def testImportFMF(self):
from fmfile import FMFLoader
table = FMFLoader.loadFMFFromFile(self.filename)
print "Testing imported SampleContainer for consistency..."
for column in ['y0', 'y1', 'y2', 'y3', 'y4', 'y5', 'y6', 'y7', 'y8']:
self.assertEqual(table[column].dimensions[0].id,
table['x'].id)
def testListofStrings2(self):
column = [['Hello', 'World'], 'World']
result = FMFLoader.column2FieldContainer('simple string', column)
expectedResult = FieldContainer(
numpy.array(['Hello, World', 'World']), longname='simple string'
)
assertEqual(result, expectedResult)
def registerFMF(self, filename, temporary=False):
"""
Extracts a SampleContainer from a given FMF file and stores it
permanently. The emd5 of the SampleContainer that has been generated
is returned.
filename -- path to the FMF file
temporary -- see registerDataContainer
"""
sc = FMFLoader.loadFMFFromFile(filename)
self.registerDataContainer(sc, temporary)
return sc.id
def registerFMF(self, filename, temporary=False):
"""
Extracts a SampleContainer from a given FMF file and stores it
permanently. The emd5 of the SampleContainer that has been generated
is returned.
filename -- path to the FMF file
temporary -- see registerDataContainer
"""
sc = FMFLoader.loadFMFFromFile(filename)
self.registerDataContainer(sc, temporary)
return sc.id
def testVariableFirstNaN(self):
column = [
('T', 'NaN', Quantity('0.5 degC')),
('T', Quantity('11.2 degC'), None)
]
result = FMFLoader.column2FieldContainer('temperature', column)
expectedResult = FieldContainer(
numpy.array([numpy.NaN, 11.2]), error=numpy.array([0.5, 0.0]),
mask = numpy.array([True, False]),
unit='1 degC', longname='temperature', shortname='T')
assertEqual(result, expectedResult)
# IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED
# TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
# PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER
# OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
# EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
# PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
# LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
# NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
u"""
"""
import sys
import unittest
sys.path.append("..")
import pkg_resources
pkg_resources.require("Pyphant")
from fmfile import FMFLoader
import pyphant.visualizers.Chart as cv
loader = FMFLoader.FMFLoader()
loader.paramFilename.value = 'Sim_abs_210nm.fmf'
data = loader.loadFMF()
v = cv.LineChart(data['absorption'])
v.figure.savefig('demoFMF.png')
def testValid(self):
result = FMFLoader.checkAndCondense(self.valid)
numpy.testing.assert_array_equal(self.x, result)
def setUp(self):
self.loader = FMFLoader.FMFLoader()
from fmfile import __path__ as path
import os
self.path = os.path.join(path[0], 'tests', 'resources', 'fmf')
def testReadSingleFile(self):
"""
Test the correct interpretation of physical constants
as definied in FMF version 1.1.
"""
consts = FMFLoader.readSingleFile(
self.FMFinput, "testReadSingleFile")[0].attributes[
'Mathematical and Physical Constants'
]
self.assertEqual(
consts[u'Speed of light'][1], str2unit("1 c", FMFversion="1.1")
)
self.assertEqual(
consts[u'Permeability of vacuum'][1],
str2unit("1 mu0", FMFversion="1.1"),
'The values differ by %s.' % (
consts[u'Permeability of vacuum'][1] -\
str2unit("1 mu0", FMFversion="1.1"),
)
)
self.assertEqual(
consts[u'Permittivity of vacuum'][1],
str2unit("1 eps0", FMFversion="1.1")
)
self.assertEqual(
consts[u'Gravitational constant'][1],
str2unit("1 G", FMFversion="1.1")
)
self.assertEqual(
consts[u'Planck constant'][1],
str2unit("1 h", FMFversion="1.1")
)
self.assertEqual(
consts[u'Planck constant / 2pi'][1],
str2unit("1 hbar", FMFversion="1.1")
)
self.assertEqual(
consts[u'Elementary charge'][1], str2unit("1 e",FMFversion="1.1"),
'The elements %s and %s do not match.' % (
consts[u'Elementary charge'][1],
str2unit("1 e", FMFversion="1.1")
)
)
self.assertEqual(
consts[u'Electron mass'][1], str2unit("1 me", FMFversion="1.1")
)
self.assertEqual(
consts[u'Proton mass'][1], str2unit("1 mp", FMFversion="1.1")
)
self.assertEqual(
consts[u'Avogadro number'][1], str2unit("1 NA", FMFversion="1.1")
)
self.assertEqual(
consts[u'Boltzmann constant'][1], str2unit("1 k",FMFversion="1.1")
)
self.assertEqual(
consts[u'Rydberg constant'][1], str2unit("1 Ryd", FMFversion="1.1")
)
consts = FMFLoader.readSingleFile(
self.FMFinput, "testReadSingleFile")[0].attributes[
'Additional constants changed from FMF version 1.0 to 1.1'
]
self.assertEqual(
consts[u'Parsec'][1], str2unit("1 pc", FMFversion="1.1")
)
self.assertEqual(
consts[u'US gallon'][1], str2unit("1 galUS", FMFversion="1.1")
)
self.assertEqual(
consts[u'Atomic mass units'][1], str2unit("1 u", FMFversion="1.1")
)
def testReadSingleFile(self):
"""
Test the correct interpretation of physical constants
as definied in FMF version 1.0.
