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source: mds-and-trees/tree-genealogy.py @ 689

Last change on this file since 689 was 689, checked in by Maciej Komosinski, 7 years ago
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[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)
[684]	245	normdiv = 2*sublines-1
[624]	246	for i in range(sublines):
[684]	247	from_pos_sub = (self.compute_value(from_pos[0], to_pos[0], 2*i/normdiv, 1),
	248	self.compute_value(from_pos[1], to_pos[1], 2*i/normdiv, 1))
	249	to_pos_sub = (self.compute_value(from_pos[0], to_pos[0], (2*i+1)/normdiv, 1),
	250	self.compute_value(from_pos[1], to_pos[1], (2*i+1)/normdiv, 1))
[624]	251	self.add_line(file, from_pos_sub, to_pos_sub, style)
[562]	252
[624]	253	def add_text(self, file, text, pos, anchor, style=''):
[626]	254	font = ImageFont.truetype("Vera.ttf", 16*self.multi)
[621]	255
[624]	256	img = Image.new('RGBA', (self.width, self.height))
	257	draw = ImageDraw.Draw(img)
	258	txtsize = draw.textsize(text, font=font)
[626]	259	pos = pos if anchor == "start" else (pos[0]-txtsize[0], pos[1])
[624]	260	draw.text(pos, text, (0,0,0), font=font)
	261	file.paste(img, (0,0), mask=img)
[622]	262
[624]	263	def compute_line_style(self, parent, child):
	264	return {'color': self.compute_property('lines', 'color', child),
	265	'width': self.compute_property('lines', 'width', child),
	266	'opacity': self.compute_property('lines', 'opacity', child)}
	267
	268	def compute_dot_style(self, node):
	269	return {'color': self.compute_property('dots', 'color', node),
	270	'r': self.compute_property('dots', 'size', node),
	271	'opacity': self.compute_property('dots', 'opacity', node)}
	272
	273	class SvgDrawer(Drawer):
[626]	274	def draw_design(self, filename, input_filename, multi=1, scale="SIMPLE"):
[624]	275	print("Drawing...")
	276	file = open(filename, "w")
	277
	278	min_width = min([x['x'] for x in self.design.positions if 'x' in x])
	279	max_width = max([x['x'] for x in self.design.positions if 'x' in x])
	280	max_height = max([x['y'] for x in self.design.positions if 'y' in x])
	281
	282	file.write('<svg xmlns:svg="http://www.w3.org/2000/svg" xmlns="http://www.w3.org/2000/svg" '
	283	'xmlns:xlink="http://www.w3.org/1999/xlink" version="1.0" '
	284	'width="' + str(self.width) + '" height="' + str(self.height) + '">')
	285
	286	self.draw_lines(file, min_width, max_width, max_height)
	287	self.draw_dots(file, min_width, max_width, max_height)
	288
	289	if scale == "SIMPLE":
	290	self.draw_scale(file, input_filename)
	291
	292	file.write("</svg>")
	293	file.close()
	294
	295	def add_text(self, file, text, pos, anchor, style=''):
	296	style = (style if style != '' else 'style="font-family: Arial; font-size: 12; fill: #000000;"')
[628]	297	# assuming font size 12, it should be taken from the style string!
