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#
# openslide-python - Python bindings for the OpenSlide library
#
# Copyright (c) 2016-2024 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 __future__ import annotations
from ctypes import ArgumentError
import re
import sys
from typing import Any
import unittest
from common import file_path
from openslide import (
OpenSlide,
OpenSlideCache,
OpenSlideError,
OpenSlideUnsupportedFormatError,
lowlevel,
)
class TestCache(unittest.TestCase):
@unittest.skipUnless(lowlevel.cache_create.available, "requires OpenSlide 4.0.0")
def test_create_cache(self) -> None:
OpenSlideCache(0)
OpenSlideCache(1)
OpenSlideCache(4 << 20)
self.assertRaises(ArgumentError, lambda: OpenSlideCache(-1))
self.assertRaises(
ArgumentError, lambda: OpenSlideCache(1.3) # type: ignore[arg-type]
)
class TestSlideWithoutOpening(unittest.TestCase):
def test_detect_format(self) -> None:
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) -> None:
self.assertRaises(
OpenSlideUnsupportedFormatError, lambda: OpenSlide('__does_not_exist')
)
self.assertRaises(
OpenSlideUnsupportedFormatError, lambda: OpenSlide('setup.py')
)
self.assertRaises(
ArgumentError,
lambda: OpenSlide(None), # type: ignore[arg-type]
)
self.assertRaises(
ArgumentError,
lambda: OpenSlide(3), # type: ignore[arg-type]
)
self.assertRaises(
OpenSlideUnsupportedFormatError, lambda: OpenSlide('unopenable.tiff')
)
@unittest.skipUnless(
sys.getfilesystemencoding() == 'utf-8',
'Python filesystem encoding is not UTF-8',
)
def test_unicode_path(self) -> None:
path = file_path('😐.svs')
for arg in path, str(path):
self.assertEqual(OpenSlide.detect_format(arg), 'aperio')
self.assertEqual(OpenSlide(arg).dimensions, (16, 16))
def test_unicode_path_bytes(self) -> None:
arg = str(file_path('😐.svs')).encode('UTF-8')
self.assertEqual(OpenSlide.detect_format(arg), 'aperio')
self.assertEqual(OpenSlide(arg).dimensions, (16, 16))
def test_operations_on_closed_handle(self) -> None:
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) -> None:
osr = OpenSlide(file_path('boxes.tiff'))
with osr:
self.assertEqual(osr.level_count, 4)
self.assertRaises(ArgumentError, lambda: osr.level_count)
class _Abstract:
# nested class to prevent the test runner from finding it
class SlideTest(unittest.TestCase):
FILENAME: str | None = None
def setUp(self) -> None:
assert self.FILENAME is not None
self.osr = OpenSlide(file_path(self.FILENAME))
def tearDown(self) -> None:
self.osr.close()
class TestSlide(_Abstract.SlideTest):
FILENAME = 'boxes.tiff'
def test_repr(self) -> None:
self.assertEqual(repr(self.osr), 'OpenSlide(%r)' % file_path('boxes.tiff'))
def test_basic_metadata(self) -> None:
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) -> None:
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)
)
@unittest.skipUnless(
lowlevel.read_icc_profile.available, "requires OpenSlide 4.0.0"
)
def test_color_profile(self) -> None:
assert self.osr.color_profile is not None # for type inference
self.assertEqual(self.osr.color_profile.profile.device_class, 'mntr')
self.assertEqual(
len(self.osr.read_region((0, 0), 0, (100, 100)).info['icc_profile']), 588
)
self.assertEqual(
len(self.osr.get_thumbnail((100, 100)).info['icc_profile']), 588
)
def test_read_region(self) -> None:
self.assertEqual(
self.osr.read_region((-10, -10), 1, (400, 400)).size, (400, 400)
)
def test_read_region_size_dimension_zero(self) -> None:
self.assertEqual(self.osr.read_region((0, 0), 1, (400, 0)).size, (400, 0))
def test_read_region_bad_level(self) -> None:
self.assertEqual(self.osr.read_region((0, 0), 4, (100, 100)).size, (100, 100))
def test_read_region_bad_size(self) -> None:
self.assertRaises(
OpenSlideError, lambda: self.osr.read_region((0, 0), 1, (400, -5))
)
@unittest.skipIf(sys.maxsize < 1 << 32, '32-bit Python')
# Disabled to avoid OOM killer on small systems, since the stdlib
# doesn't provide a way to find out how much RAM we have
def _test_read_region_2GB(self) -> None:
self.assertEqual(
self.osr.read_region((1000, 1000), 0, (32768, 16384)).size, (32768, 16384)
)
def test_thumbnail(self) -> None:
self.assertEqual(self.osr.get_thumbnail((100, 100)).size, (100, 83))
@unittest.skipUnless(lowlevel.cache_create.available, "requires OpenSlide 4.0.0")
def test_set_cache(self) -> None:
self.osr.set_cache(OpenSlideCache(64 << 10))
self.assertEqual(self.osr.read_region((0, 0), 0, (400, 400)).size, (400, 400))
self.assertRaises(
TypeError, lambda: self.osr.set_cache(None) # type: ignore[arg-type]
)
self.assertRaises(
TypeError, lambda: self.osr.set_cache(3) # type: ignore[arg-type]
)
class TestAperioSlide(_Abstract.SlideTest):
FILENAME = 'small.svs'
def test_associated_images(self) -> None:
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: Any) -> str:
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)),
)
def test_color_profile(self) -> None:
self.assertIsNone(self.osr.color_profile)
self.assertNotIn(
'icc_profile', self.osr.read_region((0, 0), 0, (100, 100)).info
)
self.assertNotIn('icc_profile', self.osr.associated_images['thumbnail'].info)
self.assertNotIn('icc_profile', self.osr.get_thumbnail((100, 100)).info)
# Requires DICOM support in OpenSlide. Use associated image ICC support as
# a proxy.
@unittest.skipUnless(
lowlevel.read_associated_image_icc_profile.available, "requires OpenSlide 4.0.0"
)
class TestDicomSlide(_Abstract.SlideTest):
FILENAME = 'boxes_0.dcm'
def test_color_profile(self) -> None:
assert self.osr.color_profile is not None # for type inference
self.assertEqual(self.osr.color_profile.profile.device_class, 'mntr')
main_profile = self.osr.read_region((0, 0), 0, (100, 100)).info['icc_profile']
associated_profile = self.osr.associated_images['thumbnail'].info['icc_profile']
self.assertEqual(len(main_profile), 456)
self.assertEqual(main_profile, associated_profile)
self.assertIs(main_profile, associated_profile)
class TestUnreadableSlide(_Abstract.SlideTest):
FILENAME = 'unreadable.svs'
def test_read_bad_region(self) -> None:
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) -> None:
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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