From ba7ae9ee20aaf081ff7688f8ee48e7b15e5282cf Mon Sep 17 00:00:00 2001
From: Tim Laibacher <tim.laibacher@idiap.ch>
Date: Wed, 1 May 2019 12:39:59 +0200
Subject: [PATCH] Add more docs and unittests
---
bob/ip/binseg/configs/__init__.py | 3 ++
bob/ip/binseg/configs/datasets/__init__.py | 3 ++
bob/ip/binseg/configs/models/__init__.py | 3 ++
bob/ip/binseg/configs/models/driulayerwise.py | 51 ++++++++++++++++++
bob/ip/binseg/data/binsegdataset.py | 2 +-
bob/ip/binseg/data/transforms.py | 10 +---
bob/ip/binseg/engine/inferencer.py | 45 ++++++++++++----
bob/ip/binseg/engine/trainer.py | 28 ++++++++--
bob/ip/binseg/modeling/driu.py | 25 +++++++--
bob/ip/binseg/modeling/hed.py | 27 +++++++---
bob/ip/binseg/modeling/m2u.py | 21 +++++++-
bob/ip/binseg/modeling/resunet.py | 19 +++++--
bob/ip/binseg/modeling/unet.py | 19 +++++--
bob/ip/binseg/script/__init__.py | 3 ++
bob/ip/binseg/script/binseg.py | 7 ++-
bob/ip/binseg/test/test_basemetrics.py | 44 +++++++++++++++
bob/ip/binseg/test/test_batchmetrics.py | 40 ++++++++++++++
bob/ip/binseg/test/test_models.py | 27 +++++++---
precision_recall_comparison.pdf | Bin 18677 -> 0 bytes
setup.py | 1 +
20 files changed, 325 insertions(+), 53 deletions(-)
create mode 100644 bob/ip/binseg/configs/__init__.py
create mode 100644 bob/ip/binseg/configs/datasets/__init__.py
create mode 100644 bob/ip/binseg/configs/models/__init__.py
create mode 100644 bob/ip/binseg/configs/models/driulayerwise.py
create mode 100644 bob/ip/binseg/test/test_basemetrics.py
create mode 100644 bob/ip/binseg/test/test_batchmetrics.py
delete mode 100644 precision_recall_comparison.pdf
diff --git a/bob/ip/binseg/configs/__init__.py b/bob/ip/binseg/configs/__init__.py
new file mode 100644
index 00000000..2ca5e07c
--- /dev/null
+++ b/bob/ip/binseg/configs/__init__.py
@@ -0,0 +1,3 @@
+# see https://docs.python.org/3/library/pkgutil.html
+from pkgutil import extend_path
+__path__ = extend_path(__path__, __name__)
\ No newline at end of file
diff --git a/bob/ip/binseg/configs/datasets/__init__.py b/bob/ip/binseg/configs/datasets/__init__.py
new file mode 100644
index 00000000..2ca5e07c
--- /dev/null
+++ b/bob/ip/binseg/configs/datasets/__init__.py
@@ -0,0 +1,3 @@
+# see https://docs.python.org/3/library/pkgutil.html
+from pkgutil import extend_path
+__path__ = extend_path(__path__, __name__)
\ No newline at end of file
diff --git a/bob/ip/binseg/configs/models/__init__.py b/bob/ip/binseg/configs/models/__init__.py
new file mode 100644
index 00000000..2ca5e07c
--- /dev/null
+++ b/bob/ip/binseg/configs/models/__init__.py
@@ -0,0 +1,3 @@
+# see https://docs.python.org/3/library/pkgutil.html
+from pkgutil import extend_path
+__path__ = extend_path(__path__, __name__)
\ No newline at end of file
diff --git a/bob/ip/binseg/configs/models/driulayerwise.py b/bob/ip/binseg/configs/models/driulayerwise.py
