. -- coding: utf-8 --

Application Program Interface (API)

Data Manipulation

bob.ip.common.data.dataset
bob.ip.common.data.loader	Data loading code
bob.ip.common.data.sample
bob.ip.common.data.utils	Common utilities
bob.ip.common.data.transforms	Image transformations for our pipelines

Datasets

Retinography

bob.ip.binseg.data.drive	DRIVE dataset for Vessel Segmentation
bob.ip.binseg.data.stare	STARE dataset for Vessel Segmentation
bob.ip.binseg.data.chasedb1	CHASE-DB1 dataset for Vessel Segmentation
bob.ip.binseg.data.hrf	HRF dataset for Vessel Segmentation
bob.ip.binseg.data.iostar	IOSTAR (training set) for Vessel and Optic-Disc Segmentation
bob.ip.binseg.data.refuge	REFUGE for Optic Disc and Cup Segmentation
bob.ip.binseg.data.drishtigs1	Drishti-GS1 for Optic Disc and Cup Segmentation
bob.ip.binseg.data.rimoner3	RIM-ONE r3 (training set) for Cup Segmentation
bob.ip.binseg.data.drionsdb	DRIONS-DB (training set) for Optic Disc Segmentation
bob.ip.binseg.data.drhagis	DRHAGIS dataset for Vessel Segmentation

Chest X-Ray

bob.ip.binseg.data.montgomery	Montgomery County dataset for Lung Segmentation
bob.ip.binseg.data.jsrt	Japanese Society of Radiological Technology dataset for Lung Segmentation
bob.ip.binseg.data.shenzhen	Shenzhen No.3 People’s Hospital dataset for Lung Segmentation
bob.ip.binseg.data.cxr8	ChestX-ray8: Hospital-scale Chest X-ray Database

Engines

bob.ip.binseg.engine
bob.ip.binseg.engine.trainer
bob.ip.binseg.engine.predictor
bob.ip.binseg.engine.evaluator	Defines functionality for the evaluation of predictions
bob.ip.binseg.engine.adabound	Implementation of the AdaBound optimizer <https://github.com/Luolc/AdaBound/blob/master/adabound/adabound.py>.

Neural Network Models

bob.ip.binseg.models
bob.ip.binseg.models.backbones
bob.ip.binseg.models.backbones.mobilenetv2
bob.ip.binseg.models.backbones.resnet
bob.ip.binseg.models.backbones.vgg
bob.ip.binseg.models.normalizer	A network model that prefixes a z-normalization step to any other module
bob.ip.binseg.models.driu
bob.ip.binseg.models.driu_bn
bob.ip.binseg.models.driu_od
bob.ip.binseg.models.driu_pix
bob.ip.binseg.models.hed
bob.ip.binseg.models.m2unet
bob.ip.binseg.models.resunet
bob.ip.binseg.models.unet
bob.ip.binseg.models.lwnet	Little W-Net
bob.ip.binseg.models.losses	Loss implementations
bob.ip.binseg.models.make_layers

Toolbox

bob.ip.common.utils
bob.ip.common.utils.checkpointer
bob.ip.common.utils.measure
bob.ip.common.utils.plot
bob.ip.common.utils.table
bob.ip.common.utils.summary

Preset Configurations

Preset configurations for baseline systems

This module contains preset configurations for baseline FCN architectures and datasets.

Models

bob.ip.binseg.configs.models.driu	DRIU Network for Vessel Segmentation
bob.ip.binseg.configs.models.driu_bn	DRIU Network for Vessel Segmentation with Batch Normalization
bob.ip.binseg.configs.models.driu_od	DRIU Network for Optic Disc Segmentation
bob.ip.binseg.configs.models.hed	HED Network for image segmentation
bob.ip.binseg.configs.models.m2unet	MobileNetV2 U-Net model for image segmentation
bob.ip.binseg.configs.models.resunet	Residual U-Net for image segmentation
bob.ip.binseg.configs.models.unet	U-Net for image segmentation
bob.ip.binseg.configs.models.lwnet	Little W-Net for image segmentation

Datasets

Standard configurations for dataset setup

bob.ip.binseg.configs.datasets.RANDOM_ROTATION = [RandomRotation(p=0.5,degrees=[-15.0, 15.0], interpolation=bilinear, expand=False, fill=0)]

Shared data augmentation based on random rotation only

bob.ip.binseg.configs.datasets.RANDOM_FLIP_JITTER = [RandomHorizontalFlip(p=0.5), RandomVerticalFlip(p=0.5), ColorJitter(p=0.5,brightness=[0.7, 1.3], contrast=[0.7, 1.3], saturation=[0.98, 1.02], hue=[-0.02, 0.02])]

Shared data augmentation transforms without random rotation

bob.ip.binseg.configs.datasets.make_subset(samples, transforms, prefixes=[], suffixes=[])

Creates a new data set, applying transforms

Note

This is a convenience function for our own dataset definitions inside this module, guaranteeting homogenity between dataset definitions provided in this package. It assumes certain strategies for data augmentation that may not be translatable to other applications.

