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source: mds-and-trees/tree-genealogy.py @ 681

Last change on this file since 681 was 681, checked in by konrad, 7 years ago
Improved the compute_depth function so now it works much faster for trees with crossover
File size: 33.1 KB

Rev	Line
[562]	1	import json
[624]	2	import math
[562]	3	import random
	4	import argparse
[624]	5	import bisect
	6	import time as timelib
	7	from PIL import Image, ImageDraw, ImageFont
[633]	8	from scipy import stats
	9	import numpy as np
[562]	10
[624]	11	class LoadingError(Exception):
	12	pass
[562]	13
[624]	14	class Drawer:
[571]	15
[624]	16	def __init__(self, design, config_file, w=600, h=800, w_margin=10, h_margin=20):
	17	self.design = design
	18	self.width = w
	19	self.height = h
	20	self.w_margin = w_margin
	21	self.h_margin = h_margin
	22	self.w_no_margs = w - 2* w_margin
	23	self.h_no_margs = h - 2* h_margin
[571]	24
[624]	25	self.colors = {
	26	'black' : {'r':0, 'g':0, 'b':0},
	27	'red' : {'r':100, 'g':0, 'b':0},
	28	'green' : {'r':0, 'g':100, 'b':0},
	29	'blue' : {'r':0, 'g':0, 'b':100},
	30	'yellow' : {'r':100, 'g':100, 'b':0},
	31	'magenta' : {'r':100, 'g':0, 'b':100},
	32	'cyan' : {'r':0, 'g':100, 'b':100},
	33	'orange': {'r':100, 'g':50, 'b':0},
	34	'purple': {'r':50, 'g':0, 'b':100}
	35	}
[562]	36
[624]	37	self.settings = {
	38	'colors_of_kinds': ['red', 'green', 'blue', 'magenta', 'yellow', 'cyan', 'orange', 'purple'],
	39	'dots': {
	40	'color': {
[628]	41	'meaning': 'Lifespan',
	42	'start': 'red',
[624]	43	'end': 'green',
	44	'bias': 1
	45	},
	46	'size': {
[628]	47	'meaning': 'EnergyEaten',
[624]	48	'start': 1,
[628]	49	'end': 6,
[624]	50	'bias': 0.5
	51	},
	52	'opacity': {
[628]	53	'meaning': 'EnergyEaten',
	54	'start': 0.2,
	55	'end': 1,
[624]	56	'bias': 1
	57	}
	58	},
	59	'lines': {
	60	'color': {
	61	'meaning': 'adepth',
	62	'start': 'black',
	63	'end': 'red',
	64	'bias': 3
	65	},
	66	'width': {
	67	'meaning': 'adepth',
[627]	68	'start': 0.1,
[624]	69	'end': 4,
	70	'bias': 3
	71	},
	72	'opacity': {
	73	'meaning': 'adepth',
	74	'start': 0.1,
	75	'end': 0.8,
	76	'bias': 5
	77	}
	78	}
	79	}
[577]	80
[624]	81	def merge(source, destination):
	82	for key, value in source.items():
	83	if isinstance(value, dict):
	84	node = destination.setdefault(key, {})
	85	merge(value, node)
	86	else:
	87	destination[key] = value
[562]	88
[624]	89	return destination
[576]	90
[624]	91	if config_file != "":
	92	with open(config_file) as config:
	93	c = json.load(config)
	94	self.settings = merge(c, self.settings)
	95	#print(json.dumps(self.settings, indent=4, sort_keys=True))
[586]	96
[624]	97	def draw_dots(self, file, min_width, max_width, max_height):
	98	for i in range(len(self.design.positions)):
	99	node = self.design.positions[i]
	100	if 'x' not in node:
	101	continue
	102	dot_style = self.compute_dot_style(node=i)
	103	self.add_dot(file, (self.w_margin+self.w_no_margs*(node['x']-min_width)/(max_width-min_width),
	104	self.h_margin+self.h_no_margs*node['y']/max_height), dot_style)
[585]	105
[624]	106	def draw_lines(self, file, min_width, max_width, max_height):
	107	for parent in range(len(self.design.positions)):
	108	par_pos = self.design.positions[parent]
	109	if not 'x' in par_pos:
	110	continue
	111	for child in self.design.tree.children[parent]:
	112	chi_pos = self.design.positions[child]
	113	if 'x' not in chi_pos:
