486. MS data, part IV: Making a stacked spectrum plot using gnuplot

In part 1, I showed you how to export MS data (MS= Mass Spectrometer/ry): http://verahill.blogspot.com.au/2013/07/474-exporting-data-from-wsearch32-and.html

In part 2, I showed you how to generate theoretical isotopic envelopes, and how to compare them with observed ones: http://verahill.blogspot.com.au/2013/07/480-ms-data-part-ii-plotting-and.html

In part 3, I showed you how to make contour plots of '3D' data -- in that particular case the extra dimension was cone voltage, but it could just as easily have been time: http://verahill.blogspot.com.au/2013/07/ms-data-part-iii-generating-matrix-by.html

In part 4, we'll use the same data as in part 3, but we'll make a stacked plot of it. This is a short post.

There is at least one other way of making a stacked plot in gnuplot, but it doesn't yield what I'd consider as being publication quality plots. It's also fairly restrictive in the type of data can be plotted. The method shown here is general and applicable to all types of data. You can e.g. use it for time-dependent NMR data...

Here's an example of a gnuplot script:

### Preamble start
set term png size 1000,500
set output 'stack.png'

set border 1
set xtics nomirror
set ytics nomirror
unset ytics

set xrange [100:3000]
set yrange [0:100]

set multiplot
set size 0.85,0.45
unset key

### Preamble over

### The stacked plot
set origin 0,0
set label "m/z" at 1500, -18
plot '0.dat' with lines lt -1

# we want the x axis to show ONLY for the first spectrum,
# so we turn it off for the remaining spectra.
# The same goes for our label (xlabel can be tricky 
# to position correctly)
unset label
set border 0
unset xtics
unset ytics

# Here we set the spacing (fx) the initial position of the second spectrum (f),
# the initial horizontal offset of the second spectrum relative to the first one (g),
# and the horizontal offset for all subsequent spectra (gy)

f=0.0025
fx=0.00
g=0.01
gy=0.02

# then we plot all the other spectra
set origin fx+0*f,gy+0*g
plot '10.dat' with lines lt -1

set origin fx+1*f,gy+1*g
plot '20.dat' with lines lt -1

set origin fx+2*f,gy+2*g
plot '30.dat' with lines lt -1

set origin fx+3*f,gy+3*g
plot '40.dat' with lines lt -1

set origin fx+4*f,gy+4*g
plot '50.dat' with lines lt -1

set origin fx+5*f,gy+5*g
plot '60.dat' with lines lt -1

set origin fx+6*f,gy+6*g
plot '70.dat' with lines lt -1

set origin fx+7*f,gy+7*g
plot '80.dat' with lines lt -1

set origin fx+8*f,gy+8*g
plot '90.dat' with lines lt -1

set origin fx+9*f,gy+9*g
plot '100.dat' with lines lt -1

set origin fx+10*f,gy+10*g
plot '110.dat' with lines lt -1

set origin fx+11*f,gy+11*g
plot '120.dat' with lines lt -1

set origin fx+12*f,gy+12*g
plot '130.dat' with lines lt -1

set origin fx+13*f,gy+13*g
plot '140.dat' with lines lt -1

set origin fx+14*f,gy+14*g
plot '150.dat' with lines lt -1

set origin fx+15*f,gy+15*g
plot '160.dat' with lines lt -1

set origin fx+16*f,gy+16*g
plot '170.dat' with lines lt -1

set origin fx+17*f,gy+17*g
plot '180.dat' with lines lt -1

set origin fx+18*f,gy+18*g
plot '190.dat' with lines lt -1

set origin fx+19*f,gy+19*g
plot '200.dat' with lines lt -1

set origin fx+20*f,gy+20*g
plot '210.dat' with lines lt -1

set origin fx+21*f,gy+21*g
plot '220.dat' with lines lt -1

set origin fx+22*f,gy+22*g
plot '230.dat' with lines lt -1

set origin fx+23*f,gy+23*g
plot '240.dat' with lines lt -1

set origin fx+24*f,gy+24*g
plot '250.dat' with lines lt -1

set origin fx+25*f,gy+25*g
plot '260.dat' with lines lt -1

set origin fx+26*f,gy+26*g
plot '270.dat' with lines lt -1

set origin fx+27*f,gy+27*g
plot '280.dat' with lines lt -1

set origin fx+28*f,gy+28*g
plot '290.dat' with lines lt -1

set origin fx+29*f,gy+29*g

plot '300.dat' with lines lt -1

and here's the plot:

If you want to make it really fancy, try this:

