CustomJS(
code="console.log('checkbox_group: ' + this.active, this.toString())"))
radio_group = RadioGroup(labels=["Option 1", "Option 2", "Option 3"], active=0)
radio_group.on_click(lambda value: print('radio_group: %s' % value))
radio_group.js_on_click(
CustomJS(
code="console.log('radio_group: ' + this.active, this.toString())"))
checkbox_button_group = CheckboxButtonGroup(
labels=["Option 1", "Option 2", "Option 3"], active=[0, 1])
checkbox_button_group.on_click(
lambda value: print('checkbox_button_group: %s' % value))
checkbox_button_group.js_on_click(
CustomJS(
code=
"console.log('checkbox_button_group: ' + this.active, this.toString())"
))
radio_button_group = RadioButtonGroup(
labels=["Option 1", "Option 2", "Option 3"], active=0)
radio_button_group.on_click(
lambda value: print('radio_button_group: %s' % value))
radio_button_group.js_on_click(
CustomJS(
code=
"console.log('radio_button_group: ' + this.active, this.toString())"))
widgetBox = WidgetBox(children=[
button,
button_disabled,
dropdown.js_on_click(CustomJS(code="console.log('dropdown: ' + this.value, this.toString())"))
dropdown_disabled = Dropdown(label="Dropdown button (disabled)", button_type="warning", disabled=True, menu=menu)
dropdown_disabled.js_on_click(CustomJS(code="console.log('dropdown_disabled: ' + this.value, this.toString())"))
#dropdown_split = Dropdown(label="Split button", button_type="danger", menu=menu, default_value="default")
#dropdown_split.js_on_click(CustomJS(code="console.log('dropdown_split: ' + this.value, this.toString())"))
checkbox_group = CheckboxGroup(labels=["Option 1", "Option 2", "Option 3"], active=[0, 1])
checkbox_group.js_on_click(CustomJS(code="console.log('checkbox_group: ' + this.active, this.toString())"))
radio_group = RadioGroup(labels=["Option 1", "Option 2", "Option 3"], active=0)
radio_group.js_on_click(CustomJS(code="console.log('radio_group: ' + this.active, this.toString())"))
checkbox_button_group = CheckboxButtonGroup(labels=["Option 1", "Option 2", "Option 3"], active=[0, 1])
checkbox_button_group.js_on_click(CustomJS(code="console.log('checkbox_button_group: ' + this.active, this.toString())"))
radio_button_group = RadioButtonGroup(labels=["Option 1", "Option 2", "Option 3"], active=0)
radio_button_group.js_on_click(CustomJS(code="console.log('radio_button_group: ' + this.active, this.toString())"))
widget_box = WidgetBox(children=[
button, button_disabled,
toggle_inactive, toggle_active,
dropdown, dropdown_disabled, #dropdown_split,
checkbox_group, radio_group,
checkbox_button_group, radio_button_group,
])
doc = Document()
doc.add_root(widget_box)
} else {
arguments[i].data.y=arguments[i].data.y_hidden;
}
arguments[i].change.emit();
}
"""
callback = CustomJS(args=sources, code=scode)
checkbox_group = CheckboxButtonGroup(
labels=["NIRCam", "NIRSpec", "NIRISS", "MIRI"],
active=[0, 1, 2, 3],
sizing_mode="scale_width",
width=800)
checkbox_group.js_on_click(callback)
spacer1 = Spacer()
spacer2 = Spacer()
l = layout([[spacer1, checkbox_group, spacer2], [plot]],
sizing_mode='scale_width')
show(l)
script, div = autoload_static(l, CDN, "etc_plot.js")
#script, div = components(l)
f = open('etc_plot.js', 'w')
f.write(script)
f.close()
def plotspectra(spectra,
zcatalog=None,
model=None,
notebook=False,
title=None):
'''
TODO: document
'''
if notebook:
bk.output_notebook()
#- If inputs are frames, convert to a spectra object
if isinstance(spectra, list) and isinstance(spectra[0],
desispec.frame.Frame):
spectra = frames2spectra(spectra)
frame_input = True
else:
frame_input = False
if frame_input and title is None:
meta = spectra.meta
title = 'Night {} ExpID {} Spectrograph {}'.format(
meta['NIGHT'],
meta['EXPID'],
meta['CAMERA'][1],
)
#- Gather spectra into ColumnDataSource objects for Bokeh
nspec = spectra.num_spectra()
cds_spectra = list()
for band in spectra.bands:
#- Set masked bins to NaN so that Bokeh won't plot them
bad = (spectra.ivar[band] == 0.0) | (spectra.mask[band] != 0)
spectra.flux[band][bad] = np.nan
cdsdata = dict(
origwave=spectra.wave[band].copy(),
plotwave=spectra.wave[band].copy(),
)
for i in range(nspec):
key = 'origflux' + str(i)
cdsdata[key] = spectra.flux[band][i]
cdsdata['plotflux'] = cdsdata['origflux0']
cds_spectra.append(bk.ColumnDataSource(cdsdata, name=band))
#- Reorder zcatalog to match input targets
#- TODO: allow more than one zcatalog entry with different ZNUM per targetid
targetids = spectra.target_ids()
if zcatalog is not None:
ii = np.argsort(np.argsort(targetids))
