From ff99eae65dfaeec1221e06572d770ebd48feb3f4 Mon Sep 17 00:00:00 2001
From: Anne Philipp <anne.philipp@univie.ac.at>
Date: Fri, 1 Jun 2018 22:34:59 +0200
Subject: [PATCH] completed application of pep8 style guide and pylint
investigations. added documentation almost everywhere
---
ECMWF_FPparameter.xlsx | Bin 20494 -> 14531 bytes
python/CONTROL_OD | 35 +
python/ControlFile.py | 68 +-
python/{ECFlexpart.py => EcFlexpart.py} | 646 ++++++++++--------
python/GribTools.py | 99 ++-
python/{MARSretrieval.py => MarsRetrieval.py} | 85 ++-
python/{UIOFiles.py => UioFiles.py} | 47 +-
python/{Disagg.py => disaggregation.py} | 20 +-
python/{getMARSdata.py => get_mars_data.py} | 102 ++-
python/install.py | 150 ++--
python/plot_retrieved.py | 395 ++++++-----
...prepareFLEXPART.py => prepare_flexpart.py} | 65 +-
python/profiling.py | 4 +-
python/submit.py | 58 +-
python/{testsuite.py => test_suite.py} | 32 +-
python/{Tools.py => tools.py} | 191 +++---
16 files changed, 1048 insertions(+), 949 deletions(-)
create mode 100644 python/CONTROL_OD
rename python/{ECFlexpart.py => EcFlexpart.py} (69%)
rename python/{MARSretrieval.py => MarsRetrieval.py} (90%)
rename python/{UIOFiles.py => UioFiles.py} (79%)
rename python/{Disagg.py => disaggregation.py} (93%)
rename python/{getMARSdata.py => get_mars_data.py} (74%)
rename python/{prepareFLEXPART.py => prepare_flexpart.py} (79%)
rename python/{testsuite.py => test_suite.py} (86%)
rename python/{Tools.py => tools.py} (78%)
diff --git a/ECMWF_FPparameter.xlsx b/ECMWF_FPparameter.xlsx
index 21bae48a2bef0dbb1dc5d02d0482921cb980a01e..20207d5a2ffdfa77f4f6686d6fc3332e284e3988 100644
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diff --git a/python/CONTROL_OD b/python/CONTROL_OD
new file mode 100644
index 0000000..f82261e
--- /dev/null
+++ b/python/CONTROL_OD
@@ -0,0 +1,35 @@
+DAY1 20151007
+DAY2 20151007
+DTIME 3
+M_TYPE AN FC FC FC FC FC AN FC FC FC FC FC AN FC FC FC FC FC AN FC FC FC FC FC
+M_TIME 00 00 00 00 00 00 06 00 00 00 00 00 12 12 12 12 12 12 18 12 12 12 12 12
+M_STEP 00 01 02 03 04 05 00 07 08 09 10 11 00 01 02 03 04 05 00 07 08 09 10 11
+M_CLASS OD
+M_STREAM OPER
+M_NUMBER OFF
+M_EXPVER 1
+M_GRID 1000
+M_LEFT -10000
+M_LOWER 30000
+M_UPPER 60000
+M_RIGHT 30000
+M_LEVEL 137
+M_LEVELIST 130/to/137
+M_RESOL 399
+M_GAUSS 0
+M_ACCURACY 16
+M_OMEGA 0
+M_OMEGADIFF 0
+M_ETA 1
+M_ETADIFF 0
+M_DPDETA 1
+M_SMOOTH 0
+M_FORMAT GRIB1
+M_ADDPAR 186/187/188/235/139/39
+PREFIX EO
+ECSTORAGE 0
+ECTRANS 1
+ECFSDIR ectmp:/${USER}/econdemand/
+MAILOPS ${USER}
+MAILFAIL ${USER}
+EOF
diff --git a/python/ControlFile.py b/python/ControlFile.py
index 8974757..2fd438d 100644
--- a/python/ControlFile.py
+++ b/python/ControlFile.py
@@ -1,7 +1,7 @@
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#************************************************************************
-# TODO AP
+# ToDo AP
# - write a test class
#************************************************************************
#*******************************************************************************
@@ -36,7 +36,28 @@
# @Class Content:
# - __init__
# - __str__
-# - tolist
+# - to_list
+#
+# @Class Attributes:
+# - start_date
+# - end_date
+# - accuracy
+# - omega
+# - cwc
+# - omegadiff
+# - etadiff
+# - level
+# - levelist
+# - step
+# - maxstep
+# - prefix
+# - makefile
+# - basetime
+# - date_chunk
+# - grib2flexpart
+# - exedir
+# - flexpart_root_scripts
+# - ecmwfdatadir
#
#*******************************************************************************
@@ -45,13 +66,14 @@
# ------------------------------------------------------------------------------
import os
import inspect
+
# software specific module from flex_extract
-import Tools
+from tools import get_list_as_string, my_error
# ------------------------------------------------------------------------------
# CLASS
# ------------------------------------------------------------------------------
-class ControlFile:
+class ControlFile(object):
'''
Class containing the information of the flex_extract CONTROL file.
@@ -113,7 +135,6 @@ class ControlFile:
data = [data[0]]
for d in dd:
data.append(d)
- pass
if len(data) == 2:
if '$' in data[1]:
setattr(self, data[0].lower(), data[1])
@@ -125,11 +146,9 @@ class ControlFile:
if var is not None:
data[1] = data[1][:i] + var + data[1][k+1:]
else:
- Tools.myerror(None,
- 'Could not find variable ' +
- data[1][j+1:k] +
- ' while reading ' +
- filename)
+ my_error(None, 'Could not find variable ' +
+ data[1][j+1:k] + ' while reading ' +
+ filename)
setattr(self, data[0].lower() + '_expanded', data[1])
else:
if data[1].lower() != 'none':
@@ -159,8 +178,8 @@ class ControlFile:
self.etadiff = '0'
if not hasattr(self, 'levelist'):
if not hasattr(self, 'level'):
- print('Warning: neither levelist nor level \
- specified in CONTROL file')
+ print 'Warning: neither levelist nor level \
+ specified in CONTROL file'
else:
self.levelist = '1/to/' + self.level
else:
@@ -223,7 +242,7 @@ class ControlFile:
return ', '.join("%s: %s" % item for item in attrs.items())
- def tolist(self):
+ def to_list(self):
'''
@Description:
Just generates a list of strings containing the attributes and
@@ -254,7 +273,7 @@ class ControlFile:
elif 'ecmwfdatadir' in item[0]:
pass
else:
- if type(item[1]) is list:
+ if isinstance(item[1], list):
stot = ''
for s in item[1]:
stot += s + ' '
@@ -264,3 +283,24 @@ class ControlFile:
l.append("%s %s" % item)
return sorted(l)
+
+ # def to_dict(self):
+ # '''
+
+ # '''
+ # parameters_dict = vars(self)
+
+ # # remove unneeded parameter
+ # parameters_dict.pop('_expanded', None)
+ # parameters_dict.pop('exedir', None)
+ # parameters_dict.pop('flexpart_root_scripts', None)
+ # parameters_dict.pop('ecmwfdatadir', None)
+
+ # parameters_dict_str = {}
+ # for key, value in parameters_dict.iteritems():
+ # if isinstance(value, list):
+ # parameters_dict_str[str(key)] = get_list_as_string(value, ' ')
+ # else:
+ # parameters_dict_str[str(key)] = str(value)
+
+ # return parameters_dict_str
diff --git a/python/ECFlexpart.py b/python/EcFlexpart.py
similarity index 69%
rename from python/ECFlexpart.py
rename to python/EcFlexpart.py
index 0537feb..4d53874 100644
--- a/python/ECFlexpart.py
+++ b/python/EcFlexpart.py
@@ -1,7 +1,7 @@
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#************************************************************************
-# TODO AP
+# ToDo AP
# - specifiy file header documentation
# - add class description in header information
# - apply classtests
@@ -20,8 +20,8 @@
# November 2015 - Leopold Haimberger (University of Vienna):
# - extended with class Control
# - removed functions mkdir_p, daterange, years_between, months_between
-# - added functions darain, dapoly, toparamId, init128, normalexit,
-# myerror, cleanup, install_args_and_control,
+# - added functions darain, dapoly, to_param_id, init128, normal_exit,
+# my_error, clean_up, install_args_and_control,
# interpret_args_and_control,
# - removed function __del__ in class EIFLexpart
# - added the following functions in EIFlexpart:
@@ -39,10 +39,10 @@
# February 2018 - Anne Philipp (University of Vienna):
# - applied PEP8 style guide
# - added documentation
-# - removed function getFlexpartTime in class ECFlexpart
+# - removed function getFlexpartTime in class EcFlexpart
# - outsourced class ControlFile
# - outsourced class MarsRetrieval
-# - changed class name from EIFlexpart to ECFlexpart
+# - changed class name from EIFlexpart to EcFlexpart
# - applied minor code changes (style)
# - removed "dead code" , e.g. retrieval of Q since it is not needed
# - removed "times" parameter from retrieve-method since it is not used
@@ -69,38 +69,57 @@
# - create
# - deacc_fluxes
#
+# @Class Attributes:
+# - dtime
+# - basetime
+# - server
+# - marsclass
+# - stream
+# - resol
+# - accuracy
+# - number
+# - expver
+# - glevelist
+# - area
+# - grid
+# - level
+# - levelist
+# - types
+# - dates
+# - area
+# - gaussian
+# - params
+# - inputdir
+# - outputfilelist
+#
#*******************************************************************************
-
+#pylint: disable=unsupported-assignment-operation
+# this is disabled because its an error in pylint for this specific case
+#pylint: disable=consider-using-enumerate
+# this is not useful in this case
# ------------------------------------------------------------------------------
# MODULES
# ------------------------------------------------------------------------------
import subprocess
import shutil
import os
-import sys
-import inspect
import glob
-import datetime
-from numpy import *
-from argparse import ArgumentParser, ArgumentDefaultsHelpFormatter
-ecapi = True
-try:
- import ecmwfapi
-except ImportError:
- ecapi = False
-from gribapi import *
+from datetime import datetime, timedelta
+import numpy as np
+from gribapi import grib_set, grib_index_select, grib_new_from_index, grib_get,\
+ grib_write, grib_get_values, grib_set_values, grib_release,\
+ grib_index_release, grib_index_get
# software specific classes and modules from flex_extract
-from GribTools import GribTools
-from Tools import init128, toparamId, silentremove, product
-from ControlFile import ControlFile
-from MARSretrieval import MARSretrieval
-import Disagg
+from Gribtools import Gribtools
+from tools import init128, to_param_id, silent_remove, product, my_error
+from MarsRetrieval import MarsRetrieval
+import disaggregation
# ------------------------------------------------------------------------------
# CLASS
# ------------------------------------------------------------------------------
-class ECFlexpart:
+class EcFlexpart(object):
'''
Class to retrieve FLEXPART specific ECMWF data.
'''
@@ -110,11 +129,11 @@ class ECFlexpart:
def __init__(self, c, fluxes=False):
'''
@Description:
- Creates an object/instance of ECFlexpart with the
+ Creates an object/instance of EcFlexpart with the
associated settings of its attributes for the retrieval.
@Input:
- self: instance of ECFlexpart
+ self: instance of EcFlexpart
The current object of the class.
c: instance of class ControlFile
@@ -141,17 +160,15 @@ class ECFlexpart:
# different mars types for retrieving data for flexpart
self.types = dict()
- try:
- if c.maxstep > len(c.type): # Pure forecast mode
- c.type = [c.type[1]]
- c.step = ['{:0>3}'.format(int(c.step[0]))]
- c.time = [c.time[0]]
- for i in range(1, c.maxstep + 1):
- c.type.append(c.type[0])
- c.step.append('{:0>3}'.format(i))
- c.time.append(c.time[0])
- except:
- pass
+
+ if c.maxstep > len(c.type): # Pure forecast mode
+ c.type = [c.type[1]]
+ c.step = ['{:0>3}'.format(int(c.step[0]))]
+ c.time = [c.time[0]]
+ for i in range(1, c.maxstep + 1):
+ c.type.append(c.type[0])
+ c.step.append('{:0>3}'.format(i))
+ c.time.append(c.time[0])
self.inputdir = c.inputdir
self.basetime = c.basetime
@@ -174,57 +191,51 @@ class ECFlexpart:
if c.basetime == '00':
btlist = [13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 0]
- if mod(i, int(c.dtime)) == 0 and \
- (c.maxstep > 24 or i in btlist):
+ if i % int(c.dtime) == 0 and c.maxstep > 24 or i in btlist:
if ty not in self.types.keys():
self.types[ty] = {'times': '', 'steps': ''}
if ti not in self.types[ty]['times']:
- if len(self.types[ty]['times']) > 0:
+ if self.types[ty]['times']:
self.types[ty]['times'] += '/'
self.types[ty]['times'] += ti
if st not in self.types[ty]['steps']:
- if len(self.types[ty]['steps']) > 0:
+ if self.types[ty]['steps']:
self.types[ty]['steps'] += '/'
self.types[ty]['steps'] += st
i += 1
- # Different grids need different retrievals
- # SH = Spherical Harmonics, GG = Gaussian Grid,
- # OG = Output Grid, ML = MultiLevel, SL = SingleLevel
- self.params = {'SH__ML': '', 'SH__SL': '',
- 'GG__ML': '', 'GG__SL': '',
- 'OG__ML': '', 'OG__SL': '',
- 'OG_OROLSM_SL': '', 'OG_acc_SL': ''}
+
self.marsclass = c.marsclass
self.stream = c.stream
self.number = c.number
self.resol = c.resol
self.accuracy = c.accuracy
self.level = c.level
- try:
+
+ if c.levelist:
self.levelist = c.levelist
- except:
+ else:
self.levelist = '1/to/' + c.level
# for gaussian grid retrieval
self.glevelist = '1/to/' + c.level
- try:
+ if c.gaussian:
self.gaussian = c.gaussian
- except:
+ else:
self.gaussian = ''
- try:
+ if c.expver:
self.expver = c.expver
- except:
+ else:
self.expver = '1'
- try:
+ if c.number:
self.number = c.number
- except:
+ else:
self.number = '0'
if 'N' in c.grid: # Gaussian output grid
@@ -249,12 +260,21 @@ class ECFlexpart:
# 3) Calculation/Retrieval of omega
# 4) Download also data for WRF
+
+ # Different grids need different retrievals
+ # SH = Spherical Harmonics, GG = Gaussian Grid,
+ # OG = Output Grid, ML = MultiLevel, SL = SingleLevel
+ self.params = {'SH__ML': '', 'SH__SL': '',
+ 'GG__ML': '', 'GG__SL': '',
+ 'OG__ML': '', 'OG__SL': '',
+ 'OG_OROLSM_SL': '', 'OG_acc_SL': ''}
+
if fluxes is False:
self.params['SH__SL'] = ['LNSP', 'ML', '1', 'OFF']
# "SD/MSL/TCC/10U/10V/2T/2D/129/172"
self.params['OG__SL'] = ["141/151/164/165/166/167/168/129/172", \
'SFC', '1', self.grid]
- if len(c.addpar) > 0:
+ if c.addpar:
if c.addpar[0] == '/':
c.addpar = c.addpar[1:]
self.params['OG__SL'][0] += '/' + '/'.join(c.addpar)
@@ -276,8 +296,8 @@ class ECFlexpart:
'{}'.format((int(self.resol) + 1) / 2)]
self.params['SH__ML'] = ['U/V/D', 'ML', self.glevelist, 'OFF']
else:
- print('Warning: This is a very costly parameter combination, \
- use only for debugging!')
