MagPy (or GeomagPy) is a Python package for analysing and displaying geomagnetic data.
Version Info: (please note: this package is still in a development state with frequent modifcations) please check the release notes.
MagPy provides tools for geomagnetic data analysis with special focus on typical data processing routines in observatories. MagPy provides methods for data format conversion, plotting and mathematical procedures with specifically geomagnetic analysis routines such as basevalue and baseline calculation and database handling. Among the supported data formats are ImagCDF, IAGA-02, WDC, IMF, IAF, BLV, and many more. Full installation also provides a graphical user interface, xmagpy.
Typical usage for reading and visualising data looks like this:
#!/usr/bin/env python
from magpy.stream import read
import magpy.mpplot as mp
stream = read(path_or_url='filename')
mp.plot(stream)
Below you will find a quick guide to usage of the MagPy package. The quickest approach can be accomplished when skipping everything except the tutorials.
1.1.1 Install NASA CDF support
- enables CDF support for formats like ImagCDF
- package details and files at http://cdf.gsfc.nasa.gov/
- download and install a recent version of CDF e.g. cdf36_2_1-setup-32.exe
- find the MagPy Windows installer here (under Downloads): http://www.conrad-observatory.at
- download and execute magpy-0.x.x.exe
- all required packages are included in the installer
-
MagPy should have a sub-folder in the Start menu. Here you will find two items:
* python -> opens a python shell ready for MagPy * xmagpy -> opens the MagPy graphical user interface
Note: NASA CDF and SpacePy only support 32 bit.
1.2.1 Install Anaconda on your operating system
- download files from https://www.continuum.io/Downloads (tested with Anaconda2 for Python 2.7)
- see https://docs.continuum.io/anaconda/install for more details
- http://cdf.gsfc.nasa.gov/
- download and install the latest cdf version for your operating system
- open the anaconda prompt or change to the anaconda2/bin directory (if not set as default)
- run './pip install spacepy'
- ... known issues: installation of spacepy eventually requires a fortran compiler
- run './pip install geomagpy'
- ...possible issues: MySQL-python problem -> install libmysqlclient-dev on linux (e.g. debian/ubuntu: sudo apt-get install libmysqlclient-dev)
-
please note that anaconda provides a full python environment with many packages not used by MagPy
-
for a "slim" installation follow the "from scratch" instructions below (for experienced users)
-
for upgrades: run './pip install geomagpy --upgrade'. Installation provides both shell based magpy and the graphical user interface xmagpy
* type "python" -> opens a python shell ready for MagPy * type "xmagpy" in a shell -> open the graphical user interface of MagPy -
adding a shortcut for xmagpy: coming soon
1.3.1 Install MacPorts
1.4.1 Install Docker (toolbox) on your operating system
- https://docs.docker.com/engine/installation/
- open a docker shell
>>> docker pull geomagpy/magpy:latest
>>> docker run -d --name magpy -p 8000:8000 geomagpy/magpy:latest
- open address http://localhost:8000 (or http://"IP of your VM":8000)
- NEW: first time access might require a token or passwd
>>> docker logs magpy
will show the token
- run python shell (not conda)
- in python shell
>>> %matplotlib inline
>>> from magpy.stream import read
>>> ...
Requirements:
- Python 2.7,3.x (xmagpy will only work with python 2.7)
Recommended:
-
Python packages:
- NasaCDF
- SpacePy
- pexpect (for SSH support)
-
Other useful Software:
- MySQL (database features)
- NetCDF4 (support is currently in preparation)
- Webserver (e.g. Apache2, PHP)
A) Get python packages and other extensions (for other distros than debian/ubuntu install similar packages):
sudo apt-get install python-numpy python-scipy python-matplotlib python-nose python-wxgtk2.8 python-wxtools python-dev build-essential python-networkx python-h5py python-f2py gfortran ncurses-dev libhdf5-serial-dev hdf5-tools libnetcdf-dev python-netcdf python-serial python-twisted owfs python-ow python-setuptools git-core mysql-server python-mysqldb libmysqlclient-dev
sudo pip install ffnet
sudo pip install pexpect
sudo pip install pyproj
B) Get CDF and Omni database support:
a) CDF (NASA): http://cdf.gsfc.nasa.gov/html/sw_and_docs.html (tested with 3.6.1.0, please check validity of commands below to make command for any future versions)
tar -zxvf cdf36_1-dist-all.tar.gz
cd cdf36*
make OS=linux ENV=gnu CURSES=yes FORTRAN=no UCOPTIONS=-O2 SHARED=yes all
sudo make INSTALLDIR=/usr/local/cdf install
b) SpacePy (Los Alamos): https://sourceforge.net/projects/spacepy/files/spacepy/ (tested with 0.1.6)
sudo pip install spacepy
C) Install MagPy
a) Using pip
sudo pip install GeomagPy
* specific version:
sudo pip install GeomagPy==v0.3.9
b) Using github (latest development versions)
git clone git://github.com/GeomagPy/MagPy.git
cd MagPy*
sudo python setup.py install
Tested on XP, Win7, Win10
a) Get a current version of Python(x,y) and install it
optionally select packages ffnet and netcdf during install - for cdf support
b) Download nasaCDF packages and install (see links above)
c) get python-spacepy package
d) download and unpack GeomagPy-x.x.x.tar.gz
e) open a command window
f) go to the unpacked directory e.g. cd c:\user\Downloads\GeomagPy
g) execute "setup.py install"
written by R. Leonhardt, R. Bailey (April 2017)
Start python. Import all stream methods and classes using:
from magpy.stream import *
Please note that this import will shadow any already existing read method.
MagPy supports the following data formats and thus conversions between them:
- WDC: World Data Centre format
- JSON: JavaScript Object Notation
- IMF: Intermagnet Format
- IAF: Intermagnet Archive Format
- NEIC: WGET data from USGS - NEIC
- IAGA: IAGA 2002 text format
- IMAGCDF: Intermagnet CDF Format
- GFZKP: GeoForschungsZentrum KP-Index format
- GSM19/GSM90: Output formats from GSM magnetometers
- POS1: POS-1 binary output
- BLV: Baseline format Intermagnet
- IYFV: Yearly mean format Intermagnet
... and many others. To get a full list, use:
from magpy.stream import *
print(PYMAG_SUPPORTED_FORMATS)
You will find several example files provided with MagPy. The cdf file is stored along with meta information in NASA's common data format (cdf). Reading this file requires a working installation of Spacepy cdf.
