Welcome to NXSDataWriter's documentation!
=========================================
|github workflow|
|docs|
|Pypi Version|
|Python Versions|
.. |github workflow| image:: https://github.com/nexdatas/nxsdatawriter/actions/workflows/tests.yml/badge.svg
:target: https://github.com/nexdatas/nxsdatawriter/actions
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.. |docs| image:: https://img.shields.io/badge/Documentation-webpages-ADD8E6.svg
:target: https://nexdatas.github.io/nxsdatawriter/index.html
:alt:
.. |Pypi Version| image:: https://img.shields.io/pypi/v/nxswriter.svg
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.. |Python Versions| image:: https://img.shields.io/pypi/pyversions/nxswriter.svg
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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
$ python setup.py install
Debian packages
"""""""""""""""
Debian `bookworm`, `bullseye`, `buster` or Ubuntu `lunar`, `jammy`, `focal` 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 **python-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.
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"description": "Welcome to NXSDataWriter's documentation!\n=========================================\n\n|github workflow|\n|docs|\n|Pypi Version|\n|Python Versions|\n\n.. |github workflow| image:: https://github.com/nexdatas/nxsdatawriter/actions/workflows/tests.yml/badge.svg\n :target: https://github.com/nexdatas/nxsdatawriter/actions\n :alt:\n\n.. |docs| image:: https://img.shields.io/badge/Documentation-webpages-ADD8E6.svg\n :target: https://nexdatas.github.io/nxsdatawriter/index.html\n :alt:\n\n.. |Pypi Version| image:: https://img.shields.io/pypi/v/nxswriter.svg\n :target: https://pypi.python.org/pypi/nxswriter\n :alt:\n\n.. |Python Versions| image:: https://img.shields.io/pypi/pyversions/nxswriter.svg\n :target: https://pypi.python.org/pypi/nxswriter/\n :alt:\n\n\nAuthors: Jan Kotanski, Eugen Wintersberger, Halil Pasic\n\n------------\nIntroduction\n------------\n\nNXSDataWriter is a Tango server which allows to store NeXuS Data in H5 files.\n\nThe server provides storing data from other Tango devices,\nvarious databases as well as passed by a user client via JSON strings.\n\nTango Server API: https://nexdatas.github.io/nxsdatawriter/doc_html\n\n| Source code: https://github.com/nexdatas/nxsdatawriter\n| Project Web page: https://nexdatas.github.io/nxsdatawriter\n| NexDaTaS Web page: https://nexdatas.github.io\n\n------------\nInstallation\n------------\n\nInstall the dependencies:\n\n| pninexus or h5py, tango, numpy, nxstools, sphinx\n\nFrom sources\n\"\"\"\"\"\"\"\"\"\"\"\"\n\nDownload the latest NexDaTaS version from\n\n| https://github.com/nexdatas/nxsdatawriter\n\nExtract sources and run\n\n.. code-block:: console\n\n\t $ python setup.py install\n\nDebian packages\n\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\n\nDebian `bookworm`, `bullseye`, `buster` or Ubuntu `lunar`, `jammy`, `focal` packages can be found in the HDRI repository.\n\nTo install the debian packages, add the PGP repository key\n\n.. code-block:: console\n\n\t $ sudo su\n\t $ 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\n\t $ chmod 644 /etc/apt/trusted.gpg.d/debian-hdri-repo.gpg\n\nand then download the corresponding source list\n\n.. code-block:: console\n\n\t $ cd /etc/apt/sources.list.d\n\t $ wget http://repos.pni-hdri.de/bookworm-pni-hdri.list\n\nTo install tango server\n\n.. code-block:: console\n\n\t $ apt-get update\n\t $ apt-get install nxswriter\n\nor\n\n.. code-block:: console\n\n\t $ apt-get update\n\t $ apt-get install nxswriter3\n\nfor older python3 releases.\n\nTo install only the python3 package\n\n.. code-block:: console\n\n\t $ apt-get update\n\t $ apt-get install python3-nxswriter\n\nand for python2\n\n.. code-block:: console\n\n\t $ apt-get update\n\t $ apt-get install python-nxswriter\n\nif exists.\n\n\n\nFrom pip\n\"\"\"\"\"\"\"\"\n\nTo install it from pip you can\n\n.. code-block:: console\n\n $ python3 -m venv myvenv\n $ . myvenv/bin/activate\n\n $ pip install nxswriter\n\nMoreover it is also good to install\n\n.. code-block:: console\n\n $ pip install pytango\n $ pip install pymysqldb\n $ pip install psycopg2-binary\n $ pip install cx-oracle\n\nSetting NeXus Writer Server\n\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\n\nTo set up NeXus Writer Server run\n\n.. code-block:: console\n\n $ nxsetup -x NXSDataWriter\n\nThe *nxsetup* command comes from the **python-nxstools** package.