In [1]:
%matplotlib qt4
import numpy as np
import hyperspy.api as hs
import matplotlib.pyplot as plt
In [2]:
s = hs.datasets.example_signals.EDS_SEM_Spectrum()
s.plot(True)
In [3]:
s = hs.datasets.example_signals.EDS_SEM_Spectrum()
s.plot()
In [4]:
s = hs.datasets.example_signals.EDS_TEM_Spectrum()
s.plot(True)
In [5]:
#Sum()
s = hs.datasets.example_signals.EDS_SEM_Spectrum()
s.sum(0).data
Out[5]:
In [6]:
#rebin()
s = hs.datasets.example_signals.EDS_SEM_Spectrum()
print(s)
print(s.rebin([512]))
In [7]:
#set_elements()
s = hs.datasets.example_signals.EDS_SEM_Spectrum()
print(s.metadata.Sample.elements)
s.set_elements(['Al'])
print(s.metadata.Sample.elements)
In [8]:
#add_elements()
s = hs.datasets.example_signals.EDS_SEM_Spectrum()
print(s.metadata.Sample.elements)
s.add_elements(['Ar'])
print(s.metadata.Sample.elements)
In [9]:
#set_lines()
s = hs.datasets.example_signals.EDS_SEM_Spectrum()
s.add_lines()
print(s.metadata.Sample.xray_lines)
s.set_lines(['Cu_Ka'])
print(s.metadata.Sample.xray_lines)
In [10]:
#add_lines()
s = hs.datasets.example_signals.EDS_SEM_Spectrum()
s.add_lines()
print(s.metadata.Sample.xray_lines)
s = hs.datasets.example_signals.EDS_SEM_Spectrum()
s.set_microscope_parameters(beam_energy=30)
s.add_lines()
print(s.metadata.Sample.xray_lines)
s = hs.datasets.example_signals.EDS_SEM_Spectrum()
s.add_lines()
print(s.metadata.Sample.xray_lines)
s.add_lines(['Cu_Ka'])
print(s.metadata.Sample.xray_lines)
In [3]:
#get_lines_intensity()
s = hs.datasets.example_signals.EDS_SEM_Spectrum()
s.get_lines_intensity(['Mn_Ka'], plot_result=True)
Out[3]:
In [4]:
#get_lines_intensity()
s = hs.datasets.example_signals.EDS_SEM_Spectrum()
s.plot(['Mn_Ka'], integration_windows=2.1)
s.get_lines_intensity(['Mn_Ka'],
integration_windows=2.1, plot_result=True)
Out[4]:
In [6]:
#get_lines_intensity()
s = hs.datasets.example_signals.EDS_SEM_Spectrum()
s.change_dtype('float')
s.set_elements(['Mn'])
s.set_lines(['Mn_Ka'])
bw = s.estimate_background_windows()
s.plot(background_windows=bw)
s.get_lines_intensity(background_windows=bw, plot_result=True)
Out[6]:
In [7]:
#estimate_integration_windows()
s = hs.datasets.example_signals.EDS_TEM_Spectrum()
s.add_lines()
iw = s.estimate_integration_windows()
s.plot(integration_windows=iw)
s.get_lines_intensity(integration_windows=iw, plot_result=True)
Out[7]:
In [9]:
#estimate_background_windows()
s = hs.datasets.example_signals.EDS_TEM_Spectrum()
s.change_dtype('float')
s.add_lines()
bw = s.estimate_background_windows(line_width=[5.0, 2.0])
s.plot(background_windows=bw)
s.get_lines_intensity(background_windows=bw, plot_result=True)
Out[9]:
In [10]:
#get_take_off()
s = hs.datasets.example_signals.EDS_SEM_Spectrum()
s.get_take_off_angle()
Out[10]:
In [11]:
#get_take_off()
s.set_microscope_parameters(tilt_stage=20.)
s.get_take_off_angle()
Out[11]:
In [12]:
#plot()
s = hs.datasets.example_signals.EDS_SEM_Spectrum()
s.plot()
s = hs.datasets.example_signals.EDS_SEM_Spectrum()
s.plot(True)
s = hs.datasets.example_signals.EDS_TEM_Spectrum()
s.add_lines()
bw = s.estimate_background_windows()
s.plot(background_windows=bw)
s = hs.datasets.example_signals.EDS_SEM_Spectrum()
s.plot(['Mn_Ka'], integration_windows='auto')
s = hs.datasets.example_signals.EDS_TEM_Spectrum()
s.add_lines()
bw = s.estimate_background_windows()
s.plot(background_windows=bw, integration_windows=2.1)
In [13]:
#get_calibration_from
ref = hs.datasets.example_signals.EDS_SEM_Spectrum()
s = hs.signals.EDSSEMSpectrum(
hs.datasets.example_signals.EDS_SEM_Spectrum().data)
print(s.axes_manager[0].scale)
s.get_calibration_from(ref)
print(s.axes_manager[0].scale)
In [14]:
#set_micro
s = hs.datasets.example_signals.EDS_SEM_Spectrum()
print('Default value %s eV' %
s.metadata.Acquisition_instrument.
SEM.Detector.EDS.energy_resolution_MnKa)
s.set_microscope_parameters(energy_resolution_MnKa=135.)
print('Now set to %s eV' %
s.metadata.Acquisition_instrument.
SEM.Detector.EDS.energy_resolution_MnKa)
In [15]:
#set_micro
s = hs.datasets.example_signals.EDS_TEM_Spectrum()
print(s.metadata.Acquisition_instrument.
TEM.Detector.EDS.energy_resolution_MnKa)
s.set_microscope_parameters(energy_resolution_MnKa=135.)
print(s.metadata.Acquisition_instrument.
TEM.Detector.EDS.energy_resolution_MnKa)
In [16]:
#get_calibration_from
ref = hs.datasets.example_signals.EDS_TEM_Spectrum()
s = hs.signals.EDSTEMSpectrum(
hs.datasets.example_signals.EDS_TEM_Spectrum().data)
print(s.axes_manager[0].scale)
s.get_calibration_from(ref)
print(s.axes_manager[0].scale)
In [4]:
#quant
s = hs.datasets.example_signals.EDS_TEM_Spectrum()
s.change_dtype('float')
s.add_lines()
kfactors = [1.450226, 5.075602] #For Fe Ka and Pt La
bw = s.estimate_background_windows(line_width=[5.0, 2.0])
s.plot(background_windows=bw)
intensities = s.get_lines_intensity(background_windows=bw)
res = s.quantification(intensities, kfactors, plot_result=True,
composition_units='atomic')
In [5]:
res[0].axes_manager.signal_size
Out[5]:
In [7]:
# Simulate a spectrum image with vacuum region
import numpy as np
s = hs.datasets.example_signals.EDS_TEM_Spectrum()
s_vac = hs.signals.BaseSignal(np.ones_like(s.data, dtype=float))*0.005
s_vac.add_poissonian_noise()
si = hs.stack([s]*3 + [s_vac])
si.vacuum_mask().data
Out[7]:
In [8]:
s = hs.datasets.example_signals.EDS_TEM_Spectrum()
si = hs.stack([s]*3)
si.change_dtype(float)
si.decomposition()
In [9]:
# Electron range in pure Copper at 30 kV in micron
hs.eds.electron_range('Cu', 30.)
Out[9]:
In [10]:
# X-ray range of Cu Ka in pure Copper at 30 kV in micron
hs.eds.xray_range('Cu_Ka', 30.)
Out[10]:
In [11]:
# X-ray range of Cu Ka in pure Carbon at 30kV in micron
hs.eds.xray_range('Cu_Ka', 30., hs.material.elements.C.
Physical_properties.density_gcm3)
Out[11]: