def make_controls(self):
button_begin = Button(icon="fast-backward", layout=Layout(width='100%'))
button_prev = Button(icon="backward", layout=Layout(width='100%'))
button_next = Button(icon="forward", layout=Layout(width='100%'))
button_end = Button(icon="fast-forward", layout=Layout(width='100%'))
self.button_play = Button(icon="play", description="Play", layout=Layout(width="100%"))
self.control_buttons = HBox([
button_begin,
button_prev,
self.position_text,
button_next,
button_end,
self.button_play,
], layout=Layout(width='100%', height="50px"))
self.control_slider = IntSlider(description=self.title,
continuous_update=False,
min=0,
max=max(self.length - 1, 0),
value=0,
style={"description_width": 'initial'},
layout=Layout(width='100%'))
## Hook them up:
button_begin.on_click(lambda button: self.goto("begin"))
button_end.on_click(lambda button: self.goto("end"))
button_next.on_click(lambda button: self.goto("next"))
button_prev.on_click(lambda button: self.goto("prev"))
self.button_play.on_click(self.toggle_play)
self.control_slider.observe(self.update_slider_control, names='value')
controls = VBox([HBox([self.control_slider, self.total_text], layout=Layout(height="40px")),
self.control_buttons], layout=Layout(width='100%'))
controls.on_displayed(lambda widget: self.initialize())
return controls
def __init__(self, atoms, xsize=500, ysize=500):
import nglview
from ipywidgets import Dropdown, FloatSlider, IntSlider, HBox, VBox
self.atoms = atoms
if isinstance(atoms[0], Atoms):
# Assume this is a trajectory or struct list
self.view = nglview.show_asetraj(atoms)
self.frm = IntSlider(value=0, min=0, max=len(atoms) - 1)
self.frm.observe(self._update_frame)
self.struct = atoms[0]
else:
# Assume this is just a single structure
self.view = nglview.show_ase(atoms)
self.struct = atoms
self.frm = None
self.colors = {}
self.view._remote_call('setSize', target='Widget',
args=['%dpx' % (xsize,), '%dpx' % (ysize,)])
self.view.add_unitcell()
self.view.add_spacefill()
self.view.camera = 'orthographic'
self.view.update_spacefill(radiusType='covalent', scale=0.7)
self.view.center()
self.asel = Dropdown(options=['All'] +
list(set(self.struct.get_chemical_symbols())),
value='All', description='Show')
self.rad = FloatSlider(value=0.8, min=0.0, max=1.5, step=0.01,
description='Ball size')
self.asel.observe(self._select_atom)
self.rad.observe(self._update_repr)
wdg = [self.asel, self.rad]
if self.frm:
wdg.append(self.frm)
self.gui = HBox([self.view, VBox(wdg)])
# Make useful shortcuts for the user of the class
self.gui.view = self.view
self.gui.control_box = self.gui.children[1]
self.gui.custom_colors = self.custom_colors
class TrajectoryPlayer(DOMWidget):
# should set default values here different from desired defaults
# so `observe` can be triggered
step = Int(0).tag(sync=True)
sync_frame = Bool(True).tag(sync=True)
interpolate = Bool(False).tag(sync=False)
delay = Float(0.0).tag(sync=True)
parameters = Dict().tag(sync=True)
iparams = Dict().tag(sync=False)
_interpolation_t = Float().tag(sync=False)
_iterpolation_type = CaselessStrEnum(['linear', 'spline']).tag(sync=False)
spin = Bool(False).tag(sync=False)
_spin_x = Int(1).tag(sync=False)
_spin_y = Int(0).tag(sync=False)
_spin_z = Int(0).tag(sync=False)
_spin_speed = Float(0.005).tag(sync=False)
camera = CaselessStrEnum(['perspective', 'orthographic'],
default_value='perspective').tag(sync=False)
_render_params = Dict().tag(sync=False)
_real_time_update = Bool(False).tag(sync=False)
widget_tab = Any(None).tag(sync=False)
widget_repr = Any(None).tag(sync=False)
widget_repr_parameters = Any(None).tag(sync=False)
widget_quick_repr = Any(None).tag(sync=False)
widget_general = Any(None).tag(sync=False)
widget_picked = Any(None).tag(sync=False)
widget_preference = Any(None).tag(sync=False)
widget_extra = Any(None).tag(sync=False)
widget_theme = Any(None).tag(sync=False)
widget_help = Any(None).tag(sync=False)
widget_export_image = Any(None).tag(sync=False)
widget_component_slider = Any(None).tag(sync=False)
widget_repr_slider = Any(None).tag(sync=False)
widget_repr_choices = Any(None).tag(sync=False)
widget_repr_control_buttons = Any(None).tag(sync=False)
widget_repr_add = Any(None).tag(sync=False)
widget_accordion_repr_parameters = Any(None).tag(sync=False)
widget_repr_parameters_dialog = Any(None).tag(sync=False)
widget_repr_name = Any(None).tag(sync=False)
widget_component_dropdown = Any(None).tag(sync=False)
widget_drag = Any(None).tag(sync=False)
def __init__(self, view, step=1, delay=100,
sync_frame=False, min_delay=40):
self._view = view
self.step = step
self.sync_frame = sync_frame
self.delay = delay
self.min_delay = min_delay
self._interpolation_t = 0.5
self._iterpolation_type = 'linear'
self.iparams = dict(
t=self._interpolation_t,
step=1,
type=self._iterpolation_type)
self._render_params = dict(factor=4,
antialias=True,
trim=False,
transparent=False)
self._widget_names = [w for w in dir(self) if w.startswith('wiget_')]
self.observe(self._on_widget_built, names=['widget_repr_parameters',
'widget_repr',
'widget_preference'])
self._movie_maker = None
def _on_widget_built(self, change):
widget = change['new']
if widget is not None:
widget.layout.padding = '5%'
def _update_padding(self, padding=default.DEFAULT_PADDING):
widget_collection = [
self.widget_general,
self.widget_repr,
self.widget_preference,
self.widget_repr_parameters,
self.widget_help,
self.widget_extra,
self.widget_picked
]
for widget in widget_collection:
if widget is not None:
widget.layout.padding = padding
def _create_all_widgets(self):
if self.widget_tab is None:
self.widget_tab = self._display()
old_index = self.widget_tab.selected_index
for index, _ in enumerate(self.widget_tab.children):
self.widget_tab.selected_index = index
self.widget_tab.selected_index = old_index
def smooth(self):
self.interpolate = True
@observe('camera')
def on_camera_changed(self, change):
camera_type = change['new']
self._view._remote_call("setParameters",
target='Stage',
kwargs=dict(cameraType=camera_type))
@property
def frame(self):
return self._view.frame
@frame.setter
def frame(self, value):
self._view.frame = value
@property
def count(self):
return self._view.count
@observe('sync_frame')
def update_sync_frame(self, change):
value = change['new']
if value:
self._view._set_sync_frame()
else:
self._view._set_unsync_frame()
@observe("delay")
def update_delay(self, change):
delay = change['new']
self._view._set_delay(delay)
@observe('parameters')
def update_parameters(self, change):
params = change['new']
self.sync_frame = params.get("sync_frame", self.sync_frame)
self.delay = params.get("delay", self.delay)
self.step = params.get("step", self.step)
@observe('_interpolation_t')
def _interpolation_t_changed(self, change):
self.iparams['t'] = change['new']
@observe('spin')
def on_spin_changed(self, change):
self.spin = change['new']
if self.spin:
self._view._set_spin([self._spin_x, self._spin_y, self._spin_z],
self._spin_speed)
else:
# stop
self._view._set_spin(None, None)
@observe('_spin_x')
def on_spin_x_changed(self, change):
self._spin_x = change['new']
if self.spin:
self._view._set_spin([self._spin_x, self._spin_y, self._spin_z],
self._spin_speed)
@observe('_spin_y')
def on_spin_y_changed(self, change):
self._spin_y = change['new']
if self.spin:
self._view._set_spin([self._spin_x, self._spin_y, self._spin_z],
self._spin_speed)
@observe('_spin_z')
def on_spin_z_changed(self, change):
self._spin_z = change['new']
if self.spin:
self._view._set_spin([self._spin_x, self._spin_y, self._spin_z],
self._spin_speed)
@observe('_spin_speed')
def on_spin_speed_changed(self, change):
self._spin_speed = change['new']
if self.spin:
self._view._set_spin([self._spin_x, self._spin_y, self._spin_z],
self._spin_speed)
def _display(self):
box_factory = [(self._make_general_box, 'General'),
(self._make_widget_repr, 'Representation'),
(self._make_widget_preference, 'Preference'),
(self._make_theme_box, 'Theme'),
(self._make_extra_box, 'Extra'),
(self._show_website, 'Help')]
tab = _make_delay_tab(box_factory, selected_index=-1)
# tab = _make_autofit(tab)
tab.layout.align_self = 'center'
tab.layout.align_items = 'stretch'
self.widget_tab = tab
return self.widget_tab
def _make_widget_tab(self):
return self._display()
def _make_button_center(self):
button = Button(description=' Center', icon='fa-bullseye')
@button.on_click
def on_click(button):
self._view.center()
return button
def _make_button_theme(self):
button = Button(description='Oceans16')
@button.on_click
def on_click(button):
from nglview import theme
display(theme.oceans16())
self._view._remote_call('cleanOutput',
target='Widget')
return button
def _make_button_reset_theme(self, hide_toolbar=False):
from nglview import theme
if hide_toolbar:
button = Button(description='Simplified Default')
@button.on_click
def on_click(button):
theme.reset(hide_toolbar=True)
else:
button = Button(description='Default')
@button.on_click
def on_click(button):
theme.reset()
return button
def _make_button_clean_error_output(self):
button = Button(description='Clear Error')
@button.on_click
def on_click(_):
js_utils.clean_error_output()
return button
def _make_widget_preference(self, width='100%'):
def make_func():
parameters = self._view._full_stage_parameters
def func(pan_speed=parameters.get('panSpeed', 0.8),
rotate_speed=parameters.get('rotateSpeed', 2),
zoom_speed=parameters.get('zoomSpeed', 1.2),
clip_dist=parameters.get('clipDist', 10),
camera_fov=parameters.get('cameraFov', 40),
clip_far=parameters.get('clipFar', 100),
clip_near=parameters.get('clipNear', 0),
fog_far=parameters.get('fogFar', 100),
fog_near=parameters.get('fogNear', 50),
impostor=parameters.get('impostor', True),
light_intensity=parameters.get('lightIntensity', 1),
quality=parameters.get('quality', 'medium'),
sample_level=parameters.get('sampleLevel', 1)):
self._view.parameters = dict(
panSpeed=pan_speed,
rotateSpeed=rotate_speed,
zoomSpeed=zoom_speed,
clipDist=clip_dist,
clipFar=clip_far,
clipNear=clip_near,
cameraFov=camera_fov,
fogFar=fog_far,
fogNear=fog_near,
impostor=impostor,
lightIntensity=light_intensity,
quality=quality,
sampleLevel=sample_level)
return func
def make_widget_box():
widget_sliders = interactive(make_func(),
pan_speed=(0, 10, 0.1),
rotate_speed=(0, 10, 1),
zoom_speed=(0, 10, 1),
clip_dist=(0, 200, 5),
clip_far=(0, 100, 1),
clip_near=(0, 100, 1),
camera_fov=(15, 120, 1),
fog_far=(0, 100, 1),
fog_near=(0, 100, 1),
light_intensity=(0, 10, 0.02),
quality=['low', 'medium', 'high'],
sample_level=(-1, 5, 1))
for child in widget_sliders.children:
if isinstance(child, (IntSlider, FloatSlider)):
child.layout.width = default.DEFAULT_SLIDER_WIDTH
return widget_sliders
if self.widget_preference is None:
widget_sliders = make_widget_box()
reset_button = Button(description='Reset')
widget_sliders.children = [reset_button,] + list(widget_sliders.children)
@reset_button.on_click
def on_click(reset_button):
self._view.parameters = self._view._original_stage_parameters
self._view._full_stage_parameters = self._view._original_stage_parameters
widget_sliders.children = [reset_button,] + list(make_widget_box().children)
self.widget_preference = _relayout_master(widget_sliders, width=width)
return self.widget_preference
def _show_download_image(self):
# "interactive" does not work for True/False in ipywidgets 4 yet.
button = Button(description=' Screenshot', icon='fa-camera')
@button.on_click
def on_click(button):
self._view.download_image()
return button
def _make_button_url(self, url, description):
button = Button(description=description)
@button.on_click
def on_click(button):
display(Javascript(js_utils.open_url_template.format(url=url)))
return button
def _show_website(self, ngl_base_url=default.NGL_BASE_URL):
buttons = [self._make_button_url(url.format(ngl_base_url), description) for url, description in
[("'http://arose.github.io/nglview/latest/'", "nglview"),
("'{}/index.html'", "NGL"),
("'{}/tutorial-selection-language.html'", "Selection"),
("'{}/tutorial-molecular-representations.html'", "Representation")]
]
self.widget_help = _make_autofit(HBox(buttons))
return self.widget_help
def _make_button_qtconsole(self):
from nglview import js_utils
button = Button(description='qtconsole',
tooltip='pop up qtconsole')
@button.on_click
def on_click(button):
js_utils.launch_qtconsole()
return button
def _make_text_picked(self):
ta = Textarea(value=json.dumps(self._view.picked), description='Picked atom')
ta.layout.width = '300px'
return ta
def _refresh(self, component_slider, repr_slider):
"""update representation and component information
"""
self._view._request_repr_parameters(component=component_slider.value,
repr_index=repr_slider.value)
self._view._remote_call('requestReprInfo', target='Widget')
self._view._handle_repr_dict_changed(change=dict(new=self._view._repr_dict))
def _make_button_repr_control(self, component_slider, repr_slider, repr_selection):
button_refresh = Button(description=' Refresh', tooltip='Get representation info', icon='fa-refresh')
button_center_selection = Button(description=' Center', tooltip='center selected atoms',
icon='fa-bullseye')
button_center_selection._ngl_name = 'button_center_selection'
button_hide = Button(description=' Hide',
icon='fa-eye-slash',
tooltip='Hide/Show current representation')
button_remove = Button(description=' Remove',
icon='fa-trash',
tooltip='Remove current representation')
button_repr_parameter_dialog = Button(description=' Dialog',
tooltip='Pop up representation parameters control dialog')
@button_refresh.on_click
def on_click_refresh(button):
self._refresh(component_slider, repr_slider)
@button_center_selection.on_click
def on_click_center(center_selection):
self._view.center_view(selection=repr_selection.value,
component=component_slider.value)
@button_hide.on_click
def on_click_hide(button_hide):
component=component_slider.value
repr_index=repr_slider.value
if button_hide.description == 'Hide':
hide = True
button_hide.description = 'Show'
else:
hide = False
button_hide.description = 'Hide'
self._view._remote_call('setVisibilityForRepr',
target='Widget',
args=[component, repr_index, not hide])
@button_remove.on_click
def on_click_remove(button_remove):
self._view._remove_representation(component=component_slider.value,
repr_index=repr_slider.value)
self._view._request_repr_parameters(component=component_slider.value,
repr_index=repr_slider.value)
@button_repr_parameter_dialog.on_click
def on_click_repr_dialog(_):
from nglview.widget_box import DraggableBox
if self.widget_repr_parameters is not None and self.widget_repr_choices:
self.widget_repr_parameters_dialog = DraggableBox([self.widget_repr_choices,
self.widget_repr_parameters])
self.widget_repr_parameters_dialog._ipython_display_()
self.widget_repr_parameters_dialog._dialog = 'on'
bbox = _make_autofit(HBox([button_refresh, button_center_selection,
button_hide, button_remove,
button_repr_parameter_dialog]))
return bbox
def _make_widget_repr(self):
self.widget_repr_name = Text(value='', description='representation')
self.widget_repr_name._ngl_name = 'repr_name_text'
repr_selection = Text(value=' ', description='selection')
repr_selection._ngl_name = 'repr_selection'
repr_selection.width = self.widget_repr_name.width = default.DEFAULT_TEXT_WIDTH
max_n_components = max(self._view.n_components-1, 0)
self.widget_component_slider = IntSlider(value=0, max=max_n_components, min=0, description='component')
self.widget_component_slider._ngl_name = 'component_slider'
cvalue = ' '
self.widget_component_dropdown = Dropdown(value=cvalue, options=[cvalue,],
description='component')
self.widget_component_dropdown._ngl_name = 'component_dropdown'
self.widget_repr_slider = IntSlider(value=0, description='representation', width=default.DEFAULT_SLIDER_WIDTH)
self.widget_repr_slider._ngl_name = 'repr_slider'
self.widget_repr_slider.visible = True
self.widget_component_slider.layout.width = default.DEFAULT_SLIDER_WIDTH
self.widget_repr_slider.layout.width = default.DEFAULT_SLIDER_WIDTH
self.widget_component_dropdown.layout.width = self.widget_component_dropdown.max_width = default.DEFAULT_TEXT_WIDTH
# turn off for now
self.widget_component_dropdown.layout.display = 'none'
self.widget_component_dropdown.description = ''
# self.widget_accordion_repr_parameters = Accordion()
self.widget_accordion_repr_parameters = Tab()
self.widget_repr_parameters = self._make_widget_repr_parameters(self.widget_component_slider,
self.widget_repr_slider,
self.widget_repr_name)
self.widget_accordion_repr_parameters.children = [self.widget_repr_parameters, Box()]
self.widget_accordion_repr_parameters.set_title(0, 'Parameters')
self.widget_accordion_repr_parameters.set_title(1, 'Hide')
self.widget_accordion_repr_parameters.selected_index = 1
checkbox_reprlist = Checkbox(value=False, description='reprlist')
checkbox_reprlist._ngl_name = 'checkbox_reprlist'
self.widget_repr_choices = self._make_repr_name_choices(self.widget_component_slider,
self.widget_repr_slider)
self.widget_repr_choices._ngl_name = 'reprlist_choices'
self.widget_repr_add = self._make_add_widget_repr(self.widget_component_slider)
def on_update_checkbox_reprlist(change):
self.widget_repr_choices.visible= change['new']
checkbox_reprlist.observe(on_update_checkbox_reprlist, names='value')
def on_repr_name_text_value_changed(change):
name = change['new'].strip()
old = change['old'].strip()
should_update = (self._real_time_update
and old and name
and name in REPRESENTATION_NAMES
and name != change['old'].strip())
if should_update:
component=self.widget_component_slider.value
repr_index=self.widget_repr_slider.value
self._view._remote_call('setRepresentation',
target='Widget',
args=[change['new'], {}, component, repr_index])
self._view._request_repr_parameters(component, repr_index)
def on_component_or_repr_slider_value_changed(change):
self._view._request_repr_parameters(component=self.widget_component_slider.value,
repr_index=self.widget_repr_slider.value)
self.widget_component_dropdown.options = tuple(self._view._ngl_component_names)
if self.widget_accordion_repr_parameters.selected_index >= 0:
self.widget_repr_parameters.name = self.widget_repr_name.value
self.widget_repr_parameters.repr_index = self.widget_repr_slider.value
self.widget_repr_parameters.component_index = self.widget_component_slider.value
def on_repr_selection_value_changed(change):
if self._real_time_update:
component = self.widget_component_slider.value
repr_index = self.widget_repr_slider.value
self._view._set_selection(change['new'],
component=component,
repr_index=repr_index)
def on_change_component_dropdown(change):
choice = change['new']
if choice:
self.widget_component_slider.value = self._view._ngl_component_names.index(choice)
self.widget_component_dropdown.observe(on_change_component_dropdown, names='value')
self.widget_repr_slider.observe(on_component_or_repr_slider_value_changed, names='value')
self.widget_component_slider.observe(on_component_or_repr_slider_value_changed, names='value')
self.widget_repr_name.observe(on_repr_name_text_value_changed, names='value')
repr_selection.observe(on_repr_selection_value_changed, names='value')
self.widget_repr_control_buttons = self._make_button_repr_control(self.widget_component_slider,
self.widget_repr_slider, repr_selection)
blank_box = Box([Label("")])
all_kids = [self.widget_repr_control_buttons,
blank_box,
self.widget_repr_add,
self.widget_component_dropdown,
self.widget_repr_name,
repr_selection,
self.widget_component_slider,
self.widget_repr_slider,
self.widget_repr_choices,
self.widget_accordion_repr_parameters
]
vbox = VBox(all_kids)
self._view._request_repr_parameters(component=self.widget_component_slider.value,
repr_index=self.widget_repr_slider.value)
self.widget_repr = _relayout_master(vbox, width='100%')
self._refresh(self.widget_component_slider, self.widget_repr_slider)
setattr(self.widget_repr, "_saved_widgets", [])
for _box in self.widget_repr.children:
if hasattr(_box, 'children'):
for kid in _box.children:
self.widget_repr._saved_widgets.append(kid)
return self.widget_repr
def _make_widget_repr_parameters(self, component_slider, repr_slider, repr_name_text=None):
name = repr_name_text.value if repr_name_text is not None else ' '
widget = self._view._display_repr(component=component_slider.value,
repr_index=repr_slider.value,
name=name)
widget._ngl_name = 'repr_parameters_box'
return widget
def _make_button_export_image(self):
slider_factor = IntSlider(value=4, min=1, max=10, description='scale')
checkbox_antialias = Checkbox(value=True, description='antialias')
checkbox_trim = Checkbox(value=False, description='trim')
checkbox_transparent = Checkbox(value=False, description='transparent')
filename_text = Text(value='Screenshot', description='Filename')
delay_text = FloatText(value=1, description='delay (s)', tooltip='hello')
start_text, stop_text, step_text = (IntText(value=0, description='start'),
IntText(value=self._view.count, description='stop'),
IntText(value=1, description='step'))
start_text.layout.max_width = stop_text.layout.max_width = step_text.layout.max_width \
= filename_text.layout.max_width = delay_text.layout.max_width = default.DEFAULT_TEXT_WIDTH
button_movie_images = Button(description='Export Images')
def download_image(filename):
self._view.download_image(factor=slider_factor.value,
antialias=checkbox_antialias.value,
trim=checkbox_trim.value,
transparent=checkbox_transparent.value,
filename=filename)
@button_movie_images.on_click
def on_click_images(button_movie_images):
for i in range(start_text.value, stop_text.value, step_text.value):
self._view.frame = i
time.sleep(delay_text.value)
download_image(filename=filename_text.value + str(i))
time.sleep(delay_text.value)
vbox = VBox([
button_movie_images,
start_text,
stop_text,
step_text,
delay_text,
filename_text,
slider_factor,
checkbox_antialias,
checkbox_trim,
checkbox_transparent,
])
form_items = _relayout(vbox, make_form_item_layout())
form = Box(form_items, layout=_make_box_layout())
# form = _relayout_master(vbox)
return form
def _make_resize_notebook_slider(self):
resize_notebook_slider = IntSlider(min=300, max=2000, description='resize notebook')
def on_resize_notebook(change):
width = change['new']
self._view._remote_call('resizeNotebook',
target='Widget',
args=[width,])
resize_notebook_slider.observe(on_resize_notebook, names='value')
return resize_notebook_slider
def _make_add_widget_repr(self, component_slider):
dropdown_repr_name = Dropdown(options=REPRESENTATION_NAMES, value='cartoon')
repr_selection = Text(value='*', description='')
repr_button = Button(description='Add', tooltip="""Add representation.
