PAN Blend imaging packages

Este programa fornece uma interface gráfica para análise científica de dados de ponto de valor real (x,y,z,valor). A princípio foi pensado para aplicações de tomografia de "Atom probe", mas se provou útil para outros tipos de aplicações.

Este metapacote instalará grandes frameworks de análise de dados astronômicos, os quais geralmente fornecem sua própria linguagem de script. Por favor, note que a Gnu Data Language tem seu próprio metapacote, astro- gdl, que o IRAF está no pacote astro-iraf, e que o framework Astropy está no metapacote astro-python3.

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.

This metapackage will install Python 3 packages for astronomy. The packages can be used for interactive analysis, or to create specific programs.

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 é usado para extrair dados de gráficos. Por exemplo, gráficos são tipicamente publicados em jornais científicos sem as tabelas dos dados reais; g3data torna fácil o processo de extração destes dados.

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 é um gerador de grade de elementos finitos 3D com um motor CAD integrado e pós-processador. Seu objetivo de design é fornecer uma ferramenta de malha rápida, leve e fácil de usar com entrada paramétrica e recursos avançados de visualização. O Gmsh é construído em torno de quatro módulos: geometria, malha, solucionador e pós-processamento. A especificação de qualquer entrada para esses módulos é feita interativamente usando a interface gráfica de usuário(a) ou em arquivos de texto ASCII usando a própria linguagem de script do Gmsh.

Consulte o manual de referência do Gmsh para obter uma visão geral mais completa dos recursos do 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.

O Gnuplot é um utilitário portável de linha de comando para funções e orientado a dados interativos que suporta diversos formatos de saída, incluindo drivers para diversas impressoras, (La)TeX, (x)fig, PostScript e outros. A saída para X11 está empacotada em gnuplot-x11.

Os arquivos de dados e funções autodefinidas podem ser manipuladas por uma linguagem interna ao estilo do C. Pode executar atenuação, ajuste de splines ou ajustes não lineares, e pode trabalhar com números complexos.

Esta metapacote serve para instalar um gnuplot completo (-qt, -x11 ou -nox).

A biblioteca gphoto2 pode ser usada por aplicações para acessar vários modelos de câmeras digitais via protocolos padrão como o "USB Mass Storage" e PTP, ou via protocolos específicos de fornecedor.

Este pacote fornece a interface em linha de comando do gphoto2.

Grace é uma ferramenta aponte-e-clique que possibilita ao usuário desenhar gráficos X-Y. Este programa antigamente era conhecido como Xmgr.

Alguns de seus recursos são: definição pelo usuário de escala dos eixos do gráfico, marcas de escala, rótulos, símbolos, estilos de linha, cores, regressão linear, splines, médias móveis, DFT/FFT, auto-correlação e correlação cruzada, modo "batch" para geração de gráficos sem acompanhamento, e suporte a exportação para PostScript, FrameMaker e diversos formatos de imagem.

Desenho de grafos trata do problema de visualizar informação estrutural construindo representações geométricas de redes e grafos abstratos. Geração automática de desenhos de grafos tem importantes aplicações em tecnologias chave tais como projeto de banco de dados, engenharia de software, VLSI, projeto de rede e interfaces visuais em outros domínios. Situações onde essas ferramentas podem ser muito úteis:

• Você precisa reestruturar um programa e precisa primeiro entender as relaçoes entre os seus tipos, procedimentos e códigos fonte
• Você precisa encontrar os gargalos em um "backbone" de internet - não apenas links individuais, mas suas relações
• Você está depurando um protocolo ou microarquitetura representada como uma máquina de estado finito e precisa descobrir como surge um certo estado de erro
• Você gostaria de procurar em um esquema de banco de dados, base de conhecimento ou programa distribuído representado graficamente
• Você gostaria de ter uma visão geral de uma coleção de documentos vinculados
• Você gostaria de descobrir padrões e comunidades de interesse em um] banco de dados de chamadas de telefone ou mensagens de e-mail

Este pacote contém as ferramentas de linha de comando.

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 é uma aplicação que

• Exibe um grande número de formatos de imagem.
• Exibe imagens 2D ou 3D (como fatias) com um zoom muito bom e com o recurso "pan".
• Funciona com multi-espectro, séries de tempo ou documentos de múltiplas páginas (e.g.: imagens de satélite, pilhas TIFF, GIFs animados e arquivos multi-componentes heterogêneos).
• Exibe todos os tipos de pixels (dados de 1-bit a 64-bit, inteiros ou ponto flutuante).
• Perfil arbitrário 1-D de imagens 2-D (ou fatias 2-D de imagens 3-D) podem ser exibidas.
• Tem suporte a mapas arbitrários de cores para todos os tipos de pixels (i.e.: exibição de cores falsas).
• Tem, por padrão, facilidades para manipulação de imagem (brilho/contraste, gama, zoom, corte, rotação, etc).
• Pode ser controlada remotamente via sockets e comandos de texto (para fácil integração em vários sistemas de análise de imagem).
• Imagens podem ser enviadas para dentro do Imview através de sockets ou memória compartilhada.
• E muito mais!

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 is a cross-platform tool for 2-D and 3-D scientific data visualization. Its features include:

• Visualization of scalar, vector and tensor data in 2 and 3 dimensions
• Easy scriptability using Python
• Easy extendability via custom sources, modules, and data filters
• Reading several file formats: VTK (legacy and XML), PLOT3D, etc.
• Saving of visualizations
• Saving rendered visualization in a variety of image formats.

MayaVi2 has been designed with scriptability and extensibility in mind. While the mayavi2 application is usable by itself, it may be used as an Envisage plugin which allows it to be embedded in user applications natively. Alternatively, it may be used as a visualization engine for any application.

This package also provides TVTK, which wraps VTK objects to provide a convenient, Pythonic API, while supporting Traits attributes and NumPy/SciPy arrays. TVTK is implemented mostly in pure Python, except for a small extension module.

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 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.

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 is a Python module that interfaces to gnuplot, the popular plotting program. It allows you to use gnuplot from within Python to plot arrays of data from memory, data files, or mathematical functions. If you use Python to perform computations or as glue' for numerical programs, you can use this module to plot data on the fly as they are computed. And the combination with Python makes it is easy to automate things, including to create crudeanimations' by plotting different datasets one after another.

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).

Pacote Python para analisar, ler e escrever arquivos no formato Microsoft OLE2 (também chamados de Structured Storage, Compound File Binary Format ou Compound Document File Format), como documentos do Microsoft Office 97-2003, vbaProject.bin em arquivos do Microsoft Office 2007+, arquivos do Image Composer e FlashPix, arquivos de mensagem do Microsoft Outlook, StickyNotes, vários formatos Microscopy, arquivos de quarentena do antivírus McAffe, 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.