def add_line_descr_f(exp, f_exp_descr):
'''
Add line for exp exp in file f_exp_descr
:param exp: new expirement name
:param f_exp_descr: file in which the new line has to be added
return: None
'''
log.info('Adding line {} in the file {}:'.format(exp, f_exp_descr))
# open file in dataframe
if not os.path.isfile(f_exp_descr):
# create dataframe
cols_exp_descr_f = [
'Experiment name', 'Platform', 'OS', 'Compiler (with version)',
'Optimisation level (-OX)', '-fast-transcendentals (y/n)',
'-no-prec-sqrt (y/n)', '-no-prec-div (y/n)', 'welch (y/n)',
'fldcor (y/n)', 'rmse (y/n)', 'emi (y/n)',
'Date of experiment (month yyyy)'
]
pd.DataFrame(columns=cols_exp_descr_f)
else:
df_exp_descr = pd.read_csv(f_exp_descr, sep=';')
# collect information from user
log.banner('Please give the following informations '
'about your experiment')
dict_line = {'Experiment name': exp}
for col_name in df_exp_descr.keys():
if col_name != 'Experiment name':
# ask the user for info
dict_line[col_name] = input('{} : '.format(col_name))
# amend the information if needed
while True:
# new dataframe containing new line for exp
df_exp_descr_new = df_exp_descr.append(dict_line, ignore_index=True)
log.banner('Here is the content of the description '
'file including your new experiment.')
log.info(df_exp_descr_new)
answ_chg = input('Is the new file right ? (y/n/abort).\n'
'If you type n, you will be able to change '
'column values\n'
'If you type abort, the process of adding '
'the experiment {} to the reference is stoped.\n'
'(y/n/abort) : '
''.format(exp))
if answ_chg.upper() == 'Y':
# save new file
df_exp_descr_new.to_csv(f_exp_descr, sep=';', index=False)
# get out of the loop
return False
elif answ_chg.upper() == 'N':
answ_col = input('Which column field you want to change ?')
if answ_col in df_exp_descr.keys():
dict_line[answ_col] = input('{} : '.format(answ_col))
else:
log.warning('{} not in columns!'.format(answ_col))
log.info('Columns are {}\n'.format(list(df_exp_descr.columns)))
elif answ_chg.upper() == 'ABORT':
exit()
return ()
def main(new_exp, p_raw_files, raw_f_subfold, p_stages, p_ref_csv_files,
wrk_dir, f_vars_to_extract, f_pattern_ref, tests, spinup, lclean,
ltestsuite, lverbose):
# init logger
logger_config.init_logger(lverbose, __file__)
log.banner('Start sanity checker')
# make all paths from user to absolute paths
wrk_dir = utils.abs_path(wrk_dir)
p_stages = utils.abs_path(p_stages)
p_ref_csv_files = utils.abs_path(p_ref_csv_files)
f_pattern_ref = utils.abs_path(f_pattern_ref)
# create directories
os.makedirs(p_stages, exist_ok=True)
os.makedirs(wrk_dir, exist_ok=True)
# go to working directory
os.chdir((wrk_dir))
log.info('Working directory is {}'.format(wrk_dir))
# data processing takes a while, check that no step is done twice
actions = utils.determine_actions_for_data_processing(
new_exp, tests, p_stages, lclean)
# create dataframe out of raw data
results_data_processing = process_data.main(
new_exp,
actions,
tests,
spinup,
p_raw_files=p_raw_files,
p_stages=p_stages,
raw_f_subfold=raw_f_subfold,
f_vars_to_extract=f_vars_to_extract,
f_pattern_ref=f_pattern_ref)
results_test, references = perform_test.main(
new_exp,
results_data_processing=results_data_processing,
p_stages=p_stages,
tests=tests,
p_ref_csv_files=p_ref_csv_files,
ltestsuite=ltestsuite,
f_vars_to_extract=f_vars_to_extract)
if 'welch' in tests:
test = 'welch'
plt.plt_welchstest(references[test].append(
results_data_processing[test], sort=False),
new_exp,
results_test[test],
p_stages=p_stages)
# Add experiment to the reference pool
#--------------------------------------------------------------------
log.banner('')
log.banner('Check results again before adding to reference pool')
log.banner('')
for test in tests:
test_cfg = test_config.get_config_of_current_test(test)
utils.print_warning_if_testresult_is_bad(test, results_test[test],
test_cfg.metric_threshold,
test_cfg.metric)
if ltestsuite:
asw = 'YES'
else:
asw = input('If you are happy with this experiment, '
'do you want to add it to the reference pool ?'
