def traits_view(self):
self.statistics_name = "Cohen's Kappa"
traits_view = View(VGroup(
HGroup(Item("statistics_name", show_label=False),
Item("info_button", show_label=False)),
Spring(),
HGroup(
Spring(),
Item("stats_view",
style="custom",
show_label=False,
width=300,
resizable=False), Spring()),
),
width=400,
resizable=True)
return traits_view
def traits_view(self):
db_table_editor = TableEditor(
columns=[
ObjectColumn(name='data_id',
label='Annotations ID',
editable=False,
width=0.65),
ObjectColumn(name='model_name', editable=False, width=0.20),
ObjectColumn(name='value',
label='Log likelihood',
editable=False,
width=0.15)
],
search=SearchIDFilter(),
editable=True,
deletable=True,
configurable=False,
sortable=True,
sort_model=False,
auto_size=False,
orientation='vertical',
show_toolbar=True,
selection_mode='row',
on_dclick=self.forward_to_model_data_view,
on_select=self.track_selection)
traits_view = View(
VGroup(
Item(
'results_table',
editor=db_table_editor,
show_label=False,
),
HGroup(
Item('open_to_main', show_label=False, width=100),
Item('delete_action',
show_label=False,
enabled_when='current_selection is not None',
width=100), Spring(),
Item('close_view', show_label=False, width=100)),
),
title='pyAnno results database',
width=800,
height=400,
resizable=True,
#buttons = [ 'OK' ],
kind='live')
return traits_view
def traits_view(self):
if is_display_small():
w_view = 350
else:
w_view = 450
info_group = VGroup(Item('_name',
label='Annotations name:',
style='readonly',
padding=0),
VGrid(Item('_nclasses',
label='Number of classes:',
style='readonly',
width=10),
Item('_labels',
label='Labels:',
style='readonly'),
Item('_nannotators',
label='Number of annotators:',
style='readonly',
width=10),
Item('_nitems',
label='Number of items:',
style='readonly'),
padding=0),
padding=0)
body = VGroup(
info_group,
Item('_'),
HGroup(
VGroup(
Spring(),
Item('frequency_plot',
style='custom',
resizable=False,
show_label=False,
width=w_view), Spring()), Spring(),
VGroup(
Spring(),
Item('edit_data',
enabled_when='annotations_are_defined',
show_label=False),
Item('save_data',
enabled_when='annotations_are_defined',
show_label=False), Spring())),
Spring(),
Item('_'),
)
traits_view = View(body)
return traits_view
def traits_view(self):
w_view = 350 if is_display_small() else 480
parameters_group = VGroup(
Item('_'),
HGroup(
VGroup(
Spring(),
Item('handler.omega_hinton_diagram',
style='custom',
resizable=False,
show_label=False,
width=w_view), Spring()), Spring(),
VGroup(Spring(), Item('handler.view_omega', show_label=False),
Spring())), Spring(), Item('_'), Spring(),
HGroup(
VGroup(
UItem('handler.theta_views'),
UItem('handler.theta_view',
style='custom',
resizable=False,
width=w_view), Spring()), Spring(),
VGroup(Spring(), UItem('handler.view_theta'), Spring())))
body = VGroup(Include('info_group'), parameters_group)
traits_view = View(body, buttons=[OKButton], resizable=True)
return traits_view
def traits_view(self):
## Model view
# adjust sizes to display size
if is_display_small():
# full view size
w_view, h_view = 1024, 768
w_data_create_group = 350
w_data_info_group = 500
h_annotations_stats = 270
else:
w_view, h_view = 1300, 850
w_data_create_group = 400
w_data_info_group = 700
h_annotations_stats = 330
model_create_group = (VGroup(HGroup(
UItem(name='model_name', width=200),
UItem(name='new_model', width=100),
UItem(name='get_info_on_model', width=100, height=25),
),
label='Create new model'))
model_group = (VGroup(
model_create_group,
VGroup(
Item('model_view', style='custom', show_label=False,
width=400),
label='Model view',
),
), )
## Data view
data_create_group = VGroup(
#Label('Open annotation file:', width=800),
HGroup(
Item('annotations_file',
style='simple',
label='Open file:',
width=w_data_create_group,
height=25), UItem('new_annotations', height=25)),
label='Load/create annotations',
show_border=False,
)
data_info_group = VGroup(
Item(
'annotations_view',
style='custom',
show_label=False,
visible_when='annotations_are_defined',
width=w_data_info_group,
),
Item('annotations_stats_view',
style='custom',
show_label=False,
visible_when='annotations_are_defined',
height=h_annotations_stats),
label='Data view',
)
data_group = (VGroup(
data_create_group,
data_info_group,
), )
## (Model,Data) view
model_data_group = (
VGroup(
#Item('info_string', show_label=False, style='readonly'),
Item('log_likelihood',
label='Log likelihood',
style='readonly'),
HGroup(
Item('ml_estimate',
enabled_when='annotations_are_defined'),
Item('map_estimate',
enabled_when='annotations_are_defined'),
Item('sample_posterior_over_accuracy',
enabled_when='annotations_are_defined'),
Item('estimate_labels',
enabled_when='annotations_are_defined'),
Spring(),
Item('add_to_database',
enabled_when='annotations_are_defined'),
Item('open_database'),
show_labels=False,
),
label='Model-data view',
))
## Full view
full_view = View(
VGroup(
HGroup(model_group, data_group),
model_data_group,
),
title='PyAnno - Models of data annotations by multiple curators',
width=w_view,
height=h_view,
resizable=False)
