The following README contains an overview about all analysis scripts used at the Conrad Observatory. A short description of each script is accompanied by dependencies and some typical schedules of the respective application. A detailed description of how the analysis scripts interact with MARTAS and MARCOS machines at the Conrad Observatory, and how different script are used for consecutive automatic data analysis is to be found in the README.md document of the MarcosScripts repository. While this "ANALYSIS" repository contains detailed descriptions and application examples of individual scripts, the "Marcos" repository README will focus on application examples for testing and production based an optimal usage of various different scripts.
| Script | Location | Schedule | Config | Monitor | Dependencies | Comments |
|---|---|---|---|---|---|---|
| magnetism_products.py | DataProducts | 5min | CONF/wic.cfg | MARTAS telegram | py2 and py3 | |
| weather_products.py | DataProducts | hourly | CONF/wic.cfg | MARTAS telegram | py2 and py3 | |
| getprimary.py | DataProducts | 5min | CONF/wic.cfg | MARTAS telegram | py2 and py3 | |
| flagging.py | DataProducts | 5min | CONF/wic.cfg | MARTAS telegram | py2 and py3 | |
| gamma_products.py | DataProducts | hourly | CONF/wic.cfg | MARTAS telegram | py2 and py3 | |
| magnetism_checkadj.py | DataProducts | daily | CONF/wic.cfg | MARTAS telegram | py2 and py3 | |
| baseline_generator.py | DataProducts | to daily | gam.cfg/swz.cfg | MARTAS telegram | py2 and py3 | |
| convert_data.py | DataProducts | hourly | wic.cfg | MARTAS telegram | py2 and py3 | |
| tg_pha.py | Info | analysis_20min | MARTAS telegram | |||
| tg_kval.py | Info | 5min | MARTAS telegram | |||
| tg_quake.py | Info | analysis_20min | MARTAS telegram | |||
| tg_base.py | Info | weekly | CONF/wic.cfg | MARTAS telegram | py3 | |
| logfiledate.py | Info | weekly | CONF/wic.cfg | MARTAS telegram | py2 ... py3 | |
| quakes_import.py | DataImport | CONF/wic.cfg | MARTAS telegram | py3 | ||
| dscovr_download_broker.py | DataImport | - | Logfile monitor | running on broker | ||
| gfzkp_download_broker.py | DataImport | - | Logfile monitor | running on broker | ||
| ace_conversion.py | DataImport | MARTAS telegram | ||||
| wbvimport.py | DataImport | MARTAS telegram | pandas, xlrd | py3 | ||
| mag_graph.py | TitleGraphs | analysis_20min | MARTAS telegram | |||
| weather_graph.py | TitleGraphs | analysis_20min | MARTAS telegram | |||
| general_graph.py | PeriodicGraphs | analysis_hourly | MARTAS telegram | py2 and py3 | ||
| tilt_graph.py | PeriodicGraphs | analysis_hourly | MARTAS telegram | |||
| supergrad_graph.py | PeriodicGraphs | analysis_hourly | MARTAS telegram | |||
| gamma_graph.py | PeriodicGraphs | analysis_hourly | MARTAS telegram | |||
| spaceweather_graph.p | PeriodicGraphs | analysis_hourly | MARTAS telegram | |||
| current_weatherchanges.py | PeriodicGraphs | analysis_hourly | MARTAS telegram | |||
| gamma.py | Projects/gamma/ | analysis_daily | MARTAS telegram | |||
| iono_analysis.py | Projects/ionit | analysis_monthly | MARTAS telegram | |||
| GeoelekTimeSeries.py | Projects/geoelectric/wenner_sgo/ | analysis_monthly | MARTAS telegram |
bash /home/cobs/ANALYSIS/DataProducts/GIC/cleanup_tempfiles.sh python /home/cobs/ANALYSIS/DataProducts/GIC/transfer_gic_anim.py python /home/cobs/ANALYSIS/DataProducts/StormDetection/StormDetector_graph.py python /home/cobs/ANALYSIS/DataProducts/gicpred/predict_GICs.py LASTGICFILE=$(ls -t /home/cobs/ANALYSIS/DataProducts/GIC/tempfiles/gicfiles/ | head -1) (cd /home/cobs/ANALYSIS/DataProducts/GIC && python src/gic_dailyplot.py -f $LASTGICFILE -m db -t station >> $TLOG 2>&1)
The folder DataProducts contains scripts which aim on the production of data sets to be published and distributed. Basically the scripts read raw data contents from sensors. Then they apply flagging and filtering routines, combine data sets from different sensors, add meta information from the database and finally export the data sets into specific formats.
