def modify_doc(doc):
""" Contains the application, including all callbacks
TODO: could the callbacks be outsourced?
:param doc:
:type doc:
"""
logger.debug('modify_doc has been called')
def get_data_frames(ie,):
""" Called one time initially, and then every time the experiment number is changed by the slider
:param ie: experiment number
:type ie: int
:returns: dataframe from stella datafile and dataframe with tau and phi and fitted values
:rtype: list of 2 pandas dataframes
"""
logger.debug('get_dataframe with ie={}'.format(ie))
fid = polymer.getfid(ie) #read FID or series of FIDs for selected experiment
try:
tau = polymer.get_tau_axis(ie) #numpy array containing the taus for experiment ie
try:
startpoint=fid_slider.range[0] #lower integration bound
endpoint = fid_slider.range[1] #upper integration bound
except NameError:
# fid_slider not initialized for first plot. Use default values:
startpoint=int(0.05*polymer.getparvalue(ie,'BS'))
endpoint = int(0.1*polymer.getparvalue(ie,'BS'))
logger.debug('fid_slider not initialized for first plot. Use default values {} and {}.'.format(startpoint, endpoint))
polymer.addparameter(ie,'fid_range',(startpoint,endpoint)) #add integration range to parameters to make it accesible
phi = get_mag_amplitude(fid, startpoint, endpoint,
polymer.getparvalue(ie,'NBLK'),
polymer.getparvalue(ie,'BS')) # list containing averaged fid amplitudes (which is proportional to a magnetization phi)
df = pd.DataFrame(data=np.c_[tau, phi], columns=['tau', 'phi']) # DataFrames are nice
df['phi_normalized'] = (df['phi'] - df['phi'].iloc[0] ) / (df['phi'].iloc[-1] - df['phi'].iloc[1] ) #Normalize magnetization,
#Note: in the normalized magnetization the magnetization build-up curves and magnetization decay curves look alike
#Note: this makes it easier for fitting as everything looks like 1 * exp(-R/time) in first order
polymer.addparameter(ie,'df_magnetization',df) # make the magnetization dataframe accesible as parameter
fit_option = 2 #mono exponential, 3 parameter fit
p0=[1.0, polymer.getparvalue(ie,'T1MX')**-1*2, 0] #choose startparameters for fitting an exponential decay
df, popt = magnetization_fit(df, p0, fit_option) # use leastsq to find optimal parameters
polymer.addparameter(ie,'popt(mono_exp)',popt) # add fitting parameters for later access
logger.info('fitfunction(t) = {} * exp(- {} * t) + {}'.format(*popt)) # print the fitting parameters to console (for convenience)
except KeyError:
logger.warning('no relaxation experiment found')
tau=np.zeros(1)
phi=np.zeros(1)
df = pd.DataFrame(data=np.c_[tau, phi], columns=['tau', 'phi'])
df['phi_normalized'] = np.zeros(1)
df['fit_phi'] = np.zeros(1)
return fid, df
def calculate_mag_dec(attr, old, new, start_ie=None):
''' Is being call from the callback for the experiment chooser
loads selected experiment visualize in plot p1 and p2
gets experiment number from the slider
writes source_fid.data from the fid from the polymer object
writes source_mag_dec.data from the dataframe
'''
ie = experiment_slider.value #get expermient number from the slider
logger.debug('calculate mag_dec for ie={}'.format(ie))
fid, df = get_data_frames(ie)
source_fid.data=ColumnDataSource.from_df(fid) #convert fid to bokeh format
source_mag_dec.data = ColumnDataSource.from_df(df)
def plot_par():
''' Creates plot for the parameters
Called with every update from the callback'''
logger.debug('creating plot for the parameters')
# read data due to selection of select_x/y
xs = par_df[select_xaxis.value ].values
ys = par_df[select_yaxis.value].values
# read titles due to name of select_x/y
x_title = select_xaxis.value.title()
y_title = select_yaxis.value.title()
# remark: many attributes in a bokeh plot cannot be modified after initialization
# for example p4.x_axis_type='datetime' does not work. keywords are a
# workaround to pass all optional arguments initially
# set optional keyword arguments, kw, for figure()
kw = dict() #initialize
if select_xaxis.value in discrete:
kw['x_range'] = sorted(set(xs))
if select_yaxis.value in discrete:
kw['y_range'] = sorted(set(ys))
if select_yaxis.value in time:
kw['y_axis_type'] = 'datetime'
if select_xaxis.value in time:
kw['x_axis_type'] = 'datetime'
kw['title']="%s vs %s" % (x_title, y_title)
# create figure using optional keywords kw
p4 = figure(plot_height=300, plot_width=600, tools='pan,box_zoom,reset',
**kw)
# set axis label
p4.xaxis.axis_label = x_title
p4.yaxis.axis_label = y_title
# strings at x axis ticks need a lot of space. solution: rotate label orientation
if select_xaxis.value in discrete:
p4.xaxis.major_label_orientation = pd.np.pi / 4 # rotates labels...
# standard size of symbols
sz = 9
# custom size of symbols due to select_size
if select_size.value != 'None':
groups = pd.qcut(pd.to_numeric(par_df[select_size.value].values), len(SIZES))
sz = [SIZES[xx] for xx in groups.codes]
# standard color
c = "#31AADE"
# custom color due to select_color
if select_color.value != 'None':
groups = pd.qcut(pd.to_numeric(par_df[select_color.value]).values, len(COLORS))
c = [COLORS[xx] for xx in groups.codes]
# create the plot using circles
p4.circle(x=xs, y=ys, color=c, size=sz, line_color="white", alpha=0.6, hover_color='white', hover_alpha=0.5)
return p4 #return the plot
def callback_update_plot_1(attr, old, new):
''' Callback for update of figure 1 in parameters tab '''
tabs.tabs[1].child.children[1] = plot_par()
print(tabs.tabs[1].child.children[1])
logger.debug('Parameter plot updated')
# p4 = plot_par()
def callback_update_p3():
logger.debug('update plot 3')
p3 = fit_mag_decay_all(polymer,par_df)
return p3
def callback_update_experiment(attr, old, new):
""" Callback for the experiment chooser
"""
ie = experiment_slider.value
logger.debug('Callback experiment update, ie={}'.format(ie))
fid_slider.end = polymer.getparvalue(ie,'BS')
try:
fid_slider.range=polymer.getparvalue(ie,'fid_range')
except:
startpoint = int(0.05 * polymer.getparvalue(ie,'BS'))
endpoint = int(0.1 * polymer.getparvalue(ie,'BS'))
fid_slider.range=(startpoint,endpoint)
calculate_mag_dec(attr,old,new)
def callback_load_more_data(attr,old,new):
''' callback for loading of data '''
# TODO: implement
logger.debug('callback for loading of data ')
logger.error('Not implemented!')
path=pathbox.value.strip()
file=filebox.value.strip()
if file=="*.sdf":
logger.info('callback for loading data. filename: {}'.format(file))
allsdf=filter(lambda x: x.endswith('.sdf'),os.listdir(path))
for f in allsdf:
sdf_list.append(sdf.StelarDataFile(f,path))
else:
sdf_list.append(sdf.StelarDataFile(file,path))
filenames=[x.file() for x in sdf_list]
filenames_df=pd.DataFrame(data=filenames,columns=['file'])
table_source.data=ColumnDataSource.from_df(filenames_df)
def callback_export_data(attr,old,new):
logger.debug('callback_export_data has been called ')
logger.error('Not implemented!')
