def _default_toolbar(figure):
pz = panzoom(figure.marks)
normal_btn = ToggleButton(icon='fa-circle-o', tooltip='Normal', value=True)
pz_btn = ToggleButton(icon='fa-arrows', tooltip='Pan and Zoom', value=False)
snapshot_btn = Button(icon='fa-thumb-tack', tooltip='Snapshot View')
reset_btn = Button(icon='fa-refresh', tooltip='Reset View')
save_btn = Button(icon='fa-save', tooltip='Save as .png Image')
def tog(btn, *args):
# Traitlets closure
def cb():
for other in args:
other.value = not btn.value
return cb
def overl(btn, value):
# Traitlets closure
def cb():
if btn.value:
figure.interaction = value
return cb
def snapshot(_):
pz.snapshot()
def reset(_):
pz.reset()
def save(_):
figure.save()
pz_btn.on_trait_change(tog(pz_btn, normal_btn))
pz_btn.on_trait_change(overl(pz_btn, pz))
normal_btn.on_trait_change(tog(normal_btn, pz_btn))
normal_btn.on_trait_change(overl(normal_btn, None))
snapshot_btn.on_click(snapshot)
reset_btn.on_click(reset)
save_btn.on_click(save)
figure.interaction = None
button_group = HBox([normal_btn, pz_btn, snapshot_btn, reset_btn, save_btn])
button_group._dom_classes = list(button_group._dom_classes) + ['btn-group']
return button_group
def _init_gui(self, **kwargs):
nframes = kwargs.pop("nframes", 1)
fields = kwargs.pop("fields", None)
tensors = kwargs.pop("tensors", None)
mainopts = super(UniverseWidget, self)._init_gui(**kwargs)
atoms = Button(description=' Fill', icon='adjust', layout=_wlo)
axis = Button(description=' Axis', icon='arrows-alt', layout=_wlo)
def _atom_3d(b):
for scn in self.active(): scn.atom_3d = not scn.atom_3d
def _axis(b):
for scn in self.active(): scn.axis = not scn.axis
atoms.on_click(_atom_3d)
axis.on_click(_axis)
atoms.active = True
atoms.disabled = False
axis.active = True
atoms.disabled = False
mainopts.update([('atom_3d', atoms), ('axis', axis),
('frame', self._frame_folder(nframes))])
if fields is not None:
folder = self._field_folder(fields, **kwargs)
self._iso_folder(folder)
self._contour_folder(folder)
folder.pop('fopts')
mainopts.update([('field', folder)])
if tensors is not None:
mainopts.update([('tensor', self._tensor_folder())])
return mainopts
def _contour_folder(self, folder):
control = Button(description=' Contours', icon='dot-circle-o')
def _cshow(b):
for scn in self.active(): scn.cont_show = not scn.cont_show
control.on_click(_cshow)
content = _ListDict([
('fopts', folder['fopts']),
('axis', Dropdown(options=['x', 'y', 'z'], value='z')),
('num', IntSlider(description='N', min=5, max=20,
value=10, step=1)),
('lim', IntRangeSlider(description='10**Limits', min=-8,
max=0, step=1, value=[-7, -1])),
('val', FloatSlider(description='Value',
min=-5, max=5, value=0))])
def _cont_axis(c):
for scn in self.active(): scn.cont_axis = c.new
def _cont_num(c):
for scn in self.active(): scn.cont_num = c.new
def _cont_lim(c):
for scn in self.active(): scn.cont_lim = c.new
def _cont_val(c):
for scn in self.active(): scn.cont_val = c.new
content['axis'].observe(_cont_axis, names='value')
content['num'].observe(_cont_num, names='value')
content['lim'].observe(_cont_lim, names='value')
content['val'].observe(_cont_val, names='value')
contour = Folder(control, content)
folder.insert(2, 'contour', contour, active=True, update=True)
class StaticFigureWrapper() :
def __init__(self,fdpi=300,fsize=(4,3),flabel="fig") :
# Set local variables
self.fdpi=fdpi
self.fsize=fsize
self.flabel=flabel
# Generate figure
self.fig = figure(dpi=self.fdpi,figsize=self.fsize)
close(self.fig)
# Generate plot axes for the figure
self.ax=self.fig.add_subplot(111)
# Create an html widget for the figure picture
self.outputHTML = HTML()
# Create save figure widget
self.btn = Button(description = 'Save %s' % flabel)
self.btn.on_click(self.btnfunc)
def btnfunc(self,btn):
self.fig.savefig('%s.png' % self.flabel , ext="png",bbox_inches='tight',dpi=self.fdpi)
def plot_to_html(self):
# write image data to a string buffer and get the PNG image bytes
self.buf = BytesIO()
self.fig.savefig(self.buf, format="png",bbox_inches='tight')
self.buf.seek(0)
return """<img src='data:image/png;base64,{}'/>""".format(b64encode(self.buf.getvalue()))
def render(self) :
self.outputHTML.value=self.plot_to_html()
return VBox([self.outputHTML,self.btn],align="center")
class ImageDownloader():
"""
Displays a widget that allows searching and downloading images from google images search
in a Jupyter Notebook or Lab.
"""
def __init__(self, path:Union[Path,str]='data'):
"Setup path to save images to, init the UI, and render the widgets."
self._path = Path(path)
self._ui = self._init_ui()
self.render()
def _init_ui(self) -> VBox:
"Initialize the widget UI and return the UI."
self._search_input = Text(placeholder="What images to search for?")
self._count_input = BoundedIntText(placeholder="How many pics?", value=10, min=1, max=5000, step=1,
layout=Layout(width='60px'))
self._size_input = Dropdown(options= _img_sizes.keys(), value='>400*300', layout=Layout(width='120px'))
self._download_button = Button(description="Search & Download", icon="download", layout=Layout(width='200px'))
self._download_button.on_click(self.on_download_button_click)
self._output = Output()
self._controls_pane = HBox([self._search_input, self._count_input, self._size_input, self._download_button],
layout=Layout(width='auto', height='40px'))
self._heading = ""
self._download_complete_heading = "<h3>Download complete. Here are a few images</h3>"
self._preview_header = widgets.HTML(self._heading, layout=Layout(height='60px'))
self._img_pane = Box(layout=Layout(display='inline'))
return VBox([self._controls_pane, self._preview_header, self._img_pane])
def render(self) -> None:
clear_output()
display(self._ui)
def clear_imgs(self) -> None:
"Clear the widget's images preview pane."
self._preview_header.value = self._heading
self._img_pane.children = tuple()
def validate_search_input(self) -> bool:
"Check if input value is empty."
input = self._search_input
if input.value == str(): input.layout = Layout(border="solid 2px red", height='auto')
else: self._search_input.layout = Layout()
return input.value != str()
def on_download_button_click(self, btn) -> None:
"Download button click handler: validate search term and download images."
term = self._search_input.value
limit = int(self._count_input.value)
size = self._size_input.value
if not self.validate_search_input(): return
self.clear_imgs()
downloaded_images = download_google_images(self._path, term, n_images=limit, size=size)
self.display_images_widgets(downloaded_images[:min(limit, 12)])
self._preview_header.value = self._download_complete_heading
self.render()
def display_images_widgets(self, fnames:list) -> None:
"Display a few preview images in the notebook"
imgs = [widgets.Image(value=open(f, 'rb').read(), width='200px') for f in fnames]
self._img_pane.children = tuple(imgs)
def _wrapper(self, *args, **kwargs): # pylint: disable=too-many-locals
result = func(self, *args, **kwargs)
if isinstance(result, rockets.RequestTask) and in_notebook():
from ipywidgets import FloatProgress, Label, HBox, VBox, Button
from IPython.display import display
progress = FloatProgress(min=0, max=1, value=0)
label = Label(value='')
button = Button(description='Cancel')
box = VBox([label, HBox([progress, button])])
display(box)
def _on_cancel(value): # pylint: disable=unused-argument
result.cancel()
def _on_progress(value):
progress.value = value.amount
label.value = value.operation
def _on_done(task): # pylint: disable=unused-argument
box.close()
button.on_click(_on_cancel)
result.add_progress_callback(_on_progress)
result.add_done_callback(_on_done)
return result
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 interactive_correlations(self):
def do_interact(data_type='expression',
sample_subset=self.default_sample_subsets,
feature_subset=self.default_feature_subset,
metric='euclidean', method='average',
list_link='',
scale_fig_by_data=True,
fig_width='', fig_height='', featurewise=False):
for k, v in locals().iteritems():
if k == 'self':
continue
sys.stdout.write('{} : {}\n'.format(k, v))
if feature_subset != "custom" and list_link != "":
raise ValueError(
"set feature_subset to \"custom\" to use list_link")
if feature_subset == "custom" and list_link == "":
raise ValueError("use a custom list name please")
if feature_subset == 'custom':
feature_subset = list_link
elif feature_subset not in self.default_feature_subsets[data_type]:
warnings.warn("This feature_subset ('{}') is not available in "
"this data type ('{}'). Falling back on all "
"features.".format(feature_subset, data_type))
return self.plot_correlations(
sample_subset=sample_subset, feature_subset=feature_subset,
data_type=data_type, scale_fig_by_data=scale_fig_by_data,
method=method, metric=metric, featurewise=featurewise)
feature_subsets = Interactive.get_feature_subsets(self,
['expression',
'splicing'])
method = ('average', 'weighted', 'single', 'complete', 'ward')
metric = ('euclidean', 'seuclidean', 'sqeuclidean', 'chebyshev',
'cosine', 'cityblock', 'mahalonobis', 'minowski', 'jaccard')
gui = interact(do_interact,
data_type=('expression', 'splicing'),
sample_subset=self.default_sample_subsets,
feature_subset=feature_subsets,
metric=metric,
method=method,
featurewise=False)
def save(w):
filename, extension = os.path.splitext(savefile.value)
self.maybe_make_directory(savefile.value)
gui.widget.result.savefig(savefile.value,
format=extension.lstrip('.'))
savefile = Text(description='savefile',
value='figures/correlations.pdf')
save_widget = Button(description='save')
gui.widget.children = list(gui.widget.children) + [savefile,
save_widget]
save_widget.on_click(save)
return gui
def _iso_folder(self, folder):
isos = Button(description=' Isosurfaces', icon='cube')
def _fshow(b):
for scn in self.active(): scn.field_show = not scn.field_show
isos.on_click(_fshow)
isofolder = Folder(isos, _ListDict([
('fopts', folder['fopts']),
('alpha', folder.pop('alpha')),
('iso', folder.pop('iso'))]))
isofolder.move_to_end('alpha', 'iso')
folder.insert(1, 'iso', isofolder, active=True)
def _init_gui(self, **kwargs):
"""Initialize generic GUI controls and observe callbacks."""
mainopts = super(DemoContainer, self)._init_gui()
geom = Button(icon='gear', description=' Mesh', layout=_wlo)
def _geom(b):
for scn in self.active():
scn.geom = not scn.geom
geom.on_click(_geom)
mainopts.update([('geom', geom),
('field', self._field_folder(**kwargs))])
return mainopts
def savebutton(fig, figpath, figname, transparent=True):
# Implement a 'save figure' button
if os.path.isfile(figpath + figname):
button = Button(description='Overwrite existing figure?')
else:
button = Button(description='Save figure.')
display(button)
# The save button
# TODO: https://stackoverflow.com/questions/10532614/can-matplotlib-add-metadata-to-saved-figures
def clicketh(b):
# http://stackoverflow.com/questions/24791709/save-a-plot-resulting-from-a-function-matplotlib-python
fig.savefig(figpath + figname, transparent=transparent)
button.on_click(clicketh)
def gen_figure(msids, group_name):
def select_next_msid(junk):
current_msid = msid_select.value
options = msid_select.options
i = options.index(current_msid)
if i < len(options) - 1:
msid_select.value=options[i + 1]
dummyfig = plt.figure(facecolor=[1,1,1],figsize=(14,8))
msid_select = Select(description='MSID:',options=msids, visible=True, padding=4)
button_next_msid = Button(description='Next', padding=4)
button_next_msid.on_click(select_next_msid)
msid_select_group = HBox(children=[msid_select, button_next_msid])
latest = DateTime().date
t1 = Text(description='Start Date:', value='2000:001:00:00:00.000', visible=True, padding=4)
t2 = Text(description='Stop Date:', value=latest, visible=True, padding=4)
time_select = Box(children=[t1, t2])
page1 = HBox(children=[msid_select_group, time_select])
wL = Checkbox(description='Plot Warning Low', value=False, visible=True, padding=4)
cL = Checkbox(description='Plot Caution Low', value=False, visible=True, padding=4)
cH = Checkbox(description='Plot Caution High', value=True, visible=True, padding=4)
wH = Checkbox(description='Plot Warning High', value=True, visible=True, padding=4)
low_select = Box(children=[wL, cL])
high_select = Box(children=[wH, cH])
page2 = HBox(children=[high_select, low_select])
stat_select = Select(description='Stat:',options=('daily', '5min', 'None'), visible=True, padding=4)
filter_bads = Checkbox(description='Filter Bad Times:', value=True, visible=True, padding=4)
group_select = Select(description='Group Name:',options=['sc', 'tel', 'isim'], visible=True, value=group_name, padding=4)
left_select = Box(children=[stat_select, filter_bads])
page3 = HBox(children=[left_select, group_select], description='Misc.')
q = interactive(plot_msid_interactive, msid=msid_select, group=group_select, tstart=t1, tstop=t2, stat=stat_select,
plot_warning_low=wL, plot_caution_low=cL, plot_caution_high=cH,
plot_warning_high=wH, remove_bads=filter_bads)
tabs = Tab(children=[page1, page2, page3])
tabs.set_title(0, 'MSID, Dates')
tabs.set_title(1, 'Limits')
tabs.set_title(2, 'Misc.')
display(tabs)
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 show_items_feature_form(table, periods):
tree = defaultdict(dict)
for period in periods:
section = period.section
tree[section.group][section.name] = period.features
def update(button, table, feature):
clear_output()
plot_items_feature(table, feature)
group_pages = []
group_titles = []
for group_title, group in tree.iteritems():
section_pages = []
section_titles = []
for section_title, features in group.iteritems():
buttons = []
for feature in features:
button = Button(description=feature.name)
button.on_click(partial(
update,
table=table,
feature=feature)
)
buttons.append(button)
section_pages.append(VBox(children=buttons))
section_titles.append(section_title)
accordion = Accordion(children=section_pages)
for index, title in enumerate(section_titles):
accordion.set_title(index, title)
group_pages.append(accordion)
group_titles.append(group_title)
accordion = Accordion(children=group_pages)
for index, title in enumerate(group_titles):
accordion.set_title(index, title)
return accordion
def _init_gui(self):
close = Button(description=' Close', icon='trash', layout=_wlo)
def _close(b): self.close()
close.on_click(_close)
frame = IntSlider(min=self._df.frame.astype(int).min(),
max=self._df.frame.astype(int).max(),
value=-1, description='Frame', layout=_wlo)
cbut = Button(description=' Columns', icon='barcode')
cols = self._df.columns.tolist()
cols = SelectMultiple(options=cols, value=cols)
def _cols(c):
self.columns = c.new
self._update_output()
cols.observe(_cols, names='value')
cfol = Folder(cbut, _ListDict([('cols', cols)]))
rbut = Button(description=' Rows', icon='bars')
rows = IntRangeSlider(min=self.indexes[0],
max=self.indexes[1],
value=[0, 50])
def _rows(c):
self.indexes = c.new
print(self.indexes)
self._update_output()
rows.observe(_rows, names='value')
rfol = Folder(rbut, _ListDict([('rows', rows)]))
return _ListDict([('close', close),
('frame', frame),
('cols', cfol),
('rows', rfol)])
def _init_ui(self) -> VBox:
"Initialize the widget UI and return the UI."
self._search_input = Text(placeholder="What images to search for?")
self._count_input = BoundedIntText(placeholder="How many pics?", value=10, min=1, max=5000, step=1,
layout=Layout(width='60px'))
self._size_input = Dropdown(options= _img_sizes.keys(), value='>400*300', layout=Layout(width='120px'))
self._download_button = Button(description="Search & Download", icon="download", layout=Layout(width='200px'))
self._download_button.on_click(self.on_download_button_click)
self._output = Output()
self._controls_pane = HBox([self._search_input, self._count_input, self._size_input, self._download_button],
layout=Layout(width='auto', height='40px'))
self._heading = ""
self._download_complete_heading = "<h3>Download complete. Here are a few images</h3>"
self._preview_header = widgets.HTML(self._heading, layout=Layout(height='60px'))
self._img_pane = Box(layout=Layout(display='inline'))
return VBox([self._controls_pane, self._preview_header, self._img_pane])
def __init__(self,fdpi=300,fsize=(4,3),flabel="fig") :
# Set local variables
self.fdpi=fdpi
self.fsize=fsize
self.flabel=flabel
# Generate figure
self.fig = figure(dpi=self.fdpi,figsize=self.fsize)
close(self.fig)
# Generate plot axes for the figure
self.ax=self.fig.add_subplot(111)
# Create an html widget for the figure picture
self.outputHTML = HTML()
# Create save figure widget
self.btn = Button(description = 'Save %s' % flabel)
self.btn.on_click(self.btnfunc)
def interactive_graph(self, data_types=('expression', 'splicing'),
sample_subsets=None,
feature_subsets=None,
featurewise=False,
cov_std_cut=(0.1, 3),
degree_cut=(0, 10),
n_pcs=(2, 100),
draw_labels=False,
feature_of_interest="RBFOX2",
weight_fun=None,
use_pc_1=True, use_pc_2=True, use_pc_3=True,
use_pc_4=True,
savefile='figures/last.graph.pdf'):
from IPython.html.widgets import interact
# not sure why nested fxns are required for this, but they are... i
# think...
def do_interact(data_type='expression',
sample_subset=self.default_sample_subsets,
feature_subset=self.default_feature_subsets,
weight_fun=NetworkerViz.weight_funs,
featurewise=False,
use_pc_1=True, use_pc_2=True, use_pc_3=True,
use_pc_4=True, degree_cut=1,
cov_std_cut=1.8, n_pcs=5,
feature_of_interest="RBFOX2",
draw_labels=False):
for k, v in locals().iteritems():
if k == 'self':
continue
sys.stdout.write('{} : {}\n'.format(k, v))
if data_type == 'expression':
assert (feature_subset in
self.expression.feature_subsets.keys())
if data_type == 'splicing':
assert (feature_subset in
self.splicing.feature_subsets.keys())
self.plot_graph(data_type=data_type,
sample_subset=sample_subset,
feature_subset=feature_subset,
featurewise=featurewise, draw_labels=draw_labels,
degree_cut=degree_cut, cov_std_cut=cov_std_cut,
n_pcs=n_pcs,
feature_of_interest=feature_of_interest,
use_pc_1=use_pc_1, use_pc_2=use_pc_2,
use_pc_3=use_pc_3,
use_pc_4=use_pc_4,
weight_function=weight_fun)
if feature_subsets is None:
feature_subsets = Interactive.get_feature_subsets(self, data_types)
if sample_subsets is None:
sample_subsets = self.default_sample_subsets
if weight_fun is None:
weight_fun = NetworkerViz.weight_funs
gui = interact(do_interact,
data_type=data_types,
sample_subset=sample_subsets,
feature_subset=feature_subsets,
featurewise=featurewise,
cov_std_cut=cov_std_cut,
degree_cut=degree_cut,
n_pcs=n_pcs,
draw_labels=draw_labels,
weight_fun=weight_fun,
feature_of_interest=feature_of_interest,
use_pc_1=use_pc_1, use_pc_2=use_pc_2,
use_pc_3=use_pc_3, use_pc_4=use_pc_4)
def save(w):
# Make the directory if it's not already there
filename, extension = os.path.splitext(savefile.value)
self.maybe_make_directory(savefile.value)
plt.gcf().savefig(savefile, format=extension.lstrip('.'))
