def _image_widget_new(self, image_data, colors=None):
b64_data = base64.b64encode(image_data)
if colors is None:
html_str = '<img src="data:image/png;base64,'+b64_data+'" width="100%" />'
else:
html_str = '''
<style>.col1 {display: none; }
.col2 {display: none; }
.col3 {display: none; }
table.show1 .col1 { display: table-cell; }
table.show2 .col2 { display: table-cell; }
table.show3 .col3 { display: table-cell; }
</style>
<script>
function toggleColumn(el, n) {
var currentClass = el.parentElement.parentElement.parentElement.parentElement.className;
if (currentClass.indexOf("show"+n) != -1) {
el.parentElement.parentElement.parentElement.parentElement.className = currentClass.replace("show"+n, "");
}
else {
el.parentElement.parentElement.parentElement.parentElement.className += " " + "show"+n;
}
}
</script>
'''
html_str += '<table style="border:0;" width="100%"><tr>'
html_str += '<th><button onclick="toggleColumn(this,2)">Toggle Colorbar</button></th><th></th></tr>'
html_str += '<tr style="border:0;paddding-right:5px;"><td style="border:0;">'
html_str += '<img src="data:image/png;base64,'+b64_data+'" / width="100%"></td>'
html_str += '<td style="border:0;" class="col2">'+self.colorbar_tabs_html(colors)+'</td></tr></table>'
image_widget = HTML(value=html_str)
image_widget.width='100%'
return image_widget
def update_global_tolerances(self):
controller = self.controller
case = self.case
pvals = self.pvals
if pvals is None:
self.tolerances_table.children = []
return
if case.is_valid(p_bounds=pvals) is False:
self.tolerances_table.children = []
return
table = HTML()
html_str = '<div><table>\n<caption>Global tolerances determined for Case ' + case.case_number + ' (' + case.signature + ') showing fold-difference to a large qualitative change{0}. </caption>\n'.format(' in log-coordinates' if self.log_coordinates is True else '')
html_str += '<tr ><th align=center rowspan=2 style="padding:0 15px 0 15px;"> Parameters </th><th colspan=2> Tolerance </th></tr>'
html_str += '<tr><td style="padding:0 15px 0 15px;"><b> Lower bound</b></td><td style="padding:0 15px 0 15px;"><b> Upper bound</b></td></tr>'
tolerances = case.measure_tolerance(pvals, log_out=self.log_coordinates)
for xi in sorted(pvals.keys()):
lower_th = 1e-15 if self.log_coordinates is False else -15
upper_th = 1e15 if self.log_coordinates is False else 15
lower, upper = tolerances[xi]
html_str += '<tr><td style="padding:0 15px 0 15px;"><b>{0}</b></td><td style="padding:0 15px 0 15px;">{1}</td><td style="padding:0 15px 0 15px;">{2}</td></tr>'.format(
xi,
lower if lower > lower_th else '-∞',
upper if upper < upper_th else '∞')
html_str += '</table><caption>'
html_str += 'Note: Global tolerance calculated based on the following values for the parameters: '
html_str += '; '.join([i + ' = ' + str(pvals[i]) for i in sorted(pvals.keys())]) + '.'
