def _default_layout(self):
return Layout(height='500px', align_self='stretch')
import ipywidgets as widgets
from ipywidgets import HBox, VBox, Layout
from IPython.display import display
from IPython.display import clear_output
#Eliminar warnings
from pandas.plotting import register_matplotlib_converters
register_matplotlib_converters()
import warnings
warnings.filterwarnings("ignore")
#Model visualization
box_layout = Layout(display='flex',
align_items='center',
width='auto',
justify_content='space-around')
#busca los ficheros netCDF en la ruta indicada
def busca_modelos(ruta):
files = [
os.path.abspath(arch.path) for arch in os.scandir(ruta)
if arch.is_file()
]
lstFiles = []
for fichero in files:
(nombreFichero, extension) = os.path.splitext(fichero)
if (extension == ".nc"):
lstFiles.append(nombre_modelo(nombreFichero))
#print (nombreFichero+extension)
def __init__(self):
tab_height = '520px'
tab_height = '550px'
tab_layout = Layout(
width='900px', # border='2px solid black',
height=tab_height) #, overflow_y='scroll')
self.output_dir = '.'
# self.output_dir = 'tmpdir'
max_frames = 1
self.svg_plot = interactive(self.plot_svg,
frame=(0, max_frames),
continuous_update=False)
svg_plot_size = '500px'
self.svg_plot.layout.width = svg_plot_size
self.svg_plot.layout.height = svg_plot_size
self.use_defaults = True
self.show_nucleus = 0 # 0->False, 1->True in Checkbox!
self.show_edge = 1 # 0->False, 1->True in Checkbox!
self.scale_radius = 1.0
self.axes_min = 0.0
self.axes_max = 2000 # hmm, this can change (TODO?)
self.fig = plt.figure(figsize=(6, 6))
# self.tab = HBox([svg_plot], layout=tab_layout)
self.max_frames = BoundedIntText(
min=0,
max=99999,
value=max_frames,
description='Max',
# layout=Layout(flex='0 1 auto', width='auto'), #Layout(width='160px'),
)
self.max_frames.observe(self.update_max_frames)
self.show_nucleus_checkbox = Checkbox(
description='nucleus',
value=False,
disabled=False,
# layout=Layout(flex='1 1 auto', width='auto'), #Layout(width='160px'),
)
self.show_nucleus_checkbox.observe(self.show_nucleus_cb)
self.show_edge_checkbox = Checkbox(
description='edge',
value=True,
disabled=False,
# layout=Layout(flex='1 1 auto', width='auto'), #Layout(width='160px'),
)
self.show_edge_checkbox.observe(self.show_edge_cb)
# row1 = HBox([Label('(select slider: drag or left/right arrows)'),
# self.max_frames, VBox([self.show_nucleus_checkbox, self.show_edge_checkbox])])
# self.max_frames, self.show_nucleus_checkbox], layout=Layout(width='500px'))
# self.tab = VBox([row1,self.svg_plot], layout=tab_layout)
self.help_label = Label('select slider: drag or left/right arrows',
layout=Layout(flex='0 1 auto', width='auto'))
# layout=Layout(flex='3 1 auto', width='auto'))
items_auto = [
self.help_label,
self.max_frames,
self.show_nucleus_checkbox,
self.show_edge_checkbox,
]
#row1 = HBox([Label('(select slider: drag or left/right arrows)'),
# max_frames, show_nucleus_checkbox, show_edge_checkbox],
# layout=Layout(width='800px'))
box_layout = Layout(display='flex',
flex_flow='row',
align_items='stretch',
width='90%')
# row1 = Box(children=items_auto, layout=box_layout)
#row1 = Box(children=items_auto)
row1 = Box([
self.help_label,
Box([
self.max_frames, self.show_nucleus_checkbox,
self.show_edge_checkbox
],
layout=Layout(border='0px solid black',
width='60%',
height='',
align_items='stretch',
flex_direction='row',
display='flex'))
])
# self.download_button = Download('svg.zip', style='warning', icon='cloud-download', tooltip='Download results', cb=self.download_cb)
#self.download_button = Download('svg.zip', style='warning', icon='cloud-download', tooltip='Download results')
# self.tab = VBox([row1, self.svg_plot], layout=tab_layout)
# self.tab = VBox([row1, self.svg_plot, self.download_button.w], layout=tab_layout)
self.tab = VBox([row1, self.svg_plot], layout=tab_layout)
def _gen_app_layout(self):
title = self._widget['title']
toggle_buttons = self._widget['toggle_buttons']
# checkbox = self._widget['checkbox']
label = self._widget['label']
fig = self._widget['fig']
topomap_fig = self._widget['topomap_fig']
dipole_amp_slider = self._widget['amplitude_slider']
tab = self._widget['tab']
output = self._widget['output']
reset_button = self._widget['reset_button']
quickstart = self._widget['quickstart_accordion']
preset = self._widget['preset_dropdown']
dipole_props_col = VBox(
[HBox([label['dipole_pos_'], label['dipole_pos']]),
HBox([label['dipole_ori_'], label['dipole_ori']])])
# dipole_amp_and_exact_sol_col = VBox(
# [label['amplitude_slider'],
# dipole_amp_slider,
# checkbox['exact_solution']])
dipole_amp_col = VBox(
[dipole_amp_slider,
label['amplitude_slider']])
grid = GridspecLayout(3, 3, grid_gap='0', width="95%")
grid[0, 0] = HBox([label['status'], label['updating']])
grid[1, 0] = preset
grid[1, -1] = reset_button
grid[2, :3] = HBox([toggle_buttons['mode_selector']],
layout=Layout(display='flex',
flex_flow='column',
align_items='center',
width='100%'))
main_tab = VBox([grid,
# dipole_amp_and_exact_sol_col]),
HBox([VBox([label['axis']['x'], fig['x'].canvas],
layout=Layout(align_items='center')),
VBox([label['axis']['y'], fig['y'].canvas],
layout=Layout(align_items='center')),
VBox([label['axis']['z'], fig['z'].canvas],
layout=Layout(align_items='center'))]),
HBox([VBox([label['topomap_mag'],
topomap_fig['mag'].canvas],
layout=Layout(align_items='center')),
VBox([label['topomap_grad'],
topomap_fig['grad'].canvas],
layout=Layout(align_items='center')),
VBox([label['topomap_eeg'],
topomap_fig['eeg'].canvas],
layout=Layout(align_items='center'))]),
dipole_amp_col,
dipole_props_col],
layout=Layout(align_items='center'))
mne_output_tab = VBox([output])
help_tab = VBox([Label('Whoops. Somebody was lazy here.')])
about_text = ('<h3>M/EEG Dipole Simulator</h3>\n'
'<p>An interactive demonstration of how dipole location '
'and orientation affect MEG and EEG sensor signals.'
'</p>\n'
'<p><b>This is still '
'<a href="https://github.com/hoechenberger/dipoles_demo/issues/26">'
'work in progress</a></b></p>\n'
'<h4>Contributors</h4>\n'
'<ul>\n'
'<li>Idea & Conceptualization: '
'<b>Maximilien Chaumon</b> '
'(<a href="https://github.com/dnacombo">GitHub</a>, '
'<a href="https://twitter.com/@cuttingEEG">Twitter)</a>'
'</li>\n'
'<li>Conceptualization & Supervision: '
'<b>Alexandre Gramfort</b> '
'(<a href="https://github.com/agramfort">GitHub</a>, '
'<a href="https://twitter.com/agramfort">Twitter</a>)'
'</li>\n'
'<li>Testing & Feedback: '
'<b>Sophie Herbst</b> '
'(<a href="https://github.com/SophieHerbst">GitHub</a>, '
'<a href="https://twitter.com/herbstso">Twitter</a>) & '
'<b>Virginie van Wassenhove</b> '
'(<a href="https://github.com/virvw">GitHub</a>, '
'<a href="https://twitter.com/virginie_vw">Twitter</a>)'
'</li>\n'
'<li>Implementation: '
'<b>Richard Höchenberger</b> '
'(<a href="https://github.com/hoechenberger">GitHub</a>, '
'<a href="https://twitter.com/RHoechenberger">Twitter</a>)'
'</li>\n'
'</ul>\n')
about_tab = VBox([HTML(about_text)])
del about_text
tab.children = [main_tab, mne_output_tab, help_tab, about_tab]
tab.set_title(0, 'Dipole Simulator')
tab.set_title(1, 'MNE-Python Output')
tab.set_title(2, 'Help')
tab.set_title(3, 'About')
app = VBox([title, quickstart, tab], layout=Layout(align_items='center'))
self._app_layout = app
def __init__(self):
items_layout = Layout (flex = '1 1 auto', width = 'auto')
self.w_title = HTML('<h3>Форма электродов</h3>')
self.w_l_x = Label('Границы изогнутой части электрода по горизонтали:')
self.w_x = FloatRangeSlider(value=[0.5,1.], min=0., max=1., step=0.02,
continuous_update=False,
readout_format='.3f', layout=items_layout)
self.w_l_y = Label('Координаты электрода по вертикали:')
self.w_l_y0 = Label('y0')
layouth = Layout(height='300px')
self.w_y0 = FloatSlider(value=0.6,
min=0.5,
max=1.0,
step=0.001,
description='y0',
disabled=False,
continuous_update=False,
orientation='vertical',
readout=True,
readout_format='.3f', layout=layouth
)
self.w_y1 = FloatSlider(value=0.6,
min=0.5,
max=1.0,
step=0.001,
description='y1',
disabled=False,
continuous_update=False,
orientation='vertical',
readout=True,
readout_format='.3f', layout=layouth
)
self.w_y2 = FloatSlider(value=0.6,
min=0.5,
max=1.0,
step=0.001,
description='y2',
disabled=False,
continuous_update=False,
orientation='vertical',
readout=True,
readout_format='.3f', layout=layouth
)
self.w_y3 = FloatSlider(value=0.6,
min=0.5,
max=1.0,
step=0.001,
description='y3',
disabled=False,
continuous_update=False,
orientation='vertical',
readout=True,
readout_format='.3f', layout=layouth
)
self.w_y4 = FloatSlider(value=0.6,
min=0.5,
max=1.0,
step=0.001,
description='y4',
disabled=False,
continuous_update=False,
orientation='vertical',
readout=True,
readout_format='.3f', layout=layouth
)
self.out_el = Output()
hbox1 = HBox([self.w_y0, self.w_y1, self.w_y2, self.w_y3, self.w_y4], layout=Layout(width='100%'))
vbox1 = VBox([self.w_l_x, self.w_x, self.w_l_y, hbox1], layout=Layout(width='50%', padding='5px'))
vbox2 = HBox([self.out_el], layout=Layout(width='50%', padding='5px'))
hbox = HBox ([vbox1, vbox2], layout=Layout(width='100%'))
self.layout = VBox([self.w_title, hbox])
self.interactive_el_form = interactive(self.el_form, x0xm=self.w_x, y0=self.w_y0, y1=self.w_y1,
y2=self.w_y2, y3=self.w_y3, y4=self.w_y4)
def create_tables():
"""Create essential cbm tables
"""
l_tb = Label("""Add a short name as prefix for the tables,
max 15 characters e.g.:escat2020.""")
try:
with open(f"{config.get_value(['paths','temp'])}tb_prefix", 'r') as f:
prefix = f.read()
except Exception:
prefix = ''
tb_prefix = Text(value=prefix,
placeholder='xx2010',
description='Table prefix:',
disabled=False)
checkboxes = {}
tbs = db_tables.tables_dict()
for key in tbs:
checkboxes[key] = Checkbox(value=True,
description=tbs[key]['name'],
disabled=False,
indent=False,
layout=Layout(width='150px'))
checkboxes["aois"].value = False
check_box = HBox([checkboxes[t] for t in checkboxes])
bt_create_tb = Button(description='Create tables',
value=False,
disabled=False,
button_style='info',
tooltip='Creat tables',
icon='fa-table')
progress = Output()
def outlog(*text):
with progress:
print(*text)
def on_tb_prefix(change):
with open(f"{config.get_value(['paths','temp'])}tb_prefix", 'w+') as f:
f.write(tb_prefix.value.replace(' ', '').lower()[:15])
tb_prefix.observe(on_tb_prefix, 'value')
@bt_create_tb.on_click
def bt_create_tb_on_click(b):
progress.clear_output()
tb_prefix_clean = tb_prefix.value.replace(' ', '').lower()[:15]
if tb_prefix.value != '':
for key in tbs:
if checkboxes[key].value is True:
if database.tb_exist(
f"{tb_prefix_clean}_{tbs[key]['table']}") is False:
sql = tbs[key]['sql'].replace('\n',
'').replace(' ', '')
database.execute_sql(sql.format(tb_prefix_clean))
outlog(
f"The table {tb_prefix_clean}_{tbs[key]['table']} is created.."
)
else:
outlog(
f"The table {tb_prefix_clean}_{tbs[key]['table']} already exist."
)
else:
outlog("Please add tables prefix.")
