Metadata-Version: 1.0
Name: GeomagPy
Version: 0.3.98
Summary: Geomagnetic analysis tools.
Home-page: http://pypi.python.org/pypi/GeomagPy/
Author: R. Leonhardt, R. Bailey, M. Miklavec
Author-email: roman.leonhardt@zamg.ac.at
License: LICENSE.txt
Description: MagPy
        =====
        
        **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. INSTALLATION
        ---------------
        
        1.1 Windows installation - WinPython Package
        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        
        1.1.1 Install NASA `CDF <https://cdf.gsfc.nasa.gov/>`__ 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
        -  Note: please use 32 bit installer.
        
        1.1.2 Install MagPy for Windows
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        
        -  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
        
        1.1.3 Post-installation information
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        
        -  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
        
        1.2 Linux/MacOs installation - Anaconda
        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        
        1.2.1 Install `Anaconda <https://www.continuum.io/downloads>`__ 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
        
        1.2.2 Install NASA CDF support
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        
        -  http://cdf.gsfc.nasa.gov/
        -  download and install the latest cdf version for your operating system
        
        1.2.3 Install MagPy and SpacePy (required for CDF support)
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        
        -  open a Terminal
        -  ... known issues: eventually change to the anaconda2/bin directory
           before running python (if not set as default)
        -  ... check by starting python in the terminal
        -  run './pip install spacepy'
        -  ... known issues: installation of spacepy eventually requires a
           fortran compiler
        -  ... e.g. Linux: install gcc
        -  ... e.g. MacOs: install gcc and gfortran
        -  run './pip install geomagpy'
        -  ... known issues: e.g. Linux: MySQL-python problem -> install
           libmysqlclient-dev on linux (e.g. debian/ubuntu: sudo apt-get install
           libmysqlclient-dev)
        
        1.2.4 Post-installation information
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        
        -  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 version==new-version'.
           Installation provides both shell based magpy and the graphical user
           interface xmagpy
        
        -  running magpy: \* type "python" in a terminal -> opens a python shell
           ready for MagPy \* type "xmagpy" in a terminal -> open the graphical
           user interface of MagPy \* !! MacOS: !! type "xmagpyw" in a terminal
           -> open the graphical user interface of MagPy (since v0.3.95)
        
        -  adding a shortcut for xmagpy: coming soon
        
        1.3 MacOs installation - MacPorts
        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        
        1.3.1 Install `MacPorts <https://www.macports.org/>`__
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        
        1.3.2 coming soon
        ^^^^^^^^^^^^^^^^^
        
        1.4 Platform independent installations - Docker
        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        
        1.4.1 Install `Docker <https://www.docker.com/>`__ (toolbox) on your operating system
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        
        ::
        
             - https://docs.docker.com/engine/installation/
        
        1.4.2 Get the MagPy Image
        ^^^^^^^^^^^^^^^^^^^^^^^^^
        
        ::
        
             - open a docker shell
        
                    >>> docker pull geomagpy/magpy:latest
                    >>> docker run -d --name magpy -p 8000:8000 geomagpy/magpy:latest
        
        1.4.3 Open a browser
        ^^^^^^^^^^^^^^^^^^^^
        
        ::
        
             - 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
                    >>> ...
        
        1.5 Install from source (experts only)
        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        
        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)
        
        1.5.1 Linux
        ^^^^^^^^^^^
        
        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
        
        1.5.2 Windows
        ^^^^^^^^^^^^^
        
        | 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::raw-latex:`\user`:raw-latex:`\Downloads`:raw-latex:`\GeomagPy`
        | g) execute "setup.py install"
        
        2. A quick guide to MagPy
        -------------------------
        
        written by R. Leonhardt, R. Bailey (April 2017)
        
        2.1 Getting started
        ~~~~~~~~~~~~~~~~~~~
        
        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.
        
        2.2 Reading and writing data
        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        
        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 <http://www.intermagnet.org>`__ CDF
           (ImagCDF) file with 1 second xyzf data
        -  ``example2``: `INTERMAGNET <http://www.intermagnet.org>`__ Archive
           format (IAF) file for one month with 1 min, 1 hour, K and mean data
        -  ``example3``: MagPy readable DI data file with data from 1 single DI
           measurement
        -  ``example4``: MagPy Basevalue file (PYSTR) with analysis results of
           several DI data
        
        2.2.1 Reading
        ^^^^^^^^^^^^^
        
        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() )
        
        2.2.2 Writing
        ^^^^^^^^^^^^^
        
        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 <http://www.intermagnet.org>`__ 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.
        
        2.2.3 Other possibilities for reading files
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        
        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')
        
        2.2.4 Selecting timerange
        ^^^^^^^^^^^^^^^^^^^^^^^^^
        
        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")
        
        .. raw:: html
        
           <!--#### 2.2.5 Tutorial
        
           For the ongoing quick example please use the following steps. This will create daily IAGA02 files within the directory. Please make sure that the directory is empty before writing data to it.
        
           A) Load example data
        
           Within the MagPy package, several example data sets are provided:
        
              example1: [INTERMAGNET] CDF (ImagCDF) file with 1 second data
              example2: [INTERMAGNET] Archive format (IAF) file with 1 min, 1 hour, K and mean data
              example3: MagPy readable DI data file with data from 1 single DI measurement
              example4: MagPy Basevalue file (PYSTR) with analysis results of several DI data
        
                   # Replace example1 with a full path, if you have your own data 
                   data = read(example1)
        
           B) Store it locally in your favorite directory
        
                   data.write('/tmp/',filenamebegins='MyExample_', format_type='IAGA')
        
           Please note that storing data in a different formt might require additional meta information. Checkout section (i) on how to deal with these aspects.-->
        
        2.3 Getting help on options and usage
        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        
        2.3.1 Python's help function
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        
        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)
        
        .. raw:: html
        
           <!--#### 2.3.2 Tutorial
        
                   help(data.fit)-->
        
        2.3.2 MagPy's logging system
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        
        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)
        
        2.4 Plotting
        ~~~~~~~~~~~~
        
        You will find some example plots at the `Conrad
        Observatory <http://www.conrad-observatory.at>`__.
        
