PAN Blend imaging packages

Ця програма надає графічний інтерфейс для наукового аналізу точкових даних з вагами (x,y,z, значення). Це в першу чергу застосування, що використовують методи атомної томографії, але може виявитися корисним і для інших застосувань.

This metapackage will install large astronomical data analysis frameworks, which usually provide their own script language. Please notice that the Gnu Data Language has its own metapackage astro-gdl, IRAF is in astro-iraf, and the Astropy framework is in the astro-python3 metapackage.

GDL (GNU Data Language) is a free replacement for the commercial software IDL (Interactive Data Language). It has full syntax compatibility with IDL 7.1 and is usable for astronomical data analysis. This metapackage will install astronomy related packages usable with GDL; especially the IDL Astronomy Users Library.

Цей збірний пакунок встановлює пакунки для астрономії для використання в Python 3. Пакунки можна використовувати для інтерактивних аналізів або створення спеціяльних програм.

The astropy package contains core functionality and some common tools needed for performing astronomy and astrophysics research with Python.

This package contains the tools that come with astropy:

• fitscheck: Detect and fix FITS standards violations
• fits2bitmap: Create a bitmap file from a FITS image.
• fitsdiff: Compare two FITS image files and report the differences in header keywords and data.
• fitsheader: Print the header(s) of one or more FITS file(s) to the standard output in a human-readable format.
• samp_hub: SAMP Hub Server.
• volint: Check a VOTable file for compliance to the VOTable specification
• wcslint: Check the WCS keywords in a FITS file for compliance against the standards

g3data використовується для отримання даних з графів. Наприклад, графи зазвичай публікуються в наукових журналах без таблиць з вихідними даними. g3data робить процес отримання цих даних простим.

Giza is a lightweight scientific plotting library built on top of cairo that provides uniform output to multiple devices. Giza also provides a mostly compatible, modern replacement for the PGPLOT graphics library.

This package contains the development files.

Gmsh — це генератор тривимірних кінцевих елементів, представлених полігонами, з вбудованими засобами САПР та після-обробкою. Програма задумана як простий інструмент створення полігональних об’єктів з можливістю введення параметрів об’єкта та сучасними засобами візуалізації. Gmsh складається з чотирьох модулів: геометрії, полігону, розв’язувача та після-обробки. Введення параметрів створюваного об’єкта у модулі здійснюється або інтерактивно — засобами графічного інтерфейсу користувача, або за допомогою текстових ASCII-файлів з використанням власної мови сценаріїв Gmsh.

Більш детальний огляд можливостей Gmsh дається у керівництві користувача Gmsh.

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.

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 metapackage is to install a full-featured gnuplot (-qt, -x11 or -nox).

The gphoto2 library can be used by applications to access various digital camera models, via standard protocols such as USB Mass Storage and PTP, or vendor-specific protocols.

This package provides the gphoto2 command-line frontend.

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, and hardcopy support for PostScript, FrameMaker and several image formats.

У вигляді діаграми можна представити саму різну структурну інформацію у вигляді геометричних форм абстрактних блоків та їх з’єднань. Автоматичне створення діаграм є ключовим елементом програми в таких галузях як проектування баз даних, мереж та програмних інтерфейсів. Вам буде корисний даний інструментарій якщо:

• Ви хочете реорганізувати програму, для чого треба по-перше зрозуміти всі існуючі взаємовідносини між типами, процедурами та файлами
• Ви хочете виявити слабкі місця опорного вузла мережі Інтернет — на системному рівні, а не тільки на рівні окремих каналів
• Ви налагоджуєте протокол або мікро-архітектуру, що зводяться до кінцевого механізму і хочете з’ясувати коли він переходить у стан «помилка»
• Ви хочете отримати наочне уявлення схеми бази даних, бази знань, або розподіленої обчислювальної системи
• Ви хочете отримати огляд групи пов’язаних між собою документів
• Ви хочете виявити шаблони та групи за інтересами на основі бази даних телефонних дзвінків або електронних листів

Цей пакунок встановлює утиліти командного рядка.

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 PDF suitable for printing (gri-pdf-doc package) and on-line by following links from the gri home page:

  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.

