update readout script for toxicity analysis

demos/0_demo/JuPedSim/readout_toxicity.py

@@ -3,80 +3,58 @@ import numpy as np
 import xml.etree.ElementTree as ET
 import math
 
+def label(quantity):
+	if quantity == 'E':
+		return 'Extinction Coefficient (1/m)'
+	if quantity == 'FED_In':
+		return 'FED Incapacitation'
+
+	#todo:
+	#"CO2 concentration (ppm)","CO concentration (ppm)",
+	#"HCN concentration (ppm)", "HCl concentration (ppm)", "FED Heat Dose",
+	#"FEC Smoke", "FIC Impairment", "FIC Incapacitation"
+
+########## change here ##########
+#number of agents
+N = 50 #todo: parse from traj.xml
+# possible quantities are: 'E','c_CO2','c_CO','c_HCl','c_HCN','FED_In','FEC_Smoke','FED_Heat','FIC_Im','FED_In'
+quantity_select = 'E'
+#################################
+
 ### traj XML readin
 tree = ET.parse('toxicity_output_jpsfire.xml')
 root = tree.getroot()
 
-### empty arrays
-t = E = co2 = co = hcn = hcl = fed_in = fec_smoke = fed_heat = fic_im = fic_in = np.array([])
-
 ### readout
+data = []
 for frame in root.iter('frame'):
     frame_id = int(frame.get('ID'))
     for agent in frame.iter('agent'):
-    	agent_id = int(agent.get('ID')) # todo: is it necessary to plot agent specifically
-    	t = np.append(t, float(agent.get('t')))
-    	E = np.append(E, float(agent.get('E')))
-    	co2 = np.append(co2, float(agent.get('c_CO2')))
-    	co = np.append(co, float(agent.get('c_CO')))
-    	hcl = np.append(hcl, float(agent.get('c_HCl')))
-    	hcn = np.append(hcn, float(agent.get('c_HCN')))
-    	fed_in = np.append(fed_in, float(agent.get('FED_In')))
-    	fec_smoke = np.append(fec_smoke, float(agent.get('FEC_Smoke')))
-    	fed_heat = np.append(fed_heat, float(agent.get('FED_Heat')))
-    	fic_im = np.append(fic_im, float(agent.get('FIC_Im')))
-    	fic_in = np.append(fic_in, float(agent.get('FED_In')))
-
-### prepare for plotting
-values = [E, co2, co, hcn, hcl, fed_in, fed_heat, fec_smoke, fic_im, fic_in]
-labels = ["Extinction Coefficient (1/m)", "CO2 concentration (ppm)","CO concentration (ppm)",
- 			"HCN concentration (ppm)", "HCl concentration (ppm)", "FED Incapacitation", "FED Heat Dose",
- 			"FEC Smoke", "FIC Impairment", "FIC Incapacitation"]
-units = ["1/m", "ppm", "ppm", "ppm", "ppm", "","","",""]
-
-max_values = []
-
-for i in values:
-	max_values.append(max(i))
-	i[i==0] = float('nan')
-
-### extinction plot
-
-plt.plot(t, E, 'bx')
+    	agent_id = int(agent.get('ID'))
+    	t = float(agent.get('t'))
+    	quantity = float(agent.get('%s' % quantity_select))
+    	data += [agent_id, t, quantity]
+data = np.array(data).reshape((-1, 3))
+
+for i in range(1,N+1):
+	
+	ids_all = data[:,0]
+	time_all = data[:,1]
+	quantity_all = data[:,2]
+
+	time_max = np.max(time_all)
+	quantity_max = np.max(quantity_all)
+
+	if i == 1:
+		plt.plot(time_all[ids_all==1], quantity_all[ids_all==1], 'b', lw=2, label = 'agent time series')
+	plt.plot(time_all[ids_all==i], quantity_all[ids_all==i], 'b', lw=2, zorder=1)
+#plt.plot([0,time_max], [1, 1], "r--", lw=2.5, label='%s threshold' %quantity_select) #threshold
+plt.plot([0,time_max], [quantity_max, quantity_max], "k--", lw=2.5, label=r'%s max.' %quantity_select)
+plt.xlabel("time [s]")
+plt.ylabel("%s" % label(quantity_select))
+plt.xlim(50) # mean premovement time
+plt.ticklabel_format(style='sci', axis='y', scilimits=(0,0))
+plt.ylim()
+plt.legend(loc=0)
+plt.savefig('toxicity_output_plot_%s.png' % quantity_select, dpi=400)
+plt.show()
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-plt.plot([0,max(t)], [max_values[0], max_values[0]], 'r-', label='max = %.2f %s' % (max_values[0], units[0]))
-plt.xlabel("Time")
-plt.ylabel(labels[0])
-plt.ylim(0)
-plt.legend()
-plt.savefig('toxicity_output_plot_0_extinction.png')
-plt.close()
-
-### concentration plot
-plt.figure(figsize=(12,9))
-
-for i in range(1,5):
-	plt.subplot(2,2,i)
-	plt.plot(t, values[i], 'bx')
-	plt.plot([0,max(t)], [max_values[i], max_values[i]], 'r-', label='max = %.2f %s' % (max_values[i], units[i]))
-	plt.xlabel("Time")
-	plt.ylabel(labels[i])
-	plt.ylim(0)
-	plt.legend()
-
-plt.savefig('toxicity_output_plot_1_concentrations.png')
-plt.close()
-
-plt.figure(figsize=(12,9))
-values2 = [fed_in, fec_smoke, fed_heat, fic_im, fic_in]
-
-for j in range(5,9):
-	plt.subplot(2,2,j-4)
-	plt.plot(t, values[j], 'bx')
-	plt.plot([0,max(t)], [max_values[j], max_values[j]], 'r-', label='max = %.3f %s' % (max_values[j], units[j]))
-	plt.xlabel("Time")
-	plt.ylabel(labels[j])
-	plt.ylim(0)
-	plt.legend()
-
-plt.savefig('toxicity_output_plot_2_FED_FEC_FIC.png')
-plt.close()
\ No newline at end of file