"""
Test ants.learn module
nptest.assert_allclose
self.assertEqual
self.assertTrue
"""
import os
import unittest
from common import run_tests
from tempfile import mktemp
# Prevent displaying figures
import matplotlib as mpl
backend_ = mpl.get_backend()
mpl.use("Agg")
import numpy as np
import numpy.testing as nptest
import ants
class TestModule_plot(unittest.TestCase):
def setUp(self):
img2d = ants.image_read(ants.get_ants_data('r16'))
img3d = ants.image_read(ants.get_ants_data('mni'))
self.imgs = [img2d, img3d]
def tearDown(self):
pass
def test_plot_example(self):
filename = mktemp(suffix='.png')
for img in self.imgs:
ants.plot(img)
ants.plot(img, overlay=img*2)
ants.plot(img, overlay=img*2)
ants.plot(img, filename=filename)
def test_extra_plot(self):
img = ants.image_read(ants.get_ants_data('r16'))
ants.plot(img, overlay=img*2, domain_image_map=ants.image_read(ants.get_data('r64')))
img = ants.image_read(ants.get_ants_data('r16'))
ants.plot(img, crop=True)
img = ants.image_read(ants.get_ants_data('mni'))
ants.plot(img, overlay=img*2,
domain_image_map=ants.image_read(ants.get_data('mni')).resample_image((4,4,4)))
img = ants.image_read(ants.get_ants_data('mni'))
ants.plot(img, overlay=img*2, reorient=True, crop=True)
def test_random(self):
img = ants.image_read(ants.get_ants_data('r16'))
img3 = ants.image_read(ants.get_data('r64'))
img2 = ants.image_read(ants.get_ants_data('mni'))
imgv = ants.merge_channels([img2])
ants.plot(img2, axis='x', scale=True, ncol=1)
ants.plot(img2, axis='y', scale=(0.05, 0.95))
ants.plot(img2, axis='z', slices=[10,20,30], title='Test', cbar=True,
cbar_vertical=True)
ants.plot(img2, cbar=True, cbar_vertical=False)
ants.plot(img, black_bg=False, title='Test', cbar=True)
imgx = img2.clone()
imgx.set_spacing((10,1,1))
ants.plot(imgx)
ants.plot(ants.get_ants_data('r16'), overlay=ants.get_data('r64'), blend=True)
with self.assertRaises(Exception):
ants.plot(ants.get_ants_data('r16'), overlay=123)
with self.assertRaises(Exception):
ants.plot(ants.get_ants_data('r16'), overlay=ants.merge_channels([img,img]))
ants.plot(ants.from_numpy(np.zeros((100,100))))
ants.plot(img.clone('unsigned int'))
ants.plot(img, domain_image_map=img3)
with self.assertRaises(Exception):
ants.plot(123)
class TestModule_plot_ortho(unittest.TestCase):
def setUp(self):
img3d = ants.image_read(ants.get_ants_data('mni'))
self.imgs = [img3d]
def tearDown(self):
pass
def test_plot_example(self):
filename = mktemp(suffix='.png')
for img in self.imgs:
ants.plot_ortho(img)
ants.plot_ortho(img, filename=filename)
def test_plot_extra(self):
img = ants.image_read(ants.get_ants_data('mni'))
ants.plot_ortho(img, overlay=img*2,
domain_image_map=ants.image_read(ants.get_data('mni')))
img = ants.image_read(ants.get_ants_data('mni'))
ants.plot_ortho(img, overlay=img*2, reorient=True, crop=True)
def test_random_params(self):
img = ants.image_read(ants.get_ants_data('mni')).resample_image((4,4,4))
img2 = ants.image_read(ants.get_data('r16'))
ants.plot_ortho(ants.get_data('mni'), overlay=ants.get_data('mni'))
with self.assertRaises(Exception):
ants.plot_ortho(123)
with self.assertRaises(Exception):
ants.plot_ortho(img2)
with self.assertRaises(Exception):
ants.plot_ortho(img, overlay=img2)
imgx = img.clone()
imgx.set_spacing((3,3,3))
ants.plot_ortho(img,overlay=imgx)
ants.plot_ortho(img.clone('unsigned int'),overlay=img, blend=True)
imgx = img.clone()
imgx.set_spacing((10,1,1))
ants.plot_ortho(imgx)
ants.plot_ortho(img, flat=True, title='Test', text='This is a test')
ants.plot_ortho(img, title='Test', text='This is a test', cbar=True)
with self.assertRaises(Exception):
ants.plot_ortho(img, domain_image_map=123)
with self.assertRaises(Exception):
ants.plot_orto(ants.merge_channels([img,img]))
class TestModule_plot_ortho_stack(unittest.TestCase):
def setUp(self):
self.img = ants.image_read(ants.get_ants_data('mni'))
def tearDown(self):
pass
def test_plot_example(self):
filename = mktemp(suffix='.png')
ants.plot_ortho_stack([self.img, self.img])
ants.plot_ortho_stack([self.img, self.img], filename=filename)
def test_extra_ortho_stack(self):
img = ants.image_read(ants.get_ants_data('mni'))
ants.plot_ortho_stack([img, img], overlays=[img*2, img*2],
domain_image_map=ants.image_read(ants.get_data('mni')))
img = ants.image_read(ants.get_ants_data('mni'))
ants.plot_ortho_stack([img, img], overlays=[img*2, img*2], reorient=True, crop=True)
class TestModule_plot_hist(unittest.TestCase):
def setUp(self):
img2d = ants.image_read(ants.get_ants_data('r16'))
img3d = ants.image_read(ants.get_ants_data('mni'))
self.imgs = [img2d, img3d]
def tearDown(self):
pass
def test_plot_example(self):
filename = mktemp(suffix='.png')
for img in self.imgs:
ants.plot_hist(img)
class TestModule_plot_grid(unittest.TestCase):
def setUp(self):
mni1 = ants.image_read(ants.get_data('mni'))
mni2 = mni1.smooth_image(1.)
