def test_save_figures():
"""Test file naming when saving figures. Requires mayavi."""
try:
from mayavi import mlab
except ImportError:
raise nose.SkipTest('Mayavi not installed')
mlab.options.offscreen = True
examples_dir = tempfile.mkdtemp()
gallery_conf = {'find_mayavi_figures': True}
mlab.test_plot3d()
plt.plot(1, 1)
fname_template = os.path.join(examples_dir, 'image{0}.png')
fig_list = sg.save_figures(fname_template, 0, gallery_conf)
assert_equal(len(fig_list), 2)
assert fig_list[0].endswith('image1.png')
assert fig_list[1].endswith('image2.png')
mlab.test_plot3d()
plt.plot(1, 1)
fig_list = sg.save_figures(fname_template, 2, gallery_conf)
assert_equal(len(fig_list), 2)
assert fig_list[0].endswith('image3.png')
assert fig_list[1].endswith('image4.png')
shutil.rmtree(examples_dir)
def test_save_figures(gallery_conf):
"""Test file naming when saving figures. Requires mayavi."""
try:
from mayavi import mlab
except ImportError:
raise pytest.skip('Mayavi not installed')
mlab.options.offscreen = True
gallery_conf.update(find_mayavi_figures=True)
mlab.test_plot3d()
plt.plot(1, 1)
fname_template = os.path.join(gallery_conf['gallery_dir'], 'image{0}.png')
image_rst, fig_num = sg.save_figures(fname_template, 0, gallery_conf)
assert fig_num == 2
assert '/image1.png' in image_rst
assert '/image2.png' in image_rst
mlab.test_plot3d()
plt.plot(1, 1)
image_rst, fig_num = sg.save_figures(fname_template, 2, gallery_conf)
assert fig_num == 2
assert '/image2.png' not in image_rst
assert '/image3.png' in image_rst
assert '/image4.png' in image_rst
shutil.rmtree(gallery_conf['gallery_dir'])
def test_save_figures():
"""Test file naming when saving figures. Requires mayavi."""
try:
from mayavi import mlab
except ImportError:
raise nose.SkipTest('Mayavi not installed')
mlab.options.offscreen = True
examples_dir = tempfile.mkdtemp()
gallery_conf = {'find_mayavi_figures': True}
mlab.test_plot3d()
plt.plot(1, 1)
fname_template = os.path.join(examples_dir, 'image{0}.png')
fig_list, _ = sg.save_figures(fname_template, 0, gallery_conf)
assert_equal(len(fig_list), 2)
assert fig_list[0].endswith('image1.png')
assert fig_list[1].endswith('image2.png')
mlab.test_plot3d()
plt.plot(1, 1)
fig_list, _ = sg.save_figures(fname_template, 2, gallery_conf)
assert_equal(len(fig_list), 2)
assert fig_list[0].endswith('image3.png')
assert fig_list[1].endswith('image4.png')
shutil.rmtree(examples_dir)
def mayavi_plt():
ml.test_plot3d()
arr = ml.screenshot()
ml.close()
plt.imshow(arr)
plt.axis('off')
plt.show()
def test_save_mayavi_figures(gallery_conf, req_mpl, req_pil):
"""Test file naming when saving figures. Requires mayavi."""
Image = _get_image()
try:
from mayavi import mlab
except ImportError:
raise pytest.skip('Mayavi not installed')
import matplotlib.pyplot as plt
mlab.options.offscreen = True
gallery_conf.update(
image_scrapers=(matplotlib_scraper, mayavi_scraper))
fname_template = os.path.join(gallery_conf['gallery_dir'], 'image{0}.png')
image_path_iterator = ImagePathIterator(fname_template)
block = ('',) * 3
block_vars = dict(image_path_iterator=image_path_iterator)
plt.axes([-0.1, -0.1, 1.2, 1.2])
plt.pcolor([[0]], cmap='Greens')
mlab.test_plot3d()
image_rst = save_figures(block, block_vars, gallery_conf)
assert len(plt.get_fignums()) == 0
assert len(image_path_iterator) == 2
assert '/image0.png' not in image_rst
assert '/image1.png' in image_rst
assert '/image2.png' in image_rst
assert '/image3.png' not in image_rst
assert not os.path.isfile(fname_template.format(0))
assert os.path.isfile(fname_template.format(1))
assert os.path.isfile(fname_template.format(2))
assert not os.path.isfile(fname_template.format(0))
with Image.open(fname_template.format(1)) as img:
pixels = np.asarray(img.convert("RGB"))
assert (pixels == [247, 252, 245]).all() # plt first
# Test next-value handling, plus image_scrapers modification
gallery_conf.update(image_scrapers=(matplotlib_scraper,))
mlab.test_plot3d()
plt.axes([-0.1, -0.1, 1.2, 1.2])
plt.pcolor([[0]], cmap='Reds')
image_rst = save_figures(block, block_vars, gallery_conf)
assert len(plt.get_fignums()) == 0
assert len(image_path_iterator) == 3
assert '/image1.png' not in image_rst
assert '/image2.png' not in image_rst
assert '/image3.png' in image_rst
assert '/image4.png' not in image_rst
assert not os.path.isfile(fname_template.format(0))
for ii in range(3):
assert os.path.isfile(fname_template.format(ii + 1))
assert not os.path.isfile(fname_template.format(4))
with Image.open(fname_template.format(3)) as img:
pixels = np.asarray(img.convert("RGB"))
assert (pixels == [255, 245, 240]).all()
def test_axes(self):
s = mlab.test_plot3d()
a = mlab.axes(s)
assert_allclose(
a.axes.ranges, [-1.5, 1.5, -1.5, 1.5, -0.5, 0.5],
rtol=0, atol=0.1
)
def test_axes(self):
s = mlab.test_plot3d()
a = mlab.axes(s)
assert_allclose(
a.axes.ranges, [-1.5, 1.5, -1.5, 1.5, -0.5, 0.5],
rtol=0, atol=0.1
)
def generate_spinning_brain_frames(trajectories, nframes_per_cycle=30, figsize=[800, 700]):
'''
Plots spike amps versus the time
Parameters
-------------
trajectories: list of dicts
list of dictionaries of trajectories fetched from ONE
nframes_per_cycle: int, optional
number of frames per cycle of spinning, default 30.
