def test_07_01_get_measurement_columns(self):
'''Test the get_measurement_columns method'''
colnames = ('Integer_Measurement', 'Float_Measurement',
'String_Measurement')
coltypes = [
cellprofiler.measurement.COLTYPE_INTEGER,
cellprofiler.measurement.COLTYPE_FLOAT,
cellprofiler.measurement.COLTYPE_VARCHAR_FORMAT % 9
]
csv_text = '''"%s","%s","%s"
1,1,1
2,1.5,"Hi"
3,1,"Hello"
4,1.7,"Hola"
5,1.2,"Bonjour"
6,1.5,"Gutentag"
7,1.1,"Hej"
8,2.3,"Bevakasha"
''' % colnames
pipeline, module, filename = self.make_pipeline(csv_text)
columns = module.get_measurement_columns(pipeline)
for colname, coltype in zip(colnames, coltypes):
self.assertTrue(
any([(column[0] == cellprofiler.measurement.IMAGE
and column[1] == colname and column[2] == coltype)
for column in columns]), 'Failed to find %s' % colname)
os.remove(filename)
def test_03_03_metadata_row_and_column_and_well(self):
csv_text = '''"Metadata_Row","Metadata_Column","Metadata_Well"
"C","03","B14"
'''
pipeline, module, filename = self.make_pipeline(csv_text)
columns = module.get_measurement_columns(pipeline)
self.assertTrue(
any([
c[0] == cellprofiler.measurement.IMAGE
and c[1] == "Metadata_Row" and c[2] == "varchar(1)"
for c in columns
]))
self.assertTrue(
any([
c[0] == cellprofiler.measurement.IMAGE
and c[1] == "Metadata_Column" and c[2] == "varchar(2)"
for c in columns
]))
self.assertTrue(
any([
c[0] == cellprofiler.measurement.IMAGE
and c[1] == "Metadata_Well" and c[2] == "varchar(3)"
for c in columns
]))
m = pipeline.run()
features = module.get_measurements(pipeline,
cellprofiler.measurement.IMAGE,
cellprofiler.measurement.C_METADATA)
for feature, expected in (("Row", "C"), ("Column", "03"), ("Well",
"B14")):
self.assertTrue(feature in features)
value = m.get_current_image_measurement('_'.join(
(cellprofiler.measurement.C_METADATA, feature)))
self.assertEqual(value, expected)
def test_get_measurement_columns(self):
module = cellprofiler.module.ObjectProcessing()
module.x_name.value = "Objects"
actual = module.get_measurement_columns(None)
expected = [
("ObjectProcessing", cellprofiler.measurement.M_LOCATION_CENTER_X,
cellprofiler.measurement.COLTYPE_FLOAT),
("ObjectProcessing", cellprofiler.measurement.M_LOCATION_CENTER_Y,
cellprofiler.measurement.COLTYPE_FLOAT),
("ObjectProcessing", cellprofiler.measurement.M_LOCATION_CENTER_Z,
cellprofiler.measurement.COLTYPE_FLOAT),
("ObjectProcessing",
cellprofiler.measurement.M_NUMBER_OBJECT_NUMBER,
cellprofiler.measurement.COLTYPE_INTEGER),
(cellprofiler.measurement.IMAGE,
cellprofiler.measurement.FF_COUNT % "ObjectProcessing",
cellprofiler.measurement.COLTYPE_INTEGER),
("Objects",
cellprofiler.measurement.FF_CHILDREN_COUNT % "ObjectProcessing",
cellprofiler.measurement.COLTYPE_INTEGER),
("ObjectProcessing",
cellprofiler.measurement.FF_PARENT % "Objects",
cellprofiler.measurement.COLTYPE_INTEGER)
]
assert actual == expected
def test_get_measurement_columns():
"""Test the get_measurement_columns method"""
colnames = ("Integer_Measurement", "Float_Measurement",
"String_Measurement")
coltypes = [
cellprofiler.measurement.COLTYPE_INTEGER,
cellprofiler.measurement.COLTYPE_FLOAT,
cellprofiler.measurement.COLTYPE_VARCHAR_FORMAT % 9,
]
csv_text = (""""%s","%s","%s"
1,1,1
2,1.5,"Hi"
3,1,"Hello"
4,1.7,"Hola"
5,1.2,"Bonjour"
6,1.5,"Gutentag"
7,1.1,"Hej"
8,2.3,"Bevakasha"
""" % colnames)
pipeline, module, filename = make_pipeline(csv_text)
columns = module.get_measurement_columns(pipeline)
for colname, coltype in zip(colnames, coltypes):
assert any([(column[0] == cellprofiler.measurement.IMAGE
and column[1] == colname and column[2] == coltype)
for column in columns]), ("Failed to find %s" % colname)
os.remove(filename)
def test_04_01_get_measurement_columns(self):
workspace, module = self.make_workspace(
dict(image=numpy.zeros((20, 10), bool)),
dict(image=numpy.zeros((20, 10), bool)),
)
assert isinstance(
module,
cellprofiler.modules.measureimageoverlap.MeasureImageOverlap)
name = TEST_IMAGE_NAME
columns = module.get_measurement_columns(workspace.pipeline)
# All columns should be unique
self.assertEqual(len(columns), len(set([x[1] for x in columns])))
# All columns should be floats and done on images
x = columns[-1]
self.assertTrue(all([x[0] == cellprofiler.measurement.IMAGE]))
self.assertTrue(all([x[2] == cellprofiler.measurement.COLTYPE_FLOAT]))
for feature in cellprofiler.modules.measureimageoverlap.FTR_ALL:
field = "_".join((
cellprofiler.modules.measureimageoverlap.C_IMAGE_OVERLAP,
feature,
name,
))
self.assertTrue(field in [x[1] for x in columns])
def test_metadata_row_and_column_and_well():
csv_text = """"Metadata_Row","Metadata_Column","Metadata_Well"
"C","03","B14"
"""
pipeline, module, filename = make_pipeline(csv_text)
columns = module.get_measurement_columns(pipeline)
assert any([
c[0] == cellprofiler.measurement.IMAGE and c[1] == "Metadata_Row"
and c[2] == "varchar(1)" for c in columns
])
assert any([
c[0] == cellprofiler.measurement.IMAGE and c[1] == "Metadata_Column"
and c[2] == "varchar(2)" for c in columns
])
assert any([
c[0] == cellprofiler.measurement.IMAGE and c[1] == "Metadata_Well"
and c[2] == "varchar(3)" for c in columns
])
m = pipeline.run()
features = module.get_measurements(pipeline,
cellprofiler.measurement.IMAGE,
