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source: mds-and-trees/tree-genealogy.py @ 707

Last change on this file since 707 was 707, checked in by konrad, 7 years ago
Added a warning message about merging nodes with a virtual parent node.
File size: 38.0 KB

Rev	Line
[562]	1	import json
[624]	2	import math
[562]	3	import random
	4	import argparse
[624]	5	import bisect
[702]	6	import copy
[624]	7	import time as timelib
	8	from PIL import Image, ImageDraw, ImageFont
[633]	9	from scipy import stats
[695]	10	from matplotlib import colors
[633]	11	import numpy as np
[562]	12
[624]	13	class LoadingError(Exception):
	14	pass
[562]	15
[624]	16	class Drawer:
[571]	17
[624]	18	def __init__(self, design, config_file, w=600, h=800, w_margin=10, h_margin=20):
	19	self.design = design
	20	self.width = w
	21	self.height = h
	22	self.w_margin = w_margin
	23	self.h_margin = h_margin
	24	self.w_no_margs = w - 2* w_margin
	25	self.h_no_margs = h - 2* h_margin
[571]	26
[695]	27	self.color_converter = colors.ColorConverter()
[562]	28
[624]	29	self.settings = {
	30	'colors_of_kinds': ['red', 'green', 'blue', 'magenta', 'yellow', 'cyan', 'orange', 'purple'],
	31	'dots': {
	32	'color': {
[628]	33	'meaning': 'Lifespan',
[700]	34	'normalize_cmap': False,
	35	'cmap': {},
[628]	36	'start': 'red',
[624]	37	'end': 'green',
	38	'bias': 1
	39	},
	40	'size': {
[628]	41	'meaning': 'EnergyEaten',
[624]	42	'start': 1,
[628]	43	'end': 6,
[624]	44	'bias': 0.5
	45	},
	46	'opacity': {
[628]	47	'meaning': 'EnergyEaten',
	48	'start': 0.2,
	49	'end': 1,
[624]	50	'bias': 1
	51	}
	52	},
	53	'lines': {
	54	'color': {
	55	'meaning': 'adepth',
[700]	56	'normalize_cmap': False,
	57	'cmap': {},
[624]	58	'start': 'black',
	59	'end': 'red',
	60	'bias': 3
	61	},
	62	'width': {
	63	'meaning': 'adepth',
[627]	64	'start': 0.1,
[624]	65	'end': 4,
	66	'bias': 3
	67	},
	68	'opacity': {
	69	'meaning': 'adepth',
	70	'start': 0.1,
	71	'end': 0.8,
	72	'bias': 5
	73	}
	74	}
	75	}
[577]	76
[624]	77	def merge(source, destination):
	78	for key, value in source.items():
	79	if isinstance(value, dict):
	80	node = destination.setdefault(key, {})
	81	merge(value, node)
	82	else:
	83	destination[key] = value
	84	return destination
[576]	85
[624]	86	if config_file != "":
	87	with open(config_file) as config:
	88	c = json.load(config)
	89	self.settings = merge(c, self.settings)
	90	#print(json.dumps(self.settings, indent=4, sort_keys=True))
[586]	91
[700]	92	self.compile_cmaps()
	93
	94	def compile_cmaps(self):
[702]	95	def normalize_and_compile_cmap(cmap):
	96	for key in cmap:
	97	for arr in cmap[key]:
	98	arr[0] = (arr[0] - cmap[key][0][0]) / (cmap[key][-1][0] - cmap[key][0][0])
	99	return colors.LinearSegmentedColormap('Custom', cmap)
[700]	100
	101	for part in ['dots', 'lines']:
[702]	102	if self.settings[part]['color']['cmap']:
	103	if self.settings[part]['color']['normalize_cmap']:
	104	cmap = self.settings[part]['color']['cmap']
	105	min = self.design.props[self.settings[part]['color']['meaning'] + "_min"]
	106	max = self.design.props[self.settings[part]['color']['meaning'] + "_max"]
[700]	107
[702]	108	for key in cmap:
	109	if cmap[key][0][0] > min:
	110	cmap[key].insert(0, cmap[key][0][:])
	111	cmap[key][0][0] = min
	112	if cmap[key][-1][0] < max:
	113	cmap[key].append(cmap[key][-1][:])
	114	cmap[key][-1][0] = max
[700]	115
[702]	116	og_cmap = normalize_and_compile_cmap(copy.deepcopy(cmap))
[700]	117
[702]	118	col2key = {'red':0, 'green':1, 'blue':2}
	119	for key in cmap:
	120	# for color from (r/g/b) #n's should be the same for all keys!
