rinexmod is a tool to batch modify the headers of GNSS data files in RINEX format and rename them correctly.
It supports Hatanaka-compressed and non-compressed files, RINEX versions 2 and 3/4, and short and long naming conventions.
It is developed in Python 3, and can be run from the command line or directly in API mode by calling a python function.
The required input metadata can come from a sitelog file, or be manually entered as arguments to the command line or the called function.
It is available under the GNU license on the following GitHub repository: https://github.com/IPGP/rinexmod
v2 - 2023-05-15 - Pierre Sakic - [email protected]
v1 - 2022-02-07 - Félix Léger - [email protected]
Last version: v3.4.0 - 2024-09-30
rinexmod.pytakes a list of RINEX Hatanaka compressed files (.d.Z or .d.gz or .rnx.gz), loops the rinex files list to modify the file's headers. It then writes them back to Hatanaka compressed format in an output folder. It also permits to rename the files, changing the four first characters of the file name with another station code. It can write those files with the long name naming convention with the --longname option.
They are stored in misc_tools folder.
-
get_m3g_sitelogs.pywill get the last version of site logs from the M3G repository and write them in an observatory-dependent subfolder. -
crzmeta.pywill extract RINEX file's header information and prompt the result. This permits to quickly access the header information without uncompressing the file manually. It's a teqc-free equivalent of teqc +meta.
The tool is designed in Python 3, and you must have it installed on your machine.
You can use pip to install the last GitHub-hosted version with the following command:
pip install git+https://github.com/IPGP/rinexmod
To use the front-end functions, you must also add the rinexmod folder in your $PATH environnement variable,
defined in your .bashrc.
If you used PIP for the installation, your can locate the folder where rinexmod has been installed with:
pip show rinexmod
at the line Location:. Usually, it is /usr/local/lib/python3.NN/dist-packages/rinexmod .
Then edit your ~/.bashrc and add it to the $PATH environnement variable
NB: Following the assisted installation procedure above, the required external modules will be automatically installed.
You need:
- Python
hatanakalibrary from M. Valgur pycountryto associate country names with their ISO abbreviations (facultative but recommended):matplotlibfor plotting samples intervals with crzmetacolorlogto get the pretty colored log outputspandasto for internal low-level data management
You can install them with:
pip install hatanaka pycountry matplotlib colorlog pandas
This is the main frontend function. It takes a list of RINEX Hatanaka compressed files (.d.Z or .d.gz or .rnx.gz), loop over the RINEX files list to modify the file's header. It then writes them back to Hatanaka-compressed format in an output folder. It also allows to rename the files, changing the four first characters of the file name with another site code. It can write those files with the long name naming convention with the --longname option.
Three ways of passing parameters to modify headers are possible: sitelog, modification_kw and station_info/lfile_apriori (from GAMIT/GLOBK software).
-
--sitelog : you pass sitelogs file. The argument must be a sitelog path or the path of a folder containing sitelogs. You then have to pass a list of files and the script will assign sitelogs to correspondig files, based on the file's name. The script will take the start and end time of each proceeded file and use them to extract from the sitelog the station instrumentation of the corresponding period and fill file's header with following infos: Four Character ID X coordinate (m) Y coordinate (m) Z coordinate (m) Receiver Type Serial Number Firmware Version Satellite System (will translate this info to one-letter code, see RinexFile.set_observable_type()) Antenna Type Serial Number Marker->ARP Up Ecc. (m) Marker->ARP East Ecc(m) Marker->ARP North Ecc(m) On-Site Agency Preferred Abbreviation Responsible Agency Preferred Abbreviation -
--modification_kw : you pass as argument the field(s) that you want to modifiy and its value. Acceptable_keywords are: marker_name, marker_number, station (legacy alias for marker_name), receiver_serial, receiver_type, receiver_fw, antenna_serial, antenna_type, antenna_X_pos, antenna_Y_pos, antenna_Z_pos, antenna_H_delta, antenna_E_delta, antenna_N_delta, operator, agency, sat_system, observables (legacy alias for sat_system), interval, filename_file_period (01H, 01D...), filename_data_freq (30S, 01S...), filename_data_source (R, S, U) -
-sti STATION_INFO, --station_info STATION_INFO Path of a GAMIT station.info file to obtain GNSS site metadata information (needs also -lfi option) -lfi LFILE_APRIORI, --lfile_apriori LFILE_APRIORI Path of a GAMIT apriori apr/L-File to obtain GNSS site position and DOMES information (needs also -sti option)
--modification_kw values will orverride the ones obtained with --sitelog and --station_info/--lfile_apriori.