cellprofiler.measurement.C_METADATA)
for feature, expected in (("Row", "C"), ("Column", "03"), ("Well", "B14")):
assert feature in features
value = m.get_current_image_measurement("_".join(
(cellprofiler.measurement.C_METADATA, feature)))
assert value == expected
def test_07_03_long_integer_column(self):
'''This is a regression test of IMG-644 where a 13-digit number got turned into an int'''
colnames = ('Long_Integer_Measurement', 'Float_Measurement', 'String_Measurement')
coltypes = [cellprofiler.measurement.COLTYPE_VARCHAR_FORMAT % 13, cellprofiler.measurement.COLTYPE_FLOAT,
cellprofiler.measurement.COLTYPE_VARCHAR_FORMAT % 9]
csv_text = '''"%s","%s","%s"
1,1,1
2,1.5,"Hi"
3,1,"Hello"
4,1.7,"Hola"
5,1.2,"Bonjour"
6,1.5,"Gutentag"
7,1.1,"Hej"
1234567890123,2.3,"Bevakasha"
''' % colnames
pipeline, module, filename = self.make_pipeline(csv_text)
columns = module.get_measurement_columns(pipeline)
fmt = "%15s %30s %20s"
print(fmt % ("Object", "Feature", "Type"))
for object_name, feature, coltype in columns:
print(fmt % (object_name, feature, coltype))
for colname, coltype in zip(colnames, coltypes):
self.assertTrue(any([(column[0] == cellprofiler.measurement.IMAGE and
column[1] == colname and
column[2] == coltype) for column in columns]),
'Failed to find %s' % colname)
os.remove(filename)
def test_07_03_long_integer_column(self):
'''This is a regression test of IMG-644 where a 13-digit number got turned into an int'''
colnames = ('Long_Integer_Measurement', 'Float_Measurement',
'String_Measurement')
coltypes = [
cellprofiler.measurement.COLTYPE_VARCHAR_FORMAT % 13,
cellprofiler.measurement.COLTYPE_FLOAT,
cellprofiler.measurement.COLTYPE_VARCHAR_FORMAT % 9
]
csv_text = '''"%s","%s","%s"
1,1,1
2,1.5,"Hi"
3,1,"Hello"
4,1.7,"Hola"
5,1.2,"Bonjour"
6,1.5,"Gutentag"
7,1.1,"Hej"
1234567890123,2.3,"Bevakasha"
''' % colnames
pipeline, module, filename = self.make_pipeline(csv_text)
columns = module.get_measurement_columns(pipeline)
fmt = "%15s %30s %20s"
print(fmt % ("Object", "Feature", "Type"))
for object_name, feature, coltype in columns:
print(fmt % (object_name, feature, coltype))
for colname, coltype in zip(colnames, coltypes):
self.assertTrue(
any([(column[0] == cellprofiler.measurement.IMAGE
and column[1] == colname and column[2] == coltype)
for column in columns]), 'Failed to find %s' % colname)
os.remove(filename)
def test_01_03_image_and_objects(image, measurements, module, objects,
workspace):
"""Test operation on an image masked by objects"""
numpy.random.seed(0)
pixels = numpy.random.uniform(size=(10, 10)).astype(numpy.float32) * 0.99
pixels[1:3, 1:3] = 1
image.pixel_data = pixels
labels = numpy.zeros((10, 10), int)
labels[1:9, 1:5] = 1
labels[1:9, 5:9] = 2
objects.segmented = labels
module.images[0].wants_objects.value = True
module.run(workspace)
assert (measurements.get_current_measurement(
cellprofiler.measurement.IMAGE,
"Intensity_TotalArea_image_objects") == 64)
assert measurements.get_current_measurement(
cellprofiler.measurement.IMAGE,
"Intensity_TotalIntensity_image_objects") == numpy.sum(pixels[1:9,
1:9])
assert (measurements.get_current_measurement(
cellprofiler.measurement.IMAGE,
"Intensity_MeanIntensity_image_objects") == numpy.sum(pixels[1:9, 1:9])
/ 64.0)
numpy.testing.assert_almost_equal(
measurements.get_current_measurement(
cellprofiler.measurement.IMAGE,
"Intensity_PercentMaximal_image_objects"),
400.0 / 64.0,
)
assert len(measurements.get_object_names()) == 1
assert measurements.get_object_names()[0] == cellprofiler.measurement.IMAGE
columns = module.get_measurement_columns(workspace.pipeline)
features = measurements.get_feature_names(cellprofiler.measurement.IMAGE)
assert len(columns) == len(features)
for column in columns:
assert column[1] in features
def test_03_01_get_measurement_columns(module):
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)
assert all([column[0] == cellprofiler.measurement.IMAGE for column in columns])
for expected_suffix in expected_suffixes:
for feature, coltype in (
(cellprofiler.modules.measureimageintensity.F_TOTAL_INTENSITY, cellprofiler.measurement.COLTYPE_FLOAT),
(cellprofiler.modules.measureimageintensity.F_MEAN_INTENSITY, cellprofiler.measurement.COLTYPE_FLOAT),
(cellprofiler.modules.measureimageintensity.F_MIN_INTENSITY, cellprofiler.measurement.COLTYPE_FLOAT),
(cellprofiler.modules.measureimageintensity.F_MAX_INTENSITY, cellprofiler.measurement.COLTYPE_FLOAT),
(cellprofiler.modules.measureimageintensity.F_TOTAL_AREA, cellprofiler.measurement.COLTYPE_INTEGER),
(cellprofiler.modules.measureimageintensity.F_PERCENT_MAXIMAL, cellprofiler.measurement.COLTYPE_FLOAT),
(cellprofiler.modules.measureimageintensity.F_MAD_INTENSITY, cellprofiler.measurement.COLTYPE_FLOAT),
(cellprofiler.modules.measureimageintensity.F_LOWER_QUARTILE, cellprofiler.measurement.COLTYPE_FLOAT),
(cellprofiler.modules.measureimageintensity.F_UPPER_QUARTILE, cellprofiler.measurement.COLTYPE_FLOAT)):
# feature names are now formatting strings
feature_name = feature % expected_suffix
assert any([(column[1] == feature_name and column[2] == coltype) for column in columns])
def test_02_get_zernike_columns():
module = (cellprofiler.modules.measureobjectintensitydistribution.
