def SVM_Classification_BeehiveSTATE(X_flat_train, y_train, X_flat_test, y_test, kerneloption='rbf'):
print('\n')
printb('Starting classification with SVM:')
Test_Preds=[]
Train_Preds=[]
Test_Preds_Proba=[]
Train_Preds_Proba=[]
Test_GroundT=[]
Train_GroundT=[]
print('\n')
printb('classification Beehive State into : Active or Missing Queen')
#train :
CLF = svm.SVC(kernel=kerneloption, probability=True)
CLF.fit(X_flat_train, y_train)
y_pred_train = CLF.predict(X_flat_train)
y_pred_proba_train = CLF.predict_proba(X_flat_train)
Train_GroundT = y_train
Train_Preds = y_pred_train
Train_Preds_Proba = y_pred_proba_train[:,1]
# test:
y_pred_test = CLF.predict(X_flat_test)
y_pred_proba_test = CLF.predict_proba(X_flat_test)
Test_GroundT= y_test
Test_Preds = y_pred_test
Test_Preds_Proba = y_pred_proba_test[:,1]
return CLF, Test_GroundT, Train_GroundT, Test_Preds, Train_Preds, Test_Preds_Proba, Train_Preds_Proba
def BalanceData_online(y_set, x_set, sample_ids_set):
## balances already processed data (X and Y, just before classifier) by replicating samples of the least represented class.
# input: y_set - binary labels of set, x_set - feature_maps of set, sample_ids_set - sample names in set, ( all have the same order!)
# output: X, Y and sample_ids with replicated samples concatenated
printb( 'Balancing training data:' )
print('will randomly replicate samples from least represented class')
x2concatenate = x_set
y2concatenate = y_set
sample_ids2concatenate = sample_ids_set
dict_items_replicate = get_items2replicate(y_set,sample_ids_set )
#print("dict_items_replicate: ",dict_items_replicate)
for i in range(len(sample_ids_set)):
if sample_ids_set[i] in dict_items_replicate.keys() :
sample_ids2concatenate =np.concatenate([sample_ids2concatenate, [sample_ids_set[i]]*dict_items_replicate[sample_ids_set[i]]])
y2concatenate = np.concatenate([y2concatenate, [y_set[i]]*dict_items_replicate[sample_ids_set[i]]])
x2concatenate = np.concatenate([x2concatenate, [x_set[i]]*dict_items_replicate[sample_ids_set[i]]])
return y2concatenate, x2concatenate, sample_ids2concatenate
def train_and_evaluate_model(model, X_train, Y_train, X_test, Y_test, y_test,
nb_epoch, batch_size, model_filename):
# y_test is labels, Y_test is categorical labels
print('Train...')
target_names = ['missing_queen', 'active']
stopping = EarlyStopping(monitor='val_accuracy', patience=50)
checkpointer = ModelCheckpoint(filepath=model_filename,
verbose=1,
save_best_only=True,
save_weights_only=False,
monitor='val_accuracy',
mode='max')
results = model.fit(X_train,
Y_train,
batch_size=batch_size,
nb_epoch=nb_epoch,
callbacks=[stopping, checkpointer],
verbose=2,
validation_data=(X_test, Y_test))
# prediction
best_model = load_model(model_filename)
probabilities = best_model.predict(X_test, batch_size=batch_size)
predictions = probabilities.argmax(axis=-1)
best_acc = accuracy_score(y_test, predictions)
print('Accuracy score (best model): {}'.format(best_acc))
#print("classification report: ", classification_report(y_test, predictions))
report = classification_report(y_test,
predictions,
target_names=target_names,
output_dict=True)
cnf_matrix = confusion_matrix(y_test, predictions)
return results, best_acc, report, cnf_matrix
def get_features_from_samples(path_audio_samples, sample_ids, raw_feature, normalization, high_level_features ):
#normalization = NO, z_norm, min_max
## function to extract features
#high_level_features = 0 or 1
#file_path = os.path.isfile(path_save_audio_labels+'matrix.mat'+'.csv')
n_samples_set = len(sample_ids) # 4
feature_Maps = []
if raw_feature== 'MFCCs20':
path_working= path_working_MFCC20
elif raw_feature=='TTBOX':
path_working= path_working_TTBox
elif raw_feature=='stft':
path_working= path_working_stft
else:
path_working= path_working_cqt
for sample in sample_ids:
# raw feature extraction:
print("sample: ",sample)
