def smoothfit(x, y, smooth=0, res=1000):
"""
Smooth data of the form f(x) = y with a spline
"""
z = y.copy()
w = isnan(z)
z[w] = 0
spl = UnivariateSpline(x, z, w=~w)
spl.set_smoothing_factor(smooth)
xs = linspace(min(x), max(x), res)
ys = spl(xs)
ys[ys < 0] = 0
if w[0]:
if len(where(~w)[0]):
first = where(~w)[0][0]
first = x[first]
first = where(xs >= first)[0][0] - 1
ys[:first] = nan
if w[-1]:
if len(where(~w)[0]):
last = where(~w)[0][-1]
last = x[last]
last = where(xs >= last)[0][0] + 1
ys[last:] = nan
return xs, ys
def grad_dist(curdata,ax):
#gaussian kernel density estimation
x=np.linspace(0,90,91)
kde=gaussian_kde(curdata)
line,=ax.plot(x,kde(x), '-', label=hl[j][0:-2]+"0")
curcolor=plt.getp(line,'color')
## #plotting histogram
## ax.hist(curdata,bins=int(max(curdata))+1,
## normed=True, histtype='step',
## color=curcolor, linewidth=0.5)
#defining splines for kd function and corresponding 1st and seconde derivatives
x=np.linspace(0,90,901)
s=UnivariateSpline(x,kde(x),s=0,k=3)
s1=UnivariateSpline(x,s(x,1),s=0,k=3)
s2=UnivariateSpline(x,s1(x,1),s=0,k=3)
#identifying local maxima (where s1=0, s2<0, and s>0.005)
maxima=s1.roots()[np.where(s2(s1.roots())<0)[0]]
maxima=maxima[np.where(s(maxima)>0.005)[0]]
#s_max=maxima[-1]
s_max=maxima[np.argmax(s(maxima))]
ax.plot(s_max, s(s_max),'o', color=curcolor)
#identifying steepest segment after maxima (where x>=maxima, s1<0)
x2=x[np.where(x>=s_max)[0]]
slope=s1(x2)
s1_min=x2[np.argmin(slope)]
ax.plot(s1_min,s(s1_min),'o', color=curcolor)
print round(s_max,1),round(s1_min,1)
return round(s_max,1),round(s1_min,1)
def find_extrema_spline(x,y,k=4,s=0,**kwargs):
"""
find local extrema of y(x) by taking derivative of spline
Parameters
----------
x,y : array-like
find extrema of y(x)
k : int
order of spline interpolation [must be >3]
s : number
s parameter sent to scipy spline interpolation (used for smoothing)
**kwargs : extra arguments to UnivariateSpline
Returns
-------
sp : UnivariateSpline object
x_max,y_max : array
value of x and y at extrema(s)
"""
sp = UVSpline(x,y,k=k,s=s,**kwargs)
x_max = sp.derivative().roots()
y_max = sp(x_max)
return sp,x_max,y_max
def fwhm(x, y, bg=[0, 100, 150, 240]):
"""
Evaluates the full width half maximum of y in units of x.
Parameters
----------
x : numpy.array
y : numpy.array
bg : list
Background sampling limits
Returns
-------
fwhm : number
Full width half maximum
"""
# xnew = copy(x)
# ynew = copy(y)
# xc = x[(x>bg[0])&(x<bg[1]) | (x>bg[2])&(x<bg[3])]
# yc = y[(x>bg[0])&(x<bg[1]) | (x>bg[2])&(x<bg[3])]
# bgfit = polyfit(xc,yc,1)
# ynew = ynew-polyval(bgfit,xnew)
xnew, ynew = rmbg(x, y, bg)
f = UnivariateSpline(xnew, ynew / max(ynew) - 0.5, s=0)
fwhm = f.roots()[1] - f.roots()[0]
return fwhm
def integrated_rate_test(mx=100., annih_prod='BB'):
# This currently doesn't work
file_path = MAIN_PATH + "/Spectrum/"
file_path += '{}'.format(int(mx)) + 'GeV_' + annih_prod + '_DMspectrum.dat'
spectrum = np.loadtxt(file_path)
imax = 0
for i in range(len(spectrum)):
if spectrum[i, 1] < 10 or i == (len(spectrum) - 1):
imax = i
break
spectrum = spectrum[0:imax, :]
Nevents = 10. ** 5.
spectrum[:, 1] /= Nevents
test = interp1d(np.log10(spectrum[:, 0] / mx), np.log10(mx * np.log(10.) * spectrum[:, 1]), kind='cubic', bounds_error=False, fill_value=0.)
test2 = interp1d(spectrum[:, 0], spectrum[:, 0] * spectrum[:, 1], kind='cubic', bounds_error=False, fill_value=0.)
e_gamma_tab = np.logspace(0., np.log10(spectrum[-1, 0]), 200)
print np.column_stack((np.log10(spectrum[:, 0] / mx), np.log10(mx * np.log(10.) * spectrum[:, 1])))
xtab = np.linspace(np.log10(1. / mx), 0., 200)
ng2 = np.trapz(10.**test(xtab) / 10. ** xtab, xtab) / np.log(10.)
mean_e2 = np.trapz(test2(e_gamma_tab), e_gamma_tab)
rate_interp = UnivariateSpline(spectrum[:, 0], spectrum[:, 1])
avg_e_interp = UnivariateSpline(spectrum[:, 0], spectrum[:, 0] * spectrum[:, 1])
num_gamma = rate_interp.integral(1., spectrum[-1, 0])
mean_e = avg_e_interp.integral(1., spectrum[-1, 0])
print 'DM Mass: ', mx
print 'Annihilation Products: ', annih_prod
print 'Number of Gammas > 1 GeV: ', num_gamma, ng2
print '<E> Gamma: ', mean_e, mean_e2
return
def fwhm(x, y, k=10, ret_roots=False):
"""
Determine full-with-half-maximum of a peaked set of points, x and y.
Assumes that there is only one peak present in the dataset. The function
uses a spline interpolation with smoothing parameter k ('s' in scipy.interpolate.UnivariateSpline).
"""
class MultiplePeaks(Exception):
pass
class NoPeaksFound(Exception):
pass
half_max = np.max(y) / 2.0
s = UnivariateSpline(x, y - half_max, s=k)
roots = s.roots()
if len(roots) > 2:
# Multiple peaks. Use the two that straddle the maximum value
maxvel = x[np.argmax(y)]
left_idx = np.argmin(maxvel - roots)
right_idx = np.argmin(roots - maxvel)
roots = np.array((roots[left_idx], roots[right_idx]))
elif len(roots) < 2:
raise NoPeaksFound("No proper peaks were found in the data set; likely "
"the dataset is flat (e.g. all zeros).")
if ret_roots:
return roots[0], roots[1]
return abs(roots[1] - roots[0])
def calc_conductance_curve(V_list,T,R_T,C_sigma):
#test_voltages = arange(-v_max,v_max,v_step)
test_currents = []
for V in V_list:
test_currents.append(calc_current(V,T,R_T,C_sigma))
#print "V: %g, current %g"%(V,test_currents[-1])
## calc conductances manually
#test_conductances = []
#for idx,V in enumerate (test_currents[1:-2]):
# if idx==0:
# print idx
# test_conductances.append((test_currents[idx+2]-test_currents[idx])/(2.0*v_step))
#
#test_voltages_G = test_voltages[1:-2]
#
# SPLINE
#
spline = UnivariateSpline(V_list,test_currents,s=0)
#print "test_conductances"
#indices = [x for x, y in enumerate(col1) if (y >0.7 or y<-0.7)]
test_conductances = []
for v_iter in V_list:
test_conductances.append(spline.derivatives(v_iter)[1])
return test_conductances
def imageSlice(image, xc, yc, width): ylen, xlen = image.shape xstart = max(0, xc - width / 2) xend = min(xlen, xc + width / 2) # I cannot get array slicing to work for the life of me slice = [] for i in range(int(xstart), int(xend)): slice.append(image[yc, i]) # https://stackoverflow.com/questions/10582795/finding-the-full-width-half-maximum-of-a-peak/10583774#10583774 shiftedSlice = [] halfMax = max(slice) / 2 baseline = numpy.mean(image) for y in slice: shiftedSlice.append(y - halfMax - baseline) x = numpy.linspace(0, width, width) spline = UnivariateSpline(x, shiftedSlice, s=0) r1, r2 = spline.roots() #r1 = 0 #r2 = 0 return (slice, r2 - r1)
def xs_interp (inp_ene, inp_xs, inp_ene_interp, plot_cs):
inp_ene = inp_ene # energies from Talys
inp_xs = inp_xs # xs from talys
inp_ene_interps = inp_ene_interp # energies for interpolation
out_xs_A = []
out_xs = np.array([]) # iterpolated xs
plot_fig = plot_cs
x_ene = np.linspace (0,660,3301)
spl = UnivariateSpline(inp_ene, inp_xs, s = 0.25)
y_xs = spl(x_ene)
for inp_ene_interp in inp_ene_interps:
out_xs_A.append(spl.__call__(inp_ene_interp))
out_xs = np.append(out_xs, out_xs_A)
# optional_plot
if plot_fig:
plt.plot (inp_ene, inp_xs, 'ro', ms = 5)
plt.plot (x_ene, y_xs, lw = 3, c = 'g', alpha = 0.6)
plt.plot (inp_ene_interps, out_xs, 'o', ms = 3)
plt.show()
return out_xs
def response(self, disturbance_vector):
""" Returns the response of the sensor due to a disturbance
The acceleration imposed to the sensor is estimatad with the following equations:
acceleration(t) = d2stress(t)/t2 * material_depth/material_prop['modulus']
And the sensor response takes into account the frequency response, estimated by a normal curve
freq_response(f) = norm(scale = self.bandwidth/2, loc=self.resonant_freq).pdf(f_array)
freq_response(f) /= max(freq_response)
response(t) = ifft(fft(acceleration) * freq_response)
Args:
disturbance_vector (list): list with a temporal array, in the 0 index, and a
stress array, in the 1 index.
Returns:
list: with two arrays, the temporal array and the voltage response array.
"""
const = self.material_depth / self.material_prop['modulus']
t_vector = disturbance_vector[0]
# using the scipy UnivariateSpline to compute the second derivative
data_spl = UnivariateSpline(t_vector, disturbance_vector[1], s=0, k=3)
acceleration = data_spl.derivative(n=2)(t_vector) * const
# we need to take the frequency response of the acceleration stimuli
N = len(disturbance_vector[1])
T = t_vector[1] - t_vector[0]
f_array = np.fft.fftfreq(N, T)
freq_acc = np.fft.fft(acceleration)
# we need to apply a filter factor related to the frequency response of the sensor
freq_response = self.frequency_response(N, (0, max(f_array)), mirror=True)[1]
voltage = np.fft.ifft(freq_acc * freq_response) * self.sensitivity
return voltage
def getCurvatureForPoints(arcLengthList, fx_s, fy_s, smoothing=None): x, x_, x__, y, y_, y__ = getFirstAndSecondDerivForTPoints(arcLengthList, fx_s, fy_s) curvature = abs(x_* y__ - y_* x__) / np.power(x_** 2 + y_** 2, 3 / 2) fCurvature = UnivariateSpline(arcLengthList, curvature, s=smoothing) dxcurvature = fCurvature.derivative(1)(arcLengthList) dx2curvature = fCurvature.derivative(2)(arcLengthList) return curvature, dxcurvature, dx2curvature
def kde_minmode(data,x,max_num_mode,min_mode_pdf):
kde=gaussian_kde(data)
f=kde.factor
f_list=np.linspace(f,(data.max()-data.min()),100)
s=UnivariateSpline(x,kde(x),s=0)
s1=UnivariateSpline(x,s(x,1),s=0)
s2=UnivariateSpline(x,s1(x,1),s=0)
extrema=s1.roots()
maxima=extrema[np.where((s2(extrema)<0)*(s(extrema)>=min_mode_pdf))]
if len(maxima)>max_num_mode:
for q in range(1,len(f_list)):
f=f_list[q]
kde2=gaussian_kde(data,bw_method=f)
s=UnivariateSpline(x,kde2(x),s=0)
s1=UnivariateSpline(x,s(x,1),s=0)
s2=UnivariateSpline(x,s1(x,1),s=0)
extrema=s1.roots()
maxima=extrema[np.where((s2(extrema)<0)*(s(extrema)>=min_mode_pdf))]
if len(maxima)<=max_num_mode:
## print 'modes: ',maxima
break
kde=gaussian_kde(data,bw_method=f)
## else:
## print maxima
return kde,maxima
def smooth(self, genome, which_x, which_y):
interpolationPointsQty = SMOOTHING_WINDOW
which_y_InterpolationNeighborhood = interpolationPointsQty / 2
minimunInterpolationNeighborhoodSize = interpolationPointsQty / 4
if which_y - interpolationPointsQty / 2 < 0:
interpolationPointsQty -= abs(which_y - which_y_InterpolationNeighborhood) * 2
which_y_InterpolationNeighborhood = interpolationPointsQty / 2
elif which_y + interpolationPointsQty / 2 > genome.getHeight() - 1:
interpolationPointsQty -= (which_y + which_y_InterpolationNeighborhood - (genome.getHeight() - 1)) * 2
which_y_InterpolationNeighborhood = interpolationPointsQty / 2
if which_y_InterpolationNeighborhood >= minimunInterpolationNeighborhoodSize:
x = np.ndarray(interpolationPointsQty)
y = np.ndarray(interpolationPointsQty)
for k in xrange(interpolationPointsQty):
poseToSmooth = which_y - which_y_InterpolationNeighborhood + k
x[k] = poseToSmooth
y[k] = genome[poseToSmooth][which_x]
spl = UnivariateSpline(x, y)
spl.set_smoothing_factor(SPLINE_SMOOTHING_FACTOR_SPLINE/10)
for k in xrange(interpolationPointsQty):
if y[k] != sysConstants.JOINT_SENTINEL:
newValue = spl(int(x[k]))
genome.setItem(int(x[k]), which_x, newValue)
def __init__(self, yp, workdir, scale, sm=200): ''' Constructor ''' yp = np.array(yp) self.l = len(yp)/2 self.xPos = (self.l-2)/2 #fPos = (self.l-2)/2 + 2 tnsc = 2/scale print tnsc plt.rcParams['font.size'] = 24 plt.rcParams['lines.linewidth'] = 2.4 self.workdir = workdir avProfilePoints = yp[:self.l] self.avx = np.append(np.append([0], np.sort(np.tanh(tnsc*avProfilePoints[:self.xPos]))),[1]) self.av = avProfilePoints[self.xPos:] sigmaProfilePoints = yp[self.l:] self.sigmax = np.append(np.append([0], np.sort(np.tanh(tnsc*sigmaProfilePoints[:self.xPos]))),[1]) self.sigma = sigmaProfilePoints[self.xPos:] self.m = UnivariateSpline(self.avx, self.av) print "Created spline with " + str(len(self.m.get_knots())) + " knots" self.s = UnivariateSpline(self.sigmax, self.sigma) print "Created spline with " + str(len(self.s.get_knots())) + " knots"
def get_derivatives(xs, ys, fd=False):
"""
return the derivatives of y(x) at the points x
if scipy is available a spline is generated to calculate the derivatives
if scipy is not available the left and right slopes are calculated, if both exist the average is returned
putting fd to zero always returns the finite difference slopes
"""
try:
if fd:
raise SplineInputError('no spline wanted')
if len(xs) < 4:
er = SplineInputError('too few data points')
raise er
from scipy.interpolate import UnivariateSpline
spline = UnivariateSpline(xs, ys)
d = spline.derivative(1)(xs)
except (ImportError, SplineInputError):
d = []
m, left, right = 0, 0, 0
for n in range(0, len(xs), 1):
try:
left = (ys[n] - ys[n-1]) / (xs[n] - xs[n-1])
m += 1
except IndexError:
pass
try:
right = (ys[n+1] - ys[n]) / (xs[n+1] - xs[n])
m += 1
except IndexError:
pass
d.append(left + right / m)
return d
def halbwertsbreite(x, y):
spline = UnivariateSpline(x, y-np.max(y)/2, s=0)
r1, r2 = spline.roots() # find the roots
lambda1 = 2*d*np.sin(np.deg2rad(r1))
lambda2 = 2*d*np.sin(np.deg2rad(r2))
E1 = h*c/lambda1
E2 = h*c/lambda2
DE = E1 - E2
print ('Halbwertswinkel: {0:.5e} deg, {1:.5e} deg'.format(r1, r2))
print ('Halbwertsbreite: {0:.5e}'.format(np.abs(r1-r2)))
print (u'Energieaufloesung: {0:.5e} eV'.format(DE))
xnew = np.linspace(min(x), max(x))
ynew = spline(xnew)
plt.plot(x, y, 'rx', label='Messdaten')
plt.plot(xnew, ynew+np.max(y)/2,'b-', label='Interpolation')
plt.axvline(r1)
plt.axvline(r2)
plt.grid()
plt.legend()
plt.xlabel("doppelter Kristallwinkel in Grad")
plt.ylabel(u"Zählrate")
class AlphaInterpolator(object):
def __init__(self, a, x, y):
# Drop NaN values to avoid fitpack errors
self._data = pd.DataFrame(np.array([a, x, y]).T, columns=["a", "x", "y"])
self._data.dropna(inplace=True)
self._create_interpolating_polynomials()
self._find_path_length()
def _create_interpolating_polynomials(self):
self.x_interp = UnivariateSpline(self._data.a, self._data.x, s=0)
self.y_interp = UnivariateSpline(self._data.a, self._data.y, s=0)
def _find_path_length(self):
dx_interp = self.x_interp.derivative()
dy_interp = self.y_interp.derivative()
ts = np.linspace(0, 1, 200)
line_length = cumtrapz(np.sqrt(dx_interp(ts) ** 2 + dy_interp(ts) ** 2), x=ts, initial=0.0)
line_length /= line_length.max()
# Here we invert the line_length (ts) function, in order to evenly
# sample the pareto front
self.l_interp = UnivariateSpline(line_length, ts, s=0)
def sample(self, num):
""" Return estimates of alpha values that evenly sample the pareto
front """
out = self.l_interp(np.linspace(0, 1, num))
out[0] = 0.0
out[-1] = 1.0
return out
def get_t_for_vols(self, vols, t_max=1000):
"""
Find the temperatures corresponding to a specific volume.
