def main(argv):
# Get command line stuff and store in a dictionary
s='verbose sumfile= indir= input_globs= tslice= nPC= sigMul= minPCFail= minRunFail= numRunFile= printVarTest popens jsonfile= mpi_enable nbin= minrange= maxrange= outfile= casejson= npick= pepsi_gm test_failure pop_tol= pop_threshold='
optkeys = s.split()
try:
opts, args = getopt.getopt(argv,"h",optkeys)
except getopt.GetoptError:
pyEnsLib.CECT_usage()
sys.exit(2)
# Set the default value for options
opts_dict = {}
opts_dict['input_globs'] = ''
opts_dict['indir'] = ''
opts_dict['tslice'] = 1
opts_dict['nPC'] = 50
opts_dict['sigMul'] = 2
opts_dict['verbose'] = False
opts_dict['minPCFail'] = 3
opts_dict['minRunFail'] = 2
opts_dict['numRunFile'] = 3
opts_dict['printVarTest'] = False
opts_dict['popens'] = False
opts_dict['jsonfile'] = ''
opts_dict['mpi_enable'] = False
opts_dict['nbin'] = 40
opts_dict['minrange'] = 0.0
opts_dict['maxrange'] = 4.0
opts_dict['outfile'] = 'testcase.result'
opts_dict['casejson'] = ''
opts_dict['npick'] = 10
opts_dict['pepsi_gm'] = False
opts_dict['test_failure'] = True
opts_dict['pop_tol'] = 3.0
opts_dict['pop_threshold'] = 0.90
# Call utility library getopt_parseconfig to parse the option keys
# and save to the dictionary
caller = 'CECT'
gmonly = False
opts_dict = pyEnsLib.getopt_parseconfig(opts,optkeys,caller,opts_dict)
popens = opts_dict['popens']
# Print out timestamp, input ensemble file and new run directory
dt=datetime.now()
verbose = opts_dict['verbose']
print('--------pyCECT--------')
print(' ')
print(dt.strftime("%A, %d. %B %Y %I:%M%p"))
print(' ')
print('Ensemble summary file = '+opts_dict['sumfile'])
print(' ')
print('Testcase file directory = '+opts_dict['indir'] )
print(' ')
print(' ')
# Create a mpi simplecomm object
if opts_dict['mpi_enable']:
me=simplecomm.create_comm()
else:
me=simplecomm.create_comm(not opts_dict['mpi_enable'])
ifiles=[]
in_files=[]
# Random pick pop files from not_pick_files list
if opts_dict['casejson']:
with open(opts_dict['casejson']) as fin:
result=json.load(fin)
in_files_first=result['not_pick_files']
in_files=random.sample(in_files_first,opts_dict['npick'])
print('Testcase files:')
print('\n'.join(in_files))
else:
wildname='*'+opts_dict['input_globs']+'*'
# Open all input files
if (os.path.exists(opts_dict['indir'])):
full_glob_str=os.path.join(opts_dict['indir'],wildname)
glob_files=glob.glob(full_glob_str)
in_files.extend(glob_files)
#in_files_temp=os.listdir(opts_dict['indir'])
in_files.sort()
if popens:
#Partition the input file list
in_files_list=me.partition(in_files,func=EqualStride(),involved=True)
else:
# Random pick non pop files
in_files_list=pyEnsLib.Random_pickup(in_files,opts_dict)
for frun_file in in_files_list:
if frun_file.find(opts_dict['indir']) != -1:
frun_temp=frun_file
else:
frun_temp=opts_dict['indir']+'/'+frun_file
if (os.path.isfile(frun_temp)):
ifiles.append(Nio.open_file(frun_temp,"r"))
else:
print("COULD NOT LOCATE FILE " +frun_temp+" EXISTING")
sys.exit()
if popens:
# Read in the included var list
Var2d,Var3d=pyEnsLib.read_jsonlist(opts_dict['jsonfile'],'ESP')
print(' ')
print('Z-score tolerance = '+'{:3.2f}'.format(opts_dict['pop_tol']))
print('ZPR = '+'{:.2%}'.format(opts_dict['pop_threshold']))
zmall,n_timeslice=pyEnsLib.compare_raw_score(opts_dict,ifiles,me.get_rank(),Var3d,Var2d)
#zmall = np.concatenate((Zscore3d,Zscore2d),axis=0)
np.set_printoptions(threshold=np.nan)
if opts_dict['mpi_enable']:
zmall = pyEnsLib.gather_npArray_pop(zmall,me,(me.get_size(),len(Var3d)+len(Var2d),len(ifiles),opts_dict['nbin']))
if me.get_rank()==0:
fout = open(opts_dict['outfile'],"w")
for i in range(me.get_size()):
for j in zmall[i]:
np.savetxt(fout,j,fmt='%-7.2e')
else:
# Read all variables from the ensemble summary file
ens_var_name,ens_avg,ens_stddev,ens_rmsz,ens_gm,num_3d,mu_gm,sigma_gm,loadings_gm,sigma_scores_gm,is_SE_sum=pyEnsLib.read_ensemble_summary(opts_dict['sumfile'])
if len(ens_rmsz) == 0:
gmonly = True
# Add ensemble rmsz and global mean to the dictionary "variables"
variables={}
if not gmonly:
for k,v in ens_rmsz.iteritems():
pyEnsLib.addvariables(variables,k,'zscoreRange',v)
for k,v in ens_gm.iteritems():
pyEnsLib.addvariables(variables,k,'gmRange',v)
# Get 3d variable name list and 2d variable name list seperately
var_name3d=[]
var_name2d=[]
for vcount,v in enumerate(ens_var_name):
if vcount < num_3d:
var_name3d.append(v)
else:
var_name2d.append(v)
# Get ncol and nlev value
npts3d,npts2d,is_SE=pyEnsLib.get_ncol_nlev(ifiles[0])
if (is_SE ^ is_SE_sum):
print('Warning: please note the ensemble summary file is different from the testing files, they use different grids')
# Compare the new run and the ensemble summary file to get rmsz score
results={}
countzscore=np.zeros(len(ifiles),dtype=np.int32)
countgm=np.zeros(len(ifiles),dtype=np.int32)
if not gmonly:
for fcount,fid in enumerate(ifiles):
otimeSeries = fid.variables
for var_name in ens_var_name:
orig=otimeSeries[var_name]
Zscore,has_zscore=pyEnsLib.calculate_raw_score(var_name,orig[opts_dict['tslice']],npts3d,npts2d,ens_avg,ens_stddev,is_SE,opts_dict,0,0,0)
if has_zscore:
# Add the new run rmsz zscore to the dictionary "results"
pyEnsLib.addresults(results,'zscore',Zscore,var_name,'f'+str(fcount))