+ print 'Warning: This is a very costly parameter combination, \
+ use only for debugging!'
self.params['GG__SL'] = ['Q', 'ML', '1', \
'{}'.format((int(self.resol) + 1) / 2)]
self.params['GG__ML'] = ['U/V/D/77', 'ML', self.glevelist, \
@@ -286,29 +306,24 @@ class ECFlexpart:
if c.omega == '1':
self.params['OG__ML'][0] += '/W'
- try:
- # add cloud water content if necessary
- if c.cwc == '1':
- self.params['OG__ML'][0] += '/CLWC/CIWC'
- except:
- pass
+ # add cloud water content if necessary
+ if c.cwc == '1':
+ self.params['OG__ML'][0] += '/CLWC/CIWC'
+
+ # add vorticity and geopotential height for WRF if necessary
+ if c.wrf == '1':
+ self.params['OG__ML'][0] += '/Z/VO'
+ if '/D' not in self.params['OG__ML'][0]:
+ self.params['OG__ML'][0] += '/D'
+ #wrf_sfc = 'sp/msl/skt/2t/10u/10v/2d/z/lsm/sst/ci/sd/stl1/ /
+ # stl2/stl3/stl4/swvl1/swvl2/swvl3/swvl4'.upper()
+ wrf_sfc = '134/235/167/165/166/168/129/172/34/31/141/ \
+ 139/170/183/236/39/40/41/42'.upper()
+ lwrt_sfc = wrf_sfc.split('/')
+ for par in lwrt_sfc:
+ if par not in self.params['OG__SL'][0]:
+ self.params['OG__SL'][0] += '/' + par
- try:
- # add vorticity and geopotential height for WRF if necessary
- if c.wrf == '1':
- self.params['OG__ML'][0] += '/Z/VO'
- if '/D' not in self.params['OG__ML'][0]:
- self.params['OG__ML'][0] += '/D'
- #wrf_sfc = 'sp/msl/skt/2t/10u/10v/2d/z/lsm/sst/ci/sd/stl1/ /
- # stl2/stl3/stl4/swvl1/swvl2/swvl3/swvl4'.upper()
- wrf_sfc = '134/235/167/165/166/168/129/172/34/31/141/ \
- 139/170/183/236/39/40/41/42'.upper()
- lwrt_sfc = wrf_sfc.split('/')
- for par in lwrt_sfc:
- if par not in self.params['OG__SL'][0]:
- self.params['OG__SL'][0] += '/' + par
- except:
- pass
else:
self.params['OG_acc_SL'] = ["LSP/CP/SSHF/EWSS/NSSS/SSR", \
'SFC', '1', self.grid]
@@ -327,7 +342,7 @@ class ECFlexpart:
momega, momegadiff, mgauss, msmooth, meta, metadiff, mdpdeta
@Input:
- self: instance of ECFlexpart
+ self: instance of EcFlexpart
The current object of the class.
c: instance of class ControlFile
@@ -351,27 +366,32 @@ class ECFlexpart:
'''
self.inputdir = c.inputdir
- area = asarray(self.area.split('/')).astype(float)
- grid = asarray(self.grid.split('/')).astype(float)
+ area = np.asarray(self.area.split('/')).astype(float)
+ grid = np.asarray(self.grid.split('/')).astype(float)
if area[1] > area[3]:
area[1] -= 360
- zyk = abs((area[3] - area[1] - 360.) + grid[1]) < 1.e-6
maxl = int((area[3] - area[1]) / grid[1]) + 1
maxb = int((area[0] - area[2]) / grid[0]) + 1
with open(self.inputdir + '/' + filename, 'w') as f:
f.write('&NAMGEN\n')
f.write(',\n '.join(['maxl = ' + str(maxl), 'maxb = ' + str(maxb),
- 'mlevel = ' + self.level,
- 'mlevelist = ' + '"' + self.levelist + '"',
- 'mnauf = ' + self.resol, 'metapar = ' + '77',
- 'rlo0 = ' + str(area[1]), 'rlo1 = ' + str(area[3]),
- 'rla0 = ' + str(area[2]), 'rla1 = ' + str(area[0]),
- 'momega = ' + c.omega, 'momegadiff = ' + c.omegadiff,
- 'mgauss = ' + c.gauss, 'msmooth = ' + c.smooth,
- 'meta = ' + c.eta, 'metadiff = ' + c.etadiff,
- 'mdpdeta = ' + c.dpdeta]))
+ 'mlevel = ' + self.level,
+ 'mlevelist = ' + '"' + self.levelist + '"',
+ 'mnauf = ' + self.resol,
+ 'metapar = ' + '77',
+ 'rlo0 = ' + str(area[1]),
+ 'rlo1 = ' + str(area[3]),
+ 'rla0 = ' + str(area[2]),
+ 'rla1 = ' + str(area[0]),
+ 'momega = ' + c.omega,
+ 'momegadiff = ' + c.omegadiff,
+ 'mgauss = ' + c.gauss,
+ 'msmooth = ' + c.smooth,
+ 'meta = ' + c.eta,
+ 'metadiff = ' + c.etadiff,
+ 'mdpdeta = ' + c.dpdeta]))
f.write('\n/\n')
@@ -385,7 +405,7 @@ class ECFlexpart:
Prepares MARS retrievals per grid type and submits them.
@Input:
- self: instance of ECFlexpart
+ self: instance of EcFlexpart
The current object of the class.
server: instance of ECMWFService or ECMWFDataServer
@@ -448,17 +468,27 @@ class ECFlexpart:
# ------ on demand path --------------------------------------------------
if self.basetime is None:
- MR = MARSretrieval(self.server,
- marsclass=self.marsclass, stream=mfstream,
- type=mftype, levtype=pv[1], levelist=pv[2],
- resol=self.resol, gaussian=gaussian,
- accuracy=self.accuracy, grid=pv[3],
- target=mftarget, area=area, date=mfdate,
- time=mftime, number=self.number, step=mfstep,
- expver=self.expver, param=pv[0])
-
- MR.displayInfo()
- MR.dataRetrieve()
+ MR = MarsRetrieval(self.server,
+ marsclass=self.marsclass,
+ stream=mfstream,
+ type=mftype,
+ levtype=pv[1],
+ levelist=pv[2],
+ resol=self.resol,
+ gaussian=gaussian,
+ accuracy=self.accuracy,
+ grid=pv[3],
+ target=mftarget,
+ area=area,
+ date=mfdate,
+ time=mftime,
+ number=self.number,
+ step=mfstep,
+ expver=self.expver,
+ param=pv[0])
+
+ MR.display_info()
+ MR.data_retrieve()
# ------ operational path ------------------------------------------------
else:
# check if mars job requests fields beyond basetime.
@@ -474,13 +504,14 @@ class ECFlexpart:
else:
tm1 = -1
- maxtime = datetime.datetime.strptime(
- mfdate.split('/')[-1] + mftime.split('/')[tm1],
- '%Y%m%d%H') + datetime.timedelta(
- hours=int(mfstep.split('/')[sm1]))
- elimit = datetime.datetime.strptime(
- mfdate.split('/')[-1] +
- self.basetime, '%Y%m%d%H')
+ maxdate = datetime.strptime(mfdate.split('/')[-1] +
+ mftime.split('/')[tm1],
+ '%Y%m%d%H')
+ istep = int(mfstep.split('/')[sm1])
+ maxtime = maxdate + timedelta(hours=istep)
+
+ elimit = datetime.strptime(mfdate.split('/')[-1] +
+ self.basetime, '%Y%m%d%H')
if self.basetime == '12':
# -------------- flux data ----------------------------
@@ -491,117 +522,157 @@ class ECFlexpart:
# if 12h <= maxtime-elimit<12h reduce time for last date
# if maxtime-elimit<12h reduce step for last time
# A split of the MARS job into 2 is likely necessary.
- maxtime = elimit - datetime.timedelta(hours=24)
- mfdate = '/'.join(('/'.join(mfdate.split('/')[:-1]),
- datetime.datetime.strftime(
- maxtime, '%Y%m%d')))
-
- MR = MARSretrieval(self.server,
- marsclass=self.marsclass,
- stream=self.stream, type=mftype,
- levtype=pv[1], levelist=pv[2],
- resol=self.resol, gaussian=gaussian,
- accuracy=self.accuracy, grid=pv[3],
- target=mftarget, area=area,
- date=mfdate, time=mftime,
- number=self.number, step=mfstep,
- expver=self.expver, param=pv[0])
-
- MR.displayInfo()
- MR.dataRetrieve()
-
- maxtime = elimit - datetime.timedelta(hours=12)
- mfdate = datetime.datetime.strftime(maxtime,
- '%Y%m%d')
+ maxtime = elimit - timedelta(hours=24)
+ mfdate = '/'.join(['/'.join(mfdate.split('/')[:-1]),
+ datetime.strftime(maxtime,
+ '%Y%m%d')])
+
+ MR = MarsRetrieval(self.server,
+ marsclass=self.marsclass,
+ stream=self.stream,
+ type=mftype,
+ levtype=pv[1],
+ levelist=pv[2],
+ resol=self.resol,
+ gaussian=gaussian,
+ accuracy=self.accuracy,
+ grid=pv[3],
+ target=mftarget,
+ area=area,
+ date=mfdate,
+ time=mftime,
+ number=self.number,
+ step=mfstep,
+ expver=self.expver,
+ param=pv[0])
+
+ MR.display_info()
+ MR.data_retrieve()
+
+ maxtime = elimit - timedelta(hours=12)
+ mfdate = datetime.strftime(maxtime, '%Y%m%d')
mftime = '00'
mftarget = self.inputdir + "/" + ftype + pk + \
'.' + mfdate + '.' + str(os.getppid()) +\
'.' + str(os.getpid()) + ".grb"
- MR = MARSretrieval(self.server,
- marsclass=self.marsclass,
- stream=self.stream, type=mftype,
- levtype=pv[1], levelist=pv[2],
- resol=self.resol, gaussian=gaussian,
- accuracy=self.accuracy, grid=pv[3],
- target=mftarget, area=area,
- date=mfdate, time=mftime,
- number=self.number, step=mfstep,
- expver=self.expver, param=pv[0])
-
- MR.displayInfo()
- MR.dataRetrieve()
+ MR = MarsRetrieval(self.server,
+ marsclass=self.marsclass,
+ stream=self.stream,
+ type=mftype,
+ levtype=pv[1],
+ levelist=pv[2],
+ resol=self.resol,
+ gaussian=gaussian,
+ accuracy=self.accuracy,
+ grid=pv[3],
+ target=mftarget,
+ area=area,
+ date=mfdate,
+ time=mftime,
+ number=self.number,
+ step=mfstep,
+ expver=self.expver,
+ param=pv[0])
+
+ MR.display_info()
+ MR.data_retrieve()
# -------------- non flux data ------------------------
else:
- MR = MARSretrieval(self.server,
- marsclass=self.marsclass,
- stream=self.stream, type=mftype,
- levtype=pv[1], levelist=pv[2],
- resol=self.resol, gaussian=gaussian,
- accuracy=self.accuracy, grid=pv[3],
- target=mftarget, area=area,
- date=mfdate, time=mftime,
- number=self.number, step=mfstep,
- expver=self.expver, param=pv[0])
-
- MR.displayInfo()
- MR.dataRetrieve()
+ MR = MarsRetrieval(self.server,
+ marsclass=self.marsclass,
+ stream=self.stream,
+ type=mftype,
+ levtype=pv[1],
+ levelist=pv[2],
+ resol=self.resol,
+ gaussian=gaussian,
+ accuracy=self.accuracy,
+ grid=pv[3],
+ target=mftarget,
+ area=area,
+ date=mfdate,
+ time=mftime,
+ number=self.number,
+ step=mfstep,
+ expver=self.expver,
+ param=pv[0])
+
+ MR.display_info()
+ MR.data_retrieve()
else: # basetime == 0 ??? #AP
- maxtime = elimit - datetime.timedelta(hours=24)
- mfdate = datetime.datetime.strftime(maxtime,'%Y%m%d')
+ maxtime = elimit - timedelta(hours=24)
+ mfdate = datetime.strftime(maxtime, '%Y%m%d')
mftimesave = ''.join(mftime)
if '/' in mftime:
times = mftime.split('/')
while ((int(times[0]) +
- int(mfstep.split('/')[0]) <= 12) and
- (pk != 'OG_OROLSM__SL') and 'acc' not in pk):
+ int(mfstep.split('/')[0]) <= 12) and
+ (pk != 'OG_OROLSM__SL') and 'acc' not in pk):
times = times[1:]
if len(times) > 1:
mftime = '/'.join(times)
else:
mftime = times[0]
- MR = MARSretrieval(self.server,
- marsclass=self.marsclass,
- stream=self.stream, type=mftype,
- levtype=pv[1], levelist=pv[2],
- resol=self.resol, gaussian=gaussian,
- accuracy=self.accuracy, grid=pv[3],
- target=mftarget, area=area,
- date=mfdate, time=mftime,
- number=self.number, step=mfstep,
- expver=self.expver, param=pv[0])
-
- MR.displayInfo()
- MR.dataRetrieve()
+ MR = MarsRetrieval(self.server,
+ marsclass=self.marsclass,
+ stream=self.stream,
+ type=mftype,
+ levtype=pv[1],
+ levelist=pv[2],
+ resol=self.resol,
+ gaussian=gaussian,
+ accuracy=self.accuracy,
+ grid=pv[3],
+ target=mftarget,
+ area=area,
+ date=mfdate,
+ time=mftime,
+ number=self.number,
+ step=mfstep,
+ expver=self.expver,
+ param=pv[0])
+
+ MR.display_info()
+ MR.data_retrieve()
if (int(mftimesave.split('/')[0]) == 0 and
- int(mfstep.split('/')[0]) == 0 and
- pk != 'OG_OROLSM__SL'):
- mfdate = datetime.datetime.strftime(elimit,'%Y%m%d')
+ int(mfstep.split('/')[0]) == 0 and
+ pk != 'OG_OROLSM__SL'):
+
+ mfdate = datetime.strftime(elimit, '%Y%m%d')
mftime = '00'
mfstep = '000'
mftarget = self.inputdir + "/" + ftype + pk + \
'.' + mfdate + '.' + str(os.getppid()) +\
'.' + str(os.getpid()) + ".grb"
- MR = MARSretrieval(self.server,
- marsclass=self.marsclass,
- stream=self.stream, type=mftype,
- levtype=pv[1], levelist=pv[2],
- resol=self.resol, gaussian=gaussian,
- accuracy=self.accuracy, grid=pv[3],
- target=mftarget, area=area,
- date=mfdate, time=mftime,
- number=self.number, step=mfstep,
- expver=self.expver, param=pv[0])
-
- MR.displayInfo()
- MR.dataRetrieve()
-
- print("MARS retrieve done... ")
+ MR = MarsRetrieval(self.server,
+ marsclass=self.marsclass,
+ stream=self.stream,
+ type=mftype,
+ levtype=pv[1],
+ levelist=pv[2],
+ resol=self.resol,
+ gaussian=gaussian,
+ accuracy=self.accuracy,
+ grid=pv[3],
+ target=mftarget,
+ area=area,
+ date=mfdate,
+ time=mftime,
+ number=self.number,
+ step=mfstep,
+ expver=self.expver,
+ param=pv[0])
+
+ MR.display_info()
+ MR.data_retrieve()
+
+ print "MARS retrieve done... "
return
@@ -620,7 +691,7 @@ class ECFlexpart:
GRIB2FLEXPART - Conversion of GRIB files to FLEXPART binary format
@Input:
- self: instance of ECFlexpart
+ self: instance of EcFlexpart
The current object of the class.
c: instance of class ControlFile
@@ -641,7 +712,7 @@ class ECFlexpart:
'''
- print('\n\nPostprocessing:\n Format: {}\n'.format(c.format))
+ print '\n\nPostprocessing:\n Format: {}\n'.format(c.format)
if c.ecapi is False:
print('ecstorage: {}\n ecfsdir: {}\n'.