\n\n-----------\nClient code\n-----------\n\nIn order to use Nexus Data Server one has to write a client code. Some simple client codes\nare in the nexdatas repository. In this section we add some\ncomments related to the client code.\n\n.. code-block:: python\n\n # To use the Tango Server we must import the tango module and\n # create DeviceProxy for the server.\n\n import tango\n\n device = \"p09/tdw/r228\"\n dpx = tango.DeviceProxy(device)\n dpx.set_timeout_millis(10000)\n\n dpx.Init()\n\n # Here device corresponds to a name of our Nexus Data Server.\n # The Init() method resets the state of the server.\n\n dpx.FileName = \"test.h5\"\n dpx.OpenFile()\n\n # We set the name of the output HDF5 file and open it.\n\n # Now we are ready to pass the XML settings describing a structure of\n # the output file as well as defining a way of data storing.\n # Examples of the XMLSettings can be found in the XMLExamples directory.\n\n with open(\"test.xml\", 'r') as fl:\n xml = fl.read()\n dpx.XMLSettings = xml\n\n dpx.JSONRecord = '{\"data\": {\"parameterA\":0.2},\n\t\t\t \"decoders\":{\"DESY2D\":\"desydecoders.desy2Ddec.desy2d\"},\n\t\t\t \"datasources\":{\n\t\t \"MCLIENT\":\"sources.DataSources.LocalClientSource\"}\n }'\n\n dpx.OpenEntry()\n\n # We read our XML settings settings from a file and pass them to the server via\n # the XMLSettings attribute. Then we open an entry group related to the XML\n # configuration. Optionally, we can also set JSONRecord, i.e. an attribute\n # which contains a global JSON string with data needed to store during opening\n # the entry and also other stages of recording. If external decoder for\n # DevEncoded data is need one can registred it passing its packages and\n # class names in JSONRecord,\n # e.g. \"desy2d\" class of \"DESY2D\" label in \"desydecoders.desy2Ddec\" package.\n # Similarly making use of \"datasources\" records of the JSON string one can\n # registred additional datasources. The OpenEntry method stores data defined\n # in the XML string with strategy=INIT.\n # The JSONRecord attribute can be changed during recording our data.\n\n # After finalization of the configuration process we can start recording\n # the main experiment data in a STEP mode.\n\n dpx.Record('{\"data\": {\"p09/counter/exp.01\":0.1, \"p09/counter/exp.02\":1.1}}')\n\n # Every time we call the Record method all nexus fields defined with\n # strategy=STEP are extended by one record unit and the assigned to them data\n # is stored. As the method argument we pass a local JSON string with the client\n # data. To record the client data one can also use the global JSONRecord string.\n # Contrary to the global JSON string the local one is only\n # valid during one record step.\n\n dpx.Record('{\"data\": {\"emittance_x\": 0.1}, \"triggers\":[\"trigger1\", \"trigger2\"] }')\n\n # If you denote in your XML configuration string some fields by additional\n # trigger attributes you may ask the server to store your data only in specific\n # record steps. This can be helpful if you want to store your data in\n # asynchronous mode. To this end you define in the local JSON string a list of\n # triggers which are used in the current record step.\n\n dpx.JSONRecord = '{\"data\": {\"parameterB\":0.3}}'\n dpx.CloseEntry()\n\n # After scanning experiment data in 'STEP' mode we close the entry.\n # To this end we call the CloseEntry method which also stores data defined\n # with strategy=FINAL. Since our HDF5 file can contain many entries we can again\n # open the entry and repeat our record procedure. If we define more than one entry\n # in one XML setting string the defined entries are recorded parallel\n # with the same steps.\n\n # Finally, we can close our output file by\n\n dpx.CloseFile()\n\nAdditionally, one can use asynchronous versions of **OpenEntry**, **Record**, **CloseEntry**, i.e.\n**OpenEntryAsynch**, **RecordAsynch**, **CloseEntryAsynch**. In this case data is stored\nin a background thread and during this writing Tango Data Server has a state *RUNNING*.\n\nIn order to build the XML configurations in the easy way the authors of the server provide\nfor this purpose a specialized GUI tool, Component Designer.\nThe attached to the server XML examples\nwas created by XMLFile class defined in XMLCreator/simpleXML.py.\n",
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