# Evaluate the new run rmsz score if is in the range of the ensemble summary rmsz zscore range
for fcount,fid in enumerate(ifiles):
countzscore[fcount]=pyEnsLib.evaluatestatus('zscore','zscoreRange',variables,'ens',results,'f'+str(fcount))
# Calculate the new run global mean
mean3d,mean2d=pyEnsLib.generate_global_mean_for_summary(ifiles,var_name3d,var_name2d,is_SE,opts_dict['pepsi_gm'],opts_dict)
means=np.concatenate((mean3d,mean2d),axis=0)
# Add the new run global mean to the dictionary "results"
for i in range(means.shape[1]):
for j in range(means.shape[0]):
pyEnsLib.addresults(results,'means',means[j][i],ens_var_name[j],'f'+str(i))
# Evaluate the new run global mean if it is in the range of the ensemble summary global mean range
for fcount,fid in enumerate(ifiles):
countgm[fcount]=pyEnsLib.evaluatestatus('means','gmRange',variables,'gm',results,'f'+str(fcount))
# Calculate the PCA scores of the new run
new_scores=pyEnsLib.standardized(means,mu_gm,sigma_gm,loadings_gm)
pyEnsLib.comparePCAscores(ifiles,new_scores,sigma_scores_gm,opts_dict)
# Print out
if opts_dict['printVarTest']:
print('*********************************************** ')
print('Variable-based testing (for reference only - not used to determine pass/fail)')
print('*********************************************** ')
for fcount,fid in enumerate(ifiles):
print(' ')
print('Run '+str(fcount+1)+":")
print(' ')
if not gmonly:
print('***'+str(countzscore[fcount])," of "+str(len(ens_var_name))+' variables are outside of ensemble RMSZ distribution***')
pyEnsLib.printsummary(results,'ens','zscore','zscoreRange',(fcount),variables,'RMSZ')
print(' ')
print('***'+str(countgm[fcount])," of "+str(len(ens_var_name))+' variables are outside of ensemble global mean distribution***')
pyEnsLib.printsummary(results,'gm','means','gmRange',fcount,variables,'global mean')
print(' ')
print('----------------------------------------------------------------------------')
if __name__ == "__main__":
main(sys.argv[1:])
print(' ')
print("Testing complete.")
def main(argv):
# Get command line stuff and store in a dictionary
s = 'verbose sumfile= indir= timeslice= nPC= sigMul= minPCFail= minRunFail= numRunFile= printVarTest'
optkeys = s.split()
try:
opts, args = getopt.getopt(argv, "h", optkeys)
except getopt.GetoptError:
pyEnsLib.CECT_usage()
sys.exit(2)
# Set the default value for options
opts_dict = {}
opts_dict['timeslice'] = 1
opts_dict['nPC'] = 50
opts_dict['sigMul'] = 2
opts_dict['verbose'] = False
opts_dict['minPCFail'] = 3
opts_dict['minRunFail'] = 2
opts_dict['numRunFile'] = 3
opts_dict['printVarTest'] = False
# Call utility library getopt_parseconfig to parse the option keys
# and save to the dictionary
caller = 'CECT'
gmonly = False
opts_dict = pyEnsLib.getopt_parseconfig(opts, optkeys, caller, opts_dict)
# Print out timestamp, input ensemble file and new run directory
dt = datetime.now()
verbose = opts_dict['verbose']
print '--------pyCECT--------'
print ' '
print dt.strftime("%A, %d. %B %Y %I:%M%p")
print ' '
print 'Ensemble summary file = ' + opts_dict['sumfile']
print ' '
print 'Cam output directory = ' + opts_dict['indir']
print ' '
print ' '
# Open all input files
ifiles = []
in_files_temp = os.listdir(opts_dict['indir'])
in_files = sorted(in_files_temp)
in_files_random = pyEnsLib.Random_pickup(in_files, opts_dict)
for frun_file in in_files_random:
if (os.path.isfile(opts_dict['indir'] + '/' + frun_file)):
ifiles.append(
Nio.open_file(opts_dict['indir'] + '/' + frun_file, "r"))
else:
print "COULD NOT LOCATE FILE " + opts_dict[
'indir'] + frun_file + " EXISTING"
sys.exit()
# Read all variables from the ensemble summary file
ens_var_name, ens_avg, ens_stddev, ens_rmsz, ens_gm, num_3d, mu_gm, sigma_gm, loadings_gm, sigma_scores_gm = pyEnsLib.read_ensemble_summary(
opts_dict['sumfile'])
if len(ens_rmsz) == 0:
gmonly = True
# Add ensemble rmsz and global mean to the dictionary "variables"
variables = {}
if not gmonly:
for k, v in ens_rmsz.iteritems():
pyEnsLib.addvariables(variables, k, 'zscoreRange', v)
for k, v in ens_gm.iteritems():
pyEnsLib.addvariables(variables, k, 'gmRange', v)
# Get 3d variable name list and 2d variable name list seperately
var_name3d = []
var_name2d = []
for vcount, v in enumerate(ens_var_name):
if vcount < num_3d:
var_name3d.append(v)
else:
var_name2d.append(v)
# Get ncol and nlev value
npts3d, npts2d, is_SE = pyEnsLib.get_ncol_nlev(ifiles[0])
# Compare the new run and the ensemble summary file to get rmsz score
results = {}
countzscore = np.zeros(len(ifiles), dtype=np.int32)
countgm = np.zeros(len(ifiles), dtype=np.int32)
if not gmonly:
for fcount, fid in enumerate(ifiles):
otimeSeries = fid.variables
for var_name in ens_var_name:
orig = otimeSeries[var_name]
Zscore, has_zscore = pyEnsLib.calculate_raw_score(
var_name, orig[opts_dict['timeslice']], npts3d, npts2d,
ens_avg, ens_stddev, is_SE)
if has_zscore:
# Add the new run rmsz zscore to the dictionary "results"
pyEnsLib.addresults(results, 'zscore', Zscore, var_name,
'f' + str(fcount))
# Evaluate the new run rmsz score if is in the range of the ensemble summary rmsz zscore range
for fcount, fid in enumerate(ifiles):
