Skip to content

Navigation Menu

Sign in
Appearance settings

Search code, repositories, users, issues, pull requests...

Provide feedback

We read every piece of feedback, and take your input very seriously.

Saved searches

Use saved searches to filter your results more quickly
Sign up
Appearance settings

JMMC-OpenDev/oitools

Repository files navigation

OITools JMMC logo

License: GPL v3 Build

This is a java library dedicated to reading / writing OIFITS files (based on the nom.tam.fits library) developed by the JMMC technical team.

See Developers corner

OIFits standard versions:

More detailed data model including dynamic columns:

Setup

  1. Download the last jar (oitools-TRUNK.jar) from release place https://github.com/JMMC-OpenDev/OITools/releases/

  2. Call:

    • type in shell:

      java -cp _path_/_to_/oitools-TRUNK-jar-with-dependencies.jar fr.jmmc.oitools.OIFitsProcessor <parameters>

    • HINT: you can define aliases in your (bashrc) as of:

      alias oip="java -cp _path_/_to_/oitools-TRUNK-jar-with-dependencies.jar fr.jmmc.oitools.OIFitsProcessor"
alias oilist="oip list"
alias oiconvert="oip convert"
alias oimerge="oip merge"

Usage & Examples

Examples are taken from the test folder

To get the command help, just type oip:

--------------------------------------------------------------------------------------
Usage: fr.jmmc.oitools.OIFitsProcessor command -o <path_output_file> <file locations>
------------- Arguments help ---------------------------------------------------------
| Key Value Description |
|------------------------------------------------------------------------------------|
| command help Show this help |
| command list List content of several oifits files |
| command list_baselines List baselines and triplets used by several oifits files |
| command dump Dump the given oifits files |
| command convert Convert the given input file |
| command merge Merge several oifits files |
|------------------------------------------------------------------------------------|
| [-l] or [-log] Enable logging (quiet by default) |
| [-v] or [-verbose] Enable logging (quiet by default) |
| [-c] or [-check] Check output file before writing |
| [-separation] <value> Separation in arcsec for the target matcher |
| [-o] or [-output] <file_path> Complete path, absolute or relative, for output file |
--------------------------------------------------------------------------------------
| Filter options available to the command merge: |
| [-target] <value> Filter result on given Targets (comma-separated) |
| [-insname] <value> Filter result on given InsNames (comma-separated) |
| [-night] <value> Filter result on given Nights (integer, comma-separated) |
| |
| [-baselines] <values> Filter result on given Baselines or Triplets (comma-separated) |
| [-mjds] <values> Filter result on given MJD ranges (comma-separated pairs) |
| [-wavelengths] <values> Filter result on given wavelength ranges (comma-separated pairs) |
| |
| <values> can be String or Range values (like 1e-6,2e-6) (comma-separated); |
| use the prefix 'not:' to have an exclusive filter |
| |
| Following columns may be available (OIFITS2 standard): |
| [-eff_wave] <values> Filter result on given column values (comma-separated) |
| [-eff_band] <values> Filter result on given column values (comma-separated) |
| [-sta_index] <values> Filter result on given column values (comma-separated) |
| [-sta_conf] <values> Filter result on given column values (comma-separated) |
| [-time] <values> Filter result on given column ranges (comma-separated pairs) |
| [-mjd] <values> Filter result on given column ranges (comma-separated pairs) |
| [-int_time] <values> Filter result on given column ranges (comma-separated pairs) |
| [-vis2data] <values> Filter result on given column ranges (comma-separated pairs) |
| [-vis2err] <values> Filter result on given column ranges (comma-separated pairs) |
| [-ucoord] <values> Filter result on given column ranges (comma-separated pairs) |
| [-vcoord] <values> Filter result on given column ranges (comma-separated pairs) |
| [-eff_wave] <values> Filter result on given column ranges (comma-separated pairs) |
| [-eff_band] <values> Filter result on given column ranges (comma-separated pairs) |
| [-hour_angle] <values> Filter result on given column ranges (comma-separated pairs) |
| [-radius] <values> Filter result on given column ranges (comma-separated pairs) |
| [-pos_angle] <values> Filter result on given column ranges (comma-separated pairs) |
| [-spatial_freq] <values> Filter result on given column ranges (comma-separated pairs) |
| [-u] <values> Filter result on given column ranges (comma-separated pairs) |
| [-v] <values> Filter result on given column ranges (comma-separated pairs) |
| [-snr_vis2] <values> Filter result on given column ranges (comma-separated pairs) |
| [-visamp] <values> Filter result on given column ranges (comma-separated pairs) |
| [-visamperr] <values> Filter result on given column ranges (comma-separated pairs) |
| [-visphi] <values> Filter result on given column ranges (comma-separated pairs) |
| [-visphierr] <values> Filter result on given column ranges (comma-separated pairs) |
| [-rvis] <values> Filter result on given column ranges (comma-separated pairs) |
| [-rviserr] <values> Filter result on given column ranges (comma-separated pairs) |
| [-ivis] <values> Filter result on given column ranges (comma-separated pairs) |
| [-iviserr] <values> Filter result on given column ranges (comma-separated pairs) |
| [-t3amp] <values> Filter result on given column ranges (comma-separated pairs) |
| [-t3amperr] <values> Filter result on given column ranges (comma-separated pairs) |
| [-t3phi] <values> Filter result on given column ranges (comma-separated pairs) |
| [-t3phierr] <values> Filter result on given column ranges (comma-separated pairs) |
| [-u1coord] <values> Filter result on given column ranges (comma-separated pairs) |
| [-v1coord] <values> Filter result on given column ranges (comma-separated pairs) |
| [-u2coord] <values> Filter result on given column ranges (comma-separated pairs) |
| [-v2coord] <values> Filter result on given column ranges (comma-separated pairs) |
| [-u1] <values> Filter result on given column ranges (comma-separated pairs) |
| [-v1] <values> Filter result on given column ranges (comma-separated pairs) |
| [-u2] <values> Filter result on given column ranges (comma-separated pairs) |
| [-v2] <values> Filter result on given column ranges (comma-separated pairs) |
| [-fluxdata] <values> Filter result on given column ranges (comma-separated pairs) |
| [-fluxerr] <values> Filter result on given column ranges (comma-separated pairs) |
| [-snr_flux] <values> Filter result on given column ranges (comma-separated pairs) |
--------------------------------------------------------------------------------------
  • oilist input_file_location [input_file_location ...] display the file content of input file(s) in CSV format files contents (granules like OiDB):

