def testGetRegion():
imagePath = utilities.externaldata(
'data/sample_jp2k_33003_TCGA-CV-7242-11A-01-TS1.1838afb1-9eee-'
'4a70-9ae3-50e3ab45e242.svs.sha512')
source = large_image_source_openslide.OpenslideFileTileSource(imagePath)
# By default, getRegion gets an image
image, mimeType = source.getRegion(scale={'magnification': 2.5})
assert mimeType == 'image/jpeg'
assert image[:len(utilities.JPEGHeader)] == utilities.JPEGHeader
# Adding a tile position request should be ignored
image2, imageFormat = source.getRegion(scale={'magnification': 2.5},
tile_position=1)
assert image == image2
# We should be able to get a NUMPY array instead
image, imageFormat = source.getRegion(scale={'magnification': 2.5},
format=constants.TILE_FORMAT_NUMPY)
assert imageFormat == constants.TILE_FORMAT_NUMPY
assert isinstance(image, numpy.ndarray)
assert image.shape == (1447, 1438, 4)
# We should be able to get a PIL image
image, imageFormat = source.getRegion(scale={'magnification': 2.5},
format=(constants.TILE_FORMAT_PIL,
constants.TILE_FORMAT_NUMPY))
assert imageFormat == constants.TILE_FORMAT_PIL
assert image.width == 1438
assert image.height == 1447
def testTilesAssociatedImages():
imagePath = utilities.externaldata(
'data/sample_svs_image.TCGA-DU-6399-01A-01-TS1.e8eb65de-d63e-42db-'
'af6f-14fefbbdf7bd.svs.sha512')
source = large_image_source_openslide.OpenslideFileTileSource(imagePath)
imageList = source.getAssociatedImagesList()
assert imageList == ['label', 'macro', 'thumbnail']
image, mimeType = source.getAssociatedImage('macro')
assert image[:len(utilities.JPEGHeader)] == utilities.JPEGHeader
# Test missing associated image
assert source.getAssociatedImage('nosuchimage') is None
def testTilesFromPowerOf3Tiles():
imagePath = utilities.externaldata(
'data/G10-3_pelvis_crop-powers-of-3.tif.sha512')
source = large_image_source_openslide.OpenslideFileTileSource(imagePath)
tileMetadata = source.getMetadata()
assert tileMetadata['tileWidth'] == 128
assert tileMetadata['tileHeight'] == 128
assert tileMetadata['sizeX'] == 3000
assert tileMetadata['sizeY'] == 5000
assert tileMetadata['levels'] == 7
utilities.checkTilesZXY(source, tileMetadata)
def testTilesFromSmallFile():
testDir = os.path.dirname(os.path.realpath(__file__))
# Using a two-channel luminance-alpha tiff should work
imagePath = os.path.join(testDir, 'test_files', 'small_la.tiff')
source = large_image_source_openslide.OpenslideFileTileSource(imagePath)
tileMetadata = source.getMetadata()
assert tileMetadata['tileWidth'] == 2
assert tileMetadata['tileHeight'] == 1
assert tileMetadata['sizeX'] == 2
assert tileMetadata['sizeY'] == 1
assert tileMetadata['levels'] == 1
utilities.checkTilesZXY(source, tileMetadata)
def testConvertPointScale():
imagePath = utilities.externaldata(
'data/sample_jp2k_33003_TCGA-CV-7242-11A-01-TS1.1838afb1-9eee-'
'4a70-9ae3-50e3ab45e242.svs.sha512')
source = large_image_source_openslide.OpenslideFileTileSource(imagePath)
point = source.getPointAtAnotherScale((500, 800), {'magnification': 5},
'mag_pixels')
assert point == (4000.0, 6400.0)
point = source.getPointAtAnotherScale((500, 800),
targetScale={'magnification': 5},
targetUnits='mag_pixels')
assert point == (62.5, 100.0)
point = source.getPointAtAnotherScale((500000, 800), {'magnification': 5},
'mag_pixels', {'magnification': 20},
'mag_pixels')
assert point == (2000000.0, 3200.0)
def testMagnification():
imagePath = utilities.externaldata(
'data/sample_jp2k_33003_TCGA-CV-7242-11A-01-TS1.1838afb1-9eee-'
'4a70-9ae3-50e3ab45e242.svs.sha512')
source = large_image_source_openslide.OpenslideFileTileSource(imagePath)
# tileMetadata = source.getMetadata()
mag = source.getNativeMagnification()
assert mag['magnification'] == 40.0
assert mag['mm_x'] == 0.000252
assert mag['mm_y'] == 0.000252
mag = source.getMagnificationForLevel()
assert mag['magnification'] == 40.0
assert mag['mm_x'] == 0.000252
assert mag['mm_y'] == 0.000252
assert mag['level'] == 7