	121	n_min = (min - cmap[key][0][0]) / (cmap[key][-1][0] - cmap[key][0][0])
	122	n_max = (max - cmap[key][0][0]) / (cmap[key][-1][0] - cmap[key][0][0])
	123
	124	min_col = og_cmap(n_min)
	125	max_col = og_cmap(n_max)
	126
	127	cmap[key][0] = [min, min_col[col2key[key]], min_col[col2key[key]]]
	128	cmap[key][-1] = [max, max_col[col2key[key]], max_col[col2key[key]]]
	129	print(self.settings[part]['color']['cmap'])
	130	self.settings[part]['color']['cmap'] = normalize_and_compile_cmap(self.settings[part]['color']['cmap'])
	131
[624]	132	def draw_dots(self, file, min_width, max_width, max_height):
	133	for i in range(len(self.design.positions)):
	134	node = self.design.positions[i]
	135	if 'x' not in node:
	136	continue
	137	dot_style = self.compute_dot_style(node=i)
	138	self.add_dot(file, (self.w_margin+self.w_no_margs*(node['x']-min_width)/(max_width-min_width),
	139	self.h_margin+self.h_no_margs*node['y']/max_height), dot_style)
[585]	140
[624]	141	def draw_lines(self, file, min_width, max_width, max_height):
	142	for parent in range(len(self.design.positions)):
	143	par_pos = self.design.positions[parent]
	144	if not 'x' in par_pos:
	145	continue
	146	for child in self.design.tree.children[parent]:
	147	chi_pos = self.design.positions[child]
	148	if 'x' not in chi_pos:
	149	continue
	150	line_style = self.compute_line_style(parent, child)
	151	self.add_line(file, (self.w_margin+self.w_no_margs*(par_pos['x']-min_width)/(max_width-min_width),
	152	self.h_margin+self.h_no_margs*par_pos['y']/max_height),
	153	(self.w_margin+self.w_no_margs*(chi_pos['x']-min_width)/(max_width-min_width),
	154	self.h_margin+self.h_no_margs*chi_pos['y']/max_height), line_style)
[585]	155
[624]	156	def draw_scale(self, file, filename):
[626]	157	self.add_text(file, "Generated from " + filename.split("\\")[-1], (5, 5), "start")
[562]	158
[624]	159	start_text = ""
	160	end_text = ""
	161	if self.design.TIME == "BIRTHS":
	162	start_text = "Birth #0"
	163	end_text = "Birth #" + str(len(self.design.positions)-1)
	164	if self.design.TIME == "REAL":
	165	start_text = "Time " + str(min(self.design.tree.time))
	166	end_text = "Time " + str(max(self.design.tree.time))
	167	if self.design.TIME == "GENERATIONAL":
[633]	168	start_text = "Depth " + str(self.design.props['adepth_min'])
	169	end_text = "Depth " + str(self.design.props['adepth_max'])
[576]	170
[626]	171	self.add_dashed_line(file, (self.width*0.7, self.h_margin), (self.width, self.h_margin))
	172	self.add_text(file, start_text, (self.width, self.h_margin), "end")
[624]	173	self.add_dashed_line(file, (self.width*0.7, self.height-self.h_margin), (self.width, self.height-self.h_margin))
[626]	174	self.add_text(file, end_text, (self.width, self.height-self.h_margin), "end")
[562]	175
[624]	176	def compute_property(self, part, prop, node):
	177	start = self.settings[part][prop]['start']
	178	end = self.settings[part][prop]['end']
	179	value = (self.design.props[self.settings[part][prop]['meaning']][node]
	180	if self.settings[part][prop]['meaning'] in self.design.props else 0 )
	181	bias = self.settings[part][prop]['bias']
	182	if prop == "color":
[700]	183	if not self.settings[part][prop]['cmap']:
	184	return self.compute_color(start, end, value, bias)
	185	else:
	186	return self.compute_color_from_cmap(self.settings[part][prop]['cmap'], value, bias)
[624]	187	else:
	188	return self.compute_value(start, end, value, bias)
[562]	189
[700]	190	def compute_color_from_cmap(self, cmap, value, bias=1):
	191	value = 1 - (1-value)**bias
	192	rgba = cmap(value)
	193	return (100rgba[0], 100rgba[1], 100*rgba[2])
	194
	195
[624]	196	def compute_color(self, start, end, value, bias=1):
	197	if isinstance(value, str):
	198	value = int(value)
[695]	199	r, g, b = self.color_converter.to_rgb(self.settings['colors_of_kinds'][value])
[624]	200	else:
[695]	201	start_color = self.color_converter.to_rgb(start)
	202	end_color = self.color_converter.to_rgb(end)
[624]	203	value = 1 - (1-value)**bias
[695]	204	r = start_color[0](1-value)+end_color[0]value
	205	g = start_color[1](1-value)+end_color[1]value
	206	b = start_color[2](1-value)+end_color[2]value
	207	return (100r, 100g, 100*b)
[562]	208
[624]	209	def compute_value(self, start, end, value, bias=1):
	210	value = 1 - (1-value)**bias
	211	return start(1-value) + endvalue
[564]	212
[624]	213	class PngDrawer(Drawer):
[626]	214
	215	def scale_up(self):
	216	self.width *= self.multi
	217	self.height *= self.multi
	218	self.w_margin *= self.multi
	219	self.h_margin *= self.multi
	220	self.h_no_margs *= self.multi
	221	self.w_no_margs *= self.multi
	222
	223	def scale_down(self):
	224	self.width /= self.multi
	225	self.height /= self.multi
	226	self.w_margin /= self.multi
	227	self.h_margin /= self.multi
	228	self.h_no_margs /= self.multi
	229	self.w_no_margs /= self.multi
	230
	231	def draw_design(self, filename, input_filename, multi=1, scale="SIMPLE"):
[624]	232	print("Drawing...")
