Merge branch 'master' into release

Author: abukaj

README.rst

@@ -13,8 +13,8 @@ PyMICE Python library
     :target: https://www.gnu.org/licenses/gpl-3.0
     :alt: License: GPL v3 badge
 
-.. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.832982.svg
-   :target: https://doi.org/10.5281/zenodo.832982
+.. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.884419.svg
+   :target: https://doi.org/10.5281/zenodo.884419
    :alt: DOI badge
 
 PyMICE is a Python® library for mice behavioural data analysis.
@@ -38,12 +38,12 @@ We ask that  that reference to our paper as well as to the library itself is
 provided in any published research making use of PyMICE.
 
 The recommended in-text citation format is:
-``PyMICE (Dzik, Puścian, et al. 2017) v. 1.2.0 (Dzik, Łęski, & Puścian 2017)``
+``PyMICE (Dzik, Puścian, et al. 2017) v. 1.2.1 (Dzik, Łęski, & Puścian 2017)``
 
 and the recommended bibliography entry format:
 
-  Dzik J. M., Łęski S., Puścian A. (July 21, 2017) "PyMICE" computer software
-  (v. 1.2.0; RRID:nlx_158570) doi: 10.5281/zenodo.832982
+  Dzik J. M., Łęski S., Puścian A. (September 5, 2017) "PyMICE" computer
+  software (v. 1.2.1; RRID:nlx_158570) doi: 10.5281/zenodo.884419
 
   Dzik J. M., Puścian A., Mijakowska Z., Radwanska K., Łęski S. (June 22, 2017)
   "PyMICE: A Python library for analysis of IntelliCage data" Behavior Research
@@ -52,13 +52,13 @@ and the recommended bibliography entry format:
 If the journal does not allow for inclusion of the `resource identifier
 <http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0146300>`_
 (RRID:nlx_158570) in the bibliography, we ask to provide it in-text:
-``PyMICE (RRID:nlx_158570) [1] v. 1.2.0 [2]``
+``PyMICE (RRID:nlx_158570) [1] v. 1.2.1 [2]``
 
   1. Dzik JM, Puścian A, Mijakowska Z, Radwanska K, Łęski S. PyMICE: A Python
      library for analysis of IntelliCage data. Behav Res Methods. 2017.
      DOI: 10.3758/s13428-017-0907-5
-  2. Dzik JM, Łęski S, Puścian A. PyMICE [computer software]. Version 1.2.0.
-     Warsaw: Nencki Institute - PAS; 2017. DOI: 10.5281/zenodo.832982
+  2. Dzik JM, Łęski S, Puścian A. PyMICE [computer software]. Version 1.2.1.
+     Warsaw: Nencki Institute - PAS; 2017. DOI: 10.5281/zenodo.884419
 
 We have provided a solution to facilitate referencing to the library. Please
 run::

lib/pymice/_ICData.py

@@ -31,7 +31,6 @@
   unicode = str
 
 import os
-import zipfile
 import csv
 import warnings
 
@@ -63,8 +62,8 @@
                       DoorHardwareEvent, LedHardwareEvent,
                       UnknownHardwareEvent, Session)
 
-from ._Tools import (timeToList, PathZipFile, warn, groupBy, isString,
-                     mapAsList)
+from ._Tools import (timeToList, ArchiveZipFile, DirectoryZipFile, warn, groupBy,
+                     isString, mapAsList)
 from ._FixTimezones import inferTimezones, LatticeOrderer
 from ._Analysis import Aggregator
 
@@ -200,10 +199,10 @@ def _appendData(self, fname):
 
     if fname.endswith('.zip') or os.path.isdir(fname):
       if isString(fname) and os.path.isdir(fname):
-        zf = PathZipFile(fname)
+        zf = DirectoryZipFile(fname)
 
       else:
-        zf = zipfile.ZipFile(fname)
+        zf = ArchiveZipFile(fname)
 
       self._loadZip(zf, source=fname)
 