x = raw_feature_fromSample( path_audio_samples+sample, raw_feature ) # x.shape: (4, 20, 2584)
# print("x.shape: ",x.shape)
# Sauvgarder les x dans un fichier .mat
b = csr_matrix(x)
savemat(path_working+ sample[:-4] + '.mat', {'b': b})
##normalization here:si on veut les résultats pour Conv1D on utlise la normalisation
##normalization here:
if not normalization == 'NO':
x_norm = featureMap_normalization_block_level(x, normalizationType = normalization)
else: x_norm = x
if high_level_features:
# high level feature extraction:
if 'MFCCs' in raw_feature:
X = compute_statistics_overMFCCs(x_norm, 'yes') # X.shape: (4 , 120)
else:
X = compute_statistics_overSpectogram(x_norm)
feature_map=X
else:
feature_map=x_norm
feature_Maps.append(feature_map)
return feature_Maps
def uniform_block_size(undersized_block, block_size_samples, method='repeat'):
lengthTofill = (block_size_samples) - (undersized_block.size)
if method == 'zero_padding':
new_block = np.pad(undersized_block, (0, lengthTofill),
'constant',
constant_values=(0))
elif method == 'mean_padding':
new_block = np.pad(undersized_block, (0, lengthTofill), 'mean')
elif method == 'repeat':
new_block = np.pad(undersized_block, (0, lengthTofill), 'reflect')
else:
print(
'methods to choose are: \'zero_padding\' ,\'mean_padding\' and \'repeat\' '
)
new_block = 0
return new_block
def plot_confusion_matrix(cm, classes,
normalize=False,
title='Confusion matrix',
cmap=plt.cm.Blues):
"""
This function prints and plots the confusion matrix.
Normalization can be applied by setting `normalize=True`.
"""
plt.imshow(cm, interpolation='nearest', cmap=cmap)
plt.title(title)
plt.colorbar()
tick_marks = np.arange(len(classes))
plt.xticks(tick_marks, classes, rotation=25)
plt.yticks(tick_marks, classes)
if normalize:
cm = cm.astype('float') / cm.sum(axis=1)[:, np.newaxis]
print("Normalized confusion matrix")
else:
print('Confusion matrix, without normalization')
print(cm)
thresh = cm.max() / 2.
for i, j in itertools.product(range(cm.shape[0]), range(cm.shape[1])):
plt.text(j, i, cm[i, j],
horizontalalignment="center",
color="white" if cm[i, j] > thresh else "black")
plt.tight_layout()
plt.ylabel('True label')
plt.xlabel('Predicted label')
def read_beeNotBee_annotations_saves_labels(audiofilename,
block_name,
blockStart,
blockfinish,
annotations_path,
threshold=0):
## function: reads corresponding annotation file (.lab) and assigns a label to one block/sample. Appends label into csv file.
##
## inputs:
## audiofilename = name of the audio file (no path), block_name = name of the sample/segment, blockStart = time point in seconds where block starts, blockfinish = time point in seconds where block ends, annotations_path = path to annotations folder (where .lab files are), threshold = value tor threshold.
##
## outputs:
## label_th= 2 element list, [0] = a label (bee / nobee) for the block and threshold considered; [1] = label strength, value that reflects the proportion of nobee interval in respect to the whole block.
# thershold gives the minimum duration of the no bee intervals we want to consider.
# trheshold=0 uses every event as notBee whatever the duration
# thershold=0.5 disregards intervals with less than half a second duration.
block_length = blockfinish - blockStart
if audiofilename.startswith('#'):
annotation_filename = audiofilename[1:-4] + '.lab'
else:
annotation_filename = audiofilename[0:-4] + '.lab'
try:
with open(annotations_path + os.sep + annotation_filename, 'r') as f:
# EXAMPLE FILE:
# CF003 - Active - Day - (223)
# 0 8.0 bee
# 8.01 15.05 nobee
# 15.06 300.0 bee
# .
#
# all files end with a dot followed by an empty line.
print(annotations_path + os.sep + annotation_filename)
lines = f.read().split('\n')
labels_th = ['bee', 0.0]
label2assign = 'bee'
label_strength = 0
intersected_s = 0
for line in lines:
if (line == annotation_filename[0:-4]) or (line
== '.') or (line
== ''):
#ignores title, '.', or empty line on the file.
