def translate(tokens, translation=None):
translations = []
inferred_meanings = None
if translation is not None:
inferred_meanings = Infer.infer(tokens, translation)
i = -1
for token in tokens:
i += 1
jp = token.word
last = i == len(tokens) - 1
if not last:
if is_sentence_ending_symbol(tokens[i + 1].word):
last = True
if is_ending(token):
translation = translate_ending(token)
translations.append(Translation(token, translation))
continue
translation = match_special(jp, last)
if translation:
translations.append(Translation(token, translation))
continue
if inferred_meanings is not None:
translation = inferred_meanings[i]
if translation is not None:
translations.append(Translation(token, translation))
continue
translation = get_translation_from_dictionary(token)
if translation:
translations.append(Translation(token, translation))
continue
if is_katakana(jp):
translations.append(Translation(token, Katakana.translate(jp)))
continue
if is_english(jp):
translations.append(Translation(token, jp))
continue
if is_number(jp):
translations.append(Translation(token, Numbers.convert(jp)))
continue
translations.append(Translation(token, token.word))
return translations
t = np.linspace(-0.1, 0.1, 300)
t_pred = np.linspace(-0.12, 0.12, 1000)
flux = Transit_aRs(lc_pars,
t) + 0.0005 * np.sin(2 * np.pi * 40 * t) + np.random.normal(
0, hp[-1], t.size)
#guess parameter values and guess uncertainties
guess_pars = hp + gp
err_pars = np.array([0.0004, 0.1, 0.0001] +
[0.00001, 0, 0.2, 0.0003, 0.02, 0.0, 0.0, 0.001, 0.])
#construct the GP
MyGP = Infer.GP(flux,
np.matrix([
t,
]).T,
p=guess_pars,
mf=Transit_aRs,
mf_args=t,
n_hp=3)
#MyGP.logPrior = lambda p: np.log(norm_dist.pdf(p[6],.10,0.02)).sum()
#make plot of the function
pylab.figure(1)
pylab.plot(MyGP.mf_args, MyGP.t, 'k.')
pylab.plot(MyGP.mf_args, MyGP.MeanFunction(), 'g-')
#get optimised parameters
#MyGP.pars = Infer.Optimise(MyGP.logPosterior,guess_pars[:],(),fixed=(np.array(err_pars) == 0)*1)
#pylab.plot(MyGP.mf_args,MyGP.MeanFunction(),'r-')
MyGP.Optimise(fp=(np.array(err_pars) == 0) * 1)
gp.logPrior = logPrior
#optimise the free parameters
gp.optimise()
gp.plot()
#can also run an MCMC by using GP.logPosterior()
ch = 10000
conv = 0.4 * ch
lims = (0, conv, 10)
Infer.MCMC_N(gp.logPosterior,
gp.p, (),
ch,
gp.ep,
N=2,
adapt_limits=lims,
glob_limits=lims)
#Infer.AffInvMCMC(gp.logPosterior,gp.p,(),500,ch/500,gp.ep*0.01,n_chains=2)
pylab.figure(2)
Infer.PlotCorrelations(conv, n_chains=2, p=np.where(np.array(gp.ep) > 0)[0])
#pylab.savefig('Correlations.png')
#get the parameters and uncertainties from the MCMC
gp.p, gp.ep = Infer.AnalyseChains(conv, n_chains=2)
#and plot
pylab.figure(1)
gp.plot()
def blink_detector(output_textfile, input_video):
Q = Queue(maxsize=7)
deque_blinks = deque(maxlen=30)
drowsy_level = "Calculating drowsiness level... "
FRAME_MARGIN_BTW_2BLINKS = 3
MIN_AMPLITUDE = 0.04
MOUTH_AR_THRESH = 0.35
MOUTH_AR_THRESH_ALERT = 0.30
MOUTH_AR_CONSEC_FRAMES = 20
EPSILON = 0.01 # for discrete derivative (avoiding zero derivative)
class Blink():
def __init__(self):
self.start = 0 #frame
self.startEAR = 1
self.peak = 0 #frame
self.peakEAR = 1
self.end = 0 #frame
self.endEAR = 0
self.amplitude = (self.startEAR + self.endEAR -
2 * self.peakEAR) / 2
self.duration = self.end - self.start + 1
self.EAR_of_FOI = 0 #FrameOfInterest
self.values = []
self.velocity = 0 #Eye-closing velocity
def eye_aspect_ratio(eye):
# compute the euclidean distances between the two sets of
# vertical eye landmarks (x, y)-coordinates
A = dist.euclidean(eye[1], eye[5])
B = dist.euclidean(eye[2], eye[4])
# compute the euclidean distance between the horizontal
# eye landmark (x, y)-coordinates
C = dist.euclidean(eye[0], eye[3])
if C < 0.1: #practical finetuning due to possible numerical issue as a result of optical flow
ear = 0.3
else:
# compute the eye aspect ratio
ear = (A + B) / (2.0 * C)
if ear > 0.45: #practical finetuning due to possible numerical issue as a result of optical flow
ear = 0.45
# return the eye aspect ratio
return ear
def mouth_aspect_ratio(mouth):
A = dist.euclidean(mouth[14], mouth[18])
C = dist.euclidean(mouth[12], mouth[16])
if C < 0.1: #practical finetuning
mar = 0.2
else:
# compute the mouth aspect ratio
mar = (A) / (C)
# return the mouth aspect ratio
return mar
def EMERGENCY(ear, COUNTER):
if ear < 0.21:
COUNTER += 1
if COUNTER >= 50:
# client.messages.create(to="+16505466275",
# from_="+15674434352",
# body="This is an emergency!")
call = client.calls.create(
twiml=
'<Response><Say>Sunny is very drowsy! This is an emergency!</Say></Response>',
to='+16505466275',
from_='+15674434352')
print(call.sid)
print('EMERGENCY SITUATION (EYES TOO LONG CLOSED)')
print(COUNTER)
COUNTER = 0
else:
COUNTER = 0
return COUNTER
def Linear_Interpolate(start, end, N):
m = (end - start) / (N + 1)
x = np.linspace(1, N, N)
y = m * (x - 0) + start
return list(y)
def Ultimate_Blink_Check():
#Given the input "values", retrieve blinks and their quantities
retrieved_blinks = []
MISSED_BLINKS = False
values = np.asarray(Last_Blink.values)
THRESHOLD = 0.4 * np.min(values) + 0.6 * np.max(
values) # this is to split extrema in highs and lows
N = len(values)
Derivative = values[1:N] - values[0:N -
1] #[-1 1] is used for derivative
i = np.where(Derivative == 0)
if len(i[0]) != 0:
for k in i[0]:
if k == 0:
Derivative[0] = -EPSILON
else:
Derivative[k] = EPSILON * Derivative[k - 1]
M = N - 1 #len(Derivative)
ZeroCrossing = Derivative[1:M] * Derivative[0:M - 1]
x = np.where(ZeroCrossing < 0)
xtrema_index = x[0] + 1
XtremaEAR = values[xtrema_index]
Updown = np.ones(
len(xtrema_index)) # 1 means high, -1 means low for each extremum
Updown[
XtremaEAR <
THRESHOLD] = -1 #this says if the extremum occurs in the upper/lower half of signal
#concatenate the beginning and end of the signal as positive high extrema
Updown = np.concatenate(([1], Updown, [1]))
XtremaEAR = np.concatenate(([values[0]], XtremaEAR, [values[N - 1]]))
xtrema_index = np.concatenate(([0], xtrema_index, [N - 1]))
##################################################################
Updown_XeroCrossing = Updown[1:len(Updown)] * Updown[0:len(Updown) - 1]
jump_index = np.where(Updown_XeroCrossing < 0)
numberOfblinks = int(len(jump_index[0]) / 2)
selected_EAR_First = XtremaEAR[jump_index[0]]
selected_EAR_Sec = XtremaEAR[jump_index[0] + 1]
selected_index_First = xtrema_index[jump_index[0]]
selected_index_Sec = xtrema_index[jump_index[0] + 1]
if numberOfblinks > 1:
MISSED_BLINKS = True
if numberOfblinks == 0:
print(Updown, Last_Blink.duration)
print(values)
print(Derivative)
for j in range(numberOfblinks):
detected_blink = Blink()
detected_blink.start = selected_index_First[2 * j]
detected_blink.peak = selected_index_Sec[2 * j]
detected_blink.end = selected_index_Sec[2 * j + 1]
detected_blink.startEAR = selected_EAR_First[2 * j]
detected_blink.peakEAR = selected_EAR_Sec[2 * j]
detected_blink.endEAR = selected_EAR_Sec[2 * j + 1]
detected_blink.duration = detected_blink.end - detected_blink.start + 1
detected_blink.amplitude = 0.5 * (
detected_blink.startEAR - detected_blink.peakEAR) + 0.5 * (
detected_blink.endEAR - detected_blink.peakEAR)
detected_blink.velocity = (
detected_blink.endEAR - selected_EAR_First[2 * j + 1]) / (
detected_blink.end - selected_index_First[2 * j + 1] + 1
) #eye opening ave velocity
retrieved_blinks.append(detected_blink)
return MISSED_BLINKS, retrieved_blinks
def Blink_Tracker(EAR, IF_Closed_Eyes, Counter4blinks, TOTAL_BLINKS, skip):
BLINK_READY = False
#If the eyes are closed
if int(IF_Closed_Eyes) == 1:
Current_Blink.values.append(EAR)
Current_Blink.EAR_of_FOI = EAR #Save to use later
if Counter4blinks > 0:
skip = False
if Counter4blinks == 0:
Current_Blink.startEAR = EAR #EAR_series[6] is the EAR for the frame of interest(the middle one)
Current_Blink.start = reference_frame - 6 #reference-6 points to the frame of interest which will be the 'start' of the blink
Counter4blinks += 1
if Current_Blink.peakEAR >= EAR: #deciding the min point of the EAR signal
Current_Blink.peakEAR = EAR
Current_Blink.peak = reference_frame - 6
# otherwise, the eyes are open in this frame
else:
if Counter4blinks < 2 and skip == False: # Wait to approve or reject the last blink
if Last_Blink.duration > 15:
FRAME_MARGIN_BTW_2BLINKS = 8
else:
FRAME_MARGIN_BTW_2BLINKS = 1
if ((reference_frame - 6) -
Last_Blink.end) > FRAME_MARGIN_BTW_2BLINKS:
# Check so the prev blink signal is not monotonic or too small (noise)
if Last_Blink.peakEAR < Last_Blink.startEAR and Last_Blink.peakEAR < Last_Blink.endEAR and Last_Blink.amplitude > MIN_AMPLITUDE and Last_Blink.start < Last_Blink.peak:
if ((Last_Blink.startEAR - Last_Blink.peakEAR) >
(Last_Blink.endEAR - Last_Blink.peakEAR) * 0.25 and
(Last_Blink.startEAR - Last_Blink.peakEAR) * 0.25 <
(Last_Blink.endEAR -
Last_Blink.peakEAR)): # the amplitude is balanced
BLINK_READY = True
#####THE ULTIMATE BLINK Check
Last_Blink.values = signal.convolve1d(
Last_Blink.values, [1 / 3.0, 1 / 3.0, 1 / 3.0],
mode='nearest')
# Last_Blink.values=signal.median_filter(Last_Blink.values, 3, mode='reflect') # smoothing the signal
[MISSED_BLINKS,
retrieved_blinks] = Ultimate_Blink_Check()
#####
TOTAL_BLINKS = TOTAL_BLINKS + len(
retrieved_blinks
) # Finally, approving/counting the previous blink candidate
###Now You can count on the info of the last separate and valid blink and analyze it
Counter4blinks = 0
print("MISSED BLINKS= {}".format(
len(retrieved_blinks)))
return retrieved_blinks, int(
TOTAL_BLINKS
), Counter4blinks, BLINK_READY, skip
else:
skip = True
print('rejected due to imbalance')
else:
skip = True
print('rejected due to noise,magnitude is {}'.format(
Last_Blink.amplitude))
print(Last_Blink.start < Last_Blink.peak)
# if the eyes were closed for a sufficient number of frames (2 or more)
# then this is a valid CANDIDATE for a blink
if Counter4blinks > 1:
Current_Blink.end = reference_frame - 7 #reference-7 points to the last frame that eyes were closed
Current_Blink.endEAR = Current_Blink.EAR_of_FOI
Current_Blink.amplitude = (Current_Blink.startEAR +
Current_Blink.endEAR -
2 * Current_Blink.peakEAR) / 2
Current_Blink.duration = Current_Blink.end - Current_Blink.start + 1
if Last_Blink.duration > 15:
FRAME_MARGIN_BTW_2BLINKS = 8
else:
FRAME_MARGIN_BTW_2BLINKS = 1
if (
Current_Blink.start - Last_Blink.end
) <= FRAME_MARGIN_BTW_2BLINKS + 1: #Merging two close blinks
print('Merging...')
frames_in_between = Current_Blink.start - Last_Blink.end - 1
print(Current_Blink.start, Last_Blink.end,
frames_in_between)
valuesBTW = Linear_Interpolate(Last_Blink.endEAR,
Current_Blink.startEAR,
frames_in_between)
Last_Blink.values = Last_Blink.values + valuesBTW + Current_Blink.values
Last_Blink.end = Current_Blink.end # update the end
Last_Blink.endEAR = Current_Blink.endEAR
if Last_Blink.peakEAR > Current_Blink.peakEAR: #update the peak
Last_Blink.peakEAR = Current_Blink.peakEAR
Last_Blink.peak = Current_Blink.peak
#update duration and amplitude
Last_Blink.amplitude = (Last_Blink.startEAR +
Last_Blink.endEAR -
2 * Last_Blink.peakEAR) / 2
Last_Blink.duration = Last_Blink.end - Last_Blink.start + 1
else: #Should not Merge (a Separate blink)
Last_Blink.values = Current_Blink.values #update the EAR list
Last_Blink.end = Current_Blink.end # update the end
Last_Blink.endEAR = Current_Blink.endEAR
Last_Blink.start = Current_Blink.start #update the start
Last_Blink.startEAR = Current_Blink.startEAR
Last_Blink.peakEAR = Current_Blink.peakEAR #update the peak
Last_Blink.peak = Current_Blink.peak
Last_Blink.amplitude = Current_Blink.amplitude
Last_Blink.duration = Current_Blink.duration
# reset the eye frame counter
Counter4blinks = 0
retrieved_blinks = 0
return retrieved_blinks, int(
TOTAL_BLINKS), Counter4blinks, BLINK_READY, skip
# initialize the frame counters and the total number of yawnings
COUNTER = 0
MCOUNTER = 0
TOTAL = 0
MTOTAL = 0
TOTAL_BLINKS = 0
Counter4blinks = 0
skip = False # to make sure a blink is not counted twice in the Blink_Tracker function
Last_Blink = Blink()
print("[INFO] loading facial landmark predictor...")
detector = dlib.get_frontal_face_detector()
#Load the Facial Landmark Detector
predictor = dlib.shape_predictor('shape_predictor_68_face_landmarks.dat')
#Load the Blink Detector
loaded_svm = pickle.load(
open('Trained_SVM_C=1000_gamma=0.1_for 7kNegSample.sav', 'rb'))
# grab the indexes of the facial landmarks for the left and
# right eye, respectively
(lStart, lEnd) = face_utils.FACIAL_LANDMARKS_IDXS["left_eye"]
(rStart, rEnd) = face_utils.FACIAL_LANDMARKS_IDXS["right_eye"]
(mStart, mEnd) = face_utils.FACIAL_LANDMARKS_IDXS["mouth"]
print("[INFO] starting video stream thread...")