You can also hit Enter in selection box""")
repr_button.layout = Layout(width='auto', flex='1 1 auto')
dropdown_repr_name.layout.width = repr_selection.layout.width = default.DEFAULT_TEXT_WIDTH
def on_click_or_submit(button_or_text_area):
self._view.add_representation(selection=repr_selection.value.strip(),
repr_type=dropdown_repr_name.value,
component=component_slider.value)
repr_button.on_click(on_click_or_submit)
repr_selection.on_submit(on_click_or_submit)
add_repr_box = HBox([repr_button, dropdown_repr_name, repr_selection])
add_repr_box._ngl_name = 'add_repr_box'
return add_repr_box
def _make_repr_playground(self):
vbox = VBox()
children = []
rep_names = REPRESENTATION_NAMES[:]
excluded_names = ['ball+stick', 'distance']
for name in excluded_names:
rep_names.remove(name)
repr_selection = Text(value='*')
repr_selection.layout.width = default.DEFAULT_TEXT_WIDTH
repr_selection_box = HBox([Label('selection'), repr_selection])
setattr(repr_selection_box, 'value', repr_selection.value)
for index, name in enumerate(rep_names):
button = ToggleButton(description=name)
def make_func():
def on_toggle_button_value_change(change, button=button):
selection = repr_selection.value
new = change['new'] # True/False
if new:
self._view.add_representation(button.description, selection=selection)
else:
self._view._remove_representations_by_name(button.description)
return on_toggle_button_value_change
button.observe(make_func(), names='value')
children.append(button)
button_clear = Button(description='clear', button_style='info',
icon='fa-eraser')
@button_clear.on_click
def on_clear(button_clear):
self._view.clear()
for kid in children:
# unselect
kid.value = False
vbox.children = children + [repr_selection, button_clear]
_make_autofit(vbox)
self.widget_quick_repr = vbox
return self.widget_quick_repr
def _make_repr_name_choices(self, component_slider, repr_slider):
repr_choices = Dropdown(options=[" ",])
def on_chose(change):
repr_name = change['new']
repr_index = repr_choices.options.index(repr_name)
repr_slider.value = repr_index
repr_choices.observe(on_chose, names='value')
repr_choices.layout.width = default.DEFAULT_TEXT_WIDTH
self.widget_repr_choices = repr_choices
return self.widget_repr_choices
def _make_drag_widget(self):
button_drag = Button(description='widget drag: off', tooltip='dangerous')
drag_nb = Button(description='notebook drag: off', tooltip='dangerous')
button_reset_notebook = Button(description='notebook: reset', tooltip='reset?')
button_dialog = Button(description='dialog', tooltip='make a dialog')
button_split_half = Button(description='split screen', tooltip='try best to make a good layout')
@button_drag.on_click
def on_drag(button_drag):
if button_drag.description == 'widget drag: off':
self._view._set_draggable(True)
button_drag.description = 'widget drag: on'
else:
self._view._set_draggable(False)
button_drag.description = 'widget drag: off'
@drag_nb.on_click
def on_drag_nb(button_drag):
if drag_nb.description == 'notebook drag: off':
js_utils._set_notebook_draggable(True)
drag_nb.description = 'notebook drag: on'
else:
js_utils._set_notebook_draggable(False)
drag_nb.description = 'notebook drag: off'
@button_reset_notebook.on_click
def on_reset(button_reset_notebook):
js_utils._reset_notebook()
@button_dialog.on_click
def on_dialog(button_dialog):
self._view._remote_call('setDialog', target='Widget')
@button_split_half.on_click
def on_split_half(button_dialog):
from nglview import js_utils
import time
js_utils._move_notebook_to_the_left()
js_utils._set_notebook_width('5%')
time.sleep(0.1)
self._view._remote_call('setDialog', target='Widget')
drag_box = HBox([button_drag, drag_nb, button_reset_notebook,
button_dialog, button_split_half])
drag_box = _make_autofit(drag_box)
self.widget_drag = drag_box
return drag_box
def _make_spin_box(self):
checkbox_spin = Checkbox(self.spin, description='spin')
spin_x_slide = IntSlider(
self._spin_x,
min=-1,
max=1,
description='spin_x')
spin_y_slide = IntSlider(
self._spin_y,
min=-1,
max=1,
description='spin_y')
spin_z_slide = IntSlider(
self._spin_z,
min=-1,
max=1,
description='spin_z')
spin_speed_slide = FloatSlider(
self._spin_speed,
min=0,
max=0.2,
step=0.001,
description='spin speed')
# spin
link((checkbox_spin, 'value'), (self, 'spin'))
link((spin_x_slide, 'value'), (self, '_spin_x'))
link((spin_y_slide, 'value'), (self, '_spin_y'))
link((spin_z_slide, 'value'), (self, '_spin_z'))
link((spin_speed_slide, 'value'), (self, '_spin_speed'))
spin_box= VBox([checkbox_spin,
spin_x_slide,
spin_y_slide,
spin_z_slide,
spin_speed_slide])
spin_box = _relayout_master(spin_box, width='75%')
return spin_box
def _make_widget_picked(self):
self.widget_picked = self._make_text_picked()
picked_box = HBox([self.widget_picked,])
return _relayout_master(picked_box, width='75%')
def _make_export_image_widget(self):
if self.widget_export_image is None:
self.widget_export_image = HBox([self._make_button_export_image()])
return self.widget_export_image
def _make_extra_box(self):
if self.widget_extra is None:
extra_list = [(self._make_drag_widget, 'Drag'),
(self._make_spin_box, 'Spin'),
(self._make_widget_picked, 'Picked'),
(self._make_repr_playground, 'Quick'),
(self._make_export_image_widget, 'Image'),
(self._make_command_box, 'Command')]
extra_box = _make_delay_tab(extra_list, selected_index=0)
self.widget_extra = extra_box
return self.widget_extra
def _make_theme_box(self):
if self.widget_theme is None:
self.widget_theme = Box([self._make_button_theme(),
self._make_button_reset_theme(hide_toolbar=False),
self._make_button_reset_theme(hide_toolbar=True),
self._make_button_clean_error_output()])
return self.widget_theme
def _make_general_box(self):
if self.widget_general is None:
step_slide = IntSlider(
value=self.step,
min=-100,
max=100,
description='step')
delay_text = IntSlider(
value=self.delay,
min=10,
max=1000,
description='delay')
toggle_button_interpolate = ToggleButton(self.interpolate, description='Smoothing',
tooltip='smoothing trajectory')
link((toggle_button_interpolate, 'value'), (self, 'interpolate'))
background_color_picker = ColorPicker(value='white', description='background')
camera_type = Dropdown(value=self.camera,
options=['perspective', 'orthographic'], description='camera')
link((step_slide, 'value'), (self, 'step'))
link((delay_text, 'value'), (self, 'delay'))
link((toggle_button_interpolate, 'value'), (self, 'interpolate'))
link((camera_type, 'value'), (self, 'camera'))
link((background_color_picker, 'value'), (self._view, 'background'))
center_button = self._make_button_center()
render_button = self._show_download_image()
qtconsole_button = self._make_button_qtconsole()
center_render_hbox = _make_autofit(HBox([toggle_button_interpolate, center_button,
render_button, qtconsole_button]))
v0_left = VBox([step_slide,
delay_text,
background_color_picker,
camera_type,
center_render_hbox,
])
v0_left = _relayout_master(v0_left, width='100%')
self.widget_general = v0_left
return self.widget_general
def _make_command_box(self):
widget_text_command = Text()
@widget_text_command.on_submit
def _on_submit_command(_):
command = widget_text_command.value
js_utils.execute(command)
widget_text_command.value = ''
return widget_text_command
def _create_all_tabs(self):
tab = self._display()
for index, _ in enumerate(tab.children):
# trigger ceating widgets
tab.selected_index = index
self.widget_extra = self._make_extra_box()
for index, _ in enumerate(self.widget_extra.children):
self.widget_extra.selected_index = index
def _simplify_repr_control(self):
for widget in self.widget_repr._saved_widgets:
if not isinstance(widget, Tab):
widget.layout.display = 'none'
self.widget_repr_choices.layout.display = 'flex'
self.widget_accordion_repr_parameters.selected_index = 0
pulse_color='#9500ff') # In[18]: map.add_layer(my_path) start_marker = Marker(location=(56.847962835674466, 35.9070110321045)) map.add_layer(start_marker) finish_marker = Marker(location=(56.881189988867625, 35.927454334450935)) map.add_layer(finish_marker) start = HTML() finish = HTML() start.value = 'Start' finish.value = 'End' start_marker.popup = start finish_marker.popup = finish zoom_slider = IntSlider(description='Zoom', min=11, max=15, value=14) jslink((zoom_slider, 'value'), (m, 'zoom')) # In[19]: widget_control = WidgetControl(widget=zoom_slider, position='topright') map.add_control(widget_control) display(map) # In[20]: print(str(map)) # In[21]: from sklearn.cluster import OPTICS
def MidpointPseudoSectionWidget():
ntx = xr.size - 2
return widgetify(DipoleDipolefun,
i=IntSlider(min=0, max=ntx - 1, step=1, value=0))
def DCIP2DfwdWidget():
return widgetify(
DC2DfwdWrapper,
xc=FloatSlider(min=-1005.0,
max=1000.0,
step=10.0,
value=0.0,
continuous_update=False),
zc=FloatSlider(min=-1000.0,
max=1000.0,
step=10.0,
value=250.0,
continuous_update=False),
ellips_a=FloatSlider(min=10.0,
max=10000.0,
step=100.0,
value=1000.0,
continuous_update=False),
ellips_b=FloatSlider(min=10.0,
max=10000.0,
step=100.0,
value=500.0,
continuous_update=False),
rhohalf=FloatText(
min=1e-8,
max=1e8,
value=1000.0,
description="$\\rho_1$",
continuous_update=False,
),
chghalf=FloatText(
min=0.0,
max=100,
value=0.0,
description="$\\eta_1$",
continuous_update=False,
),
rholayer=FloatText(
min=1e-8,
max=1e8,
value=100.0,
description="$\\rho_2$",
continuous_update=False,
),
chglayer=FloatText(
min=0.0,
max=100,
value=20.0,
description="$\\eta_2$",
continuous_update=False,
),
rhoTarget=FloatText(
min=1e-8,
max=1e8,
value=500.0,
description="$\\rho_3$",
continuous_update=False,
),
chgTarget=FloatText(
min=0.0,
max=100,
value=10.0,
description="$\\eta_3$",
continuous_update=False,
),
overburden_thick=FloatSlider(min=0.0,
max=1000.0,
step=10.0,
value=250.0,
continuous_update=False),
overburden_wide=fixed(2000.0),
target_thick=FloatSlider(min=0.0,
max=1000.0,
step=10.0,
value=200.0,
continuous_update=False),
target_wide=FloatSlider(min=0.0,
max=1000.0,
step=10.0,
value=200.0,
continuous_update=False),
predmis=ToggleButtons(options=[
"Data Without Target", "Difference", "Normalized Difference"
]),
surveyType=ToggleButtons(
options=["DipoleDipole", "PoleDipole", "DipolePole"],
desciption="Array Type",
),
which=ToggleButtons(options=["DC", "IP"], description="Survey"),
nmax=IntSlider(min=1, max=16, value=8, description="Rx per Tx"),
Scale=ToggleButtons(options=["Linear", "Log"]),
)
def init_widgets(self):
# Debug checkbox - enable logging in the Output widget
self.debug = ipywidgets.Checkbox(description="Debug")
self.debug.observe(self.controller.set_debug, names="value")
# Separate checkbox for mouse move events - they are very verbose
self.debug_move = Checkbox(description="Debug mouse move")
self.debug_move.observe(self.controller.set_debug_move, names="value")
# This is like a cell widget where loggin goes
self.output_generator = Output()
# Filename textbox
self.filename = Text(description="Filename")
self.filename.value = self.model.env_filename
self.filename.observe(self.controller.set_filename, names="value")
# Size of environment when regenerating
self.regen_width = IntSlider(
value=10,
min=5,
max=100,
step=5,
description="Regen Size (Width)",
tip="Click Regenerate after changing this")
self.regen_width.observe(self.controller.set_regen_width,
names="value")
self.regen_height = IntSlider(
value=10,
min=5,
max=100,
step=5,
description="Regen Size (Height)",
tip="Click Regenerate after changing this")
self.regen_height.observe(self.controller.set_regen_height,
names="value")
# Number of Agents when regenerating
self.regen_n_agents = IntSlider(
value=1,
min=0,
max=5,
step=1,
description="# Agents",
tip="Click regenerate or reset after changing this")
self.regen_method = RadioButtons(description="Regen\nMethod",
options=["Empty", "Random Cell"])
self.replace_agents = Checkbox(value=True,
description="Replace Agents")
self.wTab = Tab()
tab_contents = ["Regen", "Observation"]
for i, title in enumerate(tab_contents):
self.wTab.set_title(i, title)
self.wTab.children = [
VBox([
self.regen_width, self.regen_height, self.regen_n_agents,
self.regen_method
])
]
# abbreviated description of buttons and the methods they call
ldButtons = [
dict(name="Refresh",
method=self.controller.refresh,
tip="Redraw only"),
dict(name="Rotate Agent",
method=self.controller.rotate_agent,
tip="Rotate selected agent"),
dict(name="Restart Agents",
method=self.controller.reset_agents,
tip="Move agents back to start positions"),
dict(
name="Random",
method=self.controller.reset,
tip="Generate a randomized scene, including regen rail + agents"
),
dict(name="Regenerate",
method=self.controller.regenerate,
tip="Regenerate the rails using the method selected below"),
dict(name="Load", method=self.controller.load),
dict(name="Save", method=self.controller.save),
dict(name="Save as image", method=self.controller.save_image)
]
self.lwButtons = []
for dButton in ldButtons:
wButton = ipywidgets.Button(description=dButton["name"],
tooltip=dButton["tip"] if "tip"
in dButton else dButton["name"])
wButton.on_click(dButton["method"])
self.lwButtons.append(wButton)
self.wVbox_controls = VBox([self.filename, *self.lwButtons, self.wTab])
self.wMain = HBox([self.wImage, self.wVbox_controls])
class View(object):
""" The Jupyter Editor View - creates and holds the widgets comprising the Editor.
"""
def __init__(self, editor, sGL="MPL"):
self.editor = self.model = editor
self.sGL = sGL
def display(self):
self.output_generator.clear_output()
return self.wMain
def init_canvas(self):
# update the rendertool with the env
self.new_env()
self.oRT.render_env(show=False)
img = self.oRT.get_image()
self.wImage = jpy_canvas.Canvas(img)
self.yxSize = self.wImage.data.shape[:2]
self.writableData = np.copy(
self.wImage.data
) # writable copy of image - wid_img.data is somehow readonly
self.wImage.register_move(self.controller.on_mouse_move)
self.wImage.register_click(self.controller.on_click)
self.yxBase = self.oRT.gl.yxBase
self.nPixCell = self.oRT.gl.nPixCell
def init_widgets(self):
# Debug checkbox - enable logging in the Output widget
self.debug = ipywidgets.Checkbox(description="Debug")
self.debug.observe(self.controller.set_debug, names="value")
# Separate checkbox for mouse move events - they are very verbose
self.debug_move = Checkbox(description="Debug mouse move")
self.debug_move.observe(self.controller.set_debug_move, names="value")
# This is like a cell widget where loggin goes
self.output_generator = Output()
# Filename textbox
self.filename = Text(description="Filename")
self.filename.value = self.model.env_filename
self.filename.observe(self.controller.set_filename, names="value")
# Size of environment when regenerating
self.regen_width = IntSlider(
value=10,
min=5,
max=100,
step=5,
description="Regen Size (Width)",
tip="Click Regenerate after changing this")
self.regen_width.observe(self.controller.set_regen_width,
names="value")
self.regen_height = IntSlider(
value=10,
min=5,
max=100,
step=5,
description="Regen Size (Height)",
tip="Click Regenerate after changing this")
self.regen_height.observe(self.controller.set_regen_height,
names="value")
# Number of Agents when regenerating
self.regen_n_agents = IntSlider(
value=1,
min=0,
max=5,
step=1,
description="# Agents",
tip="Click regenerate or reset after changing this")
self.regen_method = RadioButtons(description="Regen\nMethod",
options=["Empty", "Random Cell"])
self.replace_agents = Checkbox(value=True,
description="Replace Agents")
self.wTab = Tab()
tab_contents = ["Regen", "Observation"]
for i, title in enumerate(tab_contents):
self.wTab.set_title(i, title)
self.wTab.children = [
VBox([
self.regen_width, self.regen_height, self.regen_n_agents,
self.regen_method
])
]
# abbreviated description of buttons and the methods they call
ldButtons = [
dict(name="Refresh",
method=self.controller.refresh,
tip="Redraw only"),
dict(name="Rotate Agent",
method=self.controller.rotate_agent,
tip="Rotate selected agent"),
dict(name="Restart Agents",
method=self.controller.reset_agents,
tip="Move agents back to start positions"),
dict(
name="Random",
method=self.controller.reset,
tip="Generate a randomized scene, including regen rail + agents"
),
dict(name="Regenerate",
method=self.controller.regenerate,
tip="Regenerate the rails using the method selected below"),
dict(name="Load", method=self.controller.load),
dict(name="Save", method=self.controller.save),
dict(name="Save as image", method=self.controller.save_image)
]
self.lwButtons = []
for dButton in ldButtons:
wButton = ipywidgets.Button(description=dButton["name"],
tooltip=dButton["tip"] if "tip"
in dButton else dButton["name"])
wButton.on_click(dButton["method"])
self.lwButtons.append(wButton)
self.wVbox_controls = VBox([self.filename, *self.lwButtons, self.wTab])
self.wMain = HBox([self.wImage, self.wVbox_controls])
def draw_stroke(self):
pass
def new_env(self):
""" Tell the view to update its graphics when a new env is created.
"""
self.oRT = rt.RenderTool(self.editor.env, gl=self.sGL)
def redraw(self):
with self.output_generator:
self.oRT.set_new_rail()
self.model.env.reset_agents()
for a in self.model.env.agents:
if hasattr(a, 'old_position') is False:
a.old_position = a.position
if hasattr(a, 'old_direction') is False:
a.old_direction = a.direction
self.oRT.render_env(agents=True,
show=False,
selected_agent=self.model.selected_agent,
show_observations=False)
img = self.oRT.get_image()
self.wImage.data = img
self.writableData = np.copy(self.wImage.data)
# the size should only be updated on regenerate at most
self.yxSize = self.wImage.data.shape[:2]
return img
def redisplay_image(self):
if self.writableData is not None:
# This updates the image in the browser to be the new edited version
self.wImage.data = self.writableData
def drag_path_element(self, x, y):
# Draw a black square on the in-memory copy of the image
if x > 10 and x < self.yxSize[1] and y > 10 and y < self.yxSize[0]:
self.writableData[(y - 2):(y + 2), (x - 2):(x + 2), :3] = 0
def xy_to_rc(self, x, y):
rc_cell = ((array([y, x]) - self.yxBase))
nX = np.floor(
(self.yxSize[0] - self.yxBase[0]) / self.model.env.height)
nY = np.floor((self.yxSize[1] - self.yxBase[1]) / self.model.env.width)
rc_cell[0] = max(
0, min(np.floor(rc_cell[0] / nY), self.model.env.height - 1))
rc_cell[1] = max(
0, min(np.floor(rc_cell[1] / nX), self.model.env.width - 1))
return rc_cell
def log(self, *args, **kwargs):
if self.output_generator:
with self.output_generator:
print(*args, **kwargs)
else:
print(*args, **kwargs)
class SequenceViewer(VBox):
def __init__(self, title, function, length, play_rate=0.5):
self.player = _Player(self, play_rate)
self.player.start()
self.title = title
self.function = function
self.length = length
self.output = Output()
self.position_text = IntText(value=0, layout=Layout(width="100%"))
self.total_text = Label(value="of %s" % self.length,
layout=Layout(width="100px"))
controls = self.make_controls()
super().__init__([controls, self.output])
def goto(self, position):
#### Position it:
if position == "begin":
self.control_slider.value = 0
elif position == "end":
self.control_slider.value = self.length - 1
elif position == "prev":
if self.control_slider.value - 1 < 0:
self.control_slider.value = self.length - 1 # wrap around
else:
self.control_slider.value = max(self.control_slider.value - 1,
0)
elif position == "next":
if self.control_slider.value + 1 > self.length - 1:
self.control_slider.value = 0 # wrap around
else:
self.control_slider.value = min(self.control_slider.value + 1,
self.length - 1)
self.position_text.value = self.control_slider.value
def toggle_play(self, button):
## toggle
if self.button_play.description == "Play":
self.button_play.description = "Stop"
self.button_play.icon = "pause"
self.player.resume()
else:
self.button_play.description = "Play"
self.button_play.icon = "play"
self.player.pause()
def make_controls(self):
button_begin = Button(icon="fast-backward",
layout=Layout(width='100%'))
button_prev = Button(icon="backward", layout=Layout(width='100%'))
button_next = Button(icon="forward", layout=Layout(width='100%'))
button_end = Button(icon="fast-forward", layout=Layout(width='100%'))
self.button_play = Button(icon="play",
description="Play",
layout=Layout(width="100%"))
self.control_buttons = HBox([
button_begin,
button_prev,
self.position_text,
button_next,
button_end,
self.button_play,
],
layout=Layout(width='100%', height="50px"))
self.control_slider = IntSlider(description=self.title,
continuous_update=False,
min=0,
max=max(self.length - 1, 0),
value=0,
style={"description_width": 'initial'},
layout=Layout(width='100%'))
## Hook them up:
button_begin.on_click(lambda button: self.goto("begin"))
button_end.on_click(lambda button: self.goto("end"))
button_next.on_click(lambda button: self.goto("next"))
button_prev.on_click(lambda button: self.goto("prev"))
self.button_play.on_click(self.toggle_play)
self.control_slider.observe(self.update_slider_control, names='value')
controls = VBox([
HBox([self.control_slider, self.total_text],
layout=Layout(height="40px")), self.control_buttons
],
layout=Layout(width='100%'))
controls.on_displayed(lambda widget: self.initialize())
return controls
def initialize(self):
results = self.function(self.control_slider.value)
try:
results = list(results)
except:
results = [results]
self.displayers = [display(x, display_id=True) for x in results]
def update_slider_control(self, change):
if change["name"] == "value":
self.position_text.value = self.control_slider.value
self.output.clear_output(wait=True)
results = self.function(self.control_slider.value)
try:
results = list(results)
except:
results = [results]
for i in range(len(self.displayers)):
self.displayers[i].update(results[i])
# ### Interactive visualization across layers
# As another way of looking at the data, run the code below to create a visualization where you can choose the class you want to look at by clicking a button to choose a particular label and scrolling across layers using the slider!
