| 1 | # Draws a genealogical tree (generates a SVG file) based on parent-child relationship information.
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| 2 | # Supports files generated by Framsticks experiments.
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| 3 |
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| 4 | import json
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| 5 | import random
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| 6 | import math
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| 7 | import argparse
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| 8 | import time as ttime
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| 9 |
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| 10 | TIME = "" # BIRTHS / GENERATIONAL / REAL
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| 11 | BALANCE = "" # MIN / DENSITY
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| 12 |
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| 13 | DOT_STYLE = "" # NONE / NORMAL / CLEAR
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| 14 |
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| 15 | JITTER = "" #
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| 16 |
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| 17 | # ------SVG---------
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| 18 | svg_file = 0
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| 19 |
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| 20 | svg_line_style = 'stroke="rgb(90%,10%,16%)" stroke-width="1" stroke-opacity="0.7"'
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| 21 | svg_mutation_line_style = 'stroke-width="1"'
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| 22 | svg_crossover_line_style = 'stroke-width="1"'
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| 23 | svg_spine_line_style = 'stroke="rgb(0%,90%,40%)" stroke-width="2" stroke-opacity="1"'
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| 24 | svg_scale_line_style = 'stroke="black" stroke-width="0.5" stroke-opacity="1" stroke-dasharray="5, 5"'
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| 25 |
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| 26 | svg_dot_style = 'r="2" stroke="black" stroke-width="0.2" fill="red"'
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| 27 | svg_clear_dot_style = 'r="2" stroke="black" stroke-width="0.4" fill="none"'
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| 28 | svg_spine_dot_style = 'r="1" stroke="black" stroke-width="0.2" fill="rgb(50%,50%,100%)"'
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| 29 |
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| 30 | svg_scale_text_style = 'style="font-family: Arial; font-size: 12; fill: #000000;"'
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| 31 |
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| 32 | def hex_to_style(hex):
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| 33 | default_style = ' stroke="black" stroke-opacity="0.5" '
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| 34 |
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| 35 | if hex[0] == "#":
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| 36 | hex = hex[1:]
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| 37 |
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| 38 | if len(hex) == 6 or len(hex) == 8:
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| 39 | try:
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| 40 | int(hex, 16)
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| 41 | except:
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| 42 | print("Invalid characters in the color's hex #" + hex + "! Assuming black.")
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| 43 | return default_style
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| 44 | red = 100*int(hex[0:2], 16)/255
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| 45 | green = 100*int(hex[2:4], 16)/255
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| 46 | blue = 100*int(hex[4:6], 16)/255
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| 47 | opacity = 0.5
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| 48 | if len(hex) == 8:
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| 49 | opacity = int(hex[6:8], 16)/255
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| 50 | return ' stroke="rgb(' +str(red)+ '%,' +str(green)+ '%,' +str(blue)+ '%)" stroke-opacity="' +str(opacity)+ '" '
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| 51 | else:
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| 52 | print("Invalid number of digits in the color's hex #" + hex + "! Assuming black.")