DESCRIPTION Checks all variometers and scalar sensors as defined in a configuration file. The first instrument in the list, which fulfills criteria on data availablility will be selected as primary instrument. Both primary instruments will be stored within a current.data json structure.
PREREQUISITES The following packegas are required: geomagpy >= 0.9.8 martas.martaslog martas.acquisitionsupport analysismethods
PARAMETERS -c configurationfile : file : too be read from GetConf2 (martas)
OUTPUT writes to current data into the data file 'current data' as defined in the configuration file
APPLICATION PERMANENTLY with cron: python getprimary.py -c /etc/marcos/analysis.cfg
DESCRIPTION This method can be used to flag data regularly, to clean up the existing falgging database, to upload new flags from files and to archive "old" flags into json file structures.
PREREQUISITES The following packegas are required: geomagpy >= 0.9.8 martas.martaslog martas.acquisitionsupport analysismethods
The upload method also works for pkl (pickle) files. However, a successful upload requires that the upload is performed with the same major python version as used for pkl creation.
PARAMETERS
| Option | Name | Type | Description |
|---|---|---|---|
| flagdict | dict | currently hardcoded into the method. Looks like { SensorNamePart : [timerange, keys, threshold, window, markall, lowlimit, highlimit]} | |
| -c | configurationfile | file | too be read from GetConf2 (martas) |
| -j | joblist | list | jobs to be performed - default "flag" (flag, clean, uploud, archive) |
| -e | endtime | date | date until analysis is performed - default "datetime.utcnow()" |
| -p | path | string | upload - path to upload directory |
| -s | sensor | string | delete - sensor of which data is deleted |
| -o | comment | string | delete - flag comment for data sets to be deleted |
OUTPUT write flags - to database etc
APPLICATION PERMANENT with cron: python flagging.py -c /etc/marcos/analysis.cfg YEARLY with cron: python flagging.py -c /etc/marcos/analysis.cfg -j archive DAILY with cron: python flagging.py -c /etc/marcos/analysis.cfg -j upload,clean -p /srv/archive/flags/uploads/ REDO: python flagging.py -c /etc/marcos/analysis.cfg -e 2020-11-22
DESCRIPTION Creates magnetism products and graphs. The new version is making use of a configuration file. magneism_products.py creates adjusted data files and if a certain time condition as defined in the configuration file is met, then quasidefinitive data is produced as well, provided actual flagging information is available. Date files are stored in the archive directory and uploaded to all connected databases. Besides adjusted and quasidefinitive data, k-values and a general two-day variation graph is created.
