def _repr_html_(self):
box = Box()
box.children = [self.value_text, self.vary_checkbox,
self.min_text, self.min_checkbox,
self.max_text, self.max_checkbox]
display(box)
box.add_class('hbox')
def _repr_html_(self):
box = HBox()
box.children = [
self.value_text, self.vary_checkbox, self.min_checkbox,
self.min_text, self.max_checkbox, self.max_text
]
display(box)
def _repr_html_(self):
box = Box()
box.children = [self.value_text, self.vary_checkbox,
self.min_text, self.min_checkbox,
self.max_text, self.max_checkbox]
display(box)
box.add_class('hbox')
def _repr_html_(self):
display(self.models_menu)
button_box = HBox()
button_box.children = [self.fit_button, self.guess_button]
display(button_box)
for pw in self.param_widgets:
display(pw)
self.plot()
def _ipython_display_(self, *pargs, **kwargs):
"""Rich display repr for this widget."""
# Call the normal display logic.
ContainerWidget._ipython_display_(self, *pargs, **kwargs)
# Call custom add/remove class logic AFTER display.
for row in self.children:
row.remove_class('widget-container')
row.remove_class('vbox')
row.add_class('row-fluid')
[c.add_class('span' + str(12/len(row.children))) for c in row.children]
def _create_cell(self, color=''):
"""Create a grid cell"""
cell = ContainerWidget()
cell.set_css({
'background': color,
'height': '100%',
'margin-right': '0px',
'margin-top': '0px',
'margin-bottom': '0px',
})
return cell
def interactive(__interact_f, **kwargs):
"""Build a group of widgets to interact with a function."""
f = __interact_f
co = kwargs.pop('clear_output', True)
kwargs_widgets = []
container = ContainerWidget()
container.result = None
container.args = []
container.kwargs = dict()
kwargs = kwargs.copy()
new_kwargs = _find_abbreviations(f, kwargs)
# Before we proceed, let's make sure that the user has passed a set of args+kwargs
# that will lead to a valid call of the function. This protects against unspecified
# and doubly-specified arguments.
getcallargs(f, **{n: v for n, v in new_kwargs})
# Now build the widgets from the abbreviations.
kwargs_widgets.extend(_widgets_from_abbreviations(new_kwargs))
kwargs_widgets.extend(
_widgets_from_abbreviations(sorted(kwargs.items(),
key=lambda x: x[0])))
# This has to be done as an assignment, not using container.children.append,
# so that traitlets notices the update. We skip any objects (such as fixed) that
# are not DOMWidgets.
c = [w for w in kwargs_widgets if isinstance(w, DOMWidget)]
container.children = c
# Build the callback
def call_f(name, old, new):
container.kwargs = {}
for widget in kwargs_widgets:
value = widget.value
container.kwargs[widget.description] = value
if co:
clear_output(wait=True)
try:
container.result = f(**container.kwargs)
except Exception as e:
ip = get_ipython()
if ip is None:
container.log.warn("Exception in interact callback: %s",
e,
exc_info=True)
else:
ip.showtraceback()
# Wire up the widgets
for widget in kwargs_widgets:
widget.on_trait_change(call_f, 'value')
container.on_displayed(lambda _: call_f(None, None, None))
return container
def __init__(self, columns, rows, debug=False, **kwargs):
"""Public constructor
PARAMETERS
----------
columns: int
rows: int
debug: bool
Use rainbow background colors for the cells.
