Debian Science Project
Summary
Data acquisition
Debian Science data acquisition packages

This metapackage will install Debian Science packages related to data acquisition. This might be used in several sciences (as for instance science-viewing and science-typesetting).

Description

For a better overview of the project's availability as a Debian package, each head row has a color code according to this scheme:

If you discover a project which looks like a good candidate for Debian Science to you, or if you have prepared an unofficial Debian package, please do not hesitate to send a description of that project to the Debian Science mailing list

Links to other tasks

Debian Science Data acquisition packages

Official Debian packages with high relevance

Engauge-digitizer
interactively extracts numbers from bitmap graphs or maps
Maintainer: Tobias Winchen
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The Engauge Digitizer tool assists in interactively extracting numbers from images of graphs. Conceptually, it is thus the opposite of a graphing tool that converts data points to graphs. It provides assistance in enhancing the image quality and matching the data points. Engauge Digitizer is used by individuals such as grad students and researchers as well engineers and employees in large government and commercial organizations for processing single files but also managing databases of thousands of image files.

Features of Engauge Digitizer include:

  • Automatic grid line removal
  • Automatic point and axis matching
  • Automatic curve tracing
  • Image processing for separating important details from background information
  • A wizard providing an interactive tutorial to explain the basic steps
  • Multiple coordinate systems in the same image can be digitized in advanced mode
  • Cubic spline interpolation between points gives more accurate curves with fewer points
  • Handling of Cartesian, polar, linear and logarithmic graphs
  • Support for drag-and-drop and copy-and-paste
  • Context sensitive help, user manual and tutorials explaining every feature
  • Preview windows to give immediate feedback while modifying settings
  • Automated line and point extraction to rapidly digitizes data
Filo
FILe and stream Operations
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The following tools are available as part of the filo package:

groupBy – mimics the “groupBy” clause in database systems.

shuffle – randomize the order of lines in a file.

stats – computes descriptive statistic on a given column of a tab-delimited file or stream.

Because their name is too generic, ‘shuffle’ and ‘stats’ are relocated in /usr/lib/filo.

G3data
extract data from scanned graphs
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g3data is used for extracting data from graphs. For example, graphs are typically published in scientific journals without tables of the actual data; g3data makes the process of extracting these data easy.

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Ghkl
diffractometer computation control application
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The hkl library is a framework for diffraction computation and diffractometer control, heavily used at the SOLEIL synchrotron. It supports various types of diffractometer geometry: Eulerian 4-circle, Eulerian 6-circle, kappa 4-circle, kappa 6-circle, and z-axis geometry. For each of these it provides several numerically computed modes, such as bisector and constant psi.

This package provides a gui on top of the hkl library.

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Jaaa
audio signal generator and spectrum analyser
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Jaaa (JACK and ALSA Audio Analyser) is an audio signal generator and spectrum analyser designed to make accurate measurements.

Jaaa allows you select on of the four inputs, 'Min' and 'Max' the min and max displayed frequencies. There can be up to two markers which helps accurately read off values in the display.

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Ktimetrace
Graphical tool to measure and graph data
Maintainer: Georges Khaznadar
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KTimeTrace is a graphical tool based on Qt that measures and displays data from data acquisition hardware. It captures samples from a data acquisition device, saving it to disk while providing a real-time graphing display.

KTimeTrace requires having a data acquisition device that is supported by Comedi in order to capture data. See the libcomedi0 package or http://stm.lbl.gov/comedi for more information about Comedi.

Libfreenect-dev
library for accessing Kinect device -- development files
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libfreenect is a cross-platform library that provides the necessary interfaces to activate, initialize, and communicate data with the Kinect hardware. Currently, the library supports access to RGB and depth video streams, motors, accelerometer and LED and provide binding in different languages (C++, Python...)

This library is the low level component of the OpenKinect project which is an open community of people interested in making use of the Xbox Kinect hardware with PCs and other devices.

This is the development package containing the libraries and header for software development with libfreenect.

Libgetdata-tools
library to read/write dirfile data - extra tools
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The GetData Project is the reference implementation of the Dirfile Standards, a filesystem-based, column-oriented database format for time-ordered binary data. The Dirfile database format is designed to provide a fast, simple format for storing and reading data.

Narval-utils
An Ada framework for Distributed Acquisition Systems (utils)
Maintainer: Xavier Grave
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NARVAL is a framework that eases setting up of experimental data acquisition. It is written in Ada, supports user plugins written in C or C++. Using NARVAL, one can distribute many processes across a network to acquire, process, store data online. Processes are of four types: producer (injects data in NARVAL framework), consumer (end of the data flow), intermediate (act as NxM switches) and stand alone actor (no data flow handling, can be used for monitoring).

This package contains shell scripts to ease narval users life.

Netcdf-bin
Programs for reading and writing NetCDF files
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Contains the programs ncdump and ncgen which convert NetCDF files to ASCII and back, respectively. NetCDF (network Common Data Form) is an interface for scientific data access and a freely-distributed software library that provides an implementation of the interface. The netCDF library also defines a machine-independent format for representing scientific data. Together, the interface, library, and format support the creation, access, and sharing of scientific data.