rinexmod will add two comment lines, one indicating the source of the modification (sitelog or arguments) and the other the modification timestamp.
rinexmod.py [-h] -i RINEXINPUT [RINEXINPUT ...] -o OUTPUTFOLDER
[-s SITELOG] [-k KEY=VALUE [KEY=VALUE ...]] [-m MARKER]
[-co COUNTRY] [-n NINECHARFILE] [-sti STATION_INFO]
[-lfi LFILE_APRIORI] [-r RELATIVE] [-nh] [-c {gz,Z,none}]
[-l] [-fs] [-fc] [-fr] [-ig] [-a] [-ol OUTPUT_LOGS] [-w]
[-v] [-t] [-u] [-fns {basic,flex,exact}]
[-mp MULTI_PROCESS] [-d] [-rm]
RinexMod takes RINEX files (v2 or v3/4, compressed or not), rename them and modifiy their headers, and write them back to a destination directory
options:
-h, --help show this help message and exit
required arguments:
-i RINEXINPUT [RINEXINPUT ...], --rinexinput RINEXINPUT [RINEXINPUT ...]
Input RINEX file(s). It can be:
1) a list file of the RINEX paths to process (generated with find or ls command for instance)
2) several RINEX files paths
3) a single RINEX file path (see -a/--alone for a single input file)
-o OUTPUTFOLDER, --outputfolder OUTPUTFOLDER
Output folder for modified RINEX files
optional arguments:
-s SITELOG, --sitelog SITELOG
Get the RINEX header values from file's site's sitelog. Provide a single sitelog path or a folder contaning sitelogs.
-k KEY=VALUE [KEY=VALUE ...], --modif_kw KEY=VALUE [KEY=VALUE ...]
Modification keywords for RINEX's header fields and/or filename.
Format: -k keyword_1='value1' keyword2='value2'.
Will override the information from the sitelog.
Acceptable keywords: comment, marker_name, marker_number, station (legacy alias for marker_name), receiver_serial, receiver_type, receiver_fw, antenna_serial, antenna_type, antenna_X_pos, antenna_Y_pos, antenna_Z_pos, antenna_H_delta, antenna_E_delta, antenna_N_delta, operator, agency, sat_system, observables (legacy alias for sat_system), interval, filename_file_period (01H, 01D...), filename_data_freq (30S, 01S...), filename_data_source (R, S, U)
-m MARKER, --marker MARKER
A four or nine-character site code that will be used to rename input files.(apply also to the header's MARKER NAME, but a custom -k marker_name='XXXX' overrides it)
-co COUNTRY, --country COUNTRY
A three-character string corresponding to the ISO 3166 Country code that will be used to rename input files. It overrides other country code sources (sitelog, --marker...). List of ISO country codes: https://en.wikipedia.org/wiki/List_of_ISO_3166_country_codes
-n NINECHARFILE, --ninecharfile NINECHARFILE
Path of a file that contains 9-char. site names (e.g. from the M3G database)
-sti STATION_INFO, --station_info STATION_INFO
Path of a GAMIT station.info file to obtain GNSS site metadata information (needs also -lfi option)
-lfi LFILE_APRIORI, --lfile_apriori LFILE_APRIORI
Path of a GAMIT apriori apr/L-File to obtain GNSS site position and DOMES information (needs also -sti option)
-r RELATIVE, --relative RELATIVE
Reconstruct files relative subfolders.You have to indicate the common parent folder, that will be replaced with the output folder
-nh, --no_hatanaka Skip high-level RINEX-specific Hatanaka compression (performed per default). See also -c 'none'
-c {gz,Z,none}, --compression {gz,Z,none}
Set low-level RINEX file compression (acceptable values : 'gz' (recommended to fit IGS standards), 'Z', 'none')
-l, --longname Rename file using long name RINEX convention (force gzip compression).
