def displayMetricEvolution(
data,
metric,
outputDir='../results/dae/neuralNetwork/resultsAnalysis/',
configuration='concatParams'):
reset_output()
p = figure(tools=TOOLS, plot_width=350, plot_height=350)
p.yaxis.axis_label = metric
p.xaxis.axis_label = 'models'
p.xaxis.axis_label_text_font_size = "12pt"
p.yaxis.axis_label_text_font_size = "12pt"
source = ColumnDataSource({
metric: data[metric],
'index': data.index.values,
'conf': data[configuration]
})
p.line('index', metric, source=source)
p.select_one(HoverTool).tooltips = [('conf', '@conf')]
output_notebook()
show(p)
output_file(outputDir + metric + 'Evolution.html')
save(p)
return True
def plot_empty(geo='state', formatting=None, output=False):
"""Generate map outline (no fill).
:param (str) geo: 'state' or 'county'
:param (dict) formatting: if custom dict is passed, update DEFAULTFORMAT with those key-values
:param (str) output: if specified, filepath to save html file. see save_plot().
:return: if output is 'bokeh', returns Bokeh object; else None """
## get default plot formatting and update if necessary
temp_format = DEFAULTFORMAT.copy()
if formatting:
temp_format.update(formatting)
## process data
shape_df = prc.shape_geojson(geo,
temp_format['simplify'],
epsg=temp_format['epsg'])
geo_src = models.GeoJSONDataSource(geojson=shape_df.to_json())
## plot and save choropleth
bkplot = initialize_plot(temp_format)
bkplot.patches('xs',
'ys',
fill_color=None,
line_color=temp_format['line_color'],
line_width=temp_format['line_width'],
source=geo_src)
if temp_format['svg']:
bkplot.output_backend = 'svg'
save_plot(bkplot, output)
## return to original state
io.reset_output()
return bkplot
def show_html_image(field_2d, output_file_name='test.html'):
"""
Plot a 2D field as image using Bokeh, output to html file only.
"""
# Needs resetting, otherwise it appends new result to old one
reset_output()
# Define ranges
xR, yR = field_2d.shape
x = np.linspace(0, xR - 1, xR)
y = np.linspace(0, yR - 1, yR)
# Generate figure canvas with tooltips
p = figure(x_range=(0, 1), y_range=(0, 1), \
tooltips=[("x", "$x"), ("y", "$y"), ("value", "@image")], \
match_aspect=True)
# Generate image
p.image(image=[field_2d], x=0, y=0, dw=1, dh=1, \
palette="Spectral11")
# Output to html file
output_file(output_file_name, title="visualization")
# Display in browser
show(p)
return None
def bok_sp(plot_dict, **kwargs):
if kwargs: figsize = kwargs['figsize']
else: figsize = (800, 400)
plot_list = []
plot_width, plot_height = figsize
i = 0
for unit, values in plot_dict.items():
p = figure(plot_width=plot_width, plot_height=plot_height)
p.xaxis.formatter = DatetimeTickFormatter()
glyph_list = []
column_list = []
for data in values:
column_name, x, y = data
g = p.line(x=x, y=y, line_width=2, color=colors[i])
i += 1
column_list.append(column_name)
glyph_list.append(g)
items = [(column, [glyph])
for column, glyph in zip(column_list, glyph_list)]
legend = Legend(items=items, location=(40, 0))
p.add_layout(legend, 'below')
plot_list.append(p)
grid = [[p] for p in plot_list]
p = gridplot(grid)
reset_output()
return p
def imshow(im, im2=None, p1=None, p2=None):
# Bokeh Plotting
io.reset_output()
io.output_file('bokeh plots.html', title='imshow')
colorImage = (len(im.shape) == 3)
if colorImage:
h, w, _ = im.shape
else:
h, w = im.shape
# Setup tools
hoverImage = models.HoverTool(tooltips=[('index', '$index'), ('(x, y)', '($x{(1.11)}, $y{(1.11)})')],
point_policy='follow_mouse')
p = plotting.figure(x_range=(0, w), y_range=(h, 0), plot_width=round(800 * w / h), plot_height=800,
x_axis_label='pixel (1 - ' + str(w) + ')', y_axis_label='pixel (1 - ' + str(h) + ')',
title='image', tools='box_zoom,pan,save,reset,wheel_zoom,crosshair',
active_scroll='wheel_zoom', active_inspect=None)
# Plot image
if colorImage: # RGB
imc = np.ones((im.shape[0], im.shape[1], 4), dtype=np.uint32) * 255
imc[:, :, 0:3] = im
img = np.empty((h, w), dtype=np.uint32)
view = img.view(dtype=np.uint8).reshape((h, w, 4))
view[:, :, :] = np.flipud(np.asarray(imc))
p.image_rgba(image=[img], x=0, y=h, dw=w, dh=h)
else:
p.image(image=[np.flip(im, 0)], x=0, y=h, dw=w, dh=h, palette=palettes.Greys256)
p.quad(top=[h], bottom=[0], left=[0], right=[w], alpha=0) # clear rectange hack for tooltip image x,y
p.add_tools(hoverImage)
# Show plot
colors = bokeh_colors(3)
if im2 is None:
if p1 is not None:
p.circle(p1[:, 0], p1[:, 1], color=colors[0], line_width=2)
if p2 is not None:
p.circle(p2[:, 0], p2[:, 1], color=colors[1], line_width=2)
p.multi_line(np.concatenate((p1[:, 0, None], p2[:, 0, None]), 1).tolist(),
np.concatenate((p1[:, 1, None], p2[:, 1, None]), 1).tolist(),
color='white', alpha=.3, line_width=1)
io.show(p) # open a browser
else:
h, w = im2.shape
q = plotting.figure(x_range=(0, w), y_range=(h, 0), plot_width=round(600 * w / h), plot_height=600,
x_axis_label='pixel (1 - ' + str(w) + ')', y_axis_label='pixel (1 - ' + str(h) + ')',
title='image', tools='box_zoom,pan,save,reset,wheel_zoom,crosshair',
active_scroll='wheel_zoom', active_inspect=None)
q.add_tools(hoverImage)
# Plot image
q.image(image=[np.flip(im2, 0)], x=0, y=h, dw=w, dh=h, palette=palettes.Greys256)
q.quad(top=[h], bottom=[0], left=[0], right=[w], alpha=0) # clear rectange hack for tooltip image x,y
# Show plots
io.show(column(p, q)) # open a browser
def clear_bokeh_memory():
"""Run garbage collection after bokeh plots in
an attempt to reduce memory usage
"""
curdoc().clear()
state.State().reset()
reset_output()
gc.collect()
def plot(file_or_df,
geoid_var,
geoid_type,
y_var,
y_type,
geolvl='county',
geolabel='name',
formatting=None,
output=False,
dropna=True):
"""Short summary.
:param (str/pd.DataFrame) file_or_df: csv filepath or pandas/geopandas DataFrame with geoid_var
:param (str) geoid_var: name of column containing the geo ID to match on
:param (str) geoid_type: 'fips' (recommended), 'cbsa', 'name', or 'abbrev' (state only)
:param (str) y_var: column name of variable to plot
:param (str) y_type: 'sequential', 'sequential_single' (hue), 'divergent', or 'categorical'
:param (str) geolvl: 'county' or 'state'
:param (str) geolabel: column name to use. default is county/state name from shapefile
:param (dict) formatting: if custom dict is passed, update DEFAULTFORMAT with those key-values
:param (str) output: if specified, filepath to save html file. see save_plot().
:param (bool) dropna: default True, if false, keeps rows where y_var is nan.
