def test_plot_surf_roi():
mesh = _generate_surf()
rng = np.random.RandomState(0)
roi1 = rng.randint(0, mesh[0].shape[0], size=5)
roi2 = rng.randint(0, mesh[0].shape[0], size=10)
parcellation = rng.rand(mesh[0].shape[0])
# plot roi
plot_surf_roi(mesh, roi_map=roi1)
plot_surf_roi(mesh, roi_map=roi1, colorbar=True)
# plot parcellation
plot_surf_roi(mesh, roi_map=parcellation)
plot_surf_roi(mesh, roi_map=parcellation, colorbar=True)
# plot roi list
plot_surf_roi(mesh, roi_map=[roi1, roi2])
plot_surf_roi(mesh, roi_map=[roi1, roi2], colorbar=True)
# plot to axes
plot_surf_roi(mesh, roi_map=roi1, ax=None, figure=plt.gcf())
# plot to axes
with tempfile.NamedTemporaryFile() as tmp_file:
plot_surf_roi(mesh, roi_map=roi1, ax=plt.gca(), figure=None,
output_file=tmp_file.name)
with tempfile.NamedTemporaryFile() as tmp_file:
plot_surf_roi(mesh, roi_map=roi1, ax=plt.gca(), figure=None,
output_file=tmp_file.name, colorbar=True)
# Save execution time and memory
plt.close()
def test_plot_surf_error():
mesh = _generate_surf()
rng = np.random.RandomState(0)
# Wrong inputs for view or hemi
assert_raises_regex(ValueError, 'view must be one of',
plot_surf, mesh, view='middle')
assert_raises_regex(ValueError, 'hemi must be one of',
plot_surf, mesh, hemi='lft')
# Wrong size of background image
assert_raises_regex(ValueError,
'bg_map does not have the same number of vertices',
plot_surf, mesh,
bg_map=rng.randn(mesh[0].shape[0] - 1, ))
# Wrong size of surface data
assert_raises_regex(ValueError,
'surf_map does not have the same number of vertices',
plot_surf, mesh,
surf_map=rng.randn(mesh[0].shape[0] + 1, ))
assert_raises_regex(ValueError,
'surf_map can only have one dimension', plot_surf,
mesh, surf_map=rng.randn(mesh[0].shape[0], 2))
def test_plot_surf_stat_map_error():
# Axes3DSubplot has no attribute 'plot_trisurf' for older versions of
# matplotlib
if LooseVersion(matplotlib.__version__) <= LooseVersion('1.3.1'):
raise SkipTest
mesh = _generate_surf()
rng = np.random.RandomState(0)
data = 10 * rng.randn(mesh[0].shape[0], )
# Try to input vmin
assert_raises_regex(ValueError,
'this function does not accept a "vmin" argument',
plot_surf_stat_map,
mesh,
stat_map=data,
vmin=0)
# Wrong size of stat map data
assert_raises_regex(ValueError,
'surf_map does not have the same number of vertices',
plot_surf_stat_map,
mesh,
stat_map=np.hstack((data, data)))
assert_raises_regex(ValueError,
'surf_map can only have one dimension',
plot_surf_stat_map,
mesh,
stat_map=np.vstack((data, data)).T)
def test_plot_surf_stat_map():
mesh = _generate_surf()
rng = np.random.RandomState(0)
bg = rng.randn(mesh[0].shape[0], )
data = 10 * rng.randn(mesh[0].shape[0], )
# Plot mesh with stat map
plot_surf_stat_map(mesh, stat_map=data)
plot_surf_stat_map(mesh, stat_map=data, colorbar=True)
plot_surf_stat_map(mesh, stat_map=data, alpha=1)
# Plot mesh with background and stat map
plot_surf_stat_map(mesh, stat_map=data, bg_map=bg)
plot_surf_stat_map(mesh, stat_map=data, bg_map=bg,
bg_on_data=True, darkness=0.5)
plot_surf_stat_map(mesh, stat_map=data, bg_map=bg, colorbar=True,
bg_on_data=True, darkness=0.5)
# Apply threshold
plot_surf_stat_map(mesh, stat_map=data, bg_map=bg,
bg_on_data=True, darkness=0.5,
threshold=0.3)
plot_surf_stat_map(mesh, stat_map=data, bg_map=bg, colorbar=True,