-fs, --force_sitelog If a single sitelog is provided, force sitelog-based header values when RINEX's header and sitelog site name do not correspond.
If several sitelogs are provided, skip badly-formated sitelogs.
-fc, --force_fake_coords
When using GAMIT station.info metadata without apriori coordinates in the L-File, gives fake coordinates at (0°,0°) to the site
-fr, --force_rnx_load
Force the loading of the input RINEX. Useful if its name is not standard
-ig, --ignore Ignore firmware changes between instrumentation periods when getting header values info from sitelogs
-a, --alone INPUT is a single/alone RINEX file (and not a list file of RINEX paths)
-ol OUTPUT_LOGS, --output_logs OUTPUT_LOGS
Folder where to write output logs. If not provided, logs will be written to OUTPUTFOLDER
-w, --write Write (RINEX version, sample rate, file period) dependant output lists
-v, --verbose Print file's metadata before and after modifications.
-t, --sort Sort the input RINEX list.
-u, --full_history Add the full history of the station in the RINEX's 'header as comment.
-fns {basic,flex,exact}, --filename_style {basic,flex,exact}
Set the RINEX filename style.
acceptable values : 'basic' (per default), 'flex', 'exact'.
* 'basic': a simple mode to apply a strict filename period (01H or 01D), being compatible with the IGS conventions.
e.g.: FNG000GLP_R_20242220000_01D_30S_MO.crx.gz
* 'flex': the filename period is tolerant and corresponds tothe actual data content,
but then can be odd (e.g. 07H, 14H...). The filename start time is rounded to the hour.
e.g.: FNG000GLP_R_20242221800_06H_30S_MO.crx.gz
* 'exact': the filename start time is strictly the one of the first epoch in the RINEX.
Useful for some specific cases needing splicing.
e.g.: FNG000GLP_R_20242221829_06H_30S_MO.crx.gz
(default: basic)
-mp MULTI_PROCESS, --multi_process MULTI_PROCESS
Number of parallel multiprocesing (default: 1, no parallelization)
-d, --debug Debug mode, stops if something goes wrong (default: False)
-rm, --remove Remove input RINEX file if the output RINEX is correctly written. Use it as your own risk. (default: False)
RinexMod 3.3.0 - GNU Public Licence v3 - P. Sakic et al. - IPGP-OVS - https://github.com/IPGP/rinexmod
./rinexmod.py -i RINEXLIST -o OUTPUTFOLDER (-k antenna_type='ANT TYPE' antenna_X_pos=9999 agency=AGN) (-m AGAL) (-r ./ROOTFOLDER/) (-f) (-v)
./rinexmod.py (-a) -i RINEXFILE -o OUTPUTFOLDER (-s ./sitelogsfolder/stationsitelog.log) (-i) (-w) (-o ./LOGFOLDER) (-v)
rinexmod can be launched directly as a Python function:
import rinexmod.rinexmod_api as rimo_api
rimo_api.rinexmod(rinexfile, outputfolder, sitelog=None, modif_kw=dict(), marker='',
country='', longname=False, force_rnx_load=False, force_sitelog=False,
ignore=False, ninecharfile=None, no_hatanaka=False, compression=None,
relative='', verbose=True, full_history=False, filename_style=False,
return_lists=None, station_info=None, lfile_apriori=None,
force_fake_coords=False):
"""
Parameters
----------
rinexfile : str
Input RINEX file to process.
outputfolder : str
Folder where to write the modified RINEX files.
sitelog : str, list of str, MetaData object, list of MetaData objects, optional
Get the RINEX header values from a sitelog.