Python-sardana
instrument control and data acquisition system - library
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Sardana is a Supervision, Control And Data Acquisition (SCADA) system for scientific installations. It is written in Python and based on the TANGO library. The hardware control and data acquisition routines can be accessed via an IPython console and a generic graphical user interface (both of which are easily extensible by the user).

Qtdmm
GUI for digital multimeter
Maintainer: Steffen Moeller
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A digital multimeter (DMM) attached to the serial port is presented under a Qt surface. The tool plots values over time, has a simple scheduler for delayed starts and logging after a threshold was reached. It supports spawning external applications, too.

Xyscan
data thief for scientists
Maintainer: Georges Khaznadar
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xyscan is a tool for the scientist in the need to extract data points, i.e. numeric values, from a plot. It allows you to scan the plots and extract data points including the size of the error bars (both in x and y). It can handle plots with linear and logarithmic scales. In fact xyscan can be used for extracting numeric values from any kind of 2D technical drawings.

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Official Debian packages with lower relevance

Comedi-source
Comedi kernel module source
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Comedi (Control and Measurement Device Interface) is a collection of device drivers for data acquisition devices. This includes most devices that have analog-to-digital (A/D) converters, digital-to-analog (D/A) converters, raw digital I/O, digital counters, and timers. Well-known manufacturers include National Instruments, Data Translation, and Measurement Computing. A list of supported devices can be found in /usr/share/doc/comedi-source/. These drivers are not included in the Linux kernel source, so if you want to use these devices with Debian, you should install this package and compile the modules.

The packages libcomedi0 and libcomedi-dev contain documentation about Comedi and Comedilib.

In order to compile these modules, you will need either the kernel sources or the Debian kernel-headers and kernel-image packages. For compile instructions, look at /usr/share/doc/comedi-source/README.Debian or the documentation for the module-assistant utility.

Gnudatalanguage
Free IDL compatible incremental compiler
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GNU Data Language (GDL) is a free IDL (Interactive Data Language) compatible incremental compiler. It has full syntax compatibility with IDL 7.1. IDL is a registered trademark of ITT Visual Information Solutions. From IDL 8.0, the following language elements are supported:

  • FOREACH loop
  • negative array indices
  • garbage collection pointers and objects
  • call methods on an object using "." (e. g. object.aMemberProcedure,arg1)

The file input output system is fully implemented. GUI support (widgets) is officially provided, but it's not complete yet.

This package contains the main commandline and interpreter frontend.

Please cite: A. Coulais, M. Schellens, J. Gales, S. Arabas, M. Boquien, P. Chanial, P. Messmer, D. Fillmore, O. Poplawski, S. Maret, G. Marchal, N. Galmiche and T. Mermet: Status of GDL - GNU Data Language. (eprint) Astronomical Data Analysis Software and Systems XIX 434:187 (2010)
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Gpsd
Global Positioning System - daemon
Maintainer: Bernd Zeimetz
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The gpsd service daemon can monitor one or more GPS devices connected to a host computer, making all data on the location and movements of the sensors available to be queried on TCP port 2947.

With gpsd, multiple GPS client applications can share access to devices without contention or loss of data. Also, gpsd responds to queries with a format that is substantially easier to parse than the different standards emitted by GPS devices.

Python-pytango
transitional dummy package for python-tango
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This is a transitional package to ease upgrades to the python-tango package. It can be safely removed.

Python-taurus
Framework for scientific/industrial CLIs and GUIs - Python2
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Taurus is a Python framework for control and data acquisition CLIs and GUIs in scientific/industrial environments. It supports multiple control systems or data sources: Tango, EPICS, spec... New control system libraries can be integrated through plugins.

This is the Python 2 version of the package.

Rt-tests
Test programs for rt kernels
Maintainer: Uwe Kleine-König
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rt-tests contains a set of programs that test and measure various components of real-time kernel behavior, such as timer latency, signal latency and the functioning of priority-inheritance mutexes. Additionally it contains hackbench, a program to generate work for the scheduler.

Rtai
Real Time Application Interface
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RTAI is a realtime extension with a broad variety of services which make realtime programmers' lifes easier. Some of them are

 choose between FIFO and RR scheduling policies on a per task basis.
 extended POSIX APIs and message queues, in kernel and user space
 semaphores can be typed as: counting, binary and resource
 a mailbox implementation
 LXRT for hard real time in user space

This is a metapackage that depends on the latest versions of the individual RTAI packages.

Tango-accesscontrol
TANGO distributed control system - accesscontrol server
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TANGO is an object oriented distributed control system. It allows communication between TANGO device processes running on the same computer or distributed over the network. These processes can provide services to the control system all over the network, such as hardware control or data processing.

This package provides a TANGO accesscontrol server. It can be used to manage the users and IP addresses that are permitted to access TANGO devices.