jj = np.argsort(zcatalog['TARGETID'])
kk = jj[ii]
zcatalog = zcatalog[kk]
#- That sequence of argsorts may feel like magic,
#- so make sure we got it right
assert np.all(zcatalog['TARGETID'] == targetids)
assert np.all(zcatalog['TARGETID'] == spectra.fibermap['TARGETID'])
#- Also need to re-order input model fluxes
if model is not None:
mwave, mflux = model
model = mwave, mflux[kk]
#- Gather models into ColumnDataSource objects, row matched to spectra
if model is not None:
mwave, mflux = model
model_obswave = mwave.copy()
model_restwave = mwave.copy()
cds_model_data = dict(
origwave=mwave.copy(),
plotwave=mwave.copy(),
plotflux=np.zeros(len(mwave)),
)
for i in range(nspec):
key = 'origflux' + str(i)
cds_model_data[key] = mflux[i]
cds_model_data['plotflux'] = cds_model_data['origflux0']
cds_model = bk.ColumnDataSource(cds_model_data)
else:
cds_model = None
#- Subset of zcatalog and fibermap columns into ColumnDataSource
target_info = list()
for i, row in enumerate(spectra.fibermap):
target_bit_names = ' '.join(desi_mask.names(row['DESI_TARGET']))
txt = 'Target {}: {}'.format(row['TARGETID'], target_bit_names)
if zcatalog is not None:
txt += '<BR/>{} z={:.4f} ± {:.4f} ZWARN={}'.format(
zcatalog['SPECTYPE'][i],
zcatalog['Z'][i],
zcatalog['ZERR'][i],
zcatalog['ZWARN'][i],
)
target_info.append(txt)
cds_targetinfo = bk.ColumnDataSource(dict(target_info=target_info),
name='targetinfo')
if zcatalog is not None:
cds_targetinfo.add(zcatalog['Z'], name='z')
plot_width = 800
plot_height = 400
# tools = 'pan,box_zoom,wheel_zoom,undo,redo,reset,save'
tools = 'pan,box_zoom,wheel_zoom,reset,save'
fig = bk.figure(height=plot_height,
width=plot_width,
title=title,
tools=tools,
toolbar_location='above',
y_range=(-10, 20))
fig.toolbar.active_drag = fig.tools[1] #- box zoom
fig.toolbar.active_scroll = fig.tools[2] #- wheel zoom
fig.xaxis.axis_label = 'Wavelength [Å]'
fig.yaxis.axis_label = 'Flux'
fig.xaxis.axis_label_text_font_style = 'normal'
fig.yaxis.axis_label_text_font_style = 'normal'
colors = dict(b='#1f77b4', r='#d62728', z='maroon')
data_lines = list()
for spec in cds_spectra:
lx = fig.line('plotwave',
'plotflux',
source=spec,
line_color=colors[spec.name])
data_lines.append(lx)
if cds_model is not None:
model_lines = list()
lx = fig.line('plotwave',
'plotflux',
source=cds_model,
line_color='black')
model_lines.append(lx)
legend = Legend(items=[
("data",
data_lines[-1::-1]), #- reversed to get blue as lengend entry
("model", model_lines),
])
else:
legend = Legend(items=[
("data",
data_lines[-1::-1]), #- reversed to get blue as lengend entry
])
fig.add_layout(legend, 'center')
fig.legend.click_policy = 'hide' #- or 'mute'
#- Zoom figure around mouse hover of main plot
zoomfig = bk.figure(
height=plot_height // 2,
width=plot_height // 2,
y_range=fig.y_range,
x_range=(5000, 5100),
# output_backend="webgl",
toolbar_location=None,
tools=[])
for spec in cds_spectra:
zoomfig.line('plotwave',
'plotflux',
source=spec,
line_color=colors[spec.name],
line_width=1,
line_alpha=1.0)
if cds_model is not None:
zoomfig.line('plotwave',
'plotflux',
source=cds_model,
line_color='black')
#- Callback to update zoom window x-range
zoom_callback = CustomJS(args=dict(zoomfig=zoomfig),
code="""
zoomfig.x_range.start = cb_obj.x - 100;
zoomfig.x_range.end = cb_obj.x + 100;
""")
fig.js_on_event(bokeh.events.MouseMove, zoom_callback)
#-----
#- Emission and absorption lines
z = zcatalog['Z'][0] if (zcatalog is not None) else 0.0
line_data, lines, line_labels = add_lines(fig, z=z)
#-----
#- Add widgets for controling plots
z1 = np.floor(z * 100) / 100
dz = z - z1
zslider = Slider(start=0.0, end=4.0, value=z1, step=0.01, title='Redshift')
dzslider = Slider(start=0.0,
end=0.01,
value=dz,
step=0.0001,
title='+ Delta redshift')
dzslider.format = "0[.]0000"
#- Observer vs. Rest frame wavelengths
waveframe_buttons = RadioButtonGroup(labels=["Obs", "Rest"], active=0)
ifiberslider = Slider(start=0, end=nspec - 1, value=0, step=1)
if frame_input:
ifiberslider.title = 'Fiber'
else:
ifiberslider.title = 'Target'
zslider_callback = CustomJS(
args=dict(
spectra=cds_spectra,
model=cds_model,
targetinfo=cds_targetinfo,
ifiberslider=ifiberslider,
zslider=zslider,
dzslider=dzslider,
waveframe_buttons=waveframe_buttons,
line_data=line_data,
lines=lines,
line_labels=line_labels,
fig=fig,
),
#- TODO: reorder to reduce duplicated code
code="""
var z = zslider.value + dzslider.value
var line_restwave = line_data.data['restwave']
var ifiber = ifiberslider.value