"""
ContainerWidget.__init__(self)
# Create the grid
self.children = self._create_grid(columns, rows, debug=debug)
# The grid should occupy the entire widget-subarea by default.
self.set_css('width', '100%')
# Manually handle height and padding changes.
self.on_trait_change(self._update_layout, ['height', 'padding'])
# Update the layout once to set initial values.
self._update_layout(None, self.height)
def __init__(self, container, caption=None, ylabel='', xlabel='', height=300, width=900):
cell_header = HTMLWidget(value=('<h3 class="chart-header">' + caption + '</h3>' if caption is not None else ''))
yaxis = HTMLWidget(value=ylabel)
area_chart = StackedAreaWidget(width=width, height=height, hide_xaxis=xlabel=='')
chart_columns = ContainerWidget(children=[yaxis, area_chart])
chart_columns.set_css('width', '100%')
xaxis = HTMLWidget(value=xlabel)
chart = ContainerWidget(children=[chart_columns, xaxis])
container.children = container.children + tuple([cell_header, chart])
chart_columns.remove_class('vbox')
chart_columns.add_class('hbox align-center center')
xaxis.add_class('x axis-label')
yaxis.add_class('y axis-label pack-center')
area_chart.add_class('area-chart')
chart.add_class('pack-center center chart-area')
self.plot = area_chart
def interactive(__interact_f, **kwargs):
"""Build a group of widgets to interact with a function."""
f = __interact_f
co = kwargs.pop('clear_output', True)
kwargs_widgets = []
container = ContainerWidget()
container.result = None
container.args = []
container.kwargs = dict()
kwargs = kwargs.copy()
new_kwargs = _find_abbreviations(f, kwargs)
# Before we proceed, let's make sure that the user has passed a set of args+kwargs
# that will lead to a valid call of the function. This protects against unspecified
# and doubly-specified arguments.
getcallargs(f, **{n:v for n,v in new_kwargs})
# Now build the widgets from the abbreviations.
kwargs_widgets.extend(_widgets_from_abbreviations(new_kwargs))
kwargs_widgets.extend(_widgets_from_abbreviations(sorted(kwargs.items(), key = lambda x: x[0])))
# This has to be done as an assignment, not using container.children.append,
# so that traitlets notices the update. We skip any objects (such as fixed) that
# are not DOMWidgets.
c = [w for w in kwargs_widgets if isinstance(w, DOMWidget)]
container.children = c
# Build the callback
def call_f(name, old, new):
container.kwargs = {}
for widget in kwargs_widgets:
value = widget.value
container.kwargs[widget.description] = value
if co:
clear_output(wait=True)
try:
container.result = f(**container.kwargs)
except Exception as e:
ip = get_ipython()
if ip is None:
container.log.warn("Exception in interact callback: %s", e, exc_info=True)
else:
ip.showtraceback()
# Wire up the widgets
for widget in kwargs_widgets:
widget.on_trait_change(call_f, 'value')
container.on_displayed(lambda _: call_f(None, None, None))
return container
def TrajectoryHeatmap(trajectory, x, y, fig=None, **kwargs):
if fig is None:
fig = pp.figure(figsize=(5,5))
ax = fig.add_subplot(1,1,1)
ax.hexbin(x, y)
ax.set_xlabel('x')
ax.set_ylabel('y')
else:
ax = fig.get_axes()[0]
heatmap = MPLFigureButton(fig=fig, height='200px');
viewer = TrajectoryView(trajectory, **kwargs)
pointToDataCoordinates = ax.transData.inverted()
kdtree = cKDTree(np.vstack((x, y)).T)
def callback(b, content):
x, y = pointToDataCoordinates.transform([content['mouseX'], content['mouseY']])
_, index = kdtree.query(x=[x, y], k=1)
print(x, y, index)
viewer.frame = index
heatmap.on_click(callback)
return ContainerWidget(children=(heatmap, viewer))
def visualize_images(images, figure_size=(7, 7), popup=False, **kwargs):
r"""
Widget that allows browsing through a list of images.
Parameters
-----------
images : `list` of :map:`Image` or subclass
The list of images to be displayed. Note that the images can have
different attributes between them, i.e. different landmark groups and
labels, different number of channels etc.
figure_size : (`int`, `int`), optional
The initial size of the plotted figures.
popup : `boolean`, optional
If enabled, the widget will appear as a popup window.
kwargs : `dict`, optional
Passed through to the viewer.
