def it_converts_to_power_of_2():
with zest.mock(worker._convert_message):
nd2 = _make_nd2(63)
m_nd2.returns(nd2)
result = worker.ims_import(src_path, ims_import_params)
assert result.field_chcy_ims(0).shape == (n_channels, n_cycles,
64, 64)
def it_scatter_gathers():
result = worker.ims_import(src_path, ims_import_params)
emitted_files = list(local.path(".").walk())
assert len(emitted_files) == 9
assert result.params == ims_import_params
assert result.n_fields == n_fields
assert result.n_channels == n_channels
assert result.n_cycles == n_cycles
def it_swaps_fields_cycles():
result = worker.ims_import(src_path, ims_import_params)
assert result.n_cycles == n_fields
assert result.n_fields == n_cycles
assert result.n_channels == n_channels
for cy in range(result.n_cycles):
assert np.all(
result.field_chcy_ims(0)[:, cy, :, :] == float(cy))
def it_respects_channel_map():
ims_import_params.dst_ch_i_to_src_ch_i = [1, 0]
result = worker.ims_import(src_path, ims_import_params)
assert result.n_fields == n_fields
assert result.n_cycles == n_cycles
assert result.n_channels == 2
assert np.all(result.field_chcy_ims(0)[0, :, :, :] == float(1))
assert np.all(result.field_chcy_ims(0)[1, :, :, :] == float(0))
def it_can_skip_cycles():
ims_import_params.start_cycle = 1
result = worker.ims_import(src_path, ims_import_params)
assert result.n_cycles == n_fields - 1
assert result.n_fields == n_cycles
assert result.n_channels == n_channels
for cy in range(result.n_cycles):
assert np.all(
result.field_chcy_ims(0)[:, cy, :, :] == float(cy + 1))
def start(self):
ims_import_params = ImsImportParams(**self.config.parameters)
ims_import_result = ims_import(
self.inputs.src_dir,
ims_import_params,
progress=self.progress,
pipeline=self,
)
ims_import_result.save()
def it_converts_to_power_of_2():
with zest.mock(worker._convert_message):
m_nd2.hook_to_call = lambda _: _make_nd2(
63, "cycle", n_fields)
result = worker.ims_import(src_path, ims_import_params)
assert result.field_chcy_ims(0).shape == (
n_channels,
n_fields,
64,
64,
)
def it_respects_channel_map():
nonlocal ims_import_params, nd2
ims_import_params = ImsImportParams(is_movie=True)
m_nd2.hook_to_call = lambda _: _make_nd2(64) # Channel mode
m_scan_nd2_files.returns(cycle_files)
m_scan_tif_files.returns([])
ims_import_params.dst_ch_i_to_src_ch_i = [1, 0]
result = worker.ims_import(src_path, ims_import_params)
assert result.n_cycles == n_fields
assert result.n_fields == n_cycles
assert result.n_channels == 2
assert np.all(result.field_chcy_ims(0)[0, :, :, :] == float(1))
assert np.all(result.field_chcy_ims(0)[1, :, :, :] == float(0))
def it_ims_import_npy():
res = worker.ims_import(".",
ims_import_params,
progress=None,
pipeline=None)
assert res.n_fields == 2 and res.n_channels == 2 and res.n_cycles == 3
def it_can_skip_cycles():
ims_import_params.start_cycle = 1
result = worker.ims_import(src_path, ims_import_params)
assert result.n_fields == n_fields
assert result.n_cycles == n_cycles - 1
assert result.n_channels == n_channels
def it_can_skip_fields():
ims_import_params.start_field = 1
result = worker.ims_import(src_path, ims_import_params)
assert result.n_fields == 2
def it_imports_src_channels():
result = worker.ims_import(src_path, ims_import_params)
assert np.all(result.field_chcy_ims(0)[0, :, :, :] == 0.0)
assert np.all(result.field_chcy_ims(0)[1, :, :, :] == 1.0)
def it_limits_fields():
ims_import_params.n_fields_limit = 1
result = worker.ims_import(src_path, ims_import_params)
assert result.n_fields == 1
