thomasaarholt

import numpy as np

machineTime = {
    'm1': {
        'p1':20,
        'p2':np.nan,
        'p3':70,
        'p4':4,
    },

thomasaarholt

import matplotlib.pyplot as plt
import numpy as np

import sympy as sp
sp.init_printing()

E0, dE, Cc = sp.symbols('E0, dE, C_c, ')
deltaZ_sigma = Cc*dE/E0#*2*sp.sqrt(2*sp.log(2)) 

zlp = 0.9

thomasaarholt

  GNU nano 2.5.3                                           File: /shared/users/thomasaar/.profile                                                                                             
PS1='$(pwd): '
echo 'Hello Thomas - edit PATH using "profile"'
echo "YOU ARE NOT IN HOME - YOU ARE ON SHARED"
# This is a comment
echo 'Enabling environment for pyprismatic'
export CPLUS_INCLUDE_PATH=/usr/local/cuda-10.0/include:$CPLUS_INCLUDE_PATH
export LD_LIBRARY_PATH=$HOME/fftw_gcc5_build/lib64:/usr/local/cuda-10.0/lib64:$HOME/prismatic_gcc5/lib:$LD_LIBRARY_PATH
export LIBRARY_PATH=$HOME/fftw_gcc5_build/lib64:/usr/local/cuda-10.0/lib64:$HOME/prismatic_gcc5/lib:$LIBRARY_PATH

thomasaarholt

"\e[A": history-search-backward
"\e[B": history-search-forward
"\e[C": forward-char
"\e[D": backward-char

thomasaarholt

from mpl_toolkits.axes_grid1 import make_axes_locatable

def colorbar(mappable):
    "mappable is img = plt.imshow()"
    ax = mappable.axes
    fig = ax.figure
    divider = make_axes_locatable(ax)
    cax = divider.append_axes("right", size="5%", pad=0.05)
    cax.aname = 'colorbar'
    return fig.colorbar(mappable, cax=cax)

thomasaarholt

from pathlib import Path
def win2lin(rpath: r"C:\Users..."):
    path = rpath.replace("\\", "/").replace(":/", "/")
    drive = path[0]
    path = Path("/mnt/") / Path(drive.lower() + path[1:])
    return path

### Example:
# >>> win2lin(r"C:\Users\myuser\Documents")
# PosixPath('/mnt/c/Users/myuser/Documents')

thomasaarholt

Timer unit: 1e-06 s

Total time: 0.265183 s
File: /mnt/c/Users/thomasaar/Documents/atomap/atomap/atom_finding_refining.py
Function: _make_model_from_atom_list at line 740

Line #      Hits         Time  Per Hit   % Time  Line Contents
==============================================================
   740                                           def _make_model_from_atom_list(
   741                                                   atom_list,

thomasaarholt

def border_elems(image_2d, pixels=1): # Input array : a, Edgewidth : W
    n = image_2d.shape[0]
    r = np.minimum(np.arange(n)[::-1], np.arange(n))
    return image_2d[np.minimum(r[:,None],r)<pixels]

def remove_integrated_edge_cells(i_points, i_record, p_record, 
                                 pixels=1, inplace=False):
    '''
    Removes any cells that touch within a number of pixels of
    the image border.

thomasaarholt

import numpy as np
import math
import copy
from tqdm import tqdm, trange
from scipy import interpolate
from scipy import ndimage
from scipy.spatial import cKDTree
import matplotlib.pyplot as plt
import hyperspy.api as hs
from hyperspy.signals import Signal1D, Signal2D

thomasaarholt

tmux attach