Parameters

• samples (list) – List of delayed samples

• transforms (list) – A list of transforms that needs to be applied to all samples in the set

• prefixes (list) – A list of data augmentation operations that needs to be applied before the transforms above

• suffixes (list) – A list of data augmentation operations that needs to be applied after the transforms above

Returns

subset – A pre-formatted dataset that can be fed to one of our engines

Return type

bob.ip.common.data.utils.SampleListDataset

bob.ip.binseg.configs.datasets.augment_subset(s, rotation_before=False)

Creates a new subset set, with data augmentation

Typically, the transforms are chained to a default set of data augmentation operations (random rotation, horizontal and vertical flips, and color jitter), but a flag allows prefixing the rotation specially (useful for some COVD training sets).

Note

This is a convenience function for our own dataset definitions inside this module, guaranteeting homogenity between dataset definitions provided in this package. It assumes certain strategies for data augmentation that may not be translatable to other applications.

Parameters

• s (bob.ip.common.data.utils.SampleListDataset) – A dataset that will be augmented

• rotation_before (py:class:bool, Optional) – A optional flag allowing you to do a rotation augmentation transform before the sequence of transforms for this dataset, that will be augmented.

Returns

subset – A pre-formatted dataset that can be fed to one of our engines

Return type

bob.ip.common.data.utils.SampleListDataset

bob.ip.binseg.configs.datasets.make_dataset(subsets, transforms)

Creates a new configuration dataset from dictionary and transforms

This function takes as input a dictionary as those that can be returned by bob.ip.common.data.dataset.JSONDataset.subsets(), or bob.ip.common.data.dataset.CSVDataset.subsets(), mapping protocol names (such as train, dev and test) to bob.ip.common.data.sample.DelayedSample lists, and a set of transforms, and returns a dictionary applying bob.ip.common.data.utils.SampleListDataset to these lists, and our standard data augmentation if a train set exists.

For example, if subsets is composed of two sets named train and test, this function will yield a dictionary with the following entries:

• __train__: Wraps the train subset, includes data augmentation (note: datasets with names starting with _ (underscore) are excluded from prediction and evaluation by default, as they contain data augmentation transformations.)

• train: Wraps the train subset, without data augmentation

• train: Wraps the test subset, without data augmentation

Note

This is a convenience function for our own dataset definitions inside this module, guaranteeting homogenity between dataset definitions provided in this package. It assumes certain strategies for data augmentation that may not be translatable to other applications.

Parameters

• subsets (dict) – A dictionary that contains the delayed sample lists for a number of named lists. If one of the keys is train, our standard dataset augmentation transforms are appended to the definition of that subset. All other subsets remain un-augmented. If one of the keys is validation, then this dataset will be also copied to the __valid__ hidden dataset and will be used for validation during training. Otherwise, if no valid subset is available, we set __valid__ to be the same as the unaugmented train subset, if one is available.

• transforms (list) – A list of transforms that needs to be applied to all samples in the set

Returns

dataset – A pre-formatted dataset that can be fed to one of our engines. It maps string names to bob.ip.common.data.utils.SampleListDataset’s.

