def test_positive_sync_offset(default_mib, lt_ctx):
udf = SumSigUDF()
sync_offset = 2
ds_with_offset = MIBDataSet(
path=MIB_TESTDATA_PATH, nav_shape=(32, 32), sync_offset=sync_offset
)
ds_with_offset.set_num_cores(4)
ds_with_offset = ds_with_offset.initialize(lt_ctx.executor)
ds_with_offset.check_valid()
p0 = next(ds_with_offset.get_partitions())
assert p0._start_frame == 2
assert p0.slice.origin == (0, 0, 0)
tileshape = Shape(
(16,) + tuple(ds_with_offset.shape.sig),
sig_dims=ds_with_offset.shape.sig.dims
)
tiling_scheme = TilingScheme.make_for_shape(
tileshape=tileshape,
dataset_shape=ds_with_offset.shape,
)
t0 = next(p0.get_tiles(tiling_scheme))
assert tuple(t0.tile_slice.origin) == (0, 0, 0)
for p in ds_with_offset.get_partitions():
for t in p.get_tiles(tiling_scheme=tiling_scheme):
pass
assert p.slice.origin == (768, 0, 0)
assert p.slice.shape[0] == 256
result = lt_ctx.run_udf(dataset=default_mib, udf=udf)
result = result['intensity'].raw_data[sync_offset:]
result_with_offset = lt_ctx.run_udf(dataset=ds_with_offset, udf=udf)
result_with_offset = result_with_offset['intensity'].raw_data[
:ds_with_offset._meta.image_count - sync_offset
]
assert np.allclose(result, result_with_offset)
def test_too_many_frames():
"""
mib files can contain more frames than the intended scanning dimensions
"""
# one full row of additional frames in the file
scan_size = (31, 32)
ds = MIBDataSet(path=MIB_TESTDATA_PATH,
tileshape=(1, 3, 256, 256),
scan_size=scan_size)
ds = ds.initialize()
ds.check_valid()
for p in ds.get_partitions():
for t in p.get_tiles():
pass
def test_missing_frames(lt_ctx):
"""
there can be some frames missing at the end
"""
# one full row of additional frames in the data set than in the file
scan_size = (33, 32)
ds = MIBDataSet(path=MIB_TESTDATA_PATH,
tileshape=(1, 3, 256, 256),
scan_size=scan_size)
ds = ds.initialize()
ds.check_valid()
for p in ds.get_partitions():
for t in p.get_tiles():
pass
def test_too_many_frames(lt_ctx):
"""
mib files can contain more frames than the intended scanning dimensions
"""
# one full row of additional frames in the file
scan_size = (31, 32)
ds = MIBDataSet(path=MIB_TESTDATA_PATH, scan_size=scan_size)
ds = ds.initialize(lt_ctx.executor)
ds.check_valid()
tileshape = Shape((16, ) + tuple(ds.shape.sig), sig_dims=ds.shape.sig.dims)
tiling_scheme = TilingScheme.make_for_shape(
tileshape=tileshape,
dataset_shape=ds.shape,
)
for p in ds.get_partitions():
for t in p.get_tiles(tiling_scheme=tiling_scheme):
pass
def test_missing_frames(lt_ctx):
"""
there can be some frames missing at the end
"""
# one full row of additional frames in the data set than in the file
scan_size = (33, 32)
ds = MIBDataSet(path=MIB_TESTDATA_PATH, scan_size=scan_size)
ds = ds.initialize(lt_ctx.executor)
ds.check_valid()
tileshape = Shape((16, ) + tuple(ds.shape.sig), sig_dims=ds.shape.sig.dims)
tiling_scheme = TilingScheme.make_for_shape(
tileshape=tileshape,
dataset_shape=ds.shape,
)
for p in ds.get_partitions():
for t in p.get_tiles(tiling_scheme=tiling_scheme):
pass