From e0943e6da6b9ff5ce2e4043bd4ec1e3af31f2863 Mon Sep 17 00:00:00 2001
From: Tim Laibacher <tim.laibacher@idiap.ch>
Date: Mon, 8 Jul 2019 09:37:18 +0200
Subject: [PATCH] Update docs
---
bob/ip/binseg/modeling/driu.py | 2 +-
bob/ip/binseg/modeling/losses.py | 8 ++++----
bob/ip/binseg/script/binseg.py | 4 +++-
bob/ip/binseg/utils/checkpointer.py | 4 +---
bob/ip/binseg/utils/plot.py | 22 ++++++++++++++++++++++
doc/covdresults.rst | 2 +-
doc/index.rst | 1 -
doc/links.rst | 9 +++++++++
doc/references.rst | 10 ----------
9 files changed, 41 insertions(+), 21 deletions(-)
delete mode 100644 doc/references.rst
diff --git a/bob/ip/binseg/modeling/driu.py b/bob/ip/binseg/modeling/driu.py
index 81ad9c4f..466d4eb0 100644
--- a/bob/ip/binseg/modeling/driu.py
+++ b/bob/ip/binseg/modeling/driu.py
@@ -24,7 +24,7 @@ class ConcatFuseBlock(nn.Module):
class DRIU(nn.Module):
"""
DRIU head module
-
+ Based on paper by `Maninis et al. (2016)`_
Parameters
----------
in_channels_list : list
diff --git a/bob/ip/binseg/modeling/losses.py b/bob/ip/binseg/modeling/losses.py
index 7bcde850..de85a581 100644
--- a/bob/ip/binseg/modeling/losses.py
+++ b/bob/ip/binseg/modeling/losses.py
@@ -7,7 +7,7 @@ from torch._jit_internal import weak_script_method
class WeightedBCELogitsLoss(_Loss):
"""
- Implements Equation 1 in [DRIU16]_. Based on ``torch.nn.modules.loss.BCEWithLogitsLoss``.
+ Implements Equation 1 in `Maninis et al. (2016)`_. Based on ``torch.nn.modules.loss.BCEWithLogitsLoss``.
Calculate sum of weighted cross entropy loss.
"""
def __init__(self, weight=None, size_average=None, reduce=None, reduction='mean', pos_weight=None):
@@ -44,7 +44,7 @@ class WeightedBCELogitsLoss(_Loss):
class SoftJaccardBCELogitsLoss(_Loss):
"""
- Implements Equation 6 in [SAT17]_. Based on ``torch.nn.modules.loss.BCEWithLogitsLoss``.
+ Implements Equation 3 in `Iglovikov et al. (2018)`_. Based on ``torch.nn.modules.loss.BCEWithLogitsLoss``.
Attributes
----------
@@ -82,7 +82,7 @@ class SoftJaccardBCELogitsLoss(_Loss):
class HEDWeightedBCELogitsLoss(_Loss):
"""
- Implements Equation 2 in [HED15]_. Based on ``torch.nn.modules.loss.BCEWithLogitsLoss``.
+ Implements Equation 2 in `He et al. (2015)`_. Based on ``torch.nn.modules.loss.BCEWithLogitsLoss``.
Calculate sum of weighted cross entropy loss.
"""
def __init__(self, weight=None, size_average=None, reduce=None, reduction='mean', pos_weight=None):
@@ -123,7 +123,7 @@ class HEDWeightedBCELogitsLoss(_Loss):
class HEDSoftJaccardBCELogitsLoss(_Loss):
"""
- Implements Equation 6 in [SAT17]_ for the hed network. Based on ``torch.nn.modules.loss.BCEWithLogitsLoss``.
+ Implements Equation 3 in `Iglovikov et al. (2018)`_ for the hed network. Based on ``torch.nn.modules.loss.BCEWithLogitsLoss``.
Attributes
----------
diff --git a/bob/ip/binseg/script/binseg.py b/bob/ip/binseg/script/binseg.py
index 47686ad3..7ddfe2af 100644
--- a/bob/ip/binseg/script/binseg.py
+++ b/bob/ip/binseg/script/binseg.py
@@ -30,7 +30,7 @@ from bob.ip.binseg.utils.plot import plot_overview
from bob.ip.binseg.utils.click import OptionEatAll
from bob.ip.binseg.utils.pdfcreator import create_pdf, get_paths
from bob.ip.binseg.utils.rsttable import create_overview_grid
-from bob.ip.binseg.utils.plot import metricsviz, overlay
+from bob.ip.binseg.utils.plot import metricsviz, overlay,savetransformedtest
logger = logging.getLogger(__name__)
@@ -397,6 +397,8 @@ def visualize(dataset, output_path, **kwargs):
metricsviz(dataset=dataset, output_path=output_path)
logger.info('Creating overlay visualizations for {}'.format(output_path))
overlay(dataset=dataset, output_path=output_path)
+ logger.info('Saving transformed test images {}'.format(output_path))
+ savetransformedtest(dataset=dataset, output_path=output_path)
# SSLTrain
diff --git a/bob/ip/binseg/utils/checkpointer.py b/bob/ip/binseg/utils/checkpointer.py
index 4da05227..e2090caa 100644
--- a/bob/ip/binseg/utils/checkpointer.py
+++ b/bob/ip/binseg/utils/checkpointer.py
@@ -11,9 +11,7 @@ from bob.ip.binseg.utils.model_serialization import load_state_dict
from bob.ip.binseg.utils.model_zoo import cache_url
class Checkpointer:
- """Adapted from [MASKRCNNBENCHMARK_18]_
-
- Copyright (c) Facebook, Inc. and its affiliates. All Rights Reserved.
