def setUp(self):
ics = np.random.laplace(size=(3, 1024))
np.random.seed(1)
mixing_matrix = np.random.random((100, 3))
s = Image(np.dot(mixing_matrix, ics).reshape((100, 32, 32)))
for (axis, name) in zip(s.axes_manager._axes, ("z", "y", "x")):
axis.name = name
s.decomposition()
self.s = s
def test_save_and_read(self):
signal_ref = Image(data_image_byte)
signal_ref.metadata.General.title = test_title
signal_ref.save(os.path.join(my_path, 'unf_files', 'example_temp.unf'),
overwrite=True)
signal = load(os.path.join(my_path, 'unf_files', 'example_temp.unf'))
np.testing.assert_equal(signal.data, signal_ref.data)
np.testing.assert_equal(signal.metadata.General.title, test_title)
nt.assert_is_instance(signal, Image)
def _request_user_input(self):
from hyperspy.signals import Image
from hyperspy.drawing.widgets import SquareWidget
mark = Image(self.metadata.marker,
axes=self.model.axes_manager._get_navigation_axes_dicts())
mark.metadata.General.title = 'SAMFire marker'
def update_when_triggered():
ind = self.model.axes_manager.indices[::-1]
isgood = self.metadata.goodness_test.test(self.model, ind)
self.active_strategy.update(ind, isgood, 0)
mark.events.data_changed.trigger(mark)
self.model.plot()
self.model.events.fitted.connect(update_when_triggered, [])
self.model._plot.signal_plot.events.closed.connect(
lambda: self.model.events.fitted.disconnect(update_when_triggered),
[])
mark.plot(navigator='slider')
w = SquareWidget(self.model.axes_manager)
w.color = 'yellow'
w.set_mpl_ax(mark._plot.signal_plot.ax)
w.connect_navigate()
def connect_other_navigation1(axes_manager):
with mark.axes_manager.events.indices_changed.suppress_callback(
connect_other_navigation2):
for ax1, ax2 in zip(mark.axes_manager.navigation_axes,
axes_manager.navigation_axes[2:]):
ax1.value = ax2.value
def connect_other_navigation2(axes_manager):
with self.model.axes_manager.events.indices_changed.suppress_callback(
connect_other_navigation1):
for ax1, ax2 in zip(
self.model.axes_manager.navigation_axes[2:],
axes_manager.navigation_axes):
ax1.value = ax2.value
mark.axes_manager.events.indices_changed.connect(
connect_other_navigation2, {'obj': 'axes_manager'})
self.model.axes_manager.events.indices_changed.connect(
connect_other_navigation1, {'obj': 'axes_manager'})
self.model._plot.signal_plot.events.closed.connect(
lambda: mark._plot.close, [])
self.model._plot.signal_plot.events.closed.connect(
lambda: self.model.axes_manager.events.indices_changed.disconnect(
connect_other_navigation1), [])
def _request_user_input(self):
from hyperspy.signals import Image
from hyperspy.drawing.widgets import SquareWidget
mark = Image(self.metadata.marker,
axes=self.model.axes_manager._get_navigation_axes_dicts())
mark.metadata.General.title = 'SAMFire marker'
def update_when_triggered():
ind = self.model.axes_manager.indices[::-1]
isgood = self.metadata.goodness_test.test(self.model, ind)
self.active_strategy.update(ind, isgood, 0)
mark.events.data_changed.trigger(mark)
self.model.plot()
self.model.events.fitted.connect(update_when_triggered, [])
self.model._plot.signal_plot.events.closed.connect(
lambda: self.model.events.fitted.disconnect(update_when_triggered),
[])
mark.plot(navigator='slider')
w = SquareWidget(self.model.axes_manager)
w.color = 'yellow'
w.set_mpl_ax(mark._plot.signal_plot.ax)
w.connect_navigate()
def connect_other_navigation1(axes_manager):