var zfit = 0.0
if(targetinfo.data['z'] != undefined) {
zfit = targetinfo.data['z'][ifiber]
}
// Observer Frame
if(waveframe_buttons.active == 0) {
var x = 0.0
for(var i=0; i<line_restwave.length; i++) {
x = line_restwave[i] * (1+z)
lines[i].location = x
line_labels[i].x = x
}
for(var i=0; i<spectra.length; i++) {
var data = spectra[i].data
var origwave = data['origwave']
var plotwave = data['plotwave']
for (var j=0; j<plotwave.length; j++) {
plotwave[j] = origwave[j]
}
spectra[i].change.emit()
}
// Update model wavelength array
if(model) {
var origwave = model.data['origwave']
var plotwave = model.data['plotwave']
for(var i=0; i<plotwave.length; i++) {
plotwave[i] = origwave[i] * (1+z) / (1+zfit)
}
model.change.emit()
}
// Rest Frame
} else {
for(i=0; i<line_restwave.length; i++) {
lines[i].location = line_restwave[i]
line_labels[i].x = line_restwave[i]
}
for (var i=0; i<spectra.length; i++) {
var data = spectra[i].data
var origwave = data['origwave']
var plotwave = data['plotwave']
for (var j=0; j<plotwave.length; j++) {
plotwave[j] = origwave[j] / (1+z)
}
spectra[i].change.emit()
}
// Update model wavelength array
if(model) {
var origwave = model.data['origwave']
var plotwave = model.data['plotwave']
for(var i=0; i<plotwave.length; i++) {
plotwave[i] = origwave[i] / (1+zfit)
}
model.change.emit()
}
}
""")
zslider.js_on_change('value', zslider_callback)
dzslider.js_on_change('value', zslider_callback)
waveframe_buttons.js_on_click(zslider_callback)
plotrange_callback = CustomJS(args=dict(
zslider=zslider,
dzslider=dzslider,
waveframe_buttons=waveframe_buttons,
fig=fig,
),
code="""
var z = zslider.value + dzslider.value
// Observer Frame
if(waveframe_buttons.active == 0) {
fig.x_range.start = fig.x_range.start * (1+z)
fig.x_range.end = fig.x_range.end * (1+z)
} else {
fig.x_range.start = fig.x_range.start / (1+z)
fig.x_range.end = fig.x_range.end / (1+z)
}
""")
waveframe_buttons.js_on_click(plotrange_callback)
smootherslider = Slider(start=0,
end=31,
value=0,
step=1.0,
title='Gaussian Sigma Smooth')
target_info_div = Div(text=target_info[0])
#-----
#- Toggle lines
lines_button_group = CheckboxButtonGroup(labels=["Emission", "Absorption"],
active=[])
lines_callback = CustomJS(args=dict(line_data=line_data,
lines=lines,
line_labels=line_labels),
code="""
var show_emission = false
var show_absorption = false
if (cb_obj.active.indexOf(0) >= 0) { // index 0=Emission in active list
show_emission = true
}
if (cb_obj.active.indexOf(1) >= 0) { // index 1=Absorption in active list
show_absorption = true
}
for(var i=0; i<lines.length; i++) {
if(line_data.data['emission'][i]) {
lines[i].visible = show_emission
line_labels[i].visible = show_emission
} else {
lines[i].visible = show_absorption
line_labels[i].visible = show_absorption
}
}
""")
lines_button_group.js_on_click(lines_callback)
# lines_button_group.js_on_change('value', lines_callback)
#-----
update_plot = CustomJS(args=dict(
spectra=cds_spectra,
model=cds_model,
targetinfo=cds_targetinfo,
target_info_div=target_info_div,
ifiberslider=ifiberslider,
smootherslider=smootherslider,
zslider=zslider,
dzslider=dzslider,
lines_button_group=lines_button_group,
fig=fig,
),
code="""
var ifiber = ifiberslider.value
var nsmooth = smootherslider.value
target_info_div.text = targetinfo.data['target_info'][ifiber]
if(targetinfo.data['z'] != undefined) {
var z = targetinfo.data['z'][ifiber]
var z1 = Math.floor(z*100) / 100
zslider.value = z1
dzslider.value = (z - z1)
}
function get_y_minmax(pmin, pmax, data) {
// copy before sorting to not impact original, and filter out NaN
var dx = data.slice().filter(Boolean)
dx.sort()
var imin = Math.floor(pmin * dx.length)
var imax = Math.floor(pmax * dx.length)
return [dx[imin], dx[imax]]
}
// Smoothing kernel
var kernel = [];
for(var i=-2*nsmooth; i<=2*nsmooth; i++) {
kernel.push(Math.exp(-(i**2)/(2*nsmooth)))
}
var kernel_offset = Math.floor(kernel.length/2)
// Smooth plot and recalculate ymin/ymax
// TODO: add smoother function to reduce duplicated code
var ymin = 0.0
var ymax = 0.0
for (var i=0; i<spectra.length; i++) {
var data = spectra[i].data
var plotflux = data['plotflux']
var origflux = data['origflux'+ifiber]
for (var j=0; j<plotflux.length; j++) {
if(nsmooth == 0) {
plotflux[j] = origflux[j]
} else {
plotflux[j] = 0.0
var weight = 0.0
// TODO: speed could be improved by moving `if` out of loop
for (var k=0; k<kernel.length; k++) {
var m = j+k-kernel_offset
if((m >= 0) && (m < plotflux.length)) {
var fx = origflux[m]
