About p3d

p3d is a general data-reduction tool intended to be used with data of fiber-fed integral field spectrographs (IFSs). The p3d spectrum viewer can be used with IFS data cubes of any origin. This tool can be useful for people who have access to astronomical data of such an instrument. Data-reduction tasks, which are performed by p3d, convert raw data of CCD detectors into extracted spectra that can thereafter be used for scientific purposes.

Version 2.10 was released 2023-01-01.

The aim with p3d is and has been to write a user-friendly tool that will reduce the time spent performing repetitive tasks in IFS data-reduction. p3d can combine several images (exposures) into one image, clean single images of cosmic-ray hits, can extract spectra using three different methods, does full error propagation through all steps, and provides graphical tools for inspection of both intermediate and final results. Release 2.10 of p3d contains tools to handle the following tasks:

• Create a master-bias image – any available prescan and overscan regions can easily be used instead.
• Clean raw data of cosmic-ray hits – two different algorithms are implemented for single images, as well as median stacking of three or more images.
• Find and trace spectra on the detector; automatically, in most cases.
• Create a dispersion mask for wavelength calibration.
• Create a dataset used to normalize (flat field) extracted spectra.
• Extract science-object data; three extraction methods are implemented.
• Perform object spectrum extraction automatically, using already reduced data products.
• Create a sensitivity function from a summed standard-star spectrum – this can be done either automatically or interactively; the sensitivity function is used to flux calibrate reduced data.
• Flux calibrate extracted data using a sensitivity function.
• Combine extracted images of separate detectors to one image (for data of the VIMOS instrument).
• Correct data for effects of differential atmospheric refraction (DAR; currently implemented for 5 instrument setups that use square-shaped spatial elements: PMAS/Larr, Spiral, VIMOS, FLAMES/Argus, and MPFS).
• Convert RSS-formated output of p3d to data cubes (currently implemented for 6 instrument setups that use square-shaped spatial elements: PMAS/Larr, Spiral, VIMOS, FLAMES, MPFS, and ERA2) or the E3d-format (all instruments).
• Combine several extracted images using the same or different exposure times, where all exposures target the same region.
• Examine reduced spectrum images or IFS data cubes of any origin (such as MUSE) with the p3d spectrum viewer.
• Fit any combination and number of emission and absorption lines in the data. The fitted data are written to binary-table fits files as well as multi-extension image files. Another provided tool (p3d_ifsfit_mosaic) can be used to view the fitted data (in the binary-table fits files) and create publication-ready plots in a large number of imaginable forms. The image files are easily opened with any fits image viewer.
• Create simulated data sets, which can then be reduced using the regular tools of p3d.
• Apply a continuum subtraction filter to data cubes.
• View automatically reduced data products "on the fly" (requires setup).

p3d also provides output and graphical tools to inspect raw data and outcome of the different tasks. Flux calibration can be done both with the routines of p3d, or with, for example, IRAF.

Tutorials are available for a number of selected instrument setups on the Documentation & Tutorials page. The tutorials cover all basic and necessary steps to configure p3d for a new instrument (one example), reduce data (three example, and visualize reduced data (three examples).

Primary Reference
The primary reference regarding the functionality, the methods, and the implementation of p3d is:
"p3d: a general data-reduction tool for fiber-fed integral-field spectrographs", C. Sandin, T. Becker, M.M. Roth, J. Gerssen, A. Monreal-Ibero, P. Böhm, and P. Weilbacher 2010, Astronomy & Astrophysics, 515, pp.A35.

This is also the reference that should be used in publications that have made use of p3d for the data reduction. Additional references and links to those references are provided on the references page; please have a look at this page to see which other references you will want to cite.

If your research benefits from the use of p3d, we would appreciate the following acknowledgement in your paper: "This research has made use of the integral-field spectroscopy data-reduction tool p3d, which is provided by the Leibniz-Institut für Astrophysik Potsdam (AIP).".