new file mode 100644
index 00000000..390145c5
--- /dev/null
+++ b/bob/ip/binseg/configs/models/driulayerwise.py
@@ -0,0 +1,51 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+from torch.optim.lr_scheduler import MultiStepLR
+from bob.ip.binseg.modeling.driu import build_driu
+import torch.optim as optim
+from torch.nn import BCEWithLogitsLoss
+from bob.ip.binseg.utils.model_zoo import modelurls
+from bob.ip.binseg.modeling.losses import WeightedBCELogitsLoss
+from bob.ip.binseg.engine.adabound import AdaBound
+
+##### Config #####
+lr = 0.001
+betas = (0.9, 0.999)
+eps = 1e-08
+weight_decay = 0
+final_lr = 0.1
+gamma = 1e-3
+eps = 1e-8
+amsbound = False
+
+scheduler_milestones = [150]
+scheduler_gamma = 0.1
+
+# model
+model = build_driu()
+
+# pretrained backbone
+pretrained_backbone = modelurls['vgg16']
+
+# optimizer
+optimizer = AdaBound(model.parameters(), lr=lr, betas=betas, final_lr=final_lr, gamma=gamma,
+ eps=eps, weight_decay=weight_decay, amsbound=amsbound)
+optim = AdaBound(
+ [
+ {"params": model.backbone.parameters(), "lr": 0.0001,"betas":betas, "final_lr":0.01, "gamma":gamma, "eps" : eps},
+ {"params": model.head.parameters(), "lr": 0.001,"betas":betas, "final_lr":0.1, "gamma":gamma, "eps" : eps},
+ ],
+ betas=betas
+ ,final_lr=final_lr
+ ,gamma=gamma
+ ,eps=eps
+ ,weight_decay=weight_decay
+ ,amsbound=amsbound
+ ,lr=0.00001
+)
+# criterion
+criterion = WeightedBCELogitsLoss(reduction='mean')
+
+# scheduler
+scheduler = MultiStepLR(optimizer, milestones=scheduler_milestones, gamma=scheduler_gamma)
diff --git a/bob/ip/binseg/data/binsegdataset.py b/bob/ip/binseg/data/binsegdataset.py
index 82725efc..27853d14 100644
--- a/bob/ip/binseg/data/binsegdataset.py
+++ b/bob/ip/binseg/data/binsegdataset.py
@@ -11,7 +11,7 @@ class BinSegDataset(Dataset):
It supports indexing such that dataset[i] can be used to get ith sample, e.g.:
img, gt, mask, name = db[0]
- Attributes
+ Parameters
----------
database : binary segmentation `bob.db.database`
diff --git a/bob/ip/binseg/data/transforms.py b/bob/ip/binseg/data/transforms.py
index 4518668d..aa20d5d4 100644
--- a/bob/ip/binseg/data/transforms.py
+++ b/bob/ip/binseg/data/transforms.py
@@ -170,8 +170,8 @@ class ColorJitter(object):
"""
Randomly change the brightness, contrast and saturation of an image.
- Attributes
- -----------
+ Parameters
+ ----------
brightness : float
How much to jitter brightness. brightness_factor
@@ -196,12 +196,6 @@ class ColorJitter(object):
@staticmethod
def get_params(brightness, contrast, saturation, hue):
- """Get a randomized transform to be applied on image.
- Arguments are same as that of __init__.
- Returns:
- Transform which randomly adjusts brightness, contrast and
- saturation in a random order.
