def __init__(self, rl_ch=12, ud_ch=13, bus=1):
self.sg = ServoGroup(rl_ch=rl_ch, ud_ch=ud_ch, bus=bus)
self.sg.reset() #Pan and tilt go to default position
#Setup various widgets
self.panel_step_move = NineButton(
button_list=['↖', '↑', '↗', '←', 'reset', '→', '↙', '↓', '↘'])
self.panel_far_move = NineButton(
button_list=['◤', '▲', '◥', '◄', 'reset', '►', '◣', '▼', '◢'])
self.image_widget = widgets.Image(
format='jpeg', width=400, height=300) #Display resolution setting
self.snap_count = widgets.IntText(description='count:',
layout=widgets.Layout(width='140px'),
value=0)
self.rl_textbox = widgets.IntText(layout=widgets.Layout(width='140px'),
value=self.sg.read()[0],
description='rl:')
self.ud_textbox = widgets.IntText(layout=widgets.Layout(width='140px'),
value=self.sg.read()[1],
description='ud:')
self.rl_slider = widgets.FloatSlider(min=-1,
max=1,
value=0,
step=0.02,
description='rl')
self.ud_slider = widgets.FloatSlider(min=-1,
max=1,
value=0,
step=0.02,
description='ud')
self.snap_dir = 'snap' #Folder name for saving snapshot
self.camera_link = None
self.press_count = 0
def main(self):
self.media_wid = widgets.ToggleButtons(options=['Lif', 'Images'],
description='Media Input',
value='Lif')
self.media_wid.observe(self.media_update, ['value'])
# self.mode_wid = widgets.ToggleButtons(options=['multi', 'single'], description='Tracking mode',tooltips=['Multiple frame tracking', 'Single frame tracking. Which singles must be specified'])
# self.mode_wid.observe(self.mode_update, ['value'])
self.fmt = widgets.Dropdown(options=['.tif', '.png', '.jpg'],
description='Frame format')
self.initial_frame = widgets.IntText(description='Initial frame')
self.nframes = widgets.IntText(description='Z Frames', value=5)
self.k = widgets.FloatSlider(min=1,
max=10,
step=0.2,
description='k (Blur)',
value=1.6)
self.edge_cutoff = widgets.FloatText(description='Edge cut')
self.plot = widgets.Checkbox(description='Show plots', value=True)
self.options.children = [self.media_wid]
def __init__(self, title="Graphics Window", width=320, height=240):
super(GraphWin, self).__init__(size=(width, height))
from calysto.display import display, Javascript
self.background_color = None
self.title = widgets.HTML("<b>%s</b>" % title)
self.mouse_x = widgets.IntText()
self.mouse_y = widgets.IntText()
self.svg_canvas = widgets.HTML(
self.get_html(onClick="window.clicked(evt, '%s', '%s')" %
(self.mouse_x.model_id, self.mouse_y.model_id)))
self.window = widgets.HBox([self.title, self.svg_canvas])
display(
Javascript("""
window.clicked = function (evt, x_model, y_model) {
var e = evt.srcElement.farthestViewportElement || evt.target;
var dim = e.getBoundingClientRect();
var x = evt.clientX - dim.left;
var y = evt.clientY - dim.top;
var manager = IPython.WidgetManager._managers[0];
var model_prom = manager.get_model(x_model);
model_prom.then(function(model) {
model.set('value', Math.round(x));
model.save_changes();
});
model_prom = manager.get_model(y_model);
model_prom.then(function(model) {
model.set('value', Math.round(y));
model.save_changes();
});
};
"""))
display(self.window)
def make_gui(self):
self.signature = signature(self.process)
label = f"<b>{self.name}</b>"
display(widgets.HTML(value=label))
for i, arg_name in enumerate(self.signature.parameters):
if i == 0:
continue
arg_type = self.signature.parameters[arg_name].annotation
wd = dict(description=arg_name, value=self.params[arg_name])
if arg_type is str:
w = widgets.Text(**wd)
elif arg_type is int:
w = widgets.IntText(**wd)
elif arg_type is float:
w = widgets.FloatText(**wd)
else:
return
w.observe(self.set_param)
display(w)
def jspecgram(snd, nt=1000, starttime=None, endtime=None,
nperseg=512, freqsmoothing=1, cmap='viridis', dynrange=(-90., -40.),
maxfreq=10e3):
nfft = int(nperseg*freqsmoothing)
d = sndplot.Spectrogram(snd, nt=nt, starttime=starttime, endtime=endtime,
nperseg=nperseg, nfft=nfft, cmap=cmap, dynrange=dynrange,
maxfreq=maxfreq)
button_play = widgets.Button(description='play')
button_play.on_click(d.play)
button_stop = widgets.Button(description='stop')
button_stop.on_click(d.stop_playing)
display(widgets.HBox((button_play, button_stop)))
drs = widgets.FloatRangeSlider(value=(-75, -35), min=-120, max=0, step=1, description='dynamic range (dB)')
drs.observe(lambda change: d.set_clim(change['new']), names='value')
display(drs)
freqs = widgets.FloatRangeSlider(value=(0, 10), min=0, max=snd.fs/2e3, step=0.1,
description='frequency range (kHz)')
freqs.observe(lambda change: d.set_freqrange(change['new']), names='value')
display(freqs)
npersegw = widgets.IntText(value=nperseg, min=1, max=4096 * 2,
description='nperseg')
npersegw.observe(lambda change: d.set_nperseg(change['new']),
names='value')
display(npersegw)
return d
def get_widgets_per_param(param, value):
if isinstance(value, float):
return (param, widgets.FloatText(
value=value,
step=0.05,
description=param.split('__')[1],
continuous_update=False,
disabled=False
))
elif isinstance(value, int):
return (param, widgets.IntText(
value=value,
step=1,
description=param.split('__')[1],
continuous_update=False,
disabled=False
))
elif isinstance(value, str):
return (param, widgets.Text(
value=value,
description=param.split('__')[1],
continuous_update=False,
disabled=False
))
else:
return None
def DrawDecisionTree(fac, datasetName, methodName):
m = GetMethodObject(fac, datasetName, methodName)
if m == None:
return None
tr = TreeReader(str(m.GetWeightFileName()))
variables = tr.getVariables()
def clicked(b):
if treeSelector.value > tr.getNTrees():
treeSelector.value = tr.getNTrees()
clear_output()
toJs = {"variables": variables, "tree": tr.getTree(treeSelector.value)}
json_str = json.dumps(toJs)
JPyInterface.JsDraw.Draw(json_str, "drawDecisionTree", True)
mx = str(tr.getNTrees() - 1)
treeSelector = widgets.IntText(value=0, font_weight="bold")
drawTree = widgets.Button(description="Draw", font_weight="bold")
label = widgets.HTML(
"<div style='padding: 6px;font-weight:bold;color:#333;'>Decision Tree [0-"
+ mx + "]:</div>")
drawTree.on_click(clicked)
container = widgets.HBox([label, treeSelector, drawTree])
display(container)
def full_list_elements(self):
retrieve_material = RetrieveMaterialMetadata(material='all')
self.list_returned = retrieve_material.full_list_material()
# import pprint
# pprint.pprint(list_returned)
box4 = widgets.HBox([
widgets.Label("List of elements",
layout=widgets.Layout(width=self.label_width)),
widgets.Select(options=self.list_returned,
layout=widgets.Layout(width='20%'))
])
box5 = widgets.HBox([
widgets.Label("Nbr Bragg Edges",
layout=widgets.Layout(width=self.label_width)),
widgets.IntText(8, layout=widgets.Layout(width='20%'))
])
vertical_box = widgets.VBox([box4, box5])
display(vertical_box)
self.list_elements_ui = box4.children[1]
self.nbr_bragg_edges_ui = box5.children[1]
def show_obs_plot_widget(data, display_fn):
from IPython import display
from ipywidgets import widgets
text_wid = widgets.IntText(value=0,
placeholder='Frame number',
description='Frame number:',
disabled=False)
slider_wid = widgets.IntSlider(value=0,
min=0,
max=len(data),
step=1,
description='Frames:',
disabled=False,
continuous_update=False,
orientation='horizontal',
readout=True,
readout_format='d')
widgets.jslink((text_wid, 'value'), (slider_wid, 'value'))
output_widget = widgets.Output(layout={'height': '250px'})
def on_value_change(change):
frame_idx = change['new']
display_fn(frame_idx)
slider_wid.observe(on_value_change, names='value')
frame_box = widgets.HBox([output_widget])
control_box = widgets.HBox([text_wid, slider_wid]) # Controls
main_box = widgets.VBox([frame_box, control_box])
display.display(main_box)
display_fn(0)
def __init__(self, Notebook):
super(Run_Dynamics_pMHC, self).__init__(Notebook)
self.widget_nputs = widgets.IntText(value=1,
description='N :',
disabled=False)
self.button_launchRun = widgets.Button(description="Run dynamics",
disabled=True)
self.notebook.dependencies_dict["generation"].append(self)
self.notebook.dependencies_dict["dynamics"] = []
self.notebook.extra_variables = {"ntries": None}
def wdim_menu():
'''
generates menu for the molecules notebook in order to display and save data of specific dimers
'''
input = widgets.Dropdown(description='Input data',
options=['Dictionary', 'Pickle', 'Text file'],
value='Dictionary')
which = widgets.IntText(description='Which dimmer')
plot = widgets.Checkbox(description='Plot', value=True)
save = widgets.Checkbox(description='Save', value=True)
return widgets.VBox([input, which, plot, save])
def g6r_menu():
'''
generates a menu for specific parameters to compute and fit the time correlation of the hexagonal order. See src.characterisation.g6.py for details
'''
input = widgets.Dropdown(description='Input data',
options=['Dictionary', 'Pickle', 'Text file'],
value='Dictionary')
nbins = widgets.IntText(description='Nbins', value=100)
bs = widgets.FloatText(description='Binwidth', value=0.25)
plot = widgets.Checkbox(description='Plot', value=True)
save = widgets.Checkbox(description='Save', value=True)
return widgets.VBox([input, nbins, bs, plot, save])
def ov_menu():
'''
generates a menu for specific parameters to compute and fit the overlap Q(t) functions. See src.characterisation.overlap.py for details
'''
input = widgets.Dropdown(description='Input data',
options=['Dictionary', 'Pickle', 'Text file'],
value='Dictionary')
plot = widgets.Checkbox(description='Plot', value=True)
fit = widgets.Checkbox(description='Fit', value=True)
points = widgets.IntText(description='No. of points', value=100)
tau = widgets.FloatText(description='$ \\tau $', value=1.)
