diff --git a/bob/ip/binseg/script/binseg.py b/bob/ip/binseg/script/binseg.py
index 5b01d03960693f7c9cffe2f0207f3758c799605e..47686ad3783e7b5241b0b8f3a43bcc1af90f563c 100644
--- a/bob/ip/binseg/script/binseg.py
+++ b/bob/ip/binseg/script/binseg.py
@@ -95,7 +95,7 @@ def binseg():
help='Number of epochs used for training',
show_default=True,
required=True,
- default=6,
+ default=1000,
cls=ResourceOption)
@click.option(
'--checkpoint-period',
@@ -103,7 +103,7 @@ def binseg():
help='Number of epochs after which a checkpoint is saved',
show_default=True,
required=True,
- default=2,
+ default=100,
cls=ResourceOption)
@click.option(
'--device',
@@ -453,7 +453,7 @@ def visualize(dataset, output_path, **kwargs):
help='Number of epochs used for training',
show_default=True,
required=True,
- default=6,
+ default=1000,
cls=ResourceOption)
@click.option(
'--checkpoint-period',
@@ -461,7 +461,7 @@ def visualize(dataset, output_path, **kwargs):
help='Number of epochs after which a checkpoint is saved',
show_default=True,
required=True,
- default=2,
+ default=100,
cls=ResourceOption)
@click.option(
'--device',
diff --git a/doc/datasets.rst b/doc/datasets.rst
index 0704149b9ca841371fa59f7b3d5c9b48a0a4ea26..2543b80163bc863e7a5762b85c20f151e16240b4 100644
--- a/doc/datasets.rst
+++ b/doc/datasets.rst
@@ -30,4 +30,12 @@ Supported Datasets
+-----+---------------+-------------+--------+-------+------+------+--------+-----+-----+----------------------------+
+Add-on: Folder-based Dataset
+============================
+
+For quick experimentation we also provide a PyTorch class that works with a
+dataset folder structure:
+
+
+
.. include:: links.rst
\ No newline at end of file
diff --git a/doc/evaluation.rst b/doc/evaluation.rst
new file mode 100644
index 0000000000000000000000000000000000000000..4a7aed35f0c6b63a50c11586a45548290787527e
--- /dev/null
+++ b/doc/evaluation.rst
@@ -0,0 +1,83 @@
+.. -*- coding: utf-8 -*-
+.. _bob.ip.binseg.evaluation:
+
+==========
+Evaluation
+==========
+
+To evaluate trained models use use ``bob binseg test`` followed by
+the model config, the dataset config and the path to the pretrained
+model via the argument ``-w``.
+
+Alternatively point to the output folder used during training via
+the ``-o`` argument. The Checkpointer will load the model as indicated
+in the file: ``last_checkpoint``.
+
+Use ``bob binseg test --help`` for more information.