# In[29]:
# Create button values
select_class = ToggleButtons(
options=['Normal','Edema', 'Non-enhancing tumor', 'Enhancing tumor'],
description='Select Class:',
disabled=False,
button_style='info',
)
# Create layer slider
select_layer = IntSlider(min=0, max=154, description='Select Layer', continuous_update=False)
# Define a function for plotting images
def plot_image(seg_class, layer):
print(f"Plotting {layer} Layer Label: {seg_class}")
img_label = classes_dict[seg_class]
mask = np.where(label_array[:,:,layer] == img_label, 255, 0)
plt.figure(figsize=(10,5))
plt.imshow(mask, cmap='gray')
plt.axis('off');
# Use the interactive() tool to create the visualization
interactive(plot_image, seg_class=select_class, layer=select_layer)
def __init__(self,
filename,
cmap='jet',
band_indices=None,
pmin=2,
pmax=98,
ts_convert=None,
title=None,
datalabel='data'):
self.ts_convert = ts_convert
self.filename = filename
with Raster(filename) as ras:
self.rows = ras.rows
self.cols = ras.cols
self.bands = ras.bands
self.epsg = ras.epsg
self.crs = ras.srs
geo = ras.raster.GetGeoTransform()
self.nodata = ras.nodata
self.format = ras.format
if self.format == 'ENVI':
self.bandnames = HDRobject(filename + '.hdr').band_names
self.slider_readout = False
self.timestamps = range(0, self.bands) if ts_convert is None else [
ts_convert(x) for x in self.bandnames
]
self.datalabel = datalabel
xlab = self.crs.GetAxisName(None, 0)
ylab = self.crs.GetAxisName(None, 1)
self.xlab = xlab.lower() if xlab is not None else 'longitude'
self.ylab = ylab.lower() if ylab is not None else 'latitude'
self.xmin = geo[0]
self.ymax = geo[3]
self.xres = geo[1]
self.yres = abs(geo[5])
self.xmax = self.xmin + self.xres * self.cols
self.ymin = self.ymax - self.yres * self.rows
self.extent = (self.xmin, self.xmax, self.ymin, self.ymax)
self.pmin, self.pmax = pmin, pmax
# define some options for display of the widget box
self.layout = Layout(display='flex',
flex_flow='column',
border='solid 2px',
align_items='stretch',
width='100%')
self.colormap = cmap
if band_indices is not None:
if len(list(set(band_indices))) != self.bands:
raise RuntimeError(
'length mismatch of unique provided band indices ({0}) '
'and image bands ({1})'.format(len(band_indices),
self.bands))
else:
self.indices = sorted(band_indices)
else:
self.indices = range(1, self.bands + 1)
# define a slider for changing a plotted image
self.slider = IntSlider(min=min(self.indices),
max=max(self.indices),
step=1,
continuous_update=False,
value=self.indices[len(self.indices) // 2],
description='band',
style={'description_width': 'initial'},
readout=self.slider_readout)
# a simple checkbox to enable/disable stacking of vertical profiles into one plot
self.checkbox = Checkbox(value=True,
description='stack vertical profiles',
indent=False)
# a button to clear the vertical profile plot
self.clearbutton = Button(description='clear vertical plot')
self.clearbutton.on_click(lambda x: self.__init_vertical_plot())
self.write_csv = Button(description='export csv')
self.write_csv.on_click(lambda x: self.__csv())
if self.format == 'ENVI':
self.sliderlabel = Label(value=self.bandnames[self.slider.value],
layout={'width': '500px'})
children = [
HBox([self.slider, self.sliderlabel]),
HBox([self.checkbox, self.clearbutton, self.write_csv])
]
else:
children = [
self.slider,
HBox([self.checkbox, self.clearbutton, self.write_csv])
]
form = VBox(children=children, layout=self.layout)
display(form)
self.fig = plt.figure(num=title)
# display of SLC amplitude
self.ax1 = self.fig.add_subplot(121)
# display of topographical phase
self.ax2 = self.fig.add_subplot(122)
# self.ax1 = plt.gca()
self.ax1.get_xaxis().get_major_formatter().set_useOffset(False)
self.ax1.get_yaxis().get_major_formatter().set_useOffset(False)
self.ax1.set_xlabel(self.xlab, fontsize=12)
self.ax1.set_ylabel(self.ylab, fontsize=12)
text_pointer = self.ylab + '={0:.2f}, ' + self.xlab + '={1:.2f}, value='
self.ax1.format_coord = lambda x, y: text_pointer.format(y, x)
# add a cross-hair to the horizontal slice plot
self.x_coord, self.y_coord = self.__img2map(0, 0)
self.lhor = self.ax1.axhline(self.y_coord, linewidth=1, color='r')
self.lver = self.ax1.axvline(self.x_coord, linewidth=1, color='r')
# set up the vertical profile plot
self.__init_vertical_plot()
# make the figure respond to mouse clicks by executing method __onclick
self.cid1 = self.fig.canvas.mpl_connect('button_press_event',
self.__onclick)
# enable interaction with the slider
out = interactive_output(self.__onslide, {'h': self.slider})
plt.tight_layout()
def _make_widget_repr(self):
# TODO: class?
if self.widget_repr is None:
self.widget_repr_name = Text(value='',
description='representation')
self.widget_repr_name._ngl_name = 'repr_name_text'
repr_selection = Text(value=' ', description='selection')
repr_selection._ngl_name = 'repr_selection'
repr_selection.width = self.widget_repr_name.width = default.DEFAULT_TEXT_WIDTH
max_n_components = max(self._view.n_components - 1, 0)
self.widget_component_slider = IntSlider(value=0,
max=max_n_components,
min=0,
description='component')
self.widget_component_slider._ngl_name = 'component_slider'
cvalue = ' '
self.widget_component_dropdown = Dropdown(value=cvalue,
options=[
cvalue,
],
description='component')
self.widget_component_dropdown._ngl_name = 'component_dropdown'
self.widget_repr_slider = IntSlider(
value=0,
description='representation',
width=default.DEFAULT_SLIDER_WIDTH)
self.widget_repr_slider._ngl_name = 'repr_slider'
self.widget_repr_slider.visible = True
self.widget_component_slider.layout.width = default.DEFAULT_SLIDER_WIDTH
self.widget_repr_slider.layout.width = default.DEFAULT_SLIDER_WIDTH
self.widget_component_dropdown.layout.width = self.widget_component_dropdown.max_width = default.DEFAULT_TEXT_WIDTH
# turn off for now
self.widget_component_dropdown.layout.display = 'none'
self.widget_component_dropdown.description = ''
# self.widget_accordion_repr_parameters = Accordion()
self.widget_accordion_repr_parameters = Tab()
self.widget_repr_parameters = self._make_widget_repr_parameters(
self.widget_component_slider, self.widget_repr_slider,
self.widget_repr_name)
self.widget_accordion_repr_parameters.children = [
self.widget_repr_parameters,
Box()
]
self.widget_accordion_repr_parameters.set_title(0, 'Parameters')
self.widget_accordion_repr_parameters.set_title(1, 'Hide')
self.widget_accordion_repr_parameters.selected_index = 1
checkbox_reprlist = Checkbox(value=False, description='reprlist')
checkbox_reprlist._ngl_name = 'checkbox_reprlist'
self.widget_repr_choices = self._make_repr_name_choices(
self.widget_component_slider, self.widget_repr_slider)
self.widget_repr_choices._ngl_name = 'reprlist_choices'
self.widget_repr_add = self._make_add_widget_repr(
self.widget_component_slider)
def on_update_checkbox_reprlist(change):
self.widget_repr_choices.visible = change['new']
checkbox_reprlist.observe(on_update_checkbox_reprlist,
names='value')
def on_repr_name_text_value_changed(change):
name = change['new'].strip()
old = change['old'].strip()
should_update = (self._real_time_update and old and name
and name in REPRESENTATION_NAMES
and name != change['old'].strip())
if should_update:
component = component_slider.value
repr_index = repr_slider.value
self._view._remote_call(
'setRepresentation',
target='Widget',
args=[change['new'], {}, component, repr_index])
self._view._request_repr_parameters(component, repr_index)
def on_component_or_repr_slider_value_changed(change):
self._view._request_repr_parameters(
component=self.widget_component_slider.value,
repr_index=self.widget_repr_slider.value)
self.widget_component_dropdown.options = tuple(
self._view._ngl_component_names)
if self.widget_accordion_repr_parameters.selected_index >= 0:
self.widget_repr_parameters.name = self.widget_repr_name.value
self.widget_repr_parameters.repr_index = self.widget_repr_slider.value
self.widget_repr_parameters.component_index = self.widget_component_slider.value
def on_repr_selection_value_changed(change):
if self._real_time_update:
component = self.widget_component_slider.value
repr_index = self.widget_repr_slider.value
self._view._set_selection(change['new'],
component=component,
repr_index=repr_index)
def on_change_component_dropdown(change):
choice = change['new']
if choice:
self.widget_component_slider.value = self._view._ngl_component_names.index(
choice)
self.widget_component_dropdown.observe(
on_change_component_dropdown, names='value')
self.widget_repr_slider.observe(
on_component_or_repr_slider_value_changed, names='value')
self.widget_component_slider.observe(
on_component_or_repr_slider_value_changed, names='value')
self.widget_repr_name.observe(on_repr_name_text_value_changed,
names='value')
repr_selection.observe(on_repr_selection_value_changed,
names='value')
self.widget_repr_control_buttons = self._make_button_repr_control(
self.widget_component_slider, self.widget_repr_slider,
repr_selection)
blank_box = Box([Label("")])
all_kids = [
self.widget_repr_control_buttons, blank_box,
self.widget_repr_add, self.widget_component_dropdown,
self.widget_repr_name, repr_selection,
self.widget_component_slider, self.widget_repr_slider,
self.widget_repr_choices, self.widget_accordion_repr_parameters
]
vbox = VBox(all_kids)
self._view._request_repr_parameters(
component=self.widget_component_slider.value,
repr_index=self.widget_repr_slider.value)
self.widget_repr = _relayout_master(vbox, width='100%')
self._refresh(self.widget_component_slider,
self.widget_repr_slider)
setattr(self.widget_repr, "_saved_widgets", [])
for _box in self.widget_repr.children:
if hasattr(_box, 'children'):
for kid in _box.children:
self.widget_repr._saved_widgets.append(kid)
return self.widget_repr
class SequenceViewer(VBox):
"""
SequenceViewer
Arguments:
title (str) - Title of sequence
function (callable) - takes an index 0 to length - 1. Function should
a displayable or list of displayables
length (int) - total number of frames in sequence
play_rate (float) - seconds to wait between frames when auto-playing.
Optional. Default is 0.5 seconds.
>>> def function(index):
... return [None]
>>> sv = SequenceViewer("Title", function, 10)
>>> ## Do this manually for testing:
>>> sv.initialize()
None
>>> ## Testing:
>>> class Dummy:
... def update(self, result):
... return result
>>> sv.displayers = [Dummy()]
>>> print("Testing"); sv.goto("begin") # doctest: +ELLIPSIS
Testing...
>>> print("Testing"); sv.goto("end") # doctest: +ELLIPSIS
Testing...
>>> print("Testing"); sv.goto("prev") # doctest: +ELLIPSIS
Testing...
>>> print("Testing"); sv.goto("next") # doctest: +ELLIPSIS
Testing...
"""
def __init__(self, title, function, length, play_rate=0.5):
self.player = _Player(self, play_rate)
self.player.start()
self.title = title
self.function = function
self.length = length
self.output = Output()
self.position_text = IntText(value=0, layout=Layout(width="100%"))
self.total_text = Label(value="of %s" % self.length, layout=Layout(width="100px"))
controls = self.make_controls()
super().__init__([controls, self.output])
def goto(self, position):
#### Position it:
if position == "begin":
self.control_slider.value = 0
elif position == "end":
self.control_slider.value = self.length - 1
elif position == "prev":
if self.control_slider.value - 1 < 0:
self.control_slider.value = self.length - 1 # wrap around
else:
self.control_slider.value = max(self.control_slider.value - 1, 0)
elif position == "next":
if self.control_slider.value + 1 > self.length - 1:
self.control_slider.value = 0 # wrap around
else:
self.control_slider.value = min(self.control_slider.value + 1, self.length - 1)
elif isinstance(position, int):
self.control_slider.value = position
self.position_text.value = self.control_slider.value
def toggle_play(self, button):
## toggle
if self.button_play.description == "Play":
self.button_play.description = "Stop"
self.button_play.icon = "pause"
self.player.resume()
else:
self.button_play.description = "Play"
self.button_play.icon = "play"
self.player.pause()
def make_controls(self):
button_begin = Button(icon="fast-backward", layout=Layout(width='100%'))
button_prev = Button(icon="backward", layout=Layout(width='100%'))
button_next = Button(icon="forward", layout=Layout(width='100%'))
button_end = Button(icon="fast-forward", layout=Layout(width='100%'))
self.button_play = Button(icon="play", description="Play", layout=Layout(width="100%"))
self.control_buttons = HBox([
button_begin,
button_prev,
self.position_text,
button_next,
button_end,
self.button_play,
], layout=Layout(width='100%', height="50px"))
self.control_slider = IntSlider(description=self.title,
continuous_update=False,
min=0,
max=max(self.length - 1, 0),
value=0,
style={"description_width": 'initial'},
layout=Layout(width='100%'))
## Hook them up:
button_begin.on_click(lambda button: self.goto("begin"))
button_end.on_click(lambda button: self.goto("end"))
button_next.on_click(lambda button: self.goto("next"))
button_prev.on_click(lambda button: self.goto("prev"))
self.button_play.on_click(self.toggle_play)
self.control_slider.observe(self.update_slider_control, names='value')
controls = VBox([HBox([self.control_slider, self.total_text], layout=Layout(height="40px")),
self.control_buttons], layout=Layout(width='100%'))
controls.on_displayed(lambda widget: self.initialize())
return controls
def initialize(self):
results = self.function(self.control_slider.value)
try:
results = list(results)
except:
results = [results]
self.displayers = [display(x, display_id=True) for x in results]
def update_slider_control(self, change):
if change["name"] == "value":
self.position_text.value = self.control_slider.value
self.output.clear_output(wait=True)
results = self.function(self.control_slider.value)
try:
results = list(results)
except:
results = [results]
for i in range(len(self.displayers)):
self.displayers[i].update(results[i])
def make_controls(self):
layout = Layout(width='100%', height="100%")
button_begin = Button(icon="fast-backward", layout=layout)
button_prev = Button(icon="backward", layout=layout)
button_next = Button(icon="forward", layout=layout)
button_end = Button(icon="fast-forward", layout=layout)
#button_prop = Button(description="Propagate", layout=Layout(width='100%'))
#button_train = Button(description="Train", layout=Layout(width='100%'))
self.button_play = Button(icon="play", description="Play", layout=layout)
step_down = Button(icon="sort-down", layout=Layout(width="95%", height="100%"))
step_up = Button(icon="sort-up", layout=Layout(width="95%", height="100%"))
up_down = HBox([step_down, step_up], layout=Layout(width="100%", height="100%"))
refresh_button = Button(icon="refresh", layout=Layout(width="25%", height="100%"))
self.position_text = IntText(value=0, layout=layout)
self.control_buttons = HBox([
button_begin,
button_prev,
#button_train,
self.position_text,
button_next,
button_end,
self.button_play,
up_down,
refresh_button
], layout=Layout(width='100%', height="100%"))
length = (len(self.net.dataset.train_inputs) - 1) if len(self.net.dataset.train_inputs) > 0 else 0
self.control_slider = IntSlider(description="Dataset index",
continuous_update=False,
min=0,
max=max(length, 0),
value=0,
layout=Layout(width='100%'))
if self.net.config["dashboard.dataset"] == "Train":
length = len(self.net.dataset.train_inputs)
else:
length = len(self.net.dataset.test_inputs)
self.total_text = Label(value="of %s" % length, layout=Layout(width="100px"))
self.zoom_slider = FloatSlider(description="Zoom",
continuous_update=False,
min=0, max=1.0,
style={"description_width": 'initial'},
layout=Layout(width="65%"),
value=self.net.config["svg_scale"] if self.net.config["svg_scale"] is not None else 0.5)
## Hook them up:
button_begin.on_click(lambda button: self.goto("begin"))
button_end.on_click(lambda button: self.goto("end"))
button_next.on_click(lambda button: self.goto("next"))
button_prev.on_click(lambda button: self.goto("prev"))
self.button_play.on_click(self.toggle_play)
self.control_slider.observe(self.update_slider_control, names='value')
refresh_button.on_click(lambda widget: (self.update_control_slider(),
self.output.clear_output(),
self.regenerate()))
step_down.on_click(lambda widget: self.move_step("down"))
step_up.on_click(lambda widget: self.move_step("up"))
self.zoom_slider.observe(self.update_zoom_slider, names='value')
self.position_text.observe(self.update_position_text, names='value')
# Put them together:
controls = VBox([HBox([self.control_slider, self.total_text], layout=Layout(height="40px")),
self.control_buttons], layout=Layout(width='100%'))
#net_page = VBox([control, self.net_svg], layout=Layout(width='95%'))
controls.on_displayed(lambda widget: self.regenerate())
return controls
def _make_widget_repr(self):
self.widget_repr_name = Text(value='', description='representation')
self.widget_repr_name._ngl_name = 'repr_name_text'
repr_selection = Text(value=' ', description='selection')
repr_selection._ngl_name = 'repr_selection'
repr_selection.width = self.widget_repr_name.width = default.DEFAULT_TEXT_WIDTH
max_n_components = max(self._view.n_components-1, 0)
self.widget_component_slider = IntSlider(value=0, max=max_n_components, min=0, description='component')
self.widget_component_slider._ngl_name = 'component_slider'
cvalue = ' '
self.widget_component_dropdown = Dropdown(value=cvalue, options=[cvalue,],
description='component')
self.widget_component_dropdown._ngl_name = 'component_dropdown'
self.widget_repr_slider = IntSlider(value=0, description='representation', width=default.DEFAULT_SLIDER_WIDTH)
self.widget_repr_slider._ngl_name = 'repr_slider'
self.widget_repr_slider.visible = True
self.widget_component_slider.layout.width = default.DEFAULT_SLIDER_WIDTH
self.widget_repr_slider.layout.width = default.DEFAULT_SLIDER_WIDTH
self.widget_component_dropdown.layout.width = self.widget_component_dropdown.max_width = default.DEFAULT_TEXT_WIDTH
# turn off for now
self.widget_component_dropdown.layout.display = 'none'
self.widget_component_dropdown.description = ''
# self.widget_accordion_repr_parameters = Accordion()
self.widget_accordion_repr_parameters = Tab()
self.widget_repr_parameters = self._make_widget_repr_parameters(self.widget_component_slider,
self.widget_repr_slider,
self.widget_repr_name)
self.widget_accordion_repr_parameters.children = [self.widget_repr_parameters, Box()]
self.widget_accordion_repr_parameters.set_title(0, 'Parameters')
self.widget_accordion_repr_parameters.set_title(1, 'Hide')
self.widget_accordion_repr_parameters.selected_index = 1
checkbox_reprlist = Checkbox(value=False, description='reprlist')
checkbox_reprlist._ngl_name = 'checkbox_reprlist'
self.widget_repr_choices = self._make_repr_name_choices(self.widget_component_slider,
self.widget_repr_slider)
self.widget_repr_choices._ngl_name = 'reprlist_choices'
self.widget_repr_add = self._make_add_widget_repr(self.widget_component_slider)
def on_update_checkbox_reprlist(change):
self.widget_repr_choices.visible= change['new']
checkbox_reprlist.observe(on_update_checkbox_reprlist, names='value')
def on_repr_name_text_value_changed(change):
name = change['new'].strip()
old = change['old'].strip()
should_update = (self._real_time_update
and old and name
and name in REPRESENTATION_NAMES
and name != change['old'].strip())
if should_update:
component=self.widget_component_slider.value
repr_index=self.widget_repr_slider.value
self._view._remote_call('setRepresentation',
target='Widget',
args=[change['new'], {}, component, repr_index])
self._view._request_repr_parameters(component, repr_index)
def on_component_or_repr_slider_value_changed(change):
self._view._request_repr_parameters(component=self.widget_component_slider.value,
repr_index=self.widget_repr_slider.value)
self.widget_component_dropdown.options = tuple(self._view._ngl_component_names)
if self.widget_accordion_repr_parameters.selected_index >= 0:
self.widget_repr_parameters.name = self.widget_repr_name.value
self.widget_repr_parameters.repr_index = self.widget_repr_slider.value
self.widget_repr_parameters.component_index = self.widget_component_slider.value
def on_repr_selection_value_changed(change):
if self._real_time_update:
component = self.widget_component_slider.value
repr_index = self.widget_repr_slider.value
self._view._set_selection(change['new'],
component=component,
repr_index=repr_index)
def on_change_component_dropdown(change):
choice = change['new']
if choice:
self.widget_component_slider.value = self._view._ngl_component_names.index(choice)
self.widget_component_dropdown.observe(on_change_component_dropdown, names='value')
self.widget_repr_slider.observe(on_component_or_repr_slider_value_changed, names='value')
self.widget_component_slider.observe(on_component_or_repr_slider_value_changed, names='value')
self.widget_repr_name.observe(on_repr_name_text_value_changed, names='value')
repr_selection.observe(on_repr_selection_value_changed, names='value')
self.widget_repr_control_buttons = self._make_button_repr_control(self.widget_component_slider,
self.widget_repr_slider, repr_selection)
blank_box = Box([Label("")])
all_kids = [self.widget_repr_control_buttons,
blank_box,
self.widget_repr_add,
self.widget_component_dropdown,
self.widget_repr_name,
repr_selection,
self.widget_component_slider,
self.widget_repr_slider,
self.widget_repr_choices,
self.widget_accordion_repr_parameters
]
vbox = VBox(all_kids)
self._view._request_repr_parameters(component=self.widget_component_slider.value,
repr_index=self.widget_repr_slider.value)
self.widget_repr = _relayout_master(vbox, width='100%')
self._refresh(self.widget_component_slider, self.widget_repr_slider)
setattr(self.widget_repr, "_saved_widgets", [])
for _box in self.widget_repr.children:
if hasattr(_box, 'children'):
for kid in _box.children:
self.widget_repr._saved_widgets.append(kid)
return self.widget_repr
class NGLDisplay:
"""Structure display class
Provides basic structure/trajectory display
in the notebook and optional gui which can be used to enhance its
usability. It is also possible to extend the functionality of the
particular instance of the viewer by adding further widgets
manipulating the structure.
