def show(self):
"""Saves the plot to a temporary file and shows it."""
if not isinstance(self._surface, cairo.ImageSurface):
sur = cairo.ImageSurface(cairo.FORMAT_ARGB32, int(self.bbox.width),
int(self.bbox.height))
ctx = cairo.Context(sur)
self.redraw(ctx)
else:
sur = self._surface
ctx = self._ctx
if self._is_dirty:
self.redraw(ctx)
with named_temporary_file(prefix="igraph", suffix=".png") as tmpfile:
sur.write_to_png(tmpfile)
config = Configuration.instance()
imgviewer = config["apps.image_viewer"]
if not imgviewer:
# No image viewer was given and none was detected. This
# should only happen on unknown platforms.
plat = platform.system()
raise NotImplementedError("showing plots is not implemented " + \
"on this platform: %s" % plat)
else:
os.system("%s %s" % (imgviewer, tmpfile))
if platform.system() == "Darwin" or self._windows_hacks:
# On Mac OS X and Windows, launched applications are likely to
# fork and give control back to Python immediately.
# Chances are that the temporary image file gets removed
# before the image viewer has a chance to open it, so
# we wait here a little bit. Yes, this is quite hackish :(
time.sleep(5)
def show(self):
"""Saves the plot to a temporary file and shows it."""
if not isinstance(self._surface, cairo.ImageSurface):
sur = cairo.ImageSurface(cairo.FORMAT_ARGB32,
int(self.bbox.width), int(self.bbox.height))
ctx = cairo.Context(sur)
self.redraw(ctx)
else:
sur = self._surface
ctx = self._ctx
if self._is_dirty:
self.redraw(ctx)
with named_temporary_file(prefix="igraph", suffix=".png") as tmpfile:
sur.write_to_png(tmpfile)
config = Configuration.instance()
imgviewer = config["apps.image_viewer"]
if not imgviewer:
# No image viewer was given and none was detected. This
# should only happen on unknown platforms.
plat = platform.system()
raise NotImplementedError("showing plots is not implemented " + \
"on this platform: %s" % plat)
else:
os.system("%s %s" % (imgviewer, tmpfile))
if platform.system() == "Darwin" or self._windows_hacks:
# On Mac OS X and Windows, launched applications are likely to
# fork and give control back to Python immediately.
# Chances are that the temporary image file gets removed
# before the image viewer has a chance to open it, so
# we wait here a little bit. Yes, this is quite hackish :(
time.sleep(5)
def main():
"""The main entry point for igraph when invoked from the command
line shell"""
config = Configuration.instance()
if config.filename:
print("Using configuration from %s" % config.filename, file=sys.stderr)
else:
print("No configuration file, using defaults", file=sys.stderr)
if "shells" in config:
parts = [part.strip() for part in config["shells"].split(",")]
shell_classes = []
available_classes = dict(
[
(k, v)
for k, v in globals().items()
if isinstance(v, type) and issubclass(v, Shell)
]
)
for part in parts:
cls = available_classes.get(part, None)
if cls is None:
print("Warning: unknown shell class `%s'" % part, file=sys.stderr)
continue
shell_classes.append(cls)
else:
shell_classes = [IPythonShell, ClassicPythonShell]
import platform
if platform.system() == "Windows":
shell_classes.insert(0, IDLEShell)
shell = None
for shell_class in shell_classes:
# pylint: disable-msg=W0703
# W0703: catch "Exception"
try:
shell = shell_class()
break
except Exception:
# Try the next one
if "Classic" in str(shell_class):
raise
pass
if isinstance(shell, Shell):
if config["verbose"]:
if shell.supports_progress_bar():
set_progress_handler(shell.get_progress_handler())
if shell.supports_status_messages():
set_status_handler(shell.get_status_handler())
shell()
else:
print("No suitable Python shell was found.", file=sys.stderr)
print("Check configuration variable `general.shells'.", file=sys.stderr)
def main():
"""The main entry point for igraph when invoked from the command
line shell"""
config = Configuration.instance()
if config.filename:
print >> sys.stderr, "Using configuration from %s" % config.filename
else:
print >> sys.stderr, "No configuration file, using defaults"
if config.has_key("shells"):
parts = [part.strip() for part in config["shells"].split(",")]
shell_classes = []
available_classes = dict([(k, v) for k, v in globals().iteritems()
if isinstance(v, type) and issubclass(v, Shell)])
for part in parts:
klass = available_classes.get(part, None)
if klass is None:
print >> sys.stderr, "Warning: unknown shell class `%s'" % part
continue
shell_classes.append(klass)
else:
shell_classes = [IPythonShell, ClassicPythonShell]
import platform
if platform.system() == "Windows":
shell_classes.insert(0, IDLEShell)
shell = None
for shell_class in shell_classes:
# pylint: disable-msg=W0703
# W0703: catch "Exception"
try:
shell = shell_class()
break
except StandardError:
# Try the next one
if "Classic" in str(shell_class):
raise
pass
if isinstance(shell, Shell):
if config["verbose"]:
if shell.supports_progress_bar():
set_progress_handler(shell.get_progress_handler())
if shell.supports_status_messages():
set_status_handler(shell.get_status_handler())
shell()
else:
print >> sys.stderr, "No suitable Python shell was found."
print >> sys.stderr, "Check configuration variable `general.shells'."
def _get_response(self, path, params={}, compressed=False):
"""Sends a request to Nexus at the given path with the given parameters
and returns a file-like object for the response. `compressed` denotes
whether we accept compressed responses."""
if self.url is None:
url = Configuration.instance()["remote.nexus.url"]
else:
url = self.url
url = "%s%s?%s" % (url, path, urlencode(params))
request = urllib2.Request(url)
if compressed:
request.add_header("Accept-Encoding", "gzip")
if self.debug:
print "[debug] Sending request: %s" % url
return self._opener.open(request)
def _get_response(self, path, params={}, compressed=False):
"""Sends a request to Nexus at the given path with the given parameters
and returns a file-like object for the response. `compressed` denotes
whether we accept compressed responses."""
if self.url is None:
url = Configuration.instance()["remote.nexus.url"]
else:
url = self.url
url = "%s%s?%s" % (url, path, urlencode(params))
request = urllib.request.Request(url)
if compressed:
request.add_header("Accept-Encoding", "gzip")
if self.debug:
print("[debug] Sending request: %s" % url)
return self._opener.open(request)
def __init__(self, target=None, bbox=None, palette=None, background=None):
"""Creates a new plot.
@param target: the target surface to write to. It can be one of the
following types:
- C{None} -- an appropriate surface will be created and the object
will be plotted there.
- C{cairo.Surface} -- the given Cairo surface will be used.
- C{string} -- a file with the given name will be created and an
appropriate Cairo surface will be attached to it.
@param bbox: the bounding box of the surface. It is interpreted
differently with different surfaces: PDF and PS surfaces will
treat it as points (1 point = 1/72 inch). Image surfaces will
treat it as pixels. SVG surfaces will treat it as an abstract
unit, but it will mostly be interpreted as pixels when viewing
the SVG file in Firefox.
@param palette: the palette primarily used on the plot if the
added objects do not specify a private palette. Must be either
an L{igraph.drawing.colors.Palette} object or a string referring
to a valid key of C{igraph.drawing.colors.palettes} (see module
L{igraph.drawing.colors}) or C{None}. In the latter case, the default
palette given by the configuration key C{plotting.palette} is used.
@param background: the background color. If C{None}, the background
will be transparent. You can use any color specification here that
is understood by L{igraph.drawing.colors.color_name_to_rgba}.
