def testNRAFromRA(self):
"""Check the array function with a RecArray instance.
"""
buffer_ = [('Cuke', 123, (45, 67)), ('Tader', 321, (76, 54))]
names = ['name', 'value', 'pair']
formats = ['a6', 'Int8', '(2,)Int16']
ra = numarray.records.array(
buffer_, names=names, formats=formats)
## buffer_, names=names, formats=formats, aligned=True)
names1 = ['newName', 'newValue', 'newPair']
nra0 = nra.array(buffer=ra, descr=zip(names1, formats))
nra1 = nra.array(buffer=buffer_, descr=zip(names1, formats))
self.assert_(common.areArraysEqual(nra0, nra1))
# Bad number of fields
badFormats = ['Int8', '(2,)Int16']
self.assertRaises(ValueError, nra.array, buffer=ra,
formats=badFormats)
# Bad format in the first field
badFormats = ['a9', 'Int8', '(2,)Int16']
self.assertRaises(ValueError, nra.array, buffer=ra,
formats=badFormats)
def testNRAFromNRA(self):
"""Check the array function with a NestedRecArray instance.
"""
nra0 = nra.array(buffer=self.buffer, descr=self.descr)
my_Descr = [('ID', 'Int64'),
('data', [('name', [('first', 'a9'), ('second', 'a9')]),
('coord', [('x', 'Float32'), ('y', 'f4'),
('z', 'f4')])])]
nra1 = nra.array(buffer=self.buffer, descr=my_Descr)
nra2 = nra.array(buffer=nra0, descr=my_Descr)
self.assert_(common.areArraysEqual(nra2, nra1))
# Bad number of fields
badDescr = [('data', [('name', [('first', 'a9'), ('second', 'a9')]),
('coord', [('x', 'Float32'), ('y', 'f4'),
('z', 'f4')])])]
self.assertRaises(ValueError, nra.array, buffer=nra0, descr=badDescr)
# Bad format in the first field
badDescr = [('ID', 'b1'),
('data', [('name', [('first', 'a9'), ('second', 'a9')]),
('coord', [('x', 'Float32'), ('y', 'f4'),
('z', 'f4')])])]
self.assertRaises(ValueError, nra.array, buffer=nra0, descr=badDescr)
def testNRAFromNRA(self):
"""Check the array function with a NestedRecArray instance.
"""
nra0 = nra.array(buffer=self.buffer, descr=self.descr)
my_Descr = [('ID', 'Int64'),
('data', [('name', [('first','a9'), ('second','a9')]),
('coord', [('x','Float32'), ('y', 'f4'), ('z', 'f4')])])]
nra1 = nra.array(buffer=self.buffer, descr=my_Descr)
nra2 = nra.array(buffer=nra0, descr=my_Descr)
self.assert_(common.areArraysEqual(nra2, nra1))
# Bad number of fields
badDescr = [
('data', [('name', [('first','a9'), ('second','a9')]),
('coord', [('x','Float32'), ('y', 'f4'), ('z', 'f4')])])]
self.assertRaises(ValueError, nra.array, buffer=nra0,
descr=badDescr)
# Bad format in the first field
badDescr = [('ID', 'b1'),
('data', [('name', [('first','a9'), ('second','a9')]),
('coord', [('x','Float32'), ('y', 'f4'), ('z', 'f4')])])]
self.assertRaises(ValueError, nra.array, buffer=nra0,
descr=badDescr)
def testGetNestedField(self):
"""Check the NestedRecArray.field method.
"""
nra0 = nra.array(descr=self.descr, buffer=self.buffer)
# Test top level nested fields
# The info field
buffer = [
[('Paco', 'Perez'), (10, 20, 30)],
[('Maria', 'Luisa'), (0, 2.0, 10)],
[('C3Peanut', 'Tofu'), (10, 30, 20)]
]
my_descr = [('name', [('first','a9'), ('second','a9')]),
('coord', [('x','Float32'), ('y', 'f4'), ('z', 'f4')])]
model = nra.array(buffer, descr=my_descr)
modelFirst = model.field('name/first')
nra1 = nra0.field('info')
nra1First = nra1.field('name/first')
nra2 = nra1.field('name')
nra3=nra2.field('first')
self.assert_(common.areArraysEqual(model, nra1))
self.assert_(common.areArraysEqual(modelFirst, nra1First))
self.assert_(common.areArraysEqual(modelFirst, nra3))
def testSetSlice(self):
"""Set a nested array slice.
"""
nra0 = nra.array(descr=self.descr, buffer=self.buffer)
buffer = [[10, (('Paco', 'Perez'), (10, 20, 30))],
[20, (('Maria', 'Luisa'), (0, 2.0, 10))],
[30, (('C3Peanut', 'Tofu'), (10, 30, 20))]]
model = nra.array(buffer, descr=self.descr)
nra0[0:3] = model[0:3]
self.assert_(common.areArraysEqual(nra0, model))
def test05c_modifyingColumns(self):
"""Checking modifying several columns using a numarray buffer."""
table = self.fileh.root.table
dtype = [('x', '(2,)i4'), ('y', '(2,2)f8'), ('z', 'u1')]
nparray = nra.array(shape=(3, ), descr=dtype)
nparray.field('x')[:] = 1
nparray.field('y')[:] = 1
nparray.field('z')[:] = 2
table.modifyColumns(3, 6, 1, nparray, ['x', 'y', 'z'])
if self.close:
self.fileh.close()
self.fileh = openFile(self.file, "a")
table = self.fileh.root.table
ycol = ones((3, 2, 2), 'Float64')
data = table.cols.y[3:6]
if common.verbose:
print "Type of read:", type(data)
print "First 3 elements of read:", data[:3]
print "Length of the data read:", len(data)
if common.verbose:
print "ycol-->", ycol
print "data-->", data
# Check that both numarray objects are equal
self.assertTrue(isinstance(data, NumArray))
# Check the type
self.assertEqual(data.type(), ycol.type())
self.assertEqual(str(data), str(ycol))
def test05c_modifyingColumns(self):
"""Checking modifying several columns using a numarray buffer."""
table = self.fileh.root.table
dtype=[('x', '(2,)i4'), ('y', '(2,2)f8'), ('z', 'u1')]
nparray = nra.array(shape=(3,), descr=dtype)
nparray.field('x')[:] = 1
nparray.field('y')[:] = 1
nparray.field('z')[:] = 2
table.modifyColumns(3, 6, 1, nparray, ['x', 'y', 'z'])
if self.close:
self.fileh.close()
self.fileh = openFile(self.file, "a")
table = self.fileh.root.table
ycol = ones((3, 2, 2), 'Float64')
data = table.cols.y[3:6]
if common.verbose:
print "Type of read:", type(data)
print "First 3 elements of read:", data[:3]
print "Length of the data read:", len(data)
if common.verbose:
print "ycol-->", ycol
print "data-->", data
# Check that both numarray objects are equal
self.assertTrue(isinstance(data, NumArray))
# Check the type
self.assertEqual(data.type(), ycol.type())
self.assertEqual(str(data), str(ycol))
def testSetRow2NestedRecord(self):
"""Check the NestedRecArray.__setitem__ with NestedRecord instances.
