Shape Data Format

[Victor]

Shape Data Format

http://www.ccpn.ac.uk/ccpn/projects/extendnmr/shape-data-format by
Rasmus Fogh — last modified 2008-12-09 17:35

Shape Data Format -- An XML format for storing shape-decomposed data.
Developed and agreed between the PRODECOMP group (Martin Billeter,
Doroteya Staykova), the MDD group (Vladislav Orekhov, Victor Jaravine)
and CCPN (Rasmus Fogh).

Standard XML format for shape-decomposed data. Intended for use as
export format for MDD and PRODECOMP, and for standard data storage
format for CCPN. What follows is a commented example:


<-- All XML attribute names are in all lower case -->

<-- Element identifiers (e.g. Decomposition number n, axis number a,
component number c, ...

are arbitrary non-negative integers. They uniquely identify that
element within its containing element) -->


<Decomposition n=0 name=something nshapes=5 ncomp=72 method=MDD>
<-- n is the Decomposition number (identifier)
method is optional. Values could be MDD or PRODECOMP if you think
that is
right -->



<Axis a=0 name=C nucleus=13C domain=time type=complex size=64
swppm=80.0 startppm=84.2 sfo=201.135773/>
<Axis a=1 name=N nucleus=15N domain=time type=complex size=256
swppm=30.0 startppm=132.1
acqtimesec=0.372 rdims=6 recursion="2 2 2 2 2 2" sfo=81.059357/>
<Axis a=2 name=HN nucleus=1H domain=freq type=real size=178
swppm=4.6 startppm=10.0
sfo=799.870544/>
...

<-- a is the axis number (identifier)
domain can be 'time' or 'freq' - the default is 'freq'.
type can be 'real' or 'complex'
size is the size in points
swppm is the spectroscopical sw in ppm (for size 128 it is the
distance between point 1 and point 129
startppm is the frequency in ppm of point 1 the lowest numbered
point.
E.g. for an HN dimension you might have swppm=4.6, startppm=10.2
For time dimensions swppm refers to sw after Fourier
transformation.
nucleus is mandatory, required for making the file independently
readable.
acqtimesec is optional, also for time dimensions
sfo is mandatory, required for making the file independently
readable. It is the spectrometer frequency in MHz.
The axes are mapped to CCPN Experiment dimension objects according
to the order of their a values-
The actual values need not be the same-->



<Projset s=0 name=hbhacanconnh ndims=5 nproj=16 >
<Axis/>
<Axis/>
...
<Projection p=0 name=s532 ndim=2 >
<Axis/>
<Axis/>
</Projection>
...
</Projset>

<-- s=0 is the number of the projection set and p=0 is the
number of the projection within the set. They work the same way
as a for axes and c for components


Projset and its contents are optional. -->



<Component c=0 ampl=1.0e3>
<Shape a=0>
1.2753233 2.00045, ...
</Shape>
<Shape a=1 rdims=4 recursion="2 2 2 8">
0.33345 7.111695, ...
</Shape>
<Shape a=2 size=12 offset=20>
0.000755, 11.51339, ...
<Peaks list=pk,intensity,pos,width>
...
</Peaks>
</Shape>
<Shape a="3 4">
0.100755, 16.51339, ...
<Peaks list=pk,intensity,pos,pos,width,width>
</Peaks>
</Shape>
<Shape a="5 6" size="17 256" offset="10 0" rdims="3 5"
recursion"2 2 8 2 2 2 2 6">
</Shape>
</Component>
<Component>
</Component>

<-- size, offset, rdims, recursion are optional. If not given, they
default to,
respectively, the axis size, 0, 1, no recursion-->

<-- Shapes can have more than one dimension. The simplest case is
given as
<Shape a="3 4"> and other parameters are deduced from the
original axes
Other parameters can be given, simply by concatenating the values
for the
dimensions. The most complicated case would be the <Shape a="5
6"...
Note that this means that axis 2 in this shape has rdims=3 and
recursion="2 2 8", while axis 3 has rdims=5, recursion="2 2 2 2
6" -->

<-- peaks are put inside the shape they refer to. They must appear
*after*
the numbers that define the shapes themselves

In parallel to intensity, pos, and width, the parameters
dintensity, dpos, dwidth, describe
a measure of the error in the corresponding parameter. These are
of course optional.-->

<Ndpeaks

list=pk,c,intensity,pos,pos,pos,pos,pos,width,width,width,width,width>
...
</Ndpeaks>

<Ndpeaks a="1 3 4"
list=pk,c,intensity,pos,pos,pos,,width,width,width,>
...
</Ndpeaks>

</Decomposition>



<-- There will be a need to give peak lists outside a Decomposition.
In these cases we will
have to add information about the axes, which decomposition, if any,
the peaks
refer to, etc. This point will be settled when the need arises, though
the Ndpeaks element would likely serve as a starting point. -->


General comments:

- For development purposes it is always possible to add new XML
attributes as well as new elements in the 'list=' of
Peaks and Ndpeaks.

- Apart from the tags in the example there are 'posppm' and
'widthppm'. 'pos'
and 'width will be positions and widths in points. dposppm and
dwidthppm are the corresponding error parameters..

- XML attributes and list elements are generally given without
surrounding quotes. Quotes are added for values that contain
whitespace.

[Vik _]

I am taking the job of re-posting here results of some agreements on the USF3 extensions.
As you can imagine there are lots of emails between many parties.

There were two additions to the format recently:

- Storing shapes in external files.

- Use for general storage of sparsely processed matrices:

see full specifications at   http://www.ccpn.ac.uk/ccpn/projects/extendnmr/shape-data-format

Victor