@@ -651,29 +722,29 @@ class ECFlexpart:
if not hasattr(c, 'destination'):
c.destination = os.getenv('DESTINATION')
print('ectrans: {}\n gateway: {}\n destination: {}\n '
- .format(c.ectrans, c.gateway, c.destination))
+ .format(c.ectrans, c.gateway, c.destination))
- print('Output filelist: \n')
- print(self.outputfilelist)
+ print 'Output filelist: \n'
+ print self.outputfilelist
if c.format.lower() == 'grib2':
for ofile in self.outputfilelist:
p = subprocess.check_call(['grib_set', '-s', 'edition=2, \
- productDefinitionTemplateNumber=8',
- ofile, ofile + '_2'])
+ productDefinitionTemplateNumber=8',
+ ofile, ofile + '_2'])
p = subprocess.check_call(['mv', ofile + '_2', ofile])
if int(c.ectrans) == 1 and c.ecapi is False:
for ofile in self.outputfilelist:
p = subprocess.check_call(['ectrans', '-overwrite', '-gateway',
- c.gateway, '-remote', c.destination,
- '-source', ofile])
+ c.gateway, '-remote', c.destination,
+ '-source', ofile])
print('ectrans:', p)
if int(c.ecstorage) == 1 and c.ecapi is False:
for ofile in self.outputfilelist:
p = subprocess.check_call(['ecp', '-o', ofile,
- os.path.expandvars(c.ecfsdir)])
+ os.path.expandvars(c.ecfsdir)])
if c.outputdir != c.inputdir:
for ofile in self.outputfilelist:
@@ -691,11 +762,11 @@ class ECFlexpart:
fname = ofile.split('/')
if '.' in fname[-1]:
l = fname[-1].split('.')
- timestamp = datetime.datetime.strptime(l[0][-6:] + l[1],
- '%y%m%d%H')
- timestamp += datetime.timedelta(hours=int(l[2]))
- cdate = datetime.datetime.strftime(timestamp, '%Y%m%d')
- chms = datetime.datetime.strftime(timestamp, '%H%M%S')
+ timestamp = datetime.strptime(l[0][-6:] + l[1],
+ '%y%m%d%H')
+ timestamp += timedelta(hours=int(l[2]))
+ cdate = datetime.strftime(timestamp, '%Y%m%d')
+ chms = datetime.strftime(timestamp, '%H%M%S')
else:
cdate = '20' + fname[-1][-8:-2]
chms = fname[-1][-2:] + '0000'
@@ -707,7 +778,7 @@ class ECFlexpart:
# generate pathnames file
pwd = os.path.abspath(c.outputdir)
- with open(pwd + '/pathnames','w') as f:
+ with open(pwd + '/pathnames', 'w') as f:
f.write(pwd + '/Options/\n')
f.write(pwd + '/\n')
f.write(pwd + '/\n')
@@ -719,9 +790,8 @@ class ECFlexpart:
os.makedirs(pwd+'/Options')
# read template COMMAND file
- with open(os.path.expandvars(
- os.path.expanduser(c.flexpart_root_scripts)) +
- '/../Options/COMMAND', 'r') as f:
+ with open(os.path.expandvars(os.path.expanduser(
+ c.flexpart_root_scripts)) + '/../Options/COMMAND', 'r') as f:
lflist = f.read().split('\n')
# find index of list where to put in the
@@ -746,10 +816,9 @@ class ECFlexpart:
# change to outputdir and start the grib2flexpart run
# afterwards switch back to the working dir
os.chdir(c.outputdir)
- p = subprocess.check_call([os.path.expandvars(
- os.path.expanduser(c.flexpart_root_scripts)) +
- '/../FLEXPART_PROGRAM/grib2flexpart',
- 'useAvailable', '.'])
+ p = subprocess.check_call([
+ os.path.expandvars(os.path.expanduser(c.flexpart_root_scripts))
+ + '/../FLEXPART_PROGRAM/grib2flexpart', 'useAvailable', '.'])
os.chdir(pwd)
return
@@ -770,10 +839,10 @@ class ECFlexpart:
"stepRange").
@Input:
- self: instance of ECFlexpart
+ self: instance of EcFlexpart
The current object of the class.
- inputfiles: instance of UIOFiles
+ inputfiles: instance of UioFiles
Contains a list of files.
c: instance of class ControlFile
@@ -795,14 +864,14 @@ class ECFlexpart:
table128 = init128(c.ecmwfdatadir +
'/grib_templates/ecmwf_grib1_table_128')
- wrfpars = toparamId('sp/mslp/skt/2t/10u/10v/2d/z/lsm/sst/ci/sd/\
+ wrfpars = to_param_id('sp/mslp/skt/2t/10u/10v/2d/z/lsm/sst/ci/sd/\
stl1/stl2/stl3/stl4/swvl1/swvl2/swvl3/swvl4',
table128)
index_keys = ["date", "time", "step"]
indexfile = c.inputdir + "/date_time_stepRange.idx"
- silentremove(indexfile)
- grib = GribTools(inputfiles.files)
+ silent_remove(indexfile)
+ grib = Gribtools(inputfiles.files)
# creates new index file
iid = grib.index(index_keys=index_keys, index_file=indexfile)
@@ -810,7 +879,7 @@ class ECFlexpart:
index_vals = []
for key in index_keys:
index_vals.append(grib_index_get(iid, key))
- print(index_vals[-1])
+ print index_vals[-1]
# index_vals looks for example like:
# index_vals[0]: ('20171106', '20171107', '20171108') ; date
# index_vals[1]: ('0', '1200', '1800', '600') ; time
@@ -841,39 +910,33 @@ class ECFlexpart:
convertFlag = True
# remove old fort.* files and open new ones
for k, f in fdict.iteritems():
- silentremove(c.inputdir + "/fort." + k)
+ silent_remove(c.inputdir + "/fort." + k)
fdict[k] = open(c.inputdir + '/fort.' + k, 'w')
cdate = str(grib_get(gid, 'date'))
time = grib_get(gid, 'time')
- type = grib_get(gid, 'type')
step = grib_get(gid, 'step')
# create correct timestamp from the three time informations
# date, time, step
- timestamp = datetime.datetime.strptime(
- cdate + '{:0>2}'.format(time/100), '%Y%m%d%H')
- timestamp += datetime.timedelta(hours=int(step))
+ timestamp = datetime.strptime(cdate + '{:0>2}'.format(time/100),
+ '%Y%m%d%H')
+ timestamp += timedelta(hours=int(step))
- cdateH = datetime.datetime.strftime(timestamp, '%Y%m%d%H')
- chms = datetime.datetime.strftime(timestamp, '%H%M%S')
+ cdateH = datetime.strftime(timestamp, '%Y%m%d%H')
if c.basetime is not None:
- slimit = datetime.datetime.strptime(
- c.start_date + '00', '%Y%m%d%H')
+ slimit = datetime.strptime(c.start_date + '00', '%Y%m%d%H')
bt = '23'
if c.basetime == '00':
bt = '00'
- slimit = datetime.datetime.strptime(
- c.end_date + bt, '%Y%m%d%H') - \
- datetime.timedelta(hours=12-int(c.dtime))
+ slimit = datetime.strptime(c.end_date + bt, '%Y%m%d%H')\
+ - timedelta(hours=12-int(c.dtime))
if c.basetime == '12':
bt = '12'
- slimit = datetime.datetime.strptime(
- c.end_date + bt, '%Y%m%d%H') - \
- datetime.timedelta(hours=12-int(c.dtime))
+ slimit = datetime.strptime(c.end_date + bt, '%Y%m%d%H')\
+ - timedelta(hours=12-int(c.dtime))
- elimit = datetime.datetime.strptime(
- c.end_date + bt, '%Y%m%d%H')
+ elimit = datetime.strptime(c.end_date + bt, '%Y%m%d%H')
if timestamp < slimit or timestamp > elimit:
continue
@@ -900,7 +963,6 @@ class ECFlexpart:
break
paramId = grib_get(gid, 'paramId')
gridtype = grib_get(gid, 'gridType')
- datatype = grib_get(gid, 'dataType')
levtype = grib_get(gid, 'typeOfLevel')
if paramId == 133 and gridtype == 'reduced_gg':
# Relative humidity (Q.grb) is used as a template only
@@ -938,7 +1000,7 @@ class ECFlexpart:
grib_write(gid, fdict['16'])
savedfields.append(paramId)
else:
- print('duplicate ' + str(paramId) + ' not written')
+ print 'duplicate ' + str(paramId) + ' not written'
try:
if c.wrf == '1':
@@ -962,16 +1024,17 @@ class ECFlexpart:
pwd = os.getcwd()
os.chdir(c.inputdir)
if os.stat('fort.21').st_size == 0 and int(c.eta) == 1:
- print('Parameter 77 (etadot) is missing, most likely it is \
- not available for this type or date/time\n')
- print('Check parameters CLASS, TYPE, STREAM, START_DATE\n')
- myerror(c, 'fort.21 is empty while parameter eta is set \
+ print 'Parameter 77 (etadot) is missing, most likely it is \
+ not available for this type or date/time\n'
+ print 'Check parameters CLASS, TYPE, STREAM, START_DATE\n'
+ my_error(c, 'fort.21 is empty while parameter eta is set \
to 1 in CONTROL file')
# create the corresponding output file fort.15
# (generated by CONVERT2) + fort.16 (paramId 167 and 168)
- p = subprocess.check_call([os.path.expandvars(
- os.path.expanduser(c.exedir)) + '/CONVERT2'], shell=True)
+ p = subprocess.check_call(
+ [os.path.expandvars(os.path.expanduser(c.exedir)) +
+ '/CONVERT2'], shell=True)
os.chdir(pwd)
# create final output filename, e.g. EN13040500 (ENYYMMDDHH)
@@ -982,7 +1045,7 @@ class ECFlexpart:
else:
suffix = cdateH[2:10]
fnout += suffix
- print("outputfile = " + fnout)
+ print "outputfile = " + fnout
self.outputfilelist.append(fnout) # needed for final processing
# create outputfile and copy all data from intermediate files
@@ -1004,11 +1067,8 @@ class ECFlexpart:
shutil.copyfileobj(
open(c.inputdir + '/fort.25', 'rb'), fout)
- try:
- if c.wrf == '1':
- fwrf.close()
- except:
- pass
+ if c.wrf == '1':
+ fwrf.close()
grib_index_release(iid)
@@ -1024,10 +1084,10 @@ class ECFlexpart:
stress data (dapoly, cubic polynomial).
@Input:
- self: instance of ECFlexpart
+ self: instance of EcFlexpart
The current object of the class.
- inputfiles: instance of UIOFiles
+ inputfiles: instance of UioFiles
Contains a list of files.
c: instance of class ControlFile
@@ -1049,19 +1109,19 @@ class ECFlexpart:
table128 = init128(c.ecmwfdatadir +
'/grib_templates/ecmwf_grib1_table_128')
- pars = toparamId(self.params['OG_acc_SL'][0], table128)
+ pars = to_param_id(self.params['OG_acc_SL'][0], table128)
index_keys = ["date", "time", "step"]
indexfile = c.inputdir + "/date_time_stepRange.idx"
- silentremove(indexfile)
- grib = GribTools(inputfiles.files)
+ silent_remove(indexfile)
+ grib = Gribtools(inputfiles.files)
# creates new index file
iid = grib.index(index_keys=index_keys, index_file=indexfile)
# read values of index keys
index_vals = []
for key in index_keys:
- key_vals = grib_index_get(iid,key)
- print(key_vals)
+ key_vals = grib_index_get(iid, key)
+ print key_vals
# have to sort the steps for disaggregation,
# therefore convert to int first
if key == 'step':
@@ -1082,6 +1142,8 @@ class ECFlexpart:
svalsdict[str(p)] = []
stepsdict[str(p)] = []
+ print 'maxstep: ', c.maxstep
+
for prod in product(*index_vals):
# e.g. prod = ('20170505', '0', '12')
# ( date ,time, step)
@@ -1091,23 +1153,19 @@ class ECFlexpart:
grib_index_select(iid, index_keys[i], prod[i])
gid = grib_new_from_index(iid)
- # do convert2 program if gid at this time is not None,
- # therefore save in hid
- hid = gid
if gid is not None:
cdate = grib_get(gid, 'date')
time = grib_get(gid, 'time')
- type = grib_get(gid, 'type')
step = grib_get(gid, 'step')
# date+time+step-2*dtime
# (since interpolated value valid for step-2*dtime)
- sdate = datetime.datetime(year=cdate/10000,
- month=mod(cdate, 10000)/100,
- day=mod(cdate, 100),
- hour=time/100)
- fdate = sdate + datetime.timedelta(
- hours=step-2*int(c.dtime))
- sdates = sdate + datetime.timedelta(hours=step)
+ sdate = datetime(year=cdate/10000,
+ month=(cdate % 10000)/100,
+ day=(cdate % 100),
+ hour=time/100)
+ fdate = sdate + timedelta(hours=step-2*int(c.dtime))
+ sdates = sdate + timedelta(hours=step)
+ elimit = None
else:
break
@@ -1125,13 +1183,14 @@ class ECFlexpart:
h = open(hnout, 'w')
else:
fnout = c.inputdir + '/flux' + fdate.strftime('%Y%m%d%H')
- gnout = c.inputdir + '/flux' + (fdate+datetime.timedelta(
- hours = int(c.dtime))).strftime('%Y%m%d%H')
+ gnout = c.inputdir + '/flux' + (fdate +
+ timedelta(hours=int(c.dtime))
+ ).strftime('%Y%m%d%H')
hnout = c.inputdir + '/flux' + sdates.strftime('%Y%m%d%H')
g = open(gnout, 'w')
h = open(hnout, 'w')
- print("outputfile = " + fnout)
+ print "outputfile = " + fnout
f = open(fnout, 'w')
# read message for message and store relevant data fields
@@ -1155,7 +1214,7 @@ class ECFlexpart:
else:
fak = 3600.
- values = (reshape(values, (nj, ni))).flatten() / fak
+ values = (np.reshape(values, (nj, ni))).flatten() / fak
vdp.append(values[:]) # save the accumulated values
if step <= int(c.dtime):
svdp.append(values[:] / int(c.dtime))
@@ -1163,7 +1222,7 @@ class ECFlexpart:
svdp.append((vdp[-1] - vdp[-2]) / int(c.dtime))
print(cparamId, atime, step, len(values),
- values[0], std(values))
+ values[0], np.std(values))
# save the 1/3-hourly or specific values
# svdp.append(values[:])
sd.append(step)
@@ -1171,9 +1230,9 @@ class ECFlexpart:
if len(svdp) >= 3:
if len(svdp) > 3:
if cparamId == '142' or cparamId == '143':
- values = Disagg.darain(svdp)
+ values = disaggregation.darain(svdp)
else:
- values = Disagg.dapoly(svdp)
+ values = disaggregation.dapoly(svdp)
if not (step == c.maxstep and c.maxstep > 12 \
or sdates == elimit):
@@ -1196,27 +1255,26 @@ class ECFlexpart:
grib_write(gid, f)
if c.basetime is not None:
- elimit = datetime.datetime.strptime(c.end_date +
- c.basetime,
- '%Y%m%d%H')
+ elimit = datetime.strptime(c.end_date +
+ c.basetime, '%Y%m%d%H')
else:
- elimit = sdate + datetime.timedelta(2*int(c.dtime))
+ elimit = sdate + timedelta(2*int(c.dtime))
# squeeze out information of last two steps contained
# in svdp
# if step+int(c.dtime) == c.maxstep and c.maxstep>12
- # or sdates+datetime.timedelta(hours = int(c.dtime))
+ # or sdates+timedelta(hours = int(c.dtime))
# >= elimit:
# Note that svdp[0] has not been popped in this case
- if (step == c.maxstep and c.maxstep > 12
- or sdates == elimit):
+ if step == c.maxstep and c.maxstep > 12 or \
+ sdates == elimit:
values = svdp[3]
grib_set_values(gid, values)
grib_set(gid, 'step', 0)
- truedatetime = fdate + datetime.timedelta(
- hours=2*int(c.dtime))
+ truedatetime = fdate + timedelta(hours=
+ 2*int(c.dtime))
grib_set(gid, 'time', truedatetime.hour * 100)
grib_set(gid, 'date', truedatetime.year * 10000 +
truedatetime.month * 100 +
@@ -1225,13 +1283,12 @@ class ECFlexpart:
#values = (svdp[1]+svdp[2])/2.
if cparamId == '142' or cparamId == '143':
- values = Disagg.darain(list(reversed(svdp)))
+ values = disaggregation.darain(list(reversed(svdp)))
else:
- values = Disagg.dapoly(list(reversed(svdp)))
+ values = disaggregation.dapoly(list(reversed(svdp)))
- grib_set(gid, 'step',0)
- truedatetime = fdate + datetime.timedelta(
- hours=int(c.dtime))
+ grib_set(gid, 'step', 0)
+ truedatetime = fdate + timedelta(hours=int(c.dtime))
grib_set(gid, 'time', truedatetime.hour * 100)
grib_set(gid, 'date', truedatetime.year * 10000 +
truedatetime.month * 100 +
@@ -1249,4 +1306,5 @@ class ECFlexpart:
grib_index_release(iid)
+ exit()
return
diff --git a/python/GribTools.py b/python/GribTools.py
index 2870334..e79e768 100644
--- a/python/GribTools.py
+++ b/python/GribTools.py
@@ -1,11 +1,5 @@
#!/usr/bin/env python
# -*- coding: utf-8 -*-
-#************************************************************************
-# TODO AP
-# - GribTools name möglicherweise etwas verwirrend.
