Debian Science Viewing packages

Fityk is a flexible and portable program for nonlinear fitting of analytical functions (especially peak-shaped) to data (usually experimental data). In other words, for nonlinear peak separation and analysis.

It was developed for analyzing diffraction patterns, but can be also used in other fields, since concepts and operations specific for crystallography are separated from the rest of the program.

Fityk offers various nonlinear fitting methods, subtracting background, calibrating data, easy placement of peaks and changing peak parameters, automation of common tasks with scripts, and much more. The main advantage of the program is flexibility - parameters of peaks can be arbitrarily bound to each other, eg. the width of a peak can be an independent variable, can be the same as the width of another peak or can be given by a complicated - common to all peaks - formula.

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.

A free IDL (Interactive Data Language) compatible incremental compiler. It has full syntax compatibility with IDL 6.0.

Gnuplot is a portable command-line driven interactive data and function plotting utility that supports lots of output formats, including drivers for many printers, (La)TeX, (x)fig, Postscript, and so on. The X11-output is packaged in gnuplot-x11.

Data files and self-defined functions can be manipulated by the internal C-like language. Can perform smoothing, spline-fitting, or nonlinear fits, and can work with complex numbers.

This package is for transition and to install a full-featured gnuplot supporting the X11-output.

Grace is a point-and-click tool that allows the user to draw X-Y plots. This is the program formerly known as Xmgr.

A few of its features are: User defined scaling, tick marks, labels, symbols, line styles, colors. Polynomial regression, splines, running averages, DFT/FFT, cross/auto-correlation. Batch mode for unattended plotting. Hardcopy support for PostScript, FrameMaker and several image formats.

Graph drawing addresses the problem of visualizing structural information by constructing geometric representations of abstract graphs and networks. Automatic generation of graph drawings has important applications in key technologies such as database design, software engineering, VLSI and network design and visual interfaces in other domains. Situations where these tools might be particularly useful include:

• you would like to restructure a program and first need to understand the relationships between its types, procedures, and source files
• you need to find the bottlenecks in an Internet backbone - not only individual links, but their relationships
• you're debugging a protocol or microarchitecture represented as a finite state machine and need to figure out how a certain error state arises
• you would like to browse a database schema, knowledge base, or distributed program represented graphically
• you would like to see an overview of a collection of linked documents
• you would like to discover patterns and communities of interest in a database of telephone calls or e-mail messages

This package contains the command-line tools.

Gri is an open-source language for scientific graphics programming. It is command-driven, as opposed to point/click. Some users consider Gri similar to LaTeX, since both provide extensive power as a reward for tolerating a learning curve. The output is industry-standard PostScript as output, suitable for inclusion in other documents.

Gri can make x-y graphs, contour graphs, and image graphs. Fine control is provided over all aspects of drawing, e.g. line widths, colors, fonts, etc. Greek letters and mathematical symbols are available in a TeX-like syntax.

Folks who write 1000-line Gri scripts usually start with something as simple as the following:

  open file.dat        # open a file
  read columns x * y   # read the 1st column as x and the 3rd as y
  draw curve           # draw the data and autoscale the axes

A full manual is also available in HTML (gri-html-doc package), in PostScript suitable for printing (gri-ps-doc package) and on-line by following links from the gri home page:

  [http://gri.sourceforge.net/](http://gri.sourceforge.net/)

Gwyddion is a modular program for Scanning Probe Microscopy (SPM) data visualization and analysis. It is primarily intended for analysis of height field data obtained by microscopy techniques like Atomic Force Microscopy (AFM), Magnetic Force Microscopy (MFM), Scanning Tunneling Microscopy (STM), Near-field Scanning Optical Microscopy (SNOM or NSOM) and others. However, it can be used for arbitrary height field and image analysis.

This package contains the main application and its modules. It also contains a GNOME (and Xfce) thumbnailer which creates previews for all file types known to Gwyddion.

Gwyddion's Python scripting interface Pygwy is also included.