savefile = Text(description='savefile')
save_widget = Button(description='save')
gui.widget.children = list(gui.widget.children) + [savefile,
save_widget]
save_widget.on_click(save)
return gui
player2Text = Label(value='Movimiento de jugador 2:',
layout=Layout(margin='0px 16px 0px 0px'))
player2TextFrom = Text(
placeholder='Desde (ej: -4,5)',
disabled=False,
layout=Layout(max_width='128px', margin='0px 16px 0px 0px')
)
player2TextTo = Text(
placeholder='Hacia (ej: -3,4)',
style={'description_width': 'initial'},
disabled=False,
layout=Layout(max_width='128px', margin='0px 16px 0px 0px')
)
player2Button = Button(
description='Mover',
disabled=False,
button_style='warning', # 'success', 'info', 'warning', 'danger' or ''
layout=Layout(max_width='80px', margin='0px 16px 0px 0px')
)
player2TextError = Label(value='')
box2_layout = Layout(display='flex',
flex_flow='row',
margin='8px 0px 8px 0px',
width='100%')
box2 = Box(children=[player2Text, player2TextFrom, player2TextTo, player2Button, player2TextError], layout=box2_layout)
# Todo
main_box_layout = Layout(display='flex',
flex_flow='column',
width='100%')
main_box = Box(children=[box2], layout=main_box_layout)
def _make_reference_widget(self):
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.width = DEFAULT_SLIDER_WIDTH
return widget_sliders
widget_sliders = make_widget_box()
reset_button = Button(description='Reset')
widget_sliders.children = [
reset_button,
] + list(widget_sliders.children)
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)
reset_button.on_click(on_click)
return widget_sliders
def __init__(self):
# Stores the respective line number and variable changes for each
# exection step
self._tracer = TimeTravelTracer()
self._current_state = None
self._debugger = None
self._code_output = HTML()
self._var_output = Output()
self._watchpoint_output = Output()
self._breakpoint_output = Output()
self._diff_slider = IntSlider(
min=1,
readout=False,
layout=Layout(width="99%"),
tooltip="Execution timeline",
)
self._diff_slider.observe(self._handle_diff_slider, names="value")
self._autoplay = Play(
tooltip="Automatic playback of the execution",
layout=Layout(height="30px"),
)
self._auto_link = jsdlink((self._autoplay, "value"),
(self._diff_slider, "value"))
self._speed_slider = IntSlider(description="Delay (ms)",
min=100,
max=1000,
step=100,
value=500)
self._speed_link = jsdlink((self._speed_slider, "value"),
(self._autoplay, "interval"))
self._reverse_autoplay = ToggleButton(
value=False,
icon="history",
tooltip="Reverse autoplay",
layout=Layout(width="40px"),
)
self._reverse_autoplay.observe(self._handle_reverse_button)
self._watchpoint_input = Text(
layout=Layout(width="150px"),
placeholder="Watch expression",
)
self._add_watchpoint = Button(
icon="plus",
tooltip="Add an expression or variable to watch",
layout=Layout(width="50px"),
)
self._add_watchpoint.on_click(self.watch_command)
self._watchpoint_dropdown = Dropdown(layout=Layout(width="150px"), )
self._remove_watchpoint = Button(
icon="trash",
tooltip="Remove a watchpoint",
layout=Layout(width="50px"),
)
self._remove_watchpoint.on_click(self.unwatch_command)
self._breakpoint_layout = GridspecLayout(3, 1)
self._add_breakpoint = Button(
icon="plus",
tooltip="Add a breakpoint",
name="breakpoint_button",
layout=Layout(width="40px"),
)
self._add_breakpoint.on_click(self._handle_breakpoint)
self._disable_breakpoint_button = Button(
icon="eye-slash",
tooltip="Disable breakpoint",
layout=Layout(width="50px"),
)
self._disable_breakpoint_button.on_click(self.disable_command)
self._remove_breakpoint_button = Button(
icon="trash",
tooltip="Remove breakpoint",
layout=Layout(width="50px"),
)
self._remove_breakpoint_button.on_click(self.delete_command)
self._breakpoint_dropdown = Dropdown(layout=Layout(width="70px"))
self._function_dropdown = Dropdown(layout=Layout(width="200px"))
self._function_dropdown.disabled = True
self._breakpoint_type = Dropdown(
options=["Line", "Function", "Conditional"],
value="Line",
layout=Layout(width="100px"),
)
self._breakpoint_type.observe(self._handle_breakpoint_type,
names="value")
self._condition_input = Text(placeholder="Enter condition",
layout=Layout(width="200px"))
self._condition_input.disabled = True
self._line_input = Text(
placeholder="Line Number",
name="line_input",
layout=Layout(width="100px"),
)
self._breakpoint_layout = VBox([
HBox([
self._add_breakpoint,
self._breakpoint_type,
self._function_dropdown,
self._line_input,
self._condition_input,
self._breakpoint_dropdown,
self._remove_breakpoint_button,
self._disable_breakpoint_button,
]),
self._breakpoint_output,
])
self._search_input = Text(placeholder="Search...")
self._search_input.observe(self._handle_search_input, names="value")
self._search_results = Output()
self._search_layout = VBox([
self._search_input,
self._search_results,
])
# Remove shadows from scrolling
style = """
<style>
.jupyter-widgets-output-area .output_scroll {
border-radius: unset !important;
-webkit-box-shadow: unset !important;
box-shadow: unset !important;
}
</style>
"""
display(HTML(style))
for key, item in self._BUTTONS.items():
self.register_button(key, **item)
self._code_layout = GridspecLayout(4, 4, grid_gap="20px")
self._code_layout[0:4, 0:3] = HBox(
[self._code_output],
layout=Layout(height="500px",
overflow_y="scroll",
border="2px solid black"),
)
self._code_layout[0:2, 3] = self._var_output
self._code_layout[2:4, 3] = VBox([
HBox([self._add_watchpoint, self._watchpoint_input]),
HBox([self._remove_watchpoint, self._watchpoint_dropdown]),
self._watchpoint_output,
])
self._code_nav_layout = VBox([
HBox([
*self.get_buttons(),
self._autoplay,
self._reverse_autoplay,
self._speed_slider,
]),
self._diff_slider,
self._code_layout,
])
self._main_layout = Tab(
[
self._code_nav_layout,
self._breakpoint_layout,
self._search_layout,
],
layout=Layout(height="650px"),
)
self._main_layout.set_title(0, "Code")
self._main_layout.set_title(1, "Breakpoints")
self._main_layout.set_title(2, "Search")
display(self._main_layout)
def __get_widgets(self, chromosomes, browser, frame=None):
if frame is None:
frame = HTML()
tracks = self.__get_tracks_name(browser)
return OrderedDict(
[
("chromosomes_list", Dropdown(options=chromosomes)),
("left_button", Button(icon="arrow-left")),
("right_button", Button(icon="arrow-right")),
("zoom_out_button", Button(icon="search-minus")),
("zoom_in_button", Button(icon="search-plus")),
(
"range_textbox",
Text(placeholder="genome range like: 'chr1:10000-20000'"),
),
("go_button", Button(description="Go")),
(
"range_slider",
IntRangeSlider(
continuous_update=False,
readout=False,
layout=Layout(width='90%'),
),
),
("range_min_label", Label("", layout=Layout(width='2%'))),
("range_max_label", Label("", layout=Layout(width='20%'))),
(
"auto_check_box",
Checkbox(
value=True,
description="Auto Range",
layout=Layout(width='120px'),
style={'description_width': 'initial'},
),
),
(
"track_min_val_float_text",
FloatText(
value=0.0001,
description="Track's min value:",
step=0.5,
disabled=True,
layout=Layout(width='30%'),
style={'description_width': 'initial'},
),
),
(
"track_max_val_float_text",
FloatText(
value=10,
description="Track's max value:",
step=0.5,
disabled=True,
layout=Layout(width='30%'),
style={'description_width': 'initial'},
),
),
(
"track_dropdown",
Dropdown(
options=[ALL_BW_MARK] + tracks,
value=ALL_BW_MARK,
description="Select track",
disabled=True,
),
),
("frame", frame),
]
)
class FileChooser(VBox):
_LBL_TEMPLATE = '<span style="margin-left:10px; color:{1};">{0}</span>'
_LBL_NOFILE = 'No file selected'
def __init__(self,
path=os.getcwd(),
filename='',
title='',
select_desc='Select',
change_desc='Change',
show_hidden=False,
directory=False,
**kwargs):
self._select_desc = select_desc
self._default_path = path
self._show_hidden = show_hidden
self._select_desc = select_desc
self._change_desc = change_desc
self._path = path
self._updir = Button(description='Up Directory')
self._dircontent = Select(rows=8,
layout=Layout(width='auto',
grid_area='dircontent'))
self._cancel = Button(description='Cancel',
layout=Layout(width='auto', display='none'))
self._select = Button(description=self._select_desc,
layout=Layout(width='auto'))
self._label = HTML(value=self._LBL_TEMPLATE.format(
self._LBL_NOFILE, 'black'),
placeholder='',
description='')
self._title = HTML(value=title)
if title is '':
self._title.layout.display = 'none'
self._updir.on_click(self._on_updir_click)
self._select.on_click(self._on_select_click)
self._cancel.on_click(self._on_cancel_click)
# Layout
self._gb = GridBox(children=[self._updir, self._dircontent],
layout=Layout(display='none',
width='500px',
grid_gap='0px 0px',
grid_template_rows='auto auto',
grid_template_columns='60% 40%',
grid_template_areas='''
'pathlist filename'
'dircontent dircontent'
'''))
self._dircontent.observe(self._on_dircontent_select, names='value')
buttonbar = HBox(children=[
self._select,
self._cancel,
self._label,
],
layout=Layout(width='auto'))
# Call setter to set initial form values
self._set_form_values(self._path)
# Call VBox super class __init__
super().__init__(children=[
self._gb,
buttonbar,
],
layout=Layout(width='auto'),
**kwargs)
def _set_form_values(self, path):
# Disable triggers to prevent selecting an entry in the Select
# box from automatically triggering a new event.
self._dircontent.unobserve(self._on_dircontent_select, names='value')
self._dircontent.options = get_dir_contents(path,
hidden=self._show_hidden)
self._dircontent.value = None
# Reenable triggers again
self._dircontent.observe(self._on_dircontent_select, names='value')
def _on_dircontent_select(self, change):
'''Handler for when a folder entry is selected'''
new_path = update_path(self._path, change['new'])
# Check if folder or file
if os.path.isdir(new_path):
self._path = new_path
#elif os.path.isfile(new_path):
# path = self._path
self._set_form_values(self._path)
def _on_updir_click(self, b):
self._path = os.path.split(self._path)[0]
self._set_form_values(self._path)
def _on_cancel_click(self, b):
self._gb.layout.display = 'none'
def _on_select_click(self, b):
'''Handler for when the select button is clicked'''
if self._gb.layout.display is 'none':
self._gb.layout.display = None
self._cancel.layout.display = None
path = self._default_path
self._set_form_values(path)
else:
self._gb.layout.display = 'none'
self._cancel.layout.display = 'none'
self._select.description = self._change_desc
#self._selected_filename = self._filename.value
# self._default_path = self._selected_path
# self._default_filename = self._selected_filename
selected_path = self._path
#if( os.path.isdir( selected_path ) ):
# self._path = selected_path
pathOK = check_plate_path(self._path)
color = 'red'
if (pathOK): color = 'green'
self._label.value = self._LBL_TEMPLATE.format(selected_path, color)
self._set_form_values(self._path)
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 __init__(self,
position: str = "bottomleft",
attr_name: str = "style",
kind: str = "stroke",
orientation: str = "horizontal",
transparent: bool = False,
a_map: Map = None,
layer: Layer = None,
place_control: bool = True):
"""Add a widget to the map that allows styling some given layer.
At the moment only the stroke color, opacity and weight can be changed
using a color picker and sliders. Dash array might follow later.
:param m: The map object to which to add a styling widget.
:param layer: The layer object which is to be styled.
:param attr_name: The layer's attribute name storing the style object.
This is usually one of: "style", "hover_style", and "point_style"
:param kind: The kind of style, either "stroke" or "fill".
:param orientation: The orientation of the UI elements, either "horizontal"
(default) or "vertical".
:param transparent: A flag to indicate if the widget background should be
transparent (default: ``False``).
:param position: The map corner where this widget will be placed.
TODO: The UI elements should reflect changes to the layer triggered by
others.
"""
assert kind in ["stroke", "fill"]
assert orientation in ["horizontal", "vertical"]
def restyle(change):
if change["type"] != "change":
return
owner = change["owner"]
style_copy = copy.copy(getattr(layer, attr_name))
attr_map = {
p: "color" if kind == "stroke" else "fillColor",
o: "opacity" if kind == "stroke" else "fillOpacity",
w: "weight"
}
if owner in [p, o, w]:
style_copy[attr_map[owner]] = owner.value
setattr(layer, attr_name, style_copy)
def close(button):
a_map.remove_control(wc)
attr = getattr(layer, attr_name)
style = getattr(layer, "style")
b = ToggleButton(description="Stroke",
value=True,
tooltip="Stroke or not?")
dummy = ToggleButton(value=not b.value)
b.layout.width = "80px"
name = "color" if kind == "stroke" else "fillColor"
p = ColorPicker(value=attr.get(name, style.get(name, "#3885ff")))
p.layout.width = "100px"
name = "opacity" if kind == "stroke" else "fillOpacity"
o = FloatSlider(min=0,
max=1,
value=attr.get(name, style.get(name, 0.5)))
o.layout.width = "200px"
w = IntSlider(min=0,
max=50,
value=attr.get("weight", style.get("weight", 5)))
w.layout.width = "200px"
layout = Layout(width="28px", height="28px", padding="0px 0px 0px 4px")
q = Button(tooltip="Close",
icon="close",
button_style="info",
layout=layout)
for el in [p, o, w] if kind == "stroke" else [p, o]:
link((dummy, "value"), (el, "disabled"))
p.observe(restyle)
o.observe(restyle)
if kind == "stroke":
w.observe(restyle)
else:
w.disabled = True
q.on_click(close)
desc = HTML(f"{kind} {attr_name}")
if orientation == "horizontal":
self.widget = HBox([desc, p, w, o, q])
elif orientation == "vertical":
self.widget = VBox([HBox([desc, q]), p, w, o])
wc = WidgetControl(widget=self.widget,
position=position,
transparent_bg=transparent)
a_map.add_control(wc)
######### Interactive ##########
################################
def interactive_plot(f):
interact = interactive(f, M = M,
bpref = bpref,
dpref = dpref,
rc = rc,
rho00 = rho00,
gpref = gpref,
continuous_update=False)
return interact
################################
########### Button #############
################################
button = Button(
description="Best Fit",
button_style='warning', # 'success', 'info', 'warning', 'danger' or ''
icon='check')
out = Output()
def on_button_clicked(_):
M.value = best_M
bpref.value = best_bpref
dpref.value = best_dpref
rho00.value = best_rho00
gpref.value = best_gpref
button.on_click(on_button_clicked)
def __init__(self,
path=os.getcwd(),
filename='',
title='',
select_desc='Select',
change_desc='Change',
show_hidden=False,
include_files=True,
include_folders=True,
**kwargs):
self._default_path = path # path.rstrip(os.path.sep)
self._default_filename = filename
self._selected_path = ''
self._selected_filename = ''
self._show_hidden = show_hidden
self._select_desc = select_desc
self._change_desc = change_desc
self._include_files = include_files
self._include_folders = include_folders
if not include_folders and not include_files:
raise ValueError("You can't exclude both files and folders")
# Widgets
self._pathlist = Dropdown(description="",
layout=Layout(width='auto',
grid_area='pathlist'))
self._filename = Text(
placeholder='output filename',
layout=Layout(
width='auto',
grid_area='filename',
visibility='visible' if self._include_files else 'hidden',
),
)
self._dircontent = Select(rows=8,
layout=Layout(width='auto',
grid_area='dircontent'))
self._cancel = Button(description='Cancel',
layout=Layout(width='auto', display='none'))
self._select = Button(description=self._select_desc,
layout=Layout(width='auto'))
self._title = HTML(value=title)
if title is '':
self._title.layout.display = 'none'
# Widget observe handlers
self._pathlist.observe(self._on_pathlist_select, names='value')
self._dircontent.observe(self._on_dircontent_select, names='value')
self._filename.observe(self._on_filename_change, names='value')
self._select.on_click(self._on_select_click)
self._cancel.on_click(self._on_cancel_click)
# Selected file label
self._label = HTML(value=self._LBL_TEMPLATE.format(
self._LBL_NOFILE if self._include_files else
self._LBL_NOFOLDER if self._include_folders else "", 'black'),
placeholder='',
description='')
# Layout
self._gb = GridBox(
children=[self._pathlist, self._filename, self._dircontent],
layout=Layout(display='none',
width='500px',
grid_gap='0px 0px',
grid_template_rows='auto auto',
grid_template_columns='60% 40%',
grid_template_areas='''
'pathlist filename'
'dircontent dircontent'
'''))
buttonbar = HBox(children=[self._select, self._cancel, self._label],
layout=Layout(width='auto'))
# Call setter to set initial form values
self._set_form_values(self._default_path, self._default_filename)
# Call VBox super class __init__
kwargs.setdefault('layout', Layout(width='auto'))
super().__init__(children=[
self._title,
self._gb,
buttonbar,
],
**kwargs)
def _create_widget(self):
self.addbtn = Button(description='Add')
self.addbtn.on_click(self.add_row_handler)
vbox = VBox([self.addbtn])
vbox.add_class('repeat-innotation')
return vbox
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 settings_panel(self):
# getMolMap calulation settings. NOTE: should only be called once.
margin = 2
num_angles_slider_text = "Number of Inverse Cone Angles to calculate:"
num_angles_slider_widget = IntSlider(value=1, min=1, max=5)
num_angles_slider = VBox(
children=[HTML(value=num_angles_slider_text), num_angles_slider_widget], margin=margin, width="100%"
)
link((self.model, "num_angles"), (num_angles_slider_widget, "value"))
sub_slider_text = "Subdivision value of the icosphere for numerical calculation:"
sub_slider_widget = IntSlider(value=5, min=1, max=9)
link((self.model, "sub"), (sub_slider_widget, "value"))
sub_slider = VBox(children=[HTML(value=sub_slider_text), sub_slider_widget], margin=margin, width="100%")
# link((sub_slider, 'value'), (i, 'value'))
# print(self.width)
# sub_slider.align = 'center'
# sub_slider.width = '100%'
# sub_slider.border_color = 'black'
# sub_slider.border_width = 2
radius_slider_text = "Cut radius measured from the central atom:"
radius_slider_widget = FloatSlider(value=0, min=0, max=10)
link((self.model, "radius"), (radius_slider_widget, "value"))
radius_slider = VBox(children=[HTML(value=radius_slider_text), radius_slider_widget], margin=margin)
atomradscale_slider_text = "Atomic radius scaling factor:"
atomradscale_slider_widget = FloatSlider(value=1, min=0, max=4)
link((self.model, "rad_scale"), (atomradscale_slider_widget, "value"))
atomradscale_slider = VBox(
children=[HTML(value=atomradscale_slider_text), atomradscale_slider_widget], margin=margin
)
excludeH_button = Checkbox(description="Exclude H from every geometry:")
link((self.model, "excludeH"), (excludeH_button, "value"))
excludeH_button.on_trait_change(self.excludeH_changed, "value")
dont = "Don't exclude any elements"