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.

It can display, edit, analyze, process, save and print 8-bit, 16-bit and 32-bit images. It can read many image formats including TIFF, GIF, JPEG, BMP, DICOM, FITS and "raw". It supports "stacks", a series of images that share a single window.

It can calculate area and pixel value statistics of user-defined selections. It can measure distances and angles. It can create density histograms and line profile plots. It supports standard image processing functions such as contrast manipulation, sharpening, smoothing, edge detection and median filtering.

Spatial calibration is available to provide real world dimensional measurements in units such as millimeters. Density or gray scale calibration is also available.

ImageJ is developed by Wayne Rasband (wayne@codon.nih.gov), is at the Research Services Branch, National Institute of Mental Health, Bethesda, Maryland, USA.

Imview це програма, яка:

• Працює з великою кількістю графічних форматів.
• Показує дво- та тривимірні (у проекціях) зображення з гарними можливостями збільшення та панорамування.
• Працює з багато-спектральними, багатосторінковими документами (наприклад: супутникові знімки поверхні, стеки TIFF, анімовані GIF та гетерогенні багато-компонентні файли).
• Показує всі типи пікселів (від 1-бітових до 64-бітових, цілі або з плаваючою точкою).
• Довільні одновимірні профілі двовимірних зображень (або двовимірні проекції тривимірних зображень) можуть бути показані.
• Підтримка довільних кольорових схем для всіх типів пікселів (наприклад: помилкові кольори дисплея).
• Має стандартні засоби для роботи із зображеннями (яскравість, контрастність, гамма, масштабування, кадрування, обертання, і т.д.).
• Може керуватись віддалено через сокети та текстові команди (для легкої інтеграції в різні системи аналізу зображень).
• Зображення можуть бути завантажені в Imview через сокети або розподіляєму пам'ять.
• Та багато іншого!

Kst is a fast real-time large-dataset viewing and plotting tool. It has basic data analysis functionality, contains many powerful built-in features and is expandable with plugins and extensions.

Spectromicroscopy combines spectral data with microscopy, where typical datasets consist of a stack of microscopic images taken across an energy range. Due to the data complexity, manual analysis can be time consuming and inefficient, whereas multivariate analysis tools not only reduce the time needed but also can uncover hidden trends in the data.

Mantis is Multivariate ANalysis Tool for Spectromicroscopy developed in Python by 2nd Look Consulting. It uses principal component analysis and cluster analysis to classify pixels according to spectral similarity.

MayaVi2 — багатоплатформовий інструмент для візуалізації наукових даних у 2-D та 3-D. Серед його можливостей:

• візуалізація скалярних, векторних і тензорних даних у 2-х та 3-х вимірах;

• просте використання сценаріїв за допомогою Python;

• легка розширюваність за допомогою додаткових джерел користувача, модулів та фільтрів даних;

• читання кількох форматів: VTK (старий та XML), PLOT3D і т.д.;

• збереження візуалізації;
• збереження візуалізацій в різних графічних форматах.

MayaVi2 був створений з думкою про розширюваність та використання сценаріїв. Але MayaVi2 є корисним застосунком сам по собі, він також може бути використаний як Передбачальний (Envisage) втулок, який дозволяє вбудовувати MayaVi2 безпосередньо у застосунки користувача. Крім того, він може бути використаний в якості рушія візуалізації для будь-якого застосунка.

Цей пакунок також впроваджує TVTK, який обертає об’єкти VTK для забезпечення зручності використання, API для мови Python, підтримуючи при цьому атрибути Traits та масиви NumPy/SciPy. TVTK реалізується в основному на чистому Python, за винятком невеликих модулів розширення.

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

On one hand, it installs several packages supporting various image file formats and image management, like DICOM (Digital Imaging and Communications in Medicine) which is the de-facto standard for medical image management, and NIFTI. On the other hand, it provides a variety of software packages that can be used for visualization and for image processing - either from a graphical user interface, the command line, or implemented in workflows.