save = widgets.Checkbox(description='Save', value=True)
return widgets.VBox([input, plot, fit, points, tau, save])
def msd_menu():
input = widgets.Dropdown(description='Input data',
options=['Dictionary', 'Pickle', 'Text file'],
value='Dictionary')
plot = widgets.Checkbox(description='Plot', value=True)
fit = widgets.Checkbox(description='Fit MSD', value=True)
points = widgets.IntText(description='Points', value=100)
vel = widgets.FloatText(description='$ \\upsilon$ (px $s^{-1}$)',
value=100)
tau = widgets.FloatText(description='$ \\tau $', value=0.5)
refs = widgets.Checkbox(description='Slope reference', value=True)
kind = widgets.Dropdown(options=['ABP', 'Quincke', 'Passive'],
description='MSD fit type',
value='ABP')
save = widgets.Checkbox(description='Save', value=True)
return widgets.VBox([input, plot, fit, kind, points, tau, vel, refs, save])
def __init__(self, model, X, y, hist=True):
self.min_value = -0.30
self.max_value = +0.30
self.step = 0.05
self.sliders = {
str(i): widgets.FloatSlider(min=self.min_value,
max=self.max_value,
step=self.step)
for i in range(16)
}
self.text = widgets.IntText()
self.sliders['index'] = self.text
self.model = model
self.X = X
self.y = y
self.hist = hist
def show_stamp_widget(masked_stamps):
from IPython import display
from ipywidgets import widgets
text_wid = widgets.IntText(value=0,
placeholder='Frame number',
description='Frame number:',
disabled=False)
slider_wid = widgets.IntSlider(value=0,
min=0,
max=len(masked_stamps),
step=1,
description='Frames:',
disabled=False,
continuous_update=False,
orientation='horizontal',
readout=True,
readout_format='d')
widgets.jslink((text_wid, 'value'), (slider_wid, 'value'))
output_widget = widgets.Output(layout={'height': '250px'})
def show_stamp(i):
fig = make_sigma_aperture_plot(masked_stamps[i])
# fig.set_size_inches(9, 2.5)
fig.suptitle(f'Frame {i:03d}', fontsize=14, y=1.06)
fig.axes[1].grid(False)
fig.axes[1].set_yticklabels([])
fig.axes[1].set_facecolor('#bbbbbb')
with output_widget:
display.clear_output()
display.display(fig)
def on_value_change(change):
frame_idx = change['new']
show_stamp(frame_idx)
slider_wid.observe(on_value_change, names='value')
frame_box = widgets.HBox([output_widget])
control_box = widgets.HBox([text_wid, slider_wid]) # Controls
main_box = widgets.VBox([frame_box, control_box])
display.display(main_box)
show_stamp(0)
def appendPVWidgets (pv = ""):
PVNameWidget = widgets.Text (description = "PV Name:", value = pv)
PVBinsWidget = widgets.Checkbox(value = False, description = 'Optimized?')
PVBinsIntWidget = widgets.IntText (value = "500", description = "# bins:", disabled = not PVBinsWidget.value)
PVRemoveWidget = widgets.Button (description = "Remove")
PVBinsWidget.observe (updateBinsText)
PVRemoveWidget.on_click(removePVHandler)
newRow = widgets.HBox ([PVNameWidget, PVBinsWidget, PVBinsIntWidget, PVRemoveWidget])
PVRemoveWidget.parent = newRow
PVBinsWidget.parent = newRow
PVWidgetList.append (newRow)
appendPVVBox.children = PVWidgetList + [appendPVWidget]
def __init__(self,
on_interact=None,
output=None,
overwrite_previous_output=True,
feedback=False,
run=True,
action_kws={},
*args,
**kwargs):
super().__init__(on_interact=on_interact,
output=output,
overwrite_previous_output=overwrite_previous_output,
feedback=feedback,
action_kws=action_kws)
self.widget = widgets.IntText(*args, **kwargs)
if run:
self.run()
def make_widgets_mat(m, n):
"""
Makes a m rows x n columns
matriz of integer Jupyter Widgets
all values initialized to zero
"""
list_elements = []
for i in range(m):
row = []
for j in range(n):
row.append(widgets.IntText(value=0))
list_elements.append(row)
rows = []
for row in list_elements:
rows.append(widgets.HBox(row))
widgets_mat = widgets.VBox(rows)
return list_elements, widgets_mat
def RandomWave():
""" Main function called by notebook
"""
noWaves_sldr = widgets.IntSlider(value=10,
min=2,
max=20,
step=1,
description='No. Waves',
continuous_update=False)
seed_Text = widgets.IntText(123, description='Seed')
filter_sldr = widgets.FloatRangeSlider(value=[minf, minf],
min=minf,
max=maxf,
description="Filter Range",
continuous_update=False)
return widgets.VBox([
widgets.HBox([noWaves_sldr, filter_sldr, seed_Text]),
widgets.interactive_output(runWaves, {
'noWaves': noWaves_sldr,
'seed': seed_Text,
'filterRange': filter_sldr
})
])
def get_cluster_params_widgets(param, value):
if isinstance(value, float):
return (param, widgets.FloatText(
value=value,
step=0.1,
description=param.split('__')[1],
disabled=False
))
elif isinstance(value, int):
return (param, widgets.IntText(
value=value,
step=1,
description=param.split('__')[1],
disabled=False
))
elif isinstance(value, str):
return (param, widgets.Text(
value=value,
description=param.split('__')[1],
disabled=False
))
else:
return None
def get_widgets_per_param(params):
for key, value in params.items():
style = {'description_width': 'initial'}
description = key.split("__")[1] if "__" in key else key
if isinstance(value, float):
yield (key,
widgets.FloatText(value=value,
step=0.05,
description=description,
continuous_update=False,
disabled=False,
layout=Layout(width="90%"),
style=style))
elif isinstance(value, bool):
yield (key,
widgets.ToggleButton(value=value,
description=description,
disabled=False,
layout=Layout(width="90%"),
style=style))
elif isinstance(value, int):
yield (key,
widgets.IntText(value=value,
step=1,
description=description,
continuous_update=False,
disabled=False,
layout=Layout(width="90%"),
style=style))
elif isinstance(value, str):
yield (key,
widgets.Text(value=value,
description=description,
continuous_update=False,
disabled=False,
layout=Layout(width="90%"),
style=style))
def __init__(self, table: DynamicTable):
super().__init__()
self.dynamic_table = table
self.col_names, self.categorical_cols = infer_columns_to_plot(
self.dynamic_table)
num_entries = len(self.dynamic_table)
num_columns = len(self.dynamic_table.colnames)
num_columns_to_plot = len(self.col_names)
num_categorical = len(self.categorical_cols)
self.name_text = widgets.Label(
f"Table name: {self.dynamic_table.name}\n", layout=field_lay)
self.entries_text = widgets.Label(
f"Number of entries: {num_entries}\n", layout=field_lay)
self.col_text = widgets.Label(
f"Number of columns: {num_columns} - real (r): {num_columns - num_categorical}, "
f"categorical (c): {num_categorical}",
layout=field_lay)
self.col_plot_text = widgets.Label(
f"Number of inspectable columns: {num_columns_to_plot}")
self.summary_text = widgets.VBox([
self.name_text, self.entries_text, self.col_text,
self.col_plot_text
])
self.col_names_display = {}
for col in self.col_names:
if col in self.categorical_cols:
self.col_names_display[f"(c) {col}"] = col
else:
self.col_names_display[f"(r) {col}"] = col
self.column_dropdown = widgets.SelectMultiple(
options=list(self.col_names_display),
description="Inspect columns",
layout=Layout(max_width="400px"),
style={"description_width": "initial"},
disabled=False,
tooltip=
"Select columns to inspect. You can select at most 1 categorical and 3 real columns."
