bluepichu

from __future__ import annotations
from collections import defaultdict

from os import path
from typing import DefaultDict, List, NamedTuple, Optional, Sequence, Set, Tuple, cast
import requests
import re
from copy import copy
from pyrsistent import m, s, v, PMap, PSet, PVector

thomasaarholt

'''
Python script to load any format supported by hyperspy directly into GMS
Must be copied and pasted into Gatan DigitalMicrograph (aka Gatan Microscopy Suite) version 3.4+
Call by `load_img(filepath)` at the bottom of the script. Can not be called outside of GMS.
Does not automatically convert the data type to EELS or EDS
Written by Thomas Aarholt, see https://gist.github.com/thomasaarholt/fccf06d56ff84cf76345b44dae30871e for newer versions
Feedback and forks are very welcome.
MUST: First import of hyperspy (or scipy) must NOT be run with "Execute on background thread" checked. One
can then swap to background thread and rerun.
v. 0.3: Added delete statements to ensure python objects don't stay in memory.

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

Using Jupyter notebook remotely via a ssh tunnel.

Especially good for running on headless devices, such as supercomputers or clusters.

Remotely:

# remote_port should be value between 8888 and 9000
jupyter notebook --no-browser --port=remote_port

Locally, new terminal window

thomasaarholt

import matplotlib.pyplot as plt

def save(filepath="image.png", fig=None):
    '''Save the current image with no whitespace
    Example filepath: "myfig.png" or r"C:\myfig.pdf" 
    Based on answers from https://stackoverflow.com/questions/11837979/
    '''
    import matplotlib.pyplot as plt
    if not fig:
        fig = plt.gcf()

bencholmes

function X = forceFFTSymmetry(X)
% forceFFTSymmetry  A function to force conjugate symmetry on an FFT such that when an
% IFFT is performed the result is a real signal.

% The function has been written to replace MATLAB's ifft(X,'symmetric'), as this function
% is not compatible with MATLAB Coder.
  
% Licensed under Creative Commons Zero (CC0) so use freely.

XStartFlipped = fliplr(X(2:floor(end/2)));

wassname

"""Another way, note this one will load the whole array into memory ."""
from keras.preprocessing.image import ImageDataGenerator
import h5py
from keras.utils.io_utils import HDF5Matrix
seed=0
batch_size=32

# we create two instances with the same arguments
data_gen_args = dict( 
    rotation_range=90.,

derricw

import numpy as np

def bin_ndarray(ndarray, new_shape, operation='sum'):
    """
    Bins an ndarray in all axes based on the target shape, by summing or
        averaging.

    Number of output dimensions must match number of input dimensions.

    Example