From 1a2b5356877cabf521c53500bd9ccf2353dca6f1 Mon Sep 17 00:00:00 2001
From: Andre Anjos <andre.dos.anjos@gmail.com>
Date: Mon, 13 Apr 2020 13:06:03 +0200
Subject: [PATCH] [data] Test correctness of images/label/masks returned by
implemented datasets; Allow special context-dependent procedures for loading
---
bob/ip/binseg/data/chasedb1/__init__.py | 7 +-
bob/ip/binseg/data/chasedb1/test.py | 31 +++-
bob/ip/binseg/data/drive/__init__.py | 9 +-
bob/ip/binseg/data/drive/test.py | 43 ++++-
bob/ip/binseg/data/hrf/__init__.py | 9 +-
bob/ip/binseg/data/hrf/test.py | 43 ++++-
bob/ip/binseg/data/iostar/__init__.py | 22 ++-
bob/ip/binseg/data/iostar/default.json | 231 ------------------------
bob/ip/binseg/data/iostar/test.py | 102 ++++++++++-
bob/ip/binseg/data/jsondataset.py | 25 ++-
bob/ip/binseg/data/stare/__init__.py | 7 +-
bob/ip/binseg/data/stare/test.py | 31 +++-
bob/ip/binseg/data/utils.py | 114 ++++++++++++
13 files changed, 401 insertions(+), 273 deletions(-)
delete mode 100644 bob/ip/binseg/data/iostar/default.json
diff --git a/bob/ip/binseg/data/chasedb1/__init__.py b/bob/ip/binseg/data/chasedb1/__init__.py
index 3ab9e993..22286f79 100644
--- a/bob/ip/binseg/data/chasedb1/__init__.py
+++ b/bob/ip/binseg/data/chasedb1/__init__.py
@@ -47,10 +47,11 @@ _protocols = [
_root_path = bob.extension.rc.get('bob.ip.binseg.chasedb1.datadir',
os.path.realpath(os.curdir))
-def _loader(s):
+def _loader(context, sample):
+ #"context" is ignore in this case - database is homogeneous
return dict(
- data=load_pil_rgb(s["data"]),
- label=load_pil_1(s["label"]),
+ data=load_pil_rgb(sample["data"]),
+ label=load_pil_1(sample["label"]),
)
dataset = JSONDataset(protocols=_protocols, root_path=_root_path, loader=_loader)
diff --git a/bob/ip/binseg/data/chasedb1/test.py b/bob/ip/binseg/data/chasedb1/test.py
index 90f196dd..a1a4af73 100644
--- a/bob/ip/binseg/data/chasedb1/test.py
+++ b/bob/ip/binseg/data/chasedb1/test.py
@@ -5,6 +5,8 @@
"""Tests for CHASE-DB1"""
import os
+
+import numpy
import nose.tools
from . import dataset
@@ -43,16 +45,41 @@ def test_protocol_consitency():
@rc_variable_set('bob.ip.binseg.chasedb1.datadir')
def test_loading():
+ from ..utils import count_bw
+ image_size = (999, 960)
+ bw_threshold_label = 0.10 #(vessels to background proportion limit)
+
def _check_sample(s):
+
data = s.data
assert isinstance(data, dict)
nose.tools.eq_(len(data), 2)
+
assert "data" in data
- nose.tools.eq_(data["data"].size, (999, 960))
+ nose.tools.eq_(data["data"].size, image_size)
nose.tools.eq_(data["data"].mode, "RGB")
+
assert "label" in data
- nose.tools.eq_(data["label"].size, (999, 960))
+ nose.tools.eq_(data["label"].size, image_size)
nose.tools.eq_(data["label"].mode, "1")
+ b, w = count_bw(data["label"])
+ assert (b+w) == numpy.prod(image_size), \
+ f"Counts of black + white ({b}+{w}) do not add up to total " \
+ f"image size ({numpy.prod(image_size)}) at '{s.key}':label"
+ assert (w/b) < bw_threshold_label, \
+ f"The proportion between black and white pixels " \
+ f"({w}/{b}={w/b:.2f}) is larger than the allowed threshold " \
+ f"of {bw_threshold_label} at '{s.key}':label - this could " \
+ f"indicate a loading problem!"
+
+ # to visualize images, uncomment the folowing code
+ # it should display an image with a faded background representing the
+ # original data, blended with green labels.