If you do not have any geomagnetic data file you can access example data by using the following command (after import *):
data = read(example1)
The data from example1 has been read into a MagPy DataStream (or stream) object. Most data processing routines in MagPy are applied to data streams.
Several example data sets are provided within the MagPy package:
example1: INTERMAGNET CDF (ImagCDF) file with 1 second xyzf dataexample2: INTERMAGNET Archive format (IAF) file for one month with 1 min, 1 hour, K and mean dataexample3: MagPy readable DI data file with data from 1 single DI measurementexample4: MagPy Basevalue file (PYSTR) with analysis results of several DI data
For a file in the same directory:
data = read(r'myfile.min')
... or for specific paths in Linux:
data = read(r'/path/to/file/myfile.min')
... or for specific paths in Windows:
data = read(r'c:\path\to\file\myfile.min')
Pathnames are related to your operating system. In this guide we will assume a Linux system. Files that are read in are uploaded to the memory and each data column (or piece of header information) is assigned to an internal variable (key). To get a quick overview of the assigned keys in any given stream (data) you can use the following method:
print(data._get_key_headers() )
After loading data from a file, we can save the data in the standard IAGA02 and IMAGCDF formats with the following commands.
To create an IAGA-02 format file, use:
data.write(r'/path/to/diretory/',format_type='IAGA')
To create an INTERMAGNET CDF (ImagCDF) file:
data.write(r'/path/to/diretory/',format_type='IMAGCDF')
The filename will be created automatically according to the defined format. By default, daily files are created and the date is added to the filename in-between the optional parameters filenamebegins and filenameends. If filenameends is missing, .txt is used as default.
To read all local files ending with .min within a directory (creates a single stream of all data):
data = read(r'/path/to/file/*.min')
Getting magnetic data directly from an online source such as the WDC:
data = read(r'ftp://thewellknownaddress/single_year/2011/fur2011.wdc')
Getting kp data from the GFZ Potsdam:
data = read(r'http://www-app3.gfz-potsdam.de/kp_index/qlyymm.tab')
(Please note: data access and usage is subjected to the terms and conditions of the individual data provider. Please make sure to read them before accessing any of these products.)
No format specifications are required for reading. If MagPy can handle the format, it will be automatically recognized.
Getting data for a specific time window for local files:
data = read(r'/path/to/files/*.min',starttime="2014-01-01", endtime="2014-05-01")
... and remote files:
data = read(r'ftp://address/fur2013.wdc',starttime="2013-01-01", endtime="2013-02-01")
Reading data from the INTERMAGNET Webservice (starting soon):
data = read('http://www.intermagnet.org/test/ws/?id=WIC')
The stream can be trimmed to a specific time interval after reading by applying the trim method, e.g. for a specific month:
data = data.trim(starttime="2013-01-01", endtime="2013-02-01")
Information on individual methods and options can be obtained as follows:
For basic functions:
help(read)
For specific methods related to e.g. a stream object "data":
help(data.fit)
Note that this requires the existence of a "data" object, which is obtained e.g. by data = read(...). The help text can also be shown by directly calling the DataStream object method using:
help(DataStream.fit)
MagPy automatically logs many function options and runtime information, which can be useful for debugging purposes. This log is saved by default in the temporary file directory of your operating system, e.g. for Linux this would be /tmp/magpy.log. The log is formatted as follows with the date, module and function in use and the message leve (INFO/WARNING/ERROR):
2017-04-22 09:50:11,308 INFO - magpy.stream - Initiating MagPy...
Messages on the WARNING and ERROR level will automatically be printed to shell. Messages for more detailed debugging are written at the DEBUG level and will not be printed to the log unless an additional handler for printing DEBUG is added.
Custom loggers can be defined by creating a logger object after importing MagPy and adding handlers (with formatting):
from magpy.stream import *
import logging
logger = logging.getLogger()
hdlr = logging.FileHandler('testlog.log')
formatter = logging.Formatter('%(asctime)s - %(name)s - %(levelname)s - %(message)s')
hdlr.setFormatter(formatter)
logger.addHandler(hdlr)
The logger can also be configured to print to shell (stdout, without formatting):
import sys
logger = logging.getLogger()
stdoutlog = logging.StreamHandler(sys.stdout)
logger.addHandler(stdoutlog)
You will find some example plots at the Conrad Observatory.
import magpy.mpplot as mp
mp.plot(data)
Select specific keys to plot:
mp.plot(data,variables=['x','y','z'])
Defining a plot title and specific colors (see help(mp.plot) for list and all options):
mp.plot(data,variables=['x','y'],plottitle="Test plot",
colorlist=['g', 'c'])
Various datasets from multiple data streams will be plotted above one another. Provide a list of streams and an array of keys:
mp.plotStreams([data1,data2],[['x','y','z'],['f']])
The flagging procedure allows the observer to mark specific data points or ranges. Falgs are useful for labelling data spikes, storm onsets, pulsations, disturbances, lightning strikes, etc. Each flag is asociated with a comment and a type number. The flagtype number ranges between 0 and 4:
- 0: normal data with comment (e.g. "Hello World")
- 1: data marked by automated analysis (e.g. spike)
- 2: data marked by observer as valid geomagnetic signature (e.g. storm onset, pulsation). Such data cannot be marked invalid by automated procedures
- 3: data marked by observer as invalid (e.g. lightning, magnetic disturbance)
- 4: merged data (e.g. data inserted from another source/instrument as defined in the comment)
Flags can be stored along with the data set (requires CDF format output) or separately in a binary archive. These flags can then be applied to the raw data again, ascertaining perfect reproducibility.
