thomasaarholt

import hyperspy.api as hs
%matplotlib qt4

s = hs.load("EELS 0eV.dm3")

s.plot() # This works!

import traitsui
traitsui.__version__
'5.0.0'

thomasaarholt

---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
<ipython-input-1-efe73691b2de> in <module>()
      2 matplotlib.use("Qt4Agg")
      3 
----> 4 import hyperspy.api as hs
      5 
      6 get_ipython().magic(u'matplotlib')

thomasaarholt

---------------------------------------------------------------------------
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)
     61 

/Users/thomas/anaconda/lib/python2.7/site-packages/matplotlib/figure.pyc in draw(self, renderer)

thomasaarholt

---------------------------------------------------------------------------
ImportError                               Traceback (most recent call last)
<ipython-input-1-5084803b0409> in <module>()
----> 1 import hyperspy.api as hs
      2 
      3 path = "/Users/thomas/Dropbox/0_DPhil/0_Data/00_TEM Data/0_Other/Test/Image"
      4 name = "EELS Metal 0eV"
      5 

/Users/thomas/anaconda/envs/c3/lib/python3.5/site-packages/hyperspy/api.py in <module>()

thomasaarholt

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.]

thomasaarholt

---------------------------------------------------------------------------
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/io.py 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

>>> %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\interactiveshell.py 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

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

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

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)
print(bin_factor)