if(fx == fx) {
plotflux[j] = plotflux[j] + fx * kernel[k]
weight += kernel[k]
}
}
}
plotflux[j] = plotflux[j] / weight
}
}
spectra[i].change.emit()
tmp = get_y_minmax(0.01, 0.99, plotflux)
ymin = Math.min(ymin, tmp[0])
ymax = Math.max(ymax, tmp[1])
}
// update model
if(model) {
var plotflux = model.data['plotflux']
var origflux = model.data['origflux'+ifiber]
for (var j=0; j<plotflux.length; j++) {
if(nsmooth == 0) {
plotflux[j] = origflux[j]
} else {
plotflux[j] = 0.0
var weight = 0.0
// TODO: speed could be improved by moving `if` out of loop
for (var k=0; k<kernel.length; k++) {
var m = j+k-kernel_offset
if((m >= 0) && (m < plotflux.length)) {
var fx = origflux[m]
if(fx == fx) {
plotflux[j] = plotflux[j] + fx * kernel[k]
weight += kernel[k]
}
}
}
plotflux[j] = plotflux[j] / weight
}
}
model.change.emit()
}
// update y_range
if(ymin<0) {
fig.y_range.start = ymin * 1.4
} else {
fig.y_range.start = ymin * 0.6
}
fig.y_range.end = ymax * 1.4
""")
smootherslider.js_on_change('value', update_plot)
ifiberslider.js_on_change('value', update_plot)
#-----
#- Add navigation buttons
navigation_button_width = 30
prev_button = Button(label="<", width=navigation_button_width)
next_button = Button(label=">", width=navigation_button_width)
prev_callback = CustomJS(args=dict(ifiberslider=ifiberslider),
code="""
if(ifiberslider.value>0) {
ifiberslider.value--
}
""")
next_callback = CustomJS(args=dict(ifiberslider=ifiberslider, nspec=nspec),
code="""
if(ifiberslider.value<nspec+1) {
ifiberslider.value++
}
""")
prev_button.js_on_event('button_click', prev_callback)
next_button.js_on_event('button_click', next_callback)
#-----
slider_width = plot_width - 2 * navigation_button_width
navigator = bk.Row(
widgetbox(prev_button, width=navigation_button_width),
widgetbox(next_button, width=navigation_button_width + 20),
widgetbox(ifiberslider, width=slider_width - 20))
bk.show(
bk.Column(
bk.Row(fig, zoomfig),
widgetbox(target_info_div, width=plot_width),
navigator,
widgetbox(smootherslider, width=plot_width // 2),
bk.Row(
widgetbox(waveframe_buttons, width=120),
widgetbox(zslider, width=plot_width // 2 - 60),
widgetbox(dzslider, width=plot_width // 2 - 60),
),
widgetbox(lines_button_group),
))
class ViewerWidgets(object):
"""
Encapsulates Bokeh widgets, and related callbacks, that are part of prospect's GUI.
Except for VI widgets
"""
def __init__(self, plots, nspec):
self.js_files = get_resources('js')
self.navigation_button_width = 30
self.z_button_width = 30
self.plot_widget_width = (plots.plot_width+(plots.plot_height//2))//2 - 40 # used for widgets scaling
#-----
#- Ifiberslider and smoothing widgets
# Ifiberslider's value controls which spectrum is displayed
# These two widgets call update_plot(), later defined
slider_end = nspec-1 if nspec > 1 else 0.5 # Slider cannot have start=end
self.ifiberslider = Slider(start=0, end=slider_end, value=0, step=1, title='Spectrum (of '+str(nspec)+')')
self.smootherslider = Slider(start=0, end=26, value=0, step=1.0, title='Gaussian Sigma Smooth')
self.coaddcam_buttons = None
self.model_select = None
def add_navigation(self, nspec):
#-----
#- Navigation buttons
self.prev_button = Button(label="<", width=self.navigation_button_width)
self.next_button = Button(label=">", width=self.navigation_button_width)
self.prev_callback = CustomJS(
args=dict(ifiberslider=self.ifiberslider),
code="""
if(ifiberslider.value>0 && ifiberslider.end>=1) {
ifiberslider.value--
}
""")
self.next_callback = CustomJS(
args=dict(ifiberslider=self.ifiberslider, nspec=nspec),
code="""
if(ifiberslider.value<nspec-1 && ifiberslider.end>=1) {
ifiberslider.value++
}
""")
self.prev_button.js_on_event('button_click', self.prev_callback)
self.next_button.js_on_event('button_click', self.next_callback)
def add_resetrange(self, viewer_cds, plots):
#-----
#- Axis reset button (superseeds the default bokeh "reset"
self.reset_plotrange_button = Button(label="Reset X-Y range", button_type="default")
reset_plotrange_code = self.js_files["adapt_plotrange.js"] + self.js_files["reset_plotrange.js"]
self.reset_plotrange_callback = CustomJS(args = dict(fig=plots.fig, xmin=plots.xmin, xmax=plots.xmax, spectra=viewer_cds.cds_spectra),
code = reset_plotrange_code)
self.reset_plotrange_button.js_on_event('button_click', self.reset_plotrange_callback)
def add_redshift_widgets(self, z, viewer_cds, plots):
## TODO handle "z" (same issue as viewerplots TBD)
#-----
#- Redshift / wavelength scale widgets
z1 = np.floor(z*100)/100
dz = z-z1