"""
nra0 = nra.array(descr=self.descr, buffer=self.buffer)
buffer = [[10, (('Paco', 'Perez'), (10, 20, 30))],
[20, (('Maria', 'Luisa'), (0, 2.0, 10))],
[30, (('C3Peanut', 'Tofu'), (10, 30, 20))]]
model = nra.array(buffer, descr=self.descr)
nra0[0] = model[0]
nra0[1] = model[1]
nra0[2] = model[2]
self.assert_(common.areArraysEqual(nra0, model))
def testSetSlice(self):
"""Set a nested array slice.
"""
nra0 = nra.array(descr=self.descr, buffer=self.buffer)
buffer = [
[10, (('Paco', 'Perez'), (10, 20, 30))],
[20, (('Maria', 'Luisa'), (0, 2.0, 10))],
[30, (('C3Peanut', 'Tofu'), (10, 30, 20))]
]
model = nra.array(buffer, descr=self.descr)
nra0[0:3] = model[0:3]
self.assert_(common.areArraysEqual(nra0, model))
def testNRAadd(self):
"""Check the addition of nested arrays.
"""
ra1 = numarray.records.array([[1, 2], [3, 4]],
formats=['Int32', 'Int32'])
ra2 = numarray.records.array([[5, 6], [7, 8]],
formats=['Int32', 'Int32'])
ra3 = ra1 + ra2
nra1 = nra.array(buffer=ra1, descr=[('c1', 'Int32'), ('c2', 'Int32')])
nra2 = nra.array(buffer=ra2, descr=[('a', 'Int32'), ('b', 'Int32')])
nra3 = nra1 + nra2
nra4 = nra1 + ra1
self.assert_(common.areArraysEqual(nra3._flatArray, ra3))
self.assertEqual(nra3.descr, nra1.descr)
self.assert_(
common.areArraysEqual(nra4._flatArray, nra1._flatArray + ra1))
self.assertRaises(TypeError, nra.NestedRecArray.__add__, nra1, 3)
def testSetRow2NestedRecord(self):
"""Check the NestedRecArray.__setitem__ with NestedRecord instances.
"""
nra0 = nra.array(descr=self.descr, buffer=self.buffer)
buffer = [
[10, (('Paco', 'Perez'), (10, 20, 30))],
[20, (('Maria', 'Luisa'), (0, 2.0, 10))],
[30, (('C3Peanut', 'Tofu'), (10, 30, 20))]
]
model = nra.array(buffer, descr=self.descr)
nra0[0] = model[0]
nra0[1] = model[1]
nra0[2] = model[2]
self.assert_(common.areArraysEqual(nra0, model))
def testNRAFromArrayList(self):
"""Check the fromarrays function.
"""
# arrayList argument is a list of lists
nra0 = nra.array(buffer=self.buffer, descr=self.descr)
nra1 = nra.fromarrays(self.array_list, formats=self.formats)
nra2 = nra.fromarrays(self.array_list,
formats=self.formats, names=self.names)
nra3 = nra.fromarrays(self.array_list, descr=self.descr)
self.assertEqual(common.areArraysEqual(nra1, nra2), False)
self.assert_(common.areArraysEqual(nra2, nra3))
self.assert_(common.areArraysEqual(nra0, nra2))
# arrayList argument is a list of NestedRecArrays
nra0 = nra.array(buffer=[[1,4],[2,4]], formats=['f8','f4'])
self.assertRaises(TypeError, nra.fromarrays,
[nra0, nra0.field('c2')], formats=[['f8','f4'],'f4'])
def testGetBottomLevelField(self):
"""Check the NestedRecArray.field method.
"""
nra0 = nra.array(descr=self.descr, buffer=self.buffer)
# Test bottom level fields
nra1 = nra0.field('info/coord/x')
ra1 = numarray.array([10, 0, 10], type='Float32')
self.assert_(common.areArraysEqual(nra1, ra1))
def testNestedRecordCreation(self):
"""Check the creation of NestedRecord instances from NestedRecArrays.
"""
nra0 = nra.array(descr=self.descr, buffer=self.buffer)
nrecord = nra0[0]
self.assert_(isinstance(nrecord, nra.NestedRecord))
self.assert_(common.areArraysEqual(nra0, nrecord.array))
self.assertEqual(nrecord.row, 0)
def testNestedRecordCreation(self):
"""Check the creation of NestedRecord instances from NestedRecArrays.
"""
nra0 = nra.array(descr=self.descr, buffer=self.buffer)
nrecord = nra0[0]
self.assert_(isinstance(nrecord, nra.NestedRecord))
self.assert_(common.areArraysEqual(nra0, nrecord.array))
self.assertEqual(nrecord.row, 0)
def testGetBottomLevelField(self):
"""Check the NestedRecArray.field method.
"""
nra0 = nra.array(descr=self.descr, buffer=self.buffer)
# Test bottom level fields
nra1 = nra0.field('info/coord/x')
ra1 = numarray.array([10, 0, 10], type='Float32')
self.assert_(common.areArraysEqual(nra1, ra1))
def testGetTopLevelFlatField(self):
"""Check the NestedRecArray.field method.
"""
nra0 = nra.array(descr=self.descr, buffer=self.buffer)
# Test top level flat fields
nra1 = nra0.field('position')
ra1 = numarray.array([1, 2, 3], type='Int64')
self.assert_(common.areArraysEqual(nra1, ra1))
def testGetTopLevelFlatField(self):
"""Check the NestedRecArray.field method.