MeasureObjectIntensityDistribution())
for wants_zernikes, ftrs in (
(
cellprofiler.modules.measureobjectintensitydistribution.
Z_MAGNITUDES,
(cellprofiler.modules.measureobjectintensitydistribution.
FF_ZERNIKE_MAGNITUDE, ),
),
(
cellprofiler.modules.measureobjectintensitydistribution.
Z_MAGNITUDES_AND_PHASE,
(
cellprofiler.modules.measureobjectintensitydistribution.
FF_ZERNIKE_MAGNITUDE,
cellprofiler.modules.measureobjectintensitydistribution.
FF_ZERNIKE_PHASE,
),
),
):
module.wants_zernikes.value = wants_zernikes
module.zernike_degree.value = 2
for i, image_name in ((0, "DNA"), (1, "Cytoplasm"), (2, "Actin")):
if i:
module.add_image()
module.images[i].image_name.value = image_name
for i, object_name, center_name in (
(0, "Nucleii", None),
(1, "Cells", "Nucleii"),
(2, "Cytoplasm", "Nucleii"),
):
if i:
module.add_object()
module.objects[i].object_name.value = object_name
columns = module.get_measurement_columns(None)
for image_name in "DNA", "Cytoplasm", "Actin":
for object_name in "Nucleii", "Cells", "Cytoplasm":
for n, m in ((0, 0), (1, 1), (2, 0), (2, 2)):
for ftr in ftrs:
name = "_".join((
cellprofiler.modules.
measureobjectintensitydistribution.M_CATEGORY,
ftr,
image_name,
str(n),
str(m),
))
col = (
object_name,
name,
cellprofiler.measurement.COLTYPE_FLOAT,
)
assert col in columns
def test_01_get_measurement_columns():
module = (cellprofiler.modules.measureobjectintensitydistribution.
MeasureObjectIntensityDistribution())
for i, image_name in ((0, "DNA"), (1, "Cytoplasm"), (2, "Actin")):
if i:
module.add_image()
module.images[i].image_name.value = image_name
for i, object_name, center_name in (
(0, "Nucleii", None),
(1, "Cells", "Nucleii"),
(2, "Cytoplasm", "Nucleii"),
):
if i:
module.add_object()
module.objects[i].object_name.value = object_name
if center_name is None:
module.objects[i].center_choice.value = (
cellprofiler.modules.measureobjectintensitydistribution.C_SELF)
else:
module.objects[i].center_choice.value = (
cellprofiler.modules.measureobjectintensitydistribution.
C_CENTERS_OF_OTHER)
module.objects[i].center_object_name.value = center_name
for i, bin_count in enumerate((4, 5, 6)):
if i:
module.add_bin_count()
module.bin_counts[i].bin_count.value = bin_count
module.bin_counts[2].wants_scaled.value = False
columns = module.get_measurement_columns(None)
column_dictionary = {}
for object_name, feature, coltype in columns:
key = (object_name, feature)
assert not (key in column_dictionary)
assert coltype == cellprofiler.measurement.COLTYPE_FLOAT
column_dictionary[key] = (object_name, feature, coltype)
for object_name in [x.object_name.value for x in module.objects]:
for image_name in [x.image_name.value for x in module.images]:
for bin_count, wants_scaled in [(x.bin_count.value,
x.wants_scaled.value)
for x in module.bin_counts]:
for bin in range(1, bin_count + (1 if wants_scaled else 2)):
for feature_fn in (
feature_frac_at_d,
feature_mean_frac,
feature_radial_cv,
):
measurement = feature_fn(bin, bin_count, image_name)
key = (object_name, measurement)
assert key in column_dictionary
del column_dictionary[key]
assert len(column_dictionary) == 0
def test_07_04_objects_measurement_columns(self):
csv_text = """%s_%s,%s_%s
Channel1-01-A-01.tif,/imaging/analysis/trunk/ExampleImages/ExampleSBSImages
""" % (
cellprofiler.measurement.C_OBJECTS_FILE_NAME,
OBJECTS_NAME,
cellprofiler.measurement.C_OBJECTS_PATH_NAME,
OBJECTS_NAME,
)
pipeline, module, filename = self.make_pipeline(csv_text)
columns = module.get_measurement_columns(pipeline)
expected_columns = (
(
cellprofiler.measurement.IMAGE,
cellprofiler.measurement.C_OBJECTS_URL + "_" + OBJECTS_NAME,
),
(
cellprofiler.measurement.IMAGE,
cellprofiler.measurement.C_OBJECTS_FILE_NAME + "_" + OBJECTS_NAME,
),
(
cellprofiler.measurement.IMAGE,
cellprofiler.measurement.C_OBJECTS_PATH_NAME + "_" + OBJECTS_NAME,
),
(
cellprofiler.measurement.IMAGE,
cellprofiler.measurement.C_COUNT + "_" + OBJECTS_NAME,
),
(OBJECTS_NAME, cellprofiler.measurement.M_LOCATION_CENTER_X),
(OBJECTS_NAME, cellprofiler.measurement.M_LOCATION_CENTER_Y),
(OBJECTS_NAME, cellprofiler.measurement.M_NUMBER_OBJECT_NUMBER),
)
for column in columns:
self.assertTrue(
any(
[
True
for object_name, feature in expected_columns
if object_name == column[0] and feature == column[1]
]
)
)
for object_name, feature in expected_columns:
self.assertTrue(
any(
[
True
for column in columns
if object_name == column[0] and feature == column[1]
]
)
)
def test_04_03_means_of_distances(self):