lk_params = dict(winSize=(13, 13),
maxLevel=2,
criteria=(cv2.TERM_CRITERIA_EPS | cv2.TERM_CRITERIA_COUNT,
10, 0.03))
EAR_series = np.zeros([13])
# Frame_series=np.linspace(1,13,13)
reference_frame = 0
First_frame = True
# top = tk.Tk()
# frame1 = Frame(top)
# frame1.grid(row=0, column=0)
# fig = plt.figure()
# ax = fig.add_subplot(111)
# plot_frame =FigureCanvasTkAgg(fig, master=frame1)
# plot_frame.get_tk_widget().pack(side=tk.BOTTOM, expand=True)
# plt.ylim([0.0, 0.5])
# line, = ax.plot(Frame_series,EAR_series)
# plot_frame.draw()
# loop over frames from the video stream
stream = cv2.VideoCapture(path)
start = datetime.datetime.now()
number_of_frames = 0
while True:
(grabbed, frame) = stream.read()
if not grabbed:
print('not grabbed')
print(number_of_frames)
break
frame = imutils.resize(frame, width=450)
# To Rotate by 90 degreees
# rows=np.shape(frame)[0]
# cols = np.shape(frame)[1]
# M = cv2.getRotationMatrix2D((cols / 2, rows / 2),-90, 1)
# frame = cv2.warpAffine(frame, M, (cols, rows))
gray = cv2.cvtColor(
frame, cv2.COLOR_BGR2GRAY) #Brighten the image(Gamma correction)
reference_frame = reference_frame + 1
gray = adjust_gamma(gray, gamma=1.5)
Q.put(frame)
end = datetime.datetime.now()
ElapsedTime = (end - start).total_seconds()
# detect faces in the grayscale frame
rects = detector(gray, 0)
if (np.size(rects) != 0):
number_of_frames = number_of_frames + 1 # we only consider frames that face is detected
First_frame = False
old_gray = gray.copy()
# determine the facial landmarks for the face region, then
# convert the facial landmark (x, y)-coordinates to a NumPy
# array
shape = predictor(gray, rects[0])
shape = face_utils.shape_to_np(shape)
###############YAWNING##################
#######################################
Mouth = shape[mStart:mEnd]
MAR = mouth_aspect_ratio(Mouth)
MouthHull = cv2.convexHull(Mouth)
#cv2.drawContours(frame, [MouthHull], -1, (255, 0, 0), 1)
if MAR > MOUTH_AR_THRESH:
MCOUNTER += 1
elif MAR < MOUTH_AR_THRESH_ALERT:
if MCOUNTER >= MOUTH_AR_CONSEC_FRAMES:
MTOTAL += 1
MCOUNTER = 0
##############YAWNING####################
#########################################
# extract the left and right eye coordinates, then use the
# coordinates to compute the eye aspect ratio for both eyes
leftEye = shape[lStart:lEnd]
rightEye = shape[rStart:rEnd]
leftEAR = eye_aspect_ratio(leftEye)
rightEAR = eye_aspect_ratio(rightEye)
# average the eye aspect ratio together for both eyes
ear = (leftEAR + rightEAR) / 2.0
#EAR_series[reference_frame]=ear
EAR_series = shift(EAR_series, -1, cval=ear)
# compute the convex hull for the left and right eye, then
# visualize each of the eyes
leftEyeHull = cv2.convexHull(leftEye)
rightEyeHull = cv2.convexHull(rightEye)
#cv2.drawContours(frame, [leftEyeHull], -1, (0, 255, 0), 1)
#cv2.drawContours(frame, [rightEyeHull], -1, (0, 255, 0), 1)
############ Show drowsiness level ########################
###########################################################
# cv2.putText(frame,f"Drowsy Level:{drowsy_level}",
# (10,250),
# cv2.FONT_HERSHEY_SIMPLEX,
# 0.5,
# [0,0,255],
# 1
# )
############HANDLING THE EMERGENCY SITATION################
###########################################################
###########################################################
COUNTER = EMERGENCY(ear, COUNTER)
# EMERGENCY SITUATION (EYES TOO LONG CLOSED) ALERT THE DRIVER IMMEDIATELY
############HANDLING THE EMERGENCY SITATION################
###########################################################
###########################################################
if Q.full() and (
reference_frame > 15
): #to make sure the frame of interest for the EAR vector is int the mid
EAR_table = EAR_series
IF_Closed_Eyes = loaded_svm.predict(EAR_series.reshape(1, -1))
if Counter4blinks == 0:
Current_Blink = Blink()
retrieved_blinks, TOTAL_BLINKS, Counter4blinks, BLINK_READY, skip = Blink_Tracker(
EAR_series[6], IF_Closed_Eyes, Counter4blinks,
TOTAL_BLINKS, skip)
if (BLINK_READY == True):
reference_frame = 20 #initialize to a random number to avoid overflow in large numbers
skip = True
#####
BLINK_FRAME_FREQ = TOTAL_BLINKS / number_of_frames
for detected_blink in retrieved_blinks:
print(detected_blink.amplitude, Last_Blink.amplitude)
print(detected_blink.duration, detected_blink.velocity)
print('-------------------')
deque_blinks.append([
BLINK_FRAME_FREQ * 100, detected_blink.amplitude,
detected_blink.duration, detected_blink.velocity
])
print(f"len(deque_blinks)={len(deque_blinks)}")
if len(deque_blinks) == 30:
deque_blinks_reshaped = np.array(
deque_blinks).reshape(1, -1, 4)
drowsy_level = Infer.how_drowsy(
deque_blinks_reshaped)
np_array_to_list = deque_blinks_reshaped.tolist()
json_file = "file.json"
json.dump(np_array_to_list,
codecs.open(json_file,
'w',
encoding='utf-8'),
sort_keys=True,
indent=4)
print(f"Drowsy Level={drowsy_level}")
if (detected_blink.velocity > 0):
with open(output_file, 'ab') as f_handle:
f_handle.write(b'\n')
np.savetxt(f_handle, [
TOTAL_BLINKS, BLINK_FRAME_FREQ * 100,
detected_blink.amplitude,