"""
nra0 = nra.array(descr=self.descr, buffer=self.buffer)
# Test top level flat fields
nra1 = nra0.field('position')
ra1 = numarray.array([1, 2, 3], type='Int64')
self.assert_(common.areArraysEqual(nra1, ra1))
def testFlattenNestedRecord(self):
"""Check the flattening of NestedRecord instances.
"""
nra0 = nra.array(descr=self.descr, buffer=self.buffer)
nrecord = nra0[0]
frecord = nrecord.asRecord()
self.assert_(isinstance(frecord, numarray.records.Record))
self.assert_(common.areArraysEqual(nra0.asRecArray(), frecord.array))
self.assertEqual(nrecord.row, frecord.row)
def testNestedRecordNestedField(self):
"""Get nested fields from nested records.
"""
nra0 = nra.array(descr=self.descr, buffer=self.buffer)
name = nra0.field('info/name')[0]
self.assertEqual(name.array._names, ['first', 'second'])
self.assertEqual(name.field('first'), 'Paco')
self.assertEqual(name.field('second'), 'Perez')
def testNRAadd(self):
"""Check the addition of nested arrays.
"""
ra1 = numarray.records.array([[1, 2], [3, 4]],
formats=['Int32', 'Int32'])
ra2 = numarray.records.array([[5, 6], [7, 8]],
formats=['Int32', 'Int32'])
ra3 = ra1 + ra2
nra1 = nra.array(buffer=ra1,
descr=[('c1', 'Int32'), ('c2', 'Int32')])
nra2 = nra.array(buffer=ra2,
descr=[('a', 'Int32'), ('b', 'Int32')])
nra3 = nra1 + nra2
nra4 = nra1 + ra1
self.assert_(common.areArraysEqual(nra3._flatArray, ra3))
self.assertEqual(nra3.descr, nra1.descr)
self.assert_(common.areArraysEqual(nra4._flatArray,
nra1._flatArray + ra1))
self.assertRaises(TypeError, nra.NestedRecArray.__add__, nra1, 3)
def testNestedRecordFlatField(self):
"""Retrieving flat fields from nested records.
"""
nra0 = nra.array(descr=self.descr, buffer=self.buffer)
position = nra0.field('position')[0]
firstName = nra0.field('info/name/first')[0]
self.assertEqual(position, 1)
self.assertEqual(firstName, 'Paco')
def testNestedRecordNestedField(self):
"""Get nested fields from nested records.
"""
nra0 = nra.array(descr=self.descr, buffer=self.buffer)
name = nra0.field('info/name')[0]
self.assertEqual(name.array._names, ['first', 'second'])
self.assertEqual(name.field('first'), 'Paco')
self.assertEqual(name.field('second'), 'Perez')
def testFlattenNestedRecord(self):
"""Check the flattening of NestedRecord instances.
"""
nra0 = nra.array(descr=self.descr, buffer=self.buffer)
nrecord = nra0[0]
frecord = nrecord.asRecord()
self.assert_(isinstance(frecord, numarray.records.Record))
self.assert_(common.areArraysEqual(nra0.asRecArray(), frecord.array))
self.assertEqual(nrecord.row, frecord.row)
def testNestedRecordFlatField(self):
"""Retrieving flat fields from nested records.
"""
nra0 = nra.array(descr=self.descr, buffer=self.buffer)
position = nra0.field('position')[0]
firstName = nra0.field('info/name/first')[0]
self.assertEqual(position, 1)
self.assertEqual(firstName, 'Paco')
def testCreateNestedRecArray(self):
"""Check the array function.
"""
flatarray = numarray.records.array(self.flat_buffer, self.flat_formats)
common.verbosePrint("""\nTesting the creation of a nested """
"""recarray: buffer + formats""")
nra1 = nra.array(formats=self.formats, buffer=self.buffer)
common.verbosePrint(
"""\nTesting the creation of a nested recarray: buffer + """
"""formats + names""")
nra2 = nra.array(names=self.names,
formats=self.formats,
buffer=self.buffer)
common.verbosePrint(
"""\nTesting the creation of a nested recarray: buffer + descr""")
nra3 = nra.array(descr=self.descr, buffer=self.buffer)
self.assertEqual(common.areArraysEqual(nra1, nra2), False)
self.assert_(common.areArraysEqual(nra2, nra3))
def testNRAFromArrayList(self):
"""Check the fromarrays function.
"""
# arrayList argument is a list of lists
nra0 = nra.array(buffer=self.buffer, descr=self.descr)
nra1 = nra.fromarrays(self.array_list, formats=self.formats)
nra2 = nra.fromarrays(self.array_list,
formats=self.formats,
names=self.names)
nra3 = nra.fromarrays(self.array_list, descr=self.descr)
self.assertEqual(common.areArraysEqual(nra1, nra2), False)
self.assert_(common.areArraysEqual(nra2, nra3))
self.assert_(common.areArraysEqual(nra0, nra2))
# arrayList argument is a list of NestedRecArrays
nra0 = nra.array(buffer=[[1, 4], [2, 4]], formats=['f8', 'f4'])
self.assertRaises(TypeError,
nra.fromarrays, [nra0, nra0.field('c2')],
formats=[['f8', 'f4'], 'f4'])
def testCreateNestedRecArray(self):
"""Check the array function.
"""
flatarray = numarray.records.array(self.flat_buffer,
self.flat_formats)
common.verbosePrint( """\nTesting the creation of a nested """
"""recarray: buffer + formats""")
nra1 = nra.array(formats=self.formats, buffer=self.buffer)
common.verbosePrint(
"""\nTesting the creation of a nested recarray: buffer + """
"""formats + names""")
nra2 = nra.array(names=self.names,
formats=self.formats, buffer=self.buffer)
common.verbosePrint(
"""\nTesting the creation of a nested recarray: buffer + descr""")
nra3 = nra.array(descr=self.descr, buffer=self.buffer)
self.assertEqual(common.areArraysEqual(nra1, nra2), False)
self.assert_(common.areArraysEqual(nra2, nra3))
def testNRAFromRA(self):
"""Check the array function with a RecArray instance.
