Initial commit

.gitignore

+### Bob defaults ###
+*~
+*.swp
+*.pyc
+*.so
+*.dylib
+bin
+eggs
+parts
+.installed.cfg
+.mr.developer.cfg
+*.egg-info
+develop-eggs
+sphinx
+dist
+.nfs*
+.gdb_history
+build
+*.egg
+src/
+record.txt
+core
+
+
+### JupyterNotebook ###
+.ipynb_checkpoints
+*/.ipynb_checkpoints/*
+
+
+### VisualStudioCode ###
+.vscode/*
+.vscode/settings.json
+.vscode/tasks.json
+.vscode/launch.json
+.vscode/extensions.json
+
+### VisualStudioCode Patch ###
+# Ignore all local history of files
+.history
\ No newline at end of file

.gitlab-ci.yml

+include: 'https://gitlab.idiap.ch/bob/bob.devtools/raw/master/bob/devtools/data/gitlab-ci/single-package.yaml'
\ No newline at end of file

LICENSE

+Copyright (c) 2016 Idiap Research Institute, http://www.idiap.ch/
+Written by Tim Laibacher <tim.laibacher@idiap.ch>
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this
+list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+this list of conditions and the following disclaimer in the documentation
+and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its contributors
+may be used to endorse or promote products derived from this software without
+specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
\ No newline at end of file

MANIFEST.in

+include README.rst buildout.cfg LICENSE version.txt requirements.txt
+recursive-include doc *.rst *.png *.ico *.txt
+recursive-include bob *.json *.csv
\ No newline at end of file

README.rst

+.. -*- coding: utf-8 -*-
+
+.. image:: https://img.shields.io/badge/docs-stable-yellow.svg
+   :target: http://beatubulatest.lab.idiap.ch/private/docs/bob/bob.db.chasedb1/stable/index.html
+.. image:: https://img.shields.io/badge/docs-latest-orange.svg
+   :target: http://beatubulatest.lab.idiap.ch/private/docs/bob/bob.db.chasedb1/master/index.html
+.. image:: https://gitlab.idiap.ch/bob/bob.db.chasedb1/badges/master/build.svg
+   :target: https://gitlab.idiap.ch/bob/bob.db.chasedb1/commits/master
+.. image:: https://gitlab.idiap.ch/bob/bob.db.chasedb1/badges/master/coverage.svg
+   :target: https://gitlab.idiap.ch/bob/bob.db.chasedb1/commits/master
+.. image:: https://img.shields.io/badge/gitlab-project-0000c0.svg
+   :target: https://gitlab.idiap.ch/bob/bob.db.chasedb1
+.. image:: https://img.shields.io/pypi/v/bob.db.chasedb1.svg
+   :target: https://pypi.python.org/pypi/bob.db.chasedb1
+
+
+====================================
+CHASE_DB1 Database Interface for Bob
+====================================
+
+This package is part of the signal-processing and machine learning toolbox
+Bob_. It provides an interface for the `CHASE_DB1 Dataset`_. This package does
+not contain the original data files, which need to be obtained through the link
+above.
+
+Installation
+------------
+
+Complete bob's `installation`_ instructions. Then, to install this
+package, run::
+
+  $ conda install bob.db.chasedb1
+
+
+Contact
+-------
+
+For questions or reporting issues to this software package, contact our
+development `mailing list`_.
+
+
+.. Place your references here:
+.. _bob: https://www.idiap.ch/software/bob
+.. _installation: https://www.idiap.ch/software/bob/install
+.. _mailing list: https://www.idiap.ch/software/bob/discuss
+.. _chase_db1 dataset: https://blogs.kingston.ac.uk/retinal/chasedb1/
\ No newline at end of file

bob/__init__.py

+# see https://docs.python.org/3/library/pkgutil.html
+from pkgutil import extend_path
+__path__ = extend_path(__path__, __name__)

bob/db/__init__.py

+# see https://docs.python.org/3/library/pkgutil.html
+from pkgutil import extend_path
+__path__ = extend_path(__path__, __name__)