continue
#print(line)
parsed_line = line.split('\t')
assert (len(parsed_line) == 3), (
'expected 3 fields in each line, got: ' +
str(len(parsed_line)))
tp0 = float(parsed_line[0])
tp1 = float(parsed_line[1])
annotation_label = parsed_line[2]
if blockfinish < tp0: # no need to read further nobee intervals since annotation line is already after block finishes
break
if annotation_label == 'nobee':
if tp1 - tp0 >= threshold: # only progress if nobee interval is longer than defined threshold.
if tp0 > blockStart and tp0 <= blockfinish and tp1 >= blockfinish:
intersected_s = intersected_s + (blockfinish - tp0)
# |____________########|########
# bs tp0 bf tp1
elif tp1 >= blockStart and tp1 < blockfinish and tp0 <= blockStart:
intersected_s = intersected_s + (tp1 - blockStart)
# #####|########_____|
# tp0 bs tp1 bf
elif tp1 >= blockStart and tp1 <= blockfinish and tp0 >= blockStart and tp0 <= blockfinish:
intersected_s = intersected_s + (tp1 - tp0)
# |_____########_____|
# bs tp0 tp1 bf
elif tp0 <= blockStart and tp1 >= blockfinish:
intersected_s = intersected_s + (blockfinish -
blockStart)
# ####|############|####
# tp0 bs bf tp1
if intersected_s > 0:
label2assign = 'nobee'
label_strength = intersected_s / block_length # proportion of nobee length in the block
labels_th = [label2assign,
round(label_strength, 3)
] # if label_strehgth ==0 --> bee segment
assert (blockfinish <= tp1), (
'the end of the request block falls outside the file: block ending: '
+ str(blockfinish) + ' end of file at: ' + str(tp1))
except FileNotFoundError as e:
print(e, '--Anotation file does not exist! label as unknown')
#print(annotation_filename=audiofilename[0:-4]+'.lab')
label2assign = 'unknown'
label_strength = -1
labels_th = [label2assign, label_strength]
except Exception as e1:
print('unknown exception: ' + str(e1))
#quit
return labels_th
def load_audioFiles_saves_segments(path_audioFiles,
path_save_audio_labels,
block_size,
thresholds,
annotations_path,
read_beeNotBee_annotations='yes',
save_audioSegments='yes'):
audiofilenames_list = [
os.path.basename(x) for x in glob.glob(path_audioFiles + '*.mp3')
]
audiofilenames_list.extend(
[os.path.basename(x) for x in glob.glob(path_audioFiles + '*.wav')])
printb("Number of audiofiles in folder: " + str(len(audiofilenames_list)))
# print("audiofilenames_list ",audiofilenames_list)
fi = 0
for file_name in audiofilenames_list:
fi = fi + 1
# print('\n')
# printb('Processing '+ file_name+' :::file number: '+str(fi)+' --------->of '+str(len(audiofilenames_list)))
offset = 0
block_id = 0
while 1:
# READ ONE BLOCK OF THE AUDIO FILE
try:
## Read one block of 60 seconds
block, sr = librosa.core.load(path_audioFiles + file_name,
offset=offset,
duration=block_size)
# print(block.shape , sr)
# print('-----------------Reading segment '+str(block_id))
except ValueError as e:
e
if 'Input signal length' in str(e):
block = np.arange(0)
except FileNotFoundError as e1:
print(e1, ' but continuing anyway')
##print("test")
if block.shape[
0] > 0: #when total length = multiple of blocksize, results that last block is 0-lenght, this if bypasses those cases.