-# - change self.filename in self.filenames!!!
-# - bis auf --init-- und index wird keine Funktion verwendet!?
-#************************************************************************
#*******************************************************************************
# @Author: Anne Fouilloux (University of Oslo)
#
@@ -35,23 +29,29 @@
#
# @Class Content:
# - __init__
-# - getkeys
-# - setkeys
+# - get_keys
+# - set_keys
# - copy
# - index
#
+# @Class Attributes:
+# - filenames
+#
#*******************************************************************************
# ------------------------------------------------------------------------------
# MODULES
# ------------------------------------------------------------------------------
import os
-from gribapi import *
+from gribapi import grib_new_from_file, grib_is_defined, grib_get, \
+ grib_release, grib_set, grib_write, grib_index_read, \
+ grib_index_new_from_file, grib_index_add_file, \
+ grib_index_write
# ------------------------------------------------------------------------------
# CLASS
# ------------------------------------------------------------------------------
-class GribTools:
+class Gribtools(object):
'''
Class for GRIB utilities (new methods) based on GRIB API
'''
@@ -61,7 +61,7 @@ class GribTools:
def __init__(self, filenames):
'''
@Description:
- Initialise an object of GribTools and assign a list
+ Initialise an object of Gribtools and assign a list
of filenames.
@Input:
@@ -72,12 +72,12 @@ class GribTools:
<nothing>
'''
- self.filename = filenames
+ self.filenames = filenames
return
- def getkeys(self, keynames, wherekeynames=[], wherekeyvalues=[]):
+ def get_keys(self, keynames, wherekeynames=[], wherekeyvalues=[]):
'''
@Description:
get keyvalues for a given list of keynames
@@ -87,10 +87,10 @@ class GribTools:
keynames: list of strings
List of keynames.
- wherekeynames: list of ???, optional
+ wherekeynames: list of strings, optional
Default value is an empty list.
- wherekeyvalues: list of ???, optional
+ wherekeyvalues: list of strings, optional
Default value is an empty list.
@Return:
@@ -98,7 +98,7 @@ class GribTools:
List of keyvalues for given keynames.
'''
- fileid = open(self.filename, 'r')
+ fileid = open(self.filenames, 'r')
return_list = []
@@ -135,8 +135,8 @@ class GribTools:
return return_list
- def setkeys(self, fromfile, keynames, keyvalues, wherekeynames=[],
- wherekeyvalues=[], strict=False, filemode='w'):
+ def set_keys(self, fromfile, keynames, keyvalues, wherekeynames=[],
+ wherekeyvalues=[], strict=False, filemode='w'):
'''
@Description:
Opens the file to read the grib messages and then write
@@ -149,16 +149,16 @@ class GribTools:
fromfile: string
Filename of the input file to read the grib messages from.
- keynames: list of ???
+ keynames: list of strings
List of keynames. Default is an empty list.
- keyvalues: list of ???
+ keyvalues: list of strings
List of keynames. Default is an empty list.
- wherekeynames: list of ???, optional
+ wherekeynames: list of strings, optional
Default value is an empty list.
- wherekeyvalues: list of ???, optional
+ wherekeyvalues: list of strings, optional
Default value is an empty list.
strict: boolean, optional
@@ -173,7 +173,7 @@ class GribTools:
<nothing>
'''
- fout = open(self.filename, filemode)
+ fout = open(self.filenames, filemode)
fin = open(fromfile)
while 1:
@@ -195,24 +195,14 @@ class GribTools:
str(grib_get(gid_in, wherekey))))
i += 1
-#AP is it secured that the order of keynames is equal to keyvalues?
if select:
i = 0
for key in keynames:
grib_set(gid_in, key, keyvalues[i])
i += 1
-#AP this is a redundant code section
-# delete the if/else :
-#
-# grib_write(gid_in, fout)
-#
- if strict:
- if select:
- grib_write(gid_in, fout)
- else:
- grib_write(gid_in, fout)
-#AP end
+ grib_write(gid_in, fout)
+
grib_release(gid_in)
fin.close()
@@ -237,10 +227,10 @@ class GribTools:
different to (False) the keynames/keyvalues list passed to the
function. Default is True.
- keynames: list of ???, optional
+ keynames: list of strings, optional
List of keynames. Default is an empty list.
- keyvalues: list of ???, optional
+ keyvalues: list of strings, optional
List of keynames. Default is an empty list.
filemode: string, optional
@@ -251,7 +241,7 @@ class GribTools:
'''
fin = open(filename_in)
- fout = open(self.filename, filemode)
+ fout = open(self.filenames, filemode)
while 1:
gid_in = grib_new_from_file(fin)
@@ -306,29 +296,24 @@ class GribTools:
iid: integer
Grib index id.
'''
- print("... index will be done")
- self.iid = None
+ print "... index will be done"
+ iid = None
- if (os.path.exists(index_file)):
- self.iid = grib_index_read(index_file)
- print("Use existing index file: %s " % (index_file))
+ if os.path.exists(index_file):
+ iid = grib_index_read(index_file)
+ print "Use existing index file: %s " % (index_file)
else:
- for file in self.filename:
- print("Inputfile: %s " % (file))
- if self.iid is None:
- self.iid = grib_index_new_from_file(file, index_keys)
+ for filename in self.filenames:
+ print "Inputfile: %s " % (filename)
+ if iid is None:
+ iid = grib_index_new_from_file(filename, index_keys)
else:
print 'in else zweig'
- grib_index_add_file(self.iid, file)
-
- if self.iid is not None:
- grib_index_write(self.iid, index_file)
-
- print('... index done')
-
- return self.iid
-
-
+ grib_index_add_file(iid, filename)
+ if iid is not None:
+ grib_index_write(iid, index_file)
+ print '... index done'
+ return iid
diff --git a/python/MARSretrieval.py b/python/MarsRetrieval.py
similarity index 90%
rename from python/MARSretrieval.py
rename to python/MarsRetrieval.py
index 3c1c5b3..eccac65 100644
--- a/python/MARSretrieval.py
+++ b/python/MarsRetrieval.py
@@ -1,9 +1,5 @@
#!/usr/bin/env python
# -*- coding: utf-8 -*-
-#************************************************************************
-# TODO AP
-# -
-#************************************************************************
#*******************************************************************************
# @Author: Anne Fouilloux (University of Oslo)
#
@@ -12,8 +8,8 @@
# @Change History:
#
# November 2015 - Leopold Haimberger (University of Vienna):
-# - optimized displayInfo
-# - optimized dataRetrieve and seperate between python and shell
+# - optimized display_info
+# - optimized data_retrieve and seperate between python and shell
# script call
#
# February 2018 - Anne Philipp (University of Vienna):
@@ -36,8 +32,29 @@
#
# @Class Content:
# - __init__
-# - displayInfo
-# - dataRetrieve
+# - display_info
+# - data_retrieve
+#
+# @Class Attributes:
+# - server
+# - marsclass
+# - dtype
+# - levtype
+# - levelist
+# - repres
+# - date
+# - resol
+# - stream
+# - area
+# - time
+# - step
+# - expver
+# - number
+# - accuracy
+# - grid
+# - gaussian
+# - target
+# - param
#
#*******************************************************************************
@@ -47,16 +64,10 @@
import subprocess
import os
-ecapi = True
-try:
- import ecmwfapi
-except ImportError:
- ecapi = False
-
# ------------------------------------------------------------------------------
# CLASS
# ------------------------------------------------------------------------------
-class MARSretrieval:
+class MarsRetrieval(object):
'''
Class for submitting MARS retrievals.
@@ -67,14 +78,14 @@ class MARSretrieval:
'''
- def __init__(self, server, marsclass = "ei", type = "", levtype = "",
- levelist = "", repres = "", date = "", resol = "", stream = "",
- area = "", time = "", step = "", expver = "1", number = "",
- accuracy = "", grid = "", gaussian = "", target = "",
- param = ""):
+ def __init__(self, server, marsclass="ei", dtype="", levtype="",
+ levelist="", repres="", date="", resol="", stream="",
+ area="", time="", step="", expver="1", number="",
+ accuracy="", grid="", gaussian="", target="",
+ param=""):
'''
@Description:
- Initialises the instance of the MARSretrieval class and
+ Initialises the instance of the MarsRetrieval class and
defines and assigns a set of the necessary retrieval parameters
for the FLEXPART input data.
A description of MARS keywords/arguments, their dependencies
@@ -83,7 +94,7 @@ class MARSretrieval:
https://software.ecmwf.int/wiki/display/UDOC/MARS+keywords
@Input:
- self: instance of MARSretrieval
+ self: instance of MarsRetrieval
For description see class documentation.
server: instance of ECMWFService (from ECMWF Web-API)
@@ -95,7 +106,7 @@ class MARSretrieval:
E4 (ERA40), OD (Operational archive), ea (ERA5).
Default is the ERA-Interim dataset "ei".
- type: string, optional
+ dtype: string, optional
Determines the type of fields to be retrieved.
Selects between observations, images or fields.
Examples for fields: Analysis (an), Forecast (fc),
@@ -274,7 +285,7 @@ class MARSretrieval:
self.server = server
self.marsclass = marsclass
- self.type = type
+ self.dtype = dtype
self.levtype = levtype
self.levelist = levelist
self.repres = repres
@@ -295,13 +306,13 @@ class MARSretrieval:
return
- def displayInfo(self):
+ def display_info(self):
'''
@Description:
Prints all class attributes and their values.
@Input:
- self: instance of MARSretrieval
+ self: instance of MarsRetrieval
For description see class documentation.
@Return:
@@ -313,14 +324,14 @@ class MARSretrieval:
# iterate through all attributes and print them
# with their corresponding values
for item in attrs.items():
- if item[0] in ('server'):
+ if item[0] in 'server':
pass
else:
- print(item[0] + ': ' + str(item[1]))
+ print item[0] + ': ' + str(item[1])
return
- def dataRetrieve(self):
+ def data_retrieve(self):
'''
@Description:
Submits a MARS retrieval. Depending on the existence of
@@ -329,7 +340,7 @@ class MARSretrieval:
are taken from the defined class attributes.
@Input:
- self: instance of MARSretrieval
+ self: instance of MarsRetrieval
For description see class documentation.
@Return:
@@ -343,7 +354,7 @@ class MARSretrieval:
# needed for the retrieval call
s = 'ret'
for k, v in attrs.iteritems():
- if k in ('server'):
+ if k in 'server':
continue
if k == 'marsclass':
k = 'class'
@@ -359,11 +370,11 @@ class MARSretrieval:
try:
self.server.execute(s, target)
except:
- print('MARS Request failed, \
- have you already registered at apps.ecmwf.int?')
+ print 'MARS Request failed, \
+ have you already registered at apps.ecmwf.int?'
raise IOError
if os.stat(target).st_size == 0:
- print('MARS Request returned no data - please check request')
+ print 'MARS Request returned no data - please check request'
raise IOError
# MARS request via extra process in shell
else:
@@ -372,14 +383,14 @@ class MARSretrieval:
stdout=subprocess.PIPE,
stderr=subprocess.PIPE, bufsize=1)
pout = p.communicate(input=s)[0]
- print(pout.decode())
+ print pout.decode()
if 'Some errors reported' in pout.decode():
- print('MARS Request failed - please check request')
+ print 'MARS Request failed - please check request'
raise IOError
if os.stat(target).st_size == 0:
- print('MARS Request returned no data - please check request')
+ print 'MARS Request returned no data - please check request'
raise IOError
return
diff --git a/python/UIOFiles.py b/python/UioFiles.py
similarity index 79%
rename from python/UIOFiles.py
rename to python/UioFiles.py
index 7b01333..dbb5409 100644
--- a/python/UIOFiles.py
+++ b/python/UioFiles.py
@@ -1,11 +1,5 @@
#!/usr/bin/env python
# -*- coding: utf-8 -*-
-#************************************************************************
-# TODO AP
-# - checken welche regelmässigen methoden auf diese Files noch angewendet werden
-# und dann hier implementieren
-# cleanup hier rein
-#************************************************************************
#*******************************************************************************
# @Author: Anne Fouilloux (University of Oslo)
#
@@ -14,15 +8,15 @@
# @Change History:
#
# November 2015 - Leopold Haimberger (University of Vienna):
-# - modified method listFiles to work with glob instead of listdir
-# - added pattern search in method listFiles
+# - modified method list_files to work with glob instead of listdir
+# - added pattern search in method list_files
#
# February 2018 - Anne Philipp (University of Vienna):
# - applied PEP8 style guide
# - added documentation
-# - optimisation of method listFiles since it didn't work correctly
+# - optimisation of method list_files since it didn't work correctly
# for sub directories
-# - additional speed up of method listFiles
+# - additional speed up of method list_files
# - modified the class so that it is initiated with a pattern instead
# of suffixes. Gives more precision in selection of files.
#
@@ -39,8 +33,12 @@
#
# @Class Content:
# - __init__
-# - listFiles
-# - deleteFiles
+# - list_files
+# - delete_files
+#
+# @Class Attributes:
+# - pattern
+# - files
#
#*******************************************************************************
@@ -48,19 +46,17 @@
# MODULES
# ------------------------------------------------------------------------------
import os
-import glob
import fnmatch
-import time
# software specific module from flex_extract
-import profiling
-from Tools import silentremove
+#import profiling
+from tools import silent_remove
# ------------------------------------------------------------------------------
# CLASS
# ------------------------------------------------------------------------------
-class UIOFiles:
+class UioFiles(object):
'''
Class to manipulate files. At initialisation it has the attribute
pattern which stores a regular expression pattern for the files associated
@@ -75,7 +71,7 @@ class UIOFiles:
Assignes a specific pattern for these files.
@Input:
- self: instance of UIOFiles
+ self: instance of UioFiles
Description see class documentation.
pattern: string
@@ -86,18 +82,19 @@ class UIOFiles:
'''
self.pattern = pattern
+ self.files = None
return
#@profiling.timefn
- def listFiles(self, path, callid=0):
+ def list_files(self, path, callid=0):
'''
@Description:
Lists all files in the directory with the matching
regular expression pattern.
@Input:
- self: instance of UIOFiles
+ self: instance of UioFiles
Description see class documentation.
path: string
@@ -131,24 +128,24 @@ class UIOFiles:
# do recursive calls for sub-direcorties
if subdirs:
for subdir in subdirs:
- self.listFiles(os.path.join(path, subdir), callid=1)
+ self.list_files(os.path.join(path, subdir), callid=1)
return
- def deleteFiles(self):
+ def delete_files(self):
'''
@Description:
Deletes the files.
@Input:
- self: instance of UIOFiles
+ self: instance of UioFiles
Description see class documentation.