+ #from ..utils import overlayed_image
+ #display = overlayed_image(data["data"], data["label"])
+ #display.show()
+ #import ipdb; ipdb.set_trace()
+ #pass
subset = dataset.subsets("default")
for s in subset["train"]: _check_sample(s)
diff --git a/bob/ip/binseg/data/drive/__init__.py b/bob/ip/binseg/data/drive/__init__.py
index f5531603..5298e661 100644
--- a/bob/ip/binseg/data/drive/__init__.py
+++ b/bob/ip/binseg/data/drive/__init__.py
@@ -36,11 +36,12 @@ _protocols = [
_root_path = bob.extension.rc.get('bob.ip.binseg.drive.datadir',
os.path.realpath(os.curdir))
-def _loader(s):
+def _loader(context, sample):
+ #"context" is ignore in this case - database is homogeneous
return dict(
- data=load_pil_rgb(s["data"]),
- label=load_pil_1(s["label"]),
- mask=load_pil_1(s["mask"]),
+ data=load_pil_rgb(sample["data"]),
+ label=load_pil_1(sample["label"]),
+ mask=load_pil_1(sample["mask"]),
)
dataset = JSONDataset(protocols=_protocols, root_path=_root_path, loader=_loader)
diff --git a/bob/ip/binseg/data/drive/test.py b/bob/ip/binseg/data/drive/test.py
index b7b291ff..f66027ef 100644
--- a/bob/ip/binseg/data/drive/test.py
+++ b/bob/ip/binseg/data/drive/test.py
@@ -5,6 +5,8 @@
"""Tests for DRIVE"""
import os
+
+import numpy
import nose.tools
from . import dataset
@@ -38,19 +40,54 @@ def test_protocol_consitency():
@rc_variable_set('bob.ip.binseg.drive.datadir')
def test_loading():
+ from ..utils import count_bw
+ image_size = (565, 584)
+ bw_threshold_label = 0.14 #(vessels to background proportion limit)
+
def _check_sample(s):
+
data = s.data
assert isinstance(data, dict)
nose.tools.eq_(len(data), 3)
+
assert "data" in data
- nose.tools.eq_(data["data"].size, (565, 584))
+ nose.tools.eq_(data["data"].size, image_size)
nose.tools.eq_(data["data"].mode, "RGB")
+
assert "label" in data
- nose.tools.eq_(data["label"].size, (565, 584))
+ nose.tools.eq_(data["label"].size, image_size)
nose.tools.eq_(data["label"].mode, "1")
+ b, w = count_bw(data["label"])
+ assert (b+w) == numpy.prod(image_size), \
+ f"Counts of black + white ({b}+{w}) do not add up to total " \
+ f"image size ({numpy.prod(image_size)}) at '{s.key}':label"
+ assert (w/b) < bw_threshold_label, \
+ f"The proportion between black and white pixels " \
+ f"({w}/{b}={w/b:.2f}) is larger than the allowed threshold " \
+ f"of {bw_threshold_label} at '{s.key}':label - this could " \
+ f"indicate a loading problem!"
+
assert "mask" in data
- nose.tools.eq_(data["mask"].size, (565, 584))
+ nose.tools.eq_(data["mask"].size, image_size)
nose.tools.eq_(data["mask"].mode, "1")
+ b, w = count_bw(data["mask"])
+ assert (b+w) == numpy.prod(image_size), \
+ f"Counts of black + white ({b}+{w}) do not add up to total " \
+ f"image size ({numpy.prod(image_size)}) at '{s.key}':mask"
+ assert w > b, \
+ f"The proportion between white and black pixels " \
+ f"({w} > {b}?) is not respected at '{s.key}':mask - " \
+ f"this could indicate a loading problem!"
+
+ # to visualize images, uncomment the folowing code
+ # it should display an image with a faded background representing the
+ # original data, blended with green labels and blue area indicating the
+ # parts to be masked out.