countzscore[fcount] = pyEnsLib.evaluatestatus(
'zscore', 'zscoreRange', variables, 'ens', results,
'f' + str(fcount))
# Calculate the new run global mean
mean3d, mean2d = pyEnsLib.generate_global_mean_for_summary(
ifiles, var_name3d, var_name2d, opts_dict['timeslice'], is_SE, verbose)
means = np.concatenate((mean3d, mean2d), axis=0)
# Add the new run global mean to the dictionary "results"
for i in range(means.shape[1]):
for j in range(means.shape[0]):
pyEnsLib.addresults(results, 'means', means[j][i], ens_var_name[j],
'f' + str(i))
# Evaluate the new run global mean if it is in the range of the ensemble summary global mean range
for fcount, fid in enumerate(ifiles):
countgm[fcount] = pyEnsLib.evaluatestatus('means', 'gmRange',
variables, 'gm', results,
'f' + str(fcount))
# Calculate the PCA scores of the new run
new_scores = pyEnsLib.standardized(means, mu_gm, sigma_gm, loadings_gm)
pyEnsLib.comparePCAscores(ifiles, new_scores, sigma_scores_gm, opts_dict)
# Print out
if opts_dict['printVarTest']:
print '*********************************************** '
print 'Variable-based testing (for reference only - not used to determine pass/fail)'
print '*********************************************** '
for fcount, fid in enumerate(ifiles):
print ' '
print 'Run ' + str(fcount + 1) + ":"
print ' '
if not gmonly:
print '***' + str(countzscore[fcount]), " of " + str(
len(ens_var_name)
) + ' variables are outside of ensemble RMSZ distribution***'
pyEnsLib.printsummary(results, 'ens', 'zscore', 'zscoreRange',
(fcount), variables, 'RMSZ')
print ' '
print '***' + str(countgm[fcount]), " of " + str(
len(ens_var_name)
) + ' variables are outside of ensemble global mean distribution***'
pyEnsLib.printsummary(results, 'gm', 'means', 'gmRange', fcount,
variables, 'global mean')
print ' '
print '----------------------------------------------------------------------------'
def main(argv):
# Get command line stuff and store in a dictionary
s = """verbose sumfile= indir= input_globs= tslice= nPC= sigMul=
minPCFail= minRunFail= numRunFile= printVarTest popens
jsonfile= mpi_enable nbin= minrange= maxrange= outfile=
casejson= npick= pepsi_gm pop_tol= web_enabled
pop_threshold= prn_std_mean fIndex= lev= eet= json_case= """
optkeys = s.split()
try:
opts, args = getopt.getopt(argv, "h", optkeys)
except getopt.GetoptError:
pyEnsLib.CECT_usage()
sys.exit(2)
# Set the default value for options
opts_dict = {}
opts_dict['input_globs'] = ''
opts_dict['indir'] = ''
opts_dict['tslice'] = 1
opts_dict['nPC'] = 50
opts_dict['sigMul'] = 2
opts_dict['verbose'] = False
opts_dict['minPCFail'] = 3
opts_dict['minRunFail'] = 2
opts_dict['numRunFile'] = 3
opts_dict['printVarTest'] = False
opts_dict['popens'] = False
opts_dict['jsonfile'] = ''
opts_dict['mpi_enable'] = False
opts_dict['nbin'] = 40
opts_dict['minrange'] = 0.0
opts_dict['maxrange'] = 4.0
opts_dict['outfile'] = 'testcase.result'
opts_dict['casejson'] = ''
opts_dict['npick'] = 10
opts_dict['pepsi_gm'] = False
opts_dict['test_failure'] = True
opts_dict['pop_tol'] = 3.0
opts_dict['pop_threshold'] = 0.90
opts_dict['prn_std_mean'] = False
opts_dict['lev'] = 0
opts_dict['eet'] = 0
opts_dict['json_case'] = ''
opts_dict['sumfile'] = ''
opts_dict['web_enabled'] = False
# Call utility library getopt_parseconfig to parse the option keys
# and save to the dictionary
caller = 'CECT'
gmonly = False
opts_dict = pyEnsLib.getopt_parseconfig(opts, optkeys, caller, opts_dict)
popens = opts_dict['popens']
#some mods for POP-ECT
if popens == True:
opts_dict['tslice'] = 0
opts_dict['numRunFile'] = 1
opts_dict['eet'] = 0
opts_dict['mpi_enable'] = False
#print opts_dict
# Create a mpi simplecomm object
if opts_dict['mpi_enable']:
me = simplecomm.create_comm()
else:
me = simplecomm.create_comm(not opts_dict['mpi_enable'])
# Print out timestamp, input ensemble file and new run directory
dt = datetime.now()
verbose = opts_dict['verbose']
if me.get_rank() == 0:
print '--------pyCECT--------'
print ' '
print dt.strftime("%A, %d. %B %Y %I:%M%p")
print ' '
if not opts_dict['web_enabled']:
print 'Ensemble summary file = ' + opts_dict['sumfile']
print ' '
print 'Testcase file directory = ' + opts_dict['indir']
print ' '
print ' '
# Ensure sensible EET value
if opts_dict['eet'] and opts_dict['numRunFile'] > opts_dict['eet']:
pyEnsLib.CECT_usage()
sys.exit(2)
ifiles = []
in_files = []
# Random pick pop files from not_pick_files list
if opts_dict['casejson']:
with open(opts_dict['casejson']) as fin:
result = json.load(fin)
in_files_first = result['not_pick_files']
in_files = random.sample(in_files_first, opts_dict['npick'])
print 'Testcase files:'
print '\n'.join(in_files)
elif opts_dict['json_case']:
json_file = opts_dict['json_case']
if (os.path.exists(json_file)):
fd = open(json_file)
metainfo = json.load(fd)
if 'CaseName' in metainfo:
casename = metainfo['CaseName']
if (os.path.exists(opts_dict['indir'])):
for name in casename:
wildname = '*.' + name + '.*'
full_glob_str = os.path.join(opts_dict['indir'],
wildname)
glob_file = glob.glob(full_glob_str)
in_files.extend(glob_file)
else:
print "ERROR: " + opts_dict['json_case'] + " does not exist."
