def snap_click(self, b=None):
w = self.widget
cy = self.cy
json = self.to_json_value()
snap = js_proxy.ProxyWidget()
self.configure_widget(snap, layout="preset", descriptor=json)
snap.embed(True, await=["cytoscape"])
def __init__(self, target):
self.target = target
w = self.widget = js_proxy.ProxyWidget()
e = self.element = w.element()
# Create JS/python parallel mapping for finding elements.
self.displays = {}
self.expanded = {}
w(e._set("DISPLAYS", {}))
self.displays_reference = e.DISPLAYS
self.jQuery = w.window().jQuery
self.display_object(None, target, expanded=True, top=True)
def __init__(self, width=500, height=500, autoRotate=False, center=(0,0,0), offset=100):
init()
w = self.w = js_proxy.ProxyWidget()
element = self.element = w.element()
window = self.window = w.window()
THREE = self.THREE = window.THREE
self.center = center
self.offset = offset
self.autoRotate = autoRotate
scene = self.scene = w.save_new("scene", THREE.Scene, [])
renderer = self.renderer = w.save_new("renderer", THREE.WebGLRenderer, [])
w(renderer.setSize(width, height))
w(renderer.setClearColor( 0xffffff, 1))
w(element.append(renderer.domElement))
def canvas(self, width=None, height=None, entropy=True):
"""
Make a jsproxy canvas widget which draws the motif using sequence_motif.js.
"""
from jp_gene_viz import js_proxy
js_proxy.load_javascript_support()
w = js_proxy.ProxyWidget()
elt = w.element()
return self.add_canvas(w,
elt,
width=width,
height=height,
entropy=entropy,
x=5,
y=5)
def explore_directory(directory):
from jp_gene_viz import js_proxy
from IPython.display import display, HTML
js_proxy.load_javascript_support()
load_highcharts = """
<script src="https://code.highcharts.com/highcharts.js"></script>
"""
display(HTML(load_highcharts))
widget = js_proxy.ProxyWidget()
elt = widget.element()
# create a chart element look up table
#widget(elt._set("PieCharts", {}))
# attach a pie chart for directory
chart = DirectoryPieChart(directory, widget, elt)
widget.flush()
display(widget)
return widget
def __init__(self,
message="Choose file",
root=".",
files=True,
folders=False,
upload=False,
dialog=True,
width=500,
*args,
**kwargs):
"""
FileChooser constructor.
Parameters
----------
message : str
Message near the top of the widget as a prompt.
root : str
The root path for the top folder to display.
files : bool
Make non-folders selectable iff true.
folders : bool
Show folders iff true.
upload : bool
Enable file upload iff true.
dialog : bool
Show in a jQueryUI dialog iff true, else inline.
width : int
Width of widget in pixels.
"""
super(FileChooser, self).__init__(*args, **kwargs)
js_context.load_if_not_loaded(["simple_upload_button.js"])
js_context.load_if_not_loaded(["server_file_chooser.js"])
self.root = root
self.upload = upload
self.files = files
self.folders = folders
self.dialog = dialog
self.message = message
self.width = width
self.widget = js_proxy.ProxyWidget()
self.layout([self.root])
def test_plot(with_box=False, with_rotator=True):
from IPython import display
import math
sp = ScatterPlot3D()
points1 = [(400 + math.sin(i * 2), math.cos(i * 3) * 1.5,
math.sin(i * 0.5)) for i in range(150)]
sp.add_series("star", 0xff0000, points1)
points2 = [(401 + math.sin(i), math.cos(i * 2), math.sin(i * 1.5) * 1.7)
for i in range(150)]
sp.add_series("openCube", 0xffff00, points2)
w = js_proxy.ProxyWidget()
window = w.window()
element = w.element()
THREE = window.THREE
new = w.save_new
scene = new("scene", THREE.Scene, [])
camera = new("camera", THREE.PerspectiveCamera, [75, 1.0, 1, 10000])
w(camera.position._set("z", 500))
# plot the scatter points
sp.plot(300, w, scene, 10)
if with_box:
geometry = new("geometry", THREE.BoxGeometry, [200, 200, 200])
#geometry = new("geometry", THREE.TetrahedronGeometry, [])
material = new("material", THREE.MeshBasicMaterial, [{
"color": 0xff00ee,
"wireframe": True
}])
mesh = new("mesh", THREE.Mesh, [geometry, material])
w(scene.add(mesh))
renderer = new("renderer", THREE.WebGLRenderer, [])
