def make_workspace(self, object_dict={}, image_dict={}):
'''Make a workspace for testing MeasureImageIntensity'''
module = M.MeasureImageIntensity()
pipeline = cpp.Pipeline()
object_set = cpo.ObjectSet()
image_set_list = cpi.ImageSetList()
image_set = image_set_list.get_image_set(0)
workspace = cpw.Workspace(pipeline, module, image_set, object_set,
cpmeas.Measurements(), image_set_list)
for key in image_dict.keys():
image_set.add(key, cpi.Image(image_dict[key]))
for key in object_dict.keys():
o = cpo.Objects()
o.segmented = object_dict[key]
object_set.add_objects(o, key)
return workspace, module
def test_03_01_get_measurement_columns(self):
module = M.MeasureImageIntensity()
image_names = ['image%d' % i for i in range(3)]
object_names = ['object%d' % i for i in range(3)]
first = True
expected_suffixes = []
for image_name in image_names:
if first:
first = False
else:
module.add_image_measurement()
im = module.images[-1]
im.image_name.value = image_name
im.wants_objects.value = False
expected_suffixes.append(image_name)
for object_name in object_names:
module.add_image_measurement()
im = module.images[-1]
im.image_name.value = image_name
im.wants_objects.value = True
im.object_name.value = object_name
expected_suffixes.append("%s_%s" % (image_name, object_name))
columns = module.get_measurement_columns(None)
self.assertTrue(all([column[0] == cpmeas.IMAGE for column in columns]))
for expected_suffix in expected_suffixes:
for feature, coltype in ((M.F_TOTAL_INTENSITY,
cpmeas.COLTYPE_FLOAT),
(M.F_MEAN_INTENSITY,
cpmeas.COLTYPE_FLOAT),
(M.F_MIN_INTENSITY, cpmeas.COLTYPE_FLOAT),
(M.F_MAX_INTENSITY, cpmeas.COLTYPE_FLOAT),
(M.F_TOTAL_AREA, cpmeas.COLTYPE_INTEGER),
(M.F_PERCENT_MAXIMAL,
cpmeas.COLTYPE_FLOAT),
(M.F_MAD_INTENSITY, cpmeas.COLTYPE_FLOAT),
(M.F_LOWER_QUARTILE,
cpmeas.COLTYPE_FLOAT),
(M.F_UPPER_QUARTILE,
cpmeas.COLTYPE_FLOAT)):
# feature names are now formatting strings
feature_name = feature % expected_suffix
self.assertTrue(
any([(column[1] == feature_name and column[2] == coltype)
for column in columns]))