wbox = VBox([l_tb, tb_prefix, check_box, bt_create_tb, progress])
return wbox
def __init__(self):
micron_units = Label(
'micron') # use "option m" (Mac, for micro symbol)
constWidth = '180px'
tab_height = '500px'
stepsize = 10
#style = {'description_width': '250px'}
style = {'description_width': '25%'}
layout = {'width': '400px'}
name_button_layout = {'width': '25%'}
widget_layout = {'width': '15%'}
units_button_layout = {'width': '15%'}
desc_button_layout = {'width': '45%'}
param_name1 = Button(description='seeding_method',
disabled=True,
layout=name_button_layout)
param_name1.style.button_color = 'lightgreen'
self.seeding_method = Text(value='box',
style=style,
layout=widget_layout)
param_name2 = Button(description='cell_default_inital_energy',
disabled=True,
layout=name_button_layout)
param_name2.style.button_color = 'tan'
self.cell_default_inital_energy = FloatText(value=7.01,
step=0.1,
style=style,
layout=widget_layout)
param_name3 = Button(description='cell_default_energy_creation_rate',
disabled=True,
layout=name_button_layout)
param_name3.style.button_color = 'lightgreen'
self.cell_default_energy_creation_rate = FloatText(
value=0.01, step=0.001, style=style, layout=widget_layout)
param_name4 = Button(description='cell_default_energy_use_rate',
disabled=True,
layout=name_button_layout)
param_name4.style.button_color = 'tan'
self.cell_default_energy_use_rate = FloatText(value=0.02,
step=0.001,
style=style,
layout=widget_layout)
param_name5 = Button(description='cell_default_cycle_energy_threshold',
disabled=True,
layout=name_button_layout)
param_name5.style.button_color = 'lightgreen'
self.cell_default_cycle_energy_threshold = FloatText(
value=10.0, step=1, style=style, layout=widget_layout)
param_name6 = Button(description='cell_default_death_energy_threshold',
disabled=True,
layout=name_button_layout)
param_name6.style.button_color = 'tan'
self.cell_default_death_energy_threshold = FloatText(
value=6, step=0.1, style=style, layout=widget_layout)
param_name7 = Button(description='cell_default_aplha',
disabled=True,
layout=name_button_layout)
param_name7.style.button_color = 'lightgreen'
self.cell_default_aplha = FloatText(value=0.0,
step=0.01,
style=style,
layout=widget_layout)
param_name8 = Button(description='cell_default_beta',
disabled=True,
layout=name_button_layout)
param_name8.style.button_color = 'tan'
self.cell_default_beta = FloatText(value=0.0,
step=0.01,
style=style,
layout=widget_layout)
param_name9 = Button(description='cell_default_gamma',
disabled=True,
layout=name_button_layout)
param_name9.style.button_color = 'lightgreen'
self.cell_default_gamma = FloatText(value=0.5,
step=0.1,
style=style,
layout=widget_layout)
param_name10 = Button(description='cell_default_rho',
disabled=True,
layout=name_button_layout)
param_name10.style.button_color = 'tan'
self.cell_default_rho = FloatText(value=0.0,
step=0.01,
style=style,
layout=widget_layout)
param_name11 = Button(description='cell_default_phi',
disabled=True,
layout=name_button_layout)
param_name11.style.button_color = 'lightgreen'
self.cell_default_phi = FloatText(value=1.0,
step=0.1,
style=style,
layout=widget_layout)
param_name12 = Button(description='cell_default_chi',
disabled=True,
layout=name_button_layout)
param_name12.style.button_color = 'tan'
self.cell_default_chi = FloatText(value=1.0,
step=0.1,
style=style,
layout=widget_layout)
param_name13 = Button(description='wound_cell_glucose_secretion_rate',
disabled=True,
layout=name_button_layout)
param_name13.style.button_color = 'lightgreen'
self.wound_cell_glucose_secretion_rate = FloatText(
value=10.0, step=1, style=style, layout=widget_layout)
param_name14 = Button(description='wound_cell_ECM_secretion_rate',
disabled=True,
layout=name_button_layout)
param_name14.style.button_color = 'tan'
self.wound_cell_ECM_secretion_rate = FloatText(value=0.0,
step=0.01,
style=style,
layout=widget_layout)
param_name15 = Button(description='anaerobic_cell_alpha',
disabled=True,
layout=name_button_layout)
param_name15.style.button_color = 'lightgreen'
self.anaerobic_cell_alpha = FloatText(value=0.0,
step=0.01,
style=style,
layout=widget_layout)
param_name16 = Button(description='anaerobic_cell_beta',
disabled=True,
layout=name_button_layout)
param_name16.style.button_color = 'tan'
self.anaerobic_cell_beta = FloatText(value=1.0,
step=0.1,
style=style,
layout=widget_layout)
param_name17 = Button(description='anaerobic_cell_gamma',
disabled=True,
layout=name_button_layout)
param_name17.style.button_color = 'lightgreen'
self.anaerobic_cell_gamma = FloatText(value=1.0,
step=0.1,
style=style,
layout=widget_layout)
param_name18 = Button(description='anaerobic_cell_rho',
disabled=True,
layout=name_button_layout)
param_name18.style.button_color = 'tan'
self.anaerobic_cell_rho = FloatText(value=0.1,
step=0.01,
style=style,
layout=widget_layout)
param_name19 = Button(description='anaerobic_cell_phi',
disabled=True,
layout=name_button_layout)
param_name19.style.button_color = 'lightgreen'
self.anaerobic_cell_phi = FloatText(value=1.0,
step=0.1,
style=style,
layout=widget_layout)
param_name20 = Button(description='anaerobic_cell_chi',
disabled=True,
layout=name_button_layout)
param_name20.style.button_color = 'tan'
self.anaerobic_cell_chi = FloatText(value=2.0,
step=0.1,
style=style,
layout=widget_layout)
param_name21 = Button(description='anaerobic_ECM_secretion_rate',
disabled=True,
layout=name_button_layout)
param_name21.style.button_color = 'lightgreen'
self.anaerobic_ECM_secretion_rate = FloatText(value=1.0,
step=0.1,
style=style,
layout=widget_layout)
param_name22 = Button(description='anaerobic_glucose_uptake_rate',
disabled=True,
layout=name_button_layout)
param_name22.style.button_color = 'tan'
self.anaerobic_glucose_uptake_rate = FloatText(value=1.0,
step=0.1,
style=style,
layout=widget_layout)
param_name23 = Button(description='aerobic_cell_alpha',
disabled=True,
layout=name_button_layout)
param_name23.style.button_color = 'lightgreen'
self.aerobic_cell_alpha = FloatText(value=1.0,
step=0.1,
style=style,
layout=widget_layout)
param_name24 = Button(description='aerobic_cell_beta',
disabled=True,
layout=name_button_layout)
param_name24.style.button_color = 'tan'
self.aerobic_cell_beta = FloatText(value=0.0,
step=0.01,
style=style,
layout=widget_layout)
param_name25 = Button(description='aerobic_cell_gamma',
disabled=True,
layout=name_button_layout)
param_name25.style.button_color = 'lightgreen'
self.aerobic_cell_gamma = FloatText(value=1.0,
step=0.1,
style=style,
layout=widget_layout)
param_name26 = Button(description='aerobic_cell_rho',
disabled=True,
layout=name_button_layout)
param_name26.style.button_color = 'tan'
self.aerobic_cell_rho = FloatText(value=0.0,
step=0.01,
style=style,
layout=widget_layout)
param_name27 = Button(description='aerobic_cell_phi',
disabled=True,
layout=name_button_layout)
param_name27.style.button_color = 'lightgreen'
self.aerobic_cell_phi = FloatText(value=1.0,
step=0.1,
style=style,
layout=widget_layout)
param_name28 = Button(description='aerobic_cell_chi',
disabled=True,
layout=name_button_layout)
param_name28.style.button_color = 'tan'
self.aerobic_cell_chi = FloatText(value=1.0,
step=0.1,
style=style,
layout=widget_layout)
param_name29 = Button(description='aerobic_ECM_secretion_rate',
disabled=True,
layout=name_button_layout)
param_name29.style.button_color = 'lightgreen'
self.aerobic_ECM_secretion_rate = FloatText(value=1.0,
step=0.1,
style=style,
layout=widget_layout)
param_name30 = Button(description='aerobic_glucose_uptake_rate',
disabled=True,
layout=name_button_layout)
param_name30.style.button_color = 'tan'
self.aerobic_glucose_uptake_rate = FloatText(value=1.0,
step=0.1,
style=style,
layout=widget_layout)
param_name31 = Button(description='aerobic_oxygen_uptake_rate',
disabled=True,
layout=name_button_layout)
param_name31.style.button_color = 'lightgreen'
self.aerobic_oxygen_uptake_rate = FloatText(value=1000.0,
step=100,
style=style,
layout=widget_layout)
param_name32 = Button(description='apoptosis_rate',
disabled=True,
layout=name_button_layout)
param_name32.style.button_color = 'tan'
self.apoptosis_rate = FloatText(value=0.01,
step=0.001,
style=style,
layout=widget_layout)
param_name33 = Button(description='proliferation_rate',
disabled=True,
layout=name_button_layout)
param_name33.style.button_color = 'lightgreen'
self.proliferation_rate = FloatText(value=0.001,
step=0.0001,
style=style,
layout=widget_layout)
param_name34 = Button(description='ECM_diffusion_coeff',
disabled=True,
layout=name_button_layout)
param_name34.style.button_color = 'tan'
self.ECM_diffusion_coeff = FloatText(value=0.01,
step=0.001,
style=style,
layout=widget_layout)
param_name35 = Button(description='ECM_decay_constant',
disabled=True,
layout=name_button_layout)
param_name35.style.button_color = 'lightgreen'
self.ECM_decay_constant = FloatText(value=1,
step=0.1,
style=style,
layout=widget_layout)
param_name36 = Button(description='glucose_diffusion_coeff',
disabled=True,
layout=name_button_layout)
param_name36.style.button_color = 'tan'
self.glucose_diffusion_coeff = FloatText(value=1.6e3,
step=100,
style=style,
layout=widget_layout)
param_name37 = Button(description='glucose_decay_constant',
disabled=True,
layout=name_button_layout)
param_name37.style.button_color = 'lightgreen'
self.glucose_decay_constant = FloatText(value=0.05,
step=0.01,
style=style,
layout=widget_layout)
units_button1 = Button(description='',
disabled=True,
layout=units_button_layout)
units_button1.style.button_color = 'lightgreen'
units_button2 = Button(description='a.u',
disabled=True,
layout=units_button_layout)
units_button2.style.button_color = 'tan'
units_button3 = Button(description='a.u/min',
disabled=True,
layout=units_button_layout)
units_button3.style.button_color = 'lightgreen'
units_button4 = Button(description='a.u/min',
disabled=True,
layout=units_button_layout)
units_button4.style.button_color = 'tan'
units_button5 = Button(description='a.u',
disabled=True,
layout=units_button_layout)
units_button5.style.button_color = 'lightgreen'
units_button6 = Button(description='a.u',
disabled=True,
layout=units_button_layout)
units_button6.style.button_color = 'tan'
units_button7 = Button(description='',
disabled=True,
layout=units_button_layout)
units_button7.style.button_color = 'lightgreen'
units_button8 = Button(description='',
disabled=True,
layout=units_button_layout)
units_button8.style.button_color = 'tan'
units_button9 = Button(description='',
disabled=True,
layout=units_button_layout)
units_button9.style.button_color = 'lightgreen'
units_button10 = Button(description='',
disabled=True,
layout=units_button_layout)
units_button10.style.button_color = 'tan'
units_button11 = Button(description='',
disabled=True,
layout=units_button_layout)
units_button11.style.button_color = 'lightgreen'
units_button12 = Button(description='',
disabled=True,
layout=units_button_layout)
units_button12.style.button_color = 'tan'
units_button13 = Button(description='1/min',
disabled=True,
layout=units_button_layout)
units_button13.style.button_color = 'lightgreen'
units_button14 = Button(description='1/min',
disabled=True,
layout=units_button_layout)
units_button14.style.button_color = 'tan'
units_button15 = Button(description='',
disabled=True,
layout=units_button_layout)
units_button15.style.button_color = 'lightgreen'
units_button16 = Button(description='',
disabled=True,
layout=units_button_layout)
units_button16.style.button_color = 'tan'
units_button17 = Button(description='',
disabled=True,
layout=units_button_layout)
units_button17.style.button_color = 'lightgreen'
units_button18 = Button(description='',
disabled=True,
layout=units_button_layout)
units_button18.style.button_color = 'tan'
units_button19 = Button(description='',
disabled=True,
layout=units_button_layout)
units_button19.style.button_color = 'lightgreen'
units_button20 = Button(description='',
disabled=True,
layout=units_button_layout)
units_button20.style.button_color = 'tan'
units_button21 = Button(description='1/min',
disabled=True,
layout=units_button_layout)
units_button21.style.button_color = 'lightgreen'
units_button22 = Button(description='1/min',
disabled=True,
layout=units_button_layout)
units_button22.style.button_color = 'tan'
units_button23 = Button(description='',
disabled=True,
layout=units_button_layout)
units_button23.style.button_color = 'lightgreen'
units_button24 = Button(description='',
disabled=True,
layout=units_button_layout)
units_button24.style.button_color = 'tan'
units_button25 = Button(description='',
disabled=True,
layout=units_button_layout)
units_button25.style.button_color = 'lightgreen'
units_button26 = Button(description='',
disabled=True,
layout=units_button_layout)
units_button26.style.button_color = 'tan'
units_button27 = Button(description='',
disabled=True,
layout=units_button_layout)
units_button27.style.button_color = 'lightgreen'
units_button28 = Button(description='',
disabled=True,
layout=units_button_layout)
units_button28.style.button_color = 'tan'
units_button29 = Button(description='1/min',
disabled=True,
layout=units_button_layout)
units_button29.style.button_color = 'lightgreen'
units_button30 = Button(description='1/min',
disabled=True,
layout=units_button_layout)
units_button30.style.button_color = 'tan'
units_button31 = Button(description='1/min',
disabled=True,
layout=units_button_layout)
units_button31.style.button_color = 'lightgreen'
units_button32 = Button(description='1/min',
disabled=True,
layout=units_button_layout)
units_button32.style.button_color = 'tan'
units_button33 = Button(description='1/min',
disabled=True,
layout=units_button_layout)
units_button33.style.button_color = 'lightgreen'
units_button34 = Button(description='um2/min',
disabled=True,
layout=units_button_layout)
units_button34.style.button_color = 'tan'
units_button35 = Button(description='1/min',
disabled=True,
layout=units_button_layout)
units_button35.style.button_color = 'lightgreen'
units_button36 = Button(description='um2/min',
disabled=True,
layout=units_button_layout)
units_button36.style.button_color = 'tan'
units_button37 = Button(description='1/min',
disabled=True,
layout=units_button_layout)
units_button37.style.button_color = 'lightgreen'
desc_button1 = Button(
description=
'Method for seeding. Can be vertical,horizontal, random, or box (default)',
disabled=True,
layout=desc_button_layout)
desc_button1.style.button_color = 'lightgreen'
desc_button2 = Button(description='Initialized energy level',
disabled=True,
layout=desc_button_layout)
desc_button2.style.button_color = 'tan'
desc_button3 = Button(
description='Energy creation rate for bacterial cells',
disabled=True,
layout=desc_button_layout)
desc_button3.style.button_color = 'lightgreen'
desc_button4 = Button(
description='Energy usage rate for bacterial cells',
disabled=True,
layout=desc_button_layout)
desc_button4.style.button_color = 'tan'
desc_button5 = Button(
description='Cycling energy threshold for bacterial cells',
disabled=True,
layout=desc_button_layout)
desc_button5.style.button_color = 'lightgreen'
desc_button6 = Button(
description='Apoptosis energy threshold for bacterial cells',
disabled=True,
layout=desc_button_layout)
desc_button6.style.button_color = 'tan'
desc_button7 = Button(
description='Energy creation Rate modifier for aerobic cells',
disabled=True,
layout=desc_button_layout)
desc_button7.style.button_color = 'lightgreen'
desc_button8 = Button(
description='Energy creation Rate modifier for anaerobic cells',
disabled=True,
layout=desc_button_layout)
desc_button8.style.button_color = 'tan'
desc_button9 = Button(
description='Energy usage modulator for bacterial cells',
disabled=True,
layout=desc_button_layout)
desc_button9.style.button_color = 'lightgreen'
desc_button10 = Button(
description='Energy degradation rate modifier for anaerobic cells',
disabled=True,
layout=desc_button_layout)
desc_button10.style.button_color = 'tan'
desc_button11 = Button(
description='Energy creation rate modulator for aerobic cells',
disabled=True,
layout=desc_button_layout)
desc_button11.style.button_color = 'lightgreen'
desc_button12 = Button(
description='Energy creation rate modulator for anaerobic cells',
disabled=True,
layout=desc_button_layout)
desc_button12.style.button_color = 'tan'
desc_button13 = Button(
description='Glucose secretion rate for wound cells',
disabled=True,
layout=desc_button_layout)
desc_button13.style.button_color = 'lightgreen'
desc_button14 = Button(
description='Glucose secretion rate for wound cells',
disabled=True,
layout=desc_button_layout)
desc_button14.style.button_color = 'tan'
desc_button15 = Button(
description='Energy Creation Rate modifier for aerobic cells',