"""
self._filename = None
self._surface_was_created = not isinstance(target, cairo.Surface)
self._need_tmpfile = False
# Several Windows-specific hacks will be used from now on, thanks
# to Dale Hunscher for debugging and fixing all that stuff
self._windows_hacks = "Windows" in platform.platform()
if bbox is None:
self.bbox = BoundingBox(600, 600)
elif isinstance(bbox, tuple) or isinstance(bbox, list):
self.bbox = BoundingBox(bbox)
else:
self.bbox = bbox
if palette is None:
config = Configuration.instance()
palette = config["plotting.palette"]
if not isinstance(palette, Palette):
palette = palettes[palette]
self._palette = palette
if target is None:
self._need_tmpfile = True
self._surface = cairo.ImageSurface(
cairo.FORMAT_ARGB32, int(self.bbox.width), int(self.bbox.height)
)
elif isinstance(target, cairo.Surface):
self._surface = target
else:
self._filename = target
_, ext = os.path.splitext(target)
ext = ext.lower()
if ext == ".pdf":
self._surface = cairo.PDFSurface(
target, self.bbox.width, self.bbox.height
)
elif ext == ".ps" or ext == ".eps":
self._surface = cairo.PSSurface(
target, self.bbox.width, self.bbox.height
)
elif ext == ".png":
self._surface = cairo.ImageSurface(
cairo.FORMAT_ARGB32, int(self.bbox.width), int(self.bbox.height)
)
elif ext == ".svg":
self._surface = cairo.SVGSurface(
target, self.bbox.width, self.bbox.height
)
else:
raise ValueError("image format not handled by Cairo: %s" % ext)
self._ctx = cairo.Context(self._surface)
self._objects = []
self._is_dirty = False
self.background = background
def plot(obj, target=None, bbox=(0, 0, 600, 600), *args, **kwds):
"""Plots the given object to the given target.
Positional and keyword arguments not explicitly mentioned here will be
passed down to the C{__plot__} method of the object being plotted.
Since you are most likely interested in the keyword arguments available
for graph plots, see L{Graph.__plot__} as well.
@param obj: the object to be plotted
@param target: the target where the object should be plotted. It can be one
of the following types:
- C{matplotib.axes.Axes} -- a matplotlib/pyplot axes in which the
graph will be plotted. Drawing is delegated to the chosen matplotlib
backend, and you can use interactive backends and matplotlib
functions to save to file as well.
- C{string} -- a file with the given name will be created and an
appropriate Cairo surface will be attached to it. The supported image
formats are: PNG, PDF, SVG and PostScript.
- C{cairo.Surface} -- the given Cairo surface will be used. This can
refer to a PNG image, an arbitrary window, an SVG file, anything that
Cairo can handle.
- C{None} -- a temporary file will be created and the object will be
plotted there. igraph will attempt to open an image viewer and show
the temporary file. This feature is deprecated from python-igraph
version 0.9.1 and will be removed in 0.10.0.
@param bbox: the bounding box of the plot. It must be a tuple with either
two or four integers, or a L{BoundingBox} object. If this is a tuple
with two integers, it is interpreted as the width and height of the plot
(in pixels for PNG images and on-screen plots, or in points for PDF,
SVG and PostScript plots, where 72 pt = 1 inch = 2.54 cm). If this is
a tuple with four integers, the first two denotes the X and Y coordinates
of a corner and the latter two denoting the X and Y coordinates of the
opposite corner.
@keyword opacity: the opacity of the object being plotted. It can be
used to overlap several plots of the same graph if you use the same
layout for them -- for instance, you might plot a graph with opacity
0.5 and then plot its spanning tree over it with opacity 0.1. To
achieve this, you'll need to modify the L{Plot} object returned with
L{Plot.add}.
@keyword palette: the palette primarily used on the plot if the
added objects do not specify a private palette. Must be either
an L{igraph.drawing.colors.Palette} object or a string referring
to a valid key of C{igraph.drawing.colors.palettes} (see module
L{igraph.drawing.colors}) or C{None}. In the latter case, the default
palette given by the configuration key C{plotting.palette} is used.
@keyword margin: the top, right, bottom, left margins as a 4-tuple.
If it has less than 4 elements or is a single float, the elements
will be re-used until the length is at least 4. The default margin
is 20 on each side.
@keyword inline: whether to try and show the plot object inline in the
current IPython notebook. Passing C{None} here or omitting this keyword
argument will look up the preferred behaviour from the
C{shell.ipython.inlining.Plot} configuration key. Note that this keyword
argument has an effect only if igraph is run inside IPython and C{target}
is C{None}.
@return: an appropriate L{Plot} object.
@see: Graph.__plot__
"""
_, plt = find_matplotlib()
if hasattr(plt, "Axes") and isinstance(target, plt.Axes):
result = MatplotlibGraphDrawer(ax=target)
result.draw(obj, *args, **kwds)
return
if not isinstance(bbox, BoundingBox):
bbox = BoundingBox(bbox)
result = Plot(target, bbox, background=kwds.get("background", "white"))
if "margin" in kwds:
bbox = bbox.contract(kwds["margin"])
del kwds["margin"]
else:
bbox = bbox.contract(20)
result.add(obj, bbox, *args, **kwds)
if target is None and _is_running_in_ipython():
# Get the default value of the `inline` argument from the configuration if
# needed
inline = kwds.get("inline")
if inline is None:
config = Configuration.instance()
inline = config["shell.ipython.inlining.Plot"]
# If we requested an inline plot, just return the result and IPython will
# call its _repr_svg_ method. If we requested a non-inline plot, show the
# plot in a separate window and return nothing
if inline:
return result
else:
result.show()
return
# We are either not in IPython or the user specified an explicit plot target,
# so just show or save the result
if target is None:
result.show()
elif isinstance(target, str):
result.save()
# Also return the plot itself
return result
def draw(self, graph, palette, *args, **kwds):
# Some abbreviations for sake of simplicity
directed = graph.is_directed()
context = self.context
# Calculate/get the layout of the graph
layout = self.ensure_layout(kwds.get("layout", None), graph)
# Determine the size of the margin on each side
margin = kwds.get("margin", 0)
try:
margin = list(margin)
except TypeError:
margin = [margin]
while len(margin) < 4:
margin.extend(margin)
# Contract the drawing area by the margin and fit the layout
bbox = self.bbox.contract(margin)
layout.fit_into(bbox, keep_aspect_ratio=kwds.get("keep_aspect_ratio", False))