)
self.column_dropdown.observe(self.max_selection)
self.nbins = widgets.IntText(10,
min=0,
description="# bins",
layout=Layout(max_width="400px"))
self.nbins.layout.visibility = "hidden"
self.show_labels = widgets.Checkbox(value=True,
description="show labels")
self.plot_controls = widgets.HBox(
[self.column_dropdown, self.nbins, self.show_labels])
self.controls = dict(col_names_display=self.column_dropdown,
nbins=self.nbins,
show_labels=self.show_labels)
out_fig = interactive_output(self.plot_hist_bar, self.controls)
bottom_panel = widgets.VBox([self.plot_controls, out_fig])
self.children = [self.summary_text, bottom_panel]
def interact(obj):
tab = widgets.Tab()
base_style = widgets.ButtonStyle()
selected_style = widgets.ButtonStyle(button_color='#DDFFDD',
font_weight='bold')
if isinstance(obj, hl.Table):
glob = widgets.Button(description='globals',
layout=widgets.Layout(width='150px',
height='30px'))
rows = widgets.Button(description='rows',
layout=widgets.Layout(width='150px',
height='200px'))
rows.style = selected_style
globals_frames = []
globals_frames.append(
widgets.HTML(
f'<p><big>Global fields, with one value in the dataset.</big></p>\n'
f'<p>Commonly used methods:</p>\n'
f'<ul>'
f'<li>{html_link("annotate_globals", "https://hail.is/docs/0.2/hail.Table.html#hail.Table.annotate_globals")}: '
f'add new global fields.</li>'
f'</ul>'))
append_struct_frames(obj.globals.dtype, globals_frames)
row_frames = []
row_frames.append(
widgets.HTML(
f'<p><big>Row fields, with one record per row of the table.</big></p>\n'
f'<p>Commonly used methods:</p>\n'
f'<ul>'
f'<li>{html_link("annotate", "https://hail.is/docs/0.2/hail.Table.html#hail.Table.annotate")}: '
f'add new fields.</li>'
f'<li>{html_link("filter", "https://hail.is/docs/0.2/hail.Table.html#hail.Table.filter")}: '
f'filter rows of the table.</li>'
f'<li>{html_link("aggregate", "https://hail.is/docs/0.2/hail.Table.html#hail.Table.aggregate")}: '
f'aggregate over rows to produce a single value.</li>'
f'</ul>'))
if len(obj.key) > 0:
row_frames.append(
widgets.HTML(f'<p><big>Key: {list(obj.key)}<big><p>'))
append_struct_frames(obj.row.dtype, row_frames)
tab.children = [
widgets.VBox(frames) for frames in [globals_frames, row_frames]
]
tab.set_title(0, 'globals')
tab.set_title(1, 'row')
tab.selected_index = 1
box = widgets.VBox([glob, rows])
buttons = [glob, rows]
else:
assert isinstance(obj, hl.MatrixTable)
glob = widgets.Button(description='globals',
layout=widgets.Layout(width='65px',
height='30px'))
cols = widgets.Button(description='cols',
layout=widgets.Layout(width='200px',
height='30px'))
rows = widgets.Button(description='rows',
layout=widgets.Layout(width='65px',
height='200px'))
entries = widgets.Button(description='entries',
layout=widgets.Layout(width='200px',
height='200px'))
entries.style = selected_style
globals_frames = []
globals_frames.append(
widgets.HTML(
f'<p><big>Global fields, with one value in the dataset.</big></p>\n'
f'<p>Commonly used methods:</p>\n'
f'<ul>'
f'<li>{html_link("annotate_globals()", "https://hail.is/docs/0.2/hail.MatrixTable.html#hail.MatrixTable.annotate_globals")}: '
f'add new global fields.</li>'
f'</ul>'))
append_struct_frames(obj.globals.dtype, globals_frames)
row_frames = []
row_frames.append(
widgets.HTML(
f'<p><big>Row fields, with one record per row in the dataset.</big></p>\n'
f'<p>Commonly used methods:</p>\n'
f'<ul>'
f'<li>{html_link("annotate_rows()", "https://hail.is/docs/0.2/hail.MatrixTable.html#hail.MatrixTable.annotate_rows")}: '
f'add new row fields. This method supports {html_link("aggregation", "https://hail.is/docs/0.2/aggregators.html")}, '
f'aggregating over entries to compute one result per row, e.g. computing the mean depth per variant.</li>'
f'<li>{html_link("filter_rows()", "https://hail.is/docs/0.2/hail.MatrixTable.html#hail.MatrixTable.filter_rows")}: '
f'filter rows in the matrix table.</li>'
f'<li>{html_link("aggregate_rows()", "https://hail.is/docs/0.2/hail.MatrixTable.html#hail.MatrixTable.aggregate_rows")}: '
f'aggregate over rows (not including entries or columns) to produce a single value, e.g. counting the number of loss-of-function variants.</li>'
f'<li>{html_link("rows()", "https://hail.is/docs/0.2/hail.MatrixTable.html#hail.MatrixTable.rows")}: '
f'return the rows as a Hail {html_link("Table", "https://hail.is/docs/0.2/hail.Table.html")}.</li>'
f'</ul>'))
if len(obj.row_key) > 0:
row_frames.append(
widgets.HTML(f'<p><big>Row key: {list(obj.row_key)}<big><p>'))
append_struct_frames(obj.row.dtype, row_frames)
col_frames = []
col_frames.append(
widgets.HTML(
f'<p><big>Column fields, with one record per column in the dataset.</big></p>\n'
f'<p>Commonly used methods:</p>\n'
f'<ul>'
f'<li>{html_link("annotate_cols()", "https://hail.is/docs/0.2/hail.MatrixTable.html#hail.MatrixTable.annotate_cols")}: '
f'add new column fields. This method supports {html_link("aggregation", "https://hail.is/docs/0.2/aggregators.html")}, '
f'aggregating over entries to compute one result per column, e.g. computing the mean depth per sample.</li>'
f'<li>{html_link("filter_cols()", "https://hail.is/docs/0.2/hail.MatrixTable.html#hail.MatrixTable.filter_cols")}: '
f'filter columns in the matrix table.</li>'
f'<li>{html_link("aggregate_cols()", "https://hail.is/docs/0.2/hail.MatrixTable.html#hail.MatrixTable.aggregate_cols")}: '
f'aggregate over columns (not including entries or rows) to produce a single value, e.g. counting the number of samples with case status.</li>'
f'<li>{html_link("cols()", "https://hail.is/docs/0.2/hail.MatrixTable.html#hail.MatrixTable.cols")}: '
f'return the columns as a Hail {html_link("Table", "https://hail.is/docs/0.2/hail.Table.html")}.'
f'</li>'
f'</ul>'))
if len(obj.col_key) > 0:
col_frames.append(
widgets.HTML(
f'<p><big>Column key: {list(obj.col_key)}<big><p>'))
append_struct_frames(obj.col.dtype, col_frames)
entry_frames = []
entry_frames.append(
widgets.HTML(
f'<p><big>Entry fields, with one record per (row, column) pair in the dataset.</big></p>\n'
f'<p>Commonly used methods:</p>\n'
f'<ul>'
f'<li>{html_link("annotate_entries()", "https://hail.is/docs/0.2/hail.MatrixTable.html#hail.MatrixTable.annotate_entries")}: '
f'add new entry fields.</li>'
f'<li>{html_link("filter_entries()", "https://hail.is/docs/0.2/hail.MatrixTable.html#hail.MatrixTable.filter_entries")}: '
f'filter entries in the matrix table, removing them from downstream operations, like aggregations.</li>'
f'<li>{html_link("aggregate_entries", "https://hail.is/docs/0.2/hail.MatrixTable.html#hail.MatrixTable.aggregate_entries")}: '
f'aggregate over entries to produce a single value, e.g. computing mean depth across an entire dataset.</li>'
f'</ul>'))
append_struct_frames(obj.entry.dtype, entry_frames)
tab.children = [
widgets.VBox(frames) for frames in
[globals_frames, row_frames, col_frames, entry_frames]
]
tab.set_title(0, 'globals')
tab.set_title(1, 'row')
tab.set_title(2, 'col')
tab.set_title(3, 'entry')
tab.selected_index = 3
box = widgets.VBox(
[widgets.HBox([glob, cols]),
widgets.HBox([rows, entries])])
buttons = [glob, rows, cols, entries]
selection_handler = widgets.IntText(tab.selected_index)
button_idx = dict(zip(buttons, range(len(buttons))))
def handle_selection(x):
if x['name'] == 'value' and x['type'] == 'change':
buttons[x['old']].style = base_style
selection = x['new']
buttons[selection].style = selected_style
tab.selected_index = selection
selection_handler.observe(handle_selection)
widgets.jslink((tab, 'selected_index'), (selection_handler, 'value'))
def button_action(b):
selection_handler.value = button_idx[b]
for button in button_idx:
button.on_click(button_action)
display(box, tab)
def cost_display(n_days=7):
users = widgets.IntText(value=8, description='Number of total users')
storage_per_user = widgets.IntText(value=10,
description='Storage per user (GB)')
mem_per_user = widgets.IntText(value=2, description="RAM per user (GB)")
machines = widgets.Dropdown(
description='Machine',
options=machines_list['Machine type'].values.tolist())
persistent = widgets.Dropdown(description="Persistent Storage?",
options={
'HDD': 'hdd',
'SSD': 'ssd'
},
value='hdd')
autoscaling = widgets.Checkbox(value=False, description='Autoscaling?')