disabled=True,
layout=desc_button_layout)
desc_button15.style.button_color = 'lightgreen'
desc_button16 = Button(
description='Energy Creation Rate modifier for anaerobic cells',
disabled=True,
layout=desc_button_layout)
desc_button16.style.button_color = 'tan'
desc_button17 = Button(
description='Energy usage modulator for bacterial cells',
disabled=True,
layout=desc_button_layout)
desc_button17.style.button_color = 'lightgreen'
desc_button18 = Button(
description='Energy degradation rate modifier for anaerobic cells',
disabled=True,
layout=desc_button_layout)
desc_button18.style.button_color = 'tan'
desc_button19 = Button(
description='Energy creation rate modulator for aerobic cells',
disabled=True,
layout=desc_button_layout)
desc_button19.style.button_color = 'lightgreen'
desc_button20 = Button(
description='Energy creation rate modulator for anaerobic cells',
disabled=True,
layout=desc_button_layout)
desc_button20.style.button_color = 'tan'
desc_button21 = Button(
description='ECM creation rate for anaerobic cells',
disabled=True,
layout=desc_button_layout)
desc_button21.style.button_color = 'lightgreen'
desc_button22 = Button(
description='Glucose uptake rate for anaerobic cells',
disabled=True,
layout=desc_button_layout)
desc_button22.style.button_color = 'tan'
desc_button23 = Button(
description='Energy Creation Rate modifier for aerobic cells',
disabled=True,
layout=desc_button_layout)
desc_button23.style.button_color = 'lightgreen'
desc_button24 = Button(
description='Energy Creation Rate modifier for anaerobic cells',
disabled=True,
layout=desc_button_layout)
desc_button24.style.button_color = 'tan'
desc_button25 = Button(
description='Energy usage modulator for bacterial cells',
disabled=True,
layout=desc_button_layout)
desc_button25.style.button_color = 'lightgreen'
desc_button26 = Button(
description='Energy degradation rate modifier for anaerobic cells',
disabled=True,
layout=desc_button_layout)
desc_button26.style.button_color = 'tan'
desc_button27 = Button(
description='Energy creation rate modulator for aerobic cells',
disabled=True,
layout=desc_button_layout)
desc_button27.style.button_color = 'lightgreen'
desc_button28 = Button(
description='Energy creation rate modulator for anaerobic cells',
disabled=True,
layout=desc_button_layout)
desc_button28.style.button_color = 'tan'
desc_button29 = Button(
description='ECM creation rate for aerobic cells',
disabled=True,
layout=desc_button_layout)
desc_button29.style.button_color = 'lightgreen'
desc_button30 = Button(
description='Glucose uptake rate for aerobic cells',
disabled=True,
layout=desc_button_layout)
desc_button30.style.button_color = 'tan'
desc_button31 = Button(
description='Oxygen uptake rate for aerobic cells',
disabled=True,
layout=desc_button_layout)
desc_button31.style.button_color = 'lightgreen'
desc_button32 = Button(
description='Apoptosis rate for bacterial cells',
disabled=True,
layout=desc_button_layout)
desc_button32.style.button_color = 'tan'
desc_button33 = Button(
description='Proliferation rate for bacterial cells',
disabled=True,
layout=desc_button_layout)
desc_button33.style.button_color = 'lightgreen'
desc_button34 = Button(description='',
disabled=True,
layout=desc_button_layout)
desc_button34.style.button_color = 'tan'
desc_button35 = Button(description='',
disabled=True,
layout=desc_button_layout)
desc_button35.style.button_color = 'lightgreen'
desc_button36 = Button(description='',
disabled=True,
layout=desc_button_layout)
desc_button36.style.button_color = 'tan'
desc_button37 = Button(description='',
disabled=True,
layout=desc_button_layout)
desc_button37.style.button_color = 'lightgreen'
row1 = [param_name1, self.seeding_method, units_button1, desc_button1]
row2 = [
param_name2, self.cell_default_inital_energy, units_button2,
desc_button2
]
row3 = [
param_name3, self.cell_default_energy_creation_rate, units_button3,
desc_button3
]
row4 = [
param_name4, self.cell_default_energy_use_rate, units_button4,
desc_button4
]
row5 = [
param_name5, self.cell_default_cycle_energy_threshold,
units_button5, desc_button5
]
row6 = [
param_name6, self.cell_default_death_energy_threshold,
units_button6, desc_button6
]
row7 = [
param_name7, self.cell_default_aplha, units_button7, desc_button7
]
row8 = [
param_name8, self.cell_default_beta, units_button8, desc_button8
]
row9 = [
param_name9, self.cell_default_gamma, units_button9, desc_button9
]
row10 = [
param_name10, self.cell_default_rho, units_button10, desc_button10
]
row11 = [
param_name11, self.cell_default_phi, units_button11, desc_button11
]
row12 = [
param_name12, self.cell_default_chi, units_button12, desc_button12
]
row13 = [
param_name13, self.wound_cell_glucose_secretion_rate,
units_button13, desc_button13
]
row14 = [
param_name14, self.wound_cell_ECM_secretion_rate, units_button14,
desc_button14
]
row15 = [
param_name15, self.anaerobic_cell_alpha, units_button15,
desc_button15
]
row16 = [
param_name16, self.anaerobic_cell_beta, units_button16,
desc_button16
]
row17 = [
param_name17, self.anaerobic_cell_gamma, units_button17,
desc_button17
]
row18 = [
param_name18, self.anaerobic_cell_rho, units_button18,
desc_button18
]
row19 = [
param_name19, self.anaerobic_cell_phi, units_button19,
desc_button19
]
row20 = [
param_name20, self.anaerobic_cell_chi, units_button20,
desc_button20
]
row21 = [
param_name21, self.anaerobic_ECM_secretion_rate, units_button21,
desc_button21
]
row22 = [
param_name22, self.anaerobic_glucose_uptake_rate, units_button22,
desc_button22
]
row23 = [
param_name23, self.aerobic_cell_alpha, units_button23,
desc_button23
]
row24 = [
param_name24, self.aerobic_cell_beta, units_button24, desc_button24
]
row25 = [
param_name25, self.aerobic_cell_gamma, units_button25,
desc_button25
]
row26 = [
param_name26, self.aerobic_cell_rho, units_button26, desc_button26
]
row27 = [
param_name27, self.aerobic_cell_phi, units_button27, desc_button27
]
row28 = [
param_name28, self.aerobic_cell_chi, units_button28, desc_button28
]
row29 = [
param_name29, self.aerobic_ECM_secretion_rate, units_button29,
desc_button29
]
row30 = [
param_name30, self.aerobic_glucose_uptake_rate, units_button30,
desc_button30
]
row31 = [
param_name31, self.aerobic_oxygen_uptake_rate, units_button31,
desc_button31
]
row32 = [
param_name32, self.apoptosis_rate, units_button32, desc_button32
]
row33 = [
param_name33, self.proliferation_rate, units_button33,
desc_button33
]
row34 = [
param_name34, self.ECM_diffusion_coeff, units_button34,
desc_button34
]
row35 = [
param_name35, self.ECM_decay_constant, units_button35,
desc_button35
]
row36 = [
param_name36, self.glucose_diffusion_coeff, units_button36,
desc_button36
]
row37 = [
param_name37, self.glucose_decay_constant, units_button37,
desc_button37
]
box_layout = Layout(display='flex',
flex_flow='row',
align_items='stretch',
width='100%')
box1 = Box(children=row1, layout=box_layout)
box2 = Box(children=row2, layout=box_layout)
box3 = Box(children=row3, layout=box_layout)
box4 = Box(children=row4, layout=box_layout)
box5 = Box(children=row5, layout=box_layout)
box6 = Box(children=row6, layout=box_layout)
box7 = Box(children=row7, layout=box_layout)
box8 = Box(children=row8, layout=box_layout)
box9 = Box(children=row9, layout=box_layout)
box10 = Box(children=row10, layout=box_layout)
box11 = Box(children=row11, layout=box_layout)
box12 = Box(children=row12, layout=box_layout)
box13 = Box(children=row13, layout=box_layout)
box14 = Box(children=row14, layout=box_layout)
box15 = Box(children=row15, layout=box_layout)
box16 = Box(children=row16, layout=box_layout)
box17 = Box(children=row17, layout=box_layout)
box18 = Box(children=row18, layout=box_layout)
box19 = Box(children=row19, layout=box_layout)
box20 = Box(children=row20, layout=box_layout)
box21 = Box(children=row21, layout=box_layout)
box22 = Box(children=row22, layout=box_layout)
box23 = Box(children=row23, layout=box_layout)
box24 = Box(children=row24, layout=box_layout)
box25 = Box(children=row25, layout=box_layout)
box26 = Box(children=row26, layout=box_layout)
box27 = Box(children=row27, layout=box_layout)
box28 = Box(children=row28, layout=box_layout)
box29 = Box(children=row29, layout=box_layout)
box30 = Box(children=row30, layout=box_layout)
box31 = Box(children=row31, layout=box_layout)
box32 = Box(children=row32, layout=box_layout)
box33 = Box(children=row33, layout=box_layout)
box34 = Box(children=row34, layout=box_layout)
box35 = Box(children=row35, layout=box_layout)
box36 = Box(children=row36, layout=box_layout)
box37 = Box(children=row37, layout=box_layout)
self.tab = VBox([
box1,
box2,
box3,
box4,
box5,
box6,
box7,
box8,
box9,
box10,
box11,
box12,
box13,
box14,
box15,
box16,
box17,
box18,
box19,
box20,
box21,
box22,
box23,
box24,
box25,
box26,
box27,
box28,
box29,
box30,
box31,
box32,
box33,
box34,
box35,
box36,
box37,
])
def make_config(self):
layout = Layout()
style = {"description_width": "initial"}
checkbox1 = Checkbox(description="Show Targets",
value=self.net.config["show_targets"],
layout=layout,
style=style)
checkbox1.observe(lambda change: self.set_attr(
self.net.config, "show_targets", change["new"]),
names='value')
checkbox2 = Checkbox(description="Errors",
value=self.net.config["show_errors"],
layout=layout,
style=style)
checkbox2.observe(lambda change: self.set_attr(
self.net.config, "show_errors", change["new"]),
names='value')
hspace = IntText(value=self.net.config["hspace"],
description="Horizontal space between banks:",
style=style,
layout=layout)
hspace.observe(lambda change: self.set_attr(self.net.config, "hspace",
change["new"]),
names='value')
vspace = IntText(value=self.net.config["vspace"],
description="Vertical space between layers:",
style=style,
layout=layout)
vspace.observe(lambda change: self.set_attr(self.net.config, "vspace",
change["new"]),
names='value')
self.feature_bank = Select(
description="Features:",
value="",
options=[""] + [
layer.name for layer in self.net.layers
if self.net._layer_has_features(layer.name)
],
rows=1)
self.feature_bank.observe(self.regenerate, names='value')
self.control_select = Select(options=['Test', 'Train'],
value='Train',
description='Dataset:',
rows=1)
self.control_select.observe(self.update_control_slider, names='value')
column1 = [
self.control_select, self.zoom_slider, hspace, vspace,
HBox([checkbox1, checkbox2]), self.feature_bank,
self.feature_columns, self.feature_scale
]
## Make layer selectable, and update-able:
column2 = []
layer = self.net.layers[-1]
self.layer_select = Select(
description="Layer:",
value=layer.name,
options=[layer.name for layer in self.net.layers],
rows=1)
self.layer_select.observe(self.update_layer_selection, names='value')
column2.append(self.layer_select)
self.layer_visible_checkbox = Checkbox(description="Visible",
value=layer.visible,
layout=layout)
self.layer_visible_checkbox.observe(self.update_layer, names='value')
column2.append(self.layer_visible_checkbox)
self.layer_colormap = Select(
description="Colormap:",
options=[""] + AVAILABLE_COLORMAPS,
value=layer.colormap if layer.colormap is not None else "",
layout=layout,
rows=1)
self.layer_colormap_image = HTML(
value="""<img src="%s"/>""" %
self.net._image_to_uri(self.make_colormap_image(layer.colormap)))
self.layer_colormap.observe(self.update_layer, names='value')
column2.append(self.layer_colormap)
column2.append(self.layer_colormap_image)
self.layer_mindim = FloatText(description="Leftmost color maps to:",
value=layer.minmax[0],
style=style)
self.layer_maxdim = FloatText(description="Rightmost color maps to:",
value=layer.minmax[1],
style=style)
self.layer_mindim.observe(self.update_layer, names='value')
self.layer_maxdim.observe(self.update_layer, names='value')
column2.append(self.layer_mindim)
column2.append(self.layer_maxdim)
output_shape = layer.get_output_shape()
self.layer_feature = IntText(value=layer.feature,
description="Feature to show:",
style=style)
self.layer_feature.observe(self.update_layer, names='value')
column2.append(self.layer_feature)
config_children = HBox([
VBox(column1, layout=Layout(width="100%")),
VBox(column2, layout=Layout(width="100%"))
])
accordion = Accordion(children=[config_children])
accordion.set_title(0, self.net.name)
accordion.selected_index = None
return accordion
def interact(self, ):
def update_plot(*args):
for b in togPlot:
self.plots[b.description] = b.value
self.init_figure()
with self.output:
clear_output(wait=True)
self.plot(self.table.get_changed_df(),
dofit=tb_plotfit.value,
cole_omega_max=ft_cc.value,
maxwell_omega_max=ft_mw.value,
g0range=frs_g0fit.value,
fitg0=tb_fitg0.value,
defaultQ=ft_quality.value,
gpmax=ft_gpmax.value)
display(self.fig)
# self.df = df
def write_df(*args):
df = self.table.get_changed_df()
self.df.update(df)
# self.table.df = self.df
self.df['plot'] = False
def save(*args):
write_df()
pickle.dump(self.df, open(t_save.value, 'wb'))
def reset_plot(*args):
df = self.table.get_changed_df()
df['plot'] = False
self.table.df = df
def update_table(*args):
self.table.df.update(self.table.get_changed_df())
self.interactive = True
self.table = qgrid.show_grid(self.df,
grid_options={
'forceFitColumns': False,
'defaultColumnWidth': 70,
})
box_layout = Layout(overflow_x='scroll',
flex_flow='row',
display='flex')
btable = Box(children=[self.table], layout=box_layout)
w = widgets.SelectMultiple(
options=self.table.get_changed_df()['file'],
value=[],
# rows=10,
description='Rheo Data Sets',
disabled=False,
layout=widgets.Layout(width='40%', height='160px'),
style={'description_width': 'initial'})
items_layout = Layout(flex='1 1 auto', width='auto')
box_layout = Layout(display='flex', flex_flow='row', width='75%')
togPlot = [
widgets.ToggleButton(description=word,
value=bool(value),
layout=items_layout,
button_style='info')
for word, value in self.plots.items()
]
plotl = Box(children=togPlot, layout=box_layout)
b_plot = widgets.Button(
description='plot',
button_style='info', # 'success', 'info', 'warning', 'danger' or ''
)
b_plot.on_click(update_plot)
tb_plotfit = widgets.ToggleButton(description='plot fit',
value=True,
button_style='info')
b_wpars = widgets.Button(
description='write fit params',
button_style='info',
)
b_wpars.on_click(write_df)
t_save = widgets.Text(value='RheoAnalysis.pkl', disabled=False)
ft_quality = widgets.FloatText(value=1,
min=0,
max=1,
step=0.2,
description='Quality:',
disabled=False,
layout=Layout(width='15%'))
b_save = widgets.Button(
description='save',
button_style='info',
)
b_save.on_click(save)
b_resetplot = widgets.Button(
description='reset plot',
button_style='info',
)
b_resetplot.on_click(reset_plot)
b_updatetable = widgets.Button(
description='update',
button_style='info',
)
b_updatetable.on_click(update_table)
# Widgets Maxwell Plot
ft_mw = widgets.FloatText(value=6,
description=r'MW: $\omega_{max}$',
disabled=False,
layout=Layout(width='15%'))
# Widgets Cole-Cole Plot
ft_cc = widgets.FloatText(value=50,
description=r'CC: $\omega_{max}$',
disabled=False,
layout=Layout(width='15%'))
ft_gpmax = widgets.FloatText(value=90,
description=r"$G'_{max}$",
disabled=False,
layout=Layout(width='15%'))
tb_fitg0 = widgets.ToggleButton(description=r'fit $G_0$',
value=False,
button_style='info')
frs_g0fit = widgets.FloatRangeSlider(
value=[6, 24],
min=1,
max=150,
step=1,
description=r'$\omega$ range:',
disabled=False,
continuous_update=False,
orientation='horizontal',
readout=True,
readout_format='.0f',
)
# Widgets Flow Curve
fls_fc_gpmin = widgets.FloatLogSlider(
value=0.02,
base=10,
min=-2, # max exponent of base
max=1, # min exponent of base
step=0.2, # exponent step
description=r'FC: GP min')
fls_fc_gpmax = widgets.FloatLogSlider(
value=0.2,
base=10,
min=-2, # max exponent of base
max=1, # min exponent of base
step=0.2, # exponent step
description='GP max')
fls_fc_etamin = widgets.FloatLogSlider(
value=1e-3,
base=10,
min=-3, # max exponent of base
max=1, # min exponent of base
step=0.2, # exponent step
description=r'FC: eta min')
fls_fc_etamax = widgets.FloatLogSlider(
value=100,
base=10,
min=-2, # max exponent of base
max=2, # min exponent of base
step=0.2, # exponent step
description='eta max')
self.cc_box = widgets.HBox([ft_cc, frs_g0fit, tb_fitg0, ft_gpmax])
self.mw_box = widgets.HBox([ft_mw, ft_quality])
self.fc_box = widgets.HBox(
[fls_fc_gpmin, fls_fc_gpmax, fls_fc_etamin, fls_fc_etamax])
self.output = widgets.Output(
layout=Layout(height='600px', width='800px', border='solid'))
gui = widgets.VBox([
widgets.HBox([
b_plot,
t_save,
b_save,
b_resetplot,
tb_plotfit,
b_wpars,
]), plotl, self.mw_box, self.cc_box, self.fc_box
])
main_window = widgets.VBox([btable, gui, self.output])
display(main_window)
def general():
"""General settings.
