mass_finder_exact_mass_text = Div(text= "Enter exact Mass (Da)", width= 150, height=30 )
mass_finder_exact_mass_sele = TextInput(value=str(mass_finder_mass.value*1000), disabled=False, width=100, height=30)
mass_finder_line_text = Div(text= "Show mz prediction", width= 150, height=30 )
mass_finder_line_sele = Toggle(label='off', active=False, width=100, height=30, callback=toggle_cb)
mass_finder_cb =CustomJS(args=dict(mass_finder_line_sele=mass_finder_line_sele, raw_mz=raw_mz, mass_finder_data=mass_finder_data, mass_finder_exact_mass_sele=mass_finder_exact_mass_sele, mass_finder_mass=mass_finder_mass, mass_finder_range_slider=mass_finder_range_slider, mfl=mfl), code=open(os.path.join(os.getcwd(), 'JS_Functions', "mass_finder_cb.js")).read())
mass_finder_exact_cb =CustomJS(args=dict(mass_finder_line_sele=mass_finder_line_sele, mass_finder_exact_mass_sele=mass_finder_exact_mass_sele, mass_finder_mass=mass_finder_mass), code=open(os.path.join(os.getcwd(), 'JS_Functions', "mass_finder_exact_cb.js")).read())
mass_finder_exact_mass_sele.js_on_change('value', mass_finder_exact_cb)
mass_finder_column=Column(mass_finder_header,mass_finder_mass, mass_finder_range_slider, Row(mass_finder_exact_mass_text,mass_finder_exact_mass_sele), Row(mass_finder_line_text, mass_finder_line_sele), visible=False)
mass_finder.js_link('active', mass_finder_column, 'visible')
mass_finder_line_sele.js_link('active', mfl, 'visible')
mass_finder_mass.js_on_change('value', mass_finder_cb)
mass_finder_line_sele.js_on_change('active', mass_finder_cb)
mass_finder_range_slider.js_on_change('value',mass_finder_cb)
### DATA PROCESSING ###
cropping = Div(text= " Range mz:", width= 150, height=30 )
# crop_max = Div(text= " ", width= 150, height=30 )
gau_name = Div(text= " Gaussian Smoothing:", width= 150, height=30 )
n_smooth_name = Div(text= " Repeats of Smoothing:", width= 150, height=30 )
# bin_name = Div(text= " Bin Every:", width= 150, height=30 )
int_name = Div(text= " Intensity Threshold (%)", width= 150, height=30 )
sub_name = Select(options=['Substract Minimum', 'Substract Line', 'Substract Curved'], name='sub_mode', value='Substract Minimum', width= 150, height=30 )
# add_name = Div(text= " Adduct Mass (Da)", width= 150, height=30 )
# dat_name = Div(text= " Data Reduction (%)", width= 150, height=30 )
#pro_name = Div(text= " bla", width= 150, height=30 )
dt_name = Div(text= " <h2>Data Processing</h2>", height=45 )
dtp_update=CustomJS(args=dict(DataProcessingParameters=DataProcessingParameters), code=open(os.path.join(os.getcwd(), 'JS_Functions', "DataProcessingParameters_update_cb.js")).read())
class ViewerVIWidgets(object):
"""
Encapsulates Bokeh widgets, and related callbacks, used for VI
"""
def __init__(self, title, viewer_cds):
self.vi_quality_labels = [ x["label"] for x in vi_flags if x["type"]=="quality" ]
self.vi_issue_labels = [ x["label"] for x in vi_flags if x["type"]=="issue" ]
self.vi_issue_slabels = [ x["shortlabel"] for x in vi_flags if x["type"]=="issue" ]
self.js_files = get_resources('js')
self.title = title
self.vi_countdown_toggle = None
#- List of fields to be recorded in output csv file, contains for each field:
# [ field name (in VI file header), associated variable in viewer_cds.cds_metadata ]
self.output_file_fields = []
for file_field in vi_file_fields:
if file_field[1] in viewer_cds.cds_metadata.data.keys() :
self.output_file_fields.append([file_field[0], file_field[1]])
def add_filename(self, username='******'):
#- VI file name
default_vi_filename = "desi-vi_"+self.title
default_vi_filename += ("_"+username)
default_vi_filename += ".csv"
self.vi_filename_input = TextInput(value=default_vi_filename, title="VI file name:")
def add_vi_issues(self, viewer_cds, widgets):
