def curve(request, id):
farmer = Location.objects.get(id=id)
longitude = farmer.lng
latitude = farmer.lat
url = "http://vedas.sac.gov.in:8080/LeanGeo/api/band_val/NDVI_PROBA?latitude=" + latitude + "&longitude=" + longitude
r = requests.get(url)
data = r.json()
x = []
y = []
num = 0
for dat in data:
x.append(dat["time"])
y.append(dat["value"])
#x = [index for index in xrange(0,len(data))]
x = ar(x)
y = ar(y)
box = np.ones(3) / 3
js = []
yhat = np.convolve(y, box, mode='same')
old_y = list(y)
new_x = []
x = list(x)
for nx in x:
new_x.append(str(nx))
new_y = []
yhat = list(yhat)
for ny in yhat:
new_y.append(ny)
data = {"x": new_x, "y": new_y, "old_y": old_y}
return JsonResponse(data)
def triangular_prism():
width = random.randint(4,12)
height = random.randint(3,6)
depth = random.randint(2,8)
points = [((0,0),(width,0)),
((width,0),(0,height)),
((0,height),(0,0))]
point1 = (width+depth, 0+depth/2)
point2 = (depth, height + depth/2)
points = points + [((width, 0), point1), ((0, height), point2), (point1, point2)]
points = ar(points)
edges_for_labels = ar([points[2][0], points[2][1], points[0][1], point1])
label_points = labels_for_shape(edges_for_labels)
labels = [str(height), str(width), str(depth)]
fig = plot_shape_byedge(points, label_points, labels)
plt.text(width/3,height/3,'Volume = ?', horizontalalignment='center', verticalalignment='center', fontsize = 'large')
r = random.randint(0, 999999999999999)
fn = 'temp_img/temp' + str(r) + '.png'
fig.savefig('media/' + fn, bbox_inches='tight', pad_inches=0, transparent=True)
question = fn
answer = str(width * height* depth)
return question, answer
def cuboid():
width = random.randint(4,12)
height = random.randint(3,6)
depth = random.randint(2,8)
units = random.choice(['mm','cm','m'])
points = [((0,0),(width,0)),
((width,0),(width,height)),
((width,height),(0, height)),
((0,height),(0,0))]
point1 = (width+depth, 0+depth/2)
point2 = (width+depth, height + depth/2)
point3 = (depth, height + depth/2)
points = points + [((width, 0), point1), ((width, height), point2), ((0, height), point3), (point1, point2), (point2, point3)]
points = ar(points)
edges_for_labels = ar([points[3][0], points[0][0], points[4][0], points[4][1]])
label_points = labels_for_shape(edges_for_labels)
labels = [str(height)+units, str(width)+units, str(depth)+units]
fig = plot_shape_byedge(points, label_points, labels)
plt.text(width/2,height/2,'Volume = ?', horizontalalignment='center', verticalalignment='center', fontsize = 'large')
r = random.randint(0, 999999999999999)
fn = 'temp_img/temp' + str(r) + '.png'
fig.savefig('media/' + fn, bbox_inches='tight', pad_inches=0, transparent=True)
question = fn
answer = '$' + str(width * height* depth) + units + '^3$'
return question, answer
def sinFit(xs, ys, paraW=None):
dataX = [float(s) for s in xs]
dataY = [float(s) for s in ys]
def sinFunction(x, a, w, p, b):
return a * sin(w * x + p) + b
x = ar(dataX)
y = ar(dataY)
def stdev(data):
ave = sum(data) / len(data)
sumI = 0
for d in data:
sumI += (d - ave)**2
return math.sqrt(sumI / (len(data) - 1))
average = sum(y) / len(y)
stv = stdev(y)
w = paraW if (paraW is not None) else 2 * math.pi / (x[-1] - x[0])
preP = [stv * math.sqrt(2), w, 0, average]
print(preP)
popt, pcov = curve_fit(sinFunction, x, y, p0=preP)
result = [i for i in popt]
print(result)
print()
return result
def peak_finder(array, lower, upper, count_offset):
'''
Peak Finder for Potassium. Needs more development
'''
points = ar(range(lower, upper))
peak = list(array[lower:upper])
counts = ar(peak)
nentries = len(points)
mean = lower + (upper - lower) / 2.0
slope = 2 * (np.log(counts[-1]) - np.log(counts[0])) / (points[-1] -
points[0])
pinit = [counts[0] / 2.0, mean, 5.0, counts[0] * count_offset, slope]
errfunc = lambda p, x, y: gaus_plus_exp(x, p) - y
pfit,pcov,infodict,errmsg,success = \
optimize.leastsq(errfunc, pinit, args=(points,counts), \
full_output=1, epsfcn=0.0001)
if (len(counts) > len(pinit)) and pcov is not None:
s_sq = (errfunc(pfit, points, counts)**
2).sum() / (len(counts) - len(pinit))
pcov = pcov * s_sq
else:
pcov = 0
error = []
for i in range(len(pfit)):
try:
error.append(np.absolute(pcov[i][i])**0.5)
except:
error.append(0.00)
pfit_leastsq = pfit
perr_leastsq = np.array(error)
return pfit_leastsq, perr_leastsq
def Generate(self):
for i in range(0, 90):
self.x.append(i / 30.)