The search is performed interpolating the V(T) dependence with a spline and
finding the roots with of V(t) - v.
It may return more than one temperature for a volume in case of non monotonic behavior.
Args:
vols: list of volumes
t_max: maximum temperature considered for the fit
Returns:
A list of lists of temperatures. For each volume more than one temperature can
be identified.
"""
if not isinstance(vols, (list, tuple, np.ndarray)):
vols = [vols]
f = self.fit_energies(0, t_max, t_max+1)
temps = []
for v in vols:
spline = UnivariateSpline(f.temp, f.min_vol - v, s=0)
temps.append(spline.roots())
return temps
def smoothing(x,y,err=None,k=5,s=None,newx=None,derivative_order=0):
# remove NaNs
idx = np.isfinite(x) & np.isfinite(y)
if idx.sum() != len(x): x=x[idx]; y=y[idx]
# if we don't need to interpolate, use same x as input
if newx is None: newx=x
if err is None:
w=None
elif err == "auto":
n=len(x)
imin = int(max(0,n/2-20))
imax = imin + 20
idx = range(imin,imax)
p = np.polyfit(x[idx],y[idx],2)
e = np.std( y[idx] - np.polyval(p,x[idx] ) )
w = np.ones_like(x)/e
else:
w=np.ones_like(x)/err
from scipy.interpolate import UnivariateSpline
if (s is not None):
s = len(x)*s
s = UnivariateSpline(x, y,w=w, k=k,s=s)
if (derivative_order==0):
return s(newx)
else:
try:
len(derivative_order)
return np.asarray([s.derivative(d)(newx) for d in derivative_order])
except:
return s.derivative(derivative_order)(newx)
def getspline_Sold(self): """Cubic spline interpolation of entropy and convective velocity. """ want = self.mass < max(self.mass)*self.mass_cut S_old = UnivariateSpline(self.mass[want], self.Sgas[want], k=self.spline_k, s=self.spline_s, ext=self.spline_ext) dS_old = S_old.derivative() vconv_Sold = UnivariateSpline(self.mass[want], self.vconv[want], k=self.spline_k, s=self.spline_s, ext=self.spline_ext) return [S_old, dS_old, vconv_Sold]
def fwhm(data, ypos=0.5):
spatial = data.sum(1)
spatial = spatial-np.min(spatial)
spatial_range = range(0, len(spatial))
spline = UnivariateSpline(spatial_range, (spatial -np.max(spatial)*ypos), s=0.1, k=3)
roots = spline.roots()
if len(roots) < 2:
return np.inf, (-np.inf, +np.inf)
return roots[-1]-roots[0], roots
def FWHM_scipy(X, Y):
"""Computing FWHM (Full width at half maximum)"""
try:
from scipy.interpolate import UnivariateSpline
spline = UnivariateSpline(X, Y, s=0)
r1, r2 = spline.roots() # find the roots
return r2 - r1 # return the difference (full width)
except ImportError:
return FWHM(X, Y)
def __init__(self, x, y, w=None, bbox=[None, None], k=3,
xname=None, xunits=None, yname=None, yunits=None):
"""Constructor.
"""
xUnivariateSplineBase.__init__(self, x, y, xname, xunits, yname, yunits)
_x = numpy.log10(x)
_y = numpy.log10(y)
UnivariateSpline.__init__(self, _x, _y, w, bbox, k, s=None)
self.__integral_spline = None
def QuasiPWeight(ReSE_A): ''' calculating the Fermi-liquid quasiparticle weight (residue) Z ''' N = len(En_A) #M = int(1e-3/dE) if dE < 1e-3 else 1 # very fine grids lead to oscillations # replace 1 with M below to dilute the grid ReSE = UnivariateSpline(En_A[int(N/2-10):int(N/2+10):1],ReSE_A[int(N/2-10):int(N/2+10):1]) dReSEdw = ReSE.derivatives(0.0)[1] Z = 1.0/(1.0-dReSEdw) return sp.array([Z,dReSEdw])
def interpolate(self, genome, which_x, which_y, wich_y_is_fixed_data=0):
interpolationPointsQty = SMOOTHING_WINDOW
which_y_InterpolationNeighborhood = interpolationPointsQty / 2
minimunInterpolationNeighborhoodSize = interpolationPointsQty / 4
array_size = 0
if which_y - which_y_InterpolationNeighborhood < 0:
interpolationPointsQty -= abs(which_y - which_y_InterpolationNeighborhood) * 2
which_y_InterpolationNeighborhood = interpolationPointsQty / 2
elif which_y + interpolationPointsQty / 2 > genome.getHeight() - 1:
interpolationPointsQty -= (which_y + which_y_InterpolationNeighborhood - (genome.getHeight() - 1)) * 2
which_y_InterpolationNeighborhood = interpolationPointsQty / 2
interpolationWindowRadius = interpolationPointsQty / 4
if which_y_InterpolationNeighborhood >= minimunInterpolationNeighborhoodSize:
array_size = interpolationPointsQty - interpolationWindowRadius * 2
if wich_y_is_fixed_data:
array_size += 1
x = np.ndarray(array_size)
y = np.ndarray(array_size)
splineIndexCounter = 0
for k in xrange(interpolationPointsQty + 1):
poseToSmooth = which_y - which_y_InterpolationNeighborhood + k
if poseToSmooth <= which_y - interpolationWindowRadius or poseToSmooth > which_y + interpolationWindowRadius:
x[splineIndexCounter] = poseToSmooth
y[splineIndexCounter] = genome[poseToSmooth][which_x]
splineIndexCounter += 1
if wich_y_is_fixed_data:
x[splineIndexCounter] = which_y
y[splineIndexCounter] = genome[which_y][which_x]
splineIndexCounter += 1
if genome[which_y - interpolationWindowRadius][which_x] == genome[which_y + interpolationWindowRadius][wich_x]:
spl = interp1d(x, y)
else:
x_order = np.argsort(x)
spl = UnivariateSpline(x_order, y)
spl.set_smoothing_factor(SPLINE_SMOOTHING_FACTOR_INTERPOLATION/10)
for k in xrange(interpolationPointsQty):
iter = which_y - which_y_InterpolationNeighborhood + k
if genome[iter][which_x] != sysConstants.JOINT_SENTINEL:
if iter > which_y - interpolationWindowRadius and iter <= which_y + interpolationWindowRadius:
if wich_y_is_fixed_data: #if fixed data do not change the which_y point
if iter != which_y:
newValue = spl(iter)
genome.setItem(iter, which_x, newValue)
else:
newValue = spl(iter)
genome.setItem(iter, which_x, newValue)
def MTF50(self, MTFx,MTFy):
'''
return object resolution as [line pairs/mm]
where MTF=50%
see http://www.imatest.com/docs/sharpness/
'''
if self.mtf_x is None:
self.MTF()
f = UnivariateSpline(self.mtf_x, self.mtf_y-0.5)
return f.roots()[0]
def find_critical_temperature(df, offset):
curve = []
temps = np.round(df.temperature,2).unique()
for temp in temps:
curve.append([temp,df.loc[np.round(df.temperature,2) == temp].TTc.mean()])
curve = np.array(curve)
curve = curve[curve[:,0].argsort()]
f = UnivariateSpline(curve[:,0],curve[:,1]-offset)
root = f.roots()
return root[0]
def interpolate_to_find_crossover(frequencies,spl):
from scipy.interpolate import UnivariateSpline
s = UnivariateSpline(frequencies,spl,s=0)
root = []
for r in s.roots():
if r>=1000 and r<=5000:
root.append(r)
if len(root)==1: return root[0]
else: return 0
def thermCond_fit_UnivariateSpline_model(T, data=[]):
# This is a fitting model for creating an equation when given a list of x,y values
x = data[0]
y = data[1]
if len(x) <= 5:
order = len(x)-1
else:
order = 5
fit = UnivariateSpline(x, y, k=order)
thermCond = fit.__call__(T)
return thermCond
def get_profile_func(self, profile_x, profile_y):
from scipy.interpolate import UnivariateSpline
profile_ = UnivariateSpline(profile_x, profile_y, k=3, s=0,
bbox=[0, 1])
integ = profile_.integral(0, 1)
def profile(o, x, slitpos):
return profile_(slitpos) / integ
return profile
if __name__ == '__main__':
start = time.time()
T = 850.0 # Unit: K
P = 1.07 * 1.0e5 # Unit: bar
moleFraction = 'C6H10:0.008, HE:0.992'
reactionIndex = 2280 # C3H5-A + C6H10 = C3H6 + C6H9
targetSpc = ['C3H6']
factorLgList = [float(i) / 100 for i in range(-50, 10, 10)]
targetMoleFractionFile = '850.txt'
[factorList,
moleFractionC3H6List] = traverseFactor(T, P, moleFraction, factorLgList,
reactionIndex, targetSpc)
para = UnivariateSpline(moleFractionC3H6List, factorList)
targetMoleFraction = readTargetMoleFraction(targetMoleFractionFile)
optimizedFactor = para(targetMoleFraction)
with open('optimizedFactor.txt', 'wb') as f:
output = csv.writer(f, delimiter=',', quoting=csv.QUOTE_ALL)
output.writerow(['Optimized F:', optimizedFactor])
output.writerow(['targetMoleFraction', targetMoleFraction])
for i in range(len(moleFractionC3H6List)):
output.writerow([factorList[i], moleFractionC3H6List[i]])
plt.plot(factorList, moleFractionC3H6List, 'r--', optimizedFactor,
targetMoleFraction, 'bs')
plt.xlabel('factor')
plt.ylabel('C3H6 Mole Fraction / ppm')
plt.savefig('factor_vs_C3H6.png')
def smooth_spline(x, y, s):
s = UnivariateSpline(x, y, s=s)
return s(x)
def __call__(self, x, nu=0):
return UnivariateSpline.__call__(self, x % self.T, nu=nu)
def find_point_in_lips(points_upper, points_lower, points_upper_inside,
points_lower_inside, rot_angle, displacement, radius):
#find where a circle with radius (radius) and center in the corner of the
#lip enconters the spline represinting the upper lip
rot_matrix = np.array([[np.cos(rot_angle),
np.sin(rot_angle)],
[-np.sin(rot_angle),
np.cos(rot_angle)]])
rot_matrix_inv = np.array([[np.cos(rot_angle), -np.sin(rot_angle)],
[np.sin(rot_angle),
np.cos(rot_angle)]])
x = points_upper[:, 0]
y = points_upper[:, 1]
rot_x, rot_y = rot_matrix.dot([x - displacement[0], y - displacement[1]])
spline = UnivariateSpline(rot_x, rot_y, s=1)
new_rot_x = np.arange(int(round(min(rot_x), 0)),
int(round(max(rot_x), 0)) + 1)
new_rot_y = spline(new_rot_x)
euclid_distance = np.sqrt(new_rot_x * new_rot_x + new_rot_y * new_rot_y)
temp = abs(euclid_distance - radius)
idx_min = np.argmin(temp) #this one takes 0.000997781753540039s
#idx_min = int(np.where(temp==temp.min())[0]) #this one takes 0.0009992122650146484s
cross_lip_rot_x_upper = new_rot_x[idx_min]
cross_lip_rot_y_upper = new_rot_y[idx_min]
new_x_upper, new_y_upper = rot_matrix_inv.dot(
[cross_lip_rot_x_upper, cross_lip_rot_y_upper])
new_x_upper = new_x_upper + displacement[0]
new_y_upper = new_y_upper + displacement[1]
new_point_upper = np.array([new_x_upper, new_y_upper])
#find the mouth openness
x = points_lower[:, 0]
y = points_lower[:, 1]
rot_x, rot_y = rot_matrix.dot([x - new_x_upper, y - new_y_upper])
spline = UnivariateSpline(rot_x, rot_y, s=1)
new_rot_x = 0 #np.arange(int(round(min(rot_x),0)),int(round(max(rot_x),0))+1)
new_rot_y = spline(new_rot_x)
cross_lip_rot_x_lower = new_rot_x
cross_lip_rot_y_lower = new_rot_y
new_x_lower, new_y_lower = rot_matrix_inv.dot(
[cross_lip_rot_x_lower, cross_lip_rot_y_lower])
new_x_lower = new_x_lower + new_x_upper
new_y_lower = new_y_lower + new_y_upper
new_point_lower = np.array([new_x_lower, new_y_lower])
#find the teeth show
x = points_upper_inside[:, 0]
y = points_upper_inside[:, 1]
rot_x, rot_y = rot_matrix.dot([x - new_x_upper, y - new_y_upper])
spline = UnivariateSpline(rot_x, rot_y, s=1)
new_rot_x = 0 #np.arange(int(round(min(rot_x),0)),int(round(max(rot_x),0))+1)
new_rot_y = spline(new_rot_x)
cross_lip_rot_x_upper_inside = new_rot_x
cross_lip_rot_y_upper_inside = new_rot_y
new_x_upper_inside, new_y_upper_inside = rot_matrix_inv.dot(
[cross_lip_rot_x_upper_inside, cross_lip_rot_y_upper_inside])
new_x_upper_inside = new_x_upper_inside + new_x_upper
new_y_upper_inside = new_y_upper_inside + new_y_upper
new_point_upper_inside = np.array([new_x_upper_inside, new_y_upper_inside])
x = points_lower_inside[:, 0]
y = points_lower_inside[:, 1]
rot_x, rot_y = rot_matrix.dot([x - new_x_upper, y - new_y_upper])
spline = UnivariateSpline(rot_x, rot_y, s=1)
new_rot_x = 0 #np.arange(int(round(min(rot_x),0)),int(round(max(rot_x),0))+1)
new_rot_y = spline(new_rot_x)
cross_lip_rot_x_lower_inside = new_rot_x
cross_lip_rot_y_lower_inside = new_rot_y
new_x_lower_inside, new_y_lower_inside = rot_matrix_inv.dot(
[cross_lip_rot_x_lower_inside, cross_lip_rot_y_lower_inside])
new_x_lower_inside = new_x_lower_inside + new_x_upper
new_y_lower_inside = new_y_lower_inside + new_y_upper
new_point_lower_inside = np.array([new_x_lower_inside, new_y_lower_inside])
#compute mouth openness and teeth show
openness = cross_lip_rot_y_lower - cross_lip_rot_y_upper #new_rot_y
theet_show = cross_lip_rot_y_lower_inside - cross_lip_rot_y_upper_inside
if theet_show < 0:
theet_show = 0
return new_point_upper, new_point_lower, new_point_upper_inside, new_point_lower_inside, openness, theet_show
import numpy as np
from scipy.interpolate import UnivariateSpline
import matplotlib.pyplot as plt
from matplotlib.backends.backend_pdf import PdfPages
pp = PdfPages('windspeed.pdf')
print("Setup Complete")
max_speeds = np.load('max-speeds.npy')
print(max_speeds)
print(max_speeds.shape)
years_nb = max_speeds.shape[0]
cprob = (np.arange(years_nb, dtype=np.float32) + 1) / (years_nb + 1)
print(cprob)
sorted_max_speeds = np.sort(max_speeds)
quantile_func = UnivariateSpline(cprob, sorted_max_speeds)
nprob = np.linspace(0, 1, 100)
fitted_max_speeds = quantile_func(nprob)
fifty_prob = 1. - 0.02
fifty_wind = quantile_func(fifty_prob)
plt.plot(sorted_max_speeds, cprob, 'o')
plt.plot(fitted_max_speeds, nprob, 'g--')
plt.plot([fifty_wind], [fifty_prob], 'o', ms=8., mfc='y', mec='y')
plt.text(30, 0.05, '$V_{50} = %.2f \, m/s$' % fifty_wind)
plt.plot([fifty_wind, fifty_wind], [plt.axis()[2], fifty_prob], 'k--')
plt.xlabel('Annual wind speed maxima [$m/s$]')
plt.ylabel('Cumulative probability')
pp.savefig()
def extrapolation_smoothing(
self,
extrapolated_data: DataArray,
rho_arr: DataArray,
):
"""Function to smooth extrapolatd data. Extrapolated data may not have
any 0th order discontinuity but 1st order discontinuities may exist.