[564]	233
[626]	234	self.multi=multi
	235	self.scale_up()
	236
[624]	237	back = Image.new('RGBA', (self.width, self.height), (255,255,255,0))
[562]	238
[624]	239	min_width = min([x['x'] for x in self.design.positions if 'x' in x])
	240	max_width = max([x['x'] for x in self.design.positions if 'x' in x])
	241	max_height = max([x['y'] for x in self.design.positions if 'y' in x])
[562]	242
[624]	243	self.draw_lines(back, min_width, max_width, max_height)
	244	self.draw_dots(back, min_width, max_width, max_height)
[562]	245
[624]	246	if scale == "SIMPLE":
	247	self.draw_scale(back, input_filename)
[564]	248
[626]	249	#back.show()
	250	self.scale_down()
	251
	252	back.thumbnail((self.width, self.height), Image.ANTIALIAS)
	253
[624]	254	back.save(filename)
[562]	255
[624]	256	def add_dot(self, file, pos, style):
	257	x, y = int(pos[0]), int(pos[1])
[626]	258	r = style['r']*self.multi
[624]	259	offset = (int(x - r), int(y - r))
	260	size = (2int(r), 2int(r))
[622]	261
[624]	262	c = style['color']
[572]	263
[624]	264	img = Image.new('RGBA', size)
	265	ImageDraw.Draw(img).ellipse((1, 1, size[0]-1, size[1]-1),
	266	(int(2.55c[0]), int(2.55c[1]), int(2.55c[2]), int(255style['opacity'])))
	267	file.paste(img, offset, mask=img)
[572]	268
[624]	269	def add_line(self, file, from_pos, to_pos, style):
	270	fx, fy, tx, ty = int(from_pos[0]), int(from_pos[1]), int(to_pos[0]), int(to_pos[1])
[626]	271	w = int(style['width'])*self.multi
[562]	272
[624]	273	offset = (min(fx-w, tx-w), min(fy-w, ty-w))
	274	size = (abs(fx-tx)+2w, abs(fy-ty)+2w)
[700]	275	if size[0] == 0 or size[1] == 0:
	276	return
[577]	277
[624]	278	c = style['color']
[622]	279
[624]	280	img = Image.new('RGBA', size)
	281	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]	282	(int(2.55c[0]), int(2.55c[1]), int(2.55c[2]), int(255style['opacity'])), w)
[624]	283	file.paste(img, offset, mask=img)
[562]	284
[624]	285	def add_dashed_line(self, file, from_pos, to_pos):
	286	style = {'color': (0,0,0), 'width': 1, 'opacity': 1}
	287	sublines = 50
	288	# TODO could be faster: compute delta and only add delta each time (but currently we do not use it often)
[684]	289	normdiv = 2*sublines-1
[624]	290	for i in range(sublines):
[684]	291	from_pos_sub = (self.compute_value(from_pos[0], to_pos[0], 2*i/normdiv, 1),
	292	self.compute_value(from_pos[1], to_pos[1], 2*i/normdiv, 1))
	293	to_pos_sub = (self.compute_value(from_pos[0], to_pos[0], (2*i+1)/normdiv, 1),
	294	self.compute_value(from_pos[1], to_pos[1], (2*i+1)/normdiv, 1))
[624]	295	self.add_line(file, from_pos_sub, to_pos_sub, style)
[562]	296
[624]	297	def add_text(self, file, text, pos, anchor, style=''):
[626]	298	font = ImageFont.truetype("Vera.ttf", 16*self.multi)
[621]	299
[624]	300	img = Image.new('RGBA', (self.width, self.height))
	301	draw = ImageDraw.Draw(img)
	302	txtsize = draw.textsize(text, font=font)
[626]	303	pos = pos if anchor == "start" else (pos[0]-txtsize[0], pos[1])
[624]	304	draw.text(pos, text, (0,0,0), font=font)
	305	file.paste(img, (0,0), mask=img)
[622]	306
[624]	307	def compute_line_style(self, parent, child):
	308	return {'color': self.compute_property('lines', 'color', child),
	309	'width': self.compute_property('lines', 'width', child),
	310	'opacity': self.compute_property('lines', 'opacity', child)}
	311
	312	def compute_dot_style(self, node):
	313	return {'color': self.compute_property('dots', 'color', node),
	314	'r': self.compute_property('dots', 'size', node),
	315	'opacity': self.compute_property('dots', 'opacity', node)}
	316
	317	class SvgDrawer(Drawer):
[626]	318	def draw_design(self, filename, input_filename, multi=1, scale="SIMPLE"):
[624]	319	print("Drawing...")
	320	file = open(filename, "w")
	321
	322	min_width = min([x['x'] for x in self.design.positions if 'x' in x])
	323	max_width = max([x['x'] for x in self.design.positions if 'x' in x])
	324	max_height = max([x['y'] for x in self.design.positions if 'y' in x])
	325
	326	file.write('<svg xmlns:svg="http://www.w3.org/2000/svg" xmlns="http://www.w3.org/2000/svg" '
	327	'xmlns:xlink="http://www.w3.org/1999/xlink" version="1.0" '
	328	'width="' + str(self.width) + '" height="' + str(self.height) + '">')
	329
	330	self.draw_lines(file, min_width, max_width, max_height)
	331	self.draw_dots(file, min_width, max_width, max_height)
	332
	333	if scale == "SIMPLE":
	334	self.draw_scale(file, input_filename)
	335
	336	file.write("</svg>")
	337	file.close()
	338
	339	def add_text(self, file, text, pos, anchor, style=''):
	340	style = (style if style != '' else 'style="font-family: Arial; font-size: 12; fill: #000000;"')
[628]	341	# assuming font size 12, it should be taken from the style string!