Load a data record with data spikes:
datawithspikes = read(example1)
Mark all spikes using the automated function flag_outlier with default options:
flaggeddata = datawithspikes.flag_outlier(timerange=timedelta(minutes=1),threshold=3)
Show flagged data in a plot:
mp.plot(flaggeddata,['f'],annotate=True)
Flag a certain time range:
flaglist = flaggeddata.flag_range(keys=['f'], starttime='2012-08-02T04:33:40',
endtime='2012-08-02T04:44:10',
flagnum=3, text="iron metal near sensor")
Apply these flags to the data:
flaggeddata = flaggeddata.flag(flaglist)
Show flagged data in a plot:
mp.plot(flaggeddata,['f'],annotate=True)
To save the data together with the list of flags to a CDF file:
flaggeddata.write('/tmp/',filenamebegins='MyFlaggedExample_', format_type='PYCDF')
To check for correct save procedure, read and plot the new file:
newdata = read("/tmp/MyFlaggedExample_*")
mp.plot(newdata,annotate=True, plottitle='Reloaded flagged CDF data')
To save the list of flags seperately from the data in a pickled binary file:
fullflaglist = flaggeddata.extractflags()
saveflags(fullflaglist,"/tmp/MyFlagList.pkl"))
These flags can be loaded in and then reapplied to the data set:
data = read(example1)
flaglist = loadflags("/tmp/MyFlagList.pkl")
data = data.flag(flaglist)
mp.plot(data,annotate=True, plottitle='Raw data with flags from file')
For some analyses it is necessary to use "clean" data, which can be produced by dropping data flagged as invalid (e.g. spikes). By default, the following method removes all data marked with flagtype numbers 1 and 3.
cleandata = flaggeddata.remove_flagged()
mp.plot(cleandata, ['f'], plottitle='Flagged data dropped')
MagPy's filter uses the settings recommended by IAGA/INTERMAGNET. Ckeck help(data.filter) for further options and definitions of filter types and pass bands.
First, get the sampling rate before filtering in seconds:
print("Sampling rate before [sec]:", cleandata.samplingrate())
Filter the data set with default parameters (filter automatically chooses the correct settings depending on the provided sanmpling rate):
filtereddata = cleandata.filter()
Get sampling rate and filtered data after filtering (please note that all filter information is added to the data's meta information dictionary (data.header):
print("Sampling rate after [sec]:", filtereddata.samplingrate())
print("Filter and pass band:", filtereddata.header.get('DataSamplingFilter',''))
Assuming vector data in columns [x,y,z] you can freely convert between xyz, hdz, and idf coordinates:
cleandata = cleandata.xyz2hdz()
If the data file contains xyz (hdz, idf) data and an independently measured f value, you can calculate delta F between the two instruments using the following:
cleandata = cleandata.delta_f()
mp.plot(cleandata,plottitle='delta F')
Mean values for certain data columns can be obtained using the mean method. The mean will only be calculated for data with the percentage of valid data (in contrast to missing data) points not falling below the value given by the percentage option (default 95). If too much data is missing, then no mean is calulated and the function returns NaN.
print(cleandata.mean('df', percentage=80))
The median can be calculated by defining the meanfunction option:
print(cleandata.mean('df', meanfunction='median'))
Constant offsets can be added to individual columns using the offset method with a dictionary defining the MagPy stream column keys and the offset to be applied (datetime.timedelta object for time column, float for all others):
offsetdata = cleandata.offset({'time':timedelta(seconds=0.19),'f':1.24})
Individual columns can also be multiplied by values provided in a dictionary:
multdata = cleandata.multiply({'x':-1})
MagPy offers the possibility to fit functions to data using either polynomial functions or cubic splines (default):
func = cleandata.fit(keys=['x','y','z'],knotstep=0.1)
mp.plot(cleandata,variables=['x','y','z'],function=func)
Time derivatives, which are useful to identify outliers and sharp changes, are calculated as follows:
diffdata = cleandata.differentiate(keys=['x','y','z'],put2keys = ['dx','dy','dz'])
mp.plot(diffdata,variables=['dx','dy','dz'])
For a summary of all supported methods, see the section List of all MagPy methods below.
MagPy supports the FMI method for determination of K indices. Please consult the MagPy publication for details on this method and application.
A month of one minute data is provided in example2, which corresponds to an INTERMAGNET IAF archive file. Reading a file in this format will load one minute data by default. Accessing hourly data and other information is described below.
data2 = read(example2)
kvals = data2.k_fmi()
The determination of K values will take some time as the filtering window is dynamically adjusted. In order to plot the original data (H component) and K values together, we now use the multiple stream plotting method plotStreams. Here you need to provide a list of streams and an array containing variables for each stream. The additional options determine the appearance of the plot (limits, bar chart):
mp.plotStreams([data2,kvals],[['x'],['var1']],
specialdict = [{},{'var1':[0,9]}],
symbollist=['-','z'],
bartrange=0.06)
'z' in symbollist refers to the second subplot (K), which should be plotted as bars rather than the standard line ('-').
Geomagnetic storm detection is supported by MagPy using two procedures based on wavelets and the Akaike Information Criterion (AIC) as outlined in detail in Bailey and Leonhardt (2016). A basic example of usage to find an SSC using a Discrete Wavelet Transform (DWT) is shown below:
from magpy.stream import read
from magpy.opt.stormdet import seekStorm
stormdata = read("LEMI025_2015-03-17.cdf") # 1s variometer data
stormdata = stormdata.xyz2hdz()
stormdata = stormdata.smooth('x', window_len=25)
detection, ssc_list = seekStorm(stormdata, method="MODWT")
print("Possible SSCs detected:", ssc_list)
The method seekStorm will return two variables: detection is True if any detection was made, while ssc_list is a list of dictionaries containing data on each detection. Note that this method alone can return a long list of possible SSCs (most incorrectly detected), particularly during active storm times. It is most useful when additional restrictions based on satellite solar wind data apply (currently only optimised for ACE data, e.g. from the NOAA website):
satdata_ace_1m = read('20150317_ace_swepam_1m.txt')
satdata_ace_5m = read('20150317_ace_epam_5m.txt')
detection, ssc_list, sat_cme_list = seekStorm(stormdata,
satdata_1m=satdata_ace_1m, satdata_5m=satdata_ace_5m,
method='MODWT', returnsat=True)
print("Possible CMEs detected:", sat_cme_list)
print("Possible SSCs detected:", ssc_list)
Methods are currently in preparation.
