def test_num_digits(self):
from jicbioimage.core.image import Image3D
self.assertEqual(Image3D._num_digits(1), 1)
self.assertEqual(Image3D._num_digits(9), 1)
self.assertEqual(Image3D._num_digits(10), 2)
self.assertEqual(Image3D._num_digits(99), 2)
self.assertEqual(Image3D._num_digits(100), 3)
def test_num_digits(self):
from jicbioimage.core.image import Image3D
self.assertEqual(Image3D._num_digits(1), 1)
self.assertEqual(Image3D._num_digits(9), 1)
self.assertEqual(Image3D._num_digits(10), 2)
self.assertEqual(Image3D._num_digits(99), 2)
self.assertEqual(Image3D._num_digits(100), 3)
def test_scaling_of_written_files(self):
from jicbioimage.core.image import Image3D, Image
directory = os.path.join(TMP_DIR, "im3d")
z0 = np.zeros((50, 50), dtype=np.uint8)
z1 = np.ones((50, 50), dtype=np.uint8)
stack = np.dstack([z0, z1])
im3d = Image3D.from_array(stack)
im3d.to_directory(directory)
im0 = Image.from_file(os.path.join(directory, "z0.png"))
im1 = Image.from_file(os.path.join(directory, "z1.png"))
self.assertTrue(np.array_equal(z0, im0))
self.assertTrue(np.array_equal(z1 * 255, im1))
z2 = np.ones((50, 50), dtype=np.uint8) * 255
stack = np.dstack([z0, z1, z2])
im3d = Image3D.from_array(stack)
im3d.to_directory(directory)
im0 = Image.from_file(os.path.join(directory, "z0.png"))
im1 = Image.from_file(os.path.join(directory, "z1.png"))
im2 = Image.from_file(os.path.join(directory, "z2.png"))
self.assertTrue(np.array_equal(z0, im0))
self.assertTrue(np.array_equal(z1, im1))
self.assertTrue(np.array_equal(z2 * 255, im1))
def test_scaling_of_written_files(self):
from jicbioimage.core.image import Image3D, Image
directory = os.path.join(TMP_DIR, "im3d")
z0 = np.zeros((50,50), dtype=np.uint8)
z1 = np.ones((50, 50), dtype=np.uint8)
stack = np.dstack([z0, z1])
im3d = Image3D.from_array(stack)
im3d.to_directory(directory)
im0 = Image.from_file(os.path.join(directory, "z0.png"))
im1 = Image.from_file(os.path.join(directory, "z1.png"))
self.assertTrue(np.array_equal(z0, im0))
self.assertTrue(np.array_equal(z1*255, im1))
z2 = np.ones((50, 50), dtype=np.uint8) * 255
stack = np.dstack([z0, z1, z2])
im3d = Image3D.from_array(stack)
im3d.to_directory(directory)
im0 = Image.from_file(os.path.join(directory, "z0.png"))
im1 = Image.from_file(os.path.join(directory, "z1.png"))
im2 = Image.from_file(os.path.join(directory, "z2.png"))
self.assertTrue(np.array_equal(z0, im0))
self.assertTrue(np.array_equal(z1, im1))
self.assertTrue(np.array_equal(z2*255, im1))
def test_from_array_with_name(self):
from jicbioimage.core.image import Image3D
ar = np.zeros((50, 50, 50), dtype=np.uint8)
im = Image3D.from_array(ar, name='Test1')
self.assertEqual(len(im.history), 0)
self.assertEqual(im.history.creation,
'Created Image3D from array as Test1')
def test_from_array(self):
from jicbioimage.core.image import Image3D
ar = np.zeros((50,50,50), dtype=np.uint8)
im = Image3D.from_array(ar)
self.assertTrue(isinstance(im, Image3D))
self.assertEqual(len(im.history), 0)
self.assertEqual(im.history.creation, 'Created Image3D from array')
def discrete_gaussian_filter(im3d, variance):
itk_im = sitk.GetImageFromArray(im3d)
gaussian_filter = sitk.DiscreteGaussianImageFilter()
gaussian_filter.SetVariance(variance)
itk_im = gaussian_filter.Execute(itk_im)
return Image3D.from_array(sitk.GetArrayFromImage(itk_im),
log_in_history=False)
def test_from_array(self):
from jicbioimage.core.image import Image3D
ar = np.zeros((50, 50, 50), dtype=np.uint8)
im = Image3D.from_array(ar)
self.assertTrue(isinstance(im, Image3D))
self.assertEqual(len(im.history), 0)
self.assertEqual(im.history.creation, 'Created Image3D from array')
def test_instantiation_from_shape_with_name(self):
from jicbioimage.core.image import Image3D
image = Image3D((50, 50, 50), name='test')
self.assertEqual(image.name, 'test')
self.assertEqual(len(image.history), 0)
self.assertEqual(
image.history.creation,
'Instantiated Image3D from shape (50, 50, 50) as test')
def test_instantiation_from_shape(self):
from jicbioimage.core.image import Image3D
image = Image3D((50, 50, 50))
self.assertTrue(isinstance(image, np.ndarray))
self.assertEqual(image.shape, (50, 50, 50))
self.assertEqual(len(image.history), 0)
self.assertEqual(image.history.creation,
'Instantiated Image3D from shape (50, 50, 50)')
