def __display_pathways_information(predicted_pathways, host,
original_model):
if util.in_ipnb():
title = "Production envelopes for %s (%s)" % (host.name,
original_model.id)
predicted_pathways.plot_production_envelopes(
original_model, title=title, objective=original_model.biomass)
def stop_loader(identifier):
if util.in_ipnb():
display(Javascript("""
jQuery("#%s").remove();
""" % identifier))
else:
logger.debug("loading only works on Jupyter notebooks")
def _oflline(self):
if self._offline_mode:
return
if self.get_option('mode') == 'offline' and in_ipnb():
from plotly.offline import init_notebook_mode
init_notebook_mode()
self._offline_mode = True
def _oflline(self):
if self._offline_mode:
return
if self.get_option('mode') == 'offline' and in_ipnb():
from plotly.offline import init_notebook_mode
init_notebook_mode()
self._offline_mode = True
def _plot_grid(self):
if util.in_ipnb():
if config.use_bokeh:
self._plot_bokeh_grid()
elif config.use_matplotlib:
self._plot_matplotlib_grid()
else:
self._plot_cli_grid()
def loading():
if util.in_ipnb():
identifier = str(uuid4())
display(HTML("""
<img class="loading" id="%s" style="margin:auto; text-align:center;" src="data:image/gif;base64,%s"/>
""" % (identifier, LOADING_IMAGE)))
return identifier
else:
logger.debug("loading only works on Jupyter notebooks")
def stats(self):
stats_data = None
if in_ipnb():
if config.use_bokeh:
stats_data = stats.BokehStatsData(self)
else:
stats_data = stats.CLIStatsData(self)
stats_data.display()
def stats(self):
stats_data = None
if in_ipnb():
if config.use_bokeh:
stats_data = stats.BokehStatsData(self)
else:
stats_data = stats.CLIStatsData(self)
stats_data.display()
def _display_on_map_static(self, index, map_name, palette="RdYlBu", **kwargs):
try:
import escher
if os.path.exists(map_name):
map_json = map_name
map_name = None
else:
map_json = None
values = self.normalized_gaps
values = values[~numpy.isnan(values)]
values = values[~numpy.isinf(values)]
data = self.solutions.iloc[index]
# Find values above decimal precision
data = data[numpy.abs(data.normalized_gaps.astype(float)) > non_zero_flux_threshold]
# Remove NaN rows
data = data[~numpy.isnan(data.normalized_gaps.astype(float))]
reaction_data = dict(data.normalized_gaps)
for rid, gap in six.iteritems(reaction_data):
if numpy.isposinf(gap):
gap = numpy.max(values)
elif numpy.isneginf(gap):
gap = numpy.min(values)
reaction_data[rid] = gap
scale = self.plot_scale(palette)
reaction_data['min'] = min(numpy.abs(values) * -1)
reaction_data['max'] = max(numpy.abs(values))
reaction_scale = [dict(type='min', color=scale[0][1], size=24),
dict(type='value', value=scale[0][0], color=scale[0][1], size=21),
dict(type='value', value=scale[1][0], color=scale[1][1], size=16),
dict(type='value', value=scale[2][0], color=scale[2][1], size=8),
dict(type='value', value=scale[3][0], color=scale[3][1], size=16),
dict(type='value', value=scale[4][0], color=scale[4][1], size=21),
dict(type='max', color=scale[4][1], size=24)]
builder = escher.Builder(map_name=map_name, map_json=map_json, reaction_data=reaction_data,
reaction_scale=reaction_scale)
if in_ipnb():
from IPython.display import display
display(builder.display_in_notebook())
else:
builder.display_in_browser()
except ImportError:
print("Escher must be installed in order to visualize maps")
def _display_on_map_static(self, index, map_name, palette="RdYlBu", **kwargs):
try:
import escher
if os.path.exists(map_name):
map_json = map_name
map_name = None
else:
map_json = None
values = self.solutions['normalized_gaps'].values
values = values[numpy.isfinite(values)]
data = self.nth_panel(index)
