class AbstractTissue(object):
'''
Initializes a abstract tissue model"
'''
def set_nr_photons(self, nr_photons):
self._mci_wrapper.set_nr_photons(nr_photons)
def set_mci_filename(self, mci_filename):
self._mci_wrapper.set_mci_filename(mci_filename)
def set_base_mco_filename(self, base_filename):
self._mci_wrapper.set_base_mco_filename(base_filename)
def get_mco_filename(self):
return self._mci_wrapper.get_base_mco_filename()
def set_wavelength(self, wavelength):
self.wavelength = wavelength
def create_mci_file(self):
self._mci_wrapper.create_mci_file()
def update_mci_file(self, wavelengths):
# set layers
for wavelength in wavelengths:
for i, ua in enumerate(self.uas):
self._mci_wrapper.set_layer(i, # layer nr
self.ns[i], # refraction index
self.uas[i](wavelength), # ua
self.usgs[i](wavelength)[0], # us
self.usgs[i](wavelength)[1], # g
self.ds[i]) # d
# now that the layers have been updated: create file
self._mci_wrapper.update_mci_file(wavelength)
create_header = False
def __str__(self):
""" Overwrite this method!
print the current model"""
model_string = ""
return model_string
def __init__(self, ns, uas, usgs, ds):
self._mci_wrapper = MciWrapper()
self.wavelength = 500.*10**9 # standard wavelength, should be set.
self.uas = uas
self.usgs = usgs
self.ds = ds
self.ns = ns
# initially create layers. these will be overwritten as soon
# as create_mci_file is called.
for i in enumerate(uas):
self._mci_wrapper.add_layer()
def __init__(self, ns, uas, usgs, ds):
self._mci_wrapper = MciWrapper()
self.wavelength = 500. * 10**9 # standard wavelength, should be set.
self.uas = uas
self.usgs = usgs
self.ds = ds
self.ns = ns
# initially create layers. these will be overwritten as soon
# as create_mci_file is called.
for i in enumerate(uas):
self._mci_wrapper.add_layer()
class AbstractTissue(object):
'''
Initializes a abstract tissue model"
'''
def set_nr_photons(self, nr_photons):
self._mci_wrapper.set_nr_photons(nr_photons)
def set_mci_filename(self, mci_filename):
self._mci_wrapper.set_mci_filename(mci_filename)
def set_mco_filename(self, mco_filename):
self._mci_wrapper.set_mco_filename(mco_filename)
def get_mco_filename(self):
return self._mci_wrapper.mco_filename
def set_wavelength(self, wavelength):
self.wavelength = wavelength
def create_mci_file(self):
# set layers
for i, ua in enumerate(self.uas):
self._mci_wrapper.set_layer(
i, # layer nr
self.ns[i], # refraction index
self.uas[i](self.wavelength), # ua
self.usgs[i](self.wavelength)[0], # us
self.usgs[i](self.wavelength)[1], # g
self.ds[i]) # d
# now that the layers have been updated: create file
self._mci_wrapper.create_mci_file()
def __str__(self):
""" Overwrite this method!
print the current model"""
model_string = ""
return model_string
def __init__(self, ns, uas, usgs, ds):
self._mci_wrapper = MciWrapper()
self.wavelength = 500. * 10**9 # standard wavelength, should be set.
self.uas = uas
self.usgs = usgs
self.ds = ds
self.ns = ns
# initially create layers. these will be overwritten as soon
# as create_mci_file is called.
for i in enumerate(uas):
self._mci_wrapper.add_layer()
def setUp(self):
self.mci_filename = "temp.mci"
self.mco_filename = "temp.mco"
# create a mci_wrapper which shall create a mci file
self.mci_wrapper = MciWrapper()
self.mci_wrapper.set_mci_filename(self.mci_filename)
self.mci_wrapper.set_mco_filename(self.mco_filename)
self.mci_wrapper.set_nr_photons(10 ** 6)
self.mci_wrapper.add_layer(1.0, 2.1, 3.2, 4.3, 5.4)
self.mci_wrapper.add_layer(6.5, 7.8, 8.9, 9.10, 10.11)
self.mci_wrapper.add_layer(100.1001, 101.10001, 102.100001,
103.1000001, 104.10000001)
self.mci_wrapper.set_layer(1, 1, 1, 1, 1, 1)
# expected mci file
self.correct_mci_filename = "./mc/data/correct.mci"
def __init__(self, ns, uas, usgs, ds):
self._mci_wrapper = MciWrapper()
self.wavelength = 500.*10**9 # standard wavelength, should be set.