+ """Adapted from `maskrcnn-benchmark`_ under MIT license
Returns
-------
diff --git a/bob/ip/binseg/utils/plot.py b/bob/ip/binseg/utils/plot.py
index db626937..e8eab7da 100644
--- a/bob/ip/binseg/utils/plot.py
+++ b/bob/ip/binseg/utils/plot.py
@@ -290,3 +290,25 @@ def overlay(dataset, output_path):
overlayed_path = os.path.join(output_path,'overlayed')
if not os.path.exists(overlayed_path): os.makedirs(overlayed_path)
overlayed.save(os.path.join(overlayed_path,name))
+
+
+def savetransformedtest(dataset, output_path):
+ """Save the test images as they are fed into the neural network.
+ Makes it easier to create overlay animations (e.g. slide)
+
+ Parameters
+ ----------
+ dataset : :py:class:`torch.utils.data.Dataset`
+ output_path : str
+ path where results and probability output images are stored. E.g. ``'DRIVE/MODEL'``
+ """
+
+ for sample in dataset:
+ # get sample
+ name = sample[0]
+ img = VF.to_pil_image(sample[1]) # PIL Image
+
+ # save to disk
+ testimg_path = os.path.join(output_path,'transformedtestimages')
+ if not os.path.exists(testimg_path): os.makedirs(testimg_path)
+ img.save(os.path.join(testimg_path,name))
diff --git a/doc/covdresults.rst b/doc/covdresults.rst
index 6dca5a6d..05c48c75 100644
--- a/doc/covdresults.rst
+++ b/doc/covdresults.rst
@@ -26,7 +26,7 @@ Dice Scores
+-------------------+---------------+---------+
| COVD-HRF | 0.8013 | 0.8036 |
+-------------------+---------------+---------+
-| COVD-HRF SSL | still running | 0.7999 |
+| COVD-HRF SSL | 0.8002 | 0.7999 |
+-------------------+---------------+---------+
| COVD-IOSTAR | 0.7934 | 0.7953 |
+-------------------+---------------+---------+
diff --git a/doc/index.rst b/doc/index.rst
index d38e7a4e..e3f54086 100644
--- a/doc/index.rst
+++ b/doc/index.rst
@@ -21,7 +21,6 @@ Users Guide
benchmarkresults
covdresults
api
- references
.. todolist::
diff --git a/doc/links.rst b/doc/links.rst
index 7b94ab06..72a0f3e1 100644
--- a/doc/links.rst
+++ b/doc/links.rst
@@ -51,3 +51,12 @@
.. REFUGE
.. _refuge: http://ai.baidu.com/broad/download?dataset=gon
+
+.. OtherPapers
+
+.. _Iglovikov et al. (2018): http://openaccess.thecvf.com/content_cvpr_2018_workshops/w4/html/Iglovikov_TernausNetV2_Fully_Convolutional_CVPR_2018_paper.html
+.. _He et al. (2015): https://doi.org/10.1109/ICCV.2015.164
+
+.. Software Tools
+
+.. _maskrcnn-benchmark: https://github.com/facebookresearch/maskrcnn-benchmark
diff --git a/doc/references.rst b/doc/references.rst
deleted file mode 100644
index 9422bbc1..00000000
--- a/doc/references.rst
+++ /dev/null
@@ -1,10 +0,0 @@
-.. vim: set fileencoding=utf-8 :
-
-===========
-References
-===========
-
-.. [HED15] *Saining Xie and Zhuowen Tu*, **Holistically-Nested Edge Detection**, in: Proceedings of IEEE International Conference on Computer Vision, 2015
-.. [SAT17] *Alexey Shvets, Vladimir Iglovikov, Alexander Rakhlin and Alexandr A. Kalinin** , in: 17th IEEE International Conference on Machine Learning and Applications (ICMLA), 2017
-.. [DRIU16] *K.K. Maninis, J. Pont-Tuset, P. Arbeláez, and L. Van Gool**, in: Medical Image Computing and Computer-Assisted Intervention (MICCAI), 2016
-.. [MASKRCNNBENCHMARK_18] **Francisco Massa and Ross Girshick**, in https://github.com/facebookresearch/maskrcnn-benchmark
\ No newline at end of file
--
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