+ #from ..utils import overlayed_image
+ #display = overlayed_image(data["data"], data["label"], data["mask"])
+ #display.show()
+ #import ipdb; ipdb.set_trace()
+ #pass
subset = dataset.subsets("default")
for s in subset["train"]: _check_sample(s)
diff --git a/bob/ip/binseg/data/hrf/__init__.py b/bob/ip/binseg/data/hrf/__init__.py
index b3d82263..8f0a387b 100644
--- a/bob/ip/binseg/data/hrf/__init__.py
+++ b/bob/ip/binseg/data/hrf/__init__.py
@@ -34,11 +34,12 @@ _protocols = [
_root_path = bob.extension.rc.get('bob.ip.binseg.hrf.datadir',
os.path.realpath(os.curdir))
-def _loader(s):
+def _loader(context, sample):
+ #"context" is ignore in this case - database is homogeneous
return dict(
- data=load_pil_rgb(s["data"]),
- label=load_pil_1(s["label"]),
- mask=load_pil_1(s["mask"]),
+ data=load_pil_rgb(sample["data"]),
+ label=load_pil_1(sample["label"]),
+ mask=load_pil_1(sample["mask"]),
)
dataset = JSONDataset(protocols=_protocols, root_path=_root_path, loader=_loader)
diff --git a/bob/ip/binseg/data/hrf/test.py b/bob/ip/binseg/data/hrf/test.py
index 9a463776..c6e44ccd 100644
--- a/bob/ip/binseg/data/hrf/test.py
+++ b/bob/ip/binseg/data/hrf/test.py
@@ -5,6 +5,8 @@
"""Tests for HRF"""
import os
+
+import numpy
import nose.tools
from . import dataset
@@ -30,19 +32,54 @@ def test_protocol_consitency():
@rc_variable_set('bob.ip.binseg.hrf.datadir')
def test_loading():
+ from ..utils import count_bw
+ image_size = (3504, 2336)
+ bw_threshold_label = 0.12 #(vessels to background proportion limit)
+
def _check_sample(s):
+
data = s.data
assert isinstance(data, dict)
nose.tools.eq_(len(data), 3)
+
assert "data" in data
- nose.tools.eq_(data["data"].size, (3504, 2336))
+ nose.tools.eq_(data["data"].size, image_size)
nose.tools.eq_(data["data"].mode, "RGB")
+
assert "label" in data
- nose.tools.eq_(data["label"].size, (3504, 2336))
+ nose.tools.eq_(data["label"].size, image_size)
nose.tools.eq_(data["label"].mode, "1")
+ b, w = count_bw(data["label"])
+ assert (b+w) == numpy.prod(image_size), \
+ f"Counts of black + white ({b}+{w}) do not add up to total " \
+ f"image size ({numpy.prod(image_size)}) at '{s.key}':label"
+ assert (w/b) < bw_threshold_label, \
+ f"The proportion between black and white pixels " \
+ f"({w}/{b}={w/b:.2f}) is larger than the allowed threshold " \
+ f"of {bw_threshold_label} at '{s.key}':label - this could " \
+ f"indicate a loading problem!"
+
assert "mask" in data
- nose.tools.eq_(data["mask"].size, (3504, 2336))
+ nose.tools.eq_(data["mask"].size, image_size)
nose.tools.eq_(data["mask"].mode, "1")
+ b, w = count_bw(data["mask"])
+ assert (b+w) == numpy.prod(image_size), \
+ f"Counts of black + white ({b}+{w}) do not add up to total " \
+ f"image size ({numpy.prod(image_size)}) at '{s.key}':mask"
+ assert w > b, \
+ f"The proportion between white and black pixels " \
+ f"({w} > {b}?) is not respected at '{s.key}':mask - " \
+ f"this could indicate a loading problem!"
+
+ # to visualize images, uncomment the folowing code
+ # it should display an image with a faded background representing the
+ # original data, blended with green labels and blue area indicating the
+ # parts to be masked out.
+ #from ..utils import overlayed_image
+ #display = overlayed_image(data["data"], data["label"], data["mask"])
+ #display.show()
+ #import ipdb; ipdb.set_trace()
+ #pass
subset = dataset.subsets("default")
for s in subset["train"]: _check_sample(s)
diff --git a/bob/ip/binseg/data/iostar/__init__.py b/bob/ip/binseg/data/iostar/__init__.py
index b8e23eb0..1654cbfd 100644
--- a/bob/ip/binseg/data/iostar/__init__.py
+++ b/bob/ip/binseg/data/iostar/__init__.py
@@ -29,6 +29,7 @@ import bob.extension
from ..jsondataset import JSONDataset
from ..loader import load_pil_rgb, load_pil_1
+from ..utils import invert_mode1_image, subtract_mode1_images
_protocols = [
pkg_resources.resource_filename(__name__, "vessel.json"),
@@ -38,12 +39,23 @@ _protocols = [
_root_path = bob.extension.rc.get('bob.ip.binseg.iostar.datadir',
os.path.realpath(os.curdir))
-def _loader(s):
- return dict(
- data=load_pil_rgb(s["data"]),
- label=load_pil_1(s["label"]),
- mask=load_pil_1(s["mask"]),
+def _loader(context, sample):
+ retval = dict(
+ data=load_pil_rgb(sample["data"]),
+ label=load_pil_1(sample["label"]),
+ mask=load_pil_1(sample["mask"]),
)
+ if context["protocol"] == "optic-disc":
+ # For optic-disc analysis, the label provided by IOSTAR raw data is the
+ # "inverted" (negative) label, and does not consider the mask region,
+ # which must be subtracted. We do this special manipulation here.
