def save_figure_widget(self, image_data, title='', caption = '', pvals=None, colors=None):
image_widget = Image()
image_widget.value = image_data
children = [i for i in self.figures_widget.children]
html_str = '<b>Figure '+str(len(children)+1)+'. '+title+'</b>' + caption
html_widget = HTML(value=html_str)
restore_pvals = Button(description='Restore Parameter Values')
restore_pvals.pvals = pvals
if pvals is None:
restore_pvals.visible = False
if old_ipython is True:
image_widget = Image()
image_widget.value = image_data
tab_widget = VBox(children=[image_widget, html_widget])
if colors is not None:
html_widgets = self.colorbar_tabs(colors)
tab_widget.description='Figure'
tab_widget = Tab(children=[tab_widget]+html_widgets)
else:
image_widget = self._image_widget_new(image_data, colors=colors)
tab_widget = VBox(children=[image_widget, html_widget])
restore_pvals.on_click(self.restore_figure_pvals)
if old_ipython is True:
wi = Popup(children=[tab_widget, restore_pvals])
else:
contents = VBox(children=[tab_widget, restore_pvals])
contents.width = '100%'
wi = Popup(children=[contents])
wi.border = '1px solid black'
children.append(wi)
self.figures_widget.children = children
if colors is not None:
if old_ipython is True:
tab_widget.set_title(0, 'Figure')
tab_widget.set_title(1, 'Colorbar')
def make_plot(self, b):
controller = self.controller
b.description = 'Creating plot... Please Wait.'
b.disabled = True
try:
b.pvals = controller.pvals.copy()
if b.plot_type.value == 'Design Space (interactive)':
self.make_interactive_plot(b)
elif b.plot_type.value == 'Design Space':
self.make_static_plot(b)
elif b.plot_type.value == 'Stability':
self.make_stability_plot(b)
elif b.plot_type.value == 'Eigenvalues':
self.make_eigenvalue_plot(b)
else:
self.make_function_plot(b)
except Exception as e:
close_button = Button(description="Close")
error_message = '<div width="200px" style="float:center; text-align:center;">'
error_message += '<b>An error occured while plotting</b></div>'
error_window = Popup(children=[HTML(value=error_message),close_button])
close_button.window = error_window
close_button.on_click(lambda x: x.window.close())
if old_ipython is False:
error_window.box_style='danger'
close_button.float = 'center'
error_window.width='250px'
error_window.height='150px'
display(error_window)
b.description = 'Add Plot'
b.disabled = False
else:
b.description = 'Add Plot'
b.disabled = False
def add_table_widget(self, table_data):
html_widget = HTML(value=table_data)
wi = Popup(children=[html_widget])
if ipy_old is True:
wi.set_css('height', '300px')
children = [i for i in self.tables_widget.children]
children.append(wi)
self.tables_widget.children = children
def add_figure_widget(self, image_data, title='', caption = '', pvals=None, colors=None):
children = [i for i in self.unsaved.children]
if len(title) > 0:
title = title + '.'
if len(caption) > 0:
caption = ' ' + caption
html_str = '<b>'+title+'</b>' + caption
html_widget = HTML(value=html_str)
save_button = Button(description='Save Figure')
save_button.image_data = image_data
save_button.title = title
save_button.caption = caption
save_button.on_click(self.save_unsaved_figure)
save_button.pvals = pvals
save_button.colors = colors
close_button = Button(description='Remove Figure')
close_button.on_click(self.remove_unsaved_figure)
restore_pvals = Button(description='Restore Parameter Values')
restore_pvals.pvals = pvals
if pvals is None:
restore_pvals.visible = False
if old_ipython is True:
image_widget = Image()
image_widget.value = image_data
tab_widget = VBox(children=[image_widget, html_widget])
if colors is not None:
html_widgets = self.colorbar_tabs(colors)
tab_widget.description='Figure'
tab_widget = Tab(children=[tab_widget]+html_widgets)
else:
image_widget = self._image_widget_new(image_data, colors=colors)
tab_widget = VBox(children=[image_widget, html_widget])
toggle = Button(description='Hide')
restore_pvals.on_click(self.restore_figure_pvals)
if old_ipython is True:
wi = Popup(children=[close_button, save_button, tab_widget, restore_pvals])
else:
contents = VBox(children=[close_button, save_button, tab_widget, restore_pvals])
contents.width = '100%'
wi = Popup(children=[contents])
wi.border = '1px solid black'
save_button.wi = wi
close_button.wi = wi
children.append(wi)
self.unsaved.children = children
if colors is not None:
if old_ipython is True:
tab_widget.set_title(0, 'Figure')
tab_widget.set_title(1, 'Colorbar')
def create_case_widget(self):
controller = self.controller
if controller.ds is None:
return
case = self.case
self.info = VBox()
self.equations = VBox()
self.log_gains = VBox()
self.parameter_table = VBox()
self.tolerances_table = VBox()
self.bounding_box_table = VBox()
calculate_pvals = Button(description='Determine values for the parameters')
calculate_pvals.visible = False
calculate_pvals.on_click(self.identify_parameters)
if case.is_valid() is True and case.is_cyclical is False:
if self.pvals is None:
calculate_pvals.visible = True
close_button = Button(description='Close Tab')
close_button.on_click(self.close_widget)
wi = Popup(children=[self.info,
self.equations,
self.log_gains,
self.bounding_box_table,
calculate_pvals,
self.parameter_table,
self.tolerances_table,
close_button])
if ipy_old is True:
wi.set_css('height', '400px')
else:
wi.width = '700px'
self.update_display()
subtitle = self.subtitle
if subtitle != '':
subtitle = ' (' + subtitle + ')'
self.title = 'Case ' + self.case.case_number + subtitle
controller.update_child(self.title, wi)
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