block_name = file_name[0:-4] + '__segment' + str(block_id)
## print(block_name)
# READ BEE NOT_BEE ANNOTATIONS:
if read_beeNotBee_annotations == 'yes':
# print('---------------------Will read BeeNotbee anotations and create labels for segment'+str(block_id))
blockStart = offset
##print("blockStart: ",blockStart)
blockfinish = offset + block_size
##print("blockfinish: ",blockfinish)
for th in thresholds:
#print("th::::::::::", th)
label_file_exists = os.path.isfile(
path_save_audio_labels + 'labels_BeeNotBee_th' +
str(th) + '.csv')
with open(path_save_audio_labels +
'labels_BeeNotBee_th' + str(th) + '.csv',
'a',
newline='') as label_file:
writer = csv.DictWriter(label_file,
fieldnames=[
'sample_name',
'segment_start',
'segment_finish',
'label_strength',
'label'
],
delimiter=',')
if not label_file_exists:
writer.writeheader()
## print("start read_beeNotBee_annotation_saves_labels")
label_block_th = read_beeNotBee_annotations_saves_labels(
file_name, block_name, blockStart, blockfinish,
annotations_path, th)
# print("label_block_th : ", label_block_th)
writer.writerow({
'sample_name': block_name,
'segment_start': blockStart,
'segment_finish': blockfinish,
'label_strength': label_block_th[1],
'label': label_block_th[0]
})
# print('-----------------Wrote label for th '+ str(th)+' seconds of segment'+str(block_id) )
# MAKE BLOCK OF THE SAME SIZE:
if block.shape[0] < block_size * sr:
block = uniform_block_size(block, block_size * sr,
'repeat')
# print('-----------------Uniformizing block length of segment'+str(block_id) )
# Save audio segment:
if save_audioSegments == 'yes' and (
not os.path.exists(path_save_audio_labels +
block_name + '.wav')
): #saves only if option is chosen and if block file doesn't already exist.
librosa.output.write_wav(
path_save_audio_labels + block_name + '.wav', block,
sr)
#print( '-----------------Saved wav file for segment '+str(block_id))
else:
#print('----------------- no more segments for this file--------------------------------------')
# print('\n')
break
offset += block_size
block_id += 1
printb(
'______________________________No more audioFiles___________________________________________________'
)
return
def report_SVM_beehiveState_results(summary_filename, path_results, thresholds, CLF, Test_GroundT, Train_GroundT, Test_Preds, Train_Preds, Test_Preds_Proba, Train_Preds_Proba, classification_idSTRING, testFilenames, chunk_size, save='yes'):
if not os.path.isfile(summary_filename):
with open(summary_filename, 'w') as csvfile:
wtr = csv.writer(csvfile, delimiter=',')
wtr.writerow(['ExperienceParameters', 'AccuracyTRAIN', 'AUC_TRAIN', 'gtACTIVEpACTIVE_TRAIN', 'gtMQUEENpACTIVE_TRAIN', 'gtACTIVEpMQUEEN_TRAIN', 'gtMQUEENpMQUEEN_TRAIN','ShannonEnthropy_TRAIN','AccuracyTEST', 'AUC_TEST','ConfusionMatrixTEST_gtACTIVEpACTIVE_gtMQUEENpACTIVE_gtACTIVEpMQUEEN_gtMQUEENpMQUEEN', 'PrecisionTEST_on_MQUEEN', 'RecallTEST_on_MQUEEN', 'PrecisionTEST_on_ACTIVE', 'RecallTEST_on_ACTIVE', 'gtACTIVEpACTIVE_TEST', 'gtMQUEENpACTIVE_TEST', 'gtACTIVEpMQUEEN_TEST', 'gtMQUEENpMQUEEN_TEST', 'ShannonEnthropyTEST','accuracyTEST_on_balancedDatasets'])