        2.4.1 Quick (and not dirty)
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^
        
        ::
        
                import magpy.mpplot as mp
                mp.plot(data)
        
        2.4.2 Some options
        ^^^^^^^^^^^^^^^^^^
        
        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'])
        
        2.4.3 Data from multiple streams
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        
        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']])
        
        .. raw:: html
        
           <!--#### 2.4.4 Tutorial
        
           Read a second stream
        
                   otherdata = read(WDC)
        
           Plot xyz data from both streams
        
                   mp.plotStreams([data,otherdata]) -->
        
        2.5 Flagging data
        ~~~~~~~~~~~~~~~~~
        
        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.
        
        2.5.1 Mark data spikes
        ^^^^^^^^^^^^^^^^^^^^^^
        
        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)
        
        2.5.2 Flag time range
        ^^^^^^^^^^^^^^^^^^^^^
        
        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)
        
        2.5.3 Save flagged data
        ^^^^^^^^^^^^^^^^^^^^^^^
        
        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')
        
        2.5.4 Save flags separately
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^
        
        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')
        
        2.5.5 Drop flagged data
        ^^^^^^^^^^^^^^^^^^^^^^^
        
        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')
        
        2.6 Basic methods
        ~~~~~~~~~~~~~~~~~
        
        2.6.1 Filtering
        ^^^^^^^^^^^^^^^
        
        MagPy's ``filter`` uses the settings recommended by
        `IAGA <http://www.iaga-aiga.org/>`__/`INTERMAGNET <http://www.intermagnet.org>`__.
        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',''))
        
        2.6.2 Coordinate transformation
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        
        Assuming vector data in columns [x,y,z] you can freely convert between
        xyz, hdz, and idf coordinates:
        
        ::
        
                cleandata = cleandata.xyz2hdz()
        
        2.6.3 Calculate delta F
        ^^^^^^^^^^^^^^^^^^^^^^^
        
        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')
        
        2.6.4 Calculate Means
        ^^^^^^^^^^^^^^^^^^^^^
        
        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'))
        
        2.6.5 Applying offsets
        ^^^^^^^^^^^^^^^^^^^^^^
        
        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})
        
        2.6.6 Scaling data
        ^^^^^^^^^^^^^^^^^^
        
        Individual columns can also be multiplied by values provided in a
        dictionary:
        
        ::
        
                multdata = cleandata.multiply({'x':-1})
        
        2.6.7 Fit functions
        ^^^^^^^^^^^^^^^^^^^
        
        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)
        
        2.6.8 Derivatives
        ^^^^^^^^^^^^^^^^^
        
        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'])
        
        2.6.9 All methods at a glance
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        
        For a summary of all supported methods, see the section **List of all
        MagPy methods** below.
        
        2.7 Geomagnetic analysis
        ~~~~~~~~~~~~~~~~~~~~~~~~
        
        2.7.1 Determination of K indices
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        
        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 <http://www.intermagnet.org>`__ 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 (``'-'``).
        
        2.7.2 Automated geomagnetic storm detection
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        
        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)
        
        2.7.3 Sq analysis
        ^^^^^^^^^^^^^^^^^
        
        Methods are currently in preparation.
        
        2.7.4 Validity check of data
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        
        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 <http://www.iaga-aiga.org/>`__, WDC, or
        `INTERMAGNET <http://www.intermagnet.org>`__. 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
        
        2.7.5 Spectral Analysis and Noise
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        
        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'])
        
        2.8 Handling multiple streams
        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        
        2.8.1 Merging streams
        ^^^^^^^^^^^^^^^^^^^^^
        
        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'``.
        
        2.8.2 Differences between streams
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        
        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'])
        
        2.9 The art of meta-information
        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        
        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 <http://www.iaga-aiga.org/>`__,
        `INTERMAGNET <http://www.intermagnet.org>`__ 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)))
        
        2.9.1 Conversion to ImagCDF - Adding meta-information
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        
        To convert data from `IAGA <http://www.iaga-aiga.org/>`__ or IAF formats
        to the new `INTERMAGNET <http://www.intermagnet.org>`__ 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')
        
        2.9.2 Providing location data
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        
        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 <https://www.epsg-registry.org/>`__ codes for coordinates. If you
        provide the geodetic references as follows, and provided that the
        `proj4 <https://github.com/OSGeo/proj.4>`__ 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
                >>>...
        
        2.9.3 Special meta-information fields
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        
        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')
        
        2.10 Data transfer
        ~~~~~~~~~~~~~~~~~~
        
        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
        
        2.10.1 Downloads
        ^^^^^^^^^^^^^^^^
        
        Use the ``read`` method as outlined above. No additional imports are
        required.
        
        2.10.2 FTP upload
        ^^^^^^^^^^^^^^^^^
        
        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.
        
        2.10.3 Secure communication protocol (SCP)
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        
        To transfer via SCP:
        
        ::
        
                mt.scptransfer('user@address:/remote/directory/','/path/to/data.cdf',passwd,timeout=60)
        
        2.10.4 Upload data to GIN
        ^^^^^^^^^^^^^^^^^^^^^^^^^
        
        Use the following command:
        
        ::
        
                mt.ginupload('/path/to/data.cdf', ginuser, ginpasswd, ginaddress, faillog=True, stdout=True)
        
        2.10.5 Avoiding real-text passwords in scripts
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        
        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')
        
        2.11 DI measurements, basevalues and baselines
        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        
        These procedures require an additional import:
        
        ::
        
                from magpy import absolutes as di
        
        2.11.1 Data structure of DI measurements
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        
        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.
        
        2.11.2 Reading DI data
        ^^^^^^^^^^^^^^^^^^^^^^
        
        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.
        
        2.11.3 Reading BLV files
        ^^^^^^^^^^^^^^^^^^^^^^^^
        
        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)
        
        2.11.4 Basevalues and baselines
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        
        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.
        
        2.11.5 Applying baselines
        ^^^^^^^^^^^^^^^^^^^^^^^^^
        
        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','')
        
        2.11.6 Saving basevalue and baseline information
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        
        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.
        
        2.12 Database support
        ~~~~~~~~~~~~~~~~~~~~~
        
        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 <https://www.mysql.com/>`__ 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 <http://www.iaga-aiga.org/>`__/`INTERMAGNET <http://www.intermagnet.org>`__
        definitive data. Furthermore, unique sensor information such as type and
        serial number is required.
        
        ::
        
                import magpy import database as mdb
        
        2.12.1 Setting up a MagPy database (using MySQL)
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        
        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';
        
        2.12.2 Initializing a MagPy database
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        
        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)
        
        2.12.3 Adding data to the database
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        
        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.
        
        2.12.4 Reading data
        ^^^^^^^^^^^^^^^^^^^
        
        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``.
        