+ retval["label"] = subtract_mode1_images(
+ invert_mode1_image(retval["label"]),
+ invert_mode1_image(retval["mask"]))
+ return retval
+ elif context["protocol"] == "vessel":
+ return retval
+ raise RuntimeError(f"Unknown protocol {context['protocol']}")
dataset = JSONDataset(protocols=_protocols, root_path=_root_path, loader=_loader)
"""IOSTAR dataset object"""
diff --git a/bob/ip/binseg/data/iostar/default.json b/bob/ip/binseg/data/iostar/default.json
deleted file mode 100644
index 87f29ad5..00000000
--- a/bob/ip/binseg/data/iostar/default.json
+++ /dev/null
@@ -1,231 +0,0 @@
-{
- "train": [
- [
- "images/01_dr.JPG",
- "manual1/01_dr.tif",
- "mask/01_dr_mask.tif"
- ],
- [
- "images/02_dr.JPG",
- "manual1/02_dr.tif",
- "mask/02_dr_mask.tif"
- ],
- [
- "images/03_dr.JPG",
- "manual1/03_dr.tif",
- "mask/03_dr_mask.tif"
- ],
- [
- "images/04_dr.JPG",
- "manual1/04_dr.tif",
- "mask/04_dr_mask.tif"
- ],
- [
- "images/05_dr.JPG",
- "manual1/05_dr.tif",
- "mask/05_dr_mask.tif"
- ],
- [
- "images/01_g.jpg",
- "manual1/01_g.tif",
- "mask/01_g_mask.tif"
- ],
- [
- "images/02_g.jpg",
- "manual1/02_g.tif",
- "mask/02_g_mask.tif"
- ],
- [
- "images/03_g.jpg",
- "manual1/03_g.tif",
- "mask/03_g_mask.tif"
- ],
- [
- "images/04_g.jpg",
- "manual1/04_g.tif",
- "mask/04_g_mask.tif"
- ],
- [
- "images/05_g.jpg",
- "manual1/05_g.tif",
- "mask/05_g_mask.tif"
- ],
- [
- "images/01_h.jpg",
- "manual1/01_h.tif",
- "mask/01_h_mask.tif"
- ],
- [
- "images/02_h.jpg",
- "manual1/02_h.tif",
- "mask/02_h_mask.tif"
- ],
- [
- "images/03_h.jpg",
- "manual1/03_h.tif",
- "mask/03_h_mask.tif"
- ],
- [
- "images/04_h.jpg",
- "manual1/04_h.tif",
- "mask/04_h_mask.tif"
- ],
- [
- "images/05_h.jpg",
- "manual1/05_h.tif",
- "mask/05_h_mask.tif"
- ]
- ],
- "test": [
- [
- "images/06_dr.JPG",
- "manual1/06_dr.tif",
- "mask/06_dr_mask.tif"
- ],
- [
- "images/07_dr.JPG",
- "manual1/07_dr.tif",
- "mask/07_dr_mask.tif"
- ],
- [
- "images/08_dr.JPG",
- "manual1/08_dr.tif",
- "mask/08_dr_mask.tif"
- ],
- [
- "images/09_dr.JPG",
- "manual1/09_dr.tif",
- "mask/09_dr_mask.tif"
- ],
- [
- "images/10_dr.JPG",
- "manual1/10_dr.tif",
- "mask/10_dr_mask.tif"
- ],
- [
- "images/11_dr.JPG",
- "manual1/11_dr.tif",
- "mask/11_dr_mask.tif"
- ],
- [
- "images/12_dr.JPG",
- "manual1/12_dr.tif",
- "mask/12_dr_mask.tif"
- ],
- [
- "images/13_dr.JPG",
- "manual1/13_dr.tif",
- "mask/13_dr_mask.tif"
- ],
- [
- "images/14_dr.JPG",
- "manual1/14_dr.tif",
- "mask/14_dr_mask.tif"
- ],
- [
- "images/15_dr.JPG",
- "manual1/15_dr.tif",
- "mask/15_dr_mask.tif"
- ],
- [
- "images/06_g.jpg",
- "manual1/06_g.tif",
- "mask/06_g_mask.tif"
- ],
- [
- "images/07_g.jpg",
- "manual1/07_g.tif",
- "mask/07_g_mask.tif"
- ],
- [
- "images/08_g.jpg",
- "manual1/08_g.tif",
- "mask/08_g_mask.tif"
- ],
- [
- "images/09_g.jpg",
- "manual1/09_g.tif",
- "mask/09_g_mask.tif"