figsize: list, [width, height], optional
size of the images, default [800, 700]
Return
------------
frames: list of numpy.darray
image in rgb for each frame
'''
fig = rendering.figure()
for index, trj in enumerate(trajectories):
if trj['coordinate_system'] == 'IBL-Allen':
brain_atlas = ba_allen
elif trj['coordinate_system'] == 'Needles-Allen':
brain_atlas = ba_needles
else:
brain_atlas = ba_allen
ins = atlas.Insertion.from_dict(trj, brain_atlas=brain_atlas)
ins = atlas.Insertion.from_dict(trj, brain_atlas=ba_allen)
mlapdv = brain_atlas.xyz2ccf(ins.xyz)
if trj['provenance'] == 'Ephys aligned histology track':
color = (0, 0, 1.) # Blue
mlab.plot3d(mlapdv[:, 1], mlapdv[:, 2], mlapdv[:, 0],
line_width=3, color=color, tube_radius=20)
frames = []
for i in range(nframes_per_cycle):
mlab.view(azimuth=0, elevation=0 - i * (360 / nframes_per_cycle))
mlab.roll(180)
mlab.test_plot3d()
f = mlab.gcf()
f.scene._lift()
frames.append(mlab.screenshot(mode='rgb', antialiased=True))
return frames
def test_udp():
"""Simple test for the UDP server."""
from mayavi import mlab
mlab.test_plot3d()
serve_udp()
def test_tcp():
"""Simple test for the TCP server."""
from mayavi import mlab
mlab.test_plot3d()
serve_tcp()
Plotting simple 3D graph with Mayavi ==================================== A simple example of the plot of a 3D graph with Mayavi in order to test the autonomy of the gallery. """ # Code source: Alex Gramfort # License: BSD 3 clause # This will show the mlab.test_mesh figure in the gallery # sphinx_gallery_thumbnail_number = 4 from mayavi import mlab mlab.test_plot3d() mlab.figure() mlab.test_contour3d() ##################################################################### # Note: this shows that inside a cell matplotlib figures are always # put before mayavi in the example HTML. In other words, the order of # plotting is not respected between matplotlib and mayavi figures mlab.figure() mlab.test_mesh() mlab.figure() mlab.test_flow()
def test_udp():
"""Simple test for the UDP server."""
from mayavi import mlab
mlab.test_plot3d()
serve_udp()
def test_tcp():
"""Simple test for the TCP server."""
from mayavi import mlab
mlab.test_plot3d()
serve_tcp()
from mayavi import mlab import vtk currfig = mlab.test_plot3d() mlab.orientation_axes() #mlab.draw() cam = currfig.scene.camera cam.zoom(1.5) #mlab.draw() mlab.show()
def test_save_mayavi_figures(gallery_conf):
"""Test file naming when saving figures. Requires mayavi."""
