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source: mds-and-trees/tree-genealogy.py @ 696

Last change on this file since 696 was 696, checked in by konrad, 7 years ago
Changes to formating of min/max values of properties
File size: 34.1 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
[695]	9	from matplotlib import colors
[633]	10	import numpy as np
[562]	11
[624]	12	class LoadingError(Exception):
	13	pass
[562]	14
[624]	15	class Drawer:
[571]	16
[624]	17	def __init__(self, design, config_file, w=600, h=800, w_margin=10, h_margin=20):
	18	self.design = design
	19	self.width = w
	20	self.height = h
	21	self.w_margin = w_margin
	22	self.h_margin = h_margin
	23	self.w_no_margs = w - 2* w_margin
	24	self.h_no_margs = h - 2* h_margin
[571]	25
[695]	26	self.color_converter = colors.ColorConverter()
[562]	27
[624]	28	self.settings = {
	29	'colors_of_kinds': ['red', 'green', 'blue', 'magenta', 'yellow', 'cyan', 'orange', 'purple'],
	30	'dots': {
	31	'color': {
[628]	32	'meaning': 'Lifespan',
	33	'start': 'red',
[624]	34	'end': 'green',
	35	'bias': 1
	36	},
	37	'size': {
[628]	38	'meaning': 'EnergyEaten',
[624]	39	'start': 1,
[628]	40	'end': 6,
[624]	41	'bias': 0.5
	42	},
	43	'opacity': {
[628]	44	'meaning': 'EnergyEaten',
	45	'start': 0.2,
	46	'end': 1,
[624]	47	'bias': 1
	48	}
	49	},
	50	'lines': {
	51	'color': {
	52	'meaning': 'adepth',
	53	'start': 'black',
	54	'end': 'red',
	55	'bias': 3
	56	},
	57	'width': {
	58	'meaning': 'adepth',
[627]	59	'start': 0.1,
[624]	60	'end': 4,
	61	'bias': 3
	62	},
	63	'opacity': {
	64	'meaning': 'adepth',
	65	'start': 0.1,
	66	'end': 0.8,
	67	'bias': 5
	68	}
	69	}
	70	}
[577]	71
[624]	72	def merge(source, destination):
	73	for key, value in source.items():
	74	if isinstance(value, dict):
	75	node = destination.setdefault(key, {})
	76	merge(value, node)
	77	else:
	78	destination[key] = value
[562]	79
[624]	80	return destination
[576]	81
[624]	82	if config_file != "":
	83	with open(config_file) as config:
	84	c = json.load(config)
	85	self.settings = merge(c, self.settings)
	86	#print(json.dumps(self.settings, indent=4, sort_keys=True))
[586]	87
[624]	88	def draw_dots(self, file, min_width, max_width, max_height):
	89	for i in range(len(self.design.positions)):
	90	node = self.design.positions[i]
	91	if 'x' not in node:
	92	continue
	93	dot_style = self.compute_dot_style(node=i)
	94	self.add_dot(file, (self.w_margin+self.w_no_margs*(node['x']-min_width)/(max_width-min_width),
	95	self.h_margin+self.h_no_margs*node['y']/max_height), dot_style)
[585]	96
[624]	97	def draw_lines(self, file, min_width, max_width, max_height):
	98	for parent in range(len(self.design.positions)):
	99	par_pos = self.design.positions[parent]
	100	if not 'x' in par_pos:
	101	continue
	102	for child in self.design.tree.children[parent]:
	103	chi_pos = self.design.positions[child]
	104	if 'x' not in chi_pos:
	105	continue
	106	line_style = self.compute_line_style(parent, child)
	107	self.add_line(file, (self.w_margin+self.w_no_margs*(par_pos['x']-min_width)/(max_width-min_width),
	108	self.h_margin+self.h_no_margs*par_pos['y']/max_height),
	109	(self.w_margin+self.w_no_margs*(chi_pos['x']-min_width)/(max_width-min_width),
	110	self.h_margin+self.h_no_margs*chi_pos['y']/max_height), line_style)
[585]	111
[624]	112	def draw_scale(self, file, filename):
[626]	113	self.add_text(file, "Generated from " + filename.split("\\")[-1], (5, 5), "start")
[562]	114
[624]	115	start_text = ""
	116	end_text = ""
	117	if self.design.TIME == "BIRTHS":
	118	start_text = "Birth #0"
	119	end_text = "Birth #" + str(len(self.design.positions)-1)