text_avg_num_machine = widgets.Text(value='',
description='Average # Machines:')
text_cost_machine = widgets.Text(value='', description='Machine Cost:')
text_cost_storage = widgets.Text(value='', description='Storage Cost:')
text_cost_total = widgets.Text(value='', description='Total Cost:')
hr = widgets.HTML(value="---")
# Define axes limits
y_max = 100.
date_stop, date_range = create_date_range(n_days)
# Create axes and extra variables for the viz
xs_hd = DateScale(
min=date_start,
max=date_stop,
)
ys_hd = LinearScale(min=0., max=y_max)
# Shading for weekends
is_weekend = np.where([ii in [6, 7] for ii in date_range.dayofweek], 1, 0)
is_weekend = is_weekend * (float(y_max) + 50.)
is_weekend[is_weekend == 0] = -10
line_fill = Lines(x=date_range,
y=is_weekend,
scales={
'x': xs_hd,
'y': ys_hd
},
colors=['black'],
fill_opacities=[.2],
fill='bottom')
# Set up hand draw widget
line_hd = Lines(x=date_range,
y=10 * np.ones(len(date_range)),
scales={
'x': xs_hd,
'y': ys_hd
},
colors=['#E46E2E'])
line_users = Lines(x=date_range,
y=10 * np.ones(len(date_range)),
scales={
'x': xs_hd,
'y': ys_hd
},
colors=['#e5e5e5'])
line_autoscale = Lines(x=date_range,
y=10 * np.ones(len(date_range)),
scales={
'x': xs_hd,
'y': ys_hd
},
colors=['#000000'])
handdraw = HandDraw(lines=line_hd)
xax = Axis(scale=xs_hd,
label='Day',
grid_lines='none',
tick_format='%b %d')
yax = Axis(scale=ys_hd,
label='Numer of Users',
orientation='vertical',
grid_lines='none')
# FIXME add `line_autoscale` when autoscale is enabled
fig = Figure(marks=[line_fill, line_hd, line_users],
axes=[xax, yax],
interaction=handdraw)
def _update_cost(change):
# Pull values from the plot
max_users = max(handdraw.lines.y)
max_buffer = max_users * 1.05 # 5% buffer
line_users.y = [max_buffer] * len(handdraw.lines.y)
if max_users > users.value:
users.value = max_users
autoscaled_users = autoscale(handdraw.lines.y)
line_autoscale.y = autoscaled_users
# Calculate costs
active_machine = machines_list[machines_list['Machine type'] ==
machines.value]
machine_cost = active_machine['Price (USD / hr)'].values.astype(
float) * 24 # To make it cost per day
users_for_cost = autoscaled_users if autoscaling.value is True else [
max_buffer
] * len(handdraw.lines.y)
num_machines = calculate_machines_needed(users_for_cost,
mem_per_user.value,
active_machine)
avg_num_machines = np.mean(num_machines)
cost_machine = integrate_cost(num_machines, machine_cost)
cost_storage = integrate_cost(
num_machines,
storage_cost[persistent.value] * storage_per_user.value)
cost_total = cost_machine + cost_storage
# Set the values
for iwidget, icost in [(text_cost_machine, cost_machine),
(text_cost_storage, cost_storage),
(text_cost_total, cost_total),
(text_avg_num_machine, avg_num_machines)]:
if iwidget is not text_avg_num_machine:
icost = locale.currency(icost, grouping=True)
else:
icost = '{:.2f}'.format(icost)
iwidget.value = icost
# Set the color
if autoscaling.value is True:
line_autoscale.colors = ['#000000']
line_users.colors = ['#e5e5e5']
else:
line_autoscale.colors = ['#e5e5e5']
line_users.colors = ['#000000']
line_hd.observe(_update_cost, names='y')
# autoscaling.observe(_update_cost) # FIXME Uncomment when we implement autoscaling
persistent.observe(_update_cost)
machines.observe(_update_cost)
storage_per_user.observe(_update_cost)
mem_per_user.observe(_update_cost)
# Show it
fig.title = 'Draw your usage pattern over time.'
# FIXME autoscaling when it's ready
display(users, machines, mem_per_user, storage_per_user, persistent, fig,
hr, text_cost_machine, text_avg_num_machine, text_cost_storage,
text_cost_total)
return fig
def old_initiate(self):
tab_children = []
###########################
# data 1 box
d1_vbox_childs = []
##
###
d1_button_next = widgets.Button(description='next measurement')
d1_button_prev = widgets.Button(description='prev measurement')
d1_button_next.on_click(self.on_d1_botton_next)
d1_button_prev.on_click(self.on_d1_botton_prev)
d1_box_h_1 = widgets.HBox([d1_button_prev, d1_button_next])
###
d1_vbox_childs.append(d1_box_h_1)
##
###
d1_text_path = widgets.Text(placeholder='path name', disabled=False)
self.d1_text_path = d1_text_path
d1_vbox_childs.append(d1_text_path)
##
d1_vbox = widgets.VBox(d1_vbox_childs)
tab_children.append({'element': d1_vbox, 'title': 'iMet'})
############################
# data 2 box
d2_vbox_childs = []
##
###
d2_button_next = widgets.Button(description='next measurement')
d2_button_prev = widgets.Button(description='prev measurement')
self.d2_dropdown_fnames = widgets.Dropdown(
options=[
1
], #[i.name for i in self.controller.data.dataset2.path2data_list],
value=1, #self.controller.data.dataset2.path2active.name,
# description='N',
disabled=False,
)
d2_button_next.on_click(self.on_d2_botton_next)
d2_button_prev.on_click(self.on_d2_botton_prev)
self.d2_dropdown_fnames.observe(self.on_change_d2_dropdown_fnames)
d2_box_h_1 = widgets.HBox(
[d2_button_prev, d2_button_next, self.d2_dropdown_fnames])
###
d2_vbox_childs.append(d2_box_h_1)
##
###
# text field showing the path
d2_text_path = widgets.Text(placeholder='path name', disabled=False)
self.d2_text_path = d2_text_path
d2_vbox_childs.append(d2_text_path)
##
d2_vbox = widgets.VBox(d2_vbox_childs)
tab_children.append({'element': d2_vbox, 'title': 'POPS'})
# others box
# Tab
tab = widgets.Tab([child['element'] for child in tab_children])
for e, child in enumerate(tab_children):
tab.set_title(e, child['title'])
# accordeon
self.accordeon_assigned = widgets.Valid(
value=False,
description='bound?',
)
self.dropdown_popssn = widgets.Dropdown(
options=['00', '14', '18'],
# value='2',
description='popssn',
disabled=False,
)
self.inttext_deltat = widgets.IntText(value=0,
description='deltat',
disabled=False)
self.inttext_deltat.observe(self.on_inttext_deltat)
self.dropdown_gps_bar_bad = widgets.Dropdown(
options=[
'gps', 'baro', 'bad', 'bad_but_usable_gps',
'bad_but_usable_baro'
],
value='gps',
description='which alt to use:',
disabled=False,
)
self.button_bind_measurements = widgets.ToggleButton(
description='bind/unbind measurements')
# button_bind_measurements.on_click(self.deprecated_on_button_bind_measurements)
self.button_bind_measurements.observe(self.on_button_bind_measurements)
accordon_box = widgets.VBox([
self.accordeon_assigned, self.dropdown_popssn, self.inttext_deltat,
self.dropdown_gps_bar_bad, self.button_bind_measurements
])
accordion_children = [accordon_box]
accordion = widgets.Accordion(children=accordion_children)
accordion.set_title(0, 'do_stuff')
# messages
self.messages = widgets.Textarea('\n'.join(self.controller._message),
layout={'width': '100%'})
# message_box = widgets.HBox([self.messages])
# OverVbox
overVbox = widgets.VBox([tab, accordion, self.messages])
display(overVbox)
####################
self.update_d1()
self.update_d2()
self.update_accordeon()
def slider(self, figsize=(10, 10), **kw):
"""
Navigate the simulation using a slider
Parameters :
------------
figsize: tuple
Size of the figures
kw: dict
Extra arguments to pass to matplotlib's imshow
"""
# -----------------------
# Define useful functions
# -----------------------
def refresh_field(force=False):
"Refresh the current field figure"
# Determine whether to do the refresh
do_refresh = False
if (self.avail_fields is not None):
if force == True or fld_refresh_toggle.value == True:
do_refresh = True
# Do the refresh
if do_refresh == True:
plt.figure(fld_figure_button.value, figsize=figsize)
plt.clf()
# When working in inline mode, in an ipython notebook,
# clear the output (prevents the images from stacking
# in the notebook)
if 'inline' in matplotlib.get_backend():
clear_output()
if fld_use_button.value == True:
i_power = fld_magnitude_button.value
vmin = fld_range_button.value[0] * 10**i_power
vmax = fld_range_button.value[1] * 10**i_power
else:
vmin = None
vmax = None
self.get_field(t=self.current_t,
output=False,
plot=True,
field=fieldtype_button.value,
coord=coord_button.value,
m=convert_to_int(mode_button.value),
slicing=slicing_button.value,
theta=theta_button.value,