#
# Regression test of issue #1409
#
# Make sure means of minimum and mean distances of children
# are recorded properly
#
i, j = numpy.mgrid[0:14, 0:30]
#
# Make the objects different sizes to exercise more code
#
parent_labels = (i >= 7) * 1 + (j >= 15) * 2 + 1
child_labels = numpy.zeros(i.shape)
numpy.random.seed(0)
# Take 12 random points and label them
child_centers = numpy.random.permutation(numpy.prod(i.shape))[:12]
child_centers = numpy.vstack((i.flatten()[child_centers],
j.flatten()[child_centers]))
child_labels[child_centers[0], child_centers[1]] = numpy.arange(1, 13)
parent_centers = numpy.array([[3, 7], [10, 7], [3, 22], [10, 22]], float)
parent_indexes = parent_labels[child_centers[0],
child_centers[1]] - 1
expected = numpy.sqrt(numpy.sum((parent_centers[parent_indexes, :] -
child_centers.transpose()) ** 2, 1))
workspace, module = self.make_workspace(parent_labels, child_labels)
self.assertTrue(isinstance(module, cellprofiler.modules.relateobjects.Relate))
module.find_parent_child_distances.value = cellprofiler.modules.relateobjects.D_CENTROID
module.wants_per_parent_means.value = True
mnames = module.get_measurements(workspace.pipeline,
PARENT_OBJECTS,
"_".join((cellprofiler.modules.relateobjects.C_MEAN, CHILD_OBJECTS)))
self.assertTrue(cellprofiler.modules.relateobjects.FF_CENTROID % PARENT_OBJECTS in mnames)
feat_mean = cellprofiler.modules.relateobjects.FF_MEAN % (CHILD_OBJECTS, cellprofiler.modules.relateobjects.FF_CENTROID % PARENT_OBJECTS)
mcolumns = module.get_measurement_columns(workspace.pipeline)
self.assertTrue(any([c[0] == PARENT_OBJECTS and c[1] == feat_mean
for c in mcolumns]))
m = workspace.measurements
m[CHILD_OBJECTS, cellprofiler.measurement.M_LOCATION_CENTER_X, 1] = child_centers[1]
m[CHILD_OBJECTS, cellprofiler.measurement.M_LOCATION_CENTER_Y, 1] = child_centers[0]
module.run(workspace)
v = m[PARENT_OBJECTS, feat_mean, 1]
plabel = m[CHILD_OBJECTS, "_".join((cellprofiler.measurement.C_PARENT, PARENT_OBJECTS)), 1]
self.assertEqual(len(v), 4)
for idx in range(4):
if numpy.any(plabel == idx + 1):
self.assertAlmostEqual(
v[idx], numpy.mean(expected[plabel == idx + 1]), 4)
def test_04_03_means_of_distances(self):
#
# Regression test of issue #1409
#
# Make sure means of minimum and mean distances of children
# are recorded properly
#
i, j = numpy.mgrid[0:14, 0:30]
#
# Make the objects different sizes to exercise more code
#
parent_labels = (i >= 7) * 1 + (j >= 15) * 2 + 1
child_labels = numpy.zeros(i.shape)
numpy.random.seed(0)
# Take 12 random points and label them
child_centers = numpy.random.permutation(numpy.prod(i.shape))[:12]
child_centers = numpy.vstack((i.flatten()[child_centers],
j.flatten()[child_centers]))
child_labels[child_centers[0], child_centers[1]] = numpy.arange(1, 13)
parent_centers = numpy.array([[3, 7], [10, 7], [3, 22], [10, 22]], float)
parent_indexes = parent_labels[child_centers[0],
child_centers[1]] - 1
expected = numpy.sqrt(numpy.sum((parent_centers[parent_indexes, :] -
child_centers.transpose()) ** 2, 1))
workspace, module = self.make_workspace(parent_labels, child_labels)
self.assertTrue(isinstance(module, cellprofiler.modules.relateobjects.Relate))
module.find_parent_child_distances.value = cellprofiler.modules.relateobjects.D_CENTROID
module.wants_per_parent_means.value = True
mnames = module.get_measurements(workspace.pipeline,
PARENT_OBJECTS,
"_".join((cellprofiler.modules.relateobjects.C_MEAN, CHILD_OBJECTS)))
self.assertTrue(cellprofiler.modules.relateobjects.FF_CENTROID % PARENT_OBJECTS in mnames)
feat_mean = cellprofiler.modules.relateobjects.FF_MEAN % (CHILD_OBJECTS, cellprofiler.modules.relateobjects.FF_CENTROID % PARENT_OBJECTS)
mcolumns = module.get_measurement_columns(workspace.pipeline)
self.assertTrue(any([c[0] == PARENT_OBJECTS and c[1] == feat_mean
for c in mcolumns]))
m = workspace.measurements
m[CHILD_OBJECTS, cellprofiler.measurement.M_LOCATION_CENTER_X, 1] = child_centers[1]
m[CHILD_OBJECTS, cellprofiler.measurement.M_LOCATION_CENTER_Y, 1] = child_centers[0]
module.run(workspace)
v = m[PARENT_OBJECTS, feat_mean, 1]
plabel = m[CHILD_OBJECTS, "_".join((cellprofiler.measurement.C_PARENT, PARENT_OBJECTS)), 1]
self.assertEqual(len(v), 4)
for idx in range(4):
if numpy.any(plabel == idx + 1):
self.assertAlmostEqual(
v[idx], numpy.mean(expected[plabel == idx + 1]), 4)
def features_and_columns_match(self, workspace):
module = workspace.module
pipeline = workspace.pipeline
measurements = workspace.measurements
object_names = [x for x in measurements.get_object_names()