### Preamble start
set term png size 1000,800
set output 'stack.png'

set border 1
set xtics nomirror
set ytics nomirror
unset ytics

set xrange [100:3000]
set yrange [0:100]

set multiplot
set size 0.85,0.25
unset key

### Preamble over

### The stacked plot
set origin 0,0
set label "m/z" at 1500, -18
plot '0.dat' with lines lt -1

# we want the x axis to show ONLY for the first spectrum,
# so we turn it off for the remaining spectra.
# The same goes for our label (xlabel can be tricky 
# to position correctly)
unset label
set border 0
unset xtics
unset ytics

# Here we set the spacing (fx) the initial position of the second spectrum (f),
# the initial horizontal offset of the second spectrum relative to the first one (g),
# and the horizontal offset for all subsequent spectra (gy)

f=0.0025
fx=0.00
g=0.01
gy=0.02

# then we plot all the other spectra
set origin fx+0*f,gy+0*g
plot '10.dat' with lines lt -1

set origin fx+1*f,gy+1*g
plot '20.dat' with lines lt -1

set origin fx+2*f,gy+2*g
plot '30.dat' with lines lt -1

set origin fx+3*f,gy+3*g
plot '40.dat' with lines lt -1

set origin fx+4*f,gy+4*g
plot '50.dat' with lines lt -1

set origin fx+5*f,gy+5*g
plot '60.dat' with lines lt -1

set origin fx+6*f,gy+6*g
plot '70.dat' with lines lt -1

set origin fx+7*f,gy+7*g
plot '80.dat' with lines lt -1

set origin fx+8*f,gy+8*g
plot '90.dat' with lines lt -1

set origin fx+9*f,gy+9*g
plot '100.dat' with lines lt -1

set origin fx+10*f,gy+10*g
plot '110.dat' with lines lt -1

set origin fx+11*f,gy+11*g
plot '120.dat' with lines lt -1

set origin fx+12*f,gy+12*g
plot '130.dat' with lines lt -1

set origin fx+13*f,gy+13*g
plot '140.dat' with lines lt -1

set origin fx+14*f,gy+14*g
plot '150.dat' with lines lt -1

set origin fx+15*f,gy+15*g
plot '160.dat' with lines lt -1

set origin fx+16*f,gy+16*g
plot '170.dat' with lines lt -1

set origin fx+17*f,gy+17*g
plot '180.dat' with lines lt -1

set origin fx+18*f,gy+18*g
plot '190.dat' with lines lt -1

set origin fx+19*f,gy+19*g
plot '200.dat' with lines lt -1

set origin fx+20*f,gy+20*g
plot '210.dat' with lines lt -1

set origin fx+21*f,gy+21*g
plot '220.dat' with lines lt -1

set origin fx+22*f,gy+22*g
plot '230.dat' with lines lt -1

set origin fx+23*f,gy+23*g
plot '240.dat' with lines lt -1

set origin fx+24*f,gy+24*g
plot '250.dat' with lines lt -1

set origin fx+25*f,gy+25*g
plot '260.dat' with lines lt -1

set origin fx+26*f,gy+26*g
plot '270.dat' with lines lt -1

set origin fx+27*f,gy+27*g
plot '280.dat' with lines lt -1

set origin fx+28*f,gy+28*g
plot '290.dat' with lines lt -1

set origin fx+29*f,gy+29*g

plot '300.dat' with lines lt -1

### second plot
set size 0.75,0.4
set origin 0.1,0.6
set xrange [800:1800]
set border 3
set xtics nomirror
set ytics nomirror
set xlabel 'm/z'
set ylabel 'Relative abundance (%)'
set title '20 V'

plot '20.dat' with lines lt -1

unset multiplot

which looks like this:

485. Arch linux - kernel 3.10 issues? Won't boot/no network.

Note: I won't show any fixes in this post. This is my farewell to Arch.

I did a full upgrade of my Arch system (amd athlon II x3 with an nvidia gf210 card) earlier today. Among the packages was kernel 3.10-2 (I think).

Turning on the computer this evening I'd get to the gdm log in screen -- with an unresponsive keyboard and mouse. I also can't log in via ssh from another computer, so the network seems not to work.

I can, however, boot using the fallback option in grub. The network still isn't working though. I use wicd. If I try to connect using wicd the system freezes and crashes.

The closest I can find is this: https://bbs.archlinux.org/viewtopic.php?id=167090 -- but I use BIOS, not EFI. And there are plenty of other differences. It does, however, seem to have to do with the new kernel.

And systemd makes troubleshooting this worse than necessary since the logs are binary. Seriously, the use of plain text files in linux for configuration and logs is one of the MAIN defining features of the OS.

