def test_user_given_cmap_with_colorbar():
img = load_mni152_template()
oslicer = OrthoSlicer(cut_coords=(0, 0, 0))
# Test with cmap given as a string
oslicer.add_overlay(img, cmap='Paired', colorbar=True)
oslicer.close()
def test_demo_ortho_slicer():
# This is only a smoke test
mp.use('template', warn=False)
import matplotlib.pyplot as plt
plt.switch_backend('template')
plt.clf()
oslicer = OrthoSlicer(cut_coords=(0, 0, 0))
img = load_mni152_template()
oslicer.add_overlay(img, cmap=plt.cm.gray)
oslicer.close()
def test_contour_fillings_levels_in_add_contours():
oslicer = OrthoSlicer(cut_coords=(0, 0, 0))
img = load_mni152_template()
# levels should be atleast 2
# If single levels are passed then we force upper level to be inf
oslicer.add_contours(img, filled=True, colors='r',
alpha=0.2, levels=[0.])
# If two levels are passed, it should be increasing from zero index
# In this case, we simply omit appending inf
oslicer.add_contours(img, filled=True, colors='b',
alpha=0.1, levels=[0., 0.2])
def test_demo_ortho_slicer():
# This is only a smoke test
oslicer = OrthoSlicer(cut_coords=(0, 0, 0))
img = load_mni152_template()
oslicer.add_overlay(img, cmap=plt.cm.gray)
oslicer.title("display mode is ortho")
oslicer.close()
def test_data_complete_mask():
"""This special case test is due to matplotlib 2.1.0.
When the data is completely masked, then we have plotting issues
See similar issue #9280 reported in matplotlib. This function
tests the patch added for this particular issue.
"""
# data is completely masked
data = np.zeros((10, 20, 30))
affine = np.eye(4)
img = nibabel.Nifti1Image(data, affine)
oslicer = OrthoSlicer(cut_coords=(0, 0, 0))
oslicer.add_overlay(img)
oslicer.close()
def test_annotations():
# Check calls to display.annotate()
# In particular, exercise some of the keyword arguments for scale bars
orthoslicer = OrthoSlicer(cut_coords=(None, None, None))
orthoslicer.annotate(size=10, left_right=True, positions=False)
orthoslicer.annotate(size=12,
left_right=False,
positions=False,
scalebar=True,
scale_size=2.5,
scale_units='cm',
scale_loc=3)
orthoslicer.close()
def test_add_markers_cut_coords_is_none():
"""Tests a special case for ``add_markers`` when ``cut_coords`` are None.
This case is used when coords are placed on glass brain.
"""
orthoslicer = OrthoSlicer(cut_coords=(None, None, None))
orthoslicer.add_markers([(0, 0, 2)])
orthoslicer.close()
def test_user_given_cmap_with_colorbar():
img = load_mni152_template()
oslicer = OrthoSlicer(cut_coords=(0, 0, 0))
# Test with cmap given as a string
oslicer.add_overlay(img, cmap='Paired', colorbar=True)
oslicer.close()
def test_annotations():
# Check calls to display.annotate()
# In particular, exercise some of the keyword arguments for scale bars
orthoslicer = OrthoSlicer(cut_coords=(None, None, None))
orthoslicer.annotate(size=10, left_right=True, positions=False)
orthoslicer.annotate(size=12, left_right=False, positions=False,
scalebar=True,
scale_size=2.5,
scale_units='cm',
scale_loc=3)
orthoslicer.close()
def test_annotations():
"""Tests for ``display.annotate()``.
In particular, exercise some of the keyword arguments for scale bars.
"""
orthoslicer = OrthoSlicer(cut_coords=(None, None, None))
orthoslicer.annotate(size=10, left_right=True, positions=False)
orthoslicer.annotate(size=12,
left_right=False,
positions=False,
scalebar=True,
scale_size=2.5,
scale_units='cm',
scale_loc=3,
frameon=True)
orthoslicer.close()
def test_demo_ortho_slicer():
# This is only a smoke test
mp.use('template', warn=False)
import pylab as pl
pl.switch_backend('template')
pl.clf()
oslicer = OrthoSlicer(cut_coords=(0, 0, 0))
img = load_mni152_template()
oslicer.add_overlay(img, cmap=pl.cm.gray)
oslicer.close()
def test_contour_fillings_levels_in_add_contours():
oslicer = OrthoSlicer(cut_coords=(0, 0, 0))
img = load_mni152_template()
# levels should be atleast 2
# If single levels are passed then we force upper level to be inf
oslicer.add_contours(img, filled=True, colors='r', alpha=0.2, levels=[0.])