self.zslider = Slider(start=-0.1, end=5.0, value=z1, step=0.01, title='Redshift rough tuning')
self.dzslider = Slider(start=0.0, end=0.0099, value=dz, step=0.0001, title='Redshift fine-tuning')
self.dzslider.format = "0[.]0000"
self.z_input = TextInput(value="{:.4f}".format(z), title="Redshift value:")
#- Observer vs. Rest frame wavelengths
self.waveframe_buttons = RadioButtonGroup(
labels=["Obs", "Rest"], active=0)
self.zslider_callback = CustomJS(
args=dict(zslider=self.zslider, dzslider=self.dzslider, z_input=self.z_input),
code="""
// Protect against 1) recursive call with z_input callback;
// 2) out-of-range zslider values (should never happen in principle)
var z1 = Math.floor(parseFloat(z_input.value)*100) / 100
if ( (Math.abs(zslider.value-z1) >= 0.01) &&
(zslider.value >= -0.1) && (zslider.value <= 5.0) ){
var new_z = zslider.value + dzslider.value
z_input.value = new_z.toFixed(4)
}
""")
self.dzslider_callback = CustomJS(
args=dict(zslider=self.zslider, dzslider=self.dzslider, z_input=self.z_input),
code="""
var z = parseFloat(z_input.value)
var z1 = Math.floor(z) / 100
var z2 = z-z1
if ( (Math.abs(dzslider.value-z2) >= 0.0001) &&
(dzslider.value >= 0.0) && (dzslider.value <= 0.0099) ){
var new_z = zslider.value + dzslider.value
z_input.value = new_z.toFixed(4)
}
""")
self.zslider.js_on_change('value', self.zslider_callback)
self.dzslider.js_on_change('value', self.dzslider_callback)
self.z_minus_button = Button(label="<", width=self.z_button_width)
self.z_plus_button = Button(label=">", width=self.z_button_width)
self.z_minus_callback = CustomJS(
args=dict(z_input=self.z_input),
code="""
var z = parseFloat(z_input.value)
if(z >= -0.09) {
z -= 0.01
z_input.value = z.toFixed(4)
}
""")
self.z_plus_callback = CustomJS(
args=dict(z_input=self.z_input),
code="""
var z = parseFloat(z_input.value)
if(z <= 4.99) {
z += 0.01
z_input.value = z.toFixed(4)
}
""")
self.z_minus_button.js_on_event('button_click', self.z_minus_callback)
self.z_plus_button.js_on_event('button_click', self.z_plus_callback)
self.zreset_button = Button(label='Reset to z_pipe')
self.zreset_callback = CustomJS(
args=dict(z_input=self.z_input, metadata=viewer_cds.cds_metadata, ifiberslider=self.ifiberslider),
code="""
var ifiber = ifiberslider.value
var z = metadata.data['Z'][ifiber]
z_input.value = z.toFixed(4)
""")
self.zreset_button.js_on_event('button_click', self.zreset_callback)
self.z_input_callback = CustomJS(
args=dict(spectra = viewer_cds.cds_spectra,
coaddcam_spec = viewer_cds.cds_coaddcam_spec,
model = viewer_cds.cds_model,
othermodel = viewer_cds.cds_othermodel,
metadata = viewer_cds.cds_metadata,
ifiberslider = self.ifiberslider,
zslider = self.zslider,
dzslider = self.dzslider,
z_input = self.z_input,
waveframe_buttons = self.waveframe_buttons,
line_data = viewer_cds.cds_spectral_lines,
lines = plots.speclines,
line_labels = plots.specline_labels,
zlines = plots.zoom_speclines,
zline_labels = plots.zoom_specline_labels,
overlap_waves = plots.overlap_waves,
overlap_bands = plots.overlap_bands,
fig = plots.fig
),
code="""
var z = parseFloat(z_input.value)
if ( z >=-0.1 && z <= 5.0 ) {
// update zsliders only if needed (avoid recursive call)
z_input.value = parseFloat(z_input.value).toFixed(4)
var z1 = Math.floor(z*100) / 100
var z2 = z-z1
if ( Math.abs(z1-zslider.value) >= 0.01) zslider.value = parseFloat(parseFloat(z1).toFixed(2))
if ( Math.abs(z2-dzslider.value) >= 0.0001) dzslider.value = parseFloat(parseFloat(z2).toFixed(4))
} else {
if (z_input.value < -0.1) z_input.value = (-0.1).toFixed(4)
if (z_input.value > 5) z_input.value = (5.0).toFixed(4)
}
var line_restwave = line_data.data['restwave']
var ifiber = ifiberslider.value
var waveshift_lines = (waveframe_buttons.active == 0) ? 1+z : 1 ;
var waveshift_spec = (waveframe_buttons.active == 0) ? 1 : 1/(1+z) ;
for(var i=0; i<line_restwave.length; i++) {
lines[i].location = line_restwave[i] * waveshift_lines
line_labels[i].x = line_restwave[i] * waveshift_lines
zlines[i].location = line_restwave[i] * waveshift_lines
zline_labels[i].x = line_restwave[i] * waveshift_lines
}
if (overlap_bands.length>0) {
for (var i=0; i<overlap_bands.length; i++) {
overlap_bands[i].left = overlap_waves[i][0] * waveshift_spec
overlap_bands[i].right = overlap_waves[i][1] * waveshift_spec
}
}
function shift_plotwave(cds_spec, waveshift) {
var data = cds_spec.data
var origwave = data['origwave']
var plotwave = data['plotwave']
if ( plotwave[0] != origwave[0] * waveshift ) { // Avoid redo calculation if not needed