@Return:
<nothing>
'''
- for f in self.files:
- silentremove(f)
+ for old_file in self.files:
+ silent_remove(old_file)
return
diff --git a/python/Disagg.py b/python/disaggregation.py
similarity index 93%
rename from python/Disagg.py
rename to python/disaggregation.py
index 20aee50..9f285c1 100644
--- a/python/Disagg.py
+++ b/python/disaggregation.py
@@ -1,7 +1,7 @@
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#************************************************************************
-# TODO AP
+# ToDo AP
# - check alist of size 4 ?
# - write a test, IMPORTANT
#************************************************************************
@@ -19,7 +19,7 @@
# - applied PEP8 style guide
# - added structured documentation
# - outsourced the disaggregation functions dapoly and darain
-# to a new module named Disagg
+# to a new module named disaggregation
#
# @License:
# (C) Copyright 2015-2018.
@@ -28,7 +28,7 @@
# which can be obtained at http://www.apache.org/licenses/LICENSE-2.0.
#
# @Module Description:
-# Disaggregation of deaccumulated flux data from an ECMWF model FG field.
+# disaggregationregation of deaccumulated flux data from an ECMWF model FG field.
# Initially the flux data to be concerned are:
# - large-scale precipitation
# - convective precipitation
@@ -69,7 +69,7 @@ def dapoly(alist):
Interpolation of deaccumulated fluxes of an ECMWF model FG field
using a cubic polynomial solution which conserves the integrals
of the fluxes within each timespan.
- Disaggregation is done for 4 accumluated timespans which generates
+ disaggregationregation is done for 4 accumluated timespans which generates
a new, disaggregated value which is output at the central point
of the 4 accumulation timespans. This new point is used for linear
interpolation of the complete timeseries afterwards.
@@ -110,7 +110,7 @@ def darain(alist):
Interpolation of deaccumulated fluxes of an ECMWF model FG rainfall
field using a modified linear solution which conserves the integrals
of the fluxes within each timespan.
- Disaggregation is done for 4 accumluated timespans which generates
+ disaggregationregation is done for 4 accumluated timespans which generates
a new, disaggregated value which is output at the central point
of the 4 accumulation timespans. This new point is used for linear
interpolation of the complete timeseries afterwards.
@@ -143,13 +143,3 @@ def darain(alist):
nfield = xac + xbd
return nfield
-
-
-
-
-
-
-
-
-
-
diff --git a/python/getMARSdata.py b/python/get_mars_data.py
similarity index 74%
rename from python/getMARSdata.py
rename to python/get_mars_data.py
index 43872cb..14f6c03 100755
--- a/python/getMARSdata.py
+++ b/python/get_mars_data.py
@@ -1,9 +1,5 @@
#!/usr/bin/env python
# -*- coding: utf-8 -*-
-#************************************************************************
-# TODO AP
-# - add function docstrings!!!!
-#************************************************************************
#*******************************************************************************
# @Author: Anne Fouilloux (University of Oslo)
#
@@ -12,10 +8,10 @@
# @Change History:
#
# November 2015 - Leopold Haimberger (University of Vienna):
-# - moved the getEIdata program into a function "getMARSdata"
+# - moved the getEIdata program into a function "get_mars_data"
# - moved the AgurmentParser into a seperate function
# - adatpted the function for the use in flex_extract
-# - renamed file to getMARSdata
+# - renamed file to get_mars_data
#
# February 2018 - Anne Philipp (University of Vienna):
# - applied PEP8 style guide
@@ -41,7 +37,7 @@
#
# @Program Content:
# - main
-# - getMARSdata
+# - get_mars_data
#
#*******************************************************************************
@@ -53,23 +49,21 @@ import sys
import datetime
import inspect
try:
- ecapi=True
+ ecapi = True
import ecmwfapi
except ImportError:
- ecapi=False
+ ecapi = False
+
+# software specific classes and modules from flex_extract
+from tools import my_error, normal_exit, interpret_args_and_control
+from EcFlexpart import EcFlexpart
+from UioFiles import UioFiles
# add path to pythonpath so that python finds its buddies
-localpythonpath = os.path.dirname(os.path.abspath(
+LOCAL_PYTHON_PATH = os.path.dirname(os.path.abspath(
inspect.getfile(inspect.currentframe())))
-if localpythonpath not in sys.path:
- sys.path.append(localpythonpath)
-
-# software specific classes and modules from flex_extract
-from ControlFile import ControlFile
-from Tools import myerror, normalexit, \
- interpret_args_and_control
-from ECFlexpart import ECFlexpart
-from UIOFiles import UIOFiles
+if LOCAL_PYTHON_PATH not in sys.path:
+ sys.path.append(LOCAL_PYTHON_PATH)
# ------------------------------------------------------------------------------
# FUNCTION
@@ -77,9 +71,9 @@ from UIOFiles import UIOFiles
def main():
'''
@Description:
- If getMARSdata is called from command line, this function controls
+ If get_mars_data is called from command line, this function controls
the program flow and calls the argumentparser function and
- the getMARSdata function for retrieving EC data.
+ the get_mars_data function for retrieving EC data.
@Input:
<nothing>
@@ -88,12 +82,12 @@ def main():
<nothing>
'''
args, c = interpret_args_and_control()
- getMARSdata(args, c)
- normalexit(c)
+ get_mars_data(c)
+ normal_exit(c)
return
-def getMARSdata(args, c):
+def get_mars_data(c):
'''
@Description:
Retrieves the EC data needed for a FLEXPART simulation.
@@ -102,9 +96,6 @@ def getMARSdata(args, c):
is set.
@Input:
- args: instance of ArgumentParser
- Contains the commandline arguments from script/program call.
-
c: instance of class ControlFile
Contains all the parameters of CONTROL file, which are e.g.:
DAY1(start_date), DAY2(end_date), DTIME, MAXSTEP, TYPE, TIME,
@@ -125,9 +116,9 @@ def getMARSdata(args, c):
if not os.path.exists(c.inputdir):
os.makedirs(c.inputdir)
- print("Retrieving EC data!")
- print("start date %s " % (c.start_date))
- print("end date %s " % (c.end_date))
+ print "Retrieving EC data!"
+ print "start date %s " % (c.start_date)
+ print "end date %s " % (c.end_date)
if ecapi:
server = ecmwfapi.ECMWFService("mars")
@@ -159,9 +150,9 @@ def getMARSdata(args, c):
# -------------- flux data ------------------------------------------------
print 'removing old flux content of ' + c.inputdir
- tobecleaned = UIOFiles('*_acc_*.' + str(os.getppid()) + '.*.grb')
- tobecleaned.listFiles(c.inputdir)
- tobecleaned.deleteFiles()
+ tobecleaned = UioFiles('*_acc_*.' + str(os.getppid()) + '.*.grb')
+ tobecleaned.list_files(c.inputdir)
+ tobecleaned.delete_files()
# if forecast for maximum one day (upto 23h) are to be retrieved,
# collect accumulation data (flux data)
@@ -171,7 +162,7 @@ def getMARSdata(args, c):
day = startm1
while day < endp1:
# retrieve MARS data for the whole period
- flexpart = ECFlexpart(c, fluxes=True)
+ flexpart = EcFlexpart(c, fluxes=True)
tmpday = day + datechunk - datetime.timedelta(days=1)
if tmpday < endp1:
dates = day.strftime("%Y%m%d") + "/to/" + \
@@ -185,7 +176,7 @@ def getMARSdata(args, c):
try:
flexpart.retrieve(server, dates, c.inputdir)
except IOError:
- myerror(c, 'MARS request failed')
+ my_error(c, 'MARS request failed')
day += datechunk
@@ -198,7 +189,7 @@ def getMARSdata(args, c):
day = start
while day <= end:
# retrieve MARS data for the whole period
- flexpart = ECFlexpart(c, fluxes=True)
+ flexpart = EcFlexpart(c, fluxes=True)
tmpday = day + datechunk - datetime.timedelta(days=1)
if tmpday < end:
dates = day.strftime("%Y%m%d") + "/to/" + \
@@ -212,39 +203,38 @@ def getMARSdata(args, c):
try:
flexpart.retrieve(server, dates, c.inputdir)
except IOError:
- myerror(c, 'MARS request failed')
+ my_error(c, 'MARS request failed')
day += datechunk
# -------------- non flux data --------------------------------------------
print 'removing old non flux content of ' + c.inputdir
- tobecleaned = UIOFiles('*__*.' + str(os.getppid()) + '.*.grb')
- tobecleaned.listFiles(c.inputdir)
- tobecleaned.deleteFiles()
+ tobecleaned = UioFiles('*__*.' + str(os.getppid()) + '.*.grb')
+ tobecleaned.list_files(c.inputdir)
+ tobecleaned.delete_files()
day = start
while day <= end:
- # retrieve all non flux MARS data for the whole period
- flexpart = ECFlexpart(c, fluxes=False)
- tmpday = day + datechunk - datetime.timedelta(days=1)
- if tmpday < end:
- dates = day.strftime("%Y%m%d") + "/to/" + \
- tmpday.strftime("%Y%m%d")
- else:
- dates = day.strftime("%Y%m%d") + "/to/" + \
- end.strftime("%Y%m%d")
+ # retrieve all non flux MARS data for the whole period
+ flexpart = EcFlexpart(c, fluxes=False)
+ tmpday = day + datechunk - datetime.timedelta(days=1)
+ if tmpday < end:
+ dates = day.strftime("%Y%m%d") + "/to/" + \
+ tmpday.strftime("%Y%m%d")
+ else:
+ dates = day.strftime("%Y%m%d") + "/to/" + \
+ end.strftime("%Y%m%d")
- print "retrieve " + dates + " in dir " + c.inputdir
+ print "retrieve " + dates + " in dir " + c.inputdir
- try:
- flexpart.retrieve(server, dates, c.inputdir)
- except IOError:
- myerror(c, 'MARS request failed')
+ try:
+ flexpart.retrieve(server, dates, c.inputdir)
+ except IOError:
+ my_error(c, 'MARS request failed')
- day += datechunk
+ day += datechunk
return
if __name__ == "__main__":
main()
-
diff --git a/python/install.py b/python/install.py
index 09cc622..835b506 100755
--- a/python/install.py
+++ b/python/install.py
@@ -1,8 +1,7 @@
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#************************************************************************
-# TODO AP
-# - localpythonpath should not be set in module load section!
+# ToDo AP
# - create a class Installation and divide installation in 3 subdefs for
# ecgate, local and cca seperatly
# - Change History ist nicht angepasst ans File! Original geben lassen
@@ -17,6 +16,7 @@
# February 2018 - Anne Philipp (University of Vienna):
# - applied PEP8 style guide
# - added documentation
+# - moved install_args_and_control in here
#
# @License:
# (C) Copyright 2015-2018.
@@ -44,23 +44,22 @@
# ------------------------------------------------------------------------------
# MODULES
# ------------------------------------------------------------------------------
-import datetime
import os
import sys
import glob
import subprocess
import inspect
-from argparse import ArgumentParser,ArgumentDefaultsHelpFormatter
-
-# add path to pythonpath so that python finds its buddies
-localpythonpath = os.path.dirname(os.path.abspath(
- inspect.getfile(inspect.currentframe())))
-if localpythonpath not in sys.path:
- sys.path.append(localpythonpath)
+from argparse import ArgumentParser, ArgumentDefaultsHelpFormatter
# software specific classes and modules from flex_extract
from ControlFile import ControlFile
+# add path to pythonpath so that python finds its buddies
+LOCAL_PYTHON_PATH = os.path.dirname(os.path.abspath(
+ inspect.getfile(inspect.currentframe())))
+if LOCAL_PYTHON_PATH not in sys.path:
+ sys.path.append(LOCAL_PYTHON_PATH)
+
# ------------------------------------------------------------------------------
# FUNCTIONS
# ------------------------------------------------------------------------------
@@ -77,14 +76,14 @@ def main():
<nothing>
'''
- os.chdir(localpythonpath)
+ os.chdir(LOCAL_PYTHON_PATH)
args, c = install_args_and_control()
if args.install_target is not None:
install_via_gateway(c, args.install_target)
else:
- print('Please specify installation target (local|ecgate|cca)')
- print('use -h or --help for help')
+ print 'Please specify installation target (local|ecgate|cca)'
+ print 'use -h or --help for help'
sys.exit()
@@ -151,25 +150,25 @@ def install_args_and_control():
try:
c = ControlFile(args.controlfile)
- except:
- print('Could not read CONTROL file "' + args.controlfile + '"')
- print('Either it does not exist or its syntax is wrong.')
- print('Try "' + sys.argv[0].split('/')[-1] +
- ' -h" to print usage information')
+ except IOError:
+ print 'Could not read CONTROL file "' + args.controlfile + '"'
+ print 'Either it does not exist or its syntax is wrong.'
+ print 'Try "' + sys.argv[0].split('/')[-1] + \
+ ' -h" to print usage information'
exit(1)
if args.install_target != 'local':
- if (args.ecgid is None or args.ecuid is None or args.gateway is None
- or args.destination is None):
- print('Please enter your ECMWF user id and group id as well as \
+ if args.ecgid is None or args.ecuid is None or args.gateway is None \
+ or args.destination is None:
+ print 'Please enter your ECMWF user id and group id as well as \
the \nname of the local gateway and the ectrans \
- destination ')
- print('with command line options --ecuid --ecgid \
- --gateway --destination')
- print('Try "' + sys.argv[0].split('/')[-1] +
- ' -h" to print usage information')
- print('Please consult ecaccess documentation or ECMWF user support \
- for further details')
+ destination '
+ print 'with command line options --ecuid --ecgid \
+ --gateway --destination'
+ print 'Try "' + sys.argv[0].split('/')[-1] + \
+ ' -h" to print usage information'
+ print 'Please consult ecaccess documentation or ECMWF user support \
+ for further details'
sys.exit(1)
else:
c.ecuid = args.ecuid
@@ -177,10 +176,8 @@ def install_args_and_control():
c.gateway = args.gateway
c.destination = args.destination
- try:
+ if args.makefile:
c.makefile = args.makefile
- except:
- pass
if args.install_target == 'local':
if args.flexpart_root_scripts is None:
@@ -239,7 +236,7 @@ def install_via_gateway(c, target):
data = 'export FLEXPART_ROOT_SCRIPTS=' + \
c.flexpart_root_scripts
else:
- data='export FLEXPART_ROOT_SCRIPTS=$HOME'
+ data = 'export FLEXPART_ROOT_SCRIPTS=$HOME'
if target.lower() != 'local':
if '--workdir' in data:
data = '#SBATCH --workdir=/scratch/ms/' + c.ecgid + \
@@ -291,16 +288,14 @@ def install_via_gateway(c, target):
fo.write('DESTINATION ' + c.destination + '\n')
fo.close()
-
-
if target.lower() == 'local':
# compile CONVERT2
if c.flexpart_root_scripts is None or c.flexpart_root_scripts == '../':
- print('Warning: FLEXPART_ROOT_SCRIPTS has not been specified')
- print('Only CONVERT2 will be compiled in ' + ecd + '/../src')
+ print 'Warning: FLEXPART_ROOT_SCRIPTS has not been specified'
+ print 'Only CONVERT2 will be compiled in ' + ecd + '/../src'
else:
c.flexpart_root_scripts = os.path.expandvars(os.path.expanduser(
- c.flexpart_root_scripts))
+ c.flexpart_root_scripts))
if os.path.abspath(ecd) != os.path.abspath(c.flexpart_root_scripts):
os.chdir('/')
p = subprocess.check_call(['tar', '-cvf',
@@ -310,7 +305,7 @@ def install_via_gateway(c, target):
ecd + 'src'])
try:
os.makedirs(c.flexpart_root_scripts + '/ECMWFDATA7.1')
- except:
+ finally:
pass
os.chdir(c.flexpart_root_scripts + '/ECMWFDATA7.1')
p = subprocess.check_call(['tar', '-xvf',
@@ -328,17 +323,18 @@ def install_via_gateway(c, target):
if flist:
p = subprocess.check_call(['rm'] + flist)
try:
- print(('Using makefile: ' + makefile))
+ print 'Using makefile: ' + makefile
p = subprocess.check_call(['make', '-f', makefile])
- p = subprocess.check_call(['ls', '-l','CONVERT2'])
- except:
- print('compile failed - please edit ' + makefile +
- ' or try another Makefile in the src directory.')
