4.2. Utilities

Besides the modules for data reduction, PAPI has a set of utilities than can be used as tools for preparing the data reduction execution; they are:

Utilities Description
check_papi_modules Check whether all python modules required by PAPI are installed
checkQuality Computes some quality values from the image (FWHM, STD, RMS)
collapse Collapse (sum) each cube of a list of files into a single 2D image
mef Utilities to convert FITS/MEF files.
eval_focus_serie Finds out the best Focus value from a focus series
genLogsheet Creates a log sheet from a set of FITS files
health Compute the Gain and Noise from a set of flat images grouped in packets and with increased level of Integration Time
imtrim Cut/crop edges of the input image
modFits Modifies a keyword inside a FITS header
skyfilter Subtracts sky background to a dither sequence of frames
spatial_noise Compute the Spatial Noise from a set of dark images grouped in pairs with the same Integration Time

4.2.1. check_papi_modules

Check whether all Python modules required by PAPI are installed. The modules currently required are:

Module Version
Numpy 1.6
PyRaf 1.1
PyFITS 3.0
Matplotlib 0.98.1
Scipy 0.10
PyQt4.QtCore 4.8
PyWCS 1.11
vo 0.7
Atpy 0.95

Example:

$ check_papi_modules.py

PAPI Python checking tool
=========================

Checking Python Version:
PAPI needs Python Version 2.Y with Y>=2.7
Your Python version 2.7.3 is fine!

Testing Python module installation for module 'atpy':
PAPI needs at least version 0.9.5
Your version 0.9.6 of 'atpy' is fine!

Testing Python module installation for module 'scipy':
PAPI needs at least version 0.10
Your version 0.10.1 of 'scipy' is fine!

Testing Python module installation for module 'pywcs':
PAPI needs at least version 1.11
Your version 1.11-4.10 of 'pywcs' is fine!

Testing Python module installation for module 'PyQt4.QtCore':
PAPI needs at least version 4.8
Your version 4.9.1 of 'PyQt4.QtCore' is fine!

Testing Python module installation for module 'vo':
PAPI needs at least version 0.7
Your version 0.8 of 'vo' is fine!

Testing Python module installation for module 'numpy':
PAPI needs at least version 1.6
Your version 1.6.2 of 'numpy' is fine!

Testing Python module installation for module 'pyraf':
PAPI needs at least version 1.1
Your version 2.0 of 'pyraf' is fine!

Testing Python module installation for module 'matplotlib':
PAPI needs at least version 0.98.1
Your version 1.1.0 of 'matplotlib' is fine!

Testing Python module installation for module 'pyfits':
PAPI needs at least version 3.0
Your version 3.1.0 of 'pyfits' is fine!

4.2.2. collapse

SYNOPSIS:

Usage: collapse.py [options] arg1 arg2 ...

Options:
-h, --help            show this help message and exit
-i INPUT_IMAGE, --input_image=INPUT_IMAGE
                        input cube image to collapse into a 2D image
-l INPUT_IMAGE_LIST, --input_image_list=INPUT_IMAGE_LIST
                        input image list to collapse into a single 2D image
-o OUTPUT_FILE, --output_file=OUTPUT_FILE
                        output filename (default = /tmp/out.fits)

DESCRIPTION:

Sum (add them up arithmetically) the planes of each cube of a list files into a single plane 2D-image. No image registration is done.

EXAMPLES:

$ collapse -i /data/mycube.fits -o /data/anymore_a_cube.fits

$ collapse -l /data/list.txt -o /data/anymore_a_cube.fits

4.2.3. mef

SYNOPSIS:

Usage: mef [options] arg1 arg2

Options:
-h, --help            show this help message and exit
-f FILE, --file=FILE  Input MEF file. It has to be a fullpath file name
-l INPUT_FILE_LIST, --input=INPUT_FILE_LIST
                      Source file list of data frames. It has to be a
                      fullpath file name.
-s OUT_SUFFIX, --suffix=OUT_SUFFIX
                      suffix to out files (default .Q%02d.fits)
-J, --join            make a join/stitch of the FITS extensions creating a
                      single FITS file
-S, --split           make a split of MEF files, adding a suffix for each
                      extension
-P, --slice           Slice a MEF-cube, adding a suffix for each plane
-G, --geirs-split     make a split of GEIRS SEF file, creating 4-single
                      files and adding a suffix for each extension
-C, --create          create a MEF (with N extensions) from a set N single
                      FITS files
-g, --geirs-convert   convert a GEIRS SEF file to a MEF FITS file with 4
                      extensions
-d OUTPUT_DIR, --output_dir=OUTPUT_DIR
                      Directory where output files will be saves.
-o OUTPUT_FILE, --output_file=OUTPUT_FILE
                      Filename of the output file created [default =
                      mef.fits].

DESCRIPTION:

Utility to convert MEF/FITS files generated by PANIC to different formats:

  • MEF -> SEF (–join)
  • SEF -> MEF (-g)
  • split a MEF/SEF (–split)
  • build MEF from N-SEFs (–create)
  • slice a MEF-cube (–slice)

EXAMPLES:

$ mef -f /tmp/myMEF_cube.fits -P -d /tmp/
$ mef -l /tmp/my_files.txt -C -d /tmp/ -o my_mef.fits

4.2.4. checkQuality

The checkQuality module computes some initial image quality estimations using SExtractor.

4.2.5. eval_focus_series

The eval_focus_series module computes the best focus estimation for a focus exposure series. It is done according to the FWHM value estimated for each frame, fitting a curve the the values pair values (FWHM,focus) and finding out the minimun.

  • Requirements

    • T-FOCUS (telescope focus) keyword value present in the header
    • (Raw) Images with enought number of stars
    • A series of images taken with covering a range of telescope focus values including the best focus value.

4.2.6. genLogsheet

4.2.7. health

4.2.8. imtrim

4.2.9. modFits

4.2.10. skyfilter

The skyfilter module uses the external package irdr_skyfilter to perform the sky background subtraction from a dither sequence of science frames. It works with almost all kind of dither sequences, even with sequences used for extended objects (T-S-T-S- ...., T-T-S-T-T-S-T-T-....)

For more details on skyfilter see the Appendix section skyfilter.

4.2.11. spatial_noise