Index: /mds-and-trees/tree-genealogy.py
===================================================================
--- /mds-and-trees/tree-genealogy.py	(revision 562)
+++ /mds-and-trees/tree-genealogy.py	(revision 562)
@@ -0,0 +1,314 @@
+# Draws a genealogical tree (generates a SVG file) based on parent-child relationship information.
+
+import json
+import random
+import math
+import argparse
+
+TIME = "GENERATIONAL"
+BALANCE = "MIN"
+
+# ------SVG---------
+svg_file = 0
+
+svg_line_style = 'stroke="rgb(90%,10%,16%)" stroke-width="1" stroke-opacity="0.8"'
+svg_dot_style = 'r="2" stroke="black" stroke-width="0.2" fill="red"'
+svg_spine_line_style = 'stroke="rgb(0%,0%,80%)" stroke-width="2" stroke-opacity="1"'
+#svg_spine_dot_style = 'r="3" stroke="black" stroke-width="0.4" fill="rgb(50%,50%,100%)"'
+svg_spine_dot_style = 'r="1" stroke="black" stroke-width="0.2" fill="rgb(50%,50%,100%)"'
+
+def svg_add_line(from_pos, to_pos, style=svg_line_style):
+    svg_file.write('<line ' + style + ' x1="' + str(from_pos[0]) + '" x2="' + str(to_pos[0]) + '" y1="' + str(from_pos[1]) + '" y2="' + str(to_pos[1]) + '" />')
+
+def svg_add_dot(pos, style=svg_dot_style):
+    svg_file.write('<circle ' + style + ' cx="' + str(pos[0]) + '" cy="' + str(pos[1]) + '" />')
+
+def svg_generate_line_style(percent):
+    from_col = [100, 70, 0]
+    to_col = [100, 0, 0]
+    # from_col = [0, 100, 50]
+    # to_col = [20, 0, 100]
+
+    percent = 1 - ((1-percent)**10)
+
+    return 'stroke="rgb(' + str(from_col[0]*(1-percent) + to_col[0]*percent) + '%,' \
+           + str(from_col[1]*(1-percent) + to_col[1]*percent) + '%,' \
+           + str(from_col[2]*(1-percent) + to_col[2]*percent) + '%)" stroke-width="1" stroke-opacity="0.8"'
+
+def svg_generate_dot_style(percent):
+    from_col = [100, 90, 0]
+    to_col = [100, 0, 0]
+    # from_col = [0, 100, 50]
+    # to_col = [20, 0, 100]
+
+    percent = 1 - ((1-percent)**10)
+
+    return 'fill="rgb(' + str(from_col[0]*(1-percent) + to_col[0]*percent) + '%,' \
+           + str(from_col[1]*(1-percent) + to_col[1]*percent) + '%,' \
+           + str(from_col[2]*(1-percent) + to_col[2]*percent) + '%)" r="1.5" stroke="black" stroke-width="0.2"' #fill-opacity="0.5"'
+
+# -------------------
+
+def load_data(dir):
+    global firstnode, nodes, inv_nodes
+    f = open(dir)
+    for line in f:
+        sline = line.split(' ', 2)
+        if len(sline) == 3:
+            if sline[1] == "[CLONE]" or sline[1] == "[MUTANT]":
+                creature = json.loads(sline[2])
+                #print("B" +str(creature))
+                if "FromID" in creature:
+                    nodes[creature["ToID"]] = creature["FromID"]
+                    if not creature["FromID"] in nodes:
+                        firstnode = creature["FromID"]
+
+    for k, v in sorted(nodes.items()):
+        inv_nodes[v] = inv_nodes.get(v, [])
+        inv_nodes[v].append(k)
+
+
+def load_simple_data(dir):
+    global firstnode, nodes, inv_nodes
+    f = open(dir)
+    for line in f:
+        sline = line.split()
+        if len(sline) > 1:
+            #if int(sline[0]) > 15000:
+            #    break
+            if sline[0] == firstnode:
+                continue
+            nodes[sline[0]] = str(max(int(sline[1]), int(firstnode)))
+        else:
+            firstnode = sline[0]
+
+    for k, v in sorted(nodes.items()):
+        inv_nodes[v] = inv_nodes.get(v, [])
+        inv_nodes[v].append(k)
+
+    #print(str(inv_nodes))
+    #quit()
+
+def compute_depth(node):
+    my_depth = 0
+    if node in inv_nodes:
+        for c in inv_nodes[node]:
+            my_depth = max(my_depth, compute_depth(c)+1)
+    depth[node] = my_depth
+    return my_depth
+
+# ------------------------------------
+
+def xmin_crowd(x1, x2, y):
+    if BALANCE == "RANDOM":
+        return (x1 if random.randrange(2) == 0 else x2)
+    elif BALANCE == "MIN":
+        x1_closest = 999999
+        x2_closest = 999999
+        for pos in positions:
+            pos = positions[pos]
+            if pos[1] == y:
+                x1_closest = min(x1_closest, abs(x1-pos[0]))
+                x2_closest = min(x2_closest, abs(x2-pos[0]))
+        return (x1 if x1_closest > x2_closest else x2)
+    elif BALANCE == "DENSITY":
+        x1_dist = 0
+        x2_dist = 0
+        for pos in positions:
+            pos = positions[pos]
+            if pos[1] > y-10 or pos[1] < y+10:
+                dy = pos[1]-y
+                dx1 = pos[0]-x1
+                dx2 = pos[0]-x2
+
+                x1_dist += math.sqrt(dy**2 + dx1**2)
+                x2_dist += math.sqrt(dy**2 + dx2**2)
+        return (x1 if x1_dist > x2_dist else x2)
+
+# ------------------------------------
+
+def prepos_children_reccurent(node):
+    for c in inv_nodes[node]:
+        #print(node + "->" + c)
+        dissimilarity = random.gauss(0,0.3)
+        if TIME == "REAL":
+            id = ""