"""
buffer_ = [('Cuke', 123, (45, 67)), ('Tader', 321, (76, 54))]
names = ['name', 'value', 'pair']
formats = ['a6', 'Int8', '(2,)Int16']
ra = numarray.records.array(buffer_, names=names, formats=formats)
## buffer_, names=names, formats=formats, aligned=True)
names1 = ['newName', 'newValue', 'newPair']
nra0 = nra.array(buffer=ra, descr=zip(names1, formats))
nra1 = nra.array(buffer=buffer_, descr=zip(names1, formats))
self.assert_(common.areArraysEqual(nra0, nra1))
# Bad number of fields
badFormats = ['Int8', '(2,)Int16']
self.assertRaises(ValueError, nra.array, buffer=ra, formats=badFormats)
# Bad format in the first field
badFormats = ['a9', 'Int8', '(2,)Int16']
self.assertRaises(ValueError, nra.array, buffer=ra, formats=badFormats)
def testNestedRecordSetNestedField(self):
"""Set nested fields of nested records.
"""
nra0 = nra.array(descr=self.descr, buffer=self.buffer)
nrecord = nra0[0]
## nra2 = nra.array(
## buffer = [['Joan', 'Clos']],
## descr = [('first', 'a9'), ('second', 'a9')])
nra2 = nra.array(buffer=[[1, (('Joan', 'Clos'), (10, 20, 30))]],
descr=self.descr)
## nrecord.setfield('info/name', nra2[0])
nrecord.setfield('info', nra2.field('info')[0])
my_buffer = [[1, (('Joan', 'Clos'), (10, 20, 30))],
[2, (('Maria', 'Luisa'), (0, 2.0, 10))],
[3, (('C3Peanut', 'Tofu'), (10.0, 30.0, 20.0))]]
nra3 = nra.array(buffer=my_buffer, descr=self.descr)
self.assert_(common.areArraysEqual(nra0, nra3))
def testNestedRecordSetFlatField(self):
"""Set flat fields of nested records.
"""
nra0 = nra.array(descr=self.descr, buffer=self.buffer)
nrecord = nra0[0]
nrecord.setfield('position', 24)
nrecord.setfield('info/name/first', 'Joan')
position = nrecord.field('position')
firstName = nrecord.field('info/name/first')
self.assertEqual(position, 24)
self.assertEqual(firstName, 'Joan')
def testNestedRecordSetFlatField(self):
"""Set flat fields of nested records.
"""
nra0 = nra.array(descr=self.descr, buffer=self.buffer)
nrecord = nra0[0]
nrecord.setfield('position', 24)
nrecord.setfield('info/name/first', 'Joan')
position = nrecord.field('position')
firstName = nrecord.field('info/name/first')
self.assertEqual(position, 24)
self.assertEqual(firstName, 'Joan')
def testNestedRecordSetNestedField(self):
"""Set nested fields of nested records.
"""
nra0 = nra.array(descr=self.descr, buffer=self.buffer)
nrecord = nra0[0]
## nra2 = nra.array(
## buffer = [['Joan', 'Clos']],
## descr = [('first', 'a9'), ('second', 'a9')])
nra2 = nra.array(
buffer = [[1, (('Joan', 'Clos'), (10, 20, 30))]],
descr = self.descr)
## nrecord.setfield('info/name', nra2[0])
nrecord.setfield('info', nra2.field('info')[0])
my_buffer = [[1, (('Joan', 'Clos'), (10, 20, 30))],
[2, (('Maria', 'Luisa'), (0, 2.0, 10))],
[3, (('C3Peanut', 'Tofu'), (10.0, 30.0, 20.0))]]
nra3 = nra.array(buffer=my_buffer, descr=self.descr)
self.assert_(common.areArraysEqual(nra0, nra3))
def testGetNestedField(self):
"""Check the NestedRecArray.field method.
"""
nra0 = nra.array(descr=self.descr, buffer=self.buffer)
# Test top level nested fields
# The info field
buffer = [[('Paco', 'Perez'), (10, 20, 30)],
[('Maria', 'Luisa'), (0, 2.0, 10)],
[('C3Peanut', 'Tofu'), (10, 30, 20)]]
my_descr = [('name', [('first', 'a9'), ('second', 'a9')]),
('coord', [('x', 'Float32'), ('y', 'f4'), ('z', 'f4')])]
model = nra.array(buffer, descr=my_descr)
modelFirst = model.field('name/first')
nra1 = nra0.field('info')
nra1First = nra1.field('name/first')
nra2 = nra1.field('name')
nra3 = nra2.field('first')
self.assert_(common.areArraysEqual(model, nra1))
self.assert_(common.areArraysEqual(modelFirst, nra1First))
self.assert_(common.areArraysEqual(modelFirst, nra3))
print repr(table.description.info2.info3)
print repr(table.description._v_nested_names)
print repr(table.description.info1._v_nested_names)
print
print "**** now some for nested records, take that ****"
print repr(table.description._v_nested_descr)
print repr(numpy.rec.array(None, shape=0,
dtype=table.description._v_nested_descr))
print repr(numpy.rec.array(None, shape=0,
dtype=table.description.info2._v_nested_descr))
# NumPy recarrays doesn't have the machinery to understand the idiom below,
# please use the above form instead.
###print repr(numpy.rec.array(None, shape=1,
### names=table.description._v_nested_names,
### formats=table.description._v_nested_formats))
from tables import nra
print repr(nra.array(None, descr=table.description._v_nested_descr))
print repr(nra.array(None, names=table.description._v_nested_names,
formats=table.description._v_nested_formats))
print
print "**** and some iteration over descriptions, too ****"
for coldescr in table.description._f_walk():
print "column-->", coldescr
print
print "**** info2 sub-structure description:\n", table.description.info2
print
print "**** table representation (long form):\n", repr(table)
# Remember to always close the file
fileh.close()
print "**** now some for nested records, take that ****"
print repr(table.description._v_nestedDescr)
print repr(
numpy.rec.array(None, shape=0, dtype=table.description._v_nestedDescr))
print repr(
numpy.rec.array(None,
shape=0,
dtype=table.description.info2._v_nestedDescr))
# NumPy recarrays doesn't have the machinery to understand the idiom below,
# please use the above form instead.
###print repr(numpy.rec.array(None, shape=1,
### names=table.description._v_nestedNames,
### formats=table.description._v_nestedFormats))
from tables import nra
print repr(nra.array(None, descr=table.description._v_nestedDescr))
print repr(
nra.array(None,
names=table.description._v_nestedNames,
formats=table.description._v_nestedFormats))
print
print "**** and some iteration over descriptions, too ****"
for coldescr in table.description._f_walk():
print "column-->", coldescr
print
print "**** info2 sub-structure description:\n", table.description.info2
print
print "**** table representation (long form):\n", ` table `
# Remember to always close the file
fileh.close()
def testGetSlice(self):
"""Get a nested array slice.
