yangyushi

def core_shell_gaussian(x, core, shell):
    """
    since we're dealing with REAL image with normally uint8 float type
    value < 1/255 --> value = 0
    let zero = 1/256
    """
    constant = shell ** 2 * 0.18033688011112042  # - shell^2 / ln(zero)
    core_shell = np.exp(- (x - core) ** 2 / constant)
    core_shell[x <= core] = 1.0  # construct core
    core_shell[x >= (core + shell)] = 0.0  # trim 4 edges of the box

yangyushi

import numpy as np
import matplotlib.pyplot as plt
import numpy as np
from mpl_toolkits.mplot3d import Axes3D
from scipy.optimize import least_squares


def get_best_rotation(r1, r2):
	"""
	calculate the best rotation to relate two sets of vectors

yangyushi

DELETE FROM raw_image WHERE id NOT IN (SELECT raw_image_id FROM result);
DELETE FROM image WHERE id NOT IN (SELECT image_id FROM result);
DELETE FROM image_parameter WHERE id NOT IN (SELECT image_parameter_id FROM result);
DELETE FROM segment_parameter WHERE id NOT IN (SELECT segment_parameter_id FROM result);
DELETE FROM result_tag WHERE id_result NOT IN (SELECT id FROM result);
VACUUM;

yangyushi

def array_to_xyz(filename, array):
    """
    Append many frames to the same xyz file that ovito can read
    The file is overwritten everytime
    array: [frame_1, frame_2, ...]
    coordinate in one frame: (dimension, number_of_particles)
    """
    if '.xyz' == filename[-4:]:
        fname = filename
    else:

yangyushi

import numpy as np
import matplotlib.pyplot as plt
from scipy import ndimage
from scipy import signal

a = np.ones((20, 20)) * 0

a[5, 5] = 1
a[10, 10] = 1
a[15, 15] = 1

yangyushi

import numpy as np
from scipy.optimize import minimize

def get_in_plane_dist_sqr(x, e1, e2):
    gamma, delta = x
    dist_sqr = gamma**2 + delta**2 - 2 * gamma * delta * (e1 @ e2)
    return dist_sqr

def get_segment_dist(r1, r2, e1, e2, L1, L2):
    """

yangyushi

def conflict(conf):
    for i in range(len(conf) - 1):
        if conf[i] == conf[-1]:
            return True
        if len(conf) - i - 1 == conf[-1] - conf[i]:
            return True
        elif len(conf) - i - 1 == conf[i] - conf[-1]:
            return True
    return False

yangyushi

ln -s /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk/System/Library/Frameworks/Tk.framework/Versions/8.5/Headers/X11 /usr/local/include/X11
./configure\
    --enable-optimizations\
    --prefix=/usr/local\
    --enable-shared\
    --with-openssl=$(brew --prefix openssl)\
    CPPFLAGS="-I/usr/local/opt/openssl/include"\
    LDFLAGS="-L/usr/local/opt/openssl/lib"

yangyushi

#!/usr/bin/env python
import re
import sys
from textwrap import dedent

STOPWORDS = [  # common stop words from package nltk
    "i", "me", "my", "myself", "we", "our", "ours", "ourselves", "you", "you're", "you've", "you'll",
    "you'd", "your", "yours", "yourself", "yourselves", "he", "him", "his", "himself", "she", "she's",
    "her", "hers", "herself", "it", "it's", "its", "itself", "they", "them", "their", "theirs",
    "themselves", "what", "which", "who", "whom", "this", "that", "that'll", "these", "those", "am",

yangyushi

./configure --with-features=huge \
            --enable-multibyte \
            --enable-rubyinterp=yes \
            --enable-python3interp=yes \
            --with-python3-config-dir=$(python3-config --configdir) \
            --enable-perlinterp=yes \
            --enable-luainterp=yes \
            --enable-cscope \
            --prefix=/usr/local