        2.12.5 Meta data
        ^^^^^^^^^^^^^^^^
        
        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')
        
        2.13 Monitoring scheduled scripts
        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        
        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 <https://www.nagios.org/>`__, you can easily create mail/SMS
        notfications of such changes, in addition to monitoring processes, live
        times, disks etc. `MARCOS <https://github.com/geomagpy/MARCOS>`__ comes
        along with some instructions on how to use Nagios/MagPy for data
        acquisition monitoring.
        
        2.14 Data acquisition support
        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        
        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 <https://github.com/geomagpy/MARTAS>`__ and
        `MARCOS <https://github.com/geomagpy/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 <http://wamp-proto.org/>`__ (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.
        
        2.15 Graphical user interface
        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        
        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 Current developments
        ~~~~~~~~~~~~~~~~~~~~~~~~~
        
        2.16.1 Exchange data objects with `ObsPy <https://github.com/obspy/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'])
        
        2.16.2 Flagging in ImagCDF
        ^^^^^^^^^^^^^^^^^^^^^^^^^^
        
        ::
        
                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)
        
        2.17 List of all MagPy methods
        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        
        Please use the help method (section 2.3) for descriptions and return
        values.
        
        +--------+---------+------------+
        | group  | method  | parameter  |
        +========+=========+============+
        | -      | **findp | name, path |
        |        | ath**   |            |
        +--------+---------+------------+
        | -      | \*\*\_p | method     |
        |        | ickle\_ |            |
        |        | method\ |            |
        |        | *\*     |            |
        +--------+---------+------------+
        | -      | \*\*\_u | func\_name |
        |        | npickle | ,          |
        |        | \_metho | obj, cls   |
        |        | d\*\*   |            |
        +--------+---------+------------+
        | stream | ****ini | self,      |
        |        | t****   | container= |
        |        |         | None,      |
        |        |         | header={}, |
        |        |         | ndarray=No |
        |        |         | ne         |
        +--------+---------+------------+
        | stream | **ext** | self,      |
        |        |         | columnstru |
        |        |         | cture      |
        +--------+---------+------------+
        | stream | **add** | self,      |
        |        |         | datlst     |
        +--------+---------+------------+
        | stream | **lengt | self       |
        |        | h**     |            |
        +--------+---------+------------+
        | stream | **repla | self,      |
        |        | ce**    | datlst     |
        +--------+---------+------------+
        | stream | **copy* | self       |
        |        | *       |            |
        +--------+---------+------------+
        | stream | ****str | self       |
        |        | ****    |            |
        +--------+---------+------------+
        | stream | ****rep | self       |
        |        | r****   |            |
        +--------+---------+------------+
        | stream | ****get | self,      |
        |        | item*** | index      |
        |        | *       |            |
        +--------+---------+------------+
        | stream | ****len | self       |
        |        | ****    |            |
        +--------+---------+------------+
        | stream | **clear | self       |
        |        | \_heade |            |
        |        | r**     |            |
        +--------+---------+------------+
        | stream | **exten | self,datls |
        |        | d**     | t,header,n |
        |        |         | darray     |
        +--------+---------+------------+
        | stream | **union | self,colum |
        |        | **      | n          |
        +--------+---------+------------+
        | stream | **remov | self       |
        |        | eduplic |            |
        |        | ates**  |            |
        +--------+---------+------------+
        | stream | **start | self,      |
        |        | **      | dateformt= |
        |        |         | None       |
        +--------+---------+------------+
        | stream | **end** | self,      |
        |        |         | dateformt= |
        |        |         | None       |
        +--------+---------+------------+
        | stream | **findt | self,time, |
        |        | ime**   | \*\*kwargs |
        +--------+---------+------------+
        | stream | \*\*\_f | self       |
        |        | ind\_t\ |            |
        |        | _limits |            |
        |        | \*\*    |            |
        +--------+---------+------------+
        | stream | \*\*\_p | self       |
        |        | rint\_k |            |
        |        | ey\_hea |            |
        |        | ders\*\ |            |
        |        | *       |            |
        +--------+---------+------------+
        | stream | \*\*\_g | self,\*\*k |
        |        | et\_key | wargs      |
        |        | \_heade |            |
        |        | rs\*\*  |            |
        +--------+---------+------------+
        | stream | \*\*\_g | self       |
        |        | et\_key |            |
        |        | \_names |            |
        |        | \*\*    |            |
        +--------+---------+------------+
        | stream | **drope | self       |
        |        | mpty**  |            |
        +--------+---------+------------+
        | stream | **fille | self,      |
        |        | mpty**  | ndarray,   |
        |        |         | keylist    |
        +--------+---------+------------+
        | stream | **sorti | self       |
        |        | ng**    |            |
        +--------+---------+------------+
        | stream | \*\*\_g | self, key, |
        |        | et\_lin | value      |
        |        | e\*\*   |            |
        +--------+---------+------------+
        | stream | \*\*\_t | self, keys |
        |        | ake\_co |            |
        |        | lumns\* |            |
        |        | \*      |            |
        +--------+---------+------------+
        | stream | \*\*\_r | self, key, |
        |        | emove\_ | value      |
        |        | lines\* |            |
        |        | \*      |            |
        +--------+---------+------------+
        | stream | \*\*\_g | self, key  |
        |        | et\_col |            |
        |        | umn\*\* |            |
        +--------+---------+------------+
        | stream | \*\*\_p | self,      |
        |        | ut\_col | column,    |
        |        | umn\*\* | key,       |
        |        |         | \*\*kwargs |
        +--------+---------+------------+
        | stream | \*\*\_m | self, key, |
        |        | ove\_co | put2key    |
        |        | lumn\*\ |            |
        |        | *       |            |
        +--------+---------+------------+
        | stream | \*\*\_d | self,key   |
        |        | rop\_co |            |
        |        | lumn\*\ |            |
        |        | *       |            |
        +--------+---------+------------+
        | stream | \*\*\_c | self, key  |
        |        | lear\_c |            |
        |        | olumn\* |            |
