def testReadLine(self):
emsa = emsaFormat.EmsaFormat()
line = r"-0.200, 0."
emsa.readLine(line)
self.assertEquals(1, len(emsa.values))
self.assertEquals(-0.2, emsa.values[0][0])
self.assertEquals(0.0, emsa.values[0][1])
line = r"#FORMAT : EMSA/MAS Spectral Data File"
emsa.readLine(line)
self.assertEquals(1, len(emsa.keywords))
self.assertEquals("FORMAT", emsa.keywords[0]["keyword"])
self.assertEquals(1, emsa.keywords[0]["order"])
line = r"#VERSION : 1.0"
emsa.readLine(line)
self.assertEquals(2, len(emsa.keywords))
self.assertEquals("VERSION", emsa.keywords[1]["keyword"])
self.assertEquals(2, emsa.keywords[1]["order"])
line = r"#TITLE : Spectrum 1"
emsa.readLine(line)
self.assertEquals(3, len(emsa.keywords))
self.assertEquals("TITLE", emsa.keywords[2]["keyword"])
self.assertEquals(3, emsa.keywords[2]["order"])
def setUp(self):
unittest.TestCase.setUp(self)
self.filepath = get_current_module_path(
__file__, "../emmff/spectra/spectrum1.emsa")
if not os.path.isfile(self.filepath):
raise SkipTest
self.emsa = emsaFormat.EmsaFormat(self.filepath)
def testReadlines(self):
emsa = emsaFormat.EmsaFormat()
filename = get_current_module_path(__file__,
"../emmff/spectra/spectrum1.emsa")
emsa.open(filename)
emsa.readLines()
self.assertEquals(30, len(emsa.keywords))
self.assertEquals(1024, len(emsa.values))
def testReadFileTEMBruker(self):
filename = get_current_module_path(
__file__, "../../test_data/TEM_Bruker/Gold-pt 2-2.msa")
if not os.path.isfile(filename):
raise SkipTest
emsa = emsaFormat.EmsaFormat()
emsa.open(filename)
emsa.readLines()
emsa.setHeader()
emsa.setSpectrumData()
self.assertNotEqual(0, len(emsa.lines))
self.assertEqual(1055, len(emsa.lines))
self.assertEqual(1024, len(emsa.values))
self.assertEqual(4096, len(emsa.getDataX()))
self.assertEqual(4096, len(emsa.getDataY()))
def testSetGetOxfordInstrumentsElement(self):
emsa = emsaFormat.EmsaFormat()
self.assertEquals(None, emsa.getOxfordInstrumentsElement())
self.assertEquals("6,8,12", self.emsa.getOxfordInstrumentsElement())
def testSetGetMagnification(self):
emsa = emsaFormat.EmsaFormat()
self.assertEquals(None, emsa.getMagnification())
self.assertEquals(250.0, self.emsa.getMagnification())
def testSetGetProbeCurrent(self):
emsa = emsaFormat.EmsaFormat()
self.assertEquals(None, emsa.getProbeCurrent())
self.assertEquals(0.0, self.emsa.getProbeCurrent())
def testSetGetRealTime(self):
emsa = emsaFormat.EmsaFormat()
self.assertEquals(None, emsa.getRealTime())
self.assertEquals(0.453241, self.emsa.getRealTime())
def testSetGetChannelOffset(self):
emsa = emsaFormat.EmsaFormat()
self.assertEquals(None, emsa.getChannelOffset())
self.assertEquals(10.0, self.emsa.getChannelOffset())
def testSetGetTime(self):
emsa = emsaFormat.EmsaFormat()
self.assertEquals(None, emsa.getTime())
self.assertEquals("16:03", self.emsa.getTime())
def testSetGetDate(self):
emsa = emsaFormat.EmsaFormat()
self.assertEquals(None, emsa.getDate())
self.assertEquals("20-NOV-2006", self.emsa.getDate())
def testSetGetTitle(self):
emsa = emsaFormat.EmsaFormat()
self.assertEquals(None, emsa.getTitle())
self.assertEquals("Spectrum 1", self.emsa.getTitle())