# Find values above decimal precision and not NaN
data = data.loc[
~numpy.isnan(data['normalized_gaps']) & (
data['normalized_gaps'].abs() > non_zero_flux_threshold)
]
data.index = data['reaction']
reaction_data = data['normalized_gaps'].copy()
reaction_data[numpy.isposinf(reaction_data)] = reaction_data.max()
reaction_data[numpy.isneginf(reaction_data)] = reaction_data.min()
reaction_data = dict(reaction_data.iteritems())
reaction_data['max'] = numpy.abs(values).max()
reaction_data['min'] = -reaction_data['max']
scale = self.plot_scale(palette)
reaction_scale = [dict(type='min', color=scale[0][1], size=24),
dict(type='value', value=scale[0][0], color=scale[0][1], size=21),
dict(type='value', value=scale[1][0], color=scale[1][1], size=16),
dict(type='value', value=scale[2][0], color=scale[2][1], size=8),
dict(type='value', value=scale[3][0], color=scale[3][1], size=16),
dict(type='value', value=scale[4][0], color=scale[4][1], size=21),
dict(type='max', color=scale[4][1], size=24)]
builder = escher.Builder(map_name=map_name, map_json=map_json, reaction_data=reaction_data,
reaction_scale=reaction_scale)
if in_ipnb():
from IPython.display import display
display(builder.display_in_notebook())
else:
builder.display_in_browser()
except ImportError:
print("Escher must be installed in order to visualize maps")
def plot_production_envelope(envelope, objective, key, grid=None, width=None, height=None, title=None,
points=None, points_colors=None, axis_font_size=None):
if util.in_ipnb():
if config.use_bokeh:
plot_production_envelope_ipython_bokeh(envelope, objective, key, grid=grid, width=width, height=height,
title=title, points=points, points_colors=points_colors,
axis_font_size=axis_font_size)
elif config.use_matplotlib:
plot_production_envelope_ipython_matplotlib(envelope, objective, key, grid=grid, width=width, height=height,
title=title, points=points, points_colors=points_colors,
axis_font_size=axis_font_size)
else:
plot_production_envelope_cli(envelope, objective, key, width=width, height=height, title=title, points=points,
points_colors=points_colors, axis_font_size=axis_font_size)
def _display_on_map_static(self, index, map_name, palette="RdYlBu", **kwargs):
try:
import escher
if os.path.exists(map_name):
map_json = map_name
map_name = None
else:
map_json = None
values = self.solutions['normalized_gaps'].values
values = values[numpy.isfinite(values)]
data = self.nth_panel(index)
# Find values above decimal precision and not NaN
data = data.loc[
~numpy.isnan(data['normalized_gaps']) &
(data['normalized_gaps'].abs() > non_zero_flux_threshold)]
data.index = data['reaction']
reaction_data = data['normalized_gaps'].copy()
reaction_data[numpy.isposinf(reaction_data)] = reaction_data.max()
reaction_data[numpy.isneginf(reaction_data)] = reaction_data.min()
reaction_data = dict(reaction_data.iteritems())
reaction_data['max'] = numpy.abs(values).max()
reaction_data['min'] = -reaction_data['max']
scale = self.plot_scale(palette)
reaction_scale = [dict(type='min', color=scale[0][1], size=24),
dict(type='value', value=scale[0][0], color=scale[0][1], size=21),
dict(type='value', value=scale[1][0], color=scale[1][1], size=16),
dict(type='value', value=scale[2][0], color=scale[2][1], size=8),
dict(type='value', value=scale[3][0], color=scale[3][1], size=16),
dict(type='value', value=scale[4][0], color=scale[4][1], size=21),
dict(type='max', color=scale[4][1], size=24)]
builder = escher.Builder(map_name=map_name, map_json=map_json, reaction_data=reaction_data,
reaction_scale=reaction_scale)
if in_ipnb():
from IPython.display import display
display(builder.display_in_notebook())