- """
transforms = []
if brightness > 0:
brightness_factor = random.uniform(max(0, 1 - brightness), 1 + brightness)
diff --git a/bob/ip/binseg/engine/inferencer.py b/bob/ip/binseg/engine/inferencer.py
index c8166a47..b57a2de0 100644
--- a/bob/ip/binseg/engine/inferencer.py
+++ b/bob/ip/binseg/engine/inferencer.py
@@ -5,20 +5,20 @@ import os
import logging
import time
import datetime
-from tqdm import tqdm
-import torch
import numpy as np
-import pickle
+import torch
import pandas as pd
+import torchvision.transforms.functional as VF
+from tqdm import tqdm
from bob.ip.binseg.utils.metric import SmoothedValue, base_metrics
from bob.ip.binseg.utils.plot import precision_recall_f1iso
-import torchvision.transforms.functional as VF
+
def batch_metrics(predictions, ground_truths, masks, names, output_folder, logger):
"""
- calculates metrics on the batch and saves it to disc
+ Calculates metrics on the batch and saves it to disc
Parameters
----------
@@ -27,7 +27,7 @@ def batch_metrics(predictions, ground_truths, masks, names, output_folder, logge
mask : :py:class:torch.Tensor
names : list
output_folder : str
- logger : logger
+ logger : :py:class:logging
Returns
-------
@@ -86,24 +86,44 @@ def batch_metrics(predictions, ground_truths, masks, names, output_folder, logge
return batch_metrics
-
def save_probability_images(predictions, names, output_folder, logger):
+ """
+ Saves probability maps as tif image
+
+ Parameters
+ ----------
+ predictions : :py:class:torch.Tensor
+ names : list
+ output_folder : str
+ logger : :py:class:logging
+ """
images_subfolder = os.path.join(output_folder,'images')
if not os.path.exists(images_subfolder): os.makedirs(images_subfolder)
for j in range(predictions.size()[0]):
img = VF.to_pil_image(predictions.cpu().data[j])
- filename = '{}_prob.gif'.format(names[j])
+ filename = '{}.tif'.format(names[j])
logger.info("saving {}".format(filename))
img.save(os.path.join(images_subfolder, filename))
-
def do_inference(
model,
data_loader,
device,
output_folder = None
):
+
+ """
+ Run inference and calculate metrics
+
+ Paramters
+ ---------
+ model : :py:class:torch.nn.Module
+ data_loader : py:class:torch.torch.utils.data.DataLoader
+ device : str
+ 'cpu' or 'cuda'
+ output_folder : str
+ """
logger = logging.getLogger("bob.ip.binseg.engine.inference")
logger.info("Start evaluation")
logger.info("Split: {}, Output folder: {}, Device: {}".format(data_loader.dataset.split, output_folder, device))
@@ -128,10 +148,12 @@ def do_inference(
start_time = time.perf_counter()
outputs = model(images)
+
# necessary check for hed architecture that uses several outputs
# for loss calculation instead of just the last concatfuse block
if isinstance(outputs,list):
outputs = outputs[-1]
+
probabilities = sigmoid(outputs)
batch_time = time.perf_counter() - start_time
@@ -140,10 +162,11 @@ def do_inference(
b_metrics = batch_metrics(probabilities, ground_truths, masks, names,results_subfolder, logger)
metrics.extend(b_metrics)
+
# Create probability images
save_probability_images(probabilities, names, output_folder, logger)
-
+ # DataFrame
df_metrics = pd.DataFrame(metrics,columns= \
["name",
"threshold",
@@ -187,7 +210,7 @@ def do_inference(
times_file = "Times.txt".format(model.name)
logger.info("saving {}".format(times_file))
-
+
with open (os.path.join(results_subfolder,times_file), "w+") as outfile:
date = datetime.datetime.now()
outfile.write("Date: {} \n".format(date.strftime("%Y-%m-%d %H:%M:%S")))