self.dont = dont
# TODO: Syncronize exclude_list_widget with excludeH button and define an event on the
# model to filter out the `dont` text.
# Alternatevily, separate this option into a checkbox and hide the exclude options
# while the button is selected.
exclude_list_text = "Exclude elements from every geometry:"
exclude_list_widget = SelectMultiple(
options=[dont] + [e.symbol for e in ELEMENTS],
selected_labels=[dont],
color="Black",
font_size=14,
height=120,
)
link((exclude_list_widget, "value"), (self.model, "excludes"))
# The dirty old SelectMultiple widget does not have an .on_trait_change method.
# So we create a new traitlet (excludes_notifier), which has an .on_trait_change method
# because it inherits HasTraits. We link the 'value' trait to excludes_notifier.excludes;
# and we bind the event handler to excludes_notifier.on_trait_change
self.excludes_notifier = ExcludesNotifier()
link((exclude_list_widget, "value"), (self.excludes_notifier, "excludes"))
self.excludes_notifier.on_trait_change(self.excludes_changed)
exclude_list = VBox(children=[HTML(value=exclude_list_text), exclude_list_widget], margin=margin)
atomrad_button = ToggleButtons(
description="Atomic radius type:",
options=["vdwrad", "covrad", "atmrad"],
background_color="AliceBlue",
margin=margin,
)
link((self.model, "rad_type"), (atomrad_button, "value"))
runbutton = Button(
description="Run calculation!",
tooltip="Click here to calculate Buried Volumes and Inverse Cone Angles!",
margin=margin * 3,
border_color="#9acfea",
# border_radius=5,
border_width=3,
font_size=20,
)
runbutton.on_click(self.run_button_clicked)
basic_tab = VBox(children=[atomrad_button, excludeH_button])
sliders = VBox(children=[num_angles_slider, atomradscale_slider, radius_slider, sub_slider])
sliders.width = "100%"
sliders.pack = "center"
advanced_tab = VBox(children=[atomrad_button, sliders, exclude_list])
main_window = Tab(children=[basic_tab, advanced_tab])
main_window.set_title(0, "Basic")
main_window.set_title(1, "Advanced")
return ControlPanel(
title="getMolMap Settings:",
children=[main_window, runbutton],
border_width=2,
border_radius=4,
margin=10,
padding=0,
)
def register_button(self, key, **kwargs):
button = Button(description="", layout=Layout(width="40px"), **kwargs)
func = getattr(self, key + "_command")
button.on_click(func)
self._BUTTONS[key]["button"] = button
class FileChooser(VBox):
_LBL_TEMPLATE = '<span style="margin-left:10px; color:{1};">{0}</span>'
_LBL_NOFILE = 'No file selected'
_LBL_NOFOLDER = 'No folder selected'
def __init__(self,
path=os.getcwd(),
filename='',
title='',
select_desc='Select',
change_desc='Change',
show_hidden=False,
include_files=True,
include_folders=True,
**kwargs):
self._default_path = path # path.rstrip(os.path.sep)
self._default_filename = filename
self._selected_path = ''
self._selected_filename = ''
self._show_hidden = show_hidden
self._select_desc = select_desc
self._change_desc = change_desc
self._include_files = include_files
self._include_folders = include_folders
if not include_folders and not include_files:
raise ValueError("You can't exclude both files and folders")
# Widgets
self._pathlist = Dropdown(description="",
layout=Layout(width='auto',
grid_area='pathlist'))
self._filename = Text(
placeholder='output filename',
layout=Layout(
width='auto',
grid_area='filename',
visibility='visible' if self._include_files else 'hidden',
),
)
self._dircontent = Select(rows=8,
layout=Layout(width='auto',
grid_area='dircontent'))
self._cancel = Button(description='Cancel',
layout=Layout(width='auto', display='none'))
self._select = Button(description=self._select_desc,
layout=Layout(width='auto'))
self._title = HTML(value=title)
if title is '':
self._title.layout.display = 'none'
# Widget observe handlers
self._pathlist.observe(self._on_pathlist_select, names='value')
self._dircontent.observe(self._on_dircontent_select, names='value')
self._filename.observe(self._on_filename_change, names='value')
self._select.on_click(self._on_select_click)
self._cancel.on_click(self._on_cancel_click)
# Selected file label
self._label = HTML(value=self._LBL_TEMPLATE.format(
self._LBL_NOFILE if self._include_files else
self._LBL_NOFOLDER if self._include_folders else "", 'black'),
placeholder='',
description='')
# Layout
self._gb = GridBox(
children=[self._pathlist, self._filename, self._dircontent],
layout=Layout(display='none',
width='500px',
grid_gap='0px 0px',
grid_template_rows='auto auto',
grid_template_columns='60% 40%',
grid_template_areas='''
'pathlist filename'
'dircontent dircontent'
'''))
buttonbar = HBox(children=[self._select, self._cancel, self._label],
layout=Layout(width='auto'))
# Call setter to set initial form values
self._set_form_values(self._default_path, self._default_filename)
# Call VBox super class __init__
kwargs.setdefault('layout', Layout(width='auto'))
super().__init__(children=[
self._title,
self._gb,
buttonbar,
],
**kwargs)
def _set_form_values(self, path, filename):
"""Set the form values"""
# Disable triggers to prevent selecting an entry in the Select
# box from automatically triggering a new event.
self._pathlist.unobserve(self._on_pathlist_select, names='value')
self._dircontent.unobserve(self._on_dircontent_select, names='value')
self._filename.unobserve(self._on_filename_change, names='value')
# Set form values
self._pathlist.options = get_subpaths(path)
self._pathlist.value = path
self._filename.value = filename
self._dircontent.options = get_dir_contents(
path,
hidden=self._show_hidden,
include_files=self._include_files,
include_folders=self._include_folders)
# If the value in the filename Text box equals a value in the
# Select box and the entry is a file then select the entry.
if ((filename in self._dircontent.options)
and os.path.isfile(os.path.join(path, filename))):
self._dircontent.value = filename
else:
self._dircontent.value = None
# Reenable triggers again
self._pathlist.observe(self._on_pathlist_select, names='value')
self._dircontent.observe(self._on_dircontent_select, names='value')
self._filename.observe(self._on_filename_change, names='value')
# Set the state of the select Button
if self._gb.layout.display is None:
selected = os.path.join(self._selected_path,
self._selected_filename)
# filename value is empty or equals the selected value
if ((filename == '') or
(os.path.join(path, filename) == selected)) \
and self._include_files:
self._select.disabled = True
else:
self._select.disabled = False
def _on_pathlist_select(self, change):
"""Handler for when a new path is selected"""
self._set_form_values(change['new'], self._filename.value)
def _on_dircontent_select(self, change):
"""Handler for when a folder entry is selected"""
new_path = update_path(self._pathlist.value, change['new'])
# Check if folder or file
if os.path.isdir(new_path):
path = new_path
filename = self._filename.value
elif os.path.isfile(new_path):
path = self._pathlist.value
filename = change['new']
self._set_form_values(path, filename)
def _on_filename_change(self, change):
"""Handler for when the filename field changes"""
self._set_form_values(self._pathlist.value, change['new'])
def _on_select_click(self, b):
"""Handler for when the select button is clicked"""
if self._gb.layout.display is 'none':
self._gb.layout.display = None
self._cancel.layout.display = None
# Show the form with the correct path and filename
if (self._selected_path and self._selected_filename) or \
(self._selected_path and not self._include_files):
path = self._selected_path
filename = self._selected_filename
else:
path = self._default_path
filename = self._default_filename
self._set_form_values(path, filename)
else:
self._gb.layout.display = 'none'
self._cancel.layout.display = 'none'
self._select.description = self._change_desc
self._selected_path = self._pathlist.value
self._selected_filename = self._filename.value
# self._default_path = self._selected_path
# self._default_filename = self._selected_filename
selected = os.path.join(self._selected_path,
self._selected_filename)
if not self._include_files and os.path.isdir(selected):
selected = selected.rstrip(os.path.sep)
if os.path.isfile(selected):
self._label.value = self._LBL_TEMPLATE.format(
selected, 'orange')
else:
self._label.value = self._LBL_TEMPLATE.format(
selected, 'green')
def _on_cancel_click(self, b):
"""Handler for when the cancel button is clicked"""
self._gb.layout.display = 'none'
self._cancel.layout.display = 'none'
self._select.disabled = False
def reset(self, path=None, filename=None):
"""Reset the form to the default path and filename"""
self._selected_path = ''
self._selected_filename = ''
self._label.value = self._LBL_TEMPLATE.format(
self._LBL_NOFILE if self._include_files else
self._LBL_NOFOLDER if self._include_folders else "", 'black')
if path is not None:
self._default_path = path.rstrip(os.path.sep)
if filename is not None:
self._default_filename = filename
self._set_form_values(self._default_path, self._default_filename)
def refresh(self):
"""Re-render the form"""
self._set_form_values(self._pathlist.value, self._filename.value)
@property
def show_hidden(self):
"""Get current number of rows"""
return self._show_hidden
@show_hidden.setter
def show_hidden(self, hidden):
"""Set number of rows"""
self._show_hidden = hidden
self.refresh()
@property
def rows(self):
"""Get current number of rows"""
return self._dircontent.rows
@rows.setter
def rows(self, rows):
"""Set number of rows"""
self._dircontent.rows = rows
@property
def title(self):
"""Get the title"""
return self._title.value
@title.setter
def title(self, title):
"""Set the title"""
self._title.value = title
if title is '':
self._title.layout.display = 'none'
else:
self._title.layout.display = None
@property
def default(self):
"""Get the default value"""
return os.path.join(self._default_path, self._default_filename)
@property
def default_path(self):
"""Get the default_path value"""
return self._default_path
@default_path.setter
def default_path(self, path):
"""Set the default_path"""
self._default_path = path.rstrip(os.path.sep)
self._default = os.path.join(self._default_path, self._filename.value)
self._set_form_values(self._default_path, self._filename.value)
@property
def default_filename(self):
"""Get the default_filename value"""
return self._default_filename
@default_filename.setter
def default_filename(self, filename):
"""Set the default_filename"""
self._default_filename = filename
self._default = os.path.join(self._pathlist.value,
self._default_filename)
self._set_form_values(self._pathlist.value, self._default_filename)
@property
def selected(self):
"""Get selected value"""
return os.path.join(self._selected_path, self._selected_filename)
@property
def selected_path(self):
"""Get selected_path value"""
return self._selected_path
@property
def selected_filename(self):
"""Get the selected_filename"""
return self._selected_filename
def __repr__(self):
str_ = ("FileChooser("
"path='{0}', "
"filename='{1}', "
"show_hidden='{2}')").format(self._default_path,
self._default_filename,
self._show_hidden)
return str_
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 get_button(**kwargs):
"""
Get Button.
"""
return Button(**kwargs)
def __init__(self, signal_components: dict):
"""
Summary:
Object constructor.
Arguments:
signal_components - dictionary with the signal components.
Returns:
Nothing.
"""
# Tab count (to keep track of the tab)
self.count = 0
self.signal_components = signal_components
# List of data displayers
self.data_displayers = [base_data_displayer_widget(signal_components)]
self.wt_data_displayers = Tab(self.data_displayers)
self.wt_data_displayers.set_title(self.count, f"Figure {self.count+1}")
self.count += 1
# Add and remove buttons
self.wb_add = Button(description='Add', disabled=False, icon='Add')
self.wb_remove = Button(description='Remove',
disabled=False,
icon='Remove')
@self.wb_add.on_click
def wb_add_on_click(b):
# Append a new data displayer
self.data_displayers.append(
base_data_displayer_widget(signal_components))
self.wt_data_displayers.children = self.data_displayers
self.wt_data_displayers.set_title(self.count,
f"Figure {self.count+1}")
self.count += 1
@self.wb_remove.on_click
def wd_remove_on_click(b):
if len(self.data_displayers) > 1:
self.data_displayers.pop()
self.count -= 1
else:
# Empty tab
self.data_displayers = [
base_data_displayer_widget(signal_components)
]
self.wt_data_displayers.children = self.data_displayers
self.wb_save = Button(description='Save', disabled=False, icon='save')
@self.wb_save.on_click
def wb_save_on_click(b):
# Create the output element in the JSON file
_dict = self.dump()
key = list(_dict.keys())[0]
value = _dict[key]
config.set_value(key, value)
self.wb_load = Button(description='Load', disabled=False, icon='load')
wfc_options = FileChooser(placeholder='Option file',
description='Option file:',
disabled=False)
self.whb_load = HBox([self.wb_load, wfc_options])
@self.wb_load.on_click
def wb_load_on_click(b):
if wfc_options.selected is not None:
optionFile = open(wfc_options.selected)
options = json.load(optionFile)
self.initialize(options)
super().__init__([self.wt_data_displayers, HBox([self.wb_add, self.wb_remove]),\
self.wb_save, self.whb_load])
class TrendsWithPickTokensGUI:
def __init__(self,
token_selector: TokensSelector,
update_handler: Callable = None):
self.token_selector: TokensSelector = token_selector
self.update_handler: Callable = update_handler
self._page_size = IntSlider(
description="Count",
min=0,
max=100,
step=1,
value=3,
continuous_update=False,
layout=Layout(width="300px"),
)
self._forward = Button(
description=">>",
button_style="Success",
layout=Layout(width="40px", color="green"),
)
self._back = Button(
description="<<",
button_style="Success",
layout=Layout(width="40px", color="green"),
)
self._split = ToggleButton(description="Split",
layout=Layout(width="80px", color="green"))
self._output = Output(layout=Layout(width="80%"))
def setup(self):
self._page_size.observe(self._update, "value")
self._split.observe(self.split_changed, "value")
self._forward.on_click(self._stepper_clicked)
self._back.on_click(self._stepper_clicked)
self.token_selector.on_selection_change_handler(self._update)
def _stepper_clicked(self, b):
_selected_indices = self.token_selector.get_selected_indices()
_current_index = min(
_selected_indices) if len(_selected_indices) > 0 else 0
if b.description == "<<":
_current_index = max(_current_index - self.page_size, 0)
if b.description == ">>":
_current_index = min(_current_index + self.page_size,
len(self.token_selector) - self.page_size)
self.token_selector.set_selected_indices(
list(range(_current_index, _current_index + self.page_size)))
def _update(self):
if self.update_handler is not None:
with self._output:
tokens = self.selected_tokens()
self.update_handler(self, tokens)
def split_changed(self, *_):
self._update()
def layout(self):
return VBox([
HBox([self._back, self._forward, self._page_size, self._split]),
HBox([self.token_selector.widget, self._output],
layout=Layout(width="98%")),
])
def display(self, trends_data: TrendsData):
self.token_selector.display(
trends_data.gof_data.most_deviating_overview)
@property
def page_size(self) -> int:
return self._page_size.value
@property
def split(self) -> bool:
return self._split.value
@property
def selected_tokens(self) -> Sequence[str]:
tokens: Sequence[str] = self.token_selector.get_selected_tokens()
if len(tokens) == 0:
tokens = self.token_selector[:self.page_size]
return tokens
@staticmethod
def create(
corpus: VectorizedCorpus,
tokens: pd.DataFrame,
n_columns: int = 3,
token_sector_cls: TokensSelector = SelectMultipleTokensSelector,
tokens_selected=None,
) -> "TrendsWithPickTokensGUI":
gui = TrendsWithPickTokensGUI(
token_selector=token_sector_cls(tokens),
update_handler=lambda tokens, split:
(tokens_selected or TrendsWithPickTokensGUI.default_tokens_plotter)
(tokens=tokens, corpus=corpus, n_columns=n_columns, split=split),
)
return gui
@staticmethod
def default_tokens_plotter(tokens: Sequence[str], corpus: VectorizedCorpus,
n_columns: int, split: bool):
indices: List[int] = [corpus.token2id[token] for token in tokens]
p = plotter.yearly_token_distribution_multiple_line_plot(
corpus,
indices,
width=1000,
height=600,
n_columns=n_columns if split else None,
)
if p is None:
return
show(p)
def _on_button_click(self, instance: widgets.Button):
self._state_index = (self._state_index + 1) % self._nStates
instance.icon = self.icon
instance.tooltip = self.tooltip
for listener in self._listeners:
listener(self.state)
def __init__(self,
path=os.getcwd(),
filename='',
title='',
select_desc='Select',
change_desc='Change',
show_hidden=False,
directory=False,
**kwargs):
self._select_desc = select_desc
self._default_path = path
self._show_hidden = show_hidden
self._select_desc = select_desc
self._change_desc = change_desc
self._path = path
self._updir = Button(description='Up Directory')
self._dircontent = Select(rows=8,
layout=Layout(width='auto',
grid_area='dircontent'))
self._cancel = Button(description='Cancel',
layout=Layout(width='auto', display='none'))
self._select = Button(description=self._select_desc,
layout=Layout(width='auto'))
self._label = HTML(value=self._LBL_TEMPLATE.format(
self._LBL_NOFILE, 'black'),
placeholder='',