	342	file.write('<text ' + style + ' text-anchor="' + anchor + '" x="' + str(pos[0]) + '" y="' + str(pos[1]+12) + '" >' + text + '</text>')
[624]	343
	344	def add_dot(self, file, pos, style):
	345	file.write('<circle ' + style + ' cx="' + str(pos[0]) + '" cy="' + str(pos[1]) + '" />')
	346
	347	def add_line(self, file, from_pos, to_pos, style):
	348	file.write('<line ' + style + ' x1="' + str(from_pos[0]) + '" x2="' + str(to_pos[0]) +
	349	'" y1="' + str(from_pos[1]) + '" y2="' + str(to_pos[1]) + '" fill="none"/>')
	350
	351	def add_dashed_line(self, file, from_pos, to_pos):
	352	style = 'stroke="black" stroke-width="0.5" stroke-opacity="1" stroke-dasharray="5, 5"'
	353	self.add_line(file, from_pos, to_pos, style)
	354
	355	def compute_line_style(self, parent, child):
	356	return self.compute_stroke_color('lines', child) + ' ' \
	357	+ self.compute_stroke_width('lines', child) + ' ' \
	358	+ self.compute_stroke_opacity(child)
	359
	360	def compute_dot_style(self, node):
	361	return self.compute_dot_size(node) + ' ' \
	362	+ self.compute_fill_opacity(node) + ' ' \
	363	+ self.compute_dot_fill(node)
	364
	365	def compute_stroke_color(self, part, node):
	366	color = self.compute_property(part, 'color', node)
	367	return 'stroke="rgb(' + str(color[0]) + '%,' + str(color[1]) + '%,' + str(color[2]) + '%)"'
	368
	369	def compute_stroke_width(self, part, node):
	370	return 'stroke-width="' + str(self.compute_property(part, 'width', node)) + '"'
	371
	372	def compute_stroke_opacity(self, node):
	373	return 'stroke-opacity="' + str(self.compute_property('lines', 'opacity', node)) + '"'
	374
	375	def compute_fill_opacity(self, node):
	376	return 'fill-opacity="' + str(self.compute_property('dots', 'opacity', node)) + '"'
	377
	378	def compute_dot_size(self, node):
	379	return 'r="' + str(self.compute_property('dots', 'size', node)) + '"'
	380
	381	def compute_dot_fill(self, node):
	382	color = self.compute_property('dots', 'color', node)
	383	return 'fill="rgb(' + str(color[0]) + '%,' + str(color[1]) + '%,' + str(color[2]) + '%)"'
	384
	385	class Designer:
	386
	387	def __init__(self, tree, jitter=False, time="GENERATIONAL", balance="DENSITY"):
	388	self.props = {}
	389
	390	self.tree = tree
	391
	392	self.TIME = time
	393	self.JITTER = jitter
	394
	395	if balance == "RANDOM":
	396	self.xmin_crowd = self.xmin_crowd_random
	397	elif balance == "MIN":
	398	self.xmin_crowd = self.xmin_crowd_min
	399	elif balance == "DENSITY":
	400	self.xmin_crowd = self.xmin_crowd_density
[562]	401	else:
[624]	402	raise ValueError("Error, the value of BALANCE does not match any expected value.")
[562]	403
[624]	404	def calculate_measures(self):
	405	print("Calculating measures...")
[679]	406	self.compute_depth()
[701]	407	self.compute_maxdepth()
[624]	408	self.compute_adepth()
	409	self.compute_children()
	410	self.compute_kind()
	411	self.compute_time()
[633]	412	self.compute_progress()
[624]	413	self.compute_custom()
[622]	414
[624]	415	def xmin_crowd_random(self, x1, x2, y):
	416	return (x1 if random.randrange(2) == 0 else x2)
[562]	417
[624]	418	def xmin_crowd_min(self, x1, x2, y):
	419	x1_closest = 999999
	420	x2_closest = 999999
	421	miny = y-3
	422	maxy = y+3
	423	i = bisect.bisect_left(self.y_sorted, miny)
	424	while True:
	425	if len(self.positions_sorted) <= i or self.positions_sorted[i]['y'] > maxy:
	426	break
	427	pos = self.positions_sorted[i]
[562]	428
[624]	429	x1_closest = min(x1_closest, abs(x1-pos['x']))
	430	x2_closest = min(x2_closest, abs(x2-pos['x']))
[562]	431
[624]	432	i += 1
	433	return (x1 if x1_closest > x2_closest else x2)
[562]	434
[624]	435	def xmin_crowd_density(self, x1, x2, y):
[690]	436	# TODO experimental - requires further work to make it less 'jumpy' and more predictable
[694]	437	CONST_LOCAL_AREA_RADIUS = 5
	438	CONST_GLOBAL_AREA_RADIUS = 10
	439	CONST_WINDOW_SIZE = 20000 #TODO should depend on the maxY ?
[690]	440	x1_dist_loc = 0
	441	x2_dist_loc = 0
	442	count_loc = 1
	443	x1_dist_glob = 0
	444	x2_dist_glob = 0
	445	count_glob = 1
[694]	446	miny = y-CONST_WINDOW_SIZE
	447	maxy = y+CONST_WINDOW_SIZE
[624]	448	i_left = bisect.bisect_left(self.y_sorted, miny)
	449	i_right = bisect.bisect_right(self.y_sorted, maxy)
[694]	450	#TODO test: maxy=y should give the same results, right?
