Trying to fix pickle

.gitignore

@@ -2,4 +2,5 @@
 .DS_Store
 *.pyc
 __pycache__
-logs/
+logs/
+data/

functions/signal_processing_functions.py

@@ -3,10 +3,16 @@
 """
 import sys
 import logging
-import resampy # to resample frequency
+
 import numpy as np
 from scipy import signal
-from multiprocessing import cpu_count
+import resampy
+import math
+try:
+    from multiprocessing import cpu_count
+except ImportError:
+    def cpu_count():
+        return 1
 
 try:
     from joblib import Parallel
@@ -100,6 +106,7 @@ def resample_acceleration(data, from_hz, to_hz, use_parallel = False, num_jobs =
 
 	# calculate number of 1 sec samples (note that hz is the frequency per second)
 	num_seconds = len(data) // from_hz
+	# num_seconds = len(data)/from_hz)
 
 	# calculate number of new samples required when data is resampled
 	num_samples = num_seconds * to_hz

infer_nw_time.py

@@ -79,11 +79,15 @@ def parse_arguments():
 
 			# read file as numpy array
 			data = np.load(file)
+			data.allow_pickle = True;
+
 			# extract raw acceleration data from numpy.
 			actigraph_acc = data['raw_data']
 
 			# read meta data from file
 			meta_data = data['meta_data']
+			if type(meta_data) is np.ndarray:
+				meta_data = meta_data.tolist()
 
 			# convert acceleration values to g values
 			actigraph_acc = rescale_log_data(log_data = actigraph_acc, acceleration_scale = meta_data['Acceleration_Scale'])

read_data.py

@@ -0,0 +1,26 @@
+import os
+import numpy as np
+import tempfile as tmp
+
+# import functions
+from functions.helper_functions import set_start, set_end, read_directory, create_directory
+from gt3x import unzip_gt3x_file, extract_info, extract_log, create_time_array, rescale_log_data
+
+
+file = "data/AI12_NEO1F09120034_2017-09-25.gt3x"
+save_folder = tmp.TemporaryDirectory()
+save_folder = save_folder.name
+delete_source_file = False
+# unzip .gt3x file and get the file location of the binary log.bin (which contains the raw data) and the info.txt which contains the meta-data
+log_bin, info_txt, _, _ = unzip_gt3x_file(f = file, save_location = save_folder, delete_source_file = delete_source_file)
+
+# get meta data from info.txt file
+meta_data = extract_info(info_txt)
+
+# read raw data from binary data
+log_data, time_data = extract_log(log_bin = log_bin, acceleration_scale = float(meta_data['Acceleration_Scale']), sample_rate = int(meta_data['Sample_Rate']), use_scaling = False)
+
+actigraph_acc = rescale_log_data(log_data = log_data, acceleration_scale = meta_data['Acceleration_Scale'])
+
+# convert time data to correct time series array with correct miliseconds values
+actigraph_time = create_time_array(time_data)

read_raw_gt3x.py

@@ -73,7 +73,7 @@ def process_gt3x_file(idx, total, file, save_folder, delete_source_file, delete_
 
 
 	# unzip .gt3x file and get the file location of the binary log.bin (which contains the raw data) and the info.txt which contains the meta-data
-	# log_bin, info_txt = unzip_gt3x_file(f = file, save_location = save_folder, delete_source_file = delete_source_file)
+	# log_bin, info_txt, _, _ = unzip_gt3x_file(f = file, save_location = save_folder, delete_source_file = delete_source_file)
 
 	# # get meta data from info.txt file
 	# meta_data = extract_info(info_txt)