description='')
self._title = HTML(value=title)
if title is '':
self._title.layout.display = 'none'
self._updir.on_click(self._on_updir_click)
self._select.on_click(self._on_select_click)
self._cancel.on_click(self._on_cancel_click)
# Layout
self._gb = GridBox(children=[self._updir, self._dircontent],
layout=Layout(display='none',
width='500px',
grid_gap='0px 0px',
grid_template_rows='auto auto',
grid_template_columns='60% 40%',
grid_template_areas='''
'pathlist filename'
'dircontent dircontent'
'''))
self._dircontent.observe(self._on_dircontent_select, names='value')
buttonbar = HBox(children=[
self._select,
self._cancel,
self._label,
],
layout=Layout(width='auto'))
# Call setter to set initial form values
self._set_form_values(self._path)
# Call VBox super class __init__
super().__init__(children=[
self._gb,
buttonbar,
],
layout=Layout(width='auto'),
**kwargs)
def __init__(self):
micron_units = Label('micron') # use "option m" (Mac, for micro symbol)
constWidth = '180px'
tab_height = '500px'
stepsize = 10
#style = {'description_width': '250px'}
style = {'description_width': '25%'}
layout = {'width': '400px'}
name_button_layout={'width':'25%'}
widget_layout = {'width': '15%'}
units_button_layout ={'width':'15%'}
desc_button_layout={'width':'45%'}
param_name1 = Button(description='tumor_radius', disabled=True, layout=name_button_layout)
param_name1.style.button_color = 'lightgreen'
self.tumor_radius = FloatText(
value=250.0,
step=10,
style=style, layout=widget_layout)
param_name2 = Button(description='oncoprotein_mean', disabled=True, layout=name_button_layout)
param_name2.style.button_color = 'tan'
self.oncoprotein_mean = FloatText(
value=1.0,
step=0.1,
style=style, layout=widget_layout)
param_name3 = Button(description='oncoprotein_sd', disabled=True, layout=name_button_layout)
param_name3.style.button_color = 'lightgreen'
self.oncoprotein_sd = FloatText(
value=0.25,
step=0.01,
style=style, layout=widget_layout)
param_name4 = Button(description='oncoprotein_min', disabled=True, layout=name_button_layout)
param_name4.style.button_color = 'tan'
self.oncoprotein_min = FloatText(
value=0.0,
step=0.01,
style=style, layout=widget_layout)
param_name5 = Button(description='oncoprotein_max', disabled=True, layout=name_button_layout)
param_name5.style.button_color = 'lightgreen'
self.oncoprotein_max = FloatText(
value=2,
step=0.1,
style=style, layout=widget_layout)
units_button1 = Button(description='micron', disabled=True, layout=units_button_layout)
units_button1.style.button_color = 'lightgreen'
units_button2 = Button(description='', disabled=True, layout=units_button_layout)
units_button2.style.button_color = 'tan'
units_button3 = Button(description='', disabled=True, layout=units_button_layout)
units_button3.style.button_color = 'lightgreen'
units_button4 = Button(description='', disabled=True, layout=units_button_layout)
units_button4.style.button_color = 'tan'
units_button5 = Button(description='', disabled=True, layout=units_button_layout)
units_button5.style.button_color = 'lightgreen'
desc_button1 = Button(description='initial tumor radius', disabled=True, layout=desc_button_layout)
desc_button1.style.button_color = 'lightgreen'
desc_button2 = Button(description='mean oncoprotein value p at start', disabled=True, layout=desc_button_layout)
desc_button2.style.button_color = 'tan'
desc_button3 = Button(description='standard deviation of oncoprotein p at start', disabled=True, layout=desc_button_layout)
desc_button3.style.button_color = 'lightgreen'
desc_button4 = Button(description='p is not allowed to fall below this value', disabled=True, layout=desc_button_layout)
desc_button4.style.button_color = 'tan'
desc_button5 = Button(description='p is not allowed to exceed this value', disabled=True, layout=desc_button_layout)
desc_button5.style.button_color = 'lightgreen'
row1 = [param_name1, self.tumor_radius, units_button1, desc_button1]
row2 = [param_name2, self.oncoprotein_mean, units_button2, desc_button2]
row3 = [param_name3, self.oncoprotein_sd, units_button3, desc_button3]
row4 = [param_name4, self.oncoprotein_min, units_button4, desc_button4]
row5 = [param_name5, self.oncoprotein_max, units_button5, desc_button5]
box_layout = Layout(display='flex', flex_flow='row', align_items='stretch', width='100%')
box1 = Box(children=row1, layout=box_layout)
box2 = Box(children=row2, layout=box_layout)
box3 = Box(children=row3, layout=box_layout)
box4 = Box(children=row4, layout=box_layout)
box5 = Box(children=row5, layout=box_layout)
self.tab = VBox([
box1,
box2,
box3,
box4,
box5,
])
class GUI(object):
_BUTTONS = {
"backstep": {
"icon": "step-backward",
"tooltip": "Step to the previous instruction",
},
"step": {
"icon": "step-forward",
"tooltip": "Step to the next instruction",
},
"previous": {
"icon": "reply",
"tooltip": "Go to th previous sourceline",
},
"next": {
"icon": "share",
"tooltip": "Go to the next sourceline",
},
"start": {
"icon": "arrow-up",
"tooltip": "Go to the start of the program",
},
"finish": {
"icon": "arrow-down",
"tooltip": "Go to the end of the program",
},
"reverse": {
"icon": "fast-backward",
"tooltip": "Continue execution backwards until breakpoint is hit",
},
"continue": {
"icon": "fast-forward",
"tooltip": "Continue execution until breakpoint is hit",
},
}
def __init__(self):
# Stores the respective line number and variable changes for each
# exection step
self._tracer = TimeTravelTracer()
self._current_state = None
self._debugger = None
self._code_output = HTML()
self._var_output = Output()
self._watchpoint_output = Output()
self._breakpoint_output = Output()
self._diff_slider = IntSlider(
min=1,
readout=False,
layout=Layout(width="99%"),
tooltip="Execution timeline",
)
self._diff_slider.observe(self._handle_diff_slider, names="value")
self._autoplay = Play(
tooltip="Automatic playback of the execution",
layout=Layout(height="30px"),
)
self._auto_link = jsdlink((self._autoplay, "value"),
(self._diff_slider, "value"))
self._speed_slider = IntSlider(description="Delay (ms)",
min=100,
max=1000,
step=100,
value=500)
self._speed_link = jsdlink((self._speed_slider, "value"),
(self._autoplay, "interval"))
self._reverse_autoplay = ToggleButton(
value=False,
icon="history",
tooltip="Reverse autoplay",
layout=Layout(width="40px"),
)
self._reverse_autoplay.observe(self._handle_reverse_button)
self._watchpoint_input = Text(
layout=Layout(width="150px"),
placeholder="Watch expression",
)
self._add_watchpoint = Button(
icon="plus",
tooltip="Add an expression or variable to watch",
layout=Layout(width="50px"),
)
self._add_watchpoint.on_click(self.watch_command)
self._watchpoint_dropdown = Dropdown(layout=Layout(width="150px"), )
self._remove_watchpoint = Button(
icon="trash",
tooltip="Remove a watchpoint",
layout=Layout(width="50px"),
)
self._remove_watchpoint.on_click(self.unwatch_command)
self._breakpoint_layout = GridspecLayout(3, 1)
self._add_breakpoint = Button(
icon="plus",
tooltip="Add a breakpoint",
name="breakpoint_button",
layout=Layout(width="40px"),
)
self._add_breakpoint.on_click(self._handle_breakpoint)
self._disable_breakpoint_button = Button(
icon="eye-slash",
tooltip="Disable breakpoint",
layout=Layout(width="50px"),
)
self._disable_breakpoint_button.on_click(self.disable_command)
self._remove_breakpoint_button = Button(
icon="trash",
tooltip="Remove breakpoint",
layout=Layout(width="50px"),
)
self._remove_breakpoint_button.on_click(self.delete_command)
self._breakpoint_dropdown = Dropdown(layout=Layout(width="70px"))
self._function_dropdown = Dropdown(layout=Layout(width="200px"))
self._function_dropdown.disabled = True
self._breakpoint_type = Dropdown(
options=["Line", "Function", "Conditional"],
value="Line",
layout=Layout(width="100px"),
)
self._breakpoint_type.observe(self._handle_breakpoint_type,
names="value")
self._condition_input = Text(placeholder="Enter condition",
layout=Layout(width="200px"))
self._condition_input.disabled = True
self._line_input = Text(
placeholder="Line Number",
name="line_input",
layout=Layout(width="100px"),
)
self._breakpoint_layout = VBox([
HBox([
self._add_breakpoint,
self._breakpoint_type,
self._function_dropdown,
self._line_input,
self._condition_input,
self._breakpoint_dropdown,
self._remove_breakpoint_button,
self._disable_breakpoint_button,
]),
self._breakpoint_output,
])
self._search_input = Text(placeholder="Search...")
self._search_input.observe(self._handle_search_input, names="value")
self._search_results = Output()
self._search_layout = VBox([
self._search_input,
self._search_results,
])
# Remove shadows from scrolling
style = """
<style>
.jupyter-widgets-output-area .output_scroll {
border-radius: unset !important;
-webkit-box-shadow: unset !important;
box-shadow: unset !important;
}
</style>
"""
display(HTML(style))
for key, item in self._BUTTONS.items():
self.register_button(key, **item)
self._code_layout = GridspecLayout(4, 4, grid_gap="20px")
self._code_layout[0:4, 0:3] = HBox(
[self._code_output],
layout=Layout(height="500px",
overflow_y="scroll",
border="2px solid black"),
)
self._code_layout[0:2, 3] = self._var_output
self._code_layout[2:4, 3] = VBox([
HBox([self._add_watchpoint, self._watchpoint_input]),
HBox([self._remove_watchpoint, self._watchpoint_dropdown]),
self._watchpoint_output,
])
self._code_nav_layout = VBox([
HBox([
*self.get_buttons(),
self._autoplay,
self._reverse_autoplay,
self._speed_slider,
]),
self._diff_slider,
self._code_layout,
])
self._main_layout = Tab(
[
self._code_nav_layout,
self._breakpoint_layout,
self._search_layout,
],
layout=Layout(height="650px"),
)
self._main_layout.set_title(0, "Code")
self._main_layout.set_title(1, "Breakpoints")
self._main_layout.set_title(2, "Search")
display(self._main_layout)
def __enter__(self, *args, **kwargs):
self._tracer.set_trace()
def __exit__(self, *args, **kwargs):
diffs, source_map = self._tracer.get_trace()
search_engine = SearchEngine()
self._debugger = TimeTravelDebugger(diffs, source_map, self.update,
search_engine)
self._debugger.start_debugger()
self._diff_slider.max = len(diffs) - 1
self._function_dropdown.options = self._debugger.source_map.keys()
def get_buttons(self, *keys):
if not keys:
return [
self._BUTTONS[key]["button"] for key in self._BUTTONS.keys()
]
return [self._BUTTONS[key]["button"] for key in keys]
def register_button(self, key, **kwargs):
button = Button(description="", layout=Layout(width="40px"), **kwargs)
func = getattr(self, key + "_command")
button.on_click(func)
self._BUTTONS[key]["button"] = button
def update(self, state=None):
if state is not None:
self._current_state = state
self._diff_slider.value = self._debugger._state_machine._exec_point
self._BUTTONS["previous"]["button"].disabled = self._debugger.at_start
self._BUTTONS["start"]["button"].disabled = self._debugger.at_start
self._BUTTONS["backstep"]["button"].disabled = self._debugger.at_start
self._BUTTONS["next"]["button"].disabled = self._debugger.at_end
self._BUTTONS["finish"]["button"].disabled = self._debugger.at_end
self._BUTTONS["step"]["button"].disabled = self._debugger.at_end
self._breakpoint_dropdown.options = [
b.id for b in self._debugger.breakpoints
]
self._watchpoint_dropdown.options = [
b.id for b in self._debugger.watchpoints
]
self.list_command()
with self._var_output:
clear_output(wait=True)
self.print_command()
with self._breakpoint_output:
clear_output(wait=True)
self.breakpoints_command()
with self._watchpoint_output:
clear_output(wait=True)
self.list_watch_command()
def log(self, *objects, sep=" ", end="\n", flush=False):
"""Like print(), but always sending to file given at initialization,
and always flushing"""
print(*objects, sep=sep, end=end, flush=True)
# COMMANDS
def print_command(self, arg=""):
"""Print all variables or pass an expression to evaluate in the
current context"""
# Shorthand such that the following code is not as lengthy
curr_vars = self._current_state
template = "|`{}`|{}|`{!r}`|"
header = "| Variable | Type | Value |"
split = "| --- | --- | --- |"
variable_table = header + "\n" + split + "\n"
variable_table += "\n".join(
template.format(var, type(curr_vars[var]), curr_vars[var])
for var in curr_vars if not var.startswith("__"))
display(Markdown(variable_table))
def step_command(self, arg=""):
""" Step to the next instruction """
self._debugger.step_forward()
def backstep_command(self, arg=""):
""" Step to the previous instruction """
self._debugger.step_backward()
def list_command(self, arg=""):
"""Show current function. If arg is given, show its source code."""
display_current_line = self._debugger.curr_line
code = self._debugger.get_source_for_func()
source_lines = open(code["filename"]).read()
css = f"""
<style>
{cssfile}
</style>
"""
lexer = lexers.get_lexer_by_name("python")
formatter = formatters.HtmlFormatter(
linenos=True,
anchorlinenos=True,
full=True,
linespans=True,
wrapcode=True,
)
coloured = highlight(source_lines, lexer=lexer, formatter=formatter)
doc = html.fromstring(coloured)
current_line_breakpoint = False
# Highlight all breakpoints on the current file
for bp in self._debugger.breakpoints:
if self._debugger.curr_diff.file_name != bp.abs_filename:
continue
if bp.breakpoint_type != BPType.FUNC:
elem = doc.get_element_by_id(f"True-{bp.lineno}", None)
if bp.lineno == display_current_line:
current_line_breakpoint = True
if elem is not None:
elem.set("class", "breakpoint")
if not bp.active:
elem.set("class", "inactive")
elem = doc.get_element_by_id(f"True-{display_current_line}", None)
if elem is not None:
if not current_line_breakpoint and not self._autoplay._playing:
elem.set("class", "currentline")
elif self._autoplay._playing:
elem.set("class", "currentline-running")
else:
elem.set("class", "hit")
coloured = html.tostring(doc).decode("utf-8").strip()
self._code_output.value = css + coloured
def next_command(self, arg=""):
""" Step to the next source line """
self._debugger.next()
def previous_command(self, arg=""):
""" Step to the previous source line """
self._debugger.previous()
def finish_command(self, arg=""):
""" Finish the current function execution """
self._debugger.finish()
def start_command(self, arg=""):
""" Go to start of the current function call """
self._debugger.start()
def continue_command(self, arg=""):
""" Continue execution forward until a breakpoint is hit """
self._debugger.continue_()
def reverse_command(self, arg=""):
""" Continue execution backward until a breakpoint is hit """
self._debugger.reverse()
def watch_command(self, change):
""" Insert a watchpoint """
arg = self._watchpoint_input.value
self._debugger.add_watchpoint(expression=arg)
self._watchpoint_input.value = ""
self.update()
def list_watch_command(self):
header = "| ID | Expression | Value |\n"
split = "|---|---|---|\n"
template = "|{}|`{}`|`{!r}`|\n"
wpstr = header + split
for wp in self._debugger.watchpoints:
wpstr += template.format(*wp)
display(Markdown(wpstr))
def unwatch_command(self, change):
""" Remove a watchpoint """
arg = self._watchpoint_dropdown.value
if not arg:
return
if not self._debugger.remove_watchpoint(int(arg)):
print(f"Watchpoint with id {arg} does not exist.")
else:
print(f"Successfully removed watchpoint {arg}.")
self.update()
def break_command(self, arg=""):
""" Insert a breakpoint at the given location """
res = None
# Find out which type of breakpoint we want to insert
if arg.isnumeric():
# Line breakpoint
res = self._debugger.add_breakpoint(arg, "line")
elif ":" not in arg:
# Function breakpoint for different file
res = self._debugger.add_breakpoint(arg, "func")
else:
filename, function_name = arg.split(":")
res = self._debugger.add_breakpoint(function_name,
"func",
filename=filename)
if res is not None:
print(f"Breakpoint {res.id} added.")
else:
print("Could not add breakpoint.")
def breakpoints_command(self, arg=""):
""" List all breakpoints """
header = "| ID | Type | Location | Status | Condition |\n"
split = "|---|---|---|---|---|\n"
bpstr = header + split
for bp in self._debugger.breakpoints:
bpstr += "|" + "|".join(bp) + "|\n"
display(Markdown(bpstr))
def delete_command(self, change):
""" Remove the given breakpoint """
arg = self._breakpoint_dropdown.value
if not arg:
return
self._debugger.remove_breakpoint(int(arg))
self.update()
def disable_command(self, arg=""):
""" Disable the given breakpoint """
arg = self._breakpoint_dropdown.value
if not arg:
return
self._debugger.disable_breakpoint(int(arg))
self.update()
def enable_command(self, arg=""):
""" Enable the given breakpoint """
self._debugger.enable_breakpoint(int(arg))
def _handle_diff_slider(self, change):
braked = self._debugger.step_to_index(
change["new"], ignore_breakpoints=self._autoplay._playing)
if braked:
self._autoplay._playing = False
def _handle_reverse_button(self, change):
self._autoplay.step = -self._autoplay.step
def _handle_breakpoint(self, change):
type = self._breakpoint_type.value
function = self._function_dropdown.value
line = self._line_input.value
condition = self._condition_input.value
if type != "Function":
if not line.isnumeric() or line is None:
self._line_input.value = ""
self._line_input.placeholder = "Please enter a valid number!"
return
if type == "Conditional":
try:
eval(condition)
except SyntaxError:
if self._condition_input.value:
self._condition_input.placeholder = "Invalid expression!"