	298	file.write('<text ' + style + ' text-anchor="' + anchor + '" x="' + str(pos[0]) + '" y="' + str(pos[1]+12) + '" >' + text + '</text>')
[624]	299
	300	def add_dot(self, file, pos, style):
	301	file.write('<circle ' + style + ' cx="' + str(pos[0]) + '" cy="' + str(pos[1]) + '" />')
	302
	303	def add_line(self, file, from_pos, to_pos, style):
	304	file.write('<line ' + style + ' x1="' + str(from_pos[0]) + '" x2="' + str(to_pos[0]) +
	305	'" y1="' + str(from_pos[1]) + '" y2="' + str(to_pos[1]) + '" fill="none"/>')
	306
	307	def add_dashed_line(self, file, from_pos, to_pos):
	308	style = 'stroke="black" stroke-width="0.5" stroke-opacity="1" stroke-dasharray="5, 5"'
	309	self.add_line(file, from_pos, to_pos, style)
	310
	311	def compute_line_style(self, parent, child):
	312	return self.compute_stroke_color('lines', child) + ' ' \
	313	+ self.compute_stroke_width('lines', child) + ' ' \
	314	+ self.compute_stroke_opacity(child)
	315
	316	def compute_dot_style(self, node):
	317	return self.compute_dot_size(node) + ' ' \
	318	+ self.compute_fill_opacity(node) + ' ' \
	319	+ self.compute_dot_fill(node)
	320
	321	def compute_stroke_color(self, part, node):
	322	color = self.compute_property(part, 'color', node)
	323	return 'stroke="rgb(' + str(color[0]) + '%,' + str(color[1]) + '%,' + str(color[2]) + '%)"'
	324
	325	def compute_stroke_width(self, part, node):
	326	return 'stroke-width="' + str(self.compute_property(part, 'width', node)) + '"'
	327
	328	def compute_stroke_opacity(self, node):
	329	return 'stroke-opacity="' + str(self.compute_property('lines', 'opacity', node)) + '"'
	330
	331	def compute_fill_opacity(self, node):
	332	return 'fill-opacity="' + str(self.compute_property('dots', 'opacity', node)) + '"'
	333
	334	def compute_dot_size(self, node):
	335	return 'r="' + str(self.compute_property('dots', 'size', node)) + '"'
	336
	337	def compute_dot_fill(self, node):
	338	color = self.compute_property('dots', 'color', node)
	339	return 'fill="rgb(' + str(color[0]) + '%,' + str(color[1]) + '%,' + str(color[2]) + '%)"'
	340
	341	class Designer:
	342
	343	def __init__(self, tree, jitter=False, time="GENERATIONAL", balance="DENSITY"):
	344	self.props = {}
	345
	346	self.tree = tree
	347
	348	self.TIME = time
	349	self.JITTER = jitter
	350
	351	if balance == "RANDOM":
	352	self.xmin_crowd = self.xmin_crowd_random
	353	elif balance == "MIN":
	354	self.xmin_crowd = self.xmin_crowd_min
	355	elif balance == "DENSITY":
	356	self.xmin_crowd = self.xmin_crowd_density
[562]	357	else:
[624]	358	raise ValueError("Error, the value of BALANCE does not match any expected value.")
[562]	359
[624]	360	def calculate_measures(self):
	361	print("Calculating measures...")
[679]	362	self.compute_depth()
[624]	363	self.compute_adepth()
	364	self.compute_children()
	365	self.compute_kind()
	366	self.compute_time()
[633]	367	self.compute_progress()
[624]	368	self.compute_custom()
[622]	369
[624]	370	def xmin_crowd_random(self, x1, x2, y):
	371	return (x1 if random.randrange(2) == 0 else x2)
[562]	372
[624]	373	def xmin_crowd_min(self, x1, x2, y):
	374	x1_closest = 999999
	375	x2_closest = 999999
	376	miny = y-3
	377	maxy = y+3
	378	i = bisect.bisect_left(self.y_sorted, miny)
	379	while True:
	380	if len(self.positions_sorted) <= i or self.positions_sorted[i]['y'] > maxy:
	381	break
	382	pos = self.positions_sorted[i]
[562]	383
[624]	384	x1_closest = min(x1_closest, abs(x1-pos['x']))
	385	x2_closest = min(x2_closest, abs(x2-pos['x']))
[562]	386
[624]	387	i += 1
	388	return (x1 if x1_closest > x2_closest else x2)
[562]	389
[624]	390	def xmin_crowd_density(self, x1, x2, y):
	391	x1_dist = 0
	392	x2_dist = 0
[682]	393	miny = y-2000
	394	maxy = y+2000
[624]	395	i_left = bisect.bisect_left(self.y_sorted, miny)
	396	i_right = bisect.bisect_right(self.y_sorted, maxy)
	397	# print("i " + str(i) + " len " + str(len(self.positions)))
	398	#
	399	# i = bisect.bisect_left(self.y_sorted, y)
	400	# i_left = max(0, i - 25)
	401	# i_right = min(len(self.y_sorted), i + 25)
[562]	402
[624]	403	def include_pos(pos):
	404	nonlocal x1_dist, x2_dist
[622]	405
[624]	406	dysq = (pos['y']-y)**2
	407	dx1 = pos['x']-x1
	408	dx2 = pos['x']-x2
[562]	409
[623]	410	x1_dist += math.sqrt(dysq + dx1**2)
	411	x2_dist += math.sqrt(dysq + dx2**2)
	412
[624]	413	# optimized to draw from all the nodes, if less than 10 nodes in the range
	414	if len(self.positions_sorted) > i_left:
	415	if i_right - i_left < 10:
	416	for j in range(i_left, i_right):
	417	include_pos(self.positions_sorted[j])
	418	else:
	419	for j in range(10):
	420	pos = self.positions_sorted[random.randrange(i_left, i_right)]
	421	include_pos(pos)
[562]	422
[624]	423	return (x1 if x1_dist > x2_dist else x2)
	424	#print(x1_dist, x2_dist)
	425	#x1_dist = x1_dist**2
	426	#x2_dist = x2_dist**2
	427	#return x1 if x1_dist+x2_dist==0 else (x1x1_dist + x2x2_dist) / (x1_dist+x2_dist) + random.gauss(0, 0.01)
	428	#return (x1 if random.randint(0, int(x1_dist+x2_dist)) < x1_dist else x2)
[571]	429
[624]	430	def calculate_node_positions(self, ignore_last=0):
	431	print("Calculating positions...")