for (var j=0; j<plotwave.length; j++) {
plotwave[j] = origwave[j] * waveshift ;
}
cds_spec.change.emit()
}
}
for(var i=0; i<spectra.length; i++) {
shift_plotwave(spectra[i], waveshift_spec)
}
if (coaddcam_spec) shift_plotwave(coaddcam_spec, waveshift_spec)
// Update model wavelength array
// NEW : don't shift model if othermodel is there
if (othermodel) {
var zref = othermodel.data['zref'][0]
var waveshift_model = (waveframe_buttons.active == 0) ? (1+z)/(1+zref) : 1/(1+zref) ;
shift_plotwave(othermodel, waveshift_model)
} else if (model) {
var zfit = 0.0
if(metadata.data['Z'] !== undefined) {
zfit = metadata.data['Z'][ifiber]
}
var waveshift_model = (waveframe_buttons.active == 0) ? (1+z)/(1+zfit) : 1/(1+zfit) ;
shift_plotwave(model, waveshift_model)
}
""")
self.z_input.js_on_change('value', self.z_input_callback)
self.waveframe_buttons.js_on_click(self.z_input_callback)
self.plotrange_callback = CustomJS(
args = dict(
z_input=self.z_input,
waveframe_buttons=self.waveframe_buttons,
fig=plots.fig,
),
code="""
var z = parseFloat(z_input.value)
// Observer Frame
if(waveframe_buttons.active == 0) {
fig.x_range.start = fig.x_range.start * (1+z)
fig.x_range.end = fig.x_range.end * (1+z)
} else {
fig.x_range.start = fig.x_range.start / (1+z)
fig.x_range.end = fig.x_range.end / (1+z)
}
"""
)
self.waveframe_buttons.js_on_click(self.plotrange_callback) # TODO: for record: is this related to waveframe bug? : 2 callbakcs for same click...
def add_oii_widgets(self, plots):
#------
#- Zoom on the OII doublet TODO mv js code to other file
# TODO: is there another trick than using a cds to pass the "oii_saveinfo" ?
# TODO: optimize smoothing for autozoom (current value: 0)
cds_oii_saveinfo = ColumnDataSource(
{'xmin':[plots.fig.x_range.start], 'xmax':[plots.fig.x_range.end], 'nsmooth':[self.smootherslider.value]})
self.oii_zoom_button = Button(label="OII-zoom", button_type="default")
self.oii_zoom_callback = CustomJS(
args = dict(z_input=self.z_input, fig=plots.fig, smootherslider=self.smootherslider,
cds_oii_saveinfo=cds_oii_saveinfo),
code = """
// Save previous setting (for the "Undo" button)
cds_oii_saveinfo.data['xmin'] = [fig.x_range.start]
cds_oii_saveinfo.data['xmax'] = [fig.x_range.end]
cds_oii_saveinfo.data['nsmooth'] = [smootherslider.value]
// Center on the middle of the redshifted OII doublet (vaccum)
var z = parseFloat(z_input.value)
fig.x_range.start = 3728.48 * (1+z) - 100
fig.x_range.end = 3728.48 * (1+z) + 100
// No smoothing (this implies a call to update_plot)
smootherslider.value = 0
""")
self.oii_zoom_button.js_on_event('button_click', self.oii_zoom_callback)
self.oii_undo_button = Button(label="Undo OII-zoom", button_type="default")
self.oii_undo_callback = CustomJS(
args = dict(fig=plots.fig, smootherslider=self.smootherslider, cds_oii_saveinfo=cds_oii_saveinfo),
code = """
fig.x_range.start = cds_oii_saveinfo.data['xmin'][0]
fig.x_range.end = cds_oii_saveinfo.data['xmax'][0]
smootherslider.value = cds_oii_saveinfo.data['nsmooth'][0]
""")
self.oii_undo_button.js_on_event('button_click', self.oii_undo_callback)
def add_coaddcam(self, plots):
#-----
#- Highlight individual-arm or camera-coadded spectra
coaddcam_labels = ["Camera-coadded", "Single-arm"]
self.coaddcam_buttons = RadioButtonGroup(labels=coaddcam_labels, active=0)
self.coaddcam_callback = CustomJS(
args = dict(coaddcam_buttons = self.coaddcam_buttons,
list_lines=[plots.data_lines, plots.noise_lines,
plots.zoom_data_lines, plots.zoom_noise_lines],
alpha_discrete = plots.alpha_discrete,
overlap_bands = plots.overlap_bands,
alpha_overlapband = plots.alpha_overlapband),
code="""
var n_lines = list_lines[0].length
for (var i=0; i<n_lines; i++) {
var new_alpha = 1
if (coaddcam_buttons.active == 0 && i<n_lines-1) new_alpha = alpha_discrete
if (coaddcam_buttons.active == 1 && i==n_lines-1) new_alpha = alpha_discrete
for (var j=0; j<list_lines.length; j++) {
list_lines[j][i].glyph.line_alpha = new_alpha
}
}
var new_alpha = 0
if (coaddcam_buttons.active == 0) new_alpha = alpha_overlapband
for (var j=0; j<overlap_bands.length; j++) {
overlap_bands[j].fill_alpha = new_alpha
}
"""
)
self.coaddcam_buttons.js_on_click(self.coaddcam_callback)
def add_metadata_tables(self, viewer_cds, show_zcat=True, template_dicts=None,
top_metadata=['TARGETID', 'EXPID']):
""" Display object-related informations
top_metadata: metadata to be highlighted in table_a
Note: "short" CDS, with a single row, are used to fill these bokeh tables.