#- Optional VI flags (issues)
self.vi_issue_input = CheckboxGroup(labels=self.vi_issue_labels, active=[])
vi_issue_code = self.js_files["CSVtoArray.js"] + self.js_files["save_vi.js"]
vi_issue_code += """
var issues = []
for (var i=0; i<vi_issue_labels.length; i++) {
if (vi_issue_input.active.indexOf(i) >= 0) issues.push(vi_issue_slabels[i])
}
if (issues.length > 0) {
cds_metadata.data['VI_issue_flag'][ifiberslider.value] = ( issues.join('') )
} else {
cds_metadata.data['VI_issue_flag'][ifiberslider.value] = " "
}
autosave_vi_localStorage(output_file_fields, cds_metadata.data, title)
cds_metadata.change.emit()
"""
self.vi_issue_callback = CustomJS(
args=dict(cds_metadata = viewer_cds.cds_metadata,
ifiberslider = widgets.ifiberslider,
vi_issue_input = self.vi_issue_input,
vi_issue_labels = self.vi_issue_labels,
vi_issue_slabels = self.vi_issue_slabels,
title = self.title, output_file_fields = self.output_file_fields),
code = vi_issue_code )
self.vi_issue_input.js_on_click(self.vi_issue_callback)
def add_vi_z(self, viewer_cds, widgets):
## TODO: z_tovi behaviour if with_vi_widget=False ..?
#- Optional VI information on redshift
self.vi_z_input = TextInput(value='', title="VI redshift:")
vi_z_code = self.js_files["CSVtoArray.js"] + self.js_files["save_vi.js"]
vi_z_code += """
cds_metadata.data['VI_z'][ifiberslider.value]=vi_z_input.value
autosave_vi_localStorage(output_file_fields, cds_metadata.data, title)
cds_metadata.change.emit()
"""
self.vi_z_callback = CustomJS(
args=dict(cds_metadata = viewer_cds.cds_metadata,
ifiberslider = widgets.ifiberslider,
vi_z_input = self.vi_z_input,
title = self.title, output_file_fields=self.output_file_fields),
code = vi_z_code )
self.vi_z_input.js_on_change('value', self.vi_z_callback)
# Copy z value from redshift slider to VI
self.z_tovi_button = Button(label='Copy z to VI')
self.z_tovi_callback = CustomJS(
args=dict(z_input=widgets.z_input, vi_z_input=self.vi_z_input),
code="""
vi_z_input.value = z_input.value
""")
self.z_tovi_button.js_on_event('button_click', self.z_tovi_callback)
def add_vi_spectype(self, viewer_cds, widgets):
#- Optional VI information on spectral type
self.vi_category_select = Select(value=' ', title="VI spectype:", options=([' '] + vi_spectypes))
# The default value set to ' ' as setting value='' does not seem to work well with Select.
vi_category_code = self.js_files["CSVtoArray.js"] + self.js_files["save_vi.js"]
vi_category_code += """
if (vi_category_select.value == ' ') {
cds_metadata.data['VI_spectype'][ifiberslider.value]=''
} else {
cds_metadata.data['VI_spectype'][ifiberslider.value]=vi_category_select.value
}
autosave_vi_localStorage(output_file_fields, cds_metadata.data, title)
cds_metadata.change.emit()
"""
self.vi_category_callback = CustomJS(
args=dict(cds_metadata=viewer_cds.cds_metadata,
ifiberslider = widgets.ifiberslider,
vi_category_select=self.vi_category_select,
title=self.title, output_file_fields=self.output_file_fields),
code=vi_category_code )
self.vi_category_select.js_on_change('value', self.vi_category_callback)
def add_vi_comment(self, viewer_cds, widgets):
#- Optional VI comment
self.vi_comment_input = TextInput(value='', title="VI comment (see guidelines):")
vi_comment_code = self.js_files["CSVtoArray.js"] + self.js_files["save_vi.js"]
vi_comment_code += """
var stored_comment = (vi_comment_input.value).replace(/./g, function(char){
if ( char==',' ) {
return ';'
} else if ( char.charCodeAt(0)<=127 ) {
return char
} else {
var char_list = ['Å','α','β','γ','δ','λ']
var char_replace = ['Angstrom','alpha','beta','gamma','delta','lambda']
for (var i=0; i<char_list.length; i++) {
if ( char==char_list[i] ) return char_replace[i]
}
return '?'