"""
def __init__(self, atoms, xsize=500, ysize=500):
import nglview
from ipywidgets import Dropdown, FloatSlider, IntSlider, HBox, VBox
self.atoms = atoms
if isinstance(atoms[0], Atoms):
# Assume this is a trajectory or struct list
self.view = nglview.show_asetraj(atoms)
self.frm = IntSlider(value=0, min=0, max=len(atoms) - 1)
self.frm.observe(self._update_frame)
self.struct = atoms[0]
else:
# Assume this is just a single structure
self.view = nglview.show_ase(atoms)
self.struct = atoms
self.frm = None
self.colors = {}
self.view._remote_call('setSize', target='Widget',
args=['%dpx' % (xsize,), '%dpx' % (ysize,)])
self.view.add_unitcell()
self.view.add_spacefill()
self.view.camera = 'orthographic'
self.view.update_spacefill(radiusType='covalent', scale=0.7)
self.view.center()
self.asel = Dropdown(options=['All'] +
list(set(self.struct.get_chemical_symbols())),
value='All', description='Show')
self.rad = FloatSlider(value=0.8, min=0.0, max=1.5, step=0.01,
description='Ball size')
self.asel.observe(self._select_atom)
self.rad.observe(self._update_repr)
wdg = [self.asel, self.rad]
if self.frm:
wdg.append(self.frm)
self.gui = HBox([self.view, VBox(wdg)])
# Make useful shortcuts for the user of the class
self.gui.view = self.view
self.gui.control_box = self.gui.children[1]
self.gui.custom_colors = self.custom_colors
def _update_repr(self, chg=None):
self.view.update_spacefill(radiusType='covalent', scale=self.rad.value)
def _update_frame(self, chg=None):
self.view.frame = self.frm.value
return
def _select_atom(self, chg=None):
sel = self.asel.value
self.view.remove_spacefill()
for e in set(self.struct.get_chemical_symbols()):
if (sel == 'All' or e == sel):
if e in self.colors:
self.view.add_spacefill(selection='#' + e,
color=self.colors[e])
else:
self.view.add_spacefill(selection='#' + e)
self._update_repr()
def custom_colors(self, clr=None):
"""
Define custom colors for some atoms. Pass a dictionary of the form
{'Fe':'red', 'Au':'yellow'} to the function.
To reset the map to default call the method without parameters.
"""
if clr:
self.colors = clr
else:
self.colors = {}
self._select_atom()
def initialize(self,
model_state,
measurements=None,
true_state=None,
landmarks=None,
robot_cov=None,
marker_cov=None,
add_aruco=False,
dt_data=0.2):
self.lock = thrd.Lock()
self.initialized = False
self.measurements = measurements
self.landmarks = landmarks
self.marker_cov = marker_cov
self.true_state = true_state
self.robot_cov = robot_cov
self.paused = False
self.cur_frame = 0
self.dt_data = dt_data
self.dt_render = dt_data
self.state = model_state
self.aruco_markers = {}
# Initialize figure
fig = plt.figure(constrained_layout=True, figsize=(14, 5))
gs = fig.add_gridspec(2, 2)
ax = fig.add_subplot(gs[:, 0])
ax2 = fig.add_subplot(gs[0, 1])
ax2.set_xlim([0, 500])
ax2.set_ylim([-5, 5])
ax2.set_title('State Error')
ax2.set_xlabel('Time')
ax2.set_ylabel('Difference between true\nand predicted value')
ax3 = fig.add_subplot(gs[1, 1])
ax3.set_title('Marker Error')
ax3.set_xlabel('Time')
ax3.set_ylabel('Avg. difference between\ntrue and predicted value')
ax3.set_xlim([0, 500])
ax3.set_ylim([-5, 5])
ax.set_xlim([-4, -1.5])
ax.set_ylim([-3.5, -1.5])
ax.tick_params(axis='both', which='major', labelsize=7)
ax.set_title('Overhead View')
ax.set_xlabel('X (m)', weight='bold')
ax.set_ylabel('Y (m)', weight='bold')
self.figure = fig
# Plot ground truth trajectory
ax.plot(self.true_state[:, 0],
self.true_state[:, 1],
c='r',
lw=1,
label='True state (from data)')
# Plot current model state
self.line, = ax.plot(self.state[0, 0],
self.state[0, 1],
c='b',
lw=1,
label='Predicted state (model)')
# Plot position error
self.pos_x_error, = ax2.plot(0,
self.true_state[0, 0] - self.state[0, 0],
label='X-coordinate')
self.pos_y_error, = ax2.plot(0,
self.true_state[0, 1] - self.state[0, 1],
label='Y-coordinate')
ax2.legend(loc='best')
self.marker_x_error, = ax3.plot(0, 0, label='X-coordinate')
self.marker_y_error, = ax3.plot(0, 0, label='Y-coordinate')
ax3.legend(loc='best')
ax.legend(loc='upper right')
# Create Robot Axes
self.robot_ax = []
self.robot_ax.append(
FancyArrowPatch((0, 0), (0.15, 0), mutation_scale=8, color='red'))
self.robot_ax.append(
FancyArrowPatch((0, 0), (0, 0.15), mutation_scale=8,
color='green'))
# Apply translation and rotation as specified by current robot state
cos_theta, sin_theta = np.cos(self.state[0, 2]), np.sin(self.state[0,
2])
Tw_r = np.eye(3)
Tw_r[0:2, 2] = self.state[0, :2]
Tw_r[0:2, 0:2] = [[cos_theta, -sin_theta], [sin_theta, cos_theta]]
Tw_r_obj = transforms.Affine2D(Tw_r)
self.ax_trans = ax.transData
self.robot_ax[0].set_transform(Tw_r_obj + self.ax_trans)
self.robot_ax[1].set_transform(self.robot_ax[0].get_transform())
ax.add_patch(self.robot_ax[0])
ax.add_patch(self.robot_ax[1])
if add_aruco:
marker_files = [
filename for filename in os.listdir('Support/images')
if filename.startswith("M")
]
marker_world_width = 0.3
for i, filename in enumerate(marker_files):
fprts = filename.split('_')
mp = np.array([float(fprts[1]), float(fprts[2])])
mi = cv2.imread('Support/images/' + filename)
ext = [mp[0]-marker_world_width/2,mp[0]+marker_world_width/2,\
mp[1]-marker_world_width/2,mp[1]+marker_world_width/2]
ax.imshow(mi, extent=ext)
ax.annotate(str(i), (mp[0], mp[1]), color='red', weight='bold')
self.aruco_markers[int(fprts[0][-1])] = mp
#Set up to plot measurements
if self.measurements is not None:
self.marker_lines = []
self.marker_lables = []
self.marker_scatter = ax.scatter(np.zeros((10, 1)),
np.zeros((10, 1)),
color='lime')
for i in range(10):
ln, = ax.plot(np.zeros((2, 1)),
np.zeros((2, 1)),
color='yellow',
alpha=0.5)
self.marker_lines.append(ln)
an = ax.annotate(str(i), (-3, -2.5),
color='green',
weight='bold')
self.marker_lables.append(an)
#Set up to plot added landmarks
if self.landmarks is not None:
self.landmarks_scatter = ax.scatter(self.landmarks[0][0, :],
self.landmarks[0][1, :],
s=80,
color='red')
if self.marker_cov is not None:
num_landmarks = self.landmarks[-1].shape[1]
self.marker_ells = []
for i in range(num_landmarks):
el = Ellipse((0, 0),
width=0.3,
height=0.3,
angle=0,
facecolor='none',
edgecolor='blue')
self.marker_ells.append(el)
ax.add_patch(el)
for i in range(self.landmarks[self.cur_frame].shape[1]):
self.marker_ells[i].set_center(
(self.landmarks[self.cur_frame][0, i],
self.landmarks[self.cur_frame][1, i]))
#Set up ellipsoid to draw robot covariance
if self.robot_cov is not None:
cov = self.robot_cov[0, :, :]
a = cov[0, 0]
b = cov[0, 1]
c = cov[1, 0]
d = cov[1, 1]
B = -(a + d)
C = (a * d - b * c)
lam1 = (-B + np.sqrt(B**2 - 4 * C)) / 2
lam2 = (-B - np.sqrt(B**2 - 4 * C)) / 2
v1 = np.array([[lam1 - d], [c]])
self.robo_ell = Ellipse(
(self.state[0, 0], self.state[0, 1]),
width=lam1,
height=lam2,
angle=np.rad2deg(np.arccos(v1[0] / np.linalg.norm(v1))))
self.robo_ell.set_facecolor('none')
self.robo_ell.set_edgecolor('blue')
ax.add_patch(self.robo_ell)
btn_play = widgets.Button(description='Play/Pause',
layout=Layout(flex='1 1 0%', width='auto'),
button_style='success')
btn_play.on_click(self.pause)
btn_prev = widgets.Button(description='<<',
layout=Layout(flex='0.3 1 0%', width='auto'),
button_style='warning')
btn_prev.on_click(self.prv)
btn_next = widgets.Button(description='>>',
layout=Layout(flex='0.3 1 0%', width='auto'),
button_style='warning')
btn_next.on_click(self.nxt)
controls = [
IntSlider(description='Frame: ',
layout=Layout(flex='3 1 0%', width='auto'),
min=0,
max=(model_state.shape[0] - 1)), btn_prev, btn_play,
btn_next
]
self.slider = controls[0]
self.slider.observe(self.slider_change, names='value')
box_layout = Layout(display='flex',
flex_flow='row',
align_items='stretch',
width='70%')
display(Box(children=controls, layout=box_layout))
if not self.is_alive():
self.start()
self.initialized = True
return [create_image(grayscott) for i in tqdm(range(n))]
frames = create_frames(500, numpy_grayscott)
# +
from ipywidgets import interact, IntSlider
def display_sequence(iframe):
return Image.fromarray(frames[iframe])
interact(display_sequence,
iframe=IntSlider(min=0,
max=len(frames)-1,
step=1,
value=0,
continuous_update=True))
# -
import imageio
frames_scaled = [np.uint8(255 * frame) for frame in frames]
imageio.mimsave('movie.gif', frames_scaled, format='gif', fps=60)
# 
# ## References
#
# - [Reaction-Diffusion by the Gray-Scott Model: Pearson's Parametrization](https://mrob.com/pub/comp/xmorphia/)
# ## Cython
class Interface():
def __init__(self,figsize=(6,6)):
self.figsize=figsize
self.size_slider=IntSlider(description='Grid Size',min=4,max=50)
display(self.size_slider)
self.nb_ob_slider=IntSlider(description='Obstacles',min=0,max=7)
display(self.nb_ob_slider)
self.gen_inst_button=Button(description='Generate Instance',margin=10)
self.gen_pos_button=Button(description='Generate Start/End Positions',margin=10)
self.gen_path_button=Button(description='Generate Path',margin=10)
self.inst_but_container=HBox(children=[self.gen_inst_button,self.gen_pos_button,self.gen_path_button])
self.inst_but_container.width = '100%'
display(self.inst_but_container)
self.show_path_button=Latex(value='Path: Value: Actions:',margin=10)
display(self.show_path_button)
self.size_slider.on_trait_change(self._on_size_slider_change,'value')
self.gen_inst_button.on_click(self._on_gen_inst_button_click)
self.gen_pos_button.on_click(self._on_pos_button_click)
self.gen_path_button.on_click(self._on_gen_path_button_click)
self.gen_path_button.disabled=True
self.gen_pos_button.disabled=True
plt.close()
plt.axis('off')
self.fig=plt.figure(figsize=self.figsize)
self.ax=self.fig.add_subplot(111)
def _on_size_slider_change(self,name,value):
self.nb_ob_slider.max=int(value)**2/2-4 #Constrain on number of obstacles
def _on_gen_inst_button_click(self,b):
self.gen_path_button.disabled=True
self.gen_pos_button.disabled=False
self.show_path_button.value='Path: Value: Actions:'
for line in self.ax.lines:
line.set_visible(False)
del(line)
#Instance Generation
self.M=self.size_slider.value
self.nb_ob=self.nb_ob_slider.value
self.A=gen_rand_instance(self.M,self.M,self.nb_ob)
self.G=gen_graph(self.A)
if hasattr(self, 'ax'):
# print self.ax
self.ax.cla()
if hasattr(self, 'start_circle'):
del(self.start_circle)
del(self.end_circle)
del(self.arrow)
colors=['white','grey']
self.ax.set_ylim([0,self.A.shape[0]])
self.ax.set_xlim([0,self.A.shape[1]])
self.ax.set_axis_off()
self.tb = Table(self.ax, bbox=[0,0,1,1])
nrows, ncols = self.A.shape
width, height = 1.0 / ncols, 1.0 / nrows
# Add cells
for (i,j),val in np.ndenumerate(self.A):
color=colors[val]
self.tb.add_cell(i, j, width, height,loc='center', facecolor=color)
# Row Labels...
for i in range(self.A.shape[0]):
self.tb.add_cell(i, -1, width, height, text=i, loc='right',
edgecolor='none', facecolor='none')
# Column Labels
for j in range(self.A.shape[1]):
self.tb.add_cell(-1, j, width, height/2, text=j, loc='center',
edgecolor='none', facecolor='none')
self.ax.add_table(self.tb)
self.ax.invert_yaxis()
#self.leg=self.ax.legend(bbox_to_anchor=(1.3, 1.05),fancybox=True)
#self.leg.get_frame().set_alpha(0.5)
#self.ax.legend()
plt.show()
def _on_pos_button_click(self,b):
for line in self.ax.lines:
line.set_visible(False)
del(line)
self.gen_path_button.disabled=False
self.start,self.end=gen_rand_positions(self.G)
#Ajout Depart
start_inst=self.start[:2][::-1]
#Ajout Direction de Depart
start_dir=self.start[2]
start_posA=start_inst
end_inst=self.end[:2][::-1]
if(start_dir==1):
start_posB=(start_posA[0],start_posA[1]-1)
if(start_dir==2):
start_posB=(start_posA[0]+1,start_posA[1])
if(start_dir==3):
start_posB=(start_posA[0],start_posA[1]+1)
if(start_dir==4):
start_posB=(start_posA[0]-1,start_posA[1])
if hasattr(self, 'start_circle'): #deja trace
self.start_circle.set_visible(True)
self.end_circle.set_visible(True)
self.arrow.set_visible(True)
self.start_circle.center=start_inst
self.arrow.set_positions(start_posA,start_posB)
self.end_circle.center=end_inst
self.show_path_button.value='Path: Value: Actions:'
else: #jamais trace encore
#Position de Depart
self.start_circle=Circle(start_inst,radius=0.5,alpha=0.8, color='g',zorder=2,label='Depart',clip_on=False)
self.ax.add_patch(self.start_circle)
#Direction de Depart
self.arrow=FancyArrowPatch(start_posA,start_posB,arrowstyle='->',color='m',mutation_scale=15.0,lw=2,zorder=3,clip_on=False)
self.ax.add_patch(self.arrow)
#Ajout Arrivee
self.end_circle=Circle(end_inst,radius=0.5,alpha=0.8, color='r',zorder=2,label='Arrivee',clip_on=False)
self.ax.add_patch(self.end_circle)
self.leg=self.ax.legend(bbox_to_anchor=(1.1, 1.05),fancybox=True)
self.leg.get_frame().set_alpha(0.5)
plt.show()
def _on_gen_path_button_click(self,b):
self.gen_path_button.disabled=True
self.result=gen_shortest_path(self.start,self.end,self.G)
self.show_path_button.value='Path: Value: '+str(self.result[0])+' Actions: '+' '.join(e for e in self.result[1])
#Ajout Chemin
for i,j in self.result[2]:
self.ax.add_line(lines.Line2D((i[1],j[1]),(i[0],j[0]),linewidth=3,zorder=1,clip_on=False))
plt.draw()
def show_opt_team(player_gw_next_eps_ext: DF,
max_budget: float,
ctx: Context,
def_budget: float = None):
def get_message(optimise_team_on, optimise_sel_on, budget,
expens_player_count, include, exclude, risk,
recommend) -> None:
message = '<span style="margin-right: 30px">'
if recommend is not None:
message += f'Recommend <strong>{recommend}</strong> transfer(s) with the highest <strong>{optimise_team_on}</strong> '
else:
message += f'Create a team with the highest <strong>{optimise_team_on}</strong> '
message += f'within the budget of <strong>£{budget:.1f}m</strong> biasing the team towards <strong>{expens_player_count}</strong> more expensive player(s) ' + \
f'and taking <strong>{risk:.0%}</strong> risk '
if len(include) > 0 and len(exclude) == 0:
message += f'while including <strong>{",".join(include)}</strong> '
elif len(include) == 0 and len(exclude) > 0:
message += f'while excluding <strong>{",".join(exclude)}</strong> '
elif len(include) > 0 and len(exclude) > 0:
message += f'while including <strong>{",".join(include)}</strong> and excluding <strong>{",".join(exclude)}</strong> '
message += f'and optimise the selection for <strong>{optimise_sel_on}</strong>.</span>'
return message
def get_players(players_text: str) -> Tuple:
return tuple([v.strip() for v in players_text.split(',')
]) if players_text != '' else ()
def get_args():
return dict(
recommend=(recommend_slider.value if has_in_team else None),
optimise_team_on='Expected Points ' + opt_for_dropdown.value,
budget=budget_slider.value,
optimise_sel_on='Expected Points ' + sel_for_dropdown.value,
expens_player_count=expens_player_slider.value,
include=get_players(include_text.value),
exclude=get_players(exclude_text.value),
risk=risk_slider.value)
def validate_include_exclude(df, include_exclude,
include_exclude_text) -> None:
include_exclude_lower = [v.lower() for v in include_exclude]
if not set(
df['Name'].str.lower().values) >= set(include_exclude_lower):
invalid_include_exclude = [
v for v in include_exclude
if v.lower() in (set(include_exclude_lower) -
set(df["Name"].str.lower().values))
]
if len(invalid_include_exclude) == 1:
raise ValueError(
f'{invalid_include_exclude[0]} in {include_exclude_text} is not a valid player name.'
)
else:
raise ValueError(
f'{", ".join(invalid_include_exclude)} in {include_exclude_text} are not valid player names.'
)
@debounce(1)
def on_value_change(change):
args = get_args()
error_html.value = ''
try:
validate_include_exclude(player_gw_next_eps_ext, args['include'],
'Include')
validate_include_exclude(player_gw_next_eps_ext, args['exclude'],
'Exclude')
message_html.value = get_message(**args)
optimise_team()
error_html.value = ''
except Exception as e:
error_html.value = f'<div class="alert alert-danger">{e}</div>'
def optimise_team():
error_html.value = f'<div class="alert alert-success">Optimising ...</div>'
with out:
out.clear_output()
summary = display_optimal_team(players_df=player_gw_next_eps_ext,
ctx=ctx,
formation=(2, 5, 5, 3),
**get_args())
display(summary)
has_in_team = 'In Team?' in player_gw_next_eps_ext.columns
horizons = get_horizons(player_gw_next_eps_ext)
if def_budget is None:
def_budget = max_budget
# Define the selector controls
opt_for_dropdown = Dropdown(description='Optimise for',
options=horizons,
value=ctx.def_next_gws)
sel_for_dropdown = Dropdown(description='Select for', options=horizons)
budget_slider = FloatSlider(value=def_budget,
min=0,
max=max_budget,
step=0.1,
description='Budget',
continuous_update=True,
readout_format='.1f')
expens_player_label = Label('Expensive players')
expens_player_slider = IntSlider(value=15,
min=1,
max=15,
step=1,
continuous_update=True,
readout_format='.0f')
include_text = Text(description='Include',
placeholder='Comma separated player names')
exclude_text = Text(description='Exclude',
placeholder='Comma separated player names')
risk_slider = FloatSlider(value=0.2,
min=0,
max=1,
step=0.1,
description='Risk',
continuous_update=True,
readout_format='.0%')
recommend_slider = IntSlider(value=1,
min=0,
max=11,
step=1,
description='Recommend',
continuous_update=True,
readout_format='.0f')
message_html = HTML()
error_html = HTML(layout=Layout(flex='1 1 0%', width='auto'))
hbox_layout = Layout(display='flex',
flex_flow='row',
align_items='stretch',
width='100%')
hboxes = []
hboxes += [
HBox([opt_for_dropdown, sel_for_dropdown] +
([recommend_slider] if has_in_team else []),
layout=hbox_layout)
]
hboxes += [
HBox([include_text, exclude_text, risk_slider], layout=hbox_layout)
]
hboxes += [
HBox([budget_slider, expens_player_label, expens_player_slider],
layout=hbox_layout)
]
for hbox in hboxes:
for widget in hbox.children:
widget.observe(on_value_change, names='value')
hboxes += [HBox([message_html])]
hboxes += [HBox([error_html])]
out = Output()
on_value_change(None)
return VBox(hboxes + [out])
latex_string += r'\\'
latex_string += '\n'
latex_string += r'\end{array}\right]$'
return display_string_as_html_in_div(latex_string, div_id=div_id)
if __name__ == "__main__":
def test_widgets(a, b, c, d, e):
print("a=", a, "b=", b, "c=", c, "d=", d, "e=", e)
ob_interactive = interactive(
test_widgets,
a=IntSlider(min=3,
max=51,
step=2,
value=17,
description='xxxxxxxxxxxxxxxxxxxxxxxxxxxx'),
b=FloatSlider(min=3,
max=51,
step=2,
value=19,
description='zzzzzzzzzzzzz'),
c=Checkbox(description="this is a check box"),
d=Label(value="This is a label"),
e=Dropdown(options=["Option 1", "Option 2", "Option 3"],
value="Option 1",
description="DropDown",
continuous_update=False))
if in_ipython_flag:
print("Testing arrange_widgets_in_grid")
def view_binding_site(pdbIds=None, groups=None, chains=None, distance=3.0):
'''A wrapper function that zooms in to a group of a protein structure and highlight
its neighbors within a certain distance.