	114	continue
	115	line_style = self.compute_line_style(parent, child)
	116	self.add_line(file, (self.w_margin+self.w_no_margs*(par_pos['x']-min_width)/(max_width-min_width),
	117	self.h_margin+self.h_no_margs*par_pos['y']/max_height),
	118	(self.w_margin+self.w_no_margs*(chi_pos['x']-min_width)/(max_width-min_width),
	119	self.h_margin+self.h_no_margs*chi_pos['y']/max_height), line_style)
[585]	120
[624]	121	def draw_scale(self, file, filename):
[626]	122	self.add_text(file, "Generated from " + filename.split("\\")[-1], (5, 5), "start")
[562]	123
[624]	124	start_text = ""
	125	end_text = ""
	126	if self.design.TIME == "BIRTHS":
	127	start_text = "Birth #0"
	128	end_text = "Birth #" + str(len(self.design.positions)-1)
	129	if self.design.TIME == "REAL":
	130	start_text = "Time " + str(min(self.design.tree.time))
	131	end_text = "Time " + str(max(self.design.tree.time))
	132	if self.design.TIME == "GENERATIONAL":
[633]	133	start_text = "Depth " + str(self.design.props['adepth_min'])
	134	end_text = "Depth " + str(self.design.props['adepth_max'])
[576]	135
[626]	136	self.add_dashed_line(file, (self.width*0.7, self.h_margin), (self.width, self.h_margin))
	137	self.add_text(file, start_text, (self.width, self.h_margin), "end")
[624]	138	self.add_dashed_line(file, (self.width*0.7, self.height-self.h_margin), (self.width, self.height-self.h_margin))
[626]	139	self.add_text(file, end_text, (self.width, self.height-self.h_margin), "end")
[562]	140
[624]	141	def compute_property(self, part, prop, node):
	142	start = self.settings[part][prop]['start']
	143	end = self.settings[part][prop]['end']
	144	value = (self.design.props[self.settings[part][prop]['meaning']][node]
	145	if self.settings[part][prop]['meaning'] in self.design.props else 0 )
	146	bias = self.settings[part][prop]['bias']
	147	if prop == "color":
	148	return self.compute_color(start, end, value, bias)
	149	else:
	150	return self.compute_value(start, end, value, bias)
[562]	151
[624]	152	def compute_color(self, start, end, value, bias=1):
	153	if isinstance(value, str):
	154	value = int(value)
	155	r = self.colors[self.settings['colors_of_kinds'][value]]['r']
	156	g = self.colors[self.settings['colors_of_kinds'][value]]['g']
	157	b = self.colors[self.settings['colors_of_kinds'][value]]['b']
	158	else:
	159	start_color = self.colors[start]
	160	end_color = self.colors[end]
	161	value = 1 - (1-value)**bias
	162	r = start_color['r'](1-value)+end_color['r']value
	163	g = start_color['g'](1-value)+end_color['g']value
	164	b = start_color['b'](1-value)+end_color['b']value
	165	return (r, g, b)
[562]	166
[624]	167	def compute_value(self, start, end, value, bias=1):
	168	value = 1 - (1-value)**bias
	169	return start(1-value) + endvalue
[564]	170
[624]	171	class PngDrawer(Drawer):
[626]	172
	173	def scale_up(self):
	174	self.width *= self.multi
	175	self.height *= self.multi
	176	self.w_margin *= self.multi
	177	self.h_margin *= self.multi
	178	self.h_no_margs *= self.multi
	179	self.w_no_margs *= self.multi
	180
	181	def scale_down(self):
	182	self.width /= self.multi
	183	self.height /= self.multi
	184	self.w_margin /= self.multi
	185	self.h_margin /= self.multi
	186	self.h_no_margs /= self.multi
	187	self.w_no_margs /= self.multi
	188
	189	def draw_design(self, filename, input_filename, multi=1, scale="SIMPLE"):
[624]	190	print("Drawing...")