w(renderer.setSize(800, 800))
w(element.append(renderer.domElement))
do_render = w(renderer.render(scene, camera))
if with_rotator:
gamma = xyz_dict(0, 0, 1)
delta = xyz_dict(1, 0, 0)
radius = 300
w(THREE.rotator(gamma, delta, radius, camera, renderer, scene))
json_sent = w.flush()
display.display(w)
return w
def __init__(self, *args, **kwargs):
super(Diagram, self).__init__(*args, **kwargs)
initialize()
mx = self.max_angle * 2
d = self.diagram = js_proxy.ProxyWidget()
xy = self.xy_slider = widgets.FloatSlider(description="XY rotation",
min=-mx,
max=mx)
xz = self.xy_slider = widgets.FloatSlider(description="XZ rotation",
min=-mx,
max=mx)
yz = self.xy_slider = widgets.FloatSlider(description="YZ rotation",
min=-mx,
max=mx)
traitlets.link((self, "xy_rotation"), (xy, "value"))
traitlets.link((self, "xz_rotation"), (xz, "value"))
traitlets.link((self, "yz_rotation"), (yz, "value"))
self.on_trait_change(self.draw_diagram, "xy_rotation")
self.on_trait_change(self.draw_diagram, "xz_rotation")
self.on_trait_change(self.draw_diagram, "yz_rotation")
self.assembly = widgets.VBox(children=[xy, xz, yz, d])
def __init__(self, dataset, *args, **kwargs):
super(Nearest, self).__init__(*args, **kwargs)
initialize()
self.dataset = dataset
feature_names = list(dataset.feature_names)
self.x_name = feature_names[0]
self.y_name = feature_names[1]
self.z_name = feature_names[2]
sc = self.scatter_plot = js_proxy.ProxyWidget()
xd = self.x_dropdown = widgets.Dropdown(
options=list(feature_names), value=self.x_name)
yd = self.y_dropdown = widgets.Dropdown(
options=list(feature_names), value=self.y_name)
zd = self.z_dropdown = widgets.Dropdown(
options=list(feature_names), value=self.z_name)
bc = self.border_checkbox = widgets.Checkbox(description="border", value=True)
tc = self.training_checkbox = widgets.Checkbox(description="training", value=True)
tstc = self.test_checkbox = widgets.Checkbox(description="test", value=True)
ns = self.n_slider = widgets.IntSlider(value=self.n_neighbors, min=1, max=20,
description="neighbors", width="50px")
ss = self.n_slider = widgets.FloatSlider(value=self.n_neighbors, min=0.2, max=0.5,
description="test size", width="50px", step=0.1)
traitlets.directional_link((ss, "value"), (self, "test_size"))
traitlets.directional_link((xd, "value"), (self, "x_name"))
traitlets.directional_link((yd, "value"), (self, "y_name"))
traitlets.directional_link((zd, "value"), (self, "z_name"))
traitlets.directional_link((bc, "value"), (self, "show_borders"))
traitlets.directional_link((ns, "value"), (self, "n_neighbors"))
traitlets.directional_link((tc, "value"), (self, "show_training"))
traitlets.directional_link((tstc, "value"), (self, "show_test"))
xd.on_trait_change(self.redraw, "value")
ss.on_trait_change(self.redraw, "value")
yd.on_trait_change(self.redraw, "value")
zd.on_trait_change(self.redraw, "value")
bc.on_trait_change(self.redraw, "value")
tc.on_trait_change(self.redraw, "value")
tstc.on_trait_change(self.redraw, "value")
ns.on_trait_change(self.redraw, "value")
controls = widgets.VBox(children=[xd, yd, zd, bc, tc, tstc, ns, ss])
self.assembly = widgets.HBox(children=[controls, sc])
def __init__(self,
viewBox="0 0 500 500",
dimension=SIDE_DEFAULT,
*pargs,
**kwargs):
super(HTML5CanvasProxy, self).__init__(*pargs, **kwargs)
self.viewBox = viewBox
self.svg_width = dimension
self.svg_height = dimension
self.on_trait_change(self.change_dimensions, "svg_width")
self.on_trait_change(self.change_dimensions, "svg_height")
self.on_trait_change(self.start_watch_event, "watch_event")
self.on_trait_change(self.stop_watch_event, "unwatch_event")
self.font = "Arial" # default
self.font_size = 10
self.font_style = ""
self.font_weight = "normal"
self.operations = []
self.assignments = {}
w = self.widget = js_proxy.ProxyWidget()
self.element = w.element()
self.empty()
def decrypt_widget():
import time
import threading
from jp_gene_viz import js_proxy
js_proxy.load_javascript_support()