IFRIT (the Ionization FRont Interactive Tool) has its origins (and hence name) in a specialized utility designed to visualize ionization fronts in cosmological numerical simulations. IFRIT, however, has outgrown its origins and now can visualize general data sets as well.

IFRIT is written in C++ and is based on two state-of-the-art toolkits: the Visualization ToolKit (VTK) and a GUI toolkit QT.

Imview is an application which

• Displays a large number of image formats.
• Displays 2D or 3D (as slices) images with a very good zoom and pan feature.
• Works with multi-spectral, time series or multi-page documents (e.g.: Satellite images, TIFF stacks, animated GIFs and heterogeneous multi-component files).
• Displays all pixel types (1-bit to 64-bit data, integer or floating point).
• Arbitrary 1-D profile of 2-D images (or of 2-D slices of 3-D images) can be displayed.
• Has support for arbitrary colourmaps for all pixel types (i.e.: false colour display).
• Has standard image manipulation facilities (brightness/contrast, gamma, zoom, crop, rotation, etc).
• Can be controlled remotely via sockets and text commands (for easy integration into various image analysis systems).
• Images can be uploaded into Imview via sockets or shared memory.
• And much more!

This is a metapackage for kst which installs all of the relevant packages.

kst is a program for examining data streams which can plot x-y plots, power spectra, histograms and equations (including equations of data streams). It can also be used to examine data in files which are being updated as data is being logged, in which case it can act as a plotter for a chart recorder.

kst also contains a command line interface for rapid analysis of large amounts of data.

LabPLot is a data plotting and analysis tool for the KDE desktop.

Its features include:

• 2D and 3D data and function plotting
• easy editing of plots
• analysis of data and functions
• support for different worksheets using MDI
• LabPLot project files
• spreadsheet for data import and editing
• filters to import over 80 image formats and export to ps, eps or pdf

Lybniz is a simple desktop graph plotter. It can currently plot three functions and allows you to navigate the plot. Functions are entered in Python notation.

MayaVi is a Python application using The Visualization Toolkit. It also provides modules which are a handy interface to VTK internals in Python. It features an easy to use GUI, and lets you save the visualized scene to PostScript file, PPM/BMP/TIFF/JPEG/PNG image, Open Inventor, VRML or RenderMan RIB files.

And a lot more! MayaVi can be easily modified to do things differently.

ParaView is an open-source, multi-platform application designed to visualize data sets of size varying from small to very large. The goals of the ParaView project include the following:

* Develop an open-source, multi-platform visualization application.
* Support distributed computation models to process large data sets.
* Create an open, flexible, and intuitive user interface.
* Develop an extensible architecture based on open standards.

ParaView runs on distributed and shared memory parallel as well as single processor systems and has been successfully tested on Windows, Mac OS X, Linux and various Unix workstations, clusters and supercomputers. Under the hood, ParaView uses the Visualization Toolkit as the data processing and rendering engine and has a user interface written using Qt.

gives standard perl the ability to COMPACTLY store and SPEEDILY manipulate the large N-dimensional data arrays which are the bread and butter of scientific computing. The idea is to turn perl in to a free, array-oriented, numerical language in the same sense as commercial packages like IDL and MatLab. One can write simple perl expressions to manipulate entire numerical arrays all at once. For example, using PDL the perl variable $a can hold a 1024x1024 floating point image, it only takes 4Mb of memory to store it and expressions like $a=sqrt($a)+2 would manipulate the whole image in a few seconds.

A simple interactive shell (perldl) is provided for command line use together with a module (PDL) for use in perl scripts. Web page: http://pdl.perl.org/

PlotDrop is designed for quick simple visualisation of 2D data series. It is intended to be used in tandem with an external filesystem browser such as GNOME's nautilus or KDE's konqueror. Files containing data are added by dragging them from the browser to the file list.

ScientificPython is a collection of Python modules that are useful for scientific computing. Most modules are rather general, others belong to specific domains and will be of interest to only a small number of users (e.g. the module Scientific.IO.PDB). Almost all modules make extensive use of Numerical Python (NumPy)

PyXPlot is a command-line graphing/plotting package with a simple interface resembling that of Gnuplot.

