spimcube 1.3.2

This package enables the exploration of datacube of spectra within a rich GUI interface.

Spimcube

spimcube provides a graphical user interface (GUI) coded with matplotlib to explore datacube of spectra, in other words, tridimensional set of data containing spectra.

Currently, the GUI is designed for datacubes obtained from a spatial mapping where a spectrum is recorded at each pixel of the map. But in futur releases, there will be tools to explore general datacube where each dimension can be: time, magnetic field, temperature, etc.

The package has three modules:

• spimclass containing the main objects implemented in the package, i.e Spim and SpimInterface.
• functions mostly functions used internally in the classes defined in spimclass.
• procedures included for personal purposes.

Spim object

Object used to initialize the set of data. It has multiple initialization methods depending on the user raw data. It possesses methods allowing for diverse kind of map plot: the default one being "spectrally filtered spatial image" with the method intensity_map.

SpimInterface object

Object that implement the GUI. It is conceived in such a way that if the user identifies interesting data points or ROI within the GUI, he can easily switch to command line interface (CLI) to manipulate those. Actually, this GUI is thought as an exploration tool for datacube before going to more thorough analysis through classical CLI.

Installation and upgrade

To install spimcube simply type in your terminal:

$ pip install spimcube

To update to the last version of the package use:

$ pip install --upgrade spimcube

Todos

• Implement a method to remove spikes from the raw data. Actually only despike.clean is used for the display but it is slow. remove_spikes is on his way!
• Implement regex formulae to read the correct parameters for initialization of Spim object directly from the file name or from file containing metadata.
• Make the code more flexible so it can handle unfinished map.

License

This project is licensed under the terms of the MIT license.