if x != cellprofiler.measurement.IMAGE]
features = [[feature
for feature in measurements.get_feature_names(object_name)
if feature not in (MEASUREMENT, IGNORED_MEASUREMENT)]
for object_name in object_names]
columns = module.get_measurement_columns(pipeline)
self.assertEqual(sum([len(f) for f in features]), len(columns))
for column in columns:
index = object_names.index(column[0])
self.assertTrue(column[1] in features[index])
def features_and_columns_match(self, workspace):
module = workspace.module
pipeline = workspace.pipeline
measurements = workspace.measurements
object_names = [x for x in measurements.get_object_names()
if x != cellprofiler.measurement.IMAGE]
features = [[feature
for feature in measurements.get_feature_names(object_name)
if feature not in (MEASUREMENT, IGNORED_MEASUREMENT)]
for object_name in object_names]
columns = module.get_measurement_columns(pipeline)
self.assertEqual(sum([len(f) for f in features]), len(columns))
for column in columns:
index = object_names.index(column[0])
self.assertTrue(column[1] in features[index])
def find_measurements(self, modules, pipeline):
"""Scan the modules for features
modules - modules to scan for features
pipeline - the pipeline they came from
returns a two tuple of
Java types, e.g., "java.lang.Integer"
A dictionary whose key is the object name and whose
value is a list of two-tuples of feature name and index into
the java types array.
"""
jtypes = ["java.lang.Integer"]
features = {}
for module in modules:
assert isinstance(module, cellprofiler.module.Module)
for column in module.get_measurement_columns(pipeline):
objects, name, dbtype = column[:3]
qualifiers = {} if len(column) < 4 else column[3]
if (objects == cellprofiler.measurement.EXPERIMENT
and qualifiers.get(
cellprofiler.measurement.MCA_AVAILABLE_POST_RUN,
False) == True):
continue
if dbtype == cellprofiler.measurement.COLTYPE_FLOAT:
jtype = "java.lang.Double"
elif dbtype == cellprofiler.measurement.COLTYPE_INTEGER:
jtype = "java.lang.Integer"
elif dbtype.startswith(
cellprofiler.measurement.COLTYPE_VARCHAR):
jtype = "java.lang.String"
else:
continue
if jtype in jtypes:
type_idx = jtypes.index(jtype)
else:
type_idx = len(jtypes)
jtypes.append(jtype)
if objects not in features:
ofeatures = features[objects] = {}
else:
ofeatures = features[objects]
if name not in ofeatures:
ofeatures[name] = type_idx
for key in features:
features[key][cellprofiler.measurement.IMAGE_NUMBER] = 0
features_out = dict([(k, v.items()) for k, v in features.items()])
return jtypes, features_out
def test_04_01_get_measurement_columns(self):
workspace, module = self.make_obj_workspace(
numpy.zeros((0, 3), int),
numpy.zeros((0, 3), int),
dict(image=numpy.zeros((20, 10), bool)),
dict(image=numpy.zeros((20, 10), bool)))
columns = module.get_measurement_columns(workspace.pipeline)
# All columns should be unique
self.assertEqual(len(columns), len(set([x[1] for x in columns])))
# All columns should be floats and done on images
self.assertTrue(all([x[0] == cellprofiler.measurement.IMAGE]))
self.assertTrue(all([x[2] == cellprofiler.measurement.COLTYPE_FLOAT]))
for feature in cellprofiler.modules.measureobjectoverlap.FTR_ALL:
field = '_'.join((cellprofiler.modules.measureobjectoverlap.C_IMAGE_OVERLAP, feature, GROUND_TRUTH_OBJ, ID_OBJ))
self.assertTrue(field in [x[1] for x in columns])
def test_get_measurement_columns(self):
module = cellprofiler.module.ObjectProcessing()
module.x_name.value = "Objects"
actual = module.get_measurement_columns(None)
expected = [
(
"ObjectProcessing",
cellprofiler.measurement.M_LOCATION_CENTER_X,
cellprofiler.measurement.COLTYPE_FLOAT
),
(
"ObjectProcessing",
cellprofiler.measurement.M_LOCATION_CENTER_Y,
cellprofiler.measurement.COLTYPE_FLOAT
),
(
"ObjectProcessing",
cellprofiler.measurement.M_LOCATION_CENTER_Z,
cellprofiler.measurement.COLTYPE_FLOAT
),
(
"ObjectProcessing",
cellprofiler.measurement.M_NUMBER_OBJECT_NUMBER,
cellprofiler.measurement.COLTYPE_INTEGER
),
(
cellprofiler.measurement.IMAGE,
cellprofiler.measurement.FF_COUNT % "ObjectProcessing",
cellprofiler.measurement.COLTYPE_INTEGER
),
(
"Objects",
cellprofiler.measurement.FF_CHILDREN_COUNT % "ObjectProcessing",
cellprofiler.measurement.COLTYPE_INTEGER
),
(
"ObjectProcessing",
cellprofiler.measurement.FF_PARENT % "Objects",
cellprofiler.measurement.COLTYPE_INTEGER
)
]
assert actual == expected
def test_04_01_get_measurement_columns(self):
workspace, module = self.make_obj_workspace(
numpy.zeros((0, 3), int), numpy.zeros((0, 3), int),