else:
builder.display_in_browser()
except ImportError:
print("Escher must be installed in order to visualize maps")
def _set_observer(self):
self.observers = []
if in_ipnb() and self.plot:
if config.use_bokeh:
if len(self.objective_function) > 1:
self.observers.append(plotters.IPythonBokehParetoPlotter(self.objective_function))
else:
self.observers.append(plotters.IPythonBokehFitnessPlotter())
else:
if config.use_bokeh:
pass
else:
pass
if self.progress:
self.observers.append(observers.ProgressObserver())
def _set_observer(self):
self.observers = []
if in_ipnb() and self.plot:
if config.use_bokeh:
if len(self.objective_function) > 1:
self.observers.append(plotters.IPythonBokehParetoPlotter(self.objective_function))
else:
self.observers.append(plotters.IPythonBokehFitnessPlotter())
else:
if config.use_bokeh:
pass
else:
pass
if self.progress:
self.observers.append(observers.ProgressObserver())
def _set_observers(self, number_of_islands):
observers = []
plotting_observer = None
if util.in_ipnb():
color_map = util.generate_colors(number_of_islands)
progress_observer = IPythonNotebookMultiprocessProgressObserver(number_of_islands=number_of_islands)
if config.use_bokeh:
plotting_observer = IPythonNotebookBokehMultiprocessPlotObserver(number_of_islands=number_of_islands,
color_map=color_map)
else:
progress_observer = CliMultiprocessProgressObserver(number_of_islands=number_of_islands)
if progress_observer is not None:
observers.append(progress_observer)
if plotting_observer is not None:
observers.append(plotting_observer)
return observers
def _set_observers(self, number_of_islands):
observers = []
plotting_observer = None
if util.in_ipnb():
color_map = util.generate_colors(number_of_islands)
progress_observer = IPythonNotebookMultiprocessProgressObserver(number_of_islands=number_of_islands)
if config.use_bokeh:
plotting_observer = IPythonNotebookBokehMultiprocessPlotObserver(number_of_islands=number_of_islands,
color_map=color_map)
else:
progress_observer = CliMultiprocessProgressObserver(number_of_islands=number_of_islands)
if progress_observer is not None:
observers.append(progress_observer)
if plotting_observer is not None:
observers.append(plotting_observer)
return observers
def display_on_map(self, map_name=None, palette="YlGnBu"):
try:
import escher
if os.path.exists(map_name):
map_json = map_name
map_name = None
else:
map_json = None
active_fluxes = {rid: flux for rid, flux in six.iteritems(self.fluxes) if abs(flux) > 10 ** -ndecimals}
values = [abs(v) for v in active_fluxes.values()]
values += [-v for v in values]
scale = self.plot_scale(values, palette)
reaction_scale = [dict(type='min', color=scale[0][1], size=24),
dict(type='value', value=scale[0][0], color=scale[0][1], size=21),
dict(type='value', value=scale[1][0], color=scale[1][1], size=16),
dict(type='value', value=scale[2][0], color=scale[2][1], size=8),
dict(type='value', value=scale[3][0], color=scale[3][1], size=16),
dict(type='value', value=scale[4][0], color=scale[4][1], size=21),
dict(type='max', color=scale[4][1], size=24)]
active_fluxes = {rid: round(flux, ndecimals) for rid, flux in six.iteritems(self.fluxes)
if abs(flux) > 10 ** -ndecimals}
active_fluxes['min'] = min(values)
active_fluxes['max'] = max(values)
builder = escher.Builder(map_name=map_name, map_json=map_json, reaction_data=active_fluxes,
reaction_scale=reaction_scale)
if in_ipnb():
from IPython.display import display
display(builder.display_in_notebook())
else:
builder.display_in_browser()
except ImportError:
print("Escher must be installed in order to visualize maps")
def display_on_map(self, map_name=None, palette="YlGnBu"):