"""
from menpo.image import MaskedImage
import matplotlib.pyplot as plt
# make sure that images is a list even with one image member
if not isinstance(images, Sized):
images = [images]
# find number of images
n_images = len(images)
# find initial groups and labels that will be passed to the landmark options
# widget creation
first_has_landmarks = images[0].landmarks.n_groups != 0
if first_has_landmarks:
initial_groups_keys, initial_labels_keys = \
_extract_groups_labels(images[0])
else:
initial_groups_keys = [' ']
initial_labels_keys = [[' ']]
# define plot function
def plot_function(name, value):
# clear current figure, but wait until the new data to be displayed are
# generated
clear_output(wait=True)
# get selected image number
im = 0
if n_images > 1:
im = image_number_wid.selected_index
# update info text widget
image_has_landmarks = images[im].landmarks.n_groups != 0
image_is_masked = isinstance(images[im], MaskedImage)
update_info(images[im], image_is_masked, image_has_landmarks,
landmark_options_wid.group)
# get the current figure id
figure_id = save_figure_wid.figure_id
# show image with selected options
new_figure_id = _plot_figure(
image=images[im], figure_id=figure_id, image_enabled=True,
landmarks_enabled=landmark_options_wid.landmarks_enabled,
image_is_masked=channel_options_wid.image_is_masked,
masked_enabled=(channel_options_wid.masked_enabled and
image_is_masked),
channels=channel_options_wid.channels,
glyph_enabled=channel_options_wid.glyph_enabled,
glyph_block_size=channel_options_wid.glyph_block_size,
glyph_use_negative=channel_options_wid.glyph_use_negative,
sum_enabled=channel_options_wid.sum_enabled,
groups=[landmark_options_wid.group],
with_labels=[landmark_options_wid.with_labels],
groups_colours=dict(), subplots_enabled=False,
subplots_titles=dict(), image_axes_mode=True,
legend_enabled=landmark_options_wid.legend_enabled,
numbering_enabled=landmark_options_wid.numbering_enabled,
x_scale=figure_options_wid.x_scale,
y_scale=figure_options_wid.x_scale,
axes_visible=figure_options_wid.axes_visible,
figure_size=figure_size, **kwargs)
# save the current figure id
save_figure_wid.figure_id = new_figure_id
# define function that updates info text
def update_info(image, image_is_masked, image_has_landmarks, group):
# Prepare masked (or non-masked) string
masked_str = 'Masked Image' if image_is_masked else 'Image'
# Display masked pixels if image is masked
masked_pixels_str = (r'{} masked pixels (attached mask {:.1%} true)'.
format(image.n_true_pixels(),
image.mask.proportion_true())
if image_is_masked else '')
# Display number of landmarks if image is landmarked
landmarks_str = (r'{} landmark points.'.
format(image.landmarks[group].lms.n_points)
if image_has_landmarks else '')
path_str = image.path if hasattr(image, 'path') else 'NO PATH'
# Create info string
info_txt = r"""
{} of size {} with {} channel{}
{}
{}
min={:.3f}, max={:.3f}
{}
""".format(masked_str, image._str_shape, image.n_channels,
's' * (image.n_channels > 1), path_str, masked_pixels_str,
image.pixels.min(), image.pixels.max(), landmarks_str)
# update info widget text
info_wid.children[1].value = _raw_info_string_to_latex(info_txt)
# create options widgets
channel_options_wid = channel_options(images[0].n_channels,
isinstance(images[0], MaskedImage),
plot_function,
masked_default=False,
toggle_show_default=True,
toggle_show_visible=False)
# The landmarks checkbox default value if the first image doesn't have
# landmarks
landmark_options_wid = landmark_options(
initial_groups_keys, initial_labels_keys, plot_function,
toggle_show_default=True, landmarks_default=first_has_landmarks,
legend_default=True, numbering_default=False, toggle_show_visible=False)
# if only a single image is passed in and it doesn't have landmarks, then
# landmarks checkbox should be disabled
landmark_options_wid.children[1].children[0].disabled = \
not first_has_landmarks
figure_options_wid = figure_options(plot_function, scale_default=1.,
show_axes_default=False,
toggle_show_default=True,
figure_scale_bounds=(0.1, 2),