	120	if self.design.TIME == "REAL":
	121	start_text = "Time " + str(min(self.design.tree.time))
	122	end_text = "Time " + str(max(self.design.tree.time))
	123	if self.design.TIME == "GENERATIONAL":
[633]	124	start_text = "Depth " + str(self.design.props['adepth_min'])
	125	end_text = "Depth " + str(self.design.props['adepth_max'])
[576]	126
[626]	127	self.add_dashed_line(file, (self.width*0.7, self.h_margin), (self.width, self.h_margin))
	128	self.add_text(file, start_text, (self.width, self.h_margin), "end")
[624]	129	self.add_dashed_line(file, (self.width*0.7, self.height-self.h_margin), (self.width, self.height-self.h_margin))
[626]	130	self.add_text(file, end_text, (self.width, self.height-self.h_margin), "end")
[562]	131
[624]	132	def compute_property(self, part, prop, node):
	133	start = self.settings[part][prop]['start']
	134	end = self.settings[part][prop]['end']
	135	value = (self.design.props[self.settings[part][prop]['meaning']][node]
	136	if self.settings[part][prop]['meaning'] in self.design.props else 0 )
	137	bias = self.settings[part][prop]['bias']
	138	if prop == "color":
	139	return self.compute_color(start, end, value, bias)
	140	else:
	141	return self.compute_value(start, end, value, bias)
[562]	142
[624]	143	def compute_color(self, start, end, value, bias=1):
	144	if isinstance(value, str):
	145	value = int(value)
[695]	146	r, g, b = self.color_converter.to_rgb(self.settings['colors_of_kinds'][value])
[624]	147	else:
[695]	148	start_color = self.color_converter.to_rgb(start)
	149	end_color = self.color_converter.to_rgb(end)
[624]	150	value = 1 - (1-value)**bias
[695]	151	r = start_color[0](1-value)+end_color[0]value
	152	g = start_color[1](1-value)+end_color[1]value
	153	b = start_color[2](1-value)+end_color[2]value
	154	return (100r, 100g, 100*b)
[562]	155
[624]	156	def compute_value(self, start, end, value, bias=1):
	157	value = 1 - (1-value)**bias
	158	return start(1-value) + endvalue
[564]	159
[624]	160	class PngDrawer(Drawer):
[626]	161
	162	def scale_up(self):
	163	self.width *= self.multi
	164	self.height *= self.multi
	165	self.w_margin *= self.multi
	166	self.h_margin *= self.multi
	167	self.h_no_margs *= self.multi
	168	self.w_no_margs *= self.multi
	169
	170	def scale_down(self):
	171	self.width /= self.multi
	172	self.height /= self.multi
	173	self.w_margin /= self.multi
	174	self.h_margin /= self.multi
	175	self.h_no_margs /= self.multi
	176	self.w_no_margs /= self.multi
	177
	178	def draw_design(self, filename, input_filename, multi=1, scale="SIMPLE"):
[624]	179	print("Drawing...")
[564]	180
[626]	181	self.multi=multi
	182	self.scale_up()
	183
[624]	184	back = Image.new('RGBA', (self.width, self.height), (255,255,255,0))
[562]	185
[624]	186	min_width = min([x['x'] for x in self.design.positions if 'x' in x])
	187	max_width = max([x['x'] for x in self.design.positions if 'x' in x])
	188	max_height = max([x['y'] for x in self.design.positions if 'y' in x])
[562]	189
[624]	190	self.draw_lines(back, min_width, max_width, max_height)
	191	self.draw_dots(back, min_width, max_width, max_height)
[562]	192
[624]	193	if scale == "SIMPLE":
	194	self.draw_scale(back, input_filename)
[564]	195
[626]	196	#back.show()
	197	self.scale_down()
	198
	199	back.thumbnail((self.width, self.height), Image.ANTIALIAS)
	200
[624]	201	back.save(filename)
[562]	202
[624]	203	def add_dot(self, file, pos, style):
	204	x, y = int(pos[0]), int(pos[1])
[626]	205	r = style['r']*self.multi
[624]	206	offset = (int(x - r), int(y - r))
	207	size = (2int(r), 2int(r))
[622]	208
[624]	209	c = style['color']
[572]	210
