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