When changing object, js code modifies these short CDS so that tables are updated.
"""
#- Sorted list of potential metadata:
metadata_to_check = ['TARGETID', 'HPXPIXEL', 'TILEID', 'COADD_NUMEXP', 'COADD_EXPTIME',
'NIGHT', 'EXPID', 'FIBER', 'CAMERA', 'MORPHTYPE']
metadata_to_check += [ ('mag_'+x) for x in viewer_cds.phot_bands ]
table_keys = []
for key in metadata_to_check:
if key in viewer_cds.cds_metadata.data.keys():
table_keys.append(key)
if 'NUM_'+key in viewer_cds.cds_metadata.data.keys():
for prefix in ['FIRST','LAST','NUM']:
table_keys.append(prefix+'_'+key)
if key in top_metadata:
top_metadata.append(prefix+'_'+key)
#- Table a: "top metadata"
table_a_keys = [ x for x in table_keys if x in top_metadata ]
self.shortcds_table_a, self.table_a = _metadata_table(table_a_keys, viewer_cds, table_width=600,
shortcds_name='shortcds_table_a', selectable=True)
#- Table b: Targeting information
self.shortcds_table_b, self.table_b = _metadata_table(['Targeting masks'], viewer_cds, table_width=self.plot_widget_width,
shortcds_name='shortcds_table_b', selectable=True)
#- Table(s) c/d : Other information (imaging, etc.)
remaining_keys = [ x for x in table_keys if x not in top_metadata ]
if len(remaining_keys) > 7:
table_c_keys = remaining_keys[0:len(remaining_keys)//2]
table_d_keys = remaining_keys[len(remaining_keys)//2:]
else:
table_c_keys = remaining_keys
table_d_keys = None
self.shortcds_table_c, self.table_c = _metadata_table(table_c_keys, viewer_cds, table_width=self.plot_widget_width,
shortcds_name='shortcds_table_c', selectable=False)
if table_d_keys is None:
self.shortcds_table_d, self.table_d = None, None
else:
self.shortcds_table_d, self.table_d = _metadata_table(table_d_keys, viewer_cds, table_width=self.plot_widget_width,
shortcds_name='shortcds_table_d', selectable=False)
#- Table z: redshift fitting information
if show_zcat is not None :
if template_dicts is not None : # Add other best fits
fit_results = template_dicts[1]
# Case of DeltaChi2 : compute it from Chi2s
# The "DeltaChi2" in rr fits is between best fits for a given (spectype,subtype)
# Convention: DeltaChi2 = -1 for the last fit.
chi2s = fit_results['CHI2'][0]
full_deltachi2s = np.zeros(len(chi2s))-1
full_deltachi2s[:-1] = chi2s[1:]-chi2s[:-1]
cdsdata = dict(Nfit = np.arange(1,len(chi2s)+1),
SPECTYPE = fit_results['SPECTYPE'][0], # [0:num_best_fits] (if we want to restrict... TODO?)
