training.rst

Training

To replicate our results use bob binseg train followed by the model config and the dataset config. Use bob binseg train --help for more information.

Note

We strongly advice training with a GPU (using -d cuda). Depending on the available GPU memory you might have to adjust your batch size (-b).

Default Dataset configs

1. Vessel:

• CHASEDB1
• CHASEDB1TEST
• COVD-DRIVE
• COVD-DRIVE_SSL
• COVD-STARE
• COVD-STARE_SSL
• COVD-IOSTARVESSEL
• COVD-IOSTARVESSEL_SSL
• COVD-HRF
• COVD-HRF_SSL
• COVD-CHASEDB1
• COVD-CHASEDB1_SSL
• DRIVE
• DRIVETEST
• HRF
• HRFTEST
• IOSTARVESSEL
• IOSTARVESSELTEST
• STARE
• STARETEST

2. Optic Disc and Cup

• DRIONSDB
• DRIONSDBTEST
• DRISHTIGS1OD
• DRISHTIGS1ODTEST
• DRISHTIGS1CUP
• DRISHTIGS1CUPTEST
• IOSTAROD
• IOSTARODTEST
• REFUGECUP
• REFUGECUPTEST
• REFUGEOD
• REFUGEODTEST
• RIMONER3CUP
• RIMONER3CUPTEST
• RIMONER3OD
• RIMONER3ODTEST

Default Model configs

• DRIU
• DRIUSSL
• DRIUOD
• HED
• M2UNet
• M2UNetSSL
• UNet

Baseline Benchmarks

#!/bin/bash
# set output directory
outputroot=`pwd`"/output"
mkdir -p $outputroot

#### Global config ####
m2u=M2UNet
hed=HED
driu=DRIU
unet=UNet
m2ussl=M2UNetSSL
driussl=DRIUSSL

#### CHASE_DB 1 ####
dataset=CHASEDB1
output=$outputroot"/"$dataset
mkdir -p $output
# batch sizes
b_m2u=6
b_hed=4
b_driu=4
b_unet=2
# Train
bob binseg train $m2u $dataset -b $b_m2u -d cuda -o $output"/"$m2u -vv
bob binseg train $hed $dataset -b $b_hed -d cuda -o $output"/"$hed -vv
bob binseg train $driu $dataset -b $b_driu -d cuda -o $output"/"$driu -vv
bob binseg train $unet $dataset -b $b_unet -d cuda -o $output"/"$unet -vv

#### DRIVE ####
dataset=DRIVE
output=$outputroot"/"$dataset
mkdir -p $output
# model configs
b_m2u=16
b_hed=8
b_driu=8
b_unet=4
# Train
bob binseg train $m2u $dataset -b $b_m2u -d cuda -o $output"/"$m2u -vv
bob binseg train $hed $dataset -b $b_hed -d cuda -o $output"/"$hed -vv
bob binseg train $driu $dataset -b $b_driu -d cuda -o $output"/"$driu -vv
bob binseg train $unet $dataset -b $b_unet -d cuda -o $output"/"$unet -vv

#### HRF ####
dataset=HRF
output=$outputroot"/"$dataset
mkdir -p $output
# model configs
b_m2u=1
b_hed=1
b_driu=1
b_unet=1
# Train
bob binseg train $m2u $dataset -b $b_m2u -d cuda -o $output"/"$m2u -vv
bob binseg train $hed $dataset -b $b_hed -d cuda -o $output"/"$hed -vv
bob binseg train $driu $dataset -b $b_driu -d cuda -o $output"/"$driu -vv
bob binseg train $unet $dataset -b $b_unet -d cuda -o $output"/"$unet -vv

#### IOSTAR VESSEL ####
dataset=IOSTARVESSEL
output=$outputroot"/"$dataset
mkdir -p $output
# model configs
b_m2u=6
b_hed=4
b_driu=4
b_unet=2
# Train
bob binseg train $m2u $dataset -b $b_m2u -d cuda -o $output"/"$m2u -vv
bob binseg train $hed $dataset -b $b_hed -d cuda -o $output"/"$hed -vv
bob binseg train $driu $dataset -b $b_driu -d cuda -o $output"/"$driu -vv
bob binseg train $unet $dataset -b $b_unet -d cuda -o $output"/"$unet -vv

#### STARE ####
dataset=STARE
output=$outputroot"/"$dataset
mkdir -p $output
# model configs
b_m2u=6
b_hed=4
b_driu=5
b_unet=2
# Train
bob binseg train $m2u $dataset -b $b_m2u -d cuda -o $output"/"$m2u -vv
bob binseg train $hed $dataset -b $b_hed -d cuda -o $output"/"$hed -vv
bob binseg train $driu $dataset -b $b_driu -d cuda -o $output"/"$driu -vv
bob binseg train $unet $dataset -b $b_unet -d cuda -o $output"/"$unet -vv