slicing_dir=slicing_dir_button.value,
vmin=vmin,
vmax=vmax,
cmap=fld_color_button.value)
def refresh_ptcl(force=False):
"Refresh the current particle figure"
# Determine whether to do the refresh
do_refresh = False
if self.avail_species is not None:
if force == True or ptcl_refresh_toggle.value == True:
do_refresh = True
# Do the refresh
if do_refresh == True:
plt.figure(ptcl_figure_button.value, figsize=figsize)
plt.clf()
# When working in inline mode, in an ipython notebook,
# clear the output (prevents the images from stacking
# in the notebook)
if 'inline' in matplotlib.get_backend():
clear_output()
if ptcl_use_button.value == True:
i_power = ptcl_magnitude_button.value
vmin = ptcl_range_button.value[0] * 10**i_power
vmax = ptcl_range_button.value[1] * 10**i_power
else:
vmin = None
vmax = None
if ptcl_yaxis_button.value == 'None':
# 1D histogram
self.get_particle(t=self.current_t,
output=False,
var_list=[ptcl_xaxis_button.value],
select=ptcl_select_widget.to_dict(),
species=ptcl_species_button.value,
plot=True,
vmin=vmin,
vmax=vmax,
cmap=ptcl_color_button.value,
nbins=ptcl_bins_button.value)
else:
# 2D histogram
self.get_particle(t=self.current_t,
output=False,
var_list=[
ptcl_xaxis_button.value,
ptcl_yaxis_button.value
],
select=ptcl_select_widget.to_dict(),
species=ptcl_species_button.value,
plot=True,
vmin=vmin,
vmax=vmax,
cmap=ptcl_color_button.value,
nbins=ptcl_bins_button.value)
def refresh_ptcl_now(b):
"Refresh the particles immediately"
refresh_ptcl(force=True)
def refresh_fld_now(b):
"Refresh the fields immediately"
refresh_field(force=True)
def change_t(name, value):
"Plot the result at the required time"
self.current_t = 1.e-15 * value
refresh_field()
refresh_ptcl()
def step_fw(b):
"Plot the result one iteration further"
if self.current_i < len(self.t) - 1:
self.current_t = self.t[self.current_i + 1]
else:
print("Reached last iteration.")
self.current_t = self.t[self.current_i]
slider.value = self.current_t * 1.e15
def step_bw(b):
"Plot the result one iteration before"
if self.current_t > 0:
self.current_t = self.t[self.current_i - 1]
else:
print("Reached first iteration.")
self.current_t = self.t[self.current_i]
slider.value = self.current_t * 1.e15
# ---------------
# Define widgets
# ---------------
# Slider
slider = widgets.FloatSlider(
min=math.ceil(1.e15 * self.tmin),
max=math.ceil(1.e15 * self.tmax),
step=math.ceil(1.e15 * (self.tmax - self.tmin)) / 20.,
description="t (fs)")
slider.on_trait_change(change_t, 'value')
# Forward button
button_p = widgets.Button(description="+")
button_p.on_click(step_fw)
# Backward button
button_m = widgets.Button(description="-")
button_m.on_click(step_bw)
# Display the time widgets
container = widgets.HBox(children=[button_m, button_p, slider])
display(container)
# Field widgets
# -------------
if (self.avail_fields is not None):
# Field type
# ----------
# Field button
fieldtype_button = widgets.ToggleButtons(
description='Field:', options=sorted(self.avail_fields.keys()))
fieldtype_button.on_trait_change(refresh_field)
# Coord button
if self.geometry == "thetaMode":
coord_button = widgets.ToggleButtons(
description='Coord:', options=['x', 'y', 'z', 'r', 't'])
elif self.geometry in ["2dcartesian", "3dcartesian"]:
coord_button = widgets.ToggleButtons(description='Coord:',
options=['x', 'y', 'z'])
coord_button.on_trait_change(refresh_field)
# Mode and theta button (for thetaMode)
mode_button = widgets.ToggleButtons(description='Mode:',
options=self.avail_circ_modes)
mode_button.on_trait_change(refresh_field)
theta_button = widgets.FloatSlider(width=140,
value=0.,
description=r'Theta:',
min=-math.pi / 2,
max=math.pi / 2)
theta_button.on_trait_change(refresh_field)
# Slicing buttons (for 3D)
slicing_dir_button = widgets.ToggleButtons(
value='y',
description='Slicing direction:',
options=['x', 'y', 'z'])
slicing_dir_button.on_trait_change(refresh_field)
slicing_button = widgets.FloatSlider(width=150,
description='Slicing:',
min=-1.,
max=1.,
value=0.)
slicing_button.on_trait_change(refresh_field)
# Plotting options
# ----------------
# Figure number
fld_figure_button = widgets.IntText(description='Figure ',
value=0,
width=50)
# Range of values
fld_range_button = widgets.FloatRangeSlider(min=-10,
max=10,
width=220)
fld_range_button.on_trait_change(refresh_field)
# Order of magnitude
fld_magnitude_button = widgets.IntText(description='x 10^',
value=9,
width=50)
fld_magnitude_button.on_trait_change(refresh_field)
# Use button
fld_use_button = widgets.Checkbox(description=' Use this range',
value=False)
fld_use_button.on_trait_change(refresh_field)
# Colormap button
fld_color_button = widgets.Select(options=sorted(
plt.cm.datad.keys()),
height=50,
width=200,
value='jet')
fld_color_button.on_trait_change(refresh_field)
# Resfresh buttons
fld_refresh_toggle = widgets.ToggleButton(
description='Always refresh', value=True)
fld_refresh_button = widgets.Button(description='Refresh now!')
fld_refresh_button.on_click(refresh_fld_now)
# Containers
# ----------
# Field type container
if self.geometry == "thetaMode":
container_fields = widgets.VBox(width=260,
children=[
fieldtype_button,
coord_button, mode_button,
theta_button
])
elif self.geometry == "2dcartesian":
container_fields = widgets.VBox(
width=260, children=[fieldtype_button, coord_button])
elif self.geometry == "3dcartesian":
container_fields = widgets.VBox(width=260,
children=[
fieldtype_button,
coord_button,
slicing_dir_button,
slicing_button
])
# Plotting options container
container_fld_plots = widgets.VBox(width=260,
children=[
fld_figure_button,
fld_range_button,
widgets.HBox(children=[
fld_magnitude_button,
fld_use_button
],
height=50),
fld_color_button
])
# Accordion for the field widgets
accord1 = widgets.Accordion(
children=[container_fields, container_fld_plots])
accord1.set_title(0, 'Field type')
accord1.set_title(1, 'Plotting options')
# Complete field container
container_fld = widgets.VBox(
width=300,
children=[
accord1,
widgets.HBox(
children=[fld_refresh_toggle, fld_refresh_button])
])
# Particle widgets
# ----------------
if (self.avail_species is not None):
# Particle quantities
# -------------------
# Species selection
ptcl_species_button = widgets.Dropdown(width=250,
options=self.avail_species)
ptcl_species_button.on_trait_change(refresh_ptcl)
# Remove charge and mass (less interesting)
avail_ptcl_quantities = [ q for q in self.avail_ptcl_quantities \
if (q in ['charge', 'mass'])==False ]
# Particle quantity on the x axis
ptcl_xaxis_button = widgets.ToggleButtons(
value='z', options=avail_ptcl_quantities)
ptcl_xaxis_button.on_trait_change(refresh_ptcl)
# Particle quantity on the y axis
ptcl_yaxis_button = widgets.ToggleButtons(
value='x', options=avail_ptcl_quantities + ['None'])
ptcl_yaxis_button.on_trait_change(refresh_ptcl)
# Particle selection
# ------------------
# 3 selection rules at maximum
ptcl_select_widget = ParticleSelectWidget(3, avail_ptcl_quantities,
refresh_ptcl)
# Plotting options
# ----------------
# Figure number
ptcl_figure_button = widgets.IntText(description='Figure ',
value=1,
width=50)
# Number of bins
ptcl_bins_button = widgets.IntSlider(description='nbins:',
min=50,
max=300,
value=100,
width=150)
ptcl_bins_button.on_trait_change(refresh_ptcl)
# Colormap button
ptcl_color_button = widgets.Select(options=sorted(
plt.cm.datad.keys()),
height=50,
width=200,
value='Blues')
ptcl_color_button.on_trait_change(refresh_ptcl)
# Range of values
ptcl_range_button = widgets.FloatRangeSlider(min=0,
max=10,
width=220,
value=(0, 5))
ptcl_range_button.on_trait_change(refresh_ptcl)
# Order of magnitude
ptcl_magnitude_button = widgets.IntText(description='x 10^',
value=9,
width=50)
ptcl_magnitude_button.on_trait_change(refresh_ptcl)
# Use button
ptcl_use_button = widgets.Checkbox(description=' Use this range',
value=False)
ptcl_use_button.on_trait_change(refresh_ptcl)
# Resfresh buttons
ptcl_refresh_toggle = widgets.ToggleButton(
description='Always refresh', value=True)
ptcl_refresh_button = widgets.Button(description='Refresh now!')