Args:
None
Returns:
update_widget : A widget for general settings.
Raises:
Error:
Example:
"""
# User settings
user_info = Label("General settings.")
values = config.read()
user_name = Text(value=values['set']['user'],
placeholder='user name',
description='User:'******'set']['email'],
placeholder='[email protected]',
description='email:',
disabled=False)
user_institution = Text(value=values['set']['institution'],
placeholder='EU-',
description='Institution:',
disabled=False)
ms_list = data_options.eu_ms()
ms = Dropdown(
options=[(ms_list[m], m) for m in ms_list] + [('', '')],
value=values['set']['member_state'],
description='Member state:',
disabled=False,
)
wbox_user = VBox([user_info, user_name, user_email, user_institution, ms],
layout=Layout(border='1px solid black'))
# System settings
sys_info = Label("System settings.")
paths_info = Label("Select the personal data folder.")
jupyterlab = Checkbox(
value=eval(values['set']['jupyterlab']),
description=
'Workin in Jupyter Lab (Uncheck for Voila and classical jupyter environment)',
disabled=False,
indent=False)
def on_jupyterlab_change(change):
config.set_value(['set', 'jupyterlab'], str(jupyterlab.value))
jupyterlab.observe(on_jupyterlab_change, 'value')
path_data = Text(value=values['paths']['data'], description='Data path:')
path_temp = Text(value=values['paths']['temp'],
description='Temp path:',
disabled=True)
files_info = Label("Select where to store the parcel IDs list file from:")
plimit_info = Label(
"Warning: No more than 25 parcels are tested, unexpected results may occur."
)
plimit = BoundedIntText(value=int(values['set']['plimit']),
max=100_000_000,
min=1,
step=1,
description='Max parcels that can be downloaded:',
disabled=False)
wbox_sys = VBox([
sys_info, jupyterlab, plimit_info, plimit, paths_info, path_data,
path_temp, files_info
],
layout=Layout(border='1px solid black'))
btn_save = Button(description='Save', icon='save')
progress = Output()
def outlog(*text):
with progress:
print(*text)
@btn_save.on_click
def btn_save_on_click(b):
progress.clear_output()
config.set_value(['set', 'user'], str(user_name.value))
config.set_value(['set', 'email'], str(user_email.value))
config.set_value(['set', 'institution'], str(user_institution.value))
config.set_value(['set', 'member_state'], str(user_email.value))
config.set_value(['set', 'plimit'], str(plimit.value))
config.set_value(['paths', 'data'], str(path_data.value))
config.set_value(['paths', 'temp'], str(path_temp.value))
outlog("The new settings are saved.")
wbox = VBox(
[clean_temp(), wbox_user, wbox_sys,
HBox([btn_save]), progress])
return wbox
def make_controls(self):
button_begin = Button(icon="fast-backward",
layout=Layout(width='100%'))
button_prev = Button(icon="backward", layout=Layout(width='100%'))
button_next = Button(icon="forward", layout=Layout(width='100%'))
button_end = Button(icon="fast-forward", layout=Layout(width='100%'))
#button_prop = Button(description="Propagate", layout=Layout(width='100%'))
#button_train = Button(description="Train", layout=Layout(width='100%'))
self.button_play = Button(icon="play",
description="Play",
layout=Layout(width="100%"))
refresh_button = Button(icon="refresh", layout=Layout(width="25%"))
self.position_text = IntText(value=0, layout=Layout(width="100%"))
self.control_buttons = HBox(
[
button_begin,
button_prev,
#button_train,
self.position_text,
button_next,
button_end,
self.button_play,
refresh_button
],
layout=Layout(width='100%', height="50px"))
length = (len(self.dataset.train_inputs) -
1) if len(self.dataset.train_inputs) > 0 else 0
self.control_slider = IntSlider(description="Dataset index",
continuous_update=False,
min=0,
max=max(length, 0),
value=0,
layout=Layout(width='100%'))
self.total_text = Label(value="of 0", layout=Layout(width="100px"))
self.zoom_slider = FloatSlider(description="Zoom",
continuous_update=False,
min=.5,
max=3,
value=self.net.config["svg_height"] /
780.0)
## Hook them up:
button_begin.on_click(lambda button: self.goto("begin"))
button_end.on_click(lambda button: self.goto("end"))
button_next.on_click(lambda button: self.goto("next"))
button_prev.on_click(lambda button: self.goto("prev"))
self.button_play.on_click(self.toggle_play)
self.control_slider.observe(self.update_slider_control, names='value')
refresh_button.on_click(lambda widget: (self.update_control_slider(
), self.output.clear_output(), self.regenerate()))
self.zoom_slider.observe(self.update_zoom_slider, names='value')
self.position_text.observe(self.update_position_text, names='value')
# Put them together:
controls = VBox([
HBox([self.control_slider, self.total_text],
layout=Layout(height="40px")), self.control_buttons
],
layout=Layout(width='100%'))
#net_page = VBox([control, self.net_svg], layout=Layout(width='95%'))
controls.on_displayed(lambda widget: self.regenerate())
return controls
def __init__(self, *args, **kwargs):
self.progress_callback = self.set_progress
super().__init__(progress_callback=self.progress_callback,
*args,
**kwargs)
fc = FileChooser()
fc.show_only_dirs = True
fc.default_path = tempfile.gettempdir()
self.ms_storage_path = fc
self.ms_upload = FileUpload()
self.peaklist_files_button = FileUpload(description='Peaklists',
accept='csv,xlsx',
multiple=False)
self.peaklist_files_button.observe(self.load_peaklist, names='value')
self.load_ms_button = Button(description='Load MS-files')
self.load_ms_button.on_click(self.search_files)
self.detect_peaks_button = Button(description="Detect Peaks")
self.detect_peaks_button.on_click(self.detect_peaks)
self.message_box = Textarea(
value='',
placeholder='Please select some files and click on Run.',
description='',
disabled=True,
layout={
'width': '90%',
'height': '500px',
'font_family': 'monospace'
})
self.run_button = Button(description="Run")
self.run_button.on_click(self.run)
self.run_button.style.button_color = 'lightgray'
self.optimize_rt_button = Button(description="Find closest peaks")
self.optimize_rt_button.on_click(self.action_optimize_rt)
self.download_button = Button(description="Export")
self.download_button.on_click(self.export_action)
self.download_button.style.button_color = 'lightgray'
self.progress_bar = Progress(min=0,
max=100,
layout=Layout(width='90%'),
description='Progress:',
bar_style='info')
self.output = widgets.Output()
tabs = Tab()
tabs.children = [
HBox([self.ms_storage_path, self.ms_upload, self.load_ms_button]),
HBox([
self.peaklist_files_button, self.detect_peaks_button,
self.optimize_rt_button
]),
]
tabs.set_title(0, 'MS-Files')
tabs.set_title(1, 'Peaklists')
self.layout = VBox([
tabs, self.message_box,
HBox([self.run_button, self.download_button]), self.progress_bar
])
class jobMaintenance:
##Debug assistance
debug = widgets.Output(style={'description_width': '120px'},
layout=Layout(width='90%'))
def __init__(self, header, jobNumberField, buildJobFunc, buildNewJobsFunc,
buildArgumentsListFunc, updateScreenFieldsFunc,
callProgramFunc, program):
self.existingJobs = []
self.jobCounter = 1
self.jobNumber = jobNumberField
self.program = program
#the buildJob function as implemented by the consuming class
self.buildJob = buildJobFunc
#the buildNewJobs function as implemented by the consuming class
self.buildNewJobs = buildNewJobsFunc
#the buildArgumentsList function as implemented by the consuming class
self.buildArgumentsList = buildArgumentsListFunc
#the updateScreenFields function as implemented by the consuming class
self.updateScreenFields = updateScreenFieldsFunc
#the callProgram function as implemented by the consuming class
self.callProgram = callProgramFunc
self.jobsList = widgets.SelectMultiple(
description='Jobs: ',
options=header,
disabled=False,
style={'description_width': 'initial'},
rows=10,
layout=Layout(width='90%'))
self.addButton = widgets.Button(description='Add',
disabled=False,
button_style='',
tooltip='Add job')
self.deleteButton = widgets.Button(description='Delete',
disabled=False,
button_style='',
tooltip='Delete job(s)')
self.selectButton = widgets.Button(description='Select',
disabled=False,
button_style='',
tooltip='Select job for editing.')
self.updateButton = widgets.Button(description='Update',
disabled=False,
button_style='',
tooltip='Update job.')
self.runAllButton = widgets.Button(description='Run All',
disabled=False,
button_style='',
tooltip='Run all jobs')
self.runProgress = widgets.IntProgress(value=0,
min=0,
max=10,
step=1,
description='Progress:',
bar_style='',
orientation='horizontal')
# addJob() - builds the new job from the input variables and updates the job list.
#
@debug.capture(clear_output=True)
def addJob(self, target):
listedJobs = self.jobsList.options
listedJobsList = list(listedJobs)
newJob = self.buildJob(self.jobCounter)
#converting to tuple, update jobsList, jobNumber
newJobTuple = (newJob, )
listedJobsList.extend(newJobTuple)
self.jobsList.options = listedJobsList
self.jobCounter = self.jobCounter + 1
self.jobNumber.value = ''
# deleteJob() - delete selected jobs from the job list.
#
@debug.capture(clear_output=True)
def deleteJob(self, target):
#obtain the listedJobs
listedJobs = self.jobsList.options
listedJobsList = list(listedJobs)
#obtain the selectedJobs
selectedJobs = self.jobsList.value
selectedJobsList = list(selectedJobs)
#remove selected jobs
for i in range(len(selectedJobsList)):
if (str(selectedJobsList[i]).startswith('Job#') == False):
listedJobsList.remove(selectedJobsList[i])
#update
self.jobsList.options = listedJobsList
self.jobNumber.value = ''
# selectJob() - update field values using the selected job in the job list
#
@debug.capture(clear_output=True)
def selectJob(self, target):
#obtain the selectedJobs
selectedJobs = self.jobsList.value
selectedJobsList = list(selectedJobs)
#can only select a single job for updating.
if len(selectedJobsList) == 1:
self.updateScreenFields(selectedJobsList[0])
# updateJob() - update the job for the displayed job number
#
@debug.capture(clear_output=True)
def updateJob(self, target):
#obtain the listedJobs
listedJobs = self.jobsList.options
listedJobsList = list(listedJobs)
#build updated job
updatedJob = self.buildJob()
updateJobNo = updatedJob['jobNumber']
for i in range(len(listedJobsList)):
#skip checking the header
if (str(listedJobsList[i]).startswith('Job#') == False):
listedJobNo = listedJobsList[i]["jobNumber"]
if listedJobNo == updateJobNo:
listedJobsList[i] = updatedJob
#update screen field
self.jobsList.options = listedJobsList
self.jobNumber.value = ''
# runAllJobs() - execute all jobs in the list.
# target - not used, exists to make to make the button call work.
#
@debug.capture(clear_output=True)
def runAllJobs(self, target):
#obtain the listedJobs
listedJobs = self.jobsList.options
listedJobsList = list(listedJobs)
self.runProgress.max = len(listedJobsList)
#Run each job, but not the Header row.
for i in range(len(listedJobsList)):
#setting progress bar to show job has started running.
if (str(listedJobsList[i]).startswith('Job#') == True):
self.runProgress.value = i + 1
if (str(listedJobsList[i]).startswith('Job#') == False):
self.callProgram(
self.program,
self.buildArgumentsList(jobToProcess=listedJobsList[i]),
listedJobsList[i]['outMrc'])
self.runProgress.value = i + 1
# addJobs() - Adds multiple jobs, when the user has specified a range of values.
# Arguments:
# fieldName - name of the field that value range has been specified
# values - specified values, ';' separated.
#
@debug.capture(clear_output=True)
def addJobs(self, fieldName, values):
#obtaining currently listed jobs
listedJobs = self.jobsList.options
listedJobsList = list(listedJobs)
newJobs = self.buildNewJobs(fieldName, values)
for i in range(len(newJobs)):
#converting to tuple
newJobTuple = (newJobs[i], )
listedJobsList.extend(newJobTuple)
#Update jobsList and jobNumber
self.jobsList.options = listedJobsList
self.jobNumber.value = ''
# buildJobWidgets()
#
def buildJobWidgets(self):
#Add fuctions to buttons.