:return: if output is 'bokeh', returns Bokeh object; else None """
## get default plot formatting and update if necessary
temp_format = DEFAULTFORMAT.copy()
if formatting:
temp_format.update(formatting)
## process data
shape_df = prc.shape_geojson(geolvl,
temp_format['simplify'],
epsg=temp_format['epsg'])
geo_df = prc.merge_to_geodf(shape_df,
file_or_df,
geoid_var,
geoid_type,
geolvl=geolvl)
if dropna:
geo_df = geo_df[geo_df[y_var].notnull()]
## make sure column name does not have spaces -- important for hover tooltip
geo_df.rename(columns={y_var: y_var.replace(' ', '_')}, inplace=True)
y_var = y_var.replace(' ', '_')
## plot and save choropleth
bkplot = initialize_plot(temp_format)
draw_choropleth_layers(bkplot, geo_df, y_var, y_type, geolabel,
temp_format)
if temp_format['svg']:
bkplot.output_backend = 'svg'
save_plot(bkplot, output)
## return to original state
io.reset_output()
return bkplot
def xyComparison(xdata,
ydata,
xlabel='Smoothness',
ylabel='Loss',
what='lossSmoothness',
outputDir='../results/dae/neuralNetwork/resultsAnalysis/'):
N = len(xdata.values)
counts = np.zeros((N, N))
for value in xdata.values:
i = ydata.values.tolist().index(value) # i for line
j = xdata.values.tolist().index(value) # j for column
counts[i, j] = 1
xname = []
yname = []
color = []
alpha = []
for i, valY in enumerate(ydata):
for j, valX in enumerate(xdata):
xname.append(valX)
yname.append(valY)
if counts[i, j] == 1: color.append('red')
else: color.append('white')
alpha.append(1)
source = ColumnDataSource(data=dict(xname=xname,
yname=yname,
colors=color,
alphas=alpha,
count=counts.flatten()))
p = figure(x_axis_location="above",
x_range=list(xdata),
y_range=list(reversed(ydata.tolist())),
tools=TOOLS)
p.grid.grid_line_color = None
p.axis.axis_line_color = None
p.axis.visible = None
p.rect('xname',
'yname',
0.9,
0.9,
source=source,
color='colors',
line_color=None)
p.select_one(HoverTool).tooltips = [('conf', '@xname')]
reset_output()
output_notebook()
show(p)
output_file(outputDir + what + 'MatrixComparison.html')
save(p)
return True
def update_notebook():
print('Repo: \'{}\': {}\nTotal commits: {}\n{} commits: {}'.format(
cloned_repo.remotes.origin.name, cloned_repo.remotes.origin.url,
len(list(cloned_repo.iter_commits('master'))), html_path,
len(list(cloned_repo.iter_commits('master', paths=html_path)))))
display(df_totals)
display(df_2016_totals)
display(mfig)
reset_output()
output_notebook()
p = vote2020_bokeh(df_totals, df_2016_totals)
show(p)
def setOutput(interactive, outputFileAddress):
reset_output()
if interactive:
print('outputting interactive to notebook.')
output_notebook()
else:
if outputFileAddress is None:
# bokio.output_file('TempBokeh.png')
print('outputting static to notebook.')
else:
output_file(outputFileAddress)
print('outputting to file.')
def intfileplot():
filesA = os.listdir(inputpath)
filesB = []
for y in filesA:
if y[-8:] == "hits.csv" and y[-10:] != "nohits.csv" and y[
-11:] != "isohits.csv":
filesB.append(y)
for y in filesB:
data, hetclassintdf = FTPM.mycsvreader(inputpath + y)
isodata = FTPM.isocsvreader(inputpath + y[:-8] + "isohits.csv")
nodata = FTPM.nohitsreader(inputpath + y[:-8] + "nohits.csv")
intplotter(data, isodata, nodata, y, hetclassintdf)
reset_output() #cleans up the cache which reduces file size
def hist(data, attribute, group, name='figure'):
output = join(os.getcwd(), 'figures', name)
output_file(output + '.html')
x = np.linspace(0, data[attribute].max(), data[attribute].max())
pdf = gaussian_kde(data[attribute])
plot = figure(title=name, x_axis_label=attribute)
hist, edges = np.histogram(data[attribute], density=True, bins=12)
plot.quad(top=hist, bottom=0, left=edges[:-1], right=edges[1:], alpha=0.4)
plot.line(x, pdf(x))
save(plot)
reset_output()
def intfileplot():
filesA = os.listdir(inputdata)
for y in filesA:
if y[-4:] == "xlsx":
df = pd.read_excel(inputdata + y)
df = df.rename(columns={
y[:-5]: 'RA',
'Error_ppm': 'Error',
'Mass': 'mz'
})
df['VKsize'] = np.sqrt((df["RA"] * 1E-5) / np.pi)
nodata = df[df['Class'] == "None"]
data = df[(df['C13'] == 0) & (df['Class'] != "None")]
isodata = df[(df['C13'] == 1) & (df['Class'] != "None")]
intplotter(data, isodata, nodata, y) #,hetclassintdf)
reset_output() #cleans up the cache which reduces file size
"""
def bokeh_plot(site, obs, obs_label, data_dict, outfile, title, resample_frequency, add_statistics=True):
'''
Plots a bokeh (interactive) daily or weekly series.
Inputs:
site: a string ID which is input to the obs and data_dict objects
obs: a pandas dataframe with columns labeled with the site IDs
data_dict: an ordered dictionary with keys each of the series you want to plot with structure:
{'series_name': {'data': pandas_dataframe, 'color': 'the color you want the timeseries to plot as'}}
outfile: path where you want to save the bokeh plot
title: title string for your plot
resample_frequency: either 'w' for weekly or 'd' for daily (this is used to decide the frequency of the plotting)
add_statistics: if True (default) will include the statistics of KGE and bias in the plot's legend
'''
reset_output()
resample_dict = {'W': 'Weekly',
'D': 'Daily'}
output_file(outfile, title=title)
p1 = figure(width=1000, height=400, x_axis_type = "datetime", title=title)
obs_resampled =obs.resample(resample_frequency, how='mean')
p1.line(obs_resampled.index.values,obs_resampled.values/100000, color='#000000', legend=obs_label, line_width=2)
for scenario in data_dict.keys():
sim = data_dict[scenario]['data'][site]
daily_kge = str(np.round(kge(sim, obs, 'D'), 2))
weekly_kge = str(np.round(kge(sim, obs, 'W'), 2))
scenario_bias = str(np.round(bias(sim, obs),2))
if add_statistics:
legend_label = scenario+', Daily KGE='+daily_kge+',\nWeekly KGE='+weekly_kge+' Bias='+scenario_bias+'%'
else:
legend_label = scenario
sim_resampled = data_dict[scenario]['data'][site].resample(resample_frequency, how='mean')
p1.line(sim_resampled.index.values, sim_resampled.values/100000,
color=data_dict[scenario]['color'], line_width=2,
legend=legend_label)
p1.grid.grid_line_alpha=0.3
p1.xaxis.axis_label = 'Date'
p1.yaxis.axis_label = 'Streamflow [CFS*100,000]'
p1.legend.label_text_font_size = '8'
window_size = 30
window = np.ones(window_size)/float(window_size)
g = vplot(p1)
save(g)
def plotCombinedPortfoliosPerf(
stratValues,
conf,
kind='gains', # Or returns
outputDir='../results/dae/portfolios/resultsAnalysis/',
benchmark=None): # Portfolios of portfolios actually
reset_output()
output_notebook()
numlines = stratValues.shape[1]
colors_list = list(reversed(RdBu10[0:numlines]))
p = figure(x_axis_type="datetime")
p.yaxis.axis_label = kind
source = ColumnDataSource(stratValues)
legs = stratValues.columns.values.tolist()
for (colr, leg) in zip(colors_list, legs):
p.line(x=stratValues.index.values,
y=leg,
source=source,
color=colr,
legend=leg)
hline = Span(location=0,
dimension='width',
line_color='black',
line_width=2)
p.renderers.extend([hline])
p.legend.orientation = "top_left"
if benchmark != None:
p.line(benchmark.gains.index.values,
benchmark.gains['cumulReturn'],
color='darkgreen',
legend='benchmark')
show(p)
output_file(outputDir + conf + '_' + kind + '.html')
save(p)
return True
def test_io_push_to_server(self):
from bokeh.io import output_server, push, curdoc, reset_output
application = Application()
with ManagedServerLoop(application) as server:
reset_output()
doc = curdoc()
doc.clear()
client_root = SomeModelInTestClientServer(foo=42)
session_id = 'test_io_push_to_server'
output_server(session_id=session_id,