self.y.append(math.sin(i/30.)+random.uniform \
(-self.noice_level,self.noice_level))
self.x = ar(self.x)
self.y = ar(self.y)
def Generate(self): for i in range(0,90): self.x.append(i/30.) self.y.append(math.sin(i/30.)+random.uniform \ (-self.noice_level,self.noice_level)) self.x = ar(self.x) self.y = ar(self.y)
def double_peak_finder(array, lower, upper):
'''
Fits double gaussian + exponential to data within some window
- fit is applied only to data within the upper/lower channel
boundaries provided as inputs
Arguments:
- full array of data
- lower and upper channel values for the fit window
Returns:
- list of fit parameters and list of parameter errors
'''
points = ar(range(lower, upper))
peak = list(array[lower:upper])
counts = ar(peak)
# Initialize fit parameters based on rough estimates of mean,sigma,amp,etc.
# - mean estimated as center of fit window - set window accordingly
# - double gaussian means shifted slightly in each direction
# - gaussian amp and expo shift estimated based on counts at left edge
# - expo slope determined using fit window boundaries
nentries = len(points)
mean = lower + (upper - lower) / 2.0
slope = 2 * (np.log(counts[-1]) - np.log(counts[0])) / (points[-1] -
points[0])
pinit = [
counts[0] / 5.0, mean - 2, 5.0, counts[0] / 5.0, mean + 2, 5.0,
counts[0], slope
]
# Currently using leastsq fit from scipy
# - see scipy documentation for more information
errfunc = lambda p, x, y: double_gaus_plus_exp(x, p) - y
pfit,pcov,infodict,errmsg,success = \
optimize.leastsq(errfunc, pinit, args=(points,counts), \
full_output=1, epsfcn=0.0001)
# Calculate fit parameter uncertainties using the covariance matrix
# and the (fit - data) variance
if (len(counts) > len(pinit)) and pcov is not None:
s_sq = (errfunc(pfit, points, counts)**
2).sum() / (len(counts) - len(pinit))
pcov = pcov * s_sq
else:
pcov = 0
error = []
for i in range(len(pfit)):
try:
# This conditional is bad!!
# Artificially sets error to zero if it's too big - remove now!
if np.absolute(pcov[i][i])**0.5 > np.absolute(pfit[i]):
error.append(0.00)
else:
error.append(np.absolute(pcov[i][i])**0.5)
except:
error.append(0.00)
pfit_leastsq = pfit
perr_leastsq = np.array(error)
return pfit_leastsq, perr_leastsq
def get_unary_vector(line, direction=1):
l = line
if l[0] == 0:
return ar([0, 1]) * direction
if l[1] == 0:
return ar([1, 0]) * direction
else:
k = l[1] / l[0]
x = (1 / (1 + 1 / k**2))**0.5
return ar([x, -x / k]) * sign_of(x) * direction
def double_peak_finder(array,lower,upper):
'''
Fits double gaussian + exponential to data within some window
- fit is applied only to data within the upper/lower channel
boundaries provided as inputs
Arguments:
- full array of data
- lower and upper channel values for the fit window
Returns:
- list of fit parameters and list of parameter errors
'''
points = ar(range(lower,upper))
peak = list(array[lower:upper])
counts = ar(peak)
# Initialize fit parameters based on rough estimates of mean,sigma,amp,etc.
# - mean estimated as center of fit window - set window accordingly
# - double gaussian means shifted slightly in each direction
# - gaussian amp and expo shift estimated based on counts at left edge
# - expo slope determined using fit window boundaries
nentries = len(points)
mean = lower + (upper - lower)/2.0
slope = 2*(np.log(counts[-1])-np.log(counts[0]))/(points[-1]-points[0])
pinit = [counts[0]/5.0,mean-2,5.0,counts[0]/5.0,mean+2,5.0,counts[0],slope]
# Currently using leastsq fit from scipy
# - see scipy documentation for more information
errfunc = lambda p, x, y: double_gaus_plus_exp(x,p) - y
pfit,pcov,infodict,errmsg,success = \
optimize.leastsq(errfunc, pinit, args=(points,counts), \
full_output=1, epsfcn=0.0001)
# Calculate fit parameter uncertainties using the covariance matrix
# and the (fit - data) variance
if (len(counts) > len(pinit)) and pcov is not None:
s_sq = (errfunc(pfit, points, counts)**2).sum()/(len(counts)-len(pinit))
pcov = pcov * s_sq
else:
pcov = 0
error = []
for i in range(len(pfit)):
try:
# This conditional is bad!!
# Artificially sets error to zero if it's too big - remove now!
if np.absolute(pcov[i][i])**0.5 > np.absolute(pfit[i]):
error.append( 0.00 )
else:
error.append(np.absolute(pcov[i][i])**0.5)
except:
error.append( 0.00 )
pfit_leastsq = pfit
perr_leastsq = np.array(error)
return pfit_leastsq, perr_leastsq
def GaussFit(X,Y,d):
LL = (np.abs(X-d.ROI_min)).argmin()
UL = (np.abs(X-d.ROI_max)).argmin() + 1
X2 = ar(X[LL:UL])
Y2 = ar(Y[LL:UL])
def gaus(x,a,x0,sigma):
return a*exp(-(x-x0)**2/(2*sigma**2))
popt,pcov = curve_fit(gaus,X2,Y2,p0=d.fit_manual)
return LL,UL,popt
def peak_finder(array, lower, upper, count_offset):
'''
Fits gaussian + exponential to data within some window
- fit is applied only to data within the upper/lower channel
boundaries provided as inputs
Arguments:
- full array of data
- lower and upper channel values for the fit window
- count_offset used to correct exponential fit parameter for the fact that the fit is not starting at the left edge of the spectrum
Returns:
- list of fit parameters and list of parameter errors
'''
points = ar(range(lower, upper))
peak = list(array[lower:upper])
counts = ar(peak)
