General bug fixes

forest/jasmine/data2mobmat.py

@@ -127,8 +127,8 @@ def collapse_data(data, itrvl, accuracylim):
                  fourth is none
     """
     data = data[data.accuracy<accuracylim]
-    t_start = np.array(data.timestamp)[0]/1000
-    t_end = np.array(data.timestamp)[-1]/1000
+    t_start = sorted(np.array(data.timestamp))[0]/1000
+    t_end = sorted(np.array(data.timestamp))[-1]/1000
     avgmat = np.empty([int(np.ceil((t_end-t_start)/itrvl))+2,4])
     sys.stdout.write("Collapse data within " + str(itrvl)+" second intervals ..."+'\n')
     IDam = 0

forest/jasmine/traj2stats.py

@@ -49,10 +49,10 @@ def gps_summaries(traj,tz_str,option):
             sys.stdout.write("Calculating the daily summary stats..." + '\n')
             time_list = stamp2datetime(traj[0,3],tz_str)
             time_list[3]=0; time_list[4]=0; time_list[5]=0
-            start_stamp = datetime2stamp(time_list,tz_str) + 3600*24
+            start_stamp = datetime2stamp(time_list,tz_str)
             time_list = stamp2datetime(traj[-1,3],tz_str)
             time_list[3]=0; time_list[4]=0; time_list[5]=0
-            end_stamp = datetime2stamp(time_list,tz_str)
+            end_stamp = datetime2stamp(time_list,tz_str) + 3600*24
             ## if it starts from 2019-3-8 11 o'clock, then our daily summary starts from 2019-3-9)
             h = (end_stamp - start_stamp)/60/60/24
             window = 60*60*24

forest/poplar/functions/log.py

@@ -112,13 +112,12 @@ def log_to_csv(log_dir, level = logging.DEBUG,
     '''
     try:
         # initialize csv
-        filepath = setup_csv(name = log_name, directory = log_dir, 
-                             header = header)
+        filepath = setup_csv(name=log_name, dirpath=log_dir, header=header)
         # configure logging output
         logging.basicConfig(format = log_format,
                             filename = filepath,
                             level = level, force = True)
         # success message
         logger.info('Writing log messages to %s.csv...' % log_name)
     except:
-        logger.warning('Unable to write logging messages.')
+        logger.warning('Unable to write logging messages.')

forest/poplar/legacy/common_funcs.py

@@ -109,7 +109,7 @@ def read_data(ID:str, study_folder: str, datastream:str, tz_str: str, time_start
                 else:
                     stamp_start1 = identifiers["timestamp"][0]/1000
             else:
-                stamp_start1 = filestamps[0]
+                stamp_start1 = sorted(filestamps)[0]
             ## now determine the starting and ending time according to the Docstring
             if time_start == None:
                 stamp_start = stamp_start1
@@ -119,12 +119,12 @@ def read_data(ID:str, study_folder: str, datastream:str, tz_str: str, time_start
             ##Last hour: look at all the subject's directories (except survey) and find the latest date for each directory
             directories = os.listdir(study_folder + "/" + ID)
             directories = list(set(directories)-set(["survey_answers","survey_timings"]))
-            lastDate = []
+            all_timestamps = []
             for i in directories:
                 files = os.listdir(study_folder + "/" + ID + "/" + i)
-                lastDate.append(files[-1])
-            stamp_end_vec = [filename2stamp(j) for j in lastDate]
-            stamp_end1 = max(stamp_end_vec)
+                all_timestamps += [filename2stamp(filename) for filename in files]
+            ordered_timestamps = sorted([timestamp for timestamp in all_timestamps if timestamp is not None])
+            stamp_end1 = ordered_timestamps[-1]
             if time_end == None:
                 stamp_end = stamp_end1
             else:

setup.py

@@ -18,7 +18,7 @@
 
 setup(
     name = 'forest',
-    version = '0.1',
+    version = '0.1.1',
     description = '--add description here--',
     long_description = readme,
     author = 'Onnela Lab',