url=("http://localhost:%d/" % server.port))
doc.add_root(client_root)
push(io_loop=server.io_loop)
server_session = server.get_session('/', session_id)
print(repr(server_session.document.roots))
assert len(server_session.document.roots) == 1
server_root = next(iter(server_session.document.roots))
assert client_root.foo == 42
assert server_root.foo == 42
# Now modify the client document and push
client_root.foo = 57
push(io_loop=server.io_loop)
server_root = next(iter(server_session.document.roots))
assert server_root.foo == 57
# Remove a root and push
doc.remove_root(client_root)
push(io_loop=server.io_loop)
assert len(server_session.document.roots) == 0
# Clean up global IO state
reset_output()
def test_io_push_to_server(self):
from bokeh.io import output_server, push, curdoc, reset_output
application = Application()
with ManagedServerLoop(application) as server:
reset_output()
doc = curdoc()
doc.clear()
client_root = SomeModelInTestClientServer(foo=42)
session_id = 'test_io_push_to_server'
output_server(session_id=session_id,
url=("http://localhost:%d/" % server.port))
doc.add_root(client_root)
push(io_loop=server.io_loop)
server_session = server.get_session('/', session_id)
print(repr(server_session.document.roots))
assert len(server_session.document.roots) == 1
server_root = next(iter(server_session.document.roots))
assert client_root.foo == 42
assert server_root.foo == 42
# Now modify the client document and push
client_root.foo = 57
push(io_loop=server.io_loop)
server_root = next(iter(server_session.document.roots))
assert server_root.foo == 57
# Remove a root and push
doc.remove_root(client_root)
push(io_loop=server.io_loop)
assert len(server_session.document.roots) == 0
# Clean up global IO state
reset_output()
def hbar(data, attribute, index, category, name=None):
output = join(os.getcwd(), 'figures', name)
output_file(output + '.html')
source = data.sort_values(by=attribute, ascending=True)
cmap = factor_cmap(category,
palette=Accent5,
factors=sorted(source[category].unique()))
plot = figure(y_range=source[index],
title=name,
x_axis_label=attribute,
tooltips=[(attribute.replace('_', ' '), f'@{attribute}')])
plot.hbar(y=index,
right=attribute,
height=0.8,
source=source,
fill_color=cmap,
line_color=cmap)
save(plot)
reset_output()
def plot_in_bokeh(x, y):
reset_output()
output_file("pathname")
fig = figure(height=300,
width=900,
responsive=True,
x_axis_type="datetime")
fig.scatter(x, y, legend="Test")
fig.y_range = Range1d(10, 40)
fig.yaxis.axis_label = "BrPM"
'''
# Setting the second y axis range name and range
fig.extra_y_ranges = {"act_level": Range1d(start=0, end=2)}
# Adding the second axis to the plot.
fig.add_layout(LinearAxis(y_range_name="act_level",axis_label="Activity level"), 'right')
fig.line(act_level_x, act_level_y, y_range_name="act_level", color="lightgrey", legend="activity level")
'''
show(fig)
def displayParameterEvolution(
groupedData,
metrics,
parameter,
configuration='concatParams',
outputDir='../results/dae/neuralNetwork/resultsAnalysis/'):
reset_output()
output_notebook()
grid = []
subGrid = []
for metric in metrics:
p = figure(tools=TOOLS)
p.xaxis.axis_label = parameter
p.yaxis.axis_label = metric
for name, group in groupedData:
tmp = group.sort(columns=parameter)
source = ColumnDataSource({
parameter: tmp[parameter],
metric: tmp[metric],
'conf': tmp[configuration]
})
p.line(parameter, metric, source=source)
p.select_one(HoverTool).tooltips = [('conf', '@conf')]
subGrid.append(p)
grid.append(subGrid)
p = gridplot(grid)
show(p)
output_file(outputDir + parameter + '.html')
save(p)
return True
def save_to_disk(p, filename, title, show_inline=True):
if show_inline:
reset_output()
output_notebook(resources=INLINE)
show(p)
reset_output()
output_file(filename, title=title)
save(p)
reset_output()
output_notebook(resources=INLINE)
def test(self):
io.reset_output()
self.assertTrue(io._state.reset.called)
def test(self):
io.reset_output()
self.assertTrue(io._state.reset.called)
def plotresults(cam, im, P, S, B, bbox):
# Bokeh Plotting
io.reset_output()
io.output_file('bokeh plots.html', title='bokeh plots')
h, w = im.shape
n = P.shape[2] # number of images
xn = list(range(0, n, 1))
# colors = bokeh_colors(n)
colorbyframe = True
colors = []
for i in np.linspace(0, 255, n, dtype=int):
colors.append(palettes.Viridis256[i])
# Setup tools
hoverImage = models.HoverTool(tooltips=[('(x, y)', '$x{1.11}, $y{1.11}')],
point_policy='follow_mouse')
# Plot image
a = plotting.figure(x_range=(0, w),
y_range=(h, 0),
plot_width=round(600 * w / h),
plot_height=600,
x_axis_label='pixel (1 - ' + str(w) + ')',
y_axis_label='pixel (1 - ' + str(h) + ')',
title=cam['filename'],
tools='box_zoom,pan,save,reset,wheel_zoom',
active_scroll='wheel_zoom',
active_inspect=None)
a.add_tools(hoverImage)
a.image(image=[np.flip(im, 0)],
x=0,
y=h,
dw=w,
dh=h,
palette=palettes.Greys256)
a.quad(top=[h], bottom=[0], left=[0], right=[w],
alpha=0) # clear rectange hack for tooltip image x,y
# Plog bounding box
a.quad(top=bbox[3],
bottom=bbox[2],
left=bbox[0],
right=bbox[1],
color=colors[1],
line_width=2,
alpha=.3)
# Plot license plate outline
a.patch(P[0, 0:4, 0], P[1, 0:4, 0], alpha=0.3, line_width=4)
# Plot points
if colorbyframe:
# i = ~np.isnan(P[0].ravel())
# c = P[4].ravel()[i].astype(int)
# fc = [colors[i] for i in c]
# a.scatter(P[0].ravel()[i], P[1].ravel()[i], size=4, fill_color=fc, line_color=None)
# a.scatter(P[2].ravel()[i], P[3].ravel()[i], size=9, fill_color=fc, fill_alpha=0.3, line_color=None)
for i in range(n - 1): # list((0, n - 1)): # plot first and last
# for i in range(n): # plot all
a.circle(P[0, :, i],
P[1, :, i],
color=colors[i],
legend='image ' + str(i),
line_width=1)
a.circle(P[2, :, i],
P[3, :, i],
color=colors[i],
size=10,
alpha=.6)
else:
a.circle(P[0].ravel(),
P[1].ravel(),
color=colors[0],
legend='Points',
line_width=2)
a.circle(P[2].ravel(),
P[3].ravel(),
color=colors[1],
legend='Reprojections',
size=10,
alpha=.6)
# Plot 2 - 3d
x, y, z = np.split(B[:, :3], 3, axis=1)
b = plotting.figure(plot_width=350,
plot_height=300,
x_axis_label='Y (m)',
y_axis_label='X (m)',
title='Position',
tools='save,reset,hover',
active_inspect='hover')
# Plot 3 - distance
c = plotting.figure(x_range=(0, n),
y_range=(0, round(S[1:, 7].max())),
plot_width=350,
plot_height=300,
x_axis_label='image',
y_axis_label='distance (m)',
title='Distance = %.2fm in %.3fs' %
(S[-1, 7], S[-1, 5] - S[0, 5]),
tools='save,reset,hover',
active_inspect='hover')
# Plot 4 - speed
d = plotting.figure(x_range=(0, n),
y_range=(0, S[1:, 8].max() + 1),
plot_width=350,
plot_height=300,
x_axis_label='image',
y_axis_label='speed (km/h)',
title='Speed = %.2f +/- %.2f km/h' %
(S[1:, 8].mean(), S[1:, 8].std()),
tools='save,reset,hover',
active_inspect='hover')
# Circles plots 2-4
b.circle(0, 0, color=colors[-1], line_width=15)
if colorbyframe:
b.scatter(x.ravel(),
z.ravel(),
fill_color=colors,
line_color=colors,
size=10)
c.scatter(xn[1:],
S[1:, 7],
fill_color=colors[1:],
line_color=colors[1:],
size=10)
d.scatter(xn[1:],
S[1:, 8],
fill_color=colors[1:],
line_color=colors[1:],
size=10)
else:
b.circle(x.ravel(), z.ravel(), color=colors[0], line_width=2)
c.circle(xn[1:], S[1:, 7], color=colors[0], line_width=2)
d.circle(xn[1:], S[1:, 8], color=colors[0], line_width=2)
# Plot lines
a.multi_line(P[0].tolist(),
P[1].tolist(),
color='white',
alpha=.7,
line_width=1)
# Show plot
io.show(column(a, row(b, c, d))) # open a browser
def assembly_chart(df, complements):
"""function to assembly the chart"""
print('starting the plot...')