return full_view
class PosteriorPlot(PyannoPlotContainer):
# data to be displayed
posterior = Array
### plot-related traits
plot_width = Float
def _plot_width_default(self):
return 450 if is_display_small() else 500
plot_height = Float
def _plot_height_default(self):
return 600 if is_display_small() else 750
colormap_low = Float(0.0)
colormap_high = Float(1.0)
origin = Str('top left')
plot_container = Instance(HPlotContainer)
plot_posterior = Instance(Plot)
def _create_colormap(self):
if self.colormap_low is None:
self.colormap_low = self.posterior.min()
if self.colormap_high is None:
self.colormap_high = self.posterior.max()
colormap = Reds(
DataRange1D(low=self.colormap_low, high=self.colormap_high))
return colormap
def _plot_container_default(self):
data = self.posterior
nannotations, nclasses = data.shape
# create a plot data object
plot_data = ArrayPlotData()
plot_data.set_data("values", data)
# create the plot
plot = Plot(plot_data, origin=self.origin)
img_plot = plot.img_plot("values",
interpolation='nearest',
xbounds=(0, nclasses),
ybounds=(0, nannotations),
colormap=self._create_colormap())[0]
ndisp = 55
img_plot.y_mapper.range.high = ndisp
img_plot.y_mapper.domain_limits = ((0, nannotations))
self._set_title(plot)
plot.padding_top = 80
# create x axis for labels
label_axis = self._create_increment_one_axis(plot, 0.5, nclasses,
'top')
label_axis.title = 'classes'
self._add_index_axis(plot, label_axis)
plot.y_axis.title = 'items'
# tweak plot aspect
goal_aspect_ratio = 2.0
plot_width = (goal_aspect_ratio * self.plot_height * nclasses / ndisp)
self.plot_width = min(max(plot_width, 200), 400)
plot.aspect_ratio = self.plot_width / self.plot_height
# add colorbar
colormap = img_plot.color_mapper
colorbar = ColorBar(index_mapper=LinearMapper(range=colormap.range),
color_mapper=colormap,
plot=img_plot,
orientation='v',
resizable='',
width=15,
height=250)
colorbar.padding_top = plot.padding_top
colorbar.padding_bottom = int(self.plot_height - colorbar.height -
plot.padding_top)
colorbar.padding_left = 0
colorbar.padding_right = 30
# create a container to position the plot and the colorbar side-by-side
container = HPlotContainer(use_backbuffer=True)
container.add(plot)
container.add(colorbar)
container.bgcolor = 0xFFFFFF # light gray: 0xEEEEEE
# add pan tools
img_plot.tools.append(
PanTool(img_plot,
constrain=True,
constrain_direction="y",
speed=7.))
self.decorate_plot(container, self.posterior)
self.plot_posterior = plot
return container
def add_markings(self,
mark_classes,
mark_name,
marker_shape,
delta_x,
delta_y,
marker_size=5,
line_width=1.,
marker_color='white'):
plot = self.plot_posterior
nannotations = plot.data.arrays['values'].shape[0]
y_name = mark_name + '_y'
x_name = mark_name + '_x'
valid = is_valid(mark_classes)
y_values = np.arange(nannotations)[valid] + delta_y + 0.5
x_values = mark_classes[valid].astype(float) + delta_x + 0.5
plot.data.set_data(y_name, y_values)
plot.data.set_data(x_name, x_values)
plot.plot((x_name, y_name),
type='scatter',
name=mark_name,
marker=marker_shape,
marker_size=marker_size,
color='transparent',
outline_color=marker_color,
line_width=line_width)
def remove_markings(self, mark_name):
self.plot_posterior.delplot(mark_name)
def _create_resizable_view(self):
# resizable_view factory, as I need to compute the height of the plot
# from the number of annotations, and I couldn't find any other way to
# do that
# "touch" posterior_plot to have it initialize
self.plot_container
if is_display_small():
height = 760
else:
height = 800
resizable_plot_item = (Item(
'plot_container',
editor=ComponentEditor(),
resizable=True,
show_label=False,
width=self.plot_width,
height=self.plot_height,
))
resizable_view = View(VGroup(
Include('instructions_group'),
resizable_plot_item,
),
width=450,
height=height,
resizable=True)
return resizable_view
def traits_view(self):
return self._create_resizable_view()
pan_instructions = Str
def _pan_instructions_default(self):
return 'Left-click and drag to navigate items'
instructions_group = VGroup(
HGroup(Spring(),
Item('instructions', style='readonly', show_label=False),
Spring()),
HGroup(Spring(),
Item('pan_instructions', style='readonly', show_label=False),
Spring()))
def traits_view(self):
if is_display_small():
w_view = 400
else:
w_view = 510
parameters_group = VGroup(
Item('_'),
HGroup(
Item('handler.edit_prior',
show_label=False,
width=100),
Spring(),
),
Item('_'),
HGroup(
VGroup(
Spring(),
Item('handler.pi_hinton_diagram',
style='custom',
resizable=False,
show_label=False,
width=w_view),
Spring(),
),
Spring(),
VGroup(
Spring(),
Item('handler.view_pi', show_label=False),
Spring()
),
),
Item('_'),
HGroup(
VGroup(
Item('handler.theta_views',
show_label=False),
Item('handler.theta_view',
style='custom',
resizable=False,
show_label=False,
width = w_view),
Spring()
),
VGroup(
Spring(),
Item('handler.view_theta', show_label=False),
Spring()
)
),
)
body = VGroup(
Include('info_group'),
parameters_group
)
traits_view = View(body, buttons=[OKButton], resizable=True)
return traits_view