        |        | \*      |            |
        +--------+---------+------------+
        | stream | \*\*\_r | self,      |
        |        | educe\_ | pointlimit |
        |        | stream\ | =100000    |
        |        | *\*     |            |
        +--------+---------+------------+
        | stream | \*\*\_r | self       |
        |        | emove\_ |            |
        |        | nancolu |            |
        |        | mns\*\* |            |
        +--------+---------+------------+
        | stream | \*\*\_a | self,      |
        |        | ic\*\*  | signal, k, |
        |        |         | debugmode= |
        |        |         | None       |
        +--------+---------+------------+
        | stream | **harmf | self,nt,   |
        |        | it**    | val,       |
        |        |         | fitdegree  |
        +--------+---------+------------+
        | stream | \*\*\_g | self, key, |
        |        | et\_max | returntime |
        |        | \*\*    | =False     |
        +--------+---------+------------+
        | stream | \*\*\_g | self, key, |
        |        | et\_min | returntime |
        |        | \*\*    | =False     |
        +--------+---------+------------+
        | stream | **ampli | self,key   |
        |        | tude**  |            |
        +--------+---------+------------+
        | stream | \*\*\_g | self, t,   |
        |        | f\*\*   | tau        |
        +--------+---------+------------+
        | stream | \*\*\_h | self, p, x |
        |        | f\*\*   |            |
        +--------+---------+------------+
        | stream | \*\*\_r | self,      |
        |        | esidual | func, y    |
        |        | \_func\ |            |
        |        | *\*     |            |
        +--------+---------+------------+
        | stream | \*\*\_t | self,      |
        |        | au\*\*  | period,    |
        |        |         | fac=0.8325 |
        |        |         | 5461       |
        +--------+---------+------------+
        | stream | \*\*\_c | self,      |
        |        | onverts | coordinate |
        |        | tream\* | ,          |
        |        | \*      | \*\*kwargs |
        +--------+---------+------------+
        | stream | \*\*\_d | self,index |
        |        | elete\* |            |
        |        | \*      |            |
        +--------+---------+------------+
        | stream | \*\*\_a | self,strea |
        |        | ppend\* | m          |
        |        | \*      |            |
        +--------+---------+------------+
        | stream | \*\*\_d | self,      |
        |        | et\_tra | period     |
        |        | nge\*\* |            |
        +--------+---------+------------+
        | stream | \*\*\_i | self, s    |
        |        | s\_numb |            |
        |        | er\*\*  |            |
        +--------+---------+------------+
        | stream | \*\*\_n | self,      |
        |        | ormaliz | column     |
        |        | e\*\*   |            |
        +--------+---------+------------+
        | stream | \*\*\_t | self, time |
        |        | esttime |            |
        |        | \*\*    |            |
        +--------+---------+------------+
        | stream | \*\*\_d | self, key  |
        |        | rop\_na |            |
        |        | ns\*\*  |            |
        +--------+---------+------------+
        | stream | \*\*\_s | self, keys |
        |        | elect\_ |            |
        |        | keys\*\ |            |
        |        | *       |            |
        +--------+---------+------------+
        | stream | \*\*\_s | self,      |
        |        | elect\_ | starttime= |
        |        | timeran | None,      |
        |        | ge\*\*  | endtime=No |
        |        |         | ne,        |
        |        |         | maxidx=-1  |
        +--------+---------+------------+
        | stream | **aic\_ | self, key, |
        |        | calc**  | \*\*kwargs |
        +--------+---------+------------+
        | stream | **basel | self,      |
        |        | ine**   | absoluteda |
        |        |         | ta,        |
        |        |         | \*\*kwargs |
        +--------+---------+------------+
        | stream | **strea | self,      |
        |        | m2dict* | keys=['dx' |
        |        | *       | ,'dy','dz' |
        |        |         | ],         |
        |        |         | dictkey='D |
        |        |         | ataBaseVal |
        |        |         | ues'       |
        +--------+---------+------------+
        | stream | **dict2 | self,dictk |
        |        | stream* | ey='DataBa |
        |        | *       | seValues'  |
        +--------+---------+------------+
        | stream | **basel | self,      |
        |        | ineAdva | absdata,   |
        |        | nced**  | baselist,  |
        |        |         | \*\*kwargs |
        +--------+---------+------------+
        | stream | **bc**  | self,      |
        |        |         | function=N |
        |        |         | one,       |
        |        |         | ctype=None |
        |        |         | ,          |
        |        |         | alpha=0.0, |
        |        |         | level='pre |
        |        |         | liminary'  |
        +--------+---------+------------+
        | stream | **binde | self,key,f |
        |        | tector* | lagnum=1,k |
        |        | *       | eystoflag= |
        |        |         | ['x'],sens |
        |        |         | orid=None, |
        |        |         | text=None, |
        |        |         | \*\*kwargs |
        +--------+---------+------------+
        | stream | **calc\ | self,      |
        |        | _f**    | \*\*kwargs |
        +--------+---------+------------+
        | stream | **daily | self,      |
        |        | means** | keys=['x', |
        |        |         | 'y','z','f |
        |        |         | '],        |
        |        |         | \*\*kwargs |
        +--------+---------+------------+
        | stream | **date\ | self,      |
        |        | _offset | offset     |
        |        | **      |            |
        +--------+---------+------------+
        | stream | **delta | self,      |
        |        | \_f**   | \*\*kwargs |
        +--------+---------+------------+
        | stream | **f\_fr | self,      |
        |        | om\_df* | \*\*kwargs |
        |        | *       |            |
        +--------+---------+------------+
        | stream | **diffe | self,      |
        |        | rentiat | \*\*kwargs |
        |        | e**     |            |
        +--------+---------+------------+
        | stream | **DWT\_ | self,key=' |
        |        | calc**  | x',wavelet |
        |        |         | ='db4',lev |
        |        |         | el=3,plot= |
        |        |         | False,outf |
        |        |         | ile=None,  |
        +--------+---------+------------+
        | stream | **event | self, key, |
        |        | logger* | values,    |
        |        | *       | compare=No |
        |        |         | ne,        |
        |        |         | stringvalu |
        |        |         | es=None,   |
        |        |         | addcomment |
        |        |         | =None,     |
        |        |         | debugmode= |
        |        |         | None       |
        +--------+---------+------------+
        | stream | **extra | self, key, |
        |        | ct**    | value,     |
        |        |         | compare=No |
        |        |         | ne,        |
        |        |         | debugmode= |
        |        |         | None       |
        +--------+---------+------------+
        | stream | **extra | self,      |
        |        | ct2**   | keys,      |
        |        |         | get='>',   |
        |        |         | func=None, |
        |        |         | debugmode= |