# Decide whether we need to calculate the curvature of edges
# automatically -- and calculate them if needed.
autocurve = kwds.get("autocurve", None)
if autocurve or (
autocurve is None
and "edge_curved" not in kwds
and "curved" not in graph.edge_attributes()
and graph.ecount() < 10000
):
from igraph import autocurve
default = kwds.get("edge_curved", 0)
if default is True:
default = 0.5
default = float(default)
kwds["edge_curved"] = autocurve(graph, attribute=None, default=default)
# Construct the vertex, edge and label drawers
vertex_drawer = self.vertex_drawer_factory(context, bbox, palette, layout)
edge_drawer = self.edge_drawer_factory(context, palette)
label_drawer = self.label_drawer_factory(context)
# Construct the visual vertex/edge builders based on the specifications
# provided by the vertex_drawer and the edge_drawer
vertex_builder = vertex_drawer.VisualVertexBuilder(graph.vs, kwds)
edge_builder = edge_drawer.VisualEdgeBuilder(graph.es, kwds)
# Determine the order in which we will draw the vertices and edges
vertex_order = self._determine_vertex_order(graph, kwds)
edge_order = self._determine_edge_order(graph, kwds)
# Draw the highlighted groups (if any)
if "mark_groups" in kwds:
mark_groups = kwds["mark_groups"]
# Deferred import to avoid a cycle in the import graph
from igraph.clustering import VertexClustering, VertexCover
# Figure out what to do with mark_groups in order to be able to
# iterate over it and get memberlist-color pairs
if isinstance(mark_groups, dict):
# Dictionary mapping vertex indices or tuples of vertex
# indices to colors
group_iter = iter(mark_groups.items())
elif isinstance(mark_groups, (VertexClustering, VertexCover)):
# Vertex clustering
group_iter = ((group, color) for color, group in enumerate(mark_groups))
elif hasattr(mark_groups, "__iter__"):
# Lists, tuples, iterators etc
group_iter = iter(mark_groups)
else:
# False
group_iter = iter({}.items())
# We will need a polygon drawer to draw the convex hulls
polygon_drawer = PolygonDrawer(context, bbox)
# Iterate over color-memberlist pairs
for group, color_id in group_iter:
if not group or color_id is None:
continue
color = palette.get(color_id)
if isinstance(group, VertexSeq):
group = [vertex.index for vertex in group]
if not hasattr(group, "__iter__"):
raise TypeError("group membership list must be iterable")
# Get the vertex indices that constitute the convex hull
hull = [group[i] for i in convex_hull([layout[idx] for idx in group])]
# Calculate the preferred rounding radius for the corners
corner_radius = 1.25 * max(vertex_builder[idx].size for idx in hull)
# Construct the polygon
polygon = [layout[idx] for idx in hull]
if len(polygon) == 2:
# Expand the polygon (which is a flat line otherwise)
a, b = Point(*polygon[0]), Point(*polygon[1])
c = corner_radius * (a - b).normalized()
n = Point(-c[1], c[0])
polygon = [a + n, b + n, b - c, b - n, a - n, a + c]
else:
# Expand the polygon around its center of mass
center = Point(
*[sum(coords) / float(len(coords)) for coords in zip(*polygon)]
)
polygon = [
Point(*point).towards(center, -corner_radius)
for point in polygon
]
# Draw the hull
context.set_source_rgba(color[0], color[1], color[2], color[3] * 0.25)
polygon_drawer.draw_path(polygon, corner_radius=corner_radius)
context.fill_preserve()
context.set_source_rgba(*color)
context.stroke()
# Construct the iterator that we will use to draw the edges
es = graph.es
if edge_order is None:
# Default edge order
edge_coord_iter = zip(es, edge_builder)
else:
# Specified edge order
edge_coord_iter = ((es[i], edge_builder[i]) for i in edge_order)
# Draw the edges
if directed:
drawer_method = edge_drawer.draw_directed_edge
else:
drawer_method = edge_drawer.draw_undirected_edge
for edge, visual_edge in edge_coord_iter:
src, dest = edge.tuple
src_vertex, dest_vertex = vertex_builder[src], vertex_builder[dest]
drawer_method(visual_edge, src_vertex, dest_vertex)
# Construct the iterator that we will use to draw the vertices
vs = graph.vs
if vertex_order is None:
# Default vertex order
vertex_coord_iter = zip(vs, vertex_builder, layout)
else:
# Specified vertex order
vertex_coord_iter = (
(vs[i], vertex_builder[i], layout[i]) for i in vertex_order
)
# Draw the vertices
drawer_method = vertex_drawer.draw
context.set_line_width(1)
for vertex, visual_vertex, coords in vertex_coord_iter:
drawer_method(visual_vertex, vertex, coords)
# Decide whether the labels have to be wrapped
wrap = kwds.get("wrap_labels")
if wrap is None:
wrap = Configuration.instance()["plotting.wrap_labels"]
wrap = bool(wrap)
# Construct the iterator that we will use to draw the vertex labels
if vertex_order is None:
# Default vertex order
vertex_coord_iter = zip(vertex_builder, layout)
else:
# Specified vertex order
vertex_coord_iter = ((vertex_builder[i], layout[i]) for i in vertex_order)
# Draw the vertex labels
for vertex, coords in vertex_coord_iter:
if vertex.label is None:
continue
# Set the font family, size, color and text
context.select_font_face(
vertex.font, cairo.FONT_SLANT_NORMAL, cairo.FONT_WEIGHT_NORMAL
)
context.set_font_size(vertex.label_size)
context.set_source_rgba(*vertex.label_color)
label_drawer.text = vertex.label
if vertex.label_dist:
# Label is displaced from the center of the vertex.
_, yb, w, h, _, _ = label_drawer.text_extents()
w, h = w / 2.0, h / 2.0
radius = vertex.label_dist * vertex.size / 2.0
# First we find the reference point that is at distance `radius'
# from the vertex in the direction given by `label_angle'.
# Then we place the label in a way that the line connecting the
# center of the bounding box of the label with the center of the
# vertex goes through the reference point and the reference
# point lies exactly on the bounding box of the vertex.
alpha = vertex.label_angle % (2 * pi)
cx = coords[0] + radius * cos(alpha)
cy = coords[1] - radius * sin(alpha)
# Now we have the reference point. We have to decide which side
# of the label box will intersect with the line that connects
# the center of the label with the center of the vertex.
if w > 0:
beta = atan2(h, w) % (2 * pi)
else:
beta = pi / 2.0
gamma = pi - beta
if alpha > 2 * pi - beta or alpha <= beta:
# Intersection at left edge of label
cx += w
cy -= tan(alpha) * w
elif alpha > beta and alpha <= gamma:
# Intersection at bottom edge of label
try:
cx += h / tan(alpha)
except:
pass # tan(alpha) == inf
cy -= h
elif alpha > gamma and alpha <= gamma + 2 * beta:
# Intersection at right edge of label
cx -= w
cy += tan(alpha) * w
else:
# Intersection at top edge of label
try:
cx -= h / tan(alpha)
except:
pass # tan(alpha) == inf
cy += h
# Draw the label
label_drawer.draw_at(cx - w, cy - h - yb, wrap=wrap)
else:
# Label is exactly in the center of the vertex
cx, cy = coords
half_size = vertex.size / 2.0
label_drawer.bbox = (
cx - half_size,
cy - half_size,
cx + half_size,
cy + half_size,
)
label_drawer.draw(wrap=wrap)
# Construct the iterator that we will use to draw the edge labels
es = graph.es
if edge_order is None:
# Default edge order
edge_coord_iter = zip(es, edge_builder)
else:
# Specified edge order
edge_coord_iter = ((es[i], edge_builder[i]) for i in edge_order)
# Draw the edge labels
for edge, visual_edge in edge_coord_iter:
if visual_edge.label is None:
continue
# Set the font family, size, color and text
context.select_font_face(
visual_edge.font, cairo.FONT_SLANT_NORMAL, cairo.FONT_WEIGHT_NORMAL
)
context.set_font_size(visual_edge.label_size)
context.set_source_rgba(*visual_edge.label_color)
label_drawer.text = visual_edge.label
# Ask the edge drawer to propose an anchor point for the label
src, dest = edge.tuple
src_vertex, dest_vertex = vertex_builder[src], vertex_builder[dest]
(x, y), (halign, valign) = edge_drawer.get_label_position(
edge, src_vertex, dest_vertex
)
# Measure the text
_, yb, w, h, _, _ = label_drawer.text_extents()
w /= 2.0
h /= 2.0
# Place the text relative to the edge
if halign == TextAlignment.RIGHT:
x -= w
elif halign == TextAlignment.LEFT:
x += w
if valign == TextAlignment.BOTTOM:
y -= h - yb / 2.0
elif valign == TextAlignment.TOP:
y += h
# Draw the edge label
label_drawer.halign = halign
label_drawer.valign = valign
label_drawer.bbox = (x - w, y - h, x + w, y + h)
label_drawer.draw(wrap=wrap)
def _collect_attributes(self, attr_spec, config=None):
"""Collects graph visualization attributes from various sources.
