Python 3 Compatibility

Author: mbrockman1

cili/cleanup.py

@@ -1,4 +1,4 @@
-from models import *
+from .models import *
 import pandas as pd
 
 #-------------------------------------------------------------
@@ -189,8 +189,8 @@ def ev_row_idxs(samples, events):
     """
     import numpy as np
     idxs = []
-    for idx, dur in events.duration.iteritems():
-        idxs.extend(range(idx, int(idx+dur)))
+    for idx, dur in events.duration.items():
+        idxs.extend(list(range(idx, int(idx+dur))))
     idxs = np.unique(idxs)
     idxs = np.intersect1d(idxs, samples.index.tolist())
     return idxs
@@ -221,7 +221,7 @@ def adjust_eyelink_recov_idxs(samples, events, z_thresh=.1, window=1000, kernel_
         threshold.
     """
     import numpy as np
-    from util import PUP_FIELDS
+    from .util import PUP_FIELDS
     # find a pupil size field to use
     p_fields = [f for f in samples.columns if f in PUP_FIELDS]
     if len(p_fields) == 0:
@@ -236,11 +236,11 @@ def adjust_eyelink_recov_idxs(samples, events, z_thresh=.1, window=1000, kernel_
     samp_count = len(samples)
     # search for drop beneath z_thresh after end index
     new_durs = []
-    for idx, dur in events.duration.iteritems():
+    for idx, dur in events.duration.items():
         try:
             s_pos = samples.index.get_loc(idx + dur)  - 1
             e_pos = samples.index[min(s_pos+window, samp_count-1)]
-        except Exception, e:
+        except Exception as e:
             # can't do much about that
             s_pos = e_pos = 0
         if s_pos == e_pos:

cili/extract.py

@@ -1,4 +1,4 @@
-from models import *
+from .models import *
 import pandas as pd
 import numpy as np
 from copy import deepcopy
@@ -64,7 +64,7 @@ def extract_event_ranges(samples, events_dataframe, start_offset=0,
     r_len = len(np.where(ev_idxs)[0]) + 1
     # we're going to make a df with a hierarchical index.
     samples['orig_idx'] = samples.index
-    midx = pd.MultiIndex.from_product([range(len(e_starts)), range(r_len)],
+    midx = pd.MultiIndex.from_product([list(range(len(e_starts))), list(range(r_len))],
         names=['event', 'onset'])
     # get all of the samples!
     # idxs = []
@@ -159,7 +159,7 @@ def extract_events(samples, events, offset=0, duration=0,
 
     # make a hierarchical index
     samples['orig_idx'] = samples.index
-    midx = pd.MultiIndex.from_product([range(len(e_starts)), range(r_dur)],
+    midx = pd.MultiIndex.from_product([list(range(len(e_starts))), list(range(r_dur))],
         names=['event', 'onset'])
     # get the samples
     df = pd.DataFrame()

cili/models.py

@@ -54,15 +54,15 @@ def __init__(self, *args, **kwargs):
 
     def save(self, save_path):
         s = pt.HDFStore(save_path)
-        for k in self.dframes.keys():
+        for k in list(self.dframes.keys()):
             s[k] = self.dframes[k]
         s.close()
 
     @classmethod
     def load_saved(cls, save_path):
         obj = cls()
         s = pt.HDFStore(save_path)
-        obj.dframes = dict([(k[1:],s[k]) for k in s.keys()])
+        obj.dframes = dict([(k[1:],s[k]) for k in list(s.keys())])
         s.close()
         return obj
 
@@ -93,7 +93,7 @@ def from_list_of_dicts(cls, events_list):
             corresponding DataFrame.
         """
         import os
-        from cPickle import load as pload
+        from pickle import load as pload
         if isinstance(events_list, str):
             if not os.path.isfile(events_list):
                 raise ValueError("Could not find file %s" % events_list)
@@ -108,13 +108,13 @@ def from_list_of_dicts(cls, events_list):
                 evd[ev["name"]] = [ev]
             else:
                 evd[ev["name"]].append(ev)
-        for k in evd.keys():
+        for k in list(evd.keys()):
             evd[k] = pd.DataFrame(evd[k])
         return cls.from_dict(evd)
 
     def _local_dir(self):
         """ add the string-like attributes from the info_axis """
-        return [c for c in self.dframes.keys()
+        return [c for c in list(self.dframes.keys())
             if isinstance(c, string_types) and isidentifier(c)]
 
     def __dir__(self):