[564]	191
[626]	192	self.multi=multi
	193	self.scale_up()
	194
[624]	195	back = Image.new('RGBA', (self.width, self.height), (255,255,255,0))
[562]	196
[624]	197	min_width = min([x['x'] for x in self.design.positions if 'x' in x])
	198	max_width = max([x['x'] for x in self.design.positions if 'x' in x])
	199	max_height = max([x['y'] for x in self.design.positions if 'y' in x])
[562]	200
[624]	201	self.draw_lines(back, min_width, max_width, max_height)
	202	self.draw_dots(back, min_width, max_width, max_height)
[562]	203
[624]	204	if scale == "SIMPLE":
	205	self.draw_scale(back, input_filename)
[564]	206
[626]	207	#back.show()
	208	self.scale_down()
	209
	210	back.thumbnail((self.width, self.height), Image.ANTIALIAS)
	211
[624]	212	back.save(filename)
[562]	213
[624]	214	def add_dot(self, file, pos, style):
	215	x, y = int(pos[0]), int(pos[1])
[626]	216	r = style['r']*self.multi
[624]	217	offset = (int(x - r), int(y - r))
	218	size = (2int(r), 2int(r))
[622]	219
[624]	220	c = style['color']
[572]	221
[624]	222	img = Image.new('RGBA', size)
	223	ImageDraw.Draw(img).ellipse((1, 1, size[0]-1, size[1]-1),
	224	(int(2.55c[0]), int(2.55c[1]), int(2.55c[2]), int(255style['opacity'])))
	225	file.paste(img, offset, mask=img)
[572]	226
[624]	227	def add_line(self, file, from_pos, to_pos, style):
	228	fx, fy, tx, ty = int(from_pos[0]), int(from_pos[1]), int(to_pos[0]), int(to_pos[1])
[626]	229	w = int(style['width'])*self.multi
[562]	230
[624]	231	offset = (min(fx-w, tx-w), min(fy-w, ty-w))
	232	size = (abs(fx-tx)+2w, abs(fy-ty)+2w)
[577]	233
[624]	234	c = style['color']
[622]	235
[624]	236	img = Image.new('RGBA', size)
	237	ImageDraw.Draw(img).line((w, w, size[0]-w, size[1]-w) if (fx-tx)*(fy-ty)>0 else (size[0]-w, w, w, size[1]-w),
[626]	238	(int(2.55c[0]), int(2.55c[1]), int(2.55c[2]), int(255style['opacity'])), w)
[624]	239	file.paste(img, offset, mask=img)
[562]	240
[624]	241	def add_dashed_line(self, file, from_pos, to_pos):
	242	style = {'color': (0,0,0), 'width': 1, 'opacity': 1}
	243	sublines = 50
	244	# TODO could be faster: compute delta and only add delta each time (but currently we do not use it often)
	245	for i in range(sublines):
	246	from_pos_sub = (self.compute_value(from_pos[0], to_pos[0], 2i/(2sublines-1), 1),
	247	self.compute_value(from_pos[1], to_pos[1], 2i/(2sublines-1), 1))
	248	to_pos_sub = (self.compute_value(from_pos[0], to_pos[0], (2i+1)/(2sublines-1), 1),
	249	self.compute_value(from_pos[1], to_pos[1], (2i+1)/(2sublines-1), 1))
	250	self.add_line(file, from_pos_sub, to_pos_sub, style)
[562]	251
[624]	252	def add_text(self, file, text, pos, anchor, style=''):
[626]	253	font = ImageFont.truetype("Vera.ttf", 16*self.multi)
[621]	254
[624]	255	img = Image.new('RGBA', (self.width, self.height))
	256	draw = ImageDraw.Draw(img)
	257	txtsize = draw.textsize(text, font=font)
[626]	258	pos = pos if anchor == "start" else (pos[0]-txtsize[0], pos[1])
[624]	259	draw.text(pos, text, (0,0,0), font=font)
	260	file.paste(img, (0,0), mask=img)
[622]	261
[624]	262	def compute_line_style(self, parent, child):
	263	return {'color': self.compute_property('lines', 'color', child),
	264	'width': self.compute_property('lines', 'width', child),
	265	'opacity': self.compute_property('lines', 'opacity', child)}
	266
	267	def compute_dot_style(self, node):
	268	return {'color': self.compute_property('dots', 'color', node),
	269	'r': self.compute_property('dots', 'size', node),
	270	'opacity': self.compute_property('dots', 'opacity', node)}
	271
	272	class SvgDrawer(Drawer):
[626]	273	def draw_design(self, filename, input_filename, multi=1, scale="SIMPLE"):
[624]	274	print("Drawing...")
	275	file = open(filename, "w")
	276
	277	min_width = min([x['x'] for x in self.design.positions if 'x' in x])
	278	max_width = max([x['x'] for x in self.design.positions if 'x' in x])
	279	max_height = max([x['y'] for x in self.design.positions if 'y' in x])
	280
	281	file.write('<svg xmlns:svg="http://www.w3.org/2000/svg" xmlns="http://www.w3.org/2000/svg" '
	282	'xmlns:xlink="http://www.w3.org/1999/xlink" version="1.0" '
	283	'width="' + str(self.width) + '" height="' + str(self.height) + '">')
	284
	285	self.draw_lines(file, min_width, max_width, max_height)
	286	self.draw_dots(file, min_width, max_width, max_height)
	287
	288	if scale == "SIMPLE":
	289	self.draw_scale(file, input_filename)
	290
	291	file.write("</svg>")
	292	file.close()
	293
	294	def add_text(self, file, text, pos, anchor, style=''):
	295	style = (style if style != '' else 'style="font-family: Arial; font-size: 12; fill: #000000;"')
[628]	296	# assuming font size 12, it should be taken from the style string!
