def testTileIteratorRetiling(self):
from girder.plugins.large_image import tilesource
from girder.plugins.large_image.models.image_item import ImageItem
file = self._uploadFile(
os.path.join(os.environ['LARGE_IMAGE_DATA'], 'sample_image.ptif'))
itemId = str(file['itemId'])
item = Item().load(itemId, user=self.admin)
source = ImageItem().tileSource(item)
# Test retiling to 500 x 400
tileCount = 0
for tile in source.tileIterator(scale={'magnification': 2.5},
format=tilesource.TILE_FORMAT_PIL,
tile_size={
'width': 500,
'height': 400
}):
tileCount += 1
self.assertEqual(tile['tile'].size,
(tile['width'], tile['height']))
self.assertEqual(tile['width'],
500 if tile['level_x'] < 7 else 148)
self.assertEqual(tile['height'],
400 if tile['level_y'] < 1 else 368)
self.assertEqual(tileCount, 16)
# Test retiling to 300 x 275 with 50 x 40 pixels overlap with trimmed
# edges
tileCount = 0
for tile in source.tileIterator(scale={'magnification': 2.5},
format=tilesource.TILE_FORMAT_PIL,
tile_size={
'width': 300,
'height': 275
},
tile_overlap={
'x': 50,
'y': 40,
'edges': True
}):
tileCount += 1
self.assertEqual(tile['tile'].size,
(tile['width'], tile['height']))
self.assertEqual(
tile['width'], 275 if not tile['level_x'] else
300 if tile['level_x'] < 14 else 173)
self.assertEqual(
tile['height'], 255
if not tile['level_y'] else 275 if tile['level_y'] < 3 else 83)
self.assertEqual(tile['tile_overlap']['left'],
0 if not tile['level_x'] else 25)
self.assertEqual(tile['tile_overlap']['right'],
25 if tile['level_x'] < 14 else 0)
self.assertEqual(tile['tile_overlap']['top'],
0 if not tile['level_y'] else 20)
self.assertEqual(tile['tile_overlap']['bottom'],
20 if tile['level_y'] < 3 else 0)
self.assertEqual(tileCount, 60)
# Test retiling to 300 x 275 with 50 x 40 pixels overlap without
# trimmed edges
tileCount = 0
for tile in source.tileIterator(scale={'magnification': 2.5},
format=tilesource.TILE_FORMAT_PIL,
tile_size={
'width': 300,
'height': 275
},
tile_overlap={
'x': 50,
'y': 40
}):
tileCount += 1
self.assertEqual(tile['tile'].size,
(tile['width'], tile['height']))
self.assertEqual(tile['width'],
300 if tile['level_x'] < 14 else 148)
self.assertEqual(tile['height'],
275 if tile['level_y'] < 3 else 63)
self.assertEqual(tile['tile_overlap']['left'],
0 if not tile['level_x'] else 25)
self.assertEqual(tile['tile_overlap']['right'],
25 if tile['level_x'] < 14 else 0)
self.assertEqual(tile['tile_overlap']['top'],
0 if not tile['level_y'] else 20)
self.assertEqual(tile['tile_overlap']['bottom'],
20 if tile['level_y'] < 3 else 0)
self.assertEqual(tileCount, 60)
# Test retiling to 300 x 275 with 51 x 41 pixels overlap with trimmed
# edges
tileCount = 0
for tile in source.tileIterator(scale={'magnification': 2.5},
format=tilesource.TILE_FORMAT_PIL,
tile_size={
'width': 300,
'height': 275
},
tile_overlap={
'x': 51,
'y': 41,
'edges': True
}):
tileCount += 1
self.assertEqual(tile['tile'].size,
(tile['width'], tile['height']))
self.assertEqual(
tile['width'], 275 if not tile['level_x'] else
300 if tile['level_x'] < 14 else 187)
self.assertEqual(
tile['height'], 255
if not tile['level_y'] else 275 if tile['level_y'] < 3 else 86)
self.assertEqual(tile['tile_overlap']['left'],
0 if not tile['level_x'] else 25)
self.assertEqual(tile['tile_overlap']['right'],
26 if tile['level_x'] < 14 else 0)
self.assertEqual(tile['tile_overlap']['top'],
0 if not tile['level_y'] else 20)
self.assertEqual(tile['tile_overlap']['bottom'],
21 if tile['level_y'] < 3 else 0)
self.assertEqual(tileCount, 60)
# Test retiling to 300 x 275 with 51 x 41 pixels overlap without
# trimmed edges
tileCount = 0
for tile in source.tileIterator(scale={'magnification': 2.5},
format=tilesource.TILE_FORMAT_PIL,
tile_size={
'width': 300,
'height': 275
},
tile_overlap={
'x': 51,
'y': 41
}):
tileCount += 1
self.assertEqual(tile['tile'].size,
(tile['width'], tile['height']))