Return type

dict

bob.ip.binseg.configs.datasets.csv	Example CSV-based custom filelist dataset
bob.ip.binseg.configs.datasets.chasedb1.first_annotator	CHASE-DB1 dataset for Vessel Segmentation (first-annotator protocol)
bob.ip.binseg.configs.datasets.chasedb1.first_annotator_768	CHASE-DB1 dataset for Vessel Segmentation
bob.ip.binseg.configs.datasets.chasedb1.first_annotator_1024	CHASE-DB1 dataset for Vessel Segmentation
bob.ip.binseg.configs.datasets.chasedb1.second_annotator	CHASE-DB1 dataset for Vessel Segmentation (second-annotator protocol)
bob.ip.binseg.configs.datasets.chasedb1.xtest	CHASE-DB1 cross-evaluation dataset
bob.ip.binseg.configs.datasets.chasedb1.mtest	CHASE-DB1 cross-evaluation dataset with matched resolution
bob.ip.binseg.configs.datasets.chasedb1.covd	COVD-CHASEDB1 for Vessel Segmentation
bob.ip.binseg.configs.datasets.drive.default	DRIVE dataset for Vessel Segmentation (default protocol)
bob.ip.binseg.configs.datasets.drive.default_768	DRIVE dataset for Vessel Segmentation (Resolution used for MTL models)
bob.ip.binseg.configs.datasets.drive.default_1024	DRIVE dataset for Vessel Segmentation (Resolution used for MTL models)
bob.ip.binseg.configs.datasets.drive.second_annotator	DRIVE dataset for Vessel Segmentation (second annotation: test only)
bob.ip.binseg.configs.datasets.drive.xtest	DRIVE cross-evaluation dataset
bob.ip.binseg.configs.datasets.drive.mtest	DRIVE cross-evaluation dataset with matched resolution
bob.ip.binseg.configs.datasets.drive.covd	COVD-DRIVE for Vessel Segmentation
bob.ip.binseg.configs.datasets.hrf.default	HRF dataset for Vessel Segmentation (default protocol)
bob.ip.binseg.configs.datasets.hrf.default_768	HRF dataset for Vessel Segmentation
bob.ip.binseg.configs.datasets.hrf.default_1024	HRF dataset for Vessel Segmentation
bob.ip.binseg.configs.datasets.hrf.xtest	HRF cross-evaluation dataset
bob.ip.binseg.configs.datasets.hrf.mtest	HRF cross-evaluation dataset with matched resolution
bob.ip.binseg.configs.datasets.hrf.default_fullres	HRF dataset for Vessel Segmentation (default protocol)
bob.ip.binseg.configs.datasets.hrf.covd	COVD-HRF for Vessel Segmentation
bob.ip.binseg.configs.datasets.iostar.vessel	IOSTAR dataset for Vessel Segmentation (default protocol)
bob.ip.binseg.configs.datasets.iostar.vessel_768	IOSTAR dataset for Vessel Segmentation (default protocol)
bob.ip.binseg.configs.datasets.iostar.vessel_xtest	IOSTAR vessel cross-evaluation dataset
bob.ip.binseg.configs.datasets.iostar.vessel_mtest	IOSTAR vessel cross-evaluation dataset with matched resolution
bob.ip.binseg.configs.datasets.iostar.optic_disc	IOSTAR dataset for Optic Disc Segmentation (default protocol)
bob.ip.binseg.configs.datasets.iostar.optic_disc_768	IOSTAR dataset for Optic Disc Segmentation
bob.ip.binseg.configs.datasets.iostar.optic_disc_512	IOSTAR dataset for Optic Disc Segmentation
bob.ip.binseg.configs.datasets.iostar.covd	COVD-IOSTAR for Vessel Segmentation
bob.ip.binseg.configs.datasets.stare.ah	STARE dataset for Vessel Segmentation (annotator AH)
bob.ip.binseg.configs.datasets.stare.ah_768	STARE dataset for Vessel Segmentation (annotator AH)
bob.ip.binseg.configs.datasets.stare.ah_1024	STARE dataset for Vessel Segmentation (annotator AH)
bob.ip.binseg.configs.datasets.stare.vk	STARE dataset for Vessel Segmentation (annotator VK)
bob.ip.binseg.configs.datasets.stare.xtest	STARE cross-evaluation dataset
bob.ip.binseg.configs.datasets.stare.mtest	STARE cross-evaluation dataset with matched resolution
bob.ip.binseg.configs.datasets.stare.covd	COVD-STARE for Vessel Segmentation
bob.ip.binseg.configs.datasets.refuge.cup	REFUGE dataset for Optic Cup Segmentation (default protocol)
bob.ip.binseg.configs.datasets.refuge.disc	REFUGE dataset for Optic Disc Segmentation (default protocol)
bob.ip.binseg.configs.datasets.refuge.cup_512	REFUGE dataset for Optic Cup Segmentation
bob.ip.binseg.configs.datasets.refuge.cup_768	REFUGE dataset for Optic Cup Segmentation