sys.exit()
print "in_files=", in_files
else:
wildname = '*' + str(opts_dict['input_globs']) + '*'
# Open all input files
if (os.path.exists(opts_dict['indir'])):
full_glob_str = os.path.join(opts_dict['indir'], wildname)
glob_files = glob.glob(full_glob_str)
in_files.extend(glob_files)
num_file = len(in_files)
if num_file == 0:
print "ERROR: no matching files for wildcard=" + wildname + " found in specified --indir"
sys.exit()
else:
print "Found " + str(
num_file) + " matching files in specified --indir"
if opts_dict['numRunFile'] > num_file:
print "ERROR: more files needed (" + str(
opts_dict['numRunFile']
) + ") than available in the indir (" + str(num_file) + ")."
sys.exit()
#in_files_temp=os.listdir(opts_dict['indir'])
in_files.sort()
#print in_files
if popens:
#Partition the input file list
in_files_list = me.partition(in_files,
func=EqualStride(),
involved=True)
else:
# Random pick non pop files
in_files_list = pyEnsLib.Random_pickup(in_files, opts_dict)
#in_files_list=in_files
for frun_file in in_files_list:
if frun_file.find(opts_dict['indir']) != -1:
frun_temp = frun_file
else:
frun_temp = opts_dict['indir'] + '/' + frun_file
if (os.path.isfile(frun_temp)):
ifiles.append(Nio.open_file(frun_temp, "r"))
else:
print "ERROR: COULD NOT LOCATE FILE " + frun_temp
sys.exit()
if opts_dict['web_enabled']:
if len(opts_dict['sumfile']) == 0:
opts_dict[
'sumfile'] = '/glade/p/cesmdata/cseg/inputdata/validation/'
opts_dict['sumfile'], machineid, compiler = pyEnsLib.search_sumfile(
opts_dict, ifiles)
if len(machineid) != 0 and len(compiler) != 0:
print ' '
print 'Validation file : machineid = ' + machineid + ', compiler = ' + compiler
print 'Found summary file : ' + opts_dict['sumfile']
print ' '
else:
print 'Warning: machine and compiler are unknown'
if popens:
# Read in the included var list
if not os.path.exists(opts_dict['jsonfile']):
print "ERROR: POP-ECT requires the specification of a valid json file via --jsonfile."
sys.exit()
Var2d, Var3d = pyEnsLib.read_jsonlist(opts_dict['jsonfile'], 'ESP')
print ' '
print 'Z-score tolerance = ' + '{:3.2f}'.format(opts_dict['pop_tol'])
print 'ZPR = ' + '{:.2%}'.format(opts_dict['pop_threshold'])
zmall, n_timeslice = pyEnsLib.pop_compare_raw_score(
opts_dict, ifiles, me.get_rank(), Var3d, Var2d)
#zmall = np.concatenate((Zscore3d,Zscore2d),axis=0)
np.set_printoptions(threshold=np.nan)
if opts_dict['mpi_enable']:
zmall = pyEnsLib.gather_npArray_pop(
zmall, me, (me.get_size(), len(Var3d) + len(Var2d),
len(ifiles), opts_dict['nbin']))
if me.get_rank() == 0:
fout = open(opts_dict['outfile'], "w")
for i in range(me.get_size()):
for j in zmall[i]:
np.savetxt(fout, j, fmt='%-7.2e')
#cam
else:
# Read all variables from the ensemble summary file
ens_var_name, ens_avg, ens_stddev, ens_rmsz, ens_gm, num_3d, mu_gm, sigma_gm, loadings_gm, sigma_scores_gm, is_SE_sum, std_gm = pyEnsLib.read_ensemble_summary(
opts_dict['sumfile'])
if len(ens_rmsz) == 0:
gmonly = True
# Add ensemble rmsz and global mean to the dictionary "variables"
variables = {}
if not gmonly:
for k, v in ens_rmsz.iteritems():
pyEnsLib.addvariables(variables, k, 'zscoreRange', v)
for k, v in ens_gm.iteritems():
pyEnsLib.addvariables(variables, k, 'gmRange', v)
# Get 3d variable name list and 2d variable name list separately
var_name3d = []
var_name2d = []
for vcount, v in enumerate(ens_var_name):
if vcount < num_3d:
var_name3d.append(v)
else:
var_name2d.append(v)
# Get ncol and nlev value
npts3d, npts2d, is_SE = pyEnsLib.get_ncol_nlev(ifiles[0])
if (is_SE ^ is_SE_sum):
print 'Warning: please note the ensemble summary file is different from the testing files, they use different grids'
# Compare the new run and the ensemble summary file to get rmsz score
results = {}
countzscore = np.zeros(len(ifiles), dtype=np.int32)
countgm = np.zeros(len(ifiles), dtype=np.int32)
if not gmonly:
for fcount, fid in enumerate(ifiles):
otimeSeries = fid.variables
for var_name in ens_var_name:
orig = otimeSeries[var_name]
Zscore, has_zscore = pyEnsLib.calculate_raw_score(
var_name, orig[opts_dict['tslice']], npts3d, npts2d,
ens_avg, ens_stddev, is_SE, opts_dict, 0, 0, 0)
if has_zscore:
# Add the new run rmsz zscore to the dictionary "results"
pyEnsLib.addresults(results, 'zscore', Zscore,
var_name, 'f' + str(fcount))
# Evaluate the new run rmsz score if is in the range of the ensemble summary rmsz zscore range
for fcount, fid in enumerate(ifiles):
countzscore[fcount] = pyEnsLib.evaluatestatus(
'zscore', 'zscoreRange', variables, 'ens', results,
'f' + str(fcount))
