def test_read(self):
l = LETCube()
l.read(self.let001)
v = create_sphere(l, name="sph", center=[10, 10, 10], radius=8)
self.assertIsNotNone(v)
logger.info("Calculating DVH")
result = l.calculate_lvh(v)
self.assertIsNotNone(result)
lvh, min_l, max_l, mean, area = result
self.assertGreater(area, 2.0)
self.assertEqual(len(lvh.shape), 1)
self.assertEqual(lvh.shape[0], 3000)
self.assertEqual(min_l, 0.0)
self.assertEqual(max_l, 1.0)
self.assertGreater(l.get_max(), 30.0)
fd, outfile = tempfile.mkstemp()
os.close(fd) # Windows needs it
os.remove(outfile) # we need only temp filename, not the file
l.write(outfile)
hed_file = outfile + LETCube.header_file_extension
dos_file = outfile + LETCube.data_file_extension
self.assertTrue(os.path.exists(hed_file))
self.assertTrue(os.path.exists(dos_file))
logger.info("Checking if output file " + hed_file + " is not empty")
self.assertGreater(os.path.getsize(hed_file), 1)
logger.info("Checking if output file " + dos_file + " is not empty")
self.assertGreater(os.path.getsize(dos_file), 1)
os.remove(hed_file)
os.remove(dos_file)
def test_read(self):
let = LETCube()
let.read(self.let001)
v = create_sphere(let, name="sph", center=[10, 10, 10], radius=8)
self.assertIsNotNone(v)
logger.info("Calculating DVH")
result = let.calculate_lvh(v)
self.assertIsNotNone(result)
lvh, min_l, max_l, mean, area = result
self.assertGreater(area, 2.0)
self.assertEqual(len(lvh.shape), 1)
self.assertEqual(lvh.shape[0], 3000)
self.assertEqual(min_l, 0.0)
self.assertEqual(max_l, 1.0)
self.assertGreater(let.get_max(), 30.0)
fd, outfile = tempfile.mkstemp()
os.close(fd) # Windows needs it
os.remove(outfile) # we need only temp filename, not the file
let.write(outfile)
hed_file = outfile + LETCube.header_file_extension
dos_file = outfile + LETCube.data_file_extension
self.assertTrue(os.path.exists(hed_file))
self.assertTrue(os.path.exists(dos_file))
logger.info("Checking if output file " + hed_file + " is not empty")
self.assertGreater(os.path.getsize(hed_file), 1)
logger.info("Checking if output file " + dos_file + " is not empty")
self.assertGreater(os.path.getsize(dos_file), 1)
os.remove(hed_file)
os.remove(dos_file)
def test_dvh_simple(self):
c = DosCube()
c.read(self.cube000)
v = create_sphere(c, name="sph", center=[10, 10, 10], radius=8)
self.assertIsNotNone(v)
logger.info("Calculating DVH simple")
x, y = volume_histogram(c.cube, v)
self.assertIsNotNone(x)
self.assertIsNotNone(y)
logger.info("Calculating DVH simple for entire cube")
x, y = volume_histogram(c.cube)
self.assertIsNotNone(x)
self.assertIsNotNone(y)
def test_dvh(self):
c = DosCube()
c.read(self.cube000)
v = create_sphere(c, name="sph", center=[10, 10, 10], radius=8)
self.assertIsNotNone(v)
logger.info("Calculating DVH")
result = c.calculate_dvh(v)
self.assertIsNotNone(result)
dvh, min_dose, max_dose, mean, area = result
self.assertGreater(area, 2.0)
self.assertEqual(len(dvh.shape), 2)
self.assertEqual(dvh.shape[1], 2)
self.assertEqual(dvh.shape[0], 1500)
self.assertEqual(min_dose, 0.0)
self.assertEqual(max_dose, 0.001)
def test_dvh(self):
c = DosCube()
c.read(self.cube000)
v = create_sphere(c, name="sph", center=[10, 10, 10], radius=8)
self.assertIsNotNone(v)
logger.info("Calculating DVH")
result = c.calculate_dvh(v)
self.assertIsNotNone(result)
dvh, min_dose, max_dose, mean, area = result
self.assertGreater(area, 2.0)
self.assertEqual(len(dvh.shape), 2)
self.assertEqual(dvh.shape[1], 2)
self.assertEqual(dvh.shape[0], 1500)
self.assertEqual(min_dose, 0.0)
self.assertEqual(max_dose, 0.001)
def _validate_voi(self) -> bool:
voi_widget = self.view.voi_layout.itemAt(0).widget()
# validate fields
if not voi_widget.validate():
return False
# check if name isn't already being used
if voi_widget.name.lower() in self.used_voi_names:
self.view.info.text = "This name is already being used by another VOI."