html_str += '</caption></div>'
table.value = html_str
save_button = Button(description='Save Global Tolerance Table')
save_button.table_data = html_str
save_button.on_click(self.save_table)
self.tolerances_table.children = [HTML(value='<br>'),
save_button,
table]
return
def update_parameter_table(self):
controller = self.controller
case = self.case
pvals = self.pvals
if pvals is None:
self.parameter_table.children = []
return
if case.is_valid(p_bounds=pvals) is False:
self.parameter_table.children = []
return
make_nominal = Button(description='Make Nominal Parameter Set')
make_nominal.on_click(self.save_parameters)
table = HTML()
html_str = '<div><table>\n<caption>Value for the parameters automatically determined for Case ' + case.case_number + ' (' + case.signature + '). </caption>\n'
html_str += '<tr ><th align=center style="padding:0 15px 0 15px;"> Parameters </th><th> Value </th>'
for xi in sorted(pvals.keys()):
html_str += '<tr><td><b>{0}</b></td><td>{1}</td></tr>'.format(
xi,
pvals[xi])
html_str += '</table></div>'
table.value = html_str
save_button = Button(description='Save Parameter Table')
save_button.table_data = html_str
save_button.on_click(self.save_table)
self.parameter_table.children = [HTML(value='<br>'),
save_button,
table,
make_nominal
]
return
def update_bounding_box(self):
controller = self.controller
case = self.case
pvals = self.pvals
if case.is_valid(p_bounds=pvals) is False:
self.bounding_box_table.children = []
return
if case.is_cyclical is True:
self.bounding_box_table.children = []
return
table = HTML()
html_str = '<div><table>\n<caption>Bounding box determined for Case ' + case.case_number + ' (' + case.signature + '){0}. </caption>\n'.format(' in log-coordinates' if self.log_coordinates is True else '')
html_str += '<tr ><th align=center rowspan=2 style="padding:0 15px 0 15px;"> Parameters </th><th colspan=2> Tolerance </th></tr>'
html_str += '<tr><td style="padding:0 15px 0 15px;"><b> Lower bound</b></td><td style="padding:0 15px 0 15px;"><b> Upper bound</b></td></tr>'
tolerances = case.bounding_box(log_out=self.log_coordinates)
for xi in sorted(tolerances.keys()):
lower_th = 1e-15 if self.log_coordinates is False else -15
upper_th = 1e15 if self.log_coordinates is False else 15
lower, upper = tolerances[xi]
html_str += '<tr><td style="padding:0 15px 0 15px;"><b>{0}</b></td><td style="padding:0 15px 0 15px;">{1}</td><td style="padding:0 15px 0 15px;">{2}</td></tr>'.format(
xi,
lower if lower > lower_th else '-∞',
upper if upper < upper_th else '∞')
html_str += '</table></div>'
table.value = html_str
save_button = Button(description='Save Bounding Box Table')
save_button.table_data = html_str
save_button.on_click(self.save_table)
self.bounding_box_table.children = [HTML(value='<br>'),
save_button,
table]
return
def update_log_gains(self):
controller = self.controller
case = self.case
if case.ssystem.solution is None:
self.log_gains.children = []
return
table = HTML()
html_str = '<div><table>\n<caption>Logarithmic gains and parameter sensitivities for Case ' + case.case_number + ' (' + case.signature + '). </caption>\n'
html_str += '<tr ><th rowspan="2" align=center style="padding:0 15px 0 15px;"> Dependent<br> Variables </th>'
html_str += '<th colspan="' + str(len(case.independent_variables)) + '" align=center style="padding:0 15px 0 15px;"> Independent Variables and Parameters</th></tr><tr align=center>'
for xi in case.independent_variables:
html_str += '<td><b>{0}</b></td>'.format(xi)
html_str += '</tr>\n'
for xd in case.dependent_variables:
html_str += '<tr><td align=center style="padding:0 15px 0 15px;"><b>{0}</b></td>'.format(xd)
for xi in case.independent_variables:
html_str += '<td align=center style="padding:0 15px 0 15px;">{0}</td>'.format(str(case.ssystem.log_gain(xd, xi)))
html_str += '</tr>\n'
html_str += '</table></div><br>'
save_button = Button(description='Save Log-Gain Table')
save_button.table_data = html_str
save_button.on_click(self.save_table)
table.value = html_str