        |        |         | None       |
        +--------+---------+------------+
        | stream | **extra | self,      |
        |        | polate* | start, end |
        |        | *       |            |
        +--------+---------+------------+
        | stream | **filte | self,\*\*k |
        |        | r**     | wargs      |
        +--------+---------+------------+
        | stream | **fit** | self,      |
        |        |         | keys,      |
        |        |         | \*\*kwargs |
        +--------+---------+------------+
        | stream | **extra | self       |
        |        | ctflags |            |
        |        | **      |            |
        +--------+---------+------------+
        | stream | **flagf | self,index |
        |        | ast**   | array,flag |
        |        |         | ,          |
        |        |         | comment,ke |
        |        |         | ys=None    |
        +--------+---------+------------+
        | stream | **flag\ | self,      |
        |        | _range* | \*\*kwargs |
        |        | *       |            |
        +--------+---------+------------+
        | stream | **flag\ | self,      |
        |        | _outlie | \*\*kwargs |
        |        | r**     |            |
        +--------+---------+------------+
        | stream | **flag* | self,      |
        |        | *       | flaglist,  |
        |        |         | removedupl |
        |        |         | icates=Fal |
        |        |         | se,        |
        |        |         | debug=Fals |
        |        |         | e          |
        +--------+---------+------------+
        | stream | **flagl | self,flagl |
        |        | iststat | ist        |
        |        | s**     |            |
        +--------+---------+------------+
        | stream | **flagl | self,flagl |
        |        | istclea | ist        |
        |        | n**     |            |
        +--------+---------+------------+
        | stream | **strea | self,      |
        |        | m2flagl | userange=T |
        |        | ist**   | rue,       |
        |        |         | flagnumber |
        |        |         | =None,     |
        |        |         | keystoflag |
        |        |         | =None,     |
        |        |         | sensorid=N |
        |        |         | one,       |
        |        |         | comment=No |
        |        |         | ne         |
        +--------+---------+------------+
        | stream | **flagl | self,      |
        |        | istmod* | mode='sele |
        |        | *       | ct',       |
        |        |         | flaglist=[ |
        |        |         | ],         |
        |        |         | parameter= |
        |        |         | 'key',     |
        |        |         | value=None |
        |        |         | ,          |
        |        |         | newvalue=N |
        |        |         | one        |
        +--------+---------+------------+
        | stream | **flagl | self,      |
        |        | istadd* | flaglist,  |
        |        | *       | sensorid,  |
        |        |         | keys,      |
        |        |         | flagnumber |
        |        |         | ,          |
        |        |         | comment,   |
        |        |         | startdate, |
        |        |         | enddate=No |
        |        |         | ne         |
        +--------+---------+------------+
        | stream | **flag\ | self, key, |
        |        | _stream | flag,      |
        |        | **      | comment,   |
        |        |         | startdate, |
        |        |         | enddate=No |
        |        |         | ne,        |
        |        |         | samplingra |
        |        |         | te=0.,     |
        |        |         | debug=Fals |
        |        |         | e          |
        +--------+---------+------------+
        | stream | **simpl | self,basev |
        |        | ebaseva | alue,\*\*k |
        |        | lue2str | wargs      |
        |        | eam**   |            |
        +--------+---------+------------+
        | stream | **func2 | self,funct |
        |        | stream* | ion,\*\*kw |
        |        | *       | args       |
        +--------+---------+------------+
        | stream | **func\ | self,funct |
        |        | _add**  | ion,\*\*kw |
        |        |         | args       |
        +--------+---------+------------+
        | stream | **func\ | self,funct |
        |        | _subtra | ion,\*\*kw |
        |        | ct**    | args       |
        +--------+---------+------------+
        | stream | **get\_ | self,      |
        |        | gaps**  | \*\*kwargs |
        +--------+---------+------------+
        | stream | **get\_ | self,      |
        |        | rotatio | xcompensat |
        |        | nangle* | ion=0,keys |
        |        | *       | =['x','y', |
        |        |         | 'z'],\*\*k |
        |        |         | wargs      |
        +--------+---------+------------+
        | stream | **get\_ | self       |
        |        | samplin |            |
        |        | g\_peri |            |
        |        | od**    |            |
        +--------+---------+------------+
        | stream | **sampl | self,      |
        |        | ingrate | \*\*kwargs |
        |        | **      |            |
        +--------+---------+------------+
        | stream | **integ | self,      |
        |        | rate**  | \*\*kwargs |
        +--------+---------+------------+
        | stream | **inter | self,      |
        |        | pol**   | keys,      |
        |        |         | \*\*kwargs |
        +--------+---------+------------+
        | stream | **k\_ex | self,      |
        |        | tend**  | \*\*kwargs |
        +--------+---------+------------+
        | stream | **k\_fm | self,      |
        |        | i**     | \*\*kwargs |
        +--------+---------+------------+
        | stream | **lines | self       |
        |        | truct2n |            |
        |        | darray* |            |
        |        | *       |            |
        +--------+---------+------------+
        | stream | **mean* | self, key, |
        |        | *       | \*\*kwargs |
        +--------+---------+------------+
        | stream | **missi | self,v,win |
        |        | ngvalue | dow\_len,t |
        |        | **      | hreshold=0 |
        |        |         | .9,fill='m |
        |        |         | ean'       |
        +--------+---------+------------+
        | stream | **MODWT | self,key=' |
        |        | \_calc* | x',wavelet |
        |        | *       | ='haar',le |
        |        |         | vel=1,plot |
        |        |         | =False,out |
        |        |         | file=None  |
        +--------+---------+------------+
        | stream | **multi | self,      |
        |        | ply**   | factors,   |
        |        |         | square=Fal |
        |        |         | se         |
        +--------+---------+------------+
        | stream | **offse | self,      |
        |        | t**     | offsets,   |
        |        |         | \*\*kwargs |
        +--------+---------+------------+
        | stream | **plot* | self,      |
        |        | *       | keys=None, |
        |        |         | debugmode= |
        |        |         | None,      |
        |        |         | \*\*kwargs |
        +--------+---------+------------+
        | stream | **power | self, key, |
        |        | spectru | debugmode= |
        |        | m**     | None,      |
        |        |         | outfile=No |
        |        |         | ne,        |
        |        |         | fmt=None,  |
        |        |         | axes=None, |
        |        |         | title=None |
        |        |         | ,\*\*kwarg |
        |        |         | s          |