[562]	432
[624]	433	def add_node(node):
	434	index = bisect.bisect_left(self.y_sorted, node['y'])
	435	self.y_sorted.insert(index, node['y'])
	436	self.positions_sorted.insert(index, node)
	437	self.positions[node['id']] = node
[572]	438
[624]	439	self.positions_sorted = [{'x':0, 'y':0, 'id':0}]
	440	self.y_sorted = [0]
	441	self.positions = [{} for x in range(len(self.tree.parents))]
	442	self.positions[0] = {'x':0, 'y':0, 'id':0}
[572]	443
[677]	444	# order by maximum depth of the parent guarantees that co child is evaluated before its parent
	445	visiting_order = [i for i in range(0, len(self.tree.parents))]
	446	visiting_order = sorted(visiting_order, key=lambda q:
	447	0 if q == 0 else max([self.props["depth"][d] for d in self.tree.parents[q]]))
[562]	448
[624]	449	start_time = timelib.time()
[566]	450
[677]	451	# for each child of the current node
[686]	452	for node_counter,child in enumerate(visiting_order, start=1):
[677]	453	# debug info - elapsed time
[685]	454	if node_counter % 100000 == 0:
	455	print("%d%%\t%d\t%g" % (node_counter*100/len(self.tree.parents), node_counter, timelib.time()-start_time))
[677]	456	start_time = timelib.time()
[562]	457
[677]	458	# using normalized adepth
	459	if self.props['adepth'][child] >= ignore_last/self.props['adepth_max']:
[621]	460
[677]	461	ypos = 0
	462	if self.TIME == "BIRTHS":
	463	ypos = child
	464	elif self.TIME == "GENERATIONAL":
	465	# one more than its parent (what if more than one parent?)
[680]	466	ypos = max([self.positions[par]['y'] for par, v in self.tree.parents[child].items()])+1 \
	467	if self.tree.parents[child] else 0
[677]	468	elif self.TIME == "REAL":
	469	ypos = self.tree.time[child]
[621]	470
[677]	471	if len(self.tree.parents[child]) == 1:
	472	# if current_node is the only parent
[687]	473	parent, similarity = [(par, v) for par, v in self.tree.parents[child].items()][0]
[621]	474
[677]	475	if self.JITTER:
[687]	476	dissimilarity = (1-similarity) + random.gauss(0, 0.5) + 0.001
[621]	477	else:
[687]	478	dissimilarity = (1-similarity) + 0.001
[677]	479	add_node({'id':child, 'y':ypos, 'x':
	480	self.xmin_crowd(self.positions[parent]['x']-dissimilarity,
	481	self.positions[parent]['x']+dissimilarity, ypos)})
	482	else:
	483	# position weighted by the degree of inheritence from each parent
	484	total_inheretance = sum([v for k, v in self.tree.parents[child].items()])
	485	xpos = sum([self.positions[k]['x']*v/total_inheretance
	486	for k, v in self.tree.parents[child].items()])
	487	if self.JITTER:
	488	add_node({'id':child, 'y':ypos, 'x':xpos + random.gauss(0, 0.1)})
	489	else:
	490	add_node({'id':child, 'y':ypos, 'x':xpos})
[621]	491
	492
[624]	493	def compute_custom(self):
	494	for prop in self.tree.props:
	495	self.props[prop] = [None for x in range(len(self.tree.children))]
[621]	496
[624]	497	for i in range(len(self.props[prop])):
	498	self.props[prop][i] = self.tree.props[prop][i]
[621]	499
[624]	500	self.normalize_prop(prop)
[562]	501
[624]	502	def compute_time(self):
	503	# simple rewrite from the tree
	504	self.props["time"] = [0 for x in range(len(self.tree.children))]
[562]	505
[624]	506	for i in range(len(self.props['time'])):
	507	self.props['time'][i] = self.tree.time[i]
[572]	508
[624]	509	self.normalize_prop('time')
[617]	510
[624]	511	def compute_kind(self):
	512	# simple rewrite from the tree
	513	self.props["kind"] = [0 for x in range(len(self.tree.children))]
[617]	514
[624]	515	for i in range (len(self.props['kind'])):
	516	self.props['kind'][i] = str(self.tree.kind[i])
[617]	517
[624]	518	def compute_depth(self):
	519	self.props["depth"] = [999999999 for x in range(len(self.tree.children))]
