thomasaarholt’s gists

thomasaarholt / lazy_align.py

Created June 14, 2017 09:28

	---------------------------------------------------------------------------
	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 / bcferror.py

Created August 22, 2017 13:27

	---------------------------------------------------------------------------
	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 / fftw.py

Created September 27, 2017 13:32

fftw prime determiner

	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 / pyprismatic_install_error.shell

Created November 13, 2017 13:26

Error when installing pyprismatic on windows

	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 / cuprismatic_crash.bash

Last active November 16, 2017 12:35

Result after cuprismatic crashing when only running on GPU

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

	Simulation parameters:
	=====================

thomasaarholt / ase_to_prismatic_writer.py

Created November 16, 2017 15:14

Python writer to create XYZ samples from ASE atoms objects

	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 / odemis_error1.py

Created November 29, 2017 13:23

	---------------------------------------------------------------------------
	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 / odemis_multistream.py

Created November 30, 2017 14:39

	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 / brokenpipe.py

Created December 4, 2017 15:36

	---------------------------------------------------------------
	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 / sync.py

Last active December 7, 2017 14:04

	### 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")

Thomas Aarholt thomasaarholt