# wait for the js to compile...
time.sleep(0.5)
from IPython.display import display
d = js_proxy.ProxyWidget()
elt = d.element()
#display(d)
window = d.window()
jQuery = window.jQuery
d(elt.width("400px").height("100px"))
d(
elt.html(
"""<input type="password" id="pw000"/> <input id="b000" type="button" value="decrypt files"/> """
))
def click_handler(id, args):
print "click"
t = threading.Timer(0.1, extract)
t.start()
def extract():
print "extracting password..."
print d.send(jQuery("#pw000").val(), pw_callback)
def pw_callback(arg):
print "... password extracted"
password = arg[0]
# print("pw="+repr(password))
decrypt(password)
callback = d.callback(click_handler, None)
d(jQuery("#b000").click(callback))
d.flush()
#display(d)
return d
def show(self):
ls = self.label_selection = self.label_selector()
sd = self.spot_display = self.display_spot_canvas()
#detail = self.detail_display = self.display_spot_canvas(width=2*self.radius, height=2*self.radius)
im_detail = self.image_detail = js_proxy.ProxyWidget()
#self.assembly = self.label_selection # testing only
info = self.info_area = widgets.Textarea(description="status")
filename = self.file_name_text = widgets.Text(
value=self.annotation_path)
savebutton = self.save_button = widgets.Button(description="save")
savebutton.on_click(self.save_click)
restorebutton = self.restore_button = widgets.Button(
description="restore")
restorebutton.on_click(self.restore_click)
nearbybutton = self.nearby_button = widgets.Button(
description="x: nearby")
nearbybutton.on_click(self.nearby_click)
file_save_widgets = [filename, savebutton, restorebutton]
if self.spots_href is not None:
spots_checkbox = self.spots_checkbox = widgets.Checkbox(
description="spots")
file_save_widgets.append(spots_checkbox)
spots_checkbox.on_trait_change(self.redraw, "value")
file_save_widgets.append(nearbybutton)
file_save = widgets.HBox(children=file_save_widgets)
work_area = widgets.HBox(children=[sd.target, ls, im_detail])
self.assembly = widgets.VBox(children=[work_area, file_save, info])
#self.assembly = widgets.HBox(children=[ls])
display(self.assembly)
self.configure_label_selector()
self.configure_image_detail()
self.add_key_bindings()
self.label_selection.flush()
if os.path.exists(self.annotation_path):
self.restore_click()
else:
self.draw_spots()
def __init__(self, data=None, slide_columns=8):
self.row_size = slide_columns
if data is None:
data = Data()
self.data = data
slides = data.slides
slide_displays = []
slide_name_to_controller = {}
slide_controllers = []
slide_rows = int(len(slides) / slide_columns)
if slide_rows * slide_columns < len(slides):
slide_rows += 1
self.slide_margin = margin = 5
row_size = 2*margin + slide_rows * (data.slide_height + margin)
col_size = 2*margin + (slide_columns) * (data.slide_width + margin)
slides_width = 2 * self.big_width
#slide_drawing = cartesian_svg.doodle(-1, -1, col_size+1, row_size+1, slides_width, margin=2)
#print "rows, cols", slide_rows, slide_columns
#print "slides dimensions", len(slides), col_size, row_size, "html width", slides_width
slide_drawing = canvas_doodle(-1, -1, col_size+1, row_size+1, slides_width, margin=2)
self.slide_drawing = slide_drawing
#slide_drawing.enable_events("click", self.slide_drawing_click)
count = 0
for slide_name in slides:
count += 1
#if count > 30:
# break
controller = Slide(slide_name, data, slide_drawing)
slide_controllers.append(controller)
