– a tool to aid blinded analysis in a lab setting

I made a tiny contribution to science this morning – a friend in neuroscience lamented that she couldn’t find any tools to automate the process of renaming a set of images for blinded analysis, so I made one.

TL;DR on what it does: you feed it a folder full of files, and it renames them all to random names while preserving their original extensions (such as .tif, .lsm, .jpeg, etc). While doing so, it creates a keyfile.csv which ties the original filename to the new, randomized filename – so that you can open up keyfile.csv in Excel, LibreOffice Calc, etc after your blind analysis is done and associate your blind results with your original data.

It’s reasonably smart and cautious – it refuses to run as root, won’t mess with dotfiles or subdirectories, won’t traverse subdirectories, won’t let you accidentally randomize the same folder twice, and spits out human-readable errors if things go wrong.

This is what it looks like in operation:

me@banshee:~$ ls -l /tmp/test
total 24
-rw-rw-r-- 1 me me 2 Oct 14 13:44 1.tif
-rw-rw-r-- 1 me me 2 Oct 14 13:44 2.tif
-rw-rw-r-- 1 me me 2 Oct 14 13:44 3.tif
-rw-rw-r-- 1 me me 2 Oct 14 13:44 4.tif
-rw-rw-r-- 1 me me 2 Oct 14 13:44 5
drwxrwxr-x 2 me me 4096 Oct 14 12:56 subdir

me@banshee:~$ /tmp/test
Renaming: 1.tif... 2.tif... 3.tif... 4.tif... 5...
5 files successfully blind renamed; keyfile saved to /tmp/test/keyfile.csv.

me@banshee:~$ ls -l /tmp/test
total 28
-rw-rw-r-- 1 me me 2 Oct 14 13:44 B4LOz.tif
-rw-rw-r-- 1 me me 2 Oct 14 13:44 Ek76e.tif
-rw-rw-r-- 1 me me 2 Oct 14 13:44 kdVFM.tif
-rw-rw-r-- 1 me me 131 Oct 14 14:02 keyfile.csv
-rw-rw-r-- 1 me me 2 Oct 14 13:44 Oklr1
drwxrwxr-x 2 me me 4096 Oct 14 12:56 subdir
-rw-rw-r-- 1 me me 2 Oct 14 13:44 wsy7e.tif

me@banshee:~$ cat /tmp/test/keyfile.csv
"Original Filename","Cloaked Filename"

There are no dependencies other than Perl itself, and the script is licensed GPLv3 – free for all to use, as in beer and as in speech. I hope this helps somebody (else); this task has got to come up frequently enough in all sorts of labwork that a free tool should be easy to find!

Future science workers: if this helped you and you’re feeling grateful, the EFF can always use a donation, whether large, small, or micro. =)

Another KVM storage comparison article

Good stuff. Nice in-depth run of several different benchmarks for everything from fileserver to mailserver to database type usage. A bit thin on the ground for configuration, and probably no surprises here if you already read my KVM storage article from 2013, but it’s always nice to get completely independent confirmation.

The author’s hardware setup was surprisingly wimpy – an AMD Phenom II with only 8GB of RAM – which may explain part of why the advanced filesystems did even more relatively poorly than expected in his testing. (ZFS did fine, but it didn’t blow the doors off of everything else the way it did in my testing, which was on a machine with four times as much RAM onboard. And btrfs absolutely tanked, across the board, whereas in my experience it’s typically more a case of “btrfs works really well until it works really badly.”) It was also interesting and gratifying to me that this article tested on CentOS, where mine tested on Ubuntu. Not that I expected any tremendous changes, but it’s always nice to see things holding up across distributions!

Thank you for the article, Gionatan – your work is appreciated!

Nagios initial configuration / NSClient++ / check_nt

A note to my future self:

Not ALL of the configs for a newly installed Nagios server are in /etc/nagios3/conf.d. Some of them are in /etc/nagios-plugins/config. In particular, the configuration for the raw check_nt command is in there, and it’s a little buggy. You’ll need to specify the correct port, and you’ll need to make it pass more than one argument along.

This is the commented-out dist definition of check_nt, followed by the correct way to define check_nt:

# 'check_nt' command definition
#define command {
# command_name check_nt
# command_line /usr/lib/nagios/plugins/check_nt -H '$HOSTADDRESS$' -v '$ARG1$'

define command {
command_name check_nt
command_line /usr/lib/nagios/plugins/check_nt -H $HOSTADDRESS$ -p 12489 -v '$ARG1$' '$ARG2$'

You’re welcome, future self. You’re welcome.