def render(root_node, img, hide_root=False):
'''main render function. hide_root option is used when render
trees as Faces
'''
mode = img.mode
orientation = img.orientation
arc_span = img.arc_span
layout_fn = img._layout_handler
parent = _TreeItem()
n2i = parent.n2i # node to items
n2f = parent.n2f # node to faces
parent.bg_layer = _EmptyItem(parent)
parent.tree_layer = _EmptyItem(parent)
parent.float_layer = _EmptyItem(parent)
parent.float_behind_layer = _EmptyItem(parent)
TREE_LAYERS = [parent.bg_layer, parent.tree_layer,
parent.float_layer, parent.float_behind_layer]
parent.bg_layer.setZValue(0)
parent.tree_layer.setZValue(2)
parent.float_behind_layer.setZValue(1)
parent.float_layer.setZValue(3)
# This could be used to handle aligned faces in internal
# nodes.
virtual_leaves = 0
if img.show_branch_length:
bl_face = faces.AttrFace("dist", fsize=8, ftype="Arial", fgcolor="black", formatter = "%0.3g")
if img.show_branch_support:
su_face = faces.AttrFace("support", fsize=8, ftype="Arial", fgcolor="darkred", formatter = "%0.3g")
if img.show_leaf_name:
na_face = faces.AttrFace("name", fsize=10, ftype="Arial", fgcolor="black")
for n in root_node.traverse(is_leaf_fn=_leaf):
set_style(n, layout_fn)
if img.show_branch_length:
faces.add_face_to_node(bl_face, n, 0, position="branch-top")
if not _leaf(n) and img.show_branch_support:
faces.add_face_to_node(su_face, n, 0, position="branch-bottom")
if _leaf(n) and n.name and img.show_leaf_name:
faces.add_face_to_node(na_face, n, 0, position="branch-right")
if _leaf(n):# or len(n.img_style["_faces"]["aligned"]):
virtual_leaves += 1
update_node_faces(n, n2f, img)
rot_step = float(arc_span) / virtual_leaves
#rot_step = float(arc_span) / len([n for n in root_node.traverse() if _leaf(n)])
# Calculate optimal branch length
if img._scale is not None:
init_items(root_node, parent, n2i, n2f, img, rot_step, hide_root)
elif img.scale is None:
# create items and calculate node dimensions skipping branch lengths
init_items(root_node, parent, n2i, n2f, img, rot_step, hide_root)
if mode == 'r':
if img.optimal_scale_level == "full":
scales = [(i.widths[1]/n.dist) for n,i in n2i.iteritems() if n.dist]
img._scale = max(scales) if scales else 0.0
else:
farthest, dist = root_node.get_farthest_leaf(topology_only=img.force_topology)
img._scale = img.tree_width / dist if dist else 0.0
update_branch_lengths(root_node, n2i, n2f, img)
else:
img._scale = crender.calculate_optimal_scale(root_node, n2i, rot_step, img)
#print "OPTIMAL circular scale", img._scale
update_branch_lengths(root_node, n2i, n2f, img)
init_items(root_node, parent, n2i, n2f, img, rot_step, hide_root)
else:
# create items and calculate node dimensions CONSIDERING branch lengths
img._scale = img.scale
init_items(root_node, parent, n2i, n2f, img, rot_step, hide_root)
#print "USING scale", img._scale
# Draw node content
for node in root_node.traverse(is_leaf_fn=_leaf):
if node is not root_node or not hide_root:
render_node_content(node, n2i, n2f, img)
# Adjust content to rect or circular layout
mainRect = parent.rect()
if mode == "c":
tree_radius = crender.render_circular(root_node, n2i, rot_step)
mainRect.adjust(-tree_radius, -tree_radius, tree_radius, tree_radius)
else:
iwidth = n2i[root_node].fullRegion.width()
iheight = n2i[root_node].fullRegion.height()
mainRect.adjust(0, 0, iwidth, iheight)
tree_radius = iwidth
# Add extra layers: aligned faces, floating faces, node
# backgrounds, etc. The order by which the following methods are
# called IS IMPORTANT
render_floatings(n2i, n2f, img, parent.float_layer, parent.float_behind_layer)
aligned_region_width = render_aligned_faces(img, mainRect, parent.tree_layer, n2i, n2f)
render_backgrounds(img, mainRect, parent.bg_layer, n2i, n2f)
