_lib/ow_utils.py

@@ -137,7 +137,7 @@ def appendDayPhase(casefile, outFn = None, sepType = ','):
 		with open(outfn, mode='w', newline ='') as out_file:
 			fieldnames = reader.fieldnames#'bl_admission bl_ucstartday bl_costartday bl_crstartday bl_restartday bl_lastknownstatus bl_duration_inpatientstay'.split(' ') # bl_duration_icustay bl_duration_ventilation bl_observationalperiod
 
-			writer = csv.DictWriter(out_file, delimiter=',', quotechar='"', quoting=csv.QUOTE_MINIMAL, fieldnames=fieldnames+'ci_d10 ci_d20 ci_death'.split(' '))
+			writer = csv.DictWriter(out_file, delimiter=',', quotechar='"', quoting=csv.QUOTE_MINIMAL, fieldnames=fieldnames+'ci_d5 ci_d10 ci_d20 ci_death'.split(' '))
 			writer.writeheader()
 			
 			for row in reader:
@@ -152,7 +152,7 @@ def appendDayPhase(casefile, outFn = None, sepType = ','):
 					
 					#out['ci_d0'] = getPhase(row, 0)
 					#out['ci_d1'] = getPhase(row, 1)
-					#out['ci_d5'] = getPhase(row, 5)
+					out['ci_d5'] = getPhase(row, 5)
 					out['ci_d10'] = getPhase(row, 10)
 					out['ci_d20'] = getPhase(row, 20)
 					out['ci_death'] = getDeath(row)

run_all.py

@@ -222,40 +222,52 @@ def addCalculatedFields(row):
 	
 	phase10 = row[f'ci_d10']
 	phase20 = row[f'ci_d20']
+	phase5 = row[f'ci_d5']
 	
 	row[f'ci_death_day10'] = row['ci_death'] == row['ci_d10'] if row['ci_death'] != '*' else '*'
 	row[f'ci_death_day20'] = row['ci_death'] == row['ci_d20'] if row['ci_death'] != '*' else '*'
+	row[f'ci_death_day5'] = row['ci_death'] == row['ci_d5'] if row['ci_death'] != '*' else '*'
 	
 	row[f'ci_hypoxaemia_day10'] = row[f'ci_hypoxaemia_{phase10}']
 	row[f'ci_hypoxaemia_day20'] = row[f'ci_hypoxaemia_{phase20}']
+	row[f'ci_hypoxaemia_day5'] = row[f'ci_hypoxaemia_{phase5}']
 				
 	row[f'ci_cardiac_output_day10'] = row[f'ci_cardiac_output_{phase10}']
 	row[f'ci_cardiac_output_day20'] = row[f'ci_cardiac_output_{phase20}']
+	row[f'ci_cardiac_output_day5'] = row[f'ci_cardiac_output_{phase5}']
 	
 	row[f'ci_coagulation_day10'] = row[f'ci_coagulation_{phase10}']
 	row[f'ci_coagulation_day20'] = row[f'ci_coagulation_{phase20}']
+	row[f'ci_coagulation_day5'] = row[f'ci_coagulation_{phase5}']
 	
 	row[f'ci_intravas_volume_day10'] = row[f'ci_intravas_volume_{phase10}']
 	row[f'ci_intravas_volume_day20'] = row[f'ci_intravas_volume_{phase20}']
+	row[f'ci_intravas_volume_day5'] = row[f'ci_intravas_volume_{phase5}']
 	
 	row[f'ci_end_organ_perf_day10'] = row[f'ci_end_organ_perf_{phase10}']
 	row[f'ci_end_organ_perf_day20'] = row[f'ci_end_organ_perf_{phase20}']
+	row[f'ci_end_organ_perf_day5'] = row[f'ci_end_organ_perf_{phase5}']
 	
 	row[f'ci_sys_immune_resp_day10'] = row[f'ci_sys_immune_resp_{phase10}']
 	row[f'ci_sys_immune_resp_day20'] = row[f'ci_sys_immune_resp_{phase20}']
+	row[f'ci_sys_immune_resp_day5'] = row[f'ci_sys_immune_resp_{phase5}']
 	
 	
 	row[f'ci_ventilator_day10'] = row[f'ci_ventilator_{phase10}']
 	row[f'ci_ventilator_day20'] = row[f'ci_ventilator_{phase20}']
+	row[f'ci_ventilator_day5'] = row[f'ci_ventilator_{phase5}']
 	