Smoothing is necessary to eliminate these higher order discontinuities.
Parameters
----------
extrapolated_data
xarray.DataArray extrapolated data to be smoothed.
Dimensions (rho, theta, t)
rho_arr
xarray.DataArray used to construct smoothing splines. Dimensions (rho)
(Must be higher or the same resolution as the rho dimension
of extrapolated_data)
Returns
-------
extrapolated_smooth_lfs_arr
Extrapolated smoothed data on low-field side (fixed theta = 0)
extrapolated_smooth_hfs_arr
Extrapolated smoothed data on high-field side (fixed theta = pi)
"""
t = extrapolated_data.coords["t"]
extrapolated_smooth_lfs = []
extrapolated_smooth_hfs = []
for ind_t, it in enumerate(extrapolated_data.coords["t"]):
variance_extrapolated_data_lfs = extrapolated_data.isel(
{"t": ind_t, "theta": 0}
).var("rho_poloidal")
variance_extrapolated_data_hfs = extrapolated_data.isel(
{"t": ind_t, "theta": 1}
).var("rho_poloidal")
extrapolated_spline_lfs = UnivariateSpline(
rho_arr,
extrapolated_data.isel(t=ind_t).sel(theta=0),
k=5,
s=0.001 * variance_extrapolated_data_lfs,
)
extrapolated_spline_hfs = UnivariateSpline(
rho_arr,
extrapolated_data.isel(t=ind_t).sel(theta=np.pi),
k=5,
s=0.001 * variance_extrapolated_data_hfs,
)
extrapolated_smooth_lfs.append(extrapolated_spline_lfs(rho_arr, 0))
extrapolated_smooth_hfs.append(extrapolated_spline_hfs(rho_arr, 0))
extrapolated_smooth_lfs_arr = DataArray(
data=extrapolated_smooth_lfs,
coords={"t": t, "rho_poloidal": rho_arr},
dims=["t", "rho_poloidal"],
)
extrapolated_smooth_hfs_arr = DataArray(
data=extrapolated_smooth_hfs,
coords={"t": t, "rho_poloidal": rho_arr},
dims=["t", "rho_poloidal"],
)
extrapolated_smooth_lfs_arr = extrapolated_smooth_lfs_arr.transpose(
"rho_poloidal", "t"
)
extrapolated_smooth_hfs_arr = extrapolated_smooth_hfs_arr.transpose(
"rho_poloidal", "t"
)
# Following section is to ensure that near the rho_poloidal=0 region, the
# extrapolated_smooth_data is constant (ie. with a first-order derivative of 0).
inv_extrapolated_smooth_hfs = DataArray(
data=np.flip(extrapolated_smooth_hfs_arr.data, axis=0),
coords={
"rho_poloidal": -1
* np.flip(extrapolated_smooth_hfs_arr.coords["rho_poloidal"].data),
"t": extrapolated_smooth_hfs_arr.coords["t"].data,
},
dims=["rho_poloidal", "t"],
)
inv_rho_arr = inv_extrapolated_smooth_hfs.coords["rho_poloidal"].data
inv_del_val = inv_rho_arr[-1]
inv_extrapolated_smooth_hfs = inv_extrapolated_smooth_hfs.drop_sel(
rho_poloidal=inv_del_val
)
extrapolated_smooth_mid_plane_arr = concat(
(inv_extrapolated_smooth_hfs, extrapolated_smooth_lfs_arr), "rho_poloidal"
)
rho_zero_ind = np.where(
np.isclose(extrapolated_smooth_mid_plane_arr.rho_poloidal.data, 0.0)
)[0][0]
smooth_central_region = extrapolated_smooth_mid_plane_arr.isel(
rho_poloidal=slice(rho_zero_ind - 2, rho_zero_ind + 3)
)
smooth_central_region.loc[:, :] = smooth_central_region.max(dim="rho_poloidal")
extrapolated_smooth_mid_plane_arr.loc[
extrapolated_smooth_mid_plane_arr.rho_poloidal.data[
rho_zero_ind - 2
] : extrapolated_smooth_mid_plane_arr.rho_poloidal.data[rho_zero_ind + 2],
:,
] = smooth_central_region
inv_extrapolated_smooth_hfs = extrapolated_smooth_mid_plane_arr.isel(
rho_poloidal=slice(0, rho_zero_ind + 1)
)
extrapolated_smooth_hfs_arr = DataArray(
data=np.flip(inv_extrapolated_smooth_hfs.data, axis=0),
coords=extrapolated_smooth_hfs_arr.coords,
dims=extrapolated_smooth_hfs_arr.dims,
)
# Ignoring mypy warning since it seems to be unaware that the xarray .loc
# method uses label-based indexing and slicing instead of integer-based.
extrapolated_smooth_lfs_arr = extrapolated_smooth_mid_plane_arr.loc[
0: # type: ignore
]
return extrapolated_smooth_lfs_arr, extrapolated_smooth_hfs_arr
def SMART_obs_calc(degree_overlap, manual_overlap):
"""
Work out how many observations are required to cover the southern sky
"""
#setting up the dec ranges
dec_range = [-72., -55., -40.5, -26.7, -13., +1.6, +18.3] #Gleam pointings
delays_range = [[0,0,0,0,6,6,6,6,12,12,12,12,18,18,18,18],\
[0,0,0,0,4,4,4,4,8,8,8,8,12,12,12,12],\
[0,0,0,0,2,2,2,2,4,4,4,4,6,6,6,6],\
[0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0],\
[6,6,6,6,4,4,4,4,2,2,2,2,0,0,0,0],\
[12,12,12,12,8,8,8,8,4,4,4,4,0,0,0,0],\
[18,18,18,18,12,12,12,12,6,6,6,6,0,0,0,0]]
print("Using GLEAM dec range: {}".format(dec_range))
"""
sweet_dec_range = [-82.8,-71.4,-63.1,-55.,-47.5,-40.4,-33.5,-26.7,-19.9,-13.,-5.9,1.6,9.7,18.6,29.4,44.8]
sweet_delays_range= [[0,0,0,0,7,7,7,7,14,14,14,14,21,21,21,21],\
[0,0,0,0,6,6,6,6,12,12,12,12,18,18,18,18],\
[0,0,0,0,5,5,5,5,10,10,10,10,15,15,15,15],\
[0,0,0,0,4,4,4,4,8,8,8,8,12,12,12,12],\
[0,0,0,0,3,3,3,3,6,6,6,6,9,9,9,9],\
[0,0,0,0,2,2,2,2,4,4,4,4,6,6,6,6],\
[0,0,0,0,1,1,1,1,2,2,2,2,3,3,3,3],\
[0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0],\
[3,3,3,3,2,2,2,2,1,1,1,1,0,0,0,0],\
[6,6,6,6,4,4,4,4,2,2,2,2,0,0,0,0],\
[9,9,9,9,6,6,6,6,3,3,3,3,0,0,0,0],\
[12,12,12,12,8,8,8,8,4,4,4,4,0,0,0,0],\
[15,15,15,15,10,10,10,10,5,5,5,5,0,0,0,0],\
[18,18,18,18,12,12,12,12,6,6,6,6,0,0,0,0],\
[21,21,21,21,14,14,14,14,7,7,7,7,0,0,0,0],\
[24,24,24,24,16,16,16,16,8,8,8,8,0,0,0,0]]
dec_range = []
delays_range =[]
sweet_spots_range = [0,2,4,7,10,12,14]
for i in sweet_spots_range:
dec_range.append(sweet_dec_range[i])
delays_range.append(sweet_delays_range[i])
print dec_range
"""
#Going to work out how many pointings are needed
#setting up some metadata requirements
time = 4800 #one hour 20 min
channels = range(107,131)
minfreq = float(min(channels))
maxfreq = float(max(channels))
centrefreq = 1.28 * (minfreq + (maxfreq-minfreq)/2) #in MHz
start_obsid = '1117624530'
start_ra = 180.
Dec_FWHM_calc = []
RA_FWHM_calc = []
for i in range(-89,89,1):
for j in range(0,361,1):
Dec_FWHM_calc.append(i)
RA_FWHM_calc.append(j)
observations = []
ra_list =[]
dec_list =[]
delays_list = []
FWHM = []
FWHM_Dec = []
pointing_count = 0
for i in range(len(dec_range)):
#calculating the FWHM at this dec
ra_sex, deg_sex = fpio.deg2sex(start_ra, dec_range[i])
cord = [start_obsid, str(ra_sex), str(deg_sex), 1, delays_range[i],centrefreq, channels]
#powout=get_beam_power(cord, zip(RA_FWHM_calc,Dec_FWHM_calc), dt=600)
names_ra_dec = np.column_stack((['source']*len(RA_FWHM_calc), RA_FWHM_calc, Dec_FWHM_calc))
powout = fpio.get_beam_power_over_time(cord, names_ra_dec, dt=600, degrees = True)
powout_RA_line = []
powout_Dec_line = []
RA_line = []
Dec_line = []
for p in range(len(powout)):
#print(int(y[i]/np.pi*180.), int(dec) )
if int(Dec_FWHM_calc[p]) == int(dec_range[i]):
powout_RA_line.append(float(powout[p]))
RA_line.append(float(RA_FWHM_calc[p]))
if int (RA_FWHM_calc[p]) == int(start_ra):
powout_Dec_line.append(float(powout[p]))
Dec_line.append(float(Dec_FWHM_calc[p]))
print("\nValues for Dec " + str(dec_range[i]))
#work out RA FWHM (not including the drift scan, 0sec observation)
if args.fwhm:
spline = UnivariateSpline(RA_line, powout_RA_line-np.max(powout_RA_line)/2., s=0)
else:
spline = UnivariateSpline(RA_line, powout_RA_line-np.full(len(powout_RA_line),0.5), s=0)
try:
r1, r2 = spline.roots()
except ValueError:
print("No FWHM for " + str(dec_range[i]) + " setting to 1000 to skip")
FWHM.append(1000.)
pointing_count -=1
else:
FWHM.append(float(r2-r1))
print("FWHM along RA at dec "+ str(dec_range[i]) + ": " + str(FWHM[i]))
#work out Dec FWHM
if args.fwhm:
spline = UnivariateSpline(Dec_line, powout_Dec_line-np.max(powout_Dec_line)/2., s=0)
r1, r2 = spline.roots()
FWHM_Dec.append(float(r2-r1))
print("FWHM along Dec at dec "+ str(dec_range[i]) + ": " + str(FWHM_Dec[i]))
deg_move = total_angle = FWHM[i] - degree_overlap*math.cos(math.radians(dec_range[i])) + \
float(time)/3600.*15.*math.cos(math.radians(dec_range[i]))
if manual_overlap is not None:
point_num_this_deg = manual_overlap[i]
else:
point_num_this_deg = int(360./deg_move) + 1
print("Number for this dec: " +str(point_num_this_deg))
deg_move = 360. / point_num_this_deg
overlap_true = FWHM[i] + float(time)/3600.*15.*math.cos(math.radians(dec_range[i])) -\
360./point_num_this_deg
print("True overlap this dec: " + str(overlap_true))
# offset every second dec range by half a FWHM in RA
for x in range(point_num_this_deg):
if i % 2 == 0:
temp_ra = start_ra + x * deg_move
observations.append(str(int(start_obsid) + int(x*deg_move*240)))
else:
temp_ra = start_ra + x * deg_move +\
deg_move / math.cos(math.radians(dec_range[i]))
observations.append(str(int(start_obsid) + int(x*deg_move*240) +\
int(deg_move*120)))
if temp_ra > 360.:
temp_ra = temp_ra -360.
ra_list.append(temp_ra)
dec_list.append(dec_range[i])
delays_list.append(delays_range[i])
total_angle += deg_move
pointing_count+=1
#Sort by ra
dec_list = [x for _,x in sorted(zip(ra_list,dec_list))]
delays_list = [x for _,x in sorted(zip(ra_list,delays_list))]
observations = [x for _,x in sorted(zip(ra_list,observations))]
ra_list = sorted(ra_list)
return observations, dec_list, ra_list, delays_list
def main():
# make output folder
try:
os.makedirs('scaler_output')
except FileExistsError:
pass
# define datasets, datasetB is scaled to match datasetA
datasetA = 'data/krogan_lab_EMAP_screens/cF3.txt'
datasetB = 'data/SGA_NxN_avg.txt'
# read in the two datasets
ints, profs, genes = read_square_dataset_small(datasetA,
"","\t",split=True,profiles = False)
b_ints, b_profs, b_genes = read_square_dataset_small(datasetB,
"","\t",split=True,profiles = False)
datasetA = datasetA.split('/')[-1].split('.')[0]
datasetB = datasetB.split('/')[-1].split('.')[0]
avalues = []; bvalues=[]
for i in ints :
if i in b_ints :
avalues.append(ints[i])
bvalues.append(b_ints[i])
asorted = sorted(avalues)
bsorted = sorted(bvalues)
# shift datasetB so that it has the same number of negative values
# as datasetA (makes it a little easier to scale)
adjustment = -bsorted[len([x for x in asorted if x < 0])]
bsorted = [x + adjustment for x in bsorted]
# plot scatter plot showing shared interactions
density_scatter_plot(ints,b_ints,'scaler_output/unscaled_scatter.png',
xlabel='S-score', ylabel='SGA score')
# record dataset information in log
with open('scaler_output/scaler_log.txt', 'w') as f:
f.write("cF3 EMAP has {} interactions\n".format(len(ints)))
f.write("SGA_NxN has {} interactions\n".format(len(b_ints)))
f.write("The sets have {} interactions in common\n".format(
len(avalues)))
f.write("Dataset correlation = {}\n".format(
np.corrcoef(avalues,bvalues)[0][1]))
f.write("Adjustment so that the SGA_NxN shared interaction "
"set has the same number of negative values as the "
"cF3 EMAP.\nadjustment={}\n".format(adjustment))
## Computing scaling values
#essentially the data is partitioned into 100 overlapping bins
#the mean value of bin[0] in datasetB is divided by the mean value of bin[0] from datasetA
#this gives a scaling factor for values in the range (min(bin[0]), max(bin[0]))
#values close to zero give unpredictable scaling factors, so they are ignored.
