def test_volume():
vol1 = imageio.imread("imageio:stent.npz")
assert vol1.shape == (256, 128, 128)
fname = os.path.join(test_dir, "stent.bsdf")
imageio.volsave(fname, vol1)
vol2 = imageio.volread(fname)
assert vol1.shape == vol2.shape
assert np.all(vol1 == vol2)
def test_volume():
vol1 = imageio.imread("imageio:stent.npz")
assert vol1.shape == (256, 128, 128)
fname = os.path.join(test_dir, "stent.bsdf")
imageio.volsave(fname, vol1)
vol2 = imageio.volread(fname)
assert vol1.shape == vol2.shape
assert np.all(vol1 == vol2)
def test_volume(test_images, tmp_path):
fname1 = test_images / "stent.npz"
vol1 = imageio.imread(fname1)
assert vol1.shape == (256, 128, 128)
fname = tmp_path / "stent.bsdf"
imageio.volsave(fname, vol1)
vol2 = imageio.volread(fname)
assert vol1.shape == vol2.shape
assert np.all(vol1 == vol2)
def test_functions():
""" Test the user-facing API functions """
# Test help(), it prints stuff, so we just check whether that goes ok
imageio.help() # should print overview
imageio.help("PNG") # should print about PNG
fname1 = get_remote_file("images/chelsea.png", test_dir)
fname2 = fname1[:-3] + "jpg"
fname3 = fname1[:-3] + "notavalidext"
open(fname3, "wb")
# Test read()
R1 = imageio.read(fname1)
R2 = imageio.read(fname1, "png")
assert R1.format is R2.format
# Fail
raises(ValueError, imageio.read, fname3) # existing but not readable
raises(FileNotFoundError, imageio.read, "notexisting.barf")
raises(IndexError, imageio.read, fname1, "notexistingformat")
# Test save()
W1 = imageio.save(fname2)
W2 = imageio.save(fname2, "JPG")
W1.close()
W2.close()
assert W1.format is W2.format
# Fail
raises(FileNotFoundError, imageio.save,
"~/dirdoesnotexist/wtf.notexistingfile")
# Test imread()
im1 = imageio.imread(fname1)
im2 = imageio.imread(fname1, "png")
assert im1.shape[2] == 3
assert np.all(im1 == im2)
# Test imsave()
if os.path.isfile(fname2):
os.remove(fname2)
assert not os.path.isfile(fname2)
imageio.imsave(fname2, im1[:, :, 0])
imageio.imsave(fname2, im1)
assert os.path.isfile(fname2)
# Test mimread()
fname3 = get_remote_file("images/newtonscradle.gif", test_dir)
ims = imageio.mimread(fname3)
assert isinstance(ims, list)
assert len(ims) > 1
assert ims[0].ndim == 3
assert ims[0].shape[2] in (1, 3, 4)
# Test protection
with raises(RuntimeError):
imageio.mimread("imageio:chelsea.png", "dummy", length=np.inf)
if IS_PYPY:
return # no support for npz format :(
# Test mimsave()
fname5 = fname3[:-4] + "2.npz"
if os.path.isfile(fname5):
os.remove(fname5)
assert not os.path.isfile(fname5)
imageio.mimsave(fname5, [im[:, :, 0] for im in ims])
imageio.mimsave(fname5, ims)
assert os.path.isfile(fname5)
# Test volread()
fname4 = get_remote_file("images/stent.npz", test_dir)
vol = imageio.volread(fname4)
assert vol.ndim == 3
assert vol.shape[0] == 256
assert vol.shape[1] == 128
assert vol.shape[2] == 128
# Test volsave()
volc = np.zeros((10, 10, 10, 3), np.uint8) # color volume
