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\title{Software Tools for 3D Spectrography}
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\author{A. P\'econtal-Rousset, R. Bacon, Y. Copin\altaffilmark{1}, E. Emsellem, P. Ferruit, E. P\'econtal}
\affil{Centre de Recherche Astronomique de Lyon, France}
\altaffiltext{1}{Institut de Physique Nucl\'eaire de Lyon, France}

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\aindex{Ferruit, P.}
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\authormark{P\'econtal-Rousset et al.}

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\keywords{spectrography: 3D, instrument modelling, Euro3D}

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%                              Abstract
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  Since the very first Tiger prototype operated at the CFHT (June
  1987), the Centre de Recherche Astronomique de Lyon (CRAL) has been
  a very active player in the development of 3D spectrographs and
  their related softwares, including data acquisition, instrument
  numerical modelling, data reduction and analysis tools. The CRAL has
  recently joined the European RTN Euro3D to promote 3D spectrography
  in Europe, and develop softwares of common interest. In this
  context, we report here on the past, on-going and future
  instrumental developments at the CRAL, as well as on the related
  software packages.
\end{abstract}

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\section{3D spectrography at the CRAL}
\subsection{1987: first experience}

The first experience of 3D spectrography for the CRAL took place at
the CFH telescope, on Mauna Kea, in June 1987. The resulting
instrument, TIGER (see below) was the first lens-array based
integral-field unit experiment, pioneering the optical principle
proposed by G. Court\`es from the Laboratoire d'Astronomie Spatiale in
Marseille (France). This successful experiment prefigured the later
large investment the CRAL devoted in such instrumentation. As an
illustration of the still alive TIGER concept, Fig.~\ref{O5-2:S1-lenset}
shows one of the lens-arrays used for the SNIFS instrument (225 lenses
only).

\subsection{The TIGER concept: the ``trick''}
The challenge for 3D spectrography is to store three-dimensional (two
spatial and one spectral) data on a two-dimensional detector (CCD).
How is this possible ? 

Using a lens-array solutions, here is the trick. First imagine you
have a uniform illumination at the entrance of the lens-array
(Fig.~\ref{O5-2:S1-trick}, left panel). The micro-lens array samples the
field and focuses the light into micro-pupils (next 4 panels). This
corresponds to the spatial sampling stage of the spectrograph, which
additionnally focuses the light into small spots (the so-called
micro-pupils), thus compacting the information and providing useful
space in between each sample. This free space is used to store the
spectral information. The micro-pupils are dispersed via a classical
spectrograph (see Fig.~\ref{O5-2:S1-trick}, last 3 panels). Assuming the
dispersion direction is aligned with the CCD columns, a problem
quickly arises with spectra from different micro-pupil overlapping
along the columns. It is solved by slightly rotating the array. In
many circumstances, it may be useful to limit the vertical range using
a filter. The overall optical concept is presented in
Fig.~\ref{O5-2:S1-optical-design}. Note that in the provided illustration,
the lenses are squares but any shape allowing good compactness (e.g.,
hexagonal) can be used (the optimal rotation angle being adapted for
each geometry).

\begin{figure}
  \epsscale{1.0} \plotone{O5-2_f1.eps}
  \caption{The micro-lens array (here the one of SNIFS), 
    the core of the lenslet-based 3D spectrograph.} 
  \label{O5-2:S1-lenset}
\end{figure}

\begin{figure}
  \epsscale{1.0} \plotone{O5-2_f2.eps}
  \caption{The ``TIGER trick'' to store 3D data on a 2D detector.} 
  \label{O5-2:S1-trick}
\end{figure}
 
\begin{figure}
  \epsscale{0.9} \plotone{O5-2_f3.eps}
  \caption{Lens-array based IFU optical design.} \label{O5-2:S1-optical-design}
\end{figure}

\subsection{TIGER at the CFHT (1987-1996)}

This instrument was a project conducted by two French teams (Lyon and
Marseille), and was originally devoted to the study of galactic
dynamics, quasars and active galactic nuclei. It allowed acquisition
of about 400 spectra of an object simultaneously. The original TIGER instrument
was a very basic device, borrowing the mechanical structure of PUMA
(Punching Machine, the ancestor of the present Multi-Object
Spectrograph), in duty at the CFHT. No specific optimization had been
achieved neither for the mechanics nor for the existing optics (Bacon
et al. 1995).

It nevertheless provided a number of spectacular results, the first
published paper including the spectral identification of the
components in the Einstein Cross (Adam et al. 1989). It also allowed
the team to investigate the capabilities of such an instrument, and to
prospect for the future. On the software side, things were also rather
preliminary. A simple toolbox was developed as a MIDAS context,
providing basic signal extractions, and requiring a high level of
human interactions. No GUI was available at that time.

