The function converts Omnirecs/Digos Datacube files to mseed or sac files and organises these in a coherent directory structure (see details) for available structures. The conversion depends on the gipptools software package (see details) provided externally.
aux_organisecubefiles(
station,
input,
output,
gipptools,
format = "sac",
pattern = "eseis",
component = "BH",
mode = "dir-wise",
fringe = "constant",
cpu,
verbose = TRUE
)A set of converted and organised seismic files written to disk.
data frame with seismic station information
See aux_stationinfofile. This data frame can also be provided
manually, in which case it must contain two elements: a first vector that
contains the Cube IDs, and a second that contains the corresponding
station IDs that will be used in the meta info and file names. If the
argument is omitted, the Cube IDs will be used as station IDs.
Character value, path to directory where the Cube
files to be processed are stored.
Character value, path to directory where output
data is written to.
Character value, path to gipptools or cubetools
directory.
Character value, output file format. One out of
"mseed" and "sac". Default is "sac".
Character value, file organisation scheme keyword.
One out of "eseis" and "seiscomp". Default is "eseis".
See details and read_data for further information.
Character vector, component code and output file
extension prefix. It is assumed that this prefix comprises two characters,
the first describing the band code, the second the instrument code. See
details for further information. Default is "BH", hence broadband
and high gain sensor. The spatial component ("E", "N", "Z") will be added
automatically. See details for a tabular overview of common band codes and
instrument codes.
Character value, mode of file conversion. One out of
"file-wise" and "dir-wise". Default is "file-wise".
See details for further important information.
Character value, option to handle data outside the
GPS-tagged time span. One out of "skip", "nominal" or
"constant". Default is "constant".
Numeric value, fraction of CPUs to use for parallel
processing. If omitted, one CPU is used.
Logical value, option to enable extended screen
output of cubetools operations. Default is FALSE. This option
might not work with Windows operating systems.
Michael Dietze
The function converts seismic data from the binary cube file format to
mseed (cf. read_mseed) or sac (cf. read_sac) and organises
the resulting files into a consistent structure, expected by 'eseis' for
convenient data handling (cf. read_data).
Currently, there are two data structure schemes supported, "eseis"
and "seiscomp". In the "eseis" case, the daily cube files are
cut to hourly files and organised in directories structured by four digit
year and three digit Julian day numbers. In each Julian day directory, the
hourly files are placed and named after the following scheme:
STATION.YEAR.JULIANDAY.HOUR.MINUTE.SECOND.COMPONENT.
The "seiscomp" case will yield daily files, which are organised by
four digit year, seismic network, seismic station, and seismic component,
each building a separate directory. In the deepest subdirectory, files are
named by: NETWORK.STATION.LOCATION.COMPONENT.TYPE.YEAR.JULIANDAY.
The component naming scheme defines the codes for the sensor's band
code (first letter) and instrument code (second letter). The third letter,
defining the spatial component, will be added automatically. For definitions
of channel codes see https://migg-ntu.github.io/SeisTomo_Tutorials/seismology/seismic-data/seismic-time-series-data.html.
The function requires that the software gipptools
(http://www.gfz-potsdam.de/en/section/geophysical-deep-sounding/infrastructure/geophysical-instrument-pool-potsdam-gipp/software/gipptools/)
is installed. Note that the gipptools are provided at regular update
intervals, including an up to date GPS leap second table, essential to
convert recently recorded files.
The Cube files will be imported in place but a series of temporary files
will be created in a temporary directory in the specified output directory.
Hence, if the routine stops due to a processing issue, one needs to delete
the temporary data manually. The path to the temporary directory will be
provided as screen output when the argument verbose = TRUE.
The Cube files can be converted in two modes: "file-wise" and
"dir-wise". In "file-wise" mode, each Cube file will be
converted individually. This option has the advantage that if one file in
a month-long sequence of records is corrupt, the conversion will not stop,
but only discard the part from the corrupted section until the file end.
The disadvantage is however, that the data before the first and after
the last GPS tags will not be converted unless the option
fringe = "constant" (by default this is the case) is used.
In "dir-wise" mode, the fringe sample issue reduces to the margins of
the total sequence of daily files but the corrupt file issue will become a
more severe danger to the success when converting a large number of files.
Specifying an input directory (input) is mandatory. That
directory should only contain the directories with the cube files to
process. Files downloaded from a Cube are usually contained in one or more
further directories, which should be moved into a single one before
running this function.
Each set of cube files from a given logger should be located in a separate
directory per logger and these directories should have the same name as
the logger IDs (logger_ID). An appropriate structure for files from
two loggers, A1A and A1B, would be something like:
input
A1A
file1.A1A
file2.A1A
A1B
file1.A1B
file2.A1B
The component definition can follow the typical keywords and key letters
defined in seismology: https://migg-ntu.github.io/SeisTomo_Tutorials/seismology/seismic-data/seismic-time-series-data.html,
hence the first letter indicating the instrument's band type and the second
letter indicating the instrument code or instrument type.
| Band code | Explanation band type |
| E | Extremely short period |
| S | Short period |
| H | High broad band |
| B | Broad band |
| M | Mid band |
| L | Long band |
| V | Very long band |
| Instrument code | Explanation |
| H | High gain seismometer |
| L | Low gain seismometer |
| G | Gravimeter |
| M | Mass position seismometer |
| N | Accelerometer |
| P | Geophone |
if (FALSE) {
## basic example with minimum effort
aux_organisecubefiles(stationfile = data.frame(logger = c("A1A", "A1B"),
station = c("ST1", "ST2")),
input = "input",
gipptools = "software/gipptools-2023.352")
}
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