[562]	451
[624]	452	def include_pos(pos):
[690]	453	nonlocal x1_dist_loc, x2_dist_loc, x1_dist_glob, x2_dist_glob, count_loc, count_glob
[562]	454
[694]	455	dysq = (pos['y']-y)**2 + 1 #+1 so 1/dysq is at most 1
	456	dx1 = math.fabs(pos['x']-x1)
	457	dx2 = math.fabs(pos['x']-x2)
	458
[690]	459	d = math.fabs(pos['x'] - (x1+x2)/2)
[623]	460
[694]	461	if d < CONST_LOCAL_AREA_RADIUS:
	462	x1_dist_loc += math.sqrt(dx1/dysq + dx1**2)
	463	x2_dist_loc += math.sqrt(dx2/dysq + dx2**2)
[690]	464	count_loc += 1
[694]	465	elif d > CONST_GLOBAL_AREA_RADIUS:
	466	x1_dist_glob += math.sqrt(dx1/dysq + dx1**2)
	467	x2_dist_glob += math.sqrt(dx2/dysq + dx2**2)
[690]	468	count_glob += 1
	469
[624]	470	# optimized to draw from all the nodes, if less than 10 nodes in the range
	471	if len(self.positions_sorted) > i_left:
	472	if i_right - i_left < 10:
	473	for j in range(i_left, i_right):
	474	include_pos(self.positions_sorted[j])
	475	else:
	476	for j in range(10):
	477	pos = self.positions_sorted[random.randrange(i_left, i_right)]
	478	include_pos(pos)
[562]	479
[690]	480	return (x1 if (x1_dist_loc-x2_dist_loc)/count_loc-(x1_dist_glob-x2_dist_glob)/count_glob > 0 else x2)
	481	#return (x1 if x1_dist +random.gauss(0, 0.00001) > x2_dist +random.gauss(0, 0.00001) else x2)
[624]	482	#print(x1_dist, x2_dist)
	483	#x1_dist = x1_dist**2
	484	#x2_dist = x2_dist**2
	485	#return x1 if x1_dist+x2_dist==0 else (x1x1_dist + x2x2_dist) / (x1_dist+x2_dist) + random.gauss(0, 0.01)
	486	#return (x1 if random.randint(0, int(x1_dist+x2_dist)) < x1_dist else x2)
[571]	487
[624]	488	def calculate_node_positions(self, ignore_last=0):
	489	print("Calculating positions...")
[562]	490
[624]	491	def add_node(node):
	492	index = bisect.bisect_left(self.y_sorted, node['y'])
	493	self.y_sorted.insert(index, node['y'])
	494	self.positions_sorted.insert(index, node)
	495	self.positions[node['id']] = node
[572]	496
[624]	497	self.positions_sorted = [{'x':0, 'y':0, 'id':0}]
	498	self.y_sorted = [0]
	499	self.positions = [{} for x in range(len(self.tree.parents))]
	500	self.positions[0] = {'x':0, 'y':0, 'id':0}
[572]	501
[677]	502	# order by maximum depth of the parent guarantees that co child is evaluated before its parent
	503	visiting_order = [i for i in range(0, len(self.tree.parents))]
[701]	504	visiting_order = sorted(visiting_order, key=lambda q:\
	505	0 if q == 0 else self.props["maxdepth"][q])
[562]	506
[624]	507	start_time = timelib.time()
[566]	508
[677]	509	# for each child of the current node
[686]	510	for node_counter,child in enumerate(visiting_order, start=1):
[677]	511	# debug info - elapsed time
[685]	512	if node_counter % 100000 == 0:
	513	print("%d%%\t%d\t%g" % (node_counter*100/len(self.tree.parents), node_counter, timelib.time()-start_time))
[677]	514	start_time = timelib.time()
[562]	515
[677]	516	# using normalized adepth
	517	if self.props['adepth'][child] >= ignore_last/self.props['adepth_max']:
[621]	518
[677]	519	ypos = 0
	520	if self.TIME == "BIRTHS":
	521	ypos = child
	522	elif self.TIME == "GENERATIONAL":
	523	# one more than its parent (what if more than one parent?)