# Initialize fit parameters based on rough estimates of mean,sigma,amp,etc.
# - mean estimated as center of fit window - set window accordingly
# - gaussian amp and expo shift estimated based on counts at left edge
# - expo slope determined using fit window boundaries
nentries = len(points)
mean = lower + (upper - lower) / 2.0
slope = 2 * (np.log(counts[-1]) - np.log(counts[0])) / (points[-1] -
points[0])
pinit = [counts[0], mean, 5.0, counts[0] * count_offset, slope]
#print('Initial parameters: amp = {0}, mean = {1}, sigma = {2}, amp2 = {3}'.format(pinit[0],pinit[1],pinit[2],pinit[3]))
# Currently using leastsq fit from scipy
# - see scipy documentation for more information
errfunc = lambda p, x, y: gaus_plus_exp(x, p) - y
pfit,pcov,infodict,errmsg,success = \
optimize.leastsq(errfunc, pinit, args=(points,counts), \
full_output=1, epsfcn=0.0001)
#print('after parameters: amp= {0}, mean ={1}, sigma = {2}, amp2 = {3}'.format(pfit[0],pfit[1],pfit[2],pfit[3]))
# Calculate fit parameter uncertainties using the covariance matrix
# and the (fit - data) variance
if (len(counts) > len(pinit)) and pcov is not None:
s_sq = (errfunc(pfit, points, counts)**
2).sum() / (len(counts) - len(pinit))
pcov = pcov * s_sq
else:
pcov = 0
error = []
for i in range(len(pfit)):
try:
error.append(np.absolute(pcov[i][i])**0.5)
except:
error.append(0.00)
pfit_leastsq = pfit
perr_leastsq = np.array(error)
return pfit_leastsq, perr_leastsq
def edge_rebound_velocity(v, segment):
if len(segment) > 2:
return edge_rebound_velocity(v, divide_segment_into_points(segment))
if segment[0][0] == segment[1][0]:
return ar([-v[0], v[1]])
if segment[0][1] == segment[1][1]:
return ar([v[0], -v[1]])
projv = projection_velocity_segment(v, segment)
return 2 * projv - v
'''global m_d
def peak_finder(array,lower,upper,count_offset):
'''
Fits gaussian + exponential to data within some window
- fit is applied only to data within the upper/lower channel
boundaries provided as inputs
Arguments:
- full array of data
- lower and upper channel values for the fit window
- count_offset used to correct exponential fit parameter for the fact that the fit is not starting at the left edge of the spectrum
Returns:
- list of fit parameters and list of parameter errors
'''
points = ar(range(lower,upper))
peak = list(array[lower:upper])
counts = ar(peak)
# Initialize fit parameters based on rough estimates of mean,sigma,amp,etc.
# - mean estimated as center of fit window - set window accordingly
# - gaussian amp and expo shift estimated based on counts at left edge
# - expo slope determined using fit window boundaries
nentries = len(points)
mean = lower + (upper - lower)/2.0
slope = 2*(np.log(counts[-1])-np.log(counts[0]))/(points[-1]-points[0])
pinit = [counts[0],mean,5.0,counts[0]*count_offset,slope]
#print('Initial parameters: amp = {0}, mean = {1}, sigma = {2}, amp2 = {3}'.format(pinit[0],pinit[1],pinit[2],pinit[3]))
# Currently using leastsq fit from scipy
# - see scipy documentation for more information
errfunc = lambda p, x, y: gaus_plus_exp(x,p)-y
pfit,pcov,infodict,errmsg,success = \
optimize.leastsq(errfunc, pinit, args=(points,counts), \
full_output=1, epsfcn=0.0001)
#print('after parameters: amp= {0}, mean ={1}, sigma = {2}, amp2 = {3}'.format(pfit[0],pfit[1],pfit[2],pfit[3]))
# Calculate fit parameter uncertainties using the covariance matrix
# and the (fit - data) variance
if (len(counts) > len(pinit)) and pcov is not None:
s_sq = (errfunc(pfit, points, counts)**2).sum()/(len(counts)-len(pinit))
pcov = pcov * s_sq
else:
pcov = 0
error = []
for i in range(len(pfit)):
try:
error.append(np.absolute(pcov[i][i])**0.5)
except:
error.append( 0.00 )
pfit_leastsq = pfit
perr_leastsq = np.array(error)
return pfit_leastsq, perr_leastsq
def singlePeakGaussianFit(xs, ys):
dataX = [float(s) for s in xs]
dataY = [float(s) for s in ys]
def gaus(x, a, x0, sigma):
return a * exp(-(x - x0) ** 2 / (2 * sigma ** 2))
x = ar(dataX)
y = ar(dataY)
mean = sum(x * y) / sum(y)
sigma = np.sqrt(sum(y * (x - mean) ** 2) / sum(y))
popt, pcov = curve_fit(gaus, x, y, p0=[1, mean, sigma])
result = [i for i in popt]
return result
def linear_line(self, seq):
popt = [0, 0, 0]
pcov = [100, 100, 100]
perr = [100, 100, 100]
try:
row_num = len(seq)
X_ = ar(range(row_num), dtype='float32')
X_ = X_.reshape((row_num, 1))
x = maxminnorm2(X_)
x = np.ravel(x)
Y_ = seq.reshape((row_num, 1))
y = maxminnorm2(Y_)
y = np.ravel(y)