csvfile.close()
# transform labels into boolean type for easiness
PRED_TEST=Test_Preds[:]
PRED_TRAIN=Train_Preds[:]
PRED_TEST_PROBA=Test_Preds_Proba[:]
PRED_TRAIN_PROBA=Train_Preds_Proba[:]
GT=Test_GroundT[:]
GT_TRAIN=Train_GroundT[:]
#Evaluate classifier:
print("Classification report for classifier %s:\n%s\n"
% (CLF, metrics.classification_report(GT, PRED_TEST)))
print("Confusion matrix:\n%s" % metrics.confusion_matrix(GT, PRED_TEST))
print('\n')
# Save classification results:
if save == 'yes':
with open(path_results+classification_idSTRING+'.csv', 'w') as csvfile:
wtr = csv.writer(csvfile, delimiter=';')
wtr.writerow( ["Classification report for classifier %s:\n%s\n"
% (CLF, metrics.classification_report(GT, PRED_TEST))])
wtr.writerow( ["Confusion matrix:\n%s" % metrics.confusion_matrix(GT, PRED_TEST)])
wtr.writerow( [" Accuracy: \n%s" % metrics.accuracy_score(GT, PRED_TEST)])
wtr.writerow( [" Area under Curve: \n%s" % metrics.roc_auc_score(GT, PRED_TEST_PROBA, average='macro', sample_weight=None)])
wtr.writerow( ["Predictions: \n"])
for p in range(len(PRED_TEST)):
wtr. writerow([testFilenames[p] +' GT: ' +str(GT[p])+ ' PRED_TEST: '+ str(PRED_TEST[p])])
# append results to summary file:
with open(summary_filename, 'a') as summaryFile:
writer=csv.writer(summaryFile, delimiter=',')
#compute parameters to show:
accuracy=metrics.accuracy_score(GT, PRED_TEST)
AccuracyTRAIN=metrics.accuracy_score(GT_TRAIN, PRED_TRAIN)
try:
gtACTIVEpACTIVE, gtMQUEENpACTIVE, gtACTIVEpMQUEEN, gtMQUEENpMQUEEN=metrics.confusion_matrix(GT, PRED_TEST).ravel()
except ValueError as e:
if sum(PRED_TEST)==len(PRED_TEST) and sum(GT)==len(PRED_TEST) :
gtACTIVEpACTIVE=0
gtMQUEENpACTIVE=0
gtACTIVEpMQUEEN=0
gtMQUEENpMQUEEN =len(PRED_TEST)
elif sum(PRED_TEST)==0 and sum(GT)==0 :
gtACTIVEpACTIVE=len(PRED_TEST)
gtMQUEENpACTIVE=0
gtACTIVEpMQUEEN=0
gtMQUEENpMQUEEN =0
elif sum(PRED_TEST)==len(PRED_TEST) and sum(GT)==0 :
gtACTIVEpACTIVE=0
gtMQUEENpACTIVE=0
gtACTIVEpMQUEEN=len(PRED_TEST)
gtMQUEENpMQUEEN =0
elif sum(PRED_TEST)==0 and sum(GT)==len(GT) :
gtACTIVEpACTIVE=0
gtMQUEENpACTIVE=len(PRED_TEST)
gtACTIVEpMQUEEN=0
gtMQUEENpMQUEEN =0
try:
gtACTIVEpACTIVE_TRAIN, gtMQUEENpACTIVE_TRAIN, gtACTIVEpMQUEEN_TRAIN, gtMQUEENpMQUEEN_TRAIN=metrics.confusion_matrix(GT_TRAIN, PRED_TRAIN).ravel()
except ValueError as e:
if sum(PRED_TRAIN)==len(PRED_TRAIN) and sum(GT_TRAIN)==len(PRED_TRAIN) :
gtACTIVEpACTIVE_TRAIN=0
gtMQUEENpACTIVE_TRAIN=0
gtACTIVEpMQUEEN_TRAIN=0
gtMQUEENpMQUEEN_TRAIN =len(PRED_TEST)
elif sum(PRED_TRAIN)==0 and sum(GT_TRAIN)==0 :
gtACTIVEpACTIVE_TRAIN=len(PRED_TRAIN)
gtMQUEENpACTIVE_TRAIN=0
gtACTIVEpMQUEEN_TRAIN=0
gtMQUEENpMQUEEN_TRAIN =0
elif sum(PRED_TRAIN)==len(PRED_TRAIN) and sum(GT_TRAIN)==0 :
gtACTIVEpACTIVE_TRAIN=0
gtMQUEENpACTIVE_TRAIN=0
gtACTIVEpMQUEEN_TRAIN=len(PRED_TRAIN)