Anyway, Arch is a fine OS. But I've been burned a few times too many now, and I am no longer young and have plenty of time and enthusiasm for this kind of stuff. I've just started installing debian instead...and for once I'm going straight for stable...

A contributing factor is that we use this computer as the family one, for watching tv, listening to music etc. And sitting down on a Sunday evening to relax and finding that the damned system won't even boot isn't a good way to end the weekend.

Anyway, if you are looking for a fix, all I can give you is my gut feeling -- downgrade. The old packages are in /var/cache/pacman/pkg

Otherwise, if you have a copy of the kernel sources, compile your own kernel and install it as shown e.g. here:
http://verahill.blogspot.com.au/2013/03/355-kernel-382-on-arch-linux-exploration.html

Why downloading the source and copying it? Because (imho) it's easier than fiddling with packages -- you can put the sources on a usb stick and copy it. But good luck, whatever method you try. I'm switching my second to last non-debian computer back to my main OS (i.e. debian). I've still got a Scientific Linux box, which I haven't booted for well over a month now...

It's 'funny' this should come less than 24 hours after me nit-picking about the use of 'stable' to describe Arch...http://news.softpedia.com/news/Arch-Linux-Is-the-First-Stable-Distro-with-Linux-Kernel-3-10-371457.shtml

484. Putting Tomato (USB) on Cisco/Linksys E2500-AU 300M

Update 18/8/2014: I've since done this on a unit with a BCM5357 chip rev 2 pkg 8 as well:

Update: the more I use it, the more I like it. I really like my old WRT54G, but I'm even happier about my fancy new E2500 since it's faster and all. Flashing them are equally easy. If you prefer some else to do it for you -- or if you want to seek independent confirmation that the router can be flashed -- look at http://flashrouters.com/ . The focus on that site seems to be dd-wrt (which is an alternative to Tomato), but they do list tomato routers too, e.g. http://www.flashrouters.com/routers/cisco-linksys-e2500-tomatousb-router

Original post:
Flashing a router is always a bit unsettling, so here's a detailed how-to.

Anyway, I managed to pick up a Linksys E2500-AU for $45 (Broadcom BCM5357 chip rev 1 pkg 8), which isn't too shabby. Some cursory searching showed that people had managed to put dd-wrt and tomato on it. While my experience with dd-wrt hasn't been that good, I've been running tomato on a linksys wrt45g for a around four years now, without any issues.

There's a number of derivatives of Tomato e.g. Tomato USB, and I'm a bit confused over what sets some of them apart. However, it seems like this Polish site is the right one for me. See here for the 'about' page.

What I'm presuming:
That you are running linux, and that you can afford to brick your router. There is always a risk associated with flashing firmware, and don't make any assumptions about the validity of the warranty...

How to:
Download the firmware:

cd ~/Downloads
wget http://tomato.groov.pl/download/K26RT-N/build5x-110-EN/Linksys%20E-series/tomato-E2500-NVRAM60K-1.28.RT-N5x-MIPSR2-110-Max.bin

With the router turned off, connect it via CAT5 cable to your computer. It should be attached to one of the LAN ports (in my case Ethernet 4) on the router. Ignore what the manual says about plugging into the WAN ('Internet') port.

Plug in power cable to the router.

On my computer I've disabled network manager (sudo rcconf, then uncheck network manager and either stop it or reboot) and my /etc/network/interfaces has this in it:

auto eth1
iface eth1 inet dhcp
ethernet-wol g

You probably won't have to worry about this. Just make sure that you don't have anything interfering with the 192.168.1.0/24 subnet.

Anyway, once you have been assigned an IP address, navigate to 192.168.1.1, and work your way through the annoying warnings:

leave the user name blank, and use admin as the password

 Here's where it get's interesting. Select the .bin file you downloaded and hit ok.

Use admin for both username and password

 I was then met with this, which at first scared me a little:

I unplugged the power from the router, and plugged it in again, and I could log in:

The first step is to erase the nvram, or you might end up with "Cannot proceed: two or more lan bridges have conflicting ip addresses or overlapping subnets" when configuring your network. To erase NVRAM go to Administration/Configuration/Restore Default Configuration - Erase all data in NVRAM memory(thorough).

 You are now ready to start setting up your router.

Go to Administration/Admin access.

Set up an admin password, turn off telnet and change the colour scheme to Tomato. Optional but recommended: disable ssh access via password -- it's better if you add your public keys here.

Go to Basic/Network, and set an SSID and a password for your wireless. Set up your network details -- in my case I have static IP. I also want the subnet to be 192.168.2.0/24 and I use MAC spoofing, which you can set up under Advanced/MAC address.

 And this is what it looks like if you connect to the router via ssh:

So far so good!