Merge branch 'develop'

loren_frank_data_processing/__init__.py

@@ -1,4 +1,5 @@
 # flake8: noqa
+from .core import Animal
 from .multiunit import (get_multiunit_dataframe,
                         get_multiunit_indicator_dataframe)
 from .neurons import (get_spike_indicator_dataframe, get_spikes_dataframe,

loren_frank_data_processing/core.py

@@ -1,17 +1,18 @@
 '''Functions for accessing data in the Frank lab format and saving
 
 '''
-
+from collections import namedtuple
 from logging import getLogger
 from os.path import join
-from sys import exit
 
 import numpy as np
 import pandas as pd
 from scipy.io import loadmat
 
 logger = getLogger(__name__)
 
+Animal = namedtuple('Animal', {'directory', 'short_name'})
+
 
 def get_data_filename(animal, day, file_type):
     '''Returns the Matlab file name assuming it is in the Raw Data
@@ -72,7 +73,7 @@ def get_epochs(animal, day):
             get_data_filename(animal, day, 'task'))
         return [(animal, day, ind + 1)
                 for ind, epoch in enumerate(task_file['task'][0, -1][0])]
-    except IOError as err:
+    except (IOError, TypeError) as err:
         logger.error('Failed to load file {0}'.format(
             get_data_filename(animal, day, 'task')))
         exit()
@@ -102,10 +103,9 @@ def get_data_structure(animal, day, file_type, variable):
     '''
     try:
         file = loadmat(get_data_filename(animal, day, file_type))
-    except IOError:
+    except (IOError, TypeError):
         logger.error('Failed to load file: {0}'.format(
             get_data_filename(animal, day, file_type)))
-        exit()
     n_epochs = file[variable][0, -1].size
     return [file[variable][0, -1][0, ind]
             for ind in np.arange(n_epochs)]

loren_frank_data_processing/tetrodes.py

@@ -3,7 +3,7 @@
 import pandas as pd
 from scipy.io import loadmat
 
-from .core import _convert_to_dict, reconstruct_time
+from .core import _convert_to_dict, reconstruct_time, logger
 
 
 def get_tetrode_info_path(animal):
@@ -53,8 +53,9 @@ def get_LFP_dataframe(tetrode_key, animals):
             data=lfp_data['data'][0, 0].squeeze(),
             index=lfp_time,
             name='electric_potential')
-    except FileNotFoundError:
-        pass
+    except (FileNotFoundError, TypeError):
+        logger.error('Failed to load file: {0}'.format(
+            get_LFP_filename(tetrode_key, animals)))
 
 
 def make_tetrode_dataframe(animals):

setup.py

@@ -8,7 +8,7 @@
 
 setup(
     name='loren_frank_data_processing',
-    version='0.3.4.dev0',
+    version='0.3.5.dev0',
     license='GPL-3.0',
     description=('Import data from Loren Frank lab'),
     author='Eric Denovellis',