detected_blink.duration,
detected_blink.velocity
],
delimiter=', ',
newline=' ',
fmt='%.4f')
Last_Blink.end = -10 # re initialization
#####
# line.set_ydata(EAR_series)
# print(EAR_series)
# plot_frame.draw()
frameMinus7 = Q.get()
# cv2.imshow("Frame", frameMinus7)
elif Q.full(
): #just to make way for the new input of the Q when the Q is full
junk = Q.get()
key = cv2.waitKey(1) & 0xFF
# if the `q` key was pressed, break from the loop
if key != 0xFF:
break
#Does not detect any face
else:
###################Using Optical Flow############
################### (Optional) ############
st = 0
st2 = 0
if (First_frame == False):
leftEye = leftEye.astype(np.float32)
rightEye = rightEye.astype(np.float32)
p1, st, err = cv2.calcOpticalFlowPyrLK(old_gray, gray, leftEye,
None, **lk_params)
p2, st2, err2 = cv2.calcOpticalFlowPyrLK(
old_gray, gray, rightEye, None, **lk_params)
if np.sum(st) + np.sum(st2) == 12 and First_frame == False:
p1 = np.round(p1).astype(np.int)
p2 = np.round(p2).astype(np.int)
#print(p1)
leftEAR = eye_aspect_ratio(p1)
rightEAR = eye_aspect_ratio(p2)
ear = (leftEAR + rightEAR) / 2.0
EAR_series = shift(EAR_series, -1, cval=ear)
#EAR_series[reference_frame] = ear
leftEyeHull = cv2.convexHull(p1)
rightEyeHull = cv2.convexHull(p2)
# cv2.drawContours(frame, [leftEyeHull], -1, (0, 255, 0), 1)
# cv2.drawContours(frame, [rightEyeHull], -1, (0, 255, 0), 1)
old_gray = gray.copy()
leftEye = p1
rightEye = p2
############HANDLING THE EMERGENCY SITATION################
###########################################################
###########################################################
COUNTER = EMERGENCY(ear, COUNTER)
############HANDLING THE EMERGENCY SITATION################
###########################################################
###########################################################
###################Using Optical Flow############
################### ############
if Q.full() and (reference_frame > 15):
EAR_table = EAR_series
IF_Closed_Eyes = loaded_svm.predict(EAR_series.reshape(1, -1))
if Counter4blinks == 0:
Current_Blink = Blink()
retrieved_blinks, TOTAL_BLINKS, Counter4blinks, BLINK_READY, skip = Blink_Tracker(
EAR_series[6], IF_Closed_Eyes, Counter4blinks,
TOTAL_BLINKS, skip)
if (BLINK_READY == True):
reference_frame = 20 #initialize to a random number to avoid overflow in large numbers
skip = True
#####
BLINK_FRAME_FREQ = TOTAL_BLINKS / number_of_frames
for detected_blink in retrieved_blinks:
print(detected_blink.amplitude, Last_Blink.amplitude)
print(detected_blink.duration, Last_Blink.duration)
print('-------------------')
with open(output_file, 'ab') as f_handle:
f_handle.write(b'\n')
np.savetxt(f_handle, [
TOTAL_BLINKS, BLINK_FRAME_FREQ * 100,
detected_blink.amplitude,
detected_blink.duration,
detected_blink.velocity
],
delimiter=', ',
newline=' ',
fmt='%.4f')
Last_Blink.end = -10 # re initialization
#####
# line.set_ydata(EAR_series)
# plot_frame.draw()
# print(EAR_series)
frameMinus7 = Q.get()
# cv2.imshow("Frame", frameMinus7)
elif Q.full():
junk = Q.get()
key = cv2.waitKey(1) & 0xFF
if key != 0xFF:
break
# do a bit of cleanup
stream.release()
cv2.destroyAllWindows()
# gp = [0.7,1.7,3.2] ep = [0.01,0.01,0.01] print "means =", m print "errs =", np.sqrt(np.diag(K)) #define MCMC parameters chain_len = 40000 conv = 20000 thin = 10 no_ch=2 #run the MCMC Infer.MCMC(LogNormalDist,gp,(m,invK,logdetK),chain_len,ep,n_chains=no_ch,adapt_limits=(5000,20000,5),glob_limits=(5000,20000,5),thin=thin) #Get parameters values/errors from chains par,par_err = Infer.AnalyseChains(conv/thin,n_chains=no_ch) bf_par = Infer.GetBestFit(n_chains=no_ch) print "Best Fit log p =", LogNormalDist(bf_par,m,invK,logdetK) #plot the chains and correlations #pylab.figure(2) #Infer.PlotChains(conv/thin,n_chains=no_ch,p=[0,2,3,4],labels=lab) pylab.figure(3) Infer.PlotCorrelations(conv/thin,n_chains=no_ch) ############ Importance sampling stage ################# #get mean and covariance from the MCMC chains m,K = Infer.NormalFromMCMC(conv/thin,n_chains=no_ch) #or use 'perfect' mean and K
#create the data set (ie training data)
time = np.arange(-0.1, 0.1, 0.001)
flux = Transit_aRs(lc_pars, time) + np.random.normal(0, wn, time.size)
#guess parameter values and guess uncertainties
guess_pars = lc_pars + [wn]
err_pars = [0.00001, 0, 0.2, 0.0003, 0.02, 0.0, 0.0, 0.001, 0.0001, 0.0001]
#plot the light curve + guess function
pylab.figure(1)
pylab.errorbar(time, flux, yerr=wn, fmt='.')
pylab.plot(time, Transit_aRs(guess_pars[:-1], time), 'r--')
#first optimise the function
guess_pars = Infer.Optimise(LogLikelihood_iid_mf,
guess_pars[:], (Transit_aRs, time, flux),
fixed=(np.array(err_pars) == 0) * 1)
#run a standard MCMC
chain_len = 40000
conv = 10000
thin = 10
no_ch = 2
adapt_lims = (2000, conv, 5)
glob_lims = (2000, conv, 5)
glob_lims = (0, 0, 0)
Infer.MCMC(LogLikelihood_iid_mf,
guess_pars[:], (Transit_aRs, time, flux),
chain_len,
err_pars,
n_chains=no_ch,
#multivariate - sum of p/2 coupled Rosenbrock functions
def InvNRosenbrock(p):
R = 0.