# rotate if necessary in circular images. flip and adjust if mirror orientation.
adjust_faces_to_tranformations(img, mainRect, n2i, n2f, TREE_LAYERS)
# Rotate main image if necessary
parent.setRect(mainRect)
parent.setPen(QtGui.QPen(QtCore.Qt.NoPen))
if img.rotation:
rect = parent.boundingRect()
x = rect.x() + (rect.width()/2.0)
y = rect.y() + (rect.height()/2.0)
parent.setTransform(QtGui.QTransform().translate(x, y).rotate(img.rotation).translate(-x, -y))
# Creates the main tree item that will act as frame for the whole image
frame = QtGui.QGraphicsRectItem()
parent.setParentItem(frame)
mainRect = parent.mapToScene(mainRect).boundingRect()
mainRect.adjust(-img.margin_left, -img.margin_top, \
img.margin_right, img.margin_bottom)
# Fix negative coordinates, so main item always starts at 0,0
topleft = mainRect.topLeft()
_x = abs(topleft.x()) if topleft.x() < 0 else 0
_y = abs(topleft.y()) if topleft.y() < 0 else 0
if _x or _y:
parent.moveBy(_x, _y)
mainRect.adjust(_x, _y, _x, _y)
# Add extra components and adjust mainRect to them
add_legend(img, mainRect, frame)
add_title(img, mainRect, frame)
add_scale(img, mainRect, frame)
frame.setRect(mainRect)
# Draws a border around the tree
if not img.show_border:
frame.setPen(QtGui.QPen(QtCore.Qt.NoPen))
else:
frame.setPen(QtGui.QPen(QtGui.QColor("black")))
return frame, n2i, n2f
def render(root_node, img, hide_root=False):
'''main render function. hide_root option is used when render
trees as Faces
'''
mode = img.mode
orientation = img.orientation
arc_span = img.arc_span
layout_fn = img._layout_handler
parent = _TreeItem()
n2i = parent.n2i # node to items
n2f = parent.n2f # node to faces
parent.bg_layer = _EmptyItem(parent)
parent.tree_layer = _EmptyItem(parent)
parent.float_layer = _EmptyItem(parent)
parent.float_behind_layer = _EmptyItem(parent)
TREE_LAYERS = [parent.bg_layer, parent.tree_layer,
parent.float_layer, parent.float_behind_layer]
parent.bg_layer.setZValue(0)
parent.tree_layer.setZValue(2)
parent.float_behind_layer.setZValue(1)
parent.float_layer.setZValue(3)
# This could be used to handle aligned faces in internal
# nodes.
virtual_leaves = 0
if img.show_branch_length:
bl_face = faces.AttrFace("dist", fsize=8, ftype="Arial", fgcolor="black", formatter = "%0.3g")
if img.show_branch_support:
su_face = faces.AttrFace("support", fsize=8, ftype="Arial", fgcolor="darkred", formatter = "%0.3g")
if img.show_leaf_name:
na_face = faces.AttrFace("name", fsize=10, ftype="Arial", fgcolor="black")
for n in root_node.traverse(is_leaf_fn=_leaf):
set_style(n, layout_fn)
if img.show_branch_length:
faces.add_face_to_node(bl_face, n, 0, position="branch-top")
if not _leaf(n) and img.show_branch_support:
faces.add_face_to_node(su_face, n, 0, position="branch-bottom")
if _leaf(n) and img.show_leaf_name:
faces.add_face_to_node(na_face, n, 0, position="branch-right")
if _leaf(n):# or len(n.img_style["_faces"]["aligned"]):
virtual_leaves += 1
update_node_faces(n, n2f, img)
rot_step = float(arc_span) / virtual_leaves
#rot_step = float(arc_span) / len([n for n in root_node.traverse() if _leaf(n)])
# Calculate optimal branch length
if img._scale is not None:
init_items(root_node, parent, n2i, n2f, img, rot_step, hide_root)
elif img.scale is None:
# create items and calculate node dimensions skipping branch lengths
init_items(root_node, parent, n2i, n2f, img, rot_step, hide_root)
if mode == 'r':
if img.optimal_scale_level == "full":
scales = [(i.widths[1]/n.dist) for n,i in n2i.iteritems() if n.dist]
img._scale = max(scales) if scales else 0.0
else:
farthest, dist = root_node.get_farthest_leaf(topology_only=img.force_topology)
img._scale = img.tree_width / dist if dist else 0.0
update_branch_lengths(root_node, n2i, n2f, img)
else:
img._scale = crender.calculate_optimal_scale(root_node, n2i, rot_step, img)
#print "OPTIMAL circular scale", img._scale
update_branch_lengths(root_node, n2i, n2f, img)
init_items(root_node, parent, n2i, n2f, img, rot_step, hide_root)
else:
# create items and calculate node dimensions CONSIDERING branch lengths
img._scale = img.scale
init_items(root_node, parent, n2i, n2f, img, rot_step, hide_root)
#print "USING scale", img._scale
# Draw node content
for node in root_node.traverse(is_leaf_fn=_leaf):
if node is not root_node or not hide_root:
render_node_content(node, n2i, n2f, img)
# Adjust content to rect or circular layout
mainRect = parent.rect()
if mode == "c":
tree_radius = crender.render_circular(root_node, n2i, rot_step)
mainRect.adjust(-tree_radius, -tree_radius, tree_radius, tree_radius)
else:
iwidth = n2i[root_node].fullRegion.width()
iheight = n2i[root_node].fullRegion.height()
mainRect.adjust(0, 0, iwidth, iheight)
tree_radius = iwidth
# Add extra layers: aligned faces, floating faces, node
# backgrounds, etc. The order by which the following methods are
# called IS IMPORTANT
render_floatings(n2i, n2f, img, parent.float_layer, parent.float_behind_layer)
aligned_region_width = render_aligned_faces(img, mainRect, parent.tree_layer, n2i, n2f)
render_backgrounds(img, mainRect, parent.bg_layer, n2i, n2f)