PyXPlot aims to improve significantly upon the quality of Gnuplot's output, producing publication-quality figures. To this end, text is rendered with all of the beauty and flexibility of the LaTeX typesetting environment.

This package includes extensive documentation and examples that can be found in the /usr/share/doc/pyxplot directory. A gallery of sample plots is available from the project's web site.

Qtiplot is a fully fledged plotting software similar to the OriginLab Origin software (See http://www.originlab.com for more informations about Origin).

It can make two and three dimensional plots of publication quality, both from datasets and functions. It can do non-linear fitting and multi-peak fitting.

Some Features:

• 3D Plots.
• Publication quality 2D plots: Error Bars, Multilayer Plots, Bar Plots, Pie Plots, Vector Plots, Contour and Image Plots.
• Statistical Plots: Box/Whiskers Diagramms, Histograms.
• Easy export of plots to vector formats (EPS, PS, PDF) and to other various image formats (BMP, JPG, PNG, TIFF).
• Powerful and versatile spreadsheets and calculations in column-logic.
• Easy ASCII-Import/Export of single or multiple files.
• Linear and non-linear curve fitting with weighting and estimation of statistical errors of the fit-parameters, using Levenberg-Marquardt, Least-Squares Algorithm or Nelder-Mead simplex minimization algorithm.
• Multi-peak fitting with Gaussian and Lorentzian peak profiles.
• Data analysis: statistics, sorting, FFT, data smoothing (Savitzky-Golay, FFT smoothing, and moving window average), data filtering (low/high/band pass and band block filters), convolution/deconvolution, correlation, interpolation, numerical integration/differentiation.
• Matrices optimized for 3D plotting.
• Templates support: all the settings for plots (2D/3D), tables and matrixes can be saved to ASCII files and restored later on for a fast editing process.
• Project files based on folders, a powerful project explorer with extensive built-in features: drag and drop, searching facilities.

Yorick is an interpreted programming language for:

• scientific simulations or calculations
• postprocessing or steering large simulation codes
• interactive scientific graphics
• reading, writing, and translating large files of numbers

The language features a compact syntax for many common array operations, so it processes large arrays of numbers very quickly and efficiently. Superficially, yorick code resembles C code, but yorick variables are never explicitly declared and have a dynamic scoping similar to many Lisp dialects. The yorick language is designed to be typed interactively at a keyboard, as well as stored in files for later use.

This package includes an emacs-based development environment, which you can launch by typing M-x yorick in emacs.

findimagedupes is a commandline utility which performs a rough "visual diff" to two images. This allows you to compare two images or a whole tree of images and determine if any are similar or identical. On common image types, findimagedupes seems to be around 98% accurate.

The Puzzle library is designed to quickly find visually similar images (GIF, PNG, JPG), even if they have been resized, recompressed, recolored or slightly modified.

This package contains the command-line tool: puzzle-diff.

This metapackage will install Debian packages which might be useful in medical image processing.

It installs several packages supporting DICOM (Digital Imaging and Communications in Medicine) which is the de-facto standard for medical image management. The standard defines data structures and services for the exchange of medical images and related information. The latest release has been published in 2008 and consists of 18 parts.

For more information, you can visit the NEMA homepage http://medical.nema.org/ .

The status of the official DICOM base standard plus all the supplements and correction items are summarized at David Clunie's webpage: http://www.dclunie.com/dicom-status/status.html where you'll find direct links to the most recent yearly edition ftp://medical.nema.org/medical/dicom/2008/ .

Carries out mapping between assorted color spaces including RGB, HSV, HLS, CIEXYZ, CIELUV, HCL (polar CIELUV), CIELAB and polar CIELAB. Qualitative, sequential, and diverging color palettes based on HCL colors are provided.

