def test_plot_markers_mpl_options():
# check if required parameters are shown in repr
_test_plot_markers_repr(markers.arrow(10, 20, 30, 40),
['x1', 'y1', 'x2', 'y2',
'edgecolor', 'arrowstyle'])
_test_plot_markers_repr(markers.ellipse(10, 20, 30, 40, color='red'),
['x', 'y', 'width', 'height',
'edgecolor'])
_test_plot_markers_repr(markers.horizontal_line(10),
['y', 'color'])
_test_plot_markers_repr(markers.horizontal_line_segment(10, 20, 30),
['x1', 'x2', 'y', 'color'])
_test_plot_markers_repr(markers.line_segment(10, 20, 30,40),
['x1', 'x2', 'y1', 'y2', 'color'])
_test_plot_markers_repr(markers.point(10, 20),
['x', 'x', 'color', 'size'])
m = markers.rectangle(10, 20, 30, 40, color='red')
_test_plot_markers_repr(m, ['edgecolor'])
# check if 'color' property is converted to 'edgecolor'
assert 'color' not in m.marker_properties
assert 'edgecolor' in m.marker_properties
assert m.marker_properties['edgecolor'] == 'red'
_test_plot_markers_repr(markers.text(10,20,"test"),
['x', 'y', 'text', 'color'])
_test_plot_markers_repr(markers.vertical_line(10),
['x', 'color'])
m = markers.vertical_line_segment(10, 20, 30)
_test_plot_markers_repr(m,['x', 'y1', 'y2', 'color'])
def test_add_several_permanent_markers(self):
s = Signal1D(np.arange(10))
m_point = markers.point(x=5, y=5)
m_line = markers.line_segment(x1=5, x2=10, y1=5, y2=10)
m_vline = markers.vertical_line(x=5)
m_vline_segment = markers.vertical_line_segment(x=4, y1=3, y2=6)
m_hline = markers.horizontal_line(y=5)
m_hline_segment = markers.horizontal_line_segment(x1=1, x2=9, y=5)
m_rect = markers.rectangle(x1=1, x2=3, y1=5, y2=10)
m_text = markers.text(x=1, y=5, text="test")
m_arrow = markers.arrow(x1=4, y1=5, x2=6, y2=6, arrowstyle='<->')
m_ellipse = markers.ellipse(x=10, y=11, width=4, height=6)
s.add_marker(m_point, permanent=True)
s.add_marker(m_line, permanent=True)
s.add_marker(m_vline, permanent=True)
s.add_marker(m_vline_segment, permanent=True)
s.add_marker(m_hline, permanent=True)
s.add_marker(m_hline_segment, permanent=True)
s.add_marker(m_rect, permanent=True)
s.add_marker(m_text, permanent=True)
s.add_marker(m_arrow, permanent=True)
s.add_marker(m_ellipse, permanent=True)
assert len(list(s.metadata.Markers)) == 10
with pytest.raises(ValueError):
s.add_marker(m_rect, permanent=True)
def _add_xray_lines_markers(self, xray_lines):
"""
Add marker on a spec.plot() with the name of the selected X-ray
lines
Parameters
----------
xray_lines: list of string
A valid list of X-ray lines
"""
line_energy = []
intensity = []
for xray_line in xray_lines:
element, line = utils_eds._get_element_and_line(xray_line)
line_energy.append(self._get_line_energy(xray_line))
relative_factor = elements_db[element][
'Atomic_properties']['Xray_lines'][line]['weight']
a_eng = self._get_line_energy(element + '_' + line[0] + 'a')
intensity.append(self.isig[a_eng].data * relative_factor)
for i in range(len(line_energy)):
line = markers.vertical_line_segment(
x=line_energy[i], y1=None, y2=intensity[i] * 0.8)
self.add_marker(line)
text = markers.text(
x=line_energy[i], y=intensity[i] * 1.1, text=xray_lines[i],
rotation=90)
self.add_marker(text)
def test_save_load_permanent_marker_all_types(self):
x1, y1, x2, y2 = 5, 2, 1, 8
s = Signal2D(np.arange(100).reshape(10, 10))
m0_list = [
markers.point(x=x1, y=y1),
markers.horizontal_line(y=y1),
markers.horizontal_line_segment(x1=x1, x2=x2, y=y1),
markers.line_segment(x1=x1, x2=x2, y1=y1, y2=y2),
markers.rectangle(x1=x1, x2=x2, y1=y1, y2=y2),
markers.text(x=x1, y=y1, text="test"),
markers.vertical_line(x=x1),
markers.vertical_line_segment(x=x1, y1=y1, y2=y2),
]
for m in m0_list:
s.add_marker(m, permanent=True)
with tempfile.TemporaryDirectory() as tmp:
filename = tmp + '/testallmarkersfile.hdf5'
s.save(filename)
s1 = load(filename)
markers_dict = s1.metadata.Markers
m0_dict_list = []
m1_dict_list = []
for m in m0_list:
m0_dict_list.append(san_dict(m._to_dictionary()))
m1_dict_list.append(
san_dict(markers_dict.get_item(m.name)._to_dictionary()))
assert len(list(s1.metadata.Markers)) == 8
for m0_dict, m1_dict in zip(m0_dict_list, m1_dict_list):
assert m0_dict == m1_dict
def test_save_load_permanent_marker_all_types(self):
x1, y1, x2, y2 = 5, 2, 1, 8
s = Signal2D(np.arange(100).reshape(10, 10))
m0_list = [
markers.point(x=x1, y=y1),
markers.horizontal_line(y=y1),
markers.horizontal_line_segment(x1=x1, x2=x2, y=y1),
markers.line_segment(x1=x1, x2=x2, y1=y1, y2=y2),
markers.rectangle(x1=x1, x2=x2, y1=y1, y2=y2),
markers.text(x=x1, y=y1, text="test"),
markers.vertical_line(x=x1),
markers.vertical_line_segment(x=x1, y1=y1, y2=y2),
]
for m in m0_list:
s.add_marker(m, permanent=True)
with tempfile.TemporaryDirectory() as tmp:
filename = tmp + '/testallmarkersfile.hdf5'
s.save(filename)
s1 = load(filename)
markers_dict = s1.metadata.Markers
m0_dict_list = []
m1_dict_list = []
for m in m0_list:
m0_dict_list.append(san_dict(m._to_dictionary()))
m1_dict_list.append(
san_dict(markers_dict.get_item(m.name)._to_dictionary()))
assert len(list(s1.metadata.Markers)) == 8
for m0_dict, m1_dict in zip(m0_dict_list, m1_dict_list):
assert m0_dict == m1_dict
def test_save_load_permanent_marker_all_types(self, tmp_path, file):
filename = tmp_path / file
s = self.s
x1, y1, x2, y2 = 5, 2, 1, 8
m0_list = [
markers.point(x=x1, y=y1),
markers.horizontal_line(y=y1),
markers.horizontal_line_segment(x1=x1, x2=x2, y=y1),
markers.line_segment(x1=x1, x2=x2, y1=y1, y2=y2),
markers.rectangle(x1=x1, x2=x2, y1=y1, y2=y2),
markers.text(x=x1, y=y1, text="test"),
markers.vertical_line(x=x1),
markers.vertical_line_segment(x=x1, y1=y1, y2=y2),
]
for m in m0_list:
s.add_marker(m, permanent=True)
s.save(filename)
s1 = load(filename)
markers_dict = s1.metadata.Markers
m0_dict_list = []
m1_dict_list = []
for m in m0_list:
m0_dict_list.append(san_dict(m._to_dictionary()))
m1_dict_list.append(
san_dict(markers_dict.get_item(m.name)._to_dictionary()))
assert len(list(s1.metadata.Markers)) == 8
for m0_dict, m1_dict in zip(m0_dict_list, m1_dict_list):
assert m0_dict == m1_dict
def add_xray_lines_markers(self, xray_lines):
"""
Add marker on a spec.plot() with the name of the selected X-ray
lines
Parameters
----------
xray_lines: list of string
A valid list of X-ray lines
"""
line_energy = []
intensity = []
for xray_line in xray_lines:
element, line = utils_eds._get_element_and_line(xray_line)
line_energy.append(self._get_line_energy(xray_line))
relative_factor = elements_db[element][
'Atomic_properties']['Xray_lines'][line]['weight']
a_eng = self._get_line_energy(element + '_' + line[0] + 'a')
intensity.append(self.isig[a_eng].data * relative_factor)
for i in range(len(line_energy)):
line = markers.vertical_line_segment(
x=line_energy[i], y1=None, y2=intensity[i] * 0.8)
self.add_marker(line)
text = markers.text(
x=line_energy[i], y=intensity[i] * 1.1, text=xray_lines[i],
rotation=90)
self.add_marker(text)
self._xray_markers[xray_lines[i]] = [line, text]
line.events.closed.connect(self._xray_marker_closed)
text.events.closed.connect(self._xray_marker_closed)
def test_vertical_horizontal_line_segment_with_None():
m0 = markers.horizontal_line_segment(None, None, 1)
m1 = markers.vertical_line_segment(1, None, None)
w = 2
h = 3
s = Signal2D(np.arange(w * h).reshape(h, w))
s.add_marker(m0)
s.add_marker(m1)
np.testing.assert_allclose(m0.marker.get_segments()[0], [[-0.5, 1.],[w - 0.5, 1.]])