popt, pcov = curve_fit(self.linear_line_func,
x,
y,
p0=[3, 1],
maxfev=10000)
#popt, pcov = curve_fit(self.linear_line_func, x, y, p0=[3, 1], maxfev=10000, bounds=(-1000,[np.inf,np.inf]))
perr = np.sqrt(np.diag(pcov))
#print perr
#print "-------------"
#print popt
#print "333-------------"
#plt.plot(x, seq, 'b+:', label='data')
#plt.plot(x, my_scipy.__linear_line_func(x, *popt), 'ro:', label='fit')
#plt.legend()
#plt.show()
except:
traceback.print_exc()
finally:
if math.isinf(perr[0]) or math.isnan(perr[0]):
return popt, [100, 100, 100]
return popt, perr
def quadraticCurve(self, seq):
popt = [0, 0, 0]
pcov = [100, 100, 100]
perr = [100, 100, 100]
try:
row_num = len(seq)
X_ = ar(range(row_num), dtype='float32')
X_ = X_.reshape((row_num, 1))
x = maxminnorm(X_)
x = np.ravel(x)
Y_ = seq.reshape((row_num, 1))
y = maxminnorm(Y_)
y = np.ravel(y)
popt, pcov = curve_fit(self.quadraticCurve_func,
x,
y,
p0=[3, 4, 3],
maxfev=1000)
perr = np.sqrt(np.diag(pcov))
#plt.plot(x, seq, 'b+:', label='data')
#plt.plot(x, my_scipy.__quadraticCurve_func(x, *popt), 'ro:', label='fit')
#plt.legend()
#plt.show()
except:
traceback.print_exc()
finally:
if math.isinf(perr[0]) or math.isnan(perr[0]):
return popt, [100, 100, 100]
return popt, perr
def labels_for_shape(points):
lbls = []
x_len = max(points[:, 0]) - min(points[:, 0])
y_len = max(points[:, 1]) - min(points[:, 1])
if y_len > x_len:
max_len = y_len
else:
max_len = x_len
centroid = (np.mean(points[:, 0]), np.mean(points[:, 1]))
print(centroid)
delta = max_len / 5
for i in range(len(points) - 1):
temp_lbls = find_label_point(points[i], points[i + 1], delta)
lbl_dists = (np.sqrt(((temp_lbls[0][0] - centroid[0])**2) +
((temp_lbls[0][1] - centroid[1])**2)),
np.sqrt(((temp_lbls[1][0] - centroid[0])**2) +
((temp_lbls[1][1] - centroid[1])**2)))
if lbl_dists[0] > lbl_dists[1]:
lbls.append(temp_lbls[0])
else:
lbls.append(temp_lbls[1])
#for lbl in temp_lbls:
#if is_in_shape([lbl],points) == False:
# lbls.append(lbl)
return ar(lbls)
def get_cell_stats(profiles):
diffs = []
mus = []
sigmas = []
for i in range(len(profiles)):
print(i)
diffs.append(np.nanmax(profiles[i]) - np.nanmin(profiles[i]))
x = ar(range(len(profiles[i])))
y = profiles[i]
# weighted arithmetic mean (corrected - check the section below)
mean = np.nansum(x * y) / np.nansum(y)
sigma = np.sqrt(np.nansum(y * (x - mean)**2) / np.nansum(y))
def Gauss(x, a, x0, sigma):
return a * np.exp(-(x - x0)**2 / (2 * sigma**2))
try:
popt, pcov = curve_fit(Gauss, x, y, p0=[np.nanmax(y), mean, sigma])
mx, mu, sigma = popt
except Exception as e:
print(e)
mu, sigma = np.nan, np.nan
mus.append(mu)
sigmas.append(sigma)
diffs = np.asarray(diffs)
mus = np.asarray(mus)
sigmas = np.asarray(sigmas)
return diffs, mus, sigmas
def GetCCS(x, y): x2 = [1/value for value in x] xaxis = ar(x2) yaxis = ar(y) slope, intercept, r_value, p_value, std_err = scipy.stats.linregress(xaxis, yaxis) K = (25.05**2)/(slope/1000) K0 = K*(273.15/T)*(P/760) Mass = content * Charge reducedMass = (Mass*Drift_Mass)/(Mass+Drift_Mass) CCS = (Charge/K0)*((1/(reducedMass*T))**0.5)*18495.88486 error = (std_err/slope)*CCS error_CCS = (error/CCS)*100 if math.isnan(CCS) == True or math.isnan(error_CCS) == True: return str(False), str(False) else: return CCS, error_CCS
def plot_shape_byedge(shape, lbl_points, lbls):
fig = plt.figure(figsize=(4, 4))
ax = fig.add_subplot(111)
for edge in shape:
plt.plot(edge[:, 0], edge[:, 1], color='#1f77b4', linewidth=4)
for i in range(len(lbls)):
plt.text(lbl_points[i][0],
lbl_points[i][1],
lbls[i],
horizontalalignment='center',
verticalalignment='center',
fontsize='xx-large')
points = []
for sh in shape:
points.append(sh[0])
points.append(sh[1])
points = ar(points)
delta = (max(points[:, 0]) - min(points[:, 0])) / 100
x_min = min(points[:, 0]) - 2
x_max = max(points[:, 0]) + 2
y_min = min(points[:, 1]) - 2
y_max = max(points[:, 1]) + 2
plt.xlim(x_min, x_max)
plt.ylim(y_min, y_max)
ax.set_aspect('equal', adjustable='box')
plt.axis('off')
return fig
def ball_ball_rebound_velocity(ball1, ball2):
center_line = ar([ball1.coords, ball2.coords])
vprojection = projection_velocity_segment(ball2.v, center_line)
m1 = ball1.mass
m2 = ball2.mass
v1 = ball1.v
v2 = vprojection #ball2.v
return ((m1 - m2) * v1 + 2 * m2 * v2) / (m1 + m2)
def get_double_peaks(rows,
number,
n=1,
lower_limit=240,
upper_limit=300,
make_plot=False):
entries = 12 * n
days = (24 / n)
i = 0
counter = 0