A common and important application used in the geomagnetism community is a general validity check of geomagnetic data to be submitted to the official data repositories IAGA, WDC, or INTERMAGNET. Please note: this is currently under development and will be extended in the near future. A 'one-click' test method will be included in xmagpy in the future, checking:
A) Validity of data formats, e.g.:
data = read('myiaffile.bin', debug=True)
B) Completeness of meta-information
C) Conformity of applied techniques to respective rules
D) Internal consistency of data
E) Optional: regional consistency
For analysis of the spectral content of data, MagPy provides two basic plotting methods. plotPS will calculate and display a power spectrum of the selected component. plotSpectrogram will plot a spectrogram of the time series. As usual, there are many options for plot window and processing parameters that can be accessed using the help method.
data = read(example1)
mp.plotPS(data,key='f')
mp.plotSpectrogram(data,['f'])
Merging data comprises combining two streams into one new stream. This includes adding a new column from another stream, filling gaps with data from another stream or replacing data from one column with data from another stream. The following example sketches the typical usage:
print("Data columns in data2:", data2._get_key_headers())
newstream = mergeStreams(data2,kvals,keys=['var1'])
print("Data columns after merging:", data2._get_key_headers())
mp.plot(newstream, ['x','y','z','var1'],symbollist=['-','-','-','z'])
If column var1 does not existing in data2 (as above), then this column is added. If column var1 had already existed, then missing data would be inserted from stream kvals. In order to replace any existing data, use option mode='replace'.
Sometimes it is necessary to examine the differences between two data streams e.g. differences between the F values of two instruments running in parallel at an observatory. The method subtractStreams is provided for this analysis:
diff = subtractStreams(data1,data2,keys=['f'])
Each data set is accompanied by a dictionary containing meta-information for this data. This dictionary is completely dynamic and can be filled freely, but there are a number of predefined fields that help the user provide essential meta-information as requested by IAGA, INTERMAGNET and other data providers. All meta information is saved only to MagPy-specific archive formats PYCDF and PYSTR. All other export formats save only specific information as required by the projected format.
The current content of this dictionary can be accessed by:
data = read(example1)
print(data.header)
Information is added/changed by using:
data.header['SensorName'] = 'FGE'
Individual information is obtained from the dictionary using standard key input:
print(data.header.get('SensorName'))
If you want to have a more readable list of the header information, do:
for key in data.header:
print ("Key: {} \t Content: {}".format(key,data.header.get(key)))
To convert data from IAGA or IAF formats to the new INTERMAGNET CDF format, you will usually need to add additional meta-information required for the new format. MagPy can assist you here, firstly by extracting and correctly adding already existing meta-information into newly defined fields, and secondly by informing you of which information needs to be added for producing the correct output format.
Example of IAGA02 to ImagCDF:
mydata = read('IAGA02-file.min')
mydata.write('/tmp',format_type='IMAGCDF')
The console output of the write command (see below) will tell you which information needs to be added (and how) in order to obtain correct ImagCDF files. Please note, MagPy will store the data in any case and will be able to read it again even if information is missing. Before submitting to a GIN, you need to make sure that the appropriate information is contained. Attributes that relate to publication of the data will not be checked at this point, and might be included later.
>>>Writing IMAGCDF Format /tmp/wic_20150828_0000_PT1M_4.cdf
>>>writeIMAGCDF: StandardLevel not defined - please specify by yourdata.header['DataStandardLevel'] = ['None','Partial','Full']
>>>writeIMAGCDF: Found F column
>>>writeIMAGCDF: given components are XYZF. Checking F column...
>>>writeIMAGCDF: analyzed F column - values are apparently independend from vector components - using column name 'S'
Now add the missing information. Selecting 'Partial' will require additional information. You will get a 'reminder' if you forget this. Please check IMAGCDF instructions on specific codes:
mydata.header['DataStandardLevel'] = 'Partial'
mydata.header['DataPartialStandDesc'] = 'IMOS-01,IMOS-02,IMOS-03,IMOS-04,IMOS-05,IMOS-06,IMOS-11,IMOS-12,IMOS-13,IMOS-14,IMOS-15,IMOS-21,IMOS-22,IMOS-31,IMOS-41'
Similar reminders to fill out complete header information will be shown for other conversions like:
mydata.write('/tmp',format_type='IAGA')
mydata.write('/tmp',format_type='IMF')
mydata.write('/tmp',format_type='IAF',coverage='month')
mydata.write('/tmp',format_type='WDC')
Providing location data usually requires information on the reference system (ellipsoid,...). By default MagPy assumes that these values are provided in WGS84/WGS84 reference system. In order to facilitate most easy referencing and conversions, MagPy supports EPSG codes for coordinates. If you provide the geodetic references as follows, and provided that the proj4 Python package is available, MagPy will automatically convert location data to the requested output format (currently WGS84).
mydata.header['DataAcquisitionLongitude'] = -34949.9
mydata.header['DataAcquisitionLatitude'] = 310087.0
mydata.header['DataLocationReference'] = 'GK M34, EPSG: 31253'
>>>...
>>>writeIMAGCDF: converting coordinates to epsg 4326
>>>...
The meta-information fields can hold much more information than required by most output formats. This includes basevalue and baseline parameters, flagging details, detailed sensor information, serial numbers and much more. MagPy makes use of these possibilities. In order to save this meta-information along with your data set you can use MagPy internal archiving format, PYCDF, which can later be converted to any of the aforementioned output formats. You can even reconstruct a full data base. Any upcoming meta-information or output request can be easily added/modified without disrupting already existing data sets and the ability to read and analyse old data. This data format is also based on Nasa CDF. ASCII outputs are also supported by MagPy, of which the PYSTR format also contains all meta information and PYASCII is the most compact. Please consider that ASCII formats require a lot of memory, especially for one second and higher resolution data.
mydata.write('/tmp',format_type='PYCDF',coverage='year')
MagPy contains a number of methods to simplify data transfer for observatory applications. Methods within the basic Python functionality can also be very useful. Using the implemented methods requires:
from magpy import transfer as mt
Use the read method as outlined above. No additional imports are required.
Files can also be uploaded to an FTP server:
mt.ftpdatatransfer(localfile='/path/to/data.cdf',ftppath='/remote/directory/',myproxy='ftpaddress or address of proxy',port=21,login='user',passwd='passwd',logfile='/path/mylog.log')
The upload methods using FTP, SCP and GIN support logging. If the data file failed to upload correctly, the path is added to a log file and, when called again, upload of the file is retried. This option is useful for remote locations with unstable network connections.