        +--------+---------+------------+
        | stream | **rando | self,perce |
        |        | mdrop** | ntage=None |
        |        |         | ,fixed\_in |
        |        |         | dicies=Non |
        |        |         | e          |
        +--------+---------+------------+
        | stream | **remov | self,      |
        |        | e**     | starttime= |
        |        |         | None,      |
        |        |         | endtime=No |
        |        |         | ne         |
        +--------+---------+------------+
        | stream | **remov | self,      |
        |        | e\_flag | \*\*kwargs |
        |        | ged**   |            |
        +--------+---------+------------+
        | stream | **remov | self,      |
        |        | e\_outl | \*\*kwargs |
        |        | ier**   |            |
        +--------+---------+------------+
        | stream | **resam | self,      |
        |        | ple**   | keys,      |
        |        |         | \*\*kwargs |
        +--------+---------+------------+
        | stream | **rotat | self,\*\*k |
        |        | ion**   | wargs      |
        +--------+---------+------------+
        | stream | **scale | self,      |
        |        | \_corre | keys,      |
        |        | ction** | scales,    |
        |        |         | \*\*kwargs |
        +--------+---------+------------+
        | stream | **selec | self,      |
        |        | tkeys** | keys,      |
        |        |         | \*\*kwargs |
        +--------+---------+------------+
        | stream | **smoot | self,      |
        |        | h**     | keys=None, |
        |        |         | \*\*kwargs |
        +--------+---------+------------+
        | stream | **spect | self,      |
        |        | rogram* | keys,      |
        |        | *       | per\_lap=0 |
        |        |         | .9,        |
        |        |         | wlen=None, |
        |        |         | log=False, |
        +--------+---------+------------+
        | stream | **stead | self, key, |
        |        | yrise** | timewindow |
        |        |         | ,          |
        |        |         | \*\*kwargs |
        +--------+---------+------------+
        | stream | **stere | self,      |
        |        | oplot** | \*\*kwargs |
        +--------+---------+------------+
        | stream | **trim* | self,      |
        |        | *       | starttime= |
        |        |         | None,      |
        |        |         | endtime=No |
        |        |         | ne,        |
        |        |         | newway=Fal |
        |        |         | se         |
        +--------+---------+------------+
        | stream | **vario | self,      |
        |        | meterco | variopath, |
        |        | rrectio | thedate,   |
        |        | n**     | \*\*kwargs |
        +--------+---------+------------+
        | stream | \*\*\_w | self,      |
        |        | rite\_f | format\_ty |
        |        | ormat\* | pe,        |
        |        | \*      | filenamebe |
        |        |         | gins,      |
        |        |         | filenameen |
        |        |         | ds,        |
        |        |         | coverage,  |
        |        |         | dateformat |
        |        |         | ,year      |
        +--------+---------+------------+
        | stream | **write | self,      |
        |        | **      | filepath,  |
        |        |         | compressio |
        |        |         | n=5,       |
        |        |         | \*\*kwargs |
        +--------+---------+------------+
        | stream | **idf2x | self,\*\*k |
        |        | yz**    | wargs      |
        +--------+---------+------------+
        | stream | **xyz2i | self,\*\*k |
        |        | df**    | wargs      |
        +--------+---------+------------+
        | stream | **xyz2h | self,\*\*k |
        |        | dz**    | wargs      |
        +--------+---------+------------+
        | stream | **hdz2x | self,\*\*k |
        |        | yz**    | wargs      |
        +--------+---------+------------+
        | -      | **coord | u,v,w,kind |
        |        | inatetr |            |
        |        | ansform |            |
        |        | **      |            |
        +--------+---------+------------+
        | -      | **isNum | s          |
        |        | ber**   |            |
        +--------+---------+------------+
        | -      | **find\ | array,valu |
        |        | _neares | e          |
        |        | t**     |            |
        +--------+---------+------------+
        | -      | **ceil\ | dt,seconds |
        |        | _dt**   |            |
        +--------+---------+------------+
        | -      | **read* | path\_or\_ |
        |        | *       | url=None,  |
        |        |         | dataformat |
        |        |         | =None,     |
        |        |         | headonly=F |
        |        |         | alse,      |
        |        |         | \*\*kwargs |
        +--------+---------+------------+
        | -      | \*\*\_r | filename,  |
        |        | ead\*\* | dataformat |
        |        |         | =None,     |
        |        |         | headonly=F |
        |        |         | alse,      |
        |        |         | \*\*kwargs |
        +--------+---------+------------+
        | -      | **savef | mylist=Non |
        |        | lags**  | e,path=Non |
        |        |         | e          |
        +--------+---------+------------+
        | -      | **loadf | path=None, |
        |        | lags**  | sensorid=N |
        |        |         | one,begin= |
        |        |         | None,      |
        |        |         | end=None   |
        +--------+---------+------------+
        | -      | **joinS | stream\_a, |
        |        | treams* | stream\_b, |
        |        | *       | \*\*kwargs |
        +--------+---------+------------+
        | -      | **appen | streamlist |
        |        | dStream |            |
        |        | s**     |            |
        +--------+---------+------------+
        | -      | **merge | stream\_a, |
        |        | Streams | stream\_b, |
        |        | **      | \*\*kwargs |
        +--------+---------+------------+
        | -      | **dms2d | dms        |
        |        | **      |            |
        +--------+---------+------------+
        | -      | **find\ | stream1,   |
        |        | _offset | stream2,   |
        |        | **      | guess\_low |
        |        |         | =-60.,     |
        |        |         | guess\_hig |
        |        |         | h=60.      |
        +--------+---------+------------+
        | -      | **diffS | stream\_a, |
        |        | treams* | stream\_b, |
        |        | *       | \*\*kwargs |
        +--------+---------+------------+
        | -      | **subtr | stream\_a, |
        |        | actStre | stream\_b, |
        |        | ams**   | \*\*kwargs |
        +--------+---------+------------+
        | -      | **stack | streamlist |
        |        | Streams | ,          |
        |        | **      | \*\*kwargs |
        +--------+---------+------------+
        | -      | **compa | stream\_a, |
        |        | reStrea | stream\_b  |
        |        | ms**    |            |
        +--------+---------+------------+
        | -      | **array | listofarra |
        |        | 2stream | ys,        |
        |        | **      | keystring, |
        |        |         | starttime= |
        |        |         | None,sr=No |
        |        |         | ne         |
        +--------+---------+------------+
        | -      | **obspy | opstream,  |
        |        | 2magpy* | keydict={} |
        |        | *       |            |
        +--------+---------+------------+
        | -      | **extra | datestring |