self.addButton.on_click(self.addJob)
self.deleteButton.on_click(self.deleteJob)
self.selectButton.on_click(self.selectJob)
self.updateButton.on_click(self.updateJob)
self.runAllButton.on_click(self.runAllJobs)
buttons = HBox([
self.addButton, self.deleteButton, self.selectButton,
self.updateButton, self.runAllButton, self.runProgress
])
return VBox([self.debug, self.jobsList, buttons])
def __init__(self):
micron_units = Label('micron') # use "option m" (Mac, for micro symbol)
constWidth = '180px'
tab_height = '500px'
stepsize = 10
#style = {'description_width': '250px'}
style = {'description_width': '25%'}
layout = {'width': '400px'}
name_button_layout={'width':'25%'}
widget_layout = {'width': '15%'}
units_button_layout ={'width':'15%'}
desc_button_layout={'width':'45%'}
param_name1 = Button(description='random_seed', disabled=True, layout=name_button_layout)
param_name1.style.button_color = 'lightgreen'
self.random_seed = IntText(
value=0,
step=1,
style=style, layout=widget_layout)
param_name2 = Button(description='immune_activation_time', disabled=True, layout=name_button_layout)
param_name2.style.button_color = 'tan'
self.immune_activation_time = FloatText(
value=20160,
step=1000,
style=style, layout=widget_layout)
param_name3 = Button(description='save_interval_after_therapy_start', disabled=True, layout=name_button_layout)
param_name3.style.button_color = 'lightgreen'
self.save_interval_after_therapy_start = FloatText(
value=3.0,
step=0.1,
style=style, layout=widget_layout)
param_name4 = Button(description='immune_o2_relative_uptake', disabled=True, layout=name_button_layout)
param_name4.style.button_color = 'tan'
self.immune_o2_relative_uptake = FloatText(
value=0.1,
step=0.01,
style=style, layout=widget_layout)
param_name5 = Button(description='immune_apoptosis_rate', disabled=True, layout=name_button_layout)
param_name5.style.button_color = 'lightgreen'
self.immune_apoptosis_rate = FloatText(
value=6.944e-5,
step=1e-05,
style=style, layout=widget_layout)
param_name6 = Button(description='immune_motility_persistence_time', disabled=True, layout=name_button_layout)
param_name6.style.button_color = 'tan'
self.immune_motility_persistence_time = FloatText(
value=10,
step=1,
style=style, layout=widget_layout)
param_name7 = Button(description='immune_migration_speed', disabled=True, layout=name_button_layout)
param_name7.style.button_color = 'lightgreen'
self.immune_migration_speed = FloatText(
value=1.0,
step=0.1,
style=style, layout=widget_layout)
param_name8 = Button(description='immune_migration_bias', disabled=True, layout=name_button_layout)
param_name8.style.button_color = 'tan'
self.immune_migration_bias = FloatText(
value=0.5,
step=0.1,
style=style, layout=widget_layout)
param_name9 = Button(description='immune_relative_adhesion', disabled=True, layout=name_button_layout)
param_name9.style.button_color = 'lightgreen'
self.immune_relative_adhesion = FloatText(
value=0,
step=0.01,
style=style, layout=widget_layout)
param_name10 = Button(description='immune_relative_repulsion', disabled=True, layout=name_button_layout)
param_name10.style.button_color = 'tan'
self.immune_relative_repulsion = FloatText(
value=5,
step=0.1,
style=style, layout=widget_layout)
param_name11 = Button(description='immune_kill_rate', disabled=True, layout=name_button_layout)
param_name11.style.button_color = 'lightgreen'
self.immune_kill_rate = FloatText(
value=0.06667,
step=0.01,
style=style, layout=widget_layout)
param_name12 = Button(description='immune_attachment_lifetime', disabled=True, layout=name_button_layout)
param_name12.style.button_color = 'tan'
self.immune_attachment_lifetime = FloatText(
value=60.0,
step=1,
style=style, layout=widget_layout)
param_name13 = Button(description='immune_attachment_rate', disabled=True, layout=name_button_layout)
param_name13.style.button_color = 'lightgreen'
self.immune_attachment_rate = FloatText(
value=0.2,
step=0.01,
style=style, layout=widget_layout)
param_name14 = Button(description='elastic_coefficient', disabled=True, layout=name_button_layout)
param_name14.style.button_color = 'tan'
self.elastic_coefficient = FloatText(
value=0.01,
step=0.001,
style=style, layout=widget_layout)
param_name15 = Button(description='number_of_immune_cells', disabled=True, layout=name_button_layout)
param_name15.style.button_color = 'lightgreen'
self.number_of_immune_cells = IntText(
value=7500,
step=100,
style=style, layout=widget_layout)
param_name16 = Button(description='initial_min_immune_distance_from_tumor', disabled=True, layout=name_button_layout)
param_name16.style.button_color = 'tan'
self.initial_min_immune_distance_from_tumor = FloatText(
value=30,
step=1,
style=style, layout=widget_layout)
param_name17 = Button(description='thickness_of_immune_seeding_region', disabled=True, layout=name_button_layout)
param_name17.style.button_color = 'lightgreen'
self.thickness_of_immune_seeding_region = FloatText(
value=75,
step=1,
style=style, layout=widget_layout)
param_name18 = Button(description='tumor_radius', disabled=True, layout=name_button_layout)
param_name18.style.button_color = 'tan'
self.tumor_radius = FloatText(
value=250,
step=10,
style=style, layout=widget_layout)
param_name19 = Button(description='tumor_mean_immunogenicity', disabled=True, layout=name_button_layout)
param_name19.style.button_color = 'lightgreen'
self.tumor_mean_immunogenicity = FloatText(
value=1.0,
step=0.1,
style=style, layout=widget_layout)
param_name20 = Button(description='tumor_immunogenicity_standard_deviation', disabled=True, layout=name_button_layout)
param_name20.style.button_color = 'tan'
self.tumor_immunogenicity_standard_deviation = FloatText(
value=0.25,
step=0.01,
style=style, layout=widget_layout)
param_name21 = Button(description='oncoprotein_saturation', disabled=True, layout=name_button_layout)
param_name21.style.button_color = 'lightgreen'
self.oncoprotein_saturation = FloatText(
value=2.0,
step=0.1,
style=style, layout=widget_layout)
param_name22 = Button(description='oncoprotein_threshold', disabled=True, layout=name_button_layout)
param_name22.style.button_color = 'tan'
self.oncoprotein_threshold = FloatText(
value=0.5,
step=0.1,
style=style, layout=widget_layout)
param_name23 = Button(description='max_attachment_distance', disabled=True, layout=name_button_layout)
param_name23.style.button_color = 'lightgreen'
self.max_attachment_distance = FloatText(
value=18.0,
step=1,
style=style, layout=widget_layout)
param_name24 = Button(description='min_attachment_distance', disabled=True, layout=name_button_layout)
param_name24.style.button_color = 'tan'
self.min_attachment_distance = FloatText(
value=14.0,
step=1,
style=style, layout=widget_layout)
units_button1 = Button(description='', disabled=True, layout=units_button_layout)
units_button1.style.button_color = 'lightgreen'
units_button2 = Button(description='min', disabled=True, layout=units_button_layout)
units_button2.style.button_color = 'tan'
units_button3 = Button(description='min', disabled=True, layout=units_button_layout)
units_button3.style.button_color = 'lightgreen'
units_button4 = Button(description='', disabled=True, layout=units_button_layout)
units_button4.style.button_color = 'tan'
units_button5 = Button(description='1/min', disabled=True, layout=units_button_layout)
units_button5.style.button_color = 'lightgreen'
units_button6 = Button(description='min', disabled=True, layout=units_button_layout)
units_button6.style.button_color = 'tan'
units_button7 = Button(description='micron/min', disabled=True, layout=units_button_layout)
units_button7.style.button_color = 'lightgreen'
units_button8 = Button(description='min', disabled=True, layout=units_button_layout)
units_button8.style.button_color = 'tan'
units_button9 = Button(description='', disabled=True, layout=units_button_layout)
units_button9.style.button_color = 'lightgreen'
units_button10 = Button(description='', disabled=True, layout=units_button_layout)
units_button10.style.button_color = 'tan'
units_button11 = Button(description='1/min', disabled=True, layout=units_button_layout)
units_button11.style.button_color = 'lightgreen'
units_button12 = Button(description='min', disabled=True, layout=units_button_layout)
units_button12.style.button_color = 'tan'
units_button13 = Button(description='1/min', disabled=True, layout=units_button_layout)
units_button13.style.button_color = 'lightgreen'
units_button14 = Button(description='1/min', disabled=True, layout=units_button_layout)
units_button14.style.button_color = 'tan'
units_button15 = Button(description='', disabled=True, layout=units_button_layout)
units_button15.style.button_color = 'lightgreen'
units_button16 = Button(description='micron', disabled=True, layout=units_button_layout)
units_button16.style.button_color = 'tan'
units_button17 = Button(description='micron', disabled=True, layout=units_button_layout)
units_button17.style.button_color = 'lightgreen'
units_button18 = Button(description='micron', disabled=True, layout=units_button_layout)
units_button18.style.button_color = 'tan'
units_button19 = Button(description='', disabled=True, layout=units_button_layout)
units_button19.style.button_color = 'lightgreen'
units_button20 = Button(description='', disabled=True, layout=units_button_layout)
units_button20.style.button_color = 'tan'
units_button21 = Button(description='', disabled=True, layout=units_button_layout)
units_button21.style.button_color = 'lightgreen'
units_button22 = Button(description='', disabled=True, layout=units_button_layout)
units_button22.style.button_color = 'tan'
units_button23 = Button(description='micron', disabled=True, layout=units_button_layout)
units_button23.style.button_color = 'lightgreen'
units_button24 = Button(description='micron', disabled=True, layout=units_button_layout)
units_button24.style.button_color = 'tan'
desc_button1 = Button(description='', disabled=True, layout=desc_button_layout)
desc_button1.style.button_color = 'lightgreen'
desc_button2 = Button(description='', disabled=True, layout=desc_button_layout)
desc_button2.style.button_color = 'tan'
desc_button3 = Button(description='', disabled=True, layout=desc_button_layout)
desc_button3.style.button_color = 'lightgreen'
desc_button4 = Button(description='', disabled=True, layout=desc_button_layout)
desc_button4.style.button_color = 'tan'
desc_button5 = Button(description='', disabled=True, layout=desc_button_layout)
desc_button5.style.button_color = 'lightgreen'
desc_button6 = Button(description='', disabled=True, layout=desc_button_layout)
desc_button6.style.button_color = 'tan'
desc_button7 = Button(description='', disabled=True, layout=desc_button_layout)
desc_button7.style.button_color = 'lightgreen'
desc_button8 = Button(description='', disabled=True, layout=desc_button_layout)
desc_button8.style.button_color = 'tan'
desc_button9 = Button(description='', disabled=True, layout=desc_button_layout)
desc_button9.style.button_color = 'lightgreen'
desc_button10 = Button(description='', disabled=True, layout=desc_button_layout)
desc_button10.style.button_color = 'tan'
desc_button11 = Button(description='', disabled=True, layout=desc_button_layout)
desc_button11.style.button_color = 'lightgreen'
desc_button12 = Button(description='', disabled=True, layout=desc_button_layout)
desc_button12.style.button_color = 'tan'
desc_button13 = Button(description='', disabled=True, layout=desc_button_layout)
desc_button13.style.button_color = 'lightgreen'
desc_button14 = Button(description='', disabled=True, layout=desc_button_layout)
desc_button14.style.button_color = 'tan'
desc_button15 = Button(description='', disabled=True, layout=desc_button_layout)
desc_button15.style.button_color = 'lightgreen'
desc_button16 = Button(description='', disabled=True, layout=desc_button_layout)
desc_button16.style.button_color = 'tan'
desc_button17 = Button(description='', disabled=True, layout=desc_button_layout)
desc_button17.style.button_color = 'lightgreen'
desc_button18 = Button(description='', disabled=True, layout=desc_button_layout)
desc_button18.style.button_color = 'tan'
desc_button19 = Button(description='', disabled=True, layout=desc_button_layout)
desc_button19.style.button_color = 'lightgreen'
desc_button20 = Button(description='', disabled=True, layout=desc_button_layout)
desc_button20.style.button_color = 'tan'
desc_button21 = Button(description='', disabled=True, layout=desc_button_layout)
desc_button21.style.button_color = 'lightgreen'
desc_button22 = Button(description='', disabled=True, layout=desc_button_layout)
desc_button22.style.button_color = 'tan'
desc_button23 = Button(description='', disabled=True, layout=desc_button_layout)
desc_button23.style.button_color = 'lightgreen'
desc_button24 = Button(description='', disabled=True, layout=desc_button_layout)
desc_button24.style.button_color = 'tan'
row1 = [param_name1, self.random_seed, units_button1, desc_button1]
row2 = [param_name2, self.immune_activation_time, units_button2, desc_button2]
row3 = [param_name3, self.save_interval_after_therapy_start, units_button3, desc_button3]
row4 = [param_name4, self.immune_o2_relative_uptake, units_button4, desc_button4]
row5 = [param_name5, self.immune_apoptosis_rate, units_button5, desc_button5]
row6 = [param_name6, self.immune_motility_persistence_time, units_button6, desc_button6]
row7 = [param_name7, self.immune_migration_speed, units_button7, desc_button7]
row8 = [param_name8, self.immune_migration_bias, units_button8, desc_button8]
row9 = [param_name9, self.immune_relative_adhesion, units_button9, desc_button9]
row10 = [param_name10, self.immune_relative_repulsion, units_button10, desc_button10]
row11 = [param_name11, self.immune_kill_rate, units_button11, desc_button11]
row12 = [param_name12, self.immune_attachment_lifetime, units_button12, desc_button12]
row13 = [param_name13, self.immune_attachment_rate, units_button13, desc_button13]
row14 = [param_name14, self.elastic_coefficient, units_button14, desc_button14]
row15 = [param_name15, self.number_of_immune_cells, units_button15, desc_button15]
row16 = [param_name16, self.initial_min_immune_distance_from_tumor, units_button16, desc_button16]
row17 = [param_name17, self.thickness_of_immune_seeding_region, units_button17, desc_button17]
row18 = [param_name18, self.tumor_radius, units_button18, desc_button18]
row19 = [param_name19, self.tumor_mean_immunogenicity, units_button19, desc_button19]
row20 = [param_name20, self.tumor_immunogenicity_standard_deviation, units_button20, desc_button20]
row21 = [param_name21, self.oncoprotein_saturation, units_button21, desc_button21]
row22 = [param_name22, self.oncoprotein_threshold, units_button22, desc_button22]
row23 = [param_name23, self.max_attachment_distance, units_button23, desc_button23]
row24 = [param_name24, self.min_attachment_distance, units_button24, desc_button24]
box_layout = Layout(display='flex', flex_flow='row', align_items='stretch', width='100%')
box1 = Box(children=row1, layout=box_layout)
box2 = Box(children=row2, layout=box_layout)
box3 = Box(children=row3, layout=box_layout)
box4 = Box(children=row4, layout=box_layout)
box5 = Box(children=row5, layout=box_layout)
box6 = Box(children=row6, layout=box_layout)
box7 = Box(children=row7, layout=box_layout)
box8 = Box(children=row8, layout=box_layout)
box9 = Box(children=row9, layout=box_layout)
box10 = Box(children=row10, layout=box_layout)
box11 = Box(children=row11, layout=box_layout)
box12 = Box(children=row12, layout=box_layout)
box13 = Box(children=row13, layout=box_layout)
box14 = Box(children=row14, layout=box_layout)
box15 = Box(children=row15, layout=box_layout)
box16 = Box(children=row16, layout=box_layout)
box17 = Box(children=row17, layout=box_layout)
box18 = Box(children=row18, layout=box_layout)
box19 = Box(children=row19, layout=box_layout)
box20 = Box(children=row20, layout=box_layout)
box21 = Box(children=row21, layout=box_layout)
box22 = Box(children=row22, layout=box_layout)
box23 = Box(children=row23, layout=box_layout)
box24 = Box(children=row24, layout=box_layout)
self.tab = VBox([
box1,
box2,
box3,
box4,
box5,
box6,
box7,
box8,
box9,
box10,
box11,
box12,
box13,
box14,
box15,
box16,
box17,
box18,
box19,
box20,
box21,
box22,
box23,
box24,
])
def _create_result_tabs(
self,
res: Dict[str, NamedRelationalAlgebraFrozenSet],
callbacks: Dict[str, Callable] = None,
):
"""Creates necessary tab pages and viewers for the specified query result `res`.
Parameters
----------
res: Dict[str, NamedRelationalAlgebraFrozenSet]
dictionary of query results with keys as result name and values as result for corresponding key.
callbacks : Dict[str, Callable], optional
dict of callback functions to display outputs in result tabs, by default None
Returns
-------
result_tabs: list
list of tab pages to be added to tab as children.
titles: list
list of titles for tab pages.
icons: list
list of icons for tab pages.
viewers: set
set of viewers for all tab pages.