	297	file.write('<text ' + style + ' text-anchor="' + anchor + '" x="' + str(pos[0]) + '" y="' + str(pos[1]+12) + '" >' + text + '</text>')
[624]	298
	299	def add_dot(self, file, pos, style):
	300	file.write('<circle ' + style + ' cx="' + str(pos[0]) + '" cy="' + str(pos[1]) + '" />')
	301
	302	def add_line(self, file, from_pos, to_pos, style):
	303	file.write('<line ' + style + ' x1="' + str(from_pos[0]) + '" x2="' + str(to_pos[0]) +
	304	'" y1="' + str(from_pos[1]) + '" y2="' + str(to_pos[1]) + '" fill="none"/>')
	305
	306	def add_dashed_line(self, file, from_pos, to_pos):
	307	style = 'stroke="black" stroke-width="0.5" stroke-opacity="1" stroke-dasharray="5, 5"'
	308	self.add_line(file, from_pos, to_pos, style)
	309
	310	def compute_line_style(self, parent, child):
	311	return self.compute_stroke_color('lines', child) + ' ' \
	312	+ self.compute_stroke_width('lines', child) + ' ' \
	313	+ self.compute_stroke_opacity(child)
	314
	315	def compute_dot_style(self, node):
	316	return self.compute_dot_size(node) + ' ' \
	317	+ self.compute_fill_opacity(node) + ' ' \
	318	+ self.compute_dot_fill(node)
	319
	320	def compute_stroke_color(self, part, node):
	321	color = self.compute_property(part, 'color', node)
	322	return 'stroke="rgb(' + str(color[0]) + '%,' + str(color[1]) + '%,' + str(color[2]) + '%)"'
	323
	324	def compute_stroke_width(self, part, node):
	325	return 'stroke-width="' + str(self.compute_property(part, 'width', node)) + '"'
	326
	327	def compute_stroke_opacity(self, node):
	328	return 'stroke-opacity="' + str(self.compute_property('lines', 'opacity', node)) + '"'
	329
	330	def compute_fill_opacity(self, node):
	331	return 'fill-opacity="' + str(self.compute_property('dots', 'opacity', node)) + '"'
	332
	333	def compute_dot_size(self, node):
	334	return 'r="' + str(self.compute_property('dots', 'size', node)) + '"'
	335
	336	def compute_dot_fill(self, node):
	337	color = self.compute_property('dots', 'color', node)
	338	return 'fill="rgb(' + str(color[0]) + '%,' + str(color[1]) + '%,' + str(color[2]) + '%)"'
	339
	340	class Designer:
	341
	342	def __init__(self, tree, jitter=False, time="GENERATIONAL", balance="DENSITY"):
	343	self.props = {}
	344
	345	self.tree = tree
	346
	347	self.TIME = time
	348	self.JITTER = jitter
	349
	350	if balance == "RANDOM":
	351	self.xmin_crowd = self.xmin_crowd_random
	352	elif balance == "MIN":
	353	self.xmin_crowd = self.xmin_crowd_min
	354	elif balance == "DENSITY":
	355	self.xmin_crowd = self.xmin_crowd_density
[562]	356	else:
[624]	357	raise ValueError("Error, the value of BALANCE does not match any expected value.")
[562]	358
[624]	359	def calculate_measures(self):
	360	print("Calculating measures...")
