def release(self, event):
if event.button == 1:
if self.radius > 0:
c = CircularROI(self.center[0], self.center[1], self.radius)
mask_dict = {}
self.set_progress(0)
for layer_artist in self.iter_data_layer_artists():
def selection(x, y):
return c.contains(x, y)
mask = get_mask_for_layer_artist(layer_artist, self.viewer,
selection, progress=self.set_progress)
mask_dict[layer_artist.layer] = mask
self.mark_selected_dict(mask_dict)
self.set_progress(-1)
self.reset()
def reg_to_roi(reg):
"""
Function to convert a region to an ROI
This might be implementable as a dictionary/registry,
but hard-coding it isn't more difficult...
"""
if isinstance(reg, regions.CirclePixelRegion):
return CircularROI(xc=reg.center.x, yc=reg.center.y, radius=reg.radius)
elif isinstance(reg, regions.PointPixelRegion):
return PointROI(x=reg.center.x, y=reg.center.y)
elif isinstance(reg, regions.RectanglePixelRegion):
if reg.angle == 0:
xmin, xmax = reg.center.x - reg.width / 2, reg.center.x + reg.width / 2
ymin, ymax = reg.center.y - reg.height / 2, reg.center.y + reg.height / 2
return RectangularROI(xmin=xmin, xmax=xmax, ymin=ymin, ymax=ymax)
else:
if hasattr(reg, 'corners'):
xverts = [c[0] for c in reg.corners]
yverts = [c[1] for c in reg.corners]
return PolygonalROI(vx=xverts, vy=yverts)
else:
raise NotImplementedError("Rectangles need to convert to polygons.")
elif isinstance(reg, regions.PolygonPixelRegion):
return PolygonalROI(vx=reg.vertices.x, vy=reg.vertices.y)
else:
raise NotImplementedError("Region {0} not recognized".format(reg))
def update_selection(self, *args):
if self.interact.brushing:
return
with self.viewer._output_widget:
if self.interact.selected_x is not None and self.interact.selected_y is not None:
x = self.interact.selected_x
y = self.interact.selected_y
# similar to https://github.com/glue-viz/glue/blob/b14ccffac6a5
# 271c2869ead9a562a2e66232e397/glue/core/roi.py#L1275-L1297
# We should now check if the radius in data coordinates is the same
# along x and y, as if so then we can return a circle, otherwise we
# should return an ellipse.
xc = x.mean()
yc = y.mean()
rx = abs(x[1] - x[0]) / 2
ry = abs(y[1] - y[0]) / 2
# We use a tolerance of 1e-2 below to match the tolerance set in glue-core
# https://github.com/glue-viz/glue/blob/6b968b352bc5ad68b95ad5e3bb25550782a69ee8/glue/viewers/matplotlib/state.py#L198
if np.allclose(rx, ry, rtol=1e-2):
roi = CircularROI(xc=xc, yc=yc, radius=rx)
else:
roi = EllipticalROI(xc=xc, yc=yc, radius_x=rx, radius_y=ry)
self.viewer.apply_roi(roi)
if self.finalize_callback is not None:
self.finalize_callback()
def on_selection(self, data, other=None):
with self.output_widget:
W = np.matrix(self.figure.matrix_world).reshape((4, 4)).T
P = np.matrix(self.figure.matrix_projection).reshape((4, 4)).T
M = np.dot(P, W)
if data['device']:
if data['type'] == 'lasso':
region = data['device']
vx, vy = zip(*region)
roi_2d = PolygonalROI(vx=vx, vy=vy)
elif data['type'] == 'circle':
x1, y1 = data['device']['begin']
x2, y2 = data['device']['end']
dx = x2 - x1
dy = y2 - y1
r = (dx**2 + dy**2)**0.5
roi_2d = CircularROI(xc=x1, yc=y1, radius=r)
elif data['type'] == 'rectangle':
x1, y1 = data['device']['begin']
x2, y2 = data['device']['end']
x = [x1, x2]
y = [y1, y2]
roi_2d = RectangularROI(xmin=min(x),
xmax=max(x),
ymin=min(y),
ymax=max(y))
roi = Projected3dROI(roi_2d, M)
self.apply_roi(roi)
def setup(self):
self.data_collection, self.viewer = get_data_collection_and_viewer()
load_wcs_data(self.data_collection)
self.viewer.add_data(self.data_collection[0])
self.viewer.add_data(self.data_collection[1])
roi = CircularROI(256, 256, 120)
py1, px1 = self.data_collection[0].pixel_component_ids
self.subset_state = RoiSubsetState(px1, py1, roi)
self.viewer.register_to_hub(self.data_collection.hub)
def release(self, event):
if event.button == 1:
if self.radius > 0:
roi = Projected3dROI(roi_2d=CircularROI(
self.center[0], self.center[1], self.radius),
projection_matrix=self.projection_matrix)
self.apply_roi(roi)
self.reset()
self.viewer.toolbar.active_tool = None
def on_mouse_release(self, event):
"""
Get the mask of selected data and get them highlighted.