bg_on_data=True, darkness=0.5,
threshold=0.3)
# Change vmax
plot_surf_stat_map(mesh, stat_map=data, vmax=5)
plot_surf_stat_map(mesh, stat_map=data, vmax=5, colorbar=True)
# Change colormap
plot_surf_stat_map(mesh, stat_map=data, cmap='cubehelix')
plot_surf_stat_map(mesh, stat_map=data, cmap='cubehelix', colorbar=True)
# Plot to axes
axes = plt.subplots(ncols=2, subplot_kw={'projection': '3d'})[1]
for ax in axes.flatten():
plot_surf_stat_map(mesh, stat_map=data, ax=ax)
axes = plt.subplots(ncols=2, subplot_kw={'projection': '3d'})[1]
for ax in axes.flatten():
plot_surf_stat_map(mesh, stat_map=data, ax=ax, colorbar=True)
fig = plot_surf_stat_map(mesh, stat_map=data, colorbar=False)
assert len(fig.axes) == 1
# symmetric_cbar
fig = plot_surf_stat_map(
mesh, stat_map=data, colorbar=True, symmetric_cbar=True)
assert len(fig.axes) == 2
yticklabels = fig.axes[1].get_yticklabels()
first, last = yticklabels[0].get_text(), yticklabels[-1].get_text()
assert float(first) == - float(last)
# no symmetric_cbar
fig = plot_surf_stat_map(
mesh, stat_map=data, colorbar=True, symmetric_cbar=False)
assert len(fig.axes) == 2
yticklabels = fig.axes[1].get_yticklabels()
first, last = yticklabels[0].get_text(), yticklabels[-1].get_text()
assert float(first) != - float(last)
# Save execution time and memory
plt.close()
def test_plot_surf():
# Axes3DSubplot has no attribute 'plot_trisurf' for older versions of
# matplotlib
if LooseVersion(matplotlib.__version__) <= LooseVersion('1.3.1'):
raise SkipTest
mesh = _generate_surf()
rng = np.random.RandomState(0)
bg = rng.randn(mesh[0].shape[0], )
# Plot mesh only
plot_surf(mesh)
# Plot mesh with background
plot_surf(mesh, bg_map=bg)
plot_surf(mesh, bg_map=bg, darkness=0.5)
plot_surf(mesh, bg_map=bg, alpha=0.5)
# Plot different views
plot_surf(mesh, bg_map=bg, hemi='right')
plot_surf(mesh, bg_map=bg, view='medial')
plot_surf(mesh, bg_map=bg, hemi='right', view='medial')
# Save execution time and memory
plt.close()
def test_plot_surf_error():
# Axes3DSubplot has no attribute 'plot_trisurf' for older versions of
# matplotlib
if LooseVersion(matplotlib.__version__) <= LooseVersion('1.3.1'):
raise SkipTest
mesh = _generate_surf()
rng = np.random.RandomState(0)
# Wrong inputs for view or hemi
assert_raises_regex(ValueError, 'view must be one of',
plot_surf, mesh, view='middle')
assert_raises_regex(ValueError, 'hemi must be one of',
plot_surf, mesh, hemi='lft')
# Wrong size of background image
assert_raises_regex(ValueError,
'bg_map does not have the same number of vertices',
plot_surf, mesh,
bg_map=rng.randn(mesh[0].shape[0] - 1, ))
# Wrong size of surface data
assert_raises_regex(ValueError,
'surf_map does not have the same number of vertices',
plot_surf, mesh,
surf_map=rng.randn(mesh[0].shape[0] + 1, ))
assert_raises_regex(ValueError,
'surf_map can only have one dimension', plot_surf,
mesh, surf_map=rng.randn(mesh[0].shape[0], 2))
def test_plot_surf_roi():
# Axes3DSubplot has no attribute 'plot_trisurf' for older versions of
# matplotlib
if LooseVersion(matplotlib.__version__) <= LooseVersion('1.3.1'):
raise SkipTest
mesh = _generate_surf()
rng = np.random.RandomState(0)
roi1 = rng.randint(0, mesh[0].shape[0], size=5)
roi2 = rng.randint(0, mesh[0].shape[0], size=10)