pass
def callback_write_table_to_file(attr,old,new): ##FIXME
logger.debug('callback_write_table_to_file has been called ')
logger.error('Not implemented!')
pass
# path=export_text.value.strip()
# exportdata=export_source.data
# CustomJS(args=dict(source=export_source),
# code=open(join(dirname(__file__), "export_csv.js")).read())
def callback_update_parameters():
''' callback for button
function to call when button is clicked
for updates parameters of polymer, since they can change during evaluation '''
logger.debug('callback for button (update parameter).')
par_df, columns, discrete, continuous, time, quantileable = polymer.scan_parameters()
select_xaxis.options=columns
select_yaxis.options=columns
select_size.options=['None']+quantileable
select_color.options=['None']+quantileable
logger.info('Starting the script')
### This is the start of the script ###
### The callbacks are above ###
#load data:
# TODO: how to handle multiple datafiles?
# New Tab for each datafile?
# dropdown selection to choose datafile
# complete new start of process? (probably not prefered)
polymer = load_data('glyzerin_d3_300K.sdf')
nr_experiments = polymer.get_number_of_experiments()
start_ie = 1 # initially set ie = 1
par_df, columns, discrete, continuous, time, quantileable = polymer.scan_parameters(20)
# for the initial call get the dataframes without callback
# they are being updated in following callbacks
fid, df = get_data_frames(start_ie)
source_fid = ColumnDataSource(data=ColumnDataSource.from_df(fid))
source_mag_dec = ColumnDataSource(data=ColumnDataSource.from_df(df))
# initialy creates the plots p1 and p2
p1, p2 = create_plot_1_and_2(source_fid, source_mag_dec)
### initiates widgets, which will call the callback on change ###
# initiate slider to choose experiment
experiment_slider = Slider(start=1, end=nr_experiments, value=1, step=1,callback_policy='mouseup', width=800) #select experiment by value
# initiate slider for the range in which fid shall be calculated
# select the intervall from which magneitization is calculated from fid
fid_slider = RangeSlider(start=1,end=polymer.getparvalue(start_ie,'BS'),
range=polymer.getparvalue(start_ie,'fid_range'),
step=1,callback_policy='mouseup', width=400)
# fit magnetization decay for all experiments
p3 = fit_mag_decay_all(polymer, par_df)
# refit mag dec with updated ranges after button push
button_refit = Button(label='Update',button_type="success")
button_refit.on_click(callback_update_p3)
# initialize empty source for experiment slider
source = ColumnDataSource(data=dict(value=[]))
# 'data' is the attribute. it's a field in source, which is a ColumnDataSource
# initiate callback_update_experiment which is the callback
source.on_change('data',callback_update_experiment) #source for experiment_slider
experiment_slider.callback = CustomJS(args=dict(source=source),code="""
source.data = { value: [cb_obj.value] }
""")#unfortunately this customjs is needed to throttle the callback in current version of bokeh
# initialize empty source for fid slider, same as above
source2 = ColumnDataSource(data=dict(range=[], ie=[]))
source2.on_change('data',calculate_mag_dec)
fid_slider.callback=CustomJS(args=dict(source=source2),code="""
source.data = { range: cb_obj.range }
""")#unfortunately this customjs is needed to throttle the callback in current version of bokeh
# same for the update button
button_scan = Button(label='Scan Parameters',button_type="success")
button_scan.on_click(callback_update_parameters)
# here comes for callbacks for x, y, size, color
select_xaxis = Select(title='X-Axis', value='ZONE', options=columns)
select_xaxis.on_change('value', callback_update_plot_1)
select_yaxis = Select(title='Y-Axis', value='TIME', options=columns)
select_yaxis.on_change('value', callback_update_plot_1)
select_size = Select(title='Size', value='None', options=['None'] + quantileable)
select_size.on_change('value', callback_update_plot_1)
select_color = Select(title='Color', value='None', options=['None'] + quantileable)
select_color.on_change('value', callback_update_plot_1)
controls_p4 = widgetbox([button_scan, select_xaxis,select_yaxis,select_color,select_size], width=150)
#p4 = plot_par()
layout_p4 = row(controls_p4,plot_par())
logger.debug('layout for parameter plot created')
####
#### TODO: write file input
#### TODO: select files to import
#### TODO: discard imported files
####
# load more data:
table_source=ColumnDataSource(data=dict())
sdf_list=[polymer]
# TODO: This is current plan, to save the different dataframes in a list, right?
filenames=[x.file() for x in sdf_list]
files_df=pd.DataFrame(data=filenames,columns=['file'])
table_source.data=ColumnDataSource.from_df(files_df)
t_columns = [
TableColumn(field='file', title='Path / Filename'),
#TableColumn(field='file', title='Filename'),
]
table=DataTable(source=table_source,columns=t_columns)
pathbox=TextInput(title="Path",value=os.path.curdir)
filebox=TextInput(title="Filename",value="*.sdf")
pathbox.on_change('value',callback_load_more_data)
filebox.on_change('value',callback_load_more_data)
layout_input=column(pathbox,filebox,table)
# Data Out: export data from figures
# & export parameters
export_source=ColumnDataSource(data=dict())
export_columns=[]
output_table=DataTable(source=export_source,columns=export_columns)
export_slider = Slider(start=1, end=4, value=3, step=1,callback_policy='mouseup', width=200) #do we need mouseup on this?
export_slider.on_change('value',callback_export_data)
export_text = TextInput(title="Path",value=os.path.curdir)
export_button = Button(label='Export to csv',button_type="success") # FIXME Callback doesn't work yet
export_button.on_click(callback_write_table_to_file)
layout_output=row(column(export_slider,export_text,export_button),output_table)
print('after layout_output')
# set the layout of the tabs
layout_p1 = column(experiment_slider, p1,
row(
column(fid_slider,p2),
column(button_refit, p3)
),
)
tab_relaxation = Panel(child = layout_p1, title = 'Relaxation')
tab_parameters = Panel(child = layout_p4, title = 'Parameters')
tab_input = Panel(child = layout_input, title = 'Data In')
tab_output = Panel(child = layout_output, title = 'Data Out')
# initialize tabs object with 3 tabs
tabs = Tabs(tabs = [tab_relaxation, tab_parameters,
tab_input, tab_output])
print('tabs')
doc.add_root(tabs)
doc.add_root(source) # i need to add source to detect changes
doc.add_root(source2)
print('tab tab')
######################################
# SET UP ALL THE WIDGETS AND CALLBACKS
######################################
source = ColumnDataSource(data=dict(value=[]))
source.on_change('data', update_data)
exptime = Slider(title="Integration Time (hours)",
value=24.,
start=1.,
end=1000.0,
step=1.0,
callback_policy='mouseup')
exptime.callback = CustomJS(args=dict(source=source),
code="""
source.data = { value: [cb_obj.value] }
""")
magnitude = Slider(title="V Band Magnitude of Object",
value=10.,
start=-10,
end=40.,
step=1.0,
callback_policy='mouseup')
magnitude.callback = CustomJS(args=dict(source=source),
code="""
source.data = { value: [cb_obj.value] }