Tango-db
TANGO distributed control system - database server
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TANGO is an object oriented distributed control system. It allows communication between TANGO device processes running on the same computer or distributed over the network. These processes can provide services to the control system all over the network, such as hardware control or data processing.

This package provides a TANGO database server using MySQL/MariaDB.

Tango-starter
TANGO distributed control system - starter server
Versions of package tango-starter
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sid9.2.5a+dfsg1-2amd64,arm64,armel,armhf,hurd-i386,i386,kfreebsd-amd64,kfreebsd-i386,mips,mips64el,mipsel,powerpc,ppc64el,s390x
wheezy7.2.6+dfsg-14amd64,armel,armhf,i386,ia64,mips,mipsel,powerpc,s390,s390x,sparc
stretch9.2.5a+dfsg1-2amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
buster9.2.5a+dfsg1-2amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
jessie8.1.2c+dfsg-5amd64,arm64,armel,armhf,i386,mips,mipsel,powerpc,ppc64el,s390x
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TANGO is an object oriented distributed control system. It allows communication between TANGO device processes running on the same computer or distributed over the network. These processes can provide services to the control system all over the network, such as hardware control or data processing.

This package provides a TANGO device control server. It can start, stop, or report the status of other TANGO components.

Xenomai-runtime
Xenomai runtime utilities
Maintainer: Roland Stigge
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Xenomai is a real-time development framework cooperating with the Linux kernel in order to provide a pervasive, interface-agnostic, hard real-time support to user-space applications, seamlessly integrated into the GNU/Linux environment. Xenomai provides its own API and emulation layers ("skins") to make migration from other RTOS easier. Examples are: pSOS+, VxWorks, VRTX, uiTRON, RTAI, POSIX.

This package contains the runtime programs and the testsuite for the Xenomai realtime system.

Unofficial packages built by somebody else

Epics
Experimental Physics and Industrial Control System
Responsible: Carlo Segre
License: EPICS base license (BSD like)

EPICS is a set of Open Source software tools, libraries and applications developed collaboratively and used worldwide to create distributed soft real-time control systems for scientific instruments such as a particle accelerators, telescopes and other large scientific experiments.

Linux-image-2.6-rt
Stock Linux kernel with RT-Preempt patch
Responsible:
License: GPL

The RT-Preempt (http://rt.wiki.kernel.org) project provides patches to make Linux kernel capable of fulfilling hard realtime requirements. The aim is to eliminate all preemptivity and reactivity problems in the kernel over the time by adding deterministic preemption points. The -rt patches are constantly being worked on for mainline by the community.

Pengutronix's Realtime Linux for Debian project provides builds of the stock Linux kernel with the RT-Preempt patch (but without Debian patches).

Remark of Debian Science team: The upstream kernel sources are not considered DFSG-free, so

the packages are available from the non-free area only.

Mx-dataacquisition
data acquisition and control system
Responsible: Carlo Segre
License: MIT

MX is a data acquisition and control system that is designed to serve several functions:

  • As a portable toolkit for writing data acquisition and control programs.
  • As a standalone system capable of controlling entire experiments.
  • As a platform for building device control servers to be used by other applications.
  • As a way of extending other control systems and of glueing disparate control systems together.

No known packages available but some record of interest (WNPP bug)

Opendap - wnpp
Java Network Data Access Protocol
Responsible: Mathieu Malaterre
License: LGPL
Debian package not available
Language: Java

OPeNDAP is a framework that simplifies all aspects of scientific data networking.

OPeNDAP provides software which makes local data accessible to remote locations regardless of local storage format.

OPeNDAP also provides tools for transforming existing applications into OPeNDAP clients (i.e., enabling them to remotely access OPeNDAP served data).

No known packages available

Hart
toolbox to generate DAQ Scicos-blocks for hardware
License: GPL
Debian package not available
Language: C
 The HART (Hardware Access in Real-Time) Toolbox can be used to
 generate Scicos-blocks for hardware that have a C/C++ interface. The
 blocks can be used under Linux for soft and hard real time tasks
 (RTAI). Blocks are provided for DAQ (COMEDI)
Plot-digitizer
digitize scanned plots of functional data
Responsible: Stuart Prescott
License: GPL
Debian package not available

An easy to use Java program that allows you to digitize data points off of scanned plots, scaled drawings, or orthographic photographs. Includes an automatic digitization feature that can automatically digitize many types of functional data.

Python-visa
control measurement devices and test equipment via GPIB, RS232, or USB
License: MIT
Debian package not available

A Python package with bindings to the "Virtual Instrument Softwares Architecture" VISA library, in order to control measurement devices and test equipment via GPIB, RS232, or USB.

Articles about pyvisa:

  • G. Varoquaux has written an interesting article describing the use of python and pyvisa for experimental control. Agile computer control of a complex experiment. Computing in Science and Engineering 10(2), 55 (2008).
  • Writing a graphical application for scientific programming using TraitsUI
*Popularitycontest results: number of people who use this package regularly (number of people who upgraded this package recently) out of 203532