np.testing.assert_allclose(m1.marker.get_segments()[0], [[1., h - 0.5],[1., -0.5]])
def test_dict2marker(self):
m_point0 = markers.point(x=5, y=5)
m_point1 = markers.point(x=(5, 10), y=(1, 5))
m_line = markers.line_segment(x1=5, x2=10, y1=5, y2=10)
m_vline = markers.vertical_line(x=5)
m_vline_segment = markers.vertical_line_segment(x=4, y1=3, y2=6)
m_hline = markers.horizontal_line(y=5)
m_hline_segment = markers.horizontal_line_segment(x1=1, x2=9, y=5)
m_rect = markers.rectangle(x1=1, x2=3, y1=5, y2=10)
m_text = markers.text(x=1, y=5, text="test")
m_point0_new = dict2marker(m_point0._to_dictionary(), m_point0.name)
m_point1_new = dict2marker(m_point1._to_dictionary(), m_point1.name)
m_line_new = dict2marker(m_line._to_dictionary(), m_line.name)
m_vline_new = dict2marker(m_vline._to_dictionary(), m_vline.name)
m_vline_segment_new = dict2marker(
m_vline_segment._to_dictionary(), m_vline_segment.name)
m_hline_new = dict2marker(m_hline._to_dictionary(), m_hline.name)
m_hline_segment_new = dict2marker(
m_hline_segment._to_dictionary(), m_hline_segment.name)
m_rect_new = dict2marker(m_rect._to_dictionary(), m_rect.name)
m_text_new = dict2marker(m_text._to_dictionary(), m_text.name)
m_point0_dict = sanitize_dict(m_point0._to_dictionary())
m_point1_dict = sanitize_dict(m_point1._to_dictionary())
m_line_dict = sanitize_dict(m_line._to_dictionary())
m_vline_dict = sanitize_dict(m_vline._to_dictionary())
m_vline_segment_dict = sanitize_dict(m_vline_segment._to_dictionary())
m_hline_dict = sanitize_dict(m_hline._to_dictionary())
m_hline_segment_dict = sanitize_dict(m_hline_segment._to_dictionary())
m_rect_dict = sanitize_dict(m_rect._to_dictionary())
m_text_dict = sanitize_dict(m_text._to_dictionary())
m_point0_new_dict = sanitize_dict(m_point0_new._to_dictionary())
m_point1_new_dict = sanitize_dict(m_point1_new._to_dictionary())
m_line_new_dict = sanitize_dict(m_line_new._to_dictionary())
m_vline_new_dict = sanitize_dict(m_vline_new._to_dictionary())
m_vline_segment_new_dict = sanitize_dict(
m_vline_segment_new._to_dictionary())
m_hline_new_dict = sanitize_dict(m_hline_new._to_dictionary())
m_hline_segment_new_dict = sanitize_dict(
m_hline_segment_new._to_dictionary())
m_rect_new_dict = sanitize_dict(m_rect_new._to_dictionary())
m_text_new_dict = sanitize_dict(m_text_new._to_dictionary())
assert m_point0_dict == m_point0_new_dict
assert m_point1_dict == m_point1_new_dict
assert m_line_dict == m_line_new_dict
assert m_vline_dict == m_vline_new_dict
assert m_vline_segment_dict == m_vline_segment_new_dict
assert m_hline_dict == m_hline_new_dict
assert m_hline_segment_dict == m_hline_segment_new_dict
assert m_rect_dict == m_rect_new_dict
assert m_text_dict == m_text_new_dict
def test_markers_auto_update():
# test data for fixed marker
pos = [1, 2, 3, 4]
# test data for auto_update marker
pos_list = np.array([[1, 3, 5], [2, 4, 6]])
pos_2d = [pos_list + pos[i] for i in range(4)]
s = Signal2D(np.arange(2 * 3 * 4 * 5).reshape(2, 3, 4, 5))
marker_list = []
for _auto_update, _pos in [(False, pos), (True, pos_2d)]:
_markers = [
markers.vertical_line(_pos[0]),
markers.horizontal_line(_pos[0]),
markers.vertical_line_segment(*(_pos[0:3])),
markers.horizontal_line_segment(*(_pos[0:3])),
markers.rectangle(*_pos),
markers.ellipse(*_pos),
markers.arrow(*_pos),
markers.line_segment(*_pos),
markers.point(_pos[0], _pos[1]),