bob/db/chasedb1/__init__.py

+#!/usr/bin/env python
+# vim: set fileencoding=utf-8 :
+
+"""
+CHASE_DB1: Retinal image database
+
+Fraz, M.M, Remagnino, P., Hoppe, A., Uyyanonvara, B., Rudnicka, A.R., Owen, C.G. and Barman S.A. (2012) An ensemble classification-based approach applied to retinal blood vessel segmentation. IEEE Transactions on Biomedical Engineering, 59(9), pp. 2538-2548.
+
+https://blogs.kingston.ac.uk/retinal/chasedb1/
+"""
+
+from .query import Database
+
+def get_config():
+  """Returns a string containing the configuration information.
+  """
+
+  import bob.extension
+  return bob.extension.get_config(__name__)
+
+# gets sphinx autodoc done right - don't remove it
+__all__ = [_ for _ in dir() if not _.startswith('_')]

bob/db/chasedb1/chasedb1_db_default.json

+{
+ "train": [
+  [
+   "Image_11L.jpg",
+   "Image_11L_1stHO.png"
+  ],
+  [
+   "Image_11R.jpg",
+   "Image_11R_1stHO.png"
+  ],
+  [
+   "Image_12L.jpg",
+   "Image_12L_1stHO.png"
+  ],
+  [
+   "Image_12R.jpg",
+   "Image_12R_1stHO.png"
+  ],
+  [
+   "Image_13L.jpg",
+   "Image_13L_1stHO.png"
+  ],
+  [
+   "Image_13R.jpg",
+   "Image_13R_1stHO.png"
+  ],
+  [
+   "Image_14L.jpg",
+   "Image_14L_1stHO.png"
+  ],
+  [
+   "Image_14R.jpg",
+   "Image_14R_1stHO.png"
+  ]
+ ],
+ "test": [
+  [
+   "Image_01L.jpg",
+   "Image_01L_1stHO.png"
+  ],
+  [
+   "Image_01R.jpg",
+   "Image_01R_1stHO.png"
+  ],
+  [
+   "Image_02L.jpg",
+   "Image_02L_1stHO.png"
+  ],
+  [
+   "Image_02R.jpg",
+   "Image_02R_1stHO.png"
+  ],
+  [
+   "Image_03L.jpg",
+   "Image_03L_1stHO.png"
+  ],
+  [
+   "Image_03R.jpg",
+   "Image_03R_1stHO.png"
+  ],
+  [
+   "Image_04L.jpg",
+   "Image_04L_1stHO.png"
+  ],
+  [
+   "Image_04R.jpg",
+   "Image_04R_1stHO.png"
+  ],
+  [
+   "Image_05L.jpg",
+   "Image_05L_1stHO.png"
+  ],
+  [
+   "Image_05R.jpg",
+   "Image_05R_1stHO.png"
+  ],
+  [
+   "Image_06L.jpg",
+   "Image_06L_1stHO.png"
+  ],
+  [
+   "Image_06R.jpg",
+   "Image_06R_1stHO.png"
+  ],
+  [
+   "Image_07L.jpg",
+   "Image_07L_1stHO.png"
+  ],
+  [
+   "Image_07R.jpg",
+   "Image_07R_1stHO.png"
+  ],
+  [
+   "Image_08L.jpg",
+   "Image_08L_1stHO.png"
+  ],
+  [
+   "Image_08R.jpg",
+   "Image_08R_1stHO.png"
+  ],
+  [
+   "Image_09L.jpg",
+   "Image_09L_1stHO.png"
+  ],
+  [
+   "Image_09R.jpg",
+   "Image_09R_1stHO.png"
+  ],
+  [
+   "Image_10L.jpg",
+   "Image_10L_1stHO.png"
+  ],
+  [
+   "Image_10R.jpg",
+   "Image_10R_1stHO.png"
+  ]
+ ]
+}
\ No newline at end of file

bob/db/chasedb1/chasedb1_test.csv

+Image_01L.jpg,Image_01L_1stHO.png
+Image_01R.jpg,Image_01R_1stHO.png
+Image_02L.jpg,Image_02L_1stHO.png
+Image_02R.jpg,Image_02R_1stHO.png
+Image_03L.jpg,Image_03L_1stHO.png
+Image_03R.jpg,Image_03R_1stHO.png
+Image_04L.jpg,Image_04L_1stHO.png
+Image_04R.jpg,Image_04R_1stHO.png
+Image_05L.jpg,Image_05L_1stHO.png
+Image_05R.jpg,Image_05R_1stHO.png
+Image_06L.jpg,Image_06L_1stHO.png
+Image_06R.jpg,Image_06R_1stHO.png
+Image_07L.jpg,Image_07L_1stHO.png
+Image_07R.jpg,Image_07R_1stHO.png
+Image_08L.jpg,Image_08L_1stHO.png
+Image_08R.jpg,Image_08R_1stHO.png
+Image_09L.jpg,Image_09L_1stHO.png
+Image_09R.jpg,Image_09R_1stHO.png
+Image_10L.jpg,Image_10L_1stHO.png
+Image_10R.jpg,Image_10R_1stHO.png
\ No newline at end of file