[680]	524	ypos = max([self.positions[par]['y'] for par, v in self.tree.parents[child].items()])+1 \
	525	if self.tree.parents[child] else 0
[677]	526	elif self.TIME == "REAL":
	527	ypos = self.tree.time[child]
[621]	528
[677]	529	if len(self.tree.parents[child]) == 1:
	530	# if current_node is the only parent
[687]	531	parent, similarity = [(par, v) for par, v in self.tree.parents[child].items()][0]
[621]	532
[677]	533	if self.JITTER:
[690]	534	dissimilarity = (1-similarity) + random.gauss(0, 0.01) + 0.001
[621]	535	else:
[687]	536	dissimilarity = (1-similarity) + 0.001
[677]	537	add_node({'id':child, 'y':ypos, 'x':
	538	self.xmin_crowd(self.positions[parent]['x']-dissimilarity,
	539	self.positions[parent]['x']+dissimilarity, ypos)})
	540	else:
	541	# position weighted by the degree of inheritence from each parent
	542	total_inheretance = sum([v for k, v in self.tree.parents[child].items()])
	543	xpos = sum([self.positions[k]['x']*v/total_inheretance
	544	for k, v in self.tree.parents[child].items()])
	545	if self.JITTER:
	546	add_node({'id':child, 'y':ypos, 'x':xpos + random.gauss(0, 0.1)})
	547	else:
	548	add_node({'id':child, 'y':ypos, 'x':xpos})
[621]	549
	550
[624]	551	def compute_custom(self):
	552	for prop in self.tree.props:
	553	self.props[prop] = [None for x in range(len(self.tree.children))]
[621]	554
[624]	555	for i in range(len(self.props[prop])):
	556	self.props[prop][i] = self.tree.props[prop][i]
[621]	557
[624]	558	self.normalize_prop(prop)
[562]	559
[624]	560	def compute_time(self):
	561	# simple rewrite from the tree
	562	self.props["time"] = [0 for x in range(len(self.tree.children))]
[562]	563
[624]	564	for i in range(len(self.props['time'])):
	565	self.props['time'][i] = self.tree.time[i]
[572]	566
[624]	567	self.normalize_prop('time')
[617]	568
[624]	569	def compute_kind(self):
	570	# simple rewrite from the tree
	571	self.props["kind"] = [0 for x in range(len(self.tree.children))]
[617]	572
[624]	573	for i in range (len(self.props['kind'])):
	574	self.props['kind'][i] = str(self.tree.kind[i])
[617]	575
[624]	576	def compute_depth(self):
	577	self.props["depth"] = [999999999 for x in range(len(self.tree.children))]
[681]	578	visited = [0 for x in range(len(self.tree.children))]
[617]	579
[624]	580	nodes_to_visit = [0]
[681]	581	visited[0] = 1
[624]	582	self.props["depth"][0] = 0
	583	while True:
[681]	584	current_node = nodes_to_visit[0]
[682]	585
[681]	586	for child in self.tree.children[current_node]:
	587	if visited[child] == 0:
	588	visited[child] = 1
	589	nodes_to_visit.append(child)
	590	self.props["depth"][child] = self.props["depth"][current_node]+1
[624]	591	nodes_to_visit = nodes_to_visit[1:]
	592	if len(nodes_to_visit) == 0:
	593	break
[617]	594
[624]	595	self.normalize_prop('depth')
[617]	596
[701]	597	def compute_maxdepth(self):
	598	self.props["maxdepth"] = [999999999 for x in range(len(self.tree.children))]
	599	visited = [0 for x in range(len(self.tree.children))]
	600
	601	nodes_to_visit = [0]
	602	visited[0] = 1
	603	self.props["maxdepth"][0] = 0
	604	while True:
	605	current_node = nodes_to_visit[0]
	606
	607	for child in self.tree.children[current_node]:
	608	if visited[child] == 0:
	609	visited[child] = 1
	610	nodes_to_visit.append(child)
	611	self.props["maxdepth"][child] = self.props["maxdepth"][current_node]+1
	612	elif self.props["maxdepth"][child] < self.props["maxdepth"][current_node]+1:
	613	self.props["maxdepth"][child] = self.props["maxdepth"][current_node]+1
	614	if child not in nodes_to_visit:
	615	nodes_to_visit.append(child)
	616
	617	nodes_to_visit = nodes_to_visit[1:]
	618	if len(nodes_to_visit) == 0:
	619	break
	620
	621	self.normalize_prop('maxdepth')
	622
[624]	623	def compute_adepth(self):
	624	self.props["adepth"] = [0 for x in range(len(self.tree.children))]
[617]	625
[679]	626	# order by maximum depth of the parent guarantees that co child is evaluated before its parent
	627	visiting_order = [i for i in range(0, len(self.tree.parents))]
[701]	628	visiting_order = sorted(visiting_order, key=lambda q: self.props["maxdepth"][q])[::-1]
[617]	629
[679]	630	for node in visiting_order:
	631	children = self.tree.children[node]
	632	if len(children) != 0:
	633	# 0 by default
	634	self.props["adepth"][node] = max([self.props["adepth"][child] for child in children])+1
[624]	635	self.normalize_prop('adepth')
[594]	636
[624]	637	def compute_children(self):
	638	self.props["children"] = [0 for x in range(len(self.tree.children))]
	639	for i in range (len(self.props['children'])):
	640	self.props['children'][i] = len(self.tree.children[i])
[562]	641
[624]	642	self.normalize_prop('children')
[564]	643
[633]	644	def compute_progress(self):
	645	self.props["progress"] = [0 for x in range(len(self.tree.children))]
	646	for i in range(len(self.props['children'])):
	647	times = sorted([self.props["time"][self.tree.children[i][j]]*100000 for j in range(len(self.tree.children[i]))])
	648	if len(times) > 4:
	649	times = [times[i+1] - times[i] for i in range(len(times)-1)]
	650	#print(times)
