# Draws a genealogical tree (generates a SVG file) based on parent-child relationship information.
import json
import random
import math
import argparse
TIME = "GENERATIONAL"
BALANCE = "MIN"
# ------SVG---------
svg_file = 0
svg_line_style = 'stroke="rgb(90%,10%,16%)" stroke-width="1" stroke-opacity="0.8"'
svg_dot_style = 'r="2" stroke="black" stroke-width="0.2" fill="red"'
svg_spine_line_style = 'stroke="rgb(0%,0%,80%)" stroke-width="2" stroke-opacity="1"'
#svg_spine_dot_style = 'r="3" stroke="black" stroke-width="0.4" fill="rgb(50%,50%,100%)"'
svg_spine_dot_style = 'r="1" stroke="black" stroke-width="0.2" fill="rgb(50%,50%,100%)"'
def svg_add_line(from_pos, to_pos, style=svg_line_style):
svg_file.write('')
def svg_add_dot(pos, style=svg_dot_style):
svg_file.write('')
def svg_generate_line_style(percent):
# hotdog
from_col = [100, 70, 0]
to_col = [60, 0, 0]
# neon
# from_col = [30, 200, 255]
# to_col = [240, 0, 220]
from_opa = 0.2
to_opa = 1.0
from_stroke = 1
to_stroke = 3
opa = from_opa*(1-percent) + to_opa*percent
stroke = from_stroke*(1-percent) + to_stroke*percent
percent = 1 - ((1-percent)**20)
return 'stroke="rgb(' + str(from_col[0]*(1-percent) + to_col[0]*percent) + '%,' \
+ str(from_col[1]*(1-percent) + to_col[1]*percent) + '%,' \
+ str(from_col[2]*(1-percent) + to_col[2]*percent) + '%)" stroke-width="' + str(stroke) + '" stroke-opacity="' + str(opa) + '"'
def svg_generate_dot_style(percent):
from_col = [100, 90, 0]
to_col = [60, 0, 0]
# neon
# from_col = [30, 200, 255]
# to_col = [240, 0, 220]
from_opa = 0.2
to_opa = 1.0
opa = from_opa*(1-percent) + to_opa*percent
percent = 1 - ((1-percent)**20)
return 'fill="rgb(' + str(from_col[0]*(1-percent) + to_col[0]*percent) + '%,' \
+ str(from_col[1]*(1-percent) + to_col[1]*percent) + '%,' \
+ str(from_col[2]*(1-percent) + to_col[2]*percent) + '%)" r="1.5" stroke="black" stroke-width="0.2" fill-opacity="' + str(opa) + '" ' \
'stroke-opacity="' + str(opa) + '"'
# -------------------
def load_data(dir):
global firstnode, nodes, inv_nodes
f = open(dir)
for line in f:
sline = line.split(' ', 2)
if len(sline) == 3:
if sline[1] == "[OFFSPRING]":
creature = json.loads(sline[2])
#print("B" +str(creature))
if "FromIDs" in creature:
assert(len(creature["FromIDs"]) == 1)
nodes[creature["ID"]] = creature["FromIDs"][0]
if not creature["FromIDs"][0] in nodes:
firstnode = creature["FromIDs"][0]
for k, v in sorted(nodes.items()):
inv_nodes[v] = inv_nodes.get(v, [])
inv_nodes[v].append(k)
def load_simple_data(dir):
global firstnode, nodes, inv_nodes
f = open(dir)
for line in f:
sline = line.split()
if len(sline) > 1:
#if int(sline[0]) > 15000:
# break
if sline[0] == firstnode:
continue
nodes[sline[0]] = str(max(int(sline[1]), int(firstnode)))
else:
firstnode = sline[0]
for k, v in sorted(nodes.items()):
inv_nodes[v] = inv_nodes.get(v, [])
inv_nodes[v].append(k)
#print(str(inv_nodes))
#quit()
def compute_depth(node):
my_depth = 0
if node in inv_nodes:
for c in inv_nodes[node]:
my_depth = max(my_depth, compute_depth(c)+1)
depth[node] = my_depth
return my_depth
# ------------------------------------
def xmin_crowd(x1, x2, y):
if BALANCE == "RANDOM":
return (x1 if random.randrange(2) == 0 else x2)
elif BALANCE == "MIN":
x1_closest = 999999
x2_closest = 999999
for pos in positions:
pos = positions[pos]
if pos[1] == y:
x1_closest = min(x1_closest, abs(x1-pos[0]))
x2_closest = min(x2_closest, abs(x2-pos[0]))
return (x1 if x1_closest > x2_closest else x2)
elif BALANCE == "DENSITY":
x1_dist = 0
x2_dist = 0
for pos in positions:
pos = positions[pos]
if pos[1] > y-10 or pos[1] < y+10:
dy = pos[1]-y
dx1 = pos[0]-x1
dx2 = pos[0]-x2
x1_dist += math.sqrt(dy**2 + dx1**2)