        |        | ctDateF |            |
        |        | romStri |            |
        |        | ng**    |            |
        +--------+---------+------------+
        | -      | **testT | time       |
        |        | imeStri |            |
        |        | ng**    |            |
        +--------+---------+------------+
        | -      | **denor | column,    |
        |        | malize* | startvalue |
        |        | *       | ,          |
        |        |         | endvalue   |
        +--------+---------+------------+
        | -      | **find\ | array,     |
        |        | _neares | value      |
        |        | t**     |            |
        +--------+---------+------------+
        | -      | **maskN | column     |
        |        | AN**    |            |
        +--------+---------+------------+
        | -      | **nan\_ | y          |
        |        | helper* |            |
        |        | *       |            |
        +--------+---------+------------+
        | -      | **neare | x          |
        |        | stPow2* |            |
        |        | *       |            |
        +--------+---------+------------+
        | -      | **test\ | time       |
        |        | _time** |            |
        +--------+---------+------------+
        | -      | **conve | lon,lat,pr |
        |        | rtGeoCo | o1,pro2    |
        |        | ordinat |            |
        |        | e**     |            |
        +--------+---------+------------+
        | mpplot | **plote | stream     |
        |        | asy**   |            |
        +--------+---------+------------+
        | mpplot | **plot\ | stream,var |
        |        | _new**  | iables=[], |
        |        |         | specialdic |
        |        |         | t={},error |
        |        |         | bars=False |
        |        |         | ,padding=0 |
        |        |         | ,noshow=Fa |
        |        |         | lse        |
        +--------+---------+------------+
        | mpplot | **plot* | stream,var |
        |        | *       | iables=[], |
        |        |         | specialdic |
        |        |         | t={},error |
        |        |         | bars=False |
        |        |         | ,padding=0 |
        |        |         | ,noshow=Fa |
        |        |         | lse        |
        +--------+---------+------------+
        | mpplot | **plotS | streamlist |
        |        | treams* | ,variables |
        |        | *       | ,padding=N |
        |        |         | one,specia |
        |        |         | ldict={},e |
        |        |         | rrorbars=N |
        |        |         | one        |
        +--------+---------+------------+
        | mpplot | **toggl | event      |
        |        | e\_sele |            |
        |        | ctor**  |            |
        +--------+---------+------------+
        | mpplot | **addFl | data,      |
        |        | ag**    | flagger,   |
        |        |         | indeciesto |
        |        |         | beflagged, |
        |        |         | variables  |
        +--------+---------+------------+
        | mpplot | **plotF | data,varia |
        |        | lag**   | bles=None, |
        |        |         | figure=Fal |
        |        |         | se         |
        +--------+---------+------------+
        | mpplot | **plotE | stream,key |
        |        | MD**    | ,verbose=F |
        |        |         | alse,plott |
        |        |         | itle=None  |
        +--------+---------+------------+
        | mpplot | **plotN | streamlist |
        |        | ormStre | ,          |
        |        | ams**   | key,       |
        |        |         | normalize= |
        |        |         | True,      |
        |        |         | normalizet |
        |        |         | =False     |
        +--------+---------+------------+
        | mpplot | **plotP | stream,key |
        |        | S**     | ,debugmode |
        |        |         | =False,out |
        |        |         | file=None, |
        |        |         | noshow=Fal |
        |        |         | se         |
        +--------+---------+------------+
        | mpplot | **plotS | mag\_strea |
        |        | atMag** | m,sat\_str |
        |        |         | eam,keys,o |
        |        |         | utfile=Non |
        |        |         | e,plottype |
        |        |         | ='disconti |
        |        |         | nuous'     |
        +--------+---------+------------+
        | mpplot | **plotS | stream,    |
        |        | pectrog | keys,      |
        |        | ram**   | NFFT=1024, |
        |        |         | detrend=ml |
        |        |         | ab.detrend |
        |        |         | \_none     |
        +--------+---------+------------+
        | mpplot | **magpy | x,         |
        |        | Specgra | NFFT=256,  |
        |        | m**     | Fs=2,      |
        |        |         | Fc=0,      |
        |        |         | detrend=ml |
        |        |         | ab.detrend |
        |        |         | \_none     |
        +--------+---------+------------+
        | mpplot | **plotS | stream,foc |
        |        | tereopl | us='all',c |
        |        | ot**    | olorlist   |
        |        |         | =          |
        |        |         | ['b','r',' |
        |        |         | g','c','m' |
        |        |         | ,'y','k']  |
        +--------+---------+------------+
        | mpplot | \*\*\_p | data,saved |
        |        | lot\*\* | pi=80,grid |
        |        |         | =True,grid |
        |        |         | color=grid |
        |        |         | color,nosh |
        |        |         | ow=False   |
        +--------+---------+------------+
        | mpplot | \*\*\_c | ax, tmax,  |
        |        | onfinex | tmin,      |
        |        | \*\*    | timeunit   |
        +--------+---------+------------+
        | mpplot | \*\*\_e | stream,    |
        |        | xtract\ | key        |
        |        | _data\_ |            |
        |        | for\_PS |            |
        |        | D\*\*   |            |
        +--------+---------+------------+
        | databa | **dbget | db,pierid, |
        | se     | Pier**  | rp, value, |
        |        |         | maxdate=No |
        |        |         | ne,        |
        |        |         | l=False,   |
        |        |         | dic='Delta |
        |        |         | Dictionary |
        |        |         | '          |
        +--------+---------+------------+
        | databa | **dbget | db,        |
        | se     | lines** | tablename, |
        |        |         | lines      |
        +--------+---------+------------+
        | databa | **dbupd | db,tablena |
        | se     | ate**   | me,        |
        |        |         | keys,      |
        |        |         | values,    |
        |        |         | condition= |
        |        |         | None       |
        +--------+---------+------------+
        | databa | **dbget | db,tablena |
        | se     | float** | me,sensori |
        |        |         | d,columnid |
        |        |         | ,revision= |
        |        |         | None       |
        +--------+---------+------------+
        | databa | **dbget | db,tablena |
        | se     | string* | me,sensori |
        |        | *       | d,columnid |
        |        |         | ,revision= |
        |        |         | None       |
        +--------+---------+------------+
        | databa | **dbupl | db,        |
        | se     | oad**   | path,stati |
        |        |         | onid,\*\*k |
        |        |         | wargs      |
        +--------+---------+------------+
        | databa | **dbini | db         |
        | se     | t**     |            |
        +--------+---------+------------+
        | databa | **dbdel | db,datainf |