bob.ip.binseg.configs.datasets.refuge.disc_512	DRISHTI-GS1 dataset for Optic Disc Segmentation (agreed by all annotators)
bob.ip.binseg.configs.datasets.refuge.disc_768	DRISHTI-GS1 dataset for Optic Disc Segmentation (agreed by all annotators)
bob.ip.binseg.configs.datasets.rimoner3.cup_exp1	RIM-ONE r3 for Optic Cup Segmentation (expert #1 annotations)
bob.ip.binseg.configs.datasets.rimoner3.cup_exp2	RIM-ONE r3 for Optic Cup Segmentation (expert #2 annotations)
bob.ip.binseg.configs.datasets.rimoner3.disc_exp1	RIM-ONE r3 for Optic Disc Segmentation (expert #1 annotations)
bob.ip.binseg.configs.datasets.rimoner3.disc_exp2	RIM-ONE r3 for Optic Disc Segmentation (expert #2 annotations)
bob.ip.binseg.configs.datasets.rimoner3.cup_exp1_512	RIM-ONE r3 for Optic Cup Segmentation (expert #1 annotations)
bob.ip.binseg.configs.datasets.rimoner3.disc_exp1_512	RIM-ONE r3 for Optic Disc Segmentation (expert #1 annotations)
bob.ip.binseg.configs.datasets.rimoner3.cup_exp1_768	RIM-ONE r3 for Optic Cup Segmentation (expert #1 annotations)
bob.ip.binseg.configs.datasets.rimoner3.disc_exp1_768	RIM-ONE r3 for Optic Disc Segmentation (expert #1 annotations)
bob.ip.binseg.configs.datasets.drishtigs1.cup_all	DRISHTI-GS1 dataset for Cup Segmentation (agreed by all annotators)
bob.ip.binseg.configs.datasets.drishtigs1.cup_all_512	DRISHTI-GS1 dataset for Cup Segmentation (agreed by all annotators)
bob.ip.binseg.configs.datasets.drishtigs1.cup_all_768	DRISHTI-GS1 dataset for Cup Segmentation (agreed by all annotators)
bob.ip.binseg.configs.datasets.drishtigs1.cup_any	DRISHTI-GS1 dataset for Cup Segmentation (agreed by any annotator)
bob.ip.binseg.configs.datasets.drishtigs1.disc_all	DRISHTI-GS1 dataset for Optic Disc Segmentation (agreed by all annotators)
bob.ip.binseg.configs.datasets.drishtigs1.disc_all_512	DRISHTI-GS1 dataset for Optic Disc Segmentation (agreed by all annotators)
bob.ip.binseg.configs.datasets.drishtigs1.disc_all_768	DRISHTI-GS1 dataset for Optic Disc Segmentation (agreed by all annotators)
bob.ip.binseg.configs.datasets.drishtigs1.disc_any	DRISHTI-GS1 dataset for Optic Disc Segmentation (agreed by any annotator)
bob.ip.binseg.configs.datasets.drionsdb.expert1	DRIONS-DB for Optic Disc Segmentation (expert #1 annotations)
bob.ip.binseg.configs.datasets.drionsdb.expert2	DRIONS-DB for Optic Disc Segmentation (expert #2 annotations)
bob.ip.binseg.configs.datasets.drionsdb.expert1_512	DRIONS-DB for Optic Disc Segmentation (expert #1 annotations)
bob.ip.binseg.configs.datasets.drionsdb.expert2_512	DRIONS-DB for Optic Disc Segmentation (expert #2 annotations)
bob.ip.binseg.configs.datasets.drionsdb.expert1_768	DRIONS-DB for Optic Disc Segmentation (expert #1 annotations)
bob.ip.binseg.configs.datasets.drionsdb.expert2_768	DRIONS-DB for Optic Disc Segmentation (expert #2 annotations)
bob.ip.binseg.configs.datasets.drhagis.default	DRHAGIS dataset for Vessel Segmentation (default protocol)
bob.ip.binseg.configs.datasets.montgomery.default	Montgomery County dataset for Lung Segmentation (default protocol)
bob.ip.binseg.configs.datasets.montgomery.xtest	Montgomery County cross-evaluation dataset
bob.ip.binseg.configs.datasets.jsrt.default	Japanese Society of Radiological Technology dataset for Lung Segmentation (default protocol)
bob.ip.binseg.configs.datasets.jsrt.xtest	JSRT CXR cross-evaluation dataset
bob.ip.binseg.configs.datasets.shenzhen.default	Shenzhen dataset for Lung Segmentation (default protocol)
bob.ip.binseg.configs.datasets.shenzhen.default_256	Shenzhen dataset for Lung Segmentation (default protocol)
bob.ip.binseg.configs.datasets.shenzhen.xtest	Shenzhen cross-evaluation dataset
bob.ip.binseg.configs.datasets.cxr8.default	CXR8 Dataset (default protocol)
bob.ip.binseg.configs.datasets.cxr8.idiap	CXR8 Dataset ("idiap" protocol - just like "default", but works at Idiap)
bob.ip.binseg.configs.datasets.cxr8.xtest	CXR8 cross-evaluation dataset
bob.ip.binseg.configs.datasets.cxr8.xtest_idiap	CXR8 cross-evaluation dataset with Idiap directory structure organisation