""")
diameter = Slider(title="Mirror Diameter (meters)",
value=10.0,
start=0.5,
end=50.,
spec = Cratio + np.random.randn(len(Cratio))*sig
planet.data = dict(lam=lam, cratio=Cratio*1e9, spec=spec*1e9, downerr=(spec-sig)*1e9, uperr=(spec+sig)*1e9)
format_button_group.active = None
######################################
# SET UP ALL THE WIDGETS AND CALLBACKS
######################################
source = ColumnDataSource(data=dict(value=[]))
source.on_change('data', update_data)
exptime = Slider(title="Integration Time (hours)", value=20., start=10., end=100.0, step=1.0, callback_policy='mouseup')
exptime.callback = CustomJS(args=dict(source=source), code="""
source.data = { value: [cb_obj.value] }
""")
distance = Slider(title="Distance (parsec)", value=10., start=2., end=50.0, step=1.0, callback_policy='mouseup')
distance.callback = CustomJS(args=dict(source=source), code="""
source.data = { value: [cb_obj.value] }
""")
radius = Slider(title="Planet Radius (R_Earth)", value=1.0, start=0.5, end=3., step=0.1, callback_policy='mouseup')
radius.callback = CustomJS(args=dict(source=source), code="""
source.data = { value: [cb_obj.value] }
""")
semimajor= Slider(title="Semi-major axis of orbit (AU)", value=1.0, start=0.2, end=2., step=0.1, callback_policy='mouseup')
semimajor.callback = CustomJS(args=dict(source=source), code="""
source.data = { value: [cb_obj.value] }
""")
exozodi = Slider(title="Number of Exozodi", value = 1.0, start=1.0, end=10., step=1., callback_policy='mouseup')
exozodi.callback = CustomJS(args=dict(source=source), code="""
def generate_gui(tsne, cut_extracellular_data, all_extra_spike_times, time_axis, cluster_info_file,
use_existing_cluster, autocor_bin_number, sampling_freq, prb_file=None, k4=False, verbose=False):
if k4:
tsne_figure_size = [1000, 800]
tsne_min_border_left = 50
spike_figure_size = [500, 500]
hist_figure_size = [500, 500]
heatmap_plot_size = [200, 800]
clusters_table_size = [400, 300]
layout_size = [1500, 1400]
slider_size = [300, 100]
user_info_size = [700, 80]
else:
tsne_figure_size = [850, 600]
tsne_min_border_left = 10
spike_figure_size = [450, 300]
hist_figure_size = [450, 300]
heatmap_plot_size = [200, 800]
clusters_table_size = [400, 400]
layout_size = [1200, 800]
slider_size = [270, 80]
user_info_size = [450, 80]
# Plots ------------------------------
# scatter plot
global non_selected_points_alpha
global selected_points_size
global non_selected_points_size
global update_old_selected_switch
global previously_selected_spike_indices
tsne_fig_tools = "pan,wheel_zoom,box_zoom,box_select,lasso_select,tap,resize,reset,save"
tsne_figure = figure(tools=tsne_fig_tools, plot_width=tsne_figure_size[0], plot_height=tsne_figure_size[1],
title='T-sne', min_border=10, min_border_left=tsne_min_border_left, webgl=True)
tsne_source = ColumnDataSource({'tsne-x': tsne[0], 'tsne-y': tsne[1]})
tsne_selected_points_glyph = Circle(x='tsne-x', y='tsne-y', size=selected_points_size,
line_alpha=0, fill_alpha=1, fill_color='red')
tsne_nonselected_points_glyph = Circle(x='tsne-x', y='tsne-y', size=non_selected_points_size,
line_alpha=0, fill_alpha=non_selected_points_alpha, fill_color='blue')
tsne_invisible_points_glyph = Circle(x='tsne-x', y='tsne-y', size=selected_points_size, line_alpha=0, fill_alpha=0)
tsne_nonselected_glyph_renderer = tsne_figure.add_glyph(tsne_source, tsne_nonselected_points_glyph,
selection_glyph=tsne_invisible_points_glyph,
nonselection_glyph=tsne_nonselected_points_glyph,
name='tsne_nonselected_glyph_renderer')
# note: the invisible glyph is required to be able to change the size of the selected points, since the
# use of selection_glyph is usefull only for colors and alphas
tsne_invinsible_glyph_renderer = tsne_figure.add_glyph(tsne_source, tsne_invisible_points_glyph,
selection_glyph=tsne_selected_points_glyph,
nonselection_glyph=tsne_invisible_points_glyph,
name='tsne_invinsible_glyph_renderer')
tsne_figure.select(BoxSelectTool).select_every_mousemove = False
tsne_figure.select(LassoSelectTool).select_every_mousemove = False
def on_tsne_data_update(attr, old, new):
global previously_selected_spike_indices
global currently_selected_spike_indices
global non_selected_points_alpha
global non_selected_points_size
global selected_points_size
global checkbox_find_clusters_of_selected_points
previously_selected_spike_indices = np.array(old['1d']['indices'])
currently_selected_spike_indices = np.array(new['1d']['indices'])
num_of_selected_spikes = len(currently_selected_spike_indices)
if num_of_selected_spikes > 0:
if verbose:
print('Num of selected spikes = ' + str(num_of_selected_spikes))
# update t-sne plot
tsne_invisible_points_glyph.size = selected_points_size
tsne_nonselected_points_glyph.size = non_selected_points_size
tsne_nonselected_points_glyph.fill_alpha = non_selected_points_alpha
# update spike plot
avg_x = np.mean(cut_extracellular_data[:, :, currently_selected_spike_indices], axis=2)
spike_mline_plot.data_source.data['ys'] = avg_x.tolist()
print('Finished avg spike plot')
# update autocorelogram
diffs, norm = crosscorrelate_spike_trains(all_extra_spike_times[currently_selected_spike_indices].astype(np.int64),
all_extra_spike_times[currently_selected_spike_indices].astype(np.int64), lag=1500)
hist, edges = np.histogram(diffs, bins=autocor_bin_number)
hist_plot.data_source.data["top"] = hist
hist_plot.data_source.data["left"] = edges[:-1] / sampling_freq
hist_plot.data_source.data["right"] = edges[1:] / sampling_freq
print('finished autocorelogram')
# update heatmap
if prb_file is not None:
print('Doing heatmap')
data = cut_extracellular_data[:, :, currently_selected_spike_indices]
final_image, (x_size, y_size) = spike_heatmap.create_heatmap(data, prb_file, rotate_90=True,
flip_ud=True, flip_lr=False)
new_image_data = dict(image=[final_image], x=[0], y=[0], dw=[x_size], dh=[y_size])
heatmap_data_source.data.update(new_image_data)
print('Finished heatmap')
tsne_source.on_change('selected', on_tsne_data_update)
# spike plot
spike_fig_tools = 'pan,wheel_zoom,box_zoom,reset,save'
spike_figure = figure(toolbar_location='below', plot_width=spike_figure_size[0], plot_height=spike_figure_size[1],
tools=spike_fig_tools, title='Spike average', min_border=10, webgl=True, toolbar_sticky=False)
num_of_channels = cut_extracellular_data.shape[0]
num_of_time_points = cut_extracellular_data.shape[1]
xs = np.repeat(np.expand_dims(time_axis, axis=0), repeats=num_of_channels, axis=0).tolist()
ys = np.ones((num_of_channels, num_of_time_points)).tolist()
spike_mline_plot = spike_figure.multi_line(xs=xs, ys=ys)
# autocorelogram plot
hist, edges = np.histogram([], bins=autocor_bin_number)
hist_fig_tools = 'pan,wheel_zoom,box_zoom,save,reset'
hist_figure = figure(toolbar_location='below', plot_width=hist_figure_size[0], plot_height=hist_figure_size[1],
tools=hist_fig_tools, title='Autocorrelogram', min_border=10, webgl=True, toolbar_sticky=False)
hist_plot = hist_figure.quad(bottom=0, left=edges[:-1], right=edges[1:], top=hist, color="#3A5785", alpha=0.5,
line_color="#3A5785")