# If two levels are passed, it should be increasing from zero index
# In this case, we simply omit appending inf
oslicer.add_contours(img,
filled=True,
colors='b',
alpha=0.1,
levels=[0., 0.2])
def test_data_complete_mask():
"""This special case test is due to matplotlib 2.1.0.
When the data is completely masked, then we have plotting issues
See similar issue #9280 reported in matplotlib. This function
tests the patch added for this particular issue.
"""
# data is completely masked
data = np.zeros((10, 20, 30))
affine = np.eye(4)
img = nibabel.Nifti1Image(data, affine)
oslicer = OrthoSlicer(cut_coords=(0, 0, 0))
oslicer.add_overlay(img)
oslicer.close()
def test_contour_fillings_levels_in_add_contours():
oslicer = OrthoSlicer(cut_coords=(0, 0, 0))
img = load_mni152_template()
# levels should be atleast 2
# If single levels are passed then we force upper level to be inf
oslicer.add_contours(img, filled=True, colors='r', alpha=0.2, levels=[0.])
# If two levels are passed, it should be increasing from zero index
# In this case, we simply omit appending inf
oslicer.add_contours(img,
filled=True,
colors='b',
alpha=0.1,
levels=[0., 0.2])
# without passing colors and alpha. In this case, default values are
# chosen from matplotlib
oslicer.add_contours(img, filled=True, levels=[0., 0.2])
# levels with only one value
oslicer.add_contours(img, filled=True, levels=[0.])
# without passing levels, should work with default levels from
# matplotlib
oslicer.add_contours(img, filled=True)
def test_add_markers_cut_coords_is_none():
# A special case test for add_markers when cut_coords are None. This
# case is used when coords are placed on glass brain
orthoslicer = OrthoSlicer(cut_coords=(None, None, None))
orthoslicer.add_markers([(0, 0, 2)])
orthoslicer.close()
def test_contour_fillings_levels_in_add_contours():
oslicer = OrthoSlicer(cut_coords=(0, 0, 0))
img = load_mni152_template()
# levels should be atleast 2
# If single levels are passed then we force upper level to be inf
oslicer.add_contours(img, filled=True, colors='r',
alpha=0.2, levels=[0.])
# If two levels are passed, it should be increasing from zero index
# In this case, we simply omit appending inf
oslicer.add_contours(img, filled=True, colors='b',
alpha=0.1, levels=[0., 0.2])
# without passing colors and alpha. In this case, default values are
# chosen from matplotlib
oslicer.add_contours(img, filled=True, levels=[0., 0.2])
# levels with only one value
oslicer.add_contours(img, filled=True, levels=[0.])
# without passing levels, should work with default levels from
# matplotlib
oslicer.add_contours(img, filled=True)
def test_add_markers_cut_coords_is_none():
# A special case test for add_markers when cut_coords are None. This
# case is used when coords are placed on glass brain
orthoslicer = OrthoSlicer(cut_coords=(None, None, None))
orthoslicer.add_markers([(0, 0, 2)])
orthoslicer.close()
def test_user_given_cmap_with_colorbar(img):
"""Test cmap provided as a string with ``OrthoSlicer``."""
oslicer = OrthoSlicer(cut_coords=(0, 0, 0))
oslicer.add_overlay(img, cmap='Paired', colorbar=True)
oslicer.close()
def test_demo_ortho_slicer():
# This is only a smoke test
oslicer = OrthoSlicer(cut_coords=(0, 0, 0))
img = load_mni152_template()
oslicer.add_overlay(img, cmap=plt.cm.gray)
oslicer.close()
def test_position_annotation_with_decimals():
"""Test of decimals position annotation with precision of 2."""
orthoslicer = OrthoSlicer(cut_coords=(0, 0, 0))
orthoslicer.annotate(positions=True, decimals=2)
orthoslicer.close()