dict(image=numpy.zeros((20, 10), bool)),
dict(image=numpy.zeros((20, 10), bool)))
columns = module.get_measurement_columns(workspace.pipeline)
# All columns should be unique
self.assertEqual(len(columns), len(set([x[1] for x in columns])))
# All columns should be floats and done on images
self.assertTrue(all([x[0] == cellprofiler.measurement.IMAGE]))
self.assertTrue(all([x[2] == cellprofiler.measurement.COLTYPE_FLOAT]))
for feature in cellprofiler.modules.measureobjectoverlap.FTR_ALL:
field = '_'.join(
(cellprofiler.modules.measureobjectoverlap.C_IMAGE_OVERLAP,
feature, GROUND_TRUTH_OBJ, ID_OBJ))
self.assertTrue(field in [x[1] for x in columns])
def test_04_01_get_measurement_columns(self):
workspace, module = self.make_workspace(
dict(image=numpy.zeros((20, 10), bool)),
dict(image=numpy.zeros((20, 10), bool)))
assert isinstance(module, cellprofiler.modules.measureimageoverlap.MeasureImageOverlap)
name = TEST_IMAGE_NAME
columns = module.get_measurement_columns(workspace.pipeline)
# All columns should be unique
self.assertEqual(len(columns), len(set([x[1] for x in columns])))
# All columns should be floats and done on images
self.assertTrue(all([x[0] == cellprofiler.measurement.IMAGE]))
self.assertTrue(all([x[2] == cellprofiler.measurement.COLTYPE_FLOAT]))
for feature in cellprofiler.modules.measureimageoverlap.FTR_ALL:
field = '_'.join((cellprofiler.modules.measureimageoverlap.C_IMAGE_OVERLAP, feature, name))
self.assertTrue(field in [x[1] for x in columns])
def test_07_02_file_name_measurement_columns(self):
'''Regression test bug IMG-315
A csv header of Image_FileName_Foo or Image_PathName_Foo should
yield column names of FileName_Foo and PathName_Foo
'''
colnames = ('Image_FileName_Foo', 'Image_PathName_Foo')
csv_text = '''"%s","%s"
"Channel1-01.tif","/imaging/analysis/2500_01_01_Jones"
"Channel1-02.tif","/imaging/analysis/2500_01_01_Jones"
''' % colnames
pipeline, module, filename = self.make_pipeline(csv_text)
try:
columns = module.get_measurement_columns(pipeline)
self.assertTrue('FileName_Foo' in [c[1] for c in columns])
self.assertTrue('PathName_Foo' in [c[1] for c in columns])
finally:
os.remove(filename)
def test_07_02_file_name_measurement_columns(self):
'''Regression test bug IMG-315
A csv header of Image_FileName_Foo or Image_PathName_Foo should
yield column names of FileName_Foo and PathName_Foo
'''
colnames = ('Image_FileName_Foo', 'Image_PathName_Foo')
csv_text = '''"%s","%s"
"Channel1-01.tif","/imaging/analysis/2500_01_01_Jones"
"Channel1-02.tif","/imaging/analysis/2500_01_01_Jones"
''' % colnames
pipeline, module, filename = self.make_pipeline(csv_text)
try:
columns = module.get_measurement_columns(pipeline)
self.assertTrue('FileName_Foo' in [c[1] for c in columns])
self.assertTrue('PathName_Foo' in [c[1] for c in columns])
finally:
os.remove(filename)
def test_file_name_measurement_columns():
"""Regression test bug IMG-315
A csv header of Image_FileName_Foo or Image_PathName_Foo should
yield column names of FileName_Foo and PathName_Foo
"""
colnames = ("Image_FileName_Foo", "Image_PathName_Foo")
csv_text = (""""%s","%s"
"Channel1-01.tif","/imaging/analysis/2500_01_01_Jones"
"Channel1-02.tif","/imaging/analysis/2500_01_01_Jones"
""" % colnames)
pipeline, module, filename = make_pipeline(csv_text)
try:
columns = module.get_measurement_columns(pipeline)
assert "FileName_Foo" in [c[1] for c in columns]
assert "PathName_Foo" in [c[1] for c in columns]
finally:
os.remove(filename)
def test_01_03_image_and_objects(image, measurements, module, objects, workspace):
'''Test operation on an image masked by objects'''
numpy.random.seed(0)
pixels = numpy.random.uniform(size=(10, 10)).astype(numpy.float32) * .99
pixels[1:3, 1:3] = 1
image.pixel_data = pixels
labels = numpy.zeros((10, 10), int)
labels[1:9, 1:5] = 1
labels[1:9, 5:9] = 2
objects.segmented = labels
module.images[0].wants_objects.value = True
module.run(workspace)
assert measurements.get_current_measurement(cellprofiler.measurement.IMAGE, "Intensity_TotalArea_image_objects") == 64
assert measurements.get_current_measurement(cellprofiler.measurement.IMAGE, "Intensity_TotalIntensity_image_objects") == numpy.sum(pixels[1:9, 1:9])
assert measurements.get_current_measurement(cellprofiler.measurement.IMAGE, "Intensity_MeanIntensity_image_objects") == numpy.sum(pixels[1:9, 1:9]) / 64.0
numpy.testing.assert_almost_equal(measurements.get_current_measurement(cellprofiler.measurement.IMAGE, "Intensity_PercentMaximal_image_objects"), 400. / 64.)