def testSetGetVersion(self):
emsa = emsaFormat.EmsaFormat()
self.assertEquals(None, emsa.getVersion())
self.assertEquals("1.0", self.emsa.getVersion())
def testIsFileValid(self):
emsa = emsaFormat.EmsaFormat()
self.assertEquals(None, emsa.isFileValid)
self.assertEquals(True, self.emsa.isFileValid)
def testSetGetFormat(self):
emsa = emsaFormat.EmsaFormat()
self.assertEquals(None, emsa.getFormat())
self.assertEquals("EMSA/MAS Spectral Data File", self.emsa.getFormat())
def testSetGetOffset(self):
emsa = emsaFormat.EmsaFormat()
self.assertEquals(None, emsa.getOffset())
self.assertEquals(-0.2, self.emsa.getOffset())
def testSetGetSignalType(self):
emsa = emsaFormat.EmsaFormat()
self.assertEquals(None, emsa.getSignalType())
self.assertEquals("EDS", self.emsa.getSignalType())
def testSetGetOwner(self):
emsa = emsaFormat.EmsaFormat()
self.assertEquals(None, emsa.getOwner())
self.assertEquals("helen", self.emsa.getOwner())
def testSetGetLiveTime(self):
emsa = emsaFormat.EmsaFormat()
self.assertEquals(None, emsa.getLiveTime())
self.assertEquals(0.34635, self.emsa.getLiveTime())
def testSetGetNumberPoints(self):
emsa = emsaFormat.EmsaFormat()
self.assertEquals(None, emsa.getNumberPoints())
self.assertEquals(1024.0, self.emsa.getNumberPoints())
def testSetGetBeamEnergy(self):
emsa = emsaFormat.EmsaFormat()
self.assertEquals(None, emsa.getBeamEnergy())
self.assertEquals(5.0, self.emsa.getBeamEnergy())
def testSetGetNumberColumns(self):
emsa = emsaFormat.EmsaFormat()
self.assertEquals(None, emsa.getNumberColumns())
self.assertEquals(1.0, self.emsa.getNumberColumns())
def testConstructor(self):
emsaFormat.EmsaFormat()
def testSetGetXUnits(self):
emsa = emsaFormat.EmsaFormat()
self.assertEquals(None, emsa.getXUnits())
self.assertEquals("keV", self.emsa.getXUnits())
def testSetGetZPosition(self):
emsa = emsaFormat.EmsaFormat()
self.assertEquals(None, emsa.getZPosition())
self.assertEquals(0.0, self.emsa.getZPosition())
def testSetGetYUnits(self):
emsa = emsaFormat.EmsaFormat()
self.assertEquals(None, emsa.getYUnits())
self.assertEquals("counts", self.emsa.getYUnits())
def testSetGetOxfordInstrumentsLabel(self):
emsa = emsaFormat.EmsaFormat()
self.assertEquals(None, emsa.getOxfordInstrumentsLabel())
self.assertEquals("8, 0.525, O", self.emsa.getOxfordInstrumentsLabel())
def testSetGetDataType(self):
emsa = emsaFormat.EmsaFormat()
self.assertEquals(None, emsa.getDataType())
self.assertEquals("XY", self.emsa.getDataType())
def testIsLineData(self):
line = ""
self.assertEqual(False,
self.emsa.isLineData(line)[0],
msg="Empty line")
self.assertEqual(None, self.emsa.isLineData(line)[1], msg="Empty line")
self.assertEqual(0, self.emsa.isLineData(line)[2], msg="Empty line")
line = None
self.assertEqual(False, self.emsa.isLineData(line)[0], msg="None line")
self.assertEqual(None, self.emsa.isLineData(line)[1], msg="None line")
self.assertEqual(0, self.emsa.isLineData(line)[2], msg="None line")
self.emsa = emsaFormat.EmsaFormat()
line = "1.2"
self.assertEqual(True, self.emsa.isLineData(line)[0], msg="Y value")
self.assertEqual('Y', self.emsa.isLineData(line)[1], msg="Y value")