ParaView — багатоплатформний застосунок з відкритими джерельними кодами, розроблений для візуалізації наборів даних як великих розмірів так і малих. Метою проекту ParaView є:

• розробка застосунку для візуалізації, багатоплатформного з відкритими джерельними кодами

• підтримка розподіленої моделі обчислень, що оперують великими обсягами даних

• створення відкритого, гнучкого та інтуїтивно зрозумілого інтерфейсу користувача

• розробка гнучкої архітектури на основі відкритих стандартів

ParaView працює на системах із розділюваною та спільною пам’яттю, а також на однопроцесорних системах, її також було успішно протестовано у Windows, Linux, MacOS та різних робочих станціях Unix, а також кластерах й суперкомп’ютерах. ParaView використовує Visualization Toolkit в якості рушія для обробки та візуалізації даних; інтерфейс користувача написаний з використанням бібліотеки Qt.

PDL 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.

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.

APLpy is a Python module aimed at producing publication-quality plots of astronomical imaging data in FITS format. The module uses Matplotlib, a powerful and interactive plotting package. It is capable of creating output files in several graphical formats, including EPS, PDF, PS, PNG, and SVG.

AstroML is a Python 3 module for machine learning and data mining built on numpy, scipy, scikit-learn, and matplotlib. It contains a growing library of statistical and machine learning routines for analyzing astronomical data in Python, loaders for several open astronomical datasets, and a large suite of examples of analyzing and visualizing astronomical datasets.

AstroML is a Python module for machine learning and data mining built on numpy, scipy, scikit-learn, and matplotlib. It contains a growing library of statistical and machine learning routines for analyzing astronomical data in Python, loaders for several open astronomical datasets, and a large suite of examples of analyzing and visualizing astronomical datasets.

This package contains the performance add-ons of the Python 3 version of the package.

The astropy package contains core functionality and some common tools needed for performing astronomy and astrophysics research with Python. It can be extended by a number of "affiliated packages" that are intended to work with the core package.

Cartopy is a Python package designed to make drawing maps for data analysis and visualisation easy.

It features:

• object oriented projection definitions
• point, line, polygon and image transformations between projections
• integration to expose advanced mapping in matplotlib with a simple and intuitive interface
• powerful vector data handling by integrating shapefile reading with Shapely capabilities

This package provides the Python 3 library.

This module can list, configure and execute CPL-based recipes from Python3. The input, calibration and output data can be specified as FITS files or as astropy fits objects in memory.

The Common Pipeline Library (CPL) comprises a set of ISO-C libraries that provide a comprehensive, efficient and robust software toolkit. It forms a basis for the creation of automated astronomical data-reduction tasks.

One of the features provided by the CPL is the ability to create data-reduction algorithms that run as plugins (dynamic libraries). These are called "recipes" and are one of the main aspects of the CPL data-reduction development environment.

Fitsio provides an easy to use object-oriented API including providing a Numpy interface to FITS files read from CFITSIO. It allows direct access to the columns of a FITS binary table which can be useful for reading large fits files. Compared to astropy.io.fits, this package is closer to the underlying cfitsio library.

Fitsio also exposes a microlanguage (implemented in CFITSIO) for making efficient SQL-like queries of tables (single tables only though–no joins or anything like that).

Gammapy is an in-development affiliated package of Astropy that builds on the core scientific Python stack to provide tools to simulate and analyse the gamma-ray sky for telescopes such as CTA, H.E.S.S., VERITAS, MAGIC, HAWC and Fermi-LAT.

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 Python library/interface.

Gnuplot.py — модуль Python для роботи з gnuplot, популярної програми побудови графіків. Дозволяє використовувати gnuplot з програм, написаних на Python, для побудови графіків, використовуючи дані в пам’яті, файли з даними або математичні функції. Якщо Ви використовуєте Python для виконання обчислень або як оболонку для обчислювальних програм, то зможете використовувати цей модуль для побудови графіків «на ходу», відразу ж після отримання даних. У поєднанні з Python можна легко автоматизувати такі завдання, як, створення «грубої» анімації, створюючи графіки різних даних один за одним.

The guiqwt Python library provides efficient 2D data-plotting features (curve/image visualization and related tools) for signal/image processing application development and interactive computing. It's based on the scientific modules NumPy and SciPy, and the PyQwt plotting widgets for PyQt4 graphical user interfaces.