# Calculate the new run global mean
mean3d, mean2d, varlist = pyEnsLib.generate_global_mean_for_summary(
ifiles, var_name3d, var_name2d, is_SE, opts_dict['pepsi_gm'],
opts_dict)
means = np.concatenate((mean3d, mean2d), axis=0)
# Add the new run global mean to the dictionary "results"
for i in range(means.shape[1]):
for j in range(means.shape[0]):
pyEnsLib.addresults(results, 'means', means[j][i],
ens_var_name[j], 'f' + str(i))
# Evaluate the new run global mean if it is in the range of the ensemble summary global mean range
for fcount, fid in enumerate(ifiles):
countgm[fcount] = pyEnsLib.evaluatestatus('means', 'gmRange',
variables, 'gm', results,
'f' + str(fcount))
# Calculate the PCA scores of the new run
new_scores, var_list, comp_std_gm = pyEnsLib.standardized(
means, mu_gm, sigma_gm, loadings_gm, ens_var_name, opts_dict,
ens_avg, me)
run_index, decision = pyEnsLib.comparePCAscores(
ifiles, new_scores, sigma_scores_gm, opts_dict, me)
# If there is failure, plot out standardized mean and compared standardized mean in box plots
if opts_dict['prn_std_mean'] and decision == 'FAILED':
import seaborn as sns
category = {
"all_outside99": [],
"two_outside99": [],
"one_outside99": [],
"all_oneside_outside1QR": []
}
b = list(pyEnsLib.chunk(ens_var_name, 10))
for f, alist in enumerate(b):
for fc, avar in enumerate(alist):
dist_995 = np.percentile(std_gm[avar], 99.5)
dist_75 = np.percentile(std_gm[avar], 75)
dist_25 = np.percentile(std_gm[avar], 25)
dist_05 = np.percentile(std_gm[avar], 0.5)
c = 0
d = 0
p = 0
q = 0
for i in range(comp_std_gm[f + fc].size):
if comp_std_gm[f + fc][i] > dist_995:
c = c + 1
elif comp_std_gm[f + fc][i] < dist_05:
d = d + 1
elif (comp_std_gm[f + fc][i] < dist_995
and comp_std_gm[f + fc][i] > dist_75):
p = p + 1
elif (comp_std_gm[f + fc][i] > dist_05
and comp_std_gm[f + fc][i] < dist_25):
q = q + 1
if c == 3 or d == 3:
category["all_outside99"].append((avar, f + fc))
elif c == 2 or d == 2:
category["two_outside99"].append((avar, f + fc))
elif c == 1 or d == 1:
category["one_outside99"].append((avar, f + fc))
if p == 3 or q == 3:
category["all_oneside_outside1QR"].append(
(avar, f + fc))
part_name = opts_dict['indir'].split('/')[-1]
if not part_name:
part_name = opts_dict['indir'].split('/')[-2]
for key in sorted(category):
list_array = []
list_array2 = []
list_var = []
value = category[key]
print "value len=", key, len(value)
for each_var in value:
list_array.append(std_gm[each_var[0]])
list_array2.append(comp_std_gm[each_var[1]])
list_var.append(each_var[0])
if len(value) != 0:
ax = sns.boxplot(data=list_array,
whis=[0.5, 99.5],
fliersize=0.0)
sns.stripplot(data=list_array2, jitter=True, color="r")
sns.plt.xticks(range(len(list_array)),
list_var,
fontsize=8,
rotation=-45)
if decision == 'FAILED':
sns.plt.savefig(part_name + "_" + key + "_fail.png")
else:
sns.plt.savefig(part_name + "_" + key + "_pass.png")
sns.plt.clf()
'''
if len(run_index)>0:
json_file=opts_dict['json_case']
if (os.path.exists(json_file)):
fd=open(json_file)
metainfo=json.load(fd)
caseindex=metainfo['CaseIndex']
enspath=str(metainfo['EnsPath'][0])
#print caseindex
if (os.path.exists(enspath)):
i=0
comp_file=[]
search = '\.[0-9]{3}\.'
for name in in_files_list:
s=re.search(search,name)
in_files_index=s.group(0)
if in_files_index[1:4] in caseindex:
ens_index=str(caseindex[in_files_index[1:4]])
wildname='*.'+ens_index+'.*'
full_glob_str=os.path.join(enspath,wildname)
glob_file=glob.glob(full_glob_str)
comp_file.extend(glob_file)
print "comp_file=",comp_file
pyEnsLib.plot_variable(in_files_list,comp_file,opts_dict,var_list,run_index,me)
'''
# Print out
if opts_dict['printVarTest']:
print '*********************************************** '
print 'Variable-based testing (for reference only - not used to determine pass/fail)'
print '*********************************************** '
for fcount, fid in enumerate(ifiles):
print ' '
print 'Run ' + str(fcount + 1) + ":"
print ' '
if not gmonly:
print '***' + str(countzscore[fcount]), " of " + str(
len(ens_var_name)
) + ' variables are outside of ensemble RMSZ distribution***'
pyEnsLib.printsummary(results, 'ens', 'zscore',
'zscoreRange', (fcount), variables,
'RMSZ')
print ' '
print '***' + str(countgm[fcount]), " of " + str(
len(ens_var_name)
) + ' variables are outside of ensemble global mean distribution***'
pyEnsLib.printsummary(results, 'gm', 'means', 'gmRange',
fcount, variables, 'global mean')
print ' '
print '----------------------------------------------------------------------------'
if me.get_rank() == 0:
print ' '
print "Testing complete."
