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. You will find a complete manual for xmagpy in the docs.
Typical usage of the basic MagPy package for reading and visualising data looks like this:
#!/usr/bin/env python
from magpy.stream import read
import magpy.mpplot as mp
stream = read('filename_or_url')
mp.plot(stream)
Below you will find a quick guide to usage of the basic MagPy package. For instructions on xmagpy please refer to the document "An introduction to XMagPy" in the docs. You can also subscribe to our information channel at Telegram for further information on updates and current issues.
Pleas note that with the publication of MagPy 1.0 the recommended python enironment is >= 3.6. The following installation instructions will assume such an environment. Particularly if you are using Python2.7 please go to the end of this sections for help.
This section is currently updated and will be ready with the publication of MagPy 1.0.
Tested for Ubuntu 18.04 and Debian Stretch (full installation with all optional packages). Please note that installation requires python 3.x.
$ sudo pip3 install geomagpy #Will install MagPy and all dependencies $ sudo pip3 install wxpython #Will install WX graphics system
If wxpython installation via pip3 fails you can try
$ sudo apt-get install python3-wxgtk4.0
You can now run XMagPy by using the following command
$ xmagpy
To upgrade to the most recent version:
$ sudo pip3 install -U geomagpy
In order to create a desktop link on linux systems please refer to instruction too be found your distribution. For Ubunutu and other Debian systems such links are created as follows:
Firstly create a file "xmagpy.desktop" which contains:
[Desktop Entry] Type=Application Name=XMagPy GenericName=GeoMagPy User Interface Exec=xmagpy Icon=/usr/local/lib/python3.7/dist-packages/magpy/gui/magpy128.xpm Terminal=false Categories=Application;Development;
Then copy this file to the systems application folder:
sudo cp xmagpy.desktop /usr/share/applications/
- we recommend Miniconda or Anaconda
- see e.g. https://docs.continuum.io/anaconda/install for more details
- before continuiung, test whether python is working. Open a terminal and run python
Open a terminal and use the following commands:
$ pip install geomagpy #Will install MagPy and all dependencies $ pip install wxpython #Will install WX graphics system for XMagPy
You can now run XMagPy from the terminal by using the following command
$ xmagpyw
Open Finder and search for xmagpyw. Copy it to the desktop. To change the icon, click on the xmagpyw link, open information and replace the image on the upper left with e.g. magpy128.jpg (also to be found using finder).
- get the MagPy Windows installer here (under Downloads): https://cobs.zamg.ac.at
- download and execute magpy-x.x.x.exe
- all required packages are included in the installer
MagPy will have a sub-folder in the Start menu. Here you will find three items:
* command -> opens a DOS shell within the Python environment e.g. for updates * python -> opens a python shell ready for MagPy * xmagpy -> opens the MagPy graphical user interface
- right-click on subfolder "command" in the start menu
- select "run as administrator"
- issue the following command "pip install -U geomagpy" (you can also specify the version e.g. pip install geomagpy==0.x.x)
- Download a most recent version of WinPython3.x
- Unpack in your home directory
- Go to the WinPython Folder and run WinPython command prompt
- issue the same commands as for MacOS installation
- to run XMagPy: use xmagpy from the WinPython command promt.
The current version of magpy is still supporting python 2.7, although it is highly recommended to switch to python >= 3.6. Installation on python 2.7 is more complex, as some packages for graphical user interface and CDF support not as well supported. Please note: None of the addtional steps is necessary for python 3.x.
Get a recent version of NasaCDF for your platform, enables CDF support for formats like ImagCDF. Package details and files can be found at http://cdf.gsfc.nasa.gov/
On Linux such installation will look like (http://cdf.gsfc.nasa.gov/html/sw_and_docs.html)
$ tar -zxvf cdf37_0-dist-all.tar.gz $ cd cdf37... $ make OS=linux ENV=gnu CURSES=yes FORTRAN=no UCOPTIONS=-O2 SHARED=yes all $ sudo make INSTALLDIR=/usr/local/cdf install
Install the following additional compilers before continuing (required for spacepy): Linux: install gcc MacOs: install gcc and gfortran
Install coordinate system transformation support:
$ sudo apt-get install libproj-dev proj-data proj-bin
On Linux this will look like:
$ sudo apt-get install python-matplotlib python-scipy python-h5py cython python-pip $ sudo apt-get install python-wxgtk3.0 # or python-wxgtk2.8 (Debian Stretch) $ sudo apt-get install python-twisted $ sudo pip install ffnet $ sudo pip install pyproj==1.9.5 $ sudo pip install pyserial $ sudo pip install service_identity $ sudo pip install ownet $ sudo pip install spacepy $ sudo pip install geomagpy
On Mac and Windows you need to download a python interpreter like Anaconda or [WinPython] and then install similar packages, particluarly the old wxpython 3.x.
1.5.1 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 (recommended is >=3.6)
Recommended: - Python packages: * wxpython (for python2.7 it needs to be 3.x or older) * NasaCDF (python 2.7 only) * SpacePy (python 2.7 only)
Other useful Software:
pyproj (for geographic coordinate systems)
MySQL (database features)
Webserver (e.g. Apache2, PHP)
git clone git://github.com/GeomagPy/MagPy.git cd magpy* sudo python setup.py install
written by R. Leonhardt, R. Bailey (April 2017)
MagPy's functionality can be accessed basically in three different ways: 1) Directly import and use the magpy package into a python environment 2) Run the graphical user interface xmagpy (xmagpyw for Mac) 3) Use predefined applications "Scripts"
The following section will primarily deal with way 1. For 2 - xmagpy - we refer to the video tutorials whcih can be found here: Section 3 contains examples for predefined applications/scripts
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: IAGA ZIP (IAGA2002, zip compressed) file with 1 second HEZ dataexample2: MagPy Archive (CDF) file with 1 sec F dataexample3: MagPy Basevalue (TXT) ascii file with DI and baseline dataexample4: INTERMAGNET ImagCDF (CDF) file with one week of 1 second dataexample5: MagPy Archive (CDF) raw data file with xyz and supporting dataexample6a: MagPy DI (txt) raw data file with DI measurementexample6b: MagPy like 6a to be used with example4flagging_example: MagPy FlagDictionary (JSON) flagging info to be used with example1recipe1_flags: MagPy FlagDictionary (JSON) to be used with cookbook recipe 1
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:
Validity of data formats, e.g.:
data = read('myiaffile.bin', debug=True)Completeness of meta-information
Conformity of applied techniques to respective rules
Internal consistency of data
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 combine the resulting baseline functions to a list:
stream = read(mydata,starttime='2016-01-01',endtime='2016-03-01') basevalues = read(mybasevalues) adoptedbasefunc = [] adoptedbasefunc.append(stream.baseline(basevalues, extradays=0, fitfunc='poly', fitdegree=1,startabs='2016-01-01',endabs='2016-02-01') adoptedbasefunc.append(stream.baseline(basevalues, extradays=0, fitfunc='spline', knotstep=0.33,startabs='2016-01-02',endabs='2016-01-03') corr = stream.bc()
The combined baseline can be plotted accordingly. Extend the function parameters with each additional segment.
mp.plot(basevalues, variables=['dx','dy','dz'], symbollist=['o','o','o'], padding=[5,0.05,5], function=adoptedbasefunc)
Adding a baseline for scalar data, which is determined from the delta F values provided within the basevalue data stream:
scalarbasefunc = [] scalarbasefunc.append(basevalues.baseline(basevalues, keys=['df'], extradays=0, fitfunc='poly', fitdegree=1,startabs='2016-01-01',endabs='2016-03-01')) plotfunc = adoptedbasefunc plotfunc.extend(scalarbasefunc) mp.plot(basevalues, variables=['dx','dy','dz','df'], symbollist=['o','o','o','o'], padding=[5,0.05,5,5], function=plotfunc)
Getting dailymeans and correction for scalar baseline can be acomplished by:
meanstream = stream.dailymeans() meanstream = meanstream.func2stream(scalarbasefunc,mode='sub',keys=['f'],fkeys=['df']) meanstream = meanstream.delta_f()
Please note that here the function originally determined from the deltaF
(df) values of the basevalue data needs to be applied to the F column
(f) from the data stream. Before saving we will also extract the
baseline parameters from the meta information, which is automatically
generated by the baseline method.
absinfo = stream.header.get('DataAbsInfo','')
fabsinfo = basevalues.header.get('DataAbsInfo','')
The following will create a BLV file:
basevalues.write('/my/path', coverage='all', format_type='BLV', diff=meanstream, year='2016', absinfo=absinfo, deltaF=fabsinfo)
Information on the adopted baselines will be extracted from option
absinfo. If several functions are provided, baseline jumps will be
automatically inserted into the BLV data file. The output of adopted
scalar baselines is configured by option deltaF. If a number is
provided, this value is assumed to represent the adopted scalar
baseline. If either 'mean' or 'median' are given (e.g.
deltaF='mean'), then the mean/median value of all delta F values in
the basevalues stream is used, requiring that such data is
contained. Providing functional parameters as stored in a
DataAbsInfo meta information field, as shown above, will calculate
and use the scalar baseline function. 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 above.
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)
MagPy comes with a steadily increasing number of applications for various purposes. These applications can be run from some command prompt and allow to simplify/automize some commonly used applications of MagPy. All applications have the same syntax, consisting of the name of application and options. The option -h is available for all applications and provides an overview about purpose and options of the application:
$> application -h
On Linux Systems all applications are added the bin directory and can be run directly from any command interface/terminal after installation of MagPy:
$> application -h
After installing MagPy/GeomagPy on Windows, three executables are found in the MagPy program folder. For running applications you have to start the MagPy "command prompt". In this terminal you will have to go to the Scripts directory:
.../> cd Scripts
And here you now can run the application of your choice using the python environment:
.../Scripts>python application -h
The available applications are briefly intruduced in the following. Please refer to "application -h" for all available options for each application.
mpconvert converts bewteen data formats based on MagPy. Typical applications are the conversion of binary data formats to readable ASCII data sets or the conversion.
Typical applications include
Convert IAGA seconds to IMAGCDF and include obligatory meta information:
mpconvert -r "/iagaseconds/wic201701*" -f IMAGCDF -c month -w "/tmp" -m "DataStandardLevel:Full,IAGACode:WIC,DataReferences:myref"Convert IMAGCDF seconds to IAF minute (using IAGA/IM filtering procedures):
mpconvert -r "/imagcdf/wic_201701_000000_PT1S_4.cdf" -f IAF -i -w "/tmp"
mpconvert -r "/srv/products/data/magnetism/definitive/wic2017/ImagCDF/wic_201708_000000_PT1S_4.cdf" -f IAF -i -w "/tmp"
Used to store encrypted credential information for automatic data transfer. So that sensitive information has not to be written in plain text in scripts or cron jobs.
Add information for ftp data transfer. This information is encrypted and can be accessed by referring to the shortcut "zamg".
addcred -t transfer -c zamg -u max -p geheim -a "ftp://ftp.remote.ac.at" -l 21