diff --git a/bob/ip/binseg/engine/trainer.py b/bob/ip/binseg/engine/trainer.py
index c84a0733..b5a60bb2 100644
--- a/bob/ip/binseg/engine/trainer.py
+++ b/bob/ip/binseg/engine/trainer.py
@@ -1,17 +1,18 @@
#!/usr/bin/env python
# -*- coding: utf-8 -*-
+import os
import logging
import time
import datetime
-from tqdm import tqdm
import torch
-import os
import pandas as pd
+from tqdm import tqdm
from bob.ip.binseg.utils.metric import SmoothedValue
from bob.ip.binseg.utils.plot import loss_curve
+
def do_train(
model,
data_loader,
@@ -24,7 +25,24 @@ def do_train(
arguments,
output_folder
):
- """ Trains the model """
+ """
+ Trains the model
+
+ Parameters
+ ----------
+ model : :py:class:torch.nn.Module
+ data_loader : py:class:torch.torch.utils.data.DataLoader
+ optimizer : py:class.torch.torch.optim.Optimizer
+ criterion : py:class.torch.nn.modules.loss._Loss
+ scheduler : py:class.torch.torch.optim._LRScheduler
+ checkpointer : bob.ip.binseg.utils.checkpointer.DetectronCheckpointer
+ checkpoint_period : int
+ device : str
+ 'cpu' or 'cuda'
+ arguments : dict
+ output_folder : str
+
+ """
logger = logging.getLogger("bob.ip.binseg.engine.trainer")
logger.info("Start training")
start_epoch = arguments["epoch"]
@@ -42,15 +60,17 @@ def do_train(
losses = SmoothedValue(len(data_loader))
epoch = epoch + 1
arguments["epoch"] = epoch
+
+ # Epoch time
start_epoch_time = time.time()
for images, ground_truths, masks, _ in tqdm(data_loader):
images = images.to(device)
ground_truths = ground_truths.to(device)
- #masks = masks.to(device)
outputs = model(images)
+
loss = criterion(outputs, ground_truths)
optimizer.zero_grad()
loss.backward()
diff --git a/bob/ip/binseg/modeling/driu.py b/bob/ip/binseg/modeling/driu.py
index b1478f63..fa367e61 100644
--- a/bob/ip/binseg/modeling/driu.py
+++ b/bob/ip/binseg/modeling/driu.py
@@ -8,6 +8,10 @@ from bob.ip.binseg.modeling.backbones.vgg import vgg16
from bob.ip.binseg.modeling.make_layers import conv_with_kaiming_uniform,convtrans_with_kaiming_uniform, UpsampleCropBlock
class ConcatFuseBlock(nn.Module):
+ """
+ Takes in four feature maps with 16 channels each, concatenates them
+ and applies a 1x1 convolution with 1 output channel.
+ """
def __init__(self):
super().__init__()
self.conv = conv_with_kaiming_uniform(4*16,1,1,1,0)
@@ -20,16 +24,18 @@ class ConcatFuseBlock(nn.Module):
class DRIU(nn.Module):
"""
DRIU head module
- Attributes
+
+ Parameters
----------
- in_channels_list (list[int]): number of channels for each feature map that is returned from backbone
+ in_channels_list : list
+ number of channels for each feature map that is returned from backbone
"""
def __init__(self, in_channels_list=None):
super(DRIU, self).__init__()
in_conv_1_2_16, in_upsample2, in_upsample_4, in_upsample_8 = in_channels_list
self.conv1_2_16 = nn.Conv2d(in_conv_1_2_16, 16, 3, 1, 1)
- # Upsample
+ # Upsample layers
self.upsample2 = UpsampleCropBlock(in_upsample2, 16, 4, 2, 0)
self.upsample4 = UpsampleCropBlock(in_upsample_4, 16, 8, 4, 0)
self.upsample8 = UpsampleCropBlock(in_upsample_8, 16, 16, 8, 0)
@@ -39,8 +45,10 @@ class DRIU(nn.Module):
def forward(self,x):
"""
- Arguments:
- x (list[Tensor]): tensor as returned from the backbone network.
+ Parameters
+ ----------
+ x : list
+ list of tensors as returned from the backbone network.
First element: height and width of input image.
Remaining elements: feature maps for each feature level.