self._condition_input.value = ""
return
except NameError:
pass
if type == "Function":
self._debugger.add_breakpoint(funcname=function)
if type == "Line":
self._debugger.add_breakpoint(lineno=line)
if type == "Conditional":
self._debugger.add_breakpoint(lineno=line, cond=condition)
self.update()
def _handle_breakpoint_type(self, change):
self._function_dropdown.disabled = change["new"] != "Function"
self._condition_input.disabled = change["new"] != "Conditional"
self._line_input.disabled = change["new"] == "Function"
def _handle_search_input(self, change):
try:
input = change["new"]
event_type, query = input.split(" ", 1)
events = self._debugger.search(event_type, query)
except:
return
with self._search_results:
clear_output()
for event in events:
goto = Button(
icon="angle-right",
layout=Layout(width="30px", height="30px"),
)
goto.on_click(lambda change: self._debugger.step_to_index(
event.exec_point, ignore_breakpoints=True))
display(HBox([goto, Label(value=str(event))]))
def __init__(self):
micron_units = Label(
'micron') # use "option m" (Mac, for micro symbol)
constWidth = '180px'
tab_height = '500px'
stepsize = 10
#style = {'description_width': '250px'}
style = {'description_width': '25%'}
layout = {'width': '400px'}
name_button_layout = {'width': '25%'}
widget_layout = {'width': '15%'}
units_button_layout = {'width': '15%'}
desc_button_layout = {'width': '45%'}
param_name1 = Button(description='persistence_time',
disabled=True,
layout=name_button_layout)
param_name1.style.button_color = 'lightgreen'
self.persistence_time = FloatText(value=10,
step=1,
style=style,
layout=widget_layout)
param_name2 = Button(description='migration_speed',
disabled=True,
layout=name_button_layout)
param_name2.style.button_color = 'tan'
self.migration_speed = FloatText(value=2,
step=0.1,
style=style,
layout=widget_layout)
param_name3 = Button(description='migration_bias',
disabled=True,
layout=name_button_layout)
param_name3.style.button_color = 'lightgreen'
self.migration_bias = FloatText(value=1.0,
step=0.1,
style=style,
layout=widget_layout)
param_name4 = Button(description='fixed_persistence',
disabled=True,
layout=name_button_layout)
param_name4.style.button_color = 'tan'
self.fixed_persistence = Checkbox(value=False,
style=style,
layout=widget_layout)
param_name5 = Button(description='number_of_cells',
disabled=True,
layout=name_button_layout)
param_name5.style.button_color = 'lightgreen'
self.number_of_cells = IntText(value=3,
step=0.1,
style=style,
layout=widget_layout)
units_button1 = Button(description='min',
disabled=True,
layout=units_button_layout)
units_button1.style.button_color = 'lightgreen'
units_button2 = Button(description='micron/min',
disabled=True,
layout=units_button_layout)
units_button2.style.button_color = 'tan'
units_button3 = Button(description='',
disabled=True,
layout=units_button_layout)
units_button3.style.button_color = 'lightgreen'
units_button4 = Button(description='',
disabled=True,
layout=units_button_layout)
units_button4.style.button_color = 'tan'
units_button5 = Button(description='',
disabled=True,
layout=units_button_layout)
units_button5.style.button_color = 'lightgreen'
desc_button1 = Button(description='mean persistence time',
disabled=True,
layout=desc_button_layout)
desc_button1.style.button_color = 'lightgreen'
desc_button2 = Button(description='migration speed',
disabled=True,
layout=desc_button_layout)
desc_button2.style.button_color = 'tan'
desc_button3 = Button(description='migration bias parameter',
disabled=True,
layout=desc_button_layout)
desc_button3.style.button_color = 'lightgreen'
desc_button4 = Button(
description=
'true if each migration path has same duration (future PhysiCell versions)',
disabled=True,
layout=desc_button_layout)
desc_button4.style.button_color = 'tan'
desc_button5 = Button(description='number of cell tracks to simulate',
disabled=True,
layout=desc_button_layout)
desc_button5.style.button_color = 'lightgreen'
row1 = [
param_name1, self.persistence_time, units_button1, desc_button1
]
row2 = [param_name2, self.migration_speed, units_button2, desc_button2]
row3 = [param_name3, self.migration_bias, units_button3, desc_button3]
row4 = [
param_name4, self.fixed_persistence, units_button4, desc_button4
]
row5 = [param_name5, self.number_of_cells, units_button5, desc_button5]
box_layout = Layout(display='flex',
flex_flow='row',
align_items='stretch',
width='100%')
box1 = Box(children=row1, layout=box_layout)
box2 = Box(children=row2, layout=box_layout)
box3 = Box(children=row3, layout=box_layout)
box4 = Box(children=row4, layout=box_layout)
box5 = Box(children=row5, layout=box_layout)
self.tab = VBox([
box1,
box2,
box3,
box4,
box5,
])
def _widget(self):
""" Create IPython widget for display within a notebook """
try:
return self._cached_widget
except AttributeError:
pass
try:
from ipywidgets import Layout, VBox, HBox, IntText, Button, HTML, Accordion
except ImportError:
self._cached_widget = None
return None
layout = Layout(width="150px")
if self.dashboard_link:
dashboard_link = (
'<p><b>Dashboard: </b><a href="%s" target="_blank">%s</a></p>\n'
% (self.dashboard_link, self.dashboard_link))
else:
dashboard_link = ""
if self.jupyter_link:
jupyter_link = (
'<p><b>Jupyter: </b><a href="%s" target="_blank">%s</a></p>\n'
% (self.jupyter_link, self.jupyter_link))
else:
jupyter_link = ""
title = "<h2>%s</h2>" % self._cluster_class_name
title = HTML(title)
dashboard = HTML(dashboard_link)
jupyter = HTML(jupyter_link)
status = HTML(self._widget_status(), layout=Layout(min_width="150px"))
if self._supports_scaling:
request = IntText(self.initial_node_count,
description="Nodes",
layout=layout)
scale = Button(description="Scale", layout=layout)
minimum = IntText(0, description="Minimum", layout=layout)
maximum = IntText(0, description="Maximum", layout=layout)
adapt = Button(description="Adapt", layout=layout)
accordion = Accordion(
[HBox([request, scale]),
HBox([minimum, maximum, adapt])],
layout=Layout(min_width="500px"),
)
accordion.selected_index = None
accordion.set_title(0, "Manual Scaling")
accordion.set_title(1, "Adaptive Scaling")
def adapt_cb(b):
self.adapt(minimum=minimum.value, maximum=maximum.value)
update()
adapt.on_click(adapt_cb)
def scale_cb(b):
with log_errors():
n = request.value
with suppress(AttributeError):
self._adaptive.stop()
self.scale(n)
update()
scale.on_click(scale_cb)
else:
accordion = HTML("")
box = VBox([title, HBox([status, accordion]), jupyter, dashboard])
self._cached_widget = box
def update():
self.close_when_disconnect()
status.value = self._widget_status()
pc = PeriodicCallback(update, 500) # , io_loop=self.loop)
self.periodic_callbacks["cluster-repr"] = pc
pc.start()
return box
class NewSageExplorer(VBox):
"""Sage Explorer in Jupyter Notebook"""
value = Any()
def __init__(self, obj=None):
"""
TESTS::
sage: from new_sage_explorer.new_sage_explorer import NewSageExplorer
sage: t = StandardTableaux(15).random_element()
sage: widget = NewSageExplorer(t)
"""
super(NewSageExplorer, self).__init__()
self.history = []
self.set_value(obj)
def compute(self):
obj = self.value
self.titlebox = ExplorerTitle(obj)
self.description = ExplorerDescription(obj)
self.props = ExplorerProperties(obj)
def handle_click(e):
self.set_value(e.source.value)
for v in self.props.children:
if type(v) == ExplorableValue:
v.clc.on_dom_event(handle_click)
self.propsbox = VBox([self.description, self.props])
self.titlebox.add_class('titlebox')
self.titlebox.add_class('lightborder')
self.visualbox = ExplorerVisual(obj)
self.visualbox.add_class('visualbox')
self.top = VBox(
[self.titlebox,
HBox(
[self.propsbox, Separator(' '), self.visualbox],
layout=Layout(margin='10px 0')
)
],
layout=Layout(border='1px solid yellow')
)
self.menusbox = ExplorerMenus(obj)
self.namingbox = ExplorerNaming(obj)
self.searchbox = ExplorerMethodSearch(obj)
self.inputbox = Text()
self.inputbutton = Button(description='-', layout=Layout(width='30px'))
self.gobutton = Button(description='Run!', tooltip='Run the method with specified arguments')
def compute_selected_method(button):
args = []
if self.inputbox.value:
args = self.inputbox.value.split(',')
try:
# if AlarmInterrupt:
# alarm(TIMEOUT)
out = self.searchbox.get_member()(obj, *args)
# if AlarmInterrupt:
# cancel_alarm()
#except AlarmInterrupt:
# self.output.value = to_html("Timeout!")
except Exception as e:
self.outputbox.output.value = 'Error: %s; input=%s' % (e, str(args))
return
self.outputbox.output.value = '$%s$' % out
self.gobutton.on_click(compute_selected_method)
self.actionbox = HBox([
self.namingbox,
Separator('.'),
self.searchbox,
Separator('('),
self.inputbox,
self.inputbutton,
Separator(')'),
self.gobutton
])
self.outputbox = ExplorerOutput(obj)
self.helpbox = ExplorerHelp(obj)
self.helpbox.update_title(self.description.content + " ..")
self.bottom = VBox([self.actionbox, self.outputbox, self.helpbox])
self.children = (self.top, self.bottom)
def set_value(self, obj):
r"""
Set new math object `obj` to the explorer.
TESTS::
sage: from new_sage_explorer.new_sage_explorer import NewSageExplorer
sage: from sage.combinat.partition import Partition
sage: p = Partition([3,3,2,1])
sage: e = NewSageExplorer(p)
sage: e.get_value()
[3, 3, 2, 1]
sage: from sage.combinat.tableau import Tableau
sage: t = Tableau([[1,2,3,4], [5,6]])
sage: e.set_value(t)
sage: e.get_value()
[[1, 2, 3, 4], [5, 6]]
"""
self.history.append(obj)
self.value = obj
self.compute()
def get_value(self):
r"""
Return math object currently explored.
TESTS::
sage: from new_sage_explorer.new_sage_explorer import NewSageExplorer
sage: from sage.combinat.partition import Partition
sage: p = Partition([3,3,2,1])
sage: e = NewSageExplorer(p)
sage: e.get_value()
[3, 3, 2, 1]
"""
return self.value
def pop_value(self):
r"""
Set again previous math object to the explorer.
TESTS::
sage: from new_sage_explorer.new_sage_explorer import NewSageExplorer
sage: from sage.combinat.partition import Partition
sage: p = Partition([3,3,2,1])
sage: e = NewSageExplorer(p)
sage: from sage.combinat.tableau import Tableau
sage: t = Tableau([[1,2,3,4], [5,6]])
sage: e.set_value(t)
sage: e.get_value()
[[1, 2, 3, 4], [5, 6]]
sage: e.pop_value()
sage: e.get_value()
[3, 3, 2, 1]
"""
if self.history:
self.history.pop()
if self.history:
self.value = self.history[-1]
else:
self.value = None
def __init__(self):
micron_units = Label(
'micron') # use "option m" (Mac, for micro symbol)
constWidth = '180px'
tab_height = '500px'
stepsize = 10
#style = {'description_width': '250px'}
style = {'description_width': '25%'}
layout = {'width': '400px'}
name_button_layout = {'width': '25%'}
widget_layout = {'width': '15%'}
units_button_layout = {'width': '15%'}
desc_button_layout = {'width': '45%'}
param_name1 = Button(description='random_seed',
disabled=True,
layout=name_button_layout)
param_name1.style.button_color = 'lightgreen'
self.random_seed = IntText(value=0,
step=1,
style=style,
layout=widget_layout)
param_name2 = Button(description='virion_uncoating_rate',
disabled=True,
layout=name_button_layout)
param_name2.style.button_color = 'tan'
self.virion_uncoating_rate = FloatText(value=0.05,
step=0.01,
style=style,
layout=widget_layout)
param_name3 = Button(description='uncoated_to_RNA_rate',
disabled=True,
layout=name_button_layout)
param_name3.style.button_color = 'lightgreen'
self.uncoated_to_RNA_rate = FloatText(value=0.05,
step=0.01,
style=style,
layout=widget_layout)
param_name4 = Button(description='protein_synthesis_rate',
disabled=True,
layout=name_button_layout)
param_name4.style.button_color = 'tan'
self.protein_synthesis_rate = FloatText(value=0.05,
step=0.01,
style=style,
layout=widget_layout)
param_name5 = Button(description='virion_assembly_rate',
disabled=True,
layout=name_button_layout)
param_name5.style.button_color = 'lightgreen'
self.virion_assembly_rate = FloatText(value=0.05,
step=0.01,
style=style,
layout=widget_layout)
param_name6 = Button(description='virion_export_rate',
disabled=True,
layout=name_button_layout)
param_name6.style.button_color = 'tan'
self.virion_export_rate = FloatText(value=0.005,
step=0.001,
style=style,
layout=widget_layout)
param_name7 = Button(description='max_infected_apoptosis_rate',
disabled=True,
layout=name_button_layout)
param_name7.style.button_color = 'lightgreen'
self.max_infected_apoptosis_rate = FloatText(value=0.001,
step=0.0001,
style=style,
layout=widget_layout)
param_name8 = Button(description='max_apoptosis_half_max',
disabled=True,
layout=name_button_layout)
param_name8.style.button_color = 'tan'
self.max_apoptosis_half_max = FloatText(value=500,
step=10,
style=style,
layout=widget_layout)
param_name9 = Button(description='apoptosis_hill_power',
disabled=True,
layout=name_button_layout)
param_name9.style.button_color = 'lightgreen'
self.apoptosis_hill_power = FloatText(value=1,
step=0.1,
style=style,
layout=widget_layout)
param_name10 = Button(description='virion_uptake_rate',
disabled=True,
layout=name_button_layout)
param_name10.style.button_color = 'tan'
self.virion_uptake_rate = FloatText(value=1,
step=0.1,
style=style,
layout=widget_layout)
param_name11 = Button(description='virus_fraction_released_at_death',
disabled=True,
layout=name_button_layout)
param_name11.style.button_color = 'lightgreen'
self.virus_fraction_released_at_death = FloatText(value=0,
step=0.01,
style=style,
layout=widget_layout)
param_name12 = Button(description='plot_scale',
disabled=True,
layout=name_button_layout)
param_name12.style.button_color = 'tan'
self.plot_scale = FloatText(value=100,
step=10,
style=style,
layout=widget_layout)
units_button1 = Button(description='',
disabled=True,
layout=units_button_layout)
units_button1.style.button_color = 'lightgreen'
units_button2 = Button(description='1/min',
disabled=True,
layout=units_button_layout)
units_button2.style.button_color = 'tan'
units_button3 = Button(description='1/min',
disabled=True,
layout=units_button_layout)
units_button3.style.button_color = 'lightgreen'
units_button4 = Button(description='1/min',
disabled=True,
layout=units_button_layout)
units_button4.style.button_color = 'tan'
units_button5 = Button(description='1/min',
disabled=True,
layout=units_button_layout)
units_button5.style.button_color = 'lightgreen'
units_button6 = Button(description='1/min',
disabled=True,
layout=units_button_layout)
units_button6.style.button_color = 'tan'
units_button7 = Button(description='1/min',
disabled=True,
layout=units_button_layout)
units_button7.style.button_color = 'lightgreen'
units_button8 = Button(description='virion',
disabled=True,
layout=units_button_layout)
units_button8.style.button_color = 'tan'
units_button9 = Button(description='',
disabled=True,
layout=units_button_layout)
units_button9.style.button_color = 'lightgreen'
units_button10 = Button(description='1/min',
disabled=True,
layout=units_button_layout)
units_button10.style.button_color = 'tan'
units_button11 = Button(description='',
disabled=True,
layout=units_button_layout)
units_button11.style.button_color = 'lightgreen'
units_button12 = Button(description='',
disabled=True,
layout=units_button_layout)
units_button12.style.button_color = 'tan'
desc_button1 = Button(description='',
tooltip='',
disabled=True,
layout=desc_button_layout)
desc_button1.style.button_color = 'lightgreen'
desc_button2 = Button(
description='rate at which an internalized virion is uncoated',
tooltip='rate at which an internalized virion is uncoated',
disabled=True,
layout=desc_button_layout)
desc_button2.style.button_color = 'tan'
desc_button3 = Button(
description=
'rate at which uncoated virion makes its mRNA available',
tooltip='rate at which uncoated virion makes its mRNA available',
disabled=True,
layout=desc_button_layout)
desc_button3.style.button_color = 'lightgreen'
desc_button4 = Button(
description='rate at mRNA creates complete set of proteins',
tooltip='rate at mRNA creates complete set of proteins',
disabled=True,
layout=desc_button_layout)
desc_button4.style.button_color = 'tan'
desc_button5 = Button(
description=
'rate at which viral proteins are assembled into complete virion',
tooltip=
'rate at which viral proteins are assembled into complete virion',
disabled=True,
layout=desc_button_layout)
desc_button5.style.button_color = 'lightgreen'
desc_button6 = Button(
description='rate at which a virion is exported from a live cell',
tooltip='rate at which a virion is exported from a live cell',
disabled=True,
layout=desc_button_layout)
desc_button6.style.button_color = 'tan'
desc_button7 = Button(
description='maximum rate of cell apoptosis due to viral infection',
tooltip='maximum rate of cell apoptosis due to viral infection',
disabled=True,
layout=desc_button_layout)
desc_button7.style.button_color = 'lightgreen'
desc_button8 = Button(
description=
'viral load at which cells reach half max apoptosis rate',
tooltip='viral load at which cells reach half max apoptosis rate',
disabled=True,
layout=desc_button_layout)
desc_button8.style.button_color = 'tan'
desc_button9 = Button(
description='Hill power for viral load apoptosis response',
tooltip='Hill power for viral load apoptosis response',
disabled=True,
layout=desc_button_layout)
desc_button9.style.button_color = 'lightgreen'
desc_button10 = Button(
description='rate coefficient for virion endocytosis',
tooltip='rate coefficient for virion endocytosis',
disabled=True,
layout=desc_button_layout)
desc_button10.style.button_color = 'tan'
desc_button11 = Button(
description='fraction of internal virus released at cell death',
tooltip='fraction of internal virus released at cell death',
disabled=True,
layout=desc_button_layout)
desc_button11.style.button_color = 'lightgreen'
desc_button12 = Button(description='scale for viral load coloring',
tooltip='scale for viral load coloring',
disabled=True,
layout=desc_button_layout)
desc_button12.style.button_color = 'tan'
row1 = [param_name1, self.random_seed, units_button1, desc_button1]
row2 = [
param_name2, self.virion_uncoating_rate, units_button2,
desc_button2
]
row3 = [
param_name3, self.uncoated_to_RNA_rate, units_button3, desc_button3
]
row4 = [
param_name4, self.protein_synthesis_rate, units_button4,
desc_button4
]
row5 = [
param_name5, self.virion_assembly_rate, units_button5, desc_button5
]
row6 = [
param_name6, self.virion_export_rate, units_button6, desc_button6
]
row7 = [
param_name7, self.max_infected_apoptosis_rate, units_button7,
desc_button7
]
row8 = [
param_name8, self.max_apoptosis_half_max, units_button8,
desc_button8
]
row9 = [
param_name9, self.apoptosis_hill_power, units_button9, desc_button9
]
row10 = [
param_name10, self.virion_uptake_rate, units_button10,
desc_button10
]
row11 = [
param_name11, self.virus_fraction_released_at_death,
units_button11, desc_button11
]
row12 = [param_name12, self.plot_scale, units_button12, desc_button12]
box_layout = Layout(display='flex',
flex_flow='row',
align_items='stretch',
width='100%')
box1 = Box(children=row1, layout=box_layout)
box2 = Box(children=row2, layout=box_layout)
box3 = Box(children=row3, layout=box_layout)
box4 = Box(children=row4, layout=box_layout)
box5 = Box(children=row5, layout=box_layout)
box6 = Box(children=row6, layout=box_layout)
box7 = Box(children=row7, layout=box_layout)
box8 = Box(children=row8, layout=box_layout)
box9 = Box(children=row9, layout=box_layout)
box10 = Box(children=row10, layout=box_layout)
box11 = Box(children=row11, layout=box_layout)
box12 = Box(children=row12, layout=box_layout)
self.tab = VBox([
box1,
box2,
box3,
box4,
box5,
box6,
box7,
box8,
box9,
box10,
box11,
box12,
])
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 _display(self):
step_slide = IntSlider(value=self.step,
min=-100,
max=100,
description='step')
delay_text = IntSlider(value=self.delay,
min=10,
max=1000,
description='delay')
checkbox_interpolate = Checkbox(self.interpolate,
description='interpolate')
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')
bg_color = ColorPicker(value='white', description='background')
bg_color.width = 100.
