setup.rst

Setup

Bob.ip.binseg

Complete bob's `installation`_ instructions. Then, to install this package

conda install bob.ip.binseg

Datasets

The package supports a range of retina fundus datasets but does not install the bob.db APIs by default, nor does it include the datasets.

To setup a datasets:

1. Download the dataset from the authors website
2. Install the corresponding bob.db package via conda install bob.db.<database>. E.g. to install the DRIVE API run conda install bob.db.drive
3. :ref:`datasetpathsetup`
4. :ref:`dsconsistency`

Dataset	Website	bob.db package
STARE	http://cecas.clemson.edu/~ahoover/stare/	bob.db.stare
DRIVE	https://www.isi.uu.nl/Research/Databases/DRIVE/	bob.db.drive
DRIONS	http://www.ia.uned.es/~ejcarmona/DRIONS-DB.html	bob.db.drionsdb
RIM-ONE	http://medimrg.webs.ull.es/research/downloads/	bob.db.rimoner3
CHASE-DB1	https://blogs.kingston.ac.uk/retinal/chasedb1/	bob.db.chasedb
HRF	https://www5.cs.fau.de/research/data/fundus-images/	bob.db.hrf
Drishti-GS	http://cvit.iiit.ac.in/projects/mip/drishti-gs/mip-dataset2/Home.php	bob.db.drishtigs1
IOSTAR	http://www.retinacheck.org/datasets	bob.db.iostar
REFUGE	https://refuge.grand-challenge.org/Details/	bob.db.refuge

Set up dataset paths

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

bob config set bob.db.drive.datadir "/path/to/drivedataset/"

To check your current setup

bob config show

This should result in an output similar to the following:

{
    "bob.db.chasedb1.datadir": "/idiap/resource/database/CHASE-DB11/",
    "bob.db.drionsdb.datadir": "/idiap/resource/database/DRIONS",
    "bob.db.drishtigs1.datadir": "/idiap/resource/database/Drishti-GS1/",
    "bob.db.drive.datadir": "/idiap/resource/database/DRIVE",
    "bob.db.hrf.datadir": "/idiap/resource/database/HRF",
    "bob.db.iostar.datadir": "/idiap/resource/database/IOSTAR/IOSTAR Vessel Segmentation Dataset/",
    "bob.db.refuge.datadir": "/idiap/resource/database/REFUGE",
    "bob.db.rimoner3.datadir": "/idiap/resource/database/RIM-ONE/RIM-ONE r3",
    "bob.db.stare.datadir": "/idiap/resource/database/STARE"
}

Test dataset consitency

To check whether the downloaded version is consistent with the structure that is expected by our bob.db packages run bob_dbmanage.py datasettocheck checkfiles E.g.:

conda activate your-conda-env-with-bob.ip.binseg
bob_dbmanage.py drive checkfiles
> checkfiles completed sucessfully