PicnicHealth.com

This is my first entry promoting something. I dislike when others do it but I am making an exception because this service has significantly helped me. The company is called PicnicHealth and their website is http://www.picnichealth.com.

Since returning from Italy last year, I have been plagued with chronic stomach dysfunction. I have seen several doctors including a specialist at John Hopkins Medical Center. I have had to go through all the pain of collating my notes, labs, imaging studies, etc.  to send to doctors and analyze myself. Its been a pain until I found this tool through an article about PicnicHeath and uBiome collaborating. I follow uBiome semi-regularly as a personal interest.

They have a legitimate DICOM viewer so all my medical imaging shows up great, including the adjustments for brightness, contrast, and movie playback controls.

Anyways, here’s a quick sample of what my health timeline looks like.

picnichealth_example

Installing Theano in Windows 7 64-bit

My instructions for installing Theano 0.6 with

  • Windows 7-64 bit
  • Anaconda 2.1.0 (Python 2.7).  This tutorial only works with 2.1.0.  I tested it with 2.2.0 and it did not work.  I have no plans to fix this issue.
  • CUDA 7.0

Steps

  1. Download Anaconda 2.1.0 from here.
  2. Install pip via command line using “pip install https://pypi.python.org/packages/source/T/Theano/Theano-0.6.0.zip#md5=0a2211b250c358809014adb945dd0ba7
  3. Create a .theanorc.txt file in your user area (C:\Users\username\.theanorc.txt) with the specified text listed below.
  4. Open Anaconda
  5. Import and test/build theano by typeing import theano and then theano.test()
  6. Sit back and relax while everything builds.

.theanorc.txt file contents (you must create at %USERDIR%/.theanorc.txt, for me this is c:\users\username\.theanorc.txt)

[global]
openmp=False
device = gpu0
floatX = float32

[blas] ldflags=

Notes

If you get an error about “CVM,” you must delete the cache files that are in C:\Users\MyUsername\AppData\Local\Theano. Once you delete everything, start python again and continue from there.

If you have path issues when trying to import theano, try using the Visual Studio 64-bit command prompt if you have it.  It sets a bunch of paths for you and “just works” for me.  For reference, the path I use is:

PATH=C:\Program Files (x86)\Microsoft Visual Studio 10.0\VC\BIN\amd64;C:\Windows\Microsoft.NET\Framework64\v4.0.30319;C:\Windows\Microsoft.NET\Framework64\v3.5;C:\Program Files (x86)\Microsoft Visual
Studio 10.0\VC\VCPackages;C:\Program Files (x86)\Microsoft Visual Studio 10.0\Common7\IDE;C:\Program Files (x86)\Microsoft Visual Studio 10.0\Common7\Tools;C:\Program Files (x86)\HTML Help Workshop;C:
\Program Files (x86)\Microsoft SDKs\Windows\v7.0A\bin\NETFX 4.0 Tools\x64;C:\Program Files (x86)\Microsoft SDKs\Windows\v7.0A\bin\x64;C:\Program Files (x86)\Microsoft SDKs\Windows\v7.0A\bin;C:\Program
 Files\NVIDIA GPU Computing Toolkit\CUDA\v7.0\bin;C:\Program Files\NVIDIA GPU Computing Toolkit\CUDA\v7.0\libnvvp;C:\Python34\Lib\site-packages\PyQt5;C:\Program Files (x86)\NVIDIA Corporation\PhysX\Co
mmon;C:\Program Files\NVIDIA GPU Computing Toolkit\CUDA\v6.5\bin;C:\Program Files\NVIDIA GPU Computing Toolkit\CUDA\v6.5\libnvvp;C:\Program Files (x86)\Intel\iCLS Client\;C:\Program Files\Intel\iCLS C
lient\;C:\Windows\system32;C:\Windows;C:\Windows\System32\Wbem;C:\Windows\System32\WindowsPowerShell\v1.0\;C:\Program Files\Intel\Intel(R) Management Engine Components\DAL;C:\Program Files\Intel\Intel
(R) Management Engine Components\IPT;C:\Program Files (x86)\Intel\Intel(R) Management Engine Components\DAL;C:\Program Files (x86)\Intel\Intel(R) Management Engine Components\IPT;C:\Program Files\MATL
AB\R2014a\bin;C:\Program Files\TortoiseHg\;C:\Program Files (x86)\Microsoft SQL Server\100\Tools\Binn\;C:\Program Files\Microsoft SQL Server\100\Tools\Binn\;C:\Program Files\Microsoft SQL Server\100\D
TS\Binn\;C:\Users\username\AppData\Local\Continuum\Anaconda;C:\Users\username\AppData\Local\Continuum\Anaconda\Scripts

Update June 11, 2015
Added link to Ananconda download