x2_dist += math.sqrt(dy**2 + dx2**2)
return (x1 if x1_dist > x2_dist else x2)
# ------------------------------------
def prepos_children_reccurent(node):
for c in inv_nodes[node]:
#print(node + "->" + c)
dissimilarity = 0.5 #random.gauss(0,0.3)
if TIME == "REAL":
id = ""
if c[0] == "c":
id = int(c[1:])
else:
id = int(c)
positions[c] = [xmin_crowd(positions[node][0]-dissimilarity, positions[node][0]+dissimilarity, id), id]
elif TIME == "GENERATIONAL":
positions[c] = [xmin_crowd(positions[node][0]-dissimilarity, positions[node][0]+dissimilarity, positions[node][1]+1), positions[node][1]+1]
for c in inv_nodes[node]:
if c in inv_nodes:
prepos_children_reccurent(c)
def prepos_children():
global max_height, max_width, min_width
positions[firstnode] = [0, 0]
prepos_children_reccurent(firstnode)
for pos in positions:
max_height = max(max_height, positions[pos][1])
max_width = max(max_width, positions[pos][0])
min_width = min(min_width, positions[pos][0])
# ------------------------------------
def draw_children_recurrent(node, max_depth):
global max_height, max_width, min_width
for c in inv_nodes[node]:
if c in inv_nodes:
draw_children_recurrent(c, max_depth)
line_style = (svg_line_style if args.mono_tree else svg_generate_line_style(depth[c]/max_depth))
dot_style = (svg_dot_style if args.mono_tree else svg_generate_dot_style(depth[c]/max_depth))
svg_add_line( (w_margin+w_no_margs*(positions[node][0]-min_width)/(max_width-min_width), h_margin+h_no_margs*positions[node][1]/max_height),
(w_margin+w_no_margs*(positions[c][0]-min_width)/(max_width-min_width), h_margin+h_no_margs*positions[c][1]/max_height), line_style)
svg_add_dot( (w_margin+w_no_margs*(positions[c][0]-min_width)/(max_width-min_width), h_margin+h_no_margs*positions[c][1]/max_height), dot_style)
def draw_children():
max_depth = 0
for k, v in depth.items():
max_depth = max(max_depth, v)
draw_children_recurrent(firstnode, max_depth)
dot_style = (svg_dot_style if args.mono_tree else svg_generate_dot_style(depth[firstnode]/max_depth))
svg_add_dot( (w_margin+w_no_margs*(positions[firstnode][0]-min_width)/(max_width-min_width), h_margin+h_no_margs*positions[firstnode][1]/max_height), dot_style)
def draw_spine_recurrent(node):
global max_height, max_width, min_width
for c in inv_nodes[node]:
if depth[c] == depth[node] - 1:
if c in inv_nodes:
draw_spine_recurrent(c)
line_style = svg_spine_line_style
svg_add_line( (w_margin+w_no_margs*(positions[node][0]-min_width)/(max_width-min_width), h_margin+h_no_margs*positions[node][1]/max_height),
(w_margin+w_no_margs*(positions[c][0]-min_width)/(max_width-min_width), h_margin+h_no_margs*positions[c][1]/max_height), line_style)
#svg_add_dot( (w_margin+w_no_margs*(positions[c][0]-min_width)/(max_width-min_width), h_margin+h_no_margs*positions[c][1]/max_height), svg_spine_dot_style)
def draw_spine():
draw_spine_recurrent(firstnode)
#svg_add_dot( (w_margin+w_no_margs*(positions[firstnode][0]-min_width)/(max_width-min_width), h_margin+h_no_margs*positions[firstnode][1]/max_height), svg_spine_dot_style)
def draw_skeleton_reccurent(node, max_depth):
global max_height, max_width, min_width
for c in inv_nodes[node]:
if depth[c] >= min_skeleton_depth or depth[c] == max([depth[q] for q in inv_nodes[node]]):
if c in inv_nodes:
draw_skeleton_reccurent(c, max_depth)
line_style = svg_spine_line_style
svg_add_line( (w_margin+w_no_margs*(positions[node][0]-min_width)/(max_width-min_width), h_margin+h_no_margs*positions[node][1]/max_height),
(w_margin+w_no_margs*(positions[c][0]-min_width)/(max_width-min_width), h_margin+h_no_margs*positions[c][1]/max_height), line_style)