means = []
sigmas = []
amps = []
while i < number * days:
if counter < days:
integration = rows[(i * entries) + 1:((i + 1) * entries) + 1]
array_lst = []
for j in integration:
array_lst.append(make_array(j))
integrated = sum(array_lst)
#print integrated
fit_pars, fit_errs = double_peak_finder(integrated, lower_limit,
upper_limit)
mean = [fit_pars[1], fit_errs[1]]
sigma = [fit_pars[2], fit_errs[2]]
amp = [fit_pars[0], fit_errs[0]]
if fit_pars[4] > fit_pars[1]:
mean = [fit_pars[4], fit_errs[4]]
sigma = [fit_pars[5], fit_errs[5]]
amp = [fit_pars[3], fit_errs[3]]
means.append(mean)
sigmas.append(sigma)
amps.append(amp)
counter += 1
i += 1
if make_plot:
fig = plt.figure()
fig.patch.set_facecolor('white')
plt.title('Spectra integrated over a day')
plt.xlabel('channels')
plt.ylabel('counts')
plt.xlim(1, 500)
x = ar(range(0, len(integrated)))
plt.plot(x, integrated, 'b:', label='data')
plt.plot(x,
double_gaus_plus_exp(x, fit_pars),
'ro:',
label='fit')
plt.legend()
plt.yscale('log')
plt.show()
else:
counter = 0
counter = 0
return means, sigmas, amps
def circle_measure(circ_or_area, r_or_d, backwards):
# plotting
radius=random.randint(1,20)
diam=2*radius
circum=diam*math.pi
area = math.pi * (radius**2)
fig = plt.figure(figsize =(2,1))
ax = fig.add_subplot(111)
ax.set_aspect('equal')
plt.axis('off')
plt.xlim(-2,2)
plt.ylim(-1.2,1.2)
circle_r = 1
circle_x = np.arange(-1.1,1.1,.0001)
circle_y = np.sqrt(circle_r**2-np.square(circle_x))
circle_x = np.append(circle_x, circle_x)
circle_y = np.append(circle_y, -1*circle_y)
n = random.randint(0,len(circle_x))
if r_or_d == 0:
rx = [0, circle_x[n]]
ry = [0, circle_y[n]]
else:
rx = [circle_x[n], -1*circle_x[n]]
ry = [circle_y[n], -1*circle_y[n]]
r = [[rx[0],ry[0]],[rx[1],ry[1]]]
label_points = labels_for_shape(ar(r))
plt.plot(circle_x, circle_y, color = '#1f77b4', linewidth = 1.5, solid_capstyle='round')
plt.plot(rx, ry, color = '#1f77b4', linewidth = 1.5,linestyle='--', solid_capstyle='round')
if r_or_d == 0:
plt.text(label_points[0][0],label_points[0][1],str(radius), horizontalalignment='center', verticalalignment='center', fontsize = 'small')
else:
plt.text(label_points[0][0],label_points[0][1],str(diam), horizontalalignment='center', verticalalignment='center', fontsize = 'small')
if circ_or_area == 0:
plt.text(-2,0.8,"C=?", fontsize = 'large')
ans = round(circum,2)
else:
plt.text(-2,0.8,"A=?", fontsize = 'large')
ans = round(area,2)
#fig.tight_layout()
r = random.randint(0, 999999999999999)
fn = 'temp_img/temp' + str(r) + '.png'
fig.savefig('media/' + fn, pad_inches=0.1, dpi=300, transparent=True, bbox_inches='tight')
#return fig
return fn, ans
def get_peaks2(rows, number=1, n=1, lower_limit=900, upper_limit=1020, make_plot = False,count_offset=100):
'''
This is for Tl-208
Applies gaussian + const fits to all data over some range of time
Arguments:
- full list of csv data input rows
- number of days to run over
- number of hours to integrate each calculation over
- lower,upper limits for fit windows
- flag to plot each fit for diagnostics
- count offset correction to fit parameters based on peak position
(peaks farther from the left edge of spectrum need bigger correction)
Returns:
- lists of means,sigmas,amps from all gaussian fits
- each entry in list includes the value and uncertainty
'''
entries = 12*n
days = (24/n)
print('making {} plots for each day'.format(days))
i = 0
counter = 0
means = []
sigmas = []
amps = []
while i < number*days:
if counter < days:
integration = rows[(i*entries)+1:((i+1)*entries)+1]
array_lst = []
for j in integration:
array_lst.append(make_array(j,12))
integrated = sum(array_lst)
#print integrated
fit_pars,fit_errs = peak_finder(integrated,lower_limit,upper_limit,count_offset)
means.append([fit_pars[1],fit_errs[1]])
sigmas.append([fit_pars[2],fit_errs[2]])
amps.append([fit_pars[0],fit_errs[0]])
counter +=1
i+=1
if make_plot:
fig = plt.figure()
fig.patch.set_facecolor('white')
plt.title('Spectra integrated over a day')
plt.xlabel('channels')
plt.ylabel('counts')
plt.xlim(1,1000)
#plt.ylim()
x = ar(range(0,len(integrated)))
plt.plot(x,integrated,'b:',label='data')
plt.plot(x,gaus_plus_const(x,fit_pars),'ro:',label='fit')
plt.legend()
plt.yscale('log')
plt.show()
else:
counter = 0
counter = 0
return means,sigmas,amps
def compose_normal_line(coefs, optcoords=None):
if type(optcoords) != type(None):
ss = compose_normal_line(coefs)
c = 0 - ss[0] * optcoords[0] - ss[1] * optcoords[1]