}
})
cds_metadata.data['VI_comment'][ifiberslider.value] = stored_comment
autosave_vi_localStorage(output_file_fields, cds_metadata.data, title)
cds_metadata.change.emit()
"""
self.vi_comment_callback = CustomJS(
args=dict(cds_metadata = viewer_cds.cds_metadata,
ifiberslider = widgets.ifiberslider,
vi_comment_input = self.vi_comment_input,
title=self.title, output_file_fields=self.output_file_fields),
code=vi_comment_code )
self.vi_comment_input.js_on_change('value',self.vi_comment_callback)
#- List of "standard" VI comment
self.vi_std_comment_select = Select(value=" ", title="Standard comment:", options=([' '] + vi_std_comments))
vi_std_comment_code = """
if (vi_std_comment_select.value != ' ') {
if (vi_comment_input.value != '') {
vi_comment_input.value = vi_comment_input.value + " " + vi_std_comment_select.value
} else {
vi_comment_input.value = vi_std_comment_select.value
}
}
"""
self.vi_std_comment_callback = CustomJS(
args = dict(vi_std_comment_select = self.vi_std_comment_select,
vi_comment_input = self.vi_comment_input),
code = vi_std_comment_code )
self.vi_std_comment_select.js_on_change('value', self.vi_std_comment_callback)
def add_vi_quality(self, viewer_cds, widgets):
#- Main VI quality widget
self.vi_quality_input = RadioButtonGroup(labels=self.vi_quality_labels)
vi_quality_code = self.js_files["CSVtoArray.js"] + self.js_files["save_vi.js"]
vi_quality_code += """
if ( vi_quality_input.active >= 0 ) {
cds_metadata.data['VI_quality_flag'][ifiberslider.value] = vi_quality_labels[vi_quality_input.active]
} else {
cds_metadata.data['VI_quality_flag'][ifiberslider.value] = "-1"
}
autosave_vi_localStorage(output_file_fields, cds_metadata.data, title)
cds_metadata.change.emit()
"""
self.vi_quality_callback = CustomJS(
args = dict(cds_metadata = viewer_cds.cds_metadata,
vi_quality_input = self.vi_quality_input,
vi_quality_labels = self.vi_quality_labels,
ifiberslider = widgets.ifiberslider,
title=self.title, output_file_fields = self.output_file_fields),
code=vi_quality_code )
self.vi_quality_input.js_on_click(self.vi_quality_callback)
def add_vi_scanner(self, viewer_cds):
#- VI scanner name
self.vi_name_input = TextInput(value=(viewer_cds.cds_metadata.data['VI_scanner'][0]).strip(), title="Your name (3-letter acronym):")
vi_name_code = self.js_files["CSVtoArray.js"] + self.js_files["save_vi.js"]
vi_name_code += """
for (var i=0; i<(cds_metadata.data['VI_scanner']).length; i++) {
cds_metadata.data['VI_scanner'][i]=vi_name_input.value
}
var newname = vi_filename_input.value
var name_chunks = newname.split("_")
newname = ( name_chunks.slice(0,name_chunks.length-1).join("_") ) + ("_"+vi_name_input.value+".csv")
vi_filename_input.value = newname
autosave_vi_localStorage(output_file_fields, cds_metadata.data, title)
"""
self.vi_name_callback = CustomJS(
args = dict(cds_metadata = viewer_cds.cds_metadata,
vi_name_input = self.vi_name_input,
vi_filename_input = self.vi_filename_input, title=self.title,
output_file_fields = self.output_file_fields),
code=vi_name_code )
self.vi_name_input.js_on_change('value', self.vi_name_callback)
def add_guidelines(self):
#- Guidelines for VI flags
vi_guideline_txt = "<B> VI guidelines </B>"
vi_guideline_txt += "<BR /> <B> Classification flags: </B>"
for flag in vi_flags :
if flag['type'] == 'quality' : vi_guideline_txt += ("<BR />  [ "+flag['label']+" ] "+flag['description'])
vi_guideline_txt += "<BR /> <B> Optional indications: </B>"
for flag in vi_flags :
if flag['type'] == 'issue' :
vi_guideline_txt += ( "<BR />  [ " + flag['label'] +
" (" + flag['shortlabel'] + ") ] " + flag['description'] )
vi_guideline_txt += "<BR /> <B> Comments: </B> <BR /> 100 characters max, avoid commas (automatically replaced by semi-columns), ASCII only."