- print('most likely GRIB_API_INCLUDE_DIR, GRIB_API_LIB '
- 'and EMOSLIB must be adapted.')
- print('Available Makefiles:')
- print(glob.glob('Makefile*'))
-
+ p = subprocess.check_call(['ls', '-l', 'CONVERT2'])
+ except subprocess.CalledProcessError as e:
+ print 'compile failed with the following error:'
+ print e.output
+ print 'please edit ' + makefile + \
+ ' or try another Makefile in the src directory.'
+ print 'most likely GRIB_API_INCLUDE_DIR, GRIB_API_LIB \
+ and EMOSLIB must be adapted.'
+ print 'Available Makefiles:'
+ print glob.glob('Makefile*')
elif target.lower() == 'ecgate':
os.chdir('/')
p = subprocess.check_call(['tar', '-cvf',
@@ -351,18 +347,24 @@ def install_via_gateway(c, target):
ecd + '../ECMWFDATA7.1.tar',
'ecgate:/home/ms/' + c.ecgid + '/' +
c.ecuid + '/ECMWFDATA7.1.tar'])
- except:
- print('ecaccess-file-put failed! Probably the eccert key has expired.')
+ except subprocess.CalledProcessError as e:
+ print 'ecaccess-file-put failed! \
+ Probably the eccert key has expired.'
+ exit(1)
+
+ try:
+ p = subprocess.check_call(['ecaccess-job-submit',
+ '-queueName',
+ target,
+ ecd + 'python/compilejob.ksh'])
+ print 'compilejob.ksh has been submitted to ecgate for \
+ installation in ' + c.ec_flexpart_root_scripts + \
+ '/ECMWFDATA7.1'
+ print 'You should get an email with subject flexcompile within \
+ the next few minutes'
+ except subprocess.CalledProcessError as e:
+ print 'ecaccess-job-submit failed!'
exit(1)
- p = subprocess.check_call(['ecaccess-job-submit',
- '-queueName',
- target,
- ecd + 'python/compilejob.ksh'])
- print('compilejob.ksh has been submitted to ecgate for '
- 'installation in ' + c.ec_flexpart_root_scripts +
- '/ECMWFDATA7.1')
- print('You should get an email with subject flexcompile within '
- 'the next few minutes')
elif target.lower() == 'cca':
os.chdir('/')
@@ -376,23 +378,27 @@ def install_via_gateway(c, target):
ecd + '../ECMWFDATA7.1.tar',
'cca:/home/ms/' + c.ecgid + '/' +
c.ecuid + '/ECMWFDATA7.1.tar'])
- except:
- print('ecaccess-file-put failed! '
- 'Probably the eccert key has expired.')
+ except subprocess.CalledProcessError as e:
+ print 'ecaccess-file-put failed! \
+ Probably the eccert key has expired.'
exit(1)
- p=subprocess.check_call(['ecaccess-job-submit',
- '-queueName',
- target,
- ecd + 'python/compilejob.ksh'])
- print('compilejob.ksh has been submitted to cca for installation in ' +
- c.ec_flexpart_root_scripts + '/ECMWFDATA7.1')
- print('You should get an email with subject flexcompile '
- 'within the next few minutes')
+ try:
+ p = subprocess.check_call(['ecaccess-job-submit',
+ '-queueName',
+ target,
+ ecd + 'python/compilejob.ksh'])
+ print 'compilejob.ksh has been submitted to cca for installation in ' +\
+ c.ec_flexpart_root_scripts + '/ECMWFDATA7.1'
+ print 'You should get an email with subject flexcompile \
+ within the next few minutes'
+ except subprocess.CalledProcessError as e:
+ print 'ecaccess-job-submit failed!'
+ exit(1)
else:
- print('ERROR: unknown installation target ', target)
- print('Valid targets: ecgate, cca, local')
+ print 'ERROR: unknown installation target ', target
+ print 'Valid targets: ecgate, cca, local'
return
diff --git a/python/plot_retrieved.py b/python/plot_retrieved.py
index b5a086f..d924c35 100755
--- a/python/plot_retrieved.py
+++ b/python/plot_retrieved.py
@@ -1,7 +1,7 @@
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#************************************************************************
-# TODO AP
+# ToDo AP
# - documentation der Funktionen
# - docu der progam functionality
# - apply pep8
@@ -18,7 +18,7 @@
# - added documentation
# - created function main and moved the two function calls for
# arguments and plotting into it
-# - added function getBasics to extract the boundary conditions
+# - added function get_basics to extract the boundary conditions
# of the data fields from the first grib file it gets.
#
# @License:
@@ -32,11 +32,11 @@
#
# @Program Content:
# - main
-# - getBasics
-# - plotRetrieved
-# - plotTS
-# - plotMap
-# - getPlotArgs
+# - get_basics
+# - plot_retrieved
+# - plot_timeseries
+# - plot_map
+# - get_plot_args
#
#*******************************************************************************
@@ -48,48 +48,36 @@ import datetime
import os
import inspect
import sys
-import glob
from argparse import ArgumentParser, ArgumentDefaultsHelpFormatter
-
-from matplotlib.pylab import *
-import matplotlib.patches as mpatches
-from mpl_toolkits.basemap import Basemap, addcyclic
-import matplotlib.colors as mcolors
-from matplotlib.font_manager import FontProperties
-from matplotlib.patches import Polygon
-import matplotlib.cm as cmx
-import matplotlib.colors as colors
-#from rasotools.utils import stats
-
-font = {'family': 'monospace', 'size': 12}
-matplotlib.rcParams['xtick.major.pad'] = '20'
-
-matplotlib.rc('font', **font)
-
-from eccodes import *
+import matplotlib
+import matplotlib.pyplot as plt
+from mpl_toolkits.basemap import Basemap
+from eccodes import codes_grib_new_from_file, codes_get, codes_release, \
+ codes_get_values
import numpy as np
-# add path to pythonpath so that python finds its buddies
-localpythonpath = os.path.dirname(os.path.abspath(
- inspect.getfile(inspect.currentframe())))
-if localpythonpath not in sys.path:
- sys.path.append(localpythonpath)
-
# software specific classes and modules from flex_extract
-from Tools import silentremove
from ControlFile import ControlFile
-#from GribTools import GribTools
-from UIOFiles import UIOFiles
+from UioFiles import UioFiles
+
+# add path to pythonpath so that python finds its buddies
+LOCAL_PYTHON_PATH = os.path.dirname(os.path.abspath(
+ inspect.getfile(inspect.currentframe())))
+if LOCAL_PYTHON_PATH not in sys.path:
+ sys.path.append(LOCAL_PYTHON_PATH)
+font = {'family': 'monospace', 'size': 12}
+matplotlib.rcParams['xtick.major.pad'] = '20'
+matplotlib.rc('font', **font)
# ------------------------------------------------------------------------------
# FUNCTION
# ------------------------------------------------------------------------------
def main():
'''
@Description:
- If plotRetrieved is called from command line, this function controls
+ If plot_retrieved is called from command line, this function controls
the program flow and calls the argumentparser function and
- the plotRetrieved function for plotting the retrieved GRIB data.
+ the plot_retrieved function for plotting the retrieved GRIB data.
@Input:
<nothing>
@@ -97,12 +85,12 @@ def main():
@Return:
<nothing>
'''
- args, c = getPlotArgs()
- plotRetrieved(args, c)
+ args, c = get_plot_args()
+ plot_retrieved(c)
return
-def getBasics(ifile, verb=False):
+def get_basics(ifile, verb=False):
"""
@Description:
An example grib file will be opened and basic information will
@@ -112,6 +100,7 @@ def getBasics(ifile, verb=False):
@Input:
ifile: string
Contains the full absolute path to the ECMWF grib file.
+
verb (opt): bool
Is True if there should be extra output in verbose mode.
Default value is False.
@@ -126,7 +115,6 @@ def getBasics(ifile, verb=False):
'jDirectionIncrementInDegrees',
'iDirectionIncrementInDegrees'
"""
- from eccodes import *
data = {}
@@ -140,37 +128,38 @@ def getBasics(ifile, verb=False):
gid = codes_grib_new_from_file(f)
# information needed from grib message
- keys = [
- 'Ni',
+ keys = ['Ni',
'Nj',
'latitudeOfFirstGridPointInDegrees',
'longitudeOfFirstGridPointInDegrees',
'latitudeOfLastGridPointInDegrees',
'longitudeOfLastGridPointInDegrees',
'jDirectionIncrementInDegrees',
- 'iDirectionIncrementInDegrees'
- ]
+ 'iDirectionIncrementInDegrees']
- if verb: print('\nInformations are: ')
+ if verb:
+ print '\nInformations are: '
for key in keys:
# Get the value of the key in a grib message.
- data[key] = codes_get(gid,key)
- if verb: print "%s = %s" % (key,data[key])
- if verb: print '\n'
+ data[key] = codes_get(gid, key)
+ if verb:
+ print "%s = %s" % (key, data[key])
+ if verb:
+ print '\n'
# Free the memory for the message referred as gribid.
codes_release(gid)
return data
-def getFilesPerDate(files, datelist):
+def get_files_per_date(files, datelist):
'''
@Description:
The filenames contain dates which are used to select a list
of files for a specific time period specified in datelist.
@Input:
- files: instance of UIOFiles
+ files: instance of UioFiles
For description see class documentation.
It contains the attribute "files" which is a list of pathes
to filenames.
@@ -184,24 +173,21 @@ def getFilesPerDate(files, datelist):
'''
filelist = []
- for file in files:
- fdate = file[-8:]
- ddate = datetime.datetime.strptime(fdate, '%y%m%d%H')
+ for filename in files:
+ filedate = filename[-8:]
+ ddate = datetime.datetime.strptime(filedate, '%y%m%d%H')
if ddate in datelist:
- filelist.append(file)
+ filelist.append(filename)
return filelist
-def plotRetrieved(args, c):
+def plot_retrieved(c):
'''
@Description:
Reads GRIB data from a specified time period, a list of levels
and a specified list of parameter.
@Input:
- args: instance of ArgumentParser
- Contains the commandline arguments from script/program call.
-
c: instance of class ControlFile
Contains all necessary information of a CONTROL file. The parameters
are: DAY1, DAY2, DTIME, MAXSTEP, TYPE, TIME, STEP, CLASS, STREAM,
@@ -228,40 +214,16 @@ def plotRetrieved(args, c):
print 'datelist: ', datelist
- c.paramIds = asarray(c.paramIds, dtype='int')
- c.levels = asarray(c.levels, dtype='int')
- c.area = asarray(c.area)
-
- # index_keys = ["date", "time", "step"]
- # indexfile = c.inputdir + "/date_time_stepRange.idx"
- # silentremove(indexfile)
- # grib = GribTools(inputfiles.files)
- # # creates new index file
- # iid = grib.index(index_keys=index_keys, index_file=indexfile)
-
- # # read values of index keys
- # index_vals = []
- # for key in index_keys:
- # index_vals.append(grib_index_get(iid, key))
- # print(index_vals[-1])
- # # index_vals looks for example like:
- # # index_vals[0]: ('20171106', '20171107', '20171108') ; date
- # # index_vals[1]: ('0', '1200', '1800', '600') ; time
- # # index_vals[2]: ('0', '12', '3', '6', '9') ; stepRange
-
-
+ c.paramIds = np.asarray(c.paramIds, dtype='int')
+ c.levels = np.asarray(c.levels, dtype='int')
+ c.area = np.asarray(c.area)
-
- #index_keys = ["date", "time", "step", "paramId"]
- #indexfile = c.inputdir + "/date_time_stepRange.idx"
- #silentremove(indexfile)
-
- files = UIOFiles(c.prefix+'*')
- files.listFiles(c.inputdir)
- ifiles = getFilesPerDate(files.files, datelist)
+ files = UioFiles(c.prefix+'*')
+ files.list_files(c.inputdir)
+ ifiles = get_files_per_date(files.files, datelist)
ifiles.sort()
- gdict = getBasics(ifiles[0], verb=False)
+ gdict = get_basics(ifiles[0], verb=False)
fdict = dict()
fmeta = dict()
@@ -273,14 +235,14 @@ def plotRetrieved(args, c):
fmeta[key] = []
fstamp[key] = []
- for file in ifiles:
- f = open(file)
- print( "Opening file for reading data --- %s" % file)
- fdate = datetime.datetime.strptime(file[-8:], "%y%m%d%H")
+ for filename in ifiles:
+ f = open(filename)
+ print "Opening file for reading data --- %s" % filename
+ fdate = datetime.datetime.strptime(filename[-8:], "%y%m%d%H")
# Load in memory a grib message from a file.
gid = codes_grib_new_from_file(f)
- while(gid is not None):
+ while gid is not None:
gtype = codes_get(gid, 'type')
paramId = codes_get(gid, 'paramId')
parameterName = codes_get(gid, 'parameterName')
@@ -289,32 +251,32 @@ def plotRetrieved(args, c):
if paramId in c.paramIds and level in c.levels:
key = '{:0>3}_{:0>3}'.format(paramId, level)
print 'key: ', key
- if len(fstamp[key]) != 0 :
+ if fstamp[key]:
for i in range(len(fstamp[key])):
if fdate < fstamp[key][i]:
fstamp[key].insert(i, fdate)
fmeta[key].insert(i, [paramId, parameterName, gtype,
- fdate, level])
- fdict[key].insert(i, flipud(reshape(
- codes_get_values(gid),
- [gdict['Nj'], gdict['Ni']])))
+ fdate, level])
+ fdict[key].insert(i, np.flipud(np.reshape(
+ codes_get_values(gid),
+ [gdict['Nj'], gdict['Ni']])))
break
elif fdate > fstamp[key][i] and i == len(fstamp[key])-1:
fstamp[key].append(fdate)
fmeta[key].append([paramId, parameterName, gtype,
- fdate, level])
- fdict[key].append(flipud(reshape(
- codes_get_values(gid),
- [gdict['Nj'], gdict['Ni']])))
+ fdate, level])
+ fdict[key].append(np.flipud(np.reshape(
+ codes_get_values(gid),
+ [gdict['Nj'], gdict['Ni']])))
break
elif fdate > fstamp[key][i] and i != len(fstamp[key])-1 \
and fdate < fstamp[key][i+1]:
fstamp[key].insert(i, fdate)
fmeta[key].insert(i, [paramId, parameterName, gtype,
- fdate, level])
- fdict[key].insert(i, flipud(reshape(
- codes_get_values(gid),
- [gdict['Nj'], gdict['Ni']])))
+ fdate, level])
+ fdict[key].insert(i, np.flipud(np.reshape(
+ codes_get_values(gid),
+ [gdict['Nj'], gdict['Ni']])))
break
else:
pass
@@ -322,7 +284,7 @@ def plotRetrieved(args, c):
fstamp[key].append(fdate)
fmeta[key].append((paramId, parameterName, gtype,
fdate, level))
- fdict[key].append(flipud(reshape(
+ fdict[key].append(np.flipud(np.reshape(
codes_get_values(gid), [gdict['Nj'], gdict['Ni']])))
codes_release(gid)
@@ -331,25 +293,21 @@ def plotRetrieved(args, c):
gid = codes_grib_new_from_file(f)
f.close()
- #print 'fstamp: ', fstamp
- #exit()
- for k in fdict.keys():
- print 'fmeta: ', len(fmeta),fmeta
+ for k in fdict.iterkeys():
+ print 'fmeta: ', len(fmeta), fmeta
fml = fmeta[k]
fdl = fdict[k]
print 'fm1: ', len(fml), fml
- #print 'fd1: ', fdl
- #print zip(fdl, fml)
for fd, fm in zip(fdl, fml):
print fm
ftitle = fm[1] + ' {} '.format(fm[-1]) + \
- datetime.datetime.strftime(fm[3], '%Y%m%d%H') #+ ' ' + stats(fd)
+ datetime.datetime.strftime(fm[3], '%Y%m%d%H')
pname = '_'.join(fm[1].split()) + '_{}_'.format(fm[-1]) + \
datetime.datetime.strftime(fm[3], '%Y%m%d%H')
- plotMap(c, fd, fm, gdict, ftitle, pname, 'png')
+ plot_map(c, fd, fm, gdict, ftitle, pname, 'png')
- for k in fdict.keys():
+ for k in fdict.iterkeys():
fml = fmeta[k]
fdl = fdict[k]
fsl = fstamp[k]
@@ -357,25 +315,35 @@ def plotRetrieved(args, c):
fm = fml[0]
fd = fdl[0]
ftitle = fm[1] + ' {} '.format(fm[-1]) + \
- datetime.datetime.strftime(fm[3], '%Y%m%d%H') #+ ' ' + stats(fd)
+ datetime.datetime.strftime(fm[3], '%Y%m%d%H')
pname = '_'.join(fm[1].split()) + '_{}_'.format(fm[-1]) + \
datetime.datetime.strftime(fm[3], '%Y%m%d%H')
- lat = -20
- lon = 20
- plotTS(c, fdl, fml, fsl, lat, lon,
- gdict, ftitle, pname, 'png')
+ lat = -20.