with mark.axes_manager.events.indices_changed.suppress_callback(
connect_other_navigation2):
for ax1, ax2 in zip(mark.axes_manager.navigation_axes,
axes_manager.navigation_axes[2:]):
ax1.value = ax2.value
def connect_other_navigation2(axes_manager):
with self.model.axes_manager.events.indices_changed.suppress_callback(
connect_other_navigation1):
for ax1, ax2 in zip(self.model.axes_manager.navigation_axes[2:],
axes_manager.navigation_axes):
ax1.value = ax2.value
mark.axes_manager.events.indices_changed.connect(
connect_other_navigation2, {'obj': 'axes_manager'})
self.model.axes_manager.events.indices_changed.connect(
connect_other_navigation1, {'obj': 'axes_manager'})
self.model._plot.signal_plot.events.closed.connect(
lambda: mark._plot.close, [])
self.model._plot.signal_plot.events.closed.connect(
lambda: self.model.axes_manager.events.indices_changed.disconnect(
connect_other_navigation1), [])
class Test2D():
def setUp(self):
self.im = Image(np.random.random((2, 3)))
def test_to_image(self):
s = self.im.to_spectrum()
assert_true(isinstance(s, Spectrum))
assert_equal(s.data.shape, self.im.data.T.shape)
assert_true(s.data.flags["C_CONTIGUOUS"])
class Test4D():
def setUp(self):
self.s = Image(np.random.random((2, 3, 4, 5)))
def test_to_image(self):
s = self.s.to_spectrum()
assert_true(isinstance(s, Spectrum))
assert_equal(s.data.shape, (3,4,5,2))
assert_true(s.data.flags["C_CONTIGUOUS"])
class Test3D:
def setUp(self):
self.im = Image(np.random.random((2, 3, 4)))
def test_to_image(self):
s = self.im.to_spectrum()
nose.tools.assert_true(isinstance(s, Spectrum))
nose.tools.assert_equal(s.data.shape, (3, 4, 2))
nose.tools.assert_true(s.data.flags["C_CONTIGUOUS"])
def test_get_data(self):
s = Image(np.zeros([3, 2, 2]))
m = markers.line_segment(x1=range(3), x2=range(3), y1=1.3, y2=1.5)
m.axes_manager = s.axes_manager
nose.tools.assert_true(m.get_data_position('x1') == 0)
nose.tools.assert_true(m.get_data_position('y1') == 1.3)
s.axes_manager[0].index = 2
nose.tools.assert_true(m.get_data_position('x1') == 2)
nose.tools.assert_true(m.get_data_position('y1') == 1.3)
class Test3D:
def setUp(self):
self.im = Image(np.random.random((2, 3, 4)))
def test_to_image(self):
s = self.im.to_spectrum()
nose.tools.assert_true(isinstance(s, Spectrum))
nose.tools.assert_equal(s.data.shape, (3, 4, 2))
nose.tools.assert_true(s.data.flags["C_CONTIGUOUS"])
def setUp(self):
np.random.seed(0) # Same random every time, Line2DROi test requires it
self.s_s = Spectrum(np.random.rand(50, 60, 4))
self.s_s.axes_manager[0].scale = 5
self.s_s.axes_manager[0].units = 'nm'
self.s_s.axes_manager[1].scale = 5
self.s_s.axes_manager[1].units = 'nm'
# 4D dataset
self.s_i = Image(np.random.rand(100, 100, 4, 4))
def test_get_data_array(self):
s = Image(np.zeros([2, 2, 2, 2]))
m = markers.line_segment(x1=[[1.1, 1.2], [1.3, 1.4]], x2=1.1, y1=1.3,
y2=1.5)
m.axes_manager = s.axes_manager
nose.tools.assert_true(m.get_data_position('x1') == 1.1)
s.axes_manager[0].index = 1
nose.tools.assert_true(m.get_data_position('x1') == 1.2)
s.axes_manager[1].index = 1
nose.tools.assert_true(m.get_data_position('x1') == 1.4)
def setUp(self):
self.im = Image(np.random.random((2, 3)))
def setUp(self):
self.s = Image(np.random.random((2, 3, 4, 5)))
def setUp(self):
self.im = Image(np.random.random((2, 3)))
def setUp(self):
self.s = Image(np.random.random((2, 3, 4, 5)))