Possible inputs are:
* list of string (sitelog file paths),
* single string (single sitelog file path or directory containing the sitelogs),
* list of MetaData object
* single MetaData object
The function will search for the latest and right sitelog
corresponding to the site.
One can force a single sitelog with force_sitelog.
The default is None.
modif_kw : dict, optional
Modification keywords for RINEX's header fields and/or filename.
Will override the information from the sitelog.
Acceptable keywords for the header fields:
* comment
* marker_name
* marker_number
* station (legacy alias for marker_name)
* receiver_serial
* receiver_type
* receiver_fw
* antenna_serial
* antenna_type
* antenna_X_pos
* antenna_Y_pos
* antenna_Z_pos
* antenna_H_delta
* antenna_E_delta
* antenna_N_delta
* operator
* agency
* sat_system (M, G, R, E, C...)
* observables (legacy alias for sat_system)
* interval
Acceptable keywords for the filename:
* filename_file_period (01H, 01D...)
* filename_data_freq (30S, 01S...)
* filename_data_source (R, S, U)
The default is dict().
marker : str, optional
A four or nine character site code that will be used to rename
input files.
Apply also to the header's MARKER NAME,
but a custom modification keyword marker_name='XXXX' overrides it
(modif_kw argument below)
The default is ''.
country : str, optional
A three character string corresponding to the ISO 3166 Country code
that will be used to rename input files.
It overrides other country code sources (sitelog, --marker...)
list of ISO country codes:
https://en.wikipedia.org/wiki/List_of_ISO_3166_country_codes
The default is ''.
longname : bool, optional
Rename file using long name RINEX convention (force gzip compression).
The default is False.
force_rnx_load : bool, optional
Force the loading of the input RINEX. Useful if its name is not standard.
The default is False.
force_sitelog : bool, optional
If a single sitelog is provided, force sitelog-based header
values when RINEX's header and sitelog site name do not correspond.
If several sitelogs are provided, skip badly-formated sitelogs.
The default is False.
ignore : bool, optional
Ignore firmware changes between instrumentation periods
when getting header values info from sitelogs. The default is False.
ninecharfile : str, optional
Path of a file that contains 9-char. site names from the M3G database.
The default is None.
no_hatanaka : bool, optional
Skip high-level RINEX-specific Hatanaka compression
(performed per default).
The default is False.
compression : str, optional
Set low-level RINEX file compression.
acceptable values : gz (recommended to fit IGS standards), 'Z', None.
The default is None.
relative : str, optional
Reconstruct files relative subfolders.
You have to indicate the common parent folder,
that will be replaced with the output folder. The default is ''.
verbose : bool, optional
set the level of verbosity
(False for the INFO level, True for the DEBUG level).
The default is True.
full_history : bool, optional
Add the full history of the station in
the RINEX's header as comment.
filename_style : str, optional
Set the RINEX filename style.
acceptable values : 'basic' (per default), 'flex', 'exact'.
* 'basic': a simple mode to apply a strict filename period (01H or 01D),
being compatible with the IGS conventions.
e.g.: `FNG000GLP_R_20242220000_01D_30S_MO.crx.gz`
* 'flex': the filename period is tolerant and corresponds to
the actual data content, but then can be odd (e.g. 07H, 14H...).
The filename start time is rounded to the hour.
e.g.: `FNG000GLP_R_20242221800_06H_30S_MO.crx.gz`
* 'exact': the filename start time is strictly the one of the
first epoch in the RINEX.
