cbare

PATH=/Users/CBare/bin:$PATH

export CLICOLOR=1
export LSCOLORS=gxBxhxDxfxhxhxhxhxcxcx

alias ls='ls -alph'
alias path='echo -e ${PATH//:/\\n}'
alias libpath='echo -e ${LD_LIBRARY_PATH//:/\\n}'
alias du='du -kh'
alias df='df -kh'

cbare

FROM ubuntu:16.04

RUN apt-get update && apt-get install -y less && apt-get install -y octave

VOLUME ["/source"]
WORKDIR /source
CMD octave

cbare

import os
from boto.s3.connection import S3Connection
from boto.s3.connection import OrdinaryCallingFormat

## retrieve AWS credentials from environment variables
aws_key = os.getenv('AWS_KEY_ID')
aws_secret = os.getenv('AWS_SECRET_KEY')

## Ordinary calling format necessary because of dots in
## bucket name. See: https://github.com/boto/boto/issues/2836

cbare

## Sample from an estimated probability density
sample.density <- function(dd, size, jitter=FALSE) {
  x <- sample(dd$x, size=size, prob=dd$y, replace=TRUE)
  if (dd$n < 2) jitter=FALSE
  if (jitter) {
    w <- mean(dd$x[2:length(dd$x)] - dd$x[1:(length(dd$x)-1)]) / 2.0
    x <- x + runif(size,-w,w)
  }
  return(x)
}

cbare

---
title: "Directionality of mPower features"
author: "J. Christopher Bare"
date: "June 6, 2016"
---

```{r imports, echo=FALSE, message=FALSE, warning=FALSE}
library(synapseClient)
library(ggplot2)
library(scales)

cbare

"""
=======================================================
 How to access Synapse from Amazon Lambda with Python
=======================================================

Here we show an example of adding a row to a Synapse table
through an AWS Lambda script.

Caveat: Any operation that requires chunked file upload
        fails on AWS Lambda. The execution environment for

cbare

"""
Combine feature extraction output .csv files
"""
import csv
import os

dir = "/home/ubuntu/mhealthx_output/feature_tables/voice_openSMILE-2.2rc1_gemaps"
data=[]
for filename in os.listdir(dir):
    print filename

cbare

## Messages for challenge scoring script.

import string
import sys
import warnings


## Module level state. You'll need to set a synapse object at least
## before using this module.
syn = None

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############################################################
##
##  Create EC2 Machines
##
##  Start up EC2 instances for each member of a Synapse
##  team, emailing them the details of their assigned
##  machine.
##
##  chris.bare@sagebase.org, November 2015
##

cbare

import json
import pandas as pd
import matplotlib.pyplot as plt

import synapseclient
from collections import OrderedDict

syn = synapseclient.Synapse()
syn.login()