#Depending on the size of your overlap you may want to tweak the number of bins
bins = 500
binsize = len(avalues) / bins
score = []; scale = []
lower_threshold = 0.05
upper_threshold = 0.99
for i in np.arange(1,bins*lower_threshold) :
start = int(i*binsize - binsize)
end = int(i*binsize + binsize)
score.append(np.mean(bsorted[start:end]))
scale.append(np.mean(asorted[start:end])/np.mean(bsorted[start:end]))
for i in np.arange(bins*upper_threshold,bins) :
start = int(i*binsize - binsize)
end = int(i*binsize + binsize)
score.append(np.mean(bsorted[start:end]))
scale.append(np.mean(asorted[start:end])/np.mean(bsorted[start:end]))
# This function creates a curve which maps scores to scaling factors
# the s=0.02 defines how close the curve fits your data points
# large values give crap curves, small values may overfit your data
# it's best to look at the resulting curve and tweak s= as appropriate
svalue = 0.02
s = UnivariateSpline(score, scale, s=svalue)
#displays the scaling values(in red) and the fitted curve (in black)
fig = plt.figure(figsize=(6, 6), dpi= 80, facecolor='w', edgecolor='k')
plt.plot(np.arange(min(score),max(score),0.01), # changed from scatter
[s(x) for x in np.arange(min(score),max(score),0.01)],
color="red")
plt.scatter(score, scale, color="black")
plt.xlim(1.1*min(score), 1.1*max(score))
plt.ylim(0.9*min(scale), 1.1*max(scale))
plt.ylabel('Scaling Factor')
plt.xlabel('SGA Score')
pylab.savefig("scaler_output/scaling_factor_curve.png")
# if the value to be scaled is larger than any value in our training set, we use
# the scaling factor from the largest observed value
def s_bounded(x) :
if x<min(score) :
x = min(score)
elif x > max(score) :
x=max(score)
return s(x)
#This function applies our scaling factor to a given value
g= lambda x : (x + adjustment) * s_bounded(x + adjustment)
for i in b_ints :
b_ints[i] = float(g(b_ints[i]))
scaled_dataset_file = "data/SGA_NxN_scaled_to_cF3.txt"
output_delimited_text(scaled_dataset_file,b_genes,b_genes,b_ints,True)
# save scaling info to log
with open('scaler_output/scaler_log.txt', 'a') as f:
f.write("Number of bins used: {}\n".format(bins))
f.write("Lower threshold for bins: {}\n".format(
lower_threshold))
f.write("Upper threshold for bins: {}\n".format(
upper_threshold))
f.write("S value for fitting spline: {}\n".format(
svalue))
f.write("max_score={}\n".format(max(score)))
f.write("min_score={}\n".format(min(score)))
# save spline for scaling full SGA in R
scores = np.arange(min(score),max(score),0.01)
scales = [float(s(x)) for x in np.arange(min(score),max(score),0.01)]
spline = pd.DataFrame(data=np.stack((scores,scales)).T,
columns=['score', 'scale'])
spline.to_csv('scaler_output/spline.txt', sep='\t', index=False)
# Plot scatter plot of shared interactions after scaling
density_scatter_plot(ints, b_ints, 'scaler_output/scaled_scatter.png',
xlabel='S-score', ylabel='Scaled SGA score')
# Make QQ Plots using the interactions before and after scaling
avalues_after_scaling = []; bvalues_after_scaling = []
for i in ints :
if i in b_ints :
avalues_after_scaling.append(ints[i])
bvalues_after_scaling.append(b_ints[i])
# qqplot_2samples puts the "2nd Sample" on the x-axis
# see documentation for statsmodels.graphics.gofplots
qqplot_scaled = qqplot_2samples(np.array(bvalues_after_scaling),
np.array(avalues_after_scaling),
xlabel='S-score Quantiles',
ylabel='Scaled SGA score Quantiles',
line='r')
pylab.savefig("scaler_output/qq_scaled.png")
qqplot_unscaled = qqplot_2samples(np.array(bvalues),
np.array(avalues),
xlabel='S-score Quantiles',
ylabel='SGA score Quantiles',
line='r')
pylab.savefig("scaler_output/qq_unscaled.png")
def Nderivat(func, x):
spl = UnivariateSpline(x, func, k=3, s=0)
derivativas = spl.derivative()
return derivativas(x)
def initialize(self, data1, data2):
from scipy.interpolate import UnivariateSpline
data1s, data2s = zip(*sorted(zip(data1, data2)))
self.sp = UnivariateSpline(data1s, data2s)
[21.504318130, 0.072918990], [21.629257560, 0.071662650],
[21.754922880, 0.070427950], [21.881318310, 0.069214520],
[22.008448090, 0.068022000], [22.136316500, 0.066850030],
[22.264927820, 0.065698250], [22.394286360, 0.064566310],
[22.524396470, 0.063453880], [22.655262520, 0.062360610],
[22.786888900, 0.061286180], [22.919280020, 0.060230260],
[23.052440330, 0.059192540], [23.186374300, 0.058172690],
[23.321086420, 0.057170410], [23.456581220, 0.056185410],
[23.592863230, 0.055217370], [23.729937040, 0.054266010],
[23.867807240, 0.053331050], [24.006478470, 0.052412190],
[24.145955370, 0.051509160], [24.286242620, 0.050621700],
[24.427344940, 0.049749520], [24.569267070, 0.048892370],
[24.712013750, 0.048049990], [24.855589790, 0.047222120],
[25.000000000, 0.046408510], [25.001000000, 0.046402940]])
cp_curve_spline = UnivariateSpline(cp_curve[:, 0], cp_curve[:, 1], ext='const')
cp_curve_spline.set_smoothing_factor(.000001)
class Nrel5MW(OneTypeWindTurbines):
def __init__(self):
OneTypeWindTurbines.__init__(self,
'Nrel5MW',
diameter=126.4,
hub_height=90,
ct_func=self._ct,
power_func=self._power,
power_unit='kW')
def _ct(self, u):
return np.interp(u, ct_curve[:, 0], ct_curve[:, 1])
def initialize(self,
data1,
data2,
frac_training_data=0.75,
max_iter=100,
s_iter_decrease=0.75,
verb=False):
from scipy.interpolate import UnivariateSpline
if verb:
print(" --------------------")
# Random subsetting of parts of the data
train_idx = random.sample(range(len(data1)),
int(len(data1) * frac_training_data))
i = 0
train_data1 = []
train_data2 = []
test_data1 = []
test_data2 = []
for d1, d2 in zip(data1, data2):
if i in train_idx:
train_data1.append(data1[i])
train_data2.append(data2[i])
else:
test_data1.append(data1[i])
test_data2.append(data2[i])
i += 1
# Sorted data points
data1s, data2s = zip(*sorted(zip(data1, data2)))
test_data1s, test_data2s = zip(*sorted(zip(test_data1, test_data2)))
train_data1s, train_data2s = zip(
*sorted(zip(train_data1, train_data2)))
# Use initial linear Smoothing to find good smoothing parameter s
smlin = SmoothingLinear()
smlin.initialize(data2, data1)
data2_lin_aligned = smlin.predict(data2)
stdev_lin = numpy.std(
numpy.array(data1) - numpy.array(data2_lin_aligned))
linear_error = stdev_lin * stdev_lin
# Perform initial spline approximation
self.s = linear_error * len(train_data1s)
self.sp = UnivariateSpline(train_data1s, train_data2s, k=3, s=self.s)
# Apply spline approximation to the testdata
test_data1_aligned = self.sp(test_data1)
test_stdev = numpy.std(
numpy.array(test_data2) - numpy.array(test_data1_aligned))
if verb:
test_median = numpy.median(
numpy.array(test_data2) - numpy.array(test_data1_aligned))
train_data1_aligned = self.sp(train_data1)
tr_stdev = numpy.std(
numpy.array(train_data2) - numpy.array(train_data1_aligned))
tr_median = numpy.median(
numpy.array(train_data2) - numpy.array(train_data1_aligned))
print(" Lin:Computed stdev", stdev_lin)
print(" Train Computed stdev", tr_stdev, "and median", tr_median)
print(" Test Computed stdev", test_stdev, "and median",
test_median)
stdev_prev = test_stdev
s_prev = self.s
s_iter = self.s
myIter = 0
for i in range(max_iter):
s_iter = s_iter * s_iter_decrease
self.sp = UnivariateSpline(train_data1s,
train_data2s,
k=3,
s=s_iter)
test_data1_aligned = self.sp(test_data1)
stdev = numpy.std(
numpy.array(test_data2) - numpy.array(test_data1_aligned))
if verb:
print(
" == Iter", s_iter, "\tstdev",
numpy.std(
numpy.array(test_data2) -
numpy.array(test_data1_aligned)))
# Stop if stdev does not improve significantly any more
#if stdev_prev - stdev < 0 or (i > 5 and (stdev_prev - stdev < 0.5)):
if stdev_prev - stdev < 0:
break
stdev_prev = stdev
s_prev = s_iter
if verb:
print(" == Done ", s_prev)
# Final spline
self.s = s_prev
self.sp = UnivariateSpline(data1s, data2s, k=3, s=self.s)
def getError(xTest, yTest, xVal, yVal, s):
#print(s)
sp = UnivariateSpline(xTest, yTest, s=s)
testError = (np.mean(np.power((sp(xTest) - yTest), 2)))
validateError = (np.mean(np.power((sp(xVal) - yVal), 2)))
return validateError
class TablePSF(object):
r"""Radially-symmetric table PSF.
This PSF represents a :math:`PSF(r)=dP / d\Omega(r)`
spline interpolation curve for a given set of offset :math:`r`
and :math:`PSF` points.
Uses `scipy.interpolate.UnivariateSpline`.
Parameters
----------
rad : `~astropy.units.Quantity` with angle units
Offset wrt source position
dp_domega : `~astropy.units.Quantity` with sr^-1 units
PSF value array
spline_kwargs : dict
Keyword arguments passed to `~scipy.interpolate.UnivariateSpline`
Notes
-----
* This PSF class works well for model PSFs of arbitrary shape (represented by a table),
but might give unstable results if the PSF has noise.
E.g. if ``dp_domega`` was estimated from histograms of real or simulated event data
with finite statistics, it will have noise and it is your responsibility
to check that the interpolating spline is reasonable.
* To customize the spline, pass keyword arguments to `~scipy.interpolate.UnivariateSpline`
in ``spline_kwargs``. E.g. passing ``dict(k=1)`` changes from the default cubic to
linear interpolation.
* TODO: evaluate spline for ``(log(rad), log(PSF))`` for numerical stability?
* TODO: merge morphology.theta class functionality with this class.
* TODO: add FITS I/O methods
* TODO: add ``normalize`` argument to ``__init__`` with default ``True``?
* TODO: ``__call__`` doesn't show up in the html API docs, but it should:
https://github.com/astropy/astropy/pull/2135
"""
def __init__(self,
rad,
dp_domega,
spline_kwargs=DEFAULT_PSF_SPLINE_KWARGS):
self._rad = Angle(rad).to('radian')
self._dp_domega = Quantity(dp_domega).to('sr^-1')
assert self._rad.ndim == self._dp_domega.ndim == 1
assert self._rad.shape == self._dp_domega.shape
# Store input arrays as quantities in default internal units
self._dp_dr = (2 * np.pi * self._rad * self._dp_domega).to('radian^-1')
self._spline_kwargs = spline_kwargs
self._compute_splines(spline_kwargs)
@classmethod
def from_shape(cls, shape, width, rad):
"""Make TablePSF objects with commonly used shapes.
This function is mostly useful for examples and testing.
Parameters
----------
shape : {'disk', 'gauss'}
PSF shape.
width : `~astropy.units.Quantity` with angle units
PSF width angle (radius for disk, sigma for Gauss).
rad : `~astropy.units.Quantity` with angle units
Offset angle
Returns
-------
psf : `TablePSF`
Table PSF
Examples
--------
>>> import numpy as np
>>> from astropy.coordinates import Angle
>>> from gammapy.irf import TablePSF
>>> TablePSF.from_shape(shape='gauss', width='0.2 deg',
... rad=Angle(np.linspace(0, 0.7, 100), 'deg'))
"""
width = Angle(width)
rad = Angle(rad)
if shape == 'disk':
amplitude = 1 / (np.pi * width.radian**2)
psf_value = np.where(rad < width, amplitude, 0)
elif shape == 'gauss':
gauss2d_pdf = Gauss2DPDF(sigma=width.radian)
psf_value = gauss2d_pdf(rad.radian)
else:
raise ValueError('Invalid shape: {}'.format(shape))
psf_value = Quantity(psf_value, 'sr^-1')
return cls(rad, psf_value)
def info(self):
"""Print basic info."""
ss = array_stats_str(self._rad.degree, 'offset')
ss += 'integral = {}\n'.format(self.integral())
for containment in [50, 68, 80, 95]:
radius = self.containment_radius(0.01 * containment)
ss += ('containment radius {} deg for {}%\n'.format(
radius.degree, containment))
return ss
# TODO: remove because it's not flexible enough?
def __call__(self, lon, lat):
"""Evaluate PSF at a 2D position.
The PSF is centered on ``(0, 0)``.
Parameters
----------
lon, lat : `~astropy.coordinates.Angle`
Longitude / latitude position
Returns
-------
psf_value : `~astropy.units.Quantity`
PSF value
"""
center = SkyCoord(0, 0, unit='radian')
point = SkyCoord(lon, lat)
rad = center.separation(point)
return self.evaluate(rad)
def kernel(self,
reference,
rad_max,
normalize=True,
discretize_model_kwargs=dict(factor=10)):
"""
Make a 2-dimensional kernel image.
The kernel image is evaluated on a cartesian grid defined by the
reference sky image.
Parameters
----------
reference : `~gammapy.image.SkyImage` or `~gammapy.cube.SkyCube`
Reference sky image or sky cube defining the spatial grid.
rad_max : `~astropy.coordinates.Angle`
Radial size of the kernel
normalize : bool
Whether to normalize the kernel.
Returns
-------
kernel : `~astropy.units.Quantity`
Kernel 2D image of Quantities
"""
from ..cube import SkyCube
rad_max = Angle(rad_max)
if isinstance(reference, SkyCube):
reference = reference.sky_image_ref
pixel_size = reference.wcs_pixel_scale()[0]
def _model(x, y):
"""Model in the appropriate format for discretize_model."""
rad = np.sqrt(x * x + y * y) * pixel_size
return self.evaluate(rad)
npix = int(rad_max.radian / pixel_size.radian)
pix_range = (-npix, npix + 1)
kernel = discretize_oversample_2D(_model,
x_range=pix_range,
y_range=pix_range,
**discretize_model_kwargs)
if normalize:
kernel = kernel / kernel.sum()
return kernel
def evaluate(self, rad, quantity='dp_domega'):
r"""Evaluate PSF.
The following PSF quantities are available:
* 'dp_domega': PDF per 2-dim solid angle :math:`\Omega` in sr^-1
.. math:: \frac{dP}{d\Omega}
* 'dp_dr': PDF per 1-dim offset :math:`r` in radian^-1
.. math:: \frac{dP}{dr} = 2 \pi r \frac{dP}{d\Omega}
Parameters
----------
rad : `~astropy.coordinates.Angle`
Offset wrt source position
quantity : {'dp_domega', 'dp_dr'}
Which PSF quantity?
Returns
-------
psf_value : `~astropy.units.Quantity`
PSF value
"""
rad = Angle(rad)
shape = rad.shape
x = np.array(rad.radian).flat
if quantity == 'dp_domega':
y = self._dp_domega_spline(x)
unit = 'sr^-1'
elif quantity == 'dp_dr':
y = self._dp_dr_spline(x)
unit = 'radian^-1'
else:
ss = 'Invalid quantity: {}\n'.format(quantity)
ss += "Choose one of: 'dp_domega', 'dp_dr'"
raise ValueError(ss)
y = np.clip(a=y, a_min=0, a_max=None)
return Quantity(y, unit).reshape(shape)
def integral(self, rad_min=None, rad_max=None):
"""Compute PSF integral, aka containment fraction.
Parameters
----------
rad_min, rad_max : `~astropy.units.Quantity` with angle units
Offset angle range
Returns
-------
integral : float
PSF integral
"""
if rad_min is None:
rad_min = self._rad[0]
else:
rad_min = Angle(rad_min)
if rad_max is None:
rad_max = self._rad[-1]
else:
rad_max = Angle(rad_max)
rad_min = self._rad_clip(rad_min)
rad_max = self._rad_clip(rad_max)
cdf_min = self._cdf_spline(rad_min)
cdf_max = self._cdf_spline(rad_max)
return cdf_max - cdf_min
def containment_radius(self, fraction):
"""Containment radius.
Parameters
----------
fraction : array_like
Containment fraction (range 0 .. 1)
Returns
-------
rad : `~astropy.coordinates.Angle`
Containment radius angle
"""
rad = self._ppf_spline(fraction)
return Angle(rad, 'radian').to('deg')
def normalize(self):
"""Normalize PSF to unit integral.
Computes the total PSF integral via the :math:`dP / dr` spline
and then divides the :math:`dP / dr` array.
"""
integral = self.integral()
self._dp_dr /= integral
# Don't divide by 0
EPS = 1e-6
rad = np.clip(self._rad.radian, EPS, None)
rad = Quantity(rad, 'radian')
self._dp_domega = self._dp_dr / (2 * np.pi * rad)
self._compute_splines(self._spline_kwargs)
def broaden(self, factor, normalize=True):
r"""Broaden PSF by scaling the offset array.
For a broadening factor :math:`f` and the offset
array :math:`r`, the offset array scaled
in the following way:
.. math::
r_{new} = f \times r_{old}
\frac{dP}{dr}(r_{new}) = \frac{dP}{dr}(r_{old})
Parameters
----------
factor : float
Broadening factor
normalize : bool
Normalize PSF after broadening
"""
self._rad *= factor
# We define broadening such that self._dp_domega remains the same
# so we only have to re-compute self._dp_dr and the slines here.
self._dp_dr = (2 * np.pi * self._rad * self._dp_domega).to('radian^-1')
self._compute_splines(self._spline_kwargs)
if normalize:
self.normalize()
def plot_psf_vs_rad(self, ax=None, quantity='dp_domega', **kwargs):
"""Plot PSF vs radius.
TODO: describe PSF ``quantity`` argument in a central place and link to it from here.
"""
import matplotlib.pyplot as plt
ax = plt.gca() if ax is None else ax
x = self._rad.to('deg')
y = self.evaluate(self._rad, quantity)
ax.plot(x.value, y.value, **kwargs)
ax.loglog()
ax.set_xlabel('Radius ({})'.format(x.unit))
ax.set_ylabel('PSF ({})'.format(y.unit))
def _compute_splines(self, spline_kwargs=DEFAULT_PSF_SPLINE_KWARGS):
"""Compute two splines representing the PSF.
* `_dp_domega_spline` is used to evaluate the 2D PSF.
* `_dp_dr_spline` is not really needed for most applications,
but is available via `eval`.
* `_cdf_spline` is used to compute integral and for normalisation.
* `_ppf_spline` is used to compute containment radii.