try:
import escher
if os.path.exists(map_name):
map_json = map_name
map_name = None
else:
map_json = None
active_fluxes = {rid: flux for rid, flux in six.iteritems(self.fluxes) if abs(flux) > 10 ** -ndecimals}
values = [abs(v) for v in active_fluxes.values()]
values += [-v for v in values]
scale = self.plot_scale(values, palette)
reaction_scale = [dict(type='min', color=scale[0][1], size=24),
dict(type='value', value=scale[0][0], color=scale[0][1], size=21),
dict(type='value', value=scale[1][0], color=scale[1][1], size=16),
dict(type='value', value=scale[2][0], color=scale[2][1], size=8),
dict(type='value', value=scale[3][0], color=scale[3][1], size=16),
dict(type='value', value=scale[4][0], color=scale[4][1], size=21),
dict(type='max', color=scale[4][1], size=24)]
active_fluxes = {rid: round(flux, ndecimals) for rid, flux in six.iteritems(self.fluxes)
if abs(flux) > 10 ** -ndecimals}
active_fluxes['min'] = min(values)
active_fluxes['max'] = max(values)
builder = escher.Builder(map_name=map_name, map_json=map_json, reaction_data=active_fluxes,
reaction_scale=reaction_scale)
if in_ipnb():
from IPython.display import display
display(builder.display_in_notebook())
else:
builder.display_in_browser()
except ImportError:
print("Escher must be installed in order to visualize maps")
def __display_pathways_information(predicted_pathways, host, original_model):
if util.in_ipnb():
title = "Production envelopes for %s (%s)" % (host.name, original_model.id)
predicted_pathways.plot_production_envelopes(original_model, title=title, objective=original_model.biomass)
def __display_compound(inchi):
if util.in_ipnb():
Designer.__display_compound_html(inchi)
def __display_product_search_result(search_result):
if util.in_ipnb():
Designer.__display_product_search_results_html(search_result)
else:
Designer.__display_product_search_results_cli(search_result)
def delta():
if util.in_ipnb():
return "Δ"
else:
return b'\xce\x94'.decode('utf-8')
def __display_compound(inchi):
if util.in_ipnb():
Designer.__display_compound_html(inchi)
for node in g.nodes():
if isinstance(node, cameo.Reaction):
labels[node] = node.name
else:
labels[node] = node.name
nx.draw_networkx_labels(g, labels=labels, pos=layout, font_size=9)
output = BytesIO()
fig.savefig(output, format='svg')
plt.close(fig)
return output.getvalue()
try:
import uuid
if not in_ipnb():
raise ImportError
class IPythonProgressBar(object):
def __init__(self, size=100, label="", color=None, fd=None):
self.progress = 0
self.size = size
self.label = label
self.color = color
self.id = None
def start(self, width='50%'):
self.id = "progress-bar-%s" % str(uuid.uuid4())
style = "width:%s;" % width
if self.color is not None:
style += "color: %s;" % self.color
def bold(message):
if util.in_ipnb():
display(HTML("<strong>%s</strong>" % message))
else:
print("\033[1m" + message + "\033[0m")
def downreg(coeff):
if util.in_ipnb():
return "↓%.3f" % coeff
else:
return str(b'\xe2\x86\x93') + "%.3f" % coeff
def knockin():
if util.in_ipnb():
return "+"
else:
return "+"
def upreg(coeff):
if util.in_ipnb():
return "↑%.3f" % coeff
else:
return b'\xe2\x86\x91'.decode('utf-8') + "%.3f" % coeff
def __init__(self, **options):
if in_ipnb():
from bokeh.io import output_notebook
output_notebook(hide_banner=True)
super(BokehPlotter, self).__init__(**options)
elif sys.version_info[0] == 3:
if sys.version_info[1] <= 3:
from importlib import find_loader as _find
else:
from importlib.util import find_spec as _find
def find_module(name):
return _find(name) is not None
_cameo_path = __path__[0]
_cameo_data_path = os.path.join(_cameo_path, 'data')