"""
my_buffer = [[1, (('Cuke', 'Skywalker'), (10, 20, 30))],
[2, (('Princess', 'Lettuce'), (0, 2.0, 10))],
[3, (('Ham', 'Solo'), (0, 2.0, 10))],
[4, (('Obi', 'Cannoli'), (0, 2.0, 10))],
[5, (('Chew', 'Brocoli'), (0, 2.0, 10))],
[6, (('Master', 'Yoda'), (0, 2.0, 10))],
[7, (('Tofu', 'Robot'), (0, 2.0, 10))],
[8, (('C3Peanut', 'Robot'), (10, 30, 20))]]
nra0 = nra.array(descr=self.descr, buffer=my_buffer)
slice_ = nra0[1:2]
model = nra.array(
[[2, (('Princess', 'Lettuce'), (0, 2.0, 10))]], descr=self.descr)
self.assert_(common.areArraysEqual(slice_, model))
slice_ = nra0[1:4]
model = nra.array(
[[2, (('Princess', 'Lettuce'), (0, 2.0, 10))],
[3, (('Ham', 'Solo'), (0, 2.0, 10))],
[4, (('Obi', 'Cannoli'), (0, 2.0, 10))]], descr=self.descr)
self.assert_(common.areArraysEqual(slice_, model))
slice_ = nra0[1:4:2]
model = nra.array(
[[2, (('Princess', 'Lettuce'), (0, 2.0, 10))],
[4, (('Obi', 'Cannoli'), (0, 2.0, 10))]], descr=self.descr)
self.assert_(common.areArraysEqual(slice_, model))
slice_ = nra0[:4]
model = nra.array(
[[1, (('Cuke', 'Skywalker'), (10, 20, 30))],
[2, (('Princess', 'Lettuce'), (0, 2.0, 10))],
[3, (('Ham', 'Solo'), (0, 2.0, 10))],
[4, (('Obi', 'Cannoli'), (0, 2.0, 10))]], descr=self.descr)
self.assert_(common.areArraysEqual(slice_, model))
slice_ = nra0[:7:3]
model = nra.array(
[[1, (('Cuke', 'Skywalker'), (10, 20, 30))],
[4, (('Obi', 'Cannoli'), (0, 2.0, 10))],
[7, (('Tofu', 'Robot'), (0, 2.0, 10))]], descr=self.descr)
self.assert_(common.areArraysEqual(slice_, model))
slice_ = nra0[:]
self.assert_(common.areArraysEqual(slice_, nra0))
slice_ = nra0[::2]
model = nra.array(
[[1, (('Cuke', 'Skywalker'), (10, 20, 30))],
[3, (('Ham', 'Solo'), (0, 2.0, 10))],
[5, (('Chew', 'Brocoli'), (0, 2.0, 10))],
[7, (('Tofu', 'Robot'), (0, 2.0, 10))]], descr=self.descr)
self.assert_(common.areArraysEqual(slice_, model))
slice_ = nra0[4:-2]
model = nra.array(
[[5, (('Chew', 'Brocoli'), (0, 2.0, 10))],
[6, (('Master', 'Yoda'), (0, 2.0, 10))]], descr=self.descr)
self.assert_(common.areArraysEqual(slice_, model))
slice_ = nra0[-1:-3]
model = nra.array(None, descr=self.descr)
self.assert_(common.areArraysEqual(slice_, model))
slice_ = nra0[-5::2]
model = nra.array(
[[4, (('Obi', 'Cannoli'), (0, 2.0, 10))],
[6, (('Master', 'Yoda'), (0, 2.0, 10))],
[8, (('C3Peanut', 'Robot'), (10, 30, 20))]], descr=self.descr)
self.assert_(common.areArraysEqual(slice_, model))
class TableNativeFlavorTestCase(common.PyTablesTestCase):
nrows = 100
dtype = [('value', 'c16'), ('y2', 'f8'),
('Info2', [('name', 'a2'), ('value', '(2,)c16'),
('y3', '(2,)f8')]), ('name', 'a2'), ('z2', 'u1')]
_infozeros = nra.array(descr=dtype, shape=3)
# Set the contents to zero (or empty strings)
_infozeros.field('value')[:] = 0
_infozeros.field('y2')[:] = 0
_infozeros.field('Info2/name')[:] = "\0"
_infozeros.field('Info2/value')[:] = 0
_infozeros.field('Info2/y3')[:] = 0
_infozeros.field('name')[:] = "\0"
_infozeros.field('z2')[:] = 0
_infoones = nra.array(descr=dtype, shape=3)
# Set the contents to one (or blank strings)
_infoones.field('value')[:] = 1
_infoones.field('y2')[:] = 1
_infoones.field('Info2/name')[:] = " "
_infoones.field('Info2/value')[:] = 1
_infoones.field('Info2/y3')[:] = 1
_infoones.field('name')[:] = " "
_infoones.field('z2')[:] = 1
def setUp(self):
# Create an instance of an HDF5 Table
self.file = tempfile.mktemp(".h5")
fileh = openFile(self.file, "w")
table = fileh.createTable(fileh.root,
'table',
TestTDescr,
expectedrows=self.nrows)
table.flavor = 'numarray'
for i in range(self.nrows):
table.row.append() # Fill 100 rows with default values
table.flush()
self.fileh = fileh
def tearDown(self):
self.fileh.close()
os.remove(self.file)
common.cleanup(self)
def test01a_basicTableRead(self):
"""Checking the return of a numarray in read()."""
if self.close:
self.fileh.close()
self.fileh = openFile(self.file, "a")
table = self.fileh.root.table
data = table[:]
if common.verbose:
print "Type of read:", type(data)
print "Formats of the record:", data._formats
print "First 3 elements of read:", data[:3]
# Check the type of the recarray
self.assertTrue(isinstance(data, records.RecArray))
# Check the value of some columns
# A flat column
col = table.cols.x[:3]
self.assertTrue(isinstance(col, NumArray))
npcol = zeros((3, 2), type="Int32")
if common.verbose:
print "Plain column:"
print "read column-->", col
print "should look like-->", npcol
self.assertTrue(allequal(col, npcol, "numarray"))
# A nested column
col = table.cols.Info[:3]
self.assertTrue(isinstance(col, records.RecArray))
npcol = self._infozeros
if common.verbose:
print "Nested column:"
print "read column-->", col
print "should look like-->", npcol
self.assertEqual(col.descr, npcol.descr)
self.assertEqual(str(col), str(npcol))
def test01b_basicTableRead(self):
"""Checking the return of a numarray in read() (strided version)."""
