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Commit f483a235 authored by Tim Laibacher's avatar Tim Laibacher
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Update docs

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......@@ -10,11 +10,11 @@ run binary-segmentation benchmarks.
PyTorch Dataset
---------------
===============
.. automodule:: bob.ip.binseg.data.binsegdataset
Transforms
----------
==========
.. note::
All transforms work with :py:class:`PIL.Image.Image` objects. We make heavy use of the
`torchvision package`_
......@@ -22,23 +22,23 @@ Transforms
.. automodule:: bob.ip.binseg.data.transforms
Losses
------
======
.. automodule:: bob.ip.binseg.modeling.losses
Training
--------
========
.. automodule:: bob.ip.binseg.engine.trainer
Checkpointer
------------
============
.. automodule:: bob.ip.binseg.utils.checkpointer
Inference and Evaluation
------------------------
========================
.. automodule:: bob.ip.binseg.engine.inferencer
Plotting
--------
========
.. automodule:: bob.ip.binseg.utils.plot
.. include:: links.rst
......@@ -11,19 +11,19 @@ F1 Scores
* Benchmark results for models: DRIU, HED, M2UNet and U-Net.
* Models are trained and tested on the same dataset using the train-test split as indicated in :ref:`bob.ip.binseg.datasets`
* standard-deviations across all test images are indicated in brakets
* Standard-deviations across all test images are indicated in brakets
+----------+-----------------+-----------------+-----------------+-----------------+-----------------+
| F1 (std) | CHASEDB1 | DRIVE | HRF1168 | IOSTAR | STARE |
+----------+-----------------+-----------------+-----------------+-----------------+-----------------+
| DRIU | 0.8114 (0.0206) | 0.8226 (0.0142) | 0.7865 (0.0545) | 0.8273 (0.0199) | 0.8286 (0.0368) |
+----------+-----------------+-----------------+-----------------+-----------------+-----------------+
| HED | 0.8111 (0.0214) | 0.8192 (0.0136) | 0.7868 (0.0576) | 0.8275 (0.0201) | 0.8250 (0.0375) |
+----------+-----------------+-----------------+-----------------+-----------------+-----------------+
| M2UNet | 0.8035 (0.0195) | 0.8051 (0.0141) | 0.7838 (0.0572) | 0.8194 (0.0201) | 0.8174 (0.0409) |
+----------+-----------------+-----------------+-----------------+-----------------+-----------------+
| UNet | 0.8136 (0.0209) | 0.8237 (0.0145) | 0.7914 (0.0516) | 0.8203 (0.0190) | 0.8306 (0.0421) |
+----------+-----------------+-----------------+-----------------+-----------------+-----------------+
+--------------------------------------------+------------------------------------------------+---------------------------------------------+-------------------------------------------+----------------------------------------------+---------------------------------------------+
| F1 (std) | :ref:`bob.ip.binseg.configs.datasets.chasedb1` | :ref:`bob.ip.binseg.configs.datasets.drive` | :ref:`bob.ip.binseg.configs.datasets.hrf` | :ref:`bob.ip.binseg.configs.datasets.iostar` | :ref:`bob.ip.binseg.configs.datasets.stare` |
+--------------------------------------------+------------------------------------------------+---------------------------------------------+-------------------------------------------+----------------------------------------------+---------------------------------------------+
| :ref:`bob.ip.binseg.configs.models.driu` | `0.8114 (0.0206) <driu_chasedb1.pth_>`_ | `0.8226 (0.0142) <driu_drive.pth_>`_ | `0.7865 (0.0545) <driu_hrf.pth_>`_ | `0.8273 (0.0199) <driu_iostar.pth_>`_ | `0.8286 (0.0368) <driu_stare.pth_>`_ |
+--------------------------------------------+------------------------------------------------+---------------------------------------------+-------------------------------------------+----------------------------------------------+---------------------------------------------+
| :ref:`bob.ip.binseg.configs.models.hed` | 0.8111 (0.0214) | 0.8192 (0.0136) | 0.7868 (0.0576) | 0.8275 (0.0201) | 0.8250 (0.0375) |
+--------------------------------------------+------------------------------------------------+---------------------------------------------+-------------------------------------------+----------------------------------------------+---------------------------------------------+
| :ref:`bob.ip.binseg.configs.models.m2unet` | `0.8035 (0.0195) <m2unet_chasedb1.pth_>`_ | `0.8051 (0.0141) <m2unet_drive.pth_>`_ | `0.7838 (0.0572) <m2unet_hrf.pth_>`_ | `0.8194 (0.0201) <m2unet_iostar.pth_>`_ | `0.8174 (0.0409) <m2unet_stare.pth_>`_ |
+--------------------------------------------+------------------------------------------------+---------------------------------------------+-------------------------------------------+----------------------------------------------+---------------------------------------------+
| :ref:`bob.ip.binseg.configs.models.unet` | 0.8136 (0.0209) | 0.8237 (0.0145) | 0.7914 (0.0516) | 0.8203 (0.0190) | 0.8306 (0.0421) |
+--------------------------------------------+------------------------------------------------+---------------------------------------------+-------------------------------------------+----------------------------------------------+---------------------------------------------+
.. figure:: img/pr_CHASEDB1.png
......@@ -65,3 +65,6 @@ F1 Scores
STARE: Precision vs Recall curve, F1 scores and
number of parameter of each model.
