Fix dependency issues

README.md

@@ -66,7 +66,7 @@ import numpy as np
 from functions.raw_non_wear_functions import cnn_nw_algorithm, hees_2013_calculate_non_wear_time, raw_baseline_calculate_non_wear_time
 
 # read raw acceleration from numpy array. Since the data was not scaled, we are dividing it by the acceleration scale to obtain acceleration values in gravity units
-raw_acc = np.load(file = os.path.join(os.sep, 'Users', 'shaheen.syed', 'PA', 'acceleration.npz'))['raw_data'] / 256.
+raw_acc = np.load(file = os.path.join(os.sep, 'Users', 'shaheen.syed', 'PA', 'acceleration.npz'), allow_pickle=True)['raw_data'] / 256.
 # how to encode wear time
 wt_encoding = 0
 # how to encode non-wear time
@@ -128,4 +128,4 @@ xyz_nw = raw_baseline_calculate_non_wear_time(raw_acc = raw_acc, std_threshold =
 # VMY baseline method
 vmu_nw = raw_baseline_calculate_non_wear_time(raw_acc = raw_acc, std_threshold = 0.004, min_interval = 105, hz = hz, use_vmu = True, nwt_encoding = nwt_encoding, wt_encoding = wt_encoding)
 
-```
+```

examples.py

@@ -9,7 +9,7 @@
 from functions.raw_non_wear_functions import cnn_nw_algorithm, hees_2013_calculate_non_wear_time, raw_baseline_calculate_non_wear_time
 
 # read raw acceleration from numpy array. Since the data was not scaled, we are dividing it by the acceleration scale to obtain acceleration values in gravity units
-raw_acc = np.load(file = os.path.join(os.sep, 'Users', 'shaheen.syed', 'PA', 'acceleration.npz'))['raw_data'] / 256.
+raw_acc = np.load(file = os.path.join(os.sep, 'Users', 'shaheen.syed', 'PA', 'acceleration.npz'), allow_pickle=True)['raw_data'] / 256.
 # how to encode wear time
 wt_encoding = 0
 # how to encode non-wear time

infer_nw_time.py

@@ -36,7 +36,7 @@ def parse_arguments():
 
 	# set the logger and start time
 	tic, process, logging = set_start()
-	
+
 	# pars command line arguments
 	args = parse_arguments()
 
@@ -78,35 +78,35 @@ def parse_arguments():
 			"""
 
 			# read file as numpy array
-			data = np.load(file)
+			data = np.load(file, allow_pickle=True)
 			# extract raw acceleration data from numpy.
 			actigraph_acc = data['raw_data']
 
 			# read meta data from file
-			meta_data = data['meta_data']
+			meta_data = data['meta_data'].item()
 
 			# convert acceleration values to g values
 			actigraph_acc = rescale_log_data(log_data = actigraph_acc, acceleration_scale = meta_data['Acceleration_Scale'])
 
-			# extract time data 
+			# extract time data
 			actigraph_time = data['time_data']
 			# convert time data to correct time series array with correct miliseconds values
 			actigraph_time = create_time_array(actigraph_time, hz = int(meta_data['Sample_Rate']))
-			
+
 			"""
 				INFER NON-WEAR TIME
 			"""
 			# call function to infer non-wear time
 			nw_vector, nw_data = cnn_nw_algorithm(	raw_acc = actigraph_acc,
 													hz = int(meta_data['Sample_Rate']),
-													cnn_model_file = cnn_model_file, 
+													cnn_model_file = cnn_model_file,
 													std_threshold = std_threshold,
 													distance_in_min = distance_in_min,
 													episode_window_sec = episode_window_sec,
 													edge_true_or_false = edge_true_or_false,
 													start_stop_label_decision = start_stop_label_decision
 													)
-			
+
 			"""
 				POST PROCESS DATA
 			"""
@@ -136,9 +136,9 @@ def parse_arguments():
 			save_csv(data = nw_data, name = 'non_wear_data_indexes', folder = os.path.dirname(file))
 			# save human readable start and stop timestamps as CSV file
 			save_csv(data = nw_data_timestamps, name = 'non_wear_data_timestamps', folder = os.path.dirname(file))
-		
+
 	else:
 		logging.warning('Folder argument not provided. Please specify the -fd or --folder argument which specifies where raw acceleration data is stored in numpy format.')
 
 	# verbose
-	set_end(tic, process)
+	set_end(tic, process)

requirements.txt

@@ -1,10 +1,10 @@
-numpy
-pandas
-joblib
-psutil
-glob2
-tensorflow>=2.0.0
-bitstring
-scipy
-resampy
-gt3x>=0.0.2
+tensorflow==2.4.1
+pandas==1.2.4
+scipy==1.6.2
+psutil==5.8.0
+glob2==0.7
+resampy==0.2.2
+joblib==1.0.1
+gt3x==0.1.1
+numpy==1.19.5
+bitstring==3.1.7