499. Briefly: Drawing NMR sequences using metapost and Mark White's pulse.mp

Since it's Friday afternoon and I'm not likely to get anything useful done in the hour that remains before going home, I might as well put up another post.

Since posting http://verahill.blogspot.com.au/2013/08/498-briefly-drawing-nmr-pulse-sequences.html I've had a look at this: http://www.celos.net/comp/pulses/

And that actually is (almost -- let's not get carried away here) exactly what I have been looking for. The main issue was that it's meant for metapost -- or rather, the main issue was my unfamiliarity with metapost. Anyway, my life is know complete.

So here's how to get started...

First 'install' the metapost script:

sudo apt-get install texlive-metapost
mkdir ~/texmf/metapost
cd ~/texmf/metapost -p
wget http://www.celos.net/comp/pulses/pulses.mp
sudo texhash

Next, time to test-drive it

mkdir ~/tmp/pulse_test -p
cd ~/tmp/pulse_test
vim test.mp

input pulses.mp

beginfig(0);
    initf;

    startline(rf,"RF");
    xline(1);
    xpulse(0.5,0.5,"90");
        ospan(-0.25,-1.0,1.5,"d1");
    xline(0.75);
    xpulse(1.0,0.5,"180");
        ospan(-0.5,-1.0,1.5,"d1");
    xline(1.0);
        ospan(0,-1.0,1.5,"vd");
    xline(1.5);
    xacq(2);
endfig;

mpost test.mp
mptopdf test.0
pdftops -eps test-0.pdf test-0.eps

Now, I somehow suspect you can embed metapost scripts directly in .tex documents, but from my brief testing I haven't quite managed to make it work.

498. Briefly: Drawing NMR pulse sequences using APSEQ and Mathematica

There are two things that have been bothering me on linux -- one is the difficulty of creating annotated PDF documents, but it seems like things are slowly improving (we still don't have a really good way of creating /editable/ annotations). Another is the issue of creating NMR pulse-sequence drawings. To be fair, it doesn't seem like the situation is much better on Windows or OSX.

Anyway, I still don't have a good way of doing this, but at least I have A way of getting it done: APSEQ. The main drawback is that it requires Mathematica, which I don't like much (I get by with octave and maxima) in addition to being proprietary. But it will do for now.

NOTE: I just needed to 'Get It Done' quickly, so I didn't spend any time looking at the following potential alternatives:
http://www.celos.net/comp/pulses/ (metapost -- which should be tex compatible, right)
https://code.google.com/p/nmrtype/ (python code)
http://nmrwiki.org/wiki/index.php?title=NMRPulse_-_pulse_sequence_drawing_extension_for_MediaWiki (the URL is fairly descriptive)
They all seem to depend on latex in some way or another.

There's also http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.187.9656&rep=rep1&type=pdf but I haven't actually found the sources.

Anyway, here's how to get started with APSEQ:

mkdir ~/tmp/apseq -p
cd ~/tmp/apseq
wget https://www.princeton.edu/~nmr/apseq/apsDistribution.tar.gz
tar xvf apsDistribution.tar.gz
cd zip.feb15/
math

Mathematica 7.0 for Linux x86 (64-bit)
Copyright 1988-2009 Wolfram Research, Inc.

In[1]:= <<nmr.auto
part01 loaded
part02 loaded
part03 loaded
part04 loaded
mscp loaded
nmr.extra loaded
nmr.auto loaded

In[2]:= draw[pulseSeq[hahn, echo]={channels[1H],pulse[90],delay[t1],pulse[180],delay[t1],delay[t2],acquire[taq]}]

Out[2]= hahn_echo.pdf

In[3]:=

which gives you something like this:

Spin echo sequence

The figure is output as a pdf, but it's easy enough to open it in inkscape and converting it to an .eps file.

497. Compiling Wine 1.7 in a chroot on debian

Here's a generic way of building Wine 1.7 which is the new testing branch. And yes, it's the instructions for 1.5.28-1.6 recycled, with a few small amendments.

See here for information about 3D acceleration using libGL/U with Wine: http://verahill.blogspot.com.au/2013/05/429-briefly-wine-libglliubglu-blender.html

Getting started:
If you set up a e.g. chroot to build 1.6 you don't need to set up a new chroot to build 1.7. In that case, skip the set-up step below and instead re-enter your existing chroot like this:

sudo mount -o bind /proc wine32/proc
sudo cp /etc/resolv.conf wine32/etc/resolv.conf
sudo chroot wine32
su sandbox

cd ~/tmp

And skip to 'Building wine'.