[681]	520	visited = [0 for x in range(len(self.tree.children))]
[617]	521
[624]	522	nodes_to_visit = [0]
[681]	523	visited[0] = 1
[624]	524	self.props["depth"][0] = 0
	525	while True:
[681]	526	current_node = nodes_to_visit[0]
[682]	527
[681]	528	for child in self.tree.children[current_node]:
	529	if visited[child] == 0:
	530	visited[child] = 1
	531	nodes_to_visit.append(child)
	532	self.props["depth"][child] = self.props["depth"][current_node]+1
[624]	533	nodes_to_visit = nodes_to_visit[1:]
	534	if len(nodes_to_visit) == 0:
	535	break
[617]	536
[624]	537	self.normalize_prop('depth')
[617]	538
[624]	539	def compute_adepth(self):
	540	self.props["adepth"] = [0 for x in range(len(self.tree.children))]
[617]	541
[679]	542	# order by maximum depth of the parent guarantees that co child is evaluated before its parent
	543	visiting_order = [i for i in range(0, len(self.tree.parents))]
	544	visiting_order = sorted(visiting_order, key=lambda q:
	545	0 if q == 0 else max([self.props["depth"][d] for d in self.tree.parents[q]]))[::-1]
[617]	546
[679]	547	for node in visiting_order:
	548	children = self.tree.children[node]
	549	if len(children) != 0:
	550	# 0 by default
	551	self.props["adepth"][node] = max([self.props["adepth"][child] for child in children])+1
[624]	552	self.normalize_prop('adepth')
[594]	553
[624]	554	def compute_children(self):
	555	self.props["children"] = [0 for x in range(len(self.tree.children))]
	556	for i in range (len(self.props['children'])):
	557	self.props['children'][i] = len(self.tree.children[i])
[562]	558
[624]	559	self.normalize_prop('children')
[564]	560
[633]	561	def compute_progress(self):
	562	self.props["progress"] = [0 for x in range(len(self.tree.children))]
	563	for i in range(len(self.props['children'])):
	564	times = sorted([self.props["time"][self.tree.children[i][j]]*100000 for j in range(len(self.tree.children[i]))])
	565	if len(times) > 4:
	566	times = [times[i+1] - times[i] for i in range(len(times)-1)]
	567	#print(times)
	568	slope, intercept, r_value, p_value, std_err = stats.linregress(range(len(times)), times)
	569	self.props['progress'][i] = slope if not np.isnan(slope) and not np.isinf(slope) else 0
	570
	571	for i in range(0, 5):
	572	self.props['progress'][self.props['progress'].index(min(self.props['progress']))] = 0
	573	self.props['progress'][self.props['progress'].index(max(self.props['progress']))] = 0
	574
	575	mini = min(self.props['progress'])
	576	maxi = max(self.props['progress'])
	577	for k in range(len(self.props['progress'])):
	578	if self.props['progress'][k] == 0:
	579	self.props['progress'][k] = mini
	580
	581	#for k in range(len(self.props['progress'])):
	582	# self.props['progress'][k] = 1-self.props['progress'][k]
	583
	584	self.normalize_prop('progress')
	585
[624]	586	def normalize_prop(self, prop):
[678]	587	noneless = [v for v in self.props[prop] if (type(v)!=str and type(v)!=list)]
[624]	588	if len(noneless) > 0:
	589	max_val = max(noneless)
	590	min_val = min(noneless)
[633]	591	print(prop, max_val, min_val)
[624]	592	self.props[prop +'_max'] = max_val
	593	self.props[prop +'_min'] = min_val
	594	for i in range(len(self.props[prop])):
	595	if self.props[prop][i] is not None:
[633]	596	qqq = self.props[prop][i]
	597	self.props[prop][i] = 0 if max_val == min_val else (self.props[prop][i] - min_val) / (max_val - min_val)
[594]	598
[624]	599	class TreeData:
	600	simple_data = None
[615]	601
[624]	602	children = []
	603	parents = []
	604	time = []
	605	kind = []
[562]	606
[624]	607	def __init__(self): #, simple_data=False):
	608	#self.simple_data = simple_data
	609	pass
[562]	610
[624]	611	def load(self, filename, max_nodes=0):
	612	print("Loading...")