gtMQUEENpMQUEEN_TRAIN =0
elif sum(PRED_TRAIN)==0 and sum(GT_TRAIN)==len(GT_TRAIN) :
gtACTIVEpACTIVE_TRAIN=0
gtMQUEENpACTIVE_TRAIN=len(PRED_TRAIN)
gtACTIVEpMQUEEN_TRAIN=0
gtMQUEENpMQUEEN_TRAIN =0
try:
ShannonEnthropy_TRAIN=-(((gtACTIVEpACTIVE_TRAIN+gtACTIVEpMQUEEN_TRAIN)/(gtACTIVEpACTIVE_TRAIN+gtMQUEENpACTIVE_TRAIN+gtACTIVEpMQUEEN_TRAIN+gtMQUEENpMQUEEN_TRAIN) )*log(((gtACTIVEpACTIVE_TRAIN+gtACTIVEpMQUEEN_TRAIN)/(gtACTIVEpACTIVE_TRAIN+gtMQUEENpACTIVE_TRAIN+gtACTIVEpMQUEEN_TRAIN+gtMQUEENpMQUEEN_TRAIN) )) + ((gtMQUEENpACTIVE_TRAIN+gtMQUEENpMQUEEN_TRAIN)/(gtACTIVEpACTIVE_TRAIN+gtMQUEENpACTIVE_TRAIN+gtACTIVEpMQUEEN_TRAIN+gtMQUEENpMQUEEN_TRAIN) )*log(((gtMQUEENpACTIVE_TRAIN+gtMQUEENpMQUEEN_TRAIN)/(gtACTIVEpACTIVE_TRAIN+gtMQUEENpACTIVE_TRAIN+gtACTIVEpMQUEEN_TRAIN+gtMQUEENpMQUEEN_TRAIN) )))
except Exception as e :
ShannonEnthropy_TRAIN=0
try:
Precision_on_MQUEEN=gtMQUEENpMQUEEN/(gtMQUEENpMQUEEN+gtACTIVEpMQUEEN)
except ZeroDivisionError as e:
Precision_on_MQUEEN=0
try:
Recall_on_MQUEEN=gtMQUEENpMQUEEN/(gtMQUEENpMQUEEN+gtMQUEENpACTIVE)
except ZeroDivisionError as e:
Recall_on_MQUEEN=0
try:
Precision_on_ACTIVE=gtACTIVEpACTIVE/(gtACTIVEpACTIVE+gtMQUEENpACTIVE)
except ZeroDivisionError as e:
Precision_on_ACTIVE=0
try:
Recall_on_ACTIVE=gtACTIVEpACTIVE/(gtACTIVEpACTIVE+gtACTIVEpMQUEEN)
except ZeroDivisionError as e:
Recall_on_ACTIVE=0
try:
ShannonEnthropy=-(((gtACTIVEpACTIVE+gtACTIVEpMQUEEN)/(gtACTIVEpACTIVE+gtMQUEENpACTIVE+gtACTIVEpMQUEEN+gtMQUEENpMQUEEN) )*log(((gtACTIVEpACTIVE+gtACTIVEpMQUEEN)/(gtACTIVEpACTIVE+gtMQUEENpACTIVE+gtACTIVEpMQUEEN+gtMQUEENpMQUEEN) )) + ((gtMQUEENpACTIVE+gtMQUEENpMQUEEN)/(gtACTIVEpACTIVE+gtMQUEENpACTIVE+gtACTIVEpMQUEEN+gtMQUEENpMQUEEN) )*log(((gtMQUEENpACTIVE+gtMQUEENpMQUEEN)/(gtACTIVEpACTIVE+gtMQUEENpACTIVE+gtACTIVEpMQUEEN+gtMQUEENpMQUEEN) )))
except Exception as e :
ShannonEnthropy=0
if ShannonEnthropy>0.9:
accuracy_on_balancedDatasets=accuracy
else:
accuracy_on_balancedDatasets=0
try:
AUC_TRAIN=metrics.roc_auc_score(GT_TRAIN, PRED_TRAIN_PROBA, average='macro', sample_weight=None)
except Exception as e:
AUC_TRAIN='error'
try:
AUC_TEST=metrics.roc_auc_score(GT, PRED_TEST_PROBA, average='macro', sample_weight=None)
except Exception as e:
AUC_TEST='error'
writer.writerow([classification_idSTRING, AccuracyTRAIN, AUC_TRAIN, gtACTIVEpACTIVE_TRAIN, gtMQUEENpACTIVE_TRAIN, gtACTIVEpMQUEEN_TRAIN, gtMQUEENpMQUEEN_TRAIN , ShannonEnthropy_TRAIN, accuracy , AUC_TEST ,metrics.confusion_matrix(GT, PRED_TEST),Precision_on_MQUEEN , Recall_on_MQUEEN, Precision_on_ACTIVE, Recall_on_ACTIVE, gtACTIVEpACTIVE, gtMQUEENpACTIVE, gtACTIVEpMQUEEN,gtMQUEENpMQUEEN, ShannonEnthropy,accuracy_on_balancedDatasets])
def extract_long_term_features_fromMEL(Mel_spectrograms, n_slices):
#n_slices must result in an equal division. so:
# total_frames=Mel_spectrograms[0].shape[-1] # total number of frames
# slice_size = total_frames//n_slices
# corrected_n_slices = total_frames / int(slice_size)
long_term_features = []