return False
ctx = self.model
center_no_offsets = [a - b for (a, b) in zip(voi_widget.center, [ctx.xoffset, ctx.yoffset, ctx.zoffset])]
if isinstance(voi_widget, SphericalVOIWidget):
voi = create_sphere(
cube=ctx,
name=voi_widget.name,
center=center_no_offsets,
radius=voi_widget.radius
)
elif isinstance(voi_widget, CuboidalVOIWidget):
voi = create_cube(
cube=ctx,
name=voi_widget.name,
center=center_no_offsets,
width=voi_widget.width,
height=voi_widget.height,
depth=voi_widget.depth,
)
elif isinstance(voi_widget, CylindricalVOIWidget):
voi = create_cylinder(
cube=ctx,
name=voi_widget.name,
center=center_no_offsets,
radius=voi_widget.radius,
depth=voi_widget.depth,
)
else:
logger.debug("VOI widget unrecognised")
return False
# validate containment in ctx
if not voi.is_fully_contained():
self.view.info.text = "VOI isn't fully contained in the given patient."
return False
return True
def _set_model_from_view(self) -> None:
ctx = self.model.ctx
vdx = self.model.vdx
list_vois = self.view.voi_scroll_area.widget().layout()
# iterating over every element of the list of vois while ignoring a trailing vertical spacer
for index in range(list_vois.count() - 1):
# the actual voi widget is embedded in the list element, we need to shell it
list_voi_element = list_vois.itemAt(index).widget()
voi_widget = list_voi_element.voi_space.itemAt(0).widget()
center_no_offsets = [
a - b for (a, b) in zip(
voi_widget.center, [ctx.xoffset, ctx.yoffset, ctx.zoffset])
]
if isinstance(voi_widget, SphericalVOIWidget):
voi = create_sphere(
cube=ctx,
name=voi_widget.name,
center=center_no_offsets,
radius=voi_widget.radius,
)
elif isinstance(voi_widget, CuboidalVOIWidget):
voi = create_cube(
cube=ctx,
name=voi_widget.name,
center=center_no_offsets,
width=voi_widget.width,
height=voi_widget.height,
depth=voi_widget.depth,
)
elif isinstance(voi_widget, CylindricalVOIWidget):
voi = create_cylinder(
cube=ctx,
name=voi_widget.name,
center=center_no_offsets,
radius=voi_widget.radius,
depth=voi_widget.depth,
)
else:
logger.debug("VOI widget unrecognised")
return
vdx.add_voi(voi)
def voxelplan_header_path(tmpdir_factory):
ctx = CtxCube()
ctx.create_empty_cube(value=0,
dimx=100,
dimy=100,
dimz=25,
pixel_size=1,
slice_distance=2,
slice_offset=0)
file_obj = tmpdir_factory.mktemp("data").join("patient")
patient_base_path = str(file_obj)
ctx.write(patient_base_path)
vdx = VdxCube(cube=ctx)
voi = create_sphere(cube=ctx,
name="target",
center=[50, 50, 25],
radius=10)
vdx.add_voi(voi)
vdx.write(patient_base_path + '.vdx')
yield patient_base_path + '.hed'
def test_dvh_simple(self):
c = DosCube()
c.read(self.cube000)
v = create_sphere(c, name="sph", center=[10, 10, 10], radius=8)
self.assertIsNotNone(v)
logger.info("Calculating DVH simple")
vh = VolHist(c, v)
self.assertIsNotNone(vh.x)
self.assertIsNotNone(vh.y)
outdir = tempfile.mkdtemp()
c.write_dicom(outdir)
f1 = os.path.join(outdir, "foobar_1.dvh")
vh.write(f1, header=True)
self.assertTrue(os.path.exists(f1))
self.assertGreater(os.path.getsize(f1), 0)
f2 = os.path.join(outdir, "foobar_2.dvh")
vh.write(f2, header=False)
self.assertTrue(os.path.exists(f2))