assert mag['scale'] == 1.0
mag = source.getMagnificationForLevel(0)
assert mag['magnification'] == 0.3125
assert mag['mm_x'] == 0.032256
assert mag['mm_y'] == 0.032256
assert mag['level'] == 0
assert mag['scale'] == 128.0
assert source.getLevelForMagnification() == 7
assert source.getLevelForMagnification(exact=True) == 7
assert source.getLevelForMagnification(40) == 7
assert source.getLevelForMagnification(20) == 6
assert source.getLevelForMagnification(0.3125) == 0
assert source.getLevelForMagnification(15) == 6
assert source.getLevelForMagnification(25) == 6
assert source.getLevelForMagnification(15, rounding='ceil') == 6
assert source.getLevelForMagnification(25, rounding='ceil') == 7
assert source.getLevelForMagnification(15, rounding=False) == 5.585
assert source.getLevelForMagnification(25, rounding=False) == 6.3219
assert source.getLevelForMagnification(45, rounding=False) == 7
assert source.getLevelForMagnification(15, rounding=None) == 5.585
assert source.getLevelForMagnification(25, rounding=None) == 6.3219
assert source.getLevelForMagnification(45, rounding=None) == 7.1699
assert source.getLevelForMagnification(mm_x=0.0005) == 6
assert source.getLevelForMagnification(mm_x=0.0005, mm_y=0.002) == 5
assert source.getLevelForMagnification(mm_x=0.0005, exact=True) is None
assert source.getLevelForMagnification(mm_x=0.000504, exact=True) == 6
assert source.getLevelForMagnification(80) == 7
assert source.getLevelForMagnification(80, exact=True) is None
assert source.getLevelForMagnification(0.1) == 0
def testTilesFromSVS():
testDir = os.path.dirname(os.path.realpath(__file__))
imagePath = os.path.join(testDir, 'test_files', 'yb10kx5k.png')
assert large_image_source_openslide.OpenslideFileTileSource.canRead(
imagePath) is False
imagePath = utilities.externaldata(
'data/sample_svs_image.TCGA-DU-6399-01A-01-TS1.e8eb65de-d63e-42db-'
'af6f-14fefbbdf7bd.svs.sha512')
assert large_image_source_openslide.OpenslideFileTileSource.canRead(
imagePath) is True
source = large_image_source_openslide.OpenslideFileTileSource(imagePath)
tileMetadata = source.getMetadata()
assert tileMetadata['tileWidth'] == 240
assert tileMetadata['tileHeight'] == 240
assert tileMetadata['sizeX'] == 31872
assert tileMetadata['sizeY'] == 13835
assert tileMetadata['levels'] == 9
utilities.checkTilesZXY(source, tileMetadata)
def testGetPixel():
imagePath = utilities.externaldata(
'data/sample_jp2k_33003_TCGA-CV-7242-11A-01-TS1.1838afb1-9eee-'
'4a70-9ae3-50e3ab45e242.svs.sha512')
source = large_image_source_openslide.OpenslideFileTileSource(imagePath)
pixel = source.getPixel(region={'left': 12125, 'top': 10640})
assert pixel == {'r': 156, 'g': 98, 'b': 138, 'a': 255}
pixel = source.getPixel(region={
'left': 3.0555,
'top': 2.68128,
'units': 'mm'
})
assert pixel == {'r': 156, 'g': 98, 'b': 138, 'a': 255}
pixel = source.getPixel(region={
'top': 10640,
'right': 12126,
'bottom': 12000
})
assert pixel == {'r': 156, 'g': 98, 'b': 138, 'a': 255}
pixel = source.getPixel(region={
'left': 12125,
'top': 10640,
'right': 13000
})
assert pixel == {'r': 156, 'g': 98, 'b': 138, 'a': 255}
pixel = source.getPixel(region={
'left': 12125,
'top': 10640
},
includeTileRecord=True)
assert 'tile' in pixel
def testTileIterator():
imagePath = utilities.externaldata(
'data/sample_jp2k_33003_TCGA-CV-7242-11A-01-TS1.1838afb1-9eee-'
'4a70-9ae3-50e3ab45e242.svs.sha512')
source = large_image_source_openslide.OpenslideFileTileSource(imagePath)
tileCount = 0
visited = {}
for tile in source.tileIterator(format=constants.TILE_FORMAT_PIL,
scale={'magnification': 5}):
# Check that we haven't loaded the tile's image yet
assert not getattr(tile, 'loaded', None)
visited.setdefault(tile['level_x'], {})[tile['level_y']] = True
tileCount += 1
assert tile['tile'].size == (tile['width'], tile['height'])
assert tile['width'] == 256 if tile['level_x'] < 11 else 61
assert tile['height'] == 256 if tile['level_y'] < 11 else 79
