def test_01_01_combine():
img = get_my_image()
inj = cellprofiler.modules.injectimage.InjectImage("my_image", img)
inj.module_num = 1
ctg = cellprofiler.modules.colortogray.ColorToGray()
ctg.module_num = 2
ctg.image_name.value = "my_image"
ctg.combine_or_split.value = cellprofiler.modules.colortogray.COMBINE
ctg.red_contribution.value = 1
ctg.green_contribution.value = 2
ctg.blue_contribution.value = 3
ctg.grayscale_name.value = "my_grayscale"
pipeline = cellprofiler.pipeline.Pipeline()
pipeline.add_module(inj)
pipeline.add_module(ctg)
pipeline.test_valid()
measurements = cellprofiler.measurement.Measurements()
object_set = cellprofiler.object.ObjectSet()
image_set_list = cellprofiler.image.ImageSetList()
workspace = Workspace(pipeline, inj, None, None, measurements,
image_set_list, None)
inj.prepare_run(workspace)
inj.prepare_group(workspace, {}, [1])
image_set = image_set_list.get_image_set(0)
inj.run(Workspace(pipeline, inj, image_set, object_set, measurements, None))
ctg.run(Workspace(pipeline, ctg, image_set, object_set, measurements, None))
grayscale = image_set.get_image("my_grayscale")
assert grayscale
img = grayscale.image
numpy.testing.assert_almost_equal(img[0, 0], 1.0 / 6.0)
numpy.testing.assert_almost_equal(img[0, 25], 1.0 / 3.0)
numpy.testing.assert_almost_equal(img[25, 0], 1.0 / 2.0)
numpy.testing.assert_almost_equal(img[25, 25], 0)
def test_split_all():
img = get_my_image()
inj = cellprofiler.modules.injectimage.InjectImage("my_image", img)
inj.set_module_num(1)
ctg = cellprofiler.modules.colortogray.ColorToGray()
ctg.set_module_num(2)
ctg.image_name.value = "my_image"
ctg.combine_or_split.value = cellprofiler.modules.colortogray.SPLIT
ctg.use_red.value = True
ctg.use_blue.value = True
ctg.use_green.value = True
ctg.red_name.value = "my_red"
ctg.green_name.value = "my_green"
ctg.blue_name.value = "my_blue"
pipeline = cellprofiler.pipeline.Pipeline()
pipeline.add_module(inj)
pipeline.add_module(ctg)
pipeline.test_valid()
measurements = cellprofiler.measurement.Measurements()
object_set = cellprofiler.object.ObjectSet()
image_set_list = cellprofiler.image.ImageSetList()
workspace = cellprofiler.workspace.Workspace(
pipeline, inj, None, None, measurements, image_set_list, None
)
inj.prepare_run(workspace)
inj.prepare_group(workspace, {}, [1])
image_set = image_set_list.get_image_set(0)
inj.run(
cellprofiler.workspace.Workspace(
pipeline, inj, image_set, object_set, measurements, None
)
)
ctg.run(
cellprofiler.workspace.Workspace(
pipeline, ctg, image_set, object_set, measurements, None
)
)
red = image_set.get_image("my_red")
assert red
img = red.image
numpy.testing.assert_almost_equal(img[0, 0], 1)
numpy.testing.assert_almost_equal(img[0, 25], 0)
numpy.testing.assert_almost_equal(img[25, 0], 0)
numpy.testing.assert_almost_equal(img[25, 25], 0)
green = image_set.get_image("my_green")
assert green
img = green.image
numpy.testing.assert_almost_equal(img[0, 0], 0)
numpy.testing.assert_almost_equal(img[0, 25], 1)
numpy.testing.assert_almost_equal(img[25, 0], 0)
numpy.testing.assert_almost_equal(img[25, 25], 0)
blue = image_set.get_image("my_blue")
assert blue
img = blue.image
numpy.testing.assert_almost_equal(img[0, 0], 0)
numpy.testing.assert_almost_equal(img[0, 25], 0)
numpy.testing.assert_almost_equal(img[25, 0], 1)
numpy.testing.assert_almost_equal(img[25, 25], 0)
def test_01_02_split_all():
img = get_my_image()
inj = cellprofiler.modules.injectimage.InjectImage("my_image", img)
inj.module_num = 1
ctg = cellprofiler.modules.colortogray.ColorToGray()
ctg.module_num = 2
ctg.image_name.value = "my_image"
ctg.combine_or_split.value = cellprofiler.modules.colortogray.SPLIT
ctg.use_red.value = True
ctg.use_blue.value = True
ctg.use_green.value = True
ctg.red_name.value = "my_red"