def to_directory(self, directory):
if not os.path.isdir(directory):
os.mkdir(directory)
xdim, ydim, zdim = self.shape
num_digits = Image3D._num_digits(zdim-1)
for z in range(zdim):
num = str(z).zfill(num_digits)
fname = "z{}.png".format(num)
fpath = os.path.join(directory, fname)
with open(fpath, "wb") as fh:
im = Image.from_array(unique_color_array(self[:, :, z]))
fh.write(im.png())
def test_to_directory(self):
from jicbioimage.core.image import Image3D
directory = os.path.join(TMP_DIR, "im3d")
im3d = Image3D((50, 50, 10))
im3d.to_directory(directory)
expected = [
"z0.png", "z1.png", "z2.png", "z3.png", "z4.png", "z5.png",
"z6.png", "z7.png", "z8.png", "z9.png"
]
actual = os.listdir(directory)
for f in expected:
self.assertTrue(f in actual)
def test_naming_with_two_digit_number(self):
from jicbioimage.core.image import Image3D
directory = os.path.join(TMP_DIR, "im3d")
im3d = Image3D((50, 50, 11))
im3d.to_directory(directory)
expected = [
"z00.png", "z01.png", "z02.png", "z03.png", "z04.png", "z05.png",
"z06.png", "z07.png", "z08.png", "z09.png", "z10.png"
]
actual = os.listdir(directory)
for f in expected:
self.assertTrue(f in actual)
def test_from_directory(self):
from jicbioimage.core.image import Image3D, Image
directory = os.path.join(TMP_DIR)
with open(os.path.join(directory, 'junk.txt'), "w") as fh:
fh.write("junk")
z0 = np.zeros((50, 50), dtype=np.uint8)
z1 = np.ones((50, 50), dtype=np.uint8) * 255
for i, z in enumerate([z0, z1]):
im = Image.from_array(z)
fpath = os.path.join(directory, "z{}.png".format(i))
with open(fpath, "wb") as fh:
fh.write(im.png())
im3d = Image3D.from_directory(TMP_DIR)
self.assertTrue(isinstance(im3d, Image3D))
self.assertEqual(im3d.shape, (50, 50, 2))
stack = np.dstack([z0, z1])
self.assertTrue(np.array_equal(im3d, stack))
def test_from_directory(self):
from jicbioimage.core.image import Image3D, Image
directory = os.path.join(TMP_DIR)
with open(os.path.join(directory, 'junk.txt'), "w") as fh:
fh.write("junk")
z0 = np.zeros((50,50), dtype=np.uint8)
z1 = np.ones((50, 50), dtype=np.uint8) * 255
for i, z in enumerate([z0, z1]):
im = Image.from_array(z)
fpath = os.path.join(directory, "z{}.png".format(i))
with open(fpath, "wb") as fh:
fh.write(im.png())
im3d = Image3D.from_directory(TMP_DIR)
self.assertTrue(isinstance(im3d, Image3D))
self.assertEqual(im3d.shape, (50, 50, 2))
stack = np.dstack([z0, z1])
self.assertTrue(np.array_equal(im3d, stack))
def test_from_array_no_history(self):
from jicbioimage.core.image import Image3D
ar = np.zeros((50, 50, 50), dtype=np.uint8)
im = Image3D.from_array(ar, log_in_history=False)
self.assertEqual(len(im.history), 0)
def filter_median(im3d):
itk_im = sitk.GetImageFromArray(im3d)
median_filter = sitk.MedianImageFilter()
itk_im = median_filter.Execute(itk_im)
return Image3D.from_array(sitk.GetArrayFromImage(itk_im),
log_in_history=False)
def get_stack(self):
return Image3D.from_directory(self.directories[self.current])
def add_height(image):
stack = np.dstack([image, image, image])
return Image3D.from_array(stack)
def gradient_magnitude(im3d):
itk_im = sitk.GetImageFromArray(im3d)
itk_im = sitk.GradientMagnitude(itk_im)
return Image3D.from_array(sitk.GetArrayFromImage(itk_im),
log_in_history=False)
def test_from_array_no_history(self):
from jicbioimage.core.image import Image3D
ar = np.zeros((50,50,50), dtype=np.uint8)
im = Image3D.from_array(ar, log_in_history=False)
self.assertEqual(len(im.history), 0)
def test_from_array_with_name(self):
from jicbioimage.core.image import Image3D
ar = np.zeros((50,50,50), dtype=np.uint8)
im = Image3D.from_array(ar, name='Test1')
self.assertEqual(len(im.history), 0)
self.assertEqual(im.history.creation, 'Created Image3D from array as Test1')
def test_instantiation_from_shape_no_history(self):
from jicbioimage.core.image import Image3D
image = Image3D((50, 50, 50), log_in_history=False)
self.assertEqual(len(image.history), 0)
def test_default_type(self):
from jicbioimage.core.image import Image3D
image = Image3D((50, 50, 50))
self.assertEqual(image.dtype, np.uint8,
'Image type not np.uint8 but {}'.format(image.dtype))
def test_default_name(self):
from jicbioimage.core.image import Image3D
image = Image3D((50, 50, 50))
self.assertTrue(image.name is None)