bw_cross_section = bw_cross_section[p:-p, p:-p]
label_cross_section, nn = label(bw_cross_section, neighbors=4, return_num=True)
if nn != 1:
main_lbl = np.unique(label_cross_section[cent_ball])
main_lbl = main_lbl[np.nonzero(main_lbl)]
if len(main_lbl)!=1:
s_inx = s_inx+direction
continue
bw_cross_section = label_cross_section==main_lbl
bound = boundary_parametrization(bw_cross_section)
if test_boundary_parametrization(bound, c_mesh) == False:
s_inx = s_inx+direction
continue
#fig, ax=plt.subplots()
#ax.plot(bound[:,1], bound[:,0], '-', linewidth=2, color='black')
if count==1:
m_curve = mean_curve(bound, bound, 2, c_mesh, 0)
max_radius = np.max(np.sum((m_curve-np.array(x.shape)/2)**2, axis=1)**0.5)
p_inx = s_inx
p_bound = bound
p_shiftX = shiftX
p_shiftY = shiftY
count = count+1
s_inx = s_inx+direction
else:
H_dist = hausdorff_distance(bound, m_curve, len(m_curve))
d_ratio = np.true_divide(H_dist, (H_dist+max_radius))
#print d_ratio
if d_ratio<H_th:
m_curve = mean_curve(bound, m_curve, count, c_mesh, 0)
max_radius = g_res*np.max(np.sum((m_curve-np.array(x.shape)/2)**2, axis=1)**0.5)
p_inx = s_inx
p_bound = bound
p_shiftX = shiftX
p_shiftY = shiftY
count = count+1
s_inx = s_inx+direction
else:
break
return p_inx, p_bound, p_shiftX, p_shiftY
def import_data(self, fn):
aoa_lim = 15
beta_lim = 15
da_lim = 21.5 / 4.
de_lim = 25
dr_lim = 30
pq_lim = 1.2
r_lim = 0.3925
num_pts = 5
alpha = np.linspace(-aoa_lim, aoa_lim, num_pts)
beta = np.linspace(-beta_lim, beta_lim, num_pts)
d_e = np.linspace(-de_lim, de_lim, num_pts)
d_a = np.linspace(-da_lim, da_lim, num_pts)
d_r = np.linspace(-dr_lim, dr_lim, num_pts)
p = np.linspace(-pq_lim, pq_lim, num_pts)
q = np.linspace(-pq_lim, pq_lim, num_pts)
r = np.linspace(-r_lim, r_lim, num_pts)
if fn[-4:] == '.csv':
self.data = pd.read_csv(fn, delimiter=',')
self.data.sort_values(
by=['AOA', 'Beta', 'd_e', 'd_a', 'd_r', 'p', 'q', 'r'],
inplace=True)
self.data.to_csv("./TODatabase_linear_sorted.csv")
self.data_array = np.zeros((5, 5, 5, 5, 5, 5, 5, 5, 6))
it = 0
for i in range(num_pts):
for j in range(num_pts):
for k in range(num_pts):
for m in range(num_pts):
for n in range(num_pts):
for pp in range(num_pts):
for qq in range(num_pts):
for rr in range(num_pts):
self.data_array[
i, j, k, m, n, pp, qq, rr,
0] = self.data.iat[it, 8]
self.data_array[
i, j, k, m, n, pp, qq, rr,
1] = self.data.iat[it, 9]
self.data_array[
i, j, k, m, n, pp, qq, rr,
2] = self.data.iat[it, 10]
self.data_array[
i, j, k, m, n, pp, qq, rr,
3] = self.data.iat[it, 11]
self.data_array[
i, j, k, m, n, pp, qq, rr,
4] = self.data.iat[it, 12]
self.data_array[
i, j, k, m, n, pp, qq, rr,
5] = self.data.iat[it, 13]
it += 1
np.save("./TODatabase_linear.npy", self.data_array)
elif fn[-4:] == '.npy':
self.data_array = np.load(fn)
mask = np.isnan(self.data_array)
self.data_array[mask] = np.interp(np.flatnonzero(mask),
np.flatnonzero(~mask),
self.data_array[~mask])
self.CX_s = rgi((alpha, beta, d_e, d_a, d_r, p, q, r),
self.data_array[:, :, :, :, :, :, :, :, 0],
bounds_error=False,
fill_value=None)
self.CY_s = rgi((alpha, beta, d_e, d_a, d_r, p, q, r),
self.data_array[:, :, :, :, :, :, :, :, 1],
bounds_error=False,
fill_value=None)
self.CZ_s = rgi((alpha, beta, d_e, d_a, d_r, p, q, r),
self.data_array[:, :, :, :, :, :, :, :, 2],
bounds_error=False,
fill_value=None)
self.Cl_s = rgi((alpha, beta, d_e, d_a, d_r, p, q, r),
self.data_array[:, :, :, :, :, :, :, :, 3],
bounds_error=False,
fill_value=None)
self.Cm_s = rgi((alpha, beta, d_e, d_a, d_r, p, q, r),
self.data_array[:, :, :, :, :, :, :, :, 4],
bounds_error=False,
fill_value=None)
self.Cn_s = rgi((alpha, beta, d_e, d_a, d_r, p, q, r),
self.data_array[:, :, :, :, :, :, :, :, 5],
bounds_error=False,
fill_value=None)