 	row[f'ci_antiviral_treat_day10'] = row[f'ci_antiviral_treat_{phase10}']
 	row[f'ci_antiviral_treat_day20'] = row[f'ci_antiviral_treat_{phase20}']
+	row[f'ci_antiviral_treat_day5'] = row[f'ci_antiviral_treat_{phase5}']
 	
 	row[f'ci_anticoag_treat_day10'] = row[f'ci_anticoag_treat_{phase10}']
 	row[f'ci_anticoag_treat_day20'] = row[f'ci_anticoag_treat_{phase20}']
+	row[f'ci_anticoag_treat_day5'] = row[f'ci_anticoag_treat_{phase5}']
 	
 	row[f'ci_antiinflam_treat_day10'] = row[f'ci_antiinflam_treat_{phase10}']	
 	row[f'ci_antiinflam_treat_day20'] = row[f'ci_antiinflam_treat_{phase20}']		
+	row[f'ci_antiinflam_treat_day5'] = row[f'ci_antiinflam_treat_{phase5}']		
 
 
 # Clean data
@@ -396,11 +408,19 @@ def doMakeBnSafe():
 scripts = [
 	clean,
 	doMakeBnSafe,
+	
+	'make_respiratory.py',
+	['validations.py', 'respiratory'],
+	
+	['validations.py', 'progressionPrevious'],
+	
 	['make_progression.py', 'nolatent'],
+	['validations.py', 'progressionNoLatent'],
 	['make_progression.py', 'latent'],
-	'make_nb.py',
-	'make_respiratory.py',
-	'validations.py',
+	['validations.py', 'progressionLatent'],
+	
+	# 'make_nb.py',
+	# 'validations.py',
 	
 	## Old/inactive
 	# 'make_structures.py',

validations.py

-import _env, csv, math, random, json, bni_netica, time, re, traceback
+import _env, csv, math, random, json, bni_netica, time, re, traceback, sys
 from bni_smile import Net
 
+toRun = None
+if len(sys.argv)>1:
+	toRun = sys.argv[1:]
+
 def openNet(fn):
 	return Net(fn)
 	# if re.search(r'\.dne', fn):
@@ -138,6 +142,30 @@ def readData(csvFn, shuffle = False):
 		
 		return data
 
+def validateScenarios(outJsonFn, netFns, data, subsets, targets, targetPosStates):
+	cachedNets = {fn:openNet(fn) for fn in netFns}
+	
+	allResults = {}
+	for subsetName, subset in subsets.items():
+		for netFn in netFns:
+			#net = Net(netFn)
+			net = cachedNets[netFn]
+			resultsKey = f'{netFn} - {subsetName}'
+			print(resultsKey)
+			try:
+				res, targetDistros = validate(net, data, targets, targetPosStates, subset = subset)
+				allResults[resultsKey] = {'res':res,'targetDistros':targetDistros}
+				print(json.dumps(res, indent='\t'))
+			except:
+				print('Error, skipping')
+				traceback.print_exc()
+	
+		# Update file after every subset
+		with open(f'bns/{outJsonFn}', 'w') as resultsFile:
+			resultsFile.write(json.dumps(allResults))
+			
+
+
 def doValidations():
 	data = readData('data/LEOSS_encoded_data_clean_bnsafe.csv')
 	netFns = [
@@ -198,27 +226,9 @@ def doValidations():
 	'All': None,
 	}
 	
-	cachedNets = {fn:openNet(fn) for fn in netFns}
+	if not toRun or 'nbtan' in toRun:
+		validateScenarios('results_nbtan.json', netFns, data, subsets, targets, targetPosStates)
 	
-	allResults = {}
-	for subsetName, subset in subsets.items():
-		for netFn in netFns:
-			#net = Net(netFn)
-			net = cachedNets[netFn]
-			resultsKey = f'{netFn} - {subsetName}'
-			print(resultsKey)
-			try:
-				res, targetDistros = validate(net, data, targets, targetPosStates, subset = subset)
-				allResults[resultsKey] = {'res':res,'targetDistros':targetDistros}
-				print(json.dumps(res, indent='\t'))
-			except:
-				print('Error, skipping')
-				traceback.print_exc()
-	
-		# Update file after every subset
-		with open('bns/results.json', 'w') as resultsFile:
-			resultsFile.write(json.dumps(allResults))
-			
 	data = readData('data/respiratory.csv')
 	netFns = [
 		'bns/respiratory/resp2_obsStructure2.dne.trained.dne',
@@ -235,23 +245,68 @@ def doValidations():
 		'All': None
 	}
 	