"""
@@ -53,6 +61,13 @@ class DRIU(nn.Module):
return out
def build_driu():
+ """
+ Adds backbone and head together
+
+ Returns
+ -------
+ model : :py:class:torch.nn.Module
+ """
backbone = vgg16(pretrained=False, return_features = [3, 8, 14, 22])
driu_head = DRIU([64, 128, 256, 512])
diff --git a/bob/ip/binseg/modeling/hed.py b/bob/ip/binseg/modeling/hed.py
index 6a3e1d8c..6a8349fd 100644
--- a/bob/ip/binseg/modeling/hed.py
+++ b/bob/ip/binseg/modeling/hed.py
@@ -8,6 +8,10 @@ from bob.ip.binseg.modeling.backbones.vgg import vgg16
from bob.ip.binseg.modeling.make_layers import conv_with_kaiming_uniform, convtrans_with_kaiming_uniform, UpsampleCropBlock
class ConcatFuseBlock(nn.Module):
+ """
+ Takes in five feature maps with one channel each, concatenates thems
+ and applies a 1x1 convolution with 1 output channel.
+ """
def __init__(self):
super().__init__()
self.conv = conv_with_kaiming_uniform(5,1,1,1,0)
@@ -20,11 +24,11 @@ class ConcatFuseBlock(nn.Module):
class HED(nn.Module):
"""
HED head module
- Attributes
+
+ Parameters
----------
- in_channels_list (list[int]): number of channels for each feature map that
- will be fed
-
+ in_channels_list : list
+ number of channels for each feature map that is returned from backbone
"""
def __init__(self, in_channels_list=None):
super(HED, self).__init__()
@@ -41,8 +45,12 @@ class HED(nn.Module):
def forward(self,x):
"""
- Arguments:
- x (list[Tensor]): feature maps for each feature level.
+ Parameters
+ ----------
+ x : list
+ list of tensors as returned from the backbone network.
+ First element: height and width of input image.
+ Remaining elements: feature maps for each feature level.
"""
hw = x[0]
conv1_2_16 = self.conv1_2_16(x[1])
@@ -56,6 +64,13 @@ class HED(nn.Module):
return out
def build_hed():
+ """
+ Adds backbone and head together
+
+ Returns
+ -------
+ model : :py:class:torch.nn.Module
+ """
backbone = vgg16(pretrained=False, return_features = [3, 8, 14, 22, 29])
hed_head = HED([64, 128, 256, 512, 512])
diff --git a/bob/ip/binseg/modeling/m2u.py b/bob/ip/binseg/modeling/m2u.py
index e3936252..13602eb3 100644
--- a/bob/ip/binseg/modeling/m2u.py
+++ b/bob/ip/binseg/modeling/m2u.py
@@ -40,9 +40,11 @@ class LastDecoderBlock(nn.Module):
class M2U(nn.Module):
"""
M2U-Net head module
- Attributes
+
+ Parameters
----------
- in_channels_list (list[int]): number of channels for each feature map that is returned from backbone
+ in_channels_list : list
+ number of channels for each feature map that is returned from backbone
"""
def __init__(self, in_channels_list=None,upsamplemode='bilinear',expand_ratio=0.15):
super(M2U, self).__init__()
@@ -67,6 +69,14 @@ class M2U(nn.Module):
m.bias.data.zero_()
def forward(self,x):
+ """
+ Parameters
+ ----------
+ x : list
+ list of tensors as returned from the backbone network.
+ First element: height and width of input image.
+ Remaining elements: feature maps for each feature level.