# heatmap plot
heatmap_plot = figure(toolbar_location='right', plot_width=1, plot_height=heatmap_plot_size[1],
x_range=(0, 1), y_range=(0, 1), title='Probe heatmap',
toolbar_sticky=False)
if prb_file is not None:
data = np.zeros(cut_extracellular_data.shape)
final_image, (x_size, y_size) = spike_heatmap.create_heatmap(data, prb_file, rotate_90=True,
flip_ud=True, flip_lr=False)
final_image[:, :, ] = 4294967295 # The int32 for the int8 255 (white)
plot_width = max(heatmap_plot_size[0], int(heatmap_plot_size[1] * y_size / x_size))
heatmap_plot = figure(toolbar_location='right', plot_width=plot_width, plot_height=heatmap_plot_size[1],
x_range=(0, x_size), y_range=(0, y_size), title='Probe heatmap',
toolbar_sticky=False)
heatmap_data_source = ColumnDataSource(data=dict(image=[final_image], x=[0], y=[0], dw=[x_size], dh=[y_size]))
heatmap_renderer = heatmap_plot.image_rgba(source=heatmap_data_source, image='image', x='x', y='y',
dw='dw', dh='dh', dilate=False)
heatmap_plot.axis.visible = None
heatmap_plot.xgrid.grid_line_color = None
heatmap_plot.ygrid.grid_line_color = None
# ---------------------------------------
# --------------- CONTROLS --------------
# Texts and Tables
# the clusters DataTable
if use_existing_cluster:
cluster_info = load_cluster_info(cluster_info_file)
else:
cluster_info = create_new_cluster_info_file(cluster_info_file, len(tsne))
cluster_info_data_source = ColumnDataSource(cluster_info)
clusters_columns = [TableColumn(field='Cluster', title='Clusters'),
TableColumn(field='Num_of_Spikes', title='Number of Spikes')]
clusters_table = DataTable(source=cluster_info_data_source, columns=clusters_columns, selectable=True,
editable=False, width=clusters_table_size[0], height=clusters_table_size[1],
scroll_to_selection=True)
def on_select_cluster_info_table(attr, old, new):
global selected_cluster_names
cluster_info = load_cluster_info(cluster_info_file)
indices = list(chain.from_iterable(cluster_info.iloc[new['1d']['indices']].Spike_Indices.tolist()))
selected_cluster_names = list(cluster_info.index[new['1d']['indices']])
old = new = tsne_source.selected
tsne_source.selected['1d']['indices'] = indices
tsne_source.trigger('selected', old, new)
user_info_edit.value = 'Selected clusters = ' + ', '.join(selected_cluster_names)
cluster_info_data_source.on_change('selected', on_select_cluster_info_table)
def update_data_table():
cluster_info_data_source = ColumnDataSource(load_cluster_info(cluster_info_file))
cluster_info_data_source.on_change('selected', on_select_cluster_info_table)
clusters_table.source = cluster_info_data_source
options = list(cluster_info_data_source.data['Cluster'])
options.insert(0, 'No cluster selected')
select_cluster_to_move_points_to.options = options
# cluster TextBox that adds cluster to the DataTable
new_cluster_name_edit = TextInput(value='give the new cluster a name',
title='Put selected points into a new cluster')
def on_text_edit_new_cluster_name(attr, old, new):
global currently_selected_spike_indices
global clusters_of_all_spikes
new_cluster_name = new_cluster_name_edit.value
spike_indices_to_delete_from_existing_clusters = {}
for spike_index in currently_selected_spike_indices:
if clusters_of_all_spikes[spike_index] != -1:
cluster_index = clusters_of_all_spikes[spike_index]
if cluster_index not in spike_indices_to_delete_from_existing_clusters:
spike_indices_to_delete_from_existing_clusters[cluster_index] = [spike_index]
else:
spike_indices_to_delete_from_existing_clusters[cluster_index].append(spike_index)
cluster_info = load_cluster_info(cluster_info_file)
for cluster_index in spike_indices_to_delete_from_existing_clusters.keys():
cluster_name = cluster_info.iloc[cluster_index].name
remove_spikes_from_cluster(cluster_info_file, cluster_name,
spike_indices_to_delete_from_existing_clusters[cluster_index], unassign=False)
add_cluster_to_cluster_info(cluster_info_file, new_cluster_name, currently_selected_spike_indices)
update_data_table()
new_cluster_name_edit.on_change('value', on_text_edit_new_cluster_name)
# user information Text
user_info_edit = TextInput(value='', title='User information',
width=user_info_size[0], height=user_info_size[1])
# Buttons ------------------------
# show all clusters Button
button_show_all_clusters = Toggle(label='Show all clusters', button_type='primary')
def on_button_show_all_clusters(state, *args):
global tsne_clusters_scatter_plot
if state:
cluster_info = load_cluster_info(cluster_info_file)
num_of_clusters = cluster_info.shape[0]
indices_list_of_lists = cluster_info['Spike_Indices'].tolist()
indices = [item for sublist in indices_list_of_lists for item in sublist]
cluster_indices = np.arange(num_of_clusters)
if verbose:
print('Showing all clusters in colors... wait for it...')
colors = []
for c in cluster_indices:
r = np.random.random(size=1) * 255
g = np.random.random(size=1) * 255
for i in np.arange(len(indices_list_of_lists[c])):
colors.append("#%02x%02x%02x" % (int(r), int(g), 50))
first_time = True
for renderer in tsne_figure.renderers:
if renderer.name == 'tsne_all_clusters_glyph_renderer':
renderer.data_source.data['fill_color'] = renderer.data_source.data['line_color'] = colors
renderer.glyph.fill_color = 'fill_color'
renderer.glyph.line_color = 'line_color'
first_time = False
break
if first_time:
tsne_clusters_scatter_plot = tsne_figure.scatter(tsne[0][indices], tsne[1][indices], size=1,
color=colors, alpha=1,
name='tsne_all_clusters_glyph_renderer')
tsne_clusters_scatter_plot.visible = True
button_show_all_clusters.label = 'Hide all clusters'
else:
if verbose:
print('Hiding clusters')
button_show_all_clusters.update()
tsne_clusters_scatter_plot.visible = False
button_show_all_clusters.label = 'Show all clusters'
button_show_all_clusters.on_click(on_button_show_all_clusters)
# select the clusters that the selected points belong to Button
# (that will then drive the selection of these spikes on t-sne through the update of the clusters_table source)
button_show_clusters_of_selected_points = Button(label='Show clusters of selected points')
def on_button_show_clusters_change():
print('Hello')
global clusters_of_all_spikes
currently_selected_spike_indices = tsne_source.selected['1d']['indices']
cluster_info = load_cluster_info(cluster_info_file)
clusters_selected = []
new_indices_to_select = []
update_data_table()
for spike_index in currently_selected_spike_indices:
if clusters_of_all_spikes[spike_index] not in clusters_selected:
clusters_selected.append(clusters_of_all_spikes[spike_index])
indices_in_cluster = cluster_info.iloc[clusters_of_all_spikes[spike_index]].Spike_Indices
new_indices_to_select.append(indices_in_cluster)
if len(new_indices_to_select) > 0:
old = clusters_table.source.selected
clusters_table.source.selected['1d']['indices'] = clusters_selected
new = clusters_table.source.selected
clusters_table.source.trigger('selected', old, new)
for c in np.arange(len(clusters_selected)):
clusters_selected[c] = cluster_info.index[clusters_selected[c]]
button_show_clusters_of_selected_points.on_click(on_button_show_clusters_change)
