def test_write_tileset(self):
image = slicedimage.TileSet(
[DimensionNames.X, DimensionNames.Y, "ch", "hyb"],
{
'ch': 2,
'hyb': 2
},
{
DimensionNames.Y: 120,
DimensionNames.X: 80
},
)
for hyb in range(2):
for ch in range(2):
tile = slicedimage.Tile(
{
DimensionNames.X: (0.0, 0.01),
DimensionNames.Y: (0.0, 0.01),
},
{
'hyb': hyb,
'ch': ch,
},
)
tile.numpy_array = np.zeros((120, 80))
tile.numpy_array[hyb, ch] = 1
image.add_tile(tile)
with tempfile.TemporaryDirectory() as tempdir:
with tempfile.NamedTemporaryFile(suffix=".json",
dir=tempdir,
delete=False) as partition_file:
partition_file_path = Path(partition_file.name)
partition_doc = slicedimage.v0_0_0.Writer(
).generate_partition_document(image,
partition_file_path.as_uri())
writer = codecs.getwriter("utf-8")
json.dump(partition_doc, writer(partition_file))
loaded = slicedimage.Reader.parse_doc(
partition_file_path.name, partition_file_path.parent.as_uri())
for hyb in range(2):
for ch in range(2):
tiles = [
_tile
for _tile in loaded.tiles(lambda tile: (tile.indices[
'hyb'] == hyb and tile.indices['ch'] == ch))
]
self.assertEqual(len(tiles), 1)
expected = np.zeros((100, 100))
expected[hyb, ch] = 1
self.assertEqual(tiles[0].numpy_array.all(),
expected.all())
self.assertIsNotNone(tiles[0].sha256)
def test_tileset_without_shapes(self):
image = slicedimage.TileSet(
[DimensionNames.X, DimensionNames.Y, "ch", "hyb"],
{'ch': 2, 'hyb': 2},
)
for hyb in range(2):
for ch in range(2):
tile = slicedimage.Tile(
{
DimensionNames.X: (0.0, 0.01),
DimensionNames.Y: (0.0, 0.01),
},
{
'hyb': hyb,
'ch': ch,
},
)
tile.numpy_array = np.zeros((120, 80))
tile.numpy_array[hyb, ch] = 1
image.add_tile(tile)
with tempfile.TemporaryDirectory() as tempdir:
with tempfile.NamedTemporaryFile(
suffix=".json", dir=tempdir, delete=False) as partition_file:
partition_file_path = Path(partition_file.name)
partition_doc = slicedimage.v0_0_0.Writer().generate_partition_document(
image, partition_file_path.as_uri())
# remove the shape information from the tiles.
for tile in partition_doc[TileSetKeys.TILES]:
del tile[TileKeys.TILE_SHAPE]
writer = codecs.getwriter("utf-8")
json.dump(partition_doc, writer(partition_file))
loaded = slicedimage.Reader.parse_doc(
partition_file_path.name, partition_file_path.parent.as_uri())
for hyb in range(2):
for ch in range(2):
tiles = [_tile
for _tile in loaded.tiles(
lambda tile: (
tile.indices['hyb'] == hyb
and tile.indices['ch'] == ch))]
self.assertEqual(len(tiles), 1)
with warnings.catch_warnings(record=True) as w:
# Cause all warnings to always be triggered. Duplicate warnings are
# normally suppressed.
warnings.simplefilter("always")
tile_shape = tiles[0].tile_shape
self.assertEqual(tile_shape, {DimensionNames.Y: 120, DimensionNames.X: 80})
self.assertEqual(len(w), 1)
self.assertIn("Decoding tile just to obtain shape", str(w[0].message))
def test_write_png(self):
image = slicedimage.TileSet(
dimensions=[DimensionNames.X, DimensionNames.Y, "ch", "hyb"],
shape={'ch': 2, 'hyb': 2},
default_tile_shape={DimensionNames.Y: 120, DimensionNames.X: 80},
)
for hyb in range(2):
for ch in range(2):
tile = slicedimage.Tile(
coordinates={
DimensionNames.X: (0.0, 0.01),
DimensionNames.Y: (0.0, 0.01),
},
indices={
'hyb': hyb,
'ch': ch,
},
)
tile.numpy_array = np.zeros((120, 80), dtype=np.uint32)
tile.numpy_array[hyb, ch] = 1
image.add_tile(tile)
with tempfile.TemporaryDirectory() as tempdir:
with tempfile.NamedTemporaryFile(
suffix=".json", dir=tempdir, delete=False) as partition_file:
# create the tileset and save it.
partition_file_path = Path(partition_file.name)
partition_doc = slicedimage.v0_0_0.Writer().generate_partition_document(
image, partition_file_path.as_uri(), tile_format=ImageFormat.PNG)
writer = codecs.getwriter("utf-8")
json.dump(partition_doc, writer(partition_file))
# construct a URL to the tileset we wrote, and load the tileset.
loaded = slicedimage.Reader.parse_doc(
partition_file_path.name, partition_file_path.parent.as_uri())
# compare the tiles we loaded to the tiles we set up.
for hyb in range(2):
for ch in range(2):
tiles = [_tile
for _tile in loaded.tiles(
lambda tile: (
tile.indices['hyb'] == hyb
and tile.indices['ch'] == ch))]
self.assertEqual(len(tiles), 1)
expected = np.zeros((120, 80), dtype=np.uint32)
expected[hyb, ch] = 1
self.assertEqual(tiles[0].numpy_array.all(), expected.all())
self.assertIsNotNone(tiles[0].sha256)
def test_write_collection(self):
image = slicedimage.TileSet(
["x", "y", "ch", "hyb"],
{'ch': 2, 'hyb': 2},
(100, 100),
)
for hyb in range(2):
for ch in range(2):
tile = slicedimage.Tile(
{
'x': (0.0, 0.01),
'y': (0.0, 0.01),
},
{
'hyb': hyb,
'ch': ch,
},
)
tile.numpy_array = numpy.zeros((100, 100))
tile.numpy_array[hyb, ch] = 1
image.add_tile(tile)
collection = slicedimage.Collection()
collection.add_partition("fov002", image)
with TemporaryDirectory() as tempdir, \
tempfile.NamedTemporaryFile(suffix=".json", dir=tempdir) as partition_file:
partition_doc = slicedimage.v0_0_0.Writer().generate_partition_document(
collection, partition_file.name)
writer = codecs.getwriter("utf-8")
json.dump(partition_doc, writer(partition_file))
partition_file.flush()
basename = os.path.basename(partition_file.name)
baseurl = "file://{}".format(os.path.dirname(partition_file.name))
loaded = slicedimage.Reader.parse_doc(basename, baseurl)
for hyb in range(2):
for ch in range(2):
tiles = [_tile
for _tile in loaded.tiles(
lambda tile: (tile.indices['hyb'] == hyb and
tile.indices['ch'] == ch))]
self.assertEqual(len(tiles), 1)
expected = numpy.zeros((100, 100))
expected[hyb, ch] = 1
self.assertEqual(tiles[0].numpy_array.all(), expected.all())
self.assertIsNotNone(tiles[0].sha256)
def test_numpy(self):
"""
Generate a tileset consisting of a single TIFF tile, and then read it.