markers.text(_pos[0], _pos[1], "test"),
]
for marker in _markers:
assert marker.auto_update is _auto_update
marker_list += _markers
assert len(marker_list) == 20
s.add_marker(marker_list)
for iy, temp_marker_list in enumerate(pos_list):
for ix, value in enumerate(temp_marker_list):
s.axes_manager.indices = (ix, iy)
for marker in marker_list:
_xy = [marker.get_data_position(ax) for ax in ('x1','y1','x2','y2')]
if marker.auto_update is False:
_xy2 = pos
else:
_xy2 = [pos_2d[i][iy, ix] for i in range(4)]
_name = marker.name
if marker.auto_update is False:
if _name == 'vertical_line':
assert _xy2[0] == _xy[0]
elif _name == 'horizontal_line':
assert _xy2[0] == _xy[1]
elif _name == 'vertical_line_segment':
assert _xy2[0:3] == [_xy[i] for i in (0,1,3)]
elif _name == 'horizontal_line_segment':
assert _xy2[0:3] == [_xy[i] for i in (0,2,1)]
elif _name in ('rectangle', 'ellipse', 'arrow', 'line_segment'):
assert _xy2 == _xy
elif _name in ('point', 'text'):
assert _xy2[0:2] == _xy[0:2]
else:
raise ValueError('Unknown marker : ' + _name)
def _test_plot_line_markers():
im = Signal2D(np.arange(100 * 100).reshape((100, 100)))
m0 = markers.vertical_line_segment(x=20, y1=30, y2=70, linewidth=4,
color='red', linestyle='dotted')
im.add_marker(m0)
m1 = markers.horizontal_line_segment(x1=30, x2=20, y=80, linewidth=8,
color='blue', linestyle='-')
im.add_marker(m1)
m2 = markers.vertical_line(50, linewidth=12, color='green')
im.add_marker(m2)
m3 = markers.horizontal_line(50, linewidth=10, color='yellow')
im.add_marker(m3)
return im
def test_save_load_vertical_line_segment_marker(self, tmp_path, file):
filename = tmp_path / file
s = self.s
x, y1, y2 = 2, 1, 3
color = 'white'
linewidth = 4.2
name = "vertical_line_segment_test"
m = markers.vertical_line_segment(
x=x, y1=y1, y2=y2, color=color, linewidth=linewidth)
m.name = name
s.add_marker(m, permanent=True)
s.save(filename)
s1 = load(filename)
m1 = s1.metadata.Markers.get_item(name)
assert san_dict(m1._to_dictionary()) == san_dict(m._to_dictionary())
def test_save_load_vertical_line_segment_marker(self):
x, y1, y2 = 2, 1, 3
color = 'white'
linewidth = 4.2
name = "vertical_line_segment_test"
s = Signal2D(np.arange(100).reshape(10, 10))
m = markers.vertical_line_segment(
x=x, y1=y1, y2=y2, color=color, linewidth=linewidth)
m.name = name
s.add_marker(m, permanent=True)
with tempfile.TemporaryDirectory() as tmp:
filename = tmp + '/test_save_vertical_line_segment_marker.hdf5'
s.save(filename)
s1 = load(filename)
m1 = s1.metadata.Markers.get_item(name)
assert san_dict(m1._to_dictionary()) == san_dict(m._to_dictionary())
def test_save_load_vertical_line_segment_marker(self):
x, y1, y2 = 2, 1, 3
color = 'white'
linewidth = 4.2
name = "vertical_line_segment_test"
s = Signal2D(np.arange(100).reshape(10, 10))
m = markers.vertical_line_segment(
x=x, y1=y1, y2=y2, color=color, linewidth=linewidth)
m.name = name
s.add_marker(m, permanent=True)
with tempfile.TemporaryDirectory() as tmp:
filename = tmp + '/test_save_vertical_line_segment_marker.hdf5'
s.save(filename)
s1 = load(filename)
m1 = s1.metadata.Markers.get_item(name)
assert san_dict(m1._to_dictionary()) == san_dict(m._to_dictionary())
def get_markers(self, labels):
'''Get the markers (vertical line segment and text box) for labelling
the edges
Parameters
----------
labels : dictionary
A dictionary with the labels as keys and their energies as values.