ctg.green_name.value = "my_green"
ctg.blue_name.value = "my_blue"
pipeline = cellprofiler.pipeline.Pipeline()
pipeline.add_module(inj)
pipeline.add_module(ctg)
pipeline.test_valid()
measurements = cellprofiler.measurement.Measurements()
object_set = cellprofiler.object.ObjectSet()
image_set_list = cellprofiler.image.ImageSetList()
workspace = Workspace(pipeline, inj, None, None, measurements,
image_set_list, None)
inj.prepare_run(workspace)
inj.prepare_group(workspace, {}, [1])
image_set = image_set_list.get_image_set(0)
inj.run(Workspace(pipeline, inj, image_set, object_set, measurements, None))
ctg.run(Workspace(pipeline, ctg, image_set, object_set, measurements, None))
red = image_set.get_image("my_red")
assert red
img = red.image
numpy.testing.assert_almost_equal(img[0, 0], 1)
numpy.testing.assert_almost_equal(img[0, 25], 0)
numpy.testing.assert_almost_equal(img[25, 0], 0)
numpy.testing.assert_almost_equal(img[25, 25], 0)
green = image_set.get_image("my_green")
assert green
img = green.image
numpy.testing.assert_almost_equal(img[0, 0], 0)
numpy.testing.assert_almost_equal(img[0, 25], 1)
numpy.testing.assert_almost_equal(img[25, 0], 0)
numpy.testing.assert_almost_equal(img[25, 25], 0)
blue = image_set.get_image("my_blue")
assert blue
img = blue.image
numpy.testing.assert_almost_equal(img[0, 0], 0)
numpy.testing.assert_almost_equal(img[0, 25], 0)
numpy.testing.assert_almost_equal(img[25, 0], 1)
numpy.testing.assert_almost_equal(img[25, 25], 0)
def test_combine():
img = get_my_image()
inj = cellprofiler.modules.injectimage.InjectImage("my_image", img)
inj.set_module_num(1)
ctg = cellprofiler.modules.colortogray.ColorToGray()
ctg.set_module_num(2)
ctg.image_name.value = "my_image"
ctg.combine_or_split.value = cellprofiler.modules.colortogray.COMBINE
ctg.red_contribution.value = 1
ctg.green_contribution.value = 2
ctg.blue_contribution.value = 3
ctg.grayscale_name.value = "my_grayscale"
pipeline = cellprofiler.pipeline.Pipeline()
pipeline.add_module(inj)
pipeline.add_module(ctg)
pipeline.test_valid()
measurements = cellprofiler.measurement.Measurements()
object_set = cellprofiler.object.ObjectSet()
image_set_list = cellprofiler.image.ImageSetList()
workspace = cellprofiler.workspace.Workspace(
pipeline, inj, None, None, measurements, image_set_list, None
)
inj.prepare_run(workspace)
inj.prepare_group(workspace, {}, [1])
image_set = image_set_list.get_image_set(0)
inj.run(
cellprofiler.workspace.Workspace(
pipeline, inj, image_set, object_set, measurements, None
)
)
ctg.run(
cellprofiler.workspace.Workspace(
pipeline, ctg, image_set, object_set, measurements, None
)
)
grayscale = image_set.get_image("my_grayscale")
assert grayscale
img = grayscale.image
numpy.testing.assert_almost_equal(img[0, 0], 1.0 / 6.0)
numpy.testing.assert_almost_equal(img[0, 25], 1.0 / 3.0)
numpy.testing.assert_almost_equal(img[25, 0], 1.0 / 2.0)
numpy.testing.assert_almost_equal(img[25, 25], 0)
def test_module_must_be_last():
"""Make sure that the pipeline is invalid if CreateBatchFiles is not last"""
#
# First, make sure that a naked CPModule tests valid
#
pipeline = cellprofiler.pipeline.Pipeline()
module = cellprofiler.module.Module()
module.set_module_num(len(pipeline.modules()) + 1)
pipeline.add_module(module)
pipeline.test_valid()
#
# Make sure that CreateBatchFiles on its own tests valid
#
pipeline = cellprofiler.pipeline.Pipeline()
module = cellprofiler.modules.createbatchfiles.CreateBatchFiles()
module.set_module_num(len(pipeline.modules()) + 1)
pipeline.add_module(module)
pipeline.test_valid()
module = cellprofiler.module.Module()
module.set_module_num(len(pipeline.modules()) + 1)
pipeline.add_module(module)
with pytest.raises(cellprofiler.setting.ValidationError):
pipeline.test_valid()