PREREQUISITES The following packegas are required: geomagpy >= 0.9.8 martas.martaslog martas.acquisitionsupport analysismethods
PARAMETERS -c configurationfile : file : too be read from GetConf2 (martas) -j joblist : string : comma separated list like adjusted,quasidefinitive,addon -l loggername : string : name for the loggerfile -e endtime : date : date until analysis is performed, default "datetime.utcnow()"
OUTPUT
APPLICATION PERMANENTLY with cron: python magnetism_products.py -c /etc/marcos/analysis.cfg REDO analysis for a time range: (startime is defined by endtime - daystodeal as given in the config file python magnetism_products.py -c /etc/marcos/analysis.cfg -e 2020-11-22
DESCRIPTION Analyses environmental data from various different sensors providing weather information. Sources are RCS raw data, RCS analyzed meteo data, ultrasonic, LNM and BM35 pressure. Creates a general METEO table called METEOSGO_adjusted, by applying various flagging methods and synop codes (LNM). Additionally, a short term current condition table is created (30min mean), two day and one year plots are generated. Beside, different measurements are compared for similarity (e.g. rain from bucket and lnm)
PREREQUISITES The following packegas are required: geomagpy >= 0.9.8 martas.martaslog martas.acquisitionsupport analysismethods
PARAMETERS -c configurationfile : file : too be read from GetConf2 (martas) -e endtime : date : date until analysis is performed default "datetime.utcnow()"
APPLICATION PERMANENTLY with cron: python weather_products.py -c /etc/marcos/analysis.cfg REDO analysis for a time range: (startime is defined by endtime - daystodeal as given in the config file python weather_products.py -c /etc/marcos/analysis.cfg -e 2020-11-22
DESCRIPTION Analyses gamma measurements. Sources are SCA gamma and METEO data. Created standard project tables and a Webservice table version.
PREREQUISITES The following packegas are required: geomagpy >= 0.9.8 martas.martaslog martas.acquisitionsupport analysismethods
PARAMETERS -c configurationfile : file : too be read from GetConf2 (martas) -e endtime : date : date until analysis is performed default "datetime.utcnow()"
APPLICATION PERMANENTLY with cron: python gamma_products.py -c /etc/marcos/analysis.cfg REDO analysis for a time range: (startime is defined by endtime - daystodeal as given in the config file python gamma_products.py -c /etc/marcos/analysis.cfg -e 2020-11-22
DESCRIPTION Compares adjusted data sets from all sensors for similarity. If not similar then a waring is send out. The same comparison is done for all F sensors using the offsets contained in the database.
PREREQUISITES The following packegas are required: geomagpy >= 0.9.8 martas.martaslog martas.acquisitionsupport analysismethods
PARAMETERS -c configurationfile : file : too be read from GetConf2 (martas) -j joblist : list : vario,scalar -e endtime : date : date until analysis is performed default "datetime.utcnow()"
APPLICATION PERMANENTLY with cron: python magnetism_checkadj.py -c /etc/marcos/analysis.cfg REDO analysis for a time range: (startime is defined by endtime - daystodeal as given in the config file python magnetism_checkadj.py -c /etc/marcos/analysis.cfg -e 2020-11-22
DESCRIPTION Create a BLV file from expected field values D,I,F. If no field values are provided then IGRF values will be obtained for the StationLocation from the obscode provided in the confguration file. Make sure that no current.data path is defined for stations. The application will calculate basevalues for the primary variometer as definied in the configuration and create a BLV outfile within the defined dipath (conf).
PREREQUISITES The following packegas are required: geomagpy >= 0.9.8 martas.martaslog martas.acquisitionsupport analysismethods
PARAMETERS -c configurationfile : file : too be read from GetConf2 (martas) -v vector : int : only provided for testing, obtaining IGRF value otherwise -t time : string : default is 1. of month, at least after the fifth day (so that data should be present)
APPLICATION Runtime: python3 baseline_generator.py -c ../conf/gam.cfg Testing: python3 baseline_generator.py -c ../conf/gam.cfg -t 2018-08-08T07:41:00 -v 64.33397725500629,4.302646668706179,48621.993688723036 -D
DESCRIPTION Converts data from a database to any specified data format. Unlike mpconvert it automatically chooses the best match containing the given sensor name fragment
PREREQUISITES The following packegas are required: geomagpy >= 0.9.8 martas.martaslog martas.acquisitionsupport analysismethods
PARAMETERS -c configurationfile : file : too be read from GetConf2 (martas)
APPLICATION PERMANENTLY with cron: python3 convert_data.py -c ~/CONF/wic.cfg -s BM35 -o /srv/products/data/meteo/pressure/
The folder TitleGraphs contains scripts to generate and assemble graphs for the homepage, particualry graphs with mixtures from fotos and real time data.
