Software for MAPS and MERLIN

T.G. Perring

ISIS Facility, Rutherford Appleton Laboratory

Outline

Plan of talk:• Overview• Brief description of the present MAPS/Het/MARI software • Challenges of MERLIN/ARCS• How we plan to re-write the software

Our aims from this meeting:• Contribute to the plans for direction of ARCS software

development• Explore cooperation in software development

– Experience + a working ARCS-like spectrometer– Fresh view of the problems of handling huge inelastic datasets

MAPS spectrometer

Position sensitive detector array

Specification:

• 20meV< EI< 2000meV

• lmod-chop = 10m

• lsam-det = 6m

• low angle bank: 3-20 high angle bank: 60

• hbar/EI = 1- 5% (FWHH)

• 40,000 detector elements 2500 time channels

108 pixels 0.4GB datasets

Background chopper

Monochromating chopper

Sample position

Overview

Inelastic scattering from single crystals:• Triple axis spectrometer: point-by-point serial operation

– Few kB of data– Every group of users writes its own least-squares fitting

algorithm from scratch– Ad-hoc cooperation only

MAPS/MERLIN/ARCS:• Parallel operation: collecting on 3D surface in 4D

S(Qspace– MAPS: raw data: 108 pixels = 0.4GB

corrected data: 1-2 x 107 = 0.1-0.2GB x 10 datasetsMERLIN, ARCS: 1-2 x 107 = 0.1-0.2GB x 100+ datasets

• Need ‘Rietveld refinement’ for inelastic scattering– Groups cannot afford to write own software– Pointless anyway: e.g. in diffraction GSAS, CCSL are trusted– We should move to a similar model of trusted black boxes

Overview(Rietveld refinement cont.)• Use entire data set to extract a limited number of parameters in a

model– Magnetic coupling constants– Force constants– Full inversion of the data: if S(Q in 4D

• Pragmatism: – In magnetism S(Q (or ''(Q is the quantity to test– Qualitative features (are there antiferromagnetic fluctuations and if so,

where ?)– Unknown processes distorting measure of goodness of fit– Rapid slicing and dicing, testing models on limited volumes of data,

testing implications for other parts of the data volume, feeding back into operation of experiment

seamless integration of simulation, visualisation and analysis programs

More formal cooperation:• Agreed data structures for instrument information, counts/ S(Q• Definitions for input/output of algorithms • Capitalise on the investment we individually make in algorithms

Current software on MAPS, HET, MARI

Planning experiment

Tobyplot

(reciprocal space viewing)

Chop

(resolution, flux)

Data reduction

HOMER

Genie-II

Visualization

MSLICE

GUI driven

Matlab

Analysis

Tobyfit (single crystals)

[Ad-hoc programs in Multi-frills

MFIT

MSCATT]

Monitoring experiment

Genie-II

OpenGenie

Tobyplot

•Reciprocal space viewing

•Mostly important for 3D systems

•but very useful for 1D, 2D, to assess access in reciprocal space

Ei=450 meVPsi=101.3°

Fortran77 + PGPLOT

VMS/Windows/Unix

CHOP

•Flux

•Resolution:

•At elastic position

•As function of

Test flux/resolution compromises

Fortran77 + PGPLOT

VMS/Windows/Unix

Monitoring an Experiment

GENIE-II

I(t) for single spectrum

rebinning, units conversion, integration

Algebra on spectra [e.g. W1=(0.3W2 + W3)/W4]

can call user-written FORTRAN algorithms

Good for quick checks during and after experiments

Still use today on MAPS

VMS only

OpenGENIE

New generation

Used on many ISIS instruments

Windows, Unix, VMS

Not the features of Matlab, IDL

Is free, however

Data reductionHOMER (au. Ray Osborn)

I(detno, t) corrects Kf/ki, efficiency(kf) S(detno, )

WHITE_VAN ( solid angle of detectors)

DIAG ( list of bad detectors)

MONO_VAN ( absolute units conversion)

Map file (detectors workspaces)

ASCII output file

(or VMS binary)

•Encapsulates years of experience of the instruments

•Scaled very well even to MAPS

$ homer/map=par:pix_981.map/mask=8900/van=8850 8900 100 -30 95 0.25

GUI interface

run info.sample parameters 2D & 1D cuts

2D slices in (Q,)

1D cuts in (Q,)

Imaging single crystal data on HET, MARI, MAPS, and IRIS (Radu Coldea (ISIS / Oak Ridge now Oxford)

MSLICE:

Least squares fitting of resolution broadened cross-section models (Toby Perring, ISIS)

TOBYFIT :