if self.close:
self.fileh.close()
self.fileh = openFile(self.file, "a")
table = self.fileh.root.table
data = table[::3]
if common.verbose:
print "Type of read:", type(data)
print "Description of the record:", data.descr
print "First 3 elements of read:", data[:3]
# Check that both numarray objects are equal
self.assertTrue(isinstance(data, records.RecArray))
# Check the value of some columns
# A flat column
col = table.cols.x[:9:3]
self.assertTrue(isinstance(col, NumArray))
npcol = zeros((3, 2), dtype="Int32")
if common.verbose:
print "Plain column:"
print "read column-->", col
print "should look like-->", npcol
self.assertTrue(allequal(col, npcol, "numarray"))
# A nested column
col = table.cols.Info[:9:3]
self.assertTrue(isinstance(col, records.RecArray))
npcol = self._infozeros
if common.verbose:
print "Nested column:"
print "read column-->", col
print "should look like-->", npcol
self.assertEqual(col.descr, npcol.descr)
self.assertEqual(str(col), str(npcol))
def test02_getWhereList(self):
"""Checking the return of numarray in getWhereList method."""
if self.close:
self.fileh.close()
self.fileh = openFile(self.file, "a")
table = self.fileh.root.table
data = table.getWhereList('z == 1')
if common.verbose:
print "Type of read:", type(data)
print "First 3 elements of read:", data[:3]
# Check that both numarray objects are equal
self.assertTrue(isinstance(data, NumArray))
# Check that all columns have been selected
self.assertEqual(len(data), 100)
# Finally, check that the contents are ok
self.assertTrue(allequal(data, arange(100, type="Int64"), "numarray"))
def test03a_readWhere(self):
"""Checking the return of numarray in readWhere method (strings)."""
table = self.fileh.root.table
table.cols.color.createIndex()
if self.close:
self.fileh.close()
self.fileh = openFile(self.file, "a")
table = self.fileh.root.table
data = table.readWhere('color == "ab"')
if common.verbose:
print "Type of read:", type(data)
print "Length of the data read:", len(data)
# Check that both numarray objects are equal
self.assertTrue(isinstance(data, records.RecArray))
# Check that all columns have been selected
self.assertEqual(len(data), self.nrows)
def test03b_readWhere(self):
"""Checking the return of numarray in readWhere method (numeric)."""
table = self.fileh.root.table
table.cols.z.createIndex()
if self.close:
self.fileh.close()
self.fileh = openFile(self.file, "a")
table = self.fileh.root.table
data = table.readWhere('z == 0')
if common.verbose:
print "Type of read:", type(data)
print "Length of the data read:", len(data)
# Check that both numarray objects are equal
self.assertTrue(isinstance(data, records.RecArray))
# Check that all columns have been selected
self.assertEqual(len(data), 0)
def test04a_createTable(self):
"""Checking the Table creation from a numarray recarray."""
npdata = self._infozeros
table = self.fileh.createTable(self.fileh.root, 'table2', npdata)
if self.close:
self.fileh.close()
self.fileh = openFile(self.file, "a")
table = self.fileh.root.table2
data = table[:]
if common.verbose:
print "Type of read:", type(data)
print "Description of the record:", data.descr
print "First 3 elements of read:", data[:3]
print "Length of the data read:", len(data)
if common.verbose:
print "npdata-->", npdata
print "data-->", data
# Check that both numarray objects are equal
self.assertTrue(isinstance(data, records.RecArray))
# Check the type
self.assertEqual(data.descr, npdata.descr)
self.assertEqual(str(data), str(npdata))
def test04b_appendTable(self):
"""Checking appending a numarray recarray."""
table = self.fileh.root.table
npdata = table[3:6]
table.append(npdata)
if self.close:
self.fileh.close()
self.fileh = openFile(self.file, "a")
table = self.fileh.root.table
data = table[-3:]
if common.verbose:
print "Type of read:", type(data)
print "Description of the record:", data.descr
print "Last 3 elements of read:", data[-3:]
print "Length of the data read:", len(data)
if common.verbose:
print "npdata-->", npdata
print "data-->", data
# Check that both numarray objects are equal
self.assertTrue(isinstance(data, records.RecArray))
# Check the type
self.assertEqual(data.descr, npdata.descr)
self.assertEqual(str(data), str(npdata))
def test05a_assignColumn(self):
"""Checking assigning to a column."""
table = self.fileh.root.table
table.cols.z[:] = ones((100, ), dtype='UInt8')
if self.close:
self.fileh.close()
self.fileh = openFile(self.file, "a")
table = self.fileh.root.table
data = table.cols.z[:]
if common.verbose:
print "Type of read:", type(data)
print "First 3 elements of read:", data[:3]
print "Length of the data read:", len(data)
# Check that both numarray objects are equal
self.assertTrue(isinstance(data, NumArray))
# Check that all columns have been selected
self.assertEqual(len(data), 100)
# Finally, check that the contents are ok
self.assertTrue(
allequal(data, ones((100, ), dtype="UInt8"), "numarray"))
def test05b_modifyingColumns(self):
"""Checking modifying several columns at once."""
table = self.fileh.root.table
xcol = ones((3, 2), 'Int32')
ycol = ones((3, 2, 2), 'Float64')
zcol = zeros((3, ), 'UInt8')
table.modifyColumns(3, 6, 1, [xcol, ycol, zcol], ['x', 'y', 'z'])
if self.close:
self.fileh.close()
self.fileh = openFile(self.file, "a")
table = self.fileh.root.table
data = table.cols.y[3:6]
if common.verbose:
print "Type of read:", type(data)
print "First 3 elements of read:", data[:3]
print "Length of the data read:", len(data)
if common.verbose:
print "ycol-->", ycol
print "data-->", data
# Check that both numarray objects are equal
self.assertTrue(isinstance(data, NumArray))
# Check the type
self.assertEqual(data.type(), ycol.type())
self.assertTrue(allequal(data, ycol, "numarray"))
def test05c_modifyingColumns(self):
"""Checking modifying several columns using a numarray buffer."""