bob/db/chasedb1/chasedb1_train.csv

+Image_11L.jpg,Image_11L_1stHO.png
+Image_11R.jpg,Image_11R_1stHO.png
+Image_12L.jpg,Image_12L_1stHO.png
+Image_12R.jpg,Image_12R_1stHO.png
+Image_13L.jpg,Image_13L_1stHO.png
+Image_13R.jpg,Image_13R_1stHO.png
+Image_14L.jpg,Image_14L_1stHO.png
+Image_14R.jpg,Image_14R_1stHO.png
\ No newline at end of file

bob/db/chasedb1/checkfiles.py

+from pathlib import Path
+import logging
+import bob.extension
+from .query import Database
+
+
+def checkfiles(args):
+    """ 
+    Check if the local database tree is consistent with the expected structure
+    """
+    
+    db = Database(args.protocol)
+    # go through all files, check if they are available on the filesystem
+    good = []
+    bad = []
+    datadir = Path(args.datadir)
+    paths = db.paths
+    for obj in paths:
+        obj = datadir.joinpath(obj)
+        if obj.exists():
+            good.append(obj)
+            logging.info(f'Found file {obj}')
+        else:
+            bad.append(obj)
+            logging.warning(f'Cannot find file {obj}')
+    # report
+    if bad:
+        logging.warning(f'{len(bad)} files (out of {len(paths)}) were not found at "{str(datadir)}" ')
+    else:
+        print('checkfiles completed sucessfully')
+
+    # return 0 for self-test
+    return 0
+
+
+def add_command(subparsers):
+    """Add specific subcommands that the action 'checkfiles' can use"""
+    from argparse import SUPPRESS
+    parser = subparsers.add_parser('checkfiles', help='Check if the local database tree is consistent with the expected structure')
+    parser.add_argument('-D', '--datadir', metavar='DIR', default=bob.extension.rc['bob.db.chasedb1.datadir'], help='path to CHASE_DB1 dataset, default uses bob config settings (to check use: bob config show).')
+    parser.add_argument('-P', '--protocol', metavar='STR', default='default',help='The train/test set protocol to use')
+    parser.add_argument('--self-test', dest="selftest", default=False, action='store_true', help=SUPPRESS)
+    parser.set_defaults(func=checkfiles) # action
\ No newline at end of file