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| 53 | return default_style
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| 54 |
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| 55 | def svg_add_line(from_pos, to_pos, style=svg_line_style):
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| 56 | svg_file.write('<line ' + style + ' x1="' + str(from_pos[0]) + '" x2="' + str(to_pos[0]) +
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| 57 | '" y1="' + str(from_pos[1]) + '" y2="' + str(to_pos[1]) + '" fill="none"/>')
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| 58 |
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| 59 | def svg_add_text(text, pos, anchor, style=svg_scale_text_style):
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| 60 | svg_file.write('<text ' + style + ' text-anchor="' + anchor + '" x="' + str(pos[0]) + '" y="' + str(pos[1]) + '" >' + text + '</text>')
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| 61 |
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| 62 | def svg_add_dot(pos, style=svg_dot_style):
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| 63 | svg_file.write('<circle ' + style + ' cx="' + str(pos[0]) + '" cy="' + str(pos[1]) + '" />')
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| 64 |
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| 65 | def svg_generate_line_style(percent):
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| 66 | # hotdog
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| 67 | from_col = [100, 70, 0]
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| 68 | to_col = [60, 0, 0]
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| 69 | # lava
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| 70 | # from_col = [100, 80, 0]
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| 71 | # to_col = [100, 0, 0]
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| 72 | # neon
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| 73 | # from_col = [30, 200, 255]
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| 74 | # to_col = [240, 0, 220]
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| 75 |
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| 76 | from_opa = 0.2
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| 77 | to_opa = 1.0
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| 78 | from_stroke = 1
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| 79 | to_stroke = 3
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| 80 |
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| 81 | opa = from_opa*(1-percent) + to_opa*percent
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| 82 | stroke = from_stroke*(1-percent) + to_stroke*percent
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| 83 |
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| 84 | percent = 1 - ((1-percent)**20)
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| 85 |
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| 86 | return 'stroke="rgb(' + str(from_col[0]*(1-percent) + to_col[0]*percent) + '%,' \
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| 87 | + str(from_col[1]*(1-percent) + to_col[1]*percent) + '%,' \
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| 88 | + str(from_col[2]*(1-percent) + to_col[2]*percent) + '%)" stroke-width="' + str(stroke) + '" stroke-opacity="' + str(opa) + '"'
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| 89 |
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| 90 | def svg_generate_dot_style(kind):
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| 91 | kinds = ["red", "lawngreen", "royalblue", "magenta", "yellow", "cyan", "white", "black"]
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| 92 |
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| 93 | r = min(2500/len(nodes), 10)
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| 94 |
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| 95 | return 'fill="' + kinds[kind] + '" r="' + str(r) + '" stroke="black" stroke-width="' + str(r/10) + '" fill-opacity="1.0" ' \
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| 96 | 'stroke-opacity="1.0"'
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| 97 |
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| 98 | # -------------------
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| 99 |
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| 100 | def load_data(dir):
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| 101 | global firstnode, nodes, inv_nodes, time
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| 102 | f = open(dir)
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| 103 | for line in f:
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| 104 | sline = line.split(' ', 1)
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| 105 | if len(sline) == 2:
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| 106 | if sline[0] == "[OFFSPRING]":
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| 107 | creature = json.loads(sline[1])
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| 108 | #print("B" +str(creature))
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| 109 | if "FromIDs" in creature:
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| 110 | if not creature["ID"] in nodes:
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| 111 | nodes[creature["ID"]] = {}
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| 112 | # we assign to each parent its contribution to the genotype of the child
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| 113 | for i in range(0, len(creature["FromIDs"])):
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| 114 | inherited = 1 #(creature["Inherited"][i] if 'Inherited' in creature else 1) #ONLY FOR NOW
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| 115 | nodes[creature["ID"]][creature["FromIDs"][i]] = inherited
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| 116 | else:
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| 117 | print("Duplicated entry for " + creature["ID"])
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| 118 | quit()
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| 119 |
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| 120 | if not creature["FromIDs"][0] in nodes and firstnode == None:
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| 121 | firstnode = creature["FromIDs"][0]
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| 122 |
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| 123 | if "Time" in creature:
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| 124 | time[creature["ID"]] = creature["Time"]
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| 125 |
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| 126 | if "Kind" in creature:
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| 127 | kind[creature["ID"]] = creature["Kind"]
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| 128 |
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| 129 | for k, v in sorted(nodes.items()):
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| 130 | for val in sorted(v):
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| 131 | inv_nodes[val] = inv_nodes.get(val, [])
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| 132 | inv_nodes[val].append(k)
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| 133 |
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| 134 | print(len(nodes))
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| 135 |
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| 136 |
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| 137 | def load_simple_data(dir):
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| 138 | global firstnode, nodes, inv_nodes
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| 139 | f = open(dir)
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| 140 | for line in f:
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| 141 | sline = line.split()
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| 142 | if len(sline) > 1:
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| 143 | #if int(sline[0]) > 15000:
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| 144 | # break