- ],
- [
- "images/10_g.jpg",
- "manual1/10_g.tif",
- "mask/10_g_mask.tif"
- ],
- [
- "images/11_g.jpg",
- "manual1/11_g.tif",
- "mask/11_g_mask.tif"
- ],
- [
- "images/12_g.jpg",
- "manual1/12_g.tif",
- "mask/12_g_mask.tif"
- ],
- [
- "images/13_g.jpg",
- "manual1/13_g.tif",
- "mask/13_g_mask.tif"
- ],
- [
- "images/14_g.jpg",
- "manual1/14_g.tif",
- "mask/14_g_mask.tif"
- ],
- [
- "images/15_g.jpg",
- "manual1/15_g.tif",
- "mask/15_g_mask.tif"
- ],
- [
- "images/06_h.jpg",
- "manual1/06_h.tif",
- "mask/06_h_mask.tif"
- ],
- [
- "images/07_h.jpg",
- "manual1/07_h.tif",
- "mask/07_h_mask.tif"
- ],
- [
- "images/08_h.jpg",
- "manual1/08_h.tif",
- "mask/08_h_mask.tif"
- ],
- [
- "images/09_h.jpg",
- "manual1/09_h.tif",
- "mask/09_h_mask.tif"
- ],
- [
- "images/10_h.jpg",
- "manual1/10_h.tif",
- "mask/10_h_mask.tif"
- ],
- [
- "images/11_h.jpg",
- "manual1/11_h.tif",
- "mask/11_h_mask.tif"
- ],
- [
- "images/12_h.jpg",
- "manual1/12_h.tif",
- "mask/12_h_mask.tif"
- ],
- [
- "images/13_h.jpg",
- "manual1/13_h.tif",
- "mask/13_h_mask.tif"
- ],
- [
- "images/14_h.jpg",
- "manual1/14_h.tif",
- "mask/14_h_mask.tif"
- ],
- [
- "images/15_h.jpg",
- "manual1/15_h.tif",
- "mask/15_h_mask.tif"
- ]
- ]
-}
\ No newline at end of file
diff --git a/bob/ip/binseg/data/iostar/test.py b/bob/ip/binseg/data/iostar/test.py
index ecedb60c..865d2eb7 100644
--- a/bob/ip/binseg/data/iostar/test.py
+++ b/bob/ip/binseg/data/iostar/test.py
@@ -5,6 +5,8 @@
"""Tests for IOSTAR"""
import os
+
+import numpy
import nose.tools
from . import dataset
@@ -41,26 +43,114 @@ def test_protocol_consitency():
@rc_variable_set('bob.ip.binseg.iostar.datadir')
-def test_loading():
+def test_loading_vessel():
+
+ from ..utils import count_bw
+ image_size = (1024, 1024)
+ bw_threshold_label = 0.11 #(vessels to background proportion limit)
def _check_sample(s):
+
data = s.data
assert isinstance(data, dict)
nose.tools.eq_(len(data), 3)
+
assert "data" in data
- nose.tools.eq_(data["data"].size, (1024, 1024))
+ nose.tools.eq_(data["data"].size, image_size)
nose.tools.eq_(data["data"].mode, "RGB")
+
assert "label" in data
- nose.tools.eq_(data["label"].size, (1024, 1024))
- nose.tools.eq_(data["label"].mode, "1")
- assert "label" in data
- nose.tools.eq_(data["label"].size, (1024, 1024))
+ nose.tools.eq_(data["label"].size, image_size)
nose.tools.eq_(data["label"].mode, "1")
+ b, w = count_bw(data["label"])
+ assert (b+w) == numpy.prod(image_size), \
+ f"Counts of black + white ({b}+{w}) do not add up to total " \
+ f"image size ({numpy.prod(image_size)}) at '{s.key}':label"
+ assert (w/b) < bw_threshold_label, \
+ f"The proportion between black and white pixels " \
+ f"({w}/{b}={w/b:.2f}) is larger than the allowed threshold " \
+ f"of {bw_threshold_label} at '{s.key}':label - this could " \
+ f"indicate a loading problem!"