"""
consts = FMFLoader.readSingleFile(
self.FMFinput,
"testReadSingleFile")[0].attributes[
'Mathematical and Physical Constants'
]
self.assertEqual(
consts[u'Speed of light'][1], str2unit("1 c", FMFversion="1.0")
)
self.assertEqual(consts[u'Speed of light'][1], str2unit("1 c"))
self.assertEqual(
consts[u'Permeability of vacuum'][1],
str2unit("1 mu0", FMFversion="1.0")
)
self.assertEqual(
consts[u'Permittivity of vacuum'][1],
str2unit("1 eps0", FMFversion="1.0")
)
self.assertEqual(
consts[u'Gravitational constant'][1],
str2unit("1 Grav", FMFversion="1.0")
)
self.assertTrue(
consts[u'Planck constant'][1],
str2unit("1 hplanck", FMFversion="1.0")
)
self.almostEqual(
consts[u'Planck constant / 2pi'][1],
str2unit("1 hbar", FMFversion="1.0")
)
self.almostEqual(
consts[u'Elementary charge'][1],
str2unit("1 e", FMFversion="1.0")
)
self.assertNotEqual(
consts[u'Elementary charge'][1], str2unit("1 e"),
"Elementary charge has been adapted to new CODATA recommendations."
)
self.assertEqual(
consts[u'Electron mass'][1], str2unit("1 me", FMFversion="1.0")
)
self.assertNotEqual(
consts[u'Electron mass'][1], str2unit("1 me"),
"Electron mass has been adapted to new CODATA recommendations."
)
self.assertEqual(
consts[u'Proton mass'][1], str2unit("1 mp", FMFversion="1.0")
)
self.assertNotEqual(
consts[u'Proton mass'][1], str2unit("1 mp"),
"Proton mass has been adapted to new CODATA recommendations."
)
self.assertEqual(
consts[u'Avogadro number'][1], str2unit("1 Nav", FMFversion="1.0")
)
self.assertEqual(
consts[u'Boltzmann constant'][1], str2unit("1 k", FMFversion="1.0")
)
consts = FMFLoader.readSingleFile(
self.FMFinput,
"testReadSingleFile")[0].attributes[
'Additional constants changed from FMF version 1.0 to 1.1'
]
self.almostEqual(
consts[u'Parsec'][1], str2unit("1 pc", FMFversion="1.0")
)
self.almostEqual(
consts[u'US gallon'][1], str2unit("1 galUS", FMFversion="1.0")
)
self.assertEqual(
consts[u'Atomic mass units'][1],
str2unit("1 amu", FMFversion="1.0")
)
def testJouleValue1_0(self):
"""Physical quantities with unit Joule are indicated by 'J'."""
result = FMFLoader.item2value(
self.inputDict['Joule'], FMFversion='1.0'
)
self.assertEqual(result, (Quantity(self.inputDict['Joule']), None))
def testComplexValue(self):
"""Imaginary numbers are indicated by 'j'."""
result = FMFLoader.item2value(self.inputDict['complexJ'])
self.assertEqual(result, (complex(self.inputDict['complexJ']), None))