This R package provides lots of plots, various labeling, axis and color scaling functions. Some of them are:

 arctext:          Display text on a circular arc.
 barhier:          Display a set of hierarchically associated variables
 barp:             A bar plotting routine
 bin.wind.records: Classify wind direction and speed records.
 centipede.plot:   Display a centipede plot
 clock24.plot:     Plot values on a 24 hour "clockface".
 color.legend:     Legend matching categories or values to colors
 dotplot.mtb:      Minitab style dotplots.
 gantt.chart:      Display a Gantt chart
 intersectDiagram: Display set intersections
 multhist:         Plot a multiple histogram, as a barplot
 polar.plot:       Plot values on a circular grid of 0 to 360 degrees.
 vectorField:      Display magnitude/direction vectors
 weighted.hist:    Display a weighted histogram

and many more. Read more about this package at http://cran.r-project.org/web/packages/plotrix/plotrix.pdf

This package includes the following CTAN packages:

 asyfig -- Commands for using Asymptote figures.
 autoarea -- Automatic computation of bounding boxes with PiCTeX.
 bardiag -- LateX package for drawing bar diagrams.
 cachepic -- Convert document fragments into graphics.
 circuitikz -- Draw electrical networks with TikZ.
 curve -- A class for making curriculum vitae.
 curve2e -- Extensions for package pict2e.
 curves -- Curves for LaTeX picture environment
 dcpic -- Commutative diagrams in a LaTeX and TeX documents.
 diagmac2 -- Diagram macros, using pict2e.
 doc-pictex -- A summary list of PicTeX documentation.
 dottex -- Use dot code in LaTeX.
 dot2texi -- Create graphs within LaTeX using the dot2tex tool.
 dratex -- General drawing macros.
 eepic -- Extensions to epic and the LaTeX drawing tools.
 epspdf -- Converter for PostScript, EPS and PDF.
 epspdfconversion -- On-the-fly conversion of EPS to PDF.
 fig4latex -- Management of figures for large LaTeX documents.
 gnuplottex -- Embed Gnuplot commands in LaTeX documents.
 miniplot -- A package for easy figure arrangement.
 pb-diagram -- A commutative diagram package using LAMSTeX or Xy-pic fonts.
 petri-nets -- A set TeX/LaTeX packages for drawing Petri nets.
 pgf-soroban -- Create images of the soroban using TikZ/PGF.
 pgfopts -- LaTeX package options with pgfkeys.
 pgfplots -- Create normal/logarithmic plots in LaTeX.
 picinpar -- Insert pictures into paragraphs.
 pict2e -- New implementation of picture commands.
 pictex -- Picture drawing macros for TeX and LaTeX.
 pictex2 -- Adds relative coordinates and improves the \plot command.
 pinlabel -- A TeX labelling package.
 pmgraph -- "Poor man's" graphics.
 randbild -- Marginal pictures.
 schemabloc -- Draw block diagrams, using Tikz.
 swimgraf -- Graphical/textual representations of swimming performances
 texdraw -- Graphical macros, using embedded PostScript.
 tikz-inet -- Draw interaction nets with TikZ
 tikz-timing -- Easy generation of timing diagrams as tikz pictures.
 tkz-doc -- Documentation macros for the TKZ series of packages.
 tkz-linknodes -- Link nodes in mathematical environments.
 tkz-tab -- Tables of signs and variations using PGF/TikZ.
 tufte-latex -- Document classes inspired by the work of Edward Tufte.
 xypic -- Flexible diagramming macros.

This package contains both runtime and development libraries. Many routines are included in pgplot for viewing scientific data. Many (about 70) output devices are supported. 2-D , 3-D , contour, image manipulation, etc. are well supported. Interactive routines are included. Both a C and a FORTRAN library are present. See http://astro.caltech.edu/~tjp/pgplot/ for more information.

This package provides tools to generate plots and labeled axes easily. It draws normal plots, logplots and semi-logplots. Axis ticks, labels, legends (in case of multiple plots) can be added with key-value options. It can cycle through a set of predefined line/marker/color specifications. In summary, its purpose is to simplify the generation of high-quality function plots, especially for use in scientific contexts (logplots).

Cassandra is a open source scientific data viewer based on VTK. Cassandra provides a dynamic interaction with the VTK pipeline and enables to load plugins dynamically in order to perform specific tasks in data manipulation and visualisation.