DESCRIPTION Script to check the creation date of the latest file matching a certain structure in a defined directory
PREREQUISITES The following packegas are required: geomagpy >= 0.9.8 martas.martaslog martas.acquisitionsupport analysismethods
PARAMETERS -c configurationfile : file : too be read from GetConf2 (martas) -p path : string : directory path to be investigated -s structure : string : match of filename structure like "*.json" or "A16.txt". Default is "" -a age : number : tolerated age (integer). Default is 1 -i iterate : string : increment of age (day, hour, minute, second). Default is day -l logger : string : name of the logger
APPLICATION Check whether most recent upload happend in the last 24 hours: python3 logfiledates.py -c /etc/marcos/analysis.cfg -p /srv/archive/flags/uploads/ -a 1 -i day') Checking for most recent succsessful AutoDIF analysis: python3 logfiledates.py -c /etc/marcos/analysis.cfg -p /srv/archive/DI/raw/ -a 1 -i day')
DESCRIPTION Creates plots for a specific sensor. PREREQUISITES The following packegas are required: geomagpy >= 0.9.8 martas.martaslog martas.acquisitionsupport analysismethods PARAMETERS -c configurationfile : file : too be read from GetConf2 (martas) -r range : int : default 2 (days) -s sensor : string : sensor or dataid -k keys : string : comma separated list of keys to be plotted -f flags : string : flags from other lists e.g. quakes, coil, etc -y style : string : plot style -l loggername : string : loggername e.g. mm-pp-tilt.log -e endtime : string : endtime (plots from endtime-range to endtime)
APPLICATION PERMANENTLY with cron: python webpage_graph.py -c /etc/marcos/analysis.cfg SensorID: python3 general_graph.py -c ../conf/wic.cfg -e 2019-01-15 -s GP20S3NSS2_012201_0001 -D DataID: python3 general_graph.py -c ../conf/wic.cfg -e 2019-01-15 -s GP20S3NSS2_012201_0001_0001 -D
Reads Kp activity indicies from Geoforschungszentrum Potsdam (GFZ) using MagPy and stores this data as CDF files.
IMPORTANT: This script is running on the data broker. CDF files are then transferred to primary and secondary servers using "file_download" routines running on the specific server.
MONITORING: This output of the script should be written to a log file. Using "monitor.py" from MARTAS, the log file can be tested for SUCCESS messages.
IMPORTANT: This script is running on the data broker. CDF files are then transferred to primary and secondary servers using "file_download" routines running on the specific server.
MONITORING: This output of the script should be written to a log file. Using "monitor.py" from MARTAS, the log file can be tested for SUCCESS messages.
Please note: This script needs to access the internet (and not the BROKER)
DESCRIPTION Downloads Earthquake data from two online sources: AT: austrian seismological service NEIC: National earthquake information center (US) PREREQUISITES The following packegas are required: geomagpy >= 0.9.8 martas.martaslog martas.acquisitionsupport analysismethods PARAMETERS -c configurationfile : file : too be read from GetConf2 (martas) -p path : string : path where to temporarly save the neic raw data
APPLICATION PERMANENTLY with cron: python3 python quakes_import.py -c /home/user/CONF/wic.cfg -p /srv/archive/external/neic/neic_quakes.d
Please note: This script makes use of a configuration file in ~/CONF It can be run however also in standalone mode by providing all necessary options. If options are provided together with cfg data, options will override configuration data.
DESCRIPTION Import raw data from csv and excel files provided for warmbad villach measurements. Imported data will be written to provided databases and/or as files within the selected directory. A subdirectory consitisting of DataID/data.cdf will be established. If file output is selected a MagPy PYCDF structure will be established.