Example where two instruments are detected: the fringe tracker GRAVITY_FT with 5 spectral channels and the science detector GRAVITY_SC with 210 spectral channels

oilist GRAVI.2016年06月23日T03:10:17.458_singlesciviscalibrated.fits
target_name s_ra s_dec t_exptime t_min t_max em_res_power em_min em_max facility_name instrument_name nb_vis nb_vis2 nb_t3 nb_channels
IRAS17216-3801 261.2771541666667 -38.066788888888894 36.54999999999172 57562.13387079336 57562.134832901625 25.75830610631207 2.0264997147023678E-6 2.347295094295987E-6 VLTI GRAVITY_FT 6 6 4 5
IRAS17216-3801 261.2771541666667 -38.066788888888894 0.0 57562.1339081338 57562.135323171286 1008.6521574069673 1.990000100704492E-6 2.4500000108673703E-6 VLTI GRAVITY_SC 6 6 4 210

⚠ Warning: Targets are gathered according to their name and positions. Due to some uncertainties from files to files, the same target maybe duplicated. In this example, the target HD45677 is miss-identified as 3 different targets with varying right ascension.

 % oilist *.fits
target_name	s_ra	s_dec	t_exptime	t_min	t_max	em_res_power	em_min	em_max	facility_name	instrument_name	nb_vis	nb_vis2	nb_t3	nb_channels
HD45677	97.071446	-13.05308	0.07500000298023224	9743.3964126119	9743.39698346838	47.39237355339858	2.841224613803206E-6	4.209076450933935E-6	VLTI	MATISSE	0	12	8	64
HD45677	97.071446	-13.05308	0.07500000298023224	29230.186422152714	29230.186875347168	47.39237355339858	2.841224613803206E-6	4.209076450933935E-6	VLTI	MATISSE	0	12	8	64
HD45677	97.071446	-13.05308	0.07500000298023224	58454.27455231501	58454.35846547426	47.39237355339858	2.841224613803206E-6	4.209076450933935E-6	VLTI	MATISSE	72	72	48	64
HD45677	97.071446	-13.05308	0.07500000298023224	58455.17619694426	58455.2241775925	47.39237355339858	2.841224613803206E-6	4.209076450933935E-6	VLTI	MATISSE	36	36	24	64
HD45677	97.071446	-13.05308	0.07500000298023224	58458.17127300924	58458.3521850002	47.39237355339858	2.841224613803206E-6	4.209076450933935E-6	VLTI	MATISSE	126	186	124	64
HD45677	97.071446	-13.05308	0.07500000298023224	58459.1170581483	58459.32373210101	47.39237355339858	2.841224613803206E-6	4.209076450933935E-6	VLTI	MATISSE	108	114	76	64
HD45677	97.071446	-13.05308	0.07500000298023224	58460.19688902766	58460.37100263876	47.39237355339858	2.841224613803206E-6	4.209076450933935E-6	VLTI	MATISSE	48	72	48	64
HD45677_1	97.072017	-13.05308	0.07500000298023224	11692.253139791668	11692.271517135014	47.39237355339858	2.841224613803206E-6	4.209076450933935E-6	VLTI	MATISSE	0	36	24	64
HD45677_1	97.072017	-13.05308	0.07500000298023224	58461.259056527546	58461.35039300915	47.39237355339858	2.841224613803206E-6	4.209076450933935E-6	VLTI	MATISSE	36	36	24	64
HD45677_1	97.072017	-13.05308	0.07500000298023224	58464.21925374992	58464.296853532614	47.39237355339858	2.841224613803206E-6	4.209076450933935E-6	VLTI	MATISSE	48	48	32	64
HD45677_1	97.072017	-13.05308	0.07500000298023224	58465.21247333342	58465.35976816349	47.39237355339858	2.841224613803206E-6	4.209076450933935E-6	VLTI	MATISSE	90	96	64	64
HD45677_1	97.072017	-13.05308	0.07500000298023224	58466.225046249856	58466.2779251908	47.39237355339858	2.841224613803206E-6	4.209076450933935E-6	VLTI	MATISSE	48	48	32	64