ptcl_refresh_button.on_click(refresh_ptcl_now)
# Containers
# ----------
# Particle quantity container
container_ptcl_quantities = widgets.VBox(width=310,
children=[
ptcl_species_button,
ptcl_xaxis_button,
ptcl_yaxis_button
])
# Particle selection container
container_ptcl_select = ptcl_select_widget.to_container()
# Plotting options container
container_ptcl_plots = widgets.VBox(width=310,
children=[
ptcl_figure_button,
ptcl_bins_button,
ptcl_range_button,
widgets.HBox(children=[
ptcl_magnitude_button,
ptcl_use_button
],
height=50),
ptcl_color_button
])
# Accordion for the field widgets
accord2 = widgets.Accordion(children=[
container_ptcl_quantities, container_ptcl_select,
container_ptcl_plots
])
accord2.set_title(0, 'Particle quantities')
accord2.set_title(1, 'Particle selection')
accord2.set_title(2, 'Plotting options')
# Complete particle container
container_ptcl = widgets.VBox(
width=370,
children=[
accord2,
widgets.HBox(
children=[ptcl_refresh_toggle, ptcl_refresh_button])
])
# Global container
if (self.avail_fields is not None) and \
(self.avail_species is not None):
global_container = widgets.HBox(
children=[container_fld, container_ptcl])
display(global_container)
elif self.avail_species is None:
display(container_fld)
elif self.avail_fields is None:
display(container_ptcl)
def slider(self,
figsize=(6, 5),
exclude_particle_records=['charge', 'mass'],
**kw):
"""
Navigate the simulation using a slider
Parameters:
-----------
figsize: tuple
Size of the figures
exclude_particle_records: list of strings
List of particle quantities that should not be displayed
in the slider (typically because they are less interesting)
kw: dict
Extra arguments to pass to matplotlib's imshow (e.g. cmap, etc.).
This will be applied both to the particle plots and field plots.
Note that `kw` sets the initial plotting options, but the user
can then still modify these options through the slider interface.
"""
# Check that the dependencies have been installed
if not dependencies_installed:
raise RuntimeError(
"Failed to load the openPMD-viewer slider.\n"
"(Make sure that ipywidgets and matplotlib are installed.)")
# -----------------------
# Define useful functions
# -----------------------
def refresh_field(change=None, force=False):
"""
Refresh the current field figure
Parameters :
------------
change: dictionary
Dictionary passed by the widget to a callback functions
whenever a change of a widget happens
(see docstring of ipywidgets.Widget.observe)
This is mainline a place holder ; not used in this function
force: bool
Whether to force the update
"""
# Determine whether to do the refresh
do_refresh = False
if (self.avail_fields is not None):
if force or fld_refresh_toggle.value:
do_refresh = True
# Do the refresh
if do_refresh:
plt.figure(fld_figure_button.value, figsize=figsize)
plt.clf()
# When working in inline mode, in an ipython notebook,
# clear the output (prevents the images from stacking
# in the notebook)
if 'inline' in matplotlib.get_backend():
if ipywidgets_version < 7:
clear_output()
else:
import warnings
warnings.warn(
"\n\nIt seems that you are using ipywidgets 7 and "
"`%matplotlib inline`. \nThis can cause issues when "
"using `slider`.\nIn order to avoid this, you "
"can either:\n- use `%matplotlib notebook`\n- or "
"downgrade to ipywidgets 6 (with `pip` or `conda`).",
UserWarning)
# Handle plotting options
kw_fld = kw.copy()
vmin, vmax = fld_color_button.get_range()
kw_fld['vmin'] = vmin
kw_fld['vmax'] = vmax
kw_fld['cmap'] = fld_color_button.cmap.value
# Determine range of the plot from widgets
plot_range = [
fld_hrange_button.get_range(),
fld_vrange_button.get_range()
]
# Call the method get_field
self.get_field(iteration=self.current_iteration,
output=False,
plot=True,
field=fieldtype_button.value,
coord=coord_button.value,
m=convert_to_int(mode_button.value),
slicing=slicing_button.value,
theta=theta_button.value,
slicing_dir=slicing_dir_button.value,
plot_range=plot_range,
**kw_fld)
def refresh_ptcl(change=None, force=False):
"""
Refresh the current particle figure
Parameters :
------------
change: dictionary
Dictionary passed by the widget to a callback functions
whenever a change of a widget happens
(see docstring of ipywidgets.Widget.observe)
This is mainline a place holder ; not used in this function
force: bool
Whether to force the update
"""
# Determine whether to do the refresh
do_refresh = False
if self.avail_species is not None:
if force or ptcl_refresh_toggle.value:
do_refresh = True
# Do the refresh
if do_refresh:
plt.figure(ptcl_figure_button.value, figsize=figsize)
plt.clf()
# When working in inline mode, in an ipython notebook,
# clear the output (prevents the images from stacking
# in the notebook)
if 'inline' in matplotlib.get_backend():
clear_output()
# Handle plotting options
kw_ptcl = kw.copy()
vmin, vmax = ptcl_color_button.get_range()
kw_ptcl['vmin'] = vmin
kw_ptcl['vmax'] = vmax
kw_ptcl['cmap'] = ptcl_color_button.cmap.value
# Determine range of the plot from widgets
plot_range = [
ptcl_hrange_button.get_range(),
ptcl_vrange_button.get_range()
]
if ptcl_yaxis_button.value == 'None':
# 1D histogram
self.get_particle(
iteration=self.current_iteration,
output=False,
var_list=[ptcl_xaxis_button.value],
select=ptcl_select_widget.to_dict(),
species=ptcl_species_button.value,
plot=True,
nbins=ptcl_bins_button.value,
plot_range=plot_range,
use_field_mesh=ptcl_use_field_button.value,
**kw_ptcl)
else:
# 2D histogram
self.get_particle(
iteration=self.current_iteration,
output=False,
var_list=[
ptcl_xaxis_button.value, ptcl_yaxis_button.value
],
select=ptcl_select_widget.to_dict(),
species=ptcl_species_button.value,
plot=True,
nbins=ptcl_bins_button.value,
plot_range=plot_range,
use_field_mesh=ptcl_use_field_button.value,
**kw_ptcl)
def refresh_field_type(change):
"""
Refresh the field type and disable the coordinates buttons
if the field is scalar.