This method can be used to collect the attributes required for graph
visualization from various sources. Attribute value sources are:
- A specific value of a Python dict belonging to a given key. This dict
is given by the argument M{self.kwds} at construction time, and
the name of the key is determined by the argument specification
given in M{attr_spec}.
- A vertex or edge sequence of a graph, given in M{self.seq}
- The global configuration, given in M{config}
- A default value when all other sources fail to provide the value.
This is also given in M{attr_spec}.
@param attr_spec: an L{AttributeSpecification} object which contains
the name of the attribute when it is coming from a
list of Python keyword arguments, the name of the
attribute when it is coming from the graph attributes
directly, the default value of the attribute and an
optional callable transformation to call on the values.
This can be used to ensure that the attributes are of
a given type.
@param config: a L{Configuration} object to be used for determining the
defaults if all else fails. If C{None}, the global
igraph configuration will be used
@return: the collected attributes
"""
kwds = self.kwds
seq = self.seq
n = len(seq)
# Special case if the attribute name is "label"
if attr_spec.name == "label":
if attr_spec.alt_name in kwds and kwds[attr_spec.alt_name] is None:
return [None] * n
# If the attribute uses an external callable to derive the attribute
# values, call it and store the results
if attr_spec.func is not None:
func = attr_spec.func
result = [func(i) for i in xrange(n)]
return result
# Get the configuration object
if config is None:
config = Configuration.instance()
# Fetch the defaults from the vertex/edge sequence
try:
attrs = seq[attr_spec.name]
except KeyError:
attrs = None
# Override them from the keyword arguments (if any)
result = kwds.get(attr_spec.alt_name, None)
if attrs:
if not result:
result = attrs
else:
if isinstance(result, str):
result = [result] * n
try:
len(result)
except TypeError:
result = [result] * n
result = [result[idx] or attrs[idx] for idx in xrange(len(result))]
# Special case for string overrides, strings are not treated
# as sequences here
if isinstance(result, str):
result = [result] * n
# If the result is still not a sequence, make it one
try:
len(result)
except TypeError:
result = [result] * n
# If it is not a list, ensure that it is a list
if not hasattr(result, "extend"):
result = list(result)
# Ensure that the length is n
while len(result) < n:
if len(result) <= n / 2:
result.extend(result)
else:
result.extend(result[0 : (n - len(result))])
# By now, the length of the result vector should be n as requested
# Get the configuration defaults
try:
default = config["plotting.%s" % attr_spec.alt_name]
except NoOptionError:
default = None
if default is None:
default = attr_spec.default
# Fill the None values with the default values
for idx in xrange(len(result)):
if result[idx] is None:
result[idx] = default
# Finally, do the transformation
if attr_spec.transform is not None:
transform = attr_spec.transform
result = [transform(x) for x in result]
return result
def __init__(self, target=None, bbox=None, palette=None, background=None):
"""Creates a new plot.
@param target: the target surface to write to. It can be one of the
following types:
- C{None} -- an appropriate surface will be created and the object
will be plotted there.
- C{cairo.Surface} -- the given Cairo surface will be used.
- C{string} -- a file with the given name will be created and an
appropriate Cairo surface will be attached to it.
@param bbox: the bounding box of the surface. It is interpreted
differently with different surfaces: PDF and PS surfaces will
treat it as points (1 point = 1/72 inch). Image surfaces will
treat it as pixels. SVG surfaces will treat it as an abstract
unit, but it will mostly be interpreted as pixels when viewing
the SVG file in Firefox.
@param palette: the palette primarily used on the plot if the
added objects do not specify a private palette. Must be either
an L{igraph.drawing.colors.Palette} object or a string referring
to a valid key of C{igraph.drawing.colors.palettes} (see module
L{igraph.drawing.colors}) or C{None}. In the latter case, the default
palette given by the configuration key C{plotting.palette} is used.
@param background: the background color. If C{None}, the background
will be transparent. You can use any color specification here that
is understood by L{igraph.drawing.colors.color_name_to_rgba}.
"""
self._filename = None
self._surface_was_created = not isinstance(target, cairo.Surface)
self._need_tmpfile = False
# Several Windows-specific hacks will be used from now on, thanks
# to Dale Hunscher for debugging and fixing all that stuff
self._windows_hacks = "Windows" in platform.platform()
if bbox is None:
self.bbox = BoundingBox(600, 600)
elif isinstance(bbox, tuple) or isinstance(bbox, list):
self.bbox = BoundingBox(bbox)
else:
self.bbox = bbox
if palette is None:
config = Configuration.instance()
palette = config["plotting.palette"]
if not isinstance(palette, Palette):
palette = palettes[palette]
self._palette = palette
if target is None:
self._need_tmpfile = True
self._surface = cairo.ImageSurface(cairo.FORMAT_ARGB32, \
int(self.bbox.width), int(self.bbox.height))
elif isinstance(target, cairo.Surface):
self._surface = target
else:
self._filename = target
_, ext = os.path.splitext(target)
ext = ext.lower()
if ext == ".pdf":
self._surface = cairo.PDFSurface(target, self.bbox.width, \
self.bbox.height)
elif ext == ".ps" or ext == ".eps":
self._surface = cairo.PSSurface(target, self.bbox.width, \
self.bbox.height)
elif ext == ".png":
self._surface = cairo.ImageSurface(cairo.FORMAT_ARGB32, \
int(self.bbox.width), int(self.bbox.height))
elif ext == ".svg":
self._surface = cairo.SVGSurface(target, self.bbox.width, \
self.bbox.height)
else:
raise ValueError("image format not handled by Cairo: %s" % ext)
self._ctx = cairo.Context(self._surface)
self._objects = []
self._is_dirty = False
self.background = background
def plot(obj, target=None, bbox=(0, 0, 600, 600), *args, **kwds):
"""Plots the given object to the given target.
Positional and keyword arguments not explicitly mentioned here will be
passed down to the C{__plot__} method of the object being plotted.
Since you are most likely interested in the keyword arguments available
for graph plots, see L{Graph.__plot__} as well.
@param obj: the object to be plotted
@param target: the target where the object should be plotted. It can be one
of the following types:
- C{None} -- an appropriate surface will be created and the object will
be plotted there.
- C{cairo.Surface} -- the given Cairo surface will be used. This can
refer to a PNG image, an arbitrary window, an SVG file, anything that
Cairo can handle.
- C{string} -- a file with the given name will be created and an
appropriate Cairo surface will be attached to it. The supported image
formats are: PNG, PDF, SVG and PostScript.
@param bbox: the bounding box of the plot. It must be a tuple with either
two or four integers, or a L{BoundingBox} object. If this is a tuple
with two integers, it is interpreted as the width and height of the plot
(in pixels for PNG images and on-screen plots, or in points for PDF,
SVG and PostScript plots, where 72 pt = 1 inch = 2.54 cm). If this is
a tuple with four integers, the first two denotes the X and Y coordinates
of a corner and the latter two denoting the X and Y coordinates of the
opposite corner.
@keyword opacity: the opacity of the object being plotted. It can be
used to overlap several plots of the same graph if you use the same
layout for them -- for instance, you might plot a graph with opacity
0.5 and then plot its spanning tree over it with opacity 0.1. To
achieve this, you'll need to modify the L{Plot} object returned with
L{Plot.add}.
@keyword palette: the palette primarily used on the plot if the
added objects do not specify a private palette. Must be either
an L{igraph.drawing.colors.Palette} object or a string referring
to a valid key of C{igraph.drawing.colors.palettes} (see module
L{igraph.drawing.colors}) or C{None}. In the latter case, the default
palette given by the configuration key C{plotting.palette} is used.
@keyword margin: the top, right, bottom, left margins as a 4-tuple.
If it has less than 4 elements or is a single float, the elements
will be re-used until the length is at least 4. The default margin
is 20 on each side.