[624]	211	img = Image.new('RGBA', size)
	212	ImageDraw.Draw(img).ellipse((1, 1, size[0]-1, size[1]-1),
	213	(int(2.55c[0]), int(2.55c[1]), int(2.55c[2]), int(255style['opacity'])))
	214	file.paste(img, offset, mask=img)
[572]	215
[624]	216	def add_line(self, file, from_pos, to_pos, style):
	217	fx, fy, tx, ty = int(from_pos[0]), int(from_pos[1]), int(to_pos[0]), int(to_pos[1])
[626]	218	w = int(style['width'])*self.multi
[562]	219
[624]	220	offset = (min(fx-w, tx-w), min(fy-w, ty-w))
	221	size = (abs(fx-tx)+2w, abs(fy-ty)+2w)
[577]	222
[624]	223	c = style['color']
[622]	224
[624]	225	img = Image.new('RGBA', size)
	226	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]	227	(int(2.55c[0]), int(2.55c[1]), int(2.55c[2]), int(255style['opacity'])), w)
[624]	228	file.paste(img, offset, mask=img)
[562]	229
[624]	230	def add_dashed_line(self, file, from_pos, to_pos):
	231	style = {'color': (0,0,0), 'width': 1, 'opacity': 1}
	232	sublines = 50
	233	# TODO could be faster: compute delta and only add delta each time (but currently we do not use it often)
[684]	234	normdiv = 2*sublines-1
[624]	235	for i in range(sublines):
[684]	236	from_pos_sub = (self.compute_value(from_pos[0], to_pos[0], 2*i/normdiv, 1),
	237	self.compute_value(from_pos[1], to_pos[1], 2*i/normdiv, 1))
	238	to_pos_sub = (self.compute_value(from_pos[0], to_pos[0], (2*i+1)/normdiv, 1),
	239	self.compute_value(from_pos[1], to_pos[1], (2*i+1)/normdiv, 1))
[624]	240	self.add_line(file, from_pos_sub, to_pos_sub, style)
[562]	241
[624]	242	def add_text(self, file, text, pos, anchor, style=''):
[626]	243	font = ImageFont.truetype("Vera.ttf", 16*self.multi)
[621]	244
[624]	245	img = Image.new('RGBA', (self.width, self.height))
	246	draw = ImageDraw.Draw(img)
	247	txtsize = draw.textsize(text, font=font)
[626]	248	pos = pos if anchor == "start" else (pos[0]-txtsize[0], pos[1])
[624]	249	draw.text(pos, text, (0,0,0), font=font)
	250	file.paste(img, (0,0), mask=img)
[622]	251
[624]	252	def compute_line_style(self, parent, child):
	253	return {'color': self.compute_property('lines', 'color', child),
	254	'width': self.compute_property('lines', 'width', child),
	255	'opacity': self.compute_property('lines', 'opacity', child)}
	256
	257	def compute_dot_style(self, node):
	258	return {'color': self.compute_property('dots', 'color', node),
	259	'r': self.compute_property('dots', 'size', node),
	260	'opacity': self.compute_property('dots', 'opacity', node)}
	261
	262	class SvgDrawer(Drawer):
[626]	263	def draw_design(self, filename, input_filename, multi=1, scale="SIMPLE"):
[624]	264	print("Drawing...")
	265	file = open(filename, "w")
	266
	267	min_width = min([x['x'] for x in self.design.positions if 'x' in x])
	268	max_width = max([x['x'] for x in self.design.positions if 'x' in x])
	269	max_height = max([x['y'] for x in self.design.positions if 'y' in x])
	270
	271	file.write('<svg xmlns:svg="http://www.w3.org/2000/svg" xmlns="http://www.w3.org/2000/svg" '
	272	'xmlns:xlink="http://www.w3.org/1999/xlink" version="1.0" '
	273	'width="' + str(self.width) + '" height="' + str(self.height) + '">')
	274
	275	self.draw_lines(file, min_width, max_width, max_height)
	276	self.draw_dots(file, min_width, max_width, max_height)
	277
	278	if scale == "SIMPLE":
	279	self.draw_scale(file, input_filename)
	280
	281	file.write("</svg>")
	282	file.close()
	283
	284	def add_text(self, file, text, pos, anchor, style=''):
	285	style = (style if style != '' else 'style="font-family: Arial; font-size: 12; fill: #000000;"')
[628]	286	# assuming font size 12, it should be taken from the style string!