# merge clusters Button
button_merge_clusters_of_selected_points = Button(label='Merge clusters of selected points')
def on_button_merge_clusters_change():
global clusters_of_all_spikes
currently_selected_spike_indices = tsne_source.selected['1d']['indices']
cluster_info = load_cluster_info(cluster_info_file)
clusters_selected = []
for spike_index in currently_selected_spike_indices:
if clusters_of_all_spikes[spike_index] not in clusters_selected:
clusters_selected.append(clusters_of_all_spikes[spike_index])
if len(clusters_selected) > 0:
clusters_selected = np.sort(clusters_selected)
clusters_selected_names = []
for cluster_index in clusters_selected:
clusters_selected_names.append(cluster_info.iloc[cluster_index].name)
cluster_name = clusters_selected_names[0]
add_cluster_to_cluster_info(cluster_info_file, cluster_name, currently_selected_spike_indices)
i = 0
for c in np.arange(1, len(clusters_selected)):
cluster_info = remove_cluster_from_cluster_info(cluster_info_file,
cluster_info.iloc[clusters_selected[c] - i].name,
unassign=False)
i = i + 1 # Every time you remove a cluster the original index of the remaining clusters drops by one
update_data_table()
user_info_edit.value = 'Clusters '+ ', '.join(clusters_selected_names) + ' merged to cluster ' + cluster_name
button_merge_clusters_of_selected_points.on_click(on_button_merge_clusters_change)
# delete cluster Button
button_delete_cluster = Button(label='Delete selected cluster(s)')
def on_button_delete_cluster():
global selected_cluster_names
for cluster_name in selected_cluster_names:
remove_cluster_from_cluster_info(cluster_info_file, cluster_name)
user_info_edit.value = 'Deleted clusters: ' + ', '.join(selected_cluster_names)
update_data_table()
button_delete_cluster.on_click(on_button_delete_cluster)
# select cluster to move selected points to Select
select_cluster_to_move_points_to = Select(title="Assign selected points to cluster:", value="No cluster selected")
options = list(cluster_info_data_source.data['Cluster'])
options.insert(0, 'No cluster selected')
select_cluster_to_move_points_to.options = options
def move_selected_points_to_cluster(attr, old, new):
global currently_selected_spike_indices
if len(currently_selected_spike_indices) > 0 and new is not 'No cluster selected':
remove_spikes_from_all_clusters(cluster_info_file, currently_selected_spike_indices)
add_spikes_to_cluster(cluster_info_file, new, currently_selected_spike_indices)
update_data_table()
select_cluster_to_move_points_to.value = 'No cluster selected'
user_info_edit.value = 'Selected clusters = ' + new
select_cluster_to_move_points_to.on_change('value', move_selected_points_to_cluster)
# undo selection button
undo_selected_points_button = Button(label='Undo last selection')
def on_button_undo_selection():
global previously_selected_spike_indices
tsne_source.selected['1d']['indices'] = previously_selected_spike_indices
old = new = tsne_source.selected
tsne_source.trigger('selected', old, new)
undo_selected_points_button.on_click(on_button_undo_selection)
# Sliders -------------------
# use the fake data trick to call the callback only when the mouse is released (mouseup only works for CustomJS)
# change visibility of non selected points Slider
slider_non_selected_visibility = Slider(start=0, end=1, value=0.2, step=.02, callback_policy='mouseup',
title='Alpha of not selected points',
width=slider_size[0], height=slider_size[1])
def on_slider_change_non_selected_visibility(attrname, old, new):
global non_selected_points_alpha
if len(source_fake_nsv.data['value']) > 0:
non_selected_points_alpha = source_fake_nsv.data['value'][0]
old = new = tsne_source.selected
tsne_source.trigger('selected', old, new)
source_fake_nsv = ColumnDataSource(data=dict(value=[]))
source_fake_nsv.on_change('data', on_slider_change_non_selected_visibility)
slider_non_selected_visibility.callback = CustomJS(args=dict(source=source_fake_nsv),
code="""
source.data = { value: [cb_obj.value] }
""")
# change size of non selected points Slider
slider_non_selected_size = Slider(start=0.5, end=10, value=2, step=0.5, callback_policy='mouseup',
title='Size of not selected points',
width=slider_size[0], height=slider_size[1])
def on_slider_change_non_selected_size(attrname, old, new):
global non_selected_points_size
if len(source_fake_nss.data['value']) > 0:
non_selected_points_size = source_fake_nss.data['value'][0]
old = new = tsne_source.selected
tsne_source.trigger('selected', old, new)
source_fake_nss = ColumnDataSource(data=dict(value=[]))
source_fake_nss.on_change('data', on_slider_change_non_selected_size)
slider_non_selected_size.callback = CustomJS(args=dict(source=source_fake_nss),
code="""
source.data = { value: [cb_obj.value] }
""")
# change size of selected points Slider
slider_selected_size = Slider(start=0.5, end=10, value=2, step=0.5, callback_policy='mouseup',
title='Size of selected points',
width=slider_size[0], height=slider_size[1])
def on_slider_change_selected_size(attrname, old, new):
global selected_points_size
if len(source_fake_ss.data['value']) > 0:
selected_points_size = source_fake_ss.data['value'][0]
old = new = tsne_source.selected
tsne_source.trigger('selected', old, new)
source_fake_ss = ColumnDataSource(data=dict(value=[]))
source_fake_ss.on_change('data', on_slider_change_selected_size)
slider_selected_size.callback = CustomJS(args=dict(source=source_fake_ss),
code="""
source.data = { value: [cb_obj.value] }
""")
# -------------------------------------------
# Layout and session setup ------------------
# align and make layout
spike_figure.min_border_top = 50
spike_figure.min_border_right = 10
hist_figure.min_border_top = 50
hist_figure.min_border_left = 10
tsne_figure.min_border_right = 50
if k4:
lay = row(column(tsne_figure,
row(slider_non_selected_visibility, slider_non_selected_size, slider_selected_size),
row(spike_figure, hist_figure),
user_info_edit),
column(clusters_table,
button_show_clusters_of_selected_points,
button_merge_clusters_of_selected_points,
button_delete_cluster,
select_cluster_to_move_points_to,
new_cluster_name_edit,
button_show_all_clusters,
undo_selected_points_button,
heatmap_plot))
else:
lay = row(column(tsne_figure,
row(spike_figure, hist_figure)),
column(row(heatmap_plot, column(slider_non_selected_visibility,
slider_non_selected_size,
slider_selected_size)),
user_info_edit),
column(clusters_table,
button_show_clusters_of_selected_points,
button_merge_clusters_of_selected_points,
button_delete_cluster,
select_cluster_to_move_points_to,
new_cluster_name_edit,
button_show_all_clusters,
undo_selected_points_button))
session = push_session(curdoc())
session.show(lay) # open the document in a browser
session.loop_until_closed() # run forever, requires stopping the interpreter in order to stop :)
# WANT TO DO THESE CUTS IN THE SUBROUTINE
#spectrum_template.data['flux_cut'] = (spectrum_template.data['f'])
#spectrum_template.data['flux_cut'][np.where(np.array(spectrum_template.data['w']) < 1200.)] = -999.
#spectrum_template.data['flux_cut'][np.where(np.array(spectrum_template.data['w']) > 1700.)] = -999.