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| 145 | if sline[0] == firstnode:
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| 146 | continue
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| 147 | nodes[sline[0]] = str(max(int(sline[1]), int(firstnode)))
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| 148 | else:
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| 149 | firstnode = sline[0]
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| 150 |
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| 151 | for k, v in sorted(nodes.items()):
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| 152 | inv_nodes[v] = inv_nodes.get(v, [])
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| 153 | inv_nodes[v].append(k)
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| 154 |
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| 155 | #print(str(inv_nodes))
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| 156 | #quit()
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| 157 |
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| 158 | def compute_depth(node):
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| 159 | my_depth = 0
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| 160 | if node in inv_nodes:
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| 161 | for c in inv_nodes[node]:
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| 162 | my_depth = max(my_depth, compute_depth(c)+1)
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| 163 | depth[node] = my_depth
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| 164 | return my_depth
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| 165 |
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| 166 | # ------------------------------------
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| 167 |
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| 168 | def xmin_crowd(x1, x2, y):
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| 169 | if BALANCE == "RANDOM":
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| 170 | return (x1 if random.randrange(2) == 0 else x2)
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| 171 | elif BALANCE == "MIN":
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| 172 | x1_closest = 999999
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| 173 | x2_closest = 999999
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| 174 | for pos in positions:
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| 175 | pos = positions[pos]
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| 176 | if pos[1] == y:
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| 177 | x1_closest = min(x1_closest, abs(x1-pos[0]))
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| 178 | x2_closest = min(x2_closest, abs(x2-pos[0]))
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| 179 | return (x1 if x1_closest > x2_closest else x2)
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| 180 | elif BALANCE == "DENSITY":
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| 181 | x1_dist = 0
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| 182 | x2_dist = 0
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| 183 | for pos in positions:
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| 184 | pos = positions[pos]
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| 185 | if pos[1] > y-10 or pos[1] < y+10:
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| 186 | dy = pos[1]-y
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| 187 | dx1 = pos[0]-x1
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| 188 | dx2 = pos[0]-x2
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| 189 |
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| 190 | x1_dist += math.sqrt(dy**2 + dx1**2)
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| 191 | x2_dist += math.sqrt(dy**2 + dx2**2)
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| 192 | return (x1 if x1_dist > x2_dist else x2)
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| 193 |
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| 194 | # ------------------------------------
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| 195 |
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| 196 | # def prepos_children_reccurent(node):
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| 197 | # global visited
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| 198 | # for c in inv_nodes[node]:
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| 199 | #
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| 200 | # # we want to visit the node just once, after all of its parents
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| 201 | # if not all_parents_visited(c):
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| 202 | # continue
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| 203 | # else:
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| 204 | # visited[c] = True
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| 205 | #
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| 206 | # cy = 0
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| 207 | # if TIME == "BIRTHS":
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| 208 | # if c[0] == "c":
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| 209 | # cy = int(c[1:])
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| 210 | # else:
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| 211 | # cy = int(c)
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| 212 | # elif TIME == "GENERATIONAL":
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| 213 | # cy = positions[node][1]+1
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| 214 | # elif TIME == "REAL":
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| 215 | # cy = time[c]
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| 216 | #
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| 217 | # if len(nodes[c]) == 1:
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| 218 | # dissimilarity = 0
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| 219 | # if JITTER == True:
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| 220 | # dissimilarity = random.gauss(0,1)
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| 221 | # else:
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| 222 | # dissimilarity = 1
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| 223 | # positions[c] = [xmin_crowd(positions[node][0]-dissimilarity, positions[node][0]+dissimilarity, cy), cy]
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| 224 | # else:
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| 225 | # vsum = sum([v for k, v in nodes[c].items()])
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| 226 | # cx = sum([positions[k][0]*v/vsum for k, v in nodes[c].items()])
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| 227 | #
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| 228 | # if JITTER == True:
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| 229 | # positions[c] = [cx + random.gauss(0, 0.1), cy]
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| 230 | # else:
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| 231 | # positions[c] = [cx, cy]
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| 232 | #
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| 233 | #
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| 234 | # if c in inv_nodes:
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| 235 | # prepos_children_reccurent(c)
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| 236 |
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| 237 | def prepos_children():
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| 238 | global max_height, max_width, min_width, visited, TIME
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| 239 |
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| 240 | print("firstnode " + firstnode)
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| 241 |
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| 242 | if not bool(time):
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| 243 | print("REAL time requested, but no real time data provided. Assuming BIRTHS time instead.")