	287	file.write('<text ' + style + ' text-anchor="' + anchor + '" x="' + str(pos[0]) + '" y="' + str(pos[1]+12) + '" >' + text + '</text>')
[624]	288
	289	def add_dot(self, file, pos, style):
	290	file.write('<circle ' + style + ' cx="' + str(pos[0]) + '" cy="' + str(pos[1]) + '" />')
	291
	292	def add_line(self, file, from_pos, to_pos, style):
	293	file.write('<line ' + style + ' x1="' + str(from_pos[0]) + '" x2="' + str(to_pos[0]) +
	294	'" y1="' + str(from_pos[1]) + '" y2="' + str(to_pos[1]) + '" fill="none"/>')
	295
	296	def add_dashed_line(self, file, from_pos, to_pos):
	297	style = 'stroke="black" stroke-width="0.5" stroke-opacity="1" stroke-dasharray="5, 5"'
	298	self.add_line(file, from_pos, to_pos, style)
	299
	300	def compute_line_style(self, parent, child):
	301	return self.compute_stroke_color('lines', child) + ' ' \
	302	+ self.compute_stroke_width('lines', child) + ' ' \
	303	+ self.compute_stroke_opacity(child)
	304
	305	def compute_dot_style(self, node):
	306	return self.compute_dot_size(node) + ' ' \
	307	+ self.compute_fill_opacity(node) + ' ' \
	308	+ self.compute_dot_fill(node)
	309
	310	def compute_stroke_color(self, part, node):
	311	color = self.compute_property(part, 'color', node)
	312	return 'stroke="rgb(' + str(color[0]) + '%,' + str(color[1]) + '%,' + str(color[2]) + '%)"'
	313
	314	def compute_stroke_width(self, part, node):
	315	return 'stroke-width="' + str(self.compute_property(part, 'width', node)) + '"'
	316
	317	def compute_stroke_opacity(self, node):
	318	return 'stroke-opacity="' + str(self.compute_property('lines', 'opacity', node)) + '"'
	319
	320	def compute_fill_opacity(self, node):
	321	return 'fill-opacity="' + str(self.compute_property('dots', 'opacity', node)) + '"'
	322
	323	def compute_dot_size(self, node):
	324	return 'r="' + str(self.compute_property('dots', 'size', node)) + '"'
	325
	326	def compute_dot_fill(self, node):
	327	color = self.compute_property('dots', 'color', node)
	328	return 'fill="rgb(' + str(color[0]) + '%,' + str(color[1]) + '%,' + str(color[2]) + '%)"'
	329
	330	class Designer:
	331
	332	def __init__(self, tree, jitter=False, time="GENERATIONAL", balance="DENSITY"):
	333	self.props = {}
	334
	335	self.tree = tree
	336
	337	self.TIME = time
	338	self.JITTER = jitter
	339
	340	if balance == "RANDOM":
	341	self.xmin_crowd = self.xmin_crowd_random
	342	elif balance == "MIN":
	343	self.xmin_crowd = self.xmin_crowd_min
	344	elif balance == "DENSITY":
	345	self.xmin_crowd = self.xmin_crowd_density
[562]	346	else:
[624]	347	raise ValueError("Error, the value of BALANCE does not match any expected value.")
[562]	348
[624]	349	def calculate_measures(self):
	350	print("Calculating measures...")
[679]	351	self.compute_depth()
[624]	352	self.compute_adepth()
	353	self.compute_children()
	354	self.compute_kind()
	355	self.compute_time()
[633]	356	self.compute_progress()
[624]	357	self.compute_custom()
[622]	358
[624]	359	def xmin_crowd_random(self, x1, x2, y):
	360	return (x1 if random.randrange(2) == 0 else x2)
[562]	361
[624]	362	def xmin_crowd_min(self, x1, x2, y):
	363	x1_closest = 999999
	364	x2_closest = 999999
	365	miny = y-3
	366	maxy = y+3
	367	i = bisect.bisect_left(self.y_sorted, miny)
	368	while True:
	369	if len(self.positions_sorted) <= i or self.positions_sorted[i]['y'] > maxy:
	370	break
	371	pos = self.positions_sorted[i]
[562]	372
[624]	373	x1_closest = min(x1_closest, abs(x1-pos['x']))
	374	x2_closest = min(x2_closest, abs(x2-pos['x']))
[562]	375
[624]	376	i += 1
	377	return (x1 if x1_closest > x2_closest else x2)
[562]	378
[624]	379	def xmin_crowd_density(self, x1, x2, y):
[690]	380	# TODO experimental - requires further work to make it less 'jumpy' and more predictable
[694]	381	CONST_LOCAL_AREA_RADIUS = 5
	382	CONST_GLOBAL_AREA_RADIUS = 10
	383	CONST_WINDOW_SIZE = 20000 #TODO should depend on the maxY ?
[690]	384	x1_dist_loc = 0
	385	x2_dist_loc = 0
	386	count_loc = 1
	387	x1_dist_glob = 0
	388	x2_dist_glob = 0
	389	count_glob = 1
[694]	390	miny = y-CONST_WINDOW_SIZE
	391	maxy = y+CONST_WINDOW_SIZE
[624]	392	i_left = bisect.bisect_left(self.y_sorted, miny)
	393	i_right = bisect.bisect_right(self.y_sorted, maxy)
[694]	394	#TODO test: maxy=y should give the same results, right?