bob/db/chasedb1/create.py

+from pathlib import Path
+import csv
+import json
+import pkg_resources
+import bob.extension
+
+
+def get_file_names(datadir):
+    """
+    Get absolute path of files in a data directory (recursively).
+    
+    Parameters
+    ----------
+    
+    data_dir : a Path object
+    
+    Returns:
+    -------
+    file_path: list
+        a sorted list of paths to all files in the given data directory. Ignores hidden files (suchs as .DS_Store)
+        
+    """
+
+    file_paths = sorted(list(datadir.glob('**/*?.*')))
+    rel_file_paths = [f.relative_to(datadir) for f in file_paths]
+    return rel_file_paths
+
+
+def read_split(file):
+    """
+    Reads a csv file with two columns: image_file_name, ground_truth_file_name.
+    
+    Returns
+    -------
+    file_list : list
+        list containing two tuples. The first one contains image file names, the second the ground truth file names
+    """
+
+    file = open(file,"r")
+    rows = csv.reader(file)
+    file_list = list(zip(*rows))
+    file.close()
+    return file_list
+
+
+def create(args):
+    """ 
+    Writes a 'database' json file to disk
+
+    Parameters
+    ----------
+    args.train   : csv containg train img, gt pairs
+    args.test    : csv containg test img,gt pairs
+    args.datadir : path to the dataset on disk
+    args.output  : name of the output file
+
+    Returns
+    -------
+    int : 0 
+
+    """
+    # read file name pairs as defined in the csv
+    basedir = Path(pkg_resources.resource_filename(__name__, ''))
+    train_split = read_split(basedir.joinpath(args.train))
+    test_split = read_split(basedir.joinpath(args.test))
+    
+    # get actual file paths and create dictionary (filname, path)
+    files = get_file_names(Path(args.datadir))
+    filedict = dict([(f.name, f) for f in files])
+
+    # map split to files
+    train_images = [str(filedict[img]) for img in train_split[0]]
+    train_ground_truths = [str(filedict[gt]) for gt in train_split[1]]
+    test_images = [str(filedict[img]) for img in test_split[0]]
+    test_ground_truths = [str(filedict[gt]) for gt in test_split[1]]
+    
+    # sense check 
+    assert len(train_images) == len(train_ground_truths)
+    assert len(test_images) == len(test_ground_truths)
+    
+    # zip together and create dict
+    train = list(zip(train_images,train_ground_truths))
+    test = list(zip(test_images,test_ground_truths))   
+    db = {'train':train,'test':test}
+    
+    # json
+    with open(basedir.joinpath(args.output),'w') as outfile:
+        json.dump(db, outfile, indent = 1)
+
+    # return 0 for self-test
+    return 0
+
+
+def add_command(subparsers):
+    """Add specific subcommands that the action "create" can use"""
+    from argparse import SUPPRESS
+
+    parser = subparsers.add_parser('create', help='Creates json file with train and test splits')
+    parser.add_argument('-D', '--datadir', metavar='DIR', default=bob.extension.rc['bob.db.chasedb1.datadir'], help='path to CHASE_DB1 dataset, default uses bob config settings (to check use: bob config show).')
+    parser.add_argument('-T', '--train', metavar='STR', default='chasedb1_train.csv', help='csv containg train img,gt pairs')
+    parser.add_argument('-E', '--test', metavar='STR', default='chasedb1_test.csv', help='csv containg test img,gt pairs')
+    parser.add_argument('-O', '--output', metavar='STR', default='chasedb1_db_default.json', help='output file name')
+    parser.add_argument('--self-test', dest="selftest", default=False, action='store_true', help=SUPPRESS)
+    parser.set_defaults(func=create) #action

bob/db/chasedb1/driver.py

+#!/usr/bin/env python
+# vim: set fileencoding=utf-8 :
+
+"""Commands the database can respond to.
+"""
+import pkg_resources
+
+from bob.db.base.driver import Interface as BaseInterface
+
+
+class Interface(BaseInterface):
+    def name(self):
+        return 'chasedb1'
+
+    def version(self):
+        return pkg_resources.require('bob.db.%s' % self.name())[0].version
+
+    def files(self):
+        """
+        List of meta-data files for the package to be downloaded/uploaded
+        
+        This function should normally return an empty list, except in case the
+        database being implemented requires download/upload of metadata files that
+        are **not** kept in its (git) repository.
+        """
+        return []
+
+    def type(self):
+        return 'text'
+
+    def add_commands(self, parser):
+        from . import __doc__ as docs
+        subparsers = self.setup_parser(parser,"CHASE_DB1 database", docs)
+
+        # checkfiles command
+        from .checkfiles import add_command as checkfiles_command
+        checkfiles_command(subparsers)
+        
+        # create command
+        from .create import add_command as create_command
+        create_command(subparsers)
+        
\ No newline at end of file