'(yes/[No])\n')
if (asw.strip().upper() == 'YES') or (asw.strip().upper() == 'Y'):
add_exp_to_ref.main(new_exp,
tests,
p_stages=p_stages,
ltestsuite=ltestsuite,
p_ref_csv_files=p_ref_csv_files)
else:
args_for_manual_execution = \
utils.derive_arguments_for_add_exp_to_ref(new_exp,
tests,
p_stages,
p_ref_csv_files)
log.info('The experiment {} is NOT added to '
'the reference pool \n'.format(new_exp))
log.info('If you want to add the experiment {} '
'to the reference pool later on, type '
'the following line when you are ready:'.format(
new_exp, new_exp))
log.info('')
log.info(
'python add_exp_to_ref.py {}'.format(args_for_manual_execution))
log.banner('')
log.banner('Sanity test finished')
log.banner('')
def main(exp,
tests,
p_stages=paths.p_stages,
p_ref_csv_files=paths.p_ref_csv_files,
ltestsuite=False,
lverbose=False):
# initialisation
new_branch_name = 'test_add_{}'.format(exp)
files_to_commit = []
# fill up file 'Exps_description.csv' with additional
# information via user input
f_exp_descr = os.path.join(p_ref_csv_files, 'Exps_description.csv')
if not ltestsuite:
add_line_descr_f(exp=exp, f_exp_descr=f_exp_descr)
files_to_commit.append(f_exp_descr)
for test in tests:
test_cfg = get_config_of_current_test(test)
csv_file = utils.clean_path(
p_stages, 'test_postproc_{}_{}.csv'.format(test, exp))
# what is the filename in the reference pool
filename_in_ref_dir = '{}_{}.csv'.format(test_cfg.ref_name, exp)
# what is the location to store that file
place_for_reference = os.path.join(p_ref_csv_files, test,
filename_in_ref_dir)
log.debug('Copy {} to {}'.format(csv_file, place_for_reference))
if not ltestsuite:
shutil.copy(csv_file, place_for_reference)
files_to_commit.append(place_for_reference)
# copy pdf with bar-plots from Welch's-test
if test == 'welch':
pdf_file = utils.clean_path(
p_stages, '{}_{}.pdf'.format(test_cfg.ref_name, exp))
# what is the name of the pdf in the reference pool
filename_in_ref_dir = '{}_plots.pdf'.format(test_cfg.ref_name)
# what is the location to store that file
place_for_reference = os.path.join(p_ref_csv_files, test,
filename_in_ref_dir)
log.debug('Copy {} to {}'.format(csv_file, place_for_reference))
files_to_commit.append(place_for_reference)
if not ltestsuite:
shutil.copy(pdf_file, place_for_reference)
# root is important to not fail during git commands
os.chdir(paths.rootdir)
# checkout new branch
if not ltestsuite:
log.info('Create and checkout new branch {}'.format(new_branch_name))
git_cmd = 'git checkout -B {}'.format(new_branch_name)
utils.shell_cmd(git_cmd, py_routine='add_exp_to_ref.py')
# commit all modified files prior in the function to git
for file in files_to_commit:
git_cmd = 'git add {}'.format(file)
log.debug(git_cmd)
utils.shell_cmd(git_cmd, py_routine=__name__)
log.debug('Commit files {}'.format(files_to_commit))
commit_message = input('Please type your commit message :')
git_cmd = 'git commit -m "{}"'.format(commit_message)
utils.shell_cmd(git_cmd, py_routine=__name__)
# Finish
log.info(
Style.GREEN(
'Files are added in the new branch: '
'{} in your local git repository.'.format(new_branch_name)))
log.info('To add the file to the official repository, '
'please perform the following steps:')
log.info('1. Push the new branch into the official repo:')
log.info(' git push --set-upstream origin {}'.format(new_branch_name))
log.info('2. On the Open Web interface (GitHub) , open a Pull Request.')