PREREQUISITES The following packages are required: pandas xlrd geomagpy >= 1.1.6 martas.martaslog martas.acquisitionsupport analysismethods APPLICATION python3 wbvimport.py -h python3 wbvimport.py -c /home/cobs/CONF/wbv.cfg -b 2023-04-01 -D COMMENTS The script joins excel and csv data (exl is only used if no csv data is present) Corrections i.e. in 2017 are hardcoded and need to be cited in the database
'''
MAILTO=""
PYTHON=/usr/bin/python3 HOME=/home/cobs LOGPATH=/var/log/magpy
#1,11,21,31,41,51 * * * * /home/cobs/MARTAS/app/threshold.py -m /etc/martas/threshold.cfg
#30 * * * * /home/cobs/MARTAS/app/monitor.py -c /etc/martas/monitor.cfg
9,19,29,39,49,59 * * * * $PYTHON /home/cobs/ANALYSIS/DataProducts/getprimary.py -c /home/cobs/CONF/wic.cfg > $LOGPATH/cron-dp-getprimary 2>&1
8,18,28,38,48,58 * * * * $PYTHON /home/cobs/ANALYSIS/DataProducts/flagging.py -c /home/cobs/CONF/wic.cfg -j flag > $LOGPATH/cron-dp-flagging 2>&1
*/10 * * * * $PYTHON /home/cobs/ANALYSIS/DataProducts/magnetism_products.py -c /home/cobs/CONF/wic.cfg > $LOGPATH/cron-dp-magprod 2>&1
4,14,24,34,44,54 * * * * $PYTHON /home/cobs/ANALYSIS/Info/tg_kval.py > $LOGPATH/cron-info-kval 2>&1
5,15,25,35,45,55 * * * * rsync -avz -e ssh find /srv/products/data/magnetism/variation/sec/ -type f -mtime -1 [email protected]:/home/cobs/SPACE/data/WICsec_v/
5,15,25,35,45,55 * * * * rsync -avz -e ssh find /srv/products/data/magnetism/variation/min/ -type f -mtime -1 [email protected]:/home/cobs/SPACE/data/WICmin_v/
5,15,25,35,45,55 * * * * rsync -avz -e ssh find /srv/products/data/magnetism/quasidefinitive/min/ -type f -mtime -5 [email protected]:/home/cobs/SPACE/data/WICmin_qd/
5,15,25,35,45,55 * * * * rsync -avz -e ssh find /srv/products/data/magnetism/quasidefinitive/sec/ -type f -mtime -5 [email protected]:/home/cobs/SPACE/data/WICsec_qd/
1,21,41 * * * * $PYTHON /home/cobs/ANALYSIS/DataImport/quakes_import.py -c /home/cobs/CONF/wic.cfg -p /srv/archive/external/neic/neic_quakes.d 2,22,42 * * * * $PYTHON /home/cobs/ANALYSIS/Info/tg_quake.py -c /home/cobs/CONF/wic.cfg
#24 * * * * $PYTHON /home/cobs/ANALYSIS/TitleGraphs/mag_graph.py >> $TLOG 2>&1 #24 * * * * $PYTHON /home/cobs/ANALYSIS/TitleGraphs/weather_graph.py >> $TLOG 2>&1 #25 * * * * $PYTHON /home/cobs/ANALYSIS/PeriodicGraphs/tilt_graph.py >> $TLOG 2>&1 #25 * * * * $PYTHON /home/cobs/ANALYSIS/PeriodicGraphs/supergrad_graph.py >> $TLOG 2>&1 #26 * * * * $PYTHON /home/cobs/ANALYSIS/PeriodicGraphs/gamma_graph.py >> $TLOG 2>&1 #26 * * * * $PYTHON /home/cobs/ANALYSIS/PeriodicGraphs/spaceweather_graph.py >> $TLOG 2>&1 #27 * * * * $PYTHON /home/cobs/ANALYSIS/PeriodicGraphs/current_weatherchanges.py >> $TLOG 2>&1 27 * * * * $PYTHON /home/cobs/ANALYSIS/Info/tg_pha.py -c /home/cobs/CONF/wic.cfg > $LOGPATH/cron-info-pha 2>&1 28 * * * * $PYTHON /home/cobs/ANALYSIS/DataProducts/weather_products.py -c /home/cobs/CONF/wic.cfg > $LOGPATH/cron-dp-weathprod 2>&1 29 * * * * $PYTHON /home/cobs/ANALYSIS/DataProducts/gamma_products.py -c /home/cobs/CONF/wic.cfg > $LOGPATH/cron-dp-gamprod 2>&1 34 * * * * $PYTHON /home/cobs/ANALYSIS/DataProducts/convert_data.py -c /home/cobs/CONF/wic.cfg -s BM35 -o /srv/products/data/meteo/pressure/ > $LOGPATH/cron-dp-convertbm35 2>&1