+ lon = 20.
+ plot_timeseries(c, fdl, fml, fsl, lat, lon, gdict,
+ ftitle, pname, 'png')
return
-def plotTS(c, flist, fmetalist, ftimestamps, lat, lon,
- gdict, ftitle, filename, fending, show=False):
+def plot_timeseries(c, flist, fmetalist, ftimestamps, lat, lon,
+ gdict, ftitle, filename, fending, show=False):
'''
@Description:
+ Creates a timeseries plot for a given lat/lon position.
@Input:
- c:
+ c: instance of class ControlFile
+ Contains all necessary information of a CONTROL file. The parameters
+ are: DAY1, DAY2, DTIME, MAXSTEP, TYPE, TIME, STEP, CLASS, STREAM,
+ NUMBER, EXPVER, GRID, LEFT, LOWER, UPPER, RIGHT, LEVEL, LEVELIST,
+ RESOL, GAUSS, ACCURACY, OMEGA, OMEGADIFF, ETA, ETADIFF, DPDETA,
+ SMOOTH, FORMAT, ADDPAR, WRF, CWC, PREFIX, ECSTORAGE, ECTRANS,
+ ECFSDIR, MAILOPS, MAILFAIL, GRIB2FLEXPART, DEBUG, INPUTDIR,
+ OUTPUTDIR, FLEXPART_ROOT_SCRIPTS
+ For more information about format and content of the parameter see
+ documentation.
- flist:
+ flist: numpy array, 2d
The actual data values to be plotted from the grib messages.
fmetalist: list of strings
@@ -385,11 +353,20 @@ def plotTS(c, flist, fmetalist, ftimestamps, lat, lon,
ftimestamps: list of datetime
Contains the time stamps.
- lat:
+ lat: float
+ The latitude for which the timeseries should be plotted.
- lon:
+ lon: float
+ The longitude for which the timeseries should be plotted.
- gdict:
+ gdict: dict
+ Contains basic informations of the ECMWF grib files, e.g.
+ 'Ni', 'Nj', 'latitudeOfFirstGridPointInDegrees',
+ 'longitudeOfFirstGridPointInDegrees',
+ 'latitudeOfLastGridPointInDegrees',
+ 'longitudeOfLastGridPointInDegrees',
+ 'jDirectionIncrementInDegrees',
+ 'iDirectionIncrementInDegrees'
ftitle: string
The title of the timeseries.
@@ -410,39 +387,36 @@ def plotTS(c, flist, fmetalist, ftimestamps, lat, lon,
t1 = time.time()
- llx = gdict['longitudeOfFirstGridPointInDegrees']
- if llx > 180. :
- llx -= 360.
- lly = gdict['latitudeOfLastGridPointInDegrees']
- dxout = gdict['iDirectionIncrementInDegrees']
- dyout = gdict['jDirectionIncrementInDegrees']
- urx = gdict['longitudeOfLastGridPointInDegrees']
- ury = gdict['latitudeOfFirstGridPointInDegrees']
- numxgrid = gdict['Ni']
- numygrid = gdict['Nj']
-
- farr = asarray(flist)
+ #llx = gdict['longitudeOfFirstGridPointInDegrees']
+ #if llx > 180. :
+ # llx -= 360.
+ #lly = gdict['latitudeOfLastGridPointInDegrees']
+ #dxout = gdict['iDirectionIncrementInDegrees']
+ #dyout = gdict['jDirectionIncrementInDegrees']
+ #urx = gdict['longitudeOfLastGridPointInDegrees']
+ #ury = gdict['latitudeOfFirstGridPointInDegrees']
+ #numxgrid = gdict['Ni']
+ #numygrid = gdict['Nj']
+
+ farr = np.asarray(flist)
#(time, lat, lon)
- lonindex = linspace(llx, urx, numxgrid)
- latindex = linspace(lly, ury, numygrid)
- #print len(lonindex), len(latindex), farr.shape
-
- #latindex = (lat + 90) * 180 / (gdict['Nj'] - 1)
- #lonindex = (lon + 179) * 360 / gdict['Ni']
- #print latindex, lonindex
+ #lonindex = linspace(llx, urx, numxgrid)
+ #latindex = linspace(lly, ury, numygrid)
-
- ts = farr[:, 0, 0]#latindex[0], lonindex[0]]
+ ts = farr[:, 0, 0]
fig = plt.figure(figsize=(12, 6.7))
plt.plot(ftimestamps, ts)
plt.title(ftitle)
- plt.savefig(c.outputdir+'/'+filename+'_TS.'+fending, facecolor=fig.get_facecolor(), edgecolor='none',format=fending)
+ plt.savefig(c.outputdir + '/' + filename + '_TS.' + fending,
+ facecolor=fig.get_facecolor(),
+ edgecolor='none',
+ format=fending)
print 'created ', c.outputdir + '/' + filename
- if show == True:
+ if show:
plt.show()
fig.clf()
plt.close(fig)
@@ -451,9 +425,10 @@ def plotTS(c, flist, fmetalist, ftimestamps, lat, lon,
return
-def plotMap(c, flist, fmetalist, gdict, ftitle, filename, fending, show=False):
+def plot_map(c, flist, fmetalist, gdict, ftitle, filename, fending, show=False):
'''
@Description:
+ Creates a basemap plot with imshow for a given data field.
@Input:
c: instance of class ControlFile
@@ -467,9 +442,12 @@ def plotMap(c, flist, fmetalist, gdict, ftitle, filename, fending, show=False):
For more information about format and content of the parameter see
documentation.
- flist
+ flist: numpy array, 2d
+ The actual data values to be plotted from the grib messages.
- fmetalist
+ fmetalist: list of strings
+ Contains some meta date for the data field to be plotted:
+ parameter id, parameter Name, grid type, datetime, level
gdict: dict
Contains basic informations of the ECMWF grib files, e.g.
@@ -503,60 +481,81 @@ def plotMap(c, flist, fmetalist, gdict, ftitle, filename, fending, show=False):
#mbaxes = fig.add_axes([0.05, 0.15, 0.8, 0.7])
llx = gdict['longitudeOfFirstGridPointInDegrees'] #- 360
- if llx > 180. :
+ if llx > 180.:
llx -= 360.
lly = gdict['latitudeOfLastGridPointInDegrees']
- dxout = gdict['iDirectionIncrementInDegrees']
- dyout = gdict['jDirectionIncrementInDegrees']
+ #dxout = gdict['iDirectionIncrementInDegrees']
+ #dyout = gdict['jDirectionIncrementInDegrees']
urx = gdict['longitudeOfLastGridPointInDegrees']
ury = gdict['latitudeOfFirstGridPointInDegrees']
- numxgrid = gdict['Ni']
- numygrid = gdict['Nj']
+ #numxgrid = gdict['Ni']
+ #numygrid = gdict['Nj']
m = Basemap(projection='cyl', llcrnrlon=llx, llcrnrlat=lly,
- urcrnrlon=urx, urcrnrlat=ury,resolution='i')
+ urcrnrlon=urx, urcrnrlat=ury, resolution='i')
- lw = 0.5
+ #lw = 0.5
m.drawmapboundary()
- x = linspace(llx, urx, numxgrid)
- y = linspace(lly, ury, numygrid)
+ #x = linspace(llx, urx, numxgrid)
+ #y = linspace(lly, ury, numygrid)
- xx, yy = m(*meshgrid(x, y))
+ #xx, yy = m(*meshgrid(x, y))
#s = m.contourf(xx, yy, flist)
s = plt.imshow(flist.T,
- extent=(llx, urx, lly, ury),
- alpha=1.0,
- interpolation='nearest'
- #vmin=vn,
- #vmax=vx,
- #cmap=my_cmap,
- #levels=levels,
- #cmap=my_cmap,
- #norm=LogNorm(vn,vx)
- )
-
- title(ftitle, y=1.08)
+ extent=(llx, urx, lly, ury),
+ alpha=1.0,
+ interpolation='nearest'
+ #vmin=vn,
+ #vmax=vx,
+ #cmap=my_cmap,
+ #levels=levels,
+ #cmap=my_cmap,
+ #norm=LogNorm(vn,vx)
+ )
+
+ plt.title(ftitle, y=1.08)
cb = m.colorbar(s, location="right", pad="10%")
- #cb.set_label('Contribution per cell (ng m$^{-3}$)',size=14)
-
- thickline = np.arange(lly,ury+1,10.)
- thinline = np.arange(lly,ury+1,5.)
- m.drawparallels(thickline,color='gray',dashes=[1,1],linewidth=0.5,labels=[1,1,1,1], xoffset=1.) # draw parallels
- m.drawparallels(np.setdiff1d(thinline,thickline),color='lightgray',dashes=[1,1],linewidth=0.5,labels=[0,0,0,0]) # draw parallels
-
- thickline = np.arange(llx,urx+1,10.)
- thinline = np.arange(llx,urx+1,5.)
- m.drawmeridians(thickline,color='gray',dashes=[1,1],linewidth=0.5,labels=[1,1,1,1],yoffset=1.) # draw meridians
- m.drawmeridians(np.setdiff1d(thinline,thickline),color='lightgray',dashes=[1,1],linewidth=0.5,labels=[0,0,0,0]) # draw meridians
+ cb.set_label('label', size=14)
+
+ thickline = np.arange(lly, ury+1, 10.)
+ thinline = np.arange(lly, ury+1, 5.)
+ m.drawparallels(thickline,
+ color='gray',
+ dashes=[1, 1],
+ linewidth=0.5,
+ labels=[1, 1, 1, 1],
+ xoffset=1.)
+ m.drawparallels(np.setdiff1d(thinline, thickline),
+ color='lightgray',
+ dashes=[1, 1],
+ linewidth=0.5,
+ labels=[0, 0, 0, 0])
+
+ thickline = np.arange(llx, urx+1, 10.)
+ thinline = np.arange(llx, urx+1, 5.)
+ m.drawmeridians(thickline,
+ color='gray',
+ dashes=[1, 1],
+ linewidth=0.5,
+ labels=[1, 1, 1, 1],
+ yoffset=1.)
+ m.drawmeridians(np.setdiff1d(thinline, thickline),
+ color='lightgray',
+ dashes=[1, 1],
+ linewidth=0.5,
+ labels=[0, 0, 0, 0])
m.drawcoastlines()
m.drawcountries()
- plt.savefig(c.outputdir+'/'+filename+'_MAP.'+fending, facecolor=fig.get_facecolor(), edgecolor='none',format=fending)
+ plt.savefig(c.outputdir + '/' + filename + '_MAP.' + fending,
+ facecolor=fig.get_facecolor(),
+ edgecolor='none',
+ format=fending)
print 'created ', c.outputdir + '/' + filename
- if show == True:
+ if show:
plt.show()
fig.clf()
plt.close(fig)
@@ -565,7 +564,7 @@ def plotMap(c, flist, fmetalist, gdict, ftitle, filename, fending, show=False):
return
-def getPlotArgs():
+def get_plot_args():
'''
@Description:
Assigns the command line arguments and reads CONTROL file
@@ -596,13 +595,13 @@ def getPlotArgs():
# the most important arguments
parser.add_argument("--start_date", dest="start_date",
help="start date YYYYMMDD")
- parser.add_argument( "--end_date", dest="end_date",
- help="end_date YYYYMMDD")
+ parser.add_argument("--end_date", dest="end_date",
+ help="end_date YYYYMMDD")
parser.add_argument("--start_step", dest="start_step",
help="start step in hours")
- parser.add_argument( "--end_step", dest="end_step",
- help="end step in hours")
+ parser.add_argument("--end_step", dest="end_step",
+ help="end step in hours")
# some arguments that override the default in the CONTROL file
parser.add_argument("--levelist", dest="levelist",
@@ -634,9 +633,8 @@ def getPlotArgs():
c = ControlFile(args.controlfile)
except IOError:
try:
- c = ControlFile(localpythonpath + args.controlfile)
-
- except:
+ c = ControlFile(LOCAL_PYTHON_PATH + args.controlfile)
+ except IOError:
print 'Could not read CONTROL file "' + args.controlfile + '"'
print 'Either it does not exist or its syntax is wrong.'
print 'Try "' + sys.argv[0].split('/')[-1] + \
@@ -681,4 +679,3 @@ def getPlotArgs():
if __name__ == "__main__":
main()
-
diff --git a/python/prepareFLEXPART.py b/python/prepare_flexpart.py
similarity index 79%
rename from python/prepareFLEXPART.py
rename to python/prepare_flexpart.py
index b1e0b86..2e5a160 100755
--- a/python/prepareFLEXPART.py
+++ b/python/prepare_flexpart.py
@@ -1,9 +1,7 @@
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#************************************************************************
-# TODO AP
-# - wieso cleanup in main wenn es in prepareflexpart bereits abgefragt wurde?
-# doppelt gemoppelt?
+# ToDo AP
# - wieso start=startm1 wenn basetime = 0 ? wenn die fluxes nicht mehr
# relevant sind? verstehe ich nicht
#************************************************************************
@@ -28,11 +26,11 @@
# - applied PEP8 style guide
# - added documentation
# - minor changes in programming style for consistence
-# - BUG: removed call of cleanup-Function after call of
+# - BUG: removed call of clean_up-Function after call of
# prepareFlexpart in main since it is already called in
# prepareFlexpart at the end!
# - created function main and moved the two function calls for
-# arguments and prepareFLEXPART into it
+# arguments and prepare_flexpart into it
#
# @License:
# (C) Copyright 2014-2018.
@@ -43,7 +41,7 @@
# @Program Functionality:
# This program prepares the final version of the grib files which are
# then used by FLEXPART. It converts the bunch of grib files extracted
-# via getMARSdata by doing for example the necessary conversion to get
+# via get_mars_data by doing for example the necessary conversion to get
# consistent grids or the disaggregation of flux data. Finally, the
# program combines the data fields in files per available hour with the
# naming convention xxYYMMDDHH, where xx should be 2 arbitrary letters
@@ -51,24 +49,25 @@
#
# @Program Content:
# - main
-# - prepareFLEXPART
+# - prepare_flexpart
#
#*******************************************************************************
# ------------------------------------------------------------------------------
# MODULES
# ------------------------------------------------------------------------------
-import shutil
import datetime
-#import time
import os
import inspect
import sys
import socket
-from argparse import ArgumentParser, ArgumentDefaultsHelpFormatter
-hostname = socket.gethostname()
-ecapi = 'ecmwf' not in hostname
+# software specific classes and modules from flex_extract
+from UioFiles import UioFiles
+from tools import interpret_args_and_control, clean_up
+from EcFlexpart import EcFlexpart
+
+ecapi = 'ecmwf' not in socket.gethostname()
try:
if ecapi:
import ecmwfapi
@@ -76,24 +75,20 @@ except ImportError:
ecapi = False
# add path to pythonpath so that python finds its buddies
-localpythonpath = os.path.dirname(os.path.abspath(
+LOCAL_PYTHON_PATH = os.path.dirname(os.path.abspath(
inspect.getfile(inspect.currentframe())))
-if localpythonpath not in sys.path:
- sys.path.append(localpythonpath)
+if LOCAL_PYTHON_PATH not in sys.path:
+ sys.path.append(LOCAL_PYTHON_PATH)
-# software specific classes and modules from flex_extract
-from UIOFiles import UIOFiles
-from Tools import interpret_args_and_control, cleanup
-from ECFlexpart import ECFlexpart
# ------------------------------------------------------------------------------
# FUNCTION
# ------------------------------------------------------------------------------
def main():
'''
@Description:
- If prepareFLEXPART is called from command line, this function controls
+ If prepare_flexpart is called from command line, this function controls
the program flow and calls the argumentparser function and
- the prepareFLEXPART function for preparation of GRIB data for FLEXPART.
