def test_3d_rgb(self):
testing_dir = os.path.join(os.path.dirname(os.path.realpath(__file__)), "testing_data")
keys = "image"
xforms = Compose(
[
LoadImaged(keys=keys),
AddChanneld(keys=keys),
ScaleIntensityd(keys=keys),
# change to RGB color image
RepeatChanneld(keys=keys, repeats=3),
]
)
image_path = os.path.join(testing_dir, "anatomical.nii")
ims = xforms({keys: image_path})
fig = pyplot.figure() # external figure
fig, _ = matshow3d(
volume=ims[keys],
fig=fig,
figsize=(2, 2),
frames_per_row=5,
every_n=2,
frame_dim=-1,
channel_dim=0,
show=False,
)
with tempfile.TemporaryDirectory() as tempdir:
tempimg = f"{tempdir}/matshow3d_rgb_test.png"
fig.savefig(tempimg)
comp = compare_images(f"{testing_dir}/matshow3d_rgb_test.png", tempimg, 5e-2)
self.assertIsNone(comp, f"value of comp={comp}") # None indicates test passed
def test_samples(self):
testing_dir = os.path.join(os.path.dirname(os.path.realpath(__file__)), "testing_data")
keys = "image"
xforms = Compose(
[
LoadImaged(keys=keys),
AddChanneld(keys=keys),
ScaleIntensityd(keys=keys),
RandSpatialCropSamplesd(keys=keys, roi_size=(8, 8, 5), random_size=True, num_samples=10),
]
)
image_path = os.path.join(testing_dir, "anatomical.nii")
xforms.set_random_state(0)
ims = xforms({keys: image_path})
fig, mat = matshow3d(
[im[keys] for im in ims], title=f"testing {keys}", figsize=(2, 2), frames_per_row=5, every_n=2, show=False
)
self.assertTrue(mat.dtype == np.float32)
with tempfile.TemporaryDirectory() as tempdir:
tempimg = f"{tempdir}/matshow3d_patch_test.png"
fig.savefig(tempimg)
comp = compare_images(f"{testing_dir}/matshow3d_patch_test.png", tempimg, 5e-2, in_decorator=True)
if comp:
print("not none comp: ", comp) # matplotlib 3.2.2
np.testing.assert_allclose(comp["rms"], 30.786983, atol=1e-3, rtol=1e-3)
else:
self.assertIsNone(comp, f"value of comp={comp}") # None indicates test passed