-	#allResults = {}
-	for subsetName, subset in subsets.items():
-		for netFn in netFns:
-			net = bni_netica.Net(netFn)
-			resultsKey = f'{netFn} - {subsetName}'
-			print(resultsKey)
-			try:
-				res, targetDistros = validate(net, data, targets, targetPosStates, subset)
-				allResults[resultsKey] = {'res':res,'targetDistros':targetDistros}
-				print(json.dumps(res, indent='\t'))
-			except Exception as e:
-				print('Error, skipping', e)
-				traceback.print_exc()
+	if not toRun or 'respiratory' in toRun:
+		validateScenarios('results_respiratory.json', netFns, data, subsets, targets, targetPosStates)
+	
+	background = ['ci_age_group_bg', 'ci_gender_bg', 'ci_metabolic_syndrome_bg', 'ci_smoking_history_bg', 'ci_diabetes_bg', 'ci_chronic_pul_disease_bg', 'ci_chronic_cardiac_disease_bg']
+	baseline = ['ci_antiviral_treat_bl', 'ci_sys_immune_resp_bl', 'ci_antiinflam_treat_bl', 'func_vas_bl', 'ci_coagulation_bl', 'ci_end_organ_perf_bl', 'func_pul_bl', 'ci_ventilator_bl', 'ci_hypoxaemia_bl', 'ci_intravas_volume_bl', 'func_car_bl', 'ci_anticoag_treat_bl', 'ci_cardiac_output_bl']
+	
+	data = readData('data/LEOSS_encoded_data_clean_trim.csv')
+	netFns = [
+		'bns/progression/previous_progression.trained.xdsl',
+		'bns/progression/previous_progression_latent.trained.xdsl',
+	]
+	targets = ['ci_death_day5', 'ci_cardiac_output_day5','ci_hypoxaemia_day5','ci_sys_immune_resp_day5']
+	targetPosStates = [1, 0, 0, 2]
+	subsets = {
+		'background': background,
+		'background+baseline': background+baseline,
+		'All': None
+	}
+	
+	if not toRun or 'progressionPrevious' in toRun:
+		validateScenarios('results_progression.json', netFns, data, subsets, targets, targetPosStates)
+	
+	
+	
+	
+	data = readData('data/LEOSS_encoded_data_clean_trim.csv')
+	netFns = [
+		'bns/progression/progression_day10.trained.xdsl',
+	]
+	targets = ['ci_death_day10', 'ci_cardiac_output_day10','ci_hypoxaemia_day10','ci_sys_immune_resp_day10']
+	targetPosStates = [1, 0, 0, 2]
+	subsets = {
+		'background': background,
+		'background+baseline': background+baseline,
+		'All': None
+	}
+	
+	if not toRun or 'progressionNoLatent' in toRun:
+		validateScenarios('results_progressionNoLatent.json', netFns, data, subsets, targets, targetPosStates)
+	netFns = [
+		'bns/progression/progression_latent_day10.trained.xdsl',
+	]
+	if not toRun or 'progressionLatent' in toRun:
+		validateScenarios('results_progressionLatent.json', netFns, data, subsets, targets, targetPosStates)
+
+	# #allResults = {}
+	# for subsetName, subset in subsets.items():
+		# for netFn in netFns:
+			# net = bni_netica.Net(netFn)
+			# resultsKey = f'{netFn} - {subsetName}'
+			# print(resultsKey)
+			# try:
+				# res, targetDistros = validate(net, data, targets, targetPosStates, subset)
+				# allResults[resultsKey] = {'res':res,'targetDistros':targetDistros}
+				# print(json.dumps(res, indent='\t'))
+			# except Exception as e:
+				# print('Error, skipping', e)
+				# traceback.print_exc()
 				
-		# Update file after every subset
-		with open('bns/results.json', 'w') as resultsFile:
-			resultsFile.write(json.dumps(allResults))
+		# # Update file after every subset
+		# with open('bns/results.json', 'w') as resultsFile:
+			# resultsFile.write(json.dumps(allResults))
 			
 	
 doValidations()
\ No newline at end of file