"""
result_tabs = []
titles = []
icons = []
# to be passed to each tab page to use viewers from the same factory
viewer_factory = ViewerFactory()
# set of all viewers for each result_tab
viewers = set()
def icon_changed(change):
icons = []
for result_tab in result_tabs:
icons.append(result_tab.icon)
self._tab.title_icons = icons
for name in sorted(res.keys()):
result_set = res[name]
result_tab = ResultTabPageWidget(name,
result_set,
viewer_factory,
layout=Layout(height="100%"))
result_tabs.append(result_tab)
titles.append(name)
icons.append(result_tab.icon)
result_tab.observe(icon_changed, names="icon")
viewers = viewers | result_tab.get_viewers()
if callbacks is not None:
for name, callback in callbacks.items():
output_tab = GraphOutputWidget(name, res, callback)
result_tabs.append(output_tab)
titles.append(name)
icons.append(output_tab.icon)
return result_tabs, titles, icons, viewers
def __init__(self, start, next_frame, L=8):
self.next_frame = next_frame
self.L = L
width = int(50 * 8 / L)
wide = str(7 * width + 24) + 'px'
wider = str(L * width + (L - 1) * 4) + 'px'
width = str(width) + 'px'
height = width
width = str(int(50 * 8 / L)) + 'px'
layout = Layout(width=width, height=height)
screen = {}
for x in range(L):
for y in range(L):
screen[x, y] = widgets.ToggleButton(description='',
button_style='',
layout=layout,
disabled=True)
screen['text'] = widgets.ToggleButton(description='',
button_style='',
layout=Layout(width=wider,
height=height),
disabled=True)
controller = {}
controller['blank'] = widgets.ToggleButton(description='',
button_style='',
layout=layout)
controller['up'] = widgets.ToggleButton(description='▲',
button_style='',
layout=layout)
controller['down'] = widgets.ToggleButton(description='▼',
button_style='',
layout=layout)
controller['left'] = widgets.ToggleButton(description='◀︎',
button_style='',
layout=layout)
controller['right'] = widgets.ToggleButton(description='►',
button_style='',
layout=layout)
controller['A'] = widgets.ToggleButton(description='A',
button_style='',
layout=layout)
controller['B'] = widgets.ToggleButton(description='B',
button_style='',
layout=layout)
controller['X'] = widgets.ToggleButton(description='X',
button_style='',
layout=layout)
controller['Y'] = widgets.ToggleButton(description='Y',
button_style='',
layout=layout)
controller['next'] = widgets.ToggleButton(description='Next',
button_style='',
layout=Layout(width=wide,
height=height))
[b, u, d, l, r, A, B, X, Y, c] = [
controller['blank'], controller['up'], controller['down'],
controller['left'], controller['right'], controller['A'],
controller['B'], controller['X'], controller['Y'],
controller['next']
]
interface = []
interface.append(
widgets.HBox([screen[x, 0]
for x in range(L)] + [b, u, b, b, b, X, b]))
interface.append(
widgets.HBox([screen[x, 1]
for x in range(L)] + [l, b, r, b, Y, b, A]))
interface.append(
widgets.HBox([screen[x, 2]
for x in range(L)] + [b, d, b, b, b, B, b]))
interface.append(widgets.HBox([screen[x, 3] for x in range(L)] + [c]))
for y in range(4, L):
interface.append(widgets.HBox([screen[x, y] for x in range(L)]))
interface.append(screen['text'])
self.screen = screen
self.controller = controller
start(self)
display(widgets.VBox(interface))
b.observe(self.given_blank)
for button in self.controller:
if button != 'blank':
self.controller[button].observe(self.given_button)
def __init__(self, nb_rows, limit=50, *args, **kwargs):
"""
Parameters
----------
nb_rows: int
total number of rows in the result set.
limit: int
number of rows to display in a page.
"""
super().__init__(*args, **kwargs)
self.__nb_rows = nb_rows if nb_rows else 1
self.page = 1
self.limit = (limit if limit and limit > 0
and limit < PaginationWidget.MAX_LIMIT else
PaginationWidget.DEFAULT_LIMIT)
self.layout.width = "400px"
if nb_rows <= limit:
self.layout.visibility = "hidden"
else:
self.layout.visibility = "visible"
nb_pages = self._get_nb_pages(self.limit)
# widget to set page number
self.__page_widget = BoundedIntText(
value=self.page,
min=1,
max=nb_pages,
step=1,
continuous_update=True,
description="page",
description_tooltip="Current page",
disabled=False,
style={"description_width": "30px"},
layout=Layout(width="90px", max_width="90px"),
)
# widget to display total number of pages.
self.__label_slash = Label(value=f"/ {nb_pages}",
layout=Layout(width="60px"))
# widget to set limit
self.__limit_widget = BoundedIntText(
value=self.limit,
min=1,
max=PaginationWidget.MAX_LIMIT,
step=1,
continuous_update=True,
description="rows",
description_tooltip=
f"Number of rows per page. Max. possible: {PaginationWidget.MAX_LIMIT}",
disabled=False,
style={"description_width": "30px"},
layout=Layout(width="90px", max_width="90px"),
)
self.__page_widget.observe(self._page_widget_changed,
names="value")
self.__limit_widget.observe(self._limit_widget_changed,
names="value")
self.children = [
self.__page_widget,
self.__label_slash,
self.__limit_widget,
]
def run_widget():
roll = widgets.ToggleButtons(
options=['Keep All', 'Drop Lowest Roll'],
description='Roll Modifications:',
style={'description_width': 'initial'},
disabled=False,
button_style='', # 'success', 'info', 'warning', 'danger' or ''
tooltips=['', ''],
)
drop_roll = widgets.IntSlider(
value=1,
min=0,
max=3,
step=1,
description='If Dropping Rolls, How Many?:',
style={'description_width': 'initial'},
layout=Layout(width='50%'),
disabled=False,
)
stat = widgets.ToggleButtons(
options=['Keep All', 'Drop Lowest Stat', 'Replace Lowest Stat'],
description='Roll Modifications:',
style={'description_width': 'initial'},
disabled=False,
button_style='', # 'success', 'info', 'warning', 'danger' or ''
tooltips=['', ''],
)
drop_stat = widgets.IntSlider(
value=1,
min=0,
max=3,
step=1,
description='If Dropping Stats, How Many?:',
style={'description_width': 'initial'},
layout=Layout(width='50%'),
disabled=False,
)
replace_stat = widgets.IntSlider(
value=18,
min=1,
max=20,
step=1,
description='If Replacing Lowest Stat, With What?:',
style={'description_width': 'initial'},
layout=Layout(width='50%'),
disabled=False,
)
n = widgets.Textarea(value='3',
placeholder='Type something',
description='Number of each Dice',
disabled=False,
style={'description_width': 'initial'},
layout=Layout(width='50%', height='100px'))
s = widgets.Textarea(value='1,2,3,4,5,6',
placeholder='Type something',
description='Sides of each Dice ',
disabled=False,
style={
'description_width': 'initial',
'width': '10%'
},
layout=Layout(width='50%', height='100px'))
name = widgets.Text(value='Roll 3d6',
placeholder='Type something',
description='Title of Policy ',
disabled=False,
style={
'description_width': 'initial',
'width': '10%'
},
layout=Layout(width='50%'))
interact_manual(runRoller,
n=n,
s=s,
roll=roll,
drop_roll=drop_roll,
stat=stat,
drop_stat=drop_stat,
replace_stat=replace_stat,
name=name)
def upload_shp(path_data):
# Upload
l_up = Label("a. Upload .shp to the server.")
accept_files = ".shp, .cpg, .dbf, .prj, .shx, .sbn, .sbx, .xml"
shp_dist_folder = Text(value=f"{path_data}vector",
placeholder='tmp/',
description='Folder:',
disabled=False)
shp_select = FileUpload(
description='Select files:',
icon='plus',
accept=accept_files,
multiple=True # True to accept multiple files upload else False
)
shp_clear = Button(value=False,
disabled=False,
button_style='info',
tooltip='Clear selections.',
icon='broom',
layout=Layout(width='40px'))
shp_upload = Button(value=False,
disabled=False,
button_style='info',
tooltip='Upload foi reference data (.shp).',
icon='fa-upload',
layout=Layout(width='40px'))
progress = Output()
def outlog(*text):
with progress:
print(*text)
@shp_clear.on_click
def shp_clear_on_click(b):
shp_select.value.clear()
shp_select._counter = 0
@shp_upload.on_click
def shp_upload_on_click(b):
progress.clear_output()
os.makedirs(shp_dist_folder.value, exist_ok=True)
for key in shp_select.value:
content = shp_select.value[key]['content']
with open(f'{shp_dist_folder.value}/{key}', 'wb') as f:
f.write(content)
outlog("All files are uploaded.")
shp_select.value.clear()
shp_select._counter = 0
shp_box = HBox([shp_dist_folder, shp_select, shp_clear, shp_upload])
# Import the .shp to the database
l_imp = Label("""b. Import uploaded .shp to the database. Add a short name,
max 15 characters for the parcels table e.g.:escat2020.""")
imp_select = Dropdown(options=[
s for s in glob.glob(f'{shp_dist_folder.value}/*') if '.shp' in s
],
description='Select .shp:',
disabled=False)
imp_refresh = Button(layout=Layout(width='35px'), icon='fa-refresh')
imp_proc = Button(
description='Import .shp file',
value=False,
disabled=False,
button_style='info',
tooltip='Run',
icon='fa-database',
)
imp_truncate = Checkbox(value=False,
description='Remove old entries',
disabled=False)
try:
with open(f"{config.get_value(['paths','temp'])}tb_prefix", 'r') as f:
name_from_prfix = f.read()
except Exception:
name_from_prfix = None
imp_tb_name = Text(value=name_from_prfix,
placeholder='ms2010',
description='Table name:',
tooltip='A short name max 10 char.',
disabled=False)
def on_imp_tb_name(change):
with open(f"{config.get_value(['paths','temp'])}tb_prefix", 'w+') as f:
f.write(imp_tb_name.value)
imp_tb_name.observe(on_imp_tb_name, 'value')
@imp_proc.on_click
def imp_proc_on_click(b):
if imp_tb_name is not None:
import subprocess
progress.clear_output()
# tb_name = imp_select.value.split('/')[-1].split('.')[0]
tb_name = imp_tb_name.value.replace(' ', '').lower()[:15]
outlog("Importing .shp to database...")
command = [
'ogr2ogr', '-f', 'PostgreSQL', 'PG:' + database.conn_str(),
'-nln', tb_name, '-nlt', 'PROMOTE_TO_MULTI', '-nlt',
'GEOMETRY', imp_select.value
]
if imp_truncate.value is True:
command.extend(['--config', 'OGR_TRUNCATE', 'YES'])
if subprocess.call(command) == 0:
progress.clear_output()
outlog(
f"Completed. Total number of rows in table '{tb_name}':",
database.exact_count(tb_name))
else:
outlog("Could not import shp file.")
else:
outlog(
"Please add a name for the parcels table (MAX 15 char e.g.: escat2020)."
)
@imp_refresh.on_click
def imp_refresh_on_click(b):
imp_select.options = [
s for s in glob.glob(f'{shp_dist_folder.value}/*') if '.shp' in s
]
imp_box = HBox(
[imp_tb_name, imp_select, imp_refresh, imp_proc, imp_truncate])
return VBox([l_up, shp_box, l_imp, imp_box, progress])
def __init__(self, player):
self.widget = ipywidgets.HTML(
value="",
placeholder='',
description='',
)
output = ipywidgets.Output()
self.player = player
def fast_backward_clicked(b):
with output:
self.player.begin()
self.player.pause()
def backward_clicked(b):
with output:
self.player.backward()
def step_backward_clicked(b):
with output:
self.player.pause()
self.player.step_backward()
def pause_clicked(b):
with output:
self.player.pause()
def step_forward_clicked(b):
with output:
self.player.pause()
self.player.step_forward()
def play_clicked(b):
with output:
self.player.play()
def fast_forward_clicked(b):
with output:
self.player.pause()
self.player.end()
# self.slider_time=ipywidgets.IntSlider(
# value=0,
# min=0,
# max=len(self.player.history),
# step=1,
# description="time:"
# )
slider = ipywidgets.FloatSlider(value=1.0,
min=0.0,
max=6.0,
step=1,
description="Speed:")
# 2puissance speed affiché ou alors nous affiché juste la valeur et pas "speed " 2** = puissance
def on_value_change(change):
value = int(change['new'])
self.player.set_fps(2**value)
slider.observe(on_value_change, names='value')
play = ipywidgets.Button(description="",
icon='fa-play',
layout=Layout(width='35px'))
fast_backward = ipywidgets.Button(description="",
icon='fa-fast-backward',
layout=Layout(width='35px'))
backward = ipywidgets.Button(description="",
icon='fa-backward',
layout=Layout(width='35px'))
step_backward = ipywidgets.Button(description="",
icon='fa-step-backward',
layout=Layout(width='35px'))
pause = ipywidgets.Button(description="",
icon='fa-pause',
layout=Layout(width='35px'))
step_forward = ipywidgets.Button(description="",
icon='fa-step-forward',
layout=Layout(width='35px'))
fast_forward = ipywidgets.Button(description="",
icon='fa-fast-forward',
layout=Layout(width='35px'))
play.on_click(play_clicked)
fast_backward.on_click(fast_backward_clicked)
backward.on_click(backward_clicked)
step_backward.on_click(step_backward_clicked)
pause.on_click(pause_clicked)
step_forward.on_click(step_forward_clicked)
fast_forward.on_click(fast_forward_clicked)
self.affichage = ipywidgets.HBox([
fast_backward, backward, step_backward, pause, step_forward, play,
fast_forward, slider
])
VBox.__init__(
self, [self.player.view, self.player.slider_time, self.affichage])
#link((self.slider_time,'value'),(self.player,'time'))
#self.widget_affichage=VBox([self.player.view,self.slider_time,self.affichage])
#self.player.time=0
self.player = player
def _init_widget(self):
state = self._state
widget = dict()
fig = dict(x=self._create_slice_fig(),
y=self._create_slice_fig(),
z=self._create_slice_fig())
widget['fig'] = fig
topomap_fig = dict(mag=create_topomap_fig(),
grad=create_topomap_fig(),
eeg=create_topomap_fig())
widget['topomap_fig'] = topomap_fig
label = dict()
label['axis'] = dict(x=HTML(f"<b>{state['label_text']['x']}</b>"),
y=HTML(f"<b>{state['label_text']['y']}</b>"),
z=HTML(f"<b>{state['label_text']['z']}</b>"))
label['topomap_mag'] = HTML(f"<b>{state['label_text']['topomap_mag']}</b>")
label['topomap_grad'] = HTML(f"<b>{state['label_text']['topomap_grad']}</b>")
label['topomap_eeg'] = HTML(f"<b>{state['label_text']['topomap_eeg']}</b>")
label['dipole_pos'] = Label('Not set')
label['dipole_ori'] = Label('Not set')
label['dipole_pos_'] = Label('Dipole origin:')
label['dipole_ori_'] = Label('Dipole orientation:')
label['status'] = Label('Status:')
label['updating'] = Label('Ready.')
widget['label'] = label
widget['tab'] = Tab(layout=Layout(width='700'))
toggle_buttons = dict(
mode_selector=ToggleButtons(
options=['Slice Browser', 'Set Dipole Origin',
'Set Dipole Orientation'],
button_style='primary',
layout=Layout(width='auto'))
)
toggle_buttons['mode_selector'].observe(self._handle_view_mode_change,
'value')
widget['toggle_buttons'] = toggle_buttons
widget['reset_button'] = Button(description='Reset',
button_style='danger',
layout=Layout(width='auto'))
widget['reset_button'].on_click(self._handle_reset_button_click)
checkbox = dict(exact_solution=Checkbox(
value=self._exact_solution,
description='Exact solution (slow!)',
tooltip='Calculate an exact forward projection. This is SLOW!'))
checkbox['exact_solution'].observe(self._toggle_exact_solution,
'value')
widget['checkbox'] = checkbox
widget['amplitude_slider'] = IntSlider(
value=int(self._state['dipole_amplitude'] * 1e9),
min=5, max=100, step=5, continuous_update=False)
widget['amplitude_slider'].observe(self._handle_amp_change,
names='value')
widget['label']['amplitude_slider'] = Label('Dipole amplitude in nAm')
widget['quickstart_text'] = HTML(
value=('<ul>'
'<li>Select the desired brain slices in the '
'<b>Slice Browser.</b></li>'
'<li>Choose the location of the dipole via '
'<b>Set Dipole Origin.</b></li>'
'<li>Orient the dipole via '
'<b>Set Dipole Orientation.</b></li>'
'<li>Adjust the <b>dipole amplitude</b> '
'using the slider below the topographic maps.</li>'
'</ul>'))
widget['quickstart_accordion'] = Accordion(
children=[widget['quickstart_text']])
widget['quickstart_accordion'].set_title(0, 'Quickstart')
widget['preset_dropdown'] = Dropdown(
options=['Select Preset…', 'Preset 1', 'Preset 2', 'Preset 3'],
value='Select Preset…',
layout=Layout(width='auto'))
widget['preset_dropdown'].observe(self._handle_preset_selection_change,
'value')
widget['title'] = HTML(value='<h2>Dipole Simulator</h2>')
widget['output'] = output_widget
return widget
def _create_ui(self):
"""Create and initialize widgets"""
# ------------
# Callbacks + logic
# ------------
def image_passes_filters(image_index):
"""Return if image should be shown."""
actual_label = int(self.dataset[image_index][1])
bo_pred_correct = bool(actual_label == self.label_to_id[self.pred_labels[image_index]])
if (bo_pred_correct and self.w_filter_correct.value) or (
not bo_pred_correct and self.w_filter_wrong.value
):
return True
return False
def button_pressed(obj):
"""Next / previous image button callback."""
step = int(obj.value)
self.vis_image_index += step
self.vis_image_index = min(
max(0, self.vis_image_index), int(len(self.pred_labels)) - 1
)
while not image_passes_filters(self.vis_image_index):
self.vis_image_index += step
if (
self.vis_image_index <= 0
or self.vis_image_index >= int(len(self.pred_labels)) - 1
):
break
self.vis_image_index = min(
max(0, self.vis_image_index), int(len(self.pred_labels)) - 1
)
self.w_image_slider.value = self.vis_image_index
self.update()
def slider_changed(obj):
"""Image slider callback.