Parameters
----------
pdbIds : list, optional
A list of PDBIDs to display
groups : list, optional
A list of groups to center at for each protein structure
chains : list, optional
A list of chains specified for each protein structure.
If no chains is specified, chain 'A' will be default to
all structures.
cutoffDistance : float, optional
The cutoff distance use the find the neighbors of specified group
'''
if pdbIds is None or groups is None:
raise ValueError("PdbIds and groups need to be specified")
if len(pdbIds) != len(groups):
raise ValueError(
"Number of structures should match with number of groups")
if type(pdbIds) == str and groups == str:
pdbIds, groups = [pdbIds], [groups]
if chains is None:
chains = ['A'] * len(pdbIds)
def view3d(i=0):
'''Simple structure viewer that zooms into a specified group and highlight
its neighbors
Parameters
----------
i (int): index of the protein if a list of PDBids
'''
print(
f"PDB: {pdbIds[i]}, group: {groups[i]}, chain: {chains[i]}, cutoffDistance: {distance}"
)
if type(groups[i]) == int:
center = {'resi': groups[i], 'chain': chains[i]}
neighbors = {
'resi': groups[i],
'chain': chains[i],
'byres': 'true',
'expand': distance
}
else:
center = {'resn': groups[i], 'chain': chains[i]}
neighbors = {
'resn': groups[i],
'chain': chains[i],
'byres': 'true',
'expand': distance
}
viewer = py3Dmol.view(query='pdb:' + pdbIds[i])
viewer.setStyle(neighbors, {'stick': {}})
viewer.setStyle(center, {'sphere': {'colorscheme': 'orangeCarbon'}})
viewer.zoomTo(neighbors)
return viewer.show()
s_widget = IntSlider(min=0,
max=len(pdbIds) - 1,
description='Structure',
continuous_update=False)
return interact(view3d, i=s_widget)
def plot(vtkfile_path, color_attribute_name, color_map=get_cmap('viridis')):
''' Generate a k3d Plot and associated controls for VTK data from file
:param vtkfile_path: the path to load vtk data from. Can be a single .vtu or a collection
:param color_attribute_name: which data array from vtk to use for plot coloring
:param color_map: a Matplotlib Colormap object or a K3D array((step, r, g, b))
:return: the generated Plot object
'''
if isinstance(color_map, Colormap):
color_map = [(x, *color_map(x)[:3]) for x in np.linspace(0, 1, 256)]
data = read_vtkfile(vtkfile_path)
size = len(data)
# getbounds: (xmin, xmax, ymin, ymax, zmin, zmax)
all_bounds = np.stack([p[1].GetBounds() for p in data])
combined_bounds = np.array([
np.min(all_bounds[:, 0]),
np.min(all_bounds[:, 2]),
np.min(all_bounds[:, 4]),
np.max(all_bounds[:, 1]),
np.max(all_bounds[:, 3]),
np.max(all_bounds[:, 5])
])
vtkplot = VTKPlot(data,
color_attribute_name=color_attribute_name,
grid_auto_fit=False,
camera_auto_fit=False,
color_map=color_map,
grid=combined_bounds)
# display needs to have been called before changing camera/grid_visible
vtkplot.display()
# could be replaced with testing if the widget is'ready'
time.sleep(0.5)
vtkplot.grid_visible = False
try:
vtkplot.menu_visibility = False
except AttributeError:
pass # k3d < 2.5.6
# guesstimate
fov_angle = 30
absx = np.abs(combined_bounds[0] - combined_bounds[3])
c_dist = np.sin((90 - fov_angle) * np.pi /
180) * absx / (2 * np.sin(fov_angle * np.pi / 180))
xhalf = (combined_bounds[0] + combined_bounds[3]) / 2
yhalf = (combined_bounds[1] + combined_bounds[4]) / 2
zhalf = (combined_bounds[2] + combined_bounds[5]) / 2
# camera[posx, posy, posz, targetx, targety, targetz, upx, upy, upz]
vtkplot.camera = (xhalf, yhalf, zhalf + c_dist, xhalf, yhalf, zhalf, 0, 1,
0)
if size > 1:
play = Play(min=0,
max=size - 1,
step=1,
value=0,
description='Timestep:')
interact(idx=play).widget(vtkplot._goto_idx)
slider = IntSlider(min=0,
max=size - 1,
step=1,
value=0,
description='Timestep:')
interact(idx=slider).widget(vtkplot._goto_idx)
widgets.jslink((play, 'value'), (slider, 'value'))
hbox = widgets.HBox([play, slider])
IPython.display.display(hbox)
return vtkplot
def interact_ometif(self):
"""Interactor for visualizing the ome.tif file at low resolution and an associated region."""
def _interact_ometif(frame, left, top, width, height):
button, text = _create_button_text_display('ometif_region_seg.png')
# get the region at 1.25x resolution for frame 0
lr_im = self.ts.getRegion(
format=large_image.tilesource.TILE_FORMAT_NUMPY,
scale={'magnification': 1.25},
frame=self.chnames[frame])[0][:, :, 0]
fig, ax = plt.subplots(ncols=2, figsize=(15, 7))
ax[0].imshow(lr_im, cmap='gray')
ax[0].set_title(f'ome.tif channel {frame} at 1.25X magnification',
fontsize=18)
# get the region and reset the fields of regions....is this the best way to do it?
region = {
'left': left,
'top': top,
'width': width,
'height': height
}
self.region = region
self.region_masks = {}
for mask_name, mask_filepath in self.masks_dict.items():
mask = fix_segmentation_mask(
imread(mask_filepath)[region['top']:region['top'] +
region['height'],
region['left']:region['left'] +
region['width'], ])
self.region_masks[mask_name] = mask
reg_im = self.ts.getRegion(
format=large_image.tilesource.TILE_FORMAT_NUMPY,
region=region,
frame=self.chnames[frame])[0][:, :, 0]
self.region_im = reg_im
ax[1].imshow(reg_im, cmap='gray')
ax[1].set_title('Image region at full magnification', fontsize=18)
ax[1].xaxis.set_visible(False)
ax[1].yaxis.set_visible(False)
plt.suptitle(
'View OME.TIF at low magnification and select region to view at full mag',
fontweight='bold',
fontsize=20)
fig.tight_layout(rect=[0, 0, 1, .9])
plt.show()
button.on_click(
partial(self.on_button_clicked,
text_widget=text,
fig_to_save=fig))
display(widgets.HBox([text, button]))
chnames = list(self.chnames.keys())
a = Dropdown(options=chnames,
value=chnames[0],
description='Channel:',
style=DESC_STYLES)
b = IntSlider(min=0,
max=self.ts.getMetadata()['sizeX'],
value=self.region['left'],
description='Region left coord:',
style=DESC_STYLES,
continuous_update=False)
c = IntSlider(min=0,
max=self.ts.getMetadata()['sizeY'],
value=self.region['top'],
description='Region top coord:',
style=DESC_STYLES,
continuous_update=False)
d = IntSlider(min=100,
max=5000,
value=self.region['width'],
description='Region width:',
style=DESC_STYLES,
continuous_update=False)
e = IntSlider(min=100,
max=5000,
value=self.region['height'],
description='Region height:',
style=DESC_STYLES,
continuous_update=False)
row1 = widgets.HBox([a])
row2 = widgets.HBox([b, d])
row3 = widgets.HBox([c, e])
ui = widgets.VBox([row1, row2, row3])
out = widgets.interactive_output(_interact_ometif, {
'frame': a,
'left': b,
'top': c,
'width': d,
'height': e
})
display(ui, out)
class Dashboard(VBox):
"""
Build the dashboard for Jupyter widgets. Requires running
in a notebook/jupyterlab.
"""
def __init__(self, net, width="95%", height="550px", play_rate=0.5):
self._ignore_layer_updates = False
self.player = _Player(self, play_rate)
self.player.start()
self.net = net
r = random.randint(1, 1000000)
self.class_id = "picture-dashboard-%s-%s" % (self.net.name, r)
self._width = width
self._height = height
## Global widgets:
style = {"description_width": "initial"}
self.feature_columns = IntText(description="Detail columns:",
value=self.net.config["dashboard.features.columns"],
min=0,
max=1024,
style=style)
self.feature_scale = FloatText(description="Detail scale:",
value=self.net.config["dashboard.features.scale"],
min=0.1,
max=10,
style=style)
self.feature_columns.observe(self.regenerate, names='value')
self.feature_scale.observe(self.regenerate, names='value')
## Hack to center SVG as justify-content is broken:
self.net_svg = HTML(value="""<p style="text-align:center">%s</p>""" % ("",), layout=Layout(
width=self._width, overflow_x='auto', overflow_y="auto",
justify_content="center"))
# Make controls first:
self.output = Output()
controls = self.make_controls()
config = self.make_config()
super().__init__([config, controls, self.net_svg, self.output])
def propagate(self, inputs):
"""
Propagate inputs through the dashboard view of the network.
"""
if dynamic_pictures_check():
return self.net.propagate(inputs, class_id=self.class_id, update_pictures=True)
else:
self.regenerate(inputs=input)
def goto(self, position):
if len(self.net.dataset.inputs) == 0 or len(self.net.dataset.targets) == 0:
return
if self.control_select.value == "Train":
length = len(self.net.dataset.train_inputs)
elif self.control_select.value == "Test":
length = len(self.net.dataset.test_inputs)
#### Position it:
if position == "begin":
self.control_slider.value = 0
elif position == "end":
self.control_slider.value = length - 1
elif position == "prev":
if self.control_slider.value - 1 < 0:
self.control_slider.value = length - 1 # wrap around
else:
self.control_slider.value = max(self.control_slider.value - 1, 0)
elif position == "next":
if self.control_slider.value + 1 > length - 1:
self.control_slider.value = 0 # wrap around
else:
self.control_slider.value = min(self.control_slider.value + 1, length - 1)
self.position_text.value = self.control_slider.value
def change_select(self, change=None):
"""
"""
self.update_control_slider(change)
self.regenerate()
def update_control_slider(self, change=None):
self.net.config["dashboard.dataset"] = self.control_select.value
if len(self.net.dataset.inputs) == 0 or len(self.net.dataset.targets) == 0:
self.total_text.value = "of 0"
self.control_slider.value = 0
self.position_text.value = 0
self.control_slider.disabled = True
self.position_text.disabled = True
for child in self.control_buttons.children:
if not hasattr(child, "icon") or child.icon != "refresh":
child.disabled = True
return
if self.control_select.value == "Test":
self.total_text.value = "of %s" % len(self.net.dataset.test_inputs)
minmax = (0, max(len(self.net.dataset.test_inputs) - 1, 0))
if minmax[0] <= self.control_slider.value <= minmax[1]:
pass # ok
else:
self.control_slider.value = 0
self.control_slider.min = minmax[0]
self.control_slider.max = minmax[1]
if len(self.net.dataset.test_inputs) == 0:
disabled = True
else:
disabled = False
elif self.control_select.value == "Train":
self.total_text.value = "of %s" % len(self.net.dataset.train_inputs)
minmax = (0, max(len(self.net.dataset.train_inputs) - 1, 0))
if minmax[0] <= self.control_slider.value <= minmax[1]:
pass # ok
else:
self.control_slider.value = 0
self.control_slider.min = minmax[0]
self.control_slider.max = minmax[1]
if len(self.net.dataset.train_inputs) == 0:
disabled = True
else:
disabled = False
self.control_slider.disabled = disabled
self.position_text.disbaled = disabled
self.position_text.value = self.control_slider.value
for child in self.control_buttons.children:
if not hasattr(child, "icon") or child.icon != "refresh":
child.disabled = disabled
def update_zoom_slider(self, change):
if change["name"] == "value":
self.net.config["svg_scale"] = self.zoom_slider.value
self.regenerate()
def update_position_text(self, change):
# {'name': 'value', 'old': 2, 'new': 3, 'owner': IntText(value=3, layout=Layout(width='100%')), 'type': 'change'}
self.control_slider.value = change["new"]
def get_current_input(self):
if self.control_select.value == "Train" and len(self.net.dataset.train_targets) > 0:
return self.net.dataset.train_inputs[self.control_slider.value]
elif self.control_select.value == "Test" and len(self.net.dataset.test_targets) > 0:
return self.net.dataset.test_inputs[self.control_slider.value]
def get_current_targets(self):
if self.control_select.value == "Train" and len(self.net.dataset.train_targets) > 0:
return self.net.dataset.train_targets[self.control_slider.value]
elif self.control_select.value == "Test" and len(self.net.dataset.test_targets) > 0:
return self.net.dataset.test_targets[self.control_slider.value]
def update_slider_control(self, change):
if len(self.net.dataset.inputs) == 0 or len(self.net.dataset.targets) == 0:
self.total_text.value = "of 0"
return
if change["name"] == "value":
self.position_text.value = self.control_slider.value
if self.control_select.value == "Train" and len(self.net.dataset.train_targets) > 0:
self.total_text.value = "of %s" % len(self.net.dataset.train_inputs)
if self.net.model is None:
return
if not dynamic_pictures_check():
self.regenerate(inputs=self.net.dataset.train_inputs[self.control_slider.value],
targets=self.net.dataset.train_targets[self.control_slider.value])
return
output = self.net.propagate(self.net.dataset.train_inputs[self.control_slider.value],
class_id=self.class_id, update_pictures=True)
if self.feature_bank.value in self.net.layer_dict.keys():
self.net.propagate_to_features(self.feature_bank.value, self.net.dataset.train_inputs[self.control_slider.value],
cols=self.feature_columns.value, scale=self.feature_scale.value, html=False)
if self.net.config["show_targets"]:
if len(self.net.output_bank_order) == 1: ## FIXME: use minmax of output bank
self.net.display_component([self.net.dataset.train_targets[self.control_slider.value]],
"targets",
class_id=self.class_id,
minmax=(-1, 1))
else:
self.net.display_component(self.net.dataset.train_targets[self.control_slider.value],
"targets",
class_id=self.class_id,
minmax=(-1, 1))
if self.net.config["show_errors"]: ## minmax is error
if len(self.net.output_bank_order) == 1:
errors = np.array(output) - np.array(self.net.dataset.train_targets[self.control_slider.value])
self.net.display_component([errors.tolist()],
"errors",
class_id=self.class_id,
minmax=(-1, 1))
else:
errors = []
for bank in range(len(self.net.output_bank_order)):
errors.append( np.array(output[bank]) - np.array(self.net.dataset.train_targets[self.control_slider.value][bank]))
self.net.display_component(errors, "errors", class_id=self.class_id, minmax=(-1, 1))
elif self.control_select.value == "Test" and len(self.net.dataset.test_targets) > 0:
self.total_text.value = "of %s" % len(self.net.dataset.test_inputs)
if self.net.model is None:
return
if not dynamic_pictures_check():
self.regenerate(inputs=self.net.dataset.test_inputs[self.control_slider.value],
targets=self.net.dataset.test_targets[self.control_slider.value])
return
output = self.net.propagate(self.net.dataset.test_inputs[self.control_slider.value],
class_id=self.class_id, update_pictures=True)
if self.feature_bank.value in self.net.layer_dict.keys():
self.net.propagate_to_features(self.feature_bank.value, self.net.dataset.test_inputs[self.control_slider.value],
cols=self.feature_columns.value, scale=self.feature_scale.value, html=False)
if self.net.config["show_targets"]: ## FIXME: use minmax of output bank
self.net.display_component([self.net.dataset.test_targets[self.control_slider.value]],
"targets",
class_id=self.class_id,
minmax=(-1, 1))
if self.net.config["show_errors"]: ## minmax is error
if len(self.net.output_bank_order) == 1:
errors = np.array(output) - np.array(self.net.dataset.test_targets[self.control_slider.value])
self.net.display_component([errors.tolist()],
"errors",
class_id=self.class_id,
minmax=(-1, 1))
else:
errors = []
for bank in range(len(self.net.output_bank_order)):
errors.append( np.array(output[bank]) - np.array(self.net.dataset.test_targets[self.control_slider.value][bank]))
self.net.display_component(errors, "errors", class_id=self.class_id, minmax=(-1, 1))
def toggle_play(self, button):
## toggle
if self.button_play.description == "Play":
self.button_play.description = "Stop"
self.button_play.icon = "pause"
self.player.resume()
else:
self.button_play.description = "Play"
self.button_play.icon = "play"
self.player.pause()
def prop_one(self, button=None):
self.update_slider_control({"name": "value"})
def regenerate(self, button=None, inputs=None, targets=None):
## Protection when deleting object on shutdown:
if isinstance(button, dict) and 'new' in button and button['new'] is None:
return
## Update the config:
self.net.config["dashboard.features.bank"] = self.feature_bank.value
self.net.config["dashboard.features.columns"] = self.feature_columns.value
self.net.config["dashboard.features.scale"] = self.feature_scale.value
inputs = inputs if inputs is not None else self.get_current_input()
targets = targets if targets is not None else self.get_current_targets()
features = None
if self.feature_bank.value in self.net.layer_dict.keys() and inputs is not None:
if self.net.model is not None:
features = self.net.propagate_to_features(self.feature_bank.value, inputs,
cols=self.feature_columns.value,
scale=self.feature_scale.value, display=False)
svg = """<p style="text-align:center">%s</p>""" % (self.net.to_svg(
inputs=inputs,
targets=targets,
class_id=self.class_id,
highlights={self.feature_bank.value: {
"border_color": "orange",
"border_width": 30,
}}))
if inputs is not None and features is not None:
html_horizontal = """
<table align="center" style="width: 100%%;">
<tr>
<td valign="top" style="width: 50%%;">%s</td>
<td valign="top" align="center" style="width: 50%%;"><p style="text-align:center"><b>%s</b></p>%s</td>
</tr>
</table>"""
html_vertical = """
<table align="center" style="width: 100%%;">
<tr>
<td valign="top">%s</td>
</tr>
<tr>
<td valign="top" align="center"><p style="text-align:center"><b>%s</b></p>%s</td>
</tr>
</table>"""
self.net_svg.value = (html_vertical if self.net.config["svg_rotate"] else html_horizontal) % (
svg, "%s details" % self.feature_bank.value, features)
else:
self.net_svg.value = svg
def make_colormap_image(self, colormap_name):
from .layers import Layer
if not colormap_name:
colormap_name = get_colormap()
layer = Layer("Colormap", 100)
minmax = layer.get_act_minmax()
image = layer.make_image(np.arange(minmax[0], minmax[1], .01),
colormap_name,
{"pixels_per_unit": 1,
"svg_rotate": self.net.config["svg_rotate"]}).resize((300, 25))
return image
def set_attr(self, obj, attr, value):
if value not in [{}, None]: ## value is None when shutting down
if isinstance(value, dict):
value = value["value"]
if isinstance(obj, dict):
obj[attr] = value
else:
setattr(obj, attr, value)
## was crashing on Widgets.__del__, if get_ipython() no longer existed
self.regenerate()
def make_controls(self):
layout = Layout(width='100%', height="100%")
button_begin = Button(icon="fast-backward", layout=layout)
button_prev = Button(icon="backward", layout=layout)
button_next = Button(icon="forward", layout=layout)
button_end = Button(icon="fast-forward", layout=layout)
#button_prop = Button(description="Propagate", layout=Layout(width='100%'))
#button_train = Button(description="Train", layout=Layout(width='100%'))
self.button_play = Button(icon="play", description="Play", layout=layout)
step_down = Button(icon="sort-down", layout=Layout(width="95%", height="100%"))
step_up = Button(icon="sort-up", layout=Layout(width="95%", height="100%"))
up_down = HBox([step_down, step_up], layout=Layout(width="100%", height="100%"))
refresh_button = Button(icon="refresh", layout=Layout(width="25%", height="100%"))
self.position_text = IntText(value=0, layout=layout)
self.control_buttons = HBox([
button_begin,
button_prev,
#button_train,
self.position_text,
button_next,
button_end,
self.button_play,
up_down,
refresh_button
], layout=Layout(width='100%', height="100%"))
length = (len(self.net.dataset.train_inputs) - 1) if len(self.net.dataset.train_inputs) > 0 else 0
self.control_slider = IntSlider(description="Dataset index",
continuous_update=False,
min=0,
max=max(length, 0),
value=0,
layout=Layout(width='100%'))
if self.net.config["dashboard.dataset"] == "Train":
length = len(self.net.dataset.train_inputs)
else:
length = len(self.net.dataset.test_inputs)
self.total_text = Label(value="of %s" % length, layout=Layout(width="100px"))
self.zoom_slider = FloatSlider(description="Zoom",
continuous_update=False,
min=0, max=1.0,
style={"description_width": 'initial'},
layout=Layout(width="65%"),
value=self.net.config["svg_scale"] if self.net.config["svg_scale"] is not None else 0.5)
## Hook them up:
button_begin.on_click(lambda button: self.goto("begin"))
button_end.on_click(lambda button: self.goto("end"))
button_next.on_click(lambda button: self.goto("next"))
button_prev.on_click(lambda button: self.goto("prev"))
self.button_play.on_click(self.toggle_play)
self.control_slider.observe(self.update_slider_control, names='value')
refresh_button.on_click(lambda widget: (self.update_control_slider(),
self.output.clear_output(),
self.regenerate()))
step_down.on_click(lambda widget: self.move_step("down"))
step_up.on_click(lambda widget: self.move_step("up"))
self.zoom_slider.observe(self.update_zoom_slider, names='value')
self.position_text.observe(self.update_position_text, names='value')
# Put them together:
controls = VBox([HBox([self.control_slider, self.total_text], layout=Layout(height="40px")),
self.control_buttons], layout=Layout(width='100%'))
#net_page = VBox([control, self.net_svg], layout=Layout(width='95%'))
controls.on_displayed(lambda widget: self.regenerate())
return controls
def move_step(self, direction):
"""
Move the layer stepper up/down through network
"""
options = [""] + [layer.name for layer in self.net.layers]
index = options.index(self.feature_bank.value)
if direction == "up":
new_index = (index + 1) % len(options)
else: ## down
new_index = (index - 1) % len(options)
self.feature_bank.value = options[new_index]
self.regenerate()
def make_config(self):
layout = Layout()
style = {"description_width": "initial"}
checkbox1 = Checkbox(description="Show Targets", value=self.net.config["show_targets"],
layout=layout, style=style)
checkbox1.observe(lambda change: self.set_attr(self.net.config, "show_targets", change["new"]), names='value')
checkbox2 = Checkbox(description="Errors", value=self.net.config["show_errors"],
layout=layout, style=style)
checkbox2.observe(lambda change: self.set_attr(self.net.config, "show_errors", change["new"]), names='value')
hspace = IntText(value=self.net.config["hspace"], description="Horizontal space between banks:",
style=style, layout=layout)
hspace.observe(lambda change: self.set_attr(self.net.config, "hspace", change["new"]), names='value')
vspace = IntText(value=self.net.config["vspace"], description="Vertical space between layers:",
style=style, layout=layout)
vspace.observe(lambda change: self.set_attr(self.net.config, "vspace", change["new"]), names='value')
self.feature_bank = Select(description="Details:", value=self.net.config["dashboard.features.bank"],
options=[""] + [layer.name for layer in self.net.layers],
rows=1)
self.feature_bank.observe(self.regenerate, names='value')
self.control_select = Select(
options=['Test', 'Train'],
value=self.net.config["dashboard.dataset"],
description='Dataset:',
rows=1
)
self.control_select.observe(self.change_select, names='value')
column1 = [self.control_select,
self.zoom_slider,
hspace,
vspace,
HBox([checkbox1, checkbox2]),
self.feature_bank,
self.feature_columns,
self.feature_scale
]
## Make layer selectable, and update-able:
column2 = []
layer = self.net.layers[-1]
self.layer_select = Select(description="Layer:", value=layer.name,
options=[layer.name for layer in
self.net.layers],
rows=1)
self.layer_select.observe(self.update_layer_selection, names='value')
column2.append(self.layer_select)
self.layer_visible_checkbox = Checkbox(description="Visible", value=layer.visible, layout=layout)
self.layer_visible_checkbox.observe(self.update_layer, names='value')
column2.append(self.layer_visible_checkbox)
self.layer_colormap = Select(description="Colormap:",
options=[""] + AVAILABLE_COLORMAPS,
value=layer.colormap if layer.colormap is not None else "", layout=layout, rows=1)
self.layer_colormap_image = HTML(value="""<img src="%s"/>""" % self.net._image_to_uri(self.make_colormap_image(layer.colormap)))
self.layer_colormap.observe(self.update_layer, names='value')
column2.append(self.layer_colormap)
column2.append(self.layer_colormap_image)
## get dynamic minmax; if you change it it will set it in layer as override:
minmax = layer.get_act_minmax()
self.layer_mindim = FloatText(description="Leftmost color maps to:", value=minmax[0], style=style)
self.layer_maxdim = FloatText(description="Rightmost color maps to:", value=minmax[1], style=style)
self.layer_mindim.observe(self.update_layer, names='value')
self.layer_maxdim.observe(self.update_layer, names='value')
column2.append(self.layer_mindim)
column2.append(self.layer_maxdim)
output_shape = layer.get_output_shape()
self.layer_feature = IntText(value=layer.feature, description="Feature to show:", style=style)
self.svg_rotate = Checkbox(description="Rotate", value=layer.visible, layout=layout)
self.layer_feature.observe(self.update_layer, names='value')
column2.append(self.layer_feature)
self.svg_rotate = Checkbox(description="Rotate network",
value=self.net.config["svg_rotate"],
style={"description_width": 'initial'},
layout=Layout(width="52%"))
self.svg_rotate.observe(lambda change: self.set_attr(self.net.config, "svg_rotate", change["new"]), names='value')
self.save_config_button = Button(icon="save", layout=Layout(width="10%"))
self.save_config_button.on_click(self.save_config)
column2.append(HBox([self.svg_rotate, self.save_config_button]))
config_children = HBox([VBox(column1, layout=Layout(width="100%")),
VBox(column2, layout=Layout(width="100%"))])
accordion = Accordion(children=[config_children])
accordion.set_title(0, self.net.name)
accordion.selected_index = None
return accordion
def save_config(self, widget=None):
self.net.save_config()
def update_layer(self, change):
"""
Update the layer object, and redisplay.