"""
from scipy.interpolate import UnivariateSpline
# Compute spline and normalize.
x, y = self._rad.value, self._dp_domega.value
self._dp_domega_spline = UnivariateSpline(x, y, **spline_kwargs)
x, y = self._rad.value, self._dp_dr.value
self._dp_dr_spline = UnivariateSpline(x, y, **spline_kwargs)
# We use the terminology for scipy.stats distributions
# http://docs.scipy.org/doc/scipy/reference/tutorial/stats.html#common-methods
# cdf = "cumulative distribution function"
self._cdf_spline = self._dp_dr_spline.antiderivative()
# ppf = "percent point function" (inverse of cdf)
# Here's a discussion on methods to compute the ppf
# http://mail.scipy.org/pipermail/scipy-user/2010-May/025237.html
y = self._rad.value
x = self.integral(Angle(0, 'rad'), self._rad)
# Since scipy 1.0 the UnivariateSpline requires that x is strictly increasing
# So only keep nodes where this is the case (and always keep the first one):
x, idx = np.unique(x, return_index=True)
y = y[idx]
# Dummy values, for cases where one really doesn't have a valid PSF.
if len(x) < 4:
x = [0, 1, 2, 3]
y = [0, 0, 0, 0]
self._ppf_spline = UnivariateSpline(x, y, **spline_kwargs)
def _rad_clip(self, rad):
"""Clip to radius support range, because spline extrapolation is unstable."""
rad = Angle(rad, 'radian').radian
rad = np.clip(rad, 0, self._rad[-1].radian)
return rad
#plt.plot(xTest,yTest,'o',label="test")
#plt.plot(xVal,yVal,'*',label="val")
#plt.legend()
#plt.show()
valErrors = []
ss = np.linspace(0.0001, 0.5, 100)
for s in ss:
valErrors.append(getFit(x, y_noise, s))
plt.plot(ss, valErrors, label="Val")
plt.legend()
plt.show()
bestS = ss[valErrors.index(min(valErrors))]
sp = UnivariateSpline(x, y_noise, s=bestS)
#m = minimize(lambda s : getError(xTest,yTest,xVal,yVal,s),x0=0.25,tol=0.00001, method='nelder-mead')
m = differential_evolution(lambda s: getFit(x, y_noise, s),
bounds=[(0, 1)],
tol=0.0001)
fitS = m.x
spFit = UnivariateSpline(x, y_noise, s=fitS)
plt.plot(x, y, label="True")
plt.plot(x, y_noise, 'o', label='Data')
plt.plot(x, sp(x), label="Spline {}".format(bestS))
plt.plot(x, spFit(x), label="fit spline {}".format(fitS))
plt.legend()
plt.show()
from numpy import linspace, exp from numpy.random import randn import matplotlib.pyplot as plt from scipy.interpolate import UnivariateSpline x = linspace(-3, 3, 100) y = exp(-x**2) + randn(100) / 10 s = UnivariateSpline(x, y, s=1) xs = linspace(-3, 3, 1000) ys = s(xs) plt.plot(x, y, '.-') plt.plot(xs, ys) plt.show()
def __init__(self, x, y, *args, **kwargs):
UnivariateSpline.__init__(self, x, y, *args, **kwargs)
self.xdata = sp.array(x)
self.ydata = sp.array(y)
from matplotlib import gridspec
import matplotlib.pyplot as plt
from scipy.stats import gaussian_kde
import numpy as np
from matplotlib import rc
rc('font', **{'family': 'serif', 'serif': ['Computer Modern']})
rc('text', usetex=True)
np.random.seed(0)
x = np.sort(np.random.rand(1000))
gx = np.sort(np.linspace(min(x), max(x), 10))
gy = np.sort(np.random.randn(10))
f = UnivariateSpline(gx, gy)
y = f(x)
n = np.random.randn(1000) * 0.1
fig = plt.figure(figsize=(5, 4))
plot_main = fig.add_subplot(111)
plot_main.plot(x, y + n, '.', color='0.75', zorder=-100)
plot_main.plot(x, y, linewidth=2, zorder=-99)
i = [10, 500, 800]
plt.errorbar(x[i],
y[i],
yerr=[0.25, 0.25, 0.25],
color='red',
linestyle='none',
def smoothing_filter(time_in,
val_in,
time_out=None,
relabel=None,
params=None):
"""
@brief Smoothing filter with relabeling and resampling features.
@details It supports evenly sampled multidimensional input signal.
Relabeling can be used to infer the value of samples at
time steps before and after the explicitly provided samples.
As a reminder, relabeling is a generalization of periodicity.
@param[in] time_in Time steps of the input signal (1D numpy array)
@param[in] val_in Sampled values of the input signal
(2D numpy array: row = sample, column = time)
@param[in] time_out Time steps of the output signal (1D numpy array)
@param[in] relabel Relabeling matrix (identity for periodic signals)
Optional: Disable if omitted
@param[in] params Parameters of the filter. Dictionary with keys:
'mixing_ratio_1': Relative time at the begining of the signal
during the output signal corresponds to a
linear mixing over time of the filtered and
original signal. (only used if relabel is omitted)
'mixing_ratio_2': Relative time at the end of the signal
during the output signal corresponds to a
linear mixing over time of the filtered and
original signal. (only used if relabel is omitted)
'smoothness'[0]: Smoothing factor to filter the begining of the signal
(only used if relabel is omitted)
'smoothness'[1]: Smoothing factor to filter the end of the signal
(only used if relabel is omitted)
'smoothness'[2]: Smoothing factor to filter the middle part of the signal
@return Filtered signal (2D numpy array: row = sample, column = time)
"""
if time_out is None:
time_out = time_in
if params is None:
params = dict()
params['mixing_ratio_1'] = 0.12
params['mixing_ratio_2'] = 0.04
params['smoothness'] = [0.0, 0.0, 0.0]
params['smoothness'][0] = 5e-3
params['smoothness'][1] = 5e-3
params['smoothness'][2] = 3e-3
if relabel is None:
mix_fit = [None, None, None]
mix_fit[0] = lambda t: 0.5 * (1 + np.sin(1 / params['mixing_ratio_1'] *
((t - time_in[0]) /
(time_in[-1] - time_in[0]
)) * np.pi - np.pi / 2))
mix_fit[1] = lambda t: 0.5 * (
1 + np.sin(1 / params['mixing_ratio_2'] *
((t - (1 - params['mixing_ratio_2']) * time_in[-1]) /
(time_in[-1] - time_in[0])) * np.pi + np.pi / 2))
mix_fit[2] = lambda t: 1
val_fit = []
for jj in range(val_in.shape[0]):
val_fit_jj = []
for kk in range(len(params['smoothness'])):
val_fit_jj.append(
UnivariateSpline(time_in,
val_in[jj],
s=params['smoothness'][kk]))
val_fit.append(val_fit_jj)
time_out_mixing = [None, None, None]
time_out_mixing_ind = [None, None, None]
time_out_mixing_ind[
0] = time_out < time_out[-1] * params['mixing_ratio_1']
time_out_mixing[0] = time_out[time_out_mixing_ind[0]]
time_out_mixing_ind[1] = time_out > time_out[-1] * (
1 - params['mixing_ratio_2'])
time_out_mixing[1] = time_out[time_out_mixing_ind[1]]
time_out_mixing_ind[2] = np.logical_and(
np.logical_not(time_out_mixing_ind[0]),
np.logical_not(time_out_mixing_ind[1]))
time_out_mixing[2] = time_out[time_out_mixing_ind[2]]
val_out = np.zeros((val_in.shape[0], len(time_out)))
for jj in range(val_in.shape[0]):
for kk in range(len(time_out_mixing)):
val_out[jj,time_out_mixing_ind[kk]] = \
(1 - mix_fit[kk](time_out_mixing[kk])) * val_fit[jj][kk](time_out_mixing[kk]) + \
mix_fit[kk](time_out_mixing[kk]) * val_fit[jj][-1](time_out_mixing[kk])
else:
time_tmp = np.concatenate(
[time_in[:-1] - time_in[-1], time_in, time_in[1:] + time_in[-1]])
val_in_tmp = np.concatenate(
[relabel.dot(val_in[:, :-1]), val_in,
relabel.dot(val_in[:, 1:])],
axis=1)
val_out = np.zeros((val_in.shape[0], len(time_out)))
for jj in range(val_in_tmp.shape[0]):
f = UnivariateSpline(time_tmp,
val_in_tmp[jj],
s=params['smoothness'][-1])
val_out[jj] = f(time_out)
return val_out
def _upsample_cam(class_activation_matrix, new_dimensions):
"""Upsamples class-activation matrix (CAM).
CAM may be 1-D, 2-D, or 3-D.
:param class_activation_matrix: numpy array containing 1-D, 2-D, or 3-D
class-activation matrix.
:param new_dimensions: numpy array of new dimensions. If matrix is
{1D, 2D, 3D}, this must be a length-{1, 2, 3} array, respectively.
:return: class_activation_matrix: Upsampled version of input.
"""
num_rows_new = new_dimensions[0]
row_indices_new = numpy.linspace(1,
num_rows_new,
num=num_rows_new,
dtype=float)
row_indices_orig = numpy.linspace(1,
num_rows_new,
num=class_activation_matrix.shape[0],
dtype=float)
if len(new_dimensions) == 1:
# interp_object = UnivariateSpline(
# x=row_indices_orig, y=numpy.ravel(class_activation_matrix),
# k=1, s=0
# )
interp_object = UnivariateSpline(
x=row_indices_orig,
y=numpy.ravel(class_activation_matrix),
k=3,
s=0)
return interp_object(row_indices_new)
num_columns_new = new_dimensions[1]
column_indices_new = numpy.linspace(1,
num_columns_new,
num=num_columns_new,
dtype=float)
column_indices_orig = numpy.linspace(1,
num_columns_new,
num=class_activation_matrix.shape[1],
dtype=float)
if len(new_dimensions) == 2:
interp_object = RectBivariateSpline(x=row_indices_orig,
y=column_indices_orig,
z=class_activation_matrix,
kx=3,
ky=3,
s=0)
return interp_object(x=row_indices_new,
y=column_indices_new,
grid=True)
num_heights_new = new_dimensions[2]
height_indices_new = numpy.linspace(1,
num_heights_new,
num=num_heights_new,
dtype=float)
height_indices_orig = numpy.linspace(1,
num_heights_new,
num=class_activation_matrix.shape[2],
dtype=float)
interp_object = RegularGridInterpolator(points=(row_indices_orig,
column_indices_orig,
height_indices_orig),
values=class_activation_matrix,
method='linear')
column_index_matrix, row_index_matrix, height_index_matrix = (
numpy.meshgrid(column_indices_new, row_indices_new,
height_indices_new))
query_point_matrix = numpy.stack(
(row_index_matrix, column_index_matrix, height_index_matrix), axis=-1)
return interp_object(query_point_matrix)
def rho2rho(self, rho_in, t_in=None, \
coord_in='rho_pol', coord_out='rho_tor', extrapolate=False):
"""Mapping from/to rho_pol, rho_tor, r_V, rho_V, Psi, r_a
r_V is the STRAHL-like radial coordinate
Input
----------
t_in : float or 1darray
time
rho_in : float, ndarray
radial coordinates, 1D (time constant) or 2D+ (time variable) of size (nt,nx,...)
coord_in: str ['rho_pol', 'rho_tor' ,'rho_V', 'r_V', 'Psi','r_a','Psi_N']
input coordinate label
coord_out: str ['rho_pol', 'rho_tor' ,'rho_V', 'r_V', 'Psi','r_a','Psi_N']
output coordinate label
extrapolate: bool
extrapolate rho_tor, r_V outside the separatrix
Output
-------
rho : 2d+ array (nt, nr, ...)
converted radial coordinate
"""
if not self.eq_open:
return
if self.debug:
print(('Remapping from %s to %s' % (coord_in, coord_out)))
if t_in is None:
t_in = self.t_eq
tarr = np.atleast_1d(t_in)
rho = np.atleast_1d(rho_in)
nt_in = np.size(tarr)
if rho.ndim == 1:
rho = np.tile(rho, (nt_in, 1))
# Trivial case
if coord_out == coord_in:
return rho
self._read_scalars()
self._read_profiles()
unique_idx, idx = self._get_nearest_index(tarr)
if coord_in in ['rho_pol', 'Psi', 'Psi_N']:
label_in = self.pf
elif coord_in == 'rho_tor':
label_in = self.tf
elif coord_in in ['rho_V', 'r_V']:
label_in = self.vol
R0 = self.ssq['Rmag']
elif coord_in in ['r_a', 'RMNMP']:
R, _ = self.rhoTheta2rz(self.pf.T, [0, np.pi], coord_in='Psi')
label_in = (R[:, 0] - R[:, 1]).T**2 / 4
else:
raise Exception('unsupported input coordinate')
if coord_out in ['rho_pol', 'Psi', 'Psi_N']:
label_out = self.pf
elif coord_out == 'rho_tor':
label_out = self.tf
elif coord_out in ['rho_V', 'r_V']:
label_out = self.vol
R0 = self.ssq['Rmag']
elif coord_out in ['r_a', 'RMNMP']:
R, _ = self.rhoTheta2rz(self.pf.T[unique_idx], [0, np.pi],
t_in=self.t_eq[unique_idx],
coord_in='Psi')
label_out = np.zeros_like(self.pf)
label_out[:, unique_idx] = (R[:, 0] - R[:, 1]).T**2 / 4
else:
raise Exception('unsupported output coordinate')
PFL = self.orientation * self.pf
PSIX = self.orientation * self.psix
PSI0 = self.orientation * self.psi0
rho_output = np.ones_like(rho) #*np.nan
for i in unique_idx:
# Calculate a normalized input and output flux
sort_wh = np.argsort(PFL[:, i])
#get rid of the point out of the separatrix
ind = (label_out[sort_wh, i] != 0) & (label_in[sort_wh, i] != 0)
ind[0] = True
sort_wh = sort_wh[ind]
sep_out, mag_out = np.interp([PSIX[i], PSI0[i]], PFL[sort_wh, i],
label_out[sort_wh, i])
sep_in, mag_in = np.interp([PSIX[i], PSI0[i]], PFL[sort_wh, i],
label_in[sort_wh, i])
if (abs(sep_out - mag_out) <
1e-4) or (abs(sep_in - mag_in) < 1e-4) or np.isnan(
sep_in * sep_out): #corrupted timepoint
#print 'corrupted'
continue
# Normalize between 0 and 1
Psi_out = (label_out[sort_wh, i] - mag_out) / (sep_out - mag_out)
Psi_in = (label_in[sort_wh, i] - mag_in) / (sep_in - mag_in)
Psi_out[(Psi_out > 1) | (Psi_out < 0)] = 0 #remove rounding errors
Psi_in[(Psi_in > 1) | (Psi_in < 0)] = 0
rho_out = np.r_[np.sqrt(Psi_out), 1]
rho_in = np.r_[np.sqrt(Psi_in), 1]
ind = (rho_out == 0) | (rho_in == 0)
rho_out, rho_in = rho_out[~ind], rho_in[~ind]
# Profiles can be noisy! smooth spline must be used
sortind = np.unique(rho_in, return_index=True)[1]
w = np.ones_like(sortind) * rho_in[sortind]
w = np.r_[w[1] / 2, w[1:], 1e3]
ratio = rho_out[sortind] / rho_in[sortind]
rho_in = np.r_[0, rho_in[sortind]]
ratio = np.r_[ratio[0], ratio]
s = UnivariateSpline(
rho_in, ratio, w=w, k=4, s=5e-3, ext=3
) #BUG s = 5e-3 can be sometimes too much, sometimes not enought :(
jt = idx == i
#print np.where(jt)[0]
#if 826 in np.where(jt)[0]:
#import IPython
#IPython.embed()
rho_ = np.copy(rho[jt])
r0_in, r0_out = 1, 1
if coord_in == 'r_V':
r0_in = np.sqrt(sep_in / (2 * np.pi**2 * R0[i]))
if coord_out == 'r_V':
embed()
r0_out = np.sqrt(sep_out / (2 * np.pi**2 * R0[i]))
if coord_in == 'RMNMP':
r0_in = np.sqrt(sep_in)
if coord_out == 'RMNMP':
r0_out = np.sqrt(sep_out)
if coord_in == 'Psi':
rho_ = np.sqrt(
np.maximum(0, (rho_ - self.psi0[i]) /
(self.psix[i] - self.psi0[i])))
if coord_in == 'Psi_N':
rho_ = np.sqrt(np.maximum(0, rho_))
# Evaluate spline
rho_output[jt] = s(rho_.flatten() / r0_in).reshape(
rho_.shape) * rho_ * r0_out / r0_in
if np.any(np.isnan(rho_output[jt])): # UnivariateSpline failed
rho_output[jt] = np.interp(rho_ / r0_in, rho_in,
ratio) * rho_ * r0_out / r0_in
if not extrapolate:
rho_output[jt] = np.minimum(rho_output[jt],
r0_out) # rounding errors
rho_output[jt] = np.maximum(0, rho_output[jt]) # rounding errors
if coord_out == 'Psi':
rho_output[jt] = rho_output[jt]**2 * (
self.psix[i] - self.psi0[i]) + self.psi0[i]
if coord_out == 'Psi_N':
rho_output[jt] = rho_output[jt]**2
return rho_output
def run_opt(layout_number, wec_method_number, wake_model, opt_alg_number,
max_wec, nsteps):
OPENMDAO_REQUIRE_MPI = False
run_number = layout_number
model = wake_model
# set model
MODELS = ['FLORIS', 'BPA', 'JENSEN', 'LARSEN']
print(MODELS[model])
# select optimization approach/method
opt_algs = ['snopt', 'ga', 'ps']
opt_algorithm = opt_algs[opt_alg_number]
# select wec method
wec_methods = ['none', 'diam', 'angle', 'hybrid']
wec_method = wec_methods[wec_method_number]
# pop_size = 760
# save and show options
show_start = False
show_end = False
save_start = False
save_end = False
save_locations = True
save_aep = True
save_time = True
rec_func_calls = True
input_directory = "../../../input_files/"
# set options for BPA
print_ti = False
sort_turbs = True
# turbine_type = 'NREL5MW' #can be 'V80' or 'NREL5MW'
turbine_type = 'V80' # can be 'V80' or 'NREL5MW'
wake_model_version = 2016
WECH = 0
if wec_method == 'diam':
output_directory = "../output_files/%s_wec_diam_max_wec_%i_nsteps_%.3f/" % (
opt_algorithm, max_wec, nsteps)
relax = True
# expansion_factors = np.array([3, 2.75, 2.5, 2.25, 2.0, 1.75, 1.5, 1.25, 1.0, 1.0])
expansion_factors = np.linspace(1.0, max_wec, nsteps)
expansion_factors = np.flip(expansion_factors)
elif wec_method == 'angle':
output_directory = "../output_files/%s_wec_angle_max_wec_%i_nsteps_%.3f/" % (
opt_algorithm, max_wec, nsteps)
relax = True
# expansion_factors = np.array([50, 40, 30, 20, 10, 0.0, 0.0])
expansion_factors = np.linspace(0.0, max_wec, nsteps)
expansion_factors = np.flip(expansion_factors)
elif wec_method == 'hybrid':
expansion_factors = np.linspace(1.0, max_wec, nsteps)
expansion_factors = np.flip(expansion_factors)
output_directory = "../output_files/%s_wec_hybrid_max_wec_%i_nsteps_%.3f/" % (
opt_algorithm, max_wec, nsteps)
relax = True
WECH = 1
elif wec_method == 'none':
relax = False
output_directory = "../output_files/%s/" % opt_algorithm
else:
raise ValueError('wec_method must be diam, angle, hybrid, or none')
# create output directory if it does not exist yet
import distutils.dir_util
distutils.dir_util.mkpath(output_directory)
differentiable = False
# for expansion_factor in np.array([5., 4., 3., 2.75, 2.5, 2.25, 2.0, 1.75, 1.5, 1.25, 1.0]):
# for expansion_factor in np.array([20., 15., 10., 5., 4., 3., 2.5, 1.25, 1.0]):
# expansion_factors = np.array([20., 10., 5., 2.5, 1.25, 1.0])
wake_combination_method = 1 # can be [0:Linear freestreem superposition,
# 1:Linear upstream velocity superposition,
# 2:Sum of squares freestream superposition,
# 3:Sum of squares upstream velocity superposition]
ti_calculation_method = 4 # can be [0:No added TI calculations,
# 1:TI by Niayifar and Porte Agel altered by Annoni and Thomas,
# 2:TI by Niayifar and Porte Agel 2016,
# 3:TI by Niayifar and Porte Agel 2016 with added soft max function,
# 4:TI by Niayifar and Porte Agel 2016 using area overlap ratio,
# 5:TI by Niayifar and Porte Agel 2016 using area overlap ratio and SM function]
if wec_method_number > 0:
ti_opt_method = 5 # can be [0:No added TI calculations,
# 1:TI by Niayifar and Porte Agel altered by Annoni and Thomas,
# 2:TI by Niayifar and Porte Agel 2016,
# 3:TI by Niayifar and Porte Agel 2016 with added soft max function,
# 4:TI by Niayifar and Porte Agel 2016 using area overlap ratio,
# 5:TI by Niayifar and Porte Agel 2016 using area overlap ratio and SM function]
else:
ti_opt_method = 5
final_ti_opt_method = 5
if opt_algorithm == 'ps':
ti_opt_method = ti_calculation_method
sm_smoothing = 700.