mni3 = mni1.smooth_image(2.)
mni4 = mni1.smooth_image(3.)
self.images3d = np.asarray([[mni1, mni2],
[mni3, mni4]])
self.images2d = np.asarray([[mni1.slice_image(2,100), mni2.slice_image(2,100)],
[mni3.slice_image(2,100), mni4.slice_image(2,100)]])
def tearDown(self):
pass
def test_plot_example(self):
ants.plot_grid(self.images3d, slices=100)
# should take middle slices if none are given
ants.plot_grid(self.images3d)
# should work with 2d images
ants.plot_grid(self.images2d)
def test_examples(self):
mni1 = ants.image_read(ants.get_data('mni'))
mni2 = mni1.smooth_image(1.)
mni3 = mni1.smooth_image(2.)
mni4 = mni1.smooth_image(3.)
images = np.asarray([[mni1, mni2],
[mni3, mni4]])
slices = np.asarray([[100, 100],
[100, 100]])
ants.plot_grid(images=images, slices=slices, title='2x2 Grid')
images2d = np.asarray([[mni1.slice_image(2,100), mni2.slice_image(2,100)],
[mni3.slice_image(2,100), mni4.slice_image(2,100)]])
ants.plot_grid(images=images2d, title='2x2 Grid Pre-Sliced')
ants.plot_grid(images.reshape(1,4), slices.reshape(1,4), title='1x4 Grid')
ants.plot_grid(images.reshape(4,1), slices.reshape(4,1), title='4x1 Grid')
# Padding between rows and/or columns
ants.plot_grid(images, slices, cpad=0.02, title='Col Padding')
ants.plot_grid(images, slices, rpad=0.02, title='Row Padding')
ants.plot_grid(images, slices, rpad=0.02, cpad=0.02, title='Row and Col Padding')
# Adding plain row and/or column labels
ants.plot_grid(images, slices, title='Adding Row Labels', rlabels=['Row #1', 'Row #2'])
ants.plot_grid(images, slices, title='Adding Col Labels', clabels=['Col #1', 'Col #2'])
ants.plot_grid(images, slices, title='Row and Col Labels',
rlabels=['Row 1', 'Row 2'], clabels=['Col 1', 'Col 2'])
# Making a publication-quality image
images = np.asarray([[mni1, mni2, mni2],
[mni3, mni4, mni4]])
slices = np.asarray([[100, 100, 100],
[100, 100, 100]])
axes = np.asarray([[0, 1, 2],
[0, 1, 2]])
ants.plot_grid(images, slices, axes, title='Publication Figures with ANTsPy',
tfontsize=20, title_dy=0.03, title_dx=-0.04,
rlabels=['Row 1', 'Row 2'],
clabels=['Col 1', 'Col 2', 'Col 3'],
rfontsize=16, cfontsize=16)
class TestModule_plot_ortho_stack(unittest.TestCase):
def setUp(self):
pass
def tearDown(self):
pass
def test_random_ortho_stack_params(self):
img = ants.image_read(ants.get_data('mni')).resample_image((4,4,4))
img2 = ants.image_read(ants.get_data('r16')).resample_image((4,4))
ants.plot_ortho_stack([ants.get_data('mni'), ants.get_data('mni')])
ants.plot_ortho_stack([ants.get_data('mni'), ants.get_data('mni')],
overlays=[ants.get_data('mni'), ants.get_data('mni')])
with self.assertRaises(Exception):
ants.plot_ortho_stack([1,2,3])
with self.assertRaises(Exception):
ants.plot_ortho_stack([img2,img2])
with self.assertRaises(Exception):
ants.plot_ortho_stack([img,img], overlays=[img2,img2])
with self.assertRaises(Exception):
ants.plot_ortho_stack([img,img], overlays=[1,2])
imgx = img.clone()
imgx.set_spacing((2,2,2))
ants.plot_ortho_stack([img,imgx])
imgx.set_spacing((2,1,1))
ants.plot_ortho_stack([imgx,img])
ants.plot_ortho_stack([img,img], scale=True, transpose=True,
title='Test', colpad=1, rowpad=1,
xyz_lines=True)
ants.plot_ortho_stack([img,img], scale=(0.05,0.95))
if __name__ == '__main__':
run_tests()