self.assertEqual(1, self.emsa.isLineData(line)[2], msg="Y value")
line = "1.2, 0.2"
self.assertEqual(True, self.emsa.isLineData(line)[0], msg="With comma")
self.assertEqual('Y', self.emsa.isLineData(line)[1], msg="With comma")
self.assertEqual(2, self.emsa.isLineData(line)[2], msg="With comma")
line = "1.2 0.2"
self.assertEqual(True, self.emsa.isLineData(line)[0], msg="With space")
self.assertEqual('Y', self.emsa.isLineData(line)[1], msg="With space")
self.assertEqual(2, self.emsa.isLineData(line)[2], msg="With space")
line = "1.2\t0.2"
self.assertEqual(True, self.emsa.isLineData(line)[0], msg="With tab")
self.assertEqual('Y', self.emsa.isLineData(line)[1], msg="With tab")
self.assertEqual(2, self.emsa.isLineData(line)[2], msg="With tab")
line = "0.2"
self.assertEqual(True,
self.emsa.isLineData(line)[0],
msg="With 1 column")
self.assertEqual('Y',
self.emsa.isLineData(line)[1],
msg="With 1 column")
self.assertEqual(1, self.emsa.isLineData(line)[2], msg="With 1 column")
line = "0.1, 0.2"
self.assertEqual(True,
self.emsa.isLineData(line)[0],
msg="With 2 column")
self.assertEqual('Y',
self.emsa.isLineData(line)[1],
msg="With 2 column")
self.assertEqual(2, self.emsa.isLineData(line)[2], msg="With 2 column")
line = "0.1, 0.2, 0.3"
self.assertEqual(True,
self.emsa.isLineData(line)[0],
msg="With 3 column")
self.assertEqual('Y',
self.emsa.isLineData(line)[1],
msg="With 3 column")
self.assertEqual(3, self.emsa.isLineData(line)[2], msg="With 3 column")
line = "0.1, 0.2, 0.3, 0.4"
self.assertEqual(True,
self.emsa.isLineData(line)[0],
msg="With 4 column")
self.assertEqual('Y',
self.emsa.isLineData(line)[1],
msg="With 4 column")
self.assertEqual(4, self.emsa.isLineData(line)[2], msg="With 4 column")
line = "0.1, 0.2, 0.3, 0.4, 0.5"
self.assertEqual(True,
self.emsa.isLineData(line)[0],
msg="With 5 column")
self.assertEqual('Y',
self.emsa.isLineData(line)[1],
msg="With 5 column")
self.assertEqual(5, self.emsa.isLineData(line)[2], msg="With 5 column")
line = "0.1, 0.2, 0.3, 0.4, 0.5, 0.6"
self.assertEqual(False,
self.emsa.isLineData(line)[0],
msg="With 6 column")
self.assertEqual(None,
self.emsa.isLineData(line)[1],
msg="With 6 column")
self.assertEqual(0, self.emsa.isLineData(line)[2], msg="With 6 column")
line = "0.1 0.2"
self.assertEqual(True,
self.emsa.isLineData(line)[0],
msg="With 2 column")
self.assertEqual('Y',
self.emsa.isLineData(line)[1],
msg="With 2 column")
self.assertEqual(2, self.emsa.isLineData(line)[2], msg="With 2 column")
line = "0.1 0.2 0.3"
self.assertEqual(True,
self.emsa.isLineData(line)[0],
msg="With 3 column")
self.assertEqual('Y',
self.emsa.isLineData(line)[1],
msg="With 3 column")
self.assertEqual(3, self.emsa.isLineData(line)[2], msg="With 3 column")
line = "0.1 0.2 0.3 0.4"
self.assertEqual(True,
self.emsa.isLineData(line)[0],
msg="With 4 column")
self.assertEqual('Y',
self.emsa.isLineData(line)[1],
msg="With 4 column")
self.assertEqual(4, self.emsa.isLineData(line)[2], msg="With 4 column")
line = "0.1 0.2 0.3 0.4 0.5"
self.assertEqual(True,
self.emsa.isLineData(line)[0],
msg="With 5 column")
self.assertEqual('Y',
self.emsa.isLineData(line)[1],