# specify the output file name
output_file("movigrama_chart.html")
# force to show only one plot when multiples executions of the code occur
# otherwise the plots will append each time one new calling is done
reset_output()
# create ColumnDataSource objects directly from Pandas data frames
source = ColumnDataSource(df)
# use the column DT as index
df.set_index('DT', inplace=True)
###########################################################################
#
# Movigrama Plot
#
###########################################################################
# build figure of the plot
p = figure(x_axis_type='datetime',
x_axis_label='days of moviment',
y_axis_label='unities movimented',
plot_width=1230,
plot_height=500,
active_scroll='wheel_zoom')
# TODO Specify X range (not all plots have 365 days of moviment)
# build the Stock Level bar
r1 = p.vbar(x='DT',
bottom=0,
top='STOCK',
width=pd.Timedelta(days=1),
fill_alpha=0.4,
color='paleturquoise',
source=source)
# build the OUT bar
p.vbar(x='DT',
bottom=0,
top='SOMA_SAI',
width=pd.Timedelta(days=1),
fill_alpha=0.8,
color='crimson',
source=source)
# build the IN bar
p.vbar(x='DT',
bottom=0,
top='SOMA_ENTRA',
width=pd.Timedelta(days=1),
fill_alpha=0.8,
color='seagreen',
source=source)
# edit title
# adds warehouse title
p.add_layout(
Title(text=complements['warehouse'],
text_font='helvetica',
text_font_size='10pt',
text_color='orangered',
text_alpha=0.5,
align='center',
text_font_style="italic"), 'above')
# adds product title
p.add_layout(
Title(text=complements['product'],
text_font='helvetica',
text_font_size='10pt',
text_color='orangered',
text_alpha=0.5,
align='center',
text_font_style="italic"), 'above')
# adds main title
p.add_layout(
Title(text='Movigrama Endicon',
text_font='helvetica',
text_font_size='16pt',
text_color='orangered',
text_alpha=0.9,
align='center',
text_font_style="bold"), 'above')
# adds horizontal line
hline = Span(location=0,
line_alpha=0.4,
dimension='width',
line_color='gray',
line_width=3)
p.renderers.extend([hline])
# adapt the range to the plot
p.x_range.range_padding = 0.1
p.y_range.range_padding = 0.1
# format the plot's outline
p.outline_line_width = 4
p.outline_line_alpha = 0.1
p.outline_line_color = 'orangered'
# format major labels
p.axis.major_label_text_color = 'gray'
p.axis.major_label_text_font_style = 'bold'
# format labels
p.axis.axis_label_text_color = 'gray'
p.axis.axis_label_text_font_style = 'bold'
# p.xgrid.grid_line_color = None # disable vertical bars
# p.ygrid.grid_line_color = None # disable horizontal bars
# change placement of minor and major ticks in the plot
p.axis.major_tick_out = 10
p.axis.minor_tick_in = -3
p.axis.minor_tick_out = 6
p.axis.minor_tick_line_color = 'gray'
# format properly the X datetime axis
p.xaxis.formatter = DatetimeTickFormatter(days=['%d/%m'],
months=['%m/%Y'],
years=['%Y'])
# iniciate hover object
hover = HoverTool()
hover.mode = "vline" # activate hover by vertical line
hover.tooltips = [("SUM-IN", "@SOMA_ENTRA"), ("SUM-OUT", "@SOMA_SAI"),
("COUNT-IN", "@TRANSACT_ENTRA"),
("COUNT-OUT", "@TRANSACT_SAI"), ("STOCK", "@STOCK"),
("DT", "@DT{%d/%m/%Y}")]
# use 'datetime' formatter for 'DT' field
hover.formatters = {"DT": 'datetime'}
hover.renderers = [r1] # display tolltip only to one render
p.add_tools(hover)
###########################################################################
#
# Demand analysis
#
###########################################################################
# change to positive values
df['out_invert'] = df['SOMA_SAI'] * -1
# moving average with n=30 days
df['MA30'] = df['out_invert'].rolling(30).mean().round(0)
# moving standard deviation with n=30 days
df['MA30_std'] = df['out_invert'].rolling(30).std().round(0)
# lower control limit for 1 sigma deviation
df['lcl_1sigma'] = (df['MA30'] - df['MA30_std'])
# upper control limit for 1 sigma deviation
df['ucl_1sigma'] = (df['MA30'] + df['MA30_std'])
source = ColumnDataSource(df)
p1 = figure(plot_width=1230,
plot_height=500,
x_range=p.x_range,
x_axis_type="datetime",
active_scroll='wheel_zoom')
# build the Sum_out bar
r1 = p1.vbar(x='DT',
top='out_invert',
width=pd.Timedelta(days=1),
color='darkred',
line_color='salmon',
fill_alpha=0.4,
source=source)
# build the moving average line
p1.line(x='DT', y='MA30', source=source)
# build the confidence interval
band = Band(base='DT',
lower='lcl_1sigma',
upper='ucl_1sigma',
source=source,
level='underlay',
fill_alpha=1.0,
line_width=1,
line_color='black')
p1.renderers.extend([band])
# adds title
p1.add_layout(
Title(text='Demand Variability',
text_font='helvetica',
text_font_size='16pt',
text_color='orangered',
text_alpha=0.5,
align='center',
text_font_style="bold"), 'above')
# adds horizontal line
hline = Span(location=0,
line_alpha=0.4,
dimension='width',
line_color='gray',
line_width=3)
p1.renderers.extend([hline])
# format the plot's outline
p1.outline_line_width = 4
p1.outline_line_alpha = 0.1
p1.outline_line_color = 'orangered'
# format major labels
p1.axis.major_label_text_color = 'gray'
p1.axis.major_label_text_font_style = 'bold'
# format labels
p1.axis.axis_label_text_color = 'gray'
p1.axis.axis_label_text_font_style = 'bold'
# change placement of minor and major ticks in the plot
p1.axis.major_tick_out = 10
p1.axis.minor_tick_in = -3
p1.axis.minor_tick_out = 6
p1.axis.minor_tick_line_color = 'gray'
# format properly the X datetime axis
p1.xaxis.formatter = DatetimeTickFormatter(days=['%d/%m'],
months=['%m/%Y'],
years=['%Y'])
# iniciate hover object
hover = HoverTool()
hover.mode = "vline" # activate hover by vertical line
hover.tooltips = [("DEMAND", '@out_invert'), ("UCL 1σ", "@ucl_1sigma"),
("LCL 1σ", "@lcl_1sigma"), ("M AVG 30d", "@MA30"),
("DT", "@DT{%d/%m/%Y}")]
# use 'datetime' formatter for 'DT' field
hover.formatters = {"DT": 'datetime'}
hover.renderers = [r1] # display tolltip only to one render
p1.add_tools(hover)
###########################################################################
#
# Demand groupped by month
#
###########################################################################
resample_M = df.iloc[:, 0:6].resample('M').sum() # resample to month
# create column date as string
resample_M['date'] = resample_M.index.strftime('%b/%y').values
# moving average with n=3 months
resample_M['MA3'] = resample_M['out_invert'].rolling(3).mean()
resample_M['MA3'] = np.ceil(resample_M.MA3) # round up the column MA3
# resample to month with mean
resample_M['mean'] = np.ceil(resample_M['out_invert'].mean())
# resample to month with standard deviation
resample_M['std'] = np.ceil(resample_M['out_invert'].std())
# moving standard deviation with n=30 days
resample_M['MA3_std'] = np.ceil(resample_M['out_invert'].rolling(3).std())
# lower control limit for 1 sigma deviation
resample_M['lcl_1sigma'] = resample_M['MA3'] - resample_M['MA3_std']
# upper control limit for 1 sigma deviation
resample_M['ucl_1sigma'] = resample_M['MA3'] + resample_M['MA3_std']