log.banner('End add_exp_to_ref for experiment {}'.format(exp))
return ()
'-v',
dest='lverbose',
action='store_true',
help='Debug output')
parser.add_argument('--testsuite',
'-ts',
dest='ltestsuite',
action='store_true',
help='Run of testsuite')
args = parser.parse_args()
# init logger
logger_config.init_logger(args.lverbose, __file__)
log.banner('Start execute {} as main()'.format(__file__))
# make all paths from user to absolute paths
args.p_stages = utils.abs_path(args.p_stages)
args.p_ref_csv_files = utils.abs_path(args.p_ref_csv_files)
main(exp=args.exp,
tests=args.tests,
p_stages=args.p_stages,
p_ref_csv_files=args.p_ref_csv_files,
ltestsuite=args.ltestsuite,
lverbose=args.lverbose)
log.banner('End execute {} as main()'.format(__file__))
def main(exp, actions, tests, spinup, p_raw_files, p_stages, raw_f_subfold,
f_vars_to_extract, f_pattern_ref):
log.banner('Start standard-postprocessing')
results_data_processing = {}
processed_netcdf_filename = {}
skip_next_step = {}
# init in case standard_postproc is skipped
for test in tests:
skip_next_step[test] = False
for test in tests:
if (actions['standard_postproc'][test]):
processed_netcdf_filename[test], skip_next_step[test] = \
standard_postproc(exp,
test=test,
spinup=spinup,
p_raw_files=p_raw_files,
raw_f_subfold=raw_f_subfold,
p_stages=p_stages,
f_vars_to_extract=f_vars_to_extract)
else:
log.info('Data already processed for test {}'.format(test))
processed_netcdf_filename[test] = utils.clean_path(
p_stages, 'standard_postproc_{}_{}.nc'.format(test, exp))
log.banner('End standard-postprocessing')
log.banner('Start conversion from NetCDF to dataframe')
if 'welch' in tests:
test = 'welch'
if (actions['test_postproc'][test] and not skip_next_step[test]):
# transforming netcdf timeseries into csv file
results_data_processing[test] = timeser_proc_nc_to_df(
exp,
filename=processed_netcdf_filename[test],
p_stages=p_stages)
else:
log.info('Processing for test {} already done'.format(test))
f_csv = os.path.join(p_stages,
'test_postproc_{}_{}.csv'.format(test, exp))
results_data_processing[test] = pd.read_csv(f_csv, sep=';')
else:
log.warning("Skip Welch's-Test")
if 'emi' in tests:
test = 'emi'
if (actions['test_postproc'][test] and not skip_next_step[test]):
results_data_processing[test] = emis_proc_nc_to_df(
exp,
filename=processed_netcdf_filename[test],
p_stages=p_stages)
else:
log.info('Processing for test {} already done'.format(test))
f_csv = os.path.join(p_stages,
'test_postproc_{}_{}.csv'.format(test, exp))
results_data_processing[test] = pd.read_csv(f_csv, sep=';')
else:
log.warning('Skip emission test')
if 'fldcor' in tests:
test = 'fldcor'
if (actions['test_postproc'][test] and not skip_next_step[test]):
f_pattern_ref = download_ref_to_stages_if_required(
f_pattern_ref, p_stages, f_vars_to_extract, test)
results_data_processing[test] = pattern_proc_nc_to_df(
exp,
filename=processed_netcdf_filename[test],
p_stages=p_stages,
reference=f_pattern_ref)
else:
log.info('Processing for test {} already done'.format(test))
f_csv = os.path.join(p_stages,
'test_postproc_{}_{}.csv'.format(test, exp))
results_data_processing[test] = pd.read_csv(f_csv, sep=';')
else:
log.warning('Skip pattern correlation test')
if 'rmse' in tests:
test = 'rmse'
if (actions['test_postproc'][test] and not skip_next_step[test]):
test = 'rmse'
f_pattern_ref = download_ref_to_stages_if_required(
f_pattern_ref, p_stages, f_vars_to_extract, test)
results_data_processing[test] = rmse_proc_nc_to_df(
exp,
filename=processed_netcdf_filename[test],
p_stages=p_stages,
reference=f_pattern_ref)
else:
log.info('Processing for test {} already done'.format(test))