msg="With 5 column")
self.assertEqual(5, self.emsa.isLineData(line)[2], msg="With 5 column")
line = "0.1 0.2 0.3 0.4 0.5 0.6"
self.assertEqual(False,
self.emsa.isLineData(line)[0],
msg="With 6 column")
self.assertEqual(None,
self.emsa.isLineData(line)[1],
msg="With 6 column")
self.assertEqual(0, self.emsa.isLineData(line)[2], msg="With 6 column")
line = "2"
self.assertEqual(True,
self.emsa.isLineData(line)[0],
msg="With integer")
self.assertEqual('Y',
self.emsa.isLineData(line)[1],
msg="With integer")
self.assertEqual(1, self.emsa.isLineData(line)[2], msg="With integer")
line = ".1"
self.assertEqual(True,
self.emsa.isLineData(line)[0],
msg="Without leading zero")
self.assertEqual('Y',
self.emsa.isLineData(line)[1],
msg="Without leading zero")
self.assertEqual(1,
self.emsa.isLineData(line)[2],
msg="Without leading zero")
line = "1.0E-6"
self.assertEqual(True,
self.emsa.isLineData(line)[0],
msg="With scinetific notation")
self.assertEqual('Y',
self.emsa.isLineData(line)[1],
msg="With scinetific notation")
self.assertEqual(1,
self.emsa.isLineData(line)[2],
msg="With scinetific notation")
line = "1.0e6"
self.assertEqual(True,
self.emsa.isLineData(line)[0],
msg="With scinetific notation")
self.assertEqual('Y',
self.emsa.isLineData(line)[1],
msg="With scinetific notation")
self.assertEqual(1,
self.emsa.isLineData(line)[2],
msg="With scinetific notation")
line = "1.0d6"
if sys.platform == 'win32' and "32 bit" in sys.version:
self.assertEqual(True,
self.emsa.isLineData(line)[0],
msg="With bad character")
self.assertEqual('Y',
self.emsa.isLineData(line)[1],
msg="With bad character")
self.assertEqual(1,
self.emsa.isLineData(line)[2],
msg="With bad character")
elif sys.platform == 'win32' and "64 bit" in sys.version:
self.assertEqual(False,
self.emsa.isLineData(line)[0],
msg="With bad character")
self.assertEqual(None,
self.emsa.isLineData(line)[1],
msg="With bad character")
self.assertEqual(0,
self.emsa.isLineData(line)[2],
msg="With bad character")
else:
self.assertEqual(False,
self.emsa.isLineData(line)[0],
msg="With bad character")
self.assertEqual(None,
self.emsa.isLineData(line)[1],
msg="With bad character")
self.assertEqual(0,
self.emsa.isLineData(line)[2],
msg="With bad character")
line = "#1.0"
self.assertEqual(False,
self.emsa.isLineData(line)[0],
msg="With leading #")
self.assertEqual(None,
self.emsa.isLineData(line)[1],
msg="With leading #")
self.assertEqual(0,
self.emsa.isLineData(line)[2],
msg="With leading #")
line = " 0.1"
self.assertEqual(True,
self.emsa.isLineData(line)[0],
msg="With leading space")
self.assertEqual('Y',
self.emsa.isLineData(line)[1],
msg="With leading space")
self.assertEqual(1,
self.emsa.isLineData(line)[2],
msg="With leading space")
line = " 0.0000, 0.0,"
flag, mode, number = self.emsa.isLineData(line)
self.assertEqual(True, flag, msg="With leading space")
self.assertEqual('Y', mode, msg="With leading space")
self.assertEqual(2, number, msg="With leading space")
def testSetGetXPerChannel(self):
emsa = emsaFormat.EmsaFormat()
self.assertEquals(None, emsa.getXPerChannel())
self.assertEquals(0.02, self.emsa.getXPerChannel())