34 * * * * rsync -avz -e ssh find /srv/archive/SGO/RCST7_20160114_0001/raw/ -type f -mtime -5 [email protected]:/home/cobs/SPACE/data/rcst7/
34 * * * * rsync -avz -e ssh find /srv/archive/SGO/RCSG0_20160114_0001/raw/ -type f -mtime -5 [email protected]:/home/cobs/SPACE/data/rcsg0/
34 * * * * rsync -avz -e ssh find /srv/archive/SGO/GAMMA_SFB867_0001/raw/ -type f -mtime -5 [email protected]:/home/cobs/SPACE/data/gamma/
35 * * * * rsync -avz -e ssh find /srv/archive/SGO/LM_TILT01_0001/raw/ -type f -mtime -5 [email protected]:/home/cobs/SPACE/data/tilt/
36 * * * * rsync -avz -e ssh find /srv/archive/SGO/LNM_0351_0001/raw/ -type f -mtime -5 [email protected]:/home/cobs/SPACE/data/lnm/
37 * * * * rsync -avz -e ssh find /srv/products/data/meteo/pressure/ -type f -mtime -5 [email protected]:/home/cobs/SPACE/data/bm35/
#1 2 * * * $PYTHON /home/cobs/ANALYSIS/DataProducts/magnetism_checkadj.py -c /home/cobs/CONF/wic.cfg #$PYTHONPATH /home/cobs/ANALYSIS/Projects/gamma/gamma.py -p /srv/projects/gamma/ -m /home/cobs/ANALYSIS/Projects/gamma/mygamma.cfg -d /srv/projects/gamma/ >> $TLOG 2>&1 #15 2 * * * $PYTHON /home/cobs/ANALYSIS/DataProducts/flagging.py -c /home/cobs/CONF/wic.cfg -j upload,clean -p /srv/archive/flags/uploads/ > $LOGPATH/cron-dp-flagdaily 2>&1
#$PYTHONPATH /home/cobs/ANALYSIS/DataProducts/logfiledates.py -c /home/cobs/CONF/wic.cfg -p /srv/archive/WIC/DI/raw/ -s "*A16_WIC.txt" -a 2 -i day -l autodif >> $TLOG
15 2 * * * rsync -avz -e ssh find /srv/archive/SGO/BGSINDCOIL_1_0001/raw/ -type f -mtime -3 [email protected]:/home/cobs/SPACE/data/induction/
15 12 * * 2 $PYTHON /home/cobs/ANALYSIS/Info/tg_base.py -c /home/cobs/CONF/wic.cfg -t /etc/martas/telegram.cfg
baseline generator schwaz: offsets determined as average of 2020-08-04 and 2020-08-06 - valid from 08-2019 until 18-07-2021
#0 3 7 * * $PYTHON $HOME/ANALYSIS/DataProducts/baseline_generator.py -c $HOME/CONF/swz.cfg -t date -d "$D" "+\%Y"-date -d "$D" "+\%m"-01T03:00:00 -o I:-0.00778,D:0.04308 -l mm-basegen-swz.log > /var/log/magpy/cron-baseline-swz.log 2>&1
0 3 7 * * $PYTHON $HOME/ANALYSIS/DataProducts/baseline_generator.py -c $HOME/CONF/swz.cfg -t date -d "$D" "+\%Y"-date -d "$D" "+\%m"-01T03:00:00 -l mm-basegen-swz.log > /var/log/magpy/cron-baseline-swz.log 2>&1
#30 2 1 2 * $PYTHON /home/cobs/ANALYSIS/DataProducts/flagging.py -c /home/cobs/CONF/wic.cfg -j archive > $LOGPATH/cron-db-flagarchive 2>&1 '''