[679]	361	self.compute_depth()
[624]	362	self.compute_adepth()
	363	self.compute_children()
	364	self.compute_kind()
	365	self.compute_time()
[633]	366	self.compute_progress()
[624]	367	self.compute_custom()
[622]	368
[624]	369	def xmin_crowd_random(self, x1, x2, y):
	370	return (x1 if random.randrange(2) == 0 else x2)
[562]	371
[624]	372	def xmin_crowd_min(self, x1, x2, y):
	373	x1_closest = 999999
	374	x2_closest = 999999
	375	miny = y-3
	376	maxy = y+3
	377	i = bisect.bisect_left(self.y_sorted, miny)
	378	while True:
	379	if len(self.positions_sorted) <= i or self.positions_sorted[i]['y'] > maxy:
	380	break
	381	pos = self.positions_sorted[i]
[562]	382
[624]	383	x1_closest = min(x1_closest, abs(x1-pos['x']))
	384	x2_closest = min(x2_closest, abs(x2-pos['x']))
[562]	385
[624]	386	i += 1
	387	return (x1 if x1_closest > x2_closest else x2)
[562]	388
[624]	389	def xmin_crowd_density(self, x1, x2, y):
	390	x1_dist = 0
	391	x2_dist = 0
[633]	392	miny = y-20
	393	maxy = y+20
[624]	394	i_left = bisect.bisect_left(self.y_sorted, miny)
	395	i_right = bisect.bisect_right(self.y_sorted, maxy)
	396	# print("i " + str(i) + " len " + str(len(self.positions)))
	397	#
	398	# i = bisect.bisect_left(self.y_sorted, y)
	399	# i_left = max(0, i - 25)
	400	# i_right = min(len(self.y_sorted), i + 25)
[562]	401
[624]	402	def include_pos(pos):
	403	nonlocal x1_dist, x2_dist
[622]	404
[624]	405	dysq = (pos['y']-y)**2
	406	dx1 = pos['x']-x1
	407	dx2 = pos['x']-x2
[562]	408
[623]	409	x1_dist += math.sqrt(dysq + dx1**2)
	410	x2_dist += math.sqrt(dysq + dx2**2)
	411
[624]	412	# optimized to draw from all the nodes, if less than 10 nodes in the range
	413	if len(self.positions_sorted) > i_left:
	414	if i_right - i_left < 10:
	415	for j in range(i_left, i_right):
	416	include_pos(self.positions_sorted[j])
	417	else:
	418	for j in range(10):
	419	pos = self.positions_sorted[random.randrange(i_left, i_right)]
	420	include_pos(pos)
[562]	421
[624]	422	return (x1 if x1_dist > x2_dist else x2)
	423	#print(x1_dist, x2_dist)
	424	#x1_dist = x1_dist**2
	425	#x2_dist = x2_dist**2
	426	#return x1 if x1_dist+x2_dist==0 else (x1x1_dist + x2x2_dist) / (x1_dist+x2_dist) + random.gauss(0, 0.01)
	427	#return (x1 if random.randint(0, int(x1_dist+x2_dist)) < x1_dist else x2)
[571]	428
[624]	429	def calculate_node_positions(self, ignore_last=0):
	430	print("Calculating positions...")
[562]	431
[624]	432	def add_node(node):
	433	index = bisect.bisect_left(self.y_sorted, node['y'])
	434	self.y_sorted.insert(index, node['y'])
	435	self.positions_sorted.insert(index, node)
	436	self.positions[node['id']] = node
[572]	437
[624]	438	self.positions_sorted = [{'x':0, 'y':0, 'id':0}]
	439	self.y_sorted = [0]
	440	self.positions = [{} for x in range(len(self.tree.parents))]
	441	self.positions[0] = {'x':0, 'y':0, 'id':0}
[572]	442
[677]	443	# order by maximum depth of the parent guarantees that co child is evaluated before its parent
	444	visiting_order = [i for i in range(0, len(self.tree.parents))]
	445	visiting_order = sorted(visiting_order, key=lambda q:
	446	0 if q == 0 else max([self.props["depth"][d] for d in self.tree.parents[q]]))
[562]	447
[624]	448	node_counter = 0
	449	start_time = timelib.time()
[566]	450
[677]	451	# for each child of the current node
	452	for child in visiting_order:
[624]	453	node_counter += 1
[677]	454	# debug info - elapsed time
[624]	455	if node_counter%1000 == 0:
[677]	456	print(str(node_counter) + " " + str(timelib.time()-start_time))
	457	start_time = timelib.time()
[562]	458
[677]	459	# using normalized adepth
	460	if self.props['adepth'][child] >= ignore_last/self.props['adepth_max']:
[621]	461
[677]	462	ypos = 0
	463	if self.TIME == "BIRTHS":
	464	ypos = child
	465	elif self.TIME == "GENERATIONAL":
	466	# one more than its parent (what if more than one parent?)
