def testInitECalibrationSpectrumRange(self):
try:
eels = SpectrumImage.EELSSpectrumImage(self.data, ZLP=False, dispersion=None, SpectrumRange=np.array([0, 1, 2, 3, 4]), channel_eV=None)
except ValueError:
self.fail("Got value error, didn't want one anyway " + traceback.format_exc())
self.assertEqual(eels.dispersion, 1)
self.assertArraysEqual(eels.SpectrumRange, np.array([0, 1, 2, 3, 4]))
def testDictifyMultipleLevels(self):
self.assertEqual(
SpectrumImage.make_dict_from_tags(['root.foo.bar = 12']),
{'root': {
'foo': {
'bar': '12'
}
}})
def testInitECalibrationChanneleVwrong(self):
with self.assertRaisesRegexp(ValueError,
'channel_eV must have length 2!'):
eels = SpectrumImage.EELSSpectrumImage(self.data,
ZLP=False,
SpectrumRange=None,
dispersion=0.3,
channel_eV=[2, 0.5, 1])
def testInitECalibrationZLPnoDispersion(self):
with self.assertRaisesRegexp(ValueError,
'Dispersion needs to be a real number!'):
eels = SpectrumImage.EELSSpectrumImage(self.data,
ZLP=True,
SpectrumRange=None,
dispersion=None,
channel_eV=None)
def testInitECalibrationChanneleV(self):
try:
eels = SpectrumImage.EELSSpectrumImage(self.data, ZLP=False, dispersion=0.3, SpectrumRange=None, channel_eV=[2, 0.5])
except ValueError:
self.fail("Got value error, didn't want one anyway")
self.assertEqual(eels.dispersion, 0.3)
self.assertAlmostEqual(eels.SpectrumRange[2], 0.5)
self.assertArraysEqual(eels.data, self.data)
def testInitECalibrationNone(self):
with self.assertRaisesRegexp(
ValueError, 'You need to input an energy calibration!'):
eels = SpectrumImage.EELSSpectrumImage(self.data,
ZLP=False,
SpectrumRange=None,
dispersion=None,
channel_eV=None)
def testInitECalibrationZLP(self):
try:
eels = SpectrumImage.EELSSpectrumImage(self.data, ZLP=True, dispersion=0.3, SpectrumRange=None, channel_eV=None)
except ValueError:
self.fail("Got value error, didn't want one anyway")
self.assertEqual(eels.dispersion, 0.3)
self.assertTrue(eels.ZLP)
self.assertArraysEqual(eels.data, self.data)
def __init__(self, SI = np.array([]), Wavelengths = np.array([]), SEM=np.array([]), survey=np.array([]), fuzzing=False): self.fuzzing = fuzzing self.SI = SpectrumImage.CLSpectrumImage(SI, Wavelengths) self.SEM = SEM self.survey = survey if self.fuzzing: reshapedSEM = np.reshape(self.SEM.data, [int(self.SEM.size[0]/4), 4, int(self.SEM.size[1]/4), 4]) self.unfuzzedSEM = Image(np.sum(np.sum(reshapedSEM, axis=1), axis=-1), calibration=self.SEM.calibration*4) else: self.unfuzzedSEM = self.SEM
def __init__(self,
SI=np.array([]),
Wavelengths=np.array([]),
SEM=np.array([]),
survey=np.array([]),
fuzzing=False):
self.fuzzing = fuzzing
self.SI = SpectrumImage.CLSpectrumImage(SI, Wavelengths * 1e9)
self.SEM = Image(SEM)
self.survey = Image(survey)
def testZLPandSpectrumRange(self):
with self.assertRaisesRegexp(
ValueError,
"You don't need to define a SpectrumRange and ZLP/dispersion!"
):
eels = SpectrumImage.EELSSpectrumImage(self.data,
ZLP=True,
SpectrumRange=np.array(
[0, 1, 2, 4, 5]),
dispersion=0.3,
channel_eV=None)
def testSpectrumRangeWrongLength(self):
with self.assertRaisesRegexp(
ValueError,
"Your SpectrumRange is not the same size as your energy axis!"
):
eels = SpectrumImage.EELSSpectrumImage(self.data,
ZLP=False,
SpectrumRange=np.array(
[0, 1, 2, 4]),
dispersion=None,
channel_eV=None)
def testDictifyCollision(self):
self.assertEqual(
SpectrumImage.make_dict_from_tags(['bar = 10', 'bar = 12']),
{'bar': '10'})
## Testing ImagePlotter
#Im = np.random.random((2000,2000))
#a = ImagePlotter.ImagePlotter(ax, Im)
#### Testing SIPlotter
#SIdata = np.random.random(size = (20,30,50))
#SIdata[:, :, 10] = 2
#SI = SpectrumImage.EELSSpectrumImage(SIdata, dispersion=0.01)
#plotter=SpectrumImagePlotter.SpectrumImagePlotter(SI)
#plt.show()
###Testing SIPlotter with real data!