bob/db/chasedb1/models.py

+from pathlib import Path
+from PIL import Image
+import bob.extension
+
+
+class FundusImage:
+    """
+    Generic fundus image object.
+    """
+
+    def __init__(self, path):
+        self.path = path
+
+
+    @property
+    def basename(self):
+        """
+        Returns the file name
+
+        Returns
+        -------
+        name : str
+        """
+        return Path(self.path).name
+
+
+    @property
+    def size(self):
+        """
+        Returns
+        -------
+        size : tuple
+                the fundus image resolution in (W, H).
+        """
+        return self.pil_image().size
+
+
+    def pil_image(self, datadir=bob.extension.rc['bob.db.chasedb1.datadir']):
+        """
+        Returns
+        -------
+        img : :py:class:`PIL.Image.Image`
+        """
+        img = Image.open(str(Path(datadir).joinpath(self.path)))
+        return img
+
+class GroundTruth:
+    """
+    Generic ground truth object.
+    
+    - Allows for thresholding in case there are multiple ground truth annotations in one bitmap
+    - Allows for "on-the-fly" drawing of ground truth annotations with a specified size
+
+
+    Parameters
+    ----------
+    path      : str
+                    relative path to the file on disk
+    threshold : float
+                    in range [0,1] used to threshold ground-truth image data with multiple classes e.g. optic disc and cup
+    drawsize  : tuple
+                    size tuple in pillow (W, H) format. Used for cases where drawing of gt is required
+    """
+
+    def __init__(self, path, threshold=None, drawsize=None):
+        self.path = path
+        self.threshold = threshold
+        self.drawsize = drawsize
+
+
+    @property
+    def basename(self):
+        """
+        Returns the file name
+
+        Returns
+        -------
+        name : str
+        """
+        return Path(self.path).name
+
+
+    @property
+    def size(self):
+        """
+        Retirms the ground truth image resolution in (W, H).
+
+        Returns
+        -------
+        size : tuple
+        """
+        return self.pil_image().size
+
+
+    def pil_image(self, datadir=bob.extension.rc['bob.db.chasedb1.datadir']):
+        """
+        Returns
+        -------
+        gt : :py:class:`PIL.Image.Image`
+                mode = '1'
+        """
+        gt = Image.open(str(Path(datadir).joinpath(self.path)))
+        gt = gt.convert(mode='1', dither=None)
+        return gt
+
+
+class Sample:
+    """
+    Generic Sample object
+
+    High level sample class that combines the objects 'FundusImage' and 'GroundTruth'
+    Allows for access of the subclass, e.g. :
+
+    .. testsetup:: *
+        
+        from bob.db.chasedb1.models import *
+
+    .. doctest::
+
+        >>> img = FundusImage('path/to/some_img.file')
+        >>> gt = GroundTruth('path/to/some_gt.file')
+        >>> mysample = Sample(img, gt)
+        >>> mysample.img.basename
+        'some_img.file'
+        >>> mysample.gt.basename
+        'some_gt.file'
+        >>> 
+
+    Parameters
+    ----------
+    img  : FundusImage
+    gt   : GroundTruth
+    """
+    
+    def __init__(self, img, gt):
+        self.img = img
+        self.gt = gt
+    
+    
+    @property
+    def paths(self):
+        """
+        Returns
+        --------
+        paths : list
+                 paths of image, ground truth
+        """
+        return self.img.path, self.gt.path

bob/db/chasedb1/query.py

+#!/usr/bin/env python
+# vim: set fileencoding=utf-8 :
+
+from PIL import Image
+import json
+from pathlib import Path
+import pkg_resources
+import itertools
+from .models import Sample, FundusImage, GroundTruth
+
+
+class FileList:
+    """
+    FileList object that loads the protocol as defined in a json file. 
+    Provides a ``__getitem__`` interface. 
+    """
+
+    def __init__(self, db_json):
+        with open(db_json,'r') as in_file:
+            self._filelist = json.load(in_file)
+    
+
+    def __getitem__(self, key):
+        # if no valid split is passed, return all paths of train and test 
+        return self._filelist.get(key, (self._filelist['train']+self._filelist['test']))
+    
+
+class Database:
+    """
+    A low level database interface to be used with PyTorch or other deep learning frameworks. 
+
+    Parameters
+    ----------
+    
+    protocol : str
+                protocol defining the train-test split.
+    """
+    
+    def __init__(self, protocol = 'default'):
+        self.protocol = protocol
+        root = Path(pkg_resources.resource_filename(__name__, ''))
+        db_json =  root.joinpath('chasedb1_db_'+self.protocol+'.json')
+        # initialize filelist
+        self._filelist = FileList(db_json)
+
+
+    @property    
+    def paths(self):
+        """
+        Returns
+        -------
+        paths : list
+                    list of all paths of all samples
+        """
+        return list(itertools.chain(*(self._filelist[None]) ))
+    
+
+    def _make_sample(self, img_path,gt_path):
+        """
+        Make a single sample object
+
+        Parameters
+        ----------
+        img_path : str
+                    relative path to image
+        gt_path  : str
+                    relative path to ground truth
+
+        Returns
+        -------
+        sample : Sample
+        """
+
+        img = FundusImage(img_path)
+        gt = GroundTruth(gt_path)
+        return Sample(img, gt)
+
+
+    def samples(self, split=None):
+        """
+        Given a split, returns a list of Sample objects.