[680]	467	ypos = max([self.positions[par]['y'] for par, v in self.tree.parents[child].items()])+1 \
	468	if self.tree.parents[child] else 0
[677]	469	elif self.TIME == "REAL":
	470	ypos = self.tree.time[child]
[621]	471
[677]	472	if len(self.tree.parents[child]) == 1:
	473	# if current_node is the only parent
	474	parent = [par for par, v in self.tree.parents[child].items()][0]
[621]	475
[677]	476	if self.JITTER:
	477	dissimilarity = random.gauss(0, 0.5)
[621]	478	else:
[677]	479	dissimilarity = 1
	480	add_node({'id':child, 'y':ypos, 'x':
	481	self.xmin_crowd(self.positions[parent]['x']-dissimilarity,
	482	self.positions[parent]['x']+dissimilarity, ypos)})
	483	else:
	484	# position weighted by the degree of inheritence from each parent
	485	total_inheretance = sum([v for k, v in self.tree.parents[child].items()])
	486	xpos = sum([self.positions[k]['x']*v/total_inheretance
	487	for k, v in self.tree.parents[child].items()])
	488	if self.JITTER:
	489	add_node({'id':child, 'y':ypos, 'x':xpos + random.gauss(0, 0.1)})
	490	else:
	491	add_node({'id':child, 'y':ypos, 'x':xpos})
[621]	492
	493
[624]	494	def compute_custom(self):
	495	for prop in self.tree.props:
	496	self.props[prop] = [None for x in range(len(self.tree.children))]
[621]	497
[624]	498	for i in range(len(self.props[prop])):
	499	self.props[prop][i] = self.tree.props[prop][i]
[621]	500
[624]	501	self.normalize_prop(prop)
[562]	502
[624]	503	def compute_time(self):
	504	# simple rewrite from the tree
	505	self.props["time"] = [0 for x in range(len(self.tree.children))]
[562]	506
[624]	507	for i in range(len(self.props['time'])):
	508	self.props['time'][i] = self.tree.time[i]
[572]	509
[624]	510	self.normalize_prop('time')
[617]	511
[624]	512	def compute_kind(self):
	513	# simple rewrite from the tree
	514	self.props["kind"] = [0 for x in range(len(self.tree.children))]
[617]	515
[624]	516	for i in range (len(self.props['kind'])):
	517	self.props['kind'][i] = str(self.tree.kind[i])
[617]	518
[624]	519	def compute_depth(self):
	520	self.props["depth"] = [999999999 for x in range(len(self.tree.children))]
[681]	521	visited = [0 for x in range(len(self.tree.children))]
[617]	522
[624]	523	nodes_to_visit = [0]
[681]	524	visited[0] = 1
[624]	525	self.props["depth"][0] = 0
[681]	526
[624]	527	while True:
[681]	528	current_node = nodes_to_visit[0]
	529	for child in self.tree.children[current_node]:
	530	if visited[child] == 0:
	531	visited[child] = 1
	532	nodes_to_visit.append(child)
	533	self.props["depth"][child] = self.props["depth"][current_node]+1
[624]	534	nodes_to_visit = nodes_to_visit[1:]
	535	if len(nodes_to_visit) == 0:
	536	break
[617]	537
[624]	538	self.normalize_prop('depth')
[617]	539
[624]	540	def compute_adepth(self):
	541	self.props["adepth"] = [0 for x in range(len(self.tree.children))]
[617]	542
[679]	543	# order by maximum depth of the parent guarantees that co child is evaluated before its parent
	544	visiting_order = [i for i in range(0, len(self.tree.parents))]
	545	visiting_order = sorted(visiting_order, key=lambda q:
	546	0 if q == 0 else max([self.props["depth"][d] for d in self.tree.parents[q]]))[::-1]
[617]	547
[679]	548	for node in visiting_order:
	549	children = self.tree.children[node]
	550	if len(children) != 0:
	551	# 0 by default
	552	self.props["adepth"][node] = max([self.props["adepth"][child] for child in children])+1
[624]	553	self.normalize_prop('adepth')
[594]	554
[624]	555	def compute_children(self):
	556	self.props["children"] = [0 for x in range(len(self.tree.children))]
	557	for i in range (len(self.props['children'])):
	558	self.props['children'][i] = len(self.tree.children[i])
[562]	559
[624]	560	self.normalize_prop('children')
[564]	561
[633]	562	def compute_progress(self):
	563	self.props["progress"] = [0 for x in range(len(self.tree.children))]
	564	for i in range(len(self.props['children'])):
	565	times = sorted([self.props["time"][self.tree.children[i][j]]*100000 for j in range(len(self.tree.children[i]))])
	566	if len(times) > 4:
	567	times = [times[i+1] - times[i] for i in range(len(times)-1)]
	568	#print(times)
	569	slope, intercept, r_value, p_value, std_err = stats.linregress(range(len(times)), times)
	570	self.props['progress'][i] = slope if not np.isnan(slope) and not np.isinf(slope) else 0
	571
	572	for i in range(0, 5):
	573	self.props['progress'][self.props['progress'].index(min(self.props['progress']))] = 0
	574	self.props['progress'][self.props['progress'].index(max(self.props['progress']))] = 0
	575
	576	mini = min(self.props['progress'])
	577	maxi = max(self.props['progress'])
	578	for k in range(len(self.props['progress'])):
	579	if self.props['progress'][k] == 0:
	580	self.props['progress'][k] = mini
	581
	582	#for k in range(len(self.props['progress'])):
	583	# self.props['progress'][k] = 1-self.props['progress'][k]
	584
	585	self.normalize_prop('progress')
	586
[624]	587	def normalize_prop(self, prop):
[678]	588	noneless = [v for v in self.props[prop] if (type(v)!=str and type(v)!=list)]
[624]	589	if len(noneless) > 0:
	590	max_val = max(noneless)
	591	min_val = min(noneless)
[633]	592	print(prop, max_val, min_val)
[624]	593	self.props[prop +'_max'] = max_val
	594	self.props[prop +'_min'] = min_val
	595	for i in range(len(self.props[prop])):
	596	if self.props[prop][i] is not None:
[633]	597	qqq = self.props[prop][i]
	598	self.props[prop][i] = 0 if max_val == min_val else (self.props[prop][i] - min_val) / (max_val - min_val)
[594]	599
[624]	600	class TreeData:
	601	simple_data = None
[615]	602
[624]	603	children = []
	604	parents = []
	605	time = []
	606	kind = []
[562]	607
[624]	608	def __init__(self): #, simple_data=False):
	609	#self.simple_data = simple_data
	610	pass
[562]	611
[624]	612	def load(self, filename, max_nodes=0):
	613	print("Loading...")