.. include:: links.rst
.. -*- coding: utf-8 -*-
.. _bob.ip.binseg.configs:
===============
Configs
===============
Dataset Configs
===============
.. _bob.ip.binseg.configs.datasets.chasedb1:
CHASEDB1
----------------
.. literalinclude:: ../bob/ip/binseg/configs/datasets/chasedb1.py
CHASEDB1TEST
----------------
.. literalinclude:: ../bob/ip/binseg/configs/datasets/chasedb1test.py
.. _bob.ip.binseg.configs.datasets.covd-drive:
COVD-DRIVE
----------------
.. literalinclude:: ../bob/ip/binseg/configs/datasets/starechasedb1iostarhrf544.py
.. _bob.ip.binseg.configs.datasets.covd-drive_ssl:
COVD-DRIVE_SSL
----------------
.. literalinclude:: ../bob/ip/binseg/configs/datasets/starechasedb1iostarhrf544ssldrive.py
.. _bob.ip.binseg.configs.datasets.covd-stare:
COVD-STARE
----------------
.. literalinclude:: ../bob/ip/binseg/configs/datasets/drivechasedb1iostarhrf608.py
.. _bob.ip.binseg.configs.datasets.covd-stare_ssl:
COVD-STARE_SSL
----------------
.. literalinclude:: ../bob/ip/binseg/configs/datasets/drivechasedb1iostarhrf608sslstare.py
.. _bob.ip.binseg.configs.datasets.covd-iostar:
COVD-IOSTARVESSEL
----------------------
.. literalinclude:: ../bob/ip/binseg/configs/datasets/drivestarechasedb1hrf1024.py
.. _bob.ip.binseg.configs.datasets.covd-iostar_ssl:
COVD-IOSTARVESSEL_SSL
----------------------
.. literalinclude:: ../bob/ip/binseg/configs/datasets/drivestarechasedb1hrf1024ssliostar.py
.. _bob.ip.binseg.configs.datasets.covd-hrf:
COVD-HRF
----------------------
.. literalinclude:: ../bob/ip/binseg/configs/datasets/drivestarechasedb1iostar1168.py
.. _bob.ip.binseg.configs.datasets.covd-hrf_ssl:
COVD-HRF_SSL
----------------------
.. literalinclude:: ../bob/ip/binseg/configs/datasets/drivestarechasedb1iostar1168sslhrf.py
.. _bob.ip.binseg.configs.datasets.covdchasedb1:
COVD-CHASEDB1
----------------------
.. literalinclude:: ../bob/ip/binseg/configs/datasets/drivestareiostarhrf960.py
.. _bob.ip.binseg.configs.datasets.covdchasedb1_ssl:
COVD-CHASEDB1_SSL
----------------------
.. literalinclude:: ../bob/ip/binseg/configs/datasets/drivestareiostarhrf960.py
.. _bob.ip.binseg.configs.datasets.drive:
DRIVE
----------------------
.. literalinclude:: ../bob/ip/binseg/configs/datasets/drive.py
DRIVETEST
----------------------
.. literalinclude:: ../bob/ip/binseg/configs/datasets/drivetest.py
.. _bob.ip.binseg.configs.datasets.hrf:
HRF
----------------------
.. literalinclude:: ../bob/ip/binseg/configs/datasets/hrf1168.py
HRFTEST
----------------------
.. literalinclude:: ../bob/ip/binseg/configs/datasets/hrftest.py
.. _bob.ip.binseg.configs.datasets.iostar:
IOSTARVESSEL
----------------------
.. literalinclude:: ../bob/ip/binseg/configs/datasets/iostarvessel.py
IOSTARVESSELTEST
----------------------
.. literalinclude:: ../bob/ip/binseg/configs/datasets/iostarvesseltest.py
.. _bob.ip.binseg.configs.datasets.stare:
STARE
----------------------
.. literalinclude:: ../bob/ip/binseg/configs/datasets/stare.py
STARETEST
----------------------
.. literalinclude:: ../bob/ip/binseg/configs/datasets/staretest.py
Model Configs
==============
.. _bob.ip.binseg.configs.models.driu:
DRIU
-----
.. literalinclude:: ../bob/ip/binseg/configs/models/driu.py
.. _bob.ip.binseg.configs.models.driubn:
DRIUBN
------
.. literalinclude:: ../bob/ip/binseg/configs/models/driubn.py
.. _bob.ip.binseg.configs.models.hed:
HED
-----
.. literalinclude:: ../bob/ip/binseg/configs/models/hed.py
.. _bob.ip.binseg.configs.models.m2unet:
M2UNet
------
.. literalinclude:: ../bob/ip/binseg/configs/models/m2unet.py
.. _bob.ip.binseg.configs.models.unet:
UNet
-----
