def _createAtom(self, enum, dflt, base='uint32', shape=()):
"""Create and check an enumerated atom."""
enumatom = tables.EnumAtom(enum, dflt, base=base, shape=shape)
sameEnum = tables.Enum(enum)
self.assertEqual(enumatom.type, 'enum')
self.assertEqual(enumatom.dtype.base.name, enumatom.base.type)
self.assertEqual(enumatom.shape, shape)
self.assertEqual(enumatom.enum, sameEnum)
def test_enum_default_persistence_black(self):
dflt = 'black'
atom = tables.EnumAtom(
self.enum, dflt, base=self.enumType, shape=())
self.h5file.create_earray('/', 'test', atom, shape=(0,),
title=self._getMethodName())
self._reopen()
self.assertEqual(
self.h5file.root.test.get_enum(), self.enum,
"Enumerated type was not restored correctly from disk.")
self.assertEqual(
self.h5file.root.test.atom.dflt, self.enum[dflt],
"The default value of enumerated type was not restored correctly "
"from disk.")
row['ballTime'] = now + 42
row['ballColor'] = 1234
tbl.flush()
COMMENT("Now print them!")
for r in tbl:
ballTime = r['ballTime']
ballColor = colors(r['ballColor']) # notice this
print "Ball extracted on %d is of color %s." % (ballTime, ballColor)
COMMENT("**** Enumerated arrays. ****")
COMMENT("This describes a range of working days.")
workingDays = {'Mon': 1, 'Tue': 2, 'Wed': 3, 'Thu': 4, 'Fri': 5}
dayRange = tables.EnumAtom(workingDays, 'Mon', base='uint16', shape=(0, 2))
COMMENT("Create an EArray of day ranges within a week.")
earr = h5f.createEArray('/', 'days', dayRange, title="Working day ranges")
earr.flavor = 'python'
COMMENT("Throw some day ranges in.")
wdays = earr.getEnum()
earr.append([(wdays.Mon, wdays.Fri), (wdays.Wed, wdays.Fri)])
COMMENT("The append method does not check values!")
earr.append([(wdays.Mon, 1234)])
COMMENT("Print the values.")
for (d1, d2) in earr:
print "From %s to %s (%d days)." % (wdays(d1), wdays(d2), d2 - d1 + 1)
def _atom(self, shape=()):
return tables.EnumAtom(
self.enum, 'red', base=self.enumType, shape=shape)
@license GPLv2
"""
import itertools
import numarray
import numpy
import sys
import tables
import Biclustering.Array
import Biclustering.Bit
import Biclustering.Sizing
NESTED = tables.Enum(['nonnested', 'nested', 'unknown'])
NESTED_ATOM = tables.EnumAtom(NESTED,
dtype='UInt8',
shape=(0, ),
flavor='numpy')
class Group(object):
def __init__(self,
file,
group,
maxConditions,
maxGenes,
create=True,
minGenes=2):
"""Creates Bicluster Table
@param file file to create Table on
@param group group to which to attach Group