self.log_gains.children = [HTML(value='<br>'),
save_button,
table]
return
def make_options_menu(self, b):
wi = b.wi
b.visible = False
b.name.visible = False
b.load.visible = False
actions = [('Enumerate Phenotypes', self.enumerate_phenotypes_menu),
('Analyze Case', self.case_report_menu),
('Intersect Phenotypes', self.case_intersect_menu),
('Co-localize Phenotypes', self.co_localize_menu),
('Create Plot', self.create_plot_menu)]
actions_h = HTML(value='<b>Actions</b>')
options_h = HTML(value='<b>Options</b>')
options = [('Edit Symbols', self.create_edit_symbols),
('Edit Parameters', self.create_edit_parameters),
('Save Data', self.save_widget_data)]
actions_w = Tab()
options_w = []
for name, method in options:
button = Button(description=name)
button.on_click(method)
## button.version = b.version
if method is None:
button.disabled = True
options_w.append(button)
edit = Button(description='Modify System')
edit.on_click(self.modify_equations_widget)
warning = HTML()
warning.value = '<font color="red"><b>Warning! Modifying system erases saved figures and tables.</b></font>'
wi.children = [actions_h, actions_w] + [options_h] + options_w + [edit, warning]
for title, method in actions:
title, widget = method(self)
children = [i for i in actions_w.children] + [widget]
actions_w.children = children
actions_w.set_title(len(children)-1, title)
self.widget.selected_index = 1
def update_info(self):
controller = self.controller
html = HTML()
html_string = '<b>Name:</b> ' + controller.name + '<br>'
html_string += '<b>Case Number:</b> ' + self.case.case_number + '<br>'
html_string += '<b>Case Signature:</b> (' + self.case.signature + ')<br>'
html_string += '<b>Valid:</b> ' + str(self.case.is_valid()) + '<br>'
html_string += '<b>Is Cyclical:</b> ' + str(self.case.is_cyclical) + '<br><hr>'
check_box = Checkbox(description='Logarithmic coordinates',
value=self.log_coordinates)
check_box.on_trait_change(self.change_logarithmic, 'value')
html.value = html_string
self.info.children = [html, check_box]
def display(self, n): # Hack!
def add_selector(_):
g.children = g.children[:-2] + tuple(
make_selector(self.sels, add_selector)) + g.children[-2:]
def get_data():
x_val, y_val = [f.value for f in c.children]
if self.debug: print(x_val, y_val)
pairs = self.pairs + [(self.x, x_val), (self.y, y_val)]
if self.debug: pprint(pairs)
return pairs
def out_sents(_):
pairs = get_data()
display(
sentences(pairs,
debug=self.debug,
limit=self.limit,
kind=self.kind))
s_l = HTMLWidget(value='Query')
self.sels = [make_selector(self.sels, add_selector) for _ in range(n)]
sels = [s_l] + self.sels
a_l = HTMLWidget(value='Aggregations')
self.aggs = make_aggregator(self.aggs, self.aggs)
aggs = [a_l] + [self.aggs]
chart_button = Button(description=' Show Chart ')
chart_button.on_click(self.chart4)
self.field_chooser = c = make_field_chooser('', [], '', [])
# clear_output(wait=True)
# display(c)
self.sent_button = sent_button = Button(description=' Show LMs ')
sent_button.on_click(out_sents)
# display(sent_button)
g = self.group = make_vgroup(sels + aggs +
[chart_button, c, sent_button])
display(self.group)
return self.group
def __init__(self, container, caption=None, ylabel='', xlabel='', height=300, width=900):
cell_header = HTMLWidget(value=('<h3 class="chart-header">' + caption + '</h3>' if caption is not None else ''))
yaxis = HTMLWidget(value=ylabel)
area_chart = StackedAreaWidget(width=width, height=height, hide_xaxis=xlabel=='')
chart_columns = ContainerWidget(children=[yaxis, area_chart])
chart_columns.set_css('width', '100%')
xaxis = HTMLWidget(value=xlabel)
chart = ContainerWidget(children=[chart_columns, xaxis])
container.children = container.children + tuple([cell_header, chart])
chart_columns.remove_class('vbox')
chart_columns.add_class('hbox align-center center')
xaxis.add_class('x axis-label')
yaxis.add_class('y axis-label pack-center')
area_chart.add_class('area-chart')
chart.add_class('pack-center center chart-area')
self.plot = area_chart