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| 244 | TIME = "BIRTHS"
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| 245 |
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| 246 | positions[firstnode] = [0, 0]
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| 247 |
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| 248 | #visited = {}
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| 249 | #visited[firstnode] = True
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| 250 |
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| 251 |
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| 252 | nodes_to_visit = [firstnode]
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| 253 |
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| 254 | ccc = 0
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| 255 | timet = ttime.time()
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| 256 |
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| 257 | while True:
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| 258 |
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| 259 | ccc += 1
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| 260 | if ccc%1000 == 0 :
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| 261 | print(str(ccc) + " " + str(ttime.time()-timet))
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| 262 | timet = ttime.time()
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| 263 |
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| 264 | current_node = nodes_to_visit[0]
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| 265 |
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| 266 | if current_node in inv_nodes:
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| 267 | for c in inv_nodes[current_node]:
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| 268 | # we want to visit the node just once, after all of its parents
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| 269 | if c not in nodes_to_visit:
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| 270 | nodes_to_visit.append(c)
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| 271 |
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| 272 | cy = 0
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| 273 | if TIME == "BIRTHS":
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| 274 | if c[0] == "c":
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| 275 | cy = int(c[1:])
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| 276 | else:
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| 277 | cy = int(c)
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| 278 | elif TIME == "GENERATIONAL":
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| 279 | cy = positions[current_node][1]+1
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| 280 | elif TIME == "REAL":
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| 281 | cy = time[c]
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| 282 |
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| 283 | if len(nodes[c]) == 1:
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| 284 | dissimilarity = 0
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| 285 | if JITTER == True:
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| 286 | dissimilarity = random.gauss(0,1)
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| 287 | else:
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| 288 | dissimilarity = 1
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| 289 | positions[c] = [xmin_crowd(positions[current_node][0]-dissimilarity, positions[current_node][0]+dissimilarity, cy), cy]
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| 290 | else:
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| 291 | vsum = sum([v for k, v in nodes[c].items()])
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| 292 | cx = sum([positions[k][0]*v/vsum for k, v in nodes[c].items()])
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| 293 |
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| 294 | if JITTER == True:
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| 295 | positions[c] = [cx + random.gauss(0, 0.1), cy]
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| 296 | else:
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| 297 | positions[c] = [cx, cy]
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| 298 |
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| 299 |
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| 300 | #if c in inv_nodes:
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| 301 | # prepos_children_reccurent(c)
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| 302 |
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| 303 | nodes_to_visit = nodes_to_visit[1:]
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| 304 | # if none left, we can stop
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| 305 | if len(nodes_to_visit) == 0:
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| 306 | break
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| 307 |
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| 308 |
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| 309 | # prepos_children_reccurent(firstnode)
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| 310 |
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| 311 | for pos in positions:
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| 312 | max_height = max(max_height, positions[pos][1])
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| 313 | max_width = max(max_width, positions[pos][0])
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| 314 | min_width = min(min_width, positions[pos][0])
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| 315 |
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| 316 | # ------------------------------------