fname6 = os.path.join(test_dir, "images", "stent2.npz")
if os.path.isfile(fname6):
os.remove(fname6)
assert not os.path.isfile(fname6)
imageio.volsave(fname6, volc)
imageio.volsave(fname6, vol)
assert os.path.isfile(fname6)
# Test mvolread()
vols = imageio.mvolread(fname4)
assert isinstance(vols, list)
assert len(vols) == 1
assert vols[0].shape == vol.shape
# Test mvolsave()
if os.path.isfile(fname6):
os.remove(fname6)
assert not os.path.isfile(fname6)
imageio.mvolsave(fname6, [volc, volc])
imageio.mvolsave(fname6, vols)
assert os.path.isfile(fname6)
# Fail for save functions
raises(ValueError, imageio.imsave, fname2, np.zeros((100, 100, 5)))
raises(ValueError, imageio.imsave, fname2, 42)
raises(ValueError, imageio.mimsave, fname5, [np.zeros((100, 100, 5))])
raises(ValueError, imageio.mimsave, fname5, [42])
raises(ValueError, imageio.volsave, fname6, np.zeros((100, 100, 100, 40)))
raises(ValueError, imageio.volsave, fname6, 42)
raises(ValueError, imageio.mvolsave, fname6, [np.zeros((90, 90, 90, 40))])
raises(ValueError, imageio.mvolsave, fname6, [42])
plt.title('Evolution of Mean IoU')
plt.xlabel('epoch')
plt.ylabel('mean intersection over union')
plt.legend(['training', 'validation'])
plt.savefig(save_dir + 'iou.png')
#%% Save some image mask pairs for visual inspection
if (False):
import itertools
import imageio
tds = iter(trainingset)
tds_raw = iter(trainingset_raw)
for i in range(3):
x, y = next(tds)
xr, yr = next(tds_raw)
imageio.volsave(save_dir + "image" + str(i) + ".tif",
x.numpy()[0, ..., 0])
y = y.numpy()[0, ...,
1] # extract foreground map and pad to original size
imageio.volsave(save_dir + "mask" + str(i) + ".tif",
np.pad(y, (44, 44)))
imageio.volsave(save_dir + "mask_raw" + str(i) + ".tif", yr)
# Generate test image and apply deformation step manualy
ti, tm = utilities.getTestImage(mask_size=(220, 220, 220), addAxis=False)
tid, tmd = random_elastic_deform(ti, tm)
imageio.volsave(save_dir + "testimage.tif", ti)
imageio.volsave(save_dir + "testmask.tif", tm)
imageio.volsave(save_dir + "testimage_deformed.tif", tid)
imageio.volsave(save_dir + "testmask_deformed.tif", tmd)
# %%
def test_functions():
""" Test the user-facing API functions """
# Test help(), it prints stuff, so we just check whether that goes ok
imageio.help() # should print overview
imageio.help('PNG') # should print about PNG
fname1 = get_remote_file('images/chelsea.png', test_dir)
fname2 = fname1[:-3] + 'jpg'
fname3 = fname1[:-3] + 'notavalidext'
open(fname3, 'wb')
# Test read()
R1 = imageio.read(fname1)
R2 = imageio.read(fname1, 'png')
assert R1.format is R2.format
# Fail
raises(ValueError, imageio.read, fname3) # existing but not readable
raises(IOError, imageio.read, 'notexisting.barf')
raises(IndexError, imageio.read, fname1, 'notexistingformat')
# Test save()
W1 = imageio.save(fname2)
W2 = imageio.save(fname2, 'JPG')
assert W1.format is W2.format
# Fail
raises(ValueError, imageio.save, 'wtf.notexistingfile')