table = self.fileh.root.table
dtype = [('x', '(2,)i4'), ('y', '(2,2)f8'), ('z', 'u1')]
nparray = nra.array(shape=(3, ), descr=dtype)
nparray.field('x')[:] = 1
nparray.field('y')[:] = 1
nparray.field('z')[:] = 2
table.modifyColumns(3, 6, 1, nparray, ['x', 'y', 'z'])
if self.close:
self.fileh.close()
self.fileh = openFile(self.file, "a")
table = self.fileh.root.table
ycol = ones((3, 2, 2), 'Float64')
data = table.cols.y[3:6]
if common.verbose:
print "Type of read:", type(data)
print "First 3 elements of read:", data[:3]
print "Length of the data read:", len(data)
if common.verbose:
print "ycol-->", ycol
print "data-->", data
# Check that both numarray objects are equal
self.assertTrue(isinstance(data, NumArray))
# Check the type
self.assertEqual(data.type(), ycol.type())
self.assertEqual(str(data), str(ycol))
def test06a_assignNestedColumn(self):
"""Checking assigning a nested column (using modifyColumn)."""
npdata = self._infoones
table = self.fileh.root.table
data = table.cols.Info[3:6]
table.modifyColumn(3, 6, 1, column=npdata, colname='Info')
if self.close:
self.fileh.close()
self.fileh = openFile(self.file, "a")
table = self.fileh.root.table
data = table.cols.Info[3:6]
if common.verbose:
print "Type of read:", type(data)
print "Description of the record:", data.descr
print "First 3 elements of read:", data[:3]
print "Length of the data read:", len(data)
if common.verbose:
print "npdata-->", npdata
print "data-->", data
# Check that both numarray objects are equal
self.assertTrue(isinstance(data, records.RecArray))
# Check the type
self.assertEqual(data.descr, npdata.descr)
self.assertEqual(str(data), str(npdata))
def test06b_assignNestedColumn(self):
"""Checking assigning a nested column (using the .cols accessor)."""
table = self.fileh.root.table
npdata = self._infoones
table.cols.Info[3:6] = npdata
if self.close:
self.fileh.close()
self.fileh = openFile(self.file, "a")
table = self.fileh.root.table
data = table.cols.Info[3:6]
if common.verbose:
print "Type of read:", type(data)
print "Description of the record:", data.descr
print "First 3 elements of read:", data[:3]
print "Length of the data read:", len(data)
if common.verbose:
print "npdata-->", npdata
print "data-->", data
# Check that both numarray objects are equal
self.assertTrue(isinstance(data, records.RecArray))
# Check the type
self.assertEqual(data.descr, npdata.descr)
self.assertEqual(str(data), str(npdata))
def test07a_modifyingRows(self):
"""Checking modifying several rows at once (using modifyRows)."""
table = self.fileh.root.table
# Read a chunk of the table
chunk = table[0:3]
# Modify it somewhat
chunk.field('y')[:] = -1
table.modifyRows(3, 6, 1, rows=chunk)
if self.close:
self.fileh.close()
self.fileh = openFile(self.file, "a")
table = self.fileh.root.table
ycol = zeros((3, 2, 2), 'Float64') - 1
data = table.cols.y[3:6]
if common.verbose:
print "Type of read:", type(data)
print "First 3 elements of read:", data[:3]
print "Length of the data read:", len(data)
if common.verbose:
print "ycol-->", ycol
print "data-->", data
# Check that both numarray objects are equal
self.assertTrue(isinstance(data, NumArray))
# Check the type
self.assertEqual(data.type(), ycol.type())
self.assertTrue(allequal(ycol, data, "numarray"))
def test07b_modifyingRows(self):
"""Checking modifying several rows at once (using cols accessor)."""
table = self.fileh.root.table
# Read a chunk of the table
chunk = table[0:3]
# Modify it somewhat
chunk.field('y')[:] = -1
table.cols[3:6] = chunk
if self.close:
self.fileh.close()
self.fileh = openFile(self.file, "a")
table = self.fileh.root.table
# Check that some column has been actually modified
ycol = zeros((3, 2, 2), 'Float64') - 1
data = table.cols.y[3:6]
if common.verbose:
print "Type of read:", type(data)
print "First 3 elements of read:", data[:3]
print "Length of the data read:", len(data)
if common.verbose:
print "ycol-->", ycol
print "data-->", data
# Check that both numarray objects are equal
self.assertTrue(isinstance(data, NumArray))
# Check the type
self.assertEqual(data.type(), ycol.type())
self.assertTrue(allequal(ycol, data, "numarray"))
def test08a_modifyingRows(self):
"""Checking modifying just one row at once (using modifyRows)."""
table = self.fileh.root.table
# Read a chunk of the table
chunk = table[3]
# Modify it somewhat
chunk.field('y')[:] = -1
table.modifyRows(6, 7, 1, chunk)
if self.close:
self.fileh.close()
self.fileh = openFile(self.file, "a")
table = self.fileh.root.table
# Check that some column has been actually modified
ycol = zeros((2, 2), 'Float64') - 1
data = table.cols.y[6]
if common.verbose:
print "Type of read:", type(data)
print "First 3 elements of read:", data[:3]
print "Length of the data read:", len(data)
if common.verbose:
print "ycol-->", ycol
print "data-->", data
# Check that both numarray objects are equal
self.assertTrue(isinstance(data, NumArray))
# Check the type
self.assertEqual(data.type(), ycol.type())
self.assertTrue(allequal(ycol, data, "numarray"))
def test08b_modifyingRows(self):
"""Checking modifying just one row at once (using cols accessor)."""
table = self.fileh.root.table
# Read a chunk of the table
chunk = table[3]
# Modify it somewhat
chunk['y'][:] = -1
table.cols[6] = chunk
if self.close:
self.fileh.close()
self.fileh = openFile(self.file, "a")
table = self.fileh.root.table
# Check that some column has been actually modified
ycol = zeros((2, 2), 'Float64') - 1
data = table.cols.y[6]
if common.verbose:
print "Type of read:", type(data)
print "First 3 elements of read:", data[:3]
print "Length of the data read:", len(data)
if common.verbose:
print "ycol-->", ycol
print "data-->", data
# Check that both numarray objects are equal
self.assertTrue(isinstance(data, NumArray))
# Check the type
self.assertEqual(data.type(), ycol.type())
self.assertTrue(allequal(ycol, data, "numarray"))
def test09a_getStrings(self):
"""Checking the return of string columns with spaces."""