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| 317 |
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| 318 | def all_parents_visited(node):
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| 319 | apv = True
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| 320 | for k, v in sorted(nodes[node].items()):
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| 321 | if not k in visited:
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| 322 | apv = False
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| 323 | break
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| 324 | return apv
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| 325 | # ------------------------------------
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| 326 |
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| 327 | def draw_children():
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| 328 | max_depth = 0
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| 329 | for k, v in depth.items():
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| 330 | max_depth = max(max_depth, v)
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| 331 |
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| 332 | nodes_to_visit = [firstnode]
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| 333 | while True:
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| 334 | current_node = nodes_to_visit[0]
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| 335 |
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| 336 | if current_node in inv_nodes:
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| 337 | for c in inv_nodes[current_node]: # inv_node => p->c
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| 338 |
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| 339 | if not c in nodes_to_visit:
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| 340 | nodes_to_visit.append(c)
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| 341 |
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| 342 | line_style = ""
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| 343 | if COLORING == "NONE":
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| 344 | line_style = svg_line_style
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| 345 | elif COLORING == "TYPE":
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| 346 | line_style = (svg_mutation_line_style if len(nodes[c]) == 1 else svg_crossover_line_style)
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| 347 | else: # IMPORTANCE, default
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| 348 | line_style = svg_generate_line_style(depth[c]/max_depth)
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| 349 |
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| 350 | svg_add_line( (w_margin+w_no_margs*(positions[current_node][0]-min_width)/(max_width-min_width), h_margin+h_no_margs*positions[current_node][1]/max_height),
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| 351 | (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)
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| 352 |
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| 353 | # we want to draw the node just once
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| 354 | if DOT_STYLE == "NONE":
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| 355 | continue
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| 356 | elif DOT_STYLE == "TYPE":
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| 357 | dot_style = svg_generate_dot_style(kind[current_node] if current_node in kind else 0) #type
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| 358 | else: # NORMAL, default
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| 359 | dot_style = svg_clear_dot_style #svg_generate_dot_style(depth[c]/max_depth)
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| 360 | svg_add_dot( (w_margin+w_no_margs*(positions[current_node][0]-min_width)/(max_width-min_width), h_margin+h_no_margs*positions[current_node][1]/max_height), dot_style)
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| 361 | #svg_add_text( str(depth[current_node]), (w_margin+w_no_margs*(positions[current_node][0]-min_width)/(max_width-min_width),
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| 362 | # h_margin+h_no_margs*positions[current_node][1]/max_height), "end")
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| 363 |
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| 364 | # we remove the current node from the list
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| 365 | nodes_to_visit = nodes_to_visit[1:]
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| 366 | # if none left, we can stop
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| 367 | if len(nodes_to_visit) == 0:
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| 368 | break
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| 369 |
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| 370 | def draw_spine():
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| 371 | nodes_to_visit = [firstnode]
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| 372 | while True:
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| 373 | current_node = nodes_to_visit[0]
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| 374 |
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| 375 | if current_node in inv_nodes:
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| 376 | for c in inv_nodes[current_node]: # inv_node => p->c
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| 377 | if depth[c] == depth[current_node] - 1:
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| 378 | if not c in nodes_to_visit:
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| 379 | nodes_to_visit.append(c)