\subsection{OASIS at the CFHT  (1997)}

OASIS (Optically Adaptative System for Imaging and Spectrography) was
the first full 3D project conducted at the CRAL (from its design to
its scientific application). It became a general user instrument
opened to the CFHT community, and took advantage of the PUEO adaptive
optics system. OASIS was a very flexible instrument, handling several
spatial and spectral samplings to match the users scientific
requirements. It has been commissioned in the summer of 1997 and
operated until 2001, with the CFH Telescope becoming a more survey
oriented facility (e.g., CFHT Legacy Survey). OASIS thus moved to the
William Herschel Telescope (4.2m, La Palma) at the beginning of 2003,
and was adapted to be used with the WHT NAOMI AO system. It now offers an
even more complete set of spectral and spatial configurations, and
should otherwise perform in a similar way as at the CFHT.

The software aspect was challenging, since OASIS has been designed a
general user instrument at the CFHT. The community was basically not
educated regarding 3D spectrography, and the versatility of OASIS only
meant more general (thus more complex) reduction algorithms. Both the
acquisition software and the data reduction were GUI oriented, and
driven by the firm goal to be as user-friendly as possible. This is
illustrated by the acquisition process, during which the observer is
asked for quantities which are meaningful to him/her, like the spatial
or spectral sampling, instead of instrumental specifications (such as
which optical component to include). This also strongly affects the
design of the GUI for the data reduction (XOasis, see
Fig.~\ref{O5-2:S1-XOasis}), which therefore shows the reduction steps in
a strict logical order. Moreover, some kind of 'history' is stored in
each processed exposure, so that a number of a priori checks can be
performed prior to its running. Last but not least, a Web server was
set up for software download
(\htmladdURL{http://www-obs.univ-lyon1.fr/~oasis}), and the users
provided with a hot-line service facility.
\begin{figure}
\epsscale{0.9}
\plotone{O5-2_f4.eps}
\caption{XOasis GUI for data reduction.} \label{O5-2:S1-XOasis}
\end{figure}

Handling complex data is not just a matter of providing an efficient
graphical user-interface. Since the instrument had multiple optical
configurations, the best way to properly and accurately extract the
user data, without a high level knowledge of the instrument, was to
implement a data extraction process based on an {\bf instrument
  numerical model}. This was probably the major software investment,
which still benefits both users and conceptors. This allows more
accurate extraction and calibration of the data, distinguishing the
different dispersion orders (for low spectral resolution
configurations) and mimicking the optical distortions and aberrations
(achromatism) of the instrument.

Two other development decisions, taken at that time, appeared to be
critical for the future: first, the elaboration of a C Input/Output
libraries handling multiple common-used formats, like FITS of course
(based on the cfitsio routines), but also MIDAS (\texttt{.bdf},
\texttt{.tbl}), IRAF (\texttt{.imh}, \texttt{.pix}) or the STSDAS
tables. The aim was to make the processed data compatible, at any
reduction step, with the user's favorite tools. Facilities to import
and export from these various formats were also provided. The second
point concerns the global architecture. Each processing module is an
executable (i.e., Unix binary), running as a stand-alone routine.
Parameters may be passed through the command line. The GUI is built as
a separate front-end passing the parameters to the module through the
command line, plus some fancy features like saving the session
history, providing an electronic logbook, etc. Given that layout,
the data reduction process can easily be operated in batch mode
through a pipeline, or via user-written shell scripts, or in
interactive mode via the GUI. All processing share the same module
basis, serving maintenance tasks.

\subsection{SAURON at the WHT (1999)}

SAURON was the first IFU dedicated to a specific science case. It is
a panoramic integral-field spectrograph for ``understanding the
formation and evolution of elliptical and lenticular galaxies and of
spiral bulges from 3D-observations''
(\htmladdURL{http://www.strw.leidenuniv.nl/sauron}). This instrument
has a large field of view and was optimized to have a high throughput
(20\% including atmosphere, telescope and detector), and to allow
simultaneous sky subtraction. SAURON has been designed for studies of
the stellar kinematics, gas kinematics, and line-strength
distributions of nearby early-type galaxies. The project was carried
out by a consortium gathering the CRAL and two European teams: the
Sterrewacht Leiden and Oxford University. The instrument was installed
at the WHT in 1999 and provided impressive results so far (de Zeeuw et
al. 2002).