"""
if self._ignore_layer_updates:
return
## The rest indicates a change to a display variable.
## We need to save the value in the layer, and regenerate
## the display.
# Get the layer:
layer = self.net[self.layer_select.value]
# Save the changed value in the layer:
layer.feature = self.layer_feature.value
layer.visible = self.layer_visible_checkbox.value
## These three, dealing with colors of activations,
## can be done with a prop_one():
if "color" in change["owner"].description.lower():
## Matches: Colormap, lefmost color, rightmost color
## overriding dynamic minmax!
layer.minmax = (self.layer_mindim.value, self.layer_maxdim.value)
layer.minmax = (self.layer_mindim.value, self.layer_maxdim.value)
layer.colormap = self.layer_colormap.value if self.layer_colormap.value else None
self.layer_colormap_image.value = """<img src="%s"/>""" % self.net._image_to_uri(self.make_colormap_image(layer.colormap))
self.prop_one()
else:
self.regenerate()
def update_layer_selection(self, change):
"""
Just update the widgets; don't redraw anything.
"""
## No need to redisplay anything
self._ignore_layer_updates = True
## First, get the new layer selected:
layer = self.net[self.layer_select.value]
## Now, let's update all of the values without updating:
self.layer_visible_checkbox.value = layer.visible
self.layer_colormap.value = layer.colormap if layer.colormap != "" else ""
self.layer_colormap_image.value = """<img src="%s"/>""" % self.net._image_to_uri(self.make_colormap_image(layer.colormap))
minmax = layer.get_act_minmax()
self.layer_mindim.value = minmax[0]
self.layer_maxdim.value = minmax[1]
self.layer_feature.value = layer.feature
self._ignore_layer_updates = False
def visualize_patch(grid,
U,
bounding_box=([0, 0], [1, 1]),
codim=2,
title=None,
legend=None,
separate_colorbars=False,
rescale_colorbars=False,
columns=2):
"""Visualize scalar data associated to a two-dimensional |Grid| as a patch plot.
The grid's |ReferenceElement| must be the triangle or square. The data can either
be attached to the faces or vertices of the grid.
Parameters
----------
grid
The underlying |Grid|.
U
|VectorArray| of the data to visualize. If `len(U) > 1`, the data is visualized
as a time series of plots. Alternatively, a tuple of |VectorArrays| can be
provided, in which case a subplot is created for each entry of the tuple. The
lengths of all arrays have to agree.
bounding_box
A bounding box in which the grid is contained.
codim
The codimension of the entities the data in `U` is attached to (either 0 or 2).
title
Title of the plot.
legend
Description of the data that is plotted. Most useful if `U` is a tuple in which
case `legend` has to be a tuple of strings of the same length.
separate_colorbars
If `True`, use separate colorbars for each subplot.
rescale_colorbars
If `True`, rescale colorbars to data in each frame.
columns
The number of columns in the visualizer GUI in case multiple plots are displayed
at the same time.
"""
assert isinstance(U, VectorArrayInterface) \
or (isinstance(U, tuple)
and all(isinstance(u, VectorArrayInterface) for u in U)
and all(len(u) == len(U[0]) for u in U))
U = (U.to_numpy().astype(np.float64, copy=False),) if isinstance(U, VectorArrayInterface) else \
tuple(u.to_numpy().astype(np.float64, copy=False) for u in U)
if not config.HAVE_MATPLOTLIB:
raise ImportError('cannot visualize: import of matplotlib failed')
if not config.HAVE_IPYWIDGETS and len(U[0]) > 1:
raise ImportError('cannot visualize: import of ipywidgets failed')
if isinstance(legend, str):
legend = (legend, )
assert legend is None or isinstance(legend,
tuple) and len(legend) == len(U)
if len(U) < 2:
columns = 1
class Plot:
def __init__(self):
if separate_colorbars:
if rescale_colorbars:
self.vmins = tuple(np.min(u[0]) for u in U)
self.vmaxs = tuple(np.max(u[0]) for u in U)
else:
self.vmins = tuple(np.min(u) for u in U)
self.vmaxs = tuple(np.max(u) for u in U)
else:
if rescale_colorbars:
self.vmins = (min(np.min(u[0]) for u in U), ) * len(U)
self.vmaxs = (max(np.max(u[0]) for u in U), ) * len(U)
else:
self.vmins = (min(np.min(u) for u in U), ) * len(U)
self.vmaxs = (max(np.max(u) for u in U), ) * len(U)
import matplotlib.pyplot as plt
rows = int(np.ceil(len(U) / columns))
self.figure = figure = plt.figure()
self.plots = plots = []
axes = []
for i, (vmin, vmax) in enumerate(zip(self.vmins, self.vmaxs)):
ax = figure.add_subplot(rows, columns, i + 1)
axes.append(ax)
plots.append(
MatplotlibPatchAxes(figure,
grid,
bounding_box=bounding_box,
vmin=vmin,
vmax=vmax,
codim=codim,
colorbar=separate_colorbars))
if legend:
ax.set_title(legend[i])
plt.tight_layout()
if not separate_colorbars:
figure.colorbar(plots[0].p, ax=axes)
def set(self, U, ind):
if rescale_colorbars:
if separate_colorbars:
self.vmins = tuple(np.min(u[ind]) for u in U)
self.vmaxs = tuple(np.max(u[ind]) for u in U)
else:
self.vmins = (min(np.min(u[ind]) for u in U), ) * len(U)
self.vmaxs = (max(np.max(u[ind]) for u in U), ) * len(U)
for u, plot, vmin, vmax in zip(U, self.plots, self.vmins,
self.vmaxs):
plot.set(u[ind], vmin=vmin, vmax=vmax)
plot = Plot()
plot.set(U, 0)
if len(U[0]) > 1:
from ipywidgets import interact, IntSlider
def set_time(t):
plot.set(U, t)
interact(set_time,
t=IntSlider(min=0, max=len(U[0]) - 1, step=1, value=0))
return plot
def make_controls(self):
layout = Layout(width='100%', height="100%")
button_begin = Button(icon="fast-backward", layout=layout)
button_prev = Button(icon="backward", layout=layout)
button_next = Button(icon="forward", layout=layout)
button_end = Button(icon="fast-forward", layout=layout)
#button_prop = Button(description="Propagate", layout=Layout(width='100%'))
#button_train = Button(description="Train", layout=Layout(width='100%'))
self.button_play = Button(icon="play",
description="Play",
layout=layout)
step_down = Button(icon="sort-down",
layout=Layout(width="95%", height="100%"))
step_up = Button(icon="sort-up",
layout=Layout(width="95%", height="100%"))
up_down = HBox([step_down, step_up],
layout=Layout(width="100%", height="100%"))
refresh_button = Button(icon="refresh",
layout=Layout(width="25%", height="100%"))
self.position_text = IntText(value=0, layout=layout)
self.control_buttons = HBox(
[
button_begin,
button_prev,
#button_train,
self.position_text,
button_next,
button_end,
self.button_play,
up_down,
refresh_button
],
layout=Layout(width='100%', height="100%"))
length = (len(self.net.dataset.train_inputs) -
1) if len(self.net.dataset.train_inputs) > 0 else 0
self.control_slider = IntSlider(description="Dataset index",
continuous_update=False,
min=0,
max=max(length, 0),
value=0,
layout=Layout(width='100%'))
if self.net.config["dashboard.dataset"] == "Train":
length = len(self.net.dataset.train_inputs)
else:
length = len(self.net.dataset.test_inputs)
self.total_text = Label(value="of %s" % length,
layout=Layout(width="100px"))
self.zoom_slider = FloatSlider(
description="Zoom",
continuous_update=False,
min=0,
max=1.0,
style={"description_width": 'initial'},
layout=Layout(width="65%"),
value=self.net.config["svg_scale"]
if self.net.config["svg_scale"] is not None else 0.5)
## Hook them up:
button_begin.on_click(lambda button: self.goto("begin"))
button_end.on_click(lambda button: self.goto("end"))
button_next.on_click(lambda button: self.goto("next"))
button_prev.on_click(lambda button: self.goto("prev"))
self.button_play.on_click(self.toggle_play)
self.control_slider.observe(self.update_slider_control, names='value')
refresh_button.on_click(lambda widget: (self.update_control_slider(
), self.output.clear_output(), self.regenerate()))
step_down.on_click(lambda widget: self.move_step("down"))
step_up.on_click(lambda widget: self.move_step("up"))
self.zoom_slider.observe(self.update_zoom_slider, names='value')
self.position_text.observe(self.update_position_text, names='value')
# Put them together:
controls = VBox([
HBox([self.control_slider, self.total_text],
layout=Layout(height="40px")), self.control_buttons
],
layout=Layout(width='100%'))
#net_page = VBox([control, self.net_svg], layout=Layout(width='95%'))
controls.on_displayed(lambda widget: self.regenerate())
return controls
class Dashboard(VBox):
"""
Build the dashboard for Jupyter widgets. Requires running
in a notebook/jupyterlab.
"""
def __init__(self, net, width="95%", height="550px", play_rate=0.5):
self._ignore_layer_updates = False
self.player = _Player(self, play_rate)
self.player.start()
self.net = net
r = random.randint(1, 1000000)
self.class_id = "picture-dashboard-%s-%s" % (self.net.name, r)
self._width = width
self._height = height
## Global widgets:
style = {"description_width": "initial"}
self.feature_columns = IntText(
description="Detail columns:",
value=self.net.config["dashboard.features.columns"],
min=0,
max=1024,
style=style)
self.feature_scale = FloatText(
description="Detail scale:",
value=self.net.config["dashboard.features.scale"],
min=0.1,
max=10,
style=style)
self.feature_columns.observe(self.regenerate, names='value')
self.feature_scale.observe(self.regenerate, names='value')
## Hack to center SVG as justify-content is broken:
self.net_svg = HTML(value="""<p style="text-align:center">%s</p>""" %
("", ),
layout=Layout(width=self._width,
overflow_x='auto',
overflow_y="auto",
justify_content="center"))
# Make controls first:
self.output = Output()
controls = self.make_controls()
config = self.make_config()
super().__init__([config, controls, self.net_svg, self.output])
def propagate(self, inputs):
"""
Propagate inputs through the dashboard view of the network.
"""
if dynamic_pictures_check():
return self.net.propagate(inputs,
class_id=self.class_id,
update_pictures=True)
else:
self.regenerate(inputs=input)
def goto(self, position):
if len(self.net.dataset.inputs) == 0 or len(
self.net.dataset.targets) == 0:
return
if self.control_select.value == "Train":
length = len(self.net.dataset.train_inputs)
elif self.control_select.value == "Test":
length = len(self.net.dataset.test_inputs)
#### Position it:
if position == "begin":
self.control_slider.value = 0
elif position == "end":
self.control_slider.value = length - 1
elif position == "prev":
if self.control_slider.value - 1 < 0:
self.control_slider.value = length - 1 # wrap around
else:
self.control_slider.value = max(self.control_slider.value - 1,
0)
elif position == "next":
if self.control_slider.value + 1 > length - 1:
self.control_slider.value = 0 # wrap around
else:
self.control_slider.value = min(self.control_slider.value + 1,
length - 1)
self.position_text.value = self.control_slider.value
def change_select(self, change=None):
"""
"""
self.update_control_slider(change)
self.regenerate()
def update_control_slider(self, change=None):
self.net.config["dashboard.dataset"] = self.control_select.value
if len(self.net.dataset.inputs) == 0 or len(
self.net.dataset.targets) == 0:
self.total_text.value = "of 0"
self.control_slider.value = 0
self.position_text.value = 0
self.control_slider.disabled = True
self.position_text.disabled = True
for child in self.control_buttons.children:
if not hasattr(child, "icon") or child.icon != "refresh":
child.disabled = True
return
if self.control_select.value == "Test":
self.total_text.value = "of %s" % len(self.net.dataset.test_inputs)
minmax = (0, max(len(self.net.dataset.test_inputs) - 1, 0))
if minmax[0] <= self.control_slider.value <= minmax[1]:
pass # ok
else:
self.control_slider.value = 0
self.control_slider.min = minmax[0]
self.control_slider.max = minmax[1]
if len(self.net.dataset.test_inputs) == 0:
disabled = True
else:
disabled = False
elif self.control_select.value == "Train":
self.total_text.value = "of %s" % len(
self.net.dataset.train_inputs)
minmax = (0, max(len(self.net.dataset.train_inputs) - 1, 0))
if minmax[0] <= self.control_slider.value <= minmax[1]:
pass # ok
else:
self.control_slider.value = 0
self.control_slider.min = minmax[0]
self.control_slider.max = minmax[1]
if len(self.net.dataset.train_inputs) == 0:
disabled = True
else:
disabled = False
self.control_slider.disabled = disabled
self.position_text.disbaled = disabled
self.position_text.value = self.control_slider.value
for child in self.control_buttons.children:
if not hasattr(child, "icon") or child.icon != "refresh":
child.disabled = disabled
def update_zoom_slider(self, change):
if change["name"] == "value":
self.net.config["svg_scale"] = self.zoom_slider.value
self.regenerate()
def update_position_text(self, change):
# {'name': 'value', 'old': 2, 'new': 3, 'owner': IntText(value=3, layout=Layout(width='100%')), 'type': 'change'}
self.control_slider.value = change["new"]
def get_current_input(self):
if self.control_select.value == "Train" and len(
self.net.dataset.train_targets) > 0:
return self.net.dataset.train_inputs[self.control_slider.value]
elif self.control_select.value == "Test" and len(
self.net.dataset.test_targets) > 0:
return self.net.dataset.test_inputs[self.control_slider.value]
def get_current_targets(self):
if self.control_select.value == "Train" and len(
self.net.dataset.train_targets) > 0:
return self.net.dataset.train_targets[self.control_slider.value]
elif self.control_select.value == "Test" and len(
self.net.dataset.test_targets) > 0:
return self.net.dataset.test_targets[self.control_slider.value]
def update_slider_control(self, change):
if len(self.net.dataset.inputs) == 0 or len(
self.net.dataset.targets) == 0:
self.total_text.value = "of 0"
return
if change["name"] == "value":
self.position_text.value = self.control_slider.value
if self.control_select.value == "Train" and len(
self.net.dataset.train_targets) > 0:
self.total_text.value = "of %s" % len(
self.net.dataset.train_inputs)
if self.net.model is None:
return
if not dynamic_pictures_check():
self.regenerate(inputs=self.net.dataset.train_inputs[
self.control_slider.value],
targets=self.net.dataset.train_targets[
self.control_slider.value])
return
output = self.net.propagate(
self.net.dataset.train_inputs[self.control_slider.value],
class_id=self.class_id,
update_pictures=True)
if self.feature_bank.value in self.net.layer_dict.keys():
self.net.propagate_to_features(
self.feature_bank.value,
self.net.dataset.train_inputs[
self.control_slider.value],
cols=self.feature_columns.value,
scale=self.feature_scale.value,
html=False)
if self.net.config["show_targets"]:
if len(self.net.output_bank_order
) == 1: ## FIXME: use minmax of output bank
self.net.display_component([
self.net.dataset.train_targets[
self.control_slider.value]
],
"targets",
class_id=self.class_id,
minmax=(-1, 1))
else:
self.net.display_component(
self.net.dataset.train_targets[
self.control_slider.value],
"targets",
class_id=self.class_id,
minmax=(-1, 1))
if self.net.config["show_errors"]: ## minmax is error
if len(self.net.output_bank_order) == 1:
errors = np.array(output) - np.array(
self.net.dataset.train_targets[
self.control_slider.value])
self.net.display_component([errors.tolist()],
"errors",
class_id=self.class_id,
minmax=(-1, 1))
else:
errors = []
for bank in range(len(self.net.output_bank_order)):
errors.append(
np.array(output[bank]) -
np.array(self.net.dataset.train_targets[
self.control_slider.value][bank]))
self.net.display_component(errors,
"errors",
class_id=self.class_id,
minmax=(-1, 1))
elif self.control_select.value == "Test" and len(
self.net.dataset.test_targets) > 0:
self.total_text.value = "of %s" % len(
self.net.dataset.test_inputs)
if self.net.model is None:
return
if not dynamic_pictures_check():
self.regenerate(inputs=self.net.dataset.test_inputs[
self.control_slider.value],
targets=self.net.dataset.test_targets[
self.control_slider.value])
return
output = self.net.propagate(
self.net.dataset.test_inputs[self.control_slider.value],
class_id=self.class_id,
update_pictures=True)
if self.feature_bank.value in self.net.layer_dict.keys():
self.net.propagate_to_features(
self.feature_bank.value,
self.net.dataset.test_inputs[
self.control_slider.value],
cols=self.feature_columns.value,
scale=self.feature_scale.value,
html=False)
if self.net.config[
"show_targets"]: ## FIXME: use minmax of output bank
self.net.display_component([
self.net.dataset.test_targets[
self.control_slider.value]
],
"targets",
class_id=self.class_id,
minmax=(-1, 1))
if self.net.config["show_errors"]: ## minmax is error
if len(self.net.output_bank_order) == 1:
errors = np.array(output) - np.array(
self.net.dataset.test_targets[
self.control_slider.value])
self.net.display_component([errors.tolist()],
"errors",
class_id=self.class_id,
minmax=(-1, 1))
else:
errors = []
for bank in range(len(self.net.output_bank_order)):
errors.append(
np.array(output[bank]) -
np.array(self.net.dataset.test_targets[
self.control_slider.value][bank]))
self.net.display_component(errors,
"errors",
class_id=self.class_id,
minmax=(-1, 1))
def toggle_play(self, button):
## toggle
if self.button_play.description == "Play":
self.button_play.description = "Stop"
self.button_play.icon = "pause"
self.player.resume()
else:
self.button_play.description = "Play"
self.button_play.icon = "play"
self.player.pause()
def prop_one(self, button=None):
self.update_slider_control({"name": "value"})
def regenerate(self, button=None, inputs=None, targets=None):
## Protection when deleting object on shutdown:
if isinstance(button,
dict) and 'new' in button and button['new'] is None:
return
## Update the config:
self.net.config["dashboard.features.bank"] = self.feature_bank.value
self.net.config[
"dashboard.features.columns"] = self.feature_columns.value
self.net.config["dashboard.features.scale"] = self.feature_scale.value
inputs = inputs if inputs is not None else self.get_current_input()
targets = targets if targets is not None else self.get_current_targets(
)
features = None
if self.feature_bank.value in self.net.layer_dict.keys(
) and inputs is not None:
if self.net.model is not None:
features = self.net.propagate_to_features(
self.feature_bank.value,
inputs,
cols=self.feature_columns.value,
scale=self.feature_scale.value,
display=False)
svg = """<p style="text-align:center">%s</p>""" % (self.net.to_svg(
inputs=inputs,
targets=targets,
class_id=self.class_id,
highlights={
self.feature_bank.value: {
"border_color": "orange",
"border_width": 30,
}
}))
if inputs is not None and features is not None:
html_horizontal = """
<table align="center" style="width: 100%%;">
<tr>
<td valign="top" style="width: 50%%;">%s</td>
<td valign="top" align="center" style="width: 50%%;"><p style="text-align:center"><b>%s</b></p>%s</td>