	651	slope, intercept, r_value, p_value, std_err = stats.linregress(range(len(times)), times)
	652	self.props['progress'][i] = slope if not np.isnan(slope) and not np.isinf(slope) else 0
	653
	654	for i in range(0, 5):
	655	self.props['progress'][self.props['progress'].index(min(self.props['progress']))] = 0
	656	self.props['progress'][self.props['progress'].index(max(self.props['progress']))] = 0
	657
	658	mini = min(self.props['progress'])
	659	maxi = max(self.props['progress'])
	660	for k in range(len(self.props['progress'])):
	661	if self.props['progress'][k] == 0:
	662	self.props['progress'][k] = mini
	663
	664	#for k in range(len(self.props['progress'])):
	665	# self.props['progress'][k] = 1-self.props['progress'][k]
	666
	667	self.normalize_prop('progress')
	668
[624]	669	def normalize_prop(self, prop):
[678]	670	noneless = [v for v in self.props[prop] if (type(v)!=str and type(v)!=list)]
[624]	671	if len(noneless) > 0:
	672	max_val = max(noneless)
	673	min_val = min(noneless)
[697]	674	print("%s: [%g, %g]" % (prop, min_val, max_val))
[624]	675	self.props[prop +'_max'] = max_val
	676	self.props[prop +'_min'] = min_val
	677	for i in range(len(self.props[prop])):
	678	if self.props[prop][i] is not None:
[633]	679	qqq = self.props[prop][i]
	680	self.props[prop][i] = 0 if max_val == min_val else (self.props[prop][i] - min_val) / (max_val - min_val)
[594]	681
[624]	682	class TreeData:
	683	simple_data = None
[615]	684
[624]	685	children = []
	686	parents = []
	687	time = []
	688	kind = []
[562]	689
[624]	690	def __init__(self): #, simple_data=False):
	691	#self.simple_data = simple_data
	692	pass
[562]	693
[624]	694	def load(self, filename, max_nodes=0):
	695	print("Loading...")
[576]	696
[624]	697	CLI_PREFIX = "Script.Message:"
	698	default_props = ["Time", "FromIDs", "ID", "Operation", "Inherited"]
[576]	699
[707]	700	merged_with_virtual_parent = []
	701
[633]	702	self.ids = {}
[628]	703	def get_id(id, createOnError = True):
	704	if createOnError:
[633]	705	if id not in self.ids:
	706	self.ids[id] = len(self.ids)
[628]	707	else:
[633]	708	if id not in self.ids:
[628]	709	return None
[701]	710
[633]	711	return self.ids[id]
[576]	712
[624]	713	file = open(filename)
[576]	714
[624]	715	# counting the number of expected nodes
	716	nodes = 0
	717	for line in file:
	718	line_arr = line.split(' ', 1)
	719	if len(line_arr) == 2:
	720	if line_arr[0] == CLI_PREFIX:
	721	line_arr = line_arr[1].split(' ', 1)
	722	if line_arr[0] == "[OFFSPRING]":
	723	nodes += 1
[562]	724
[624]	725	nodes = min(nodes, max_nodes if max_nodes != 0 else nodes)+1
	726	self.parents = [{} for x in range(nodes)]
	727	self.children = [[] for x in range(nodes)]
	728	self.time = [0] * nodes
	729	self.kind = [0] * nodes
[628]	730	self.life_lenght = [0] * nodes
[624]	731	self.props = {}
[562]	732
[688]	733	print("nodes: %d" % len(self.parents))
[562]	734
[624]	735	file.seek(0)
	736	loaded_so_far = 0
	737	lasttime = timelib.time()
	738	for line in file:
	739	line_arr = line.split(' ', 1)
	740	if len(line_arr) == 2:
	741	if line_arr[0] == CLI_PREFIX:
	742	line_arr = line_arr[1].split(' ', 1)
	743	if line_arr[0] == "[OFFSPRING]":
[682]	744	try:
	745	creature = json.loads(line_arr[1])
	746	except ValueError:
	747	print("Json format error - the line cannot be read. Breaking the loading loop.")
	748	# fixing arrays by removing the last element
	749	# ! assuming that only the last line is broken !
	750	self.parents.pop()
	751	self.children.pop()
	752	self.time.pop()
	753	self.kind.pop()
	754	self.life_lenght.pop()
	755	nodes -= 1
	756	break
	757
[624]	758	if "FromIDs" in creature:
[562]	759
[624]	760	# make sure that ID's of parents are lower than that of their children
	761	for i in range(0, len(creature["FromIDs"])):
[633]	762	if creature["FromIDs"][i] not in self.ids:
[627]	763	get_id("virtual_parent")
[562]	764
[624]	765	creature_id = get_id(creature["ID"])
	766
	767	# debug
	768	if loaded_so_far%1000 == 0:
	769	#print(". " + str(creature_id) + " " + str(timelib.time() - lasttime))
	770	lasttime = timelib.time()
	771
	772	# we assign to each parent its contribution to the genotype of the child
	773	for i in range(0, len(creature["FromIDs"])):
[633]	774	if creature["FromIDs"][i] in self.ids:
[627]	775	parent_id = get_id(creature["FromIDs"][i])
	776	else:
[707]	777	if creature["FromIDs"][i] not in merged_with_virtual_parent:
	778	merged_with_virtual_parent.append(creature["FromIDs"][i])
[627]	779	parent_id = get_id("virtual_parent")
[687]	780	inherited = (creature["Inherited"][i] if 'Inherited' in creature else 1)
[624]	781	self.parents[creature_id][parent_id] = inherited
	782
	783	if "Time" in creature:
	784	self.time[creature_id] = creature["Time"]
	785
	786	if "Kind" in creature:
	787	self.kind[creature_id] = creature["Kind"]
	788
	789	for prop in creature:
	790	if prop not in default_props:
	791	if prop not in self.props:
[628]	792	self.props[prop] = [0 for i in range(nodes)]
[624]	793	self.props[prop][creature_id] = creature[prop]
	794
	795	loaded_so_far += 1
	796	else:
	797	raise LoadingError("[OFFSPRING] misses the 'FromIDs' field!")