f_csv = os.path.join(p_stages,
'test_postproc_{}_{}.csv'.format(test, exp))
results_data_processing[test] = pd.read_csv(f_csv, sep=';')
else:
log.warning('Skip Rmse test')
log.banner('End conversion from NetCDF to dataframe')
return (results_data_processing)
def standard_postproc(exp, test, spinup, p_raw_files, raw_f_subfold, p_stages,
f_vars_to_extract):
'''
Perfom standard post-processing using cdo
Arguments:
exp = experiment name
test = name of current test to process data
spinup = number of files (from begining of simulation)
to ignore du to model spinup
p_raw_files = path to raw model output
raw_f_subfold = subfolder in p_raw_files with model output
[p_raw_files]/[raw_f_subfold]
p_stages = directory where processing steps are stored
f_vars_to_extract = csv file containg the variables to proceed
returns:
netCDF filename containing the fields as defined in f_vars_to_extract
'''
log.info('Postprocess data using CDO for test {}'.format(test))
# check that exp is defined
if exp is None:
log.error('Experiment is not defined.\n exp = {}'.format(exp))
# get variables to process:
p_test_vars_proc = os.path.join(paths.p_f_vars_proc, test)
full_p_f_vars = utils.clean_path(p_test_vars_proc, f_vars_to_extract)
df_vars = pd.read_csv(full_p_f_vars, sep=',')
# define expressions
df_vars['expr'] = df_vars['var'] + '=' + df_vars['formula']
# name of output file
ofile_tot = os.path.join(p_stages,
'standard_postproc_{}_{}.nc'.format(test, exp))
# initialisation
files_error = [] # list files giving error
files_proceed = [] # list of files where data are collected
# sometimes data is stored in a folder called Raw
p_raw_folder = os.path.join(p_raw_files, exp, raw_f_subfold)
# SPECIAL CASE, echam specific :
# if the folder containing the Raw files have been deleted,
# but folder 'Data' contains already global annual means
if not os.path.isdir(p_raw_folder):
log.warning('The folder containing the raw data '
'has been deleted : {}'.format(p_raw_folder))
p_altern_timeser_fold = os.path.join(p_raw_files, exp, 'Data')
if test == 'welch':
time_series_altern_fold = glob.glob(
os.path.join(p_altern_timeser_fold, 'timeser_daint_*.nc'))
if test == 'fldcor' or test == 'rmse':
time_series_altern_fold = glob.glob(
os.path.join(p_altern_timeser_fold, 'multi_annual_means_*.nc'))
if test == 'emi':
time_series_altern_fold = glob.glob(
os.path.join(p_altern_timeser_fold, 'emi_*.nc'))
if len(time_series_altern_fold) < 1:
log.error('Could not find files in alternative directory '
'{}'.format(time_series_altern_fold))
else:
log.info('The alternative folder has been found instead: '
'{}'.format(p_altern_timeser_fold))
log.warning('This section of code is only tested for ECHAM! '
'It is not recommended to use it for other cases')
if len(time_series_altern_fold) == 1:
index_ts = 0
if len(time_series_altern_fold) > 1:
for (i, item) in enumerate(time_series_altern_fold):
print(i, item)
index_ts = int(
input('Please type the index of the file'
' to use (negative means '
'none of them) : '))
# If index positive, copy the time serie and exit
if index_ts >= 0:
log.info('File used : {}'.format(
time_series_altern_fold[index_ts]))
cdo_cmd = ('cdo -L -chname,CDNC,burden_CDNC '
'-chname,ICNC,burden_ICNC '
'-chname,SCF,SCRE -chname,LCF,LCRE '
'{} {}'.format(time_series_altern_fold[index_ts],
ofile_tot))
utils.shell_cmd(cdo_cmd, py_routine=__name__)
# convert netCDF to dataframe,
# therefore skip next processing step
if test == 'welch':
timeser_proc_nc_to_df(exp,
ofile_tot,
p_stages,
already_a_timeseries=True)
skip_next_steps = True
else:
skip_next_steps = False
log.warning('Leave ECHAM-only code-section! '
'You are save again...')