@@ -349,8 +348,9 @@ def _loadZip(self, zf, source=None):
 
   def _extractSessions(self, zf):
     try:
-      fh = self._openZipFile(zf, 'Sessions.xml')
-      dom = minidom.parse(fh)
+      with self._findAndOpenZipFile(zf, 'Sessions.xml') as fh:
+        dom = minidom.parse(fh)
+
       aos = dom.getElementsByTagName('ArrayOfSession')[0]
       ss = aos.getElementsByTagName('Session')
       sessions = []
@@ -416,55 +416,39 @@ def _getZipLoader(self, zf):
 
 
   def _checkVersion(self, zf):
-    fh = self._openZipFile(zf, 'DataDescriptor.xml')
-    dom = minidom.parse(fh)
+    with self._findAndOpenZipFile(zf, 'DataDescriptor.xml') as fh:
+      dom = minidom.parse(fh)
+
     dd = dom.getElementsByTagName('DataDescriptor')[0]
     version = dd.getElementsByTagName('Version')[0]
     versionStr = version.childNodes[0]
     assert versionStr.nodeType == versionStr.TEXT_NODE
     return versionStr.nodeValue.strip().lower()
 
   def _fromZipCSV(self, zf, path, source=None, oldLabels=None):
-    return self._fromCSV(self._openZipFile(zf, path + '.txt'),
-                         source=source,
-                         convert=self._convertZip.get(path),
-                         oldLabels=oldLabels)
+    with self._findAndOpenZipFile(zf, path + '.txt') as fh:
+      return self._fromCSV(fh,
+                           source=source,
+                           convert=self._convertZip.get(path),
+                           oldLabels=oldLabels)
 
   @staticmethod
-  def _openZipFile(zf, path):
+  def _findAndOpenZipFile(zf, path):
     try:
-      fh = zf.open(path)
+      return zf.open(path)
 
     except KeyError:
-      fh = zf.open('IntelliCage/' + path)
-
-    if sys.version_info >= (3, 0):
-      # if sys.version_info < (3, 2):
-      #   # XXX: Python3 monkey-path
-      #   fh.readable = lambda: True
-      #   fh.writable = lambda: False
-      #   fh.seekable = lambda: False
-      #   fh.read1 = items_file.read
-      #   #io.BytesIO(fh.read())
-      return io.TextIOWrapper(fh)
+      return zf.open('IntelliCage/' + path)
 
-    return fh
+  def _fromCSV(self, fh, source=None, convert=None, oldLabels=None):
+    return self.__fromCSV(list(csv.reader(fh, delimiter='\t')),
+                          source,
+                          convert,
+                          oldLabels)
 
-  @staticmethod
-  def _fromCSV(fname, source=None, convert=None, oldLabels=None):
-    if isString(fname):
-      fname = open(fname, 'rb')
-
-    reader = csv.reader(fname, delimiter='\t')
-    data = list(reader)
-    fname.close()
-
-    return Loader.__fromCSV(data, source, convert, oldLabels)
-
-  @staticmethod
-  def __fromCSV(data, source, convert, oldLabels):
+  def __fromCSV(self, data, source, convert, oldLabels):
     if len(data) == 0:
-      return
+      return None
 
     labels = data.pop(0)
     if isinstance(oldLabels, set):
@@ -476,7 +460,7 @@ def __fromCSV(data, source, convert, oldLabels):
       return dict((l, []) for l in labels)
 
     emptyStringToNone(data)
-    return Loader.__DictOfColumns(labels, data, source, convert)
+    return self.__DictOfColumns(labels, data, source, convert)
 
   class __DictOfColumns(dict):
     def __init__(self, labels, rows, source, conversions):
@@ -755,75 +739,6 @@ def _appendDataSource(self, dataSource):
 
     self._buildCache()
 