Parameter
---------
change: dictionary
Dictionary passed by the widget to a callback functions
whenever a change of a widget happens
(see docstring of ipywidgets.Widget.observe)
"""
if self.avail_fields[change['new']] == 'scalar':
coord_button.disabled = True
elif self.avail_fields[change['new']] == 'vector':
coord_button.disabled = False
refresh_field()
def refresh_species(change=None):
"""
Refresh the particle species buttons by populating them
with the available records for the current species
Parameter
---------
change: dictionary
Dictionary passed by the widget to a callback functions
whenever a change of a widget happens
(see docstring of ipywidgets.Widget.observe)
"""
# Deactivate the particle refreshing to avoid callback
# while modifying the widgets
saved_refresh_value = ptcl_refresh_toggle.value
ptcl_refresh_toggle.value = False
# Get available records for this species
avail_records = [
q for q in self.avail_record_components[
ptcl_species_button.value]
if q not in exclude_particle_records
]
# Update the plotting buttons
ptcl_xaxis_button.options = avail_records
ptcl_yaxis_button.options = avail_records + ['None']
if ptcl_xaxis_button.value not in ptcl_xaxis_button.options:
ptcl_xaxis_button.value = avail_records[0]
if ptcl_yaxis_button.value not in ptcl_yaxis_button.options:
ptcl_yaxis_button.value = 'None'
# Update the selection widgets
for dropdown_button in ptcl_select_widget.quantity:
dropdown_button.options = avail_records
# Put back the previous value of the refreshing button
ptcl_refresh_toggle.value = saved_refresh_value
def change_iteration(change):
"Plot the result at the required iteration"
# Find the closest iteration
self._current_i = abs(self.iterations - change['new']).argmin()
self.current_iteration = self.iterations[self._current_i]
refresh_field()
refresh_ptcl()
def step_fw(b):
"Plot the result one iteration further"
if self._current_i < len(self.t) - 1:
self.current_iteration = self.iterations[self._current_i + 1]
else:
self.current_iteration = self.iterations[self._current_i]
slider.value = self.current_iteration
def step_bw(b):
"Plot the result one iteration before"
if self._current_i > 0:
self.current_iteration = self.iterations[self._current_i - 1]
else:
self.current_iteration = self.iterations[self._current_i]
slider.value = self.current_iteration
# ---------------
# Define widgets
# ---------------
# Slider
iteration_min = self.iterations.min()
iteration_max = self.iterations.max()
step = max(int((iteration_max - iteration_min) / 20.), 1)
slider = widgets.IntSlider(description="iteration",
min=iteration_min,
max=iteration_max + step,
step=step)
slider.observe(change_iteration, names='value', type='change')
set_widget_dimensions(slider, width=500)
# Forward button
button_p = widgets.Button(description="+")
set_widget_dimensions(button_p, width=40)
button_p.on_click(step_fw)
# Backward button
button_m = widgets.Button(description="-")
set_widget_dimensions(button_m, width=40)
button_m.on_click(step_bw)
# Display the time widgets
container = widgets.HBox(children=[button_m, button_p, slider])
display(container)
# Field widgets
# -------------
if (self.avail_fields is not None):
# Field type
# ----------
# Field button
fieldtype_button = create_toggle_buttons(
description='Field:', options=sorted(self.avail_fields.keys()))
fieldtype_button.observe(refresh_field_type, 'value', 'change')
# Coord button
if self.geometry == "thetaMode":
coord_button = create_toggle_buttons(
description='Coord:', options=['x', 'y', 'z', 'r', 't'])
elif self.geometry in \
["1dcartesian", "2dcartesian", "3dcartesian"]:
coord_button = create_toggle_buttons(description='Coord:',
options=['x', 'y', 'z'])
coord_button.observe(refresh_field, 'value', 'change')
# Mode and theta button (for thetaMode)
mode_button = create_toggle_buttons(description='Mode:',
options=self.avail_circ_modes)
mode_button.observe(refresh_field, 'value', 'change')
theta_button = widgets.FloatSlider(value=0.,
min=-math.pi / 2,
max=math.pi / 2)
set_widget_dimensions(theta_button, width=190)
theta_button.observe(refresh_field, 'value', 'change')
# Slicing buttons (for 3D)
slicing_dir_button = create_toggle_buttons(
value=self.axis_labels[0],
options=self.axis_labels,
description='Slice normal:')
slicing_dir_button.observe(refresh_field, 'value', 'change')
slicing_button = widgets.FloatSlider(min=-1., max=1., value=0.)
set_widget_dimensions(slicing_button, width=180)
slicing_button.observe(refresh_field, 'value', 'change')
# Plotting options
# ----------------
# Figure number
fld_figure_button = widgets.IntText(value=0)
set_widget_dimensions(fld_figure_button, width=50)
# Colormap button
fld_color_button = ColorBarSelector(
refresh_field,
default_cmap=kw.get('cmap', 'viridis'),
default_vmin=kw.get('vmin', -5.e9),
default_vmax=kw.get('vmax', 5.e9))
# Range buttons
fld_hrange_button = RangeSelector(refresh_field,
default_value=10.,
title='Horizontal axis:')
fld_vrange_button = RangeSelector(refresh_field,
default_value=10.,
title='Vertical axis:')
# Refresh buttons
fld_refresh_toggle = widgets.ToggleButton(
description='Always refresh', value=True)
fld_refresh_button = widgets.Button(description='Refresh now!')
fld_refresh_button.on_click(partial(refresh_field, force=True))
# Containers
# ----------
# Field type container
if self.geometry == "thetaMode":
container_fields = widgets.VBox(children=[
fieldtype_button, coord_button, mode_button,
add_description('Theta:', theta_button)
])
elif self.geometry in ["1dcartesian", "2dcartesian"]:
container_fields = widgets.VBox(
children=[fieldtype_button, coord_button])
elif self.geometry == "3dcartesian":
container_fields = widgets.VBox(children=[
fieldtype_button, coord_button, slicing_dir_button,
add_description("Slicing:", slicing_button)
])
set_widget_dimensions(container_fields, width=330)
# Plotting options container
container_fld_cbar = fld_color_button.to_container()
container_fld_hrange = fld_hrange_button.to_container()
container_fld_vrange = fld_vrange_button.to_container()
if self.geometry == "1dcartesian":
container_fld_plots = widgets.VBox(children=[
add_description("<b>Figure:</b>", fld_figure_button),
container_fld_vrange, container_fld_hrange
])
else:
container_fld_plots = widgets.VBox(children=[
add_description("<b>Figure:</b>",
fld_figure_button), container_fld_cbar,
container_fld_vrange, container_fld_hrange
])
set_widget_dimensions(container_fld_plots, width=330)
# Accordion for the field widgets
accord1 = widgets.Accordion(
children=[container_fields, container_fld_plots])
accord1.set_title(0, 'Field type')
accord1.set_title(1, 'Plotting options')
# Complete field container
container_fld = widgets.VBox(children=[
accord1,
widgets.HBox(children=[fld_refresh_toggle, fld_refresh_button])
])
set_widget_dimensions(container_fld, width=370)
# Particle widgets
# ----------------
if (self.avail_species is not None):
# Particle quantities
# -------------------
# Species selection
ptcl_species_button = widgets.Dropdown(options=self.avail_species)
set_widget_dimensions(ptcl_species_button, width=250)
ptcl_species_button.observe(refresh_species, 'value', 'change')
# Get available records for this species
avail_records = [
q for q in self.avail_record_components[
ptcl_species_button.value]
if q not in exclude_particle_records
]
# Particle quantity on the x axis
ptcl_xaxis_button = create_toggle_buttons(options=avail_records)
ptcl_xaxis_button.observe(refresh_ptcl, 'value', 'change')
# Particle quantity on the y axis
ptcl_yaxis_button = create_toggle_buttons(options=avail_records +
['None'],
value='None')
ptcl_yaxis_button.observe(refresh_ptcl, 'value', 'change')
# Particle selection
# ------------------
# 3 selection rules at maximum
ptcl_select_widget = ParticleSelectWidget(3, avail_records,
refresh_ptcl)
# Plotting options
# ----------------
# Figure number
ptcl_figure_button = widgets.IntText(value=1)
set_widget_dimensions(ptcl_figure_button, width=50)
# Number of bins
ptcl_bins_button = widgets.IntText(value=100)
set_widget_dimensions(ptcl_bins_button, width=60)
ptcl_bins_button.observe(refresh_ptcl, 'value', 'change')
# Colormap button
ptcl_color_button = ColorBarSelector(
refresh_ptcl,
default_cmap=kw.get('cmap', 'Blues'),
default_vmin=kw.get('vmin', -5.e9),
default_vmax=kw.get('vmax', 5.e9))
# Range buttons
ptcl_hrange_button = RangeSelector(refresh_ptcl,
default_value=10.,
title='Horizontal axis:')
ptcl_vrange_button = RangeSelector(refresh_ptcl,
default_value=10.,
title='Vertical axis:')
# Use field mesh buttons
ptcl_use_field_button = widgets.ToggleButton(
description=' Use field mesh', value=True)
ptcl_use_field_button.observe(refresh_ptcl, 'value', 'change')
# Resfresh buttons
ptcl_refresh_toggle = widgets.ToggleButton(
description='Always refresh', value=True)
ptcl_refresh_button = widgets.Button(description='Refresh now!')