# rotate if necessary in circular images. flip and adjust if mirror orientation.
adjust_faces_to_tranformations(img, mainRect, n2i, n2f, TREE_LAYERS)
# Rotate main image if necessary
parent.setRect(mainRect)
parent.setPen(QtGui.QPen(QtCore.Qt.NoPen))
if img.rotation:
rect = parent.boundingRect()
x = rect.x() + (rect.width()/2.0)
y = rect.y() + (rect.height()/2.0)
parent.setTransform(QtGui.QTransform().translate(x, y).rotate(img.rotation).translate(-x, -y))
# Creates the main tree item that will act as frame for the whole image
frame = QtGui.QGraphicsRectItem()
parent.setParentItem(frame)
mainRect = parent.mapToScene(mainRect).boundingRect()
mainRect.adjust(-img.margin_left, -img.margin_top, \
img.margin_right, img.margin_bottom)
# Fix negative coordinates, so main item always starts at 0,0
topleft = mainRect.topLeft()
_x = abs(topleft.x()) if topleft.x() < 0 else 0
_y = abs(topleft.y()) if topleft.y() < 0 else 0
if _x or _y:
parent.moveBy(_x, _y)
mainRect.adjust(_x, _y, _x, _y)
# Add extra components and adjust mainRect to them
add_legend(img, mainRect, frame)
add_title(img, mainRect, frame)
add_scale(img, mainRect, frame)
frame.setRect(mainRect)
# Draws a border around the tree
if not img.show_border:
frame.setPen(QtGui.QPen(QtCore.Qt.NoPen))
else:
frame.setPen(QtGui.QPen(QtGui.QColor("black")))
return frame, n2i, n2f
def set_node_size(node, n2i, n2f, img):
scale = img.scale
min_separation = img.min_leaf_separation
item = n2i[node]
if img.force_topology:
branch_length = item.branch_length = float(scale)
else:
branch_length = item.branch_length = float(node.dist * scale)
# Organize faces by groups
faceblock = update_node_faces(node, n2f, img)
aligned_height = 0
if _leaf(node):
if img.mode == "r":
aligned_height = faceblock["aligned"].h
elif img.mode == "c":
# aligned faces in circular mode are adjusted afterwords. The
# min radius of the largest aligned faces will be calculated.
pass
# Total height required by the node. I cannot sum up the height of
# all elements, since the position of some of them are forced to
# be on top or at the bottom of branches. This fact can produce
# and unbalanced nodeRegion center. Here, I only need to know
# about the imbalance size to correct node height. The center will
# be calculated later according to the parent position.
top_half_h = ( (node.img_style["size"]/2) +
node.img_style["hz_line_width"]/2 +
faceblock["branch-top"].h )
bottom_half_h =( (node.img_style["size"]/2) +
node.img_style["hz_line_width"]/2 +
faceblock["branch-bottom"].h )
h1 = top_half_h + bottom_half_h
h2 = max(faceblock["branch-right"].h, \
aligned_height, \
min_separation )
h = max(h1, h2)
imbalance = abs(top_half_h - bottom_half_h)
if imbalance > h2/2:
h += imbalance - (h2/2)
# This adds a vertical margin around the node elements
h += img.branch_vertical_margin
# Total width required by the node
w = sum([max(branch_length + node.img_style["size"],
faceblock["branch-top"].w + node.img_style["size"],
faceblock["branch-bottom"].w + node.img_style["size"],
),
faceblock["branch-right"].w]
)
w += node.img_style["vt_line_width"]
# rightside faces region
item.facesRegion.setRect(0, 0, faceblock["branch-right"].w, h)
# Node region
item.nodeRegion.setRect(0, 0, w, h)
# This is the node total region covered by the node
item.fullRegion.setRect(0, 0, w, h)
