The simplest usage exports all data for GCDIR (/data/site-instrument). It uses the gcwerks-report.conf and peak.list files in the config directory:
gcexport GCDIR
A custom report.conf and peak.list may be used:
gcexport GCDIR -format report.conf -peaklist peak.list
Instead of report.conf, the fields to export may be specified on the command-line:
gcexport GCDIR time type port co2_C n2o_C
Here exporting data for run type air on inlet port 1:
gcexport GCDIR -type air -port 1 -format report.conf -peaklist peak.list
gcexport options
- -format report.conf: use report.conf to define the fields to export rather than the default config/gcwerks-report.conf file. If this is not specified, fields to export may be specified on the command-line.
- -peaklist peak.list: use peak.list for species to export instead of config/peak.list.
- -csv: export as comma-separated values and values reported with on more decimal place (note: -csv implies -noflags)
- -noheader: export data without a header
- -headerfile filename.txt: uses the contents of filename.txt as an additional header
These options select data to be reported (by date range, run type, standard tank, etc.).
- -type type: match run type
- -tank tank: match first part of tank name (e.g. “-tank -J”)
- -stdtank tank: match first part of standard tank name
- -port N: match port number
- -mean N: select N-minute mean for CRDS data (N=1,5,20,60)
- -mindate yymmdd: starting date (may be yymmdd.hhmm)
- -maxdate yymmdd: ending date
These options affect how missing or flagged data are reported.
- -skipmissing: Do not report fields not in the database. Normally fields which are not in the database are reported as a column containg all NaNs (for fixed format).
- -nanvalue -999: report this value instead of NaN
- -noflags: Prevents display of flags and flagged values are reported as NaN.
report.conf and peak.list example
The default config/gcwerks-report.conf file contains the default export (or GCWerks report) format. It also contains a complete commented list of possible fields to export. This file may be copied to a local directory to create a custom report.conf file.
Example report.conf:
#name flag format csv_format #---------- ---------- ------ ---------- time - 4 2 type tank # %s_C %s_flag 9.2 %s_stdev %s_N
Only the first column is required in the report.conf file. The two format columns over-ride the default format for each field.
Example peak.list:
co2 n2o
Using the above report.conf and peak.list would results in exported columns:
time type tank co2_C co2_stdev co2_N n2o_C n2o_stdev n2o_N
Flags and -noflags
If a field has a flag associated (%s_C %s_flag above), the flag is displayed after the value:
123.456F - flag = 'F' (flagged value) 123.456* - flag = '*' (filtered value)
Time formats
The following time format numbers may be used in the report.conf file.
- 1: yyyy-mm-dd hh:mm
- 2: yyyy-mm-dd hh:mm:ss
- 3: yymmdd hhmm
- 4: yymmdd hhmmss
- 5: yyyy mm dd hh mm
- 6: yyyy mm dd hh mm ss
- 7: yyyy.ffffff (year and fractional year)