# Check that we have loaded the tile's image
assert getattr(tile, 'loaded', None) is True
assert tileCount == 144
assert len(visited) == 12
assert len(visited[0]) == 12
# Check with a non-native magnfication with exact=True
tileCount = 0
for _tile in source.tileIterator(scale={
'magnification': 4,
'exact': True
}):
tileCount += 1
assert tileCount == 0
# Check with a non-native (but factor of 2) magnfication with exact=True
for _tile in source.tileIterator(scale={
'magnification': 2.5,
'exact': True
}):
tileCount += 1
assert tileCount == 0
# Check with a native magnfication with exact=True
for _tile in source.tileIterator(scale={
'magnification': 5,
'exact': True
}):
tileCount += 1
assert tileCount == 144
# Check with a non-native magnfication without resampling
tileCount = 0
for tile in source.tileIterator(format=constants.TILE_FORMAT_PIL,
scale={'magnification': 2},
resample=False):
tileCount += 1
assert tile['tile'].size == (tile['width'], tile['height'])
assert tile['width'] == 256 if tile['level_x'] < 11 else 61
assert tile['height'] == 256 if tile['level_y'] < 11 else 79
assert tileCount == 144
assert source.getTileCount(format=constants.TILE_FORMAT_PIL,
scale={'magnification': 2},
resample=False) == 144
# Check with a non-native magnfication with resampling
tileCount = 0
for tile in source.tileIterator(format=constants.TILE_FORMAT_PIL,
scale={'magnification': 2},
resample=True):
tileCount += 1
assert tile['tile'].size == (tile['width'], tile['height'])
assert tile['width'] == 256 if tile['level_x'] < 4 else 126
assert tile['height'] == 256 if tile['level_y'] < 4 else 134
assert tileCount == 25
assert source.getTileCount(format=constants.TILE_FORMAT_PIL,
scale={'magnification': 2},
resample=True) == 25
# Check that the default is with resampling
tileCount = len(
list(
source.tileIterator(format=constants.TILE_FORMAT_PIL,
scale={'magnification': 2})))
assert tileCount == 25
assert source.getTileCount(format=constants.TILE_FORMAT_PIL,
scale={'magnification': 2}) == 25
# Asking for exact scale should result in no tiles.
assert source.getTileCount(format=constants.TILE_FORMAT_PIL,
scale={
'magnification': 2,
'exact': True
}) == 0
# Ask for numpy array as results
tileCount = 0
for tile in source.tileIterator(scale={'magnification': 5}):
tileCount += 1
assert isinstance(tile['tile'], numpy.ndarray)
assert tile['tile'].shape == (256 if tile['level_y'] < 11 else 79,
256 if tile['level_x'] < 11 else 61, 4)
assert tile['tile'].dtype == numpy.dtype('uint8')
assert tileCount == 144
# Ask for either PIL or IMAGE data, we should get PIL data
tileCount = 0
for tile in source.tileIterator(scale={'magnification': 5},
format=(constants.TILE_FORMAT_PIL,
constants.TILE_FORMAT_IMAGE),
encoding='JPEG'):
tileCount += 1
assert isinstance(tile['tile'], PIL.Image.Image)
assert tileCount == 144
# Ask for PNGs
tileCount = 0
for tile in source.tileIterator(scale={'magnification': 5},
format=constants.TILE_FORMAT_IMAGE,
encoding='PNG'):
tileCount += 1
assert not isinstance(tile['tile'], PIL.Image.Image)
assert tile['tile'][:len(utilities.PNGHeader)] == utilities.PNGHeader
assert tileCount == 144
def testRegionsWithMagnification():
imagePath = utilities.externaldata(
'data/sample_svs_image.TCGA-DU-6399-01A-01-TS1.e8eb65de-d63e-42db-'
'af6f-14fefbbdf7bd.svs.sha512')
source = large_image_source_openslide.OpenslideFileTileSource(imagePath)
params = {
'region': {
'width': 2000,
'height': 1500
},
'output': {
'maxWidth': 1000,
'maxHeight': 1000
},
'encoding': 'PNG'
}
image, mimeType = source.getRegion(**params)
assert image[:len(utilities.PNGHeader)] == utilities.PNGHeader
(width, height) = struct.unpack('!LL', image[16:24])
assert width == 1000
assert height == 750
# test magnification
params = {
'region': {
'width': 2000,
'height': 1500
},
'scale': {
'magnification': 15
},
'encoding': 'PNG'
}
image, mimeType = source.getRegion(**params)
assert image[:len(utilities.PNGHeader)] == utilities.PNGHeader