self.assertGreater(os.path.getsize(f2), 0)
logger.info("Calculating DVH simple for entire cube")
vh = VolHist(c)
self.assertIsNotNone(vh.x)
self.assertIsNotNone(vh.y)
f3 = os.path.join(outdir, "foobar_3.dvh")
vh.write(f3, header=True)
self.assertTrue(os.path.exists(f3))
self.assertGreater(os.path.getsize(f3), 0)
f4 = os.path.join(outdir, "foobar_4.dvh")
vh.write(f4, header=False)
self.assertTrue(os.path.exists(f4))
self.assertGreater(os.path.getsize(f4), 0)
shutil.rmtree(outdir)
def test_dvh_simple(self):
c = DosCube()
c.read(self.cube000)
v = create_sphere(c, name="sph", center=[10, 10, 10], radius=8)
self.assertIsNotNone(v)
logger.info("Calculating DVH simple")
vh = VolHist(c, v)
self.assertIsNotNone(vh.x)
self.assertIsNotNone(vh.y)
outdir = tempfile.mkdtemp()
c.write_dicom(outdir)
f1 = os.path.join(outdir, "foobar_1.dvh")
vh.write(f1, header=True)
self.assertTrue(os.path.exists(f1))
self.assertGreater(os.path.getsize(f1), 0)
f2 = os.path.join(outdir, "foobar_2.dvh")
vh.write(f2, header=False)
self.assertTrue(os.path.exists(f2))
self.assertGreater(os.path.getsize(f2), 0)
logger.info("Calculating DVH simple for entire cube")
vh = VolHist(c)
self.assertIsNotNone(vh.x)
self.assertIsNotNone(vh.y)
f3 = os.path.join(outdir, "foobar_3.dvh")
vh.write(f3, header=True)
self.assertTrue(os.path.exists(f3))
self.assertGreater(os.path.getsize(f3), 0)
f4 = os.path.join(outdir, "foobar_4.dvh")
vh.write(f4, header=False)
self.assertTrue(os.path.exists(f4))
self.assertGreater(os.path.getsize(f4), 0)
shutil.rmtree(outdir)
def test_create_voi_sphere(self):
logger.info("Creating CT cube from path " + self.cube000)
c = pt.CtxCube()
c.read(self.cube000)
logger.info("Generating and adding sphere VOI")
v = create_sphere(c, name="cube3", center=[10, 10, 10], radius=8)
self.assertEqual(v.number_of_slices(), 6)
logger.info("Checking Voi vdx_string method")
self.assertGreater(len(v.vdx_string()), 1)
logger.info("Checking Voi get_slice_at_pos method, non-existent slice")
self.assertIsNone(v.get_slice_at_pos(137))
logger.info("Checking Voi get_slice_at_pos method, good slice")
s = v.get_slice_at_pos(11)
self.assertIsNotNone(s)
logger.info("Checking Slice vdx_string method")
self.assertGreater(len(s.vdx_string()), 1)
logger.info("Checking Slice number_of_contours method")
self.assertEqual(s.number_of_contours(), 1)
logger.info("Checking Contour create_dicom_contours method")
dicom_cont = s.create_dicom_contours(v.cube.create_dicom())
self.assertEqual(len(dicom_cont), 1)
contour = s.contours[0]
logger.info("Checking Contour calculate_center method")
center, area = contour.calculate_center()
self.assertAlmostEqual(center[0], 10.0)
self.assertAlmostEqual(center[1], 10.0)
self.assertAlmostEqual(center[2], 12.0) # TODO why 12 ?
self.assertGreater(area, 100.0)
logger.info("Checking Contour vdx_string method")
self.assertGreater(len(contour.vdx_string()), 1)
logger.info("Checking Contour number_of_points method")
self.assertEqual(contour.number_of_points(), 99)
logger.info("Checking Contour has_childs method")
self.assertFalse(
contour.has_childs()) # TODO why doesn't have children ?
