This is a java library dedicated to reading / writing OIFITS files (based on the nom.tam.fits library) developed by the JMMC technical team.
More detailed data model including dynamic columns:
Download the last jar (oitools-TRUNK.jar
) from release place https://github.com/JMMC-OpenDev/OITools/releases/
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"
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) |
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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.2016-06-23T03:10:17.458_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.2016-06-23T03:10:17.458_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.2016-06-23T03:10:17.458_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
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 |
-------------------------------------------------------------------------