+
+E.g. run inference on model M2U-Net on the DRIVE test set:
+
+.. code-block:: bash
+
+ # Point directly to saved model via -w argument:
+ bob binseg test M2UNet DRIVETEST -o /outputfolder/for/results -w /direct/path/to/weight/model_final.pth
+
+ # Use training output path (requries last_checkpoint file to be present)
+ # The evaluation results will be stored in the same folder
+ bob binseg test M2UNet DRIVETEST -o /DRIVE/M2UNet/output
+
+
+Pretrained Models
+=================
+
+Due to storage limitations we only provide weights of a subset
+of all evaluated models, namely all DRIU and M2U-Net variants:
+
+
+https://dl.dropboxusercontent.com/s/wnyjzmhhep2smjl/retinanet_MobileNetV2-FPN_1x.pth
+
++--------------------+------------------------------------------------------------------------------------------------------+--------------------------------------------------------------------------------------------------------------------+
+| | DRIU | M2UNet |
++--------------------+------------------------------------------------------------------------------------------------------+--------------------------------------------------------------------------------------------------------------------+
+| DRIVE | `DRIU_DRIVE.pth <https://dl.dropboxusercontent.com/s/rggn9ebj38c06uf/DRIU_DRIVE.pth>`_ | `M2UNet_DRIVE.pth <https://dl.dropboxusercontent.com/s/55xply8jm0g2skp/M2UNet_DRIVE.pth>`_ |
++--------------------+------------------------------------------------------------------------------------------------------+--------------------------------------------------------------------------------------------------------------------+
+| COVD-DRIVE | | |
++--------------------+------------------------------------------------------------------------------------------------------+--------------------------------------------------------------------------------------------------------------------+
+| COVD-DRIVE SSL | | |
++--------------------+------------------------------------------------------------------------------------------------------+--------------------------------------------------------------------------------------------------------------------+
+| STARE | `DRIU_STARE.pth <https://dl.dropboxusercontent.com/s/sw5ivfzgz5djirc/DRIU_STARE.pth>`_ | `M2UNet_STARE.pth <https://dl.dropboxusercontent.com/s/pc9wb8r7tjvg06p/M2UNet_STARE.pth>`_ |
++--------------------+------------------------------------------------------------------------------------------------------+--------------------------------------------------------------------------------------------------------------------+
+| COVD-STARE | | `M2UNet_COVD-STARE.pth <https://dl.dropboxusercontent.com/s/vh1trws2nxqt65y/M2UNet_COVD-STARE.pth>`_ |
++--------------------+------------------------------------------------------------------------------------------------------+--------------------------------------------------------------------------------------------------------------------+
+| COVD-STARE SSL | | `M2UNet_COVD-STARE_SSL.pth <https://dl.dropboxusercontent.com/s/slcvfgf1saf7t19/M2UNet_COVD-STARE_SSL.pth>`_ |
++--------------------+------------------------------------------------------------------------------------------------------+--------------------------------------------------------------------------------------------------------------------+
+| CHASE_DB1 | `DRIU_CHASEDB1.pth <https://dl.dropboxusercontent.com/s/15gxvhdtq0gw074/DRIU_CHASEDB1.pth>`_ | `M2UNet_CHASEDB1.pth <https://dl.dropboxusercontent.com/s/jqq0z9boi17nhqf/M2UNet_CHASEDB1.pth>`_ |
++--------------------+------------------------------------------------------------------------------------------------------+--------------------------------------------------------------------------------------------------------------------+
+| COVD-CHASE_DB1 | | `M2UNet_COVD-CHASEDB1.pth <https://dl.dropboxusercontent.com/s/pvbp0qky13q5o11/M2UNet_COVD-CHASEDB1.pth>`_ |