# fake source for managing callbacks
source = ColumnDataSource(data=dict(value=[]))
source.on_change('data', update_data)
# Set up widgets and their callbacks (faking the mouseup policy via "source" b/c functional callback doesn't do that.
template = Select(title="Template Spectrum", value="QSO", options=["QSO", "10 Myr Starburst", "O5V Star", "G2V Star", "Classical T Tauri", "M1 Dwarf", "Orion Nebula", \
"Starburst, No Dust", "Starburst, E(B-V) = 0.6"])
redshift = Slider(title="Redshift", value=0.0, start=0., end=1.0, step=0.02, callback_policy='mouseup')
redshift.callback = CustomJS(args=dict(source=source), code="""
source.data = { value: [cb_obj.value] }
""")
magnitude = Slider(title="Magnitude [AB]", value=21., start=15., end=25.0, step=0.1, callback_policy='mouseup')
magnitude.callback = CustomJS(args=dict(source=source), code="""
source.data = { value: [cb_obj.value] }
""")
grating = Select(title="Grating / Setting", value="G150M (R = 30,000)", \
options=["G120M (R = 30,000)", "G150M (R = 30,000)", "G180M (R = 30,000)", "G155L (R = 5,000)", "G145LL (R = 500)"])
aperture= Slider(title="Aperture (meters)", value=12., start=2., end=20.0, step=1.0, callback_policy='mouseup')
aperture.callback = CustomJS(args=dict(source=source), code="""
source.data = { value: [cb_obj.value] }
""")
exptime = Slider(title="Exposure Time [hr]", value=1.0, start=0.1, end=10.0, step=0.1, callback_policy='mouseup')
exptime.callback = CustomJS(args=dict(source=source), code="""
source.data = { value: [cb_obj.value] }
""")
life_points.data['r'] = np.array(life_points.data['alpha']) * 0. + (
0.3 * i + 0.5)
# Set up widgets with "fake" callbacks
fake_callback_source1 = ColumnDataSource(data=dict(value=[]))
fake_callback_source1.on_change('data', update_data)
aperture = Slider(title="Aperture (meters)",
value=12.,
start=4.,
end=20.0,
step=4.0,
callback_policy='mouseup',
width=400)
aperture.callback = CustomJS(args=dict(source=fake_callback_source1),
code="""
source.data = { value: [cb_obj.value] }
""")
contrast = Slider(title="Log (Contrast)",
value=-10,
start=-11.0,
end=-9,
step=1.0,
callback_policy='mouseup',
width=400)
contrast.callback = CustomJS(args=dict(source=fake_callback_source1),
code="""
source.data = { value: [cb_obj.value] }
""")
iwa = Slider(title="Inner Working Angle (l/D)",
value=1.5,
start=1.5,
link.style.visibility = 'hidden';
link.dispatchEvent(new MouseEvent('click'));
}
} else {
alert('No data selected!');
}
""")
data_freq.on_change('data', data_freq_sld_callback)
data_freq_sld.on_change('value', data_freq_on_title)
data_freq_sld.callback = CustomJS(args=dict(
data_freq=data_freq,
conn_status=conn_status,
),
code="""
if(!conn_status.value) {
console.log("This application must be connected to ESP device to change it's acquisition frequency.");
}
data_freq.data = { value: [cb_obj.value] }
""")
##############################################################################
# Periodic streaming update call
def periodic_stream():
global new_data
if new_data:
util.doc_next_tick(doc,
// Emit data source for plot to be updated
source.change.emit();
"""
# Done! Not too bad. Now let's define the arguments for the callback function
# Define arguments for JavaScript callback function
cb_args = {'source': source, 'sSlider': s_select, 'xoSlider': x_init}
# Asign arguments to function
cb = CustomJS(args=cb_args, code=cb_script)
# Now we must assign this callback function to each of the sliders. What this means is that we must indicate that every time the slider value is changed, the `JavaScript` callback function must be executed.
# Assign callback function to widgets
x_init.callback = cb
s_select.callback = cb
x_init.js_on_change('value', cb)
s_select.js_on_change('value', cb)
# Alright. Now everything is setup for our interactive plot! Now we just need to define the bokeh plot.
# Define bokeh axis
x_allele_ax = bokeh.plotting.figure(width=300,
height=275,
x_axis_label='time (a.u.)',
y_axis_label='allele frequency',
y_range=[-0.05, 1.05])
# Populate the plot with our line coming from the Data Source
x_allele_ax.line(x='time', y='x_allele', line_width=2, source=source)
s=float(slider_smooth.value)) # t=x_knots,
source_spline.data = dict(x=x, y=splev(x, tck))
p.line('x', 'y', color="red", source=source_spline)
source_knots.data = dict(x=tck[0])
# cs = CubicSpline(sorted_x, sorted_y, axis=0, bc_type='natural', extrapolate=None)
# source_spline = ColumnDataSource(data=dict(x=x, y=cs(x)))
# This way the slider triggers only when hte mouse is released
# Otherwise at higher curve orders with many points it could get slow
# source_dummy is just used to trigger the callback to update_source_spline
source_dummy = ColumnDataSource(data=dict(value=[]))
source_dummy.on_change('data', update_source_spline)
# slider_smooth.on_change('value', update_source_spline)
slider_smooth.callback = CustomJS(args=dict(source_dummy=source_dummy),
code="""
source_dummy.data = { value: [cb_obj.value] }
""")
def display_event():
return CustomJS(args=dict(p=p, source_datapoints_JS=source_datapoints),
code="""
function distance(p1, p2) {
return Math.sqrt( Math.pow(p1[0]-p2[0] , 2) + Math.pow(p1[1]-p2[1], 2) );
}
var x_scale = p.inner_width / (p.x_range.end - p.x_range.start)
var y_scale = p.inner_height / (p.y_range.end - p.y_range.start)
var CIRCLE_RADIUS = %s;
def plot_datatable(df):
df = df.copy()
# deal with some atomic mass values of the form '[98]'
df['atomic mass'] = df['atomic mass'].str.extract('([\d\.]+)').astype(
float)
columns = [
TableColumn(field='atomic number', title='Atomic Number'),
TableColumn(field='symbol', title='Symbol'),
TableColumn(field='name', title='Name'),
TableColumn(field='metal', title='Type'),
TableColumn(field='atomic mass', title='Atomic Mass')
]
column_names = [tc.field for tc in columns]
source = ColumnDataSource(df[column_names])
original_source = ColumnDataSource(df)
data_table = DataTable(source=source,
columns=columns,
height=600,
editable=False)
widget_callback_code = """
var filtered_data = filtered_source.get('data');
var original_data = original_source.get('data');
var element_type = element_type_select.get('value');
var min_mass = min_mass_slider.get('value');
// now construct the new data object based on the filtered values
for (var key in original_data) {
filtered_data[key] = [];
for (var i = 0; i < original_data[key].length; ++i) {
if ((element_type === "ALL" || original_data["metal"][i] === element_type) &&
(original_data['atomic mass'][i] >= min_mass)) {
filtered_data[key].push(original_data[key][i]);
}
}
}
target_obj.trigger('change');
filtered_source.trigger('change');
"""
# define the filter widgets, without callbacks for now
element_type_list = ['ALL'] + df['metal'].unique().tolist()
