Extending sfftk

Adding A Segmentation File Format

There are four (4) steps involved.

• Create a reader
• Create a format adapter
• Add test data
• Write unit tests

Step I: Create a reader

Write a reader module and place it in sfftk.readers package. The reader module may implement a single class that provides a simple API to segmentation files. There is not predefined structure on how to handle reading the file. However, the reader module must implement a get_data(fn, *args, **kwargs) function that takes the name of a file as a string. The name of the module should be the extension followed by the word ‘reader’ e.g. for Segger files it is segreader.py.

Step II: Create a format adapter

Write a format module and place it in the sfftk.formats package. This module adapts the reader in Step II to the schema (EMDB-SFF data model) API. The name of the module must be simply the extension of the file format e.g. for Segger files it is seg.py. The module uses the inherits segmentation parts from the classes defined in sfftk.formats.base module and have names indicating the segmentation format e.g. for Segger seg.py has a SeggerSegmentation class that inherits from the generic Segmentation class which provides a way to hook functionality required of all custom segmentation representations. This module will then tie the segmentation file format API defined in readers with the schema (EMDB-SFF data model) API.

Step III: Add test data

Provide an example segmentation in the sfftk.test_data package.

Step IV: Write tests

Write unit tests and add them to the sfftk.unittests.test_formats module. Each format that you add should implement a read and convert test method (respectively called test_<format>_read and test_<format>_convert. See the sfftk.unittests.test_formats module for examples.

Once all this components are in place conversion to XML, HDF5 and JSON should be automatic.

$ sff convert file.<format> -f sff

$ sff convert file.<format> -f hff

$ sff convert file.<format> -f json

Also, tests can be run as follows:

$ sff tests format

$ sff test formats