# t_interpolation = FloatSlider(value=0.5, min=0, max=1.0, step=0.1)
interpolation_type = Dropdown(value=self._iterpolation_type,
options=['linear', 'spline'])
camera_type = Dropdown(value=self.camera,
options=['perspective', 'orthographic'],
description='camera')
link((step_slide, 'value'), (self, 'step'))
link((delay_text, 'value'), (self, 'delay'))
link((checkbox_interpolate, 'value'), (self, 'interpolate'))
# link((t_interpolation, 'value'), (self, '_interpolation_t'))
link((interpolation_type, 'value'), (self, '_iterpolation_type'))
link((camera_type, 'value'), (self, 'camera'))
link((bg_color, 'value'), (self._view, 'background'))
# 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'))
qtconsole_button = self._make_button_qtconsole()
ibox = HBox([checkbox_interpolate, interpolation_type])
center_button = self._make_button_center()
render_button = self._show_download_image()
center_render_hbox = HBox([center_button, render_button])
v0_left = VBox([
step_slide,
delay_text,
bg_color,
ibox,
camera_type,
center_render_hbox,
qtconsole_button,
])
spin_box = VBox([
checkbox_spin, spin_x_slide, spin_y_slide, spin_z_slide,
spin_speed_slide
])
drag_button = Button(description='widget drag: off',
tooltip='dangerous')
def on_drag(drag_button):
if drag_button.description == 'widget drag: off':
self._view._set_draggable(True)
drag_button.description = 'widget drag: on'
else:
self._view._set_draggable(False)
drag_button.description = 'widget drag: off'
drag_nb = Button(description='notebook drag: off', tooltip='dangerous')
def on_drag_nb(drag_button):
if drag_nb.description == 'notebook drag: off':
self._view._set_notebook_draggable(True)
drag_nb.description = 'notebook drag: on'
else:
self._view._set_notebook_draggable(False)
drag_nb.description = 'notebook drag: off'
reset_nb = Button(description='notebook: reset', tooltip='reset?')
def on_reset(reset_nb):
self._view._reset_notebook()
dialog_button = Button(description='dialog', tooltip='make a dialog')
def on_dialog(dialog_button):
self._view._remote_call('setDialog', target='Widget')
lucky_button = Button(description='lucky',
tooltip='try best to make a good layout')
def on_being_lucky(dialog_button):
self._view._move_notebook_to_the_right()
self._view._remote_call('setDialog', target='Widget')
drag_button.on_click(on_drag)
drag_nb.on_click(on_drag_nb)
reset_nb.on_click(on_reset)
dialog_button.on_click(on_dialog)
lucky_button.on_click(on_being_lucky)
drag_box = HBox(
[drag_button, drag_nb, reset_nb, dialog_button, lucky_button])
gen_box = HBox([
v0_left,
])
theme_box = Box(
[self._make_button_theme(),
self._make_button_reset_theme()])
hide_box = Box([])
help_url_box = self._show_website()
picked_box = HBox([
self.picked_widget,
])
component_slider = get_widget_by_name(self.repr_widget,
'component_slider')
repr_add_widget = self._make_add_repr_widget(component_slider)
repr_box = HBox([self.repr_widget, repr_add_widget])
repr_playground = self._make_selection_repr_buttons()
export_image_box = HBox([self._make_button_export_image()])
extra_list = [(drag_box, 'Drag'), (spin_box, 'spin_box'),
(picked_box, 'picked atom'),
(repr_playground, 'quick repr'),
(export_image_box, 'Image')]
extra_box = Tab([w for w, _ in extra_list])
[
extra_box.set_title(i, title)
for i, (_, title) in enumerate(extra_list)
]
box_couple = [(gen_box, 'General'), (repr_box, 'Representation'),
(self._preference_widget, 'Preference'),
(theme_box, 'Theme'), (extra_box, 'Extra'),
(hide_box, 'Hide'), (help_url_box, 'Help')]
for box in gen_box.children:
make_default_slider_width(box)
make_default_slider_width(self._preference_widget)
tab = Tab([box for box, _ in box_couple])
[tab.set_title(i, title) for i, (_, title) in enumerate(box_couple)]
return tab
class Core:
# All constants that will be injected into global scope in the user"s cell
global_constants = {
"pi": pi
}
# All methods/fields from this class that will be exposed as global in user"s scope
global_fields = {
"canvas", "size", "width", "height",
"mouse_x", "mouse_y", "mouse_is_pressed",
"fill_style", "stroke_style",
"clear", "background",
"rect", "square", "fill_rect", "stroke_rect", "clear_rect",
"fill_text", "stroke_text", "text_align",
"draw_line",
"circle", "fill_circle", "stroke_circle", "fill_arc", "stroke_arc",
"print"
}
# All methods that user will be able to define and override
global_methods = {
"draw", "setup",
"mouse_down", "mouse_up", "mouse_moved"
}
def __init__(self, globals_dict):
self.status_text = display(Code(""), display_id=True)
self._globals_dict = globals_dict
self._methods = {}
self.stop_button = Button(description="Stop")
self.stop_button.on_click(self.on_stop_button_clicked)
self.canvas = Canvas()
self.output_text = ""
self.width, self.height = DEFAULT_CANVAS_SIZE
self.mouse_x = 0
self.mouse_y = 0
self.mouse_is_pressed = False
### Properties ###
@property
def mouse_x(self):
return self._globals_dict["mouse_x"]
@mouse_x.setter
def mouse_x(self, val):
self._globals_dict["mouse_x"] = val
@property
def mouse_y(self):
return self._globals_dict["mouse_y"]
@mouse_y.setter
def mouse_y(self, val):
self._globals_dict["mouse_y"] = val
@property
def mouse_is_pressed(self):
return self._globals_dict["mouse_is_pressed"]
@mouse_is_pressed.setter
def mouse_is_pressed(self, val):
self._globals_dict["mouse_is_pressed"] = val
@property
def width(self):
return self._globals_dict["width"]
@width.setter
def width(self, val):
self._globals_dict["width"] = val
self.canvas.width = val
@property
def height(self):
return self._globals_dict["height"]
@height.setter
def height(self, val):
self._globals_dict["height"] = val
self.canvas.height = val
### Library init ###
# Updates last activity time
@staticmethod
def refresh_last_activity():
global _sparkplug_last_activity
_sparkplug_last_activity = time.time()
# Creates canvas and starts thread
def start(self, methods):
self._methods = methods
draw = self._methods.get("draw", None)
if draw:
self.print_status("Running...")
display(self.stop_button)
else:
self.print_status("Done drawing")
display(self.canvas)
self.output_text_code = display(Code(self.output_text), display_id=True)
self.canvas.on_mouse_down(self.on_mouse_down)
self.canvas.on_mouse_up(self.on_mouse_up)
self.canvas.on_mouse_move(self.on_mouse_move)
thread = threading.Thread(target=self.loop)
thread.start()
def stop(self, message="Stopped"):
global _sparkplug_running
if not _sparkplug_running:
return
_sparkplug_running = False
self.print_status(message)
# Assuming we're using IPython to draw the canvas through the display() function.
# Commenting this out for now, it throws exception since it does not derive BaseException
# raise IpyExit
# Loop method that handles drawing and setup
def loop(self):
global _sparkplug_active_thread_id, _sparkplug_running
# Set active thread to this thread. This will stop any other active thread.
current_thread_id = threading.current_thread().native_id
_sparkplug_active_thread_id = current_thread_id
_sparkplug_running = True
self.refresh_last_activity()
draw = self._methods.get("draw", None)
setup = self._methods.get("setup", None)
if setup:
try:
setup()
except Exception as e:
self.print_status("Error in setup() function: " + str(e))
return
while _sparkplug_running:
if _sparkplug_active_thread_id != current_thread_id or time.time() - _sparkplug_last_activity > NO_ACTIVITY_THRESHOLD:
self.stop("Stopped due to inactivity")
return
if not draw:
return
with hold_canvas(self.canvas):
try:
draw()
except Exception as e:
self.print_status("Error in draw() function: " + str(e))
return
time.sleep(1 / FRAME_RATE)
# Prints status to embedded error box
def print_status(self, msg):
self.status_text.update(Code(msg))
# Prints output to embedded output box
def print(self, msg):
global _sparkplug_running
self.output_text += str(msg) + "\n"
if _sparkplug_running:
self.output_text_code.update(Code(self.output_text))
# Update mouse_x, mouse_y, and call mouse_down handler
def on_mouse_down(self, x, y):
self.refresh_last_activity()
self.mouse_x, self.mouse_y = int(x), int(y)
self.mouse_is_pressed = True
mouse_down = self._methods.get("mouse_down", None)
if mouse_down:
mouse_down()
# Update mouse_x, mouse_y, and call mouse_up handler
def on_mouse_up(self, x, y):
self.refresh_last_activity()
self.mouse_x, self.mouse_y = int(x), int(y)
self.mouse_is_pressed = False
mouse_up = self._methods.get("mouse_up", None)
if mouse_up:
mouse_up()
# Update mouse_x, mouse_y, and call mouse_moved handler
def on_mouse_move(self, x, y):
self.refresh_last_activity()
self.mouse_x, self.mouse_y = int(x), int(y)
mouse_moved = self._methods.get("mouse_moved", None)
if mouse_moved:
mouse_moved()
def on_stop_button_clicked(self, button):
self.stop()
### Global functions ###
# Sets canvas size
def size(self, *args):
if len(args) == 2:
self.width = args[0]
self.height = args[1]
# Sets fill style
# 1 arg: HTML string value
# 3 args: r, g, b are int between 0 and 255
# 4 args: r, g, b, a, where r, g, b are ints between 0 and 255, and a (alpha) is a float between 0 and 1.0
def fill_style(self, *args):
self.canvas.fill_style = self.parse_color("fill_style", *args)
def stroke_style(self, *args):
self.canvas.stroke_style = self.parse_color("stroke_style", *args)
# Combines fill_rect and stroke_rect into one wrapper function
def rect(self, *args):
self.check_coords("rect", *args)
self.canvas.fill_rect(*args)
self.canvas.stroke_rect(*args)
# Similar to self.rect wrapper, except only accepts x, y and size
def square(self, *args):
self.check_coords("square", *args, width_only=True)
rect_args = (*args, args[2]) # Copy the width arg into the height
self.rect(*rect_args)
# Draws filled rect
def fill_rect(self, *args):
self.check_coords("fill_rect", *args)
self.canvas.fill_rect(*args)
# Strokes a rect
def stroke_rect(self, *args):
self.check_coords("stroke_rect", *args)
self.canvas.stroke_rect(*args)
#Clears a rect
def clear_rect(self, *args):
self.check_coords('clear_rect', *args)
self.canvas.clear_rect(*args)
# Draws circle at given coordinates
def circle(self, *args):
self.check_coords("circle", *args, width_only=True)
arc_args = self.arc_args(*args)
self.canvas.fill_arc(*arc_args)
self.canvas.stroke_arc(*arc_args)
# Draws filled circle
def fill_circle(self, *args):
self.check_coords("fill_circle", *args, width_only=True)
arc_args = self.arc_args(*args)
self.canvas.fill_arc(*arc_args)
# Draws circle stroke
def stroke_circle(self, *args):
self.check_coords("stroke_circle", *args, width_only=True)
arc_args = self.arc_args(*args)
self.canvas.stroke_arc(*arc_args)
def fill_arc(self, *args):
self.canvas.fill_arc(*args)
def stroke_arc(self, *args):
self.canvas.stroke_arc(*args)
def fill_text(self, *args):
self.canvas.font = "{px}px sans-serif".format(px = args[4])
self.canvas.fill_text(args[0:3])
self.canvas.font = "12px sans-serif"
def stroke_text(self, *args):
self.canvas.font = "{px}px sans-serif".format(px = args[4])
self.canvas.stroke_text(args[0:3])
self.canvas.font = "12px sans-serif"
def text_align(self, *args):
self.canvas.text_align(*args)
def draw_line(self, *args):
if len(args) == 4:
self.canvas.line_width = args[4]
else:
self.canvas.line_width = 1
self.canvas.begin_path()
self.canvas.move_to(args[0],args[1])
self.canvas.line_to(args[2],args[4])
self.canvas.close_path()
# Clears canvas
def clear(self, *args):
self.canvas.clear()
# Draws background on canvas
def background(self, *args):
old_fill = self.canvas.fill_style
argc = len(args)
if argc == 3:
if ((not type(args[0]) is int) or (not type(args[1]) is int) or (not type(args[2]) is int)):
raise TypeError("Enter Values between 0 and 255(integers only) for all 3 values")
elif (not (args[0] >= 0 and args[0] <= 255) or not (args[1] >= 0 and args[1] <= 255) or not (
args[2] >= 0 and args[2] <= 255)):
raise TypeError("Enter Values between 0 and 255(integers only) for all 3 values")
self.clear()
self.fill_style(args[0], args[1], args[2])
self.fill_rect(0, 0, self.width, self.height)
elif argc == 1:
if (not type(args[0]) is str):
raise TypeError("Enter colour value in Hex i.e #000000 for black and so on")
self.clear()
self.fill_style(args[0])
self.fill_rect(0, 0, self.width, self.height)
elif argc == 4:
if ((not type(args[0]) is int) or (not type(args[1]) is int) or (not type(args[2]) is int) or (
not type(args[3]) is float)):
raise TypeError("Enter Values between 0 and 255(integers only) for all 3 values")
elif (not (args[0] >= 0 and args[0] <= 255) or not (args[1] >= 0 and args[1] <= 255) or not (
args[2] >= 0 and args[2] <= 255) or not (args[3] >= 0.0 and args[3] <= 1.0)):
raise TypeError(
"Enter Values between 0 and 255(integers only) for all 3 values and a value between 0.0 and 1.0 for opacity(last argument")
self.clear()
self.fill_style(args[0], args[1], args[2], args[3])
self.fill_rect(0, 0, self.width, self.height)
self.canvas.fill_style = old_fill
### Helper Functions ###
# Tests if input is numeric
# Note: No support for complex numbers
def check_type_is_num(self, n, func_name=None):
if not isinstance(n, (int, float)):
msg = "Expected {} to be a number".format(n)
if func_name:
msg = "{} expected {} to be a number".format(func_name, self.quote_if_string(n))
raise TypeError(msg)
# Tests if input is an int
def check_type_is_int(self, n, func_name=None):
if type(n) is not int:
msg = "Expected {} to be an int".format(n)
if func_name:
msg = "{} expected {} to be an int".format(func_name, self.quote_if_string(n))
raise TypeError(msg)
