Setup

Complete Bob’s installation instructions. Then, to install this package, do this:

$ conda activate <myenv>
(<myenv>) $ conda install bob.ip.binseg

Note

The value <myenv> should correspond to the name of the environment where you initially installed your Bob packages.

Datasets

The package supports a range of retina fundus datasets, but does not include the raw data itself, which you must procure.

To setup a dataset, do the following:

  1. Download the dataset from the authors website (see Supported Datasets for download links and details), unpack it and store the directory leading to the uncompressed directory structure.

    Warning

    Our dataset connectors expect you provide “root” paths of raw datasets as you unpack them in their pristine state. Changing the location of files within a dataset distribution will likely cause execution errors.

  2. For each dataset that you are planning to use, set the datadir to the root path where it is stored. E.g.:

    (<myenv>) $ bob config set bob.ip.binseg.drive.datadir "/path/to/drive"
    

    To check supported raw datasets and your current setup, do the following:

    (<myenv>) $ bob binseg dataset list
    Supported datasets:
    - drive: bob.ip.binseg.drive.datadir = "/Users/andre/work/bob/dbs/drive"
    * stare: bob.ip.binseg.stare.datadir (not set)
    

    This command will show the set location for each configured dataset, and the variable names for each supported dataset which has not yet been setup.

  3. To check whether the downloaded version is consistent with the structure that is expected by this package, run bob binseg dataset check <dataset>, where <dataset> should be replaced by the dataset programmatic name. E.g., to check DRIVE files, use:

    (<myenv>) $ bob binseg dataset check drive
    ...
    

    If there are problems on the current file organisation, this procedure should detect and highlight which files are missing (cannot be loaded).