def execute(self,
image,
function,
mask=None,
custom_repeats=None,
scale=None,
module=None):
'''Run the morph module on an input and return the resulting image'''
INPUT_IMAGE_NAME = 'input'
OUTPUT_IMAGE_NAME = 'output'
if module is None:
module = morph.Morph()
module.functions[0].function.value = function
module.image_name.value = INPUT_IMAGE_NAME
module.output_image_name.value = OUTPUT_IMAGE_NAME
if custom_repeats is None:
module.functions[0].repeats_choice.value = morph.R_ONCE
elif custom_repeats == -1:
module.functions[0].repeats_choice.value = morph.R_FOREVER
else:
module.functions[0].repeats_choice.value = morph.R_CUSTOM
module.functions[0].custom_repeats.value = custom_repeats
if scale is not None:
module.functions[0].scale.value = scale
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)
image_set.add(INPUT_IMAGE_NAME, cpi.Image(image, mask=mask))
module.run(workspace)
output = image_set.get_image(OUTPUT_IMAGE_NAME)
return output.pixel_data
def test_04_09_strel_square(self):
r = np.random.RandomState()
r.seed(49)
module = morph.Morph()
module.functions[0].structuring_element.value = morph.SE_SQUARE
strel = cpmorph.strel_square(7)
pixel_data = r.uniform(size=(20, 30)) > .5
expected = scind.binary_dilation(pixel_data, strel)
result = self.execute(pixel_data, morph.F_DILATE, scale=7,
module=module)
np.testing.assert_array_equal(expected, result)
def test_04_01_strel_arbitrary(self):
r = np.random.RandomState()
r.seed(41)
strel = r.uniform(size=(5, 3)) > .5
module = morph.Morph()
module.functions[0].structuring_element.value = morph.SE_ARBITRARY
module.functions[0].strel.value_text = cps.BinaryMatrix.to_value(strel)
pixel_data = r.uniform(size=(20, 30)) > .5
expected = scind.binary_dilation(pixel_data, strel)
result = self.execute(pixel_data, morph.F_DILATE, module=module)
np.testing.assert_array_equal(expected, result)
def test_04_08_strel_disk(self):
r = np.random.RandomState()
r.seed(48)
module = morph.Morph()
module.functions[0].structuring_element.value = morph.SE_RECTANGLE
module.functions[0].width.value = 5
module.functions[0].height.value = 9
strel = cpmorph.strel_rectangle(5, 9)
pixel_data = r.uniform(size=(20, 30)) > .5
expected = scind.binary_dilation(pixel_data, strel)
result = self.execute(pixel_data, morph.F_DILATE, module=module)
np.testing.assert_array_equal(expected, result)
def test_04_06_strel_pair(self):
r = np.random.RandomState()
r.seed(46)
module = morph.Morph()
module.functions[0].structuring_element.value = morph.SE_PAIR
module.functions[0].x_offset.value = -1
module.functions[0].y_offset.value = 4
strel = cpmorph.strel_pair(-1, 4)
pixel_data = r.uniform(size=(20, 30)) > .5
expected = scind.binary_dilation(pixel_data, strel)
result = self.execute(pixel_data, morph.F_DILATE, module=module)
np.testing.assert_array_equal(expected, result)
def test_04_07_strel_periodicline(self):
r = np.random.RandomState()
r.seed(43)
module = morph.Morph()
module.functions[0].structuring_element.value = morph.SE_PERIODIC_LINE
module.functions[0].x_offset.value = 4
module.functions[0].y_offset.value = -3
strel = cpmorph.strel_periodicline(4, -3, 3)
pixel_data = r.uniform(size=(20, 30)) > .5
expected = scind.binary_dilation(pixel_data, strel)
result = self.execute(pixel_data, morph.F_DILATE, scale=30,
module=module)
np.testing.assert_array_equal(expected, result)