# Tests if input is a float
# allow_int: Set to True to allow ints as a float. Defaults to True.
def check_type_is_float(self, n, func_name=None, allow_int=True):
if type(n) is not float:
if not allow_int or type(n) is not int:
msg = "Expected {} to be a float".format(n)
if func_name:
msg = "{} expected {} to be a float".format(func_name, self.quote_if_string(n))
raise TypeError(msg)
@staticmethod
def quote_if_string(val):
if type(val) is str:
return "\"{}\"".format(val)
else:
return val
# Parse a string, rgb or rgba input into an HTML color string
def parse_color(self, func_name, *args):
argc = len(args)
if argc == 1:
return args[0]
elif argc == 3 or argc == 4:
color_args = args[:3]
for col in color_args:
self.check_type_is_int(col, func_name)
color_args = np.clip(color_args, 0, 255)
if argc == 3:
return "rgb({}, {}, {})".format(*color_args)
else:
# Clip alpha between 0 and 1
alpha_arg = args[3]
self.check_type_is_float(alpha_arg, func_name)
alpha_arg = np.clip(alpha_arg, 0, 1.0)
return "rgba({}, {}, {}, {})".format(*color_args, alpha_arg)
else:
raise TypeError("{} expected {}, {} or {} arguments, got {}".format(func_name, 1, 3, 4, argc))
# Check a set of 4 args are valid coordinates
# x, y, w, h
def check_coords(self, func_name, *args, width_only=False):
argc = len(args)
if argc != 4 and not width_only:
raise TypeError("{} expected {} arguments for x, y, w, h, got {} arguments".format(func_name, 4, argc))
elif argc != 3 and width_only:
raise TypeError("{} expected {} arguments for x, y, size, got {} arguments".format(func_name, 3, argc))
for arg in args:
self.check_type_is_float(arg, func_name)
# Convert a tuple of circle args into arc args
def arc_args(self, *args):
return (args[0], args[1], args[2] / 2, 0, 2 * pi)
def _make_repr_widget(self):
button_refresh = Button(description='Refresh',
tooltip='Get representation info')
button_update = Button(
description='Update',
tooltip='Update representation by updating rinfo box')
button_remove = Button(description='Remove',
tooltip='Remove current representation')
button_hide = Button(description='Hide',
tooltip='Hide/Show current representation')
button_center_selection = Button(description='Center',
tooltip='center selected atoms')
button_center_selection._ngl_name = 'button_center_selection'
bbox = HBox([
button_refresh, button_center_selection, button_hide, button_remove
])
repr_name_text = Text(value='', description='')
repr_name_text._ngl_name = 'repr_name_text'
repr_selection = Text(value='', description='')
repr_selection._ngl_name = 'repr_selection'
repr_selection.width = repr_name_text.width = DEFAULT_TEXT_WIDTH
repr_info_box = VBox([repr_name_text, repr_selection])
repr_info_box._ngl_name = 'repr_info_box'
component_slider = IntSlider(value=0, description='component')
component_slider._ngl_name = 'component_slider'
component_slider.visible = False
cvalue = ' '
component_dropdown = Dropdown(value=cvalue,
options=[
cvalue,
],
description='component')
component_dropdown._ngl_name = 'component_dropdown'
repr_slider = IntSlider(value=0,
description='representation',
width=DEFAULT_SLIDER_WIDTH)
repr_slider._ngl_name = 'repr_slider'
repr_slider.visible = True
repr_text_info = Textarea(value='',
description='representation parameters')
repr_text_info.visible = False
checkbox_repr_text = Checkbox(value=False,
description='show parameters')
checkbox_repr_text.visible = False
repr_text_box = VBox([checkbox_repr_text, repr_text_info])
repr_text_box._ngl_name = 'repr_text_box'
checkbox_reprlist = Checkbox(value=False, description='reprlist')
checkbox_reprlist._ngl_name = 'checkbox_reprlist'
reprlist_choices = self._make_repr_name_choices(
component_slider, repr_slider)
reprlist_choices._ngl_name = 'reprlist_choices'
def on_update_checkbox_reprlist(change):
reprlist_choices.visible = change['new']
checkbox_reprlist.observe(on_update_checkbox_reprlist, names='value')
def on_click_refresh(button):
self._view._request_repr_parameters(
component=component_slider.value, repr_index=repr_slider.value)
self._view._remote_call('requestReprInfo', target='Widget')
button_refresh.on_click(on_click_refresh)
def on_click_update(button):
parameters = json.loads(
repr_text_info.value.replace("False",
"false").replace("True", "true"))
self._view.update_representation(component=component_slider.value,
repr_index=repr_slider.value,
**parameters)
self._view._set_selection(repr_selection.value,
component=component_slider.value,
repr_index=repr_slider.value)
button_update.on_click(on_click_update)
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_remove.on_click(on_click_remove)
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'
elif button_hide.description == 'Show':
hide = False
button_hide.description = 'Hide'
else:
raise ValueError("must be Hide or Show")
self._view._remote_call('setVisibilityForRepr',
target='Widget',
args=[component, repr_index, not hide])
button_hide.on_click(on_click_hide)
def on_click_center(center_selection):
self._view.center_view(selection=repr_selection.value,
component=component_slider.value)
button_center_selection.on_click(on_click_center)
def on_change_repr_name(change):
name = change['new'].strip()
old = change['old'].strip()
should_update = (self._real_time_update and old and name
and name in REPR_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 update_slider_info(change):
self._view._request_repr_parameters(
component=component_slider.value, repr_index=repr_slider.value)
component_dropdown.options = tuple(self._view._ngl_component_names)
def on_change_selection(change):
if self._real_time_update:
component = component_slider.value
repr_index = 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:
component_slider.value = self._view._ngl_component_names.index(
choice)
component_dropdown.observe(on_change_component_dropdown, names='value')
def on_change_checkbox_repr_text(change):
repr_text_info.visible = change['new']
repr_slider.observe(update_slider_info, names='value')
component_slider.observe(update_slider_info, names='value')
repr_name_text.observe(on_change_repr_name, names='value')
repr_selection.observe(on_change_selection, names='value')
checkbox_repr_text.observe(on_change_checkbox_repr_text, names='value')
# HC
repr_parameters_box = self._make_repr_parameter_slider()
repr_parameters_box._ngl_name = 'repr_parameters_box'
# NOTE: if you update below list, make sure to update _make_repr_parameter_slider
# or refactor
# try to "refresh"
vbox = VBox([
component_dropdown, bbox, repr_info_box, component_slider,
repr_slider, reprlist_choices, repr_text_box, repr_parameters_box
])
self._view._request_repr_parameters(component=component_slider.value,
repr_index=repr_slider.value)
return vbox
PARADIM_UI = {}
PARADIM_UI['s0'] = {}
PARADIM_UI['s0']['pwd'] = MyPassword(description='MARCC Password',
name='MARCC Password',
value=PARADIM['PWD'])
PARADIM_UI['s0']['code'] = ui.String(description='GOOGLE AUTH Code',
name='GOOGLE AUTH Code',
value=PARADIM['CODE'])
PARADIM_UI['s0']['user'] = ui.String(description='Marcc User name',
name='Marcc User name',
value=PARADIM['USER'])
PARADIM_UI['s0']['folder'] = ui.String(description='Working folder',
name='Working folder',
value=PARADIM['TUTORIAL_NAME'])
PARADIM_UI['s0']['button'] = Button(description='Connect')
PARADIM_UI['s0']['button'].w = Box([PARADIM_UI['s0']['button']])
PARADIM_UI['s0']['status'] = ui.String(name='Status',
description='Status',
value='')
PARADIM_UI['s0']['status'].dd.layout = Layout(width='100%')
PARADIM_UI['s0']['status'].disabled = True
PARADIM_UI['s0']['display'] = ui.Form([
PARADIM_UI['s0']['user'],
PARADIM_UI['s0']['pwd'],
PARADIM_UI['s0']['code'],
PARADIM_UI['s0']['folder'],
PARADIM_UI['s0']['button'],
PARADIM_UI['s0']['status'],
],
name='MARCC Credentials')
def interactive_classifier(self, data_types=('expression', 'splicing'),
sample_subsets=None,
feature_subsets=None,
categorical_variables=None,
predictor_types=None,
score_coefficient=(0.1, 20),
draw_labels=False):
def do_interact(data_type,
sample_subset,
feature_subset,
predictor_type=default_classifier,
categorical_variable='outlier',
score_coefficient=2,
plot_violins=False,
show_point_labels=False):
for k, v in locals().iteritems():
if k == 'self':
continue
sys.stdout.write('{} : {}\n'.format(k, v))
self.plot_classifier(trait=categorical_variable,
feature_subset=feature_subset,
sample_subset=sample_subset,
predictor_name=predictor_type,
score_coefficient=score_coefficient,
data_type=data_type,
plot_violins=plot_violins,
show_point_labels=show_point_labels)
if feature_subsets is None:
feature_subsets = Interactive.get_feature_subsets(self, data_types)
feature_subsets.insert(0, 'variant')
if sample_subsets is None:
sample_subsets = self.default_sample_subsets
if categorical_variables is None:
categorical_variables = [i for i in self.default_sample_subsets if
not i.startswith(
"~") and i != 'all_samples']
if predictor_types is None:
predictor_types = \
self.predictor_config_manager.predictor_configs.keys()
# self.plot_study_sample_legend()
gui = interact(do_interact,
data_type=data_types,
sample_subset=sample_subsets,
feature_subset=feature_subsets,
categorical_variable=categorical_variables,
score_coefficient=score_coefficient,
draw_labels=draw_labels,
predictor_type=predictor_types)
def save(w):
# Make the directory if it's not already there
filename, extension = os.path.splitext(savefile.value)
self.maybe_make_directory(savefile.value)
gui.widget.result.fig_reduced.savefig(savefile.value,
format=extension)
# add "violins" after the provided filename, but before the
# extension
violins_file = '{}.{}'.format("_".join([filename, 'violins']),
extension)
try:
gui.widget.result.fig_violins.savefig(
violins_file, format=extension.lstrip('.'))
except AttributeError:
pass
savefile = Text(description='savefile')
save_widget = Button(description='save')
gui.widget.children = list(gui.widget.children) + [savefile,
save_widget]
save_widget.on_click(save)
return gui
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 interactive_pca(self, data_types=('expression', 'splicing'),
sample_subsets=None,
feature_subsets=None,
color_samples_by=None,
featurewise=False,
x_pc=(1, 10), y_pc=(1, 10),
show_point_labels=False,
list_link='', plot_violins=False,
scale_by_variance=True,
savefile='figures/last.pca.pdf'):
def do_interact(data_type='expression',
sample_subset=self.default_sample_subsets,
feature_subset=self.default_feature_subsets,
featurewise=False,
list_link='',
x_pc=1, y_pc=2,
plot_violins=False,
show_point_labels=False,
color_samples_by=self.metadata.phenotype_col,
bokeh=False,
scale_by_variance=True,
most_variant_features=False,
std_multiplier=(0, 5.0)):
for k, v in locals().iteritems():
if k == 'self':
continue
sys.stdout.write('{} : {}\n'.format(k, v))
if feature_subset != "custom" and list_link != "":
raise ValueError(
"Set feature_subset to \"custom\" to use list_link")
if feature_subset == "custom" and list_link == "":
raise ValueError("Use a custom list name please")
if feature_subset == 'custom':
feature_subset = link_to_list(list_link)
elif feature_subset not in self.default_feature_subsets[data_type]:
warnings.warn("This feature_subset ('{}') is not available in "
"this data type ('{}'). Falling back on all "
"features.".format(feature_subset, data_type))
return self.plot_pca(sample_subset=sample_subset,
data_type=data_type,
featurewise=featurewise,
x_pc=x_pc, y_pc=y_pc,
show_point_labels=show_point_labels,
feature_subset=feature_subset,
plot_violins=plot_violins,
color_samples_by=color_samples_by,
bokeh=bokeh, std_multiplier=std_multiplier,
scale_by_variance=scale_by_variance,
most_variant_features=most_variant_features)
# self.plot_study_sample_legend()
if feature_subsets is None:
feature_subsets = Interactive.get_feature_subsets(self, data_types)
if sample_subsets is None:
sample_subsets = self.default_sample_subsets
color_samples_by = self.metadata.data.columns.tolist()
gui = interact(do_interact,
data_type=data_types,
sample_subset=sample_subsets,
feature_subset=feature_subsets + ['custom'],
featurewise=featurewise,
x_pc=x_pc, y_pc=y_pc,
show_point_labels=show_point_labels,
list_link=list_link, plot_violins=plot_violins,
color_samples_by=color_samples_by,
scale_by_variance=scale_by_variance)
def save(w):
# Make the directory if it's not already there
filename, extension = os.path.splitext(savefile.value)
self.maybe_make_directory(savefile.value)
gui.widget.result.fig_reduced.savefig(savefile.value,
format=extension)
# add "violins" after the provided filename, but before the
# extension
violins_file = '{}.{}'.format("_".join([filename, 'violins']),
extension)
try:
gui.widget.result.fig_violins.savefig(
violins_file, format=extension.lstrip('.'))
except AttributeError:
pass
savefile = Text(description='savefile')
save_widget = Button(description='save')
gui.widget.children = list(gui.widget.children) + [savefile,
save_widget]
save_widget.on_click(save)
return gui
class Dbfs(object):
"""Database browser implementation
Args:
dbutils (DBUtils): DBUtils object (for fs only)
"""
def __init__(self, dbutils):
self.dbutils = dbutils
self.running = False
def create(self, rows=30, path="/", height="400px"):
if self.running:
print("dbfs browser already running. Use close() first")
return
self.path = path
self.flist = Select(options=[],
disabled=False,
layout={"height": height})
self.flist.observe(self.on_click, names="value")
self.refresh = Button(icon="refresh", layout={"width": "40px"})
self.refresh.on_click(self.on_refresh)
self.path_view = Output()
self.preview = Output(
layout={
"width": "800px",
"height": height,
"overflow": "scroll",
"border": "1px solid gray",
})
self.up = Button(icon="arrow-up", layout={"width": "40px"})
self.up.on_click(self.on_up)
display(
VBox([
HBox([self.refresh, self.up, self.path_view]),
HBox([self.flist, self.preview]),
]))
self.update()
self.running = True
def convertBytes(self, fsize):
"""Convert bytes to largest unit
Args:
fsize (int): Size in bytes
Returns:
tuple: size of largest unit, largest unit
"""
size = fsize
unit = "B"
if size > 1024 * 1024 * 1024 * 10:
size = int(size / 1024.0 / 1024.0 / 1024.0)
unit = "GB"
elif size > 1024 * 1024 * 10:
size = int(size / 1024.0 / 1024.0)
unit = "MB"
elif size > 1024 * 10:
size = int(size / 1024.0)
unit = "KB"
return (size, unit)
def update(self):
"""Update the view when an element was selected"""
self.path_view.clear_output()
self.preview.clear_output()
with self.path_view:
print("updating ...")
try:
fobjs = self.dbutils.fs.ls(self.path)
except Exception as ex:
with self.path_view:
print("Error: Cannot access folder")
return False
self.show_path(self.path)
dirs = sorted([fobj.name for fobj in fobjs if fobj.isDir()],
key=lambda x: x.lower())
files = sorted(
[
"%s (%d %s)" % ((fobj.name, ) + self.convertBytes(fobj.size))
for fobj in fobjs if not fobj.isDir()
],
key=lambda x: x[0].lower(),
)
self.flist.options = [""] + dirs + files
return True
def show_path(self, path):
"""Show path in output widget
Args:
path (str): Currently selected path
"""
self.path_view.clear_output()
with self.path_view:
print("dbfs:" + re.sub(r"\s\(.*?\)$", "", path))
def show_preview(self, path):
"""Show preview of csv, md or txt in output widget
Args:
path (str): Currently selected path
"""
real_path = re.sub(r"\s\(.*?\)$", "", path)
parts = real_path.split(".")
if len(parts) > 0 and parts[-1].lower() in [
"md",
"html",
"csv",
"txt",
"sh",
"sql",
"py",
"scala",
"json",
"jpg",
"jpeg",
"png",
"gif",
]:
ext = parts[-1].lower()
filename = "/dbfs" + real_path
# text = self.dbutils.fs.head(real_path)
self.preview.clear_output()
with self.preview:
if ext == "html":
display(HTML(filename=filename))
elif ext in ["py", "sh", "sql", "scala"]:
display(Code(filename=filename))
elif ext in ["jpg", "jpeg", "png", "gif"]:
display(Image(filename=filename))
elif ext == "md":
display(Markdown(filename=filename))
elif ext == "csv":
df = pd.read_csv(filename)
display(df)
else:
with open(filename, "r") as fd:
print(fd.read())
def on_refresh(self, b):
"""Refresh handler
Args:
b (ipywidgets.Button): clicked button
"""
self.update()
def on_up(self, b):
"""Up handler
Args:
b (ipywidgets.Button): clicked button
"""
new_path = os.path.dirname(self.path.rstrip("/"))
if new_path != self.path:
self.path = new_path
self.update()
def on_click(self, change):
"""Click handler providing db and parent as context
Args:
db (str): database name
parent (object): parent object
"""
new_path = os.path.join(self.path, change["new"])
if change["old"] is not None:
if len(change["new"]) > 0 and change["new"][-1] == "/":
old_path = self.path
self.path = new_path
if not self.update():
self.path = old_path
else:
self.show_path(new_path)
self.show_preview(new_path)
def close(self):
"""Close view"""
self.running = False
def compute(self):
obj = self.value
self.titlebox = ExplorerTitle(obj)
self.description = ExplorerDescription(obj)
self.props = ExplorerProperties(obj)
def handle_click(e):
self.set_value(e.source.value)
for v in self.props.children:
if type(v) == ExplorableValue:
v.clc.on_dom_event(handle_click)
self.propsbox = VBox([self.description, self.props])
self.titlebox.add_class('titlebox')
self.titlebox.add_class('lightborder')
self.visualbox = ExplorerVisual(obj)
self.visualbox.add_class('visualbox')
self.top = VBox(
[self.titlebox,
HBox(
[self.propsbox, Separator(' '), self.visualbox],
layout=Layout(margin='10px 0')
)
],
layout=Layout(border='1px solid yellow')
)
self.menusbox = ExplorerMenus(obj)
self.namingbox = ExplorerNaming(obj)
self.searchbox = ExplorerMethodSearch(obj)
self.inputbox = Text()
self.inputbutton = Button(description='-', layout=Layout(width='30px'))
self.gobutton = Button(description='Run!', tooltip='Run the method with specified arguments')
def compute_selected_method(button):
args = []
if self.inputbox.value:
args = self.inputbox.value.split(',')
try:
# if AlarmInterrupt:
# alarm(TIMEOUT)
out = self.searchbox.get_member()(obj, *args)
# if AlarmInterrupt:
# cancel_alarm()
#except AlarmInterrupt:
# self.output.value = to_html("Timeout!")
except Exception as e:
self.outputbox.output.value = 'Error: %s; input=%s' % (e, str(args))
return
self.outputbox.output.value = '$%s$' % out
self.gobutton.on_click(compute_selected_method)
self.actionbox = HBox([
self.namingbox,
Separator('.'),
self.searchbox,
Separator('('),
self.inputbox,
self.inputbutton,
Separator(')'),
self.gobutton
])
self.outputbox = ExplorerOutput(obj)
self.helpbox = ExplorerHelp(obj)
self.helpbox.update_title(self.description.content + " ..")