This is the Python 3 version of the package.

HyperSpy is an open source Python library for the interactive analysis of multidimensional datasets that can be described as multidimensional arrays of a given signal (for example, a 2D array of spectra, also known as a spectrum image).

HyperSpy makes it straightforward to apply analytical procedures that operate on an individual signal to multidimensional arrays, as well as providing easy access to analytical tools that exploit the multidimensionality of the dataset.

Its modular structure makes it easy to add features to analyze many different types of signals.

Imexam is an affiliated package of AstroPy. It was designed to be a lightweight library which enables users to explore data using common methods which are consistent across viewers. It can be used from a command line interface, through a Jupyter notebook or through a Jupyter console. It can be used with multiple viewers, such as DS9 or Ginga, or without a viewer as a simple library to make plots and grab quick photometry information.

Fast, interactive, multi-dimensional image viewer for Python. It's designed for browsing, annotating, and analyzing large multi-dimensional images. It's built on top of Qt (for the GUI), vispy (for performant GPU-based rendering), and the scientific Python stack (numpy, scipy).

Python package to parse, read and write Microsoft OLE2 files (also called Structured Storage, Compound File Binary Format or Compound Document File Format), such as Microsoft Office 97-2003 documents, vbaProject.bin in MS Office 2007+ files, Image Composer and FlashPix files, Outlook MSG files, StickyNotes, several Microscopy file formats, McAfee antivirus quarantine files, etc.

Photutils contains functions for:

• estimating the background and background rms in astronomical images
• detecting sources in astronomical images
• estimating morphological parameters of those sources (e.g., centroid and shape parameters)
• performing aperture and PSF photometry

This package contains the Python 3 version of the package.

PyQtGraph is a pure-python graphics and GUI library built on PyQt4 and numpy. It is intended for use in mathematics / scientific / engineering applications. Despite being written entirely in Python, the library is very fast due to its heavy leverage of numpy for number crunching and Qt's GraphicsView framework for fast display.

This is the Python 3 version of the package.

Seaborn is a library for making attractive and informative statistical graphics in Python. It is built on top of matplotlib and tightly integrated with the PyData stack, including support for numpy and pandas data structures and statistical routines from scipy and statsmodels.

Some of the features that seaborn offers are

• Several built-in themes that improve on the default matplotlib aesthetics
• Tools for choosing color palettes to make beautiful plots that reveal patterns in your data
• Functions for visualizing univariate and bivariate distributions or for comparing them between subsets of data
• Tools that fit and visualize linear regression models for different kinds of independent and dependent variables
• A function to plot statistical timeseries data with flexible estimation and representation of uncertainty around the estimate
• High-level abstractions for structuring grids of plots that let you easily build complex visualizations

This is the Python 3 version of the package.

scikit-image is a collection of image processing algorithms for Python. It performs tasks such as image loading, filtering, morphology, segmentation, color conversions, and transformations.

This package provides the Python 3 module.

The specutils package implements base classes and utilities for interacting with astronomical spectra in Python and the Astropy project. It is intended for eventual merger with the astropy package, but for now is being developed independently.

Vispy is a high-performance interactive 2D/3D data visualization library.

Vispy leverages the computational power of modern Graphics Processing Units (GPUs) through the OpenGL library to display very large datasets.

This package provides VisPy for the Python 3 interpreter.

Willow is a simple image library that combines the APIs of Pillow, Wand and OpenCV. It converts the image between the libraries when necessary.

Willow currently has basic resize and crop operations, face and feature detection and animated GIF support. New operations and library integrations can also be easily implemented.