[576]	614
[624]	615	CLI_PREFIX = "Script.Message:"
	616	default_props = ["Time", "FromIDs", "ID", "Operation", "Inherited"]
[576]	617
[633]	618	self.ids = {}
[628]	619	def get_id(id, createOnError = True):
	620	if createOnError:
[633]	621	if id not in self.ids:
	622	self.ids[id] = len(self.ids)
[628]	623	else:
[633]	624	if id not in self.ids:
[628]	625	return None
[633]	626	return self.ids[id]
[576]	627
[624]	628	file = open(filename)
[576]	629
[624]	630	# counting the number of expected nodes
	631	nodes = 0
	632	for line in file:
	633	line_arr = line.split(' ', 1)
	634	if len(line_arr) == 2:
	635	if line_arr[0] == CLI_PREFIX:
	636	line_arr = line_arr[1].split(' ', 1)
	637	if line_arr[0] == "[OFFSPRING]":
	638	nodes += 1
[562]	639
[624]	640	nodes = min(nodes, max_nodes if max_nodes != 0 else nodes)+1
	641	self.parents = [{} for x in range(nodes)]
	642	self.children = [[] for x in range(nodes)]
	643	self.time = [0] * nodes
	644	self.kind = [0] * nodes
[628]	645	self.life_lenght = [0] * nodes
[624]	646	self.props = {}
[562]	647
[624]	648	print(len(self.parents))
[562]	649
[624]	650	file.seek(0)
	651	loaded_so_far = 0
	652	lasttime = timelib.time()
	653	for line in file:
	654	line_arr = line.split(' ', 1)
	655	if len(line_arr) == 2:
	656	if line_arr[0] == CLI_PREFIX:
	657	line_arr = line_arr[1].split(' ', 1)
	658	if line_arr[0] == "[OFFSPRING]":
	659	creature = json.loads(line_arr[1])
	660	if "FromIDs" in creature:
[562]	661
[624]	662	# make sure that ID's of parents are lower than that of their children
	663	for i in range(0, len(creature["FromIDs"])):
[633]	664	if creature["FromIDs"][i] not in self.ids:
[627]	665	get_id("virtual_parent")
[562]	666
[624]	667	creature_id = get_id(creature["ID"])
	668
	669	# debug
	670	if loaded_so_far%1000 == 0:
	671	#print(". " + str(creature_id) + " " + str(timelib.time() - lasttime))
	672	lasttime = timelib.time()
	673
	674	# we assign to each parent its contribution to the genotype of the child
	675	for i in range(0, len(creature["FromIDs"])):
[633]	676	if creature["FromIDs"][i] in self.ids:
[627]	677	parent_id = get_id(creature["FromIDs"][i])
	678	else:
	679	parent_id = get_id("virtual_parent")
[624]	680	inherited = 1 #(creature["Inherited"][i] if 'Inherited' in creature else 1) #ONLY FOR NOW
	681	self.parents[creature_id][parent_id] = inherited
	682
	683	if "Time" in creature:
	684	self.time[creature_id] = creature["Time"]
	685
	686	if "Kind" in creature:
	687	self.kind[creature_id] = creature["Kind"]
	688
	689	for prop in creature:
	690	if prop not in default_props:
	691	if prop not in self.props:
[628]	692	self.props[prop] = [0 for i in range(nodes)]
[624]	693	self.props[prop][creature_id] = creature[prop]
	694
	695	loaded_so_far += 1
	696	else:
	697	raise LoadingError("[OFFSPRING] misses the 'FromIDs' field!")