figure_scale_step=0.1,
figure_scale_visible=True,
toggle_show_visible=False)
info_wid = info_print(toggle_show_default=True,
toggle_show_visible=False)
initial_figure_id = plt.figure()
save_figure_wid = save_figure_options(initial_figure_id,
toggle_show_default=True,
toggle_show_visible=False)
# define function that updates options' widgets state
def update_widgets(name, value):
# get new groups and labels, update landmark options and format them
group_keys, labels_keys = _extract_groups_labels(images[value])
update_landmark_options(landmark_options_wid, group_keys,
labels_keys, plot_function)
format_landmark_options(landmark_options_wid, container_padding='6px',
container_margin='6px',
container_border='1px solid black',
toggle_button_font_weight='bold',
border_visible=False)
# update channel options
update_channel_options(channel_options_wid,
n_channels=images[value].n_channels,
image_is_masked=isinstance(images[value],
MaskedImage))
# create final widget
if n_images > 1:
# image selection slider
image_number_wid = animation_options(
index_min_val=0, index_max_val=n_images-1,
plot_function=plot_function, update_function=update_widgets,
index_step=1, index_default=0,
index_description='Image Number', index_minus_description='<',
index_plus_description='>', index_style='buttons',
index_text_editable=True, loop_default=True, interval_default=0.3,
toggle_show_title='Image Options', toggle_show_default=True,
toggle_show_visible=False)
# final widget
cont_wid = TabWidget(children=[info_wid, channel_options_wid,
landmark_options_wid,
figure_options_wid, save_figure_wid])
wid = ContainerWidget(children=[image_number_wid, cont_wid])
button_title = 'Images Menu'
else:
# final widget
wid = TabWidget(children=[info_wid, channel_options_wid,
landmark_options_wid, figure_options_wid,
save_figure_wid])
button_title = 'Image Menu'
# create popup widget if asked
if popup:
wid = PopupWidget(children=[wid], button_text=button_title)
# display final widget
display(wid)
# set final tab titles
tab_titles = ['Image info', 'Channels options', 'Landmarks options',
'Figure options', 'Save figure']
if popup:
if n_images > 1:
for (k, tl) in enumerate(tab_titles):
wid.children[0].children[1].set_title(k, tl)
else:
for (k, tl) in enumerate(tab_titles):
wid.children[0].set_title(k, tl)
else:
if n_images > 1:
for (k, tl) in enumerate(tab_titles):
wid.children[1].set_title(k, tl)
else:
for (k, tl) in enumerate(tab_titles):
wid.set_title(k, tl)
# align-start the image number widget and the rest
if n_images > 1:
wid.add_class('align-start')
# format options' widgets
if n_images > 1:
format_animation_options(image_number_wid, index_text_width='0.5cm',
container_padding='6px',
container_margin='6px',
container_border='1px solid black',
toggle_button_font_weight='bold',
border_visible=False)
format_channel_options(channel_options_wid, container_padding='6px',
container_margin='6px',
container_border='1px solid black',
toggle_button_font_weight='bold',
border_visible=False)
format_landmark_options(landmark_options_wid, container_padding='6px',
container_margin='6px',
container_border='1px solid black',
toggle_button_font_weight='bold',
border_visible=False)
format_figure_options(figure_options_wid, container_padding='6px',
container_margin='6px',
container_border='1px solid black',
toggle_button_font_weight='bold',
border_visible=False)
format_info_print(info_wid, font_size_in_pt='9pt', container_padding='6px',
container_margin='6px',
container_border='1px solid black',
toggle_button_font_weight='bold', border_visible=False)
format_save_figure_options(save_figure_wid, container_padding='6px',
container_margin='6px',
container_border='1px solid black',
toggle_button_font_weight='bold',
tab_top_margin='0cm', border_visible=False)
# update widgets' state for image number 0
update_widgets('', 0)
# Reset value to trigger initial visualization
landmark_options_wid.children[1].children[1].value = False
def visualize_shapes(shapes, figure_size=(7, 7), popup=False, **kwargs):
r"""
Widget that allows browsing through a list of shapes.