self.uas = uas
self.usgs = usgs
self.ds = ds
self.ns = ns
# initially create layers. these will be overwritten as soon
# as create_mci_file is called.
for i in enumerate(uas):
self._mci_wrapper.add_layer()
def test_mci_wrapper_book_example_2(self):
"""see if our result matches the one from
Biomedical Optics
Principles and Imaging
page 56 (Table 3.2)"""
# create a book_p56_mci which shall create a mci file
book_p56_mci = MciWrapper()
book_p56_mci.set_mci_filename(self.mci_filename)
book_p56_mci.set_mco_filename(self.mco_filename)
book_p56_mci.set_nr_photons(10**6)
book_p56_mci.add_layer(1.5, 1000, 9000, 0., 1)
mcml_path, mcml_file = os.path.split(path_to_gpumcml)
if os.path.isfile(path_to_gpumcml):
book_p56_mci.create_mci_file()
sim_wrapper = SimWrapper()
sim_wrapper.set_mci_filename(self.mci_filename)
sim_wrapper.set_mcml_executable(path_to_gpumcml)
sim_wrapper.run_simulation()
self.assertTrue(os.path.isfile(mcml_path + "/" + self.mco_filename),
"mco file was created")
refl = get_total_reflectance(os.path.join(mcml_path,
self.mco_filename))
self.assertAlmostEqual(refl, 0.26, delta=0.01,
msg="correct reflectance determined " +
"according to book table 3.2")
class Test(unittest.TestCase):
def setUp(self):
self.mci_filename = "temp.mci"
self.mco_filename = "temp.mco"
# create a mci_wrapper which shall create a mci file
self.mci_wrapper = MciWrapper()
self.mci_wrapper.set_mci_filename(self.mci_filename)
self.mci_wrapper.set_mco_filename(self.mco_filename)
self.mci_wrapper.set_nr_photons(10 ** 6)
self.mci_wrapper.add_layer(1.0, 2.1, 3.2, 4.3, 5.4)
self.mci_wrapper.add_layer(6.5, 7.8, 8.9, 9.10, 10.11)
self.mci_wrapper.add_layer(100.1001, 101.10001, 102.100001,
103.1000001, 104.10000001)
self.mci_wrapper.set_layer(1, 1, 1, 1, 1, 1)
# expected mci file
self.correct_mci_filename = "./mc/data/correct.mci"
# path to the externaly installed mcml simulation. This is machine
# dependent. Thus tests depending on the execution of mcml will only
# be performed if this file exists.
# Should the file be located somewhere else on your computer,
# change this path to your actual location.
def tearDown(self):
os.remove(self.mci_filename)
mcml_path, mcml_file = os.path.split(path_to_gpumcml)
created_mco_file = mcml_path + "/" + self.mco_filename
if os.path.isfile(created_mco_file):
os.remove(created_mco_file)
def test_mci_wrapper(self):
self.mci_wrapper.create_mci_file()
self.assertTrue(os.path.isfile(self.mci_filename),
"mci file was created")
self.assertTrue(filecmp.cmp(self.mci_filename,
self.correct_mci_filename, shallow=False),
"the written mci file is the same as the stored " +
"reference file")
@unittest.skipIf(skip_gpu_tests, "skip if gpumcml not installed")
def test_sim_wrapper(self):
mcml_path, mcml_file = os.path.split(path_to_gpumcml)
if os.path.isfile(path_to_gpumcml):
self.mci_wrapper.create_mci_file()
sim_wrapper = SimWrapper()
sim_wrapper.set_mci_filename(self.mci_filename)
sim_wrapper.set_mcml_executable(path_to_gpumcml)
sim_wrapper.run_simulation()
self.assertTrue(os.path.isfile(os.path.join(mcml_path,
self.mco_filename)),
"mco file was created")
@unittest.skipIf(skip_gpu_tests, "skip if gpumcml not installed")
def test_mci_wrapper_book_example(self):
"""see if our result matches the one from
Biomedical Optics
Principles and Imaging
page 55 (Table 3.1)"""
# create a book_p55_mci which shall create a mci file
book_p55_mci = MciWrapper()
book_p55_mci.set_mci_filename(self.mci_filename)
book_p55_mci.set_mco_filename(self.mco_filename)
book_p55_mci.set_nr_photons(10**6)
book_p55_mci.add_layer(1, 1000, 9000, 0.75, 0.0002)
mcml_path, mcml_file = os.path.split(path_to_gpumcml)
if os.path.isfile(path_to_gpumcml):
book_p55_mci.create_mci_file()
sim_wrapper = SimWrapper()
sim_wrapper.set_mci_filename(self.mci_filename)
sim_wrapper.set_mcml_executable(path_to_gpumcml)
sim_wrapper.run_simulation()
self.assertTrue(os.path.isfile(mcml_path + "/" + self.mco_filename),
"mco file was created")
refl = get_diffuse_reflectance(os.path.join(mcml_path,
self.mco_filename))
self.assertAlmostEqual(refl, 0.09734, 3,
"correct reflectance determined " +
"according to book table 3.1")
@unittest.skipIf(skip_gpu_tests, "skip if gpumcml not installed")
def test_mci_wrapper_book_example_2(self):
"""see if our result matches the one from
Biomedical Optics
Principles and Imaging
page 56 (Table 3.2)"""
# create a book_p56_mci which shall create a mci file
book_p56_mci = MciWrapper()
book_p56_mci.set_mci_filename(self.mci_filename)
book_p56_mci.set_mco_filename(self.mco_filename)
book_p56_mci.set_nr_photons(10**6)
book_p56_mci.add_layer(1.5, 1000, 9000, 0., 1)
mcml_path, mcml_file = os.path.split(path_to_gpumcml)
if os.path.isfile(path_to_gpumcml):
book_p56_mci.create_mci_file()
sim_wrapper = SimWrapper()
sim_wrapper.set_mci_filename(self.mci_filename)
sim_wrapper.set_mcml_executable(path_to_gpumcml)
sim_wrapper.run_simulation()
self.assertTrue(os.path.isfile(mcml_path + "/" + self.mco_filename),
"mco file was created")
refl = get_total_reflectance(os.path.join(mcml_path,
self.mco_filename))
self.assertAlmostEqual(refl, 0.26, delta=0.01,
msg="correct reflectance determined " +
"according to book table 3.2")