element_type_select = Select(title="Element Type:",
value=element_type_list[0],
options=element_type_list)
min_mass_slider = Slider(start=0,
end=df['atomic mass'].max(),
value=1,
step=1,
title="minimum atomic mass")
# now define the callback objects now that the filter widgets exist
arg_dct = dict(filtered_source=source,
original_source=original_source,
element_type_select=element_type_select,
min_mass_slider=min_mass_slider,
target_obj=data_table)
generic_callback = CustomJS(args=arg_dct, code=widget_callback_code)
# connect the callbacks to the filter widgets
element_type_select.callback = generic_callback
min_mass_slider.callback = generic_callback
# create a button to collect the filtered results
# for now, just send json to new window
send_button_callback_code = """
var filtered_data = filtered_source.get('data');
var action_items = [];
for (var i = 0; i < filtered_data['atomic number'].length; ++i) {
var item = new Object();
for (var key in filtered_data) {
item[key] = filtered_data[key][i]
}
action_items.push(item);
}
var new_window = window.open("data:text/html," + encodeURIComponent(JSON.stringify(action_items)),
"_blank", "location=yes,height=570,width=520,scrollbars=yes,status=yes");
new_window.focus();
"""
send_button_callback = CustomJS(args=dict(filtered_source=source),
code=send_button_callback_code)
send_button = Button(label="Send",
type="success",
callback=send_button_callback)
input_widgets = HBox(children=[
HBox(children=[
element_type_select,
]),
HBox(children=[min_mass_slider]),
HBox(children=[send_button]),
])
p = vplot(input_widgets, data_table)
show(p)
end=len(ch2_data[0]),
value=1,
step=1,
title="Peak Slider")
peak_start = Span(
location=slider2.value,
dimension='height',
line_color='red',
line_dash='dashed',
line_width=1)
p.add_layout(peak_start)
slider2.callback = CustomJS(args=dict(span=peak_start, slider=slider2), code="""
span.location = slider.value;
""")
cb_up = CustomJS(args=dict(span=peak_start, slider=slider2), code="""
span.location = span.location + 1;
slider.value = span.location;
""")
cb_down = CustomJS(args=dict(span=peak_start, slider=slider2), code="""
span.location = span.location - 1;
slider.value = span.location;
""")
button_up = Button(label=">", callback=cb_up)
button_down = Button(label="<", callback=cb_down)
button_group = RadioButtonGroup(
d16, d17, d18, d19, d20
])
source = ColumnDataSource(data=dict(value=[]))
source.on_change('data', update_data)
# Set up widgets
aperture = Slider(title="Aperture (meters)",
value=12.,
start=4.,
end=20.0,
step=4.0,
callback_policy='mouseup')
aperture.callback = CustomJS(args=dict(source=source),
code="""
source.data = { value: [cb_obj.value] }
""")
contrast = Slider(title="Log (Contrast)",
value=-10,
start=-11.0,
end=-9,
step=1.0,
callback_policy='mouseup')
contrast.callback = CustomJS(args=dict(source=source),
code="""
source.data = { value: [cb_obj.value] }
""")
iwa = Slider(title="Inner Working Angle (l/D)",
value=1.5,
start=1.5,
end=4.0,
######################################
# SET UP ALL THE WIDGETS AND CALLBACKS
######################################
source = ColumnDataSource(data=dict(value=[]))
source.on_change('data', update_data)
exptime = Slider(title="Integration Time (hours)",
value=20.,
start=10.,
end=100.0,
step=1.0,
callback_policy='mouseup')
exptime.callback = CustomJS(args=dict(source=source),
code="""
source.data = { value: [cb_obj.value] }
""")
distance = Slider(title="Distance (parsec)",
value=10.,
start=2.,
end=50.0,
step=1.0,
callback_policy='mouseup')
distance.callback = CustomJS(args=dict(source=source),
code="""
source.data = { value: [cb_obj.value] }
""")
radius = Slider(title="Planet Radius (R_Earth)",
value=1.0,
start=0.5,
end=3.,
def create_ui(self, data):
self.logger.info("number of data items %d", len(data))
# Create data source and data table
# path, score, software_id, featcnt, featfreq, app name, app path, decision, status, comment, active in play, still voilating
decision_editor = SelectEditor(options=[
"Unprocessed", "GPL Violation", "LGPL Violation",
"Open Source App", "False Positive", "False Negative (LGPL)",
"False Negative (GPL)"
])
status_editor = SelectEditor(options=[
"Unprocessed", "Emailed", "Confirmed", "Denied", "Authorized"
])
if self.app_info:
columns = [
TableColumn(field="myindex", title="Id"),
TableColumn(field="path", title="File Path"),
TableColumn(field="score", title="Score"),
TableColumn(field="normscore",
title="NormScore",
formatter=NumberFormatter(format="0.00")),
TableColumn(field="partial", title="PartialMatch"),
TableColumn(field="repo_id", title="Repo ID"),
TableColumn(field="software_name", title="OSS"),
TableColumn(field="version", title="Version"),
TableColumn(
field="featcnt",
title="FeatCount",
),
TableColumn(
field="featfreq",
title="FeatFreq",
),
TableColumn(field="package_name", title="Package"),
TableColumn(field="app_path", title="App Path"),
TableColumn(field="app_count", title="App Count"),
TableColumn(field="decision",
title="Decision",
editor=decision_editor),
TableColumn(field="status",
title="Status",
editor=status_editor),
TableColumn(field="comment", title="Comment"),
# I am not sure whether we should add these two fields here.
# TableColumn(field="active", title="Active in Play"),
# TableColumn(field="still_violating", title="Still Violating"),
]
else:
template_str = '<a href="' + self.REPO_URL + '/<%= value %>"><%= value %></a>'
columns = [
TableColumn(
field="myindex",
title="Id",
),
TableColumn(field="name", title="Name"),
TableColumn(field="score",
title="Score",
formatter=NumberFormatter(format="0.00")),
TableColumn(field="normscore",
title="NormScore",
formatter=NumberFormatter(format="0.00")),
TableColumn(field="partial", title="PartialMatch"),
TableColumn(field="repo_id", title="RepoID"),
TableColumn(
field="software_name",
title="OSS",
formatter=HTMLTemplateFormatter(template=template_str)),
TableColumn(field="featcnt",
title="FeatCount",
formatter=NumberFormatter(format="0,000,000")),
TableColumn(field="featfreq",
title="FeatFreq",
formatter=NumberFormatter(format="0,000,000")),
TableColumn(field="version", title="Version"),
TableColumn(field="decision",
title="Decision",
editor=decision_editor),
TableColumn(field="status",
title="Status",
editor=status_editor),
TableColumn(field="comment", title="Comment"),
TableColumn(field="path", title="Path"),
]
# source is the displayed table, and can be modified by user
# original_source is the original data, it is the base, and can only be modified by the program
self.source = ColumnDataSource(self._data)
self.original_source = ColumnDataSource(self._data)
self.data_table = DataTable(source=self.source,
columns=columns,
width=2000,
height=2000,
editable=True,
sortable=True) # Disable sortable for now!