The XSauron software shares with XOasis most of the data reduction
modules (with different parameter values for the instrument numerical
model). It has been enhanced with new analysis tools developed by the
consortium. But as a survey instrument, SAURON also required the
building of a true pipeline. A first ``linear'' pipeline (based
mostly on Tcl modules plus a global wrapper) was developed in Lyon,
and a more robust pipeline (Jython, etc) is being tested at the
Sterrewacht Leiden.

\subsection{SNIFS at UH (2004)}

A recent addition to the suite of IFUs developed in Lyon is the
Supernova Integral Field Spectrograph (SNIFS), another science-case
dedicated instrument (Aldering et al. 2002). SNIFS has been designed
to provide a systematic spectroscopic follow-up of Supernovae Ia. This
project is a partnership between LBNL (Berkeley), LPNHE (Paris), IPNL
(Lyon) and CRAL. The instrument will be operated for 3 years at the UH
Telescope (Hawaii), for a total of 20 percent of the nights.

SNIFS is a two-channel optical spectrograph equipped with a micro-lens
array (TIGER type) integral field unit (Lantz et al. 2003). The blue
channel will cover 3500--5700~\AA, while the red channel will cover
5300--10500~\AA. SNIFS includes a photometry camera run in parallel
with the spectrograph; it allows photometric normalization of the
spectrographic observations even under non-photometric sky conditions.
SNIFS is also equipped with a calibration unit for the spectrograph
which will provide the relevant spectral flats and arc exposures.
The intended operational mode for SNIFS is quasi queue observing.
Target coordinates and exposure sequences are generated automatically.

On the software side, this was the first time a full numerical
simulation of the instrument was used to confirm building options and
to deeply check the data reduction process before the instrument 
is put in operation (Bonnaud et al., this conference). Given the heavy use of
the instrument, a fully-automated processing pipeline is being
designed by the IPNL team, based on previous XOasis and XSauron
reduction modules, as well as a scheduler, built by the LBNL team, to
afford and optimize the observational procedure.

\section{The new generation: using slices}

\begin{figure}
\epsscale{0.5}
\plotone{O5-2_f5.eps}
\caption{Slices prototype tested in the CRAL} \label{O5-2:S2-slices}
\end{figure}
\begin{figure}
\epsscale{0.55}
\plotone{O5-2_f6.eps}
\caption{Image slicer optical concept (from Allington Smith et Content, Univ. of Durham)} \label{O5-2:S2-slices-optics}
\end{figure}
To avoid spectra to be polluted by the other dispersion orders (low
dispersion configurations), but also to increase data compactness on
the detector, the CRAL investigates a new type of 3D spectrographs
using slicers (see Fig.~\ref{O5-2:S2-slices}, the active surface being on
the left). Each slice cuts a strip in the field of view. Each strip
is then dispersed and gathered on a detector, with a slight shift with
respect to the previous one induced by the slight angle given to the
slices (see Fig.~\ref{O5-2:S2-slices-optics}). The current corresponding
studies held in the CRAL are:

\begin{description}
\item[MUSE Phase A study (VLT-2)] The major scientific goal is deep
  spectrographic observations of high-$z$ galaxies, in particular of
  Ly$\alpha$ emitters. The Principal Investigator of the MUSE project
  is R. Bacon (CRAL). The field of view being rather large for such a
  spectrograph (1 square arc-minute), the field is sampled in 24
  sub-fields, which thus results in 24 spectrographic channels. CRAL
  is in charge of many software aspects, AIP (Postdam) being
  responsible for the data reduction package.
  
\item[NIRSpec (JWST)] NIRSpec provides users of JWST with the ability
  to obtain simultaneous spectra of more than a hundred objects in a 9
  square arc-minute field of view. The baseline spectrograph will take
  advantage of a micro-electromechanical system (MEMS) to provide
  dynamic aperture shutter masks. The CRAL is involved in the phase A
  study for an IFU mode, and deeply involved in the instrument
  numerical model (Gnata et al. 2004).
  
\item[ESA prototype] Slicer feasibility study for NIRSpec.
  
\item[SNAP] The Supernova/Acceleration Probe (SNAP) Mission is
  expected to provide an understanding of the mechanism driving the
  acceleration of the universe. The satellite observatory is capable
  of measuring up to 2,000 distant supernovae during the three-year
  mission lifetime. The CRAL is involved in calibration scenarii and
  performance evaluations.