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

• Cross platform: works natively on Windows, Mac OS X and Linux/Unix systems
• Fully Python scriptable
• OpenGL based 3D plotting
• Publication quality plots and easy export to various image formats (EMF, EPS, PS, PDF, SVG, BMP, JPG, PNG, TIFF, etc ...)
• Easy integration with LaTeX typesetting system
• Powerful and versatile spreadsheets with column-logic calculations and easy import/export of multiple files
• One-click access to extensive built-in data analysis routines
• Advanced statistical analysis: Student's t-Test, ANOVA, chi-square test for variance, normality test (Shapiro-Wilk)
• Linear and nonlinear curve fitting with weighting and estimation of statistical errors of the fit-parameters
• Multi-peak fitting
• Image analysis tools
• Templates support: all settings for plots, tables and matrices can be saved and restored later on for a fast editing process
• Project files based on folders, a powerful project explorer with built-in drag and drop and searching facilities
• Full import of Excel workbooks and Open Document Format spreadsheets, dBase, SQLite and Microsoft Access databases

RasMol is a molecular graphics program intended for the visualisation of proteins, nucleic acids and small molecules. The program is aimed at display, teaching and generation of publication quality images.

The program reads in a molecule coordinate file and interactively displays the molecule on the screen in a variety of colour schemes and molecule representations. Currently available representations include depth-cued wireframes, 'Dreiding' sticks, spacefilling (CPK) spheres, ball and stick, solid and strand biomolecular ribbons, atom labels and dot surfaces.

Supported input file formats include Protein Data Bank (PDB), Tripos Associates' Alchemy and Sybyl Mol2 formats, Molecular Design Limited's (MDL) Mol file format, Minnesota Supercomputer Center's (MSC) XYZ (XMol) format, CHARMm format, CIF format and mmCIF format files.

This package installs two versions of RasMol, rasmol-gtk has a modern GTK-based user interface and rasmol-classic is the version with the old Xlib GUI.

RELION (for REgularised LIkelihood OptimisatioN) is a stand-alone computer program for Maximum A Posteriori refinement of (multiple) 3D reconstructions or 2D class averages in cryo-electron microscopy.

RELION provides a GUI, several command-line tools in parallel (MPI) and serial versions, optionally with CUDA/GPU support.

relion provides the serial and parallel (MPI) command-line tools without CUDA/GPU support.

RELION (for REgularised LIkelihood OptimisatioN) is a stand-alone computer program for Maximum A Posteriori refinement of (multiple) 3D reconstructions or 2D class averages in cryo-electron microscopy.

RELION provides a GUI, several command-line tools in parallel (MPI) and serial versions, optionally with CUDA/GPU support.

relion-gui provides the graphical user interface without CUDA/GPU support.

Bayesian analysis of blinking and bleaching, or 3B microscopy, is a method which analyses data in which many overlapping fluorophores undergo bleaching and blinking events, giving the structure at enhanced resolution. By using a Hidden Markov Model (HMM), it allows useful information to be obtained from data that would be impossible to analyse with standard localisation analysis techniques.

This package contains the command-line tool.

Bayesian analysis of blinking and bleaching, or 3B microscopy, is a method which analyses data in which many overlapping fluorophores undergo bleaching and blinking events, giving the structure at enhanced resolution. By using a Hidden Markov Model (HMM), it allows useful information to be obtained from data that would be impossible to analyse with standard localisation analysis techniques.

This package contains the ImageJ plugin.

Veusz is a 2D and 3D scientific plotting and graphing package, designed to produce publication-ready PDF, SVG, Postscript and bitmap output. Veusz provides a GUI, command line and scripting interface (based on Python) to its plotting facilities. The plots are built using an object-based system to provide a consistent interface.

This package includes the main executable, documentation and examples.

RELION (for REgularised LIkelihood OptimisatioN) is a stand-alone computer program for Maximum A Posteriori refinement of (multiple) 3D reconstructions or 2D class averages in cryo-electron microscopy.

RELION provides a GUI, several command-line tools in parallel (MPI) and serial versions, optionally with CUDA/GPU support.

relion-cuda provides the serial and parallel (MPI) command-line tools with CUDA/GPU support.

RELION (for REgularised LIkelihood OptimisatioN) is a stand-alone computer program for Maximum A Posteriori refinement of (multiple) 3D reconstructions or 2D class averages in cryo-electron microscopy.

RELION provides a GUI, several command-line tools in parallel (MPI) and serial versions, optionally with CUDA/GPU support.

relion-gui-cuda provides the graphical user interface with CUDA/GPU support.

MoviePy is a Python library for video editing: cutting, concatenations, title insertions, video compositing (a.k.a. non-linear editing), video processing, and creation of custom effects.