setup.rst

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 install the bob.db iterator APIs by default, or includes the raw data itself, which you must procure.

To setup a dataset, do the following:

1. Download the dataset from the authors website (see :ref:`bob.ip.binseg.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. Install the corresponding bob.db package (package names are marked on :ref:`bob.ip.binseg.datasets`) with the following command:

   # replace "<package>" by the corresponding package name
   (<myenv>) $ conda install <package>
   # example:
   (<myenv>) $ conda install bob.db.drive #to install DRIVE iterators

3. 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.db.drive.datadir "/path/to/drivedataset/"

   To check your current setup, do the following:

   (<myenv>) $ bob config show
   {
       "bob.db.chasedb1.datadir": "/path/to/chasedb1/",
       "bob.db.drionsdb.datadir": "/path/to/drionsdb",
       "bob.db.drive.datadir": "/path/to/drive",
       "bob.db.hrf.datadir": "/path/to/hrf",
   }

   This command will show the set location for each configured dataset. These paths are automatically used by the dataset iterators provided by the bob.db packages to find the raw datafiles.

4. To check whether the downloaded version is consistent with the structure that is expected by our bob.db packages, run bob_dbmanage.py <dataset> checkfiles, where <dataset> should be replaced by the dataset programmatic name. E.g., to check DRIVE files, use:

   (<myenv>) $ bob_dbmanage.py drive checkfiles
   > checkfiles completed sucessfully

   If there are problems on the current file organisation, this procedure should detect and highlight which files are missing.

   Tip

   The programmatic name of datasets follow the bob.db.<dataset> nomenclature. For example, the programmatic name of CHASE-DB1 is chasedb1, because the package name implementing iterators to its files is bob.db.chasedb1.