E.g. for EELS edges it could be {'Mn_L2': 651.0, 'Cr_L3': 575.0}.
Returns
-------
vls : list
A list contains HyperSpy's vertical line segment marker
txs : list
A list contains HyperSpy's text marker
'''
xytext = self._get_textbox_pos(labels)
vls = []
txs = []
for xyt in xytext:
vl = markers.vertical_line_segment(x=xyt[0],
y1=xyt[1],
y2=xyt[2],
color=xyt[4])
tx = markers.text(x=xyt[0],
y=xyt[1],
text=self._text_parser(xyt[3]),
color=xyt[4],
**self.edge_label_style)
vl.events.closed.connect(self.signal._edge_marker_closed)
tx.events.closed.connect(self.signal._edge_marker_closed)
vl.auto_update = True
tx.auto_update = True
vls.append(vl)
txs.append(tx)
return vls, txs
def test_add_several_permanent_markers(self):
s = Signal1D(np.arange(10))
m_point = markers.point(x=5, y=5)
m_line = markers.line_segment(x1=5, x2=10, y1=5, y2=10)
m_vline = markers.vertical_line(x=5)
m_vline_segment = markers.vertical_line_segment(x=4, y1=3, y2=6)
m_hline = markers.horizontal_line(y=5)
m_hline_segment = markers.horizontal_line_segment(x1=1, x2=9, y=5)
m_rect = markers.rectangle(x1=1, x2=3, y1=5, y2=10)
m_text = markers.text(x=1, y=5, text="test")
s.add_marker(m_point, permanent=True)
s.add_marker(m_line, permanent=True)
s.add_marker(m_vline, permanent=True)
s.add_marker(m_vline_segment, permanent=True)
s.add_marker(m_hline, permanent=True)
s.add_marker(m_hline_segment, permanent=True)
s.add_marker(m_rect, permanent=True)
s.add_marker(m_text, permanent=True)
assert len(list(s.metadata.Markers)) == 8
with pytest.raises(ValueError):
s.add_marker(m_rect, permanent=True)
def test_add_several_permanent_markers(self, mpl_cleanup):
s = Signal1D(np.arange(10))
m_point = markers.point(x=5, y=5)
m_line = markers.line_segment(x1=5, x2=10, y1=5, y2=10)
m_vline = markers.vertical_line(x=5)
m_vline_segment = markers.vertical_line_segment(x=4, y1=3, y2=6)
m_hline = markers.horizontal_line(y=5)
m_hline_segment = markers.horizontal_line_segment(x1=1, x2=9, y=5)
m_rect = markers.rectangle(x1=1, x2=3, y1=5, y2=10)
m_text = markers.text(x=1, y=5, text="test")
s.add_marker(m_point, permanent=True)
s.add_marker(m_line, permanent=True)
s.add_marker(m_vline, permanent=True)
s.add_marker(m_vline_segment, permanent=True)
s.add_marker(m_hline, permanent=True)
s.add_marker(m_hline_segment, permanent=True)
s.add_marker(m_rect, permanent=True)
s.add_marker(m_text, permanent=True)
assert len(list(s.metadata.Markers)) == 8
with pytest.raises(ValueError):
s.add_marker(m_rect, permanent=True)