+
+ assert "mask" in data
+ nose.tools.eq_(data["mask"].size, image_size)
+ nose.tools.eq_(data["mask"].mode, "1")
+ b, w = count_bw(data["mask"])
+ assert (b+w) == numpy.prod(image_size), \
+ f"Counts of black + white ({b}+{w}) do not add up to total " \
+ f"image size ({numpy.prod(image_size)}) at '{s.key}':mask"
+ assert w > b, \
+ f"The proportion between white and black pixels " \
+ f"({w} > {b}?) is not respected at '{s.key}':mask - " \
+ f"this could indicate a loading problem!"
+
+ # to visualize images, uncomment the folowing code
+ # it should display an image with a faded background representing the
+ # original data, blended with green labels and blue area indicating the
+ # parts to be masked out.
+ #from ..utils import overlayed_image
+ #display = overlayed_image(data["data"], data["label"], data["mask"])
+ #display.show()
+ #import ipdb; ipdb.set_trace()
+ #pass
subset = dataset.subsets("vessel")
for s in subset["train"]: _check_sample(s)
for s in subset["test"]: _check_sample(s)
+
+@rc_variable_set('bob.ip.binseg.iostar.datadir')
+def test_loading_optic_disc():
+
+ from ..utils import count_bw
+ image_size = (1024, 1024)
+ bw_threshold_label = 0.04 #(optic-disc to background proportion limit)
+
+ def _check_sample(s):
+
+ data = s.data
+ assert isinstance(data, dict)
+ nose.tools.eq_(len(data), 3)
+
+ assert "data" in data
+ nose.tools.eq_(data["data"].size, image_size)
+ nose.tools.eq_(data["data"].mode, "RGB")
+
+ assert "label" in data
+ nose.tools.eq_(data["label"].size, image_size)
+ nose.tools.eq_(data["label"].mode, "1")
+ b, w = count_bw(data["label"])
+ assert (b+w) == numpy.prod(image_size), \
+ f"Counts of black + white ({b}+{w}) do not add up to total " \
+ f"image size ({numpy.prod(image_size)}) at '{s.key}':label"
+ assert (w/b) < bw_threshold_label, \
+ f"The proportion between black and white pixels " \
+ f"({w}/{b}={w/b:.2f}) is larger than the allowed threshold " \
+ f"of {bw_threshold_label} at '{s.key}':label - this could " \
+ f"indicate a loading problem!"
+
+ assert "mask" in data
+ nose.tools.eq_(data["mask"].size, image_size)
+ nose.tools.eq_(data["mask"].mode, "1")
+ b, w = count_bw(data["mask"])
+ assert (b+w) == numpy.prod(image_size), \
+ f"Counts of black + white ({b}+{w}) do not add up to total " \
+ f"image size ({numpy.prod(image_size)}) at '{s.key}':mask"
+ assert w > b, \
+ f"The proportion between white and black pixels " \
+ f"({w} > {b}?) is not respected at '{s.key}':mask - " \
+ f"this could indicate a loading problem!"
+
+ # to visualize images, uncomment the folowing code
+ # it should display an image with a faded background representing the
+ # original data, blended with green labels and blue area indicating the
+ # parts to be masked out.
+ #from ..utils import overlayed_image
+ #display = overlayed_image(data["data"], data["label"], data["mask"])
+ #display.show()
+ #import ipdb; ipdb.set_trace()
+ #pass
+
subset = dataset.subsets("optic-disc")
for s in subset["train"]: _check_sample(s)
for s in subset["test"]: _check_sample(s)
diff --git a/bob/ip/binseg/data/jsondataset.py b/bob/ip/binseg/data/jsondataset.py
index 6ce86a20..01121ec1 100644
--- a/bob/ip/binseg/data/jsondataset.py
+++ b/bob/ip/binseg/data/jsondataset.py
@@ -14,7 +14,7 @@ from .sample import DelayedSample
class JSONDataset:
"""
- Generic multi-protocol filelist dataset
+ Generic multi-protocol filelist dataset that yields samples
To create a new dataset, you need to provide one or more JSON formatted
filelists (one per protocol) with the following contents:
@@ -66,11 +66,18 @@ class JSONDataset:
Where:
- * ``data``: absolute or relative path leading to original image
+ * ``data``: absolute or relative path leading to original image, in RGB
+ format
* ``label``: (optional) absolute or relative path with manual segmentation
- information
+ information. This image will be converted to a binary image. This
+ dataset shall always yield label images in which white pixels (value=1)
+ indicate the **presence** of the object, and black pixels (value=0), its
+ absence.