++--------------------+------------------------------------------------------------------------------------------------------+--------------------------------------------------------------------------------------------------------------------+
+| COVD-CHASE_DB1 SSL | | `M2UNet_COVD-CHASEDB1_SSL.pth <https://dl.dropboxusercontent.com/s/qx7mm5h8ywm98fi/M2UNet_COVD-CHASEDB1_SSL.pth>`_ |
++--------------------+------------------------------------------------------------------------------------------------------+--------------------------------------------------------------------------------------------------------------------+
+| IOSTARVESSEL | `DRIU_IOSTARVESSEL.pth <https://dl.dropboxusercontent.com/s/dx1dp8g4nct5r2z/DRIU_IOSTARVESSEL.pth>`_ | `M2UNet_IOSTARVESSEL.pth <https://dl.dropboxusercontent.com/s/g9jyvar9x8vvihr/M2UNet_IOSTARVESSEL.pth>`_ |
++--------------------+------------------------------------------------------------------------------------------------------+--------------------------------------------------------------------------------------------------------------------+
+| COVD-IOSTAR | | `M2UNet_COVD-IOSTAR.pth <https://dl.dropboxusercontent.com/s/t5b2qomq6ey8i9t/M2UNet_COVD-IOSTAR.pth>`_ |
++--------------------+------------------------------------------------------------------------------------------------------+--------------------------------------------------------------------------------------------------------------------+
+| COVD-IOSTAR SSL | | `M2UNet_COVD-IOSTAR_SSL.pth <https://dl.dropboxusercontent.com/s/70ynm2k3bpkj4mq/M2UNet_COVD-IOSTAR_SSL.pth>`_ |
++--------------------+------------------------------------------------------------------------------------------------------+--------------------------------------------------------------------------------------------------------------------+
+| HRF | `DRIU_HRF1168.pth <https://dl.dropboxusercontent.com/s/c02m2zyby1zndqx/DRIU_HRF1168.pth>`_ | `M2UNet_HRF1168.pth <https://dl.dropboxusercontent.com/s/g34g6nai1rsgbsc/M2UNet_HRF1168.pth>`_ |
++--------------------+------------------------------------------------------------------------------------------------------+--------------------------------------------------------------------------------------------------------------------+
+| COVD-HRF | | `M2UNet_COVD-HRF.pth <https://dl.dropboxusercontent.com/s/o3edhljeidl6fvi/M2UNet_COVD-HRF.pth>`_ |
++--------------------+------------------------------------------------------------------------------------------------------+--------------------------------------------------------------------------------------------------------------------+
+| COVD-HRF SSL | | `M2UNet_COVD-HRF_SSL.pth <https://dl.dropboxusercontent.com/s/2e0aq8a5vbop2yx/M2UNet_COVD-HRF_SSL.pth>`_ |
++--------------------+------------------------------------------------------------------------------------------------------+--------------------------------------------------------------------------------------------------------------------+
+
+
+
+To run evaluation of pretrained models pass url as ``-w`` argument. E.g.:
+
+.. code-block:: bash
+
+ bob binseg test DRIU DRIVETEST -o Evaluation_DRIU_DRIVE -w https://dl.dropboxusercontent.com/s/rggn9ebj38c06uf/DRIU_DRIVE.pth
+ bob binseg test M2UNet DRIVETEST -o Evaluation_M2UNet_DRIVE -w https://dl.dropboxusercontent.com/s/55xply8jm0g2skp/M2UNet_DRIVE.pth
+
+
+
diff --git a/doc/index.rst b/doc/index.rst
index c19b48eaba56c1d134694231dded4a3c4fe34d04..45df43d42f497d68086af6f1167c5772f1482862 100644
--- a/doc/index.rst
+++ b/doc/index.rst
@@ -13,12 +13,15 @@ Users Guide
.. toctree::
:maxdepth: 2
-
+
+ setup
datasets
+ training
+ evaluation
benchmarkresults
api
references
.. todolist::
-.. include:: links.rst
\ No newline at end of file
+.. include:: links.rst
diff --git a/doc/links.rst b/doc/links.rst