\end{description}

\section{The growing amount of data}
One of the major challenges IFU software will face in the next years,
as for many other instruments used for surveys, is the data flow.
The amount of data produced at once is growing continuously, as shown
in Table~\ref{O5-2:data_tbl}. Parallel processing would be straightforward
for instruments having multiple channels, like MUSE. But some software
improvements or new tools will be required to handle these data, such
as data mining tools. One cannot imagine checking data quality
of 90,000 spectra without any robust tools detecting some unexpected
feature for you, nor trying to view at once the full dataset.
\begin{deluxetable}{lrrrr}
\scriptsize
\tablecaption{Increasing volume of data per exposure for IFU\label{O5-2:data_tbl}}
\tablehead{
\colhead{Instr.} & \colhead{Year} & \colhead{Nb spectra} & \colhead{Nb pixels} & \colhead{Volume (in Mb)} }
\startdata
Tiger & 1987 & 572 & 270 & 0.59\nl
Oasis & 1997 & 1200 & 360 & 1.65\nl
Sauron & 1999 & 1577 & 540 & 3.25\nl
Vimos\tablenotemark{*} & 2002 & 6400 & 550 & 13.42\nl
Muse & 2008 & 90 000 & 4096 & 1406.25\nl
\enddata
\tablenotetext{*}{Not a CRAL-made IFU, given for comparison with Muse.}
\end{deluxetable}

\section{Reaching the EURO3D RTN\ldots}

The goal of the Euro3D Research \& Training Network, founded by the
European Commission, is to convert integral-field spectrography from a
technique reserved to experts to a common-user and powerful
observational tool. The RTN is a partnership between 11 partner
institutes, namely: AIP (Potsdam; PI of the RTN being Martin M.
Roth), Cambridge, Durham, ESO Garching, MPE Garching, Leiden, CRAL
(Lyon), LAM (Marseille), Milano, Paris and IAC (Tenerife), alltogether
operating 14 different IFUs.

To promote 3D spectrography in Europe, the RTN will train 10 post-doc
during two years, focus on common scientific projects (7 have been
identified) and develop state-of-the-art data analysis software.

Here is the list of the software work-packages the RTN is in charge
of:
\begin{itemize}
\item{\bf Data format and software specifications} Data format definition
  (including FITS format, FITS keyword list), software requirements
  (e.g., platforms, code structure, language, interfaces)

\item{\bf 3D Visualization} (Sanchez et al. 2004) Input/output of data
  files, data cube transformation, display/plotting options,
  extracting spectra and monochromatic images, GUI

\item{\bf Line fitting tool} Emission lines, gas kinematics, line ratios,
  line deblending, global data cube fitting, automated fitting
  processes

\item{\bf Crowded field 3D spectrography} Accurate background subtraction,
  spectrography of faint point sources on high surface brightness
  distribution: testing, interpolation techniques, PSF-fitting
  techniques

\item{\bf 3D mosaicing} Combination of multiple exposures to increase S/N
  and/or FOV, ``shift and stare'' mode, dithering

\item{\bf Data cube exploration, data mining} 3D data scape, surveys, 3D
  archives, object finding for specific signatures, serendipitous
  discoveries

\item{\bf 3D deconvolution} High spatial resolution, deconvolution
  techniques, deconvolution guiding using high resolution images, PSF
  restoration techniques
  
\item{\bf 3D cross correlation} Galaxy kinematics, radial velocity maps,
  radial velocities derived from absorption and emission lines, low
  signal-to-noise spectra, template spectra
\end{itemize}

\subsection{Euro3D data format }
As integral field spectrographs become more common around the world
and in Europe in particular, the need for a common data format was
recognized as a critical asset which would benefit all potential
users. Here, we present the Euro3D format that is adapted as a
post-instrumental-signature-removal format for all instruments within
the Euro3D network. It follows the FITS standard, and includes several
extensions all of them being binary FITS tables.
Fig.~\ref{O5-2:S4-E3D-format} is intended to provide a comprehensive
overview of the format. It consists mainly of a binary table
extension, storing each spatial sample (spaxel: SPAtial piXture
ELement) ID, its coordinates and the associated data, ie. signal, data
quality and variance. A second extension contains the group
description, in case several kinds of spaxels have been glued in a
single datacube. For detailed information on this format, please
refer to Kissler-Patig et al. 2003 and to the Euro3D Data Format
Definition Document on the Euro3D Web server
(\htmladdURL{http://www.aip.de/Euro3D}).
\begin{figure}
\epsscale{0.9}
\plotone{O5-2_f7.eps}
\caption{Euro3D file format} \label{O5-2:S4-E3D-format}
\end{figure}


\subsection{E3D LCL I/O library}

Since the development time-scales for the Euro3D analysis tools are
short, the I/O library needed to be available quickly. It was decided
to use an existing library, the Lyon IFU I/O library, as a starting
point. This I/O library is part of a larger software ``suite''
developed in Lyon. The Lyon C Library (LCL) results from the
extension by A.~P\'econtal-Rousset of the IFU I/O library to include
the Euro3D-format specific I/O and others dedicated routines to handle
new features, like groups or spaxels. It provides transparent access
to FITS files (including E3D datacubes), and benefits from already
existing features such as command-line arguments and error handling
tools.