@keyword inline: whether to try and show the plot object inline in the
current IPython notebook. Passing ``None`` here or omitting this keyword
argument will look up the preferred behaviour from the
C{shell.ipython.inlining.Plot} configuration key. Note that this keyword
argument has an effect only if igraph is run inside IPython and C{target}
is C{None}.
@return: an appropriate L{Plot} object.
@see: Graph.__plot__
"""
if not isinstance(bbox, BoundingBox):
bbox = BoundingBox(bbox)
result = Plot(target, bbox, background="white")
if "margin" in kwds:
bbox = bbox.contract(kwds["margin"])
del kwds["margin"]
else:
bbox = bbox.contract(20)
result.add(obj, bbox, *args, **kwds)
if IN_IPYTHON and target is None:
# Get the default value of the `inline` argument from the configuration if
# needed
inline = kwds.get("inline")
if inline is None:
config = Configuration.instance()
inline = config["shell.ipython.inlining.Plot"]
# If we requested an inline plot, just return the result and IPython will
# call its _repr_svg_ method. If we requested a non-inline plot, show the
# plot in a separate window and return nothing
if inline:
return result
else:
result.show()
return
# We are either not in IPython or the user specified an explicit plot target,
# so just show or save the result
if target is None:
result.show()
elif isinstance(target, basestring):
result.save()
# Also return the plot itself
return result
def draw(self, graph, palette, *args, **kwds):
# Some abbreviations for sake of simplicity
directed = graph.is_directed()
context = self.context
# Calculate/get the layout of the graph
layout = self.ensure_layout(kwds.get("layout", None), graph)
# Determine the size of the margin on each side
margin = kwds.get("margin", 0)
try:
margin = list(margin)
except TypeError:
margin = [margin]
while len(margin)<4:
margin.extend(margin)
# Contract the drawing area by the margin and fit the layout
bbox = self.bbox.contract(margin)
layout.fit_into(bbox, keep_aspect_ratio=kwds.get("keep_aspect_ratio", False))
# Decide whether we need to calculate the curvature of edges
# automatically -- and calculate them if needed.
autocurve = kwds.get("autocurve", None)
if autocurve or (autocurve is None and \
"edge_curved" not in kwds and "curved" not in graph.edge_attributes() \
and graph.ecount() < 10000):
from igraph import autocurve
default = kwds.get("edge_curved", 0)
if default is True:
default = 0.5
default = float(default)
kwds["edge_curved"] = autocurve(graph, attribute=None, default=default)
# Construct the vertex, edge and label drawers
vertex_drawer = self.vertex_drawer_factory(context, bbox, palette, layout)
edge_drawer = self.edge_drawer_factory(context, palette)
label_drawer = self.label_drawer_factory(context)
# Construct the visual vertex/edge builders based on the specifications
# provided by the vertex_drawer and the edge_drawer
vertex_builder = vertex_drawer.VisualVertexBuilder(graph.vs, kwds)
edge_builder = edge_drawer.VisualEdgeBuilder(graph.es, kwds)
# Determine the order in which we will draw the vertices and edges
vertex_order = self._determine_vertex_order(graph, kwds)
edge_order = self._determine_edge_order(graph, kwds)
# Draw the highlighted groups (if any)
if "mark_groups" in kwds:
mark_groups = kwds["mark_groups"]
# Deferred import to avoid a cycle in the import graph
from igraph.clustering import VertexClustering, VertexCover
# Figure out what to do with mark_groups in order to be able to
# iterate over it and get memberlist-color pairs
if isinstance(mark_groups, dict):
# Dictionary mapping vertex indices or tuples of vertex
# indices to colors
group_iter = mark_groups.iteritems()
elif isinstance(mark_groups, (VertexClustering, VertexCover)):
# Vertex clustering
group_iter = (
(group, color) for color, group in enumerate(mark_groups)
)
elif hasattr(mark_groups, "__iter__"):
# Lists, tuples, iterators etc
group_iter = iter(mark_groups)
else:
# False
group_iter = {}.iteritems()
# We will need a polygon drawer to draw the convex hulls
polygon_drawer = PolygonDrawer(context, bbox)
# Iterate over color-memberlist pairs
for group, color_id in group_iter:
if not group or color_id is None:
continue
color = palette.get(color_id)
if isinstance(group, VertexSeq):
group = [vertex.index for vertex in group]
if not hasattr(group, "__iter__"):
raise TypeError("group membership list must be iterable")
# Get the vertex indices that constitute the convex hull
hull = [group[i] for i in convex_hull([layout[idx] for idx in group])]
# Calculate the preferred rounding radius for the corners
corner_radius = 1.25 * max(vertex_builder[idx].size for idx in hull)
# Construct the polygon
polygon = [layout[idx] for idx in hull]
if len(polygon) == 2:
# Expand the polygon (which is a flat line otherwise)
a, b = Point(*polygon[0]), Point(*polygon[1])
c = corner_radius * (a-b).normalized()
n = Point(-c[1], c[0])
polygon = [a + n, b + n, b - c, b - n, a - n, a + c]
else:
# Expand the polygon around its center of mass
center = Point(*[sum(coords) / float(len(coords))
for coords in zip(*polygon)])
polygon = [Point(*point).towards(center, -corner_radius)
for point in polygon]
# Draw the hull
context.set_source_rgba(color[0], color[1], color[2],
color[3]*0.25)
polygon_drawer.draw_path(polygon, corner_radius=corner_radius)
context.fill_preserve()
context.set_source_rgba(*color)
context.stroke()
# Construct the iterator that we will use to draw the edges
es = graph.es
if edge_order is None:
# Default edge order
edge_coord_iter = izip(es, edge_builder)
else:
# Specified edge order
edge_coord_iter = ((es[i], edge_builder[i]) for i in edge_order)
# Draw the edges
if directed:
drawer_method = edge_drawer.draw_directed_edge
else:
drawer_method = edge_drawer.draw_undirected_edge
for edge, visual_edge in edge_coord_iter:
src, dest = edge.tuple
src_vertex, dest_vertex = vertex_builder[src], vertex_builder[dest]
drawer_method(visual_edge, src_vertex, dest_vertex)
# Construct the iterator that we will use to draw the vertices
vs = graph.vs
if vertex_order is None:
# Default vertex order
vertex_coord_iter = izip(vs, vertex_builder, layout)
else:
# Specified vertex order
vertex_coord_iter = ((vs[i], vertex_builder[i], layout[i])
for i in vertex_order)
# Draw the vertices
drawer_method = vertex_drawer.draw
context.set_line_width(1)
for vertex, visual_vertex, coords in vertex_coord_iter:
drawer_method(visual_vertex, vertex, coords)
# Decide whether the labels have to be wrapped
wrap = kwds.get("wrap_labels")
if wrap is None:
wrap = Configuration.instance()["plotting.wrap_labels"]
wrap = bool(wrap)
# Construct the iterator that we will use to draw the vertex labels
if vertex_order is None:
# Default vertex order
vertex_coord_iter = izip(vertex_builder, layout)
else:
# Specified vertex order
vertex_coord_iter = ((vertex_builder[i], layout[i])
for i in vertex_order)
# Draw the vertex labels
for vertex, coords in vertex_coord_iter:
if vertex.label is None:
continue
# Set the font family, size, color and text
context.select_font_face(vertex.font, \
cairo.FONT_SLANT_NORMAL, cairo.FONT_WEIGHT_NORMAL)
context.set_font_size(vertex.label_size)
context.set_source_rgba(*vertex.label_color)
label_drawer.text = vertex.label
if vertex.label_dist:
# Label is displaced from the center of the vertex.
_, yb, w, h, _, _ = label_drawer.text_extents()
w, h = w/2.0, h/2.0
radius = vertex.label_dist * vertex.size / 2.