print ' '
def main(argv):
# Get command line stuff and store in a dictionary
s='verbose sumfile= indir= timeslice= nPC= sigMul= minPCFail= minRunFail= numRunFile= printVarTest'
optkeys = s.split()
try:
opts, args = getopt.getopt(argv,"h",optkeys)
except getopt.GetoptError:
pyEnsLib.CECT_usage()
sys.exit(2)
# Set the default value for options
opts_dict = {}
opts_dict['timeslice'] = 1
opts_dict['nPC'] = 50
opts_dict['sigMul'] = 2
opts_dict['verbose'] = False
opts_dict['minPCFail'] = 3
opts_dict['minRunFail'] = 2
opts_dict['numRunFile'] = 3
opts_dict['printVarTest'] = False
# Call utility library getopt_parseconfig to parse the option keys
# and save to the dictionary
caller = 'CECT'
gmonly = False
opts_dict = pyEnsLib.getopt_parseconfig(opts,optkeys,caller,opts_dict)
# Print out timestamp, input ensemble file and new run directory
dt=datetime.now()
verbose = opts_dict['verbose']
print '--------pyCECT--------'
print ' '
print dt.strftime("%A, %d. %B %Y %I:%M%p")
print ' '
print 'Ensemble summary file = '+opts_dict['sumfile']
print ' '
print 'Cam output directory = '+opts_dict['indir']
print ' '
print ' '
# Open all input files
ifiles=[]
in_files_temp=os.listdir(opts_dict['indir'])
in_files=sorted(in_files_temp)
in_files_random=pyEnsLib.Random_pickup(in_files,opts_dict)
for frun_file in in_files_random:
if (os.path.isfile(opts_dict['indir'] +'/'+ frun_file)):
ifiles.append(Nio.open_file(opts_dict['indir']+'/'+frun_file,"r"))
else:
print "COULD NOT LOCATE FILE " +opts_dict['indir']+frun_file+" EXISTING"
sys.exit()
# Read all variables from the ensemble summary file
ens_var_name,ens_avg,ens_stddev,ens_rmsz,ens_gm,num_3d,mu_gm,sigma_gm,loadings_gm,sigma_scores_gm=pyEnsLib.read_ensemble_summary(opts_dict['sumfile'])
if len(ens_rmsz) == 0:
gmonly = True
# Add ensemble rmsz and global mean to the dictionary "variables"
variables={}
if not gmonly:
for k,v in ens_rmsz.iteritems():
pyEnsLib.addvariables(variables,k,'zscoreRange',v)
for k,v in ens_gm.iteritems():
pyEnsLib.addvariables(variables,k,'gmRange',v)
# Get 3d variable name list and 2d variable name list seperately
var_name3d=[]
var_name2d=[]
for vcount,v in enumerate(ens_var_name):
if vcount < num_3d:
var_name3d.append(v)
else:
var_name2d.append(v)
# Get ncol and nlev value
npts3d,npts2d,is_SE=pyEnsLib.get_ncol_nlev(ifiles[0])
# Compare the new run and the ensemble summary file to get rmsz score
results={}
countzscore=np.zeros(len(ifiles),dtype=np.int32)
countgm=np.zeros(len(ifiles),dtype=np.int32)
if not gmonly:
for fcount,fid in enumerate(ifiles):
otimeSeries = fid.variables
for var_name in ens_var_name:
orig=otimeSeries[var_name]
Zscore,has_zscore=pyEnsLib.calculate_raw_score(var_name,orig[opts_dict['timeslice']],npts3d,npts2d,ens_avg,ens_stddev,is_SE)
if has_zscore:
# Add the new run rmsz zscore to the dictionary "results"
pyEnsLib.addresults(results,'zscore',Zscore,var_name,'f'+str(fcount))
# Evaluate the new run rmsz score if is in the range of the ensemble summary rmsz zscore range
for fcount,fid in enumerate(ifiles):
countzscore[fcount]=pyEnsLib.evaluatestatus('zscore','zscoreRange',variables,'ens',results,'f'+str(fcount))
# Calculate the new run global mean
mean3d,mean2d=pyEnsLib.generate_global_mean_for_summary(ifiles,var_name3d,var_name2d,opts_dict['timeslice'],is_SE,verbose)
means=np.concatenate((mean3d,mean2d),axis=0)
# Add the new run global mean to the dictionary "results"
for i in range(means.shape[1]):
for j in range(means.shape[0]):
pyEnsLib.addresults(results,'means',means[j][i],ens_var_name[j],'f'+str(i))
# Evaluate the new run global mean if it is in the range of the ensemble summary global mean range
for fcount,fid in enumerate(ifiles):
countgm[fcount]=pyEnsLib.evaluatestatus('means','gmRange',variables,'gm',results,'f'+str(fcount))
# Calculate the PCA scores of the new run
new_scores=pyEnsLib.standardized(means,mu_gm,sigma_gm,loadings_gm)
pyEnsLib.comparePCAscores(ifiles,new_scores,sigma_scores_gm,opts_dict)
# Print out
if opts_dict['printVarTest']:
print '*********************************************** '
print 'Variable-based testing (for reference only - not used to determine pass/fail)'
print '*********************************************** '
for fcount,fid in enumerate(ifiles):
print ' '
print 'Run '+str(fcount+1)+":"
print ' '
if not gmonly:
print '***'+str(countzscore[fcount])," of "+str(len(ens_var_name))+' variables are outside of ensemble RMSZ distribution***'
pyEnsLib.printsummary(results,'ens','zscore','zscoreRange',(fcount),variables,'RMSZ')
print ' '
print '***'+str(countgm[fcount])," of "+str(len(ens_var_name))+' variables are outside of ensemble global mean distribution***'
pyEnsLib.printsummary(results,'gm','means','gmRange',fcount,variables,'global mean')
print ' '
print '----------------------------------------------------------------------------'
def main(argv):
# Get command line stuff and store in a dictionary
s="""verbose sumfile= indir= input_globs= tslice= nPC= sigMul=
minPCFail= minRunFail= numRunFile= printVarTest popens
jsonfile= mpi_enable nbin= minrange= maxrange= outfile=
casejson= npick= pepsi_gm test_failure pop_tol= web_enabled
pop_threshold= prn_std_mean fIndex= lev= eet= json_case= """
optkeys = s.split()
try:
opts, args = getopt.getopt(argv,"h",optkeys)
except getopt.GetoptError:
pyEnsLib.CECT_usage()
sys.exit(2)
# Set the default value for options
opts_dict = {}
opts_dict['input_globs'] = ''