HD45677_2	97.072587	-13.05308	0.07500000298023224	58462.2034310185	58462.37512025083	47.39237355339858	2.841224613803206E-6	4.209076450933935E-6	VLTI	MATISSE	114	120	80	64
HD45677_2	97.072587	-13.05308	0.07500000298023224	58463.31136550928	58463.36339001964	47.39237355339858	2.841224613803206E-6	4.209076450933935E-6	VLTI	MATISSE	30	48	32	64

This can be fixed by ajusting the separation of the target matcher using the keyword -separation <value> (default: 1 arcsec ):

% oilist -separation 10 *.fits
target_name	s_ra	s_dec	t_exptime	t_min	t_max	em_res_power	em_min	em_max	facility_name	instrument_name	nb_vis	nb_vis2	nb_t3	nb_channels
HD45677	97.071446	-13.05308	0.07500000298023224	9743.3964126119	9743.39698346838	47.39237355339858	2.841224613803206E-6	4.209076450933935E-6	VLTI	MATISSE	0	12	8	64
HD45677	97.071446	-13.05308	0.07500000298023224	11692.253139791668	11692.271517135014	47.39237355339858	2.841224613803206E-6	4.209076450933935E-6	VLTI	MATISSE	0	36	24	64
HD45677	97.071446	-13.05308	0.07500000298023224	29230.186422152714	29230.186875347168	47.39237355339858	2.841224613803206E-6	4.209076450933935E-6	VLTI	MATISSE	0	12	8	64
HD45677	97.071446	-13.05308	0.07500000298023224	58454.27455231501	58454.35846547426	47.39237355339858	2.841224613803206E-6	4.209076450933935E-6	VLTI	MATISSE	72	72	48	64
HD45677	97.071446	-13.05308	0.07500000298023224	58455.17619694426	58455.2241775925	47.39237355339858	2.841224613803206E-6	4.209076450933935E-6	VLTI	MATISSE	36	36	24	64
HD45677	97.071446	-13.05308	0.07500000298023224	58458.17127300924	58458.3521850002	47.39237355339858	2.841224613803206E-6	4.209076450933935E-6	VLTI	MATISSE	126	186	124	64
HD45677	97.071446	-13.05308	0.07500000298023224	58459.1170581483	58459.32373210101	47.39237355339858	2.841224613803206E-6	4.209076450933935E-6	VLTI	MATISSE	108	114	76	64
HD45677	97.071446	-13.05308	0.07500000298023224	58460.19688902766	58460.37100263876	47.39237355339858	2.841224613803206E-6	4.209076450933935E-6	VLTI	MATISSE	48	72	48	64
HD45677	97.071446	-13.05308	0.07500000298023224	58461.259056527546	58461.35039300915	47.39237355339858	2.841224613803206E-6	4.209076450933935E-6	VLTI	MATISSE	36	36	24	64
HD45677	97.071446	-13.05308	0.07500000298023224	58462.2034310185	58462.37512025083	47.39237355339858	2.841224613803206E-6	4.209076450933935E-6	VLTI	MATISSE	114	120	80	64
HD45677	97.071446	-13.05308	0.07500000298023224	58463.31136550928	58463.36339001964	47.39237355339858	2.841224613803206E-6	4.209076450933935E-6	VLTI	MATISSE	30	48	32	64
HD45677	97.071446	-13.05308	0.07500000298023224	58464.21925374992	58464.296853532614	47.39237355339858	2.841224613803206E-6	4.209076450933935E-6	VLTI	MATISSE	48	48	32	64
HD45677	97.071446	-13.05308	0.07500000298023224	58465.21247333342	58465.35976816349	47.39237355339858	2.841224613803206E-6	4.209076450933935E-6	VLTI	MATISSE	90	96	64	64
HD45677	97.071446	-13.05308	0.07500000298023224	58466.225046249856	58466.2779251908	47.39237355339858	2.841224613803206E-6	4.209076450933935E-6	VLTI	MATISSE	48	48	32	64
  • oip list_baselines display similar information as oilist plus the station/baselines used.