+ """
decode4 = self.decode4(x[5],x[4]) # 96, 32
decode3 = self.decode3(decode4,x[3]) # 64, 24
decode2 = self.decode2(decode3,x[2]) # 44, 16
@@ -75,6 +85,13 @@ class M2U(nn.Module):
return decode1
def build_m2unet():
+ """
+ Adds backbone and head together
+
+ Returns
+ -------
+ model : :py:class:torch.nn.Module
+ """
backbone = MobileNetV2(return_features = [1,3,6,13], m2u=True)
m2u_head = M2U(in_channels_list=[16, 24, 32, 96])
diff --git a/bob/ip/binseg/modeling/resunet.py b/bob/ip/binseg/modeling/resunet.py
index 7ee94961..38f66cdd 100644
--- a/bob/ip/binseg/modeling/resunet.py
+++ b/bob/ip/binseg/modeling/resunet.py
@@ -12,9 +12,11 @@ from bob.ip.binseg.modeling.backbones.resnet import resnet50
class ResUNet(nn.Module):
"""
UNet head module for ResNet backbones
- Attributes
+
+ Parameters
----------
- in_channels_list (list[int]): number of channels for each feature map that is returned from backbone
+ in_channels_list : list
+ number of channels for each feature map that is returned from backbone
"""
def __init__(self, in_channels_list=None, pixel_shuffle=False):
super(ResUNet, self).__init__()
@@ -36,8 +38,10 @@ class ResUNet(nn.Module):
def forward(self,x):
"""
- Arguments:
- x (list[Tensor]): tensor as returned from the backbone network.
+ Parameters
+ ----------
+ x : list
+ list of tensors as returned from the backbone network.
First element: height and width of input image.
Remaining elements: feature maps for each feature level.
"""
@@ -51,6 +55,13 @@ class ResUNet(nn.Module):
return out
def build_res50unet():
+ """
+ Adds backbone and head together
+
+ Returns
+ -------
+ model : :py:class:torch.nn.Module
+ """
backbone = resnet50(pretrained=False, return_features = [2, 4, 5, 6, 7])
unet_head = ResUNet([64, 256, 512, 1024, 2048],pixel_shuffle=False)
model = nn.Sequential(OrderedDict([("backbone", backbone), ("head", unet_head)]))
diff --git a/bob/ip/binseg/modeling/unet.py b/bob/ip/binseg/modeling/unet.py
index 9be2b498..d0db666b 100644
--- a/bob/ip/binseg/modeling/unet.py
+++ b/bob/ip/binseg/modeling/unet.py
@@ -12,9 +12,11 @@ from bob.ip.binseg.modeling.backbones.vgg import vgg16
class UNet(nn.Module):
"""
UNet head module
- Attributes
+
+ Parameters
----------
- in_channels_list (list[int]): number of channels for each feature map that is returned from backbone
+ in_channels_list : list
+ number of channels for each feature map that is returned from backbone
"""
def __init__(self, in_channels_list=None, pixel_shuffle=False):
super(UNet, self).__init__()
@@ -30,8 +32,10 @@ class UNet(nn.Module):
def forward(self,x):
"""
- Arguments:
- x (list[Tensor]): tensor as returned from the backbone network.
+ Parameters
+ ----------
+ x : list
+ list of tensors as returned from the backbone network.
First element: height and width of input image.
Remaining elements: feature maps for each feature level.