return ar([ss[0], ss[1], c])
else:
if coefs[0] == 0:
return ar([1, 0, 0])
if coefs[1] == 0:
return ar([0, 1, 0])
else:
if coefs[1] != 1:
return compose_normal_line(ar(coefs) / coefs[1])
a = -1 / coefs[0]
b = coefs[1]
return ar([a, b, 0])
def get_peaks(rows,
number=1,
n=1,
lower_limit=240,
upper_limit=300,
make_plot=False,
count_offset=100):
'''
Gets single gaussian peaks in the specified window
number is the number of days of spectras to go through
n is the number of hours that each spectra is integrated over
lower_limit, upper_limit set the window to look for a peak inside
'''
entries = 12 * n
days = (24 / n)
print('making {} plots for each day'.format(days))
i = 0
counter = 0
means = []
sigmas = []
amps = []
while i < number * days:
if counter < days:
integration = rows[(i * entries) + 1:((i + 1) * entries) + 1]
array_lst = []
for j in integration:
array_lst.append(make_array(j))
integrated = sum(array_lst)
#print integrated
fit_pars, fit_errs = peak_finder(integrated, lower_limit,
upper_limit, count_offset)
means.append([fit_pars[1], fit_errs[1]])
sigmas.append([fit_pars[2], fit_errs[2]])
amps.append([fit_pars[0], fit_errs[0]])
counter += 1
i += 1
if make_plot:
fig = plt.figure()
fig.patch.set_facecolor('white')
plt.title('Spectra integrated over a day')
plt.xlabel('channels')
plt.ylabel('counts')
plt.xlim(1, 500)
#plt.ylim()
x = ar(range(0, len(integrated)))
plt.plot(x, integrated, 'b:', label='data')
plt.plot(x, gaus_plus_exp(x, fit_pars), 'ro:', label='fit')
plt.legend()
plt.yscale('log')
plt.show()
else:
counter = 0
counter = 0
return means, sigmas, amps
def getDistanceData():
Q = []
g = 'BoundaryDistanceArray.csv'
with open('{}'.format(g), 'rb') as mycvsfile:
thedatareader = csv.reader(mycvsfile)
for row in thedatareader:
Q.append(row)
A = Q
A = ar(A)
A = A.astype(numpy.float)
return A
def rotate(self, angle=3.14159 / 4):
# Calculating the center
x = 0
y = 0
vertex_count = 0
for point in self.vertex_list:
x += point[0]
y += point[1]
vertex_count += 1
x = x / vertex_count
y = y / vertex_count
center = (x, y)
# Rotating
self.vertex_list = dot(
ar(self.vertex_list) - center,
ar([[cos(angle), sin(angle)], [-sin(angle),
cos(angle)]])) + center
def importFile(fileLoc):
'''
This code will open up the txt files containing the data.
Parameters:
fileLoc - the file location as a string
Returns:
two arrays of integers:
the first array (channel) is uncalibrated energy
channel
the second array (counts) is number of counts
'''
with open(fileLoc, 'r') as data:
counts = []
channel = []
linenum = 0
for line in data:
n = ""
for char in line:
if char != '\n' and char != ' ':
n += char
counts.append(n)
linenum += 1
for i in range(linenum - 28):
channel.append(i)
counts = counts[12:2060]
i = 0
for num in counts:
num = int(num)
counts[i] = num
i += 1
channels = ar(channel)
counts = ar(counts)
for i in range(
300
): #replacing counts on low end channels with all 0s to remove noise
counts[i] = 0
return channel, counts
def get_away_direction(ball1, ball2):
central_segment = ar([ball1.coords, ball2.coords])
if ball1.coords[0] < ball2.coords[0]:
direction = -1
elif ball1.coords[0] > ball2.coords[0]:
direction = 1
elif ball1.coords[1] < ball2.coords[1]:
direction = -1
else:
direction = 1
return get_unary_vector(compose_equation_line(central_segment), direction)
def shortest_segment_point_segment(point, segment):
if len(segment) > 2:
return shortest_segment_point_segment(
point, divide_segment_into_points(segment))
try:
if len(point[0]) > 1:
return shortest_segment_point_segment(segment, point)
except:
pass
vect1 = segment[0] - point
vect2 = segment[1] - point
try:
if cos_vect(vect1, segment[0] - segment[1]) <= 0:
return ar([point, segment[0]])
if cos_vect(vect2, segment[1] - segment[0]) <= 0:
return ar([point, segment[1]])
except:
a = 9
normal = compose_normal_line(compose_equation_line(segment), point)
return ar(
[point,
find_intersection(normal, compose_equation_line(segment))])
def main(in_fid):
big_list = make_big_list(in_fid)
test_list = [float(x) for x in big_list]
print test_list
m,s = norm.fit(test_list)
n = len(test_list)
x = ar(range(n))
y = ar(test_list)
"""
n = len(test_list)
x = ar(range(n))
y = ar(test_list)
mean = sum(x * y) / n
sigma = np.sqrt(sum(y * (x - mean)**2) / n)
#popt ,pcov = curve_fit(gaus, x, y, p0=[max(y), mean, sigma])
"""
popt ,pcov = curve_fit(gaus, x, y, p0=[203, m, s])
print popt