parcellation = rng.rand(mesh[0].shape[0])
# plot roi
plot_surf_roi(mesh, roi_map=roi1)
# plot parcellation
plot_surf_roi(mesh, roi_map=parcellation)
# plot roi list
plot_surf_roi(mesh, roi_map=[roi1, roi2])
# plot to axes
plot_surf_roi(mesh, roi_map=roi1, ax=None, figure=plt.gcf())
# plot to axes
with tempfile.NamedTemporaryFile() as tmp_file:
plot_surf_roi(mesh,
roi_map=roi1,
ax=plt.gca(),
figure=None,
output_file=tmp_file.name)
# Save execution time and memory
plt.close()
def test_plot_surf_roi():
# Axes3DSubplot has no attribute 'plot_trisurf' for older versions of
# matplotlib
if LooseVersion(matplotlib.__version__) <= LooseVersion('1.3.1'):
raise SkipTest
mesh = _generate_surf()
rng = np.random.RandomState(0)
roi1 = rng.randint(0, mesh[0].shape[0], size=5)
roi2 = rng.randint(0, mesh[0].shape[0], size=10)
parcellation = rng.rand(mesh[0].shape[0])
# plot roi
plot_surf_roi(mesh, roi_map=roi1)
# plot parcellation
plot_surf_roi(mesh, roi_map=parcellation)
# plot roi list
plot_surf_roi(mesh, roi_map=[roi1, roi2])
# plot to axes
plot_surf_roi(mesh, roi_map=roi1, ax=None, figure=plt.gcf())
# plot to axes
with tempfile.NamedTemporaryFile() as tmp_file:
plot_surf_roi(mesh, roi_map=roi1, ax=plt.gca(), figure=None,
output_file=tmp_file.name)
# Save execution time and memory
plt.close()
def test_plot_surf_error():
mesh = _generate_surf()
rng = np.random.RandomState(0)
# Wrong inputs for view or hemi
assert_raises_regex(ValueError,
'view must be one of',
plot_surf,
mesh,
view='middle')
assert_raises_regex(ValueError,
'hemi must be one of',
plot_surf,
mesh,
hemi='lft')
# Wrong size of background image
assert_raises_regex(ValueError,
'bg_map does not have the same number of vertices',
plot_surf,
mesh,
bg_map=rng.randn(mesh[0].shape[0] - 1, ))
# Wrong size of surface data
assert_raises_regex(ValueError,
'surf_map does not have the same number of vertices',
plot_surf,
mesh,
surf_map=rng.randn(mesh[0].shape[0] + 1, ))
assert_raises_regex(ValueError,
'surf_map can only have one dimension',
plot_surf,
mesh,
surf_map=rng.randn(mesh[0].shape[0], 2))
def test_plot_surf():
# Axes3DSubplot has no attribute 'plot_trisurf' for older versions of
# matplotlib
if LooseVersion(matplotlib.__version__) <= LooseVersion('1.3.1'):
raise SkipTest
mesh = _generate_surf()
rng = np.random.RandomState(0)
bg = rng.randn(mesh[0].shape[0], )
# Plot mesh only
plot_surf(mesh)
# Plot mesh with background
plot_surf(mesh, bg_map=bg)
plot_surf(mesh, bg_map=bg, darkness=0.5)
plot_surf(mesh, bg_map=bg, alpha=0.5)
# Plot different views
plot_surf(mesh, bg_map=bg, hemi='right')
plot_surf(mesh, bg_map=bg, view='medial')
plot_surf(mesh, bg_map=bg, hemi='right', view='medial')
# Save execution time and memory
plt.close()
def test_plot_surf_stat_map_error():
mesh = _generate_surf()
rng = np.random.RandomState(0)
data = 10 * rng.randn(mesh[0].shape[0], )
# Try to input vmin
assert_raises_regex(ValueError,
'this function does not accept a "vmin" argument',
plot_surf_stat_map,
mesh,
stat_map=data,
vmin=0)
# Wrong size of stat map data
assert_raises_regex(ValueError,
'surf_map does not have the same number of vertices',
plot_surf_stat_map,
mesh,
stat_map=np.hstack((data, data)))
assert_raises_regex(ValueError,
'surf_map can only have one dimension',
plot_surf_stat_map,
mesh,