Need to wrap in try statement to avoid errors when slider value is not a number.
"""
try:
self.vis_image_index = int(obj["new"]["value"])
self.update()
except Exception:
pass
# ------------
# UI - image + controls (left side)
# ------------
w_next_image_button = widgets.Button(description="下一张")
w_next_image_button.value = "1"
w_next_image_button.layout = Layout(width="80px")
w_next_image_button.on_click(button_pressed)
w_previous_image_button = widgets.Button(description="上一张")
w_previous_image_button.value = "-1"
w_previous_image_button.layout = Layout(width="80px")
w_previous_image_button.on_click(button_pressed)
self.w_filename = widgets.Text(
value="", description="名称:", layout=Layout(width="200px")
)
self.w_path = widgets.Text(
value="", description="路径:", layout=Layout(width="200px")
)
self.w_image_slider = IntSlider(
min=0,
max=len(self.pred_labels) - 1,
step=1,
value=self.vis_image_index,
continuous_update=False,
)
self.w_image_slider.observe(slider_changed)
self.w_image_header = widgets.Text("", layout=Layout(width="130px"))
self.w_img = widgets.Image()
self.w_img.layout.width = f"{self.IM_WIDTH}px"
w_header = widgets.HBox(
children=[
w_previous_image_button,
w_next_image_button,
self.w_image_slider,
self.w_filename,
self.w_path,
]
)
# ------------
# UI - info (right side)
# ------------
w_filter_header = widgets.HTML(
value="Filters (use Image +1/-1 buttons for navigation):"
)
self.w_filter_correct = widgets.Checkbox(
value=True, description="正确分类图像"
)
self.w_filter_wrong = widgets.Checkbox(
value=True, description="错误分类图像"
)
w_gt_header = widgets.HTML(value="真实值:")
self.w_gt_label = widgets.Text(value="")
self.w_gt_label.layout.width = "360px"
w_pred_header = widgets.HTML(value="预测值:")
self.w_pred_labels = widgets.Textarea(value="")
self.w_pred_labels.layout.height = "200px"
self.w_pred_labels.layout.width = "360px"
w_scores_header = widgets.HTML(value="分类得分:")
self.w_scores = bqpyplot.figure()
self.w_scores.layout.height = "250px"
self.w_scores.layout.width = "370px"
self.w_scores.fig_margin = {
"top": 5,
"bottom": 80,
"left": 30,
"right": 5,
}
# Combine UIs into tab widget
w_info = widgets.VBox(
children=[
w_filter_header,
self.w_filter_correct,
self.w_filter_wrong,
w_gt_header,
self.w_gt_label,
w_pred_header,
self.w_pred_labels,
w_scores_header,
self.w_scores,
]
)
w_info.layout.padding = "20px"
self.ui = widgets.Tab(
children=[
widgets.VBox(
children=[
w_header,
widgets.HBox(children=[self.w_img, w_info]),
]
)
]
)
self.ui.set_title(0, "模型结果分析系统")
# Fill UI with content
self.update()
def __init__(self,
path=os.getcwd(),
filename='',
title='',
select_desc='Select',
load_desc='Load',
change_desc='Change',
show_hidden=False,
select_default=False,
use_dir_icons=False,
show_only_dirs=False,
filter_pattern=None,
**kwargs):
"""Initialize FileChooser object."""
self._default_path = path.rstrip(os.path.sep)
self._default_filename = filename
self._selected_path = None
self._selected_filename = None
self._show_hidden = show_hidden
self._select_desc = select_desc
self._load_desc = load_desc
self._change_desc = change_desc
self._callback = None
self._select_default = select_default
self._use_dir_icons = use_dir_icons
self._show_only_dirs = show_only_dirs
self._filter_pattern = filter_pattern
# Widgets
self._pathlist = Dropdown(description="",
layout=Layout(width='auto',
grid_area='pathlist'))
self._filename = Text(
placeholder='output filename',
layout=Layout(width='auto',
grid_area='filename',
display=(None, "none")[self._show_only_dirs]),
disabled=self._show_only_dirs)
self._dircontent = Select(rows=8,
layout=Layout(width='auto',
height=FC_SCROLLBOX_HEIGHT,
grid_area='dircontent'))
self._cancel = Button(description='Cancel',
layout=Layout(width='auto', display='none'))
self._select = Button(description=self._select_desc,
layout=Layout(width='auto'))
self._title = HTML(value=title)
if title == '':
self._title.layout.display = 'none'
# Widget observe handlers
self._pathlist.observe(self._on_pathlist_select, names='value')
self._dircontent.observe(self._on_dircontent_select, names='value')
self._filename.observe(self._on_filename_change, names='value')
self._select.on_click(self._on_select_click)
self._cancel.on_click(self._on_cancel_click)
# Selected file label
self._label = HTML(value=self._LBL_TEMPLATE.format(
self._LBL_NOFILE, 'black'),
placeholder='',
description='')
# Layout
self._gb = GridBox(
children=[self._pathlist, self._filename, self._dircontent],
layout=Layout(display='none',
width=FC_WIDTH,
grid_gap='0px 0px',
grid_template_rows='auto auto',
grid_template_columns='60% 40%',
grid_template_areas='''
'pathlist {}'
'dircontent dircontent'
'''.format(
('filename', 'pathlist')[self._show_only_dirs])))
buttonbar = HBox(children=[self._select, self._cancel, self._label],
layout=Layout(width='auto'))
# Call setter to set initial form values
self._set_form_values(self._default_path, self._default_filename)
# Use the defaults as the selected values
if self._select_default:
self._apply_selection()
# Call VBox super class __init__
super().__init__(children=[
self._title,
self._gb,
buttonbar,
],
layout=Layout(width='auto'),
**kwargs)
def dsc_config(dsc_value):
values = config.read()
ds_db = Dropdown(
options=list(values['db'].keys()),
value="main",
description='Database:',
disabled=False,
layout=Layout(width='200px')
)
try:
with open(normpath(join(f"{values['paths']['temp']}", 'tb_prefix')),
'r') as f:
code_value = f.read().split('_')[0]
except Exception:
code_value = dsc_value.split('_')[0]
ds_code = Combobox(
value=code_value,
placeholder='abc',
options=[m for m in data_options.eu_ms()] + [''],
description='AOI code:',
ensure_option=False,
disabled=False,
layout=Layout(width='200px'),
tooltip='Lowercase AOI code name for the dataset (5chr max).'
)
ds_year = BoundedIntText(
value=int(dsc_value.split('_')[1]),
min=1980,
max=2100,
step=1,
description='Dataset year:',
disabled=False,
layout=Layout(width='180px')
)
ds_desc = Text(
value=values['dataset'][dsc_value]['description'],
description='Description:',
disabled=False
)
info_map_text = ["Set default map view options. ",
"You can get automatically the dataset ",
"center coordinates."]
lat, lon = values['dataset'][dsc_value]['center'].split(",")
map_cent_lat = FloatText(
value=float(lat),
description='Lat:',
disabled=False,
layout=Layout(width='160px')
)
map_cent_lon = FloatText(
value=float(lon),
description='Lon:',
disabled=False,
layout=Layout(width='160px')
)
map_zoom = BoundedIntText(
value=values['dataset'][dsc_value]['zoom'],
min=0,
max=20,
step=1,
description='Zoom:',
disabled=False,
layout=Layout(width='140px')
)
bt_get_center = Button(
layout=Layout(width='40px'),
icon='bullseye',
tooltip='Get center point from database.'
)
ds_box = HBox([ds_code, ds_year, ds_desc, ds_db])
map_box = HBox([Label("Map center: "), map_cent_lat,
map_cent_lon, bt_get_center, map_zoom])
info_config = Label(
"""Change 'AOI code' or 'Year' value to create a new configuration set or
leave the same 'AOI code' value to configure the selected one.""")
db_set = values['dataset'][dsc_value]['db']
def get_tb_list():
tbls = db.tables(db_set, None, False)
if tbls is None:
return []
else:
return tbls
tb_dc = Dropdown(
options=get_tb_list(),
value=config.autoselect(
values['dataset'][dsc_value]['tables']['dias_catalog'],
get_tb_list(), False),
description='DIAS catalog:',
disabled=False
)
tb_pr = Dropdown(
options=get_tb_list(),
value=config.autoselect(
values['dataset'][dsc_value]['tables']['parcels'],
get_tb_list(), False),
description='Parcels:',
disabled=False
)
def get_pr_columns():
try:
colms = db.table_columns(tb_pr.value, ds_db.value, None)
if colms is None:
return []
else:
return colms
except Exception:
return []
tc_id = Dropdown(
options=get_pr_columns(),
value=config.autoselect(
values['dataset'][dsc_value]['pcolumns']['parcels_id'],
get_pr_columns(), False),
description='Parcels ID:',
disabled=False,
layout=Layout(width='180px')
)
tc_cn = Dropdown(
options=get_pr_columns(),
value=config.autoselect(
values['dataset'][dsc_value]['pcolumns']['crop_names'],
get_pr_columns(), False),
description='Crop names:',
disabled=False,
layout=Layout(width='180px')
)
tc_cc = Dropdown(
options=get_pr_columns(),
value=config.autoselect(
values['dataset'][dsc_value]['pcolumns']['crop_codes'],
get_pr_columns(), False),
description='Crop codes:',
disabled=False,
layout=Layout(width='180px')
)
def on_tb_pr_change(change):
tc_id.options = get_pr_columns()
tc_cn.options = get_pr_columns()
tc_cc.options = get_pr_columns()
tb_pr.observe(on_tb_pr_change, 'value')
tb_s2 = Dropdown(
options=get_tb_list(),
value=config.autoselect(
values['dataset'][dsc_value]['tables']['s2'],
get_tb_list(), False),
description='S2 signatures:',
disabled=False
)
tb_bs = Dropdown(
options=get_tb_list(),
value=config.autoselect(
values['dataset'][dsc_value]['tables']['bs'],
get_tb_list(), False),
description='Backscattering:',
disabled=False
)
tb_6c = Dropdown(
options=get_tb_list(),
value=config.autoselect(
values['dataset'][dsc_value]['tables']['c6'],
get_tb_list(), False),
description='6 day coherence:',
disabled=False
)
wb_save = Button(
description='Save',
disabled=False,
icon='save'
)
@bt_get_center.on_click
def bt_get_center_on_click(b):
import json
center_json = json.loads(
db_queries.getTableCentroid(tb_pr.value)['center'][0])
map_cent_lat.value = round(center_json['coordinates'][1], 2)
map_cent_lon.value = round(center_json['coordinates'][0], 2)
map_zoom.value = 10
@wb_save.on_click
def wb_save_on_click(b):
progress.clear_output()
dscode = ds_code.value
config.set_value(['dataset', f'{dscode}_{str(ds_year.value)}',
'tables', 'dias_catalog'], str(tb_dc.value))
config.set_value(['dataset', f'{dscode}_{str(ds_year.value)}',
'tables', 'parcels'], str(tb_pr.value))
config.set_value(['dataset', f'{dscode}_{str(ds_year.value)}',
'pcolumns', 'parcels_id'], str(tc_id.value))
config.set_value(['dataset', f'{dscode}_{str(ds_year.value)}',
'pcolumns', 'crop_names'], str(tc_cn.value))
config.set_value(['dataset', f'{dscode}_{str(ds_year.value)}',
'pcolumns', 'crop_codes'], str(tc_cc.value))
config.set_value(['dataset', f'{dscode}_{str(ds_year.value)}',
'tables', 's2'], str(tb_s2.value))
config.set_value(['dataset', f'{dscode}_{str(ds_year.value)}',
'tables', 'bs'], str(tb_bs.value))
config.set_value(['dataset', f'{dscode}_{str(ds_year.value)}',
'tables', 'c6'], str(tb_6c.value))
config.set_value(['dataset', f'{dscode}_{str(ds_year.value)}',
'db'], str(ds_db.value))
config.set_value(['dataset', f'{dscode}_{str(ds_year.value)}',
'description'], str(ds_desc.value))
config.set_value(
['dataset', f'{dscode}_{str(ds_year.value)}', 'center'],
f"{map_cent_lat.value},{map_cent_lon.value}")
config.set_value(['dataset', f'{dscode}_{str(ds_year.value)}',
'zoom'], str(map_zoom.value))
config.set_value(['set', 'dataset'],
f'{dscode}_{str(ds_year.value)}')
config.set_value(['set', 'ds_year'], str(ds_year.value))
values = config.read()
ds_c = values['set']['dataset']
dsc.options = [d for d in values['dataset']]
dsc.value = ds_c
outlog("The configurations are saved.")
db_box = HBox([VBox([Label('Tables:'),
tb_pr, tb_dc, tb_s2, tb_bs, tb_6c]),
VBox([Label('Columns:'),
HBox([tc_id, tc_cn, tc_cc])])])
return VBox([info_config, ds_box, db_box,
Label(''.join(info_map_text)), map_box, wb_save])
def __init__(self):
# размерность задачи
items_layout = Layout (flex = '1 1 auto', width = 'auto')
self.w_title = HTML('<h3>Параметры задачи</h3>')
self.w_l_dim = Label('Размерность задачи:')
self.w_dim = ToggleButtons(
options=['2', '3'],
value = '2',
#description=' ',
disabled=False,
button_style='', # 'success', 'info', 'warning', 'danger' or ''
tooltips=['Плоская двухмерная задача', 'Трехмерная осесимметричная задача'],
layout=items_layout
)
chg.r0=1e-6
self.w_l_r0 = Label('Радиус заряда:')
self.w_r0 =SelectionSlider(
options=['1e-6', '1e-5', '1e-4', '1e-3', '1e-2'],
value='1e-6',
#description=' ',
disabled=False,
continuous_update=False,
orientation='horizontal',
readout=True, layout=items_layout
)
chg.alpha = 0
self.w_l_alpha = Label(r"Параметр регуляризации ($\alpha$):")
self.w_alpha =SelectionSlider(
options=['0', '1e-6', '1e-4', '1e-2', '1e-1', '0.5', '1.0'],
value='0',
#description=' ',
disabled=False,
continuous_update=False,
orientation='horizontal',
readout=True, layout=items_layout
)
chg.n = 100
self.w_l_n = Label('Число разбиений области:')
self.w_n = SelectionSlider(
options=['20', '50', '100', '200', '400', '500', '1000'],
value='100',
#description=' ',
disabled=False,
continuous_update=False,
orientation='horizontal',
readout=True, layout=items_layout
)
chg.minmaxxy=(0., 0, 1.,1.)