(width, height) = struct.unpack('!LL', image[16:24])
assert width == 750
assert height == 562
# test magnification with exact requirements
params = {
'region': {
'width': 2000,
'height': 1500
},
'scale': {
'magnification': 15,
'exact': True
},
'encoding': 'PNG'
}
image, mimeType = source.getRegion(**params)
assert len(image) == 0
params = {
'region': {
'width': 2000,
'height': 1500
},
'scale': {
'magnification': 10,
'exact': True
},
'encoding': 'PNG'
}
image, mimeType = source.getRegion(**params)
assert image[:len(utilities.PNGHeader)] == utilities.PNGHeader
(width, height) = struct.unpack('!LL', image[16:24])
assert width == 500
assert height == 375
def testConvertRegionScale():
imagePath = utilities.externaldata(
'data/sample_jp2k_33003_TCGA-CV-7242-11A-01-TS1.1838afb1-9eee-'
'4a70-9ae3-50e3ab45e242.svs.sha512')
source = large_image_source_openslide.OpenslideFileTileSource(imagePath)
# If we aren't using pixels as our units and don't specify a target
# unit, this should do nothing. This source image is 23021 x 23162
sourceRegion = {'width': 0.8, 'height': 0.7, 'units': 'fraction'}
targetRegion = source.convertRegionScale(sourceRegion)
assert sourceRegion == targetRegion
# Units must be valid
with pytest.raises(ValueError):
source.convertRegionScale({'units': 'unknown'})
with pytest.raises(ValueError):
source.convertRegionScale(sourceRegion, targetUnits='unknown')
# We can convert to pixels
targetRegion = source.convertRegionScale(
sourceRegion, targetScale={'magnification': 2.5}, targetUnits='pixels')
assert int(targetRegion['width']) == 1151
assert int(targetRegion['height']) == 1013
assert targetRegion['units'] == 'mag_pixels'
# Now use that to convert to a different magnification
sourceRegion = targetRegion
sourceScale = {'magnification': 2.5}
# Test other conversions
targetScale = {'magnification': 1.25}
targetRegion = source.convertRegionScale(sourceRegion, sourceScale,
targetScale)
assert int(targetRegion['width']) == 18417
assert int(targetRegion['height']) == 16213
assert targetRegion['units'] == 'base_pixels'
targetRegion = source.convertRegionScale(sourceRegion,
sourceScale,
targetScale,
targetUnits='fraction')
assert targetRegion['width'] == pytest.approx(0.8, 1.0e-4)
assert targetRegion['height'] == pytest.approx(0.7, 1.0e-4)
assert targetRegion['units'] == 'fraction'
targetRegion = source.convertRegionScale(sourceRegion,
sourceScale,
targetScale,
targetUnits='mm')
assert targetRegion['width'] == pytest.approx(4.6411, 1.0e-3)
assert targetRegion['height'] == pytest.approx(4.0857, 1.0e-3)
assert targetRegion['units'] == 'mm'
targetRegion = source.convertRegionScale(sourceRegion,
sourceScale,
None,
targetUnits='mm')
assert targetRegion['width'] == pytest.approx(4.6411, 1.0e-3)
assert targetRegion['height'] == pytest.approx(4.0857, 1.0e-3)
assert targetRegion['units'] == 'mm'
targetRegion = source.convertRegionScale(sourceRegion,
sourceScale,
targetScale,
targetUnits='pixels')
assert int(targetRegion['width']) == 575
assert int(targetRegion['height']) == 506
assert targetRegion['units'] == 'mag_pixels'
# test getRegionAtAnotherScale
image, imageFormat = source.getRegionAtAnotherScale(
sourceRegion,
sourceScale,
targetScale,
format=constants.TILE_FORMAT_NUMPY)
assert imageFormat == constants.TILE_FORMAT_NUMPY
assert isinstance(image, numpy.ndarray)
assert image.shape == (506, 575, 4)
with pytest.raises(TypeError):
source.getRegionAtAnotherScale(sourceRegion,
sourceScale,
region=sourceRegion,
format=constants.TILE_FORMAT_NUMPY)
# test tileIteratorAtAnotherScale
tileCount = 0
for _tile in source.tileIteratorAtAnotherScale(
sourceRegion,
sourceScale,
targetScale,
format=constants.TILE_FORMAT_NUMPY,
resample=False):
tileCount += 1
assert tileCount == 72
with pytest.raises(TypeError):
for _tile in source.tileIteratorAtAnotherScale(
sourceRegion,
sourceScale,
region=sourceRegion,
format=constants.TILE_FORMAT_NUMPY):
tileCount += 1