stat_map=np.vstack((data, data)).T)
def test_plot_surf_roi_error():
mesh = _generate_surf()
rng = np.random.RandomState(0)
roi_idx = rng.randint(0, mesh[0].shape[0], size=5)
# Wrong input
assert_raises_regex(ValueError,
'roi_map does not have the same number of vertices',
plot_surf_roi, mesh,
roi_map=roi_idx)
def test_plot_surf_roi_error():
mesh = _generate_surf()
rng = np.random.RandomState(0)
roi_idx = rng.randint(0, mesh[0].shape[0], size=5)
# Wrong input
assert_raises_regex(ValueError,
'roi_map does not have the same number of vertices',
plot_surf_roi,
mesh,
roi_map=roi_idx)
def test_plot_surf_roi_error():
mesh = _generate_surf()
rng = np.random.RandomState(0)
roi1 = rng.randint(0, mesh[0].shape[0], size=5)
roi2 = rng.randint(0, mesh[0].shape[0], size=10)
# Wrong input
assert_raises_regex(ValueError,
'Invalid input for roi_map',
plot_surf_roi, mesh,
roi_map={'roi1': roi1, 'roi2': roi2})
def test_plot_surf_roi_error():
mesh = _generate_surf()
rng = np.random.RandomState(0)
roi1 = rng.randint(0, mesh[0].shape[0], size=5)
roi2 = rng.randint(0, mesh[0].shape[0], size=10)
# Wrong input
assert_raises_regex(ValueError,
'Invalid input for roi_map',
plot_surf_roi,
mesh,
roi_map={
'roi1': roi1,
'roi2': roi2
})
def test_plot_surf_stat_map():
# Axes3DSubplot has no attribute 'plot_trisurf' for older versions of
# matplotlib
if LooseVersion(matplotlib.__version__) <= LooseVersion('1.3.1'):
raise SkipTest
mesh = _generate_surf()
rng = np.random.RandomState(0)
bg = rng.randn(mesh[0].shape[0], )
data = 10 * rng.randn(mesh[0].shape[0], )
# Plot mesh with stat map
plot_surf_stat_map(mesh, stat_map=data)
plot_surf_stat_map(mesh, stat_map=data, alpha=1)
# Plot mesh with background and stat map
plot_surf_stat_map(mesh, stat_map=data, bg_map=bg)
plot_surf_stat_map(mesh,
stat_map=data,
bg_map=bg,
bg_on_stat=True,
darkness=0.5)
# Apply threshold
plot_surf_stat_map(mesh,
stat_map=data,
bg_map=bg,
bg_on_stat=True,
darkness=0.5,
threshold=0.3)
# Change vmax
plot_surf_stat_map(mesh, stat_map=data, vmax=5)
# Change colormap
plot_surf_stat_map(mesh, stat_map=data, cmap='cubehelix')
# Plot to axes
axes = plt.subplots(ncols=2, subplot_kw={'projection': '3d'})[1]
for ax in axes.flatten():
plot_surf_stat_map(mesh, stat_map=data, ax=ax)
# Save execution time and memory
plt.close()
def test_plot_surf_stat_map_error():
mesh = _generate_surf()
rng = np.random.RandomState(0)
data = 10 * rng.randn(mesh[0].shape[0], )
# Try to input vmin
assert_raises_regex(ValueError,
'this function does not accept a "vmin" argument',
plot_surf_stat_map, mesh, stat_map=data, vmin=0)
# Wrong size of stat map data
assert_raises_regex(ValueError,
'surf_map does not have the same number of vertices',
plot_surf_stat_map, mesh,
stat_map=np.hstack((data, data)))
assert_raises_regex(ValueError,
'surf_map can only have one dimension',
plot_surf_stat_map, mesh,
stat_map=np.vstack((data, data)).T)
def test_plot_surf_roi():
mesh = _generate_surf()
rng = np.random.RandomState(0)
roi1 = rng.randint(0, mesh[0].shape[0], size=5)
roi2 = rng.randint(0, mesh[0].shape[0], size=10)
parcellation = rng.rand(mesh[0].shape[0])
# plot roi
plot_surf_roi(mesh, roi_map=roi1)
plot_surf_roi(mesh, roi_map=roi1, colorbar=True)
# plot parcellation
plot_surf_roi(mesh, roi_map=parcellation)