[576]	613
[624]	614	CLI_PREFIX = "Script.Message:"
	615	default_props = ["Time", "FromIDs", "ID", "Operation", "Inherited"]
[576]	616
[633]	617	self.ids = {}
[628]	618	def get_id(id, createOnError = True):
	619	if createOnError:
[633]	620	if id not in self.ids:
	621	self.ids[id] = len(self.ids)
[628]	622	else:
[633]	623	if id not in self.ids:
[628]	624	return None
[633]	625	return self.ids[id]
[576]	626
[624]	627	file = open(filename)
[576]	628
[624]	629	# counting the number of expected nodes
	630	nodes = 0
	631	for line in file:
	632	line_arr = line.split(' ', 1)
	633	if len(line_arr) == 2:
	634	if line_arr[0] == CLI_PREFIX:
	635	line_arr = line_arr[1].split(' ', 1)
	636	if line_arr[0] == "[OFFSPRING]":
	637	nodes += 1
[562]	638
[624]	639	nodes = min(nodes, max_nodes if max_nodes != 0 else nodes)+1
	640	self.parents = [{} for x in range(nodes)]
	641	self.children = [[] for x in range(nodes)]
	642	self.time = [0] * nodes
	643	self.kind = [0] * nodes
[628]	644	self.life_lenght = [0] * nodes
[624]	645	self.props = {}
[562]	646
[688]	647	print("nodes: %d" % len(self.parents))
[562]	648
[624]	649	file.seek(0)
	650	loaded_so_far = 0
	651	lasttime = timelib.time()
	652	for line in file:
	653	line_arr = line.split(' ', 1)
	654	if len(line_arr) == 2:
	655	if line_arr[0] == CLI_PREFIX:
	656	line_arr = line_arr[1].split(' ', 1)
	657	if line_arr[0] == "[OFFSPRING]":
[682]	658	try:
	659	creature = json.loads(line_arr[1])
	660	except ValueError:
	661	print("Json format error - the line cannot be read. Breaking the loading loop.")
	662	# fixing arrays by removing the last element
	663	# ! assuming that only the last line is broken !
	664	self.parents.pop()
	665	self.children.pop()
	666	self.time.pop()
	667	self.kind.pop()
	668	self.life_lenght.pop()
	669	nodes -= 1
	670	break
	671
[624]	672	if "FromIDs" in creature:
[562]	673
[624]	674	# make sure that ID's of parents are lower than that of their children
	675	for i in range(0, len(creature["FromIDs"])):
[633]	676	if creature["FromIDs"][i] not in self.ids:
[627]	677	get_id("virtual_parent")
[562]	678
[624]	679	creature_id = get_id(creature["ID"])
	680
	681	# debug
	682	if loaded_so_far%1000 == 0:
	683	#print(". " + str(creature_id) + " " + str(timelib.time() - lasttime))
	684	lasttime = timelib.time()
	685
	686	# we assign to each parent its contribution to the genotype of the child
	687	for i in range(0, len(creature["FromIDs"])):
[633]	688	if creature["FromIDs"][i] in self.ids:
[627]	689	parent_id = get_id(creature["FromIDs"][i])
	690	else:
	691	parent_id = get_id("virtual_parent")
[687]	692	inherited = (creature["Inherited"][i] if 'Inherited' in creature else 1)
[624]	693	self.parents[creature_id][parent_id] = inherited
	694
	695	if "Time" in creature:
	696	self.time[creature_id] = creature["Time"]
	697
	698	if "Kind" in creature:
	699	self.kind[creature_id] = creature["Kind"]
	700
	701	for prop in creature:
	702	if prop not in default_props:
	703	if prop not in self.props:
[628]	704	self.props[prop] = [0 for i in range(nodes)]
[624]	705	self.props[prop][creature_id] = creature[prop]
	706
	707	loaded_so_far += 1
	708	else:
	709	raise LoadingError("[OFFSPRING] misses the 'FromIDs' field!")