Example showing that the stations used are: A0 B2 C1 D0 and the file contains all combinaison of baselines and triplets:

oip list_baselines GRAVI.2016年06月23日T03:10:17.458_singlesciviscalibrated.fits
instrument_name	em_min	em_max	night_id	target_name	s_ra	s_dec	mjds	baselines
GRAVITY_FT	2.0264997147023678E-6	2.347295094295987E-6	57562	IRAS17216-3801	261.2771541666667	-38.066788888888894	[57562.133866,57562.136111] [57562.133947,57562.136748] [57562.13412,57562.13522] [57562.13412,57562.135231] [57562.13412,57562.135243] [57562.134745,57562.135336] [57562.13478,57562.135243] [57562.13478,57562.135498] [57562.134815,57562.135266] [57562.134826,57562.135266] 	A0 B2 C1 D0 B2-A0 C1-A0 C1-B2 C1-D0 D0-A0 D0-B2 C1-B2-A0 C1-D0-A0 C1-D0-B2 D0-B2-A0
GRAVITY_SC	1.990000100704492E-6	2.4500000108673703E-6	57562	IRAS17216-3801	261.2771541666667	-38.066788888888894	[57562.13390,57562.136343] [57562.13397,57562.133981] [57562.13397,57562.137454] [57562.135312,57562.13544] 	A0 B2 C1 D0 B2-A0 C1-A0 C1-B2 C1-D0 D0-A0 D0-B2 C1-B2-A0 C1-D0-A0 C1-D0-B2 D0-B2-A0
  • oip dump print headers of all HDUs.

  • oimerge -o <output_file_path> input_file_location [input_file_location ...] merge multiple files with filter support, targets are gathered and merged into a single OI_TARGET table.

    Available filters are (multiple arguments must be comma separated):

    • -target
    • -insname
    • -night
    • -mjds
    • -baselines
    • -wavelength

  • Extracting flux from Gravity science instrument at wavelengths between 2.15 and 2.2 μm*:

% oimerge -insname GRAVITY_SC -baselines A0,B2,C1,D0 -wavelengths 2.15E-6,2.20E-6 -o output.fits GRAVI.2016年06月23日T03:10:17.458_singlesciviscalibrated.fits
Writing: output.fits
% oilist output.fits
target_name	s_ra	s_dec	t_exptime	t_min	t_max	em_res_power	em_min	em_max	facility_name	instrument_name	nb_vis	nb_vis2	nb_t3	nb_channels
IRAS17216-3801	261.2771541666667	-38.066788888888894	300.0	57562.133972453696	57562.133972453696	988.1521592210469	2.1506698431039695E-6	2.1990908862790093E-6	VLTI	GRAVITY_SC	0	0	0	23

OIFitsViewer

You may also define some other aliases to dump main informations of your oifits files through XML or TSV format or check content

 alias oiv="java -cp _path_/_to_/oitools-TRUNK-jar-with-dependencies.jar fr.jmmc.oitools.OIFitsViewer"
 alias oicheck="oiv -check"

To get the command help, just type oiv:

No file location given in arguments.
-------------------------------------------------------------------------
Usage: fr.jmmc.oitools.OIFitsViewer [-f|-format] [-v|-verbose] [-t|-tsv] <file locations>
------------- Arguments help --------------------------------------------
| Key Value Description |
|-----------------------------------------------------------------------|
| [-h|-help] Show arguments help |
| [-l] or [-log] Enable logging (quiet by default) |
| [-f] or [-format] Use the number formatter |
| [-v] or [-verbose] Dump all column data |
| [-t] or [-tsv] Dump object table in tsv format |
| [-c] or [-check] Check only given file(s) |
| [-g] or [-granule] Use Granules to get target metadata |
-------------------------------------------------------------------------

About

OiTools is a Java library dedicated to reading / writing OIFITS files

Topics

Resources

License

Stars

Watchers

Forks

Packages

No packages published

Contributors 6

Languages

AltStyle によって変換されたページ (->オリジナル) /