for i in range(len(p) / 2):
R += 100. * (p[2 * i]**2 - p[2 * i + 1])**2. + (p[2 * i] - 1.)**2.
return -0.4 * R
gp = [1., 1., 1., 1., 1., 1., 1., 1.]
ep = [0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1]
gp = np.array(gp) + np.random.normal(0, 1, len(gp))
#first optimise the function
gp = Infer.Optimise(InvNRosenbrock, gp[:], (), fixed=(np.array(ep) == 0) * 1)
#run a normal MCMC
chain_len = 50000
conv = 2000
thin = 1
no_ch = 3
adapt_lims = (200, conv, 10)
glob_lims = (200, conv, 10)
Infer.MCMC(InvNRosenbrock,
gp[:], (),
chain_len,
ep,
n_chains=no_ch,
adapt_limits=adapt_lims,
glob_limits=glob_lims,
pylab.figure(1)
pylab.errorbar(time, flux, yerr=wn, fmt='.')
pylab.plot(time, Transit_aRs(guess_pars[:-1], time), 'r--')
#define MCMC parameters
chain_len = 20000
conv = 10000
thin = 10
no_ch = 2
adapt_lims = (2000, 10000, 3)
glob_lims = (2000, 20000, 10)
#first optimise the function and get parameter errors from the conditionals
guess_pars, err_pars = Infer.ConditionalErrors(LogLikelihood_iid_mf,
guess_pars,
err_pars,
(Transit_aRs, time, flux),
plot=0,
opt=True)
Infer.MCMC(LogLikelihood_iid_mf,
guess_pars, (Transit_aRs, time, flux),
chain_len,
err_pars,
n_chains=no_ch,
adapt_limits=adapt_lims,
glob_limits=glob_lims,
thin=thin)
par, par_err = Infer.AnalyseChains(conv / thin, n_chains=no_ch)
#plot the chains and correlations
#pylab.figure(2)
#Infer.PlotChains(conv/thin,n_chains=no_ch,p=[0,2,3,4],labels=lab)
#guess parameter values and guess uncertainties
guess_pars = lc_pars + [wn]
err_pars = [0.00001, 0, 0.2, 0.0003, 0.02, 0.0, 0.0, 0.00001, 0.00001, 0.00001]
#plot the light curve + guess function
pylab.figure(1)
pylab.errorbar(time, flux, yerr=wn, fmt='.')
pylab.plot(time, Transit_aRs(guess_pars[:-1], time), 'r--')
#first optimise the function
#guess_pars = Infer.Optimise(LogLikelihood_iid_mf,guess_pars[:],(Transit_aRs,time,flux),fixed=(np.array(err_pars) == 0)*1)
#find the conditional errors to seed an MCMC
pylab.figure(2)
p, e = Infer.ConditionalErrors(LogLikelihood_iid_mf,
guess_pars,
err_pars, (Transit_aRs, time, flux),
plot=1)
#run the MCMC
#define MCMC parameters
chain_len = 100000
conv = 50000
thin = 10
no_ch = 2
adapt_lims = (0, 0, 0)
glob_lims = (2000, 100000, 4)
Infer.MCMC(LogLikelihood_iid_mf,
p, (Transit_aRs, time, flux),
chain_len,
e,
n_chains=no_ch,
# MyMCMC.Ballpark(lf,pl,pu,(f,x,y),5000,filename="testfile",log_proposal=[1,1,1,1]) # pg = MyMCMC.ExtractBallpark(filename="testfile") #plot test function pylab.figure(1) pylab.plot(x,y,'k.') pylab.plot(x,f(p[:3],x),'r-') pylab.plot(x,f(pg[:3],x),'g--') #plot guess function #run the MCMC (using C version) MyMCMC.MCMC(lf,pg,(f,x,y),chain_len,dp,n_chains=no_ch,glob_limits=limits,adapt_limits=limits) #Get parameters values/errors from chains par,par_err = MyMCMC.AnalyseChains(conv,n_chains=no_ch) print #run the PyMCMC Infer.MCMC(lf,pg,(f,x,y),chain_len,dp,n_chains=no_ch,glob_limits=limits,adapt_limits=limits,thin=thin) #Get parameters values/errors from chains par,par_err = Infer.AnalyseChains(conv/thin,n_chains=no_ch) print #plot fitted function pylab.figure(1) pylab.plot(x,f(par[:3],x),'b-') # pylab.figure(2) # Infer.PlotChains(conv/thin,n_chains=no_ch) pylab.figure(3) Infer.PlotCorrelations(conv/thin,n_chains=no_ch,n_samples=1000) raw_input()
lc_pars = [.0,2.5,11.,.1,0.6,0.2,0.3,1.,0.] hp = [0.0003,0.01,0.0003] #create the data set (ie training data) t = np.linspace(-0.1,0.1,300) t_pred = np.linspace(-0.12,0.12,1000) flux = Transit_aRs(lc_pars,t) + np.random.normal(0,hp[-1],t.size) #guess parameter values and guess uncertainties