def createThread(threadIndex, queryString, pcdbFileName, outputDir):
paddedNum = ('%0' + str(config.numDivisionDigits) + 'd') % threadIndex
minTime = helper.interpolate(threadIndex, config.numSearchDivisions,
config.startTime, config.endTime)
maxTime = helper.interpolate(threadIndex + 1, config.numSearchDivisions,
config.startTime, config.endTime)
return FlickrDownloaderThread(queryString, pcdbFileName,
minTime, maxTime,
outputDir, paddedNum)
def data_confidence(patients, patient, code):
# Attributes
length_arr = 0
arr_ = []
list_ = []
isAnalyzable = False
# All patients
for i in patients[:70]:
df_ = i.data.loc[i.data['CODE'] == code]
arr_.append(len(df_))
length_arr = arr_
avg_len = math.ceil(((np.sum(length_arr)) / (len(length_arr))))
# Our patient
for i in patient.data:
patient_df = patient.data.loc[patient.data['CODE'] == code]
pat_len = len(patient_df)
pat_val_arr = patient_df[['VALUE']]
# Confidence Model (comparing all patients to THE patient)
threshold = avg_len * 0.6
if pat_len < threshold:
pass
elif (pat_len > threshold and pat_len < avg_len):
pat_val_arr_expanded = helper.interpolate(pat_val_arr, avg_len)
print("-----------------")
print("| Patient #", patient.getPatientId(), " |")
print("|", len(pat_val_arr_expanded), " |")
print("|", len(patient_df[['VALUE']]), " |")
print("-----------------")
isAnalyzable = True
elif pat_len > avg_len:
isAnalyzable = True
#print(avg_len)
return isAnalyzable
def get_mfcc(signal1, signal2, count, label, uuid, subject):
"""
This function takes the input signals and converts them to MFCCs and saves the converted representations to
a destination directory in the hdf5 format.
:param signal1:
:param signal2:
:param count:
:param label:
:param uuid:
:param subject:
:return:
"""
destination = "../data/{}/".format(des_string)
if show_plot:
line1, = mp.plot(signal1 / 1000., label="Channel 1")
_, = mp.plot(signal2 / 1000., label="Channel 2")
mp.rcParams.update({'font.size': 20})
mp.locator_params(axis='y', nticks=3)
mp.yticks()
mp.xlabel("Samples (4000 per second)")
mp.legend(handler_map={line1: HandlerLine2D(numpoints=4)})
mp.ylabel("Milli volts")
mp.show()
m1_array = [signal1]
m2_array = [signal2]
"""
One in every n is in test and one in every n is in validation. Other (n-2) are in training.
"""
test_data = (count % test_fraction) == 1
validation_data = (count % test_fraction) == 2
if not test_data and not validation_data:
"""
Data augmentation step. Data augmentation is only done for the training dataset, not for testing or validation.
"""
for noise in noises:
for coefficient in noise_coefficients:
# Add moise to the signal
m1_array.append(add_noise(signal1, float(coefficient), noise))
m2_array.append(add_noise(signal2, float(coefficient), noise))
if apply_shift:
# SHIFT RIGHT
m1_array.append(np.roll(signal1, int(len(signal1) * 0.05)))
m2_array.append(np.roll(signal2, int(len(signal2) * 0.05)))
# SHIFT LEFT
m1_array.append(np.roll(signal1, int(len(signal1) * 0.05 * -1)))
m2_array.append(np.roll(signal2, int(len(signal2) * 0.05 * -1)))
if apply_stretch:
# Stretch the signal
m1_array.append(stretch(signal1, 0.8))
m2_array.append(stretch(signal2, 0.8))
m1_array.append(stretch(signal1, 1.2))
m2_array.append(stretch(signal2, 1.2))
for i in range(len(m1_array)):
"""
Convert the original and augmented data to their MFCC representations.
"""
signal1 = m1_array[i]
signal2 = m2_array[i]
if len(signal1) < 1:
continue
m1 = mfcc(signal1,
samplerate=sampling_frequency,
numcep=numcep,
nfilt=nfilt,
highfreq=highfreq)
m2 = mfcc(signal2,
samplerate=sampling_frequency,
numcep=numcep,
nfilt=nfilt,
highfreq=highfreq)
if i == 0:
lengths.append(len(m1))
if show_plot:
print(len(m1), len(m1[0]))
if apply_interpolation:
# Use interpolation to make the converted data have the same sizes
m1 = interpolate(m1, new_length)
m2 = interpolate(m2, new_length)
if apply_padding:
# Use padding to make the converted data have the same sizes
m1 = pad(m1, new_length, True)
m2 = pad(m2, new_length, True)
if apply_stack:
# Stack the signals to make them comparable to multi-channel inputs to the models. Helpful for CNNs.
signal = np.dstack((m1, m2))
else:
m1 = m1.T
m2 = m2.T
signal = np.concatenate((m1, m2))
signal = signal.T
normalize(signal, axis=0)
if show_plot:
"""
Show converted MFCC representations
"""
if i == 1:
fig, ax = mp.subplots()
mfcc_data = np.swapaxes(m1, 0, 1)
ax.imshow(mfcc_data, interpolation='nearest', origin='lower')
ax.set_title('MFCC Representation of Channel 1')
mp.xlabel("Time Frames")
mp.ylabel("Mel Bands")
mp.show()
fig, ax = mp.subplots()
mfcc_data = np.swapaxes(m2, 0, 1)
ax.imshow(mfcc_data, interpolation='nearest', origin='lower')
ax.set_title('MFCC Representation of Channel 2')
mp.xlabel("Time Frames")
mp.ylabel("Mel Bands")
mp.show()
"""
Round the converted signals to 4 decimal places only. Made unreachable for now.
"""
if False:
signal = np.round(signal, decimals=4)
"""
Save the files
"""
data = {"label": labels.index(label), "signal": signal}
if not os.path.exists(destination):
os.makedirs(destination)
sub_destination = destination + subject + "/"
if not os.path.exists(sub_destination):
os.makedirs(sub_destination)
if not os.path.exists(sub_destination + label):
os.makedirs(sub_destination + label)
if not os.path.exists(sub_destination + label + "/test"):
os.makedirs(sub_destination + label + "/test")
if not os.path.exists(sub_destination + label + "/validation"):
os.makedirs(sub_destination + label + "/validation")
if test_data:
file_location = "{}{}/test/{}_{}_{}.hdf5".format(
sub_destination, label, uuid, str(count), str(i))
elif validation_data:
file_location = "{}{}/validation/{}_{}_{}.hdf5".format(
sub_destination, label, uuid, count, str(i))
else:
file_location = "{}{}/{}_{}_{}.hdf5".format(
sub_destination, label, uuid, str(count), str(i))
with h5py.File(file_location, 'w') as f:
for k, v in data.items():
f.create_dataset(k, data=np.array(v, dtype=float))
return
def splitQuery(self, numImages, minTime, maxTime, splitAttempts):
targetNumChunks = math.ceil(numImages / config.targetPhotosPerPage)
for chunk in range(0, targetNumChunks):
newMin = helper.interpolate(chunk, targetNumChunks, minTime, maxTime)
newMax = helper.interpolate(chunk + 1, targetNumChunks, minTime, maxTime)
self.queryTimeRange(newMin, newMax, splitAttempts + 1)