Simultaneous fitting to many 2D or 1D data sets

Text-based interface for entering:instrumentsample parameterscross-section parameters

MSLICE and TOBYFITIntegral part of the operation of the spectrometer - ‘Tertiary spectrometer’

MSLICE: Visualisation of 3D data in 2D slices, 1D cuts

Can generate ‘backgrounds’ from selected parts of the data

MATLAB as front end:

GUI

Graphics

manipulating data structures, ad-hoc programming

FORTRAN77 for speed of operation of algorithms

PC with 1GB RAM, 500MHz+ necessary

TOBYFIT: Fitting and simulationtest ideas by feeding S(detno, ) to MSLICE

Hold an experiment in a parameter file

Fortran + PGPLOT

Runs on VMS, Windows, UNIX

Communicate via ASCII files: 1 for data, 1 for detector parameters

other sample & instrument parameters

Challenges offered by future instrumentation

•Physics a function of 4 variables: C(x1,x2,x3,x4)•Instrument gathers data on a 3D volume in that 4D space•Data gathered on a fine non-Cartesian grid

•0.1-0.2 Gbyte•MAPS: usually ~10 settings in an experiment

•fine data on 3D surface, coarse in 4th dimension•ARCS/MERLIN: 100+ settings

•fine in all 4 dimensions (scan Ei, or crystal orientation)•10-20GByte complete data set

•Data has low statistics - need techniques to pick out features in data•will always need real-time slicing and dicing of data

[too many ways of being led astray or being deceived]•will be doing this after going back to home institution

Visualisation: a hierarchy of views•View 4D data:

•? How do that ?•Define integration interval along any one dimension, and then:

•View 3D data:•isosurfaces + slider control for

•intensity levels • rotation and viewpoint•binning along the three axes • smoothing, image processing control

•Move a plane through the 3D volume: define integration interval along one of the remaining dimensions, and then:

•View 2D data:•Contour plots, mountain plots, + slider controls for

•contouring levels • interval scaling (linear, log, sqrt …)•binning along the two axes

•Move a line across the plane, defining a thickness, and then•View 1D data:

•overplotting, fine comparison•book-keeping of titles of the plots ...On raw counts, white beam files,… as well as

S(Q,)

Instrument resolution, modelling•Must be able to simulate results of experiments and view results in same way as data (number crunching)

•Must perform on-line analysis (resolution-convoluted model fitting,multiple scattering) within framework of same package (even more number crunching)

•flexibility: fit on limited volume of data, simulate for whole dataset, slice-and-dice in same way as data to try out ideas

•User wants one-stop shopI(det,t)

Sexp(Q,w) * inst

S calc(Q,w)

Convolve with

instrument

Compare, fit

Visualisation,

algebra on 1,2,3,4D

+ Tobyplot MkII

Issues•Number crunching - more than the typical user institute will have

•huge storage requirements (not just the raw data)

•data management a real problem - we already create hundreds of cuts

•thumbnails when click on file•database functions (select by date, temperature, field, scan of a parameter…)•history of analysis stored in file

•well-defined data structures needed•ease interact seamlessly with other programs

•deconvolution, modelling•user-written algorithms easy to write

•define appropriate methods and algebras•(addition, subtraction, background generation, symmetrization…)

•not just GUIs:•scripting must always be possible•maximises flexibility

Our plansExisting programs need to rewritten

•F77, getting unmaintainable, monolithic,functionality insufficient, grown organically, written independently

•Define NeXus files to hold all processed files

•1D,2D,3D,4D data + all relevant instrument information (detectors etc.)

•sufficient information for MCSTAS simulation

•include raw data files eventually

•Mirror the data structures in Fortran95 + methods

•Fortran95 for speedy algorithms[number crunching for visualisation (MSLICE-2), fitting (Tobyfit-2)]

•MATLAB for graphics, language for manipulation and scripting - the glue[+access to all features of MATLAB for ad-hoc manipulations]

TGP, SMB + inst. Scientists + part effort from 2 post-docs (25-50% effort from each)

(plans cont.)About to start working with E-Science centre at Rutherford Laboratory

•funding to implement grid based applications for science within the laboratory

•demonstration projects:•data portal to distributed data stores•graphics processing and number-crunching•ISIS projects chosen to focus the development for real applications

•aim to isolate user from where the work is done - no need for their own Beowulf cluster

•user will have a front end - in our case we want MATLABbut also web-based interface (oceanography, space science)•Ensures that one version is maintained •assumes high-speed networks•[GLOBUS toolkit to isolate user from location of resources]

•ISIS: full effort of ISIS computing staff member + post-doc effort of E-Science centre