def test_group_on_two():
groups, workspace = make_image_sets(
(
("Plate", ("P-12345", "P-23456")),
("Well", ("A01", "A02", "A03")),
("Site", ("1", "2", "3", "4")),
),
(
(
"DNA",
"Wavelength",
"1",
cellprofiler.pipeline.Pipeline.ImageSetChannelDescriptor.
CT_GRAYSCALE,
),
(
"GFP",
"Wavelength",
"1",
cellprofiler.pipeline.Pipeline.ImageSetChannelDescriptor.
CT_GRAYSCALE,
),
),
)
groups.wants_groups.value = True
groups.grouping_metadata[0].metadata_choice.value = "Plate"
groups.add_grouping_metadata()
groups.grouping_metadata[1].metadata_choice.value = "Site"
assert groups.prepare_run(workspace)
m = workspace.measurements
assert isinstance(m, cellprofiler.measurement.Measurements)
image_numbers = m.get_image_numbers()
pipeline = workspace.pipeline
assert isinstance(pipeline, cellprofiler.pipeline.Pipeline)
key_list, groupings = pipeline.get_groupings(workspace)
assert len(key_list) == 2
assert key_list[0] == "Metadata_Plate"
assert key_list[1] == "Metadata_Site"
assert len(groupings) == 8
idx = 0
for plate in ("P-12345", "P-23456"):
for site in ("1", "2", "3", "4"):
grouping, image_set_list = groupings[idx]
idx += 1
assert grouping["Metadata_Plate"] == plate
assert grouping["Metadata_Site"] == site
assert len(image_set_list) == 3
ftr = "_".join((cellprofiler.measurement.C_FILE_NAME, "DNA"))
for image_number in image_set_list:
file_name = m[cellprofiler.measurement.IMAGE, ftr,
image_number]
p, w, s, rest = file_name.split("_")
assert p == plate
assert s == site
def test_compute_no_groups():
groups, workspace = make_image_sets(
(
("Plate", ("P-12345", "P-23456")),
("Well", ("A01", "A02", "A03")),
("Site", ("1", "2", "3", "4")),
),
(
(
"DNA",
"Wavelength",
"1",
cellprofiler.pipeline.Pipeline.ImageSetChannelDescriptor.CT_GRAYSCALE,
),
(
"GFP",
"Wavelength",
"1",
cellprofiler.pipeline.Pipeline.ImageSetChannelDescriptor.CT_GRAYSCALE,
),
),
)
groups = cellprofiler.modules.groups.Groups()
groups.wants_groups.value = False
m = workspace.measurements
assert isinstance(m, cellprofiler.measurement.Measurements)
image_numbers = m.get_image_numbers()
expected_file_names = m[
cellprofiler.measurement.IMAGE,
cellprofiler.measurement.C_FILE_NAME + "_" + "DNA",
image_numbers,
]
assert groups.prepare_run(workspace)
assert len(image_numbers) == 2 * 3 * 4
output_file_names = m[
cellprofiler.measurement.IMAGE,
cellprofiler.measurement.C_FILE_NAME + "_" + "DNA",
image_numbers,
]
assert list(expected_file_names) == list(output_file_names)
def test_group_on_one():
groups = cellprofiler.modules.groups.Groups()
groups, workspace = make_image_sets(
(
("Plate", ("P-12345", "P-23456")),
("Well", ("A01", "A02", "A03")),
("Site", ("1", "2", "3", "4")),
),
(
(
"DNA",
"Wavelength",
"1",
cellprofiler.pipeline.Pipeline.ImageSetChannelDescriptor.CT_GRAYSCALE,
),
(
"GFP",
"Wavelength",
"1",
cellprofiler.pipeline.Pipeline.ImageSetChannelDescriptor.CT_GRAYSCALE,
),
),
)
groups.wants_groups.value = True
groups.grouping_metadata[0].metadata_choice.value = "Plate"
groups.prepare_run(workspace)
m = workspace.measurements
assert isinstance(m, cellprofiler.measurement.Measurements)
image_numbers = m.get_image_numbers()
assert len(image_numbers) == 24
numpy.testing.assert_array_equal(
numpy.hstack([numpy.ones(12, int), numpy.ones(12, int) * 2]),
m[
cellprofiler.measurement.IMAGE,
cellprofiler.measurement.GROUP_NUMBER,
image_numbers,
],
)
numpy.testing.assert_array_equal(
numpy.hstack([numpy.arange(1, 13)] * 2),
m[
cellprofiler.measurement.IMAGE,
cellprofiler.measurement.GROUP_INDEX,
image_numbers,
],
)
pipeline = workspace.pipeline
assert isinstance(pipeline, cellprofiler.pipeline.Pipeline)
key_list, groupings = pipeline.get_groupings(workspace)
assert len(key_list) == 1
assert key_list[0] == "Metadata_Plate"
assert len(groupings) == 2
for group_number, plate, (grouping, image_set_list) in zip(
(1, 2), ("P-12345", "P-23456"), groupings
):
assert grouping == dict(Metadata_Plate=plate)
assert len(image_set_list) == 3 * 4
assert list(image_set_list) == list(
range((group_number - 1) * 12 + 1, group_number * 12 + 1)
)
for image_number in range(1 + (group_number - 1) * 12, 1 + group_number * 12):
for image_name in ("DNA", "GFP"):
ftr = "_".join((cellprofiler.measurement.C_FILE_NAME, image_name))
assert m[cellprofiler.measurement.IMAGE, ftr, image_number].startswith(
plate
)