# First we find the reference point that is at distance `radius'
# from the vertex in the direction given by `label_angle'.
# Then we place the label in a way that the line connecting the
# center of the bounding box of the label with the center of the
# vertex goes through the reference point and the reference
# point lies exactly on the bounding box of the vertex.
alpha = vertex.label_angle % (2*pi)
cx = coords[0] + radius * cos(alpha)
cy = coords[1] - radius * sin(alpha)
# Now we have the reference point. We have to decide which side
# of the label box will intersect with the line that connects
# the center of the label with the center of the vertex.
if w > 0:
beta = atan2(h, w) % (2*pi)
else:
beta = pi/2.
gamma = pi - beta
if alpha > 2*pi-beta or alpha <= beta:
# Intersection at left edge of label
cx += w
cy -= tan(alpha) * w
elif alpha > beta and alpha <= gamma:
# Intersection at bottom edge of label
try:
cx += h / tan(alpha)
except:
pass # tan(alpha) == inf
cy -= h
elif alpha > gamma and alpha <= gamma + 2*beta:
# Intersection at right edge of label
cx -= w
cy += tan(alpha) * w
else:
# Intersection at top edge of label
try:
cx -= h / tan(alpha)
except:
pass # tan(alpha) == inf
cy += h
# Draw the label
label_drawer.draw_at(cx-w, cy-h-yb, wrap=wrap)
else:
# Label is exactly in the center of the vertex
cx, cy = coords
half_size = vertex.size / 2.
label_drawer.bbox = (cx - half_size, cy - half_size,
cx + half_size, cy + half_size)
label_drawer.draw(wrap=wrap)
# Construct the iterator that we will use to draw the edge labels
es = graph.es
if edge_order is None:
# Default edge order
edge_coord_iter = izip(es, edge_builder)
else:
# Specified edge order
edge_coord_iter = ((es[i], edge_builder[i]) for i in edge_order)
# Draw the edge labels
for edge, visual_edge in edge_coord_iter:
if visual_edge.label is None:
continue
# Set the font family, size, color and text
context.select_font_face(visual_edge.font, \
cairo.FONT_SLANT_NORMAL, cairo.FONT_WEIGHT_NORMAL)
context.set_font_size(visual_edge.label_size)
context.set_source_rgba(*visual_edge.label_color)
label_drawer.text = visual_edge.label
# Ask the edge drawer to propose an anchor point for the label
src, dest = edge.tuple
src_vertex, dest_vertex = vertex_builder[src], vertex_builder[dest]
(x, y), (halign, valign) = \
edge_drawer.get_label_position(edge, src_vertex, dest_vertex)
# Measure the text
_, yb, w, h, _, _ = label_drawer.text_extents()
w /= 2.0
h /= 2.0
# Place the text relative to the edge
if halign == TextAlignment.RIGHT:
x -= w
elif halign == TextAlignment.LEFT:
x += w
if valign == TextAlignment.BOTTOM:
y -= h - yb / 2.0
elif valign == TextAlignment.TOP:
y += h
# Draw the edge label
label_drawer.halign = halign
label_drawer.valign = valign
label_drawer.bbox = (x-w, y-h, x+w, y+h)
label_drawer.draw(wrap=wrap)
def draw(self, graph, palette, *args, **kwds):
# Some abbreviations for sake of simplicity
directed = graph.is_directed()
context = self.context
# Calculate/get the layout of the graph
layout = self.ensure_layout(kwds.get("layout", None), graph)
# Determine the size of the margin on each side
margin = kwds.get("margin", 0)
try:
margin = list(margin)
except TypeError:
margin = [margin]
while len(margin)<4:
margin.extend(margin)
# margin = [x + 20. for x in margin[:4]]
# Contract the drawing area by the margin and fit the layout
bbox = self.bbox.contract(margin)
layout.fit_into(bbox, keep_aspect_ratio=False)
# Decide whether we need to calculate the curvature of edges
# automatically -- and calculate them if needed.
autocurve = kwds.get("autocurve", None)
if autocurve or (autocurve is None and \
"edge_curved" not in kwds and "curved" not in graph.edge_attributes() \
and graph.ecount() < 10000):
from igraph import autocurve
default = kwds.get("edge_curved", 0)
if default is True:
default = 0.5
default = float(default)
kwds["edge_curved"] = autocurve(graph, attribute=None, default=default)
# Construct the visual vertex/edge builders
class VisualVertexBuilder(AttributeCollectorBase):
"""Collects some visual properties of a vertex for drawing"""
_kwds_prefix = "vertex_"
color = ("green", palette.get)
label = None
label_angle = -pi/2
label_dist = 0.0
label_color = ("black", palette.get)
label_size = 14.0
position = dict(func=layout.__getitem__)
shape = ("circle", ShapeDrawerDirectory.resolve_default)
size = 20.0
# RON EDIT ---------------------
edge_color = ("#444", palette.get)
edge_size = 2.0
# ------------------------------
class VisualEdgeBuilder(AttributeCollectorBase):
"""Collects some visual properties of an edge for drawing"""
_kwds_prefix = "edge_"
arrow_size = 1.0
arrow_width = 1.0
color = ("#444", palette.get)
curved = (0.0, ArrowEdgeDrawer._curvature_to_float)
width = 1.0
vertex_builder = VisualVertexBuilder(graph.vs, kwds)
edge_builder = VisualEdgeBuilder(graph.es, kwds)
# Draw the highlighted groups (if any)
if "mark_groups" in kwds:
mark_groups = kwds["mark_groups"]
# Figure out what to do with mark_groups in order to be able to
# iterate over it and get memberlist-color pairs
if isinstance(mark_groups, dict):
group_iter = mark_groups.iteritems()
elif hasattr(mark_groups, "__iter__"):
# Lists, tuples, iterators etc
group_iter = iter(mark_groups)
else:
# False
group_iter = {}.iteritems()
# We will need a polygon drawer to draw the convex hulls
polygon_drawer = PolygonDrawer(context, bbox)
# Iterate over color-memberlist pairs
for group, color_id in group_iter:
if not group or color_id is None:
continue
color = palette.get(color_id)
if isinstance(group, VertexSeq):
group = [vertex.index for vertex in group]
if not hasattr(group, "__iter__"):
raise TypeError("group membership list must be iterable")
# Get the vertex indices that constitute the convex hull
hull = [group[i] for i in convex_hull([layout[idx] for idx in group])]
# Calculate the preferred rounding radius for the corners
corner_radius = 1.25 * max(vertex_builder[idx].size for idx in hull)
# Construct the polygon
polygon = [layout[idx] for idx in hull]
if len(polygon) == 2:
# Expand the polygon (which is a flat line otherwise)
a, b = Point(*polygon[0]), Point(*polygon[1])
c = corner_radius * (a-b).normalized()
n = Point(-c[1], c[0])
polygon = [a + n, b + n, b - c, b - n, a - n, a + c]
else:
# Expand the polygon around its center of mass
center = Point(*[sum(coords) / float(len(coords))
for coords in zip(*polygon)])
polygon = [Point(*point).towards(center, -corner_radius)
for point in polygon]
# Draw the hull
context.set_source_rgba(color[0], color[1], color[2],
color[3]*0.25)
polygon_drawer.draw_path(polygon, corner_radius=corner_radius)
context.fill_preserve()
context.set_source_rgba(*color)
context.stroke()
# Draw the edges
edge_drawer = self.edge_drawer_factory(context)
if directed:
drawer_method = edge_drawer.draw_directed_edge
else:
drawer_method = edge_drawer.draw_undirected_edge
for edge, visual_edge in izip(graph.es, edge_builder):
src, dest = edge.tuple
src_vertex, dest_vertex = vertex_builder[src], vertex_builder[dest]
drawer_method(visual_edge, src_vertex, dest_vertex)
# Calculate the desired vertex order
if "vertex_order" in kwds:
# Vertex order specified explicitly
vertex_order = kwds["vertex_order"]
elif kwds.get("vertex_order_by") is not None:
# Vertex order by another attribute
vertex_order_by = kwds["vertex_order_by"]
if isinstance(vertex_order_by, tuple):
vertex_order_by, reverse = vertex_order_by
if isinstance(reverse, basestring) and reverse.lower().startswith("asc"):
reverse = False
else:
reverse = bool(reversed)
else:
reverse = False
attrs = graph.vs[vertex_order_by]
vertex_order = sorted(range(graph.vcount()), key=attrs.__getitem__,
reverse=reverse)
del attrs
else:
# Default vertex order
vertex_order = None
if vertex_order is None:
# Default vertex order
vertex_coord_iter = izip(vertex_builder, layout)
else:
# Specified vertex order
vertex_coord_iter = ((vertex_builder[i], layout[i])
for i in vertex_order)
# RON EDIT ---------------------
# Draw the vertices
context.set_line_width(1)
for vertex, coords in vertex_coord_iter:
vertex.shape.draw_path(context, coords[0], coords[1], vertex.size)
context.set_source_rgba(*vertex.color)
context.fill_preserve()
#print vertex.edge_color
context.set_source_rgba(*vertex.edge_color)
context.set_line_width(vertex.edge_size)
context.stroke()
# ------------------------------
# Draw the vertex labels
context.select_font_face("sans-serif", cairo.FONT_SLANT_NORMAL, \
cairo.FONT_WEIGHT_NORMAL)
wrap = kwds.get("wrap_labels", None)
if wrap is None:
wrap = Configuration.instance()["plotting.wrap_labels"]
else:
wrap = bool(wrap)
if vertex_order is None:
# Default vertex order
vertex_coord_iter = izip(vertex_builder, layout)
else:
# Specified vertex order
vertex_coord_iter = ((vertex_builder[i], layout[i])
for i in vertex_order)
label_drawer = self.label_drawer_factory(context)
for vertex, coords in vertex_coord_iter:
if vertex.label is None:
continue
context.set_font_size(vertex.label_size)
context.set_source_rgba(*vertex.label_color)
label_drawer.text = vertex.label
if vertex.label_dist:
# Label is displaced from the center of the vertex.
_, yb, w, h, _, _ = label_drawer.text_extents()
w, h = w/2.0, h/2.0
radius = vertex.label_dist * vertex.size / 2.
# First we find the reference point that is at distance `radius'
# from the vertex in the direction given by `label_angle'.
# Then we place the label in a way that the line connecting the
# center of the bounding box of the label with the center of the
# vertex goes through the reference point and the reference
# point lies exactly on the bounding box of the vertex.
alpha = vertex.label_angle % (2*pi)
cx = coords[0] + radius * cos(alpha)
cy = coords[1] - radius * sin(alpha)
# Now we have the reference point. We have to decide which side
# of the label box will intersect with the line that connects
# the center of the label with the center of the vertex.
if w > 0:
beta = atan2(h, w) % (2*pi)
else:
beta = pi/2.
gamma = pi - beta
if alpha > 2*pi-beta or alpha <= beta:
# Intersection at left edge of label
cx += w
cy -= tan(alpha) * w
elif alpha > beta and alpha <= gamma:
# Intersection at bottom edge of label
try:
cx += h / tan(alpha)
except:
pass # tan(alpha) == inf
cy -= h
elif alpha > gamma and alpha <= gamma + 2*beta:
# Intersection at right edge of label
cx -= w
cy += tan(alpha) * w
else:
# Intersection at top edge of label
try:
cx -= h / tan(alpha)
except:
pass # tan(alpha) == inf
cy += h
# Draw the label
label_drawer.draw_at(cx-w, cy-h-yb, wrap=wrap)
else:
# Label is exactly in the center of the vertex
cx, cy = coords
half_size = vertex.size / 2.
label_drawer.bbox = (cx - half_size, cy - half_size,
cx + half_size, cy + half_size)
label_drawer.draw(wrap=wrap)
def _collect_attributes(self, attr_spec, config=None):
"""Collects graph visualization attributes from various sources.
This method can be used to collect the attributes required for graph
visualization from various sources. Attribute value sources are:
- A specific value of a Python dict belonging to a given key. This dict
is given by the argument M{self.kwds} at construction time, and
the name of the key is determined by the argument specification
given in M{attr_spec}.
- A vertex or edge sequence of a graph, given in M{self.seq}
- The global configuration, given in M{config}
- A default value when all other sources fail to provide the value.
This is also given in M{attr_spec}.
@param attr_spec: an L{AttributeSpecification} object which contains
the name of the attribute when it is coming from a
list of Python keyword arguments, the name of the
attribute when it is coming from the graph attributes
directly, the default value of the attribute and an
optional callable transformation to call on the values.
This can be used to ensure that the attributes are of
a given type.
@param config: a L{Configuration} object to be used for determining the
defaults if all else fails. If C{None}, the global
igraph configuration will be used
@return: the collected attributes
"""
kwds = self.kwds
seq = self.seq
n = len(seq)
# Special case if the attribute name is "label"
if attr_spec.name == "label":
if attr_spec.alt_name in kwds and kwds[attr_spec.alt_name] is None:
return [None] * n
# If the attribute uses an external callable to derive the attribute
# values, call it and store the results
if attr_spec.func is not None:
func = attr_spec.func
result = [func(i) for i in range(n)]
return result
# Get the configuration object
if config is None:
config = Configuration.instance()
# Fetch the defaults from the vertex/edge sequence
try:
attrs = seq[attr_spec.name]
except KeyError:
attrs = None
# Override them from the keyword arguments (if any)
result = kwds.get(attr_spec.alt_name, None)
if attrs:
if not result:
result = attrs
else:
if isinstance(result, str):
result = [result] * n
try:
len(result)
except TypeError:
result = [result] * n
result = [result[idx] or attrs[idx] \
for idx in range(len(result))]
# Special case for string overrides, strings are not treated
# as sequences here
if isinstance(result, str):
result = [result] * n
# If the result is still not a sequence, make it one
try:
len(result)
except TypeError:
result = [result] * n
# If it is not a list, ensure that it is a list
if not hasattr(result, "extend"):
result = list(result)
# Ensure that the length is n
while len(result) < n:
if len(result) <= n / 2:
result.extend(result)
else:
result.extend(result[0:(n - len(result))])
# By now, the length of the result vector should be n as requested
# Get the configuration defaults
try:
default = config["plotting.%s" % attr_spec.alt_name]
except NoOptionError:
default = None
if default is None:
default = attr_spec.default
# Fill the None values with the default values
for idx in range(len(result)):
if result[idx] is None:
result[idx] = default
# Finally, do the transformation
if attr_spec.transform is not None:
transform = attr_spec.transform
result = [transform(x) for x in result]
return result
def draw(self, graph, palette, *args, **kwds):
# Some abbreviations for sake of simplicity
directed = graph.is_directed()
context = self.context
# Calculate/get the layout of the graph
layout = self.ensure_layout(kwds.get("layout", None), graph)
# Determine the size of the margin on each side
margin = kwds.get("margin", 0)
try:
margin = list(margin)
except TypeError:
margin = [margin]
while len(margin) < 4:
margin.extend(margin)
# margin = [x + 20. for x in margin[:4]]
# Contract the drawing area by the margin and fit the layout
bbox = self.bbox.contract(margin)
layout.fit_into(bbox, keep_aspect_ratio=False)