[562]	395
[624]	396	def include_pos(pos):
[690]	397	nonlocal x1_dist_loc, x2_dist_loc, x1_dist_glob, x2_dist_glob, count_loc, count_glob
[562]	398
[694]	399	dysq = (pos['y']-y)**2 + 1 #+1 so 1/dysq is at most 1
	400	dx1 = math.fabs(pos['x']-x1)
	401	dx2 = math.fabs(pos['x']-x2)
	402
[690]	403	d = math.fabs(pos['x'] - (x1+x2)/2)
[623]	404
[694]	405	if d < CONST_LOCAL_AREA_RADIUS:
	406	x1_dist_loc += math.sqrt(dx1/dysq + dx1**2)
	407	x2_dist_loc += math.sqrt(dx2/dysq + dx2**2)
[690]	408	count_loc += 1
[694]	409	elif d > CONST_GLOBAL_AREA_RADIUS:
	410	x1_dist_glob += math.sqrt(dx1/dysq + dx1**2)
	411	x2_dist_glob += math.sqrt(dx2/dysq + dx2**2)
[690]	412	count_glob += 1
	413
[624]	414	# optimized to draw from all the nodes, if less than 10 nodes in the range
	415	if len(self.positions_sorted) > i_left:
	416	if i_right - i_left < 10:
	417	for j in range(i_left, i_right):
	418	include_pos(self.positions_sorted[j])
	419	else:
	420	for j in range(10):
	421	pos = self.positions_sorted[random.randrange(i_left, i_right)]
	422	include_pos(pos)
[562]	423
[690]	424	return (x1 if (x1_dist_loc-x2_dist_loc)/count_loc-(x1_dist_glob-x2_dist_glob)/count_glob > 0 else x2)
	425	#return (x1 if x1_dist +random.gauss(0, 0.00001) > x2_dist +random.gauss(0, 0.00001) else x2)
[624]	426	#print(x1_dist, x2_dist)
	427	#x1_dist = x1_dist**2
	428	#x2_dist = x2_dist**2
	429	#return x1 if x1_dist+x2_dist==0 else (x1x1_dist + x2x2_dist) / (x1_dist+x2_dist) + random.gauss(0, 0.01)
	430	#return (x1 if random.randint(0, int(x1_dist+x2_dist)) < x1_dist else x2)
[571]	431
[624]	432	def calculate_node_positions(self, ignore_last=0):
	433	print("Calculating positions...")
[562]	434
[624]	435	def add_node(node):
	436	index = bisect.bisect_left(self.y_sorted, node['y'])
	437	self.y_sorted.insert(index, node['y'])
	438	self.positions_sorted.insert(index, node)
	439	self.positions[node['id']] = node
[572]	440
[624]	441	self.positions_sorted = [{'x':0, 'y':0, 'id':0}]
	442	self.y_sorted = [0]
	443	self.positions = [{} for x in range(len(self.tree.parents))]
	444	self.positions[0] = {'x':0, 'y':0, 'id':0}
[572]	445
[677]	446	# order by maximum depth of the parent guarantees that co child is evaluated before its parent
	447	visiting_order = [i for i in range(0, len(self.tree.parents))]
	448	visiting_order = sorted(visiting_order, key=lambda q:
	449	0 if q == 0 else max([self.props["depth"][d] for d in self.tree.parents[q]]))
[562]	450
[624]	451	start_time = timelib.time()
[566]	452
[677]	453	# for each child of the current node
[686]	454	for node_counter,child in enumerate(visiting_order, start=1):
[677]	455	# debug info - elapsed time
[685]	456	if node_counter % 100000 == 0:
	457	print("%d%%\t%d\t%g" % (node_counter*100/len(self.tree.parents), node_counter, timelib.time()-start_time))
[677]	458	start_time = timelib.time()
[562]	459
[677]	460	# using normalized adepth
	461	if self.props['adepth'][child] >= ignore_last/self.props['adepth_max']:
[621]	462
[677]	463	ypos = 0
	464	if self.TIME == "BIRTHS":
	465	ypos = child
	466	elif self.TIME == "GENERATIONAL":
	467	# one more than its parent (what if more than one parent?)