# Test imread()
im1 = imageio.imread(fname1)
im2 = imageio.imread(fname1, 'png')
assert im1.shape[2] == 3
assert np.all(im1 == im2)
# Test imsave()
if os.path.isfile(fname2):
os.remove(fname2)
assert not os.path.isfile(fname2)
imageio.imsave(fname2, im1[:, :, 0])
imageio.imsave(fname2, im1)
assert os.path.isfile(fname2)
# Test mimread()
fname3 = get_remote_file('images/newtonscradle.gif', test_dir)
ims = imageio.mimread(fname3)
assert isinstance(ims, list)
assert len(ims) > 1
assert ims[0].ndim == 3
assert ims[0].shape[2] in (1, 3, 4)
if IS_PYPY:
return # no support for npz format :(
# Test mimsave()
fname5 = fname3[:-4] + '2.npz'
if os.path.isfile(fname5):
os.remove(fname5)
assert not os.path.isfile(fname5)
imageio.mimsave(fname5, [im[:, :, 0] for im in ims])
imageio.mimsave(fname5, ims)
assert os.path.isfile(fname5)
# Test volread()
fname4 = get_remote_file('images/stent.npz', test_dir)
vol = imageio.volread(fname4)
assert vol.ndim == 3
assert vol.shape[0] == 256
assert vol.shape[1] == 128
assert vol.shape[2] == 128
# Test volsave()
volc = np.zeros((10, 10, 10, 3), np.uint8) # color volume
fname6 = fname4[:-4] + '2.npz'
if os.path.isfile(fname6):
os.remove(fname6)
assert not os.path.isfile(fname6)
imageio.volsave(fname6, volc)
imageio.volsave(fname6, vol)
assert os.path.isfile(fname6)
# Test mvolread()
vols = imageio.mvolread(fname4)
assert isinstance(vols, list)
assert len(vols) == 1
assert vols[0].shape == vol.shape
# Test mvolsave()
if os.path.isfile(fname6):
os.remove(fname6)
assert not os.path.isfile(fname6)
imageio.mvolsave(fname6, [volc, volc])
imageio.mvolsave(fname6, vols)
assert os.path.isfile(fname6)
# Fail for save functions
raises(ValueError, imageio.imsave, fname2, np.zeros((100, 100, 5)))
raises(ValueError, imageio.imsave, fname2, 42)
raises(ValueError, imageio.mimsave, fname5, [np.zeros((100, 100, 5))])
raises(ValueError, imageio.mimsave, fname5, [42])
raises(ValueError, imageio.volsave, fname4, np.zeros((100, 100, 100, 40)))
raises(ValueError, imageio.volsave, fname4, 42)
raises(ValueError, imageio.mvolsave, fname4, [np.zeros((90, 90, 90, 40))])
raises(ValueError, imageio.mvolsave, fname4, [42])
def test_functions(test_images, tmp_path):
"""Test the user-facing API functions"""
# Test help(), it prints stuff, so we just check whether that goes ok
imageio.help() # should print overview
imageio.help("PNG") # should print about PNG
fname1 = test_images / "chelsea.png"
fname2 = tmp_path / fname1.with_suffix(".jpg").name
fname3 = tmp_path / fname1.with_suffix(".notavalidext").name
open(fname3, "wb")
# Test read()
R1 = imageio.read(fname1)
R2 = imageio.read(fname1, "png")
# this tests if the highest priority png plugin and the highest
# priority fallback plugin match.
# Do we really what to enforce this?
assert type(R1) is type(R2)
raises(ValueError, imageio.read, fname3) # existing but not readable
raises(IndexError, imageio.read, fname1, "notexistingformat")