#svg_add_dot( (w_margin+w_no_margs*(positions[c][0]-min_width)/(max_width-min_width), h_margin+h_no_margs*positions[c][1]/max_height),
# svg_spine_dot_style)
def draw_skeleton():
max_depth = 0
for k, v in depth.items():
max_depth = max(max_depth, v)
draw_skeleton_reccurent(firstnode, max_depth)
#svg_add_dot( (w_margin+w_no_margs*(positions[firstnode][0]-min_width)/(max_width-min_width), h_margin+h_no_margs*positions[firstnode][1]/max_height),
# svg_spine_dot_style)
##################################################### main #####################################################
args = 0
h = 800
w = 600
h_margin = 10
w_margin = 10
h_no_margs = h - 2* h_margin
w_no_margs = w - 2* w_margin
max_height = 0
max_width = 0
min_width = 9999999999
min_skeleton_depth = 0
firstnode = ""
nodes = {}
inv_nodes = {}
positions = {}
depth = {}
def main():
global svg_file, min_skeleton_depth, args, TIME, BALANCE
parser = argparse.ArgumentParser(description='Process some integers.')
parser.add_argument('--in', dest='input', required=True, help='input file with stuctured evolutionary data')
parser.add_argument('--out', dest='output', required=True, help='output file for the evolutionary tree')
draw_tree_parser = parser.add_mutually_exclusive_group(required=False)
draw_tree_parser.add_argument('--draw-tree', dest='draw_tree', action='store_true', help='whether drawing the full tree should be skipped')
draw_tree_parser.add_argument('--no-draw-tree', dest='draw_tree', action='store_false')
draw_skeleton_parser = parser.add_mutually_exclusive_group(required=False)
draw_skeleton_parser.add_argument('--draw-skeleton', dest='draw_skeleton', action='store_true', help='whether the skeleton of the tree should be drawn')
draw_skeleton_parser.add_argument('--no-draw-skeleton', dest='draw_skeleton', action='store_false')
draw_spine_parser = parser.add_mutually_exclusive_group(required=False)
draw_spine_parser.add_argument('--draw-spine', dest='draw_spine', action='store_true', help='whether the spine of the tree should be drawn')
draw_spine_parser.add_argument('--no-draw-spine', dest='draw_spine', action='store_false')
#TODO: better names for those parameters
parser.add_argument('--time', default='REAL', dest='time', help='values on vertical axis (REAL/GENERATIONAL)')
parser.add_argument('--balance', default='MIN',dest='balance', help='method of placing node in the tree (RANDOM/MIN/DENSITY)')
mono_tree_parser = parser.add_mutually_exclusive_group(required=False)
mono_tree_parser.add_argument('--mono-tree', dest='mono_tree', action='store_true', help='whether the tree should be drawn with a single color')
mono_tree_parser.add_argument('--no-mono-tree', dest='mono_tree', action='store_false')
parser.add_argument('--min-skeleton-depth', type=int, default=2, dest='min_skeleton_depth', help='minimal distance from the leafs for the nodes in the skeleton')
parser.add_argument('--seed', type=int, dest='seed', help='seed for the random number generator (-1 for random)')
parser.add_argument('--simple-data', type=bool, dest='simple_data', help='input data are given in a simple format (#child #parent)')
parser.set_defaults(mono_tree=False)
parser.set_defaults(draw_tree=True)
parser.set_defaults(draw_skeleton=False)
parser.set_defaults(draw_spine=False)
parser.set_defaults(seed=-1)
args = parser.parse_args()
TIME = args.time
BALANCE = args.balance
dir = args.input
min_skeleton_depth = args.min_skeleton_depth
seed = args.seed
if seed == -1:
seed = random.randint(0, 10000)
random.seed(seed)
print("seed:", seed)
if args.simple_data:
load_simple_data(dir)
else:
load_data(dir)
compute_depth(firstnode)
svg_file = open(args.output, "w")
svg_file.write('")
svg_file.close()
main()