return (ofile_tot, skip_next_steps)
# NORMAL CASE
else:
log.info('Analyse files in : {}'.format(p_raw_folder))
log.banner('Time for a coffee...')
# loop over output stream
for stream in df_vars['file'].unique():
# extract all lines with file f
df_file = df_vars[df_vars.file == stream]
# list all available files in p_raw_files/exp/raw_f_subfold
#which have stream f
# restart files and {}m.format(stream) e.g. echamm.nc
# files are not considered
final_p_raw_files = os.path.join(p_raw_folder,
'*_*{}*.nc'.format(stream))
ifiles = [
fn for fn in glob.glob(final_p_raw_files) if sum([
s in os.path.basename(fn)
for s in ['stream', '{}m'.format(stream)]
]) == 0
]
if len(ifiles) == 0:
log.warning('No raw files found for stream {} at address : \n'
'{}'.format(stream, final_p_raw_files))
# sort files in chronoligcal order
# (this will be needed for doing yearmean properly)
ifiles.sort()
print_statistics_of_raw_files(ifiles, stream, exp)
# remove spin-up files
log.info('Remove first {} months of data '
'due to model spinup'.format(spinup))
ifiles = ifiles[int(spinup):]
# output file for stream f
ofile_str = '{}_{}.nc'.format(exp, stream)
# variables to extract form netcdf
# files (this is needed for optimization)
variables = variables_to_extract(vars_in_expr=df_file.formula.values)
# Extract variables needed from big files
log.info('Extract variables from file: {}'.format(stream))
# initialization
tmp_selvar_files = [] # list to store the ifiles
for ifile in ifiles:
# basename of ifile
ifile_bsn = os.path.basename(ifile)
log.debug('File {}'.format(ifile_bsn))
tmp_selvar_file = 'tmp_extract_{}'.format(ifile_bsn)
cdo_cmd = 'cdo selvar,{} {} {}'.format(','.join(variables), ifile,
tmp_selvar_file)
out_status, out_mess = utils.shell_cmd(cdo_cmd,
py_routine=__name__,
lowarn=True)
if out_status == 0:
tmp_selvar_files.append(tmp_selvar_file)
else:
files_error.append(ifile_bsn)
# Merge all the monthly files together
log.info('Copy {} files'.format(stream))
tmp_merged = 'tmp_{}_{}.nc'.format(exp, stream)
if os.path.isfile(tmp_merged):
os.remove(tmp_merged)
cdo_cmd = 'cdo -copy {} {}'.format(' '.join(tmp_selvar_files),
tmp_merged)
utils.shell_cmd(cdo_cmd, py_routine=__name__)
# compute needed variables
log.info('Compute variables for file : {}'.format(stream))
if os.path.isfile(ofile_str):
os.remove(ofile_str)
expr_str = ';'.join((df_file.expr.values))
cdo_cmd = 'cdo -L -setctomiss,-9e+33 -expr,"{}" {} {}'.format(
expr_str, tmp_merged, ofile_str)
utils.shell_cmd(cdo_cmd, py_routine=__name__)
# keep trace of output file per stream
files_proceed.append(ofile_str)
# cleaning
[os.remove(f) for f in tmp_selvar_files]
os.remove(tmp_merged)
# merge all stream files
if os.path.isfile(ofile_tot):
os.remove(ofile_tot)
cdo_cmd = 'cdo merge {} {}'.format(' '.join(files_proceed), ofile_tot)
utils.shell_cmd(cdo_cmd, py_routine=__name__)
[os.remove(f) for f in files_proceed]
# Finish
if len(files_error) != 0:
log.warning('Files with a problem: {}'.format(','.join(files_error)))
log.info('Postprocess data using CDO for test {} finished. \n '
'Output here : {}'.format(test, ofile_tot))
# return name of output file
return (ofile_tot, False)
def main(new_exp, results_data_processing, tests, p_stages, p_ref_csv_files,
ltestsuite, f_vars_to_extract):
df_exp = {}
df_ref = {}
p_csv_files = {}
testresult_csv = {}
df_result = {}
for test in tests:
log.info('Prepare references for test {}'.format(test))
test_cfg = get_config_of_current_test(test)
results_data_processing[test]['exp'] = new_exp
# list of paths to all csv files
p_csv_files[test] = glob.glob(
os.path.join(p_ref_csv_files, test,
'{}_*csv'.format(test_cfg.ref_name)))
if len(p_csv_files[test]) == 0:
log.error('No reference files found in {}'.format(p_ref_csv_files))
log.debug('{} reference(s) found for test \
{}'.format(len(p_csv_files[test]), test))
# create big dataframe containing all reference exps
df_ref[test] = create_big_df(test_cfg.ref_name,
list_csv_files=p_csv_files[test])
# Exclude all the non-desired variables (1) var from file, 2) exp)
full_p_f_vars = os.path.join(paths.p_f_vars_proc, test,
f_vars_to_extract)
vars_to_analyse = list(
pd.read_csv(full_p_f_vars, sep=',')['var'].values)
vars_to_analyse.append('exp')
try:
df_ref[test] = df_ref[test][vars_to_analyse]
except KeyError as e:
log.warning(e)
log.error('Variables defined in {} are not contained in reference \
{}'.format(utils.rel_path(f_vars_to_extract),
utils.rel_path(p_ref_csv_files)))
df_exp[test] = results_data_processing[test][vars_to_analyse]
log.info('References for test {} prepared'.format(test))
testresult_csv[test] = os.path.join(
p_stages, 'result_{}_{}.csv'.format(test, new_exp))
if test == 'welch':
log.banner('')
log.banner("Perform Welch's t-test for each variable")
log.banner('')
df_result[test] = welch_test(
df_a=df_ref[test],
df_b=df_exp[test],
filename_student_test=testresult_csv[test])
df_result[test]['p-value [%]'] = df_result[test]['p-value'] * 100.
if test == 'fldcor':
log.banner('')
log.banner("Perform fldcor test for each variable")
log.banner('')
df_result[test] = pattern_correlation(df_exp[test], test_cfg)
if test == 'emi':
log.banner('')
log.banner("Perform emission test for each variable")
log.banner('')
df_result[test] = emissions(df_exp[test], df_ref[test], test_cfg)
if test == 'rmse':
log.banner('')
log.banner("Perform rmse test for each variable")
log.banner('')
df_result[test] = rmse(df_exp[test], test_cfg)
df_result[test] = sort_level_metric(df_result[test],
test_cfg.metric_threshold,
test_cfg.metric)
df_result[test] = add_color_df_result(df_result[test],
test_cfg.metric_threshold)
print_warning_color(df_result[test], test_cfg.metric_threshold,
test_cfg.metric)
if ltestsuite:
for test in tests:
test_cfg = get_config_of_current_test(test)
utils.exit_if_testresult_is_bad(test, df_result[test],
test_cfg.metric_threshold,
test_cfg.metric)
return df_result, df_ref