Christer Sandin gave a presentation with the title "Integral-Field Spectroscopy Data Reduction Made Easy with p3d" in October 2010, at the STScI-workshop "IFUs in the era of JWST". Please, follow this link and watch the presentation.

p3d is written in the IDL language of Harris / EXELIS Visual Information Solutions – p3d can consequently be used on three platforms: Linux, Mac OSX, and Windows. While p3d is licensed under GPLv3 and can be used freely with the help of provided tools, IDL is in itself a proprietary program.

We refer to p3d as a general tool since it has been developed to work with any fiber-fed integral field unit (IFU) of any IFS. Currently, the software has been configured and tested with the following instruments:

• PMAS – placed on the 3.5m telescope at the Calar Alto Observatory in southern Spain. p3d supports data of both the old 2kx4k CCD and the new 4kx4k CCD.
• The Mitchell Spectrograph [VIRUS-P] – placed on the 2.7m Harlan J. Smith telescope at the McDonald Observatory in west Texas.
• VIRUS-W – currently placed on the 2.7m Harlan J. Smith telescope at the McDonald Observatory in west Texas.
• SPIRAL and SAMI of the AAOMEGA spectrograph – placed on the 3.9m telescope at the Australian Astronomical Observatory.
• VIMOS – placed on the third unit telescope (UT3) at the VLT in Chile. p3d supports data using the medium- and the high-resolution (MR and HR) gratings. Data sampled both before and after the instrument refurbish about October 2010 are supported.
• FLAMES – placed on the second unit telescope (UT2) at the VLT in Chile. p3d supports data using the ARGUS IFU as well as the two mini-IFU configurations. Data sampled both before and after the instrument refurbish in 2007 are supported.
• MPFS – placed on the 6m SAO Big Telescope Alt-azimuth (BTA) near Mount Pastukhov in the Caucasus Mountains in Russia. p3d has been setup to work with the newer CCD.
• GMOS-N and GMOS-S – placed on the Gemini North telescope on top of Mauna Kea on the Big Island of Hawaií, and the Gemini South telescope on top of Cerro Pachon in Chile; both telescopes belong to the Gemini Observatory. p3d supports data using the two one-slit modes; i.e. the red and the blue slits. The two-slit mode is (logistically) more complex to handle, which is why it is not (yet) supported.
• INTEGRAL, which has been a set of IFUs connected to the WYFFOS spectrograph at the 4.2m William Herschel Telescope (WHT) (of the Isaac Newton Group of Telescopes) at the Roque de los Muchachos Observatory on the island of La Palma. p3d supports both the older single-detector as well as the newer two-detector configurations.
• ERA2, which is an life-sciences integral-field spectrograph in development at the AIP.
• MRS1, MRS2, R10E-Atik, & PlasMark/Andor which are life-sciences integral-field spectrograph IFUs in development at the AIP.
• PRAXIS, which is an experimental setup.
• MUSE, The Multi Unit Spectroscopic Explorer is a second generation instrument placed on the fourth unit telescope (UT4) at the VLT in Chile. Use the p3d spectrum viewer to study and analyze reduced MUSE data cubes of any size (the amount of available RAM defines the limiting size on the cube that can be viewed). Additionally, the tool p3d_d11 can be used on data cubes such as those of MUSE to subtract the continuum.
• MOSMS, 3D-Cancerspec, & PlasMark; these are setups meant to create simulated raw data of required properties. The simulated raw data can be reduced with the tools of p3d.

A tool as complex as p3d is never finished. There are several parts of p3d, which could be extended and improved upon. Additional tools could be written in order to optimize the control and analysis of the outcome. p3d can also, if required, be configured for more instruments. If and how this will happen at large depends on the interest of the community. Please, tell us if there is some functionality missing, in your opinion, or if you need support for another instrument. We are scientists with limited resources, but we will do what we can to help you out. We do consider taking on people with a suitable expertise in our development team.

The p3d team
ninth version, for php 5.4: 2018-03-15
eighth version, for release 2.5: 2017-06-28
seventh version, for release 2.3: 2015-12-16
sixth version, for release 2.2: 2012-12-13
fifth version, for release 2.1.2: 2012-04-23
fourth version, for release 2.1: 2011-11-24
third version, for release 2.0: 2011-06-20
second version, for release 2.0a: 2011-01-26
first version: 2010-02-04