[628]	698	if line_arr[0] == "[DIED]":
	699	creature = json.loads(line_arr[1])
	700	creature_id = get_id(creature["ID"], False)
	701	if creature_id is not None:
	702	for prop in creature:
	703	if prop not in default_props:
	704	if prop not in self.props:
	705	self.props[prop] = [0 for i in range(nodes)]
	706	self.props[prop][creature_id] = creature[prop]
[624]	707
[628]	708
[624]	709	if loaded_so_far >= max_nodes and max_nodes != 0:
	710	break
	711
	712	for k in range(len(self.parents)):
	713	v = self.parents[k]
	714	for val in self.parents[k]:
	715	self.children[val].append(k)
	716
[562]	717	depth = {}
[577]	718	kind = {}
[562]	719
	720	def main():
	721
[624]	722	parser = argparse.ArgumentParser(description='Draws a genealogical tree (generates a SVG file) based on parent-child relationship '
	723	'information from a text file. Supports files generated by Framsticks experiments.')
[615]	724	parser.add_argument('-i', '--in', dest='input', required=True, help='input file name with stuctured evolutionary data')
[624]	725	parser.add_argument('-o', '--out', dest='output', required=True, help='output file name for the evolutionary tree (SVG/PNG/JPG/BMP)')
	726	parser.add_argument('-c', '--config', dest='config', default="", help='config file name ')
[562]	727
[624]	728	parser.add_argument('-W', '--width', default=600, type=int, dest='width', help='width of the output image (600 by default)')
[626]	729	parser.add_argument('-H', '--height', default=800, type=int, dest='height', help='height of the output image (800 by default)')
	730	parser.add_argument('-m', '--multi', default=1, type=int, dest='multi', help='multisampling factor (applicable only for raster images)')
[562]	731
[620]	732	parser.add_argument('-t', '--time', default='GENERATIONAL', dest='time', help='values on vertical axis (BIRTHS/GENERATIONAL(d)/REAL); '
[614]	733	'BIRTHS: time measured as the number of births since the beginning; '
[571]	734	'GENERATIONAL: time measured as number of ancestors; '
	735	'REAL: real time of the simulation')
[620]	736	parser.add_argument('-b', '--balance', default='DENSITY', dest='balance', help='method of placing nodes in the tree (RANDOM/MIN/DENSITY(d))')
[624]	737	parser.add_argument('-s', '--scale', default='SIMPLE', dest='scale', help='type of timescale added to the tree (NONE(d)/SIMPLE)')
[571]	738	parser.add_argument('-j', '--jitter', dest="jitter", action='store_true', help='draw horizontal positions of children from the normal distribution')
[624]	739	parser.add_argument('-p', '--skip', dest="skip", type=int, default=0, help='skip last P levels of the tree (0 by default)')
	740	parser.add_argument('-x', '--max-nodes', type=int, default=0, dest='max_nodes', help='maximum number of nodes drawn (starting from the first one)')
[562]	741	parser.add_argument('--seed', type=int, dest='seed', help='seed for the random number generator (-1 for random)')
	742
	743	parser.set_defaults(draw_tree=True)
	744	parser.set_defaults(draw_skeleton=False)
	745	parser.set_defaults(draw_spine=False)
	746
	747	parser.set_defaults(seed=-1)
	748
	749	args = parser.parse_args()
	750
[620]	751	TIME = args.time.upper()
	752	BALANCE = args.balance.upper()
	753	SCALE = args.scale.upper()
[571]	754	JITTER = args.jitter
[620]	755	if not TIME in ['BIRTHS', 'GENERATIONAL', 'REAL']\
	756	or not BALANCE in ['RANDOM', 'MIN', 'DENSITY']\
	757	or not SCALE in ['NONE', 'SIMPLE']:
	758	print("Incorrect value of one of the parameters! Closing the program.") #TODO don't be lazy, figure out which parameter is wrong...
	759	return
[562]	760
	761	dir = args.input
	762	seed = args.seed
	763	if seed == -1:
	764	seed = random.randint(0, 10000)
	765	random.seed(seed)
	766	print("seed:", seed)
	767
[624]	768	tree = TreeData()
	769	tree.load(dir, max_nodes=args.max_nodes)
[562]	770
[624]	771	designer = Designer(tree, jitter=JITTER, time=TIME, balance=BALANCE)
	772	designer.calculate_measures()
	773	designer.calculate_node_positions(ignore_last=args.skip)
[562]	774
[624]	775	if args.output.endswith(".svg"):
	776	drawer = SvgDrawer(designer, args.config, w=args.width, h=args.height)
	777	else:
	778	drawer = PngDrawer(designer, args.config, w=args.width, h=args.height)
[626]	779	drawer.draw_design(args.output, args.input, multi=args.multi, scale=SCALE)
[562]	780
	781
	782	main()

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