self.assertEqual(tile['width'],
300 if tile['level_x'] < 14 else 162)
self.assertEqual(tile['height'],
275 if tile['level_y'] < 3 else 66)
self.assertEqual(tile['tile_overlap']['left'],
0 if not tile['level_x'] else 25)
self.assertEqual(tile['tile_overlap']['right'],
26 if tile['level_x'] < 14 else 0)
self.assertEqual(tile['tile_overlap']['top'],
0 if not tile['level_y'] else 20)
self.assertEqual(tile['tile_overlap']['bottom'],
21 if tile['level_y'] < 3 else 0)
self.assertEqual(tileCount, 60)
def testTileIteratorSingleTile(self):
from girder.plugins.large_image.models.image_item import ImageItem
file = self._uploadFile(
os.path.join(os.environ['LARGE_IMAGE_DATA'], 'sample_image.ptif'))
itemId = str(file['itemId'])
item = Item().load(itemId, user=self.admin)
source = ImageItem().tileSource(item)
# Test getting a single tile
sourceRegion = {
'width': 0.7,
'height': 0.6,
'left': 0.15,
'top': 0.2,
'units': 'fraction'
}
tileCount = 0
for tile in source.tileIterator(region=sourceRegion,
scale={'magnification': 5},
tile_position=25):
tileCount += 1
self.assertEqual(tile['tile_position']['position'], 25)
self.assertEqual(tile['tile_position']['level_x'], 8)
self.assertEqual(tile['tile_position']['level_y'], 2)
self.assertEqual(tile['tile_position']['region_x'], 4)
self.assertEqual(tile['tile_position']['region_y'], 1)
self.assertEqual(tile['iterator_range']['level_x_min'], 4)
self.assertEqual(tile['iterator_range']['level_y_min'], 1)
self.assertEqual(tile['iterator_range']['level_x_max'], 25)
self.assertEqual(tile['iterator_range']['level_y_max'], 5)
self.assertEqual(tile['iterator_range']['region_x_max'], 21)
self.assertEqual(tile['iterator_range']['region_y_max'], 4)
self.assertEqual(tile['iterator_range']['position'], 84)
self.assertEqual(tileCount, 1)
tiles = list(
source.tileIterator(region=sourceRegion,
scale={'magnification': 5},
tile_position={'position': 25}))
self.assertEqual(len(tiles), 1)
self.assertEqual(tiles[0]['tile_position']['position'], 25)
tiles = list(
source.tileIterator(region=sourceRegion,
scale={'magnification': 5},
tile_position={
'level_x': 8,
'level_y': 2
}))
self.assertEqual(len(tiles), 1)
self.assertEqual(tiles[0]['tile_position']['position'], 25)
tiles = list(
source.tileIterator(region=sourceRegion,
scale={'magnification': 5},
tile_position={
'region_x': 4,
'region_y': 1
}))
self.assertEqual(len(tiles), 1)
self.assertEqual(tiles[0]['tile_position']['position'], 25)
tiles = list(
source.tileIterator(region=sourceRegion,
scale={'magnification': 5},
tile_position={'position': 90}))
self.assertEqual(len(tiles), 0)
def testTileIterator(self):
from girder.plugins.large_image import tilesource
from girder.plugins.large_image.models.image_item import ImageItem
file = self._uploadFile(
os.path.join(
os.environ['LARGE_IMAGE_DATA'],
'sample_jp2k_33003_TCGA-CV-7242-'
'11A-01-TS1.1838afb1-9eee-4a70-9ae3-50e3ab45e242.svs'))
itemId = str(file['itemId'])
item = Item().load(itemId, user=self.admin)
source = ImageItem().tileSource(item)
tileCount = 0
visited = {}
for tile in source.tileIterator(format=tilesource.TILE_FORMAT_PIL,
scale={'magnification': 5}):
# Check that we haven't loaded the tile's image yet
self.assertFalse(getattr(tile, 'loaded', None))
visited.setdefault(tile['level_x'], {})[tile['level_y']] = True
tileCount += 1
self.assertEqual(tile['tile'].size,
(tile['width'], tile['height']))
self.assertEqual(tile['width'],
256 if tile['level_x'] < 11 else 61)
self.assertEqual(tile['height'],
256 if tile['level_y'] < 11 else 79)
# Check that we have loaded the tile's image
self.assertTrue(getattr(tile, 'loaded', None))
self.assertEqual(tileCount, 144)
self.assertEqual(len(visited), 12)
self.assertEqual(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
self.assertEqual(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
self.assertEqual(tileCount, 0)
# Check with a native magnfication with exact=True
for tile in source.tileIterator(scale={