plot_surf_roi(mesh, roi_map=parcellation, colorbar=True)
# plot roi list
plot_surf_roi(mesh, roi_map=[roi1, roi2])
plot_surf_roi(mesh, roi_map=[roi1, roi2], colorbar=True)
# plot to axes
plot_surf_roi(mesh, roi_map=roi1, ax=None, figure=plt.gcf())
# plot to axes
with tempfile.NamedTemporaryFile() as tmp_file:
plot_surf_roi(mesh,
roi_map=roi1,
ax=plt.gca(),
figure=None,
output_file=tmp_file.name)
with tempfile.NamedTemporaryFile() as tmp_file:
plot_surf_roi(mesh,
roi_map=roi1,
ax=plt.gca(),
figure=None,
output_file=tmp_file.name,
colorbar=True)
# Save execution time and memory
plt.close()
def test_plot_surf_error():
# Axes3DSubplot has no attribute 'plot_trisurf' for older versions of
# matplotlib
if LooseVersion(matplotlib.__version__) <= LooseVersion('1.3.1'):
raise SkipTest
mesh = _generate_surf()
rng = np.random.RandomState(0)
# Wrong inputs for view or hemi
assert_raises_regex(ValueError,
'view must be one of',
plot_surf,
mesh,
view='middle')
assert_raises_regex(ValueError,
'hemi must be one of',
plot_surf,
mesh,
hemi='lft')
# Wrong size of background image
assert_raises_regex(ValueError,
'bg_map does not have the same number of vertices',
plot_surf,
mesh,
bg_map=rng.randn(mesh[0].shape[0] - 1, ))
# Wrong size of surface data
assert_raises_regex(ValueError,
'surf_map does not have the same number of vertices',
plot_surf,
mesh,
surf_map=rng.randn(mesh[0].shape[0] + 1, ))
assert_raises_regex(ValueError,
'surf_map can only have one dimension',
plot_surf,
mesh,
surf_map=rng.randn(mesh[0].shape[0], 2))
def test_plot_surf_stat_map():
# Axes3DSubplot has no attribute 'plot_trisurf' for older versions of
# matplotlib
if LooseVersion(matplotlib.__version__) <= LooseVersion('1.3.1'):
raise SkipTest
mesh = _generate_surf()
rng = np.random.RandomState(0)
bg = rng.randn(mesh[0].shape[0], )
data = 10 * rng.randn(mesh[0].shape[0], )
# Plot mesh with stat map
plot_surf_stat_map(mesh, stat_map=data)
plot_surf_stat_map(mesh, stat_map=data, alpha=1)
# Plot mesh with background and stat map
plot_surf_stat_map(mesh, stat_map=data, bg_map=bg)
plot_surf_stat_map(mesh, stat_map=data, bg_map=bg,
bg_on_stat=True, darkness=0.5)
# Apply threshold
plot_surf_stat_map(mesh, stat_map=data, bg_map=bg,
bg_on_stat=True, darkness=0.5,
threshold=0.3)
# Change vmax
plot_surf_stat_map(mesh, stat_map=data, vmax=5)
# Change colormap
plot_surf_stat_map(mesh, stat_map=data, cmap='cubehelix')
# Plot to axes
axes = plt.subplots(ncols=2, subplot_kw={'projection': '3d'})[1]
for ax in axes.flatten():
plot_surf_stat_map(mesh, stat_map=data, ax=ax)
# Save execution time and memory
plt.close()
def test_plot_surf():
mesh = _generate_surf()
rng = np.random.RandomState(0)
bg = rng.randn(mesh[0].shape[0], )
# Plot mesh only
plot_surf(mesh)
# Plot mesh with background
plot_surf(mesh, bg_map=bg)
plot_surf(mesh, bg_map=bg, darkness=0.5)
plot_surf(mesh, bg_map=bg, alpha=0.5)
# Plot different views
plot_surf(mesh, bg_map=bg, hemi='right')
plot_surf(mesh, bg_map=bg, view='medial')
plot_surf(mesh, bg_map=bg, hemi='right', view='medial')
# Plot with colorbar
plot_surf(mesh, bg_map=bg, colorbar=True)
# Save execution time and memory
plt.close()
def test_plot_surf():
mesh = _generate_surf()
rng = np.random.RandomState(0)
bg = rng.randn(mesh[0].shape[0], )
# Plot mesh only
plot_surf(mesh)