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| 380 | line_style = svg_spine_line_style
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| 381 | svg_add_line( (w_margin+w_no_margs*(positions[current_node][0]-min_width)/(max_width-min_width), h_margin+h_no_margs*positions[current_node][1]/max_height),
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| 382 | (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)
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| 383 |
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| 384 | # we remove the current node from the list
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| 385 | nodes_to_visit = nodes_to_visit[1:]
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| 386 | # if none left, we can stop
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| 387 | if len(nodes_to_visit) == 0:
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| 388 | break
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| 389 |
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| 390 | def draw_skeleton():
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| 391 | nodes_to_visit = [firstnode]
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| 392 | while True:
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| 393 | current_node = nodes_to_visit[0]
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| 394 |
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| 395 | if current_node in inv_nodes:
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| 396 | for c in inv_nodes[current_node]: # inv_node => p->c
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| 397 | if depth[c] >= min_skeleton_depth:
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| 398 | if not c in nodes_to_visit:
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| 399 | nodes_to_visit.append(c)
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| 400 | line_style = svg_spine_line_style
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| 401 | svg_add_line( (w_margin+w_no_margs*(positions[current_node][0]-min_width)/(max_width-min_width), h_margin+h_no_margs*positions[current_node][1]/max_height),
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| 402 | (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)
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| 403 |
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| 404 | # we remove the current node from the list
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| 405 | nodes_to_visit = nodes_to_visit[1:]
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| 406 | # if none left, we can stop
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| 407 | if len(nodes_to_visit) == 0:
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| 408 | break
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| 409 |
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| 410 | # ------------------------------------
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| 411 |
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| 412 | def draw_scale(filename ,type):
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| 413 |
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| 414 | svg_add_text("Generated from " + filename.split("\\")[-1], (5, 15), "start")
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| 415 |
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| 416 | svg_add_line( (w*0.7, h_margin), (w, h_margin), svg_scale_line_style)
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|---|
| 417 | start_text = ""
|
|---|
| 418 | if TIME == "BIRTHS":
|
|---|
| 419 | start_text = "Birth #" + str(min([int(k[1:]) for k, v in nodes.items()]))
|
|---|
| 420 | if TIME == "REAL":
|
|---|
| 421 | start_text = "Time " + str(min([v for k, v in time.items()]))
|
|---|
| 422 | if TIME == "GENERATIONAL":
|
|---|
| 423 | start_text = "Depth " + str(min([v for k, v in depth.items()]))
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|---|
| 424 | svg_add_text( start_text, (w, h_margin + 15), "end")
|
|---|
| 425 |
|
|---|
| 426 | svg_add_line( (w*0.7, h-h_margin), (w, h-h_margin), svg_scale_line_style)
|
|---|
| 427 | end_text = ""
|
|---|
| 428 | if TIME == "BIRTHS":
|
|---|
| 429 | end_text = "Birth #" + str(max([int(k[1:]) for k, v in nodes.items()]))
|
|---|
| 430 | if TIME == "REAL":
|
|---|
| 431 | end_text = "Time " + str(max([v for k, v in time.items()]))
|
|---|
| 432 | if TIME == "GENERATIONAL":
|
|---|
| 433 | end_text = "Depth " + str(max([v for k, v in depth.items()]))
|
|---|
| 434 | svg_add_text( end_text, (w, h-h_margin + 15), "end")
|
|---|
| 435 |
|
|---|
| 436 |
|
|---|
| 437 | ##################################################### main #####################################################
|
|---|
| 438 |
|
|---|
| 439 | args = 0
|
|---|
| 440 |
|
|---|
| 441 | h = 800
|
|---|
| 442 | w = 600
|
|---|
| 443 | h_margin = 20
|
|---|
| 444 | w_margin = 10
|
|---|
| 445 | h_no_margs = h - 2* h_margin
|
|---|
| 446 | w_no_margs = w - 2* w_margin
|
|---|
| 447 |
|
|---|
| 448 | max_height = 0
|
|---|
| 449 | max_width = 0
|
|---|
| 450 | min_width = 9999999999
|
|---|
| 451 |
|
|---|
| 452 | min_skeleton_depth = 0
|
|---|
| 453 |
|
|---|
| 454 | firstnode = None
|
|---|
| 455 | nodes = {}
|
|---|
| 456 | inv_nodes = {}
|
|---|
| 457 | positions = {}
|
|---|
| 458 | visited= {}
|
|---|
| 459 | depth = {}
|
|---|
| 460 | time = {}
|
|---|
| 461 | kind = {}
|
|---|
| 462 |
|
|---|
| 463 | def main():
|
|---|
| 464 | global svg_file, min_skeleton_depth, args, \
|
|---|
| 465 | TIME, BALANCE, DOT_STYLE, COLORING, JITTER, \
|
|---|
| 466 | svg_mutation_line_style, svg_crossover_line_style
|
|---|
| 467 |
|
|---|
| 468 | parser = argparse.ArgumentParser(description='Draws a genealogical tree (generates a SVG file) based on parent-child relationship information from a text file. Supports files generated by Framsticks experiments.')