+ the prepare_flexpart function for preparation of GRIB data for FLEXPART.
@Input:
<nothing>
@@ -102,14 +97,14 @@ def main():
<nothing>
'''
args, c = interpret_args_and_control()
- prepareFLEXPART(args, c)
+ prepare_flexpart(args, c)
return
-def prepareFLEXPART(args, c):
+def prepare_flexpart(args, c):
'''
@Description:
- Lists all grib files retrieved from MARS with getMARSdata and
+ Lists all grib files retrieved from MARS with get_mars_data and
uses prepares data for the use in FLEXPART. Specific data fields
are converted to a different grid and the flux data are going to be
disaggregated. The data fields are collected by hour and stored in
@@ -156,27 +151,27 @@ def prepareFLEXPART(args, c):
# one day ahead of the start date and
# one day after the end date is needed
startm1 = start - datetime.timedelta(days=1)
- endp1 = end + datetime.timedelta(days=1)
+# endp1 = end + datetime.timedelta(days=1)
# get all files with flux data to be deaccumulated
- inputfiles = UIOFiles('*OG_acc_SL*.' + c.ppid + '.*')
- inputfiles.listFiles(c.inputdir)
+ inputfiles = UioFiles('*OG_acc_SL*.' + c.ppid + '.*')
+ inputfiles.list_files(c.inputdir)
# create output dir if necessary
if not os.path.exists(c.outputdir):
os.makedirs(c.outputdir)
# deaccumulate the flux data
- flexpart = ECFlexpart(c, fluxes=True)
+ flexpart = EcFlexpart(c, fluxes=True)
flexpart.write_namelist(c, 'fort.4')
flexpart.deacc_fluxes(inputfiles, c)
- print('Prepare ' + start.strftime("%Y%m%d") +
- "/to/" + end.strftime("%Y%m%d"))
+ print 'Prepare ' + start.strftime("%Y%m%d") + \
+ "/to/" + end.strftime("%Y%m%d")
# get a list of all files from the root inputdir
- inputfiles = UIOFiles('????__??.*' + c.ppid + '.*')
- inputfiles.listFiles(c.inputdir)
+ inputfiles = UioFiles('????__??.*' + c.ppid + '.*')
+ inputfiles.list_files(c.inputdir)
# produce FLEXPART-ready GRIB files and
# process GRIB files -
@@ -184,16 +179,16 @@ def prepareFLEXPART(args, c):
if c.basetime == '00':
start = startm1
- flexpart = ECFlexpart(c, fluxes=False)
+ flexpart = EcFlexpart(c, fluxes=False)
flexpart.create(inputfiles, c)
flexpart.process_output(c)
# check if in debugging mode, then store all files
# otherwise delete temporary files
if int(c.debug) != 0:
- print('Temporary files left intact')
+ print 'Temporary files left intact'
else:
- cleanup(c)
+ clean_up(c)
return
diff --git a/python/profiling.py b/python/profiling.py
index b20e6e6..526c17f 100644
--- a/python/profiling.py
+++ b/python/profiling.py
@@ -1,7 +1,7 @@
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#************************************************************************
-# TODO AP
+# ToDo AP
# - check of license of book content
#************************************************************************
#*******************************************************************************
@@ -65,7 +65,7 @@ def timefn(fn):
t1 = time.time()
result = fn(*args, **kwargs)
t2 = time.time()
- print("@timefn:" + fn.func_name + " took " + str(t2 - t1) + " seconds")
+ print "@timefn:" + fn.func_name + " took " + str(t2 - t1) + " seconds"
return result
diff --git a/python/submit.py b/python/submit.py
index 0685103..fcf5735 100755
--- a/python/submit.py
+++ b/python/submit.py
@@ -1,15 +1,5 @@
#!/usr/bin/env python
# -*- coding: utf-8 -*-
-#************************************************************************
-# TODO AP
-#
-# - Change History ist nicht angepasst ans File! Original geben lassen
-# - dead code ? what to do?
-# - seperate operational and reanlysis for clarification
-# - divide in two submits , ondemand und operational
-# -
-#************************************************************************
-
#*******************************************************************************
# @Author: Anne Fouilloux (University of Oslo)
#
@@ -36,7 +26,7 @@
# This program is the main program of flex_extract and controls the
# program flow.
# If it is supposed to work locally then it works through the necessary
-# functions getMARSdata and prepareFlexpart. Otherwise it prepares
+# functions get_mars_data and prepareFlexpart. Otherwise it prepares
# a shell job script which will do the necessary work on the
# ECMWF server and is submitted via ecaccess-job-submit.
#
@@ -51,19 +41,19 @@
# ------------------------------------------------------------------------------
import os
import sys
-import glob
import subprocess
import inspect
-# add path to pythonpath so that python finds its buddies
-localpythonpath = os.path.dirname(os.path.abspath(
- inspect.getfile(inspect.currentframe())))
-if localpythonpath not in sys.path:
- sys.path.append(localpythonpath)
# software specific classes and modules from flex_extract
-from Tools import interpret_args_and_control, normalexit
-from getMARSdata import getMARSdata
-from prepareFLEXPART import prepareFLEXPART
+from tools import interpret_args_and_control, normal_exit
+from get_mars_data import get_mars_data
+from prepare_flexpart import prepare_flexpart
+
+# add path to pythonpath so that python finds its buddies
+LOCAL_PYTHON_PATH = os.path.dirname(os.path.abspath(
+ inspect.getfile(inspect.currentframe())))
+if LOCAL_PYTHON_PATH not in sys.path:
+ sys.path.append(LOCAL_PYTHON_PATH)
# ------------------------------------------------------------------------------
# FUNCTIONS
@@ -83,17 +73,19 @@ def main():
@Return:
<nothing>
'''
- calledfromdir = os.getcwd()
+
+ called_from_dir = os.getcwd()
args, c = interpret_args_and_control()
+
# on local side
if args.queue is None:
if c.inputdir[0] != '/':
- c.inputdir = os.path.join(calledfromdir, c.inputdir)
+ c.inputdir = os.path.join(called_from_dir, c.inputdir)
if c.outputdir[0] != '/':
- c.outputdir = os.path.join(calledfromdir, c.outputdir)
- getMARSdata(args, c)
- prepareFLEXPART(args, c)
- normalexit(c)
+ c.outputdir = os.path.join(called_from_dir, c.outputdir)
+ get_mars_data(args, c)
+ prepare_flexpart(args, c)
+ normal_exit(c)
# on ECMWF server
else:
submit(args.job_template, c, args.queue)
@@ -138,11 +130,10 @@ def submit(jtemplate, c, queue):
insert_point = lftext.index('EOF')
# put all parameters of ControlFile instance into a list
- clist = c.tolist()
+ clist = c.to_list() # ondemand
colist = [] # operational
mt = 0
-#AP wieso 2 for loops?
for elem in clist:
if 'maxstep' in elem:
mt = int(elem.split(' ')[1])
@@ -151,8 +142,7 @@ def submit(jtemplate, c, queue):
if 'start_date' in elem:
elem = 'start_date ' + '${MSJ_YEAR}${MSJ_MONTH}${MSJ_DAY}'
if 'end_date' in elem:
-#AP Fehler?! Muss end_date heissen
- elem = 'start_date ' + '${MSJ_YEAR}${MSJ_MONTH}${MSJ_DAY}'
+ elem = 'end_date ' + '${MSJ_YEAR}${MSJ_MONTH}${MSJ_DAY}'
if 'base_time' in elem:
elem = 'base_time ' + '${MSJ_BASETIME}'
if 'time' in elem and mt > 24:
@@ -172,11 +162,13 @@ def submit(jtemplate, c, queue):
try:
p = subprocess.check_call(['ecaccess-job-submit', '-queueName',
queue, 'job.ksh'])
- except:
- print('ecaccess-job-submit failed, probably eccert has expired')
+ except subprocess.CalledProcessError as e:
+ print 'ecaccess-job-submit failed!'
+ print 'Error Message: '
+ print e.output
exit(1)
- print('You should get an email with subject flex.hostname.pid')
+ print 'You should get an email with subject flex.hostname.pid'
return
diff --git a/python/testsuite.py b/python/test_suite.py
similarity index 86%
rename from python/testsuite.py
rename to python/test_suite.py
index 199fa89..c20b5f8 100755
--- a/python/testsuite.py
+++ b/python/test_suite.py
@@ -1,11 +1,9 @@
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#************************************************************************
-# TODO AP
-#
+# ToDo AP
# - provide more tests
# - provide more documentation
-# -
#************************************************************************
#*******************************************************************************
@@ -27,7 +25,7 @@
#
# @Program Functionality:
# This script triggers the ECMWFDATA test suite. Call with
-# testsuite.py [test group]
+# test_suite.py [test group]
#
# @Program Content:
#
@@ -45,9 +43,9 @@ import subprocess
# PROGRAM
# ------------------------------------------------------------------------------
try:
- taskfile = open('testsuite.json')
-except:
- print 'could not open suite definition file testsuite.json'
+ taskfile = open('test_suite.json')
+except IOError:
+ print 'could not open suite definition file test_suite.json'
exit()
if not os.path.isfile('../src/CONVERT2'):
@@ -72,14 +70,14 @@ jobfailed = 0
for g in groups:
try:
tk, tv = g, tasks[g]
- except:
- continue
+ finally:
+ pass
garglist = []
for ttk, ttv in tv.iteritems():
if isinstance(ttv, basestring):
if ttk != 'script':
garglist.append('--' + ttk)
- if '$' == ttv[0]:
+ if ttv[0] == '$':
garglist.append(os.path.expandvars(ttv))
else:
garglist.append(ttv)
@@ -88,11 +86,11 @@ for g in groups:
arglist = []
for tttk, tttv in ttv.iteritems():
if isinstance(tttv, basestring):
- arglist.append('--' + tttk)
- if '$' in tttv[0]:
- arglist.append(os.path.expandvars(tttv))
- else:
- arglist.append(tttv)
+ arglist.append('--' + tttk)
+ if '$' in tttv[0]:
+ arglist.append(os.path.expandvars(tttv))
+ else:
+ arglist.append(tttv)
print 'Command: ', ' '.join([tv['script']] + garglist + arglist)
o = '../test/' + tk + '_' + ttk + '_' + '_'.join(ttv.keys())
print 'Output will be sent to ', o
@@ -100,7 +98,7 @@ for g in groups:
try:
p = subprocess.check_call([tv['script']] + garglist + arglist,
stdout=f, stderr=f)
- except:
+ except subprocess.CalledProcessError as e:
f.write('\nFAILED\n')
print 'FAILED'
jobfailed += 1
@@ -110,5 +108,3 @@ for g in groups:
print 'Test suite tasks completed'
print str(jobcounter-jobfailed) + ' successful, ' + str(jobfailed) + ' failed'
print 'If tasks have been submitted via ECACCESS please check emails'
-
-#print tasks
diff --git a/python/Tools.py b/python/tools.py
similarity index 78%
rename from python/Tools.py
rename to python/tools.py
index 24e9e02..b74fd68 100644
--- a/python/Tools.py
+++ b/python/tools.py
@@ -1,10 +1,10 @@
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#************************************************************************
-# TODO AP
-# - check myerror
-# - check normalexit
-# - check getListAsString
+# ToDo AP
+# - check my_error
+# - check normal_exit
+# - check get_list_as_string
# - seperate args and control interpretation
#************************************************************************
#*******************************************************************************
@@ -14,17 +14,17 @@
#
# @Change History:
# October 2014 - Anne Fouilloux (University of Oslo)
-# - created functions silentremove and product (taken from ECMWF)
+# - created functions silent_remove and product (taken from ECMWF)
#
# November 2015 - Leopold Haimberger (University of Vienna)
-# - created functions: interpret_args_and_control, cleanup
-# myerror, normalexit, init128, toparamId
+# - created functions: interpret_args_and_control, clean_up
+# my_error, normal_exit, init128, to_param_id
#
# April 2018 - Anne Philipp (University of Vienna):
# - applied PEP8 style guide
# - added documentation
-# - moved all functions from file FlexpartTools to this file Tools
-# - added function getListAsString
+# - moved all functions from file Flexparttools to this file tools
+# - added function get_list_as_string
#
# @License:
# (C) Copyright 2014-2018.
@@ -38,14 +38,14 @@
#
# @Module Content:
# - interpret_args_and_control
-# - cleanup
-# - myerror
-# - normalexit
+# - clean_up
+# - my_error
+# - normal_exit
# - product
-# - silentremove
+# - silent_remove
# - init128
-# - toparamId
-# - getListAsString
+# - to_param_id
+# - get_list_as_string
#
#*******************************************************************************
@@ -56,10 +56,11 @@ import os
import errno
import sys
import glob
+import inspect
+import subprocess
import traceback
-from numpy import *
-from gribapi import *
from argparse import ArgumentParser, ArgumentDefaultsHelpFormatter
+import numpy as np
# software specific class from flex_extract
from ControlFile import ControlFile
@@ -122,13 +123,13 @@ def interpret_args_and_control():
help="root directory for storing output files")
parser.add_argument("--flexpart_root_scripts", dest="flexpart_root_scripts",
help="FLEXPART root directory (to find grib2flexpart \
- and COMMAND file)\n\ Normally ECMWFDATA resides in \
+ and COMMAND file)\n Normally ECMWFDATA resides in \
the scripts directory of the FLEXPART distribution")
- # this is only used by prepareFLEXPART.py to rerun a postprocessing step
+ # this is only used by prepare_flexpart.py to rerun a postprocessing step
parser.add_argument("--ppid", dest="ppid",
help="Specify parent process id for \
- rerun of prepareFLEXPART")
+ rerun of prepare_flexpart")
# arguments for job submission to ECMWF, only needed by submit.py
parser.add_argument("--job_template", dest='job_template',
@@ -151,20 +152,22 @@ def interpret_args_and_control():
c = ControlFile(args.controlfile)
except IOError:
try:
- c = ControlFile(localpythonpath + args.controlfile)
- except:
- print('Could not read CONTROL file "' + args.controlfile + '"')
- print('Either it does not exist or its syntax is wrong.')
- print('Try "' + sys.argv[0].split('/')[-1] +
- ' -h" to print usage information')
+ LOCAL_PYTHON_PATH = os.path.dirname(os.path.abspath(
+ inspect.getfile(inspect.currentframe())))
+ c = ControlFile(LOCAL_PYTHON_PATH + args.controlfile)
+ except IOError:
+ print 'Could not read CONTROL file "' + args.controlfile + '"'
+ print 'Either it does not exist or its syntax is wrong.'
+ print 'Try "' + sys.argv[0].split('/')[-1] + \
+ ' -h" to print usage information'
exit(1)
# check for having at least a starting date
if args.start_date is None and getattr(c, 'start_date') is None:
- print('start_date specified neither in command line nor \
- in