PingjunChen

#!/usr/bin/env bash

# A bash script for converting all the files in a directory to pyramidal tiff
# Pass the directory the images are stored in as an argument
# But it will put the images in the current directory ... to be fixed

if [ $# -lt 3 ]; then
    echo 'Usage: tile <directory> <extension> <desired_prefix>'
else
    echo 'Looking for all files in directory: $1/'

PingjunChen

Clear sonsole

Ctrl+l

Set working directory

setwd(dir)

Get working directory

getwd()

Clear environment

remove(list = ls())

How to use a package

install.packages('fortunes') # install

PingjunChen

# -*- coding: utf-8 -*-

__author__ = "Pingjun Chen"
__email__ =  "[email protected]"

import os, sys, pdb

def organize_images(txt_path, image_path):
	with open(txt_path) as f:
		content = f.readlines()

PingjunChen

# -*- coding: utf-8 -*-
__author__ = "Pingjun Chen"
__email__ =  "[email protected]"

import os, sys, pdb
import numpy as np
from scipy import misc
import matplotlib.pyplot as plt
from skimage import io
import openslide

PingjunChen

# -*- coding: utf-8 -*-
__author__ = "Pingjun Chen"
__email__ =  "[email protected]"

import os, sys, pdb
import json

# load json file
json_in = json.load(open('***.json'))