def test_surface_measurement_voxelsize_mm(self):
import imtools.surface_measurement as sm
import scipy
# data 1
data1 = np.zeros([30, 40, 55])
voxelsize_mm1 = [1, 1, 1]
data1[10:20, 10:20, 10:20] = 1
data1[13:18, 13:18, 10:15] = 0
# data 2
voxelsize_mm2 = [0.1, 0.2, 0.3]
data2 = scipy.ndimage.interpolation.zoom(data1,
zoom=1.0 /
np.asarray(voxelsize_mm2),
order=0)
# import sed3
# ed = sed3.sed3(data1)
# ed.show()
# ed = sed3.sed3(data2)
# ed.show()
Sv1 = sm.surface_density(data1, voxelsize_mm1)
Sv2 = sm.surface_density(data2, voxelsize_mm2)
self.assertGreater(Sv1, Sv2 * 0.9)
self.assertLess(Sv1, Sv2 * 1.1)
def test_surface_measurement(self):
import imtools.surface_measurement as sm
# box
data1 = np.zeros([30, 30, 30])
voxelsize_mm = [1, 1, 1]
data1[10:20, 10:20, 10:20] = 1
Sv1 = sm.surface_density(data1, voxelsize_mm)
# box without small box on corner
data2 = np.zeros([30, 30, 30])
voxelsize_mm = [1, 1, 1]
data2[10:20, 10:20, 10:20] = 1
data2[10:15, 10:15, 10:15] = 0
Sv2 = sm.surface_density(data2, voxelsize_mm)
self.assertEqual(Sv2, Sv1)
# box with hole in one edge
data3 = np.zeros([30, 30, 30])
voxelsize_mm = [1, 1, 1]
data3[10:20, 10:20, 10:20] = 1
data3[13:18, 13:18, 10:15] = 0
Sv3 = sm.surface_density(data3, voxelsize_mm)
self.assertGreater(Sv3, Sv1)
def test_surface_measurement_use_aoi(self):
"""
Test of AOI. In Sv2 is AOI half in compare with Sv1.
Sv1 should be half of Sv2
"""
data1 = np.zeros([30, 60, 60])
aoi = np.zeros([30, 60, 60])
aoi[:30, :60, :30] = 1
voxelsize_mm = [1, 1, 1]
data1[10:20, 10:20, 10:20] = 1
data1[13:18, 13:18, 10:15] = 0
Sv1 = sm.surface_density(data1, voxelsize_mm, aoi=None)
Sv2 = sm.surface_density(data1, voxelsize_mm, aoi=aoi)
self.assertGreater(2*Sv1, Sv2*0.9)
self.assertLess(2*Sv1, Sv2*1.1)
def test_surface_density_gensei_data(self):
import io3d.datasets
dr = io3d.datareader.DataReader()
datap = dr.Get3DData(io3d.datasets.join_path('gensei_slices/'),
dataplus_format=True)
# total object volume fraction: 0.081000
# total object volume [(mm)^3]: 81.000000
# total object surface fraction [1/(mm)]: 0.306450
# total object surface [(mm)^2]: 306.449981
segmentation = (datap['data3d'] > 100).astype(np.int8)
voxelsize_mm = [0.2, 0.2, 0.2]
volume = np.sum(segmentation) * np.prod(voxelsize_mm)
Sv = sm.surface_density(segmentation, voxelsize_mm)
self.assertGreater(volume, 80)
self.assertLess(volume, 85)
self.assertGreater(Sv, 0.3)
self.assertLess(Sv, 0.4)
def test_surface_density_gensei_data(self):
import imtools.surface_measurement as sm
import io3d
import imtools.sample_data
data_path = 'sample_data/gensei_slices/'
if not os.path.exists(data_path):
imtools.sample_data.get("gensei_slices", 'sample_data/')
dr = io3d.datareader.DataReader()
datap = dr.Get3DData(datapath=data_path, dataplus_format=True)
# total object volume fraction: 0.081000
# total object volume [(mm)^3]: 81.000000
# total object surface fraction [1/(mm)]: 0.306450
# total object surface [(mm)^2]: 306.449981
segmentation = (datap['data3d'] > 100).astype(np.int8)
voxelsize_mm = [0.2, 0.2, 0.2]
volume = np.sum(segmentation) * np.prod(voxelsize_mm)
Sv = sm.surface_density(segmentation, voxelsize_mm)
self.assertGreater(volume, 80)
self.assertLess(volume, 85)
self.assertGreater(Sv, 0.3)
self.assertLess(Sv, 0.4)