def test_plot_markers_threshold(threshold, coords):
"""Smoke test for plot_markers with different threshold values."""
plot_markers([1, 2, 3, 4],
coords,
node_threshold=threshold,
display_mode='x')
plt.close()
def test_plot_markers_tuple_node_coords(coords):
"""Smoke test for plot_markers with node coordinates passed as a list
of tuples.
"""
plot_markers([1, 2, 3, 4], [tuple(coord) for coord in coords],
display_mode='x')
plt.close()
def test_plot_markers_cmap(cmap, vmin, vmax, coords):
"""Smoke test for plot_markers with different cmaps."""
plot_markers([1, 2, 3, 4],
coords,
node_cmap=cmap,
node_vmin=vmin,
node_vmax=vmax,
display_mode='x')
plt.close()
def test_plot_markers_bound_error(vmin, vmax, coords):
"""Tests that a ValueError is raised when vmin and vmax
have inconsistent values.
"""
with pytest.raises(ValueError):
plot_markers([1, 2, 2, 4],
coords,
node_vmin=vmin,
node_vmax=vmax,
display_mode='x')
def test_plot_markers_node_kwargs(coords):
"""Smoke test for plot_markers testing that node_kwargs is working
and does not interfere with alpha.
"""
node_kwargs = dict(marker='s')
plot_markers([1, 2, 3, 4],
coords,
alpha=.1,
node_kwargs=node_kwargs,
display_mode='x')
plt.close()
def test_plot_markers_saving_to_file(coords, tmpdir):
"""Smoke test for plot_markers and file saving."""
filename = str(tmpdir.join('test.png'))
display = plot_markers([1, 2, 3, 4],
coords,
output_file=filename,
display_mode='x')
assert display is None
assert (os.path.isfile(filename) and os.path.getsize(filename) > 0)
plt.close()
def test_plot_markers_node_sizes_lyrz_display(node_size, coords):
"""Tests for plot_markers and 'lyrz' display mode.
Tests that markers are plotted with the requested size
with display_mode='lyrz'. (See issue #3012 and PR #3013).
"""
display = plot_markers([1, 2, 3, 4],
coords,
display_mode="lyrz",
node_size=node_size)
for d, axes in display.axes.items():
display_sizes = axes.ax.collections[0].get_sizes()
if d == 'l':
expected_sizes = node_size[-2:]
elif d == 'r':
expected_sizes = node_size[:-2]
else:
expected_sizes = node_size
assert np.all(display_sizes == expected_sizes)
plt.close()
# Note the 1. on the matrix diagonal: These are the signals variances, set
# to 1. by the `spheres_masker`. Hence the covariance of the signal is a
# correlation matrix.
###############################################################################
# Sometimes, the information in the correlation matrix is overwhelming and
# aggregating edge strength from the graph would help. Use the function
# `nilearn.plotting.plot_markers` to visualize this information.
# calculate normalized, absolute strength for each node
node_strength = np.sum(np.abs(matrix), axis=0)
node_strength /= np.max(node_strength)
plotting.plot_markers(
node_strength,
coords,
title='Node strength for absolute value of edges for Power atlas',
)
###############################################################################
# From the correlation matrix, we observe that there is a positive and negative
# structure. We could make two different plots, one for the positive and one for
# the negative structure.
from matplotlib.pyplot import cm
# clip connectivity matrix to preserve positive and negative edges
positive_edges = np.clip(matrix, 0, matrix.max())
negative_edges = np.clip(matrix, matrix.min(), 0)
# calculate strength for positive edges
def test_plot_markers_node_sizes(node_size, coords):
"""Smoke test for plot_markers with different node sizes."""
plot_markers([1, 2, 3, 4], coords, node_size=node_size, display_mode='x')
plt.close()
def test_plot_markers_node_values(node_values, coords):
"""Smoke test for plot_markers with different node values."""
plot_markers(node_values, coords, display_mode='x')
plt.close()
def test_plot_markers_threshold_errors(coords):
"""Tests that a ValueError is raised when node_threshold is
higher than the max node_value.
"""
with pytest.raises(ValueError, match="Provided 'node_threshold' value"):
plot_markers([1, 2, 2, 4], coords, node_threshold=5, display_mode='x')
def test_plot_markers_node_values_errors(coords):
"""Tests that a TypeError is raised when node_values is wrong type."""
with pytest.raises(TypeError):
plot_markers(['1', '2', '3', '4'], coords, display_mode='x')
def test_plot_markers_dimension_mismatch(matrix, coords):
"""Tests that an error is raised in plot_markers when the length of
node_values mismatches with node_coords.
"""
with pytest.raises(ValueError, match="Dimension mismatch"):
plot_markers(matrix, coords, display_mode='x')