#plt.plot(x, y)
plt.plot(x,gaus(x,*popt),'ro:',label='fit')
plt.show()
import pylab as plb
import matplotlib.pyplot as plt
from scipy.optimize import curve_fit
from scipy import asarray as ar,exp
x = ar(range(10)) # [0,1,2,3,4,5,6,7,8,9]
y = ar([0,1,2,3,4,5,4,3,2,1])
n = len(x) #the number of data
mean = sum(x*y)/n #note this correction
suma = sum(y*z)
sigma = sum(y*(x-mean)**2)/n #note this correction
def gaus(x,a,x0,sigma):
return a*exp(-(x-x0)**2/(2*sigma**2))
popt,pcov = curve_fit(gaus,x,y,p0=[1,mean,sigma])
resultado = gaus(3, 1, 2, 4)
print 'x:', x
print 'suma', suma
"""
plt.plot(x,y,'b+:',label='data')
plt.plot(x,gaus(x,*popt),'ro:',label='fit')
plt.legend()
plt.title('Fig. 3 - Fit for Time Constant')
plt.xlabel('Time (s)')
plt.ylabel('Voltage (V)')
def get_double_peaks(rows, number, n=1, lower_limit=480, upper_limit=600, make_plot = False):
'''
Applies double gaussian + expo fits to all data over some range of time
Arguments:
- full list of csv data input rows
- number of days to run over
- number of hours to integrate each calculation over
- lower,upper limits for fit windows
- flag to plot each fit for diagnostics
Returns:
- list of means,sigmas,amps for second gaussian in fit
- that's the Bi peak, so this is hard coded to work for a specific case
- each entry in list includes the value and uncertainty
'''
entries = 12*n
days = (24/n)
i = 0
counter = 0
means = []
sigmas = []
amps = []
while i < number*days:
if counter < days:
integration = rows[(i*entries)+1:((i+1)*entries)+1]
array_lst = []
for j in integration:
array_lst.append(make_array(j,12))
integrated = sum(array_lst)
#print integrated
fit_pars, fit_errs = double_peak_finder(integrated,lower_limit,upper_limit)
mean = [fit_pars[1],fit_errs[1]]
sigma = [fit_pars[2],fit_errs[2]]
amp = [fit_pars[0],fit_errs[0]]
if fit_pars[4] > fit_pars[1]:
mean = [fit_pars[4],fit_errs[4]]
sigma = [fit_pars[5],fit_errs[5]]
amp = [fit_pars[3],fit_errs[3]]
means.append(mean)
sigmas.append(sigma)
amps.append(amp)
counter+=1
i+=1
if make_plot:
fig = plt.figure()
fig.patch.set_facecolor('white')
plt.title('Spectra integrated over a day')
plt.xlabel('channels')
plt.ylabel('counts')
plt.xlim(1,1000)
x = ar(range(0,len(integrated)))
plt.plot(x,integrated,'b:',label='data')
plt.plot(x,double_gaus_plus_exp(x,fit_pars),'ro:',label='fit')
plt.legend()
plt.yscale('log')
plt.show()
else:
counter = 0
counter = 0
return means, sigmas, amps
import pylab as plb
import matplotlib.pyplot as plt
from scipy.optimize import curve_fit
from scipy import asarray as ar, exp
from math import sqrt
x = ar(range(10))
y = ar([0, 1, 2, 3, 4, 5, 4, 3, 2, 1])
n = len(x) # the number of data
mean = sum(x * y) / n # note this correction
sigma = sqrt(sum(y * (x - mean) ** 2) / n) # note this correction
def gaus(x, a, x0, sigma):
return a * exp(-(x - x0) ** 2 / (2 * sigma ** 2))
popt, pcov = curve_fit(gaus, x, y, p0=[1, mean, sigma])
plt.plot(x, y, "b+:", label="data")
plt.plot(x, gaus(x, *popt), "ro:", label="fit")
plt.legend()
plt.title("Fig. 3 - Fit for Time Constant")
plt.xlabel("Time (s)")
plt.ylabel("Voltage (V)")
plt.show()
def main():
logging.basicConfig(level=logging.DEBUG,
format='%(asctime)s [%(levelname)s] %(message)s',
datefmt='%Y-%m-%d %H:%M:%S')
logging.info('*** Starting: Compute STR ***')
db = connect()
components_to_compute = get_components_to_compute(db)
mov_stack = get_config(db, "mov_stack")
if mov_stack.count(',') == 0:
mov_stacks = [int(mov_stack), ]
else:
mov_stacks = [int(mi) for mi in mov_stack.split(',')]
goal_sampling_rate = float(get_config(db, "cc_sampling_rate"))
maxlag = float(get_config(db, "maxlag"))
export_format = get_config(db, 'export_format')
if export_format == "BOTH":
extension = ".MSEED"
else:
extension = "."+export_format
# First we reset all DTT jobs to "T"odo if the REF is new for a given pair
# for station1, station2 in get_station_pairs(db, used=True):
# sta1 = "%s.%s" % (station1.net, station1.sta)
# sta2 = "%s.%s" % (station2.net, station2.sta)
# pair = "%s:%s" % (sta1, sta2)
# if is_dtt_next_job(db, jobtype='DTT', ref=pair):
# logging.info(
# "We will recompute all STR based on the new REF for %s" % pair)
# reset_dtt_jobs(db, pair)
# update_job(db, "REF", pair, jobtype='DTT', flag='D')
filters = get_filters(db, all=False)
# Then we compute the jobs
while is_dtt_next_job(db, flag='T', jobtype='MWCS'):
jobs = get_dtt_next_job(db, flag='T', jobtype='MWCS')
if not len(jobs):