"""
@@ -44,6 +48,13 @@ class UNet(nn.Module):
return out
def build_unet():
+ """
+ Adds backbone and head together
+
+ Returns
+ -------
+ model : :py:class:torch.nn.Module
+ """
backbone = vgg16(pretrained=False, return_features = [3, 8, 14, 22, 29])
unet_head = UNet([64, 128, 256, 512, 512], pixel_shuffle=False)
diff --git a/bob/ip/binseg/script/__init__.py b/bob/ip/binseg/script/__init__.py
index e69de29b..2ca5e07c 100644
--- a/bob/ip/binseg/script/__init__.py
+++ b/bob/ip/binseg/script/__init__.py
@@ -0,0 +1,3 @@
+# see https://docs.python.org/3/library/pkgutil.html
+from pkgutil import extend_path
+__path__ = extend_path(__path__, __name__)
\ No newline at end of file
diff --git a/bob/ip/binseg/script/binseg.py b/bob/ip/binseg/script/binseg.py
index d57406f7..8fc667b1 100644
--- a/bob/ip/binseg/script/binseg.py
+++ b/bob/ip/binseg/script/binseg.py
@@ -75,6 +75,7 @@ def binseg():
)
@click.option(
'--pretrained-backbone',
+ '-t',
required=True,
cls=ResourceOption
)
@@ -122,6 +123,8 @@ def train(model
,checkpoint_period
,device
,**kwargs):
+ """ Train a model """
+
if not os.path.exists(output_path): os.makedirs(output_path)
# PyTorch dataloader
@@ -198,7 +201,7 @@ def test(model
,batch_size
,dataset
, **kwargs):
-
+ """ Run inference and evalaute the model performance """
# PyTorch dataloader
data_loader = DataLoader(
@@ -257,7 +260,7 @@ def testcheckpoints(model
,dataset
, **kwargs):
-
+ """ Run inference and evaluate all checkpoints saved for a model"""
# PyTorch dataloader
data_loader = DataLoader(
dataset = dataset
diff --git a/bob/ip/binseg/test/test_basemetrics.py b/bob/ip/binseg/test/test_basemetrics.py
new file mode 100644
index 00000000..bf478ac7
--- /dev/null
+++ b/bob/ip/binseg/test/test_basemetrics.py
@@ -0,0 +1,44 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+import unittest
+import numpy as np
+from bob.ip.binseg.utils.metric import base_metrics
+import random
+
+class Tester(unittest.TestCase):
+ """
+ Unit test for base metrics
+ """
+ def setUp(self):
+ self.tp = random.randint(1, 100)
+ self.fp = random.randint(1, 100)
+ self.tn = random.randint(1, 100)
+ self.fn = random.randint(1, 100)
+
+ def test_precision(self):
+ precision = base_metrics(self.tp, self.fp, self.tn, self.fn)[0]
+ self.assertEqual((self.tp)/(self.tp + self.fp),precision)
+
+ def test_recall(self):
+ recall = base_metrics(self.tp, self.fp, self.tn, self.fn)[1]
+ self.assertEqual((self.tp)/(self.tp + self.fn),recall)
+
+ def test_specificity(self):
+ specificity = base_metrics(self.tp, self.fp, self.tn, self.fn)[2]
+ self.assertEqual((self.tn)/(self.tn + self.fp),specificity)
+
+ def test_accuracy(self):
+ accuracy = base_metrics(self.tp, self.fp, self.tn, self.fn)[3]
+ self.assertEqual((self.tp + self.tn)/(self.tp + self.tn + self.fp + self.fn), accuracy)
+
+ def test_jaccard(self):
+ jaccard = base_metrics(self.tp, self.fp, self.tn, self.fn)[4]
+ self.assertEqual(self.tp / (self.tp+self.fp+self.fn), jaccard)
+
+ def test_f1(self):
+ f1 = base_metrics(self.tp, self.fp, self.tn, self.fn)[5]
+ self.assertEqual((2.0 * self.tp ) / (2.0 * self.tp + self.fp + self.fn ),f1)
+
+if __name__ == '__main__':
+ unittest.main()
\ No newline at end of file
diff --git a/bob/ip/binseg/test/test_batchmetrics.py b/bob/ip/binseg/test/test_batchmetrics.py
new file mode 100644
index 00000000..93d573e8
--- /dev/null
+++ b/bob/ip/binseg/test/test_batchmetrics.py
@@ -0,0 +1,40 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+import unittest
