thomasaarholt

---------------------------------------------------------------------------
IndexError                                Traceback (most recent call last)
<ipython-input-4-f890f17f75fd> in <module>()
----> 1 s.align_zero_loss_peak()

C:\ProgramData\Miniconda3\lib\site-packages\hyperspy\_signals\eels.py in align_zero_loss_peak(self, calibrate, also_align, print_stats, subpixel, mask, signal_range, show_progressbar, **kwargs)
    287 
    288         zlpc = estimate_zero_loss_peak_centre(self, mask, signal_range)
--> 289         mean_ = without_nans(zlpc.data).mean()
    290         if print_stats is True:

thomasaarholt

---------------------------------------------------------------------------
TraitError                                Traceback (most recent call last)
<ipython-input-88-3fc0a0685cf7> in <module>()
----> 1 img, s = hs.load("8.bcf")

C:\ProgramData\Miniconda3\envs\35\lib\site-packages\hyperspy\io.py in load(filenames, signal_type, stack, stack_axis, new_axis_name, lazy, **kwds)
    241             objects = [load_single_file(filename, lazy=lazy,
    242                                         **kwds)
--> 243                        for filename in filenames]
    244 

thomasaarholt

def check_if_number_is_fftw_prime(numb):
    import sympy
    factors = sympy.ntheory.factorint(numb)
    if len(factors) > 5:
        return False
    primes = factors.keys()
    if max(primes) > 13:
        return False
    n11 = 0
    n13 = 0

thomasaarholt

λ pip install pyprismatic
Collecting pyprismatic
  Using cached PyPrismatic-1.1.15.tar.gz
Collecting numpy>=1.13.0 (from pyprismatic)
  Using cached numpy-1.13.3-cp35-none-win_amd64.whl
Collecting matplotlib>=2.0.2 (from pyprismatic)
  Using cached matplotlib-2.1.0-cp35-cp35m-win_amd64.whl
Requirement already satisfied: pytz in c:\programdata\miniconda3\lib\site-packages (from matplotlib>=2.0.2->pyprismatic)
Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in c:\programdata\miniconda3\lib\site-packages (from matplotlib>=2.0.2->pyprismatic)
Requirement already satisfied: python-dateutil>=2.0 in c:\programdata\miniconda3\lib\site-packages (from matplotlib>=2.0.2->pyprismatic)

thomasaarholt

[I 13:34:12.255 NotebookApp] Adapting to protocol v5.1 for kernel 879c9343-88fe-43f2-a9d7-9416223907b7                                                                                   
COMPILED FOR GPU                                                                                                                                                                         
                                                                                                                                                                                         
Simulation parameters:                                                                                                                                                                   
=====================                                                                                                                                                                    
                                                                                              

thomasaarholt

def save_cell_for_prismatic(sample, name, path=""):
    "Auto-adds 'prismatic' to filename"
	import os
	import numpy as np
    
	if path == "":
		path = os.getcwd()
	
    name += "_Prismatic"
	total = np.zeros(len(sample.numbers), dtype=[('Z', 'int8'), ("x", 'float'), ("y", 'float'), ("z", 'float'), ('occ', 'int'), ('dw', 'float')])

thomasaarholt

---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
<ipython-input-18-0e1e17072b32> in <module>()
----> 1 SED, SI = acquirer.start()
      2 #plt.imshow(a)

<ipython-input-16-abe1af516896> in start(self)
    197         '''
    198         #SE = self.acquire_large_SE_image()
--> 199         SED, SI = self.acquire_cube()

thomasaarholt

sem = model.getComponent(name="SEM Detector")
spec = model.getComponent(name="UV Spectrometer")
stream = SEMSpectrumMDStream("test", sem, spec)

---------------------------------------------------------------
AssertionError                Traceback (most recent call last)
<ipython-input-173-dab28defdbf6> in <module>()
      1 sem = model.getComponent(name="SEM Detector")
      2 spec = model.getComponent(name="UV Spectrometer")
----> 3 stream = SEMSpectrumMDStream("thomas", sem, spec)

thomasaarholt

---------------------------------------------------------------
ConnectionClosedError         Traceback (most recent call last)
<ipython-input-16-248a991767f8> in <module>()
----> 1 SE, SI  = acquirer.start()

/home/sparc/development/notebooks_thomas/tools_acquire.py in start(self)
    252         '''
    253         #SE = self.acquire_large_SE_image()
--> 254         SED, SI = self.acquire_cube()
    255         return SED, SI

thomasaarholt

### The intention is to create a script that acquires both from the secondary electron detector
### and the CL detector (UV spectrometer) whilst scanning over a rectangular grid on the sample.

# In order to define the various streams, I import the following
from odemis.acq.stream import SEMStream, CameraStream, SEMMDStream
from odemis import model

escan = model.getComponent(name="SEM E-beam")
sed = model.getComponent(name="SEM Detector")
spec = model.getComponent(name="UV Spectrometer")