if ti_calculation_method == 0:
calc_k_star_calc = False
else:
calc_k_star_calc = True
if ti_opt_method == 0:
calc_k_star_opt = False
else:
calc_k_star_opt = True
nRotorPoints = 1
wind_rose_file = 'nantucket' # can be one of: 'amalia', 'nantucket', 'directional
TI = 0.108
k_calc = 0.3837 * TI + 0.003678
# k_calc = 0.022
# k_opt = 0.04
shear_exp = 0.31
# air_density = 1.1716 # kg/m^3
air_density = 1.225 # kg/m^3 (from Jen)
if turbine_type == 'V80':
# define turbine size
rotor_diameter = 80. # (m)
hub_height = 70.0
z_ref = 80.0 # m
z_0 = 0.0
# load performance characteristics
cut_in_speed = 4. # m/s
cut_out_speed = 25. # m/s
rated_wind_speed = 16. # m/s
rated_power = 2000. # kW
generator_efficiency = 0.944
ct_curve_data = np.loadtxt(input_directory +
'mfg_ct_vestas_v80_niayifar2016.txt',
delimiter=",")
ct_curve_wind_speed = ct_curve_data[:, 0]
ct_curve_ct = ct_curve_data[:, 1]
# air_density = 1.1716 # kg/m^3
Ar = 0.25 * np.pi * rotor_diameter**2
# cp_curve_wind_speed = ct_curve[:, 0]
power_data = np.loadtxt(input_directory +
'niayifar_vestas_v80_power_curve_observed.txt',
delimiter=',')
# cp_curve_cp = niayifar_power_model(cp_curve_wind_speed)/(0.5*air_density*cp_curve_wind_speed**3*Ar)
cp_curve_cp = power_data[:, 1] * (1E6) / (0.5 * air_density *
power_data[:, 0]**3 * Ar)
cp_curve_wind_speed = power_data[:, 0]
cp_curve_spline = UnivariateSpline(cp_curve_wind_speed,
cp_curve_cp,
ext='const')
cp_curve_spline.set_smoothing_factor(.0001)
elif turbine_type == 'NREL5MW':
# define turbine size
rotor_diameter = 126.4 # (m)
hub_height = 90.0
z_ref = 80.0 # m
z_0 = 0.0
# load performance characteristics
cut_in_speed = 3. # m/s
cut_out_speed = 25. # m/s
rated_wind_speed = 11.4 # m/s
rated_power = 5000. # kW
generator_efficiency = 0.944
filename = input_directory + "NREL5MWCPCT_dict.p"
# filename = "../input_files/NREL5MWCPCT_smooth_dict.p"
import pickle
data = pickle.load(open(filename, "rb"), encoding='latin1')
ct_curve = np.zeros([data['wind_speed'].size, 2])
ct_curve_wind_speed = data['wind_speed']
ct_curve_ct = data['CT']
# cp_curve_cp = data['CP']
# cp_curve_wind_speed = data['wind_speed']
loc0 = np.where(data['wind_speed'] < 11.55)
loc1 = np.where(data['wind_speed'] > 11.7)
cp_curve_cp = np.hstack([data['CP'][loc0], data['CP'][loc1]])
cp_curve_wind_speed = np.hstack(
[data['wind_speed'][loc0], data['wind_speed'][loc1]])
cp_curve_spline = UnivariateSpline(cp_curve_wind_speed,
cp_curve_cp,
ext='const')
cp_curve_spline.set_smoothing_factor(.000001)
else:
raise ValueError("Turbine type is undefined.")
# load starting locations
layout_directory = input_directory
layout_data = np.loadtxt(
layout_directory +
"layouts/round_38turbs/nTurbs38_spacing5_layout_%i.txt" %
layout_number)
# layout_data = np.loadtxt(layout_directory + "layouts/grid_16turbs/nTurbs16_spacing5_layout_%i.txt" % layout_number)
# layout_data = np.loadtxt(layout_directory+"layouts/nTurbs9_spacing5_layout_%i.txt" % layout_number)
turbineX = layout_data[:, 0] * rotor_diameter + rotor_diameter / 2.
turbineY = layout_data[:, 1] * rotor_diameter + rotor_diameter / 2.
turbineX_init = np.copy(turbineX)
turbineY_init = np.copy(turbineY)
nTurbines = turbineX.size
# create boundary specifications
boundary_radius = 0.5 * (rotor_diameter * 4000. / 126.4 - rotor_diameter
) # 1936.8
center = np.array([boundary_radius, boundary_radius]) + rotor_diameter / 2.
start_min_spacing = 5.
nVertices = 1
boundary_center_x = center[0]
boundary_center_y = center[1]
xmax = np.max(turbineX)
ymax = np.max(turbineY)
xmin = np.min(turbineX)
ymin = np.min(turbineY)
boundary_radius_plot = boundary_radius + 0.5 * rotor_diameter
plot_round_farm(turbineX,
turbineY,
rotor_diameter, [boundary_center_x, boundary_center_y],
boundary_radius,
show_start=show_start)
# quit()
# initialize input variable arrays
nTurbs = nTurbines
rotorDiameter = np.zeros(nTurbs)
hubHeight = np.zeros(nTurbs)
axialInduction = np.zeros(nTurbs)
Ct = np.zeros(nTurbs)
Cp = np.zeros(nTurbs)
generatorEfficiency = np.zeros(nTurbs)
yaw = np.zeros(nTurbs)
minSpacing = 2. # number of rotor diameters
# define initial values
for turbI in range(0, nTurbs):
rotorDiameter[turbI] = rotor_diameter # m
hubHeight[turbI] = hub_height # m
axialInduction[turbI] = 1.0 / 3.0
Ct[turbI] = 4.0 * axialInduction[turbI] * (1.0 - axialInduction[turbI])
# print(Ct)
Cp[turbI] = 4.0 * 1.0 / 3.0 * np.power((1 - 1.0 / 3.0), 2)
generatorEfficiency[turbI] = generator_efficiency
yaw[turbI] = 0. # deg.
# Define flow properties
if wind_rose_file is 'nantucket':
# windRose = np.loadtxt(input_directory + 'nantucket_windrose_ave_speeds.txt')
windRose = np.loadtxt(input_directory +
'nantucket_wind_rose_for_LES.txt')
windDirections = windRose[:, 0]
windSpeeds = windRose[:, 1]
windFrequencies = windRose[:, 2]
size = np.size(windDirections)
elif wind_rose_file is 'amalia':
windRose = np.loadtxt(
input_directory +
'windrose_amalia_directionally_averaged_speeds.txt')
windDirections = windRose[:, 0]
windSpeeds = windRose[:, 1]
windFrequencies = windRose[:, 2]
size = np.size(windDirections)
elif wind_rose_file is 'directional':
windRose = np.loadtxt(input_directory + 'directional_windrose.txt')
windDirections = windRose[:, 0]
windSpeeds = windRose[:, 1]
windFrequencies = windRose[:, 2]
size = np.size(windDirections)
elif wind_rose_file is '1d':
windDirections = np.array([270.])
windSpeeds = np.array([8.0])
windFrequencies = np.array([1.0])
size = np.size(windDirections)
else:
size = 20
windDirections = np.linspace(0, 270, size)
windFrequencies = np.ones(size) / size
wake_model_options = {
'nSamples': 0,
'nRotorPoints': nRotorPoints,
'use_ct_curve': True,
'ct_curve_ct': ct_curve_ct,
'ct_curve_wind_speed': ct_curve_wind_speed,
'interp_type': 1,
'use_rotor_components': False,
'differentiable': differentiable,
'verbose': False,
'variant': "CosineFortran"
}
if MODELS[model] == 'BPA':
# initialize problem
prob = om.Problem(
model=OptAEP(nTurbines=nTurbs,
nDirections=windDirections.size,
nVertices=nVertices,
minSpacing=minSpacing,
differentiable=differentiable,
use_rotor_components=False,
wake_model=gauss_wrapper,
params_IdepVar_func=add_gauss_params_IndepVarComps,
params_IdepVar_args={'nRotorPoints': nRotorPoints},
wake_model_options=wake_model_options,
cp_points=cp_curve_cp.size,
cp_curve_spline=cp_curve_spline,
record_function_calls=True,
runparallel=False))
elif MODELS[model] == 'FLORIS':
# initialize problem
prob = om.Problem(
model=OptAEP(nTurbines=nTurbs,
nDirections=windDirections.size,
nVertices=nVertices,
minSpacing=minSpacing,
differentiable=differentiable,
use_rotor_components=False,
wake_model=floris_wrapper,
cp_points=cp_curve_cp.size,
params_IdepVar_func=add_floris_params_IndepVarComps,
params_IdepVar_args={},
record_function_calls=True))
elif MODELS[model] == 'JENSEN':
# initialize problem
prob = om.Problem(
model=OptAEP(nTurbines=nTurbs,
nDirections=windDirections.size,
nVertices=nVertices,
minSpacing=minSpacing,
differentiable=False,
use_rotor_components=False,
wake_model=jensen_wrapper,
wake_model_options=wake_model_options,
params_IdepVar_func=add_jensen_params_IndepVarComps,
params_IdepVar_args={},
runparallel=False,
record_function_calls=True))
else:
ValueError(
'The %s model is not currently available. Please select BPA or FLORIS'
% (MODELS[model]))
# prob.model.deriv_options['type'] = 'fd'
# prob.model.deriv_options['form'] = 'central'
# prob.model.deriv_options['step_size'] = 1.0e-8
# prob.model.linear_solver = om.LinearBlockGS()
# prob.model.linear_solver.options['iprint'] = 0
# prob.model.linear_solver.options['maxiter'] = 5
#
# prob.model.nonlinear_solver = om.NonlinearBlockGS()
# prob.model.nonlinear_solver.options['iprint'] = 0
# prob.model.linear_solver = om.DirectSolver()
prob.driver = om.pyOptSparseDriver()
if opt_algorithm == 'snopt':
# set up optimizer
prob.driver.options['optimizer'] = 'SNOPT'
prob.driver.options['gradient method'] = 'snopt_fd'
# set optimizer options
prob.driver.opt_settings['Verify level'] = 3
# set optimizer options
prob.driver.opt_settings['Major optimality tolerance'] = 1e-4
prob.driver.opt_settings[
'Print file'] = output_directory + 'SNOPT_print_multistart_%iturbs_%sWindRose_%idirs_%sModel_RunID%i.out' % (
nTurbs, wind_rose_file, size, MODELS[model], run_number)
prob.driver.opt_settings[
'Summary file'] = output_directory + 'SNOPT_summary_multistart_%iturbs_%sWindRose_%idirs_%sModel_RunID%i.out' % (
nTurbs, wind_rose_file, size, MODELS[model], run_number)
prob.model.add_constraint('sc',
lower=np.zeros(
int(((nTurbs - 1.) * nTurbs / 2.))),
scaler=1E-2) # ,
# active_tol=(2. * rotor_diameter) ** 2)
prob.model.add_constraint('boundaryDistances',
lower=(np.zeros(1 * turbineX.size)),
scaler=1E-2) # ,
# active_tol=2. * rotor_diameter)
prob.driver.options['dynamic_derivs_sparsity'] = True
elif opt_algorithm == 'ga':
prob.driver.options['optimizer'] = 'NSGA2'
prob.driver.opt_settings['PrintOut'] = 1
prob.driver.opt_settings['maxGen'] = 50000
prob.driver.opt_settings['PopSize'] = 10 * nTurbines * 2
# prob.driver.opt_settings['pMut_real'] = 0.001
prob.driver.opt_settings['xinit'] = 1
prob.driver.opt_settings['rtol'] = 1E-4
prob.driver.opt_settings['atol'] = 1E-4
prob.driver.opt_settings['min_tol_gens'] = 200
prob.driver.opt_settings['file_number'] = run_number
prob.model.add_constraint('sc',
lower=np.zeros(
int(((nTurbs - 1.) * nTurbs / 2.))),
scaler=1E-2)
prob.model.add_constraint('boundaryDistances',
lower=(np.zeros(1 * turbineX.size)),
scaler=1E-2)
elif opt_algorithm == 'ps':
prob.driver.options['optimizer'] = 'ALPSO'
prob.driver.opt_settings['fileout'] = 1
prob.driver.opt_settings[
'filename'] = output_directory + 'ALPSO_summary_multistart_%iturbs_%sWindRose_%idirs_%sModel_RunID%i.out' % (
nTurbs, wind_rose_file, size, MODELS[model], run_number)
prob.driver.opt_settings['maxOuterIter'] = 10000
prob.driver.opt_settings['SwarmSize'] = 24
prob.driver.opt_settings[
'xinit'] = 1 # Initial Position Flag (0 - no position, 1 - position given)
prob.driver.opt_settings[
'Scaling'] = 1 # Design Variables Scaling Flag (0 - no scaling, 1 - scaling between [-1, 1])
# prob.driver.opt_settings['rtol'] = 1E-3 # Relative Tolerance for Lagrange Multipliers
#
# prob.driver.opt_settings['atol'] = 1E-2 # Absolute Tolerance for Lagrange Function
#
# prob.driver.opt_settings['dtol'] = 1E-1 # Relative Tolerance in Distance of All Particles to Terminate (GCPSO)
#
# prob.driver.opt_settings['itol'] = 1E-3 # Absolute Tolerance for Inequality constraints
#
# prob.driver.opt_settings['dynInnerIter'] = 1 # Dynamic Number of Inner Iterations Flag
prob.model.add_constraint('sc',
lower=np.zeros(
int(((nTurbs - 1.) * nTurbs / 2.))),
scaler=1E-2)
prob.model.add_constraint('boundaryDistances',
lower=(np.zeros(1 * turbineX.size)),
scaler=1E-2)
# prob.driver.add_objective('obj', scaler=1E0)
prob.model.add_objective('obj', scaler=1E0)
# select design variables
prob.model.add_design_var('turbineX',
scaler=1E3,
lower=np.zeros(nTurbines),
upper=np.ones(nTurbines) * 3. * boundary_radius)
prob.model.add_design_var('turbineY',
scaler=1E3,
lower=np.zeros(nTurbines),
upper=np.ones(nTurbines) * 3. * boundary_radius)
# prob.model.ln_solver.options['single_voi_relevance_reduction'] = True
# prob.model.ln_solver.options['mode'] = 'rev'
# if run_number == 0:
# # set up recorder
# recorder = SqliteRecorder(output_directory+'recorder_database_run%i' % run_number)
# recorder.options['record_params'] = True
# recorder.options['record_metadata'] = False
# recorder.options['record_unknowns'] = True
# recorder.options['record_derivs'] = False
# recorder.options['includes'] = ['turbineX', 'turbineY', 'AEP']
# prob.driver.add_recorder(recorder)
# recorder = om.SqliteRecorder(output_directory + 'recorded_data.sql')
# # prob.driver.add_recorder(recorder)
# # prob.driver.recording_options['includes'] = ['']
# # prob.driver.recording_options['excludes'] = ['*']
# # prob.driver.recording_options['record_constraints'] = False
# # prob.driver.recording_options['record_derivatives'] = False
# # prob.driver.recording_options['record_desvars'] = False
# # prob.driver.recording_options['record_inputs'] = False
# # prob.driver.recording_options['record_model_metadata'] = True
# # prob.driver.recording_options['record_objectives'] = False
# # prob.driver.recording_options['record_responses'] = False
# set up profiling
# from plantenergy.GeneralWindFarmComponents import WindFarmAEP
# methods = [
# ('*', (WindFarmAEP,))
# ]
#
# iprofile.setup(methods=methods)
print("almost time for setup")
tic = time.time()
print("entering setup at time = ", tic)
prob.setup(check=True)
toc = time.time()
print("setup complete at time = ", toc)
# print the results
print(('Problem setup took %.03f sec.' % (toc - tic)))
# assign initial values to design variables
prob['turbineX'] = np.copy(turbineX)
prob['turbineY'] = np.copy(turbineY)
for direction_id in range(0, windDirections.size):
prob['yaw%i' % direction_id] = yaw
# assign values to constant inputs (not design variables)
prob['rotorDiameter'] = rotorDiameter
prob['hubHeight'] = hubHeight
prob['axialInduction'] = axialInduction
prob['generatorEfficiency'] = generatorEfficiency
prob['windSpeeds'] = windSpeeds
prob['air_density'] = air_density
prob['windDirections'] = windDirections
prob['windFrequencies'] = windFrequencies
prob['Ct_in'] = Ct
prob['Cp_in'] = Cp
prob['cp_curve_cp'] = cp_curve_cp
prob['cp_curve_wind_speed'] = cp_curve_wind_speed
cutInSpeeds = np.ones(nTurbines) * cut_in_speed
prob['cut_in_speed'] = cutInSpeeds
ratedPowers = np.ones(nTurbines) * rated_power
prob['rated_power'] = ratedPowers
# assign values to turbine states
prob['cut_in_speed'] = np.ones(nTurbines) * cut_in_speed
prob['cut_out_speed'] = np.ones(nTurbines) * cut_out_speed
prob['rated_power'] = np.ones(nTurbines) * rated_power
prob['rated_wind_speed'] = np.ones(nTurbines) * rated_wind_speed
prob['use_power_curve_definition'] = True
prob['gen_params:CTcorrected'] = True
prob['gen_params:CPcorrected'] = True
# assign boundary values
prob['boundary_center'] = np.array([boundary_center_x, boundary_center_y])
prob['boundary_radius'] = boundary_radius
if MODELS[model] is 'BPA':
prob['model_params:wake_combination_method'] = np.copy(
wake_combination_method)
prob['model_params:ti_calculation_method'] = np.copy(
ti_calculation_method)
prob['model_params:wake_model_version'] = np.copy(wake_model_version)
prob['model_params:wec_factor'] = 1.0
prob['model_params:wec_spreading_angle'] = 0.0
prob['model_params:calc_k_star'] = np.copy(calc_k_star_calc)
prob['model_params:sort'] = np.copy(sort_turbs)
prob['model_params:z_ref'] = np.copy(z_ref)
prob['model_params:z_0'] = np.copy(z_0)
prob['model_params:ky'] = np.copy(k_calc)
prob['model_params:kz'] = np.copy(k_calc)
prob['model_params:print_ti'] = np.copy(print_ti)
prob['model_params:shear_exp'] = np.copy(shear_exp)
prob['model_params:I'] = np.copy(TI)
prob['model_params:sm_smoothing'] = np.copy(sm_smoothing)
prob['model_params:WECH'] = WECH
if nRotorPoints > 1:
prob['model_params:RotorPointsY'], prob[
'model_params:RotorPointsZ'] = sunflower_points(nRotorPoints)
elif MODELS[model] is 'Jensen':
prob['model_params:spread_angle'] = 20.0
prob.run_model()
AEP_init_calc = np.copy(prob['AEP'])
print(AEP_init_calc * 1E-6)
if MODELS[model] is 'BPA':
prob['model_params:ti_calculation_method'] = np.copy(ti_opt_method)
prob['model_params:calc_k_star'] = np.copy(calc_k_star_opt)
prob.run_model()
AEP_init_opt = np.copy(prob['AEP'])
AEP_run_opt = np.copy(AEP_init_opt)
print(AEP_init_opt * 1E-6)
config.obj_func_calls_array[:] = 0.0
config.sens_func_calls_array[:] = 0.0
expansion_factor_last = 0.0
tict = time.time()
if relax:
for expansion_factor, i in zip(
expansion_factors,
np.arange(0, expansion_factors.size)): # best so far
# print("func calls: ", config.obj_func_calls_array, np.sum(config.obj_func_calls_array))
# print("grad func calls: ", config.sens_func_calls_array, np.sum(config.sens_func_calls_array))
# AEP_init_run_opt = prob['AEP']
if expansion_factor_last == expansion_factor:
ti_opt_method = np.copy(final_ti_opt_method)
print("starting run with exp. fac = ", expansion_factor)
if opt_algorithm == 'snopt':
prob.driver.opt_settings['Print file'] = output_directory + \
'SNOPT_print_multistart_%iturbs_%sWindRose_%idirs_%sModel_RunID%i_EF%.3f_TItype%i.out' % (
nTurbs, wind_rose_file, size, MODELS[model], run_number,
expansion_factor, ti_opt_method)
prob.driver.opt_settings['Summary file'] = output_directory + \
'SNOPT_summary_multistart_%iturbs_%sWindRose_%idirs_%sModel_RunID%i_EF%.3f_TItype%i.out' % (
nTurbs, wind_rose_file, size, MODELS[model], run_number,
expansion_factor, ti_opt_method)
elif opt_algorithm == 'ps':
prob.driver.opt_settings[
'filename'] = output_directory + 'ALPSO_summary_multistart_%iturbs_%sWindRose_%idirs_%sModel_RunID%i.out' % (
nTurbs, wind_rose_file, size, MODELS[model],
run_number)
turbineX = np.copy(prob['turbineX'])
turbineY = np.copy(prob['turbineY'])
prob['turbineX'] = np.copy(turbineX)
prob['turbineY'] = np.copy(turbineY)
if MODELS[model] is 'BPA':
prob['model_params:ti_calculation_method'] = np.copy(
ti_opt_method)
prob['model_params:calc_k_star'] = np.copy(calc_k_star_opt)
if wec_method == 'diam':
prob['model_params:wec_factor'] = np.copy(expansion_factor)
elif wec_method == "hybrid":
prob['model_params:wec_factor'] = np.copy(expansion_factor)
elif wec_method == 'angle':
prob['model_params:wec_spreading_angle'] = np.copy(
expansion_factor)
# run the problem
print('start %s run' % (MODELS[model]))
tic = time.time()
# iprofile.start()
config.obj_func_calls_array[prob.comm.rank] = 0.0
config.sens_func_calls_array[prob.comm.rank] = 0.0
prob.run_driver()
# quit()
toc = time.time()
obj_calls = np.copy(config.obj_func_calls_array[0])
sens_calls = np.copy(config.sens_func_calls_array[0])
# iprofile.stop()
toc = time.time()
# print(np.sum(config.obj_func_calls_array))
# print(np.sum(config.sens_func_calls_array))
print('end %s run' % (MODELS[model]))
run_time = toc - tic
# print(run_time, expansion_factor)
AEP_run_opt = np.copy(prob['AEP'])
# print("AEP improvement = ", AEP_run_opt / AEP_init_opt)
if MODELS[model] is 'BPA':
prob['model_params:wec_factor'] = 1.0
prob['model_params:wec_spreading_angle'] = 0.0
prob['model_params:ti_calculation_method'] = np.copy(
ti_calculation_method)
prob['model_params:calc_k_star'] = np.copy(calc_k_star_calc)
prob.run_model()
AEP_run_calc = np.copy(prob['AEP'])
# print("compare: ", aep_run, prob['AEP'])
print("AEP calc improvement = ", AEP_run_calc / AEP_init_calc)
if prob.model.comm.rank == 0:
# if save_aep:
# np.savetxt(output_directory + '%s_multistart_aep_results_%iturbs_%sWindRose_%idirs_%sModel_RunID%i_EF%.3f.txt' % (
# opt_algorithm, nTurbs, wind_rose_file, size, MODELS[model], run_number, expansion_factor),
# np.c_[AEP_init, prob['AEP']],
# header="Initial AEP, Final AEP")
if save_locations:
np.savetxt(
output_directory +
'%s_multistart_locations_%iturbs_%sWindRose_%idirs_%s_run%i_EF%.3f_TItype%i.txt'
% (opt_algorithm, nTurbs, wind_rose_file, size,
MODELS[model], run_number, expansion_factor,
ti_opt_method),
np.c_[turbineX_init, turbineY_init, prob['turbineX'],
prob['turbineY']],
header=
"initial turbineX, initial turbineY, final turbineX, final turbineY"
)
# if save_time:
# np.savetxt(output_directory + '%s_multistart_time_%iturbs_%sWindRose_%idirs_%s_run%i_EF%.3f.txt' % (
# opt_algorithm, nTurbs, wind_rose_file, size, MODELS[model], run_number, expansion_factor),
# np.c_[run_time],
# header="run time")
if save_time and save_aep and rec_func_calls:
output_file = output_directory + '%s_multistart_rundata_%iturbs_%sWindRose_%idirs_%s_run%i.txt' \
% (opt_algorithm, nTurbs, wind_rose_file, size, MODELS[model], run_number)
f = open(output_file, "a")
if i == 0:
header = "run number, exp fac, ti calc, ti opt, aep init calc (kW), aep init opt (kW), " \
"aep run calc (kW), aep run opt (kW), run time (s), obj func calls, sens func calls"
else:
header = ''
np.savetxt(f,
np.c_[run_number, expansion_factor,
ti_calculation_method, ti_opt_method,
AEP_init_calc, AEP_init_opt, AEP_run_calc,
AEP_run_opt, run_time, obj_calls,
sens_calls],
header=header)
f.close()
expansion_factor_last = expansion_factor
else:
# run the problem
print('start %s run' % (MODELS[model]))
# cProfile.run('prob.run_driver()')
if MODELS[model] is 'BPA':
# prob['model_params:wec_factor'] = 1.
prob['model_params:ti_calculation_method'] = np.copy(ti_opt_method)
prob['model_params:calc_k_star'] = np.copy(calc_k_star_opt)
tic = time.time()
# cProfile.run('prob.run_driver()')
config.obj_func_calls_array[prob.comm.rank] = 0.0
config.sens_func_calls_array[prob.comm.rank] = 0.0
prob.run_driver()
# quit()
toc = time.time()
obj_calls = np.copy(config.obj_func_calls_array[0])
sens_calls = np.copy(config.sens_func_calls_array[0])
run_time = toc - tic
AEP_run_opt = np.copy(prob['AEP'])
# print("AEP improvement = ", AEP_run_calc / AEP_init_calc)
if MODELS[model] is 'BPA':
prob['model_params:wec_factor'] = 1.0
prob['model_params:wec_spreading_angle'] = 0.0
prob['model_params:ti_calculation_method'] = np.copy(
ti_calculation_method)
prob['model_params:calc_k_star'] = np.copy(calc_k_star_calc)
prob.run_model()
AEP_run_calc = np.copy(prob['AEP'])
if prob.model.comm.rank == 0:
if save_locations:
np.savetxt(
output_directory +
'%s_multistart_locations_%iturbs_%sWindRose_%idirs_%s_run%i.txt'
% (opt_algorithm, nTurbs, wind_rose_file, size,
MODELS[model], run_number),
np.c_[turbineX_init, turbineY_init, prob['turbineX'],
prob['turbineY']],
header=
"initial turbineX, initial turbineY, final turbineX, final turbineY"
)
if save_time and save_aep and rec_func_calls:
output_file = output_directory + '%s_multistart_rundata_%iturbs_%sWindRose_%idirs_%s_run%i.txt' \
% (opt_algorithm, nTurbs, wind_rose_file, size, MODELS[model], run_number)
f = open(output_file, "a")
header = "run number, ti calc, ti opt, aep init calc (kW), aep init opt (kW), " \
"aep run calc (kW), aep run opt (kW), run time (s), obj func calls, sens func calls"
np.savetxt(f,
np.c_[run_number, ti_calculation_method,
ti_opt_method, AEP_init_calc, AEP_init_opt,
AEP_run_calc, AEP_run_opt, run_time,
obj_calls, sens_calls],
header=header)
f.close()
turbineX_end = np.copy(prob['turbineX'])
turbineY_end = np.copy(prob['turbineY'])
toct = time.time()
total_time = toct - tict
if prob.model.comm.rank == 0:
# print the results
print(('Opt. calculation took %.03f sec.' % (toct - tict)))
for direction_id in range(0, windDirections.size):
print('yaw%i (deg) = ' % direction_id,
prob['yaw%i' % direction_id])
print('turbine X positions in wind frame (m): %s' % prob['turbineX'])
print('turbine Y positions in wind frame (m): %s' % prob['turbineY'])
print('wind farm power in each direction (kW): %s' % prob['dirPowers'])
print('Initial AEP (kWh): %s' % AEP_init_opt)
print('Final AEP (kWh): %s' % AEP_run_calc)
print('AEP improvement: %s' % (AEP_run_calc / AEP_init_calc))
plot_round_farm(turbineX_end,
turbineY_end,
rotor_diameter, [boundary_center_x, boundary_center_y],
boundary_radius,
show_start=show_end)
return 0
RA_line.append(temp_ra_line)
else:
if abs(ny[p]*180/np.pi + 0.001 - dec) < 0.5*float(res):
powout_RA_line.append(float(nz[p]))
RA_line.append(180. - float(nx[p])*180/np.pi)
#if ra_offset it needs to be restarted because it'll start at 180 not 0
if args.ra_offset:
powout_RA_line = [x for _,x in sorted(zip(RA_line,powout_RA_line))]
RA_line = sorted(RA_line)
#janky fix because there's two 360 values at the end
RA_line = [0.] + RA_line[:-1]
powout_RA_line = [powout_RA_line[-1]] + powout_RA_line[:-1]
spline = UnivariateSpline(RA_line, powout_RA_line-np.max(powout_RA_line)/2., s=0)
if len(spline.roots()) != 2:
#print(spline.roots())
#print(ra,dec)
r1 = spline.roots()[-1]
r2 = spline.roots()[0]
else:
r1 = spline.roots()[0]
r2 = spline.roots()[1]
diff = r2 - r1
if diff > 180. and dec != -72.0:
diff = r1 - (r2 -360)
max_ra = r1 - (diff)/2.
else:
max_ra = r1 + (diff)/2.
plotting=(i == 2))
print("histograms made")
plt.figure(-1)
#plt.scatter(redshift[id_ == True], colors[i][id_ == True], s = 0.01, color = 'b', label = "Blue")
#plt.scatter(redshift[id_ == False], colors[i][id_ == False], s = 0.01, color = 'r', label = "Red")
z_edges = np.linspace(min_z, max_z, num=z_step)
z_middles = z_edges[:-1] + (z_edges[1] - z_edges[0]) / 2.
idx = (cuts > 0.0) & (cuts < 1.5)
z_middles = z_middles[idx]
cuts = cuts[idx]
red_con = red_con[idx]
blue_con = blue_con[idx]
if (i == 2):
spl = UnivariateSpline(z_middles, cuts)
rrange = np.linspace(0, 0.35, 1000)
plt.plot(rrange, spl(rrange), 'k-', lw=0.3, label="spline")
plt.ylim([0, 3])
plt.xlim([0.03, 0.33])
plt.legend()
plt.xlabel("z")
plt.ylabel(labels[i])
plt.savefig("%s/%s_vs_z.pdf" % (output_dir, labels[i]))
idx = (red_con > 0.0) & (blue_con > 0.0)
red_con = red_con[idx]
blue_con = blue_con[idx]
contamination = np.sum(red_con) / np.sum(red_con + blue_con)
def MC_variations(dummy,map_id=18388,padding_ratio=a.padding_ratio,map_size=a.map_size,\ sep=a.sep,N_sims=a.N_sims,noise_power=a.noise_power,FWHM=a.FWHM,\ slope=a.slope,lMin=a.lMin,lMax=a.lMax,KKmethod=a.KKmethod): """Compute MC values of estimated quantities (yanked from PaddedPower.padded_estimates)""" print 'Starting %s' %dummy # First compute high-resolution B-mode map from padded-real space map with desired padding ratio from .PaddedPower import MakePaddedPower Bpow=MakePaddedPower(map_id,padding_ratio=padding_ratio,map_size=map_size,sep=sep) # Input directory: inDir=a.root_dir+'%sdeg%s/' %(map_size,sep) # Compute the noise power map using the B-mode map as a template from .NoisePower import noise_map noiseMap=noise_map(powMap=Bpow.copy(),noise_power=noise_power,FWHM=FWHM,windowFactor=Bpow.windowFactor) # Compute total map totMap=Bpow.copy() totMap.powerMap=Bpow.powerMap+noiseMap.powerMap # Apply the KK estimators from .KKtest import zero_estimator #A_est,fs_est,fc_est,Afs_est,Afc_est=zero_estimator(totMap.copy(),lMin=lMin,lMax=lMax,slope=slope,factor=1e-10,FWHM=FWHM,noise_power=noise_power,KKmethod=KKmethod) # (Factor is expected monpole amplitude (to speed convergence)) # Compute anisotropy fraction and angle #ang_est=0.25*180./np.pi*np.arctan(Afs_est/Afc_est) # in degrees #frac_est=np.sqrt(fs_est**2.+fc_est**2.) ## Run MC Simulations # First compute 1D power spectrum by binning in annuli from hades.PowerMap import oneD_binning l_cen,mean_pow = oneD_binning(totMap.copy(),0.8*a.lMin,1.*a.lMax,0.8*a.l_step,binErr=False,windowFactor=Bpow.windowFactor) # gives central binning l and mean power in annulus using window function corrections (from unpaddded map) # Compute univariate spline model fit to 1D power spectrum from scipy.interpolate import UnivariateSpline spline_fun = UnivariateSpline(np.log10(l_cen),np.log10(mean_pow),k=4) # compute spline of log data def model_power(ell): return 10.**spline_fun(np.log10(ell)) # this estimates 1D spectrum for any ell # Initialise arrays A_MC,fs_MC,fc_MC,Afs_MC,Afc_MC,epsilon_MC,ang_MC=[],[],[],[],[],[],[] from hades.NoisePower import single_MC for n in range(N_sims): # for each MC map MC_map=single_MC(totMap.copy(),model_power,windowFactor=Bpow.windowFactor) # create random map from isotropic spectrum output=zero_estimator(MC_map.copy(),lMin=lMin,lMax=lMax,slope=slope,factor=1e-10,FWHM=FWHM,noise_power=noise_power,KKmethod=KKmethod) # compute MC anisotropy parameters A_MC.append(output[0]) fs_MC.append(output[1]) fc_MC.append(output[2]) Afs_MC.append(output[3]) Afc_MC.append(output[4]) epsilon_MC.append(np.sqrt(output[1]**2.+output[2]**2.)) ang_MC.append(0.25*180./np.pi*np.arctan(output[3]/output[4])) return A_MC,fs_MC,fc_MC,Afs_MC,Afc_MC,epsilon_MC,ang_MC
def lrs_distortion(input_model, reference_files):
"""
The LRS-FIXEDSLIT and LRS-SLITLESS WCS pipeline.
Transform from subarray (x, y) to (v2, v3, lambda) using
the "specwcs" and "distortion" reference files.
"""
# subarray to full array transform
subarray2full = subarray_transform(input_model)
# full array to v2v3 transform for the ordinary imager
with DistortionModel(reference_files['distortion']) as dist:
distortion = dist.model
# Combine models to create subarray to v2v3 distortion
if subarray2full is not None:
subarray_dist = subarray2full | distortion
else:
subarray_dist = distortion
# Read in the reference table data and get the zero point (SIAF reference point)
# of the LRS in the subarray ref frame
# We'd like to open this file as a DataModel, so we can consolidate
# the S3 URI handling to one place. The S3-related code here can
# be removed once that has been changed.
if s3_utils.is_s3_uri(reference_files['specwcs']):
ref = fits.open(s3_utils.get_object(reference_files['specwcs']))
else:
ref = fits.open(reference_files['specwcs'])
with ref:
lrsdata = np.array([d for d in ref[1].data])
# Get the zero point from the reference data.
# The zero_point is X, Y (which should be COLUMN, ROW)
# These are 1-indexed in CDP-7 (i.e., SIAF convention) so must be converted to 0-indexed
if input_model.meta.exposure.type.lower() == 'mir_lrs-fixedslit':
zero_point = ref[0].header['imx'] - 1, ref[0].header['imy'] - 1
elif input_model.meta.exposure.type.lower() == 'mir_lrs-slitless':
zero_point = ref[0].header['imxsltl'] - 1, ref[0].header['imysltl'] - 1
# Transform to slitless subarray from full array
zero_point = subarray2full.inverse(zero_point[0], zero_point[1])
# In the lrsdata reference table, X_center,y_center,wavelength describe the location of the
# centroid trace along the detector in pixels relative to nominal location.
# x0,y0(ul) x1,y1 (ur) x2,y2(lr) x3,y3(ll) define corners of the box within which the distortion
# and wavelength calibration was derived
xcen = lrsdata[:, 0]
ycen = lrsdata[:, 1]
wavetab = lrsdata[:, 2]
x0 = lrsdata[:, 3]
y0 = lrsdata[:, 4]
x1 = lrsdata[:, 5]
y2 = lrsdata[:, 8]
# If in fixed slit mode, define the bounding box using the corner locations provided in
# the CDP reference file.
if input_model.meta.exposure.type.lower() == 'mir_lrs-fixedslit':
bb_sub = ((np.floor(x0.min() + zero_point[0]) - 0.5, np.ceil(x1.max() + zero_point[0]) + 0.5),
(np.floor(y2.min() + zero_point[1]) - 0.5, np.ceil(y0.max() + zero_point[1]) + 0.5))
# If in slitless mode, define the bounding box X locations using the subarray x boundaries
# and the y locations using the corner locations in the CDP reference file. Make sure to
# omit the 4 reference pixels on the left edge of slitless subarray.
if input_model.meta.exposure.type.lower() == 'mir_lrs-slitless':
bb_sub = ((input_model.meta.subarray.xstart - 1 + 4 - 0.5, input_model.meta.subarray.xsize - 1 + 0.5),
(np.floor(y2.min() + zero_point[1]) - 0.5, np.ceil(y0.max() + zero_point[1]) + 0.5))
# Find the ROW of the zero point
row_zero_point = zero_point[1]
# The inputs to the "detector_to_v2v3" transform are
# - the indices in x spanning the entire image row
# - y is the y-value of the zero point
# This is equivalent of making a vector of x, y locations for
# every pixel in the reference row
const1d = models.Const1D(row_zero_point)
const1d.inverse = models.Const1D(row_zero_point)
det_to_v2v3 = models.Identity(1) & const1d | subarray_dist
# Now deal with the fact that the spectral trace isn't perfectly up and down along detector.
# This information is contained in the xcenter/ycenter values in the CDP table, but we'll handle it
# as a simple rotation using a linear fit to this relation provided by the CDP.
z = np.polyfit(xcen, ycen, 1)
slope = 1. / z[0]
traceangle = np.arctan(slope) * 180. / np.pi # trace angle in degrees
rot = models.Rotation2D(traceangle) # Rotation model
# Now include this rotation in our overall transform
# First shift to a frame relative to the trace zeropoint, then apply the rotation
# to correct for the curved trace. End in a rotated frame relative to zero at the reference point
# and where yrot is aligned with the spectral trace)
xysubtoxyrot = models.Shift(-zero_point[0]) & models.Shift(-zero_point[1]) | rot
# Next shift back to the subarray frame, and then map to v2v3
xyrottov2v3 = models.Shift(zero_point[0]) & models.Shift(zero_point[1]) | det_to_v2v3
# The two models together
xysubtov2v3 = xysubtoxyrot | xyrottov2v3
# Work out the spectral component of the transform
# First compute the reference trace in the rotated-Y frame
xcenrot, ycenrot = rot(xcen, ycen)
# The input table of wavelengths isn't perfect, and the delta-wavelength
# steps show some unphysical behaviour
# Therefore fit with a spline for the ycenrot->wavelength transform
# Reverse vectors so that yinv is increasing (needed for spline fitting function)
yrev = ycenrot[::-1]
wrev = wavetab[::-1]
# Spline fit with enforced smoothness
spl = UnivariateSpline(yrev, wrev, s=0.002)
# Evaluate the fit at the rotated-y reference points
wavereference = spl(yrev)
# wavereference now contains the wavelengths corresponding to regularly-sampled ycenrot, create the model
wavemodel = models.Tabular1D(lookup_table=wavereference, points=yrev, name='waveref',
bounds_error=False, fill_value=np.nan)
# Now construct the inverse spectral transform.
# First we need to create a spline going from wavereference -> ycenrot
spl2 = UnivariateSpline(wavereference[::-1], ycenrot, s=0.002)
# Make a uniform grid of wavelength points from min to max, sampled according
# to the minimum delta in the input table
dw = np.amin(np.absolute(np.diff(wavereference)))
wmin = np.amin(wavereference)
wmax = np.amax(wavereference)
wgrid = np.arange(wmin, wmax, dw)
# Evaluate the rotated y locations of the grid
ygrid = spl2(wgrid)
# ygrid now contains the rotated y pixel locations corresponding to
# regularly-sampled wavelengths, create the model
wavemodel.inverse = models.Tabular1D(lookup_table=ygrid, points=wgrid, name='waverefinv',
bounds_error=False, fill_value=np.nan)
# Wavelength barycentric correction
try:
velosys = input_model.meta.wcsinfo.velosys
except AttributeError:
pass
else:
if velosys is not None:
velocity_corr = velocity_correction(input_model.meta.wcsinfo.velosys)
wavemodel = wavemodel | velocity_corr
log.info("Applied Barycentric velocity correction : {}".format(velocity_corr[1].amplitude.value))
# Construct the full distortion model (xsub,ysub -> v2,v3,wavelength)
lrs_wav_model = xysubtoxyrot | models.Mapping([1], n_inputs=2) | wavemodel
dettotel = models.Mapping((0, 1, 0, 1)) | xysubtov2v3 & lrs_wav_model
# Construct the inverse distortion model (v2,v3,wavelength -> xsub,ysub)
# Transform to get xrot from v2,v3
v2v3toxrot = subarray_dist.inverse | xysubtoxyrot | models.Mapping([0], n_inputs=2)
# wavemodel.inverse gives yrot from wavelength
# v2,v3,lambda -> xrot,yrot
xform1 = v2v3toxrot & wavemodel.inverse
dettotel.inverse = xform1 | xysubtoxyrot.inverse
# Bounding box is the subarray bounding box, because we're assuming subarray coordinates passed in
dettotel.bounding_box = bb_sub[::-1]
return dettotel
def D_p(self, N):
yn11 = self.sol()[:, 4]
ynn11 = UnivariateSpline(self.n1, yn11, k=3, s=0)
return ynn11(N)
err = err2[:, 0]
nn_err = np.loadtxt('./NNerr.csv', delimiter=',')
nn_err = np.abs(nn_err)
print(np.mean(err))
print(np.max(err))
print(np.min(err))
print(np.mean(nn_err))
print(np.max(nn_err))
print(np.min(nn_err))
plt.plot(Y_pred[:, 0], label='PLS预测辛烷值')
plt.plot(trainY[:, 0], label='实际辛烷值')
ecdf = sm.distributions.ECDF(err)
x = np.linspace(min(err), max(err))
y = ecdf(x)
func = UnivariateSpline(x, y)
xnew = np.arange(min(err), max(err), 0.000001)
ynew = func(xnew)**q
plt.plot(xnew, ynew, 'b-', label='PLS')
ecdf = sm.distributions.ECDF(nn_err)
x = np.linspace(min(nn_err), max(nn_err))
y = ecdf(x)
func = UnivariateSpline(x, y)
xnew = np.arange(min(err), max(err), 0.000001)
ynew = func(xnew)**q
plt.plot(xnew, ynew, 'r-', label='BP')
plt.xlabel('相对误差')
plt.ylabel('累积概率')
plt.title('CDF')
while k < data_set[j][0][-1]:
output_x.append(k)
k += step_size
output_y = t(output_x)
for m in range(len(output_x)):
line = str(output_x[m])
line = line+" "+str(output_y[m])+"\n"
output.write(line)
single_orb = []
single_orb.append(output_x)
single_orb.append(output_y)
# store single_orb into data_set
output_set.append(single_orb)
# open graphs to show final output
# comment out below to circumvent graphing
v = UnivariateSpline(output_x, output_y, k=5, s=0.0)
psi_d = v(output_x,1)
psi_dd = v(output_x,2)
psi_ddd = v(output_x,3)
pyl.close()
pyl.figure(1)
pyl.subplot(511)
pyl.title('compare input (red) and output (blue)' )
pyl.xlabel('r')
pyl.ylabel('Psi(r)')
pyl.semilogy(data_set[j][0], data_set[j][1],'-r')
pyl.semilogy(output_set[j][0], output_set[j][1],'-b')
pyl.subplot(512)
pyl.xlabel('r')
pyl.ylabel('Psi(r)')
pyl.plot(data_set[j][0], data_set[j][1],'-r')
def get_Paz(self, az_data, R_data, jns):
"""
Computes probability of line of sight acceleration at projected R : P(az|R)
"""
# Under construction !!!
# Return P(az|R)
az_data = abs(az_data) # Consider only positive values
# Assumes units of az [m/s^2] if self.G ==0.004302, else models units
# Conversion factor from [pc (km/s)^2/Msun] -> [m/s^2]
az_fac = 1. / 3.0857e10 if (self.G == 0.004302) else 1
if (R_data < self.rt):
nz = self.nstep # Number of z value equal to number of r values
zt = sqrt(self.rt**2 - R_data**2) # maximum z value at R
z = numpy.logspace(log10(self.r[1]), log10(zt), nz)
spl_Mr = UnivariateSpline(self.r, self.mc, s=0,
ext=1) # Spline for enclosed mass
r = sqrt(R_data**2 + z**2) # Local r array
az = self.G * spl_Mr(r) * z / r**3 # Acceleration along los
az[-1] = self.G * spl_Mr(
self.rt) * zt / self.rt**3 # Ensure non-zero final data point
az *= az_fac # convert to [m/s^2]
az_spl = UnivariateSpline(
z, az, k=4, s=0,
ext=1) # 4th order needed to find max (can be done easier?)
zmax = az_spl.derivative().roots(
) # z where az = max(az), can be done without 4th order spline?
azt = az[-1] # acceleration at the max(z) = sqrt(r_t**2 - R**2)
# Setup spline for rho(z)
if jns == 0 and self.nmbin == 1:
rho = self.rho
else:
rho = self.rhoj[jns]
rho_spl = UnivariateSpline(self.r, rho, ext=1, s=0)
rhoz = rho_spl(sqrt(z**2 + R_data**2))
rhoz_spl = UnivariateSpline(z, rhoz, ext=1, s=0)
# Now compute P(a_z|R)
# There are 2 possibilities depending on R:
# (1) the maximum acceleration occurs within the cluster boundary, or
# (2) max(a_z) = a_z,t (this happens when R ~ r_t)
nr, k = nz, 3 # bit of experimenting
# Option (1): zmax < max(z)
if len(zmax) > 0:
zmax = zmax[
0] # Take first entry for the rare cases with multiple peaks
# Set up 2 splines for the inverse z(a_z) for z < zmax and z > zmax
z1 = numpy.linspace(z[0], zmax, nr)
z2 = (numpy.linspace(zmax, z[-1],
nr))[::-1] # Reverse z for ascending az
z1_spl = UnivariateSpline(az_spl(z1), z1, k=k, s=0, ext=1)
z2_spl = UnivariateSpline(az_spl(z2), z2, k=k, s=0, ext=1)
# Option 2: zmax = max(z)
else:
zmax = z[-1]
z1 = numpy.linspace(z[0], zmax, nr)
z1_spl = UnivariateSpline(az_spl(z1), z1, k=k, s=0, ext=1)
# Maximum acceleration along this los
azmax = az_spl(zmax)
# Now determine P(az_data|R)
if (az_data < azmax):
z1 = max([z1_spl(az_data),
z[0]]) # first radius where az = az_data
Paz = rhoz_spl(z1) / abs(az_spl.derivatives(z1)[1])
if (az_data > azt):
# Find z where a_z = a_z,t
z2 = z2_spl(az_data)
Paz += rhoz_spl(z2) / abs(az_spl.derivatives(z2)[1])
# Normalize to 1
Paz /= rhoz_spl.integral(0, zt)
self.z = z
self.az = az
self.Paz = Paz
self.azmax = azmax
self.zmax = zmax
else:
self.Paz = 0
else:
self.Paz = 0
return