source = ColumnDataSource(resample_M)
p2 = figure(plot_width=1230,
plot_height=500,
x_range=FactorRange(factors=list(resample_M.date)),
title='demand groupped by month')
colors = factor_cmap('date',
palette=Category20_20,
factors=list(resample_M.date))
p2.vbar(x='date',
top='out_invert',
width=0.8,
fill_color=colors,
fill_alpha=0.8,
source=source,
legend=value('OUT'))
p2.line(x='date',
y='MA3',
color='red',
line_width=3,
line_dash='dotted',
source=source,
legend=value('MA3'))
p2.line(x='date',
y='mean',
color='blue',
line_width=3,
line_dash='dotted',
source=source,
legend=value('mean'))
band = Band(base='date',
lower='lcl_1sigma',
upper='ucl_1sigma',
source=source,
level='underlay',
fill_alpha=1.0,
line_width=1,
line_color='black')
labels1 = LabelSet(x='date',
y='MA3',
text='MA3',
level='glyph',
y_offset=5,
source=source,
render_mode='canvas',
text_font_size="8pt",
text_color='darkred')
labels2 = LabelSet(x='date',
y='out_invert',
text='out_invert',
level='glyph',
y_offset=5,
source=source,
render_mode='canvas',
text_font_size="8pt",
text_color='gray')
low_box = BoxAnnotation(
top=resample_M['mean'].iloc[0] -
resample_M['std'].iloc[0], # analysis:ignore
fill_alpha=0.1,
fill_color='red')
mid_box = BoxAnnotation(
bottom=resample_M['mean'].iloc[0] -
resample_M['std'].iloc[0], # analysis:ignore
top=resample_M['mean'].iloc[0] +
resample_M['std'].iloc[0], # analysis:ignore
fill_alpha=0.1,
fill_color='green')
high_box = BoxAnnotation(
bottom=resample_M['mean'].iloc[0] +
resample_M['std'].iloc[0], # analysis:ignore
fill_alpha=0.1,
fill_color='red')
p2.renderers.extend([band, labels1, labels2, low_box, mid_box, high_box])
p2.legend.click_policy = "hide"
p2.legend.background_fill_alpha = 0.4
p2.add_layout(
Title(text='Demand Grouped by Month',
text_font='helvetica',
text_font_size='16pt',
text_color='orangered',
text_alpha=0.5,
align='center',
text_font_style="bold"), 'above')
# adds horizontal line
hline = Span(location=0,
line_alpha=0.4,
dimension='width',
line_color='gray',
line_width=3)
p2.renderers.extend([hline])
# format the plot's outline
p2.outline_line_width = 4
p2.outline_line_alpha = 0.1
p2.outline_line_color = 'orangered'
# format major labels
p2.axis.major_label_text_color = 'gray'
p2.axis.major_label_text_font_style = 'bold'
# format labels
p2.axis.axis_label_text_color = 'gray'
p2.axis.axis_label_text_font_style = 'bold'
# change placement of minor and major ticks in the plot
p2.axis.major_tick_out = 10
p2.axis.minor_tick_in = -3
p2.axis.minor_tick_out = 6
p2.axis.minor_tick_line_color = 'gray'
# iniciate hover object
# TODO develop hoverTool
# hover = HoverTool()
# hover.mode = "vline" # activate hover by vertical line
# hover.tooltips = [("SUM-IN", "@SOMA_ENTRA"),
# ("SUM-OUT", "@SOMA_SAI"),
# ("COUNT-IN", "@TRANSACT_ENTRA"),
# ("COUNT-OUT", "@TRANSACT_SAI"),
# ("STOCK", "@STOCK")]
# hover.renderers = [r1] # display tolltip only to one render
# p2.add_tools(hover)
###########################################################################
#
# Plot figures
#
###########################################################################
# put the results in a column and show
show(column(p, p1, p2))
# show(p) # plot action
print('plot finished')
def connect_to_server(self):
try:
output_server("dreaml")
except ConnectionError:
reset_output()
print "Failed to connect to bokeh server"
def plot(self,
front: List[S],
reference: List[S] = None,
output: str = '',
show: bool = True) -> None:
# This is important to purge front (if any) between calls
reset_output()
# Set up figure
self.figure_xy = Figure(output_backend='webgl',
sizing_mode='scale_width',
title=self.plot_title,
tools=self.plot_tools)
self.figure_xy.scatter(x='x',
y='y',
legend='solution',
fill_alpha=0.7,
source=self.source)
self.figure_xy.xaxis.axis_label = self.xaxis_label
self.figure_xy.yaxis.axis_label = self.yaxis_label
x_values, y_values, z_values = self.get_objectives(front)
if self.number_of_objectives == 2:
# Plot reference solution list (if any)
if reference:
ref_x_values, ref_y_values, _ = self.get_objectives(reference)
self.figure_xy.line(x=ref_x_values,
y=ref_y_values,
legend='reference',
color='green')
# Push front to server
self.source.stream({
'x': x_values,
'y': y_values,
'str': [s.__str__() for s in front]
})
self.doc.add_root(column(self.figure_xy))
else:
# Add new figures for each axis
self.figure_xz = Figure(title='xz',
output_backend='webgl',
sizing_mode='scale_width',
tools=self.plot_tools)
self.figure_xz.scatter(x='x',
y='z',
legend='solution',
fill_alpha=0.7,
source=self.source)
self.figure_xz.xaxis.axis_label = self.xaxis_label
self.figure_xz.yaxis.axis_label = self.zaxis_label
self.figure_yz = Figure(title='yz',
output_backend='webgl',
sizing_mode='scale_width',
tools=self.plot_tools)
self.figure_yz.scatter(x='y',
y='z',
legend='solution',
fill_alpha=0.7,
source=self.source)
self.figure_yz.xaxis.axis_label = self.yaxis_label
self.figure_yz.yaxis.axis_label = self.zaxis_label
# Plot reference solution list (if any)
if reference:
ref_x_values, ref_y_values, ref_z_values = self.get_objectives(
reference)
self.figure_xy.line(x=ref_x_values,
y=ref_y_values,
legend='reference',
color='green')
self.figure_xz.line(x=ref_x_values,
y=ref_z_values,
legend='reference',
color='green')
self.figure_yz.line(x=ref_y_values,
y=ref_z_values,
legend='reference',
color='green')
# Push front to server
self.source.stream({
'x': x_values,
'y': y_values,
'z': z_values,
'str': [s.__str__() for s in front]
})
self.doc.add_root(
row(self.figure_xy, self.figure_xz, self.figure_yz))
self.client.push(self.doc)
if output:
self.__save(output)
if show:
self.client.show()
def plot_process_tree(
data: pd.DataFrame,
schema: ProcSchema = None,
output_var: str = None,
legend_col: str = None,
show_table: bool = False,
**kwargs,
) -> Tuple[figure, LayoutDOM]:
"""
Plot a Process Tree Visualization.
Parameters
----------
data : pd.DataFrame
DataFrame containing one or more Process Trees
schema : ProcSchema, optional
The data schema to use for the data set, by default None
(if None the schema is inferred)
output_var : str, optional
Output variable for selected items in the tree,
by default None
legend_col : str, optional
The column used to color the tree items, by default None
show_table: bool
Set to True to show a data table, by default False.
Other Parameters
----------------
height : int, optional
The height of the plot figure
(the default is 700)
width : int, optional
The width of the plot figure (the default is 900)
title : str, optional
Title to display (the default is None)
Returns
-------
Tuple[figure, LayoutDOM]:
figure - The main bokeh.plotting.figure
Layout - Bokeh layout structure.
Raises
------
ProcessTreeSchemaException
If the data set schema is not valid for the plot.
Notes
-----
The `output_var` variable will be overwritten with any selected
values.
