omsi Package

Subpackages

The omsi package defines the main BASTet software stack used, e.g., by the OpenMSI project. It contains a large range of functionality for interacting analyses, OpenMSI HDF5 data files, analysis workflows and other related infrastructure. The following is a rough overview of the various packages and modules

  • Analysis omsi.analysis Package containing the base classes that facilitate the integration of new analysis with the BASTet software stack (e.g, the file format) and collection of specific analysis functionality.
omsi.analysis Package containing the base classes that facilitate the integration of new analysis with the BASTet software stack (e.g, the file format) and collection of specific analysis functionality.
omsi.analysis.compound_stats Package containing shared third-party code modules included here to reduce the need for external dependencies when only small parts of external code are used.
omsi.analysis.findpeaks Package of peak-finding related analysis modules.
omsi.analysis.msi_filtering Module with third-party modules, functions, classes used by some of the analysis modules in the containing package.
omsi.analysis.multivariate_stats Multivariate statistics analysis
  • Data Format omsi.dataformat Package for implementation and specification of file formats. In particular this package contains the base API for interacting with OpenMSI HDF5 datasets.
omsi.dataformat Package for implementation and specification of file formats.
omsi.dataformat.omsi_file Module for specification of the OpenMSI file API.
  • Workflow omsi.workflow Package with modules for specification and execution of analysis tasks and complex analysis workflows.
omsi.workflow Package with modules for specification and execution of analysis tasks and complex analysis workflows.
omsi.worflow.dirver
omsi.workflow.executor Package with executors of analysis workflows.
  • Data Structures omsi.datastructure Package with a collection of various data structures and related classes used throughout the software stack, e.g., for metadata, analysis parameter data, runtime information data etc.
omsi.datastructures Package with a collection of various data structures and related classes used throughout the software stack, e.g., for metadata, analysis parameter data, runtime information data etc.
omsi.datastructures.metadata Package with metadata datastructures
  • Shared omsi.shared Package used to implement shared functionality and helper functions.
omsi.shared Package used to implement shared functionality and helper functions.
omsi.shared.thirdparty
  • Tools omsi.tools Package for collecting tools (e.g,. command-line programs) to help with particular tasks. This includes, e.g, tools for data conversion, document generation, etc.
omsi.tools Package for collecting tools (e.g,.
omsi.tools.misc Collection of miscellaneous tools.
  • Templates omsi.templates This package provides a collection of code templates to ease the development of additional components, e.g., analysis modules. As such, this package is NOT intended for direct usage but is rather just a library of code templates.
omsi.templates This package provides a collection of code templates to ease the development of additional components, e.g., analysis modules.
  • Examples omsi.examples Package with a collection of various misc. example scripts.
omsi.examples Package with a collection of various misc.