[680]	468	ypos = max([self.positions[par]['y'] for par, v in self.tree.parents[child].items()])+1 \
	469	if self.tree.parents[child] else 0
[677]	470	elif self.TIME == "REAL":
	471	ypos = self.tree.time[child]
[621]	472
[677]	473	if len(self.tree.parents[child]) == 1:
	474	# if current_node is the only parent
[687]	475	parent, similarity = [(par, v) for par, v in self.tree.parents[child].items()][0]
[621]	476
[677]	477	if self.JITTER:
[690]	478	dissimilarity = (1-similarity) + random.gauss(0, 0.01) + 0.001
[621]	479	else:
[687]	480	dissimilarity = (1-similarity) + 0.001
[677]	481	add_node({'id':child, 'y':ypos, 'x':
	482	self.xmin_crowd(self.positions[parent]['x']-dissimilarity,
	483	self.positions[parent]['x']+dissimilarity, ypos)})
	484	else:
	485	# position weighted by the degree of inheritence from each parent
	486	total_inheretance = sum([v for k, v in self.tree.parents[child].items()])
	487	xpos = sum([self.positions[k]['x']*v/total_inheretance
	488	for k, v in self.tree.parents[child].items()])
	489	if self.JITTER:
	490	add_node({'id':child, 'y':ypos, 'x':xpos + random.gauss(0, 0.1)})
	491	else:
	492	add_node({'id':child, 'y':ypos, 'x':xpos})
[621]	493
	494
[624]	495	def compute_custom(self):
	496	for prop in self.tree.props:
	497	self.props[prop] = [None for x in range(len(self.tree.children))]
[621]	498
[624]	499	for i in range(len(self.props[prop])):
	500	self.props[prop][i] = self.tree.props[prop][i]
[621]	501
[624]	502	self.normalize_prop(prop)
[562]	503
[624]	504	def compute_time(self):
	505	# simple rewrite from the tree
	506	self.props["time"] = [0 for x in range(len(self.tree.children))]
[562]	507
[624]	508	for i in range(len(self.props['time'])):
	509	self.props['time'][i] = self.tree.time[i]
[572]	510
[624]	511	self.normalize_prop('time')
[617]	512
[624]	513	def compute_kind(self):
	514	# simple rewrite from the tree
	515	self.props["kind"] = [0 for x in range(len(self.tree.children))]
[617]	516
[624]	517	for i in range (len(self.props['kind'])):
	518	self.props['kind'][i] = str(self.tree.kind[i])
[617]	519
[624]	520	def compute_depth(self):
	521	self.props["depth"] = [999999999 for x in range(len(self.tree.children))]
[681]	522	visited = [0 for x in range(len(self.tree.children))]
[617]	523
[624]	524	nodes_to_visit = [0]
[681]	525	visited[0] = 1
[624]	526	self.props["depth"][0] = 0
	527	while True:
[681]	528	current_node = nodes_to_visit[0]
[682]	529
[681]	530	for child in self.tree.children[current_node]:
	531	if visited[child] == 0:
	532	visited[child] = 1
	533	nodes_to_visit.append(child)
	534	self.props["depth"][child] = self.props["depth"][current_node]+1
[624]	535	nodes_to_visit = nodes_to_visit[1:]
	536	if len(nodes_to_visit) == 0:
	537	break
[617]	538
[624]	539	self.normalize_prop('depth')
[617]	540
[624]	541	def compute_adepth(self):
	542	self.props["adepth"] = [0 for x in range(len(self.tree.children))]
[617]	543
[679]	544	# order by maximum depth of the parent guarantees that co child is evaluated before its parent
	545	visiting_order = [i for i in range(0, len(self.tree.parents))]
	546	visiting_order = sorted(visiting_order, key=lambda q:
	547	0 if q == 0 else max([self.props["depth"][d] for d in self.tree.parents[q]]))[::-1]
[617]	548
[679]	549	for node in visiting_order:
	550	children = self.tree.children[node]
	551	if len(children) != 0:
	552	# 0 by default
	553	self.props["adepth"][node] = max([self.props["adepth"][child] for child in children])+1
[624]	554	self.normalize_prop('adepth')
[594]	555
[624]	556	def compute_children(self):
	557	self.props["children"] = [0 for x in range(len(self.tree.children))]
	558	for i in range (len(self.props['children'])):
	559	self.props['children'][i] = len(self.tree.children[i])
[562]	560
[624]	561	self.normalize_prop('children')
[564]	562
[633]	563	def compute_progress(self):
	564	self.props["progress"] = [0 for x in range(len(self.tree.children))]
	565	for i in range(len(self.props['children'])):
	566	times = sorted([self.props["time"][self.tree.children[i][j]]*100000 for j in range(len(self.tree.children[i]))])
	567	if len(times) > 4:
	568	times = [times[i+1] - times[i] for i in range(len(times)-1)]
	569	#print(times)
	570	slope, intercept, r_value, p_value, std_err = stats.linregress(range(len(times)), times)
	571	self.props['progress'][i] = slope if not np.isnan(slope) and not np.isinf(slope) else 0
	572
	573	for i in range(0, 5):
	574	self.props['progress'][self.props['progress'].index(min(self.props['progress']))] = 0
	575	self.props['progress'][self.props['progress'].index(max(self.props['progress']))] = 0
	576
	577	mini = min(self.props['progress'])
	578	maxi = max(self.props['progress'])
	579	for k in range(len(self.props['progress'])):
	580	if self.props['progress'][k] == 0:
	581	self.props['progress'][k] = mini
	582
	583	#for k in range(len(self.props['progress'])):
	584	# self.props['progress'][k] = 1-self.props['progress'][k]
	585
	586	self.normalize_prop('progress')
	587
[624]	588	def normalize_prop(self, prop):
[678]	589	noneless = [v for v in self.props[prop] if (type(v)!=str and type(v)!=list)]
[624]	590	if len(noneless) > 0:
	591	max_val = max(noneless)
	592	min_val = min(noneless)
[696]	593	print(prop + ": <" + str(min_val) + "; " + str(max_val) + ">")
[624]	594	self.props[prop +'_max'] = max_val
	595	self.props[prop +'_min'] = min_val
	596	for i in range(len(self.props[prop])):
	597	if self.props[prop][i] is not None:
[633]	598	qqq = self.props[prop][i]
	599	self.props[prop][i] = 0 if max_val == min_val else (self.props[prop][i] - min_val) / (max_val - min_val)
[594]	600
[624]	601	class TreeData:
	602	simple_data = None
[615]	603
[624]	604	children = []
	605	parents = []
	606	time = []
	607	kind = []
[562]	608
[624]	609	def __init__(self): #, simple_data=False):
	610	#self.simple_data = simple_data
	611	pass
[562]	612
[624]	613	def load(self, filename, max_nodes=0):
	614	print("Loading...")