Combined Vessel Dataset (COVD) and Semi-Supervised Learning (SSL)

COVD-:

### COVD-DRIVE ####
dataset=COVD-DRIVE
output=$outputroot"/"$dataset
mkdir -p $output
# model configs
driu=DRIU
m2u=M2UNet
b_driu=4
b_m2u=8
# Train
bob binseg train $driu $dataset -b $b_driu -d cuda -o $output"/"$driu -vv
bob binseg train $m2u $dataset -b $b_m2u -d cuda -o $output"/"$m2u -vv

### COVD-STARE ####
dataset=COVD-STARE
output=$outputroot"/"$dataset
mkdir -p $output
# model configs
driu=DRIU
m2u=M2UNet
b_driu=4
b_m2u=4
# Train
bob binseg train $driu $dataset -b $b_driu -d cuda -o $output"/"$driu -vv
bob binseg train $m2u $dataset -b $b_m2u -d cuda -o $output"/"$m2u -vv

### COVD-IOSTAR ####
dataset=COVD-IOSTARVESSEL
output=$outputroot"/"$dataset
mkdir -p $output
# model configs
driu=DRIU
m2u=M2UNet
b_driu=4
b_m2u=4
# Train
bob binseg train $driu $dataset -b $b_driu -d cuda -o $output"/"$driu -vv
bob binseg train $m2u $dataset -b $b_m2u -d cuda -o $output"/"$m2u -vv

### COVD-CHASEDB1 ####
dataset=COVD-CHASEDB1
output=$outputroot"/"$dataset
mkdir -p $output
# model configs
driu=DRIU
m2u=M2UNet
b_driu=4
b_m2u=4
# Train
bob binseg train $driu $dataset -b $b_driu -d cuda -o $output"/"$driu -vv
bob binseg train $m2u $dataset -b $b_m2u -d cuda -o $output"/"$m2u -vv

### COVD-HRF ####
dataset=COVD-HRF
output=$outputroot"/"$dataset
mkdir -p $output
# model configs
driu=DRIU
m2u=M2UNet
b_driu=2
b_m2u=4
# Train
bob binseg train $driu $dataset -b $b_driu -d cuda -o $output"/"$driu -vv
bob binseg train $m2u $dataset -b $b_m2u -d cuda -o $output"/"$m2u -vv

COVD-SSL:

### COVD-DRIVE_SSL ####
dataset=COVD-DRIVE_SSL
output=$outputroot"/"$dataset
mkdir -p $output
# model configs
driu=DRIUSSL
m2u=M2UNetSSL
b_driu=4
b_m2u=4
# Train
bob binseg ssltrain $driu $dataset -b $b_driu -d cuda -o $output"/"$driu -vv
bob binseg ssltrain $m2u $dataset -b $b_m2u -d cuda -o $output"/"$m2u -vv

### COVD-STARE_SSL ####
dataset=COVD-STARE_SSL
output=$outputroot"/"$dataset
mkdir -p $output
# model configs
driu=DRIUSSL
m2u=M2UNetSSL
b_driu=4
b_m2u=4
# Train
bob binseg ssltrain $driu $dataset -b $b_driu -d cuda -o $output"/"$driu -vv
bob binseg ssltrain $m2u $dataset -b $b_m2u -d cuda -o $output"/"$m2u -vv

### COVD-IOSTAR_SSL ####
dataset=COVD-IOSTARVESSEL_SSL
output=$outputroot"/"$dataset
mkdir -p $output
# model configs
driu=DRIUSSL
m2u=M2UNetSSL
b_driu=1
b_m2u=2
# Train
bob binseg ssltrain $driu $dataset -b $b_driu -d cuda -o $output"/"$driu -vv
bob binseg ssltrain $m2u $dataset -b $b_m2u -d cuda -o $output"/"$m2u -vv

### COVD-CHASEDB1_SSL ####
dataset=COVD-CHASEDB1_SSL
output=$outputroot"/"$dataset
mkdir -p $output
# model configs
driu=DRIUSSL
m2u=M2UNetSSL
b_driu=1
b_m2u=2
# Train
bob binseg ssltrain $driu $dataset -b $b_driu -d cuda -o $output"/"$driu -vv
bob binseg ssltrain $m2u $dataset -b $b_m2u -d cuda -o $output"/"$m2u -vv


### COVD-HRF_SSL ####
dataset=COVD-HRF_SSL
output=$outputroot"/"$dataset
mkdir -p $output
# model configs
driu=DRIUSSL
m2u=M2UNetSSL
b_driu=1
b_m2u=2
# Train
bob binseg ssltrain $driu $dataset -b $b_driu -d cuda -o $output"/"$driu -vv
bob binseg ssltrain $m2u $dataset -b $b_m2u -d cuda -o $output"/"$m2u -vv

Using your own configs

Instead of the default configs you can pass the full path of your customized dataset and model config.

bob binseg train /path/to/model/config.py /path/to/dataset/config.py