try:
from mayavi import mlab
except ImportError:
raise pytest.skip('Mayavi not installed')
import matplotlib.pyplot as plt
mlab.options.offscreen = True
gallery_conf.update(
image_scrapers=(matplotlib_scraper, mayavi_scraper))
fname_template = os.path.join(gallery_conf['gallery_dir'], 'image{0}.png')
image_path_iterator = ImagePathIterator(fname_template)
block = ('',) * 3
block_vars = dict(image_path_iterator=image_path_iterator)
plt.axes([-0.1, -0.1, 1.2, 1.2])
plt.pcolor([[0]], cmap='Greens')
mlab.test_plot3d()
image_rst = save_figures(block, block_vars, gallery_conf)
assert len(plt.get_fignums()) == 0
assert len(image_path_iterator) == 2
assert '/image0.png' not in image_rst
assert '/image1.png' in image_rst
assert '/image2.png' in image_rst
assert '/image3.png' not in image_rst
assert not os.path.isfile(fname_template.format(0))
assert os.path.isfile(fname_template.format(1))
assert os.path.isfile(fname_template.format(2))
assert not os.path.isfile(fname_template.format(0))
with Image.open(fname_template.format(1)) as img:
pixels = np.asarray(img.convert("RGB"))
assert (pixels == [247, 252, 245]).all() # plt first
# Test next-value handling, plus image_scrapers modification
gallery_conf.update(image_scrapers=(matplotlib_scraper,))
mlab.test_plot3d()
plt.axes([-0.1, -0.1, 1.2, 1.2])
plt.pcolor([[0]], cmap='Reds')
image_rst = save_figures(block, block_vars, gallery_conf)
assert len(plt.get_fignums()) == 0
assert len(image_path_iterator) == 3
assert '/image1.png' not in image_rst
assert '/image2.png' not in image_rst
assert '/image3.png' in image_rst
assert '/image4.png' not in image_rst
assert not os.path.isfile(fname_template.format(0))
for ii in range(3):
assert os.path.isfile(fname_template.format(ii + 1))
assert not os.path.isfile(fname_template.format(4))
with Image.open(fname_template.format(3)) as img:
pixels = np.asarray(img.convert("RGB"))
assert (pixels == [255, 245, 240]).all()
# custom finders
gallery_conf.update(image_scrapers=[lambda x, y, z: ''])
image_rst = save_figures(block, block_vars, gallery_conf)
assert len(image_path_iterator) == 3
# degenerate
gallery_conf.update(image_scrapers=['foo'])
with pytest.raises(ValueError, match='Unknown image scraper'):
_complete_gallery_conf(
gallery_conf, gallery_conf['gallery_dir'], True, False)
gallery_conf.update(
image_scrapers=[lambda x, y, z: y['image_path_iterator'].next()])
with pytest.raises(RuntimeError, match='did not produce expected image'):
save_figures(block, block_vars, gallery_conf)
gallery_conf.update(image_scrapers=[lambda x, y, z: 1.])
with pytest.raises(TypeError, match='was not a string'):
save_figures(block, block_vars, gallery_conf)
def test_save_mayavi_figures(gallery_conf):
"""Test file naming when saving figures. Requires mayavi."""
try:
from mayavi import mlab
except ImportError:
raise pytest.skip('Mayavi not installed')
import matplotlib.pyplot as plt
mlab.options.offscreen = True
gallery_conf.update(image_scrapers=(matplotlib_scraper, mayavi_scraper))
fname_template = os.path.join(gallery_conf['gallery_dir'], 'image{0}.png')
image_path_iterator = ImagePathIterator(fname_template)
block = ('', ) * 3
block_vars = dict(image_path_iterator=image_path_iterator)
plt.axes([-0.1, -0.1, 1.2, 1.2])
plt.pcolor([[0]], cmap='Greens')
mlab.test_plot3d()
image_rst = save_figures(block, block_vars, gallery_conf)
assert len(plt.get_fignums()) == 0
assert len(image_path_iterator) == 2
assert '/image0.png' not in image_rst
assert '/image1.png' in image_rst
assert '/image2.png' in image_rst
assert '/image3.png' not in image_rst
assert not os.path.isfile(fname_template.format(0))
assert os.path.isfile(fname_template.format(1))
assert os.path.isfile(fname_template.format(2))
assert not os.path.isfile(fname_template.format(0))
with Image.open(fname_template.format(1)) as img:
pixels = np.asarray(img.convert("RGB"))
assert (pixels == [247, 252, 245]).all() # plt first
# Test next-value handling, plus image_scrapers modification
gallery_conf.update(image_scrapers=(matplotlib_scraper, ))
mlab.test_plot3d()
plt.axes([-0.1, -0.1, 1.2, 1.2])
plt.pcolor([[0]], cmap='Reds')
image_rst = save_figures(block, block_vars, gallery_conf)
assert len(plt.get_fignums()) == 0
assert len(image_path_iterator) == 3
assert '/image1.png' not in image_rst
assert '/image2.png' not in image_rst
assert '/image3.png' in image_rst
assert '/image4.png' not in image_rst
assert not os.path.isfile(fname_template.format(0))
for ii in range(3):
assert os.path.isfile(fname_template.format(ii + 1))
assert not os.path.isfile(fname_template.format(4))
with Image.open(fname_template.format(3)) as img:
pixels = np.asarray(img.convert("RGB"))
assert (pixels == [255, 245, 240]).all()
# custom finders
gallery_conf.update(image_scrapers=[lambda x, y, z: ''])
image_rst = save_figures(block, block_vars, gallery_conf)
assert len(image_path_iterator) == 3
# degenerate
gallery_conf.update(image_scrapers=['foo'])
with pytest.raises(ValueError, match='Unknown image scraper'):
_complete_gallery_conf(gallery_conf, gallery_conf['gallery_dir'], True,
False)
gallery_conf.update(
image_scrapers=[lambda x, y, z: y['image_path_iterator'].next()])
with pytest.raises(RuntimeError, match='did not produce expected image'):
save_figures(block, block_vars, gallery_conf)
gallery_conf.update(image_scrapers=[lambda x, y, z: 1.])
with pytest.raises(TypeError, match='was not a string'):
save_figures(block, block_vars, gallery_conf)