ptcl_refresh_button.on_click(partial(refresh_ptcl, force=True))
# Containers
# ----------
# Particle quantity container
container_ptcl_quantities = widgets.VBox(children=[
ptcl_species_button, ptcl_xaxis_button, ptcl_yaxis_button
])
set_widget_dimensions(container_ptcl_quantities, width=310)
# Particle selection container
container_ptcl_select = ptcl_select_widget.to_container()
# Plotting options container
container_ptcl_fig = widgets.HBox(children=[
add_description("<b>Figure:</b>", ptcl_figure_button),
add_description("Bins:", ptcl_bins_button)
])
container_ptcl_cbar = ptcl_color_button.to_container()
container_ptcl_hrange = ptcl_hrange_button.to_container()
container_ptcl_vrange = ptcl_vrange_button.to_container()
container_ptcl_plots = widgets.VBox(children=[
container_ptcl_fig, container_ptcl_cbar, container_ptcl_vrange,
container_ptcl_hrange, ptcl_use_field_button
])
set_widget_dimensions(container_ptcl_plots, width=310)
# Accordion for the field widgets
accord2 = widgets.Accordion(children=[
container_ptcl_quantities, container_ptcl_select,
container_ptcl_plots
])
accord2.set_title(0, 'Particle quantities')
accord2.set_title(1, 'Particle selection')
accord2.set_title(2, 'Plotting options')
# Complete particle container
container_ptcl = widgets.VBox(children=[
accord2,
widgets.HBox(
children=[ptcl_refresh_toggle, ptcl_refresh_button])
])
set_widget_dimensions(container_ptcl, width=370)
# Global container
if (self.avail_fields is not None) and \
(self.avail_species is not None):
global_container = widgets.HBox(
children=[container_fld, container_ptcl])
display(global_container)
elif self.avail_species is None:
display(container_fld)
elif self.avail_fields is None:
display(container_ptcl)
def __init__(self, nmrproblem=None):
super().__init__()
if not isinstance(nmrproblem, nmrProblem.NMRproblem):
self.nmrproblem = nmrproblem
self.df = pd.DataFrame()
else:
self.nmrproblem = nmrproblem
self.df = nmrproblem.df
# create debug label widget for output
self.debugLabel = widgets.Label(value="",
layout=widgets.Layout(width="400px"))
# create save problem widgets
self.saveProblemButtonW = widgets.Button(description="Save Problem")
# widgets to obtain problem working directory
self.prDirW = widgets.Text(value='',
placeholder='problem directory',
description='problem directory',
disabled=False)
self.prDirB = widgets.Button(description='Set Directory')
self.upload_problemdir = ipywidgets.widgets.FileUpload(
multiple=True,
description="Open Existing Problem ",
description_tooltip="choose all files in problem directory",
layout=widgets.Layout(width='300px'))
self.problemNameL = widgets.Label(value=" Problem Name",
layout=widgets.Layout(width='100px'))
self.spacerL = widgets.Label(value=" ",
layout=widgets.Layout(width='50px'))
self.problemNameW = widgets.Text(value="Problem Name",
description="",
layout=widgets.Layout(width='150px'))
self.newproblemB = widgets.Button(description="Start New Problem")
self.prDirLayout = widgets.HBox([
self.upload_problemdir, self.spacerL, self.problemNameL,
self.problemNameW, self.spacerL, self.newproblemB
])
# widgets to obtain info on the molecule
# number and tye of atoms in molecule
# number of proton resonances in molecule
# number of carbon resonance in molecule
self.moleculeAtomsW = widgets.Text(value='',
placeholder='atoms in molecule',
description='atoms',
disabled=False)
self.pGrpsW = widgets.IntText(value=1,
placeholder='H1 groups in spectrum',
description='H1 groups',
disabled=False)
self.cGrpsW = widgets.IntText(value=1,
description='C13 groups',
disabled=False)
self.moleculesSubmitB = widgets.Button(description="Update Molecule")
self.moleculeLayout = widgets.VBox([
self.moleculeAtomsW, self.pGrpsW, self.cGrpsW,
self.moleculesSubmitB
])
# widgets to set 1D spectral parameters for proton and carbon
self.pLabelW = widgets.Label("$^{1}H$")
self.pSpecWidthW = widgets.FloatText(value=12.0,
tooltip='proton spectral width',
description='sw (ppm)',
disabled=False)
self.pObsFreqW = widgets.FloatText(value=400.0,
description='obs (MHz)',
disabled=False)
self.pTofW = widgets.FloatText(value=5.0,
description='tof (ppm)',
diabled=False)
self.pSizeW = widgets.IntText(value=32768,
description='size (pts)',
disabled=False)
self.pLineBroadeningW = widgets.FloatText(value=0.5,
description='lb (Hz)',
disabled=False)
self.cLabelW = widgets.Label("$^{13}C$")
self.cSpecWidthW = widgets.FloatText(value=210.0,
description='sw (ppm)',
disabled=False)
self.cObsFreqW = widgets.FloatText(value=100.0,
description='obs (MHz)',
disabled=False)
self.cTofW = widgets.FloatText(value=5.0,
description='tof (ppm)',
diabled=False)
self.cSizeW = widgets.IntText(value=32768,
description='size (pts)',
disabled=False)
self.cLineBroadeningW = widgets.FloatText(value=0.5,
description='lb (Hz)',
disabled=False)
self.specSubmitB = widgets.Button(description="Update Spectra")
self.specLayout = widgets.HBox([
widgets.VBox([
self.pLabelW, self.pObsFreqW, self.pSpecWidthW, self.pTofW,
self.pSizeW, self.pLineBroadeningW, self.specSubmitB
]),
widgets.VBox([
self.cLabelW, self.cObsFreqW, self.cSpecWidthW, self.cTofW,
self.cSizeW, self.cLineBroadeningW
])
])
self.old = 'All'
self.new = 'ALL'
self.toggleDF = widgets.ToggleButtons(
options=['All', 'integrals-ppm', 'COSY', 'HSQC-HMBC'],
description='Display:',
disabled=False,
button_style='',
tooltips=[
'Show full Dataframe', 'Show COSY Input',
'Show HSQC/HMBC Input'
])
self.sheet1 = ipysheet.from_dataframe(self.df)
self.toggleDF.observe(self.toggleValue)
self.dfWarningTextW = widgets.Label("Table Messages: OK")
self.dfUpdateTableB = widgets.Button(description="update table")
self.dfRunAnalysisB = widgets.Button(description="update and run")
self.dfButtonsLayout = widgets.HBox(
[self.dfUpdateTableB, self.dfRunAnalysisB])
self.dfLayout = widgets.VBox([
self.toggleDF, self.dfWarningTextW, self.sheet1,
self.dfButtonsLayout
])
self.accordion = widgets.Accordion(children=[
self.prDirLayout, self.moleculeLayout, self.specLayout,
self.dfLayout
])
self.accordion.set_title(0, "Problem Directory")
self.accordion.set_title(1, "Molecule")
self.accordion.set_title(2, "Spectroscopy")
self.accordion.set_title(3, "DataSet")
self.page1 = widgets.VBox(
[self.accordion, self.saveProblemButtonW, self.debugLabel])
self.H1C131DplotsLayout = widgets.VBox(
[widgets.Output(), self.saveProblemButtonW])
self.ymlTitle = widgets.HTML("yml description of problem")
self.ymlText = widgets.Textarea(
layout=widgets.Layout(width="400px", height="500px"))
self.problemYML = widgets.VBox([self.ymlTitle, self.ymlText])
self.children = [self.page1, self.H1C131DplotsLayout, self.problemYML]
self.set_title(0, 'Problem Setup')
self.set_title(1, 'Problem Plots')
self.set_title(2, 'Problem YML')
self.upload_problemdir.observe(
lambda change: self.on_upload_problemdir(change), names='value')
self.moleculesSubmitB.on_click(self.onButtonClicked)
self.specSubmitB.on_click(self.onButtonClicked)
self.dfUpdateTableB.on_click(self.onButtonClicked)
self.dfRunAnalysisB.on_click(self.onButtonClicked)
self.saveProblemButtonW.on_click(self.onButtonClicked)
self.newproblemB.on_click(self.onButtonClicked)
def __init__(
self,
input_data: Units,
trials: pynwb.epoch.TimeIntervals = None,
unit_index=0,
unit_controller=None,
ntt=1000,
):
self.units = input_data
super().__init__()
if trials is None:
self.trials = self.get_trials()
if self.trials is None:
self.children = [widgets.HTML("No trials present")]
return
else:
self.trials = trials
if unit_controller is None:
self.unit_ids = self.units.id.data[:]
n_units = len(self.unit_ids)
self.unit_controller = widgets.Dropdown(
options=[(str(self.unit_ids[x]), x) for x in range(n_units)],
value=unit_index,
description="unit",
layout=Layout(width="200px"),
)
self.trial_event_controller = make_trial_event_controller(
self.trials, layout=Layout(width="200px")
)
self.start_ft = widgets.FloatText(
-0.5, step=0.1, description="start (s)", layout=Layout(width="200px"),
description_tooltip = 'Start time for calculation before or after (negative or positive) the reference point (aligned to)'
)
self.end_ft = widgets.FloatText(
1.0, step=0.1, description="end (s)", layout=Layout(width="200px"),
description_tooltip = 'End time for calculation before or after (negative or positive) the reference point (aligned to).'
)
self.psth_type_radio = widgets.RadioButtons(
options=["histogram", "gaussian"], layout=Layout(width="100px")
)
self.bins_ft = widgets.IntText(
30, min=0, description="# bins", layout=Layout(width="150px")
)
self.gaussian_sd_ft = widgets.FloatText(
0.05,
min=0.001,
description="sd (s)",
layout=Layout(width="150px"),
active=False,
step=0.01,
)
self.gas = self.make_group_and_sort(window=False, control_order=False)
self.controls = dict(
ntt=fixed(ntt),
index=self.unit_controller,
end=self.end_ft,
start=self.start_ft,
start_label=self.trial_event_controller,
gas=self.gas,
plot_type=self.psth_type_radio,
sigma_in_secs=self.gaussian_sd_ft,
nbins=self.bins_ft
# progress_bar=fixed(progress_bar)
)
out_fig = interactive_output(self.update, self.controls)
self.children = [
widgets.HBox(
[
widgets.VBox(
[
self.gas,
widgets.HBox(
[
self.psth_type_radio,
widgets.VBox([self.gaussian_sd_ft, self.bins_ft]),
]
),
]
),
widgets.VBox(
[
self.unit_controller,
self.trial_event_controller,
self.start_ft,
self.end_ft,
]
),
]
),
out_fig,
]