The LCL is written in ANSI~C (callable from C++), and the systematic
use of the GNU \texttt{autoconf} and \texttt{automake} tools insures
good portability to any Unix system. The low-level FITS I/O access
routines use the \texttt{cfitsio} library
(\htmladdURL{http://heasarc.gsfc.nasa.gov/docs/software/fitsio/fitsio.html})
implying very good FITS compliance (even if the FITS format
evolves), and a high reliability and long-term maintenance (see
Fig.~\ref{O5-2:S4-E3D-IOlibs}).

\begin{figure}
\epsscale{0.7}
\plotone{O5-2_f8.eps}
\caption{Euro3D I/O libraries} \label{O5-2:S4-E3D-IOlibs}
\end{figure}

The latest stable version (presently only distributed internally) can
be downloaded from the Euro3D website (\url{www.aip.de/Euro3D},
cf.~password protected internal pages). What you can get there is:
\begin{itemize}
\item The \emph{Euro3D LCL library} software package with its
  installation guide,
\item The \emph{Euro3D library cookbooks}: documentation on how to use
  the LCL library, along with examples,
\item The \emph{Euro3D developer guide}: documentation on how to set
  up the Euro3D Development Environment, and a template architecture.
\end{itemize}
The Euro3D I/O Lyon C Library is now made available inside the Euro3D
RTN. It has not yet been released externally, but people interested
in such features are encouraged to contact the RTN PI or Arlette
P\'econtal-Rousset.

%-----------------------------------------------------------------------
%                             References
%-----------------------------------------------------------------------
% List your references below within the reference environment
% (i.e. between the \begin{references} and \end{references} tags).
% Each new reference should begin with a \reference command which sets
% up the proper indentation. Observe the following order when listing
% bibliographical information for each reference:  author name(s),
% publication year, journal name, volume, and page number for
% articles. Note that many journal names are available as macros; see
% the User Guide listing "macro-ized" journals.  
%
% EXAMPLE:  \reference Hagiwara, K., \& Zeppenfeld, D.\  1986, 
%                Nucl.Phys., 274, 1
%           \reference H\'enon, M.\  1961, Ann.d'Ap., 24, 369
%           \reference King, I.\ R.\  1966, \aj, 71, 276
%           \reference King, I.\ R.\  1975, in Dynamics of Stellar 
%                Systems, ed.\ A.\ Hayli (Dordrecht: Reidel), 99
%           \reference Tody, D.\  1998, \adassvii, 146
%           \reference Zacharias, N.\ \& Zacharias, M.\ 2003,
%                \adassxii, \paperref{P7.6}
% 
% Note the following tricks used in the example above:
%
%   o  \& is used to format an ampersand symbol (&).
%   o  \'e puts an accent agu over the letter e. See the User Guide
%      and the sample files for details on formatting special
%      characters. 
%   o  "\ " after a period prevents LaTeX from interpreting the period 
%      as an end of a sentence.
%   o  \aj is a macro that expands to "Astron. J."  See the User Guide
%      for a full list of journal macros
%   o  \adassvii is a macro that expands to the full title, editor,
%      and publishing information for the ADASS VII conference
%      proceedings. Such macros are defined for ADASS conferences I
%      through XI.
%   o  When referencing a paper in the current volume, use the
%      \adassxii and \paperref macros. The argument to \paperref is
%      the paper ID code for the paper you are referencing. See the 
%      note in the "Paper ID Code" section above for details on how to 
%      determine the paper ID code for the paper you reference. 
%
\begin{references}
\reference Adam, G. et al. 1989, Astronomy and Astrophysics, 208, 15-18
\reference Aldering, G. et al. 2002, SPIE Proceedings ``Survey and
Other Telescope Technologies and Discoveries'', 4836, 61-72 
\reference Bacon, R. et al. 1995, Astronomy and Astrophysics Supplement, 113, 347
\reference de Zeeuw P.T. et al. 2002, MNRAS, 329, 513
\reference Gnata, X. 2004, \adassxiii, \paperref{O5-3}
\reference Kissler-Patig, M. et al., 2003, Astron. Nachr., (in press)
\reference Lantz, B. et al., 2003, SPIE Proceedings ``Optical systems design'' (in press)
\reference Pecontal-Rousset, A. et al. 2003, Astron. Nachr., (in press) 
\reference Sanchez, S. 2004, \adassxiii, \paperref{D10}
\end{references}

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