'magnification': 5,
'exact': True
}):
tileCount += 1
self.assertEqual(tileCount, 144)
# Check with a non-native magnfication without resampling
tileCount = 0
for tile in source.tileIterator(format=tilesource.TILE_FORMAT_PIL,
scale={'magnification': 2}):
tileCount += 1
self.assertEqual(tile['tile'].size,
(tile['width'], tile['height']))
self.assertEqual(tile['width'],
256 if tile['level_x'] < 11 else 61)
self.assertEqual(tile['height'],
256 if tile['level_y'] < 11 else 79)
self.assertEqual(tileCount, 144)
# Check with a non-native magnfication with resampling
tileCount = 0
for tile in source.tileIterator(format=tilesource.TILE_FORMAT_PIL,
scale={'magnification': 2},
resample=True):
tileCount += 1
self.assertEqual(tile['tile'].size,
(tile['width'], tile['height']))
self.assertEqual(tile['width'],
256 if tile['level_x'] < 4 else 126)
self.assertEqual(tile['height'],
256 if tile['level_y'] < 4 else 134)
self.assertEqual(tileCount, 25)
# Ask for numpy array as results
tileCount = 0
for tile in source.tileIterator(scale={'magnification': 5}):
tileCount += 1
self.assertTrue(isinstance(tile['tile'], numpy.ndarray))
self.assertEqual(tile['tile'].shape,
(256 if tile['level_y'] < 11 else 79,
256 if tile['level_x'] < 11 else 61, 4))
self.assertEqual(tile['tile'].dtype, numpy.dtype('uint8'))
self.assertEqual(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=(tilesource.TILE_FORMAT_PIL,
tilesource.TILE_FORMAT_IMAGE),
encoding='JPEG'):
tileCount += 1
self.assertTrue(isinstance(tile['tile'], PIL.Image.Image))
self.assertEqual(tileCount, 144)
# Ask for PNGs
tileCount = 0
for tile in source.tileIterator(scale={'magnification': 5},
format=tilesource.TILE_FORMAT_IMAGE,
encoding='PNG'):
tileCount += 1
self.assertFalse(isinstance(tile['tile'], PIL.Image.Image))
self.assertEqual(tile['tile'][:len(common.PNGHeader)],
common.PNGHeader)
self.assertEqual(tileCount, 144)
# Use a ptif to test getting tiles as images
file = self._uploadFile(
os.path.join(os.environ['LARGE_IMAGE_DATA'], 'sample_image.ptif'))
itemId = str(file['itemId'])
item = Item().load(itemId, user=self.admin)
source = ImageItem().tileSource(item)
# Ask for either PIL or IMAGE data, we should get image data
tileCount = 0
jpegTileCount = 0
for tile in source.tileIterator(scale={'magnification': 2.5},
format=(tilesource.TILE_FORMAT_PIL,
tilesource.TILE_FORMAT_IMAGE),
encoding='JPEG'):
tileCount += 1
if not isinstance(tile['tile'], PIL.Image.Image):
self.assertEqual(tile['tile'][:len(common.JPEGHeader)],
common.JPEGHeader)
jpegTileCount += 1
self.assertEqual(tileCount, 45)
self.assertGreater(jpegTileCount, 0)
# Ask for PNGs
tileCount = 0
for tile in source.tileIterator(scale={'magnification': 2.5},
format=tilesource.TILE_FORMAT_IMAGE,
encoding='PNG'):
tileCount += 1
self.assertEqual(tile['tile'][:len(common.PNGHeader)],
common.PNGHeader)
self.assertEqual(tileCount, 45)
# Ask for TIFFs
tileCount = 0
for tile in source.tileIterator(scale={'magnification': 2.5},
format=tilesource.TILE_FORMAT_IMAGE,
encoding='TIFF'):
tileCount += 1
self.assertEqual(tile['tile'][:len(common.TIFFHeader)],
common.TIFFHeader)
self.assertEqual(tileCount, 45)
# Test some internal properties
self.assertEqual(len(source._tiffDirectories), 9)
info = source._tiffDirectories[-1]._tiffInfo
self.assertEqual(info['bitspersample'], 8)
self.assertEqual(info['compression'], 7)
self.assertEqual(info['imagelength'], 12288)
self.assertEqual(info['imagewidth'], 58368)
self.assertEqual(info['istiled'], 1)
self.assertEqual(info['jpegcolormode'], 0)
self.assertEqual(info['jpegquality'], 75)
self.assertEqual(info['jpegtablesmode'], 3)
self.assertEqual(info['orientation'], 1)
self.assertEqual(info['photometric'], 6)
self.assertEqual(info['planarconfig'], 1)
self.assertEqual(info['samplesperpixel'], 3)
self.assertEqual(info['tilelength'], 256)
self.assertEqual(info['tilewidth'], 256)