Otherwise do this:
Setting up the Chroot

sudo apt-get install debootstrap
mkdir $HOME/tmp/architectures/wine32 -p
cd $HOME/tmp/architectures
sudo debootstrap --arch i386 wheezy $HOME/tmp/architectures/wine32 http://ftp.au.debian.org/debian/
sudo mount -o bind /proc wine32/proc
sudo cp /etc/resolv.conf wine32/etc/resolv.conf
sudo chroot wine32

You're now in the chroot:

apt-get update
apt-get install locales sudo vim
echo 'export LC_ALL="C"'>>/etc/bash.bashrc
echo 'export LANG="C"'>>/etc/bash.bashrc
echo '127.0.0.1 localhost beryllium' >> /etc/hosts
source /etc/bash.bashrc
adduser sandbox
usermod -g sudo sandbox
echo 'Defaults !tty_tickets' >> /etc/sudoers
su sandbox
cd ~/

Replace 'beryllium' with the name your host system (it's just to suppress error messages)

---

Building Wine
While still in the chroot, continue (the i386 is ok; don't worry about it -- you don't actually need it):

sudo apt-get install libx11-dev:i386 libfreetype6-dev:i386 libxcursor-dev:i386 libxi-dev:i386 libxxf86vm-dev:i386 libxrandr-dev:i386 libxinerama-dev:i386 libxcomposite-dev:i386 libglu-dev:i386 libosmesa-dev:i386 libglu-dev:i386 libosmesa-dev:i386 libdbus-1-dev:i386 libgnutls-dev:i386 libncurses-dev:i386 libsane-dev:i386 libv4l-dev:i386 libgphoto2-2-dev:i386 liblcms2-dev:i386 libgstreamer-plugins-base0.10-dev:i386 libcapi20-dev:i386 libcups2-dev:i386 libfontconfig-dev:i386 libgsm1-dev:i386 libtiff-dev:i386 libpng-dev:i386 libjpeg-dev:i386 libmpg123-dev:i386 libopenal-dev:i386 libldap-dev:i386 libxrender-dev:i386 libxml2-dev:i386 libxslt-dev:i386 libhal-dev:i386 gettext:i386 prelink:i386 bzip2:i386 bison:i386 flex:i386 oss4-dev:i386 checkinstall:i386 ocl-icd-libopencl1:i386 opencl-headers:i386 libasound2-dev:i386 build-essential

mkdir ~/tmp
cd ~/tmp
wget http://prdownloads.sourceforge.net/wine/wine-1.7.0.tar.bz2

tar xvf wine-1.7.0.tar.bz2
cd wine-1.7.0/
./configure
time make -j3
sudo checkinstall --install=no

checkinstall 1.6.2, Copyright 2009 Felipe Eduardo Sanchez Diaz Duran
           This software is released under the GNU GPL.


The package documentation directory ./doc-pak does not exist. 
Should I create a default set of package docs?  [y]: 

Preparing package documentation...OK

Please write a description for the package.
End your description with an empty line or EOF.
>> wine 1.7.0
>> 

*****************************************
**** Debian package creation selected ***
*****************************************

This package will be built according to these values: 

0 -  Maintainer: [ root@beryllium ]
1 -  Summary: [ wine 1.7.0]
2 -  Name:    [ wine ]
3 -  Version: [ 1.7.0]
4 -  Release: [ 1 ]
5 -  License: [ GPL ]
6 -  Group:   [ checkinstall ]
7 -  Architecture: [ i386 ]
8 -  Source location: [ wine-1.7.0 ]
9 -  Alternate source location: [  ]
10 - Requires: [  ]
11 - Provides: [ wine ]
12 - Conflicts: [  ]
13 - Replaces: [  ]

Checkinstall takes a little while (In particular this step: 'Copying files to the temporary directory...').

**********************************************************************

 Done. The new package has been saved to

 /home/sandbox/tmp/wine-1.7.0/wine_1.7.0-1_i386.deb
 You can install it in your system anytime using:

      dpkg -i wine_1.7.0-1_i386.deb

**********************************************************************

---

Installing Wine

Exit the chroot

sandbox@beryllium:~/tmp/wine-1.7.0$ exit
exit
root@beryllium:/# exit
exit
me@beryllium:~/tmp/architectures$ 

On your host system
 Enable multiarch* and install ia32-libs, since you've built a proper 32 bit binary:

sudo dpkg --add-architecture i386
sudo apt-get update
sudo apt-get install ia32-libs libgstreamer-plugins-base0.10-0

*At some point I think ia32-libs may be replaced by proper multiarch packages, but maybe not. So we're kind of doing both here.

 Copy the .deb package and install it

sudo cp wine32/home/sandbox/tmp/wine-1.7.0/wine_1.7.0-1_i386.deb .
sudo chown $USER wine_1.7.0-1_i386.deb
sudo dpkg -i wine_1.7.0-1_i386.deb

---