Parameters
-----------
shapes : `list` of :map:`LandmarkManager` or subclass
The list of shapes to be displayed. Note that the shapes can have
different attributes between them, i.e. different landmark groups and
labels etc.
figure_size : (`int`, `int`), optional
The initial size of the plotted figures.
popup : `boolean`, optional
If enabled, the widget will appear as a popup window.
kwargs : `dict`, optional
Passed through to the viewer.
"""
import matplotlib.pyplot as plt
# make sure that shapes is a list even with one shape member
if not isinstance(shapes, list):
shapes = [shapes]
# find number of shapes
n_shapes = len(shapes)
# find initial groups and labels that will be passed to the landmark options
# widget creation
first_has_landmarks = shapes[0].n_groups != 0
if first_has_landmarks:
initial_groups_keys, initial_labels_keys = \
_exrtact_group_labels_landmarks(shapes[0])
else:
initial_groups_keys = [' ']
initial_labels_keys = [[' ']]
# Define plot function
def plot_function(name, value):
# clear current figure, but wait until the new data to be displayed are
# generated
clear_output(wait=True)
# get params
s = 0
if n_shapes > 1:
s = image_number_wid.selected_index
axis_mode = axes_mode_wid.value
x_scale = figure_options_wid.x_scale
y_scale = figure_options_wid.y_scale
axes_visible = figure_options_wid.axes_visible
# get the current figure id
figure_id = plt.figure(save_figure_wid.figure_id.number)
# plot
if (landmark_options_wid.landmarks_enabled and
landmark_options_wid.group != ' '):
# invert axis if image mode is enabled
if axis_mode == 1:
plt.gca().invert_yaxis()
# plot
shapes[s].view(
group=landmark_options_wid.group,
with_labels=landmark_options_wid.with_labels,
image_view=axis_mode == 1,
render_legend=landmark_options_wid.legend_enabled,
render_numbering=landmark_options_wid.numbering_enabled,
**kwargs)
plt.hold(False)
plt.gca().axis('equal')
# set figure size
plt.gcf().set_size_inches([x_scale, y_scale] *
np.asarray(figure_size))
# turn axis on/off
if not axes_visible:
plt.axis('off')
plt.show()
# save the current figure id
save_figure_wid.figure_id = figure_id
# info_wid string
if landmark_options_wid.group != ' ':
info_txt = r"""
{} landmark points.
Shape range: {:.1f} x {:.1f}.
Shape centre: {:.1f} x {:.1f}.
Shape norm is {:.2f}.
""".format(shapes[s][landmark_options_wid.group][None].n_points,
shapes[s][landmark_options_wid.group][None].range()[0],
shapes[s][landmark_options_wid.group][None].range()[1],
shapes[s][landmark_options_wid.group][None].centre()[0],
shapes[s][landmark_options_wid.group][None].centre()[1],
shapes[s][landmark_options_wid.group][None].norm())
else:
info_txt = "There are no landmarks."