+import numpy as np
+from bob.ip.binseg.engine.inferencer import batch_metrics
+import random
+import shutil, tempfile
+import logging
+import torch
+
+class Tester(unittest.TestCase):
+ """
+ Unit test for batch metrics
+ """
+ def setUp(self):
+ self.tp = random.randint(1, 100)
+ self.fp = random.randint(1, 100)
+ self.tn = random.randint(1, 100)
+ self.fn = random.randint(1, 100)
+ self.predictions = torch.rand(size=(2,1,420,420))
+ self.ground_truths = torch.randint(low=0, high=2, size=(2,1,420,420))
+ self.masks = None
+ self.names = ['Bob','Tim']
+ self.output_folder = tempfile.mkdtemp()
+ self.logger = logging.getLogger(__name__)
+
+ def tearDown(self):
+ # Remove the temporary folder after the test
+ shutil.rmtree(self.output_folder)
+
+ def test_batch_metrics(self):
+ bm = batch_metrics(self.predictions, self.ground_truths, self.masks, self.names, self.output_folder, self.logger)
+ self.assertEqual(len(bm),2*100)
+ for metric in bm:
+ # check whether f1 score agree
+ self.assertAlmostEqual(metric[-1],2*(metric[-6]*metric[-5])/(metric[-6]+metric[-5]))
+
+if __name__ == '__main__':
+ unittest.main()
\ No newline at end of file
diff --git a/bob/ip/binseg/test/test_models.py b/bob/ip/binseg/test/test_models.py
index bf796565..a5f37d3f 100644
--- a/bob/ip/binseg/test/test_models.py
+++ b/bob/ip/binseg/test/test_models.py
@@ -6,27 +6,42 @@ import unittest
import numpy as np
from bob.ip.binseg.modeling.driu import build_driu
from bob.ip.binseg.modeling.hed import build_hed
+from bob.ip.binseg.modeling.unet import build_unet
+from bob.ip.binseg.modeling.resunet import build_res50unet
class Tester(unittest.TestCase):
"""
Unit test for model architectures
"""
- x = torch.randn(1, 3, 544, 544)
- hw = np.array(x.shape)[[2,3]]
+ def setUp(self):
+ self.x = torch.randn(1, 3, 544, 544)
+ self.hw = np.array(self.x.shape)[[2,3]]
def test_driu(self):
model = build_driu()
- out = model(Tester.x)
+ out = model(self.x)
out_hw = np.array(out.shape)[[2,3]]
- self.assertEqual(Tester.hw.all(), out_hw.all())
+ self.assertEqual(self.hw.all(), out_hw.all())
def test_hed(self):
model = build_hed()
- out = model(Tester.x)
+ out = model(self.x)
# NOTE: HED outputs a list of length 4. We test only for the last concat-fuse layer
out_hw = np.array(out[4].shape)[[2,3]]
- self.assertEqual(Tester.hw.all(), out_hw.all())
+ self.assertEqual(self.hw.all(), out_hw.all())
+
+ def test_unet(self):
+ model = build_unet()
+ out = model(self.x)
+ out_hw = np.array(out.shape)[[2,3]]
+ self.assertEqual(self.hw.all(), out_hw.all())
+
+ def test_resunet(self):
+ model = build_res50unet()
+ out = model(self.x)
+ out_hw = np.array(out.shape)[[2,3]]
+ self.assertEqual(self.hw.all(), out_hw.all())
if __name__ == '__main__':
diff --git a/precision_recall_comparison.pdf b/precision_recall_comparison.pdf
deleted file mode 100644
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diff --git a/setup.py b/setup.py
index 8c8bb0bf..eb8429e7 100644
--- a/setup.py
+++ b/setup.py
@@ -59,6 +59,7 @@ setup(
'M2UNet = bob.ip.binseg.configs.models.m2unet',
'UNet = bob.ip.binseg.configs.models.unet',
'ResUNet = bob.ip.binseg.configs.models.resunet',
+ 'ShapeResUNet = bob.ip.binseg.configs.models.shaperesunet',
'DRIUADABOUND = bob.ip.binseg.configs.models.driuadabound',
'DRIVETRAIN = bob.ip.binseg.configs.datasets.drivetrain',
'DRIVECROPTRAIN = bob.ip.binseg.configs.datasets.drivecroptrain',
--
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