"""
image = slicedimage.TileSet(
[DimensionNames.X, DimensionNames.Y, "ch", "hyb"],
{
'ch': 1,
'hyb': 1
},
{
DimensionNames.Y: 120,
DimensionNames.X: 80
},
)
tile = slicedimage.Tile(
{
DimensionNames.X: (0.0, 0.01),
DimensionNames.Y: (0.0, 0.01),
},
{
'hyb': 0,
'ch': 0,
},
)
tile.numpy_array = np.random.randint(0,
65535,
size=(120, 80),
dtype=np.uint16)
image.add_tile(tile)
with tempfile.TemporaryDirectory() as tempdir:
tempdir_path = Path(tempdir)
tileset_path = tempdir_path / "tileset.json"
partition_doc = slicedimage.v0_0_0.Writer(
).generate_partition_document(image, (tempdir_path /
"tileset.json").as_uri())
with open(fspath(tileset_path), "w") as fh:
json.dump(partition_doc, fh)
result = slicedimage.Reader.parse_doc("tileset.json",
tempdir_path.as_uri())
self.assertTrue(
np.array_equal(
list(result.tiles())[0].numpy_array, tile.numpy_array))
def test_numpy(self):
"""
Generate a tileset consisting of a single NUMPY tile. Deposit it where the HTTP server can
find the tileset, and fetch it.
"""
image = slicedimage.TileSet(
["x", "y", "ch", "hyb"],
{'ch': 1, 'hyb': 1},
(100, 100),
)
tile = slicedimage.Tile(
{
'x': (0.0, 0.01),
'y': (0.0, 0.01),
},
{
'hyb': 0,
'ch': 0,
},
)
tile.numpy_array = np.random.randint(0, 65535, size=(100, 100), dtype=np.uint16)
image.add_tile(tile)
partition_path = os.path.join(self.tempdir.name, "tileset.json")
partition_doc = slicedimage.v0_0_0.Writer().generate_partition_document(
image, partition_path)
with open(partition_path, "w") as fh:
json.dump(partition_doc, fh)
result = slicedimage.Reader.parse_doc(
"tileset.json",
"http://localhost:{port}/".format(port=self.port),
allow_caching=False,
)
self.assertTrue(np.array_equal(list(result.tiles())[0].numpy_array, tile.numpy_array))
def test_multi_directory_write_collection(self):
"""Test that we can write collections with a directory hierarchy."""
image = slicedimage.TileSet(
["x", "y", "ch", "hyb"],
{'ch': 2, 'hyb': 2},
{'y': 120, 'x': 80},
)
for hyb in range(2):
for ch in range(2):
tile = slicedimage.Tile(
{
'x': (0.0, 0.01),
'y': (0.0, 0.01),
},
{
'hyb': hyb,
'ch': ch,
},
)
tile.numpy_array = np.zeros((120, 80))
tile.numpy_array[hyb, ch] = 1
image.add_tile(tile)
collection = slicedimage.Collection()
collection.add_partition("fov002", image)
def partition_path_generator(parent_toc_path, toc_name):
directory = parent_toc_path.parent / toc_name
directory.mkdir()
return directory / "{}.json".format(parent_toc_path.stem)
def tile_opener(tileset_path, tile, ext):
directory_path = tempfile.mkdtemp(dir=str(tileset_path.parent))
return tempfile.NamedTemporaryFile(
suffix=".{}".format(ext),
prefix="{}-".format(tileset_path.stem),
dir=directory_path,
delete=False,
)
with tempfile.TemporaryDirectory() as tempdir:
with tempfile.NamedTemporaryFile(
suffix=".json", dir=tempdir, delete=False) as partition_file:
partition_file_path = Path(partition_file.name)
partition_doc = slicedimage.v0_0_0.Writer().generate_partition_document(
collection, partition_file_path.as_uri(),
partition_path_generator=partition_path_generator,
tile_opener=tile_opener,
)
writer = codecs.getwriter("utf-8")
json.dump(partition_doc, writer(partition_file))
loaded = slicedimage.Reader.parse_doc(
partition_file_path.name, partition_file_path.parent.as_uri())
for hyb in range(2):
for ch in range(2):
tiles = [
_tile
for _tile in loaded.tiles(
lambda tile: (
tile.indices['hyb'] == hyb
and tile.indices['ch'] == ch))]
self.assertEqual(len(tiles), 1)
expected = np.zeros((100, 100))
expected[hyb, ch] = 1
self.assertEqual(tiles[0].numpy_array.all(), expected.all())
self.assertIsNotNone(tiles[0].sha256)