|
|---|
| 469 | parser.add_argument('-i', '--in', dest='input', required=True, help='input file name with stuctured evolutionary data')
|
|---|
| 470 | parser.add_argument('-o', '--out', dest='output', required=True, help='output file name for the evolutionary tree (SVG format)')
|
|---|
| 471 | draw_tree_parser = parser.add_mutually_exclusive_group(required=False)
|
|---|
| 472 | draw_tree_parser.add_argument('--draw-tree', dest='draw_tree', action='store_true', help='whether drawing the full tree should be skipped')
|
|---|
| 473 | draw_tree_parser.add_argument('--no-draw-tree', dest='draw_tree', action='store_false')
|
|---|
| 474 |
|
|---|
| 475 | draw_skeleton_parser = parser.add_mutually_exclusive_group(required=False)
|
|---|
| 476 | draw_skeleton_parser.add_argument('--draw-skeleton', dest='draw_skeleton', action='store_true', help='whether the skeleton of the tree should be drawn')
|
|---|
| 477 | draw_skeleton_parser.add_argument('--no-draw-skeleton', dest='draw_skeleton', action='store_false')
|
|---|
| 478 |
|
|---|
| 479 | draw_spine_parser = parser.add_mutually_exclusive_group(required=False)
|
|---|
| 480 | draw_spine_parser.add_argument('--draw-spine', dest='draw_spine', action='store_true', help='whether the spine of the tree should be drawn')
|
|---|
| 481 | draw_spine_parser.add_argument('--no-draw-spine', dest='draw_spine', action='store_false')
|
|---|
| 482 |
|
|---|
| 483 | #TODO: better names for those parameters
|
|---|
| 484 | parser.add_argument('-t', '--time', default='GENERATIONAL', dest='time', help='values on vertical axis (BIRTHS/GENERATIONAL(d)/REAL); '
|
|---|
| 485 | 'BIRTHS: time measured as the number of births since the beginning; '
|
|---|
| 486 | 'GENERATIONAL: time measured as number of ancestors; '
|
|---|
| 487 | 'REAL: real time of the simulation')
|
|---|
| 488 | parser.add_argument('-b', '--balance', default='DENSITY', dest='balance', help='method of placing nodes in the tree (RANDOM/MIN/DENSITY(d))')
|
|---|
| 489 | parser.add_argument('-s', '--scale', default='NONE', dest='scale', help='type of timescale added to the tree (NONE(d)/SIMPLE)')
|
|---|
| 490 | parser.add_argument('-c', '--coloring', default='IMPORTANCE', dest="coloring", help='method of coloring the tree (NONE/IMPORTANCE(d)/TYPE)')
|
|---|
| 491 | parser.add_argument('-d', '--dots', default='TYPE', dest='dots', help='method of drawing dots (individuals) (NONE/NORMAL/TYPE(d))')
|
|---|
| 492 | parser.add_argument('-j', '--jitter', dest="jitter", action='store_true', help='draw horizontal positions of children from the normal distribution')
|
|---|
| 493 |
|
|---|
| 494 | parser.add_argument('--color-mut', default="#000000", dest="color_mut", help='color of clone/mutation lines in rgba (e.g. #FF60B240) for TYPE coloring')
|
|---|
| 495 | parser.add_argument('--color-cross', default="#660198", dest="color_cross", help='color of crossover lines in rgba (e.g. #FF60B240) for TYPE coloring')