# fix - if matplotlib is installed it is not possible to import cameo without importing matplotlib on jupyter notebook.
if find_module("matplotlib") and in_ipnb():
from IPython import get_ipython
ipython = get_ipython()
ipython.magic("matplotlib inline")
system_info = get_system_info()
from ._version import get_versions
__version__ = get_versions()['version']
del get_versions
from cameo.io import load_model
from cameo import models
def display_pathway(pathway, i):
notice("Pathway %i" % i)
if in_ipnb():
display(pathway.data_frame)
else:
print(pathway.data_frame)
def delta():
if util.in_ipnb():
return "Δ"
else:
return b'\xce\x94'.decode('utf-8')
def display_pathway(pathway, i):
notice("Pathway %i" % i)
if in_ipnb():
display(pathway.data_frame)
else:
print(pathway.data_frame)
def _display(self):
if in_ipnb():
from IPython.display import display
return display
for node in g.nodes():
if isinstance(node, cameo.Reaction):
labels[node] = node.name
else:
labels[node] = node.name
nx.draw_networkx_labels(g, labels=labels, pos=layout, font_size=9)
output = BytesIO()
fig.savefig(output, format='svg')
plt.close(fig)
return output.getvalue()
try:
import uuid
if not in_ipnb():
raise ImportError
class IPythonProgressBar(object):
def __init__(self, size=100, label="", color=None, fd=None):
self.progress = 0
self.size = size
self.label = label
self.color = color
self.id = None
def start(self, width='50%'):
self.id = "progress-bar-%s" % str(uuid.uuid4())
style = "width:%s;" % width
if self.color is not None:
style += "color: %s;" % self.color
def downreg(coeff):
if util.in_ipnb():
return "↓%.3f" % coeff
else:
return b'\xe2\x86\x93'.decode('utf-8') + "%.3f" % coeff
def __display_product_search_result(search_result):
if util.in_ipnb():
Designer.__display_product_search_results_html(search_result)
else:
Designer.__display_product_search_results_cli(search_result)
def upreg(coeff):
if util.in_ipnb():
return "↑%.3f" % coeff
else:
return str(b'\xe2\x86\x91') + "%.3f" % coeff
def downreg(coeff):
if util.in_ipnb():
return "↓%.3f" % coeff
else:
return b'\xe2\x86\x93'.decode('utf-8') + "%.3f" % coeff
def notice(message):
if util.in_ipnb():
display(HTML("<span>%s</span>" % message))
else:
print(message)
elif sys.version_info[0] == 3:
if sys.version_info[1] <= 3:
from importlib import find_loader as _find
else:
from importlib.util import find_spec as _find
def find_module(name):
return _find(name) is not None
_cameo_path = __path__[0]
_cameo_data_path = os.path.join(_cameo_path, 'data')
# fix - if matplotlib is installed it is not possible to import cameo without importing matplotlib on jupyter notebook.
if find_module("matplotlib") and in_ipnb():
from IPython import get_ipython
ipython = get_ipython()
ipython.magic("matplotlib inline")
system_info = get_system_info()
from ._version import get_versions
__version__ = get_versions()['version']
del get_versions
from cameo.io import load_model
from cameo import models
def __init__(self, **options):
if in_ipnb():
from bokeh.io import output_notebook
output_notebook(hide_banner=True)
super(BokehPlotter, self).__init__(**options)
def _display_on_map_static(self,
index,
map_name,
palette="RdYlBu",
**kwargs):
try:
import escher
if os.path.exists(map_name):
map_json = map_name
map_name = None
else:
map_json = None
values = self.normalized_gaps
values = values[~numpy.isnan(values)]
values = values[~numpy.isinf(values)]
data = self.solutions.iloc[index]
# Find values above decimal precision
data = data[numpy.abs(data.normalized_gaps.astype(float)) >
non_zero_flux_threshold]
# Remove NaN rows
data = data[~numpy.isnan(data.normalized_gaps.astype(float))]
reaction_data = dict(data.normalized_gaps)
for rid, gap in six.iteritems(reaction_data):
if numpy.isposinf(gap):
gap = numpy.max(values)
elif numpy.isneginf(gap):
gap = numpy.min(values)
reaction_data[rid] = gap
scale = self.plot_scale(palette)
reaction_data['min'] = min(numpy.abs(values) * -1)
reaction_data['max'] = max(numpy.abs(values))
reaction_scale = [
dict(type='min', color=scale[0][1], size=24),
dict(type='value',
value=scale[0][0],
color=scale[0][1],
size=21),
dict(type='value',
value=scale[1][0],
color=scale[1][1],
size=16),
dict(type='value',
value=scale[2][0],
color=scale[2][1],
size=8),
dict(type='value',
value=scale[3][0],
color=scale[3][1],
size=16),
dict(type='value',
value=scale[4][0],
color=scale[4][1],
size=21),
dict(type='max', color=scale[4][1], size=24)
]
builder = escher.Builder(map_name=map_name,
map_json=map_json,
reaction_data=reaction_data,
reaction_scale=reaction_scale)
if in_ipnb():
from IPython.display import display
display(builder.display_in_notebook())
else:
builder.display_in_browser()
except ImportError:
print("Escher must be installed in order to visualize maps")
def delta():
if util.in_ipnb():
return "Δ"
else:
return str(b'\xce\x94')
def upreg(coeff):
if util.in_ipnb():
return "↑%.3f" % coeff
else:
return b'\xe2\x86\x91'.decode('utf-8') + "%.3f" % coeff