info_wid.children[1].value = _raw_info_string_to_latex(info_txt)
# create options widgets
# The landmarks checkbox default value if the first image doesn't have
# landmarks
landmark_options_wid = landmark_options(
initial_groups_keys, initial_labels_keys, plot_function,
toggle_show_default=True, landmarks_default=first_has_landmarks,
legend_default=True, numbering_default=False, toggle_show_visible=False)
# if only a single image is passed in and it doesn't have landmarks, then
# landmarks checkbox should be disabled
landmark_options_wid.children[1].children[0].disabled = \
not first_has_landmarks
figure_options_wid = figure_options(plot_function, scale_default=1.,
show_axes_default=False,
toggle_show_default=True,
toggle_show_visible=False)
axes_mode_wid = RadioButtonsWidget(values={'Image': 1, 'Point cloud': 2},
description='Axes mode:', value=1)
axes_mode_wid.on_trait_change(plot_function, 'value')
ch = list(figure_options_wid.children)
ch.insert(3, axes_mode_wid)
figure_options_wid.children = ch
info_wid = info_print(toggle_show_default=True, toggle_show_visible=False)
initial_figure_id = plt.figure()
save_figure_wid = save_figure_options(initial_figure_id,
toggle_show_default=True,
toggle_show_visible=False)
# define function that updates options' widgets state
def update_widgets(name, value):
# get new groups and labels, update landmark options and format them
group_keys, labels_keys = _exrtact_group_labels_landmarks(shapes[value])
update_landmark_options(landmark_options_wid, group_keys,
labels_keys, plot_function)
format_landmark_options(landmark_options_wid, container_padding='6px',
container_margin='6px',
container_border='1px solid black',
toggle_button_font_weight='bold',
border_visible=False)
# create final widget
if n_shapes > 1:
# image selection slider
image_number_wid = animation_options(
index_min_val=0, index_max_val=n_shapes-1,
plot_function=plot_function, update_function=update_widgets,
index_step=1, index_default=0,
index_description='Shape Number', index_minus_description='<',
index_plus_description='>', index_style='buttons',
index_text_editable=True, loop_default=True, interval_default=0.3,
toggle_show_title='Shape Options', toggle_show_default=True,
toggle_show_visible=False)
# final widget
cont_wid = TabWidget(children=[info_wid, landmark_options_wid,
figure_options_wid, save_figure_wid])
wid = ContainerWidget(children=[image_number_wid, cont_wid])
button_title = 'Shapes Menu'
else:
# final widget
wid = TabWidget(children=[info_wid, landmark_options_wid,
figure_options_wid, save_figure_wid])
button_title = 'Shape Menu'
# create popup widget if asked
if popup:
wid = PopupWidget(children=[wid], button_text=button_title)
# display final widget
display(wid)
# set final tab titles
tab_titles = ['Shape info', 'Landmarks options', 'Figure options',
'Save figure']
if popup:
if n_shapes > 1:
for (k, tl) in enumerate(tab_titles):
wid.children[0].children[1].set_title(k, tl)
else:
for (k, tl) in enumerate(tab_titles):
wid.children[0].set_title(k, tl)
else:
if n_shapes > 1:
for (k, tl) in enumerate(tab_titles):
wid.children[1].set_title(k, tl)
else:
for (k, tl) in enumerate(tab_titles):
wid.set_title(k, tl)
# align-start the image number widget and the rest
if n_shapes > 1:
wid.add_class('align-start')
# format options' widgets
if n_shapes > 1:
format_animation_options(image_number_wid, index_text_width='0.5cm',
container_padding='6px',
container_margin='6px',
container_border='1px solid black',
toggle_button_font_weight='bold',
border_visible=False)
format_landmark_options(landmark_options_wid, container_padding='6px',
container_margin='6px',
container_border='1px solid black',
toggle_button_font_weight='bold',
border_visible=False)
format_figure_options(figure_options_wid, container_padding='6px',
container_margin='6px',
container_border='1px solid black',
toggle_button_font_weight='bold',
border_visible=False)
format_info_print(info_wid, font_size_in_pt='9pt', container_padding='6px',
container_margin='6px',
container_border='1px solid black',
toggle_button_font_weight='bold', border_visible=False)
format_save_figure_options(save_figure_wid, container_padding='6px',
container_margin='6px',
container_border='1px solid black',
toggle_button_font_weight='bold',
tab_top_margin='0cm', border_visible=False)
# update widgets' state for image number 0
update_widgets('', 0)
# Reset value to trigger initial visualization
landmark_options_wid.children[1].children[1].value = False
def _repr_html_(self):
box = HBox()
box.children = [self.value_text, self.vary_checkbox,
self.min_checkbox, self.min_text,
self.max_checkbox, self.max_text]
display(box)