guess_pars = hp + lc_pars err_pars = np.array([0.00001,1,0.0001] + [0.00001,0,0.2,0.0003,0.02,0.0,0.0,0.001,0.0001]) X = np.matrix([t,]).T X_pred = np.matrix([t_pred,]).T MyGP = Infer.GP(flux,X,p=guess_pars,mf=Transit_aRs,mf_args=t,n_hp=3) #make plot of the function pylab.figure(1) pylab.plot(MyGP.mf_args,MyGP.t,'k.') pylab.plot(MyGP.mf_args,MyGP.mf(lc_pars,MyGP.mf_args),'g-') start = time.time() for i in range(100): gp = np.array(guess_pars) + np.random.normal(0,1) * err_pars # print gp lik = MyGP.logPosterior(gp) # print lik print " t = %.2f s" % (time.time()-start) MyGP.pars = Infer.Optimise(MyGP.logPosterior,guess_pars[:],(),fixed=(np.array(err_pars) == 0)*1)
#create the data set (ie training data) time = np.linspace(-0.1,0.1,300) flux = Transit_aRs(lc_pars,time) + np.random.normal(0,wn,time.size) #guess parameter values and guess uncertainties guess_pars = lc_pars + [wn] err_pars = [0.0001,0,0.05,0.003,0.002,0.0,0.0,0.01,0.0001,0.00010] #plot the light curve + guess function pylab.figure(1) pylab.errorbar(time,flux,yerr=wn,fmt='.') pylab.plot(time,Transit_aRs(guess_pars[:-1],time),'r--') #first optimise the function guess_pars = Infer.Optimise(Posterior,guess_pars[:],(Transit_aRs,time,flux),fixed=(np.array(err_pars) == 0)*1,method='BFGS') #run a normal MCMC chain_len = 60000 conv = 30000 thin = 10 no_ch=3 adapt_lims = (2000,conv,10) glob_lims = (2000,conv,10) # Infer.MCMC(Posterior,guess_pars[:],(Transit_aRs,time,flux),chain_len,err_pars,n_chains=no_ch,adapt_limits=adapt_lims,glob_limits=glob_lims,thin=thin) # #Get parameters values/errors from chains # par,par_err = Infer.AnalyseChains(conv/thin,n_chains=no_ch) # bf_par = Infer.GetBestFit(n_chains=no_ch) # print "Best Fit log p =", LogLikelihood_iid_mf(bf_par,Transit_aRs,time,flux) # pylab.figure(3) # Infer.PlotCorrelations(conv/thin,n_chains=no_ch,p=np.where(np.array(par_err)>0.)[0])
chain_len = 100000
conv = 50000
thin = 10
no_ch = 2
adapt_lims = (10000, 40000, 3)
glob_lims = (2000, 100000, 4)
#first optimise the function
#guess_pars = Infer.Optimise(LogLikelihood_iid_mf,guess_pars[:],(Transit_aRs,time,flux),fixed=(np.array(err_pars) == 0)*1)
#run the MCMC with orthogonal steps
Infer.MCMC(LogLikelihood_iid_mf,
guess_pars[:], (Transit_aRs, time, flux),
chain_len,
err_pars,
n_chains=no_ch,
adapt_limits=adapt_lims,
glob_limits=glob_lims,
thin=thin,
orth=True)
#Get parameters values/errors from chains
par, par_err = Infer.AnalyseChains(conv / thin, n_chains=no_ch)
#run the MCMC with covariant steps
Infer.MCMC(LogLikelihood_iid_mf,
guess_pars[:], (Transit_aRs, time, flux),
chain_len,
err_pars,
n_chains=no_ch,
adapt_limits=adapt_lims,
glob_limits=glob_lims,
pylab.plot(x, Model3(par3[:-1], x), 'r--')
#MCMC params
chain_len = 25000
conv = 10000
thin = 10
no_ch = 2
limits = (conv / 4, conv, 3)
#first try the linear model
gp = par1[:]
ep = [0.001, 0.001, 0.001]
Infer.MCMC(LogLikelihood_iid_mf,
gp, (Model1, x, y),
chain_len,
ep,
n_chains=no_ch,
adapt_limits=limits,
glob_limits=limits,
thin=thin)
par, par_err = Infer.AnalyseChains(conv / thin, n_chains=no_ch)
pylab.plot(x, Model1(par[:-1], x), 'b')
m, K = Infer.NormalFromMCMC(conv / thin, n_chains=no_ch)
E1, par, par_err = Infer.ImportanceSamp(LogLikelihood_iid_mf, (Model1, x, y),
m, K, chain_len)
E1, par, par_err = Infer.ImportanceSamp(LogLikelihood_iid_mf, (Model1, x, y),
m, 3. * K, chain_len)
#now try the quadratic model
gp = par2[:]
ep = [0.001, 0.001, 0.001, 0.001]
Infer.MCMC(LogLikelihood_iid_mf,
#plot the light curve + guess function
pylab.figure(1)
pylab.errorbar(time, flux, yerr=wn, fmt='.')