# Note: This is actually a test of Requests. We should probably
# migrate or remove it.
raises(FileNotFoundError, imageio.read, "notexisting.barf")
# Test save()
W1 = imageio.save(fname2)
W2 = imageio.save(fname2, "JPG")
W1.close()
W2.close()
assert type(W1) is type(W2)
# Fail
raises(FileNotFoundError, imageio.save,
"~/dirdoesnotexist/wtf.notexistingfile")
# Test imread()
im1 = imageio.imread(fname1)
im2 = imageio.imread(fname1, "png")
assert im1.shape[2] == 3
assert np.all(im1 == im2)
# Test imsave()
if os.path.isfile(fname2):
os.remove(fname2)
assert not os.path.isfile(fname2)
imageio.imsave(fname2, im1[:, :, 0])
imageio.imsave(fname2, im1)
assert os.path.isfile(fname2)
# Test mimread()
fname3 = test_images / "newtonscradle.gif"
ims = imageio.mimread(fname3)
assert isinstance(ims, list)
assert len(ims) > 1
assert ims[0].ndim == 3
assert ims[0].shape[2] in (1, 3, 4)
# Test protection
with raises(RuntimeError):
imageio.mimread(test_images / "chelsea.png", "dummy", length=np.inf)
if IS_PYPY:
return # no support for npz format :(
# Test mimsave()
fname5 = str(fname3.with_suffix(""))
fname5 += "2.npz"
if os.path.isfile(fname5):
os.remove(fname5)
assert not os.path.isfile(fname5)
imageio.mimsave(fname5, [im[:, :, 0] for im in ims])
imageio.mimsave(fname5, ims)
assert os.path.isfile(fname5)
# Test volread()
fname4 = test_images / "stent.npz"
vol = imageio.volread(fname4)
assert vol.ndim == 3
assert vol.shape[0] == 256
assert vol.shape[1] == 128
assert vol.shape[2] == 128
# Test volsave()
volc = np.zeros((10, 10, 10, 3), np.uint8) # color volume
fname6 = tmp_path / "stent2.npz"
if os.path.isfile(fname6):
os.remove(fname6)
assert not os.path.isfile(fname6)
imageio.volsave(fname6, volc)
imageio.volsave(fname6, vol)
assert os.path.isfile(fname6)
# Test mvolread()
vols = imageio.mvolread(fname4)
assert isinstance(vols, list)
assert len(vols) == 1
assert vols[0].shape == vol.shape
# Test mvolsave()
if os.path.isfile(fname6):
os.remove(fname6)
assert not os.path.isfile(fname6)
imageio.mvolsave(fname6, [volc, volc])
imageio.mvolsave(fname6, vols)
assert os.path.isfile(fname6)
# Fail for save functions
raises(ValueError, imageio.imsave, fname2, np.zeros((100, 100, 5)))
raises(ValueError, imageio.imsave, fname2, 42)
raises(ValueError, imageio.mimsave, fname5, [np.zeros((100, 100, 5))])
raises(ValueError, imageio.mimsave, fname5, [42])
raises(ValueError, imageio.volsave, fname6, np.zeros((100, 100, 100, 40)))
raises(ValueError, imageio.volsave, fname6, 42)
raises(ValueError, imageio.mvolsave, fname6, [np.zeros((90, 90, 90, 40))])
raises(ValueError, imageio.mvolsave, fname6, [42])
import numpy as np
import time
if __name__ == "__main__":
image_path = "./images/3d_example.tif"
volume_write_path = "./results/3d_results.tif"
projection_before_enhance_write_path = "./results/3d_projection_before.png"
projection_after_enhance_write_path = "./results/3d_projection_after.png"
smooth_degree = 0.006
# -- read image
image = imageio.volread(image_path)
image = image / np.max(image)
# -- enhance
tic = time.time()
enhanced_image, enhance_hist = cane_3d(image, smooth_degree)
toc = time.time()
print("Enhancement done: {:.2f}s. The image is of size {}*{}*{}".
