def default_mib():
scan_size = (32, 32)
ds = MIBDataSet(path=MIB_TESTDATA_PATH,
tileshape=(1, 3, 256, 256),
scan_size=scan_size)
ds = ds.initialize()
return ds
def test_mib_dist(dist_ctx):
scan_size = (32, 32)
ds = MIBDataSet(path=MIB_TESTDATA_PATH, scan_size=scan_size)
ds = ds.initialize(dist_ctx.executor)
analysis = dist_ctx.create_sum_analysis(dataset=ds)
results = dist_ctx.run(analysis)
assert results[0].raw_data.shape == (256, 256)
def test_mib_dist(dist_ctx):
scan_size = (32, 32)
ds = MIBDataSet(path="/data/default.mib",
tileshape=(1, 3, 256, 256),
scan_size=scan_size)
ds = ds.initialize(dist_ctx.executor)
analysis = dist_ctx.create_sum_analysis(dataset=ds)
results = dist_ctx.run(analysis)
assert results[0].raw_data.shape == (256, 256)
def test_not_too_many_files(lt_ctx):
ds = MIBDataSet(path=MIB_TESTDATA_PATH, scan_size=(32, 32))
with mock.patch(
'libertem.io.dataset.mib.glob',
side_effect=lambda p: ["/a/%d.mib" % i for i in range(256)]):
with pytest.warns(None) as record:
ds._filenames()
assert len(record) == 0
def test_too_many_files(lt_ctx):
ds = MIBDataSet(path=MIB_TESTDATA_PATH, scan_size=(32, 32))
with mock.patch(
'libertem.io.dataset.mib.glob',
side_effect=lambda p: ["/a/%d.mib" % i for i in range(256 * 256)]):
with pytest.warns(RuntimeWarning) as record:
ds._filenames()
assert len(record) == 1
assert "Saving data in many small files" in record[0].message.args[0]
def test_read_at_boundaries(default_mib, lt_ctx):
scan_size = (32, 32)
ds_odd = MIBDataSet(path=MIB_TESTDATA_PATH, scan_size=scan_size)
ds_odd = ds_odd.initialize(lt_ctx.executor)
sumjob_odd = lt_ctx.create_sum_analysis(dataset=ds_odd)
res_odd = lt_ctx.run(sumjob_odd)
sumjob = lt_ctx.create_sum_analysis(dataset=default_mib)
res = lt_ctx.run(sumjob)
assert np.allclose(res[0].raw_data, res_odd[0].raw_data)
def test_detect(lt_ctx):
params = MIBDataSet.detect_params(MIB_TESTDATA_PATH, lt_ctx.executor)["parameters"]
assert params == {
"path": MIB_TESTDATA_PATH,
"nav_shape": (1024,),
"sig_shape": (256, 256)
}
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
def open(self):
ds = MIBDataSet(path=self._path, nav_shape=self._nav_shape)
ds.initialize(MITExecutor())
print("dataset shape: %s" % (ds.shape, ))
self._ds = ds
self._warmup()
def test_detect(lt_ctx):
params = MIBDataSet.detect_params(MIB_TESTDATA_PATH,
lt_ctx.executor)["parameters"]
assert params == {
"path": MIB_TESTDATA_PATH,
}
def default_mib(lt_ctx):
scan_size = (32, 32)
ds = MIBDataSet(path=MIB_TESTDATA_PATH, scan_size=scan_size)
ds = ds.initialize(lt_ctx.executor)
return ds
def test_detect():
params = MIBDataSet.detect_params(MIB_TESTDATA_PATH)
assert params == {"path": MIB_TESTDATA_PATH, "tileshape": (1, 3, 256, 256)}
def test_detect(lt_ctx):
params = MIBDataSet.detect_params(MIB_TESTDATA_PATH, lt_ctx.executor)
assert params == {"path": MIB_TESTDATA_PATH, "tileshape": (1, 3, 256, 256)}