assert len(measurements.get_object_names()) == 1
assert measurements.get_object_names()[0] == cellprofiler.measurement.IMAGE
columns = module.get_measurement_columns(workspace.pipeline)
features = measurements.get_feature_names(cellprofiler.measurement.IMAGE)
assert len(columns) == len(features)
for column in columns:
assert column[1] in features
def test_04_01_get_measurement_columns(self):
workspace, module = self.make_workspace(
dict(image=numpy.zeros((20, 10), bool)),
dict(image=numpy.zeros((20, 10), bool)))
assert isinstance(module, cellprofiler.modules.measureimageoverlap.MeasureImageOverlap)
module.object_name_GT.value = GROUND_TRUTH_OBJ
module.object_name_ID.value = ID_OBJ
for obj_or_img, name in ((O_IMG, TEST_IMAGE_NAME),
(O_OBJ, "_".join((GROUND_TRUTH_OBJ, ID_OBJ)))):
module.obj_or_img.value = obj_or_img
columns = module.get_measurement_columns(workspace.pipeline)
# All columns should be unique
self.assertEqual(len(columns), len(set([x[1] for x in columns])))
# All columns should be floats and done on images
self.assertTrue(all([x[0] == cellprofiler.measurement.IMAGE]))
self.assertTrue(all([x[2] == cellprofiler.measurement.COLTYPE_FLOAT]))
for feature in cellprofiler.modules.measureimageoverlap.FTR_ALL:
field = '_'.join((cellprofiler.modules.measureimageoverlap.C_IMAGE_OVERLAP, feature, name))
self.assertTrue(field in [x[1] for x in columns])
def test_00_00_zeros(image, measurements, module, workspace):
'''Test operation on a completely-masked image'''
image.pixel_data = numpy.zeros((10, 10))
image.mask = numpy.zeros((10, 10), bool)
module.run(workspace)
assert measurements.get_current_measurement(cellprofiler.measurement.IMAGE, "Intensity_TotalArea_image") == 0
assert len(measurements.get_object_names()) == 1
assert measurements.get_object_names()[0] == cellprofiler.measurement.IMAGE
columns = module.get_measurement_columns(workspace.pipeline)
features = measurements.get_feature_names(cellprofiler.measurement.IMAGE)
assert len(columns) == len(features)
for column in columns:
assert column[1] in features
def test_get_measurement_columns(self):
module = cellprofiler.module.ImageSegmentation()
module.x_name.value = "Image"
actual = module.get_measurement_columns(None)
expected = [
("ImageSegmentation", cellprofiler.measurement.M_LOCATION_CENTER_X,
cellprofiler.measurement.COLTYPE_FLOAT),
("ImageSegmentation", cellprofiler.measurement.M_LOCATION_CENTER_Y,
cellprofiler.measurement.COLTYPE_FLOAT),
("ImageSegmentation", cellprofiler.measurement.M_LOCATION_CENTER_Z,
cellprofiler.measurement.COLTYPE_FLOAT),
("ImageSegmentation",
cellprofiler.measurement.M_NUMBER_OBJECT_NUMBER,
cellprofiler.measurement.COLTYPE_INTEGER),
(cellprofiler.measurement.IMAGE,
cellprofiler.measurement.FF_COUNT % "ImageSegmentation",
cellprofiler.measurement.COLTYPE_INTEGER)
]
assert actual == expected
def test_00_00_zeros(image, measurements, module, workspace):
'''Test operation on a completely-masked image'''
image.pixel_data = numpy.zeros((10, 10))
image.mask = numpy.zeros((10, 10), bool)
module.run(workspace)
assert measurements.get_current_measurement(
cellprofiler.measurement.IMAGE, "Intensity_TotalArea_image") == 0
assert len(measurements.get_object_names()) == 1
assert measurements.get_object_names()[0] == cellprofiler.measurement.IMAGE
columns = module.get_measurement_columns(workspace.pipeline)
features = measurements.get_feature_names(cellprofiler.measurement.IMAGE)
assert len(columns) == len(features)
for column in columns:
assert column[1] in features
def test_get_measurement_columns():
workspace, module = make_obj_workspace(
numpy.zeros((0, 3), int),
numpy.zeros((0, 3), int),
dict(image=numpy.zeros((20, 10), bool)),
dict(image=numpy.zeros((20, 10), bool)),
)
columns = module.get_measurement_columns(workspace.pipeline)
# All columns should be unique
assert len(columns) == len(set([x[1] for x in columns]))
# All columns should be floats and done on images
x = columns[-1]
assert all([x[0] == cellprofiler.measurement.IMAGE])
assert all([x[2] == cellprofiler.measurement.COLTYPE_FLOAT])
for feature in cellprofiler.modules.measureobjectoverlap.FTR_ALL:
field = "_".join((
cellprofiler.modules.measureobjectoverlap.C_IMAGE_OVERLAP,
feature,
GROUND_TRUTH_OBJ,
ID_OBJ,
))
assert field in [x[1] for x in columns]
def test_07_04_objects_measurement_columns(self):
csv_text = """%s_%s,%s_%s
Channel1-01-A-01.tif,/imaging/analysis/trunk/ExampleImages/ExampleSBSImages
""" % (cellprofiler.measurement.C_OBJECTS_FILE_NAME, OBJECTS_NAME,
cellprofiler.measurement.C_OBJECTS_PATH_NAME, OBJECTS_NAME)
pipeline, module, filename = self.make_pipeline(csv_text)
columns = module.get_measurement_columns(pipeline)
expected_columns = (
(cellprofiler.measurement.IMAGE, cellprofiler.measurement.C_OBJECTS_URL + "_" + OBJECTS_NAME),