[628]	798	if line_arr[0] == "[DIED]":
	799	creature = json.loads(line_arr[1])
	800	creature_id = get_id(creature["ID"], False)
	801	if creature_id is not None:
	802	for prop in creature:
	803	if prop not in default_props:
	804	if prop not in self.props:
	805	self.props[prop] = [0 for i in range(nodes)]
	806	self.props[prop][creature_id] = creature[prop]
[624]	807
[628]	808
[624]	809	if loaded_so_far >= max_nodes and max_nodes != 0:
	810	break
	811
[707]	812	print("WARNING: merging individuals: " + str(merged_with_virtual_parent) + " with a virtual parent node!")
	813
[624]	814	for k in range(len(self.parents)):
	815	v = self.parents[k]
	816	for val in self.parents[k]:
	817	self.children[val].append(k)
	818
[562]	819	depth = {}
[577]	820	kind = {}
[562]	821
	822	def main():
	823
[624]	824	parser = argparse.ArgumentParser(description='Draws a genealogical tree (generates a SVG file) based on parent-child relationship '
	825	'information from a text file. Supports files generated by Framsticks experiments.')
[615]	826	parser.add_argument('-i', '--in', dest='input', required=True, help='input file name with stuctured evolutionary data')
[624]	827	parser.add_argument('-o', '--out', dest='output', required=True, help='output file name for the evolutionary tree (SVG/PNG/JPG/BMP)')
	828	parser.add_argument('-c', '--config', dest='config', default="", help='config file name ')
[562]	829
[624]	830	parser.add_argument('-W', '--width', default=600, type=int, dest='width', help='width of the output image (600 by default)')
[626]	831	parser.add_argument('-H', '--height', default=800, type=int, dest='height', help='height of the output image (800 by default)')
	832	parser.add_argument('-m', '--multi', default=1, type=int, dest='multi', help='multisampling factor (applicable only for raster images)')
[562]	833
[620]	834	parser.add_argument('-t', '--time', default='GENERATIONAL', dest='time', help='values on vertical axis (BIRTHS/GENERATIONAL(d)/REAL); '
[614]	835	'BIRTHS: time measured as the number of births since the beginning; '
[571]	836	'GENERATIONAL: time measured as number of ancestors; '
	837	'REAL: real time of the simulation')
[620]	838	parser.add_argument('-b', '--balance', default='DENSITY', dest='balance', help='method of placing nodes in the tree (RANDOM/MIN/DENSITY(d))')
[624]	839	parser.add_argument('-s', '--scale', default='SIMPLE', dest='scale', help='type of timescale added to the tree (NONE(d)/SIMPLE)')
[571]	840	parser.add_argument('-j', '--jitter', dest="jitter", action='store_true', help='draw horizontal positions of children from the normal distribution')
[624]	841	parser.add_argument('-p', '--skip', dest="skip", type=int, default=0, help='skip last P levels of the tree (0 by default)')
	842	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]	843	parser.add_argument('--seed', type=int, dest='seed', help='seed for the random number generator (-1 for random)')
	844
	845	parser.set_defaults(draw_tree=True)
	846	parser.set_defaults(draw_skeleton=False)
	847	parser.set_defaults(draw_spine=False)
	848
	849	parser.set_defaults(seed=-1)
	850
	851	args = parser.parse_args()
	852
[620]	853	TIME = args.time.upper()
	854	BALANCE = args.balance.upper()
	855	SCALE = args.scale.upper()
[571]	856	JITTER = args.jitter
[620]	857	if not TIME in ['BIRTHS', 'GENERATIONAL', 'REAL']\
	858	or not BALANCE in ['RANDOM', 'MIN', 'DENSITY']\
	859	or not SCALE in ['NONE', 'SIMPLE']:
[683]	860	print("Incorrect value of one of the parameters! (time or balance or scale).") #user has to figure out which parameter is wrong...
[620]	861	return
[562]	862
	863	dir = args.input
	864	seed = args.seed
	865	if seed == -1:
	866	seed = random.randint(0, 10000)
	867	random.seed(seed)
[689]	868	print("randomseed:", seed)
[562]	869
[624]	870	tree = TreeData()
	871	tree.load(dir, max_nodes=args.max_nodes)
[562]	872
[682]	873
[624]	874	designer = Designer(tree, jitter=JITTER, time=TIME, balance=BALANCE)
	875	designer.calculate_measures()
	876	designer.calculate_node_positions(ignore_last=args.skip)
[562]	877
[624]	878	if args.output.endswith(".svg"):
	879	drawer = SvgDrawer(designer, args.config, w=args.width, h=args.height)
	880	else:
	881	drawer = PngDrawer(designer, args.config, w=args.width, h=args.height)
[626]	882	drawer.draw_design(args.output, args.input, multi=args.multi, scale=SCALE)
[562]	883
	884
	885	main()

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