assert slide_name not in slide_name_to_controller
slide_name_to_controller[slide_name] = controller
self.slide_controllers = slide_controllers
controller_rows = []
available_controllers = list(slide_controllers)
while available_controllers:
row_list = available_controllers[:self.row_size]
available_controllers = available_controllers[self.row_size:]
controller_rows.append(row_list)
self.controller_rows = controller_rows
self.slide_name_to_controller = slide_name_to_controller
#tsne_drawing = cartesian_svg.doodle(-TSNE_RADIUS-1, -TSNE_RADIUS-1, TSNE_RADIUS+1, TSNE_RADIUS+1, self.big_width, margin=4)
tsne_drawing = canvas_doodle(-TSNE_RADIUS-1, -TSNE_RADIUS-1, TSNE_RADIUS+1, TSNE_RADIUS+1, self.big_width, margin=4)
self.tsne_drawing = tsne_drawing
#tsne_events = "click mouseover mouseout"
#tsne_events = "click"
#print "enabling tsne events", tsne_events
#tsne_drawing.enable_events(tsne_events, self.tsne_event_callback)
#big_slide_drawing = cartesian_svg.doodle(-1, -1, data.slide_width+1, data.slide_height+1, self.big_width, margin=4)
big_slide_drawing = canvas_doodle(-1, -1, data.slide_width+1, data.slide_height+1, self.big_width, margin=4)
self.big_slide_drawing = big_slide_drawing
# make dialog
w = js_proxy.ProxyWidget()
e = w.element()
w(e.html("Temporary content for dialog").dialog())
w(e.dialog("close"))
w.flush()
self.dialog = w
big_assembly = widgets.HBox(children=[tsne_drawing.target.widget, big_slide_drawing.target.widget])
self.assembly = widgets.VBox(children=[big_assembly, slide_drawing.target.widget, self.dialog])
self.tsne_controller = TSNE(data, tsne_drawing)
self.slide_controller_rows = slide_controllers
self.chosen_slide = slides[0]
self.chosen_indicator = None
self.events_enabled = False
self.reset_bookkeeping()
def label_selector(self):
w = js_proxy.ProxyWidget()
return w
def configure_widget(self, w=None, layout="cose", descriptor=None):
if w is None:
self.widget = js_proxy.ProxyWidget()
w = self.widget
element = w.element()
w(element.empty())
# set up an event callback helper
w.save_function(
"event_cb", ["callback"], """
//debugger;
return function(evt) {
//debugger;
var cyTarget = evt.cyTarget;
if (cyTarget && cyTarget.data) {
var result = evt.cyTarget.data();
if (result) {
result.type = evt.type;
result.shiftKey = evt.originalEvent.shiftKey;
result.isNode = cyTarget.isNode();
result.isEdge = cyTarget.isEdge();
return callback(result);
}
}
return callback({});
}
""")
self.element = element = w.element()
window = w.window()
cytoscape = window.cytoscape
jQuery = window.jQuery
w(
element._set(
"target",
jQuery("<div></div>").height("600px").width("800px").
#html("cytoscape target div").
appendTo(element)))
#nodes = [{"data": {"id": "n", "label": "cytoscape"}}]
if descriptor is None:
nodes = []
edges = []
elements = {"nodes": nodes, "edges": edges}
descriptor = {
"container": element.target._get(0),
"style": STYLE,
"elements": elements,
"layout": {
"name": layout,
"padding": 5
}
}
else:
descriptor = copy.deepcopy(descriptor)
descriptor["container"] = element.target._get(0)
descriptor["layout"]["name"] = layout
w(element._set("cy_container", cytoscape(descriptor)))
w(element.height("600px").width("800px"))
self.cy = cy = element.cy_container
clickcallback = element.event_cb(
w.callback(self.clickhandler, data="click", level=3))
self.getter = cy._get("$")
# only add events in live mode
if w == self.widget:
w(cy.on('click', clickcallback))
return w