:param event:
"""
# Get the visible datasets
if event.button == 1 and self.mode and self.mode is not 'point':
visible_data, visual = self.get_visible_data()
data = self.get_map_data()
if len(self.line_pos) == 0:
self.lasso_reset()
return
elif self.mode is 'lasso':
# Note, we use points_inside_poly here instead of calling e.g.
# matplotlib directly, because we include some optimizations
# in points_inside_poly
vx, vy = np.array(self.line_pos).transpose()
x, y = data.transpose()
mask = points_inside_poly(x, y, vx, vy)
elif self.mode is 'ellipse':
xmin, ymin = np.min(self.line_pos[:, 0]), \
np.min(self.line_pos[:, 1])
xmax, ymax = np.max(self.line_pos[:, 0]), \
np.max(self.line_pos[:, 1])
# (xc, yc, radius)
c = CircularROI((xmax+xmin)/2., (ymax+ymin)/2., (xmax-xmin)/2.)
mask = c.contains(data[:, 0], data[:, 1])
elif self.mode is 'rectangle':
xmin, ymin = np.min(self.line_pos[:, 0]), \
np.min(self.line_pos[:, 1])
xmax, ymax = np.max(self.line_pos[:, 0]), \
np.max(self.line_pos[:, 1])
r = RectangularROI(xmin, xmax, ymin, ymax)
mask = r.contains(data[:, 0], data[:, 1])
else:
raise ValueError("Unknown mode: {0}".format(self.mode))
# Mask matches transposed volume data set rather than the original one.
# The ravel here is to make mask compatible with ElementSubsetState input.
new_mask = np.reshape(mask, self.trans_ones_data.shape)
new_mask = np.ravel(np.transpose(new_mask))
self.mark_selected(new_mask, self.visible_data)
self.lasso_reset()
def test_circular_roi(self):
subset_state = RoiSubsetState(self.data.pixel_component_ids[1],
self.data.pixel_component_ids[0],
CircularROI(1, 3.5, 0.75))
self.dc.new_subset_group(subset_state=subset_state, label='circular')
reg = self.data.get_selection_definition(format='astropy-regions')
assert isinstance(reg, CirclePixelRegion)
assert_equal(reg.center.x, 1)
assert_equal(reg.center.y, 3.5)
assert_equal(reg.radius, 0.75)
def on_selection(self, data, other=None):
if data['type'] != self.selector:
return
if data['device']:
with self.viewer.output_widget:
x1, y1 = data['device']['begin']
x2, y2 = data['device']['end']
dx = x2 - x1
dy = y2 - y1
r = (dx**2 + dy**2)**0.5
roi_2d = CircularROI(xc=x1, yc=y1, radius=r)
roi = Projected3dROI(roi_2d, self.projection_matrix)
self.viewer.apply_roi(roi)
def on_mouse_release(self, event):
# Get the visible datasets
if event.button == 1 and self.mode is not None:
visible_data, visual = self.get_visible_data()
data = self.get_map_data()
if len(self.line_pos) == 0:
self.lasso_reset()
return
elif self.mode is 'lasso':
selection_path = path.Path(self.line_pos, closed=True)
mask = selection_path.contains_points(data)
elif self.mode is 'ellipse':
xmin, ymin = np.min(self.line_pos[:,
0]), np.min(self.line_pos[:,
1])
xmax, ymax = np.max(self.line_pos[:,
0]), np.max(self.line_pos[:,
1])
c = CircularROI((xmax + xmin) / 2., (ymax + ymin) / 2.,
(xmax - xmin) / 2.) # (xc, yc, radius)
mask = c.contains(data[:, 0], data[:, 1])
elif self.mode is 'rectangle':
xmin, ymin = np.min(self.line_pos[:,
0]), np.min(self.line_pos[:,
1])
xmax, ymax = np.max(self.line_pos[:,
0]), np.max(self.line_pos[:,
1])
r = RectangularROI(xmin, xmax, ymin, ymax)