# Plot mesh with background
plot_surf(mesh, bg_map=bg)
plot_surf(mesh, bg_map=bg, darkness=0.5)
plot_surf(mesh, bg_map=bg, alpha=0.5)
# Plot different views
plot_surf(mesh, bg_map=bg, hemi='right')
plot_surf(mesh, bg_map=bg, view='medial')
plot_surf(mesh, bg_map=bg, hemi='right', view='medial')
# Plot with colorbar
plot_surf(mesh, bg_map=bg, colorbar=True)
# Save execution time and memory
plt.close()
def test_plot_surf_stat_map_error():
# Axes3DSubplot has no attribute 'plot_trisurf' for older versions of
# matplotlib
if LooseVersion(matplotlib.__version__) <= LooseVersion('1.3.1'):
raise SkipTest
mesh = _generate_surf()
rng = np.random.RandomState(0)
data = 10 * rng.randn(mesh[0].shape[0], )
# Try to input vmin
assert_raises_regex(ValueError,
'this function does not accept a "vmin" argument',
plot_surf_stat_map, mesh, stat_map=data, vmin=0)
# Wrong size of stat map data
assert_raises_regex(ValueError,
'surf_map does not have the same number of vertices',
plot_surf_stat_map, mesh,
stat_map=np.hstack((data, data)))
assert_raises_regex(ValueError,
'surf_map can only have one dimension',
plot_surf_stat_map, mesh,
stat_map=np.vstack((data, data)).T)
def test_plot_surf_stat_map():
mesh = _generate_surf()
rng = np.random.RandomState(0)
bg = rng.randn(mesh[0].shape[0], )
data = 10 * rng.randn(mesh[0].shape[0], )
# Plot mesh with stat map
plot_surf_stat_map(mesh, stat_map=data)
plot_surf_stat_map(mesh, stat_map=data, colorbar=True)
plot_surf_stat_map(mesh, stat_map=data, alpha=1)
# Plot mesh with background and stat map
plot_surf_stat_map(mesh, stat_map=data, bg_map=bg)
plot_surf_stat_map(mesh,
stat_map=data,
bg_map=bg,
bg_on_data=True,
darkness=0.5)
plot_surf_stat_map(mesh,
stat_map=data,
bg_map=bg,
colorbar=True,
bg_on_data=True,
darkness=0.5)
# Apply threshold
plot_surf_stat_map(mesh,
stat_map=data,
bg_map=bg,
bg_on_data=True,
darkness=0.5,
threshold=0.3)
plot_surf_stat_map(mesh,
stat_map=data,
bg_map=bg,
colorbar=True,
bg_on_data=True,
darkness=0.5,
threshold=0.3)
# Change vmax
plot_surf_stat_map(mesh, stat_map=data, vmax=5)
plot_surf_stat_map(mesh, stat_map=data, vmax=5, colorbar=True)
# Change colormap
plot_surf_stat_map(mesh, stat_map=data, cmap='cubehelix')
plot_surf_stat_map(mesh, stat_map=data, cmap='cubehelix', colorbar=True)
# Plot to axes
axes = plt.subplots(ncols=2, subplot_kw={'projection': '3d'})[1]
for ax in axes.flatten():
plot_surf_stat_map(mesh, stat_map=data, ax=ax)
axes = plt.subplots(ncols=2, subplot_kw={'projection': '3d'})[1]
for ax in axes.flatten():
plot_surf_stat_map(mesh, stat_map=data, ax=ax, colorbar=True)
fig = plot_surf_stat_map(mesh, stat_map=data, colorbar=False)
assert len(fig.axes) == 1
# symmetric_cbar
fig = plot_surf_stat_map(mesh,
stat_map=data,
colorbar=True,
symmetric_cbar=True)
assert len(fig.axes) == 2
yticklabels = fig.axes[1].get_yticklabels()
first, last = yticklabels[0].get_text(), yticklabels[-1].get_text()
assert float(first) == -float(last)
# no symmetric_cbar
fig = plot_surf_stat_map(mesh,
stat_map=data,
colorbar=True,
symmetric_cbar=False)
assert len(fig.axes) == 2
yticklabels = fig.axes[1].get_yticklabels()
first, last = yticklabels[0].get_text(), yticklabels[-1].get_text()
assert float(first) != -float(last)
# Save execution time and memory
plt.close()