* ``mask``: (optional) absolute or relative path with a mask that indicates
- valid regions in the image where automatic segmentation should occur
+ valid regions in the image where automatic segmentation should occur.
+ This image will be converted to a binary image. This dataset shall
+ always yield mask images in which white pixels (value=1) indicate the
+ **valid** regions of the mask, and black pixels (value=0), invalid parts.
Relative paths are interpreted with respect to the location where the JSON
file is or to an optional ``root_path`` parameter, that can be provided.
@@ -97,8 +104,11 @@ class JSONDataset:
relative paths.
loader : object
- A function that receives, as input, a dictionary with ``{key: path}``
- entries, and returns a dictionary with the loaded data
+ A function that receives, as input, a context dictionary (with a
+ "protocol" and "subset" keys indicating which protocol and subset are
+ being served), and a dictionary with ``{key: path}`` entries, and
+ returns a dictionary with the loaded data. It shall respect the
+ loading principles of data, label and mask objects as stated above.
"""
@@ -173,6 +183,7 @@ class JSONDataset:
for subset, samples in data.items():
delayeds = []
+ context = dict(protocol=protocol, subset=subset)
for k in samples:
if isinstance(k, dict):
@@ -194,7 +205,7 @@ class JSONDataset:
if not os.path.isabs(v):
abs_item[k] = os.path.join(self.root_path, v)
- load = functools.partial(self.loader, abs_item)
+ load = functools.partial(self.loader, context, abs_item)
delayeds.append(DelayedSample(load, key=key))
retval[subset] = delayeds
diff --git a/bob/ip/binseg/data/stare/__init__.py b/bob/ip/binseg/data/stare/__init__.py
index 3aa38840..6885fc4d 100644
--- a/bob/ip/binseg/data/stare/__init__.py
+++ b/bob/ip/binseg/data/stare/__init__.py
@@ -40,10 +40,11 @@ _protocols = [
_root_path = bob.extension.rc.get('bob.ip.binseg.stare.datadir',
os.path.realpath(os.curdir))
-def _loader(s):
+def _loader(context, sample):
+ #"context" is ignore in this case - database is homogeneous
return dict(
- data=load_pil_rgb(s["data"]),
- label=load_pil_1(s["label"]),
+ data=load_pil_rgb(sample["data"]),
+ label=load_pil_1(sample["label"]),
)
dataset = JSONDataset(protocols=_protocols, root_path=_root_path, loader=_loader)
diff --git a/bob/ip/binseg/data/stare/test.py b/bob/ip/binseg/data/stare/test.py
index 0a60cd60..4db5d97f 100644
--- a/bob/ip/binseg/data/stare/test.py
+++ b/bob/ip/binseg/data/stare/test.py
@@ -5,6 +5,8 @@
"""Tests for STARE"""
import os
+
+import numpy
import nose.tools
from . import dataset
@@ -43,16 +45,41 @@ def test_protocol_consitency():
@rc_variable_set('bob.ip.binseg.stare.datadir')
def test_loading():
+ from ..utils import count_bw
+ image_size = (700, 605)
+ bw_threshold_label = 0.19 #(vessels to background proportion limit)
+
def _check_sample(s):
+
data = s.data
assert isinstance(data, dict)
nose.tools.eq_(len(data), 2)
+
assert "data" in data
- nose.tools.eq_(data["data"].size, (700, 605))
+ nose.tools.eq_(data["data"].size, image_size)
nose.tools.eq_(data["data"].mode, "RGB")
+
assert "label" in data
- nose.tools.eq_(data["label"].size, (700, 605))
+ nose.tools.eq_(data["label"].size, image_size)
nose.tools.eq_(data["label"].mode, "1")
+ b, w = count_bw(data["label"])
+ assert (b+w) == numpy.prod(image_size), \
+ f"Counts of black + white ({b}+{w}) do not add up to total " \
+ f"image size ({numpy.prod(image_size)}) at '{s.key}':label"
+ assert (w/b) < bw_threshold_label, \
+ f"The proportion between black and white pixels " \
+ f"({w}/{b}={w/b:.2f}) is larger than the allowed threshold " \
+ f"of {bw_threshold_label} at '{s.key}':label - this could " \
+ f"indicate a loading problem!"