To transfer via SCP:
mt.scptransfer('user@address:/remote/directory/','/path/to/data.cdf',passwd,timeout=60)
Use the following command:
mt.ginupload('/path/to/data.cdf', ginuser, ginpasswd, ginaddress, faillog=True, stdout=True)
In order to avoid using real-text password in scripts, MagPy comes along with a simple encryption routine.
from magpy.opt import cred as mpcred
Credentials will be saved to a hidden file with encrypted passwords. To add information for data transfer to a machine called 'MyRemoteFTP' with an IP of 192.168.0.99:
mpcred.cc('transfer', 'MyRemoteFTP', user='user', passwd='secure', address='192.168.0.99', port=21)
Extracting passwd information within your data transfer scripts:
user = mpcred.lc('MyRemoteFTP', 'user')
password = mpcred.lc('MyRemoteFTP','passwd')
These procedures require an additional import:
from magpy import absolutes as di
Please check example3, which is an example DI file. You can create these DI files by using the input sheet from xmagpy or the online input sheet provided by the Conrad Observatory. If you want to use this service, please contact the Observatory staff. Also supported are DI-files from the AUTODIF.
Reading and analyzing DI data requires valid DI file(s). For correct analysis, variometer data and scalar field information needs to be provided as well. Checkout help(di.absoluteAnalysis) for all options. The analytical procedures are outlined in detail in the MagPy article (citation). A typical analysis looks like:
diresult = di.absoluteAnalysis('/path/to/DI/','path/to/vario/','path/to/scalar/')
Path to DI can either point to a single file, a directory or even use wildcards to select data from a specific observatory/pillar. Using the examples provided along with MagPy, the analysis line looks like
diresult = di.absoluteAnalysis(example3,example2,example2)
Calling this method will provide terminal output as follows and a stream object diresult which can be used for further analyses.
>>>...
>>>Analyzing manual measurement from 2015-03-25
>>>Vector at: 2015-03-25 08:18:00+00:00
>>>Declination: 3:53:46, Inclination: 64:17:17, H: 21027.2, Z: 43667.9, F: 48466.7
>>>Collimation and Offset:
>>>Declination: S0: -3.081, delta H: -6.492, epsilon Z: -61.730
>>>Inclination: S0: -1.531, epsilon Z: -60.307
>>>Scalevalue: 1.009 deg/unit
>>>Fext with delta F of 0.0 nT
>>>Delta D: 0.0, delta I: 0.0
Fext indicates that F values have been used from a separate file and not provided along with DI data. Delta values for F, D, and I have not been provided either. diresult is a stream object containing average D, I and F values, the collimation angles, scale factors and the base values for the selected variometer, beside some additional meta information provided in the data input form.
Basevalues:
blvdata = read('/path/myfile.blv')
mp.plot(blvdata, symbollist=['o','o','o'])
Adopted baseline:
bldata = read('/path/myfile.blv',mode='adopted')
mp.plot(bldata)
Basevalues as obtained in (2.11.2) or (2.11.3) are stored in a normal data stream object, therefore all analysis methods outlined above can be applied to this data. The diresult object contains D, I, and F values for each measurement in columns x,y,z. Basevalues for H, D and Z related to the selected variometer are stored in columns dx,dy,dz. In example4, you will find some more DI analysis results. To plot these basevalues we can use the following plot command, where we specify the columns, filled circles as plotsymbols and also define a minimum spread of each y-axis of +/- 5 nT for H and Z, +/- 0.05 deg for D.
basevalues = read(example4)
mp.plot(basevalues, variables=['dx','dy','dz'], symbollist=['o','o','o'], padding=[5,0.05,5])
Fitting a baseline can be easily accomplished with the fit method. First we test a linear fit to the data by fitting a polynomial function with degree 1.
func = basevalues.fit(['dx','dy','dz'],fitfunc='poly', fitdegree=1)
mp.plot(basevalues, variables=['dx','dy','dz'], symbollist=['o','o','o'], padding=[5,0.05,5], function=func)
We then fit a spline function using 3 knotsteps over the timerange (the knotstep option is always related to the given timerange).
func = basevalues.fit(['dx','dy','dz'],fitfunc='spline', knotstep=0.33)
mp.plot(basevalues, variables=['dx','dy','dz'], symbollist=['o','o','o'], padding=[5,0.05,5], function=func)
Hint: a good estimate on the necessary fit complexity can be obtained by looking at delta F values. If delta F is mostly constant, then the baseline should also not be very complex.
The baseline method provides a number of options to assist the observer in determining baseline corrections and realted issues. The basic building block of the baseline method is the fit function as discussed above. Lets first load raw vectorial geomagnetic data, the absevalues of which are contained in above example:
rawdata = read(example5)
Now we can apply the basevalue information and the spline function as tested above:
func = rawdata.baseline(basevalues, extradays=0, fitfunc='spline',
knotstep=0.33,startabs='2015-09-01',endabs='2016-01-22')
The baseline method will determine and return a fit function between the two given timeranges based on the provided basevalue data blvdata. The option extradays allows for adding days before and after start/endtime for which the baseline function will be extrapolated. This option is useful for providing quasi-definitive data. When applying this method, a number of new meta-information attributes will be added, containing basevalues and all functional parameters to describe the baseline. Thus, the stream object still contains uncorrected raw data, but all baseline correction information is now contained within its meta data. To apply baseline correction you can use the bc method:
corrdata = rawdata.bc()
If baseline jumps/breaks are necessary due to missing data, you can call the baseline function for each independent segment and then join the corrected streams:
stream_a = read(mydata,starttime='2016-01-01',endtime='2016-02-01')
func = stream_a.baseline(blvdata, extradays=0, fitfunc='spline', knotstep=0.3,startabs='2016-01-01',endabs='2016-02-01')
corr = stream_a.bc()
stream_b = read(mydata,starttime='2016-02-01',endtime='2016-03-01')
func_b = stream.baseline(blvdata, extradays=0, fitfunc='poly', degree=1,startabs='2016-02-01',endabs='2016-03-01')
corr_b = stream_b.bc()
func.extend(func_b)
corr.extend(corr_b)
mp.plot(basevalues, variables=['dx','dy','dz'], symbollist=['o','o','o'], padding=[5,0.05,5], function=func)
The combined baseline can be plotted accordingly. Extend the function parameters with each additional segment.
