npyoung

# update install packages
yum update -y

# install build tools 
yum install make automake gcc gcc-c++ kernel-devel git-core -y 

# install python 2.7 and change default python symlink 
yum install python27-devel -y 
rm /usr/bin/python
ln -s /usr/bin/python2.7 /usr/bin/python 

npyoung

Dialog.create("Process interleaved ratiometric movie");
Dialog.addString("Experiment name:", "expt");
Dialog.addNumber("Background", 1600)
Dialog.show()
expt_name = Dialog.getString();
background = Dialog.getNumber();
 
expt_dir = getDirectory("Choose a save directory");
 
id = getImageID();

npyoung

#!/usr/bin/env python
import argparse, os
from libtiff import TIFF
import moviepy.editor as mpy
import numpy as np
from skimage.color import gray2rgb

if __name__ == '__main__':
    ap = argparse.ArgumentParser()
    ap.add_argument('input_stack', help="Path to a tiff stack file")

npyoung

"""
This demonstration assumes you have already installed Pymba and followed the installation instructions there:
https://github.com/morefigs/pymba

MoviePy is used to save the frames to a video file for later viewing, while the frame's mean intensity is
printed in real time. MoviePy can be installed from pip nicely.
"""
import pymba
from moviepy.video.io.ffmpeg_writer import FFMPEG_VideoWriter as VidWriter
from skimage.color import gray2rgb

npyoung

from serial import Serial
from time import sleep

class DG4(object):
    """Control a Sutter Lambda DG-4 over serial interface"""
    SWITCH_TO_SERIAL = 238 # switch the DG4 to serial mode, DG4 hangs until it receives the next serial command
    FREEZE_DISPLAY = 218
    TURN_DISPLAY_ON = 219
    OPEN_SHUTTER = 170
    ND_ADJ_MARKER = 171 # DATANUM = 171 MARKER BETWEEN 235 OR 236 IN N.D. ADJUST

npyoung

def timeshuffle_bootstrap(dview, statistic, data, axis=-1, n_boot=1000):
    """Perform bootstrap resampling to assess the significance of a statistic by reshuffling in time.
    
    Args:
        dview: IPython client (i.e. dview = IPython.parallel.Client()[:]) for parallelization.
        statistic: Function that takes the dataset and computes some statistic (or array of statistics).
        data: Data from which the statistic is computed.
        axis: Axis in the data the shuffle along (usually time).
    """
    T = data.shape[axis]

npyoung

from os.path import join as pjoin
from os.path import isdir
from os import listdir
from argparse import ArgumentParser
from neo.io import TdtIO, NeoHdf5IO
from progressbar import ProgressBar


if __name__ == '__main__':
    parser = ArgumentParser(description="Convert a Tucker-Davis Technologies (TDT) to Neo's HDF5 format.")

npyoung

sudo -i
apt-get update
apt-get upgrade -y
apt-get install htop git
apt-get install python-dev pkg-config build-essential libfreetype6-dev libpng-dev libatlas-base-dev
wget "https://bootstrap.pypa.io/get-pip.py" | python
rm "get-pip.py"
pip install numpy scipy matplotlib seaborn scikit-image jupyter ipyparallel ipywidgets libtiff s4cmd

npyoung

*.ipynb filter=stripoutput

npyoung

#!/usr/bin/env bash                                                                                                                

FILEPATH=$@                                                                                                                        
   
git filter-branch --force --index-filter "git rm --cached --ignore-unmatch $FILEPATH" --prune-empty --tag-name-filter cat -- --all