for sample in Mel_spectrograms:
print(sample.shape)
sliced_sample = np.array_split(sample, n_slices, 1 )
print(len(sliced_sample))
print(sliced_sample[0].shape)
stacked_averaged_slices = []
for i in range(len(sliced_sample)):
stacked_averaged_slices.append(np.mean(sliced_sample[i],1))
print(stacked_averaged_slices[i].shape)
#pdb.set_trace()
print(len(stacked_averaged_slices))
long_term_features.append(stacked_averaged_slices)
print(len(long_term_features))
print(len(long_term_features[0]))
print(long_term_features[0][0].shape)
return long_term_features
path_save_audio_stft= path+ 'dataset_BeeNoBee_2_second'+str(block_size)+'sec'+'\\stft_matrix.mat'+os.sep
nbits = 16;
MAX_VAL = pow(2,(nbits-1)) * 1.0;
target_names=['missing_queen', 'active']
#-----------------------------------STFT+CNN -----------------------------------#
ruche1,Y1,labels1, sample_ids1, ruche2,Y2,labels2, sample_ids2, ruche3,Y3,labels3, sample_ids3, ruche4,Y4,labels4, sample_ids4=get_list_samples_name_('b', path_save_audio_stft)
# save the model history in a list after fitting so we can plot later
model_history=[]
val_accuracy=[]
for i in range(4):
fold= i+1
print("Training on Fold :", fold)
x_train, x_test, y_train, y_test,sample_ids_train, sample_ids_test=cross_validation_4folds(fold, ruche1,Y1, ruche2,Y2, ruche3,Y3, ruche4,Y4 , sample_ids1 , sample_ids2 , sample_ids3 , sample_ids4)
print(len(x_train), len(x_test), len(y_train), len(y_test))
# Read a sparse matrix
x_train2=[]
x_test2=[]
for l in range(len(x_train)):
x_train2.append(x_train[l].todense())
for l in range(len(x_test)):
x_test2.append(x_test[l].todense())
X_train= np.array(x_train2)
x_Test= np.array(x_test2)
y_train=np.array(y_train)
y_test= np.array(y_test)
X_test, y_test = constrainedsplit(y_train, x_Test, y_test, 0.7)
def fit_and_evaluate(train_x, val_x, train_y, val_y, EPOCHS=50, BATCH_SIZE=145 ):
model=None
model=deep_model(( 20,44, 1))
results= model.fit(train_x, train_y, epochs=EPOCHS, batch_size= BATCH_SIZE, callbacks=[early_stopping, model_checkpoint], verbose=1, validation_split=0.1)
print("Val Score :", model.evaluate(val_x, val_y))
return results
def StoreExcel(dic):
checklis = []
if os.path.isfile('./MFCC/Name_Label_MFCCfeature.xlsx'):
xls = load_workbook('./MFCC/Name_Label_MFCCfeature.xlsx')
print("file existed ")
try:
df = pd.read_excel('./MFCC/Name_Label_MFCCfeature.xlsx',
delimiter="\t")
# 取出第一行(Name)
check = df.iloc[:, 0]
for i in check:
if i in checklis:
continue
else:
checklis.append(i)
except Exception as e:
print("An error found but ignored", e)
else:
xls = openpyxl.Workbook()
#以下是儲存進excel
sheet = xls.get_sheet_by_name('Sheet') #生成excel的方法
x, y = 1, 1
sheet.cell(row=x, column=y, value='Name')
sheet.cell(row=x, column=y + 1, value='Labal')
x, y = 2, 1
#判斷全新一列 塞值
tmp = 'A' + str(x)
while True:
if sheet[tmp].value != None:
x += 1
tmp = 'A' + str(x)
#print(ws[tmp].value)
else:
break
for name in dic:
if name[0:-4] in checklis:
print('this file has been used , Pass!')