</tr>
</table>"""
html_vertical = """
<table align="center" style="width: 100%%;">
<tr>
<td valign="top">%s</td>
</tr>
<tr>
<td valign="top" align="center"><p style="text-align:center"><b>%s</b></p>%s</td>
</tr>
</table>"""
self.net_svg.value = (
html_vertical if self.net.config["svg_rotate"] else
html_horizontal) % (svg, "%s details" %
self.feature_bank.value, features)
else:
self.net_svg.value = svg
def make_colormap_image(self, colormap_name):
from .layers import Layer
if not colormap_name:
colormap_name = get_colormap()
layer = Layer("Colormap", 100)
minmax = layer.get_act_minmax()
image = layer.make_image(np.arange(
minmax[0], minmax[1], .01), colormap_name, {
"pixels_per_unit": 1,
"svg_rotate": self.net.config["svg_rotate"]
}).resize((300, 25))
return image
def set_attr(self, obj, attr, value):
if value not in [{}, None]: ## value is None when shutting down
if isinstance(value, dict):
value = value["value"]
if isinstance(obj, dict):
obj[attr] = value
else:
setattr(obj, attr, value)
## was crashing on Widgets.__del__, if get_ipython() no longer existed
self.regenerate()
def make_controls(self):
layout = Layout(width='100%', height="100%")
button_begin = Button(icon="fast-backward", layout=layout)
button_prev = Button(icon="backward", layout=layout)
button_next = Button(icon="forward", layout=layout)
button_end = Button(icon="fast-forward", layout=layout)
#button_prop = Button(description="Propagate", layout=Layout(width='100%'))
#button_train = Button(description="Train", layout=Layout(width='100%'))
self.button_play = Button(icon="play",
description="Play",
layout=layout)
step_down = Button(icon="sort-down",
layout=Layout(width="95%", height="100%"))
step_up = Button(icon="sort-up",
layout=Layout(width="95%", height="100%"))
up_down = HBox([step_down, step_up],
layout=Layout(width="100%", height="100%"))
refresh_button = Button(icon="refresh",
layout=Layout(width="25%", height="100%"))
self.position_text = IntText(value=0, layout=layout)
self.control_buttons = HBox(
[
button_begin,
button_prev,
#button_train,
self.position_text,
button_next,
button_end,
self.button_play,
up_down,
refresh_button
],
layout=Layout(width='100%', height="100%"))
length = (len(self.net.dataset.train_inputs) -
1) if len(self.net.dataset.train_inputs) > 0 else 0
self.control_slider = IntSlider(description="Dataset index",
continuous_update=False,
min=0,
max=max(length, 0),
value=0,
layout=Layout(width='100%'))
if self.net.config["dashboard.dataset"] == "Train":
length = len(self.net.dataset.train_inputs)
else:
length = len(self.net.dataset.test_inputs)
self.total_text = Label(value="of %s" % length,
layout=Layout(width="100px"))
self.zoom_slider = FloatSlider(
description="Zoom",
continuous_update=False,
min=0,
max=1.0,
style={"description_width": 'initial'},
layout=Layout(width="65%"),
value=self.net.config["svg_scale"]
if self.net.config["svg_scale"] is not None else 0.5)
## Hook them up:
button_begin.on_click(lambda button: self.goto("begin"))
button_end.on_click(lambda button: self.goto("end"))
button_next.on_click(lambda button: self.goto("next"))
button_prev.on_click(lambda button: self.goto("prev"))
self.button_play.on_click(self.toggle_play)
self.control_slider.observe(self.update_slider_control, names='value')
refresh_button.on_click(lambda widget: (self.update_control_slider(
), self.output.clear_output(), self.regenerate()))
step_down.on_click(lambda widget: self.move_step("down"))
step_up.on_click(lambda widget: self.move_step("up"))
self.zoom_slider.observe(self.update_zoom_slider, names='value')
self.position_text.observe(self.update_position_text, names='value')
# Put them together:
controls = VBox([
HBox([self.control_slider, self.total_text],
layout=Layout(height="40px")), self.control_buttons
],
layout=Layout(width='100%'))
#net_page = VBox([control, self.net_svg], layout=Layout(width='95%'))
controls.on_displayed(lambda widget: self.regenerate())
return controls
def move_step(self, direction):
"""
Move the layer stepper up/down through network
"""
options = [""] + [layer.name for layer in self.net.layers]
index = options.index(self.feature_bank.value)
if direction == "up":
new_index = (index + 1) % len(options)
else: ## down
new_index = (index - 1) % len(options)
self.feature_bank.value = options[new_index]
self.regenerate()
def make_config(self):
layout = Layout()
style = {"description_width": "initial"}
checkbox1 = Checkbox(description="Show Targets",
value=self.net.config["show_targets"],
layout=layout,
style=style)
checkbox1.observe(lambda change: self.set_attr(
self.net.config, "show_targets", change["new"]),
names='value')
checkbox2 = Checkbox(description="Errors",
value=self.net.config["show_errors"],
layout=layout,
style=style)
checkbox2.observe(lambda change: self.set_attr(
self.net.config, "show_errors", change["new"]),
names='value')
hspace = IntText(value=self.net.config["hspace"],
description="Horizontal space between banks:",
style=style,
layout=layout)
hspace.observe(lambda change: self.set_attr(self.net.config, "hspace",
change["new"]),
names='value')
vspace = IntText(value=self.net.config["vspace"],
description="Vertical space between layers:",
style=style,
layout=layout)
vspace.observe(lambda change: self.set_attr(self.net.config, "vspace",
change["new"]),
names='value')
self.feature_bank = Select(
description="Details:",
value=self.net.config["dashboard.features.bank"],
options=[""] + [layer.name for layer in self.net.layers],
rows=1)
self.feature_bank.observe(self.regenerate, names='value')
self.control_select = Select(
options=['Test', 'Train'],
value=self.net.config["dashboard.dataset"],
description='Dataset:',
rows=1)
self.control_select.observe(self.change_select, names='value')
column1 = [
self.control_select, self.zoom_slider, hspace, vspace,
HBox([checkbox1, checkbox2]), self.feature_bank,
self.feature_columns, self.feature_scale
]
## Make layer selectable, and update-able:
column2 = []
layer = self.net.layers[-1]
self.layer_select = Select(
description="Layer:",
value=layer.name,
options=[layer.name for layer in self.net.layers],
rows=1)
self.layer_select.observe(self.update_layer_selection, names='value')
column2.append(self.layer_select)
self.layer_visible_checkbox = Checkbox(description="Visible",
value=layer.visible,
layout=layout)
self.layer_visible_checkbox.observe(self.update_layer, names='value')
column2.append(self.layer_visible_checkbox)
self.layer_colormap = Select(
description="Colormap:",
options=[""] + AVAILABLE_COLORMAPS,
value=layer.colormap if layer.colormap is not None else "",
layout=layout,
rows=1)
self.layer_colormap_image = HTML(
value="""<img src="%s"/>""" %
self.net._image_to_uri(self.make_colormap_image(layer.colormap)))
self.layer_colormap.observe(self.update_layer, names='value')
column2.append(self.layer_colormap)
column2.append(self.layer_colormap_image)
## get dynamic minmax; if you change it it will set it in layer as override:
minmax = layer.get_act_minmax()
self.layer_mindim = FloatText(description="Leftmost color maps to:",
value=minmax[0],
style=style)
self.layer_maxdim = FloatText(description="Rightmost color maps to:",
value=minmax[1],
style=style)
self.layer_mindim.observe(self.update_layer, names='value')
self.layer_maxdim.observe(self.update_layer, names='value')
column2.append(self.layer_mindim)
column2.append(self.layer_maxdim)
output_shape = layer.get_output_shape()
self.layer_feature = IntText(value=layer.feature,
description="Feature to show:",
style=style)
self.svg_rotate = Checkbox(description="Rotate",
value=layer.visible,
layout=layout)
self.layer_feature.observe(self.update_layer, names='value')
column2.append(self.layer_feature)
self.svg_rotate = Checkbox(description="Rotate network",
value=self.net.config["svg_rotate"],
style={"description_width": 'initial'},
layout=Layout(width="52%"))
self.svg_rotate.observe(lambda change: self.set_attr(
self.net.config, "svg_rotate", change["new"]),
names='value')
self.save_config_button = Button(icon="save",
layout=Layout(width="10%"))
self.save_config_button.on_click(self.save_config)
column2.append(HBox([self.svg_rotate, self.save_config_button]))
config_children = HBox([
VBox(column1, layout=Layout(width="100%")),
VBox(column2, layout=Layout(width="100%"))
])
accordion = Accordion(children=[config_children])
accordion.set_title(0, self.net.name)
accordion.selected_index = None
return accordion
def save_config(self, widget=None):
self.net.save_config()
def update_layer(self, change):
"""
Update the layer object, and redisplay.
"""
if self._ignore_layer_updates:
return
## The rest indicates a change to a display variable.
## We need to save the value in the layer, and regenerate
## the display.
# Get the layer:
layer = self.net[self.layer_select.value]
# Save the changed value in the layer:
layer.feature = self.layer_feature.value
layer.visible = self.layer_visible_checkbox.value
## These three, dealing with colors of activations,
## can be done with a prop_one():
if "color" in change["owner"].description.lower():
## Matches: Colormap, lefmost color, rightmost color
## overriding dynamic minmax!
layer.minmax = (self.layer_mindim.value, self.layer_maxdim.value)
layer.minmax = (self.layer_mindim.value, self.layer_maxdim.value)
layer.colormap = self.layer_colormap.value if self.layer_colormap.value else None
self.layer_colormap_image.value = """<img src="%s"/>""" % self.net._image_to_uri(
self.make_colormap_image(layer.colormap))
self.prop_one()
else:
self.regenerate()
def update_layer_selection(self, change):
"""
Just update the widgets; don't redraw anything.
"""
## No need to redisplay anything
self._ignore_layer_updates = True
## First, get the new layer selected:
layer = self.net[self.layer_select.value]
## Now, let's update all of the values without updating:
self.layer_visible_checkbox.value = layer.visible
self.layer_colormap.value = layer.colormap if layer.colormap != "" else ""
self.layer_colormap_image.value = """<img src="%s"/>""" % self.net._image_to_uri(
self.make_colormap_image(layer.colormap))
minmax = layer.get_act_minmax()
self.layer_mindim.value = minmax[0]
self.layer_maxdim.value = minmax[1]
self.layer_feature.value = layer.feature
self._ignore_layer_updates = False
# Pie chart, where the slices will be ordered and plotted counter-clockwise:
labels = 'Agree', 'Disagree'
sizes = [np.sum(discrepancyMapping==1),np.sum(discrepancyMapping==0)]
fig1, ax1 = plt.subplots()
ax1.pie(sizes, labels=labels, autopct='%1.3f%%',
shadow=True, startangle=90)
ax1.axis('equal') # Equal aspect ratio ensures that pie is drawn as a circle.
plt.show()
#update the plot via input values
def update(xOffset, yOffset):
naieveOceanMaskMoved = np.roll(naieveOceanMask,yOffset,0)
naieveOceanMaskMoved = np.roll(naieveOceanMaskMoved,xOffset,1)
plot_mapDiscrepancy(obtainedOceanMask,naieveOceanMaskMoved)
#establish interactivity
interact(update, xOffset=IntSlider(min=-30, max=30, step=1,continuous_update=False), yOffset=IntSlider(min=-30, max=30, step=1,continuous_update=False))
# It seems that the lowest mismatch percentage you can get is around 17%, which occurs at -28 x offset and -9 y offset. What accounts for the remaining mismatch? Part of it likely has to do with how our mask was made (and the threshold value we chose), and that it likely wasnn't entirely perfect.
#
# One major source of discrepancy is the fact that sea ice is not the color of water, but is not included in the purpose-made land mask we obtained either. Hence our algorithm considers it "land" (because it is not the color of water), even though the gray colored mask (the provided mask) is specific to land (which ice does not count as).
#
# Finally, one final source is likely that the two maps, even if they were to have their equator and prime maridian lined up, may not be warped (reshaped from a surface that covers a sphere) in exactly the same way. Theoretically we could attempt to apply a **nonlinear warp** (we'll come back to this concept in later lessons) to try and align the two images, but this would be beyond the scope of this introduction to digital image representations and masks.
# #### How this relates to neuroimaging
#
#
# In the next lesson we will see a more complex version of a mask, one which is not binary, but instead features multiple different categories. That is, instead of just trying to label one thing (i.e. "water") we will try and use the same general approach to label multiple things. This capability is something that is used in neuroimaging quite frequently. For example, we often wish to label particular parts of a neuroimaging scan as being some specific part of the brain (e.g. "frontal lobe", "angular gyrus", or "thalamus" etc.). We'll explore this possibility in 2D with another map in the next lesson. In later lessons we'll explicitly look at these "multi category masks" (i.e. **parcellations**) in brains.
def nb_view_patches(Yr,
A,
C,
S,
b,
f,
d1,
d2,
YrA=None,
image_neurons=None,
thr=0.99,
denoised_color=None,
cmap='jet'):
"""
Interactive plotting utility for ipython notebook
Args:
Yr: np.ndarray
movie
A,C,b,f: np.ndarrays
outputs of matrix factorization algorithm
d1,d2: floats
dimensions of movie (x and y)
YrA: np.ndarray
ROI filtered residual as it is given from update_temporal_components
If not given, then it is computed (K x T)
image_neurons: np.ndarray
image to be overlaid to neurons (for instance the average)
thr: double
threshold regulating the extent of the displayed patches
denoised_color: string or None
color name (e.g. 'red') or hex color code (e.g. '#F0027F')
cmap: string
name of colormap (e.g. 'viridis') used to plot image_neurons
"""
# PREPROCESSING
nr, T = C.shape
nA2 = np.ravel(np.power(A,
2).sum(0)) if type(A) == np.ndarray else np.ravel(
A.power(2).sum(0))
b = np.squeeze(b)
f = np.squeeze(f)
if YrA is None:
Y_r = np.array(
spdiags(old_div(1, nA2), 0, nr, nr) *
(A.T * np.matrix(Yr) -
(A.T * np.matrix(b[:, np.newaxis])) * np.matrix(f[np.newaxis]) -
A.T.dot(A) * np.matrix(C)) + C)
else:
Y_r = C + YrA
x = np.arange(T)
if image_neurons is None:
image_neurons = A.mean(1).reshape((d1, d2), order='F')
coors = get_contours(A, (d1, d2), thr)
cc1 = [cor['coordinates'][:, 0] for cor in coors]
cc2 = [cor['coordinates'][:, 1] for cor in coors]
c1 = cc1[0]
c2 = cc2[0]
# PLOTTING
fig, axes = plt.subplots(2)
axes[0].imshow(image_neurons, cmap='gray')
axes[0].set_title('Neural map')
axes[1].plot(C[0], label='C: raw traces', c='blue')
axes[1].plot(Y_r[0], label='Y_r: residuals', c='red')
axes[1].plot(S[0], label='S: deconvolved activity', c='green')
plt.legend()
axes[1].set_xlabel('t [frames]')
# WIDGETS
neuron_nr_slider = IntSlider(description='Neuron Number',
value=0,
min=0,
max=len(C) - 1)
def neuron_nr_handler(*args):
i = neuron_nr_slider.value
axes[1].clear()
axes[1].plot(C[i], label='C: raw traces', c='blue')
axes[1].plot(Y_r[i], label='Y_r: residuals', c='red')
axes[1].plot(S[i], label='S: deconvolved activity', c='green')
plt.legend()
axes[1].set_xlabel('t [frames]')
neuron_nr_slider.observe(neuron_nr_handler, 'value')
widgets = [neuron_nr_slider]
return fig, widgets
class NGLDisplay:
"""Structure display class
Provides basic structure/trajectory display
in the notebook and optional gui which can be used to enhance its
usability. It is also possible to extend the functionality of the
particular instance of the viewer by adding further widgets
manipulating the structure.
"""
def __init__(self, atoms, xsize=500, ysize=500):
import nglview
import nglview.color
from ipywidgets import Dropdown, FloatSlider, IntSlider, HBox, VBox
self.atoms = atoms
if isinstance(atoms[0], Atoms):
# Assume this is a trajectory or struct list
self.view = nglview.show_asetraj(atoms, default=False)
self.frm = IntSlider(value=0, min=0, max=len(atoms) - 1)
self.frm.observe(self._update_frame)
self.struct = atoms[0]
else:
# Assume this is just a single structure
self.view = nglview.show_ase(atoms, default=False)
self.struct = atoms
self.frm = None
self.colors = {}
self.view._remote_call('setSize', target='Widget',
args=['%dpx' % (xsize,), '%dpx' % (ysize,)])
self.view.add_unitcell()
self.view.add_spacefill()
self.view.camera = 'orthographic'
self.view.parameters = { "clipDist": 0 }
self.view.center()
self.asel = Dropdown(options=['All'] +
list(set(self.struct.get_chemical_symbols())),
value='All', description='Show')
self.csel = Dropdown(options=nglview.color.COLOR_SCHEMES,
value='element', description='Color scheme')
self.rad = FloatSlider(value=0.5, min=0.0, max=1.5, step=0.01,
description='Ball size')
self.asel.observe(self._select_atom)
self.csel.observe(self._update_repr)
self.rad.observe(self._update_repr)
self.view.update_spacefill(radiusType='covalent',
radiusScale=0.5,
color_scheme=self.csel.value,
color_scale='rainbow')
wdg = [self.asel, self.csel, self.rad]
if self.frm:
wdg.append(self.frm)
self.gui = HBox([self.view, VBox(wdg)])
# Make useful shortcuts for the user of the class
self.gui.view = self.view
self.gui.control_box = self.gui.children[1]
self.gui.custom_colors = self.custom_colors
def _update_repr(self, chg=None):
self.view.update_spacefill(radiusType='covalent',
radiusScale=self.rad.value,
color_scheme=self.csel.value,
color_scale='rainbow')
def _update_frame(self, chg=None):
self.view.frame = self.frm.value
return
def _select_atom(self, chg=None):
sel = self.asel.value
self.view.remove_spacefill()
for e in set(self.struct.get_chemical_symbols()):
if (sel == 'All' or e == sel):
if e in self.colors:
self.view.add_spacefill(selection='#' + e,
color=self.colors[e])
else:
self.view.add_spacefill(selection='#' + e)
self._update_repr()
def custom_colors(self, clr=None):
"""
Define custom colors for some atoms. Pass a dictionary of the form
{'Fe':'red', 'Au':'yellow'} to the function.
To reset the map to default call the method without parameters.
"""
if clr:
self.colors = clr
else:
self.colors = {}
self._select_atom()
from ipywidgets import IntSlider, Text, VBox
from IPython.display import display
s = IntSlider(max=200, value=100)
t = Text()
def update_text(change):
t.value = str(s.value ** 2)
s.observe(update_text, names='value')
display(VBox([s, t]))
def _create_controls(
self,
time: Union[pd.DatetimeIndex, pd.TimedeltaIndex, List[pd.Timestamp]],
reference_system: str,
show_data_labels: bool,
show_labels: bool,
show_origins: bool,
show_traces: bool,
show_vectors: bool,
show_wireframe: bool,
):
"""Create the control panel.
