add graph-based traversal density

analyzers/__init__.py

@@ -9,7 +9,7 @@ from .analyzer.locomotion import LocomotionActionAnalyzer, CacheSequenceAnalyzer
 from .analyzer.mask import MaskSpatials
 from .render import Render
 from .render.biogames import SimulationRoundsRender, BoardDurationHistRender, BoardDurationBoxRender, \
-	ActivityMapperRender, StoreRender, SimulationOrderRender
+	ActivityMapperRender, StoreRender, SimulationOrderRender, SimulationGroupRender
 from .render.default import PrintRender, JSONRender, TrackRender, HeatMapRender
 from .render.locomotion import LocomotionActionRelativeRender, LocomotionActionAbsoluteRender, \
 	LocomotionActionRatioRender
@@ -49,7 +49,8 @@ __MAPPING__ = {
 	],
 	SimulationOrderAnalyzer: [
 		JSONRender,
-SimulationOrderRender
+#SimulationOrderRender,
+SimulationGroupRender
 	]
 }
 

analyzers/render/biogames.py

@@ -4,22 +4,73 @@ from typing import List, Tuple
 
 import matplotlib.pyplot as plt
 import os
+import numpy as np
+from scipy.interpolate import interp1d
+import networkx as nx
+import itertools
 
 from analyzers import Store, BiogamesStore, SimulationOrderAnalyzer
 from . import Render
 from .. import Result, SimulationRoundsAnalyzer, BoardDurationAnalyzer, ActivityMapper
 
+def add_edge(graph, src, dest):
+	if graph.has_edge(src, dest):
+		weight = graph.get_edge_data(src, dest)['weight'] + 1
+	else:
+		weight = 1
+	graph.add_edge(tuple(src),tuple(dest),weight=weight)
+
+def pairs(iterable):
+	a,b = itertools.tee(iterable)
+	next(b,None)
+	return zip(a,b)
 
 def plot(src_data: List[Tuple[str, List[int]]], ylabel="simulation rounds", title="simulation retries",
          rotation='vertical'):
 	names, datas = list(zip(*src_data))
-	plt.boxplot(datas, labels=names)
+	#plt.boxplot(datas, labels=names, showfliers=False, showmeans=True, meanline=True)
+	rand = np.random.rand(len(datas),len(datas[0]))
+	plt.plot(datas+rand, linewidth=.2)
 	plt.xticks(rotation=rotation)
 	# plt.margins()
 	plt.ylabel(ylabel)
 	plt.title(title)
 	plt.show()
 
+def graph_plot(src_data: List[Tuple[str, List[int]]], ylabel="simulation rounds", title="sequential simulation retries",
+         rotation='vertical'):
+	g = nx.Graph()
+	for group in src_data:
+		for i in pairs(enumerate(group)):
+			add_edge(g, i[0], i[1])
+	positions = {}
+	for node in g.nodes():
+		positions[node] = node
+	widths = [x[2]/10.0 for x in g.edges.data('weight')]
+	print(max(widths))
+	nx.draw_networkx_edges(g, positions, width=widths)
+	#rand = np.random.rand(len(datas),len(datas[0]))
+	#plt.plot(datas+rand, linewidth=.2)
+	plt.xticks(rotation=rotation)
+	# plt.margins()
+	plt.ylabel(ylabel)
+	plt.title(title)
+	plt.show()
+
+def graph_fit(src_data, deg=5):
+	plt.title("polyfit(x,y,deg="+str(deg)+")")
+	for i in src_data:
+		#plt.plot(i)
+		count = len(i)
+		xp = np.linspace(0, count-1, num=count, endpoint=True)
+		#fit = np.poly1d(np.polyfit(range(len(i)), i, deg=deg))
+		#plt.plot(xp, fit(xp), linewidth=0.1)
+		xnew = np.linspace(0, count-1, num=count*20, endpoint=True)
+		f = interp1d(xp, i, kind='quadratic')
+		
+		plt.plot(range(count), i, '.', markersize=1)
+		plt.plot(xnew, f(xnew), linewidth=0.2)
+	plt.show()
 
 class SimulationRoundsRender(Render):
 	def render(self, results: List[Result]):
@@ -101,4 +152,13 @@ class SimulationOrderRender(Render):
 		#plot(enumerate([r.get() for r in self.filter(results)]))
 		plot(list(data.items()), ylabel="simulation retries", title="sequential simulation retries", rotation=None)
 
+	result_types = [SimulationOrderAnalyzer]
+
+
+class SimulationGroupRender(Render):
+	def render(self, results: List[Result]):
+		data = [r.get() for r in self.filter(results)]
+		#graph_plot(list(data), ylabel="simulation retries", title="sequential simulation retries", rotation=None)
+		graph_fit(list(data))
+
 	result_types = [SimulationOrderAnalyzer]

biogames2.json

@@ -68,8 +68,8 @@
     "type": "Biogames",
     "url": "http://0.0.0.0:5000/game2/instance/log/list/",
     "login_url": "http://localhost:5000/game2/auth/json-login",
-    "username": "dev",
-    "password": "dev",
+    "username": "ba",
+    "password": "853451",
     "host":"http://0.0.0.0:5000"
   }
 }

log_analyzer.py

@@ -17,6 +17,7 @@ requests_log.setLevel(logging.WARN)
 
 def process_log(log_id: str, settings: LogSettings) -> List[Analyzer]:
 	logfile: str = "data/inst_{id}.{format}".format(id=log_id, format=settings.log_format)
+	logfile = log_id
 	loader = LOADERS[settings.log_format]()
 	try:
 		loader.load(logfile)
@@ -54,6 +55,11 @@ if __name__ == '__main__':
 		#	"fe1331481f85560681f86827ec",
 			"fe1331481f85560681f86827ec"]
 		#"fec57041458e6cef98652df625", ]
+	log_ids = []
+	with open("/home/clemens/git/ma/test/filtered") as src:
+		for line in src:
+			line = line.strip()
+			log_ids.append(line)
 	store: ResultStore = ResultStore()
 	for log_id in log_ids:
 		for analysis in process_log(log_id, settings):

static/progress/my.js

@@ -1,11 +1,11 @@
 $.getJSON("tmp3.json", function (data) {
     var list = $("<ul />");
     var maps = {};
-    $.each(data, function (key, value) {
+    $.each(data, function (index, entry) {
         //key: instance_id, value: AnlysisResult
         //value.result.instance: InstanceConfig_id
         // console.log(key, value[0].result.store[0].timestamp);
-        $.each(value[0].result.store, function (index, entry) {
+        //$.each(value[0].result.store, function (index, entry) {
             //console.log(entry);
             var time = new Date(entry.timestamp);
             var item = $("<li>", {html: entry.sequence + " @ " + time.toLocaleDateString() + " "+ time.toLocaleTimeString()});
@@ -44,7 +44,7 @@ $.getJSON("tmp3.json", function (data) {
             });
             container.appendTo(item);
             item.appendTo(list);
-        });
+        //});
     });
     list.appendTo("body");
     var slider = $("<input />", {type: "range" })