[628]	710	if line_arr[0] == "[DIED]":
	711	creature = json.loads(line_arr[1])
	712	creature_id = get_id(creature["ID"], False)
	713	if creature_id is not None:
	714	for prop in creature:
	715	if prop not in default_props:
	716	if prop not in self.props:
	717	self.props[prop] = [0 for i in range(nodes)]
	718	self.props[prop][creature_id] = creature[prop]
[624]	719
[628]	720
[624]	721	if loaded_so_far >= max_nodes and max_nodes != 0:
	722	break
	723
	724	for k in range(len(self.parents)):
	725	v = self.parents[k]
	726	for val in self.parents[k]:
	727	self.children[val].append(k)
	728
[562]	729	depth = {}
[577]	730	kind = {}
[562]	731
	732	def main():
	733
[624]	734	parser = argparse.ArgumentParser(description='Draws a genealogical tree (generates a SVG file) based on parent-child relationship '
	735	'information from a text file. Supports files generated by Framsticks experiments.')
[615]	736	parser.add_argument('-i', '--in', dest='input', required=True, help='input file name with stuctured evolutionary data')
[624]	737	parser.add_argument('-o', '--out', dest='output', required=True, help='output file name for the evolutionary tree (SVG/PNG/JPG/BMP)')
	738	parser.add_argument('-c', '--config', dest='config', default="", help='config file name ')
[562]	739
[624]	740	parser.add_argument('-W', '--width', default=600, type=int, dest='width', help='width of the output image (600 by default)')
[626]	741	parser.add_argument('-H', '--height', default=800, type=int, dest='height', help='height of the output image (800 by default)')
	742	parser.add_argument('-m', '--multi', default=1, type=int, dest='multi', help='multisampling factor (applicable only for raster images)')
[562]	743
[620]	744	parser.add_argument('-t', '--time', default='GENERATIONAL', dest='time', help='values on vertical axis (BIRTHS/GENERATIONAL(d)/REAL); '
[614]	745	'BIRTHS: time measured as the number of births since the beginning; '
[571]	746	'GENERATIONAL: time measured as number of ancestors; '
	747	'REAL: real time of the simulation')
[620]	748	parser.add_argument('-b', '--balance', default='DENSITY', dest='balance', help='method of placing nodes in the tree (RANDOM/MIN/DENSITY(d))')
[624]	749	parser.add_argument('-s', '--scale', default='SIMPLE', dest='scale', help='type of timescale added to the tree (NONE(d)/SIMPLE)')
[571]	750	parser.add_argument('-j', '--jitter', dest="jitter", action='store_true', help='draw horizontal positions of children from the normal distribution')
[624]	751	parser.add_argument('-p', '--skip', dest="skip", type=int, default=0, help='skip last P levels of the tree (0 by default)')
	752	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]	753	parser.add_argument('--seed', type=int, dest='seed', help='seed for the random number generator (-1 for random)')
	754
	755	parser.set_defaults(draw_tree=True)
	756	parser.set_defaults(draw_skeleton=False)
	757	parser.set_defaults(draw_spine=False)
	758
	759	parser.set_defaults(seed=-1)
	760
	761	args = parser.parse_args()
	762
[620]	763	TIME = args.time.upper()
	764	BALANCE = args.balance.upper()
	765	SCALE = args.scale.upper()
[571]	766	JITTER = args.jitter
[620]	767	if not TIME in ['BIRTHS', 'GENERATIONAL', 'REAL']\
	768	or not BALANCE in ['RANDOM', 'MIN', 'DENSITY']\
	769	or not SCALE in ['NONE', 'SIMPLE']:
[683]	770	print("Incorrect value of one of the parameters! (time or balance or scale).") #user has to figure out which parameter is wrong...
[620]	771	return
[562]	772
	773	dir = args.input
	774	seed = args.seed
	775	if seed == -1:
	776	seed = random.randint(0, 10000)
	777	random.seed(seed)
[689]	778	print("randomseed:", seed)
[562]	779
[624]	780	tree = TreeData()
	781	tree.load(dir, max_nodes=args.max_nodes)
[562]	782
[682]	783
[624]	784	designer = Designer(tree, jitter=JITTER, time=TIME, balance=BALANCE)
	785	designer.calculate_measures()
	786	designer.calculate_node_positions(ignore_last=args.skip)
[562]	787
[624]	788	if args.output.endswith(".svg"):
	789	drawer = SvgDrawer(designer, args.config, w=args.width, h=args.height)
	790	else:
	791	drawer = PngDrawer(designer, args.config, w=args.width, h=args.height)
[626]	792	drawer.draw_design(args.output, args.input, multi=args.multi, scale=SCALE)
[562]	793
	794
	795	main()

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