# Decide whether we need to calculate the curvature of edges
# automatically -- and calculate them if needed.
autocurve = kwds.get("autocurve", None)
if autocurve or (autocurve is None and \
"edge_curved" not in kwds and "curved" not in graph.edge_attributes() \
and graph.ecount() < 10000):
from igraph import autocurve
default = kwds.get("edge_curved", 0)
if default is True:
default = 0.5
default = float(default)
kwds["edge_curved"] = autocurve(graph,
attribute=None,
default=default)
# Construct the visual vertex/edge builders
class VisualVertexBuilder(AttributeCollectorBase):
"""Collects some visual properties of a vertex for drawing"""
_kwds_prefix = "vertex_"
color = ("red", palette.get)
frame_color = ("black", palette.get)
frame_width = 1.0
label = None
label_angle = -pi / 2
label_dist = 0.0
label_color = ("black", palette.get)
label_size = 14.0
position = dict(func=layout.__getitem__)
shape = ("circle", ShapeDrawerDirectory.resolve_default)
size = 20.0
class VisualEdgeBuilder(AttributeCollectorBase):
"""Collects some visual properties of an edge for drawing"""
_kwds_prefix = "edge_"
arrow_size = 1.0
arrow_width = 1.0
color = ("#444", palette.get)
curved = (0.0, ArrowEdgeDrawer._curvature_to_float)
width = 1.0
vertex_builder = VisualVertexBuilder(graph.vs, kwds)
edge_builder = VisualEdgeBuilder(graph.es, kwds)
# Draw the highlighted groups (if any)
if "mark_groups" in kwds:
mark_groups = kwds["mark_groups"]
# Figure out what to do with mark_groups in order to be able to
# iterate over it and get memberlist-color pairs
if isinstance(mark_groups, dict):
group_iter = mark_groups.iteritems()
elif hasattr(mark_groups, "__iter__"):
# Lists, tuples, iterators etc
group_iter = iter(mark_groups)
else:
# False
group_iter = {}.iteritems()
# We will need a polygon drawer to draw the convex hulls
polygon_drawer = PolygonDrawer(context, bbox)
# Iterate over color-memberlist pairs
for group, color_id in group_iter:
if not group or color_id is None:
continue
color = palette.get(color_id)
if isinstance(group, VertexSeq):
group = [vertex.index for vertex in group]
if not hasattr(group, "__iter__"):
raise TypeError("group membership list must be iterable")
# Get the vertex indices that constitute the convex hull
hull = [
group[i]
for i in convex_hull([layout[idx] for idx in group])
]
# Calculate the preferred rounding radius for the corners
corner_radius = 1.25 * max(vertex_builder[idx].size
for idx in hull)
# Construct the polygon
polygon = [layout[idx] for idx in hull]
if len(polygon) == 2:
# Expand the polygon (which is a flat line otherwise)
a, b = Point(*polygon[0]), Point(*polygon[1])
c = corner_radius * (a - b).normalized()
n = Point(-c[1], c[0])
polygon = [a + n, b + n, b - c, b - n, a - n, a + c]
else:
# Expand the polygon around its center of mass
center = Point(*[
sum(coords) / float(len(coords))
for coords in zip(*polygon)
])
polygon = [
Point(*point).towards(center, -corner_radius)
for point in polygon
]
# Draw the hull
context.set_source_rgba(color[0], color[1], color[2],
color[3] * 0.25)
polygon_drawer.draw_path(polygon, corner_radius=corner_radius)
context.fill_preserve()
context.set_source_rgba(*color)
context.stroke()
# Draw the edges
edge_drawer = self.edge_drawer_factory(context)
if directed:
drawer_method = edge_drawer.draw_directed_edge
else:
drawer_method = edge_drawer.draw_undirected_edge
for edge, visual_edge in izip(graph.es, edge_builder):
src, dest = edge.tuple
src_vertex, dest_vertex = vertex_builder[src], vertex_builder[dest]
drawer_method(visual_edge, src_vertex, dest_vertex)
# Calculate the desired vertex order
if "vertex_order" in kwds:
# Vertex order specified explicitly
vertex_order = kwds["vertex_order"]
elif kwds.get("vertex_order_by") is not None:
# Vertex order by another attribute
vertex_order_by = kwds["vertex_order_by"]
if isinstance(vertex_order_by, tuple):
vertex_order_by, reverse = vertex_order_by
if isinstance(
reverse,
basestring) and reverse.lower().startswith("asc"):
reverse = False
else:
reverse = bool(reversed)
else:
reverse = False
attrs = graph.vs[vertex_order_by]
vertex_order = sorted(range(graph.vcount()),
key=attrs.__getitem__,
reverse=reverse)
del attrs
else:
# Default vertex order
vertex_order = None
if vertex_order is None:
# Default vertex order
vertex_coord_iter = izip(vertex_builder, layout)
else:
# Specified vertex order
vertex_coord_iter = ((vertex_builder[i], layout[i])
for i in vertex_order)
# Draw the vertices
context.set_line_width(1)
for vertex, coords in vertex_coord_iter:
vertex.shape.draw_path(context, \
coords[0], coords[1], vertex.size)
context.set_source_rgba(*vertex.color)
context.fill_preserve()
context.set_source_rgba(*vertex.frame_color)
context.set_line_width(vertex.frame_width)
context.stroke()
# Draw the vertex labels
context.select_font_face("sans-serif", cairo.FONT_SLANT_NORMAL, \
cairo.FONT_WEIGHT_NORMAL)
wrap = kwds.get("wrap_labels", None)
if wrap is None:
wrap = Configuration.instance()["plotting.wrap_labels"]
else:
wrap = bool(wrap)
if vertex_order is None:
# Default vertex order
vertex_coord_iter = izip(vertex_builder, layout)
else:
# Specified vertex order
vertex_coord_iter = ((vertex_builder[i], layout[i])
for i in vertex_order)
label_drawer = self.label_drawer_factory(context)
for vertex, coords in vertex_coord_iter:
if vertex.label is None:
continue
context.set_font_size(vertex.label_size)
context.set_source_rgba(*vertex.label_color)
label_drawer.text = vertex.label
if vertex.label_dist:
# Label is displaced from the center of the vertex.
_, yb, w, h, _, _ = label_drawer.text_extents()
w, h = w / 2.0, h / 2.0
radius = vertex.label_dist * vertex.size / 2.
# First we find the reference point that is at distance `radius'
# from the vertex in the direction given by `label_angle'.
# Then we place the label in a way that the line connecting the
# center of the bounding box of the label with the center of the
# vertex goes through the reference point and the reference
# point lies exactly on the bounding box of the vertex.
alpha = vertex.label_angle % (2 * pi)
cx = coords[0] + radius * cos(alpha)
cy = coords[1] - radius * sin(alpha)
# Now we have the reference point. We have to decide which side
# of the label box will intersect with the line that connects
# the center of the label with the center of the vertex.
if w > 0:
beta = atan2(h, w) % (2 * pi)
else:
beta = pi / 2.
gamma = pi - beta
if alpha > 2 * pi - beta or alpha <= beta:
# Intersection at left edge of label
cx += w
cy -= tan(alpha) * w
elif alpha > beta and alpha <= gamma:
# Intersection at bottom edge of label
try:
cx += h / tan(alpha)
except:
pass # tan(alpha) == inf
cy -= h
elif alpha > gamma and alpha <= gamma + 2 * beta:
# Intersection at right edge of label
cx -= w
cy += tan(alpha) * w
else:
# Intersection at top edge of label
try:
cx -= h / tan(alpha)
except:
pass # tan(alpha) == inf
cy += h
# Draw the label
label_drawer.draw_at(cx - w, cy - h - yb, wrap=wrap)
else:
# Label is exactly in the center of the vertex
cx, cy = coords
half_size = vertex.size / 2.
label_drawer.bbox = (cx - half_size, cy - half_size,
cx + half_size, cy + half_size)
label_drawer.draw(wrap=wrap)