if self.close:
self.fileh.close()
self.fileh = openFile(self.file, "a")
table = self.fileh.root.table
rdata = table.getWhereList('color == "ab"')
data = table.readCoordinates(rdata)
if common.verbose:
print "Type of read:", type(data)
print "Description of the record:", data.descr
print "First 3 elements of read:", data[:3]
# Check that both numarray objects are equal
self.assertTrue(isinstance(data, records.RecArray))
# Check that all columns have been selected
self.assertEqual(len(data), 100)
# Finally, check that the contents are ok
for idata in data.field('color'):
self.assertEqual(idata, "ab")
def test09b_getStrings(self):
"""Checking the return of string columns with spaces. (modify)"""
if self.close:
self.fileh.close()
self.fileh = openFile(self.file, "a")
table = self.fileh.root.table
for i in range(50):
table.cols.color[i] = "a "
table.flush()
data = table[:]
if common.verbose:
print "Type of read:", type(data)
print "Description of the record:", data.descr
print "First 3 elements of read:", data[:3]
# Check that both numarray objects are equal
self.assertTrue(isinstance(data, records.RecArray))
# Check that all columns have been selected
self.assertEqual(len(data), 100)
# Finally, check that the contents are ok
for i in range(100):
idata = data.field('color')[i]
if i >= 50:
self.assertEqual(idata, "ab")
else:
self.assertEqual(idata, "a")
def test09c_getStrings(self):
"""Checking the return of string columns with spaces. (append)"""
if self.close:
self.fileh.close()
self.fileh = openFile(self.file, "a")
table = self.fileh.root.table
row = table.row
for i in range(50):
row["color"] = "a " # note the trailing spaces
row.append()
table.flush()
if self.close:
self.fileh.close()
self.fileh = openFile(self.file, "a")
data = self.fileh.root.table[:]
if common.verbose:
print "Type of read:", type(data)
print "Description of the record:", data.descr
print "First 3 elements of read:", data[:3]
# Check that both numarray objects are equal
self.assertTrue(isinstance(data, records.RecArray))
# Check that all columns have been selected
self.assertEqual(len(data), 150)
# Finally, check that the contents are ok
# Finally, check that the contents are ok
for i in range(150):
idata = data.field('color')[i]
if i < 100:
self.assertEqual(idata, "ab")
else:
self.assertEqual(idata, "a")
def testGetSlice(self):
"""Get a nested array slice.
"""
my_buffer = [[1, (('Cuke', 'Skywalker'), (10, 20, 30))],
[2, (('Princess', 'Lettuce'), (0, 2.0, 10))],
[3, (('Ham', 'Solo'), (0, 2.0, 10))],
[4, (('Obi', 'Cannoli'), (0, 2.0, 10))],
[5, (('Chew', 'Brocoli'), (0, 2.0, 10))],
[6, (('Master', 'Yoda'), (0, 2.0, 10))],
[7, (('Tofu', 'Robot'), (0, 2.0, 10))],
[8, (('C3Peanut', 'Robot'), (10, 30, 20))]]
nra0 = nra.array(descr=self.descr, buffer=my_buffer)
slice_ = nra0[1:2]
model = nra.array([[2, (('Princess', 'Lettuce'), (0, 2.0, 10))]],
descr=self.descr)
self.assert_(common.areArraysEqual(slice_, model))
slice_ = nra0[1:4]
model = nra.array(
[[2, (('Princess', 'Lettuce'),
(0, 2.0, 10))], [3, (('Ham', 'Solo'), (0, 2.0, 10))],
[4, (('Obi', 'Cannoli'), (0, 2.0, 10))]],
descr=self.descr)
self.assert_(common.areArraysEqual(slice_, model))
slice_ = nra0[1:4:2]
model = nra.array(
[[2, (('Princess', 'Lettuce'),
(0, 2.0, 10))], [4, (('Obi', 'Cannoli'), (0, 2.0, 10))]],
descr=self.descr)
self.assert_(common.areArraysEqual(slice_, model))
slice_ = nra0[:4]
model = nra.array(
[[1, (('Cuke', 'Skywalker'),
(10, 20, 30))], [2, (('Princess', 'Lettuce'), (0, 2.0, 10))],
[3, (('Ham', 'Solo'),
(0, 2.0, 10))], [4, (('Obi', 'Cannoli'), (0, 2.0, 10))]],
descr=self.descr)
self.assert_(common.areArraysEqual(slice_, model))
slice_ = nra0[:7:3]
model = nra.array(
[[1, (('Cuke', 'Skywalker'),
(10, 20, 30))], [4, (('Obi', 'Cannoli'), (0, 2.0, 10))],
[7, (('Tofu', 'Robot'), (0, 2.0, 10))]],
descr=self.descr)
self.assert_(common.areArraysEqual(slice_, model))
slice_ = nra0[:]
self.assert_(common.areArraysEqual(slice_, nra0))
slice_ = nra0[::2]
model = nra.array(
[[1, (('Cuke', 'Skywalker'),
(10, 20, 30))], [3, (('Ham', 'Solo'), (0, 2.0, 10))],
[5, (('Chew', 'Brocoli'),
(0, 2.0, 10))], [7, (('Tofu', 'Robot'), (0, 2.0, 10))]],
descr=self.descr)
self.assert_(common.areArraysEqual(slice_, model))
slice_ = nra0[4:-2]
model = nra.array(
[[5, (('Chew', 'Brocoli'),
(0, 2.0, 10))], [6, (('Master', 'Yoda'), (0, 2.0, 10))]],
descr=self.descr)
self.assert_(common.areArraysEqual(slice_, model))
slice_ = nra0[-1:-3]
model = nra.array(None, descr=self.descr)
self.assert_(common.areArraysEqual(slice_, model))
slice_ = nra0[-5::2]
model = nra.array(
[[4, (('Obi', 'Cannoli'),
(0, 2.0, 10))], [6, (('Master', 'Yoda'), (0, 2.0, 10))],
[8, (('C3Peanut', 'Robot'), (10, 30, 20))]],
descr=self.descr)
self.assert_(common.areArraysEqual(slice_, model))