opts_dict['indir'] = ''
opts_dict['tslice'] = 1
opts_dict['nPC'] = 50
opts_dict['sigMul'] = 2
opts_dict['verbose'] = False
opts_dict['minPCFail'] = 3
opts_dict['minRunFail'] = 2
opts_dict['numRunFile'] = 3
opts_dict['printVarTest'] = False
opts_dict['popens'] = False
opts_dict['jsonfile'] = ''
opts_dict['mpi_enable'] = False
opts_dict['nbin'] = 40
opts_dict['minrange'] = 0.0
opts_dict['maxrange'] = 4.0
opts_dict['outfile'] = 'testcase.result'
opts_dict['casejson'] = ''
opts_dict['npick'] = 10
opts_dict['pepsi_gm'] = False
opts_dict['test_failure'] = True
opts_dict['pop_tol'] = 3.0
opts_dict['pop_threshold'] = 0.90
opts_dict['prn_std_mean'] = False
opts_dict['lev'] = 0
opts_dict['eet'] = 0
opts_dict['json_case'] = ''
opts_dict['sumfile'] = ''
opts_dict['web_enabled'] = False
# Call utility library getopt_parseconfig to parse the option keys
# and save to the dictionary
caller = 'CECT'
gmonly = False
opts_dict = pyEnsLib.getopt_parseconfig(opts,optkeys,caller,opts_dict)
popens = opts_dict['popens']
# Create a mpi simplecomm object
if opts_dict['mpi_enable']:
me=simplecomm.create_comm()
else:
me=simplecomm.create_comm(not opts_dict['mpi_enable'])
# Print out timestamp, input ensemble file and new run directory
dt=datetime.now()
verbose = opts_dict['verbose']
if me.get_rank()==0:
print '--------pyCECT--------'
print ' '
print dt.strftime("%A, %d. %B %Y %I:%M%p")
print ' '
if not opts_dict['web_enabled']:
print 'Ensemble summary file = '+opts_dict['sumfile']
print ' '
print 'Testcase file directory = '+opts_dict['indir']
print ' '
print ' '
# Ensure sensible EET value
if opts_dict['eet'] and opts_dict['numRunFile'] > opts_dict['eet']:
pyEnsLib.CECT_usage()
sys.exit(2)
ifiles=[]
in_files=[]
# Random pick pop files from not_pick_files list
if opts_dict['casejson']:
with open(opts_dict['casejson']) as fin:
result=json.load(fin)
in_files_first=result['not_pick_files']
in_files=random.sample(in_files_first,opts_dict['npick'])
print 'Testcase files:'
print '\n'.join(in_files)
elif opts_dict['json_case']:
json_file=opts_dict['json_case']
if (os.path.exists(json_file)):
fd=open(json_file)
metainfo=json.load(fd)
if 'CaseName' in metainfo:
casename=metainfo['CaseName']
if (os.path.exists(opts_dict['indir'])):
for name in casename:
wildname='*.'+name+'.*'
full_glob_str=os.path.join(opts_dict['indir'],wildname)
glob_file=glob.glob(full_glob_str)
in_files.extend(glob_file)
else:
print "Error: "+opts_dict['json_case']+" does not exist"
sys.exit()
print "in_files=",in_files
else:
wildname='*'+opts_dict['input_globs']+'*'
# Open all input files
if (os.path.exists(opts_dict['indir'])):
full_glob_str=os.path.join(opts_dict['indir'],wildname)
glob_files=glob.glob(full_glob_str)
in_files.extend(glob_files)
num_file=len(in_files)
if opts_dict['numRunFile'] > num_file:
print "You requested more numRunFile than it is available at the indir, please change"
sys.exit()
#in_files_temp=os.listdir(opts_dict['indir'])
in_files.sort()
if popens:
#Partition the input file list
in_files_list=me.partition(in_files,func=EqualStride(),involved=True)
else:
# Random pick non pop files
in_files_list=pyEnsLib.Random_pickup(in_files,opts_dict)
#in_files_list=in_files
for frun_file in in_files_list:
if frun_file.find(opts_dict['indir']) != -1:
frun_temp=frun_file
else:
frun_temp=opts_dict['indir']+'/'+frun_file
if (os.path.isfile(frun_temp)):
ifiles.append(Nio.open_file(frun_temp,"r"))
else:
print "COULD NOT LOCATE FILE " +frun_temp+" EXISTING"
sys.exit()
if opts_dict['web_enabled']:
if len(opts_dict['sumfile'])==0:
opts_dict['sumfile']='/glade/p/cesmdata/cseg/inputdata/validation/'
opts_dict['sumfile'],machineid,compiler=pyEnsLib.search_sumfile(opts_dict,ifiles)
if len(machineid)!=0 and len(compiler)!=0:
print ' '
print 'Validation file : machineid = '+machineid+', compiler = '+compiler
print 'Found summery file : '+opts_dict['sumfile']
print ' '
else:
print 'Warning: machineid and compiler are unknown'
if popens:
# Read in the included var list
Var2d,Var3d=pyEnsLib.read_jsonlist(opts_dict['jsonfile'],'ESP')
print ' '
print 'Z-score tolerance = '+'{:3.2f}'.format(opts_dict['pop_tol'])
print 'ZPR = '+'{:.2%}'.format(opts_dict['pop_threshold'])
zmall,n_timeslice=pyEnsLib.compare_raw_score(opts_dict,ifiles,me.get_rank(),Var3d,Var2d)
#zmall = np.concatenate((Zscore3d,Zscore2d),axis=0)
np.set_printoptions(threshold=np.nan)
if opts_dict['mpi_enable']:
zmall = pyEnsLib.gather_npArray_pop(zmall,me,(me.get_size(),len(Var3d)+len(Var2d),len(ifiles),opts_dict['nbin']))
if me.get_rank()==0:
fout = open(opts_dict['outfile'],"w")
for i in range(me.get_size()):
for j in zmall[i]:
np.savetxt(fout,j,fmt='%-7.2e')
else:
# Read all variables from the ensemble summary file
ens_var_name,ens_avg,ens_stddev,ens_rmsz,ens_gm,num_3d,mu_gm,sigma_gm,loadings_gm,sigma_scores_gm,is_SE_sum,std_gm=pyEnsLib.read_ensemble_summary(opts_dict['sumfile'])
if len(ens_rmsz) == 0:
gmonly = True
# Add ensemble rmsz and global mean to the dictionary "variables"
variables={}
if not gmonly:
for k,v in ens_rmsz.iteritems():
pyEnsLib.addvariables(variables,k,'zscoreRange',v)
for k,v in ens_gm.iteritems():
pyEnsLib.addvariables(variables,k,'gmRange',v)
# Get 3d variable name list and 2d variable name list seperately
var_name3d=[]
var_name2d=[]
for vcount,v in enumerate(ens_var_name):
if vcount < num_3d:
var_name3d.append(v)
else:
var_name2d.append(v)