Useful for some specific cases needing splicing.
e.g.: `FNG000GLP_R_20242221829_06H_30S_MO.crx.gz`
The default is 'basic'.
return_lists : dict, optional
Specific option for file distribution through a GLASS node.
Store the rinexmoded RINEXs in a dictionary
to activates it, give a dict as input (an empty one - dict() works)
The default is None.
station_info: str, optional
Path of a GAMIT station.info file to obtain GNSS site
metadata information (needs also lfile_apriori option)
lfile_apriori: str, optional
Path of a GAMIT apriori apr/L-File to obtain GNSS site
position and DOMES information (needs also station_info option)
force_fake_coords: bool, optional
When using GAMIT station.info metadata without apriori coordinates
in the L-File, gives fake coordinates at (0°,0°) to the site
remove: bool, optional
Remove input RINEX file if the output RINEX is correctly written
The default is False.
Raises
------
RinexModInputArgsError
Something is wrong with the input arguments.
RinexFileError
Something is wrong with the input RINEX File.
Returns
-------
outputfile : str
the path of the rinexmoded RINEX
OR
return_lists : dict
a dictionary of rinexmoded RINEXs for GLASS distribution.
Extract metadata from crz file.
With -p option, will plot the file's samples intervals
EXAMPLE:
./crzmeta.py RINEXFILE (-p)
This script will get the last version of sitelogs from M3G repository and write them in an observatory dependent subfolder set in 'observatories'. The -d --delete option will delete the old version to get only the last version even in a name-changing case.
USE :
* OUTPUTFOLDER : Folder where to write the downloaded sitelogs.
OPTION :
* -d : delete : Delete old sitelogs in storage folder. This permits to have only the last version, as version changing sitelogs changes of name.
EXAMPLE:
./get_m3g_sitelogs.py OUTPUTFOLDER (-d)
rinexmod will prompt errors when arguments are wrong. Apart from this, it will prompt and save to file errors and waring occurring on specific files from the rinex list. Here are the error codes :
01 - The specified file does not exists
That means that the input file containing a list of rinex files is wrong and references a file that is not present. It can also mean that the file was deleted between the list generation and the script launch, but this case should be quite rare.
02 - Not an observation Rinex file
The file name does not correspond to the classic pattern (it doesn't match the regular expression for new and old convention naming model ). Most of time, it's because it is not a d rinex file (for example, navigation file).
03 - Invalid or empty Zip file
The Zip file is corrupted or empty
04 - Invalid Compressed Rinex file
The CRX Hatanaka file is corrupted.
05 - Less than two epochs in the file, reject
Not enought data in the file to extract a sample rate, and data not relevant because insufficient. Reject the file.
30 - Input and output folders are the same !
The file will not be proceeded as rinexmod does not modify files inplace. Check your outputfolder.
31 - The subfolder can not be reconstructed for file
The script tries to find the 'reconstruct' subfolder in the file's path to replace it with outputfolder, and does not find it.
32 - Station's country not retrevied, will not be properly renamed
When using --name option, that will rename file with rinex long name convention, it needs to retrieve the file's country. It tries to do so using an external file of list of 9 char ids. the concerned rinex file's station seems to be absent from this station list file.
33 - File\'s station does not correspond to provided sitelog - use -f option to force
The station name retrieved from the provided sitelog does not correspond to the station's name retrieved from the file's headers. Do not process.
34 - File's station does not correspond to provided sitelog, processing anyway
The station name retrieved from the provided sitelog does not correspond to the station's name retrieved from the file's headers. As the --force option was provided, the file has been processed.
35 - No instrumentation corresponding to the data period on the sitelog
There is no continuous instrumentation period in the sitelog taht corresponds to the rinex file's dates. We can thus not fill the header.
36 - Instrumentation cames from merged periods of sitelog with different firmwares, processing anyway
We provided the --ignore option, so the consecutive periods of instrumentation for witch only the firmware version of the receiver has changed have been merged. We used this period to fill this file's header.