index 2398e1c87eeebc3a0e8aba0d27ee8b3a1231acfd..7b94ab0645774c0e00d9c1f15065d4f093fb9be0 100644
--- a/doc/links.rst
+++ b/doc/links.rst
@@ -4,7 +4,7 @@
.. _idiap: http://www.idiap.ch
.. _bob: http://www.idiap.ch/software/bob
-.. _installation: https://www.idiap.ch/software/bob/install
+.. _installation: https://www.idiap.ch/software/bob/docs/bob/docs/stable/bob/bob/doc/install.html
.. _mailing list: https://www.idiap.ch/software/bob/discuss
.. _torchvision package: https://github.com/pytorch/vision
diff --git a/doc/setup.rst b/doc/setup.rst
new file mode 100644
index 0000000000000000000000000000000000000000..5b5de78fa7bdd1fd30192f9d14b2df4ab2bd92b9
--- /dev/null
+++ b/doc/setup.rst
@@ -0,0 +1,91 @@
+.. -*- coding: utf-8 -*-
+.. _bob.ip.binseg.setup:
+
+=========
+Setup
+=========
+
+Bob.ip.binseg
+=============
+
+Complete bob's `installation`_ instructions. Then, to install this
+package
+
+.. code-block:: bash
+
+ conda install bob.ip.binseg
+
+Dataset Links
+=============
+
++------------+----------------------------------------------------------------------+
+| Dataset | Website |
++------------+----------------------------------------------------------------------+
+| STARE | http://cecas.clemson.edu/~ahoover/stare/ |
++------------+----------------------------------------------------------------------+
+| DRIVE | https://www.isi.uu.nl/Research/Databases/DRIVE/ |
++------------+----------------------------------------------------------------------+
+| DRIONS | http://www.ia.uned.es/~ejcarmona/DRIONS-DB.html |
++------------+----------------------------------------------------------------------+
+| RIM-ONE | http://medimrg.webs.ull.es/research/downloads/ |
++------------+----------------------------------------------------------------------+
+| CHASE-DB1 | https://blogs.kingston.ac.uk/retinal/chasedb1/ |
++------------+----------------------------------------------------------------------+
+| HRF | https://www5.cs.fau.de/research/data/fundus-images/ |
++------------+----------------------------------------------------------------------+
+| Drishti-GS | http://cvit.iiit.ac.in/projects/mip/drishti-gs/mip-dataset2/Home.php |
++------------+----------------------------------------------------------------------+
+| IOSTAR | http://www.retinacheck.org/datasets |
++------------+----------------------------------------------------------------------+
+| REFUGE | https://refuge.grand-challenge.org/Details/ |
++------------+----------------------------------------------------------------------+
+
+Setting up dataset paths
+========================
+
+For each dataset that you are planning to use, set the datadir to
+the path where it is stored. E.g.:
+
+.. code-block:: bash
+
+ bob config set bob.db.drive.datadir "/path/to/drivedataset/"
+
+To check your current setup
+
+.. code-block:: bash
+
+ bob config show
+
+This should result in an output similar to the following:
+
+.. code-block:: bash
+
+ {
+ "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"
+ }
+
+
+
+Testing 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.:
+
+.. code-block:: sh
+
+ conda activate your-conda-env-with-bob.ip.binseg
+ bob_dbmanage.py drive checkfiles
+ > checkfiles completed sucessfully
+
+.. include:: links.rst
diff --git a/doc/training.rst b/doc/training.rst
new file mode 100644
index 0000000000000000000000000000000000000000..ce9fbc2136a493d807dcb92e4a710ab5fcd14f5b
--- /dev/null
+++ b/doc/training.rst
@@ -0,0 +1,322 @@
+.. -*- coding: utf-8 -*-
+.. _bob.ip.binseg.training:
+
+
+========
+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
+===================
+
+.. code-block:: bash
+
+ #!/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-:
+
+.. code-block:: bash
+
+ ### 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:
+
+.. code-block:: bash
+
+ ### 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.