SUBTYPE = fit_results['SUBTYPE'][0],
Z = [ "{:.4f}".format(x) for x in fit_results['Z'][0] ],
ZERR = [ "{:.4f}".format(x) for x in fit_results['ZERR'][0] ],
ZWARN = fit_results['ZWARN'][0],
CHI2 = [ "{:.1f}".format(x) for x in fit_results['CHI2'][0] ],
DELTACHI2 = [ "{:.1f}".format(x) for x in full_deltachi2s ])
self.shortcds_table_z = ColumnDataSource(cdsdata, name='shortcds_table_z')
columns_table_z = [ TableColumn(field=x, title=t, width=w) for x,t,w in [ ('Nfit','Nfit',5), ('SPECTYPE','SPECTYPE',70), ('SUBTYPE','SUBTYPE',60), ('Z','Z',50) , ('ZERR','ZERR',50), ('ZWARN','ZWARN',50), ('DELTACHI2','Δχ2(N+1/N)',70)] ]
self.table_z = DataTable(source=self.shortcds_table_z, columns=columns_table_z,
selectable=False, index_position=None, width=self.plot_widget_width)
self.table_z.height = 3 * self.table_z.row_height
else :
self.shortcds_table_z, self.table_z = _metadata_table(viewer_cds.zcat_keys, viewer_cds,
table_width=self.plot_widget_width, shortcds_name='shortcds_table_z', selectable=False)
else :
self.table_z = Div(text="Not available ")
self.shortcds_table_z = None
def add_specline_toggles(self, viewer_cds, plots):
#-----
#- Toggle lines
self.speclines_button_group = CheckboxButtonGroup(
labels=["Emission lines", "Absorption lines"], active=[])
self.majorline_checkbox = CheckboxGroup(
labels=['Show only major lines'], active=[])
self.speclines_callback = CustomJS(
args = dict(line_data = viewer_cds.cds_spectral_lines,
lines = plots.speclines,
line_labels = plots.specline_labels,
zlines = plots.zoom_speclines,
zline_labels = plots.zoom_specline_labels,
lines_button_group = self.speclines_button_group,
majorline_checkbox = self.majorline_checkbox),
code="""
var show_emission = false
var show_absorption = false
if (lines_button_group.active.indexOf(0) >= 0) { // index 0=Emission in active list
show_emission = true
}
if (lines_button_group.active.indexOf(1) >= 0) { // index 1=Absorption in active list
show_absorption = true
}
for(var i=0; i<lines.length; i++) {
if ( !(line_data.data['major'][i]) && (majorline_checkbox.active.indexOf(0)>=0) ) {
lines[i].visible = false
line_labels[i].visible = false
zlines[i].visible = false
zline_labels[i].visible = false
} else if (line_data.data['emission'][i]) {
lines[i].visible = show_emission
line_labels[i].visible = show_emission
zlines[i].visible = show_emission
zline_labels[i].visible = show_emission
} else {
lines[i].visible = show_absorption
line_labels[i].visible = show_absorption
zlines[i].visible = show_absorption
zline_labels[i].visible = show_absorption
}
}
"""
)
self.speclines_button_group.js_on_click(self.speclines_callback)
self.majorline_checkbox.js_on_click(self.speclines_callback)
def add_model_select(self, viewer_cds, template_dicts, num_approx_fits, with_full_2ndfit=True):
#------
#- Select secondary model to display
model_options = ['Best fit', '2nd best fit']
for i in range(1,1+num_approx_fits) :
ith = 'th'
if i==1 : ith='st'
if i==2 : ith='nd'
if i==3 : ith='rd'
model_options.append(str(i)+ith+' fit (approx)')
if with_full_2ndfit is False :
model_options.remove('2nd best fit')
for std_template in ['QSO', 'GALAXY', 'STAR'] :
model_options.append('STD '+std_template)
self.model_select = Select(value=model_options[0], title="Other model (dashed curve):", options=model_options)
model_select_code = self.js_files["interp_grid.js"] + self.js_files["smooth_data.js"] + self.js_files["select_model.js"]
self.model_select_callback = CustomJS(
args = dict(ifiberslider = self.ifiberslider,
model_select = self.model_select,
fit_templates=template_dicts[0],
cds_othermodel = viewer_cds.cds_othermodel,
cds_model_2ndfit = viewer_cds.cds_model_2ndfit,
cds_model = viewer_cds.cds_model,
fit_results=template_dicts[1],
std_templates=template_dicts[2],
median_spectra = viewer_cds.cds_median_spectra,
smootherslider = self.smootherslider,
z_input = self.z_input,
cds_metadata = viewer_cds.cds_metadata),
code = model_select_code)
self.model_select.js_on_change('value', self.model_select_callback)
def add_update_plot_callback(self, viewer_cds, plots, vi_widgets, template_dicts):
#-----
#- Main js code to update plots
update_plot_code = (self.js_files["adapt_plotrange.js"] + self.js_files["interp_grid.js"] +
self.js_files["smooth_data.js"] + self.js_files["coadd_brz_cameras.js"] +
self.js_files["update_plot.js"])
# TMP handling of template_dicts
the_fit_results = None if template_dicts is None else template_dicts[1] # dirty
self.update_plot_callback = CustomJS(
args = dict(
spectra = viewer_cds.cds_spectra,
coaddcam_spec = viewer_cds.cds_coaddcam_spec,
model = viewer_cds.cds_model,
othermodel = viewer_cds.cds_othermodel,
model_2ndfit = viewer_cds.cds_model_2ndfit,
metadata = viewer_cds.cds_metadata,
fit_results = the_fit_results,
shortcds_table_z = self.shortcds_table_z,
shortcds_table_a = self.shortcds_table_a,
shortcds_table_b = self.shortcds_table_b,
shortcds_table_c = self.shortcds_table_c,
shortcds_table_d = self.shortcds_table_d,
ifiberslider = self.ifiberslider,
smootherslider = self.smootherslider,
z_input = self.z_input,
fig = plots.fig,
imfig_source = plots.imfig_source,
imfig_urls = plots.imfig_urls,
model_select = self.model_select,
vi_comment_input = vi_widgets.vi_comment_input,
vi_std_comment_select = vi_widgets.vi_std_comment_select,
vi_name_input = vi_widgets.vi_name_input,
vi_quality_input = vi_widgets.vi_quality_input,
vi_quality_labels = vi_widgets.vi_quality_labels,
vi_issue_input = vi_widgets.vi_issue_input,
vi_z_input = vi_widgets.vi_z_input,
vi_category_select = vi_widgets.vi_category_select,
vi_issue_slabels = vi_widgets.vi_issue_slabels
),
code = update_plot_code
)
self.smootherslider.js_on_change('value', self.update_plot_callback)
self.ifiberslider.js_on_change('value', self.update_plot_callback)