mask = r.contains(data[:, 0], data[:, 1])
else:
raise ValueError("Unknown mode: {0}".format(self.mode))
self.mark_selected(mask, visible_data)
self.lasso_reset()
def test_or_region(self):
subset_state1 = RoiSubsetState(self.data.pixel_component_ids[1],
self.data.pixel_component_ids[0],
RectangularROI(1, 5, 2, 6))
subset_state2 = RoiSubsetState(self.data.pixel_component_ids[1],
self.data.pixel_component_ids[0],
CircularROI(4.75, 5.75, 0.5))
or_subset_state = OrState(subset_state1, subset_state2)
self.dc.new_subset_group(subset_state=or_subset_state, label='orstate')
reg = self.data.get_selection_definition(format='astropy-regions')
assert isinstance(reg, CompoundPixelRegion)
assert isinstance(reg.region1, RectanglePixelRegion)
assert isinstance(reg.region2, CirclePixelRegion)
assert reg.contains(PixCoord(4.5, 5.5))
assert reg.contains(PixCoord(3, 4))
assert reg.contains(PixCoord(5.1, 6.1))
assert not reg.contains(PixCoord(11, 12))
def update_selection(self, *args):
if self.interact.brushing:
return
with self.viewer._output_widget:
if self.interact.selected_x is not None and self.interact.selected_y is not None:
x = self.interact.selected_x
y = self.interact.selected_y
# similar to https://github.com/glue-viz/glue/blob/b14ccffac6a5
# 271c2869ead9a562a2e66232e397/glue/core/roi.py#L1275-L1297
# We should now check if the radius in data coordinates is the same
# along x and y, as if so then we can return a circle, otherwise we
# should return an ellipse.
xc = x.mean()
yc = y.mean()
rx = abs(x[1] - x[0])/2
ry = abs(y[1] - y[0])/2
if np.allclose(rx, ry):
roi = CircularROI(xc=xc, yc=yc, radius=rx)
else:
roi = EllipticalROI(xc=xc, yc=yc, radius_x=rx, radius_y=ry)
self.viewer.apply_roi(roi)
if self.finalize_callback is not None:
self.finalize_callback()
def release(self, event):
if event.button == 1:
if self.radius > 0:
c = CircularROI(self.center[0], self.center[1], self.radius)
indices_dict = {}
for layer_artist in self.iter_data_layer_artists():
data = get_map_data(layer_artist, self.viewer)
mask = c.contains(data[:, 0], data[:, 1])
shape_mask = np.reshape(mask,
layer_artist.layer.shape[::-1])
shape_mask = np.ravel(np.transpose(shape_mask))
indices_dict[layer_artist.layer] = np.where(shape_mask)[0]
self.mark_selected_dict(indices_dict)
self.reset()
def test_invalid_combos(self):
good_subset = RoiSubsetState(self.data.pixel_component_ids[1],
self.data.pixel_component_ids[0],
RectangularROI(1, 5, 2, 6))
bad_subset = RoiSubsetState(self.data.pixel_component_ids[1],
self.data.main_components[0],
CircularROI(4.75, 5.75, 0.5))
and_sub = AndState(good_subset, bad_subset)
or_sub = OrState(good_subset, bad_subset)
xor_sub = XorState(good_subset, bad_subset)
multior = MultiOrState([good_subset, bad_subset])
self.dc.new_subset_group(subset_state=and_sub, label='and')
self.dc.new_subset_group(subset_state=or_sub, label='or')
self.dc.new_subset_group(subset_state=xor_sub, label='xor')
self.dc.new_subset_group(subset_state=multior, label='multior')
expected_error = 'Subset state yatt should be y pixel coordinate'
with pytest.raises(ValueError) as exc:
self.data.get_selection_definition(subset_id='and',
format='astropy-regions')