"""
check_kwargs(kwargs, _DEFAULT_KWARGS)
reset_output()
output_notebook()
data, schema, levels, n_rows = _pre_process_tree(data, schema)
if schema is None:
raise ProcessTreeSchemaException(
"Could not infer schema from data set.")
source = ColumnDataSource(data=data)
# Get legend/color bar map
fill_map, color_bar = _create_fill_map(source, legend_col)
max_level = max(levels) + 3
min_level = min(levels)
plot_height: int = kwargs.pop("height", 700)
plot_width: int = kwargs.pop("width", 900)
title: str = kwargs.pop("title", "ProcessTree")
if color_bar:
title += " (color bar = {legend_col})"
visible_range = int(plot_height / 35)
y_start_range = (n_rows - visible_range, n_rows + 1)
b_plot = figure(
title=title,
plot_width=plot_width,
plot_height=plot_height,
x_range=(min_level, max_level),
y_range=y_start_range,
tools=["ypan", "reset", "save", "tap"],
toolbar_location="above",
)
hover = HoverTool(tooltips=_get_tool_tips(schema),
formatters={"TimeGenerated": "datetime"})
b_plot.add_tools(hover)
# dodge to align rectangle with grid
rect_x = dodge("Level", 1.75, range=b_plot.x_range)
rect_plot_params = dict(width=3.5,
height=0.95,
source=source,
fill_alpha=0.4,
fill_color=fill_map)
if color_bar:
b_plot.add_layout(color_bar, "right")
elif legend_col:
rect_plot_params["legend_field"] = legend_col
rect_plot = b_plot.rect(x=rect_x, y="Row", **rect_plot_params)
if legend_col and not color_bar:
b_plot.legend.title = legend_col
text_props = {
"source": source,
"text_align": "left",
"text_baseline": "middle"
}
def x_dodge(x_offset):
return dodge("Level", x_offset, range=b_plot.x_range)
def y_dodge(y_offset):
return dodge("Row", y_offset, range=b_plot.y_range)
b_plot.text(x=x_dodge(0.1),
y=y_dodge(-0.2),
text="cmd",
text_font_size="7pt",
**text_props)
b_plot.text(x=x_dodge(0.1),
y=y_dodge(0.25),
text="Exe",
text_font_size="8pt",
**text_props)
b_plot.text(x=x_dodge(1.8),
y=y_dodge(0.25),
text="PID",
text_font_size="8pt",
**text_props)
# Plot options
_set_plot_option_defaults(b_plot)
b_plot.xaxis.ticker = sorted(levels)
b_plot.xgrid.ticker = sorted(levels)
b_plot.hover.renderers = [rect_plot] # only hover element boxes
# Selection callback
if output_var is not None:
get_selected = _create_js_callback(source, output_var)
b_plot.js_on_event("tap", get_selected)
box_select = BoxSelectTool(callback=get_selected)
b_plot.add_tools(box_select)
range_tool = _create_vert_range_tool(
data=source,
min_y=0,
max_y=n_rows,
plot_range=b_plot.y_range,
width=90,
height=plot_height,
x_col="Level",
y_col="Row",
fill_map=fill_map,
)
plot_elems = row(b_plot, range_tool)
if show_table:
data_table = _create_data_table(source, schema, legend_col)
plot_elems = column(plot_elems, data_table)
show(plot_elems)
return b_plot, plot_elems
def _return_html_comps(plots):
script, divs = components(plots)
reset_output()
return script, divs, get_bokeh_version()
def tradingRepartitionDay(portfolio, absGain, conf):
reset_output()
output_file(
'../results/dae/portfolios/resultsAnalysis/tradingRepartitionDay_' +
conf + '.html')
count, sell, buyy, days = getMetricsDay(portfolio, absGain)
colorRange = OrRd9[0:5] + list(reversed(YlGn9[0:5]))
colors = []
for day in absGain.index.values:
if absGain[day] < -5000: colors.append(0)
elif absGain[day] >= -5000 and absGain[day] <= -2500: colors.append(1)
elif absGain[day] > -2500 and absGain[day] <= -1000: colors.append(2)
elif absGain[day] > -1000 and absGain[day] <= -500: colors.append(3)
elif absGain[day] > -500 and absGain[day] < 0: colors.append(4)
elif absGain[day] == 0: colors.append(-1)
elif absGain[day] > 0 and absGain[day] <= 500: colors.append(5)
elif absGain[day] > 500 and absGain[day] <= 1000: colors.append(6)
elif absGain[day] > 1000 and absGain[day] <= 2500: colors.append(7)
elif absGain[day] > 2500 and absGain[day] <= 5000: colors.append(8)
elif absGain[day] > 5000: colors.append(9)
xRange = []
yRange = []
for line in range(int(np.floor(absGain.shape[0] / 20) + 1)):
for column in range(20):
xRange.append(str(column))
yRange.append(str(line))
type_color = []
for i, color in enumerate(colors):
if color != -1: type_color.append(colorRange[colors[i]])
else: type_color.append('grey')
source = ColumnDataSource(data=dict(xGroup=xRange,
yGroup=yRange,
absGain=absGain,
days=days,
count=count,
sell=sell,
buyy=buyy,
type_color=type_color))
p = figure(
title="Trading repartition by day",
tools=TOOLS,
x_range=[str(x) for x in range(20)],
y_range=list(
reversed([
str(x)
for x in range(int(np.floor(portfolio.shape[0] / 20) + 1))
])))
p.outline_line_color = None
p.plot_width = 1800
p.plot_height = 1800
p.rect('xGroup',
'yGroup',
0.9,
0.9,
source=source,
fill_alpha=0.6,
color="type_color")
text_props = {
"source": source,
"angle": 0,
"color": "black",
"text_align": "center",
"text_baseline": "middle"
}
p.text(x='xGroup',
y='yGroup',
text='days',
text_font_size="9pt",
**text_props)
p.axis.visible = None
p.grid.grid_line_color = None
p.select_one(HoverTool).tooltips = [("day", "@days"),
("% actions involved", "@count"),
("sold", "@sell"), ("bought", "@buyy"),
("absGain", "@absGain")]
save(p)
show(p)
return True
def tradingRepartitionAction(portfolio, conf):
reset_output()
output_notebook()
count, minn, maxx, sellPerc, buyyPerc, name = getMetricsAction(portfolio)
colorRange = list(reversed(PuBu9))
colors = []
for stock in portfolio.columns.values:
if count[stock] < 0.01: colors.append(0)
elif count[stock] >= 0.01 and count[stock] <= 0.4: colors.append(1)
elif count[stock] > 0.4 and count[stock] <= 0.5: colors.append(2)
elif count[stock] > 0.5 and count[stock] <= 0.6: colors.append(3)
elif count[stock] > 0.6 and count[stock] <= 0.7: colors.append(4)
elif count[stock] > 0.7 and count[stock] <= 0.8: colors.append(5)
elif count[stock] > 0.8 and count[stock] <= 0.9: colors.append(6)
elif count[stock] > 0.9 and count[stock] <= 0.95: colors.append(7)
elif count[stock] > 0.95: colors.append(8)
xRange = []
yRange = []
for line in range(int(np.floor(portfolio.shape[1] / 10) + 1)):
for column in range(10):
xRange.append(str(column))
yRange.append(str(line))
source = ColumnDataSource(data=dict(
xGroup=xRange,
yGroup=yRange,
name=name,
count=count,
minn=minn,
maxx=maxx,
sellPerc=sellPerc,
buyyPerc=buyyPerc,
type_color=[colorRange[colors[i]] for i in range(portfolio.shape[1])]))
p = figure(
title="Trading repartition by action",
tools=TOOLS,
x_range=[str(x) for x in range(10)],
y_range=list(
reversed([
str(x)
for x in range(int(np.floor(portfolio.shape[1] / 10) + 1))
])))
p.outline_line_color = None
p.plot_width = 1200
p.rect('xGroup',
'yGroup',
0.9,
0.9,
source=source,
fill_alpha=0.6,
color="type_color")
text_props = {
"source": source,
"angle": 0,
"color": "black",
"text_align": "center",
"text_baseline": "middle"
}
p.text(x='xGroup',
y='yGroup',
text='name',
text_font_size="9pt",
**text_props)
p.axis.visible = None
p.grid.grid_line_color = None
p.select_one(HoverTool).tooltips = [("name", "@name"),
("participation", "@count"),
("min weight", "@minn"),
("max weight", "@maxx"),
("sellPerc", "@sellPerc"),
("buyyPerc", "@buyyPerc")]
show(p)
output_file(
'../results/dae/portfolios/resultsAnalysis/tradingRepartitionAction_' +
conf + '.html')
save(p)
return True
def make_interactive_scatter_plot(df,
x_col='coord_x',
y_col='coord_y',
color_col=None,
size_col=None,
hover_cols=[],
palette_type='categorical',
color_bar=False,
plot_width=1200,
plot_height=800,
max_lvls=20,
plot_title='Title',
plot_name='test.html'):
"""
Makes and saves interactive scatter plot to a file.