+
+.. code-block:: bash
+
+ bob binseg train /path/to/model/config.py /path/to/dataset/config.py
+
+
+
diff --git a/setup.py b/setup.py
index 593a4d782a66fee45bd3f236d63340858aefacc9..44a23e1f588c69e2d631a9666f54957a21b8f175 100644
--- a/setup.py
+++ b/setup.py
@@ -55,21 +55,28 @@ setup(
'visualize = bob.ip.binseg.script.binseg:visualize',
],
- #bob hed train configurations
+ #bob train configurations
'bob.ip.binseg.config': [
'DRIU = bob.ip.binseg.configs.models.driu',
- 'DRIUSSL = bob.ip.binseg.configs.models.driussl'
+ 'DRIUSSL = bob.ip.binseg.configs.models.driussl',
'DRIUOD = bob.ip.binseg.configs.models.driuod',
'HED = bob.ip.binseg.configs.models.hed',
'M2UNet = bob.ip.binseg.configs.models.m2unet',
+ 'M2UNetSSL = bob.ip.binseg.configs.models.m2unetssl',
'UNet = bob.ip.binseg.configs.models.unet',
'ResUNet = bob.ip.binseg.configs.models.resunet',
- 'ShapeResUNet = bob.ip.binseg.configs.models.shaperesunet',
- 'ALLVESSEL544 = bob.ip.binseg.configs.datasets.allvessel544',
- 'ALLVESSEL544TEST = bob.ip.binseg.configs.datasets.allvessel544test',
'CHASEDB1 = bob.ip.binseg.configs.datasets.chasedb1',
'CHASEDB1TEST = bob.ip.binseg.configs.datasets.chasedb1test',
- 'CHASEDB1544TEST = bob.ip.binseg.configs.datasets.chasedb1544test',
+ 'COVD-DRIVE = bob.ip.binseg.configs.datasets.starechasedb1iostarhrf544',
+ 'COVD-DRIVE_SSL = bob.ip.binseg.configs.datasets.starechasedb1iostarhrf544ssldrive',
+ 'COVD-STARE = bob.ip.binseg.configs.datasets.drivechasedb1iostarhrf608',
+ 'COVD-STARE_SSL = bob.ip.binseg.configs.datasets.drivechasedb1iostarhrf608sslstare',
+ 'COVD-IOSTARVESSEL = bob.ip.binseg.configs.datasets.drivestarechasedb1hrf1024',
+ 'COVD-IOSTARVESSEL_SSL = bob.ip.binseg.configs.datasets.drivestarechasedb1hrf1024ssliostar',
+ 'COVD-HRF = bob.ip.binseg.configs.datasets.drivestarechasedb1iostar1168',
+ 'COVD-HRF_SSL = bob.ip.binseg.configs.datasets.drivestarechasedb1iostar1168sslhrf',
+ 'COVD-CHASEDB1 = bob.ip.binseg.configs.datasets.drivestareiostarhrf960',
+ 'COVD-CHASEDB1_SSL = bob.ip.binseg.configs.datasets.drivestareiostarhrf960sslchase',
'DRIONSDB = bob.ip.binseg.configs.datasets.drionsdb',
'DRIONSDBTEST = bob.ip.binseg.configs.datasets.drionsdbtest',
'DRISHTIGS1OD = bob.ip.binseg.configs.datasets.dristhigs1od',
@@ -78,14 +85,12 @@ setup(
'DRISHTIGS1CUPTEST = bob.ip.binseg.configs.datasets.dristhigs1cuptest',
'DRIVE = bob.ip.binseg.configs.datasets.drive',
'DRIVETEST = bob.ip.binseg.configs.datasets.drivetest',
- 'HRF = bob.ip.binseg.configs.datasets.hrf',
+ 'HRF = bob.ip.binseg.configs.datasets.hrf1168',
'HRFTEST = bob.ip.binseg.configs.datasets.hrftest',
- 'HRF544TEST = bob.ip.binseg.configs.datasets.hrf544test',
'IOSTAROD = bob.ip.binseg.configs.datasets.iostarod',
'IOSTARODTEST = bob.ip.binseg.configs.datasets.iostarodtest',
'IOSTARVESSEL = bob.ip.binseg.configs.datasets.iostarvessel',
'IOSTARVESSELTEST = bob.ip.binseg.configs.datasets.iostarvesseltest',
- 'IOSTARVESSEL544TEST = bob.ip.binseg.configs.datasets.iostarvessel544test',
'REFUGECUP = bob.ip.binseg.configs.datasets.refugecup',
'REFUGECUPTEST = bob.ip.binseg.configs.datasets.refugecuptest',
'REFUGEOD = bob.ip.binseg.configs.datasets.refugeod',
@@ -96,7 +101,6 @@ setup(
'RIMONER3ODTEST = bob.ip.binseg.configs.datasets.rimoner3odtest',
'STARE = bob.ip.binseg.configs.datasets.stare',
'STARETEST = bob.ip.binseg.configs.datasets.staretest',
- 'STARE544TEST = bob.ip.binseg.configs.datasets.stare544test',
]
},