def test_ome_tiff_reader(
resources_dir,
filename,
expected_shape,
expected_dims,
select_scene,
):
# Get file
f = resources_dir / filename
# Read file
img = OmeTiffReader(f, S=select_scene)
# Check that there are no open file pointers after init
proc = Process()
assert str(f) not in [f.path for f in proc.open_files()]
# Check basics
# Check that OME Metadata matches the dask data array shape and dims order
dim_size_getters = {
Dimensions.Scene: img.size_s,
Dimensions.Time: img.size_t,
Dimensions.Channel: img.size_c,
Dimensions.SpatialZ: img.size_z,
Dimensions.SpatialY: img.size_y,
Dimensions.SpatialX: img.size_x,
}
for d, getter in dim_size_getters.items():
if d in expected_dims:
assert getter() == img.dask_data.shape[img.dims.index(d)]
assert img.dims == expected_dims
assert img.is_ome()
assert img.metadata
assert img.shape == expected_shape
assert img.dask_data.shape == expected_shape
assert img.size(expected_dims) == expected_shape
# Will error because those dimensions don't exist in the file
with pytest.raises(exceptions.InvalidDimensionOrderingError):
assert img.size("ABCDEFG") == expected_shape
# Check that there are no open file pointers after basics
assert str(f) not in [f.path for f in proc.open_files()]
# Check array
assert isinstance(img.data, np.ndarray)
assert img.data.shape == expected_shape
# Check that there are no open file pointers after retrieval
assert str(f) not in [f.path for f in proc.open_files()]
def test_get_channel_names(resources_dir, filename, scene, expected_channel_names):
# Get file
f = resources_dir / filename
# Read file
img = OmeTiffReader(f)
# Check that there are no open file pointers after init
proc = Process()
assert str(f) not in [f.path for f in proc.open_files()]
# Check channel names
assert img.get_channel_names(scene) == expected_channel_names
# Check that there are no open file pointers after check
assert str(f) not in [f.path for f in proc.open_files()]
def test_ome_tiff_reader(resources_dir, filename, expected_shape,
expected_dims, select_scene, expected_chunksize,
expected_task_count):
# Get file
f = resources_dir / filename
# Read file
img = OmeTiffReader(f, S=select_scene)
# Check that there are no open file pointers after init
proc = Process()
assert str(f) not in [f.path for f in proc.open_files()]
# Check basics
with Profiler() as prof:
# Check that OME Metadata matches the dask data array shape and dims order
dim_size_getters = {
Dimensions.Scene: img.size_s,
Dimensions.Time: img.size_t,
Dimensions.Channel: img.size_c,
Dimensions.SpatialZ: img.size_z,
Dimensions.SpatialY: img.size_y,
Dimensions.SpatialX: img.size_x
}
for d, getter in dim_size_getters.items():
if d in expected_dims:
assert getter() == img.dask_data.shape[img.dims.index(d)]
assert img.dims == expected_dims
assert img.is_ome()
assert img.metadata
assert img.dask_data.shape == expected_shape
assert img.dask_data.chunksize == expected_chunksize
# Check that basic details don't require task computation
assert len(prof.results) == 0
# Check that there are no open file pointers after basics
assert str(f) not in [f.path for f in proc.open_files()]
# Check computed type is numpy array, computed shape is expected shape, and task count is expected
with Profiler() as prof:
assert isinstance(img.data, np.ndarray)
assert img.data.shape == expected_shape
assert len(prof.results) == expected_task_count
# Check that there are no open file pointers after retrieval
assert str(f) not in [f.path for f in proc.open_files()]
def test_writerShapeComparison(resources_dir):
"""
Test to check that OmeTiffWriter saves arrays that are reflexive with OmeTiffReader
"""
with OmeTiffWriter(resources_dir / filename,
overwrite_file=True) as writer:
writer.save(image)
output = OmeTiffReader(resources_dir / filename).data
assert output.shape == image.shape[1:]
def test_size_functions(resources_dir, filename, s, t, c, z, y, x):
# Get file
f = resources_dir / filename
# Init reader
img = OmeTiffReader(f)
# Check sizes
assert img.size_s() == s
assert img.size_t() == t
assert img.size_c() == c
assert img.size_z() == z
assert img.size_y() == y
assert img.size_x() == x
def test_dimensionOrder(resources_dir, dims, expected_t, expected_c,
expected_z, expected_y, expected_x):
with OmeTiffWriter(resources_dir / filename,
overwrite_file=True) as writer:
writer.save(image, dimension_order=dims)
reader = OmeTiffReader(resources_dir / filename)
output = reader.data
t = reader.size_t()
c = reader.size_c()
z = reader.size_z()
y = reader.size_y()
x = reader.size_x()
os.remove(resources_dir / filename)
assert output.shape == image.shape[1:]
assert x == expected_x
assert y == expected_y
assert z == expected_z
assert c == expected_c
assert t == expected_t