# edge case, should only occur when is_next returns true, but
# get_next receives no jobs (heavily parallelised calls).
time.sleep(np.random.random())
continue
pair = jobs[0].pair
refs, days = zip(*[[job.ref, job.day] for job in jobs])
logging.info(
"There are MWCS jobs for some days to recompute for %s" % pair)
ref_name = pair.replace('.', '_').replace(':', '_')
sta1, sta2 = pair.split(':')
station1 = sta1.split(".")
station2 = sta2.split(".")
station1 = get_station(db, station1[0], station1[1])
station2 = get_station(db, station2[0], station2[1])
dtt_lag = get_config(db, "dtt_lag")
dtt_v = float(get_config(db, "dtt_v"))
dtt_minlag = float(get_config(db, "dtt_minlag"))
dtt_width = float(get_config(db, "dtt_width"))
dtt_sides = get_config(db, "dtt_sides")
if dtt_lag == "static":
minlag = dtt_minlag
else:
minlag = get_interstation_distance(station1, station2, station1.coordinates) / dtt_v
maxlag2 = minlag + dtt_width
print("betweeen", minlag, "and", maxlag2)
for f in get_filters(db, all=False):
filterid = int(f.ref)
for mov_stack in mov_stacks:
for components in components_to_compute:
rf = os.path.join("STACKS", "%02i" %
filterid, "REF", components, ref_name + extension)
if os.path.isfile(rf):
ref = read(rf)[0].data
mid = int(goal_sampling_rate*maxlag)
ref[mid-int(minlag*goal_sampling_rate):mid+int(minlag*goal_sampling_rate)] *= 0.
ref[:mid-int(maxlag2*goal_sampling_rate)] *= 0.
ref[mid+int(maxlag2*goal_sampling_rate):] *= 0.
alldays = []
alldeltas = []
allcoefs = []
allerrs = []
str_range = 0.5 ### HARD CODE!!! ###
nstr = 1001 ### HARD CODE!!! ###
ref_stretched, deltas = stretch_mat_creation(ref,
str_range=str_range,
nstr=nstr)
for day in days:
df = os.path.join(
"STACKS", "%02i" % filterid, "%03i_DAYS" %
mov_stack, components, ref_name, str(day) + extension)
if os.path.isfile(df):
cur = read(df)[0].data ### read the current mseed file ###
cur[mid-int(minlag*goal_sampling_rate):mid+int(minlag*goal_sampling_rate)] *= 0.
cur[:mid-int(maxlag2*goal_sampling_rate)] *= 0.
cur[mid+int(maxlag2*goal_sampling_rate):] *= 0. ### replace with zeroes at all
### times outside minlag to maxlag
logging.debug(
'Processing Stretching for: %s.%s.%02i - %s - %02i days' %
(ref_name, components, filterid, day, mov_stack))
coeffs =[]
for i in range(ref_stretched.shape[0]):
ci = np.corrcoef(cur,ref_stretched[i])[0,1]
coeffs.append(ci)
tday = datetime.datetime.strptime(day, "%Y-%m-%d")
alldays.append(tday)
alldeltas.append(deltas[np.argmax(coeffs)])
allcoefs.append(np.max(coeffs))
###### gaussian fit ######
def gauss_function(x, a, x0, sigma):
return a*np.exp(-(x-x0)**2/(2*sigma**2))
x = ar(range(len(coeffs)))
ymax_index = coeffs.index(np.max(coeffs))
ymin = np.min(coeffs)
coeffs_shift = []
for i in coeffs:
i += np.absolute(ymin) # make all points above zero
coeffs_shift.append(i)
n = len(coeffs)
x0 = sum(x)/n
sigma = (sum((x-x0)**2)/n)**0.5
try:
popt, pcov = curve_fit(gauss_function, x, coeffs_shift, [ymax_index, x0, sigma])
FWHM = 2 * ((2*np.log(2))**0.5)*popt[2] # convert sigma (popt[2]) to FWHM
error = FWHM / 2 ### error is half width at full maximum
except RuntimeError:
error = np.nan # gaussian fit failed
allerrs.append(error)
df = pd.DataFrame(np.array([alldeltas,allcoefs,allerrs]).T, index=alldays, columns=["Delta", "Coeff", "Error"],)
output = os.path.join('STR', "%02i" % filterid, "%03i_DAYS" % mov_stack, components)
if not os.path.isdir(output):
os.makedirs(output)
df.to_csv(os.path.join(output, "%s.csv" % ref_name), index_label="Date")
# THIS SHOULD BE IN THE API
updated = False
mappings = [{'ref': job.ref, 'flag': "D"} for job in jobs]
while not updated:
try:
db.bulk_update_mappings(Job, mappings)
db.commit()
updated = True
except:
time.sleep(np.random.random())
pass
logging.info('*** Finished: Compute STR ***')