Parameters
----------
time : pandas.DatetimeIndex, pandas.TimedeltaIndex, List[pandas.Timestamp], or \
LocalCoordinateSystem
The time steps that should be plotted initially
reference_system : str
Name of the initial reference system. If `None` is provided, the root system
of the `CoordinateSystemManager` instance will be used
show_data_labels : bool
If `True`, the data labels will be shown initially
show_labels : bool
If `True`, the coordinate system labels will be shown initially
show_origins : bool
If `True`, the coordinate systems' origins will be shown initially
show_traces : bool
If `True`, the coordinate systems' traces will be shown initially
show_vectors : bool
If `True`, the coordinate systems' axis vectors will be shown initially
show_wireframe : bool
If `True`, spatial data containing mesh data will be drawn as wireframe
"""
num_times = 1
disable_time_widgets = True
lo = Layout(width="200px")
# create widgets
if time is not None:
num_times = len(time)
disable_time_widgets = False
play = Play(
min=0,
max=num_times - 1,
value=self._current_time_index,
step=1,
)
time_slider = IntSlider(
min=0,
max=num_times - 1,
value=self._current_time_index,
description="Time:",
)
reference_dropdown = Dropdown(
options=self._csm.coordinate_system_names,
value=reference_system,
description="Reference:",
disabled=False,
)
data_dropdown = Dropdown(
options=SpatialDataVisualizer.visualization_methods,
value="auto",
description="data repr.:",
disabled=False,
layout=lo,
)
lo = Layout(width="200px")
vectors_cb = Checkbox(value=show_vectors,
description="show vectors",
layout=lo)
origin_cb = Checkbox(value=show_origins,
description="show origins",
layout=lo)
traces_cb = Checkbox(value=show_traces,
description="show traces",
layout=lo)
labels_cb = Checkbox(value=show_labels,
description="show labels",
layout=lo)
wf_cb = Checkbox(value=show_wireframe,
description="show wireframe",
layout=lo)
data_labels_cb = Checkbox(value=show_data_labels,
description="show data labels",
layout=lo)
jslink((play, "value"), (time_slider, "value"))
play.disabled = disable_time_widgets
time_slider.disabled = disable_time_widgets
# callback functions
def _reference_callback(change):
self.update_reference_system(change["new"])
def _time_callback(change):
self.update_time_index(change["new"])
def _vectors_callback(change):
self.show_vectors(change["new"])
def _origins_callback(change):
self.show_origins(change["new"])
def _traces_callback(change):
self.show_traces(change["new"])
def _labels_callback(change):
self.show_labels(change["new"])
def _data_callback(change):
self.set_data_visualization_method(change["new"])
def _data_labels_callback(change):
self.show_data_labels(change["new"])
def _wireframe_callback(change):
self.show_wireframes(change["new"])
# register callbacks
time_slider.observe(_time_callback, names="value")
reference_dropdown.observe(_reference_callback, names="value")
vectors_cb.observe(_vectors_callback, names="value")
origin_cb.observe(_origins_callback, names="value")
traces_cb.observe(_traces_callback, names="value")
labels_cb.observe(_labels_callback, names="value")
data_dropdown.observe(_data_callback, names="value")
data_labels_cb.observe(_data_labels_callback, names="value")
wf_cb.observe(_wireframe_callback, names="value")
# create control panel
row_1 = HBox([time_slider, play, reference_dropdown])
row_2 = HBox([vectors_cb, origin_cb, traces_cb, labels_cb])
if len(self._data_vis) > 0:
row_3 = HBox([data_dropdown, wf_cb, data_labels_cb])
return VBox([row_1, row_2, row_3])
return VBox([row_1, row_2])
def _intermediate(target):
# based on the target mask get the labels for the rest of the interactors
target_mask = self.region_masks[target]
def _interact_object(target_mask, pred, label, threshold=0.5):
button, text = _create_button_text_display(
'object_comparison.png')
# get the target and prediction images
pred_mask = self.region_masks[pred]
# calculate the iou matrix
iou = intersection_over_union(target_mask, pred_mask)[0]
# threshold the iou
match = iou > threshold
# create a copy of the raw image in rgb
im = gray_to_rgb(normalize_image(self.region_im.copy()))
# each row in the match array represents a target object
match_row = match[label - 1, :]
# get prediction labels where there is intersection
_pred_labels = np.where(match_row)[0]
# color codes as before - white for agreement, red for false positive, and blue for false negative
target_mask = target_mask == label
im[target_mask, :] = [0, 0, 255]
# get indices where target mask is True
row_i, col_i = np.where(target_mask)
# color the matched predicted labels as red
for _pred_label in _pred_labels:
pred_mask = pred_mask == _pred_label + 1
im[pred_mask, :] = [255, 0, 0]
im[pred_mask & target_mask, :] = [255, 255, 255]
# get indices where pred mask is True and append row_i, col_i
row_j, col_j = np.where(pred_mask)
row_i, col_i = np.concatenate(
(row_i, row_j)), np.concatenate((col_i, col_j))
# chop the region for a closer look =)
# pad the edges of teh chopped regionpixels on each edge but threshold
min_y, min_x, max_y, max_x = np.min(row_i), np.min(
col_i), np.max(row_i), np.max(col_i)
pad = 30
min_y = max(0, min_y - pad)
min_x = max(0, min_x - pad)
max_x += pad
max_y += pad
chopped_im = im[min_y:max_y, min_x:max_x, :]
print(
'White -> Agreement, Blue -> False Negative, Red -> False Positive'
)
print(
f'{len(pred_labels)} predicted object(s) overlap that pass iou threshold'
)
# plot the images
fig, ax = plt.subplots(ncols=2, figsize=(15, 7))
ax[0].imshow(im)
ax[0].xaxis.set_visible(False)
ax[0].yaxis.set_visible(False)
ax[1].imshow(chopped_im)
ax[1].xaxis.set_visible(False)
ax[1].yaxis.set_visible(False)
plt.show()
button.on_click(
partial(self.on_button_clicked,
text_widget=text,
fig_to_save=fig))
display(widgets.HBox([text, button]))
_ = interact(_interact_object,
target_mask=fixed(target_mask),
pred=Dropdown(options=pred_labels,
value=pred_label,
description='Prediction mask:',
style=DESC_STYLES),
label=IntSlider(
value=1,
min=1,
max=len(np.unique(target_mask)) - 1,
continuous_update=False,
description='Nuclei Label',
style={'description_width': 'initial'}),
threshold=FloatSlider(value=0.5,
min=0.,
max=1.,
continuous_update=False))
def _default_plotter(self, mask_background=False, **kwargs):
"""
Plot three orthogonal views.
This is called by nifti_plotter, you shouldn't call it directly.
"""
plt.gcf().clear()
plt.ioff() # disable interactive mode
data_array = self.data.get_data()
if not ((data_array.ndim == 3) or (data_array.ndim == 4)):
raise ValueError('Input image should be 3D or 4D')
# mask the background
if mask_background:
# TODO: add the ability to pass 'mne' to use a default brain mask
# TODO: split this out into a different function
if data_array.ndim == 3:
labels, n_labels = scipy.ndimage.measurements.label(
(np.round(data_array) == 0))
else: # 4D
labels, n_labels = scipy.ndimage.measurements.label(
(np.round(data_array).max(axis=3) == 0))
mask_labels = [
lab for lab in range(1, n_labels + 1)
if (np.any(labels[[0, -1], :, :] == lab)
| np.any(labels[:, [0, -1], :] == lab)
| np.any(labels[:, :, [0, -1]] == lab))
]
if data_array.ndim == 3:
data_array = np.ma.masked_where(np.isin(labels, mask_labels),
data_array)
else:
data_array = np.ma.masked_where(
np.broadcast_to(
np.isin(labels, mask_labels)[:, :, :, np.newaxis],
data_array.shape), data_array)
# init sliders for the various dimensions
for dim, label in enumerate(['x', 'y', 'z']):
if label not in kwargs.keys():
kwargs[label] = IntSlider(value=(data_array.shape[dim] - 1) /
2,
min=0,
max=data_array.shape[dim] - 1,
continuous_update=False)
if (data_array.ndim == 3) or (data_array.shape[3] == 1):
kwargs['t'] = fixed(0) # time is fixed
else: # 4D
kwargs['t'] = IntSlider(value=0,
min=0,
max=data_array.shape[3] - 1,
continuous_update=False)
interact(self._plot_slices, data=fixed(data_array), **kwargs)
plt.close() # clear plot
plt.ion() # return to interactive state
dot_data = tree.export_graphviz(
clf,
out_file=None,
feature_names=X.columns,
class_names=list(y_encoder.classes_),
filled=True,
rounded=True,
special_characters=True,
)
graph = graphviz.Source(dot_data)
display(SVG(graph.pipe(format='svg')))
inter = interactive(
plot_tree,
max_depth=IntSlider(min=1, max=15),
min_samples_leaf=IntSlider(min=1, max=25, value=10),
)
display(inter)
# -
# # Explorando las particiones
#
# [dtreeviz](https://github.com/parrt/dtreeviz) permite explorar un poco mas los árboles. Es un poco más visual que su contraparte de sklearn. Veamos las reglas aprendidas por cada nodo.
# +
X, y, df, y_encoder = feature_engineering(dataset)
clf = get_tree(X, y)
viz = dtreeviz.dtreeviz(
clf,
def _init_widget(self):
state = self._state
widget = dict()
fig = dict(x=self._create_slice_fig(),
y=self._create_slice_fig(),
z=self._create_slice_fig())
widget['fig'] = fig
topomap_fig = dict(mag=create_topomap_fig(),
grad=create_topomap_fig(),
eeg=create_topomap_fig())
widget['topomap_fig'] = topomap_fig
label = dict()
label['axis'] = dict(x=HTML(f"<b>{state['label_text']['x']}</b>"),
y=HTML(f"<b>{state['label_text']['y']}</b>"),
z=HTML(f"<b>{state['label_text']['z']}</b>"))
label['topomap_mag'] = HTML(
f"<b>{state['label_text']['topomap_mag']}</b>")
label['topomap_grad'] = HTML(
f"<b>{state['label_text']['topomap_grad']}</b>")
label['topomap_eeg'] = HTML(
f"<b>{state['label_text']['topomap_eeg']}</b>")
label['dipole_pos'] = Label('Not set')
label['dipole_ori'] = Label('Not set')
label['dipole_pos_'] = Label('Dipole origin:')
label['dipole_ori_'] = Label('Dipole orientation:')
label['status'] = Label('Status:')
label['updating'] = Label('Ready.')
widget['label'] = label
widget['tab'] = Tab(layout=Layout(width='700'))
toggle_buttons = dict(
mode_selector=ToggleButtons(options=[
'Slice Browser', 'Set Dipole Origin', 'Set Dipole Orientation'
],
button_style='primary',
layout=Layout(width='auto')))
toggle_buttons['mode_selector'].observe(self._handle_view_mode_change,
'value')
widget['toggle_buttons'] = toggle_buttons
widget['reset_button'] = Button(description='Reset',
button_style='danger',
layout=Layout(width='auto'))
widget['reset_button'].on_click(self._handle_reset_button_click)
checkbox = dict(exact_solution=Checkbox(
value=self._exact_solution,
description='Exact solution (slow!)',
tooltip='Calculate an exact forward projection. This is SLOW!'))
checkbox['exact_solution'].observe(self._toggle_exact_solution,
'value')
widget['checkbox'] = checkbox
widget['amplitude_slider'] = IntSlider(value=int(
self._state['dipole_amplitude'] * 1e9),
min=5,
max=100,
step=5,
continuous_update=False)
widget['amplitude_slider'].observe(self._handle_amp_change,
names='value')
widget['label']['amplitude_slider'] = Label('Dipole amplitude in nAm')
widget['quickstart_text'] = HTML(value=(
'<ul>'
'<li>Select the desired brain slices in the '
'<b>Slice Browser (or use a preset).</b></li>'
'<li>Choose the location of the dipole via '
'<b>Set Dipole Origin.</b></li>'
'<li>Orient the dipole via '
'<b>Set Dipole Orientation.</b></li>'
'<li>Adjust the <b>dipole amplitude</b> '
'using the slider below the topographic maps.</li>'
'</ul>\n'
'<p><b>This application is still '
'<a href="https://github.com/hoechenberger/dipoles_demo/issues/26">'
'work in progress</a>.</b></p>'))
widget['quickstart_accordion'] = Accordion(
children=[widget['quickstart_text']])
widget['quickstart_accordion'].set_title(0, 'Quickstart')
widget['preset_dropdown'] = Dropdown(
options=['Select Preset…', 'Preset 1', 'Preset 2', 'Preset 3'],
value='Select Preset…',
layout=Layout(width='auto'))
widget['preset_dropdown'].observe(self._handle_preset_selection_change,
'value')
widget['title'] = HTML(value='<h2>Dipole Simulator</h2>')
widget['output'] = output_widget
return widget
def view_structure(pdbIds,
bioAssembly=False,
style='cartoon',
color='spectrum'):
'''A wrapper function that simply displays a list of protein structures using
ipywidgets and py3Dmol
Parameters
----------
pdbIds : list
A list of PDBIDs to display
bioAssembly : bool
display bioAssembly
style : str, optional
Style of 3D structure (stick line cross sphere cartoon VDW MS)
color : str, optional
Color of 3D structure
'''
if type(pdbIds) == str:
pdbIds = [pdbIds]
def view3d(i=0):
'''Simple structure viewer that uses py3Dmol to view PDB structure by
indexing the list of PDBids
Parameters
----------
i (int): index of the protein if a list of PDBids
'''
print(f"PdbID: {pdbIds[i]}, Style: {style}")
if '.' not in pdbIds[i]:
viewer = py3Dmol.view(query='pdb:' + pdbIds[i],
options={'doAssembly': bioAssembly})
viewer.setStyle({style: {'color': color}})
viewer.setStyle({'hetflag': True},
{'stick': {
'singleBond': False
}})
else:
pdbid, chainid = pdbIds[i].split('.')
viewer = py3Dmol.view(query='pdb:' + pdbid,
options={'doAssembly': bioAssembly})
viewer.setStyle({})
viewer.setStyle({'chain': chainid}, {style: {'color': color}})
viewer.setStyle({
'chain': chainid,
'hetflag': True
}, {'stick': {
'singleBond': False
}})
viewer.zoomTo({'chain': chainid})
return viewer.show()
s_widget = IntSlider(min=0,
max=len(pdbIds) - 1,
description='Structure',
continuous_update=False)
return interact(view3d, i=s_widget)
class Dashboard:
def __init__(self, df, map_file, province_id_to_name) -> None:
self.df = df
self.yearly_df = self.df.pipe(self.reshape_with_period_cols)
self.years = list(self.yearly_df.columns)
self.sc_x = LinearScale()
self.sc_y = LinearScale()
self.col_scale = ColorScale(scheme="Greens")
self.geomap = self.create_map(map_file)
self.lineplot = self.create_lineplot()
self.province_id_to_name = province_id_to_name.copy()
self.year_slider = IntSlider(
description="year",
min=1995,
max=2001,
continuous_update=False,
layout=Layout(width="100%"),
)
def create_map(self, map_file):
first_year = self.years[0]
first_provincial_income_proportion = self.get_provincial_income_proportion(
first_year)
sc_geo = Mercator(scale_factor=7000, center=(5.5, 53.0))
tooltip = Tooltip(fields=["name"], labels=["province"])
return Map(
map_data=topo_load(map_file),
scales={
"projection": sc_geo,
"color": self.col_scale
},
colors={"default_color": "Grey"},
color=first_provincial_income_proportion,
tooltip=tooltip,
interactions={
"click": "select",
"hover": "tooltip"
},
visible=True,
)
def create_map_figure(self):
ax_col = ColorAxis(scale=self.col_scale,
label="ratio",
tick_format="0.2f")
return Figure(
marks=[self.geomap],
axes=[ax_col],
title="Wealth of The Netherlands",
layout={
"min_width": "400px",
"width": "auto",
"min_height": "400px",
"width": "auto",
},
)
def create_lineplot(self):
return Lines(
x=self.years,
y=[],
scales={
"x": self.sc_x,
"y": self.sc_y
},
display_legend=True,
)
def create_lineplot_figure(self):
ax_x = Axis(scale=self.sc_x, label="Year", tick_values=self.years)
ax_y = Axis(scale=self.sc_y,
orientation="vertical",
label="Thousands (Euro)")
return Figure(
marks=[self.lineplot],
axes=[ax_x, ax_y],
title="Income per Year (Click a province to show)",
layout={
"min_width": "400px",
"width": "auto",
"min_height": "400px",
"height": "auto",
},
)
def plot_yearly_income_per_province(self, *_):
"""
on_event, when a province is clicked
"""
if self.geomap.selected is not None and len(self.geomap.selected) > 0:
selected_provinces = self.geomap.selected
self.lineplot.y = self.yearly_df.loc[selected_provinces]
self.lineplot.labels = [
self.province_id_to_name[province_id]
for province_id in selected_provinces
]
else:
self.lineplot.labels = []
self.lineplot.y = []
def update_income(self, *_):
"""
on_event, when a year slider is changed
"""
year = self.year_slider.value
id_to_income = self.get_provincial_income_proportion(year)
geomap_color_scale = self.geomap.scales["color"]
geomap_color_scale.min = min(id_to_income.values())
geomap_color_scale.max = max(id_to_income.values())
self.geomap.color = id_to_income
def reshape_with_period_cols(_, input_df):
"""
To get a yearly dataframe, in which years are pivoted as columns
"""
input_df = input_df.pivot(index="province_id",
columns="period")[["income"]]
# Drop higher column level, i.e income
input_df.columns = input_df.columns.droplevel()
return input_df
def get_provincial_income_proportion(self, year: int) -> Dict[int, float]:
is_within_year = self.df["period"] == year
yearly_income = self.df[is_within_year]
income_proportion = yearly_income["income"] / sum(
yearly_income["income"])
id_to_income = dict(
zip(yearly_income["province_id"], income_proportion))
return id_to_income
def build(self):
self.geomap.observe(self.plot_yearly_income_per_province, "selected")
play_button = Play(min=1995,
max=2001,
interval=1000,
layout=Layout(width="100%"))
self.year_slider.observe(self.update_income, "value")
jslink((play_button, "value"), (self.year_slider, "value"))
map_figure = self.create_map_figure()
lineplot_figure = self.create_lineplot_figure()
return VBox([
HBox([play_button, self.year_slider]), map_figure, lineplot_figure
])
class SequenceViewer(VBox):
"""
SequenceViewer
Arguments:
title (str) - Title of sequence
function (callable) - takes an index 0 to length - 1. Function should
a displayable or list of displayables
length (int) - total number of frames in sequence
play_rate (float) - seconds to wait between frames when auto-playing.
Optional. Default is 0.5 seconds.
>>> def function(index):
... return [None]
>>> sv = SequenceViewer("Title", function, 10)
>>> ## Do this manually for testing:
>>> sv.initialize()
None
>>> ## Testing:
>>> class Dummy:
... def update(self, result):
... return result
>>> sv.displayers = [Dummy()]
>>> print("Testing"); sv.goto("begin") # doctest: +ELLIPSIS
Testing...
>>> print("Testing"); sv.goto("end") # doctest: +ELLIPSIS
Testing...
>>> print("Testing"); sv.goto("prev") # doctest: +ELLIPSIS
Testing...
>>> print("Testing"); sv.goto("next") # doctest: +ELLIPSIS
Testing...
"""
def __init__(self, title, function, length, play_rate=0.5):
self.player = _Player(self, play_rate)
self.player.start()
self.title = title
self.function = function
self.length = length
self.output = Output()
self.position_text = IntText(value=0, layout=Layout(width="100%"))
self.total_text = Label(value="of %s" % self.length,
layout=Layout(width="100px"))
controls = self.make_controls()
super().__init__([controls, self.output])
def goto(self, position):
#### Position it:
if position == "begin":
self.control_slider.value = 0
elif position == "end":
self.control_slider.value = self.length - 1
elif position == "prev":
if self.control_slider.value - 1 < 0:
self.control_slider.value = self.length - 1 # wrap around
else:
self.control_slider.value = max(self.control_slider.value - 1,
0)
elif position == "next":
if self.control_slider.value + 1 > self.length - 1:
self.control_slider.value = 0 # wrap around
else:
self.control_slider.value = min(self.control_slider.value + 1,
self.length - 1)
elif isinstance(position, int):
self.control_slider.value = position
self.position_text.value = self.control_slider.value
def toggle_play(self, button):
## toggle
if self.button_play.description == "Play":
self.button_play.description = "Stop"
self.button_play.icon = "pause"
self.player.resume()
else:
self.button_play.description = "Play"
self.button_play.icon = "play"
self.player.pause()
def make_controls(self):
button_begin = Button(icon="fast-backward",
layout=Layout(width='100%'))
button_prev = Button(icon="backward", layout=Layout(width='100%'))
button_next = Button(icon="forward", layout=Layout(width='100%'))
button_end = Button(icon="fast-forward", layout=Layout(width='100%'))
self.button_play = Button(icon="play",
description="Play",
layout=Layout(width="100%"))
self.control_buttons = HBox([
button_begin,
button_prev,
self.position_text,
button_next,
button_end,
self.button_play,
],
layout=Layout(width='100%', height="50px"))
self.control_slider = IntSlider(description=self.title,
continuous_update=False,
min=0,
max=max(self.length - 1, 0),
value=0,
style={"description_width": 'initial'},
layout=Layout(width='100%'))
## Hook them up:
button_begin.on_click(lambda button: self.goto("begin"))
button_end.on_click(lambda button: self.goto("end"))
button_next.on_click(lambda button: self.goto("next"))
button_prev.on_click(lambda button: self.goto("prev"))
self.button_play.on_click(self.toggle_play)
self.control_slider.observe(self.update_slider_control, names='value')
controls = VBox([
HBox([self.control_slider, self.total_text],
layout=Layout(height="40px")), self.control_buttons
],
layout=Layout(width='100%'))
controls.on_displayed(lambda widget: self.initialize())
return controls
def initialize(self):
results = self.function(self.control_slider.value)
try:
results = list(results)
except:
results = [results]
self.displayers = [display(x, display_id=True) for x in results]
def update_slider_control(self, change):
if change["name"] == "value":
self.position_text.value = self.control_slider.value
self.output.clear_output(wait=True)
results = self.function(self.control_slider.value)
try:
results = list(results)
except:
results = [results]
for i in range(len(self.displayers)):
self.displayers[i].update(results[i])
def _make_resize_notebook_slider(self):
resize_notebook_slider = IntSlider(min=300, max=2000, description='resize notebook')
def on_resize_notebook(change):
width = change['new']
self._view._remote_call('resizeNotebook',
target='Widget',
args=[width,])
resize_notebook_slider.observe(on_resize_notebook, names='value')
return resize_notebook_slider
def __init__(self,figsize=(6,6)):
self.figsize=figsize
self.size_slider=IntSlider(description='Grid Size',min=4,max=50)
display(self.size_slider)
self.nb_ob_slider=IntSlider(description='Obstacles',min=0,max=7)
display(self.nb_ob_slider)
self.gen_inst_button=Button(description='Generate Instance',margin=10)
self.gen_pos_button=Button(description='Generate Start/End Positions',margin=10)
self.gen_path_button=Button(description='Generate Path',margin=10)
self.inst_but_container=HBox(children=[self.gen_inst_button,self.gen_pos_button,self.gen_path_button])
self.inst_but_container.width = '100%'
display(self.inst_but_container)
self.show_path_button=Latex(value='Path: Value: Actions:',margin=10)
display(self.show_path_button)
self.size_slider.on_trait_change(self._on_size_slider_change,'value')
self.gen_inst_button.on_click(self._on_gen_inst_button_click)
self.gen_pos_button.on_click(self._on_pos_button_click)
self.gen_path_button.on_click(self._on_gen_path_button_click)
self.gen_path_button.disabled=True
self.fig=plt.figure(figsize=self.figsize)
self.ax=self.fig.add_subplot(111)
self.A=np.zeros((4,4),dtype='int')
self.replot_grid()
self.cid=self.fig.canvas.mpl_connect('button_press_event',self.onclick)
self.mod=False
def __init__(self,figsize=(6,6)):
self.figsize=figsize
self.size_slider=IntSlider(description='Grid Size',min=4,max=50)
display(self.size_slider)
self.nb_ob_slider=IntSlider(description='Obstacles',min=0,max=7)
display(self.nb_ob_slider)
self.gen_inst_button=Button(description='Generate Instance',margin=10)
self.gen_pos_button=Button(description='Generate Start/End Positions',margin=10)
self.gen_path_button=Button(description='Generate Path',margin=10)
self.inst_but_container=HBox(children=[self.gen_inst_button,self.gen_pos_button,self.gen_path_button])
self.inst_but_container.width = '100%'
display(self.inst_but_container)
self.show_path_button=Latex(value='Path: Value: Actions:',margin=10)
display(self.show_path_button)
self.size_slider.on_trait_change(self._on_size_slider_change,'value')
self.gen_inst_button.on_click(self._on_gen_inst_button_click)
self.gen_pos_button.on_click(self._on_pos_button_click)
self.gen_path_button.on_click(self._on_gen_path_button_click)
self.gen_path_button.disabled=True
self.gen_pos_button.disabled=True
plt.close()
plt.axis('off')
self.fig=plt.figure(figsize=self.figsize)
self.ax=self.fig.add_subplot(111)