|
|---|
| 496 |
|
|---|
| 497 | 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')
|
|---|
| 498 | parser.add_argument('--seed', type=int, dest='seed', help='seed for the random number generator (-1 for random)')
|
|---|
| 499 |
|
|---|
| 500 | parser.add_argument('--simple-data', type=bool, dest='simple_data', help='input data are given in a simple format (#child #parent)')
|
|---|
| 501 |
|
|---|
| 502 | parser.set_defaults(draw_tree=True)
|
|---|
| 503 | parser.set_defaults(draw_skeleton=False)
|
|---|
| 504 | parser.set_defaults(draw_spine=False)
|
|---|
| 505 |
|
|---|
| 506 | parser.set_defaults(seed=-1)
|
|---|
| 507 |
|
|---|
| 508 | args = parser.parse_args()
|
|---|
| 509 |
|
|---|
| 510 | TIME = args.time.upper()
|
|---|
| 511 | BALANCE = args.balance.upper()
|
|---|
| 512 | DOT_STYLE = args.dots.upper()
|
|---|
| 513 | COLORING = args.coloring.upper()
|
|---|
| 514 | SCALE = args.scale.upper()
|
|---|
| 515 | JITTER = args.jitter
|
|---|
| 516 | if not TIME in ['BIRTHS', 'GENERATIONAL', 'REAL']\
|
|---|
| 517 | or not BALANCE in ['RANDOM', 'MIN', 'DENSITY']\
|
|---|
| 518 | or not DOT_STYLE in ['NONE', 'NORMAL', 'TYPE']\
|
|---|
| 519 | or not COLORING in ['NONE', 'IMPORTANCE', 'TYPE']\
|
|---|
| 520 | or not SCALE in ['NONE', 'SIMPLE']:
|
|---|
| 521 | print("Incorrect value of one of the parameters! Closing the program.") #TODO don't be lazy, figure out which parameter is wrong...
|
|---|
| 522 | return
|
|---|
| 523 |
|
|---|
| 524 |
|
|---|
| 525 | svg_mutation_line_style += hex_to_style(args.color_mut)
|
|---|
| 526 | svg_crossover_line_style += hex_to_style(args.color_cross)
|
|---|
| 527 |
|
|---|
| 528 | dir = args.input
|
|---|
| 529 | min_skeleton_depth = args.min_skeleton_depth
|
|---|
| 530 | seed = args.seed
|
|---|
| 531 | if seed == -1:
|
|---|
| 532 | seed = random.randint(0, 10000)
|
|---|
| 533 | random.seed(seed)
|
|---|
| 534 | print("seed:", seed)
|
|---|
| 535 |
|
|---|
| 536 | if args.simple_data:
|
|---|
| 537 | load_simple_data(dir)
|
|---|
| 538 | else:
|
|---|
| 539 | load_data(dir)
|
|---|
| 540 |
|
|---|
| 541 | compute_depth(firstnode)
|
|---|
| 542 |
|
|---|
| 543 | svg_file = open(args.output, "w")
|
|---|
| 544 | svg_file.write('<svg xmlns:svg="http://www.w3.org/2000/svg" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" version="1.0" '
|
|---|
| 545 | 'width="' + str(w) + '" height="' + str(h) + '">')
|
|---|
| 546 |
|
|---|
| 547 | prepos_children()
|
|---|
| 548 |
|
|---|
| 549 | if args.draw_tree:
|
|---|
| 550 | draw_children()
|
|---|
| 551 | if args.draw_skeleton:
|
|---|
| 552 | draw_skeleton()
|
|---|
| 553 | if args.draw_spine:
|
|---|
| 554 | draw_spine()
|
|---|
| 555 |
|
|---|
| 556 | draw_scale(dir, SCALE)
|
|---|
| 557 |
|
|---|
| 558 | svg_file.write("</svg>")
|
|---|
| 559 | svg_file.close()
|
|---|
| 560 |
|
|---|
| 561 | main()
|
|---|