[576]	615
[624]	616	CLI_PREFIX = "Script.Message:"
	617	default_props = ["Time", "FromIDs", "ID", "Operation", "Inherited"]
[576]	618
[633]	619	self.ids = {}
[628]	620	def get_id(id, createOnError = True):
	621	if createOnError:
[633]	622	if id not in self.ids:
	623	self.ids[id] = len(self.ids)
[628]	624	else:
[633]	625	if id not in self.ids:
[628]	626	return None
[633]	627	return self.ids[id]
[576]	628
[624]	629	file = open(filename)
[576]	630
[624]	631	# counting the number of expected nodes
	632	nodes = 0
	633	for line in file:
	634	line_arr = line.split(' ', 1)
	635	if len(line_arr) == 2:
	636	if line_arr[0] == CLI_PREFIX:
	637	line_arr = line_arr[1].split(' ', 1)
	638	if line_arr[0] == "[OFFSPRING]":
	639	nodes += 1
[562]	640
[624]	641	nodes = min(nodes, max_nodes if max_nodes != 0 else nodes)+1
	642	self.parents = [{} for x in range(nodes)]
	643	self.children = [[] for x in range(nodes)]
	644	self.time = [0] * nodes
	645	self.kind = [0] * nodes
[628]	646	self.life_lenght = [0] * nodes
[624]	647	self.props = {}
[562]	648
[688]	649	print("nodes: %d" % len(self.parents))
[562]	650
[624]	651	file.seek(0)
	652	loaded_so_far = 0
	653	lasttime = timelib.time()
	654	for line in file:
	655	line_arr = line.split(' ', 1)
	656	if len(line_arr) == 2:
	657	if line_arr[0] == CLI_PREFIX:
	658	line_arr = line_arr[1].split(' ', 1)
	659	if line_arr[0] == "[OFFSPRING]":
[682]	660	try:
	661	creature = json.loads(line_arr[1])
	662	except ValueError:
	663	print("Json format error - the line cannot be read. Breaking the loading loop.")
	664	# fixing arrays by removing the last element
	665	# ! assuming that only the last line is broken !
	666	self.parents.pop()
	667	self.children.pop()
	668	self.time.pop()
	669	self.kind.pop()
	670	self.life_lenght.pop()
	671	nodes -= 1
	672	break
	673
[624]	674	if "FromIDs" in creature:
[562]	675
[624]	676	# make sure that ID's of parents are lower than that of their children
	677	for i in range(0, len(creature["FromIDs"])):
[633]	678	if creature["FromIDs"][i] not in self.ids:
[627]	679	get_id("virtual_parent")
[562]	680
[624]	681	creature_id = get_id(creature["ID"])
	682
	683	# debug
	684	if loaded_so_far%1000 == 0:
	685	#print(". " + str(creature_id) + " " + str(timelib.time() - lasttime))
	686	lasttime = timelib.time()
	687
	688	# we assign to each parent its contribution to the genotype of the child
	689	for i in range(0, len(creature["FromIDs"])):
[633]	690	if creature["FromIDs"][i] in self.ids:
[627]	691	parent_id = get_id(creature["FromIDs"][i])
	692	else:
	693	parent_id = get_id("virtual_parent")
[687]	694	inherited = (creature["Inherited"][i] if 'Inherited' in creature else 1)
[624]	695	self.parents[creature_id][parent_id] = inherited
	696
	697	if "Time" in creature:
	698	self.time[creature_id] = creature["Time"]
	699
	700	if "Kind" in creature:
	701	self.kind[creature_id] = creature["Kind"]
	702
	703	for prop in creature:
	704	if prop not in default_props:
	705	if prop not in self.props:
[628]	706	self.props[prop] = [0 for i in range(nodes)]
[624]	707	self.props[prop][creature_id] = creature[prop]
	708
	709	loaded_so_far += 1
	710	else:
	711	raise LoadingError("[OFFSPRING] misses the 'FromIDs' field!")