self.w_l_minmaxxy = Label('Область для расчета и отображения потенциала (x, y):')
self.w_minmaxx = FloatRangeSlider(value=[0.,1.],
min=0,
max=2.0,
#description='xmin, xmax',
step=0.01,
disabled=False,
continuous_update=False,
orientation='horizontal',
readout=True,
readout_format='.2f', layout=items_layout)
self.w_minmaxy = FloatRangeSlider(value=[0.,1.],
min=0,
max=2.0,
#description='ymin, ymax',
step=0.02,
disabled=False,
continuous_update=False,
orientation='horizontal',
readout=True,
readout_format='.2f', layout=items_layout)
chg.minmaxarea=(0.2, 0.2, 0.9,0.9)
self.w_l_minmaxarea = Label('Область для расчета напряженности (x, y):')
self.w_minmaxxarea = FloatRangeSlider(value=[0.2,0.9],
min=0,
max=1.0,
#description='xmin, xmax',
step=0.01,
disabled=False,
continuous_update=False,
orientation='horizontal',
readout=True,
readout_format='.2f', layout=items_layout)
self.w_minmaxyarea = FloatRangeSlider(value=[0.2,0.9],
min=0,
max=1.2,
#description='ymin, ymax',
step=0.005,
disabled=False,
continuous_update=False,
orientation='horizontal',
readout=True,
readout_format='.3f', layout=items_layout)
self.w_l_na = Label('Разбиений для аппроксимации электродов:')
chg.na = 50
self.w_na = IntSlider(
value=chg.na,
min=20,
max=250,
step=2,
#description=' ',
disabled=False,
continuous_update=False,
orientation='horizontal',
readout=True,
readout_format='d', layout=items_layout
)
chg.c = None
self.l_c = Label('')
self.update_label('cond', chg.c, self.l_c)
chg.err = None
self.l_err = Label('')
self.update_label('err', chg.err, self.l_err)
chg.E = None
self.l_E = Label('')
self.update_label('E', chg.E, self.l_E)
chg.t = None
self.l_t = Label('')
self.update_label('t', chg.t, self.l_t)
self.l_msg=HTML('<b></b>')
self.l_var = Label('Вариант:')
self.w_dsc = Textarea(value='',
placeholder='Введите пояснения по варианту расчета',
description='',
disabled=False
)
self.btn0 = Button(description ='Пересчитать поле', button_style='primary')
self.btn01 = Button(description ='Emax/Emin', button_style='primary', disabled=True)
self.out0 = Output()
self.btn02 = Button(description='Сохранить', disabled=False)
vb01= VBox([self.w_l_dim, self.w_dim,
self.w_l_r0, self.w_r0,
self.w_l_alpha, self.w_alpha,
self.w_l_n, self.w_n,
self.w_l_minmaxxy, self.w_minmaxx, self.w_minmaxy,
self.w_l_minmaxarea, self.w_minmaxxarea, self.w_minmaxyarea],
layout=Layout(width='47%'))
vb02 = VBox([self.w_l_na, self.w_na, self.l_var, self.w_dsc,
self.l_c, self.l_err, self.l_E , self.l_t, self.l_msg ], layout=Layout(width='47%'))
hbox =HBox([vb01, vb02],
layout=Layout(justify_content='space-between'))
hbox2 = HBox([self.btn0, self.btn01, self.btn02])
self.layout = VBox([self.w_title, hbox, hbox2, self.out0], layout=Layout(width='100%'))
# инициализация
self.get_data()
def _create_title(self, title, tab_controls):
"""Creates title controls for this tab widget.
- Adds title label
- Adds download button for query result. Disabled if one of the following conditions hold:
* query result contains ExplicitVBR or ExplicitVBROverlay type column
* number of rows in the query result exceeds DOWNLOAD_THRESHOLD
- Adds paginator if there exists no ExplicitVBR or ExplicitVBROverlay type column
- Adds any controls related to column types in the result set
Parameters
----------
title: str
result set title.
tab_controls: list
list of controls related to columns in the result set.
"""
# initialize widgets
# add title label
title_label = HTML(f"<h3>{title}</h3>",
layout=Layout(padding="0px 5px 5px 0px"))
self._hbox_title = HBox(layout=Layout(justify_content="space-between",
align_items="center"))
# create download link
dw = NlDownloadLink(layout=Layout(
width="30px",
max_width="30px",
min_width="30px",
margin="5px 5px 5px 0",
padding="0 0 0 0",
flex="0 1 0",
align_self="center",
))
hbox_table_info = HBox(
[title_label, dw],
layout=Layout(justify_content="flex-start", align_items="center"),
)
if not self._columns_manager.hasVBRColumn:
if self._total_nb_rows <= ResultTabPageWidget.DOWNLOAD_THRESHOLD:
dw.filename = f"{title}.csv.gz"
dw.mimetype = "application/gz"
dw.tooltip = f"Download {dw.filename} file."
def clicked(event):
dw.content = gzip.compress(
self._df.to_csv(index=False).encode())
dw.on_click(clicked)
else:
dw.disabled = True
dw.tooltip = "Not available for download due to size!"
# add paginator if there exist no ExplicitVBR or ExplicitVBROverlay column
paginator = PaginationWidget(
self._df.shape[0], layout=Layout(padding="0px 0px 0px 50px"))
self._limit = paginator.limit
paginator.observe(self._page_number_changed, names="page")
paginator.observe(self._limit_changed, names="limit")
hbox_table_info.children = hbox_table_info.children + (paginator, )
else:
dw.tooltip = "Not available for download due to column type!"
dw.disabled = True
self._limit = self._total_nb_rows
return [hbox_table_info, HBox(tab_controls)]
def interact_distributions():
from ipywidgets import FloatSlider, Label, GridBox, interactive, Layout, VBox, \
HBox, Checkbox, IntSlider, Box, Button, widgets
fx0=FloatSlider(value=2, description=" ", min=.5, max=4., step=.2, continuous_update=False,
layout=Layout(width='auto', grid_area='vx0'))
fy0=FloatSlider(value=3, description=" ", min=.5, max=4., step=.2, continuous_update=False,
layout=Layout(width='auto', grid_area='vy0'))
fs0=FloatSlider(value=1, description=" ", min=.1, max=4., step=.2, continuous_update=False,
layout=Layout(width='auto', grid_area='vs0'))
fd0=FloatSlider(value=.9, description=" ", min=-2., max=2., step=.1, continuous_update=False,
layout=Layout(width='auto', grid_area='vd0'))
fx1=FloatSlider(value=2, description=" ", min=.5, max=4., step=.2, continuous_update=False,
layout=Layout(width='auto', grid_area='vx1'))
fy1=FloatSlider(value=2, description=" ", min=.5, max=4., step=.2, continuous_update=False,
layout=Layout(width='auto', grid_area='vy1'))
fs1=FloatSlider(value=1, description=" ", min=.1, max=4., step=.2, continuous_update=False,
layout=Layout(width='auto', grid_area='vs1'))
fd1=FloatSlider(value=-.3, description=" ", min=-2., max=2., step=.1, continuous_update=False,
layout=Layout(width='auto', grid_area='vd1'))
fdummy = FloatSlider(value=2, description= " ", min=1, max=4, step=1)
l = lambda s,p, w="auto": Label(s, layout=Layout(width=w, grid_area=p))
bay = Checkbox(value=False, description='show NATURAL frontiers',disabled=False, indent=False,
layout=Layout(width="80%"))
resample = Button(description="resample data points")
from IPython.core.display import clear_output
def resample_onclick(_):
global do_resample_points
do_resample_points = True
tmp = fdummy.value
fdummy.value = tmp+(1 if tmp<3 else -1)
do_resample_points = False
resample.on_click(resample_onclick)
w = interactive(display_distributions,
x0=fx0, y0=fy0, s0=fs0, d0=fd0,
x1=fx1, y1=fy1, s1=fs1, d1=fd1, show_bayesians=bay, dummy=fdummy,
continuous_update=False)
w.children[-1].layout=Layout(width='auto', grid_area='fig')
controls = Box([bay, resample],
layout=Layout(grid_area="ctr",
display="flex-flow",
justify_content="flex-start",
flex_flow="column",
align_items = 'flex-start'))
gb =GridBox(children=[fx0, fy0, fs0, fd0, fx1, fy1, fs1, fd1,
l("AMERICAN TRILOBYTE", "h0"), l("AFRICAN TRILOBYTE", "h1"),
l("size", "lx0"),l("weight", "ly0"), l("spread", "ls0"), l("tilt", "ld0"),
l("size", "lx1"),l("weight", "ly1"), l("spread", "ls1"), l("tilt", "ld1"),
controls
],
layout=Layout(
width='100%',
grid_template_rows='auto auto auto auto auto auto auto',
grid_template_columns='5% 30% 5% 30% 30%',
grid_template_areas='''
"h0 h0 h1 h1 ."
"lx0 vx0 lx1 vx1 ."
"ly0 vy0 ly1 vy1 ctr"
"ls0 vs0 ls1 vs1 ctr"
"ld0 vd0 ld1 vd1 ctr"
"fig fig fig fig fig"
''')
)
def limit_fd0(*args):
fd0.max = fs0.value+fs0.value*0.5
fd0.min = -fs0.value*0.5
def limit_fd1(*args):
fd1.max = fs1.value+fs1.value*0.5
fd1.min = -fs1.value*0.5
fs0.observe(limit_fd0, "value")
fd0.observe(limit_fd0, "value")
fs1.observe(limit_fd1, "value")
fd1.observe(limit_fd1, "value")
w.children[0].value=1
widget1 = VBox([gb, w.children[-1]])
display(widget1)
return fx0, fy0, fs0, fd0, fx1, fy1, fs1, fd1
def __init__(self, *args, **kwargs):
super().__init__(*args, **kwargs)
# tab widget that displays each resultset in an individual tab
self._tab = NlIconTab(layout=Layout(height="460px"))
# viewers necessary for each resultset, can be shared among resultsets
self._viewers = None
def __init__(
self,
origin_time: datetime = None,
before: int = 60,
after: int = 10,
max_before: int = 600,
max_after: int = 100,
label: str = None,
units: str = "min",
auto_display: bool = False,
):
"""
Create new instance of QueryTime.
Parameters
----------
origin_time : datetime, optional
The origin time (the default is `datetime.utcnow()`)
label : str, optional
The description to display
(the default is 'Select time ({units}) to look back')
before : int, optional
The default number of `units` before the `origin_time`
(the default is 60)
after : int, optional
The default number of `units` after the `origin_time`
(the default is 10)
max_before : int, optional
The largest value for `before` (the default is 600)
max_after : int, optional
The largest value for `after` (the default is 100)
units : str, optional
Time unit (the default is 'min')
Permissable values are 'day', 'hour', 'minute', 'second'
These can all be abbreviated down to initial characters
('d', 'm', etc.)
auto_display : bool, optional
Whether to display on instantiation (the default is False)
"""
self._label = "Set query time boundaries" if label is None else label
self._time_unit = _parse_time_unit(units)
max_before = abs(max_before)
max_after = abs(max_after)
before = abs(before)
after = abs(after)
if max_before < before:
before = max_before
if max_after < after:
after = max_after
# default to now
self.origin_time = datetime.utcnow() if origin_time is None else origin_time
# Calculate time offsets from origin
self._query_start = self.origin_time - timedelta(
0, before * self._time_unit.value
)
self._query_end = self.origin_time + timedelta(0, after * self._time_unit.value)
# Create widgets
self._w_origin_dt = widgets.DatePicker(
description="Origin Date", disabled=False, value=self.origin_time.date()
)
self._w_origin_tm = widgets.Text(
description="Time (24hr)",
disabled=False,
value=str(self.origin_time.time()),
)
range_desc = "Time Range ({}):".format(self._time_unit.name)
self._w_tm_range = widgets.IntRangeSlider(
value=[-before, after],
min=-max_before,
max=max_after,
step=1,
description=range_desc,
disabled=False,
continuous_update=True,
orientation="horizontal",
readout=True,
readout_format="d",
layout=Layout(width="80%"),
style=self._label_style,
)
self._w_start_time_txt = widgets.Text(
value=self._query_start.isoformat(sep=" "),
description="Query start time (UTC):",
layout=Layout(width="50%"),
style=self._label_style,
)
self._w_end_time_txt = widgets.Text(
value=self._query_end.isoformat(sep=" "),
description="Query end time (UTC) : ",
layout=Layout(width="50%"),
style=self._label_style,
)
self._w_tm_range.observe(self._time_range_change, names="value")
self._w_origin_dt.observe(self._update_origin, names="value")
self._w_origin_tm.observe(self._update_origin, names="value")
if auto_display:
self.display()
def getTS(self, startDate, endDate):
ndays = (endDate - startDate).days + 1
if self.init:
ndays += 1
currentDate = startDate
delta = timedelta(days=1)
self.df = pd.DataFrame(columns=[
'datetime', 'AOD', 'DUST_PM', 'SALT_PM', 'ORG_CARB', 'BLK_CARB',
'SO4', 'PM2.5'
])
with self.out_cp:
self.out_cp.clear_output()
pbar = IntProgress(min=0, max=int(ndays))
pbar.description = 'Progress:'
info1 = Label('0%')
info2 = Label(' ')
display(
VBox([
HBox([pbar, info1]),
HBox([info2], layout=Layout(justify_content='center'))
]))
progVal = 0
if self.init:
info2.value = 'Initializing NASA Earth Data Connection..'
self.initSession()
self.init = False
pbar.value += 1
progVal += 1
info1.value = '{:.1f}%'.format(
(float(progVal) / float(ndays)) * 100.0)
self.lonlatToIndex(self.plon, self.plat)
while currentDate <= endDate:
url = self.getUrlMERRA(currentDate)
info2.value = 'Accessing data for {}'.format(currentDate)
dataset = open_url(url, session=self.session)
aod = np.squeeze(dataset['TOTEXTTAU'][:, self.ilat, self.ilon])
dust_pm = np.squeeze(
dataset['DUSMASS25'][:, self.ilat,
self.ilon]) * 1000000000.0
salt_pm = np.squeeze(
dataset['SSSMASS25'][:, self.ilat,
self.ilon]) * 1000000000.0
org_carb = np.squeeze(
dataset['OCSMASS'][:, self.ilat, self.ilon]) * 1000000000.0
blk_carb = np.squeeze(
dataset['BCSMASS'][:, self.ilat, self.ilon]) * 1000000000.0
so4 = np.squeeze(dataset['SO4SMASS'][:, self.ilat,
self.ilon]) * 1000000000.0
pm25 = (1.375 * so4 + 1.6 * org_carb + blk_carb + dust_pm +
salt_pm)
dt = pd.date_range(currentDate, periods=24, freq='H')
vardict = {
'datetime': dt,
'AOD': aod,
'DUST_PM': dust_pm,
'SALT_PM': salt_pm,
'ORG_CARB': org_carb,
'BLK_CARB': blk_carb,
'SO4': so4,
'PM2.5': pm25
}
df_add = pd.DataFrame(vardict)
self.df = pd.concat([self.df, df_add])
currentDate += delta
progVal += 1
info1.value = '{:.1f}%'.format(
(float(progVal) / float(ndays)) * 100.0)
pbar.value += 1
self.stateChange = False