+
+ # to visualize images, uncomment the folowing code
+ # it should display an image with a faded background representing the
+ # original data, blended with green labels.
+ #from ..utils import overlayed_image
+ #display = overlayed_image(data["data"], data["label"])
+ #display.show()
+ #import ipdb; ipdb.set_trace()
+ #pass
subset = dataset.subsets("default")
for s in subset["train"]: _check_sample(s)
diff --git a/bob/ip/binseg/data/utils.py b/bob/ip/binseg/data/utils.py
index 0e1c8842..d8ab2299 100644
--- a/bob/ip/binseg/data/utils.py
+++ b/bob/ip/binseg/data/utils.py
@@ -4,6 +4,10 @@
"""Common utilities"""
+import numpy
+import PIL.Image
+import PIL.ImageOps
+import PIL.ImageChops
import torch
import torch.utils.data
@@ -11,6 +15,116 @@ import torch.utils.data
from .transforms import Compose, ToTensor
+def count_bw(b):
+ """Calculates totals of black and white pixels in a binary image
+
+
+ Parameters
+ ----------
+
+ b : PIL.Image.Image
+ A PIL image in mode "1" to be used for calculating positives and
+ negatives
+
+ Returns
+ -------
+
+ black : int
+ Number of black pixels in the binary image
+
+ white : int
+ Number of white pixels in the binary image
+ """
+
+ boolean_array = numpy.array(b)
+ white = boolean_array.sum()
+ return (boolean_array.size-white), white
+
+
+def invert_mode1_image(img):
+ """Inverts a binary PIL image (mode == ``"1"``)"""
+
+ return PIL.ImageOps.invert(img.convert("RGB")).convert(mode="1",
+ dither=None)
+
+
+def subtract_mode1_images(img1, img2):
+ """Returns a new image that represents ``img1 - img2``"""
+
+ return PIL.ImageChops.subtract(img1, img2)
+
+
+def overlayed_image(img, label, mask=None, label_color=(0, 255, 0),
+ mask_color=(0, 0, 255), alpha=0.4):
+ """Creates an image showing existing labels and masko
+
+ This function creates a new representation of the input image ``img``
+ overlaying a green mask for labelled objects, and a red mask for parts of
+ the image that should be ignored (negative mask). By looking at this
+ representation, it shall be possible to verify if the dataset/loader is
+ yielding images correctly.
+
+
+ Parameters
+ ----------
+
+ img : PIL.Image.Image
+ An RGB PIL image that represents the original image for analysis
+
+ label : PIL.Image.Image
+ A PIL image in mode "1" that represents the labelled elements in the
+ image. White pixels represent the labelled object. Black pixels
+ represent background.
+
+ mask : py:class:`PIL.Image.Image`, Optional
+ A PIL image in mode "1" that represents the mask for the image. White
+ pixels indicate where content should be used, black pixels, content to
+ be ignored.
+
+ label_color : py:class:`tuple`, Optional
+ A tuple with three integer entries indicating the RGB color to be used
+ for labels
+
+ mask_color : py:class:`tuple`, Optional
+ A tuple with three integer entries indicating the RGB color to be used
+ for the mask-negative (black parts in the original mask).
+
+ alpha : py:class:`float`, Optional
+ A float that indicates how much of blending should be performed between
+ the label, mask and the original image.
+
+
+ Returns
+ -------
+
+ image : PIL.Image.Image
+ A new image overlaying the original image, object labels (in green) and
+ what is to be considered parts to be **masked-out** (i.e. a
+ representation of a negative of the mask).
+
+ """
+
+ # creates a representation of labels with the right color
+ label_colored = PIL.ImageOps.colorize(label.convert("L"), (0, 0, 0),
+ label_color)
+
+ # blend image and label together - first blend to get vessels drawn with a
+ # slight "label_color" tone on top, then composite with original image, not
+ # to loose brightness.
+ retval = PIL.Image.blend(img, label_colored, alpha)
+ retval = PIL.Image.composite(img, retval,
+ invert_mode1_image(label))
+
+ # creates a representation of the mask negative with the right color
+ if mask is not None:
+ antimask_colored = PIL.ImageOps.colorize(mask.convert("L"), mask_color,
+ (0, 0, 0))
+ tmp = PIL.Image.blend(retval, antimask_colored, alpha)
+ retval = PIL.Image.composite(retval, tmp, mask)
+
+ return retval
+
+
class SampleList2TorchDataset(torch.utils.data.Dataset):
"""PyTorch dataset wrapper around Sample lists
--
GitLab