.. literalinclude:: ../bob/ip/binseg/configs/models/unet.py
.. _bob.ip.binseg.configs.models.driussl:
DRIUSSL
--------
.. literalinclude:: ../bob/ip/binseg/configs/models/driussl.py
.. _bob.ip.binseg.configs.models.m2unetssl:
M2UNetSSL
---------
.. literalinclude:: ../bob/ip/binseg/configs/models/m2unetssl.py
......@@ -38,4 +38,4 @@ dataset folder structure:
.. include:: links.rst
\ No newline at end of file
.. include:: links.rst
......@@ -35,39 +35,39 @@ of all evaluated models, namely all DRIU and M2U-Net variants:
+--------------------+------------------------------------------------------------------------------------------------------+--------------------------------------------------------------------------------------------------------------------+
| | 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 | | `M2UNet_COVD-DRIVE.pth <https://dl.dropboxusercontent.com/s/x5wb84uao8nlx44/M2UNet_COVD-DRIVE.pth>`_ |
+--------------------+------------------------------------------------------------------------------------------------------+--------------------------------------------------------------------------------------------------------------------+
| COVD-DRIVE SSL | | `M2UNet_COVD-DRIVE_SSL.pth <https://dl.dropboxusercontent.com/s/hp7fg6bct0i3awr/M2UNet_COVD-DRIVE_SSL.pth>`_ |
+--------------------+------------------------------------------------------------------------------------------------------+--------------------------------------------------------------------------------------------------------------------+
| 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>`_ |
+--------------------+------------------------------------------------------------------------------------------------------+--------------------------------------------------------------------------------------------------------------------+
+--------------------+--------------------+--------------------------------------------------------------------------------------------------------------------+
| | DRIU | M2UNet |
+--------------------+--------------------+--------------------------------------------------------------------------------------------------------------------+
| DRIVE | `DRIU_DRIVE.pth`_ | |
+--------------------+--------------------+--------------------------------------------------------------------------------------------------------------------+
| COVD-DRIVE | | `M2UNet_COVD-DRIVE.pth <https://dl.dropboxusercontent.com/s/x5wb84uao8nlx44/M2UNet_COVD-DRIVE.pth>`_ |
+--------------------+--------------------+--------------------------------------------------------------------------------------------------------------------+
| COVD-DRIVE SSL | | `M2UNet_COVD-DRIVE_SSL.pth <https://dl.dropboxusercontent.com/s/hp7fg6bct0i3awr/M2UNet_COVD-DRIVE_SSL.pth>`_ |
+--------------------+--------------------+--------------------------------------------------------------------------------------------------------------------+
| STARE | 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_ | `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_IOSTAR.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_HRF.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>`_ |
+--------------------+--------------------+--------------------------------------------------------------------------------------------------------------------+
......@@ -80,3 +80,4 @@ To run evaluation of pretrained models pass url as ``-w`` argument. E.g.:
.. include:: links.rst
......@@ -22,6 +22,7 @@ Users Guide
evaluation
benchmarkresults
covdresults
configs
api
.. todolist::
......
