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https://github.com/nexdatas/nxsdatawriter

NXSDataWriter Tango server dedicated to store data in NeXuS/HDF5 files
https://github.com/nexdatas/nxsdatawriter

hdf5 nexusformat python tango

Last synced: 10 months ago
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NXSDataWriter Tango server dedicated to store data in NeXuS/HDF5 files

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README 

          
Welcome to NXSDataWriter's documentation!

=========================================



|github workflow|

|docs|

|Pypi Version|

|Python Versions|



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   :target: https://github.com/nexdatas/nxsdatawriter/actions

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.. |Pypi Version| image:: https://img.shields.io/pypi/v/nxswriter.svg

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                  :alt:



.. |Python Versions| image:: https://img.shields.io/pypi/pyversions/nxswriter.svg

                     :target: https://pypi.python.org/pypi/nxswriter/

                     :alt:



Authors: Jan Kotanski, Eugen Wintersberger, Halil Pasic



------------

Introduction

------------



NXSDataWriter is a Tango server which allows to store NeXuS Data in H5 files.



The server provides storing data from other Tango devices,

various databases as well as passed by a user client via JSON strings.



Tango Server API: https://nexdatas.github.io/nxsdatawriter/doc_html



| Source code: https://github.com/nexdatas/nxsdatawriter

| Project Web page: https://nexdatas.github.io/nxsdatawriter

| NexDaTaS Web page: https://nexdatas.github.io



------------

Installation

------------



Install the dependencies:



|    pninexus or h5py, tango, numpy, nxstools, sphinx



From sources

""""""""""""



Download the latest NexDaTaS version from



|    https://github.com/nexdatas/nxsdatawriter



Extract sources and run



.. code-block:: console



	  $ python3 setup.py install



Debian packages

"""""""""""""""



Debian `bookworm`, `bullseye`, `buster`  or Ubuntu `oracular`,  `noble`, `jammy`  packages can be found in the HDRI repository.



To install the debian packages, add the PGP repository key



.. code-block:: console



	  $ sudo su

	  $ curl -s http://repos.pni-hdri.de/debian_repo.pub.gpg | gpg --no-default-keyring --keyring gnupg-ring:/etc/apt/trusted.gpg.d/debian-hdri-repo.gpg --import

	  $ chmod 644 /etc/apt/trusted.gpg.d/debian-hdri-repo.gpg



and then download the corresponding source list



.. code-block:: console



	  $ cd /etc/apt/sources.list.d

	  $ wget http://repos.pni-hdri.de/bookworm-pni-hdri.list



To install tango server



.. code-block:: console



	  $ apt-get update

	  $ apt-get install nxswriter



or



.. code-block:: console



	  $ apt-get update

	  $ apt-get install nxswriter3



for older python3 releases.



To install only the python3 package



.. code-block:: console



	  $ apt-get update

	  $ apt-get install python3-nxswriter



and for python2



.. code-block:: console



	  $ apt-get update

	  $ apt-get install python-nxswriter



if exists.



From pip

""""""""



To install it from pip you can



.. code-block:: console



   $ python3 -m venv myvenv

   $ . myvenv/bin/activate



   $ pip install nxswriter



Moreover it is also good to install



.. code-block:: console



   $ pip install pytango

   $ pip install pymysqldb

   $ pip install psycopg2-binary

   $ pip install cx-oracle



Setting NeXus Writer Server

"""""""""""""""""""""""""""



To set up  NeXus Writer Server run



.. code-block:: console



          $ nxsetup -x NXSDataWriter



The *nxsetup* command comes from the **python3-nxstools** package.



-----------

Client code

-----------



In order to use Nexus Data Server one has to write a client code. Some simple client codes

are in the  nexdatas repository. In this section we add some

comments related to the client code.



.. code-block:: python



   # To use the Tango Server we must import the tango module and

   # create DeviceProxy for the server.



   import tango



   device = "p09/tdw/r228"

   dpx = tango.DeviceProxy(device)

   dpx.set_timeout_millis(10000)



   dpx.Init()



   # Here device corresponds to a name of our Nexus Data Server.

   # The Init() method resets the state of the server.



   dpx.FileName = "test.h5"

   dpx.OpenFile()



   # We set the name of the output HDF5 file and open it.



   # Now we are ready to pass the XML settings describing a structure of

   # the output file as well as defining a way of data storing.

   # Examples of the XMLSettings can be found in the XMLExamples directory.



   with open("test.xml", 'r') as fl:

       xml = fl.read()

   dpx.XMLSettings = xml



   dpx.JSONRecord = '{"data": {"parameterA":0.2},

			 "decoders":{"DESY2D":"desydecoders.desy2Ddec.desy2d"},

			 "datasources":{

		              "MCLIENT":"sources.DataSources.LocalClientSource"}

   }'



   dpx.OpenEntry()



   # We read our XML settings settings from a file and pass them to the server via

   # the XMLSettings attribute. Then we open an entry group related to the XML

   # configuration. Optionally, we can also set JSONRecord, i.e. an attribute

   # which contains a global JSON string with data needed to store during opening

   # the entry and also other stages of recording. If external decoder for

   # DevEncoded data is need one can registred it passing its packages and

   # class names in JSONRecord,

   # e.g. "desy2d" class of "DESY2D" label in "desydecoders.desy2Ddec" package.

   # Similarly making use of "datasources" records of the JSON string one can

   # registred additional datasources. The OpenEntry method stores data defined

   # in the XML string with strategy=INIT.

   # The JSONRecord attribute can be changed during recording our data.



   # After finalization of the configuration process we can start recording

   # the main experiment data in a STEP mode.



   dpx.Record('{"data": {"p09/counter/exp.01":0.1, "p09/counter/exp.02":1.1}}')



   # Every time we call the Record method all nexus fields defined with

   # strategy=STEP are extended by one record unit and the assigned to them data

   # is stored. As the method argument we pass a local JSON string with the client

   # data. To record the client data one can also use the global JSONRecord string.

   # Contrary to the global JSON string the local one is only

   # valid during one record step.



   dpx.Record('{"data": {"emittance_x": 0.1},  "triggers":["trigger1", "trigger2"]  }')



   # If you denote in your XML configuration string some fields by additional

   # trigger attributes you may ask the server to store your data only in specific

   # record steps. This can be helpful if you want to store your data in

   # asynchronous mode. To this end you define in the local JSON string a list of

   # triggers which are used in the current record step.



   dpx.JSONRecord = '{"data": {"parameterB":0.3}}'

   dpx.CloseEntry()



   # After scanning experiment data in 'STEP' mode we close the entry.

   # To this end we call the CloseEntry method which also stores data defined

   # with strategy=FINAL. Since our HDF5 file can contain many entries we can again

   # open the entry and repeat our record procedure. If we define more than one entry

   # in one XML setting string the defined entries are recorded parallel

   # with the same steps.



   # Finally, we can close our output file by



   dpx.CloseFile()



Additionally, one can use asynchronous versions of **OpenEntry**, **Record**, **CloseEntry**, i.e.

**OpenEntryAsynch**, **RecordAsynch**, **CloseEntryAsynch**. In this case data is stored

in a background thread and during this writing Tango Data Server has a state *RUNNING*.



In order to build the XML configurations in the easy way the authors of the server provide

for this purpose a specialized GUI tool, Component Designer.

The attached to the server XML examples

was created by XMLFile class defined in XMLCreator/simpleXML.py.