+            if c[0] == "c":
+                id = int(c[1:])
+            else:
+                id = int(c)
+            positions[c] = [xmin_crowd(positions[node][0]-dissimilarity, positions[node][0]+dissimilarity, id), id]
+        elif TIME == "GENERATIONAL":
+            positions[c] = [xmin_crowd(positions[node][0]-dissimilarity, positions[node][0]+dissimilarity, positions[node][1]+1), positions[node][1]+1]
+
+    for c in inv_nodes[node]:
+        if c in inv_nodes:
+            prepos_children_reccurent(c)
+
+def prepos_children():
+    global max_height, max_width, min_width
+
+    positions[firstnode] = [0, 0]
+
+    prepos_children_reccurent(firstnode)
+
+    for pos in positions:
+        max_height = max(max_height, positions[pos][1])
+        max_width = max(max_width, positions[pos][0])
+        min_width = min(min_width, positions[pos][0])
+
+# ------------------------------------
+
+def draw_children_recurrent(node, max_depth):
+    global max_height, max_width, min_width
+    for c in inv_nodes[node]:
+        if c in inv_nodes:
+            draw_children_recurrent(c, max_depth)
+        svg_add_line( (w_margin+w_no_margs*(positions[node][0]-min_width)/(max_width-min_width), h_margin+h_no_margs*positions[node][1]/max_height),
+            (w_margin+w_no_margs*(positions[c][0]-min_width)/(max_width-min_width), h_margin+h_no_margs*positions[c][1]/max_height),
+                      (svg_line_style if args.mono_tree else svg_generate_line_style(depth[c]/max_depth)))
+        svg_add_dot( (w_margin+w_no_margs*(positions[c][0]-min_width)/(max_width-min_width), h_margin+h_no_margs*positions[c][1]/max_height),
+                     (svg_dot_style if args.mono_tree else svg_generate_dot_style(depth[c]/max_depth)))
+def draw_children():
+    max_depth = 0
+    for k, v in depth.items():
+            max_depth = max(max_depth, v)
+    draw_children_recurrent(firstnode, max_depth)
+    svg_add_dot( (w_margin+w_no_margs*(positions[firstnode][0]-min_width)/(max_width-min_width), h_margin+h_no_margs*positions[firstnode][1]/max_height),
+                 (svg_dot_style if args.mono_tree else svg_generate_dot_style(depth[firstnode]/max_depth)))
+
+def draw_spine_recurrent(node):
+    global max_height, max_width, min_width
+    for c in inv_nodes[node]:
+        if depth[c] == depth[node] - 1:
+            if c in inv_nodes:
+                draw_spine_recurrent(c)
+            svg_add_line( (w_margin+w_no_margs*(positions[node][0]-min_width)/(max_width-min_width), h_margin+h_no_margs*positions[node][1]/max_height),
+                (w_margin+w_no_margs*(positions[c][0]-min_width)/(max_width-min_width), h_margin+h_no_margs*positions[c][1]/max_height), svg_spine_line_style)
+            #svg_add_dot( (w_margin+w_no_margs*(positions[c][0]-min_width)/(max_width-min_width), h_margin+h_no_margs*positions[c][1]/max_height), svg_spine_dot_style)
+def draw_spine():
+    draw_spine_recurrent(firstnode)
+    #svg_add_dot( (w_margin+w_no_margs*(positions[firstnode][0]-min_width)/(max_width-min_width), h_margin+h_no_margs*positions[firstnode][1]/max_height), svg_spine_dot_style)
+
+def draw_skeleton_reccurent(node, max_depth):
+    global max_height, max_width, min_width
+    for c in inv_nodes[node]:
+        if depth[c] >= min_skeleton_depth or depth[c] == max([depth[q] for q in inv_nodes[node]]):
+            if c in inv_nodes:
+                draw_skeleton_reccurent(c, max_depth)
+            svg_add_line( (w_margin+w_no_margs*(positions[node][0]-min_width)/(max_width-min_width), h_margin+h_no_margs*positions[node][1]/max_height),
+                (w_margin+w_no_margs*(positions[c][0]-min_width)/(max_width-min_width), h_margin+h_no_margs*positions[c][1]/max_height),
+                          svg_spine_line_style)
+            #svg_add_dot( (w_margin+w_no_margs*(positions[c][0]-min_width)/(max_width-min_width), h_margin+h_no_margs*positions[c][1]/max_height),
+            #             svg_spine_dot_style)
+def draw_skeleton():
+    max_depth = 0
+    for k, v in depth.items():
+            max_depth = max(max_depth, v)
+
+    draw_skeleton_reccurent(firstnode, max_depth)
+    #svg_add_dot( (w_margin+w_no_margs*(positions[firstnode][0]-min_width)/(max_width-min_width), h_margin+h_no_margs*positions[firstnode][1]/max_height),
+    #             svg_spine_dot_style)
+
+
+
+
+##################################################### main #####################################################
+
+args = 0
+
+h = 800
+w = 600
+h_margin = 10
+w_margin = 10
+h_no_margs = h - 2* h_margin
+w_no_margs = w - 2* w_margin
+
+max_height = 0
+max_width = 0
+min_width = 9999999999
+
+min_skeleton_depth = 0
+
+firstnode = ""
+nodes = {}
+inv_nodes = {}
+positions = {}
+depth = {}
+
+def main():
+    global svg_file, min_skeleton_depth, args, TIME, BALANCE
+
+    parser = argparse.ArgumentParser(description='Process some integers.')