format(toc - tic, image.shape[0], image.shape[1], image.shape[2]))
# -- write results
before_project = (np.max(image, axis=0)*255).astype(np.uint8)
after_project = (np.max(enhanced_image, axis=0)*255).astype(np.uint8)
imageio.volsave(volume_write_path, (enhanced_image * 255).astype(np.uint8))
imageio.imwrite(projection_before_enhance_write_path, before_project)
imageio.imwrite(projection_after_enhance_write_path, after_project)
def test_functions():
""" Test the user-facing API functions """
# Test help(), it prints stuff, so we just check whether that goes ok
imageio.help() # should print overview
imageio.help('PNG') # should print about PNG
fname1 = get_remote_file('images/chelsea.png', test_dir)
fname2 = fname1[:-3] + 'jpg'
fname3 = fname1[:-3] + 'notavalidext'
open(fname3, 'wb')
# Test read()
R1 = imageio.read(fname1)
R2 = imageio.read(fname1, 'png')
assert R1.format is R2.format
# Fail
raises(ValueError, imageio.read, fname3) # existing but not readable
raises(IOError, imageio.read, 'notexisting.barf')
raises(IndexError, imageio.read, fname1, 'notexistingformat')
# Test save()
W1 = imageio.save(fname2)
W2 = imageio.save(fname2, 'JPG')
assert W1.format is W2.format
# Fail
raises(ValueError, imageio.save, 'wtf.notexistingfile')
# Test imread()
im1 = imageio.imread(fname1)
im2 = imageio.imread(fname1, 'png')
assert im1.shape[2] == 3
assert np.all(im1 == im2)
# Test imsave()
if os.path.isfile(fname2):
os.remove(fname2)
assert not os.path.isfile(fname2)
imageio.imsave(fname2, im1[:, :, 0])
imageio.imsave(fname2, im1)
assert os.path.isfile(fname2)
# Test mimread()
fname3 = get_remote_file('images/newtonscradle.gif', test_dir)
ims = imageio.mimread(fname3)
assert isinstance(ims, list)
assert len(ims) > 1
assert ims[0].ndim == 3
assert ims[0].shape[2] in (1, 3, 4)
if IS_PYPY:
return # no support for npz format :(
# Test mimsave()
fname5 = fname3[:-4] + '2.npz'
if os.path.isfile(fname5):
os.remove(fname5)
assert not os.path.isfile(fname5)
imageio.mimsave(fname5, [im[:, :, 0] for im in ims])
imageio.mimsave(fname5, ims)
assert os.path.isfile(fname5)
# Test volread()
fname4 = get_remote_file('images/stent.npz', test_dir)
vol = imageio.volread(fname4)
assert vol.ndim == 3
assert vol.shape[0] == 256
assert vol.shape[1] == 128
assert vol.shape[2] == 128
# Test volsave()
volc = np.zeros((10, 10, 10, 3), np.uint8) # color volume
fname6 = fname4[:-4] + '2.npz'
if os.path.isfile(fname6):
os.remove(fname6)
assert not os.path.isfile(fname6)
imageio.volsave(fname6, volc)
imageio.volsave(fname6, vol)
assert os.path.isfile(fname6)
# Test mvolread()
vols = imageio.mvolread(fname4)
assert isinstance(vols, list)
assert len(vols) == 1
assert vols[0].shape == vol.shape
# Test mvolsave()
if os.path.isfile(fname6):
os.remove(fname6)
assert not os.path.isfile(fname6)
imageio.mvolsave(fname6, [volc, volc])
imageio.mvolsave(fname6, vols)
assert os.path.isfile(fname6)
# Fail for save functions
raises(ValueError, imageio.imsave, fname2, np.zeros((100, 100, 5)))
raises(ValueError, imageio.imsave, fname2, 42)
raises(ValueError, imageio.mimsave, fname5, [np.zeros((100, 100, 5))])
raises(ValueError, imageio.mimsave, fname5, [42])
raises(ValueError, imageio.volsave, fname4, np.zeros((100, 100, 100, 40)))
raises(ValueError, imageio.volsave, fname4, 42)