The following will create a BLV file:
diresult.write('/my/path',coverage='all',format_type='BLV',diff=meanstream,year='2016')
The meanstream stream contains daily averages of delta F values between variometer and F measurements and the baseline adoption data in the meta-information. You can, however, provide all this information manually as well. The typical way to obtain such a meanstream is sketched below:
finaldata = mergeStreams(vectordata_corr, scalardata, ['f'])
finaldata = finaldata.delta_f()
meanstream = finaldata.filter(filter_width=timedelta(days=1),filter_type='flat',resampleoffset=timedelta(hours=12), resample_period=43200, missingdata='mean')
MagPy supports database access and many methods for optimizing data treatment in connection with databases. Among many other benefits, using a database simplifies many typical procedures related to meta-information. Currently, MagPy supports MySQL databases. To use these features, you need to have MySQL installed on your system. In the following we provide a brief outline of how to set up and use this optional addition. Please note that a proper usage of the database requires sensor-specific information. In geomagnetism, it is common to combine data from different sensors into one file structure. In this case, such data needs to remain separate for database usage and is only combined when producing IAGA/INTERMAGNET definitive data. Furthermore, unique sensor information such as type and serial number is required.
import magpy import database as mdb
Open mysql (e.g. Linux: mysql -u root -p mysql) and create a new database. Replace #DB-NAME with your database name (e.g. MyDB). After creation, you will need to grant priviledges to this database to a user of your choice. Please refer to official MySQL documentations for details and further commands.
mysql> CREATE DATABASE #DB-NAME;
mysql> GRANT ALL PRIVILEGES ON #DB-NAME.* TO '#USERNAME'@'%' IDENTIFIED BY '#PASSWORD';
Connecting to a database using MagPy is done using following command:
db = mdb.mysql.connect(host="localhost",user="#USERNAME",passwd="#PASSWORD",db="#DB-NAME")
mdb.dbinit(db)
Examples of useful meta-information:
iagacode = 'WIC'
data = read(example1)
gsm = data.selectkeys(['f'])
fge = data.selectkeys(['x','y','z'])
gsm.header['SensorID'] = 'GSM90_12345_0002'
gsm.header['StationID'] = iagacode
fge.header['SensorID'] = 'FGE_22222_0001'
fge.header['StationID'] = iagacode
mdb.writeDB(db,gsm)
mdb.writeDB(db,fge)
All available meta-information will be added automatically to the relevant database tables. The SensorID scheme consists of three parts: instrument (GSM90), serial number (12345), and a revision number (0002) which might change in dependency of maintenance, calibration, etc. As you can see in the example above, we separate data from different instruments, which we recommend particularly for high resolution data, as frequency and noise characteristics of sensor types will differ.
To read data from an established database:
data = mdb.readDB(db,'GSM90_12345_0002')
Options e.g. starttime='' and endtime='' are similar as for normal read.
An often used application of database connectivity with MagPy will be to apply meta-information stored in the database to data files before submission. The following command demostrates how to extract all missing meta-information from the database for the selected sensor and add it to the header dictionary of the data object.
rawdata = read('/path/to/rawdata.bin')
rawdata.header = mdb.dbfields2dict(db,'FGE_22222_0001')
rawdata.write(..., format_type='IMAGCDF')
Automated analysis can e easily accomplished by adding a series of MagPy commands into a script. A typical script could be:
# read some data and get means
data = read(example1)
mean_f = data.mean('f')
# import monitor method
from magpy.opt import Analysismonitor
analysisdict = Analysismonitor(logfile='/var/log/anamon.log')
analysisdict = analysisdict.load()
# check some arbitray threshold
analysisdict.check({'data_threshold_f_GSM90': [mean_f,'>',20000]})
If provided criteria are invalid, then the logfile is changed accordingly. This method can assist you particularly in checking data actuality, data contents, data validity, upload success, etc. In combination with an independent monitoring tool like Nagios, you can easily create mail/SMS notfications of such changes, in addition to monitoring processes, live times, disks etc. MARCOS comes along with some instructions on how to use Nagios/MagPy for data acquisition monitoring.
MagPy contains a couple of packages which can be used for data acquisition, collection and organization. These methods are primarily contained in two applications: MARTAS and MARCOS. MARTAS (Magpy Automated Realtime Acquisition System) supports communication with many common instruments (e.g. GSM, LEMI, POS1, FGE, and many non-magnetic instruments) and transfers serial port signals to WAMP (Web Application Messaging Protocol), which allows for real-time data access using e.g. WebSocket communication through the internet. MARCOS (Magpy's Automated Realtime Collection and Organistaion System) can access such real-time streams and also data from many other sources and supports the observer by storing, analyzing, archiving data, as well as monitoring all processes. Details on these two applications can be found elsewhere.
Many of the above mentioned methods are also available within the graphical user interface of MagPy. To use this check the installation instructions for your operating system. You will find Video Tutorials online (to be added) describing its usage for specific analyses.
2.16.1 Exchange data objects with ObsPy
MagPy supports the exchange of data with ObsPy, the seismological toolbox. Data objects of both python packages are very similar. Note: ObsPy assumes regular spaced time intervals. Please be careful if this is not the case with your data. The example below shows a simple import routine, on how to read a seed file and plot a spectrogram (which you can identically obtain from ObsPy as well). Conversions to MagPy allow for vectorial analyses, and geomagnetic applications. Conversions to ObsPy are useful for effective high frequency analysis, requiring evenly spaced time intervals, and for exporting to seismological data formats.
from obspy import read as obsread
seeddata = obsread('/path/to/seedfile')
magpydata = obspy2magpy(seeddata,keydict={'ObsPyColName': 'x'})
mp.plotSpectrogram(magpydata,['x'])
datawithspikes = read(example1)
flaggeddata = datawithspikes.flag_outlier(keys=['f'],timerange=timedelta(minutes=1),threshold=3)
mp.plot(flaggeddata,['f'],annotate=True)
flaggeddata.write(tmpdir,format_type='IMAGCDF',addflags=True)
The addflags option denotes that flagging information will be added to the ImagCDF format. Please note that this is still under development and thus content and format specifications may change. So please use it only for test purposes and not for archiving. To read and view flagged ImagCDF data, just use the normal read command, and activate annotation for plotting.