cili/util.py

@@ -6,7 +6,7 @@
 from time import sleep
 import numpy as np
 
-from models import *
+from .models import *
 
 ASC_SFIELDS_EYE = {
     'l':[('onset', np.int64),
@@ -174,10 +174,10 @@ def pandas_df_from_txt(file_path):
     # accordingly. It would be nice if the dtypes would work in read_csv, but
     # so far no luck...
     df = pd.read_csv(file_path, sep="\t", index_col="TIMESTAMP", low_memory=False, na_values=["."],)
-    fields = [str(x) for x in df.dtypes.keys()]
-    dtypes = dict([(d, object) for d in fields if not d in TXT_FIELDS.keys()])
-    dtypes.update(dict([(k, v) for k, v in TXT_FIELDS.iteritems() if k in fields]))
-    nums = [k for k, v in dtypes.iteritems() if v not in [object]]
+    fields = [str(x) for x in list(df.dtypes.keys())]
+    dtypes = dict([(d, object) for d in fields if not d in list(TXT_FIELDS.keys())])
+    dtypes.update(dict([(k, v) for k, v in TXT_FIELDS.items() if k in fields]))
+    nums = [k for k, v in dtypes.items() if v not in [object]]
     ints = [k for k in nums if dtypes[k] in TXT_INT_TYPES]
     df[nums] = df[nums].convert_objects(convert_numeric=True)
     df[ints] = df[ints].astype(np.int64)
@@ -233,9 +233,9 @@ def pandas_dfs_from_asc(file_path):
 
 def pandas_df_from_lines(csv_lines, dtypes, ignore):
     import pandas as pd
-    import cStringIO
-    c = cStringIO.StringIO("".join(csv_lines))
-    fields, dts = zip(*dtypes)
+    import io
+    c = io.StringIO("".join(csv_lines))
+    fields, dts = list(zip(*dtypes))
     # use_names = [n for n in fields if not n in ignore]
     df = pd.read_csv(c,
                      delim_whitespace=True,
@@ -404,14 +404,14 @@ def list_run_corruption(asc_dir):
     vals = {}
     for i, fn in enumerate(files):
         vals[os.path.basename(fn)] = file_checks[i]
-    print "\nDropout by File:"
+    print("\nDropout by File:")
     pprint(vals)
 
 def constrain_events(samples, events):
     """ adjusts start times of any events that overflow sample bounds"""
     lowtime = samples.index[0]
     hightime = samples.index[-1]
-    enames = events.dframes.keys()
+    enames = list(events.dframes.keys())
     for en in enames:
         df = events.dframes[en]
         idxs = np.where(df.index < lowtime)[0]
@@ -435,7 +435,7 @@ def main(argv=None):
     try:
         try:
             opts, args = getopt.getopt(argv[1:], "d:", ["dir", "dropout"])
-        except getopt.error, msg:
+        except getopt.error as msg:
             raise Usage(msg="\n"+str(msg))
         # option processing
         drop_check = False
@@ -452,12 +452,12 @@ def main(argv=None):
         if drop_check and asc_dir:
             list_run_corruption(asc_dir)
             return
-    except Usage, err:
+    except Usage as err:
         f_str = sys.argv[0].split("/")[-1] + ":"
         lfs = len(f_str)
         f_str = "%s\n%s\n%s\n" % ("-"*lfs, f_str, "-"*lfs)
-        print >> sys.stderr, f_str + str(err.msg)
-        print >> sys.stderr, "-------------------\nfor help use --help\n-------------------"
+        print(f_str + str(err.msg), file=sys.stderr)
+        print("-------------------\nfor help use --help\n-------------------", file=sys.stderr)
         return 2
 
 if __name__ == '__main__':

tests/test_extract.py

@@ -4,7 +4,7 @@
 from nose.tools import assert_equal, assert_true, assert_raises, raises
 from numpy.testing import assert_array_equal
 
-from config import *
+from .config import *
 from cili.extract import *
 from cili.util import load_eyelink_dataset, pandas_dfs_from_asc
 

tests/test_util.py

@@ -5,7 +5,7 @@
 from pandas.util.testing import assert_frame_equal
 from nose.tools import assert_equal, assert_true, assert_raises, raises
 
-from config import *
+from .config import *
 from cili.util import load_eyelink_dataset, pandas_dfs_from_asc
 
 # Unit tests for the util module. Paths to data files assume tests
@@ -154,7 +154,7 @@ def test_event_types():
     # make sure the full list of events is there
     ds, es = pandas_dfs_from_asc(paths['binoRemote500'])
     test_evs = ['END', 'EFIX', 'EBLINK', 'START', 'ESACC', 'MSG']
-    assert_array_equal(es.dframes.keys(), test_evs)
+    assert_array_equal(list(es.dframes.keys()), test_evs)
 
 def test_end_fields():
     ds, es = pandas_dfs_from_asc(paths['binoRemote500'])