# selector or filters
# reference link for callback: https://gist.github.com/dennisobrien/450d7da20daaba6d39d0
min_matching_score_slider = Slider(start=0,
end=2,
value=0.3,
step=.01,
title="Minimum Matching Score")
max_matching_score_slider = Slider(start=0,
end=2,
value=0.7,
step=.01,
title="Maximum Matching Score")
featfreq_slider = Slider(start=0,
end=10000,
value=0,
step=1,
title="Minimum Matching Num of Features")
featcnt_slider = Slider(start=0,
end=10000,
value=50,
step=1,
title="Minimum Feature Count is OSS")
kind_select = Select(value="All", options=["All", "Java", "Native"])
file_select = Select(value="Name", options=["Name", "MD5", "Path"])
search_input = TextInput(value=None,
title="Enter library to search",
callback=None)
search_button = Button(label="Search", button_type="success")
download_callback_code = """
var data = source.get('data');
var filetext = 'Id,File Name,Matching Score,Normalized Matching Score,Repo ID,Software Name,Feature Count,Feature Freq.,Version,Decision,Status,Comment,File Path\\n';
var order = ['myindex', 'name', 'score', 'normscore', 'repo_id', 'software_name', 'featcnt', 'featfreq', 'version', 'decision', 'status', 'comment', 'path'];
for (var i = 0; i < data['path'].length; ++i) {
var currRow = [];
for (var item in order) {
key = order[item]
currRow.push(data[key][i]);
}
var joined = currRow.join().concat('\\n');
filetext = filetext.concat(joined);
}
var filename = 'violations.csv';
var blob = new Blob([filetext], { type: 'text/csv;charset=utf-8;' });
//addresses IE
if (navigator.msSaveBlob) {
//navigator.msSaveBlob(blob, filename);
}
else {
var link = document.createElement("a");
link = document.createElement('a');
link.href = URL.createObjectURL(blob);
link.download = filename;
link.target = "_blank";
link.style.visibility = 'hidden';
link.dispatchEvent(new MouseEvent('click'));
}
"""
# enable downloading of results as a csv file
download_button = Button(label="Download", button_type="success")
download_button.callback = CustomJS(args=dict(source=self.source),
code=download_callback_code)
# enable comparison of selected rows
compare_button = Button(label="Compare", button_type="success")
compare_button.on_click(self.compare_callback)
# update on change
#controls = [min_matching_score_slider, max_matching_score_slider, featfreq_slider, \
# featcnt_slider, kind_select, file_select, button]
#for item in controls:
# item.on_change('value', lambda attr, old, new: self.update_source(item))
combined_callback_code = """
var data = source.get('data');
var original_data = original_source.get('data');
var min_score = min_matching_score_slider.get('value');
var max_score = max_matching_score_slider.get('value');
var search_input = search_input.get('value');
var min_featfreq = featfreq_slider.get('value');
var min_featcnt = featcnt_slider.get('value');
var kind = kind_select.get('value');
console.log("min score: " + min_score + ", max score: " + max_score + ", min_featfreq: " + min_featfreq + ", min_featcnt" + min_featcnt + ", kind" + kind);
var java_suffix = ".dex";
var native_suffix = ".so";
console.log("searchinput: " + search_input);
var re;
if (search_input) {
re = new RegExp(search_input);
} else {
re = new RegExp(".*");
}
for (var key in original_data) {
data[key] = [];
for (var i = 0; i < original_data['path'].length; ++i) {
if ((original_data['normscore'][i] >= min_score) && (original_data['normscore'][i] <= max_score) && (original_data['featfreq'][i] >= min_featfreq) &&
(original_data['featcnt'][i] >= min_featcnt)) {
// filter by java
if (kind == "Java" && original_data['path'][i].indexOf(java_suffix, original_data['path'][i].length - java_suffix.length) === -1)
continue;
// filter by native
if (kind == "Native" && original_data['path'][i].indexOf(native_suffix, original_data['path'][i].length - native_suffix.length) === -1)
continue;
// filter by search regex
if (!re.test(original_data['name'][i])) {
console.log("mismatch: " + original_data['name'][i]);
continue;
}
// this row is the expected kind
data[key].push(original_data[key][i]);
}
}
}
source.trigger('change');
target.trigger('change');
"""
generic_callback = CustomJS(args=dict(
source=self.source,
original_source=self.original_source,
search_input=search_input,
max_matching_score_slider=max_matching_score_slider,
min_matching_score_slider=min_matching_score_slider,
featfreq_slider=featfreq_slider,
featcnt_slider=featcnt_slider,
kind_select=kind_select,
target=self.data_table),
code=combined_callback_code)
min_matching_score_slider.callback = generic_callback
max_matching_score_slider.callback = generic_callback
featfreq_slider.callback = generic_callback
featcnt_slider.callback = generic_callback
search_button.callback = generic_callback
kind_select.callback = generic_callback
# install callback when a row gets selected
self.source.on_change('selected', self.selected_callback)
###########################################################
# Main
###########################################################
controls = [min_matching_score_slider, max_matching_score_slider, featfreq_slider, \
featcnt_slider, kind_select, file_select, search_input, search_button, \
download_button, compare_button]
plots_box = widgetbox(*controls, width=800, sizing_mode="fixed")
layout = column(plots_box, self.data_table, sizing_mode="fixed")
return layout
from bokeh.io import curdoc
from bokeh.layouts import column
from bokeh.plotting import figure
from bokeh.models.callbacks import CustomJS
from bokeh.models.sources import ColumnDataSource
from bokeh.models.widgets import Slider
# this is the real callback that we want to happen on slider mouseup
def cb(attr, old, new):
print("UPDATE", source.data['value'])
#p.x_range=range(0, int(source.data['value']))
# This data source is just used to communicate / trigger the real callback
source = ColumnDataSource(data=dict(value=[]))
source.on_change('data', cb)
# a figure, just for example
p = figure(x_range=(0,1), y_range=(0,1))
# add a slider with a CustomJS callback and a mouseup policy to update the source
slider = Slider(start=1, end=10, value=1, step=0.1, callback_policy='mouseup')
slider.callback = CustomJS(args=dict(source=source), code="""
source.data = { value: [cb_obj.value] }
""")
curdoc().add_root(column(slider, p))
# make sure to add the source explicitly
curdoc().add_root(source)
# x axis selection box
x_axis_selector_title = Div(text="""X Axis:""", height=10)
x_axis_selector = RadioButtonGroup(labels=x_axis_options, active=0)
x_axis_selector.on_click(change_x_axis)
# toggle second axis button
toggle_second_axis_button = Button(label="Toggle Second Axis", button_type="success")
toggle_second_axis_button.on_click(toggle_second_axis)
# averaging slider
# This data source is just used to communicate / trigger the real callback
averaging_slider_dummy_source = ColumnDataSource(data=dict(value=[]))
averaging_slider_dummy_source.on_change('data', update_averaging)
averaging_slider = Slider(title="Averaging window", start=1, end=101, step=10, callback_policy='mouseup')
averaging_slider.callback = CustomJS(args=dict(source=averaging_slider_dummy_source), code="""
source.data = { value: [cb_obj.value] }
""")
# group properties checkbox
group_cb = CheckboxGroup(labels=["Show statistics bands", "Ungroup signals"], active=[])
group_cb.on_click(toggle_group_property)
# color selector
color_selector_title = Div(text="""Select Color:""")
crsource = ColumnDataSource(data=dict(x=crx, y=cry, crcolor=crcolor, RGBs=crRGBs))
color_selector = figure(x_range=(0, color_resolution), y_range=(0, 10),
plot_width=300, plot_height=40,
tools='tap')
color_selector.axis.visible = False
color_range = color_selector.rect(x='x', y='y', width=1, height=10,
color='crcolor', source=crsource)
######################################
# SET UP ALL THE WIDGETS AND CALLBACKS
######################################
source = ColumnDataSource(data=dict(value=[]))
source.on_change('data', update_data)
exptime = Slider(title="Integration Time (hours)",
value=24.,
start=1.,
end=1000.0,
step=1.0,
callback_policy='mouseup')
exptime.callback = CustomJS(args=dict(source=source),
code="""
source.data = { value: [cb_obj.value] }
""")
distance = Slider(title="Log Distance (parsec)",
value=1.,
start=-5.3,
end=10.0,
step=0.1,
callback_policy='mouseup')
distance.callback = CustomJS(args=dict(source=source),
code="""
source.data = { value: [cb_obj.value] }
""")
radius = Slider(title="Log Object Radius (R_Sun)",
value=0,
start=-10,
end=20.,