self.vi_guideline_div = Div(text=vi_guideline_txt)
def add_vi_storage(self, viewer_cds, widgets):
#- Save VI info to CSV file
self.save_vi_button = Button(label="Download VI", button_type="success")
save_vi_code = self.js_files["FileSaver.js"] + self.js_files["CSVtoArray.js"] + self.js_files["save_vi.js"]
save_vi_code += """
download_vi_file(output_file_fields, cds_metadata.data, vi_filename_input.value)
"""
self.save_vi_callback = CustomJS(
args = dict(cds_metadata = viewer_cds.cds_metadata,
output_file_fields = self.output_file_fields,
vi_filename_input = self.vi_filename_input),
code=save_vi_code )
self.save_vi_button.js_on_event('button_click', self.save_vi_callback)
#- Recover auto-saved VI data in browser
self.recover_vi_button = Button(label="Recover auto-saved VI", button_type="default")
recover_vi_code = self.js_files["CSVtoArray.js"] + self.js_files["recover_autosave_vi.js"]
self.recover_vi_callback = CustomJS(
args = dict(title=self.title, output_file_fields=self.output_file_fields,
cds_metadata = viewer_cds.cds_metadata,
ifiber = widgets.ifiberslider.value, vi_comment_input = self.vi_comment_input,
vi_name_input=self.vi_name_input, vi_quality_input=self.vi_quality_input,
vi_issue_input=self.vi_issue_input,
vi_issue_slabels=self.vi_issue_slabels, vi_quality_labels=self.vi_quality_labels),
code = recover_vi_code )
self.recover_vi_button.js_on_event('button_click', self.recover_vi_callback)
#- Clear all auto-saved VI
self.clear_vi_button = Button(label="Clear all auto-saved VI", button_type="default")
self.clear_vi_callback = CustomJS( args = dict(), code = """
localStorage.clear()
""" )
self.clear_vi_button.js_on_event('button_click', self.clear_vi_callback)
def add_vi_table(self, viewer_cds):
#- Show VI in a table
vi_table_columns = [
TableColumn(field="VI_quality_flag", title="Flag", width=40),
TableColumn(field="VI_issue_flag", title="Opt.", width=50),
TableColumn(field="VI_z", title="VI z", width=50),
TableColumn(field="VI_spectype", title="VI spectype", width=150),
TableColumn(field="VI_comment", title="VI comment", width=200)
]
self.vi_table = DataTable(source=viewer_cds.cds_metadata, columns=vi_table_columns, width=500)
self.vi_table.height = 10 * self.vi_table.row_height
def add_countdown(self, vi_countdown):
#- VI countdown
assert vi_countdown > 0
self.vi_countdown_callback = CustomJS(args=dict(vi_countdown=vi_countdown), code="""
if ( (cb_obj.label).includes('Start') ) { // Callback doesn't do anything after countdown started
var countDownDate = new Date().getTime() + (1000 * 60 * vi_countdown);
var countDownLoop = setInterval(function(){
var now = new Date().getTime();
var distance = countDownDate - now;
if (distance<0) {
cb_obj.label = "Time's up !";
clearInterval(countDownLoop);
} else {
var days = Math.floor(distance / (1000 * 60 * 60 * 24));
var hours = Math.floor((distance % (1000 * 60 * 60 * 24)) / (1000 * 60 * 60));
var minutes = Math.floor((distance % (1000 * 60 * 60)) / (1000 * 60));
var seconds = Math.floor((distance % (1000 * 60)) / 1000);
//var stuff = days + "d " + hours + "h " + minutes + "m " + seconds + "s ";
var stuff = minutes + "m " + seconds + "s ";
cb_obj.label = "Countdown: " + stuff;
}
}, 1000);
}
""")
self.vi_countdown_toggle = Toggle(label='Start countdown ('+str(vi_countdown)+' min)', active=False, button_type="success")
self.vi_countdown_toggle.js_on_change('active', self.vi_countdown_callback)
