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

echo 'Hello Thomas - edit PATH using "profile"'

alias ls="ls --color"

alias cd..='cd ../'                         # Go back 1 directory level (for fast typers)
alias cd...='cd ../../'
alias ..='cd ../'                           # Go back 1 directory level
alias ...='cd ../../'                       # Go back 2 directory levels
alias .3='cd ../../../'                     # Go back 3 directory levels
alias .4='cd ../../../../'                  # Go back 4 directory levels

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