# Get ncol and nlev value
npts3d,npts2d,is_SE=pyEnsLib.get_ncol_nlev(ifiles[0])
if (is_SE ^ is_SE_sum):
print 'Warning: please note the ensemble summary file is different from the testing files, they use different grids'
# Compare the new run and the ensemble summary file to get rmsz score
results={}
countzscore=np.zeros(len(ifiles),dtype=np.int32)
countgm=np.zeros(len(ifiles),dtype=np.int32)
if not gmonly:
for fcount,fid in enumerate(ifiles):
otimeSeries = fid.variables
for var_name in ens_var_name:
orig=otimeSeries[var_name]
Zscore,has_zscore=pyEnsLib.calculate_raw_score(var_name,orig[opts_dict['tslice']],npts3d,npts2d,ens_avg,ens_stddev,is_SE,opts_dict,0,0,0)
if has_zscore:
# Add the new run rmsz zscore to the dictionary "results"
pyEnsLib.addresults(results,'zscore',Zscore,var_name,'f'+str(fcount))
# Evaluate the new run rmsz score if is in the range of the ensemble summary rmsz zscore range
for fcount,fid in enumerate(ifiles):
countzscore[fcount]=pyEnsLib.evaluatestatus('zscore','zscoreRange',variables,'ens',results,'f'+str(fcount))
# Calculate the new run global mean
mean3d,mean2d,varlist=pyEnsLib.generate_global_mean_for_summary(ifiles,var_name3d,var_name2d,is_SE,opts_dict['pepsi_gm'],opts_dict)
means=np.concatenate((mean3d,mean2d),axis=0)
# Add the new run global mean to the dictionary "results"
for i in range(means.shape[1]):
for j in range(means.shape[0]):
pyEnsLib.addresults(results,'means',means[j][i],ens_var_name[j],'f'+str(i))
# Evaluate the new run global mean if it is in the range of the ensemble summary global mean range
for fcount,fid in enumerate(ifiles):
countgm[fcount]=pyEnsLib.evaluatestatus('means','gmRange',variables,'gm',results,'f'+str(fcount))
# Calculate the PCA scores of the new run
new_scores,var_list,comp_std_gm=pyEnsLib.standardized(means,mu_gm,sigma_gm,loadings_gm,ens_var_name,opts_dict,ens_avg,me)
run_index,decision=pyEnsLib.comparePCAscores(ifiles,new_scores,sigma_scores_gm,opts_dict,me)
# If there is failure, plot out standardized mean and compared standardized mean in box plots
if opts_dict['prn_std_mean'] and decision == 'FAILED':
import seaborn as sns
category={"all_outside99":[],"two_outside99":[],"one_outside99":[],"all_oneside_outside1QR":[]}
b=list(pyEnsLib.chunk(ens_var_name,10))
for f,alist in enumerate(b):
for fc,avar in enumerate(alist):
dist_995=np.percentile(std_gm[avar],99.5)
dist_75=np.percentile(std_gm[avar],75)
dist_25=np.percentile(std_gm[avar],25)
dist_05=np.percentile(std_gm[avar],0.5)
c=0
d=0
p=0
q=0
for i in range(comp_std_gm[f+fc].size):
if comp_std_gm[f+fc][i]>dist_995:
c=c+1
elif comp_std_gm[f+fc][i]<dist_05:
d=d+1
elif (comp_std_gm[f+fc][i]<dist_995 and comp_std_gm[f+fc][i]>dist_75):
p=p+1
elif (comp_std_gm[f+fc][i]>dist_05 and comp_std_gm[f+fc][i]<dist_25):
q=q+1
if c == 3 or d == 3:
category["all_outside99"].append((avar,f+fc))
elif c == 2 or d == 2:
category["two_outside99"].append((avar,f+fc))
elif c == 1 or d == 1:
category["one_outside99"].append((avar,f+fc))
if p == 3 or q == 3:
category["all_oneside_outside1QR"].append((avar,f+fc))
part_name=opts_dict['indir'].split('/')[-1]
if not part_name:
part_name=opts_dict['indir'].split('/')[-2]
for key in sorted(category):
list_array=[]
list_array2=[]
list_var=[]
value=category[key]
print "value len=",key,len(value)
for each_var in value:
list_array.append(std_gm[each_var[0]])
list_array2.append(comp_std_gm[each_var[1]])
list_var.append(each_var[0])
if len(value) !=0 :
ax=sns.boxplot(data=list_array,whis=[0.5,99.5],fliersize=0.0)
sns.stripplot(data=list_array2,jitter=True,color="r")
sns.plt.xticks(range(len(list_array)),list_var,fontsize=8,rotation=-45)
if decision == 'FAILED':
sns.plt.savefig(part_name+"_"+key+"_fail.png")
else:
sns.plt.savefig(part_name+"_"+key+"_pass.png")
sns.plt.clf()
'''
if len(run_index)>0:
json_file=opts_dict['json_case']
if (os.path.exists(json_file)):
fd=open(json_file)
metainfo=json.load(fd)
caseindex=metainfo['CaseIndex']
enspath=str(metainfo['EnsPath'][0])
#print caseindex
if (os.path.exists(enspath)):
i=0
comp_file=[]
search = '\.[0-9]{3}\.'
for name in in_files_list:
s=re.search(search,name)
in_files_index=s.group(0)
if in_files_index[1:4] in caseindex:
ens_index=str(caseindex[in_files_index[1:4]])
wildname='*.'+ens_index+'.*'
full_glob_str=os.path.join(enspath,wildname)
glob_file=glob.glob(full_glob_str)
comp_file.extend(glob_file)
print "comp_file=",comp_file
pyEnsLib.plot_variable(in_files_list,comp_file,opts_dict,var_list,run_index,me)
'''
# Print out
if opts_dict['printVarTest']:
print '*********************************************** '
print 'Variable-based testing (for reference only - not used to determine pass/fail)'
print '*********************************************** '
for fcount,fid in enumerate(ifiles):
print ' '
print 'Run '+str(fcount+1)+":"
print ' '
if not gmonly:
print '***'+str(countzscore[fcount])," of "+str(len(ens_var_name))+' variables are outside of ensemble RMSZ distribution***'
pyEnsLib.printsummary(results,'ens','zscore','zscoreRange',(fcount),variables,'RMSZ')
print ' '
print '***'+str(countgm[fcount])," of "+str(len(ens_var_name))+' variables are outside of ensemble global mean distribution***'
pyEnsLib.printsummary(results,'gm','means','gmRange',fcount,variables,'global mean')
print ' '
print '----------------------------------------------------------------------------'
if me.get_rank() == 0:
print ' '
print "Testing complete."
print ' '