def test_06_01_get_measurement_columns(self):
module = F.FlagImage()
module.add_flag()
module.flags[0].category.value = 'Foo'
module.flags[0].feature_name.value = 'Bar'
module.flags[1].category.value = 'Hello'
module.flags[1].feature_name.value = 'World'
columns = module.get_measurement_columns(None)
self.assertEqual(len(columns), 2)
self.assertTrue(all([column[0] == cpmeas.IMAGE and
column[1] in ("Foo_Bar", "Hello_World") and
column[2] == cpmeas.COLTYPE_INTEGER
for column in columns]))
self.assertNotEqual(columns[0][1], columns[1][1])
categories = module.get_categories(None, 'foo')
self.assertEqual(len(categories), 0)
categories = module.get_categories(None, cpmeas.IMAGE)
self.assertEqual(len(categories), 2)
self.assertTrue('Foo' in categories)
self.assertTrue('Hello' in categories)
self.assertEqual(len(module.get_measurements(None, cpmeas.IMAGE, 'Whatever')), 0)
for category, feature in (('Foo', 'Bar'), ('Hello', 'World')):
features = module.get_measurements(None, cpmeas.IMAGE, category)
self.assertEqual(len(features), 1)
self.assertEqual(features[0], feature)
def test_09_01_batch(self):
orig_path = '/foo/bar'
def fn_alter_path(path, **varargs):
self.assertEqual(path, orig_path)
return '/imaging/analysis'
module = F.FlagImage()
rd = module.flags[0].measurement_settings[0].rules_directory
rd.dir_choice = cps.ABSOLUTE_FOLDER_NAME
rd.custom_path = orig_path
module.prepare_to_create_batch(None, fn_alter_path)
self.assertEqual(rd.custom_path, '/imaging/analysis')
def make_workspace(self, image_measurements, object_measurements):
"""Make a workspace with a FlagImage module and the given measurements
image_measurements - a sequence of single image measurements. Use
image_measurement_name(i) to get the name of
the i th measurement
object_measurements - a seequence of sequences of object measurements.
These are stored under object, OBJECT_NAME with
measurement name object_measurement_name(i) for
the i th measurement.
returns module, workspace
"""
module = F.FlagImage()
measurements = cpmeas.Measurements()
for i in range(len(image_measurements)):
measurements.add_image_measurement(image_measurement_name(i),
image_measurements[i])
for i in range(len(object_measurements)):
measurements.add_measurement(
OBJECT_NAME,
object_measurement_name(i),
np.array(object_measurements[i]),
)
flag = module.flags[0]
self.assertTrue(isinstance(flag, cps.SettingsGroup))
flag.category.value = MEASUREMENT_CATEGORY
flag.feature_name.value = MEASUREMENT_FEATURE
module.module_num = 1
pipeline = cpp.Pipeline()
def callback(caller, event):
self.assertFalse(isinstance(event, cpp.RunExceptionEvent))
pipeline.add_listener(callback)
pipeline.add_module(module)
image_set_list = cpi.ImageSetList()
image_set = image_set_list.get_image_set(0)
workspace = cpw.Workspace(pipeline, module, image_set, cpo.ObjectSet(),
measurements, image_set_list)
return module, workspace