self.bottom = VBox([self.actionbox, self.outputbox, self.helpbox])
self.children = (self.top, self.bottom)
def __init__(self):
micron_units = Label(
'micron') # use "option m" (Mac, for micro symbol)
constWidth = '180px'
tab_height = '500px'
stepsize = 10
#style = {'description_width': '250px'}
style = {'description_width': '25%'}
layout = {'width': '400px'}
name_button_layout = {'width': '25%'}
widget_layout = {'width': '15%'}
units_button_layout = {'width': '15%'}
desc_button_layout = {'width': '45%'}
menv_var1 = Button(description='oxygen (mmHg)',
disabled=True,
layout=name_button_layout)
menv_var1.style.button_color = 'tan'
param_name1 = Button(description='diffusion_coefficient',
disabled=True,
layout=name_button_layout)
self.oxygen_diffusion_coefficient = FloatText(value=100000.000000,
step=10000,
style=style,
layout=widget_layout)
param_name2 = Button(description='decay_rate',
disabled=True,
layout=name_button_layout)
self.oxygen_decay_rate = FloatText(value=.1,
step=0.01,
style=style,
layout=widget_layout)
param_name3 = Button(description='initial_condition',
disabled=True,
layout=name_button_layout)
self.oxygen_initial_condition = FloatText(value=38.0,
style=style,
layout=widget_layout)
param_name4 = Button(description='Dirichlet_boundary_condition',
disabled=True,
layout=name_button_layout)
self.oxygen_Dirichlet_boundary_condition = FloatText(
value=38.0, style=style, layout=widget_layout)
self.oxygen_Dirichlet_boundary_condition_toggle = Checkbox(
description='on/off',
disabled=False,
style=style,
layout=widget_layout)
menv_var2 = Button(description='chemoattractant',
disabled=True,
layout=name_button_layout)
menv_var2.style.button_color = 'lightgreen'
param_name5 = Button(description='diffusion_coefficient',
disabled=True,
layout=name_button_layout)
self.chemoattractant_diffusion_coefficient = FloatText(
value=1000, step=100, style=style, layout=widget_layout)
param_name6 = Button(description='decay_rate',
disabled=True,
layout=name_button_layout)
self.chemoattractant_decay_rate = FloatText(value=.1,
step=0.01,
style=style,
layout=widget_layout)
param_name7 = Button(description='initial_condition',
disabled=True,
layout=name_button_layout)
self.chemoattractant_initial_condition = FloatText(
value=0, style=style, layout=widget_layout)
param_name8 = Button(description='Dirichlet_boundary_condition',
disabled=True,
layout=name_button_layout)
self.chemoattractant_Dirichlet_boundary_condition = FloatText(
value=0, style=style, layout=widget_layout)
self.chemoattractant_Dirichlet_boundary_condition_toggle = Checkbox(
description='on/off',
disabled=False,
style=style,
layout=widget_layout)
menv_var3 = Button(description='therapeutic',
disabled=True,
layout=name_button_layout)
menv_var3.style.button_color = 'tan'
param_name9 = Button(description='diffusion_coefficient',
disabled=True,
layout=name_button_layout)
self.therapeutic_diffusion_coefficient = FloatText(
value=1000, step=100, style=style, layout=widget_layout)
param_name10 = Button(description='decay_rate',
disabled=True,
layout=name_button_layout)
self.therapeutic_decay_rate = FloatText(value=.15625,
step=0.01,
style=style,
layout=widget_layout)
param_name11 = Button(description='initial_condition',
disabled=True,
layout=name_button_layout)
self.therapeutic_initial_condition = FloatText(value=0,
style=style,
layout=widget_layout)
param_name12 = Button(description='Dirichlet_boundary_condition',
disabled=True,
layout=name_button_layout)
self.therapeutic_Dirichlet_boundary_condition = FloatText(
value=0, style=style, layout=widget_layout)
self.therapeutic_Dirichlet_boundary_condition_toggle = Checkbox(
description='on/off',
disabled=False,
style=style,
layout=widget_layout)
self.calculate_gradient = Checkbox(description='calculate_gradients',
disabled=False,
layout=desc_button_layout)
self.track_internal = Checkbox(description='track_in_agents',
disabled=False,
layout=desc_button_layout)
# ------- micronenv info
menv_units_button1 = Button(description='micron^2/min',
disabled=True,
layout=units_button_layout)
menv_units_button2 = Button(description='1/min',
disabled=True,
layout=units_button_layout)
menv_units_button3 = Button(description='mmHg',
disabled=True,
layout=units_button_layout)
menv_units_button4 = Button(description='mmHg',
disabled=True,
layout=units_button_layout)
menv_units_button5 = Button(description='micron^2/min',
disabled=True,
layout=units_button_layout)
menv_units_button6 = Button(description='1/min',
disabled=True,
layout=units_button_layout)
units_button1 = Button(description='',
disabled=True,
layout=units_button_layout)
units_button2 = Button(description='',
disabled=True,
layout=units_button_layout)
menv_units_button9 = Button(description='micron^2/min',
disabled=True,
layout=units_button_layout)
menv_units_button10 = Button(description='1/min',
disabled=True,
layout=units_button_layout)
units_button3 = Button(description='',
disabled=True,
layout=units_button_layout)
units_button4 = Button(description='',
disabled=True,
layout=units_button_layout)
row_oxygen = [
menv_var1,
]
row1 = [
param_name1, self.oxygen_diffusion_coefficient, menv_units_button1
]
row2 = [param_name2, self.oxygen_decay_rate, menv_units_button2]
row3 = [param_name3, self.oxygen_initial_condition, menv_units_button3]
row4 = [
param_name4, self.oxygen_Dirichlet_boundary_condition,
menv_units_button4, self.oxygen_Dirichlet_boundary_condition_toggle
]
row_chemoattractant = [
menv_var2,
]
row5 = [
param_name5, self.chemoattractant_diffusion_coefficient,
menv_units_button5
]
row6 = [
param_name6, self.chemoattractant_decay_rate, menv_units_button6
]
row7 = [
param_name7, self.chemoattractant_initial_condition, units_button1
]
row8 = [
param_name8, self.chemoattractant_Dirichlet_boundary_condition,
units_button2,
self.chemoattractant_Dirichlet_boundary_condition_toggle
]
row_therapeutic = [
menv_var3,
]
row9 = [
param_name9, self.therapeutic_diffusion_coefficient,
menv_units_button9
]
row10 = [
param_name10, self.therapeutic_decay_rate, menv_units_button10
]
row11 = [
param_name11, self.therapeutic_initial_condition, units_button3
]
row12 = [
param_name12, self.therapeutic_Dirichlet_boundary_condition,
units_button4, self.therapeutic_Dirichlet_boundary_condition_toggle
]
row13 = [
self.calculate_gradient,
]
row14 = [
self.track_internal,
]
box_layout = Layout(display='flex',
flex_flow='row',
align_items='stretch',
width='100%')
box_oxygen = Box(children=row_oxygen, layout=box_layout)
box1 = Box(children=row1, layout=box_layout)
box2 = Box(children=row2, layout=box_layout)
box3 = Box(children=row3, layout=box_layout)
box4 = Box(children=row4, layout=box_layout)
box_chemoattractant = Box(children=row_chemoattractant,
layout=box_layout)
box5 = Box(children=row5, layout=box_layout)
box6 = Box(children=row6, layout=box_layout)
box7 = Box(children=row7, layout=box_layout)
box8 = Box(children=row8, layout=box_layout)
box_therapeutic = Box(children=row_therapeutic, layout=box_layout)
box9 = Box(children=row9, layout=box_layout)
box10 = Box(children=row10, layout=box_layout)
box11 = Box(children=row11, layout=box_layout)
box12 = Box(children=row12, layout=box_layout)
box13 = Box(children=row13, layout=box_layout)
box14 = Box(children=row14, layout=box_layout)
self.tab = VBox([
box_oxygen,
box1,
box2,
box3,
box4,
box_chemoattractant,
box5,
box6,
box7,
box8,
box_therapeutic,
box9,
box10,
box11,
box12,
box13,
box14,
])
def _init_gui(self, **kwargs):
"""Initialize generic GUI controls and observe callbacks."""
mainopts = super(TensorContainer, self)._init_gui(**kwargs)
scn = self.scenes[0]
alo = Layout(width='74px')
rlo = Layout(width='235px')
if self._df is not None:
scn.txx = self._df.loc[0,'xx']
scn.txy = self._df.loc[0,'xy']
scn.txz = self._df.loc[0,'xz']
scn.tyx = self._df.loc[0,'yx']
scn.tyy = self._df.loc[0,'yy']
scn.tyz = self._df.loc[0,'yz']
scn.tzx = self._df.loc[0,'zx']
scn.tzy = self._df.loc[0,'zy']
scn.tzz = self._df.loc[0,'zz']
xs = [FloatText(value=scn.txx , layout=alo),
FloatText(value=scn.txy , layout=alo),
FloatText(value=scn.txz , layout=alo)]
ys = [FloatText(value=scn.tyx , layout=alo),
FloatText(value=scn.tyy , layout=alo),
FloatText(value=scn.tyz , layout=alo)]
zs = [FloatText(value=scn.tzx , layout=alo),
FloatText(value=scn.tzy , layout=alo),
FloatText(value=scn.tzz , layout=alo)]
#scale = FloatSlider(max=10.0, step=0.01, readout=True, value=1.0)
opt = [0] if self._df is None else [int(x) for x in self._df.index.values]
tensorIndex = Dropdown(options=opt, value=opt[0], layout=rlo)
tdxlabel = Label(value='Select the tensor index:')
def _x0(c):
for scn in self.active(): scn.txx = c.new
def _x1(c):
for scn in self.active(): scn.txy = c.new
def _x2(c):
for scn in self.active(): scn.txz = c.new
def _y0(c):
for scn in self.active(): scn.tyx = c.new
def _y1(c):
for scn in self.active(): scn.tyy = c.new
def _y2(c):
for scn in self.active(): scn.tyz = c.new
def _z0(c):
for scn in self.active(): scn.tzx = c.new
def _z1(c):
for scn in self.active(): scn.tzy = c.new
def _z2(c):
for scn in self.active(): scn.tzz = c.new
xs[0].observe(_x0, names='value')
xs[1].observe(_x1, names='value')
xs[2].observe(_x2, names='value')
ys[0].observe(_y0, names='value')
ys[1].observe(_y1, names='value')
ys[2].observe(_y2, names='value')
zs[0].observe(_z0, names='value')
zs[1].observe(_z1, names='value')
zs[2].observe(_z2, names='value')
rlo = Layout(width='234px')
xbox = HBox(xs, layout=rlo)
ybox = HBox(ys, layout=rlo)
zbox = HBox(zs, layout=rlo)
geom = Button(icon='cubes', description=' Geometry', layout=_wlo)
def _change_tensor(tdx=0):
carts = ['x','y','z']
for i, bra in enumerate(carts):
for j, ket in enumerate(carts):
if i == 0:
xs[j].value = self._df.loc[tdx,bra+ket]
elif i == 1:
ys[j].value = self._df.loc[tdx,bra+ket]
elif i == 2:
zs[j].value = self._df.loc[tdx,bra+ket]
def _geom(b):
for scn in self.active(): scn.geom = not scn.geom
def _tdx(c):
for scn in self.active(): scn.tdx = c.new
_change_tensor(c.new)
geom.on_click(_geom)
tensorIndex.observe(_tdx, names="value")
mainopts.update([('geom', geom),
('tlbl', tdxlabel),
('tidx', tensorIndex),
('xbox', xbox),
('ybox', ybox),
('zbox', zbox)])
return mainopts
def calendar(path):
def show_imgs():
print(f"Crop name: {crop_name}, Area: {area:.2f} sqm")
def multi_bands_imgs(bands, fname):
df = view_images.create_df(ci_path, pid, ci_band.value)
rows = round((df.shape[0] / columns) + 0.5)
fig = plt.figure(figsize=(16, 4 * rows))
for i, row in df.iterrows():
fig.add_subplot(rows, columns, i + 1)
str_date = str(row['date'].date()).replace('-', '')
img_png = f"{ci_path}{fname}_{str_date}.png"
# Create color image if it does not exist
# Merge bands (images path, export image path, bands list)
if not os.path.isfile(img_png):
imgs_path = f"{ci_path}{row['imgs']}"
view_images.merge_bands(imgs_path, img_png, bands)
with rasterio.open(img_png, format='PNG') as img:
"""extracts the EPSG spatial reference"""
overlay_date(img, row['date'].date()) # Add date overlay.
ax = plt.gca()
if show_parcel.value:
ax.add_patch(overlay_parcel(img, info_data))
plt.axis('off') # Turn of axis.
pA, pB = np.percentile(img.read(1),
tuple(ci_percent.value))
# Strech image to A - B percentile.
stack = [
exposure.rescale_intensity(img.read()[i, :, :],
in_range=(pA, pB))
for i in range(len(bands))
]
rgb_enhanced = np.dstack(stack)
show(np.uint16(rgb_enhanced.transpose(2, 0, 1) / 300),
ax=ax,
transform=img.transform)
return plt.show()
def ndvi_imgs(bands, fname):
df = view_images.create_df(ci_path, pid, ci_band.value)
rows = round((df.shape[0] / columns) + 0.5)
fig = plt.figure(figsize=(16, 4 * rows))
for i, row in df.iterrows():
fig.add_subplot(rows, columns, i + 1)
str_date = str(row['date'].date()).replace('-', '')
img_png = f"{ci_path}{fname}_{str_date}.png"
imgs_path = f"{ci_path}{row['imgs']}"
b4f = f"{imgs_path}.B04.tif"
b4 = rasterio.open(b4f, format='GTiff')
ndvi = view_images.calc_ndvi(imgs_path, img_png, bands)
overlay_date(b4, row['date'].date()) # Add date overlay.
ax = plt.gca()
if show_parcel.value:
ax.add_patch(overlay_parcel(b4, info_data))
plt.axis('off') # Turn of axis.
pA, pB = np.percentile(ndvi, tuple(ci_percent.value))
show(ndvi,
ax=ax,
transform=b4.transform,
cmap=ci_cmaps.value,
vmin=pA,
vmax=pB)
b4.close()
return plt.show()
def single_band(band):
df = view_images.create_df(ci_path, pid, ci_band.value)
rows = round((df.shape[0] / columns) + 0.5)
fig = plt.figure(figsize=(16, 4 * rows))
for i, row in df.iterrows():
img_gtif = f"{ci_path}{row['imgs']}.{ci_band.value[0]}.tif"
with rasterio.open(img_gtif, format='GTiff') as img:
fig.add_subplot(rows, columns, i + 1)
overlay_date(img, row['date'].date())
plt.axis('off')
ax = plt.gca()
if show_parcel.value:
ax.add_patch(overlay_parcel(img, info_data))
img_read = img.read(1)
pA, pB = np.percentile(img_read, tuple(ci_percent.value))
show(img.read(1),
ax=ax,
transform=img.transform,
cmap=data_options.cmaps(ci_band.value[0]),
vmin=pA,
vmax=pB)
return plt.show()
if len(ci_band.value) == 1:
single_band(ci_band.value[0])
elif ci_band.value == ['B04', 'B08']:
ndvi_imgs(ci_band.value, 'NDVI')
else:
multi_bands_imgs(ci_band.value, ('').join(ci_band.value))
def overlay_date(img, date):
date_text = plt.text(
img.bounds.left + ((img.bounds.right - img.bounds.left) / 6.5),
img.bounds.top - ((img.bounds.top - img.bounds.bottom) / 6.5),
date,
color='yellow',
weight='bold',
size=12,
bbox=dict(boxstyle="round", ec='yellow', fc='black', alpha=0.2))
return date_text
def overlay_parcel(img, info_data):
img_epsg = img.crs.to_epsg()
geo_json = view_spatial.trasform_geometry(info_data, img_epsg)
patche = [
PolygonPatch(feature,
edgecolor="yellow",
facecolor="none",
linewidth=2) for feature in [geo_json]
]
return patche[0]
# Images options.
file_info = glob.glob(f"{path}*_information.json")[0]
with open(file_info, 'r') as f:
info_data = json.loads(f.read())
pid = info_data['ogc_fid'][0]
crop_name = info_data['cropname'][0]
area = info_data['area'][0]
ci_path = f"{path}{pid}_chip_images/"
columns = 4
available_options = view_images.available_options(path, pid)
ci_band = Dropdown(
options=available_options,
description='Select band:',
disabled=False,
)
ci_cmaps = Dropdown(options=data_options.color_maps(),
value='RdYlGn_r',
description='Color map:',
disabled=False,
layout=Layout(width='15%'))
ci_percent = IntRangeSlider(
value=[2, 98],
min=0,
max=100,
step=1,
description='%:',
disabled=False,
continuous_update=False,
orientation='horizontal',
readout=True,
readout_format='d',
)
show_parcel = Checkbox(value=True,
description='Show parcel',
disabled=False,
indent=False,
layout=Layout(width='100px'))
ci_cloud = Checkbox(value=False,
description='Cloud free',
disabled=True,
indent=False,
layout=Layout(width='140px'))
btn_ci = Button(value=False,
description='Show images',
disabled=False,
button_style='info',
tooltip='Refresh output',
icon='')
ci_out = Output()
@btn_ci.on_click
def btn_ci_on_click(b):
btn_ci.description = 'Refresh'
btn_ci.icon = 'refresh'
with ci_out:
ci_out.clear_output()
show_imgs()
wbox_ci_cloud = HBox([])
if len([val for key, val in available_options if 'SCL' in val]) > 0:
wbox_ci_cloud = HBox([ci_cloud])
wbox_ci = HBox([btn_ci, ci_band, show_parcel, ci_percent, wbox_ci_cloud])
def ci_band_change(change):
if len(ci_band.value) == 1:
if ci_band.value[0] in ['B02', 'B03', 'B04', 'B08']:
wbox_ci.children = [btn_ci, ci_band, show_parcel, ci_percent]
show_parcel.value = True
else:
wbox_ci.children = [btn_ci, ci_band, ci_percent]
show_parcel.value = False
elif ci_band.value == ['B04', 'B08']:
wbox_ci.children = [
btn_ci, ci_band, show_parcel, ci_cmaps, ci_percent,
wbox_ci_cloud
]
show_parcel.value = True
else:
wbox_ci.children = [
btn_ci, ci_band, show_parcel, ci_percent, wbox_ci_cloud
]
show_parcel.value = True
ci_band.observe(ci_band_change, 'value')
wbox = VBox([wbox_ci, ci_out])
return wbox
def _tensor_folder(self):
alo = Layout(width='70px')
rlo = Layout(width='220px')
scale = FloatSlider(max=10.0, step=0.001, readout=True, value=1.0)
xs = [Text(layout=alo,disabled=True),
Text(layout=alo,disabled=True),
Text(layout=alo,disabled=True)]
ys = [Text(layout=alo,disabled=True),
Text(layout=alo,disabled=True),
Text(layout=alo,disabled=True)]
zs = [Text(layout=alo,disabled=True),
Text(layout=alo,disabled=True),
Text(layout=alo,disabled=True)]
cs = [Text(layout=alo,disabled=True),
Text(layout=alo,disabled=True),
Text(layout=alo,disabled=True)]
cidx = HBox([Text(disabled=True,description='Atom Index',layout=rlo)])
xbox = HBox(xs, layout=rlo)
ybox = HBox(ys, layout=rlo)
zbox = HBox(zs, layout=rlo)
cbox = HBox(cs, layout=rlo)
tens = Button(description=' Tensor', icon='bank')
tensor_cont = VBox([xbox,ybox,zbox])
tensorIndex = Dropdown(options=[0],value=0,description='Tensor')
# sceneIndex = Dropdown(options=[0],value=0,description='Scene')
ten_label = Label(value="Change selected tensor:")
sel_label = Label(value="Selected tensor in gray frame")
cod_label = Label(value="Center of selected tensor: (x,y,z)")
tensor = []
self.coords = []
def _changeTensor(tensor, tdx):
carts = ['x','y','z']
for i,bra in enumerate(carts):
for j,ket in enumerate(carts):
tensor_cont.children[i].children[j].disabled=False
tensor_cont.children[i].children[j].value = \
str(tensor[0][tdx][bra+ket])
tensor_cont.children[i].children[j].disabled=True
adx = tensor[0][tdx]['atom']
cidx.children[0].value = str(adx)
cbox.children[0].value = str(self.coords[0][int(adx)])
cbox.children[1].value = str(self.coords[1][int(adx)])
cbox.children[2].value = str(self.coords[2][int(adx)])
# scale.value = tensor[0][tdx]['scale']
def _tens(c):
for scn in self.active(): scn.tens = not scn.tens
self.coords = self._filter_coords()
# sceneIndex.options = [x for x in range(len(self.active()))]
# sceneIndex.value = sceneIndex.options[0]
tensor = self.active()[0].tensor_d
tensorIndex.options = [x for x in range(len(tensor[0]))]
tensorIndex.value = tensorIndex.options[0]
tdx = tensorIndex.value
_changeTensor(tensor, tdx)
def _scale(c):
for scn in self.active(): scn.scale = c.new
# tdx = tensorIndex.value
# tensor = self.active()[0].tensor_d
# tensor[0][tdx]['scale'] = c.new
def _idx(c):
for scn in self.active(): scn.tidx = c.new
tensor = self.active()[0].tensor_d
tdx = c.new
_changeTensor(tensor, tdx)
# def _sdx(c):
# tensor = self.active()[sceneIndex.value].tensor_d
# tensorIndex.options = [x for x in range(len(tensor[0]))]
# tensorIndex.value = tensorIndex.options[0]
# tdx = tensorIndex.value
# _changeTensor(tensor, tdx)
tens.on_click(_tens)
scale.observe(_scale, names='value')
tensorIndex.observe(_idx, names='value')
# sceneIndex.observe(_sdx, names='value')
content = _ListDict([
('scale', scale),
('ten', ten_label),
# ('sdx', sceneIndex),
('tdx', tensorIndex),
('tensor', tensor_cont),
('sel', sel_label),
('cidx', cidx),
('center', cod_label),
('coord', cbox)])
return Folder(tens, content)
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)