pylab.plot(time, Transit_aRs(guess_pars[:-1], time), 'r--')
#define MCMC parameters
chain_len = 100000
conv = 20000
thin = 10
no_ch = 5
#run the MCMC
Infer.MCMC(LogLikelihood_iid_mf,
guess_pars, (Transit_aRs, time, flux),
chain_len,
err_pars,
n_chains=no_ch,
adapt_limits=(5000, 20000, 3),
glob_limits=(5000, 20000, 3),
thin=thin)
#Get parameters values/errors from chains
par, par_err = Infer.AnalyseChains(conv / thin, n_chains=no_ch)
#plot the chains and correlations
lab = [r'$T_0$', r'$a/R\star$', r'$\rho$', r'$b$']
#pylab.figure(2)
#Infer.PlotChains(conv/thin,n_chains=no_ch,p=[0,2,3,4],labels=lab)
pylab.figure(3)
Infer.PlotCorrelations(conv / thin, n_chains=no_ch, p=[0, 2, 3, 4], labels=lab)
#plot fitted function
optimizer = RAdam.RAdam(t.parameters(), lr=args.lr)
elif args.optimizer == 'Adam':
optimizer = torch.optim.Adam(t.parameters(), lr=args.lr)
t = t.double()
train_mse = []
test_mse = [10000]
for ij in range(epochs):
loss_list = []
for i, batch in enumerate(train_data_loader):
optimizer.zero_grad()
in_batch = batch['in'].to(device)
out = t(in_batch)
loss = lossfn(batch['out'].to(device), out)
loss_list.append(loss)
loss.backward()
optimizer.step()
print('Avg. Training Loss in ' + str(ij) + 'th epoch :- ',
sum(loss_list) / len(loss_list))
train_mse.append(sum(loss_list) / len(loss_list))
loss_list = []
test_mse.append(
Infer.evaluate(t,
loss=args.loss,
test_dataset=test_dataset,
args_from_train=args))
if test_mse[-1] == min(test_mse):
print('saving:- ', test_mse[-1])
torch.save(t.state_dict(), args.param_file)
#gpar = tpar
#epar = np.array([0.000,0.0,0.0,0.01,0.0,0.0,0.0,0.0001,0.00001,0.0000])
#create arrays for bound and fixed parameters (optional)
fixed = (epar == 0) * 1
bounds = np.array([(None, None) for i in range(len(tpar))])
bounds[4][0] = 0.
#create data (time and flux)
t = np.linspace(-0.05, 0.05, 1000)
f = MF.Transit_aRs(tpar[:-1], t) + np.random.normal(0, tpar[-1], t.size)
#perform LM fit to the data
p, pe, wn, K, logE = Infer.LevMar(MF.Transit_aRs,
gpar[:-1], (t, ),
f,
fixed=fixed[:-1],
bounds=None)
print K
print K.shape
print np.sqrt(K.diagonal())
print pe
print np.sqrt(K.diagonal()) == np.hstack([pe, 0.])
#get residuals
resid = f - MF.Transit_aRs(p, t)
#compare with MCMC fit - use LM values as inputs
lims = (0, 4000, 4)
MCMC_p = list(p) + [
wn,
#test the N parallel chain code
chain_len = 11000
conv = 10000
thin = 1
lims = (0, conv, 4)
ext_len = 1000
max_ext = 50
N = 4
import time as timer
start = timer.time()
Infer.MCMC_N(LogLikelihood_iid_mf,
guess_pars, (Transit_aRs, time, flux),
chain_len,
err_pars,
N=N,
adapt_limits=lims,
glob_limits=lims,
thin=thin,
ext_len=ext_len,
max_ext=max_ext)
ts = timer.time() - start
st1 = "t = %dm %.2fs" % (ts // 60., ts % 60.)
#MCMCParallelCPU.MCMCParallel(LogLikelihood_iid_mf,guess_pars,(Transit_aRs,time,flux),chain_len,err_pars,N=N,adapt_limits=lims,glob_limits=lims,thin=thin,ext_len=ext_len,max_ext=100)
par, par_err = Infer.AnalyseChains(conv, n_chains=N)
pylab.figure(2)
Infer.PlotCorrelations(conv, n_chains=N)
#check against normal version
# chain_len = 10000
# conv = 4000
# lims = (0,conv,4)
import Infer
#create example with some noise/systematics
tpar = [0,3.0,10,0.1,0.2,0.2,0.2,1.0,0.0]
time = np.linspace(-0.1,0.1,300)
flux = MF.Transit_aRs(tpar,time) + 0.001*np.sin(2*np.pi*40*time) + np.random.normal(0.,0.0005,time.size)
#construct the GP
gp = GeePea.GP(time,flux,p=tpar+[0.1,0.01,0.001],mf=MF.Transit_aRs)
gp.opt() #optimise
#run quick MCMC to test predictions:
ch_len = 10000
lims = (0,5000,10)
epar = [0,0,0,0.001,0,0,0,0,0,] + [0.001,0.01,0.001]
Infer.MCMC_N(gp.logPosterior,gp.p,(),ch_len,epar,adapt_limits=lims,glob_limits=lims,chain_filenames=['test_chain'])
p,perr = Infer.AnalyseChains(lims[1],chain_filenames=['test_chain'])
X = Infer.GetSamples(5000,100,chain_filenames=['test_chain']) #get samples from the chains
os.remove('test_chain.npy')
#standard plot
pylab.figure()
gp.plot()
#pylab.savefig('test.pdf')
#density plot for single parameter set
pylab.figure()
f,ferr = gp.predict()
GeePea.PlotDensity(time,f,ferr)
pylab.plot(time,flux,'ro',ms=3)
epar = [
par_noise,
] * 7 + [
0.0,
]
epar[2] = 0
fp = [0, 0, 0, 0, 0, 0, 0, 1]
wn = 0.6
f = mf(par, time) + np.random.normal(0, wn, time.size)
##########################################################################################
#fit with levenburg marquardt
NM_temp = Infer.Optimise(MF.LogLikelihood_iid_mf,
np.concatenate([par_guess, [
wn,
]]), (mf, time, f),
fixed=fp)
LM1 = opt.leastsq(LM_ErrFunc,
NM_temp[:-1],
args=(mf, time, f, 1),
full_output=1)
rescale1 = (f - mf(LM1[0], time)).std()
LM1_par = LM1[0]
LM1_epar = np.sqrt(np.diag(LM1[1])) * rescale1
#fit with least squares - again a levenberg marquardt method (trust region is similar idea)
LM2 = opt.least_squares(LM_ErrFunc,
par_guess,
args=(mf, time, f, 1),
method='trf',