raises(ValueError, imageio.mvolsave, fname4, [np.zeros((90, 90, 90, 40))])
raises(ValueError, imageio.mvolsave, fname4, [42])
def test_functions():
""" Test the user-facing API functions """
# Test help(), it prints stuff, so we just check whether that goes ok
imageio.help() # should print overview
imageio.help("PNG") # should print about PNG
fname1 = get_remote_file("images/chelsea.png", test_dir)
fname2 = fname1[:-3] + "jpg"
fname3 = fname1[:-3] + "notavalidext"
open(fname3, "wb")
# Test read()
R1 = imageio.read(fname1)
R2 = imageio.read(fname1, "png")
assert R1.format is R2.format
# Fail
raises(ValueError, imageio.read, fname3) # existing but not readable
raises(FileNotFoundError, imageio.read, "notexisting.barf")
raises(IndexError, imageio.read, fname1, "notexistingformat")
# Test save()
W1 = imageio.save(fname2)
W2 = imageio.save(fname2, "JPG")
W1.close()
W2.close()
assert W1.format is W2.format
# Fail
raises(FileNotFoundError, imageio.save, "~/dirdoesnotexist/wtf.notexistingfile")
# Test imread()
im1 = imageio.imread(fname1)
im2 = imageio.imread(fname1, "png")
assert im1.shape[2] == 3
assert np.all(im1 == im2)
# Test imsave()
if os.path.isfile(fname2):
os.remove(fname2)
assert not os.path.isfile(fname2)
imageio.imsave(fname2, im1[:, :, 0])
imageio.imsave(fname2, im1)
assert os.path.isfile(fname2)
# Test mimread()
fname3 = get_remote_file("images/newtonscradle.gif", test_dir)
ims = imageio.mimread(fname3)
assert isinstance(ims, list)
assert len(ims) > 1
assert ims[0].ndim == 3
assert ims[0].shape[2] in (1, 3, 4)
# Test protection
with raises(RuntimeError):
imageio.mimread("imageio:chelsea.png", "dummy", length=np.inf)
if IS_PYPY:
return # no support for npz format :(
# Test mimsave()
fname5 = fname3[:-4] + "2.npz"
if os.path.isfile(fname5):
os.remove(fname5)
assert not os.path.isfile(fname5)
imageio.mimsave(fname5, [im[:, :, 0] for im in ims])
imageio.mimsave(fname5, ims)
assert os.path.isfile(fname5)
# Test volread()
fname4 = get_remote_file("images/stent.npz", test_dir)
vol = imageio.volread(fname4)
assert vol.ndim == 3
assert vol.shape[0] == 256
assert vol.shape[1] == 128
assert vol.shape[2] == 128
# Test volsave()
volc = np.zeros((10, 10, 10, 3), np.uint8) # color volume
fname6 = os.path.join(test_dir, "images", "stent2.npz")
if os.path.isfile(fname6):
os.remove(fname6)
assert not os.path.isfile(fname6)
imageio.volsave(fname6, volc)
imageio.volsave(fname6, vol)
assert os.path.isfile(fname6)
# Test mvolread()
vols = imageio.mvolread(fname4)
assert isinstance(vols, list)
assert len(vols) == 1
assert vols[0].shape == vol.shape
# Test mvolsave()
if os.path.isfile(fname6):
os.remove(fname6)
assert not os.path.isfile(fname6)
imageio.mvolsave(fname6, [volc, volc])
imageio.mvolsave(fname6, vols)
assert os.path.isfile(fname6)
# Fail for save functions
raises(ValueError, imageio.imsave, fname2, np.zeros((100, 100, 5)))
raises(ValueError, imageio.imsave, fname2, 42)
raises(ValueError, imageio.mimsave, fname5, [np.zeros((100, 100, 5))])
raises(ValueError, imageio.mimsave, fname5, [42])
raises(ValueError, imageio.volsave, fname6, np.zeros((100, 100, 100, 40)))
raises(ValueError, imageio.volsave, fname6, 42)
raises(ValueError, imageio.mvolsave, fname6, [np.zeros((90, 90, 90, 40))])
raises(ValueError, imageio.mvolsave, fname6, [42])