assert exc.value.args[0] == expected_error
with pytest.raises(ValueError) as exc:
self.data.get_selection_definition(subset_id='or',
format='astropy-regions')
assert exc.value.args[0] == expected_error
with pytest.raises(ValueError) as exc:
self.data.get_selection_definition(subset_id='xor',
format='astropy-regions')
assert exc.value.args[0] == expected_error
with pytest.raises(ValueError) as exc:
self.data.get_selection_definition(subset_id='multior',
format='astropy-regions')
assert exc.value.args[0] == expected_error
def test_datetime64_support(self, tmpdir):
self.data.add_component(np.array([100, 200, 300, 400], dtype='M8[D]'),
't1')
self.data.add_component(np.array([200, 300, 400, 500], dtype='M8[D]'),
't2')
self.viewer.add_data(self.data)
self.viewer.state.x_att = self.data.id['t1']
self.viewer.state.y_att = self.data.id['y']
# Matplotlib deals with dates by converting them to the number of days
# since 01-01-0001, so we can check that the limits are correctly
# converted (and not 100 to 400)
assert self.viewer.axes.get_xlim() == (719248.0, 719578.0)
assert self.viewer.axes.get_ylim() == (3.2 - 0.015, 3.5 + 0.015)
# Apply an ROI selection in plotting coordinates
roi = RectangularROI(xmin=719313, xmax=719513, ymin=3, ymax=4)
self.viewer.apply_roi(roi)
# Check that the two middle elements are selected
assert_equal(self.data.subsets[0].to_mask(), [0, 1, 1, 0])
# Now do the same with the y axis
self.viewer.state.y_att = self.data.id['t2']
assert self.viewer.axes.get_xlim() == (719248.0, 719578.0)
assert self.viewer.axes.get_ylim() == (719348.0, 719678.0)
# Apply an ROI selection in plotting coordinates
edit = self.session.edit_subset_mode
edit.edit_subset = []
roi = CircularROI(xc=719463, yc=719563, radius=200)
self.viewer.apply_roi(roi)
assert_equal(self.data.subsets[1].to_mask(), [0, 1, 1, 1])
# Make sure that the Qt labels look ok
self.viewer.state.y_att = self.data.id['y']
options = self.viewer.options_widget().ui
assert options.valuetext_x_min.text() == '1970-03-27'
assert options.valuetext_x_max.text() == '1971-02-20'
assert options.valuetext_y_min.text() == '3.185'
assert options.valuetext_y_max.text() == '3.515'
# Make sure that we can set the xmin/xmax to a string date
assert_equal(self.viewer.state.x_min, np.datetime64('1970-03-27', 'D'))
options.valuetext_x_min.setText('1970-04-14')
options.valuetext_x_min.editingFinished.emit()
assert self.viewer.axes.get_xlim() == (719266.0, 719578.0)
assert_equal(self.viewer.state.x_min, np.datetime64('1970-04-14', 'D'))
# Make sure that everything works fine after saving/reloading
filename = tmpdir.join('test_datetime64.glu').strpath
self.session.application.save_session(filename)
with open(filename, 'r') as f:
session = f.read()
state = GlueUnSerializer.loads(session)
ga = state.object('__main__')
viewer = ga.viewers[0][0]
options = viewer.options_widget().ui
assert_equal(self.viewer.state.x_min, np.datetime64('1970-04-14', 'D'))
assert options.valuetext_x_min.text() == '1970-04-14'
assert options.valuetext_x_max.text() == '1971-02-20'
assert options.valuetext_y_min.text() == '3.185'
assert options.valuetext_y_max.text() == '3.515'