-# # TO BE MOVED TO DEBUG MODULE
-# import matplotlib.pyplot as plt
-# import matplotlib.patches as patches
-# from matplotlib.path import Path
-# import matplotlib.ticker
-#   def _plotData(self):
-#     # FIXME: obsoleted
-#     #fig, ax = plt.subplots()
-#     ax = plt.gca()
-#     ax.xaxis.set_major_formatter(matplotlib.ticker.FuncFormatter(lambda x, y: hTime(x)))
-#     plt.xticks(rotation=10)
-#     labels = []
-#     yticks = []
-#     times = []
-#     for i, dataSource in enumerate(self._dataSources):
-#       labels.append(str(i))
-#       start = dataSource.getStart()
-#       end = dataSource.getEnd()
-#       #plt.broken_barh([(start, end - start)], [i - 0.4, 0.8])
-#       times.extend([start, end])
-#       dataSource.plotChannel(i + 0.6, i + 1.4)
-#       yticks.append(i)
-#
-#     plt.yticks(yticks, labels)
-#     start = min(times)
-#     end = max(times)
-#     span = end - start
-#     plt.xlim(start - 0.1 * span, end + 0.1 * span)
-#     plt.ylim(0, len(self._dataSources) + 1)
-#
-#   def _plotChannelR(self, top=1., bottom=0.):
-#     h = top - bottom
-#     l = len(self._dataSources)
-#     h2 = h / l
-#     starts, ends = [], []
-#
-#     for i, dataSource in enumerate(self._dataSources):
-#       start, end = dataSource._plotChannelR(bottom + i * h2, bottom + (i + 1) * h2)
-#       starts.append(start)
-#       ends.append(end)
-#
-#     if self.maskTimeStart is not None and self.maskTimeEnd is not None:
-#       left = self.maskTimeStart if self.maskTimeStart is not None else self.getStart()
-#       right = self.maskTimeEnd if self.maskTimeEnd is not None else self.getEnd()
-#       ax = plt.gca()
-#       codes = [Path.MOVETO, Path.LINETO]
-#       verts = [(left, top), (right, top)]
-#       if self.maskTimeEnd is not None:
-#         codes.append(Path.LINETO)
-#         ends.append(self.maskTimeEnd)
-#
-#       else:
-#         codes.append(Path.MOVETO)
-#
-#       verts.append((right, bottom))
-#       codes.append(Path.LINETO)
-#       verts.append((left, bottom))
-#       if self.maskTimeStart is not None:
-#         verts.append((left, top))
-#         codes.append(Path.CLOSEPOLY)
-#         starts.append(self.maskTimeStart)
-#
-#       path = Path(verts, codes)
-#       patch = patches.PathPatch(path, facecolor='none', edgecolor='red')
-#       ax.add_patch(patch)
-#
-#
-#     return min(starts), max(ends)
-
 
 class ICSide(int):
   #__slots__ = ('__Corner',)

lib/pymice/_Tools.py

@@ -32,21 +32,33 @@
 from operator import attrgetter
 
 import pytz
-
-#from numbers import Number
-#import numpy as np
-#if not issubclass(np.floating, Number):
-#  Number.register(np.floating)
+import zipfile
 
 from ._FixTimezones import LatticeOrderer
 
-# XXX: isString, mapAsList are imported from elsewhere
-if sys.version_info >= (3, 0):
+# XXX: imported objects are imported from elsewhere
+if sys.version_info.major >= 3:
   from ._Python3.Tools import isString, mapAsList
 
+  import io
+
+  class ArchiveZipFile(zipfile.ZipFile):
+    def open(self, *args, **kwargs):
+      return io.TextIOWrapper(super(ArchiveZipFile, self).open(*args, **kwargs))
+      # if sys.version_info < (3, 2):
+      #   # XXX: Python3 monkey-path
+      #   fh.readable = lambda: True
+      #   fh.writable = lambda: False
+      #   fh.seekable = lambda: False
+      #   fh.read1 = items_file.read
+      #   #io.BytesIO(fh.read())
+
 else:
   from ._Python2.Tools import isString, mapAsList
 
+  class ArchiveZipFile(zipfile.ZipFile):
+    pass
+
 
 def timeString(x, tz=None):
   return datetime.fromtimestamp(x, tz).strftime('%Y-%m-%d %H:%M:%S.%f%z')
@@ -165,6 +177,7 @@ def timeToList(tStr):
   #return map(int, tokens[:5] + [seconds, round(decimal * 1000000)])
   return LatticeOrderer.Node(map(int, tokens[:5] + [seconds, round(decimal * 1000000)]))
 
+
 class timeListList(list):
   def __eq__(self, x):
     return self[0] == x[0]
@@ -185,7 +198,7 @@ def __gt__(self, x):
     return self[0] > x[0]
 
 
-class PathZipFile(object):
+class DirectoryZipFile(object):
   """
   A class emulating zipfile.ZipFile behaviour with filesystem directories.
   """
@@ -201,14 +214,6 @@ def open(self, name, mode='r'):
       raise KeyError(name)
 
 
-
-
-
-
-
-
-
-
 def groupBy(objects, getKey=lambda x: x, requiredKeys=()):
   """
   >>> import operator

test/testData.py

@@ -1314,6 +1314,11 @@ def testGetOrderedHwTypes(self):
     self.assertEqual(['Air', 'Air', 'LED', 'Door', 'Door', 'LED'],
                      [h.Type for h in self.data.getHardwareEvents(order='DateTime')])
 
+
+class LoadUncompressedIntelliCagePlus3DataTest(LoadIntelliCagePlus3DataTest):
+  DATA_FILE = 'icp3_data'
+
+
 class LoadEmptyDataTest(LoaderIntegrationTest):
   DATA_FILE = 'empty_data.zip'