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#
# openslide-python - Python bindings for the OpenSlide library
#
# Copyright (c) 2016 Benjamin Gilbert
#
# This library is free software; you can redistribute it and/or modify it
# under the terms of version 2.1 of the GNU Lesser General Public License
# as published by the Free Software Foundation.
#
# This library is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
# or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public
# License for more details.
#
# You should have received a copy of the GNU Lesser General Public License
# along with this library; if not, write to the Free Software Foundation,
# Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
#
from ctypes import ArgumentError
from openslide import (OpenSlide, OpenSlideError,
OpenSlideUnsupportedFormatError)
from PIL import Image
import re
import sys
import unittest
from . import (file_path, have_optimizations, image_dimensions_cannot_be_zero,
skip_if)
# Tests should be written to be compatible with Python 2.6 unittest.
class TestSlideWithoutOpening(unittest.TestCase):
def test_detect_format(self):
self.assertTrue(
OpenSlide.detect_format(file_path('__missing_file')) is None)
self.assertTrue(
OpenSlide.detect_format(file_path('../setup.py')) is None)
self.assertEqual(
OpenSlide.detect_format(file_path('boxes.tiff')),
'generic-tiff')
def test_open(self):
self.assertRaises(OpenSlideUnsupportedFormatError,
lambda: OpenSlide('__does_not_exist'))
self.assertRaises(OpenSlideUnsupportedFormatError,
lambda: OpenSlide('setup.py'))
self.assertRaises(OpenSlideError,
lambda: OpenSlide('unopenable.tiff'))
def test_operations_on_closed_handle(self):
osr = OpenSlide(file_path('boxes.tiff'))
props = osr.properties
associated = osr.associated_images
osr.close()
self.assertRaises(ArgumentError,
lambda: osr.read_region((0, 0), 0, (100, 100)))
self.assertRaises(ArgumentError, lambda: osr.close())
self.assertRaises(ArgumentError, lambda: props['openslide.vendor'])
self.assertRaises(ArgumentError, lambda: associated['label'])
def test_context_manager(self):
osr = OpenSlide(file_path('boxes.tiff'))
with osr:
self.assertEqual(osr.level_count, 4)
self.assertRaises(ArgumentError, lambda: osr.level_count)
class _SlideTest(object):
def setUp(self):
self.osr = OpenSlide(file_path(self.FILENAME))
def tearDown(self):
self.osr.close()
class TestSlide(_SlideTest, unittest.TestCase):
FILENAME = 'boxes.tiff'
def test_repr(self):
self.assertEqual(repr(self.osr),
'OpenSlide(%r)' % file_path('boxes.tiff'))
def test_basic_metadata(self):
self.assertEqual(self.osr.level_count, 4)
self.assertEqual(self.osr.level_dimensions,
((300, 250), (150, 125), (75, 62), (37, 31)))
self.assertEqual(self.osr.dimensions, (300, 250))
self.assertEqual(len(self.osr.level_downsamples), self.osr.level_count)
self.assertEqual(self.osr.level_downsamples[0:2], (1, 2))
self.assertAlmostEqual(self.osr.level_downsamples[2], 4, places=0)
self.assertAlmostEqual(self.osr.level_downsamples[3], 8, places=0)
self.assertEqual(self.osr.get_best_level_for_downsample(0.5), 0)
self.assertEqual(self.osr.get_best_level_for_downsample(3), 1)
self.assertEqual(self.osr.get_best_level_for_downsample(37), 3)
def test_properties(self):
self.assertEqual(self.osr.properties['openslide.vendor'],
'generic-tiff')
self.assertRaises(KeyError,
lambda: self.osr.properties['__does_not_exist'])
# test __len__ and __iter__
self.assertEqual(len([v for v in self.osr.properties]),
len(self.osr.properties))
self.assertEqual(repr(self.osr.properties),
'<_PropertyMap %r>' % dict(self.osr.properties))
def test_read_region(self):
self.assertEqual(self.osr.read_region((-10, -10), 1, (400, 400)).size,
(400, 400))
@skip_if(image_dimensions_cannot_be_zero, 'Pillow issue #2259')
def test_read_region_size_dimension_zero(self):
self.assertEqual(self.osr.read_region((0, 0), 1, (400, 0)).size,
(400, 0))
def test_read_region_bad_level(self):
self.assertEqual(self.osr.read_region((0, 0), 4, (100, 100)).size,
(100, 100))
def test_read_region_bad_size(self):
self.assertRaises(OpenSlideError,
lambda: self.osr.read_region((0, 0), 1, (400, -5)))
# Disabled to avoid OOM killer on small systems, since the stdlib
# doesn't provide a way to find out how much RAM we have
@skip_if(sys.maxsize < 1 << 32, '32-bit Python')
# Also skips Pillow < 2.1.0
@skip_if(have_optimizations and not hasattr(Image, 'PILLOW_VERSION'),
'broken on PIL')
def _test_read_region_2GB(self):
self.assertEqual(
self.osr.read_region((1000, 1000), 0, (32768, 16384)).size,
(32768, 16384))
@skip_if(have_optimizations, 'only relevant --without-performance')
@skip_if(sys.maxsize < 1 << 32, '32-bit Python')
def test_read_region_2GB_width(self):
self.assertRaises(ValueError,
lambda: self.osr.read_region((1000, 1000), 0, (1 << 29, 1)))
def test_thumbnail(self):
self.assertEqual(self.osr.get_thumbnail((100, 100)).size, (100, 83))
class TestAperioSlide(_SlideTest, unittest.TestCase):
FILENAME = 'small.svs'
def test_associated_images(self):
self.assertEqual(self.osr.associated_images['thumbnail'].size,
(16, 16))
self.assertRaises(KeyError,
lambda: self.osr.associated_images['__missing'])
# test __len__ and __iter__
self.assertEqual(len([v for v in self.osr.associated_images]),
len(self.osr.associated_images))
def mangle_repr(o):
return re.sub('0x[0-9a-fA-F]+', '(mangled)', repr(o))
self.assertEqual(mangle_repr(self.osr.associated_images),
'<_AssociatedImageMap %s>' % mangle_repr(
dict(self.osr.associated_images)))
class TestUnreadableSlide(_SlideTest, unittest.TestCase):
FILENAME = 'unreadable.svs'
def test_read_bad_region(self):
self.assertEqual(self.osr.properties['openslide.vendor'], 'aperio')
self.assertRaises(OpenSlideError,
lambda: self.osr.read_region((0, 0), 0, (16, 16)))
# verify that errors are sticky
self.assertRaises(OpenSlideError,
lambda: self.osr.properties['openslide.vendor'])
def test_read_bad_associated_image(self):
self.assertEqual(self.osr.properties['openslide.vendor'], 'aperio')
# Prints "JPEGLib: Bogus marker length." to stderr due to
# https://github.com/openslide/openslide/issues/36
self.assertRaises(OpenSlideError,
lambda: self.osr.associated_images['thumbnail'])
# verify that errors are sticky
self.assertRaises(OpenSlideError,
lambda: self.osr.properties['openslide.vendor'])
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