+    parser.add_argument('--in', dest='input', required=True, help='input file with stuctured evolutionary data')
+    parser.add_argument('--out', dest='output', required=True, help='output file for the evolutionary tree')
+    draw_tree_parser = parser.add_mutually_exclusive_group(required=False)
+    draw_tree_parser.add_argument('--draw-tree', dest='draw_tree', action='store_true', help='whether drawing the full tree should be skipped')
+    draw_tree_parser.add_argument('--no-draw-tree', dest='draw_tree', action='store_false')
+
+    draw_skeleton_parser = parser.add_mutually_exclusive_group(required=False)
+    draw_skeleton_parser.add_argument('--draw-skeleton', dest='draw_skeleton', action='store_true', help='whether the skeleton of the tree should be drawn')
+    draw_skeleton_parser.add_argument('--no-draw-skeleton', dest='draw_skeleton', action='store_false')
+
+    draw_spine_parser = parser.add_mutually_exclusive_group(required=False)
+    draw_spine_parser.add_argument('--draw-spine', dest='draw_spine', action='store_true', help='whether the spine of the tree should be drawn')
+    draw_spine_parser.add_argument('--no-draw-spine', dest='draw_spine', action='store_false')
+
+    #TODO: better names for those parameters
+    parser.add_argument('--time', default='REAL', dest='time', help='values on vertical axis (REAL/GENERATIONAL)')
+    parser.add_argument('--balance', default='MIN',dest='balance', help='method of placing node in the tree (RANDOM/MIN/DENSITY)')
+
+    mono_tree_parser = parser.add_mutually_exclusive_group(required=False)
+    mono_tree_parser.add_argument('--mono-tree', dest='mono_tree', action='store_true', help='whether the tree should be drawn with a single color')
+    mono_tree_parser.add_argument('--no-mono-tree', dest='mono_tree', action='store_false')
+
+    parser.add_argument('--min-skeleton-depth', type=int, default=2, dest='min_skeleton_depth', help='minimal distance from the leafs for the nodes in the skeleton')
+    parser.add_argument('--seed', type=int, dest='seed', help='seed for the random number generator (-1 for random)')
+
+    parser.add_argument('--simple-data', type=bool, dest='simple_data', help='input data are given in a simple format (#child #parent)')
+
+    parser.set_defaults(mono_tree=False)
+    parser.set_defaults(draw_tree=True)
+    parser.set_defaults(draw_skeleton=False)
+    parser.set_defaults(draw_spine=False)
+
+    parser.set_defaults(seed=-1)
+
+    args = parser.parse_args()
+
+    TIME = args.time
+    BALANCE = args.balance
+
+    dir = args.input
+    min_skeleton_depth = args.min_skeleton_depth
+    seed = args.seed
+    if seed == -1:
+        seed = random.randint(0, 10000)
+    random.seed(seed)
+    print("seed:", seed)
+
+    if args.simple_data:
+        load_simple_data(dir)
+    else:
+        load_data(dir)
+
+    compute_depth(firstnode)
+
+    svg_file = open(args.output, "w")
+    svg_file.write('<svg xmlns:svg="http://www.w3.org/2000/svg" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" version="1.0" '
+                   'width="' + str(w) + '" height="' + str(h) + '">')
+
+    prepos_children()
+
+    if args.draw_tree:
+        draw_children()
+    if args.draw_skeleton:
+        draw_skeleton()
+    if args.draw_spine:
+        draw_spine()
+
+    svg_file.write("</svg>")
+    svg_file.close()
+
+main()
+