folder = '/home/isobel/Documents/McMaster/EELS/2016-07-28/Sq2R_(1,7)/'
filebase = 'EELS Spectrum Image (dark ref corrected).dm3'
s = hp.load(folder + filebase)
eels = SpectrumImage.EELSSpectrumImage(s.data)
#PSF = Spectrum.EELSSpectrum.LoadFromCSV('/home/isobel/Documents/McMaster/EELS/2016-07-27/SI3/Processed/Spectrum_ZLP.csv')
#print(np.shape(PSF.intensity))
p1 = SpectrumImagePlotter.SpectrumImagePlotter(eels, filepath=folder)
#eels2 = eels.RLDeconvolution(2, PSF)
#p2 = SpectrumImagePlotter.SpectrumImagePlotter(eels2)
p1.ShowPlot()
folderCL = '/home/isobel/Documents/McMaster/CL/T9-3_Sq1A_(1,3)/'
fileCL = 'T9-3_Sq1A_(1,3)h_Gr800at750_30keV_Ap3Spot4_2s_noQWP_noPol_full2.h5'
cl = CLSpectrumData.CLDataSet.LoadFromFile(folderCL + fileCL)
plotter = SpectrumImagePlotter.SpectrumImagePlotter(cl.SI)
plt.show()
#plotter.extractedim.SaveImgAsPNG('/home/isobel/Documents/McMaster/PythonCodes/DataAnalysis/testIm.png', plotter.extractedim.Imglim)
def testDictifyOneLevel(self):
self.assertEqual(SpectrumImage.make_dict_from_tags(['root = 65']),
{'root': '65'})
# raise ValueError("No intersection! Fix it!")
# h_edge = sorted((r1.xmin, r1.xmax, r2.xmin, r2.xmax))
# v_edge = sorted((r1.ymin, r1.ymax, r2.ymin, r2.ymax))
# return Rectangle(h_edge[1], v_edge[1], h_edge[2], v_edge[2])
#print("Will's rectangle stuff")
#r1=Rectangle(0,0,10,10)
#r2=Rectangle(2,2,17,17)
#print(FindRectangleIntersectionWillsWay(r1, r2))
################End of Will's thing
#maxcorners = np.roll(np.transpose((p1.size, p2.size, p3.size, p4.size)), 1, axis = 0)
#overlapcorners = (np.max(offsets, axis = 1), np.min(maxcorners+offsets, axis = 1))
#p2_alignedtest = p2.data[overlapcorners[0][1] - offsets[1][1]:overlapcorners[1][1]-offsets[1][1], overlapcorners[0][0] - offsets[0][1]:overlapcorners[1][0] - offsets[0][1]]
#print(offsets)
AlignCrop.AlignCrop((p1, p2, SpectrumImage.SpectrumImage(data.chelsea(), 'nm'),
SpectrumImage.SpectrumImage(data.astronaut(), 'nm')),
offsets)
fig = plt.figure()
ax = plt.axes([0, 0, 1, 1])
ax.imshow(p3.data, interpolation='none', cmap='gray')
ax.imshow(p1.data, interpolation='none', cmap='Reds', alpha=0.2)
#ax.imshow(p4_aligned, interpolation = 'none', cmap = 'hot', alpha = 0.2)
#ax.imshow(p1_aligned, alpha = 0.2, cmap = 'Blues', interpolation = 'none')
#ax.imshow(mask, cmap = 'gray', alpha = 0.8)
ax.axis('off')
plt.show()
def testDictifyEmptyValue(self):
self.assertEqual(SpectrumImage.make_dict_from_tags(['root = ']),
{'root': ''})
raise ValueError("No intersection! Fix it!")
h_edge = sorted((r1.xmin, r1.xmax, r2.xmin, r2.xmax))
v_edge = sorted((r1.ymin, r1.ymax, r2.ymin, r2.ymax))
return Rectangle(h_edge[1], v_edge[1], h_edge[2], v_edge[2])
#print "Will's rectangle stuff"
#r1=Rectangle(0,0,10,10)
#r2=Rectangle(2,2,17,17)
#print FindRectangleIntersectionWillsWay(r1, r2)
################End of Will's thing
#maxcorners = np.roll(np.transpose((p1.size, p2.size, p3.size, p4.size)), 1, axis = 0)
#overlapcorners = (np.max(offsets, axis = 1), np.min(maxcorners+offsets, axis = 1))
#p2_alignedtest = p2.data[overlapcorners[0][1] - offsets[1][1]:overlapcorners[1][1]-offsets[1][1], overlapcorners[0][0] - offsets[0][1]:overlapcorners[1][0] - offsets[0][1]]
print(offsets)
AlignCrop.AlignCrop((p1, p2, SpectrumImage.SpectrumImage(
data.chelsea()), SpectrumImage.SpectrumImage(data.astronaut())), offsets)
fig = plt.figure()
ax = plt.axes([0, 0, 1, 1])
ax.imshow(p3.data, interpolation='none', cmap='gray')
ax.imshow(p1.data, interpolation='none', cmap='Reds', alpha=0.2)
#ax.imshow(p4_aligned, interpolation = 'none', cmap = 'hot', alpha = 0.2)
#ax.imshow(p1_aligned, alpha = 0.2, cmap = 'Blues', interpolation = 'none')
#ax.imshow(mask, cmap = 'gray', alpha = 0.8)
ax.axis('off')
plt.show()
def testDictifyMultipleValues(self):
self.assertEqual(
SpectrumImage.make_dict_from_tags(['foo = 12', 'bar = 16']), {
'foo': '12',
'bar': '16'
})