contour.print_child(level=0)
logger.info("Test of Voi get_min_max method")
s_min, s_max = v.get_min_max()
self.assertIsNotNone(s_min)
self.assertIsNotNone(s_max)
# TODO check why get_min_max returns tuple, not a number
self.assertEqual(s_max[2], 18.0)
self.assertEqual(s_min[2], 3.0)
logger.info(
"Subsequent test of Voi get_min_max method, as it modifies the object"
)
s_min, s_max = v.get_min_max()
self.assertIsNotNone(s_min)
self.assertIsNotNone(s_max)
# TODO check why get_min_max returns tuple, not a number
self.assertEqual(s_max[2], 18.0)
self.assertEqual(s_min[2], 3.0)
logger.info("Test of Voi get_2d_slice method (sagittal)")
s2 = v.get_2d_slice(plane=pt.Voi.sagittal, depth=10.0)
self.assertIsNotNone(s2)
logger.info("Test of Voi get_2d_slice method (coronal)")
s3 = v.get_2d_slice(plane=pt.Voi.coronal, depth=5.0)
self.assertIsNotNone(s3)
logger.info("Test of Voi get_2d_projection_on_basis method")
v.get_2d_projection_on_basis(basis=((1, 0, 0), (0, 2, 0)))
logger.info("Test of Voi create_point_tree method")
v.create_point_tree()
self.assertIsNotNone(v.points)
self.assertEqual(len(v.points), 496)
logger.info("Test of Voi get_row_intersections method")
isec = v.get_row_intersections(pos=(10, 10, 9))
self.assertIsNotNone(isec)
self.assertEqual(len(isec), 2)
logger.info("Test of Voi get_voi_cube method")
vc = v.get_voi_cube()
self.assertIsNotNone(vc)
center_pos = v.calculate_center()
self.assertAlmostEqual(center_pos[0], 10.0)
def test_create_voi_sphere(self):
logger.info("Creating CT cube from path " + self.cube000)
c = pt.CtxCube()
c.read(self.cube000)
logger.info("Generating and adding sphere VOI")
v = create_sphere(c, name="cube3", center=[10, 10, 10], radius=8)
self.assertEqual(v.number_of_slices(), 6)
logger.info("Checking Voi vdx_string method")
self.assertGreater(len(v.vdx_string()), 1)
logger.info("Checking Voi get_slice_at_pos method, non-existent slice")
self.assertIsNone(v.get_slice_at_pos(137))
logger.info("Checking Voi get_slice_at_pos method, good slice")
s = v.get_slice_at_pos(11)
self.assertIsNotNone(s)
logger.info("Checking Slice vdx_string method")
self.assertGreater(len(s.vdx_string()), 1)
logger.info("Checking Slice number_of_contours method")
self.assertEqual(s.number_of_contours(), 1)
logger.info("Checking Contour create_dicom_contours method")
dicom_cont = s.create_dicom_contours(v.cube.create_dicom())
self.assertEqual(len(dicom_cont), 1)
contour = s.contours[0]
logger.info("Checking Contour calculate_center method")
center, area = contour.calculate_center()
self.assertAlmostEqual(center[0], 10.0)
self.assertAlmostEqual(center[1], 10.0)
self.assertAlmostEqual(center[2], 12.0) # TODO why 12 ?
self.assertGreater(area, 100.0)
logger.info("Checking Contour vdx_string method")
self.assertGreater(len(contour.vdx_string()), 1)
logger.info("Checking Contour number_of_points method")
self.assertEqual(contour.number_of_points(), 99)
logger.info("Checking Contour has_childs method")
self.assertFalse(contour.has_childs()) # TODO why doesn't have children ?
contour.print_child(level=0)
logger.info("Test of Voi get_min_max method")
s_min, s_max = v.get_min_max()
self.assertIsNotNone(s_min)
self.assertIsNotNone(s_max)
# TODO check why get_min_max returns tuple, not a number
self.assertEqual(s_max[2], 18.0)
self.assertEqual(s_min[2], 3.0)
logger.info("Subsequent test of Voi get_min_max method, as it modifies the object")
s_min, s_max = v.get_min_max()
self.assertIsNotNone(s_min)
self.assertIsNotNone(s_max)
# TODO check why get_min_max returns tuple, not a number
self.assertEqual(s_max[2], 18.0)
self.assertEqual(s_min[2], 3.0)
logger.info("Test of Voi get_2d_slice method (sagittal)")
s2 = v.get_2d_slice(plane=pt.Voi.sagittal, depth=10.0)
self.assertIsNotNone(s2)
logger.info("Test of Voi get_2d_slice method (coronal)")
s3 = v.get_2d_slice(plane=pt.Voi.coronal, depth=5.0)
self.assertIsNotNone(s3)
logger.info("Test of Voi get_2d_projection_on_basis method")
v.get_2d_projection_on_basis(basis=((1, 0, 0), (0, 2, 0)))
logger.info("Test of Voi create_point_tree method")
v.create_point_tree()
self.assertIsNotNone(v.points)
self.assertEqual(len(v.points), 496)
logger.info("Test of Voi get_row_intersections method")
isec = v.get_row_intersections(pos=(10, 10, 9))
self.assertIsNotNone(isec)
self.assertEqual(len(isec), 2)
logger.info("Test of Voi get_voi_cube method")
vc = v.get_voi_cube()
self.assertIsNotNone(vc)
center_pos = v.calculate_center()
self.assertAlmostEqual(center_pos[0], 10.0)