(cellprofiler.measurement.IMAGE, cellprofiler.measurement.C_OBJECTS_FILE_NAME + "_" + OBJECTS_NAME),
(cellprofiler.measurement.IMAGE, cellprofiler.measurement.C_OBJECTS_PATH_NAME + "_" + OBJECTS_NAME),
(cellprofiler.measurement.IMAGE, cellprofiler.measurement.C_COUNT + "_" + OBJECTS_NAME),
(OBJECTS_NAME, cellprofiler.measurement.M_LOCATION_CENTER_X),
(OBJECTS_NAME, cellprofiler.measurement.M_LOCATION_CENTER_Y),
(OBJECTS_NAME, cellprofiler.measurement.M_NUMBER_OBJECT_NUMBER))
for column in columns:
self.assertTrue(any([
True for object_name, feature in expected_columns
if object_name == column[0] and feature == column[1]]))
for object_name, feature in expected_columns:
self.assertTrue(any([
True for column in columns
if object_name == column[0] and feature == column[1]]))
def test_07_01_get_measurement_columns(self):
'''Test the get_measurement_columns method'''
colnames = ('Integer_Measurement', 'Float_Measurement', 'String_Measurement')
coltypes = [cellprofiler.measurement.COLTYPE_INTEGER, cellprofiler.measurement.COLTYPE_FLOAT,
cellprofiler.measurement.COLTYPE_VARCHAR_FORMAT % 9]
csv_text = '''"%s","%s","%s"
1,1,1
2,1.5,"Hi"
3,1,"Hello"
4,1.7,"Hola"
5,1.2,"Bonjour"
6,1.5,"Gutentag"
7,1.1,"Hej"
8,2.3,"Bevakasha"
''' % colnames
pipeline, module, filename = self.make_pipeline(csv_text)
columns = module.get_measurement_columns(pipeline)
for colname, coltype in zip(colnames, coltypes):
self.assertTrue(any([(column[0] == cellprofiler.measurement.IMAGE and
column[1] == colname and
column[2] == coltype) for column in columns]),
'Failed to find %s' % colname)
os.remove(filename)
def test_get_measurement_columns(self):
module = cellprofiler.module.ImageSegmentation()
module.x_name.value = "Image"
actual = module.get_measurement_columns(None)
expected = [
(
"ImageSegmentation",
cellprofiler.measurement.M_LOCATION_CENTER_X,
cellprofiler.measurement.COLTYPE_FLOAT
),
(
"ImageSegmentation",
cellprofiler.measurement.M_LOCATION_CENTER_Y,
cellprofiler.measurement.COLTYPE_FLOAT
),
(
"ImageSegmentation",
cellprofiler.measurement.M_LOCATION_CENTER_Z,
cellprofiler.measurement.COLTYPE_FLOAT
),
(
"ImageSegmentation",
cellprofiler.measurement.M_NUMBER_OBJECT_NUMBER,
cellprofiler.measurement.COLTYPE_INTEGER
),
(
cellprofiler.measurement.IMAGE,
cellprofiler.measurement.FF_COUNT % "ImageSegmentation",
cellprofiler.measurement.COLTYPE_INTEGER
)
]
assert actual == expected
def test_03_03_metadata_row_and_column_and_well(self):
csv_text = '''"Metadata_Row","Metadata_Column","Metadata_Well"
"C","03","B14"
'''
pipeline, module, filename = self.make_pipeline(csv_text)
columns = module.get_measurement_columns(pipeline)
self.assertTrue(any([c[0] == cellprofiler.measurement.IMAGE and
c[1] == "Metadata_Row" and
c[2] == "varchar(1)" for c in columns]))
self.assertTrue(any([c[0] == cellprofiler.measurement.IMAGE and
c[1] == "Metadata_Column" and
c[2] == "varchar(2)" for c in columns]))
self.assertTrue(any([c[0] == cellprofiler.measurement.IMAGE and
c[1] == "Metadata_Well" and
c[2] == "varchar(3)" for c in columns]))
m = pipeline.run()
features = module.get_measurements(pipeline, cellprofiler.measurement.IMAGE,
cellprofiler.measurement.C_METADATA)
for feature, expected in (("Row", "C"),
("Column", "03"),
("Well", "B14")):
self.assertTrue(feature in features)
value = m.get_current_image_measurement('_'.join((cellprofiler.measurement.C_METADATA, feature)))
self.assertEqual(value, expected)
def test_03_01_get_measurement_columns(module):
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)
assert all(
[column[0] == cellprofiler.measurement.IMAGE for column in columns])
for expected_suffix in expected_suffixes:
for feature, coltype in (
(cellprofiler.modules.measureimageintensity.F_TOTAL_INTENSITY,
cellprofiler.measurement.COLTYPE_FLOAT),
(cellprofiler.modules.measureimageintensity.F_MEAN_INTENSITY,
cellprofiler.measurement.COLTYPE_FLOAT),
(cellprofiler.modules.measureimageintensity.F_MIN_INTENSITY,
cellprofiler.measurement.COLTYPE_FLOAT),
(cellprofiler.modules.measureimageintensity.F_MAX_INTENSITY,
cellprofiler.measurement.COLTYPE_FLOAT),
(cellprofiler.modules.measureimageintensity.F_TOTAL_AREA,
cellprofiler.measurement.COLTYPE_INTEGER),
(cellprofiler.modules.measureimageintensity.F_PERCENT_MAXIMAL,
cellprofiler.measurement.COLTYPE_FLOAT),
(cellprofiler.modules.measureimageintensity.F_MAD_INTENSITY,
cellprofiler.measurement.COLTYPE_FLOAT),
(cellprofiler.modules.measureimageintensity.F_LOWER_QUARTILE,
cellprofiler.measurement.COLTYPE_FLOAT),
(cellprofiler.modules.measureimageintensity.F_UPPER_QUARTILE,
cellprofiler.measurement.COLTYPE_FLOAT)):
# feature names are now formatting strings
feature_name = feature % expected_suffix
assert any([(column[1] == feature_name and column[2] == coltype)
for column in columns])