continue # 此檔案已經存過 略過
currentname = name[0:-4]
# 判斷狀況
if 'NO' in currentname or 'Missing' in currentname:
currentlabel = 'Missing Queen'
else:
currentlabel = 'Active'
# 存進excel格子
# 存 名稱 & 狀態
y = 1
sheet.cell(row=x, column=y, value=currentname)
sheet.cell(row=x, column=y + 1, value=currentlabel)
y = 3
# 存 feature
for feature in dic[name]:
sheet.cell(row=x, column=y, value=feature)
y += 1
x += 1
# MFCC特徵數值
x, y = 1, 3
for count in range(1, 121):
tmps = count
sheet.cell(row=x, column=y, value=tmps)
y += 1
Excelname = 'Name_Label_MFCCfeature.xlsx'
xls.save('./MFCC/' + Excelname)
print(Excelname + " have Done")
def load_audioFiles_saves_segments(audiofilenames_list,
path_audioFiles,
path_save_audio_labels,
block_size,
save_audioSegments='yes'):
printb("Number of audiofiles in folder: " + str(len(audiofilenames_list)))
fi = 0 #目前檔案第0個
#操作方式: 逐檔載入,一個音檔中設置開始時間offset從0開始,到指定每個音檔分段時間duration(block_size=60s),然後進到while 1,
#將音檔輸出成wav(等於此音檔的序列被輸出,剩下的序列是從offset+block_size開始)&資訊存進csv後,序列還有資料就再執行一次,
#當序列<0則表示此音檔已經完全輸出,則跳出while 1 ,繼續處理下一個音檔
for file_name in audiofilenames_list:
fi = fi + 1
print('\n')
printb('Processing ' + file_name + ' :::file number: ' +
str(fi) + ' ----->of ' + str(len(audiofilenames_list)))
offset = 0
block_id = 0
# 處理前先判斷是否已經處理過,若以處理過則跳過
exitfile = fileisexitornot(path_save_audio_labels)
# 用第一個切割的音段名稱來判斷是否需要處理此音檔
first_block_name = file_name[0:-4] + '__segment' + str(
block_id) + '.wav'
if first_block_name in exitfile:
print('this file has been used')
continue
while 1:
# READ ONE BLOCK OF THE AUDIO FILE
try: #try除錯用
#加載音檔 (音檔位置,offset:以此時間開始讀取,duration:持續讀取時間) 回傳音檔序列,sr=採樣率
block, sr = librosa.core.load(path_audioFiles + file_name,
offset=offset,
duration=block_size)
print('-----Reading segment ' + str(block_id))
except ValueError as e:
e
if 'Input signal length' in str(e):
block = np.arange(0)
except FileNotFoundError as e1:
print(e1, ' but continuing anyway')
if block.shape[0] > 0:
#when total length = multiple of blocksize, results that last block is 0-lenght, this if bypasses those cases.
block_name = file_name[0:-4] + '__segment' + str(block_id)
print(block_name)
#testing
#在此產生state_label.csv並將名稱跟label狀態加入
states = ['active', 'missing queen', 'swarm']
label_file_exists = os.path.isfile(path_save_audio_labels +
'state_labels' +
'.csv') #判斷檔案是否存在
with open(path_save_audio_labels + 'state_labels' + '.csv',
'a',
newline='') as label_file: #label_file檔案讀寫
writer = csv.DictWriter(
label_file,
fieldnames=['sample_name', 'label'],
delimiter=',') #定義欄位sample_name, label
if not label_file_exists: #假如檔案不存在
writer.writeheader() #寫入欄位
csvreader = csv.DictReader(label_file)
try:
for row in csvreader:
print(row['sample_name'])
except:
pass
#270
label_state = read_HiveState_fromSampleName(
block_name, states)
writer.writerow({
'sample_name': block_name,
'label': label_state
})
# READ BEE NOT_BEE ANNOTATIONS: 將音檔資訊.lab儲存進csv
# MAKE BLOCK OF THE SAME SIZE:
if block.shape[0] < block_size * sr:
pass
# Save audio segment:
if save_audioSegments == 'yes' and (
not os.path.exists(path_save_audio_labels +
block_name + '.wav')
): #saves only if option is chosen and if block file doesn't already exist.
#將音檔序列輸出為.wav文件
librosa.output.write_wav(
path_save_audio_labels + block_name + '.wav', block,
sr)
print('-----Saved wav file for segment ' + str(block_id))
else:
print('-----no more segments for this file-----')
print('\n')
break
offset += block_size
block_id += 1
printb('_____No more audioFiles_____')
return