df: data frame for plotting
color_col: what column of df as the color label
x_col: what column of df to plot along x axis
y_col: what column of df to plot along y axis
hover_cols: what columns of df to come up when hovering over point
palette_type: either 'categorical' or 'sequential'
plot_width: how wide is the output plot
plot_height: how high is the output plot
max_lvls: maximum number of categorical levels to plot. Chooses different palettes depending on the levels. Must be between 2 and 40
plot_title: Title of the output plot
plot_name: What name/path to save the output plot
"""
from bokeh.io import output_file, show, reset_output
from bokeh.plotting import figure, show
from bokeh.models import HoverTool, ColumnDataSource, CategoricalColorMapper, BasicTicker
from bokeh.transform import transform
reset_output()
source = ColumnDataSource(data=df)
if palette_type == 'categorical':
if color_bar:
raise ValueError(
"Must set palette_type='sequential' if specifying a color bar")
n_levels = len(df[color_col].unique())
factors = sorted(list(df[color_col].unique()))
colors = get_palette(min(n_levels, max_lvls),
palette_type=palette_type)
color_mapper = CategoricalColorMapper(factors=factors, palette=colors)
elif palette_type == 'sequential':
colors = get_palette(9, palette_type=palette_type)
color_mapper = LinearColorMapper(low=df[color_col].min(),
high=df[color_col].max(),
palette=colors)
hover_tooltips = [(o, "@" + o) for o in hover_cols]
hover = HoverTool(tooltips=hover_tooltips)
p = figure(plot_width=plot_width,
plot_height=plot_height,
tools=[hover, 'pan', 'box_zoom', 'wheel_zoom', 'reset'],
title=plot_title)
if size_col is None:
p.circle(x_col,
y_col,
size=10,
source=source,
fill_color=transform(color_col, color_mapper))
else:
p.circle(x_col,
y_col,
size=size_col,
source=source,
fill_color=transform(color_col, color_mapper))
if color_bar:
color_bar = ColorBar(color_mapper=color_mapper,
ticker=BasicTicker(),
location=(0, 0))
p.add_layout(color_bar, 'right')
output_file(plot_name)
show(p)
def graph(gui, daysList, nightsList, masterBlock, plotVertices = True, showDragWarn = False):
bulkvertices = []
vertX = []
vertY = []
masterX = []
masterY = []
airX = []
airY = []
monResList = []
#Clears previous graphs from memory
reset_output()
if plotVertices:
#Add daytime period delimiting lines if appropriate
if gui.restrictSearchBV.get() is True:
for day in daysList:
if len(day.vertices) > 0:
#Add vertex at 0 to mark begining of day
bulkvertices.append(coreC.vert(day.vertices[0].index, np.nan, day.vertices[0].vertType))
#Get all vertices from bouts
bulkvertices += day.vertices
#Add vertex at 0 to mark end of day
bulkvertices.append(coreC.vert(day.vertices[-1].index, np.nan, day.vertices[-1].vertType))
#Else compile vertices for entire input file
else:
bulkvertices = masterBlock.vertices
#Compile index number and temperature of all vertices
for vertex in bulkvertices:
vertX.append(gui.masterList[vertex.index][gui.dataPointCol])
vertY.append(vertex.temp)
#Output to HTML file
output_file(gui.graphName)
else:
output_file(os.path.join(gui.coreDir, "misc_files", "tempGraph.html"))
#Create column data source for vertex data so it can be manipulated in the interactive plot
boutsSourceData = ColumnDataSource(data = dict(x = vertX, y = vertY))
#Compile index number and temperature for every line in input file
for line in gui.masterList:
masterX.append(int(line[gui.dataPointCol]))
masterY.append(float(line[gui.tempsCol]))
#Compile air temperature if a valid column is present
if gui.airValid is True:
airX.append(int(line[gui.dataPointCol]))
airY.append(float(line[gui.airTempCol]))
#Set plot dimensions
if gui.plotDimVar.get() is 1:
#Get monitor resolution if "auto" selected
for monitor in get_monitors():
monResList.append(str(monitor))
#Extract monitor width and height
resRE = re.search("(\d+)x(\d+)", monResList[0])
monX = int(resRE.group(1))
monY = int(resRE.group(2))
plotX = (monX - 200)
plotY = (monY - 200)
#Get user dimension values if "manual" selected
else:
plotX = int(gui.plotDimXE.get())
plotY = int(gui.plotDimYE.get())
#Initialize hover tool (provides information about individual datapoints)
hover = HoverTool(tooltips=[("Data Point", "$x{int}"), ("Temperature", "$y")])
#(flag) may not be neccessary
# for y in masterY:
# float(y)
#Get name of plot
if plotVertices:
plotName = gui.graphName[:-5]
else:
#Get input file root name
tempRE = re.search((".*\."), os.path.basename(os.path.normpath(gui.inputFileAdvE.get())))
#Assign default plot name
if tempRE:
plotName = tempRE.group(0)[:-1]
else:
plotName = os.path.basename(os.path.normpath(gui.inputFileAdvE.get()))
#Detect best y axis range
if gui.airValid is True:
yMin = (float(min(min(masterY), min(airY))) - 2)
yMax = (float(max(max(masterY), max(airY))) + 2)
else:
yMin = (float(min(masterY)) - 2)
yMax = (float(max(masterY)) + 2)
#Create core plot
plot = figure(tools = [hover, "box_zoom, wheel_zoom, pan, reset, save"],
x_range = [int(masterX[0]), int(masterX[len(masterX) - 1])],
y_range = [yMin, yMax],
# y_range = [float(min((float(min(airY)), float(min(masterY)))) - 2), (max(max(airY), max(masterY)) + 2)],
title = plotName,
x_axis_label= "Data Point", y_axis_label = "Temperature (C)", plot_width = plotX, plot_height = plotY)
#Add vertical lines delimiting days
if gui.showDayDelimsBV.get() is True:
for day in daysList:
vline = Span(location = int(gui.masterList[day.start][gui.dataPointCol]), dimension = "height",
line_color = gui.dayMarkerColorVar.get(), line_width = float(gui.dayMarkerSize_E.get()), line_alpha = 0.6)
plot.renderers.extend([vline])
#Get size settings from GUI
plot.title.text_font_size = (gui.titleFontSizeE.get() + "pt")
plot.axis.axis_label_text_font_size = (gui.axisTitleFontSizeE.get() + "pt")
plot.axis.major_label_text_font_size = (gui.axisLabelFontSizeE.get() + "pt")
plot.axis.major_tick_line_width = int(gui.axisTickSizeE.get())
plot.axis.minor_tick_line_width = int(gui.axisTickSizeE.get())
plot.axis.major_tick_out = int(gui.axisTickSizeE.get())
plot.axis.minor_tick_out = int(gui.axisTickSizeE.get())
#Append vertex x and y values to data dictionary
data = {"x": [], "y": []}
for x in vertX: data["x"].append(x)
for y in vertY: data["y"].append(y)
#Generate table with vertex information
src = ColumnDataSource(data)
columns = [
TableColumn(field = "x", title = "Data Point"),
TableColumn(field = "y", title = "Temperature")
]
data_table = DataTable(source = src, columns = columns, width = 500, height = 20000)
if gui.editModeBV.get():
#Show drag warning if applicable
if showDragWarn:
dragWarn(gui)
#Plot air temperatures
if gui.showAirTempBV.get() is True and gui.airValid:
# plot.circle(airX, airY, size = 5, color = "black", alpha = 1, legend = "Air Temeprature")
plot.line(airX, airY, line_width = float(gui.airTempSize_E.get()), color = gui.airTempColorVar.get(), line_alpha = 1, legend = "Air Temeprature")
#Plot egg temperatures
plot.circle(masterX, masterY, size = float(gui.eggTempPointSize_E.get()), color = gui.eggTempPointColorVar.get(), legend = "Egg Temperature")
plot.line(masterX, masterY, line_width = float(gui.eggTempLineSize_E.get()), color = gui.eggTempLineColorVar.get())
#Plot verticies as large circles if edit mode selected
renderer = plot.circle (
"x",
"y",
size = (float(gui.boutSize_E.get()) * 3),
color = "black",
fill_color = gui.boutColorVar.get(),
fill_alpha = 0.8,
legend = "Prediced Incubation Shift",
source = src
)
draw_tool = PointDrawTool(renderers = [renderer], empty_value = 1)
plot.add_tools(draw_tool)
plot.toolbar.active_drag = draw_tool
#Else plot verticies as lines
else:
#Plot air temperatures
if gui.showAirTempBV.get() is True and gui.airValid:
# plot.circle(airX, airY, size = 5, color = "black", alpha = 1, legend = "Air Temeprature")
plot.line(airX, airY, line_width = float(gui.airTempSize_E.get()), color = gui.airTempColorVar.get(), line_alpha = 1, legend = "Air Temeprature")
#Plot egg temperatures
plot.circle(masterX, masterY, size = float(gui.eggTempPointSize_E.get()), color = gui.eggTempPointColorVar.get(), legend = "Egg Temperature")
plot.line(masterX, masterY, line_width = float(gui.eggTempLineSize_E.get()), color = gui.eggTempLineColorVar.get())
#Add vertices
plot.line("x", "y", line_width = float(gui.boutSize_E.get()), legend = "Detected Bout", line_color = gui.boutColorVar.get(), source = boutsSourceData)
if gui.showGridBV.get() is False:
plot.grid.visible = False
plot.legend.label_text_font_size = (gui.legendFontSizeE.get() + "pt")
plot.background_fill_color = None
plot.border_fill_color = None
# plot.outline_color = None
#Generate plot
show(column(plot, widgetbox(data_table)))
return df
#path = r'D:/Documents/DataScience/Portfolio/criticalrole_webscraper_knowledgegraph/'
result_df = pd.read_csv('critrole_w2v_model_output.csv')
result_df = DataFrame_StringOfInts2ListOfInts(result_df,
['word_most_similar_indices'])
#result_df['word_most_similar_indices'] = result_df['word_most_similar_indices'].apply(ast.literal_eval)
result_df['coords'] = list(zip(result_df['dim0'], result_df['dim1']))
result_pos = result_df['coords'].to_dict()
result_links = result_df['word_most_similar_indices'].to_dict()
result_cds = ColumnDataSource(result_df)
G = nx.from_dict_of_lists(result_links)
reset_output()
#output_notebook()
#output_file('critrole_w2v_visualizer.html')
# We could use figure here but don't want all the axes and titles
plot = Plot(x_range=Range1d(-2, 2), y_range=Range1d(-2, 2))
# Create a Bokeh graph from the NetworkX input using nx.spring_layout
#nx.set_node_attributes(G, result_pos, 'coord')
graph = from_networkx(G, layout_function=result_pos)
graph.node_renderer.glyph = Circle(size=4, fill_color='#2b83ba', line_width=0)
graph.edge_renderer.glyph = MultiLine(line_color="#cccccc",
line_alpha=0.8,
line_width=0)
def modify_doc(doc):
reset_output(state=None)
print("Entering modify_doc ...")
global ecg_idx, ecg_filtered, crr_idx
df = pd.read_csv(os.path.join(
app.config['UPLOAD_FOLDER'], app.config['CUR_FILE']))
ecg_clean = df['P02S ECG']
ecg_idx = [i for i in range(len(ecg_clean))]
ecg_filtered = bandpass(ecg_clean, lf, hf, 250, 2, False)
ecg_filtered = np.interp(
ecg_filtered, (ecg_filtered.min(), ecg_filtered.max()), (-1, +1))
# ecg_filtered = scale(ecg_filtered, axis=0, with_mean=True,
# with_std=True, copy=True)
min_g = min(ecg_filtered)
max_g = max(ecg_filtered)
file_name_div = Div(text='Processing on file: ' +
app.config['CUR_FILE'].split('/')[-1])
div = Div(text="Quality")
radio_group = RadioGroup(
labels=["Good", "Boderline", "Poor"], active=2)
button_nxt_unit = Button(label="Next Unit", button_type="success")
skip_unit = RadioGroup(
labels=["Save This Unit", "Skip This Unit"], active=0)
marker_line_st = ColumnDataSource(data=dict(x=[0, 0], y=[min_g, max_g]))
marker_line_en = ColumnDataSource(data=dict(x=[0, 0], y=[min_g, max_g]))
s2 = ColumnDataSource(data=dict(x=[], y=[]))
sx = figure(width=1300, height=300, title="ecg_filtered "+str(lf) +
"-"+str(hf)+"Hz", x_axis_label='time', y_axis_label='acc')
sx.line(ecg_idx, ecg_filtered, legend="ecg_filtered "+str(lf) +
"-"+str(hf)+"Hz", line_color="red", line_width=1)
sx.line('x', 'y', source=marker_line_st,
legend="current unit ", line_color="blue", line_width=1)
sx.line('x', 'y', source=marker_line_en,
legend="current unit ", line_color="blue", line_width=1)
sx1 = figure(width=800, height=300, title="ecg_filtered "+str(lf) +
"-"+str(hf)+"Hz", x_axis_label='time', y_axis_label='acc')
sx1.line('x', 'y', source=s2, legend="ecg_filtered unit "+str(lf) +
"-"+str(hf)+"Hz", line_color="red", line_width=1)
peaks, _ = find_peaks(ecg_filtered, distance=150)
crr_idx = 0
marked_file = open(os.path.join(
app.config['MARKED_FOLDER'], app.config['CUR_FILE'][:-4] + '_' +
str(datetime.datetime.now().strftime("%Y-%m-%d_%H:%M:%S")) + '.txt'), 'w')
marked_file.write(app.config['CUR_FILE'] + '\n')
marked_file.write('P02S ECG' + '\n')
marked_file.write(str(len(peaks) - 1) + '\n')
res_df = {}
def my_nxt_unit_handler():
global crr_idx, ecg_filtered
if (crr_idx < len(peaks) - 1):
#save unit data
if(skip_unit.active == 0 and crr_idx > 0):
out_fn = os.path.join(
app.config['MARKED_FOLDER'], radio_group.labels[radio_group.active],
app.config['CUR_FILE'][:-4]+'_P2SECG_'+str(crr_idx)+'.json')
print(out_fn)
with open(out_fn, "w") as write_file:
json.dump(res_df, write_file)
st = int(max(0, peaks[crr_idx] -
(peaks[crr_idx + 1] - peaks[crr_idx]) / 2))
en = int(
min(peaks[crr_idx] + (peaks[crr_idx + 1] - peaks[crr_idx]) / 2, ecg_idx[-1]))
unit_idx = ecg_idx[st:en]
unit_data = ecg_filtered[st:en]
s2.data['x'] = unit_idx
s2.data['y'] = unit_data
marker_line_st.data['x'] = [st, st]
marker_line_en.data['x'] = [en, en]
print("crr marked quality: ", radio_group.labels[radio_group.active])
marked_file.write(str(st) + '\t' + str(en) + '\t' + str(en - st) + '\t' +
str(radio_group.labels[radio_group.active]) + '\n')
res_df['file_name'] = app.config['CUR_FILE']
res_df['unit_number'] = crr_idx
res_df['size'] = en - st +1
res_df['data'] = list(unit_data)
res_df['signal_name'] = 'P02S ECG'
res_df['quality'] = radio_group.labels[radio_group.active]
crr_idx += 1
if crr_idx == len(peaks)-1:
marked_file.close()
button_nxt_unit.on_click(my_nxt_unit_handler)
graphs = column(
list(itertools.chain.from_iterable([[sx, sx1, widgetbox(div)]])))
doc.add_root(widgetbox(file_name_div))
doc.add_root(graphs)
doc.add_root(row(widgetbox(radio_group), widgetbox(
button_nxt_unit), widgetbox(skip_unit)))
doc.theme = Theme(filename=os.path.join(THIS_FILE_PATH, "theme.yaml"))