[628]	712	if line_arr[0] == "[DIED]":
	713	creature = json.loads(line_arr[1])
	714	creature_id = get_id(creature["ID"], False)
	715	if creature_id is not None:
	716	for prop in creature:
	717	if prop not in default_props:
	718	if prop not in self.props:
	719	self.props[prop] = [0 for i in range(nodes)]
	720	self.props[prop][creature_id] = creature[prop]
[624]	721
[628]	722
[624]	723	if loaded_so_far >= max_nodes and max_nodes != 0:
	724	break
	725
	726	for k in range(len(self.parents)):
	727	v = self.parents[k]
	728	for val in self.parents[k]:
	729	self.children[val].append(k)
	730
[562]	731	depth = {}
[577]	732	kind = {}
[562]	733
	734	def main():
	735
[624]	736	parser = argparse.ArgumentParser(description='Draws a genealogical tree (generates a SVG file) based on parent-child relationship '
	737	'information from a text file. Supports files generated by Framsticks experiments.')
[615]	738	parser.add_argument('-i', '--in', dest='input', required=True, help='input file name with stuctured evolutionary data')
[624]	739	parser.add_argument('-o', '--out', dest='output', required=True, help='output file name for the evolutionary tree (SVG/PNG/JPG/BMP)')
	740	parser.add_argument('-c', '--config', dest='config', default="", help='config file name ')
[562]	741
[624]	742	parser.add_argument('-W', '--width', default=600, type=int, dest='width', help='width of the output image (600 by default)')
[626]	743	parser.add_argument('-H', '--height', default=800, type=int, dest='height', help='height of the output image (800 by default)')
	744	parser.add_argument('-m', '--multi', default=1, type=int, dest='multi', help='multisampling factor (applicable only for raster images)')
[562]	745
[620]	746	parser.add_argument('-t', '--time', default='GENERATIONAL', dest='time', help='values on vertical axis (BIRTHS/GENERATIONAL(d)/REAL); '
[614]	747	'BIRTHS: time measured as the number of births since the beginning; '
[571]	748	'GENERATIONAL: time measured as number of ancestors; '
	749	'REAL: real time of the simulation')
[620]	750	parser.add_argument('-b', '--balance', default='DENSITY', dest='balance', help='method of placing nodes in the tree (RANDOM/MIN/DENSITY(d))')
[624]	751	parser.add_argument('-s', '--scale', default='SIMPLE', dest='scale', help='type of timescale added to the tree (NONE(d)/SIMPLE)')
[571]	752	parser.add_argument('-j', '--jitter', dest="jitter", action='store_true', help='draw horizontal positions of children from the normal distribution')
[624]	753	parser.add_argument('-p', '--skip', dest="skip", type=int, default=0, help='skip last P levels of the tree (0 by default)')
	754	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]	755	parser.add_argument('--seed', type=int, dest='seed', help='seed for the random number generator (-1 for random)')
	756
	757	parser.set_defaults(draw_tree=True)
	758	parser.set_defaults(draw_skeleton=False)
	759	parser.set_defaults(draw_spine=False)
	760
	761	parser.set_defaults(seed=-1)
	762
	763	args = parser.parse_args()
	764
[620]	765	TIME = args.time.upper()
	766	BALANCE = args.balance.upper()
	767	SCALE = args.scale.upper()
[571]	768	JITTER = args.jitter
[620]	769	if not TIME in ['BIRTHS', 'GENERATIONAL', 'REAL']\
	770	or not BALANCE in ['RANDOM', 'MIN', 'DENSITY']\
	771	or not SCALE in ['NONE', 'SIMPLE']:
[683]	772	print("Incorrect value of one of the parameters! (time or balance or scale).") #user has to figure out which parameter is wrong...
[620]	773	return
[562]	774
	775	dir = args.input
	776	seed = args.seed
	777	if seed == -1:
	778	seed = random.randint(0, 10000)
	779	random.seed(seed)
[689]	780	print("randomseed:", seed)
[562]	781
[624]	782	tree = TreeData()
	783	tree.load(dir, max_nodes=args.max_nodes)
[562]	784
[682]	785
[624]	786	designer = Designer(tree, jitter=JITTER, time=TIME, balance=BALANCE)
	787	designer.calculate_measures()
	788	designer.calculate_node_positions(ignore_last=args.skip)
[562]	789
[624]	790	if args.output.endswith(".svg"):
	791	drawer = SvgDrawer(designer, args.config, w=args.width, h=args.height)
	792	else:
	793	drawer = PngDrawer(designer, args.config, w=args.width, h=args.height)
[626]	794	drawer.draw_design(args.output, args.input, multi=args.multi, scale=SCALE)
[562]	795
	796
	797	main()

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