......@@ -60,3 +60,29 @@
.. Software Tools
.. _maskrcnn-benchmark: https://github.com/facebookresearch/maskrcnn-benchmark
.. Pretrained models
.. _driu_chasedb1.pth: https://dl.dropboxusercontent.com/s/15gxvhdtq0gw074/DRIU_CHASEDB1.pth
.. _driu_drive.pth: https://dl.dropboxusercontent.com/s/rggn9ebj38c06uf/DRIU_DRIVE.pth
.. _driu_hrf.pth: https://dl.dropboxusercontent.com/s/c02m2zyby1zndqx/DRIU_HRF1168.pth
.. _driu_stare.pth: https://dl.dropboxusercontent.com/s/sw5ivfzgz5djirc/DRIU_STARE.pth
.. _driu_iostar.pth: https://dl.dropboxusercontent.com/s/dx1dp8g4nct5r2z/DRIU_IOSTARVESSEL.pth
.. _m2unet_chasedb1.pth: https://dl.dropboxusercontent.com/s/jqq0z9boi17nhqf/M2UNet_CHASEDB1.pth
.. _m2unet_drive.pth: https://dl.dropboxusercontent.com/s/55xply8jm0g2skp/M2UNet_DRIVE.pth
.. _m2unet_hrf.pth: https://dl.dropboxusercontent.com/s/g34g6nai1rsgbsc/M2UNet_HRF1168.pth
.. _m2unet_stare.pth: https://dl.dropboxusercontent.com/s/pc9wb8r7tjvg06p/M2UNet_STARE.pth
.. _m2unet_iostar.pth: https://dl.dropboxusercontent.com/s/g9jyvar9x8vvihr/M2UNet_IOSTARVESSEL.pth
.. _m2unet_covd-drive.pth: https://dl.dropboxusercontent.com/s/x5wb84uao8nlx44/M2UNet_COVD-DRIVE.pth
.. _m2unet_covd-drive_ssl.pth: https://dl.dropboxusercontent.com/s/hp7fg6bct0i3awr/M2UNet_COVD-DRIVE_SSL.pth
.. _m2unet_covd-stare.pth: https://dl.dropboxusercontent.com/s/vh1trws2nxqt65y/M2UNet_COVD-STARE.pth
.. _m2unet_covd-stare_ssl.pth: https://dl.dropboxusercontent.com/s/slcvfgf1saf7t19/M2UNet_COVD-STARE_SSL.pth
.. _m2unet_covd-chaesdb1.pth: https://dl.dropboxusercontent.com/s/pvbp0qky13q5o11/M2UNet_COVD-CHASEDB1.pth
.. _m2unet_covd-chaesdb1_ssl.pth: https://dl.dropboxusercontent.com/s/qx7mm5h8ywm98fi/M2UNet_COVD-CHASEDB1_SSL.pth
.. _m2unet_covd-hrf.pth: https://dl.dropboxusercontent.com/s/o3edhljeidl6fvi/M2UNet_COVD-HRF.pth
.. _m2unet_covd-hrf_ssl.pth: https://dl.dropboxusercontent.com/s/2e0aq8a5vbop2yx/M2UNet_COVD-HRF_SSL.pth
.. _m2unet_covd-iostar.pth: https://dl.dropboxusercontent.com/s/t5b2qomq6ey8i9t/M2UNet_COVD-IOSTAR.pth
.. _m2unet_covd-iostar_ssl.pth: https://dl.dropboxusercontent.com/s/70ynm2k3bpkj4mq/M2UNet_COVD-IOSTAR_SSL.pth
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