def testCachesClear(self):
large_image.cache_util.cache._tileCache = None
large_image.cache_util.cache._tileLock = None
config.setConfig('cache_backend', 'python')
self.ExampleWithMetaclass('test')
getTileCache()
assert cachesInfo()['test']['used'] == 1
cachesClear()
assert cachesInfo()['test']['used'] == 0
def cacheClear(self, params):
before = cache_util.cachesInfo()
cache_util.cachesClear()
after = cache_util.cachesInfo()
return {
'cacheCleared': datetime.datetime.utcnow(),
'before': before,
'after': after
}
def testCachesKeyLock(self):
cachesClear()
assert cachesInfo()['test']['used'] == 0
starttime = time.time()
with concurrent.futures.ThreadPoolExecutor(max_workers=3) as executor:
executor.map(self.ExampleWithMetaclass, [3, 3, 2])
endtime = time.time()
# This really should be close to 3
assert endtime - starttime < 6
assert cachesInfo()['test']['used'] == 2
def testInternalMetadata():
import large_image_source_bioformats
imagePath = utilities.externaldata('data/HENormalN801.czi.sha512')
source = large_image_source_bioformats.BioformatsFileTileSource(imagePath)
metadata = source.getInternalMetadata()
assert 'sizeColorPlanes' in metadata
source = None
cachesClear()
def cacheClear(self, params):
before = cache_util.cachesInfo()
cache_util.cachesClear()
after = cache_util.cachesInfo()
# Add a small delay to give the memcached time to clear
stoptime = time.time() + 5
while time.time() < stoptime and any(after[key]['used'] for key in after):
time.sleep(0.1)
after = cache_util.cachesInfo()
return {'cacheCleared': datetime.datetime.utcnow(), 'before': before, 'after': after}
def testInternalMetadata():
import large_image_source_bioformats
imagePath = datastore.fetch('HENormalN801.czi')
source = large_image_source_bioformats.open(imagePath)
metadata = source.getInternalMetadata()
assert 'sizeColorPlanes' in metadata
source = None
cachesClear()
def testCachesInfo(self):
cachesClear()
large_image.cache_util.cache._tileCache = None
large_image.cache_util.cache._tileLock = None
assert cachesInfo()['test']['used'] == 0
assert 'tileCache' not in cachesInfo()
self.ExampleWithMetaclass('test')
assert cachesInfo()['test']['used'] == 1
config.setConfig('cache_backend', 'python')
getTileCache()
assert 'tileCache' in cachesInfo()
large_image.cache_util.cache._tileCache = None
large_image.cache_util.cache._tileLock = None
config.setConfig('cache_backend', 'memcached')
getTileCache()
# memcached shows an items record as well
assert 'items' in cachesInfo()['tileCache']
def testTilesFromBioformats():
import large_image_source_bioformats
imagePath = utilities.externaldata('data/HENormalN801.czi.sha512')
source = large_image_source_bioformats.BioformatsFileTileSource(imagePath)
tileMetadata = source.getMetadata()
assert tileMetadata['tileWidth'] == 1024
assert tileMetadata['tileHeight'] == 1024
assert tileMetadata['sizeX'] == 50577
assert tileMetadata['sizeY'] == 17417
assert tileMetadata['levels'] == 7
assert tileMetadata['magnification'] == pytest.approx(20, 1)
utilities.checkTilesZXY(source, tileMetadata)
source = None
cachesClear()
def testTilesFromBioformats():
import large_image_source_bioformats
imagePath = datastore.fetch('HENormalN801.czi')
source = large_image_source_bioformats.open(imagePath)
tileMetadata = source.getMetadata()
assert tileMetadata['tileWidth'] == 1024
assert tileMetadata['tileHeight'] == 1024
assert tileMetadata['sizeX'] == 50577
assert tileMetadata['sizeY'] == 17417
assert tileMetadata['levels'] == 7
assert tileMetadata['magnification'] == pytest.approx(20, 1)
utilities.checkTilesZXY(source, tileMetadata)
source = None
cachesClear()
def testTilesFromPIL():
# Ensure this test can run in any order
cachesClear()
imagePath = datastore.fetch('sample_Easy1.png')
# Test with different max size options.
config.setConfig('max_small_image_size', 100)
assert large_image_source_pil.canRead(imagePath) is False
# Allow images bigger than our test
config.setConfig('max_small_image_size', 2048)
assert large_image_source_pil.canRead(imagePath) is True
source = large_image_source_pil.open(imagePath)
tileMetadata = source.getMetadata()
assert tileMetadata['tileWidth'] == 1790
assert tileMetadata['tileHeight'] == 1046
assert tileMetadata['sizeX'] == 1790
assert tileMetadata['sizeY'] == 1046
assert tileMetadata['levels'] == 1
assert tileMetadata['magnification'] is None
assert tileMetadata['mm_x'] is None
assert tileMetadata['mm_y'] is None
utilities.checkTilesZXY(source, tileMetadata)
def testBelowLevelTilesFromOpenJPEG():
from large_image.cache_util import cachesClear
imagePath = datastore.fetch('JK-kidney_B-gal_H3_4C_1-500sec.jp2')
origMin = large_image_source_openjpeg.OpenjpegFileTileSource._minTileSize
origMax = large_image_source_openjpeg.OpenjpegFileTileSource._maxTileSize
large_image_source_openjpeg.OpenjpegFileTileSource._minTileSize = 64
large_image_source_openjpeg.OpenjpegFileTileSource._maxTileSize = 64
# Clear the cache to make sure we use our required max tile size.
cachesClear()
source = large_image_source_openjpeg.open(imagePath)
tileMetadata = source.getMetadata()
assert tileMetadata['tileWidth'] == 64
assert tileMetadata['tileHeight'] == 64
assert tileMetadata['sizeX'] == 16384
assert tileMetadata['sizeY'] == 14848
assert tileMetadata['levels'] == 9
assert tileMetadata['magnification'] == 40
utilities.checkTilesZXY(source, tileMetadata)
large_image_source_openjpeg.OpenjpegFileTileSource._minTileSize = origMin
large_image_source_openjpeg.OpenjpegFileTileSource._maxTileSize = origMax
cachesClear()
def testTiffClosed(self):
# test the Tiff files are properly closed.
orig_del = TiledTiffDirectory.__del__
orig_init = TiledTiffDirectory.__init__
self.delCount = 0
self.initCount = 0
def countDelete(*args, **kwargs):
self.delCount += 1
orig_del(*args, **kwargs)
def countInit(*args, **kwargs):
self.initCount += 1
orig_init(*args, **kwargs)
imagePath = utilities.externaldata('data/sample_image.ptif.sha512')
cachesClear()
gc.collect(2)
TiledTiffDirectory.__del__ = countDelete
TiledTiffDirectory.__init__ = countInit
self.initCount = 0
self.delCount = 0
source = large_image.getTileSource(imagePath)
assert source is not None
assert self.initCount == 12
assert self.delCount < 12
# Create another source; we shouldn't init it again, as it should be
# cached.
source = large_image.getTileSource(imagePath)
assert source is not None
assert self.initCount == 12
assert self.delCount < 12
source = None
# Clear the cache to free references and force garbage collection
cachesClear()
gc.collect(2)
cachesClear()
assert self.delCount == 12