new = read('/tmp/cnb_20120802_000000_PT1S_1.cdf')
mp.plot(new,['f'],annotate=True)
Please use the help method (section 2.3) for descriptions and return values.
| group | method | parameter |
|---|---|---|
| - | findpath | name, path |
| - | _pickle_method | method |
| - | _unpickle_method | func_name, obj, cls |
| stream | init | self, container=None, header={},ndarray=None |
| stream | ext | self, columnstructure |
| stream | add | self, datlst |
| stream | length | self |
| stream | replace | self, datlst |
| stream | copy | self |
| stream | str | self |
| stream | repr | self |
| stream | getitem | self, index |
| stream | len | self |
| stream | clear_header | self |
| stream | extend | self,datlst,header,ndarray |
| stream | union | self,column |
| stream | removeduplicates | self |
| stream | start | self, dateformt=None |
| stream | end | self, dateformt=None |
| stream | findtime | self,time,**kwargs |
| stream | _find_t_limits | self |
| stream | _print_key_headers | self |
| stream | _get_key_headers | self,**kwargs |
| stream | _get_key_names | self |
| stream | dropempty | self |
| stream | fillempty | self, ndarray, keylist |
| stream | sorting | self |
| stream | _get_line | self, key, value |
| stream | _take_columns | self, keys |
| stream | _remove_lines | self, key, value |
| stream | _get_column | self, key |
| stream | _put_column | self, column, key, **kwargs |
| stream | _move_column | self, key, put2key |
| stream | _drop_column | self,key |
| stream | _clear_column | self, key |
| stream | _reduce_stream | self, pointlimit=100000 |
| stream | _remove_nancolumns | self |
| stream | _aic | self, signal, k, debugmode=None |
| stream | harmfit | self,nt, val, fitdegree |
| stream | _get_max | self, key, returntime=False |
| stream | _get_min | self, key, returntime=False |
| stream | amplitude | self,key |
| stream | _gf | self, t, tau |
| stream | _hf | self, p, x |
| stream | _residual_func | self, func, y |
| stream | _tau | self, period, fac=0.83255461 |
| stream | _convertstream | self, coordinate, **kwargs |
| stream | _delete | self,index |
| stream | _append | self,stream |
| stream | _det_trange | self, period |
| stream | _is_number | self, s |
| stream | _normalize | self, column |
| stream | _testtime | self, time |
| stream | _drop_nans | self, key |
| stream | _select_keys | self, keys |
| stream | _select_timerange | self, starttime=None, endtime=None, maxidx=-1 |
| stream | aic_calc | self, key, **kwargs |
| stream | baseline | self, absolutedata, **kwargs |
| stream | stream2dict | self, keys=['dx','dy','dz'], dictkey='DataBaseValues' |
| stream | dict2stream | self,dictkey='DataBaseValues' |
| stream | baselineAdvanced | self, absdata, baselist, **kwargs |
| stream | bc | self, function=None, ctype=None, alpha=0.0,level='preliminary' |
| stream | bindetector | self,key,flagnum=1,keystoflag=['x'],sensorid=None,text=None,**kwargs |
| stream | calc_f | self, **kwargs |
| stream | dailymeans | self, keys=['x','y','z','f'], **kwargs |
| stream | date_offset | self, offset |
| stream | delta_f | self, **kwargs |
| stream | f_from_df | self, **kwargs |
| stream | differentiate | self, **kwargs |
| stream | DWT_calc | self,key='x',wavelet='db4',level=3,plot=False,outfile=None, |
| stream | eventlogger | self, key, values, compare=None, stringvalues=None, addcomment=None, debugmode=None |
| stream | extract | self, key, value, compare=None, debugmode=None |
| stream | extract2 | self, keys, get='>', func=None, debugmode=None |
| stream | extrapolate | self, start, end |
| stream | filter | self,**kwargs |
| stream | fit | self, keys, **kwargs |
| stream | extractflags | self |
| stream | flagfast | self,indexarray,flag, comment,keys=None |
| stream | flag_range | self, **kwargs |
| stream | flag_outlier | self, **kwargs |
| stream | flag | self, flaglist, removeduplicates=False, debug=False |
| stream | flagliststats | self,flaglist |
| stream | flaglistclean | self,flaglist |
| stream | stream2flaglist | self, userange=True, flagnumber=None, keystoflag=None, sensorid=None, comment=None |
| stream | flaglistmod | self, mode='select', flaglist=[], parameter='key', value=None, newvalue=None |
| stream | flaglistadd | self, flaglist, sensorid, keys, flagnumber, comment, startdate, enddate=None |
| stream | flag_stream | self, key, flag, comment, startdate, enddate=None, samplingrate=0., debug=False |
| stream | simplebasevalue2stream | self,basevalue,**kwargs |
| stream | func2stream | self,function,**kwargs |
| stream | func_add | self,function,**kwargs |
| stream | func_subtract | self,function,**kwargs |
| stream | get_gaps | self, **kwargs |
| stream | get_rotationangle | self, xcompensation=0,keys=['x','y','z'],**kwargs |
| stream | get_sampling_period | self |
| stream | samplingrate | self, **kwargs |
| stream | integrate | self, **kwargs |
| stream | interpol | self, keys, **kwargs |
| stream | k_extend | self, **kwargs |
| stream | k_fmi | self, **kwargs |
| stream | linestruct2ndarray | self |
| stream | mean | self, key, **kwargs |
| stream | missingvalue | self,v,window_len,threshold=0.9,fill='mean' |
| stream | MODWT_calc | self,key='x',wavelet='haar',level=1,plot=False,outfile=None |
| stream | multiply | self, factors, square=False |
| stream | offset | self, offsets, **kwargs |
| stream | plot | self, keys=None, debugmode=None, **kwargs |
| stream | powerspectrum | self, key, debugmode=None, outfile=None, fmt=None, axes=None, title=None,**kwargs |
| stream | randomdrop | self,percentage=None,fixed_indicies=None |
| stream | remove | self, starttime=None, endtime=None |
| stream | remove_flagged | self, **kwargs |
| stream | remove_outlier | self, **kwargs |
| stream | resample | self, keys, **kwargs |
| stream | rotation | self,**kwargs |
| stream | scale_correction | self, keys, scales, **kwargs |
| stream | selectkeys | self, keys, **kwargs |
| stream | smooth | self, keys=None, **kwargs |
| stream | spectrogram | self, keys, per_lap=0.9, wlen=None, log=False, |
| stream | steadyrise | self, key, timewindow, **kwargs |
| stream | stereoplot | self, **kwargs |
| stream | trim | self, starttime=None, endtime=None, newway=False |
| stream | variometercorrection | self, variopath, thedate, **kwargs |
| stream | _write_format | self, format_type, filenamebegins, filenameends, coverage, dateformat,year |
| stream | write | self, filepath, compression=5, **kwargs |
| stream | idf2xyz | self,**kwargs |
| stream | xyz2idf | self,**kwargs |
| stream | xyz2hdz | self,**kwargs |
| stream | hdz2xyz | self,**kwargs |
| - | coordinatetransform | u,v,w,kind |
| - | isNumber | s |
| - | find_nearest | array,value |
| - | ceil_dt | dt,seconds |
| - | read | path_or_url=None, dataformat=None, headonly=False, **kwargs |
| - | _read | filename, dataformat=None, headonly=False, **kwargs |
| - | saveflags | mylist=None,path=None |
| - | loadflags | path=None,sensorid=None,begin=None, end=None |
| - | joinStreams | stream_a,stream_b, **kwargs |
| - | appendStreams | streamlist |
| - | mergeStreams | stream_a, stream_b, **kwargs |
| - | dms2d | dms |
| - | find_offset | stream1, stream2, guess_low=-60., guess_high=60. |
| - | diffStreams | stream_a, stream_b, **kwargs |
| - | subtractStreams | stream_a, stream_b, **kwargs |
| - | stackStreams | streamlist, **kwargs |
| - | compareStreams | stream_a, stream_b |
| - | array2stream | listofarrays, keystring,starttime=None,sr=None |
| - | obspy2magpy | opstream, keydict={} |
| - | extractDateFromString | datestring |
| - | testTimeString | time |
| - | denormalize | column, startvalue, endvalue |
| - | find_nearest | array, value |
| - | maskNAN | column |
| - | nan_helper | y |
| - | nearestPow2 | x |
| - | test_time | time |
| - | convertGeoCoordinate | lon,lat,pro1,pro2 |
| mpplot | ploteasy | stream |
| mpplot | plot_new | stream,variables=[],specialdict={},errorbars=False,padding=0,noshow=False |
| mpplot | plot | stream,variables=[],specialdict={},errorbars=False,padding=0,noshow=False |
| mpplot | plotStreams | streamlist,variables,padding=None,specialdict={},errorbars=None |
| mpplot | toggle_selector | event |
| mpplot | addFlag | data, flagger, indeciestobeflagged, variables |
| mpplot | plotFlag | data,variables=None,figure=False |
| mpplot | plotEMD | stream,key,verbose=False,plottitle=None |
| mpplot | plotNormStreams | streamlist, key, normalize=True, normalizet=False |
| mpplot | plotPS | stream,key,debugmode=False,outfile=None,noshow=False |
| mpplot | plotSatMag | mag_stream,sat_stream,keys,outfile=None,plottype='discontinuous' |
| mpplot | plotSpectrogram | stream, keys, NFFT=1024, detrend=mlab.detrend_none |
| mpplot | magpySpecgram | x, NFFT=256, Fs=2, Fc=0, detrend=mlab.detrend_none |
| mpplot | plotStereoplot | stream,focus='all',colorlist = ['b','r','g','c','m','y','k'] |
| mpplot | _plot | data,savedpi=80,grid=True,gridcolor=gridcolor,noshow=False |
| mpplot | _confinex | ax, tmax, tmin, timeunit |
| mpplot | _extract_data_for_PSD | stream, key |
| database | dbgetPier | db,pierid, rp, value, maxdate=None, l=False, dic='DeltaDictionary' |
| database | dbgetlines | db, tablename, lines |
| database | dbupdate | db,tablename, keys, values, condition=None |
| database | dbgetfloat | db,tablename,sensorid,columnid,revision=None |
| database | dbgetstring | db,tablename,sensorid,columnid,revision=None |
| database | dbupload | db, path,stationid,**kwargs |
| database | dbinit | db |
| database | dbdelete | db,datainfoid,**kwargs |
| database | dbdict2fields | db,header_dict,**kwargs |
| database | dbfields2dict | db,datainfoid |
| database | dbalter | db |
| database | dbselect | db, element, table, condition=None, expert=None, debug=False |
| database | dbcoordinates | db, pier, epsgcode='epsg:4326' |
| database | dbsensorinfo | db,sensorid,sensorkeydict=None,sensorrevision = '0001' |
| database | dbdatainfo | db,sensorid,datakeydict=None,tablenum=None,defaultstation='WIC',updatedb=True |
| database | writeDB | db, datastream, tablename=None, StationID=None, mode='replace', revision=None, debug=False, **kwargs |
| database | dbsetTimesinDataInfo | db, tablename,colstr,unitstr |
| database | dbupdateDataInfo | db, tablename, header |
| database | stream2db | db, datastream, noheader=None, mode=None, tablename=None, **kwargs |
| database | readDB | db, table, starttime=None, endtime=None, sql=None |
| database | db2stream | db, sensorid=None, begin=None, end=None, tableext=None, sql=None |
| database | diline2db | db, dilinestruct, mode=None, **kwargs |
| database | db2diline | db,**kwargs |
| database | applyDeltas | db, stream |
| database | getBaseline | db,sensorid, date=None |
| database | flaglist2db | db,flaglist,mode=None,sensorid=None,modificationdate=None |
| database | db2flaglist | db,sensorid, begin=None, end=None, comment=None, flagnumber=-1, key=None, removeduplicates=False |
| database | string2dict | string |
| tranfer | _checklogfile | logfile |
| tranfer | ftpdatatransfer | **kwargs |
| tranfer | _missingvals | myproxy, port, login, passwd, logfile |
| tranfer | scptransfer | src,dest,passwd,**kwargs |
| tranfer | ssh_remotefilelist | remotepath, filepat, user, host, passwd |
| tranfer | ginupload | filename=None, user=None, password=None, url=None,**kwargs |
| tranfer | ftpdirlist | **kwargs |
| tranfer | ftpremove | **kwargs |
| tranfer | ftpget | ftpaddress,ftpname,ftppasswd,remotepath,localpath,identifier,port=None,**kwargs |