        | se     | ete**   | oid,\*\*kw |
        |        |         | args       |
        +--------+---------+------------+
        | databa | **dbdic | db,header\ |
        | se     | t2field | _dict,\*\* |
        |        | s**     | kwargs     |
        +--------+---------+------------+
        | databa | **dbfie | db,datainf |
        | se     | lds2dic | oid        |
        |        | t**     |            |
        +--------+---------+------------+
        | databa | **dbalt | db         |
        | se     | er**    |            |
        +--------+---------+------------+
        | databa | **dbsel | db,        |
        | se     | ect**   | element,   |
        |        |         | table,     |
        |        |         | condition= |
        |        |         | None,      |
        |        |         | expert=Non |
        |        |         | e,         |
        |        |         | debug=Fals |
        |        |         | e          |
        +--------+---------+------------+
        | databa | **dbcoo | db, pier,  |
        | se     | rdinate | epsgcode=' |
        |        | s**     | epsg:4326' |
        +--------+---------+------------+
        | databa | **dbsen | db,sensori |
        | se     | sorinfo | d,sensorke |
        |        | **      | ydict=None |
        |        |         | ,sensorrev |
        |        |         | ision      |
        |        |         | = '0001'   |
        +--------+---------+------------+
        | databa | **dbdat | db,sensori |
        | se     | ainfo** | d,datakeyd |
        |        |         | ict=None,t |
        |        |         | ablenum=No |
        |        |         | ne,default |
        |        |         | station='W |
        |        |         | IC',update |
        |        |         | db=True    |
        +--------+---------+------------+
        | databa | **write | db,        |
        | se     | DB**    | datastream |
        |        |         | ,          |
        |        |         | tablename= |
        |        |         | None,      |
        |        |         | StationID= |
        |        |         | None,      |
        |        |         | mode='repl |
        |        |         | ace',      |
        |        |         | revision=N |
        |        |         | one,       |
        |        |         | debug=Fals |
        |        |         | e,         |
        |        |         | \*\*kwargs |
        +--------+---------+------------+
        | databa | **dbset | db,        |
        | se     | Timesin | tablename, |
        |        | DataInf | colstr,uni |
        |        | o**     | tstr       |
        +--------+---------+------------+
        | databa | **dbupd | db,        |
        | se     | ateData | tablename, |
        |        | Info**  | header     |
        +--------+---------+------------+
        | databa | **strea | db,        |
        | se     | m2db**  | datastream |
        |        |         | ,          |
        |        |         | noheader=N |
        |        |         | one,       |
        |        |         | mode=None, |
        |        |         | tablename= |
        |        |         | None,      |
        |        |         | \*\*kwargs |
        +--------+---------+------------+
        | databa | **readD | db, table, |
        | se     | B**     | starttime= |
        |        |         | None,      |
        |        |         | endtime=No |
        |        |         | ne,        |
        |        |         | sql=None   |
        +--------+---------+------------+
        | databa | **db2st | db,        |
        | se     | ream**  | sensorid=N |
        |        |         | one,       |
        |        |         | begin=None |
        |        |         | ,          |
        |        |         | end=None,  |
        |        |         | tableext=N |
        |        |         | one,       |
        |        |         | sql=None   |
        +--------+---------+------------+
        | databa | **dilin | db,        |
        | se     | e2db**  | dilinestru |
        |        |         | ct,        |
        |        |         | mode=None, |
        |        |         | \*\*kwargs |
        +--------+---------+------------+
        | databa | **db2di | db,\*\*kwa |
        | se     | line**  | rgs        |
        +--------+---------+------------+
        | databa | **apply | db, stream |
        | se     | Deltas* |            |
        |        | *       |            |
        +--------+---------+------------+
        | databa | **getBa | db,sensori |
        | se     | seline* | d,         |
        |        | *       | date=None  |
        +--------+---------+------------+
        | databa | **flagl | db,flaglis |
        | se     | ist2db* | t,mode=Non |
        |        | *       | e,sensorid |
        |        |         | =None,modi |
        |        |         | ficationda |
        |        |         | te=None    |
        +--------+---------+------------+
        | databa | **db2fl | db,sensori |
        | se     | aglist* | d,         |
        |        | *       | begin=None |
        |        |         | ,          |
        |        |         | end=None,  |
        |        |         | comment=No |
        |        |         | ne,        |
        |        |         | flagnumber |
        |        |         | =-1,       |
        |        |         | key=None,  |
        |        |         | removedupl |
        |        |         | icates=Fal |
        |        |         | se         |
        +--------+---------+------------+
        | databa | **strin | string     |
        | se     | g2dict* |            |
        |        | *       |            |
        +--------+---------+------------+
        | tranfe | \*\*\_c | logfile    |
        | r      | hecklog |            |
        |        | file\*\ |            |
        |        | *       |            |
        +--------+---------+------------+
        | tranfe | **ftpda | \*\*kwargs |
        | r      | tatrans |            |
        |        | fer**   |            |
        +--------+---------+------------+
        | tranfe | \*\*\_m | myproxy,   |
        | r      | issingv | port,      |
        |        | als\*\* | login,     |
        |        |         | passwd,    |
        |        |         | logfile    |
        +--------+---------+------------+
        | tranfe | **scptr | src,dest,p |
        | r      | ansfer* | asswd,\*\* |
        |        | *       | kwargs     |
        +--------+---------+------------+
        | tranfe | **ssh\_ | remotepath |
        | r      | remotef | ,          |
        |        | ilelist | filepat,   |
        |        | **      | user,      |
        |        |         | host,      |
        |        |         | passwd     |
        +--------+---------+------------+
        | tranfe | **ginup | filename=N |
        | r      | load**  | one,       |
        |        |         | user=None, |
        |        |         | password=N |
        |        |         | one,       |
        |        |         | url=None,\ |
        |        |         | *\*kwargs  |
        +--------+---------+------------+
        | tranfe | **ftpdi | \*\*kwargs |
        | r      | rlist** |            |
        +--------+---------+------------+
        | tranfe | **ftpre | \*\*kwargs |
        | r      | move**  |            |
        +--------+---------+------------+
        | tranfe | **ftpge | ftpaddress |
        | r      | t**     | ,ftpname,f |
        |        |         | tppasswd,r |
        |        |         | emotepath, |
        |        |         | localpath, |
        |        |         | identifier |
        |        |         | ,port=None |
        |        |         | ,\*\*kwarg |
        |        |         | s          |
        +--------+---------+------------+
        
        
Platform: UNKNOWN
