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Thomas Aarholt thomasaarholt

  • University of Oslo
  • Oslo, Norway
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View gist:d8fa0a53c7cca210d857
import hyperspy.api as hs
%matplotlib qt4
s = hs.load("EELS 0eV.dm3")
s.plot() # This works!
import traitsui
View gist:805a2e120ca00669fe6c
ValueError Traceback (most recent call last)
<ipython-input-1-efe73691b2de> in <module>()
2 matplotlib.use("Qt4Agg")
----> 4 import hyperspy.api as hs
6 get_ipython().magic(u'matplotlib')
View gist:607c33992bcbbae497fa
AttributeError Traceback (most recent call last)
/Users/thomas/anaconda/lib/python2.7/site-packages/matplotlib/artist.pyc in draw_wrapper(artist, renderer, *args, **kwargs)
57 def draw_wrapper(artist, renderer, *args, **kwargs):
58 before(artist, renderer)
---> 59 draw(artist, renderer, *args, **kwargs)
60 after(artist, renderer)
/Users/thomas/anaconda/lib/python2.7/site-packages/matplotlib/figure.pyc in draw(self, renderer)
ImportError Traceback (most recent call last)
<ipython-input-1-5084803b0409> in <module>()
----> 1 import hyperspy.api as hs
3 path = "/Users/thomas/Dropbox/0_DPhil/0_Data/00_TEM Data/0_Other/Test/Image"
4 name = "EELS Metal 0eV"
/Users/thomas/anaconda/envs/c3/lib/python3.5/site-packages/hyperspy/ in <module>()
import hyperspy.api as hs
s = hs.load("MO")
# Get peak energy
Zr_Peak = 330.
O_peak = 532.
# Create signals with enough background and signal length to fit the components.
s_Zr = s.isig[Zr_Peak - 40.:Zr_Peak + 60.]
s_O = s.isig[O_peak - 40.:O_peak + 60.]
OSError Traceback (most recent call last)
<ipython-input-14-240ac4daefae> in <module>()
1 spectra[0].save("test2.hdf5")
----> 2 abc = hs.load("test2.hdf5")
/Users/thomas/Dropbox/0_Git/GitHub Desktop/hyperspy/hyperspy/ in load(filenames, record_by, signal_type, signal_origin, stack, stack_axis, new_axis_name, mmap, mmap_dir, **kwds)
212 objects = [load_single_file(filename,
213 **kwds)
--> 214 for filename in filenames]
thomasaarholt / Hyperspy Windows
Last active May 23, 2016
Error with a fresh single-user 64-bit install of Hyperspy 0.8.4
View Hyperspy Windows
>>> %matplotlib
RuntimeError Traceback (most recent call last)
<ipython-input-3-fc39d5fd4eba> in <module>()
----> 1 get_ipython().magic('matplotlib')
C:\Users\EMGroup\AppData\Local\HyperSpy WinPython Bundle 0.8.4\python-3.4.4.amd64\lib\site-packages\IPython\core\ in magic(self, arg_s)
2161 magic_name, _, magic_arg_s = arg_s.partition(' ')
2162 magic_name = magic_name.lstrip(prefilter.ESC_MAGIC)
-> 2163 return self.run_line_magic(magic_name, magic_arg_s)
thomasaarholt /
Created Jun 1, 2016
Functions to remove high-energy cosmic ray spikes in EELS data
def median_from_neighbors(energy_slice, x, y=""):
"""Takes the median of the value of the list neighbors"""
import numpy as np
return(np.median(find_cell_neighbors(energy_slice, x,y)))
def find_cell_neighbors(data, X, Y, r=1):
"""Finds value of neighbors of a index in the SI, excluding the centre and any values outside the edges of the SI"""
adjacent = []
if Y == "":
thomasaarholt /
Created Jun 7, 2016
Function for binning a Hyperspy Signal
def mybin(s, xbin=1, ybin=1, sbin=1):
"""Return spectrum s binned by factors xbin, ybin, sbin"""
if (xbin < 1) or (ybin < 1) or (sbin < 1):
raise ValueError("One of your binnings is smaller than 1. For signal axis to remain constant, leave as 1")
if all(n==1 for n in (xbin, ybin, sbin)):
print("Not binning because all binnings == 1")
return s # End Early
# Get signal channels
thomasaarholt /
Created Jun 7, 2016
Part of my script to make two signals the same length
SI_dispersion = check_energy_dispersion(bss_spectra[0])
bin_mlls = False
bin_factor = 1
for s in mlls_objects:
mlls_dispersion = check_energy_dispersion(s)
if SI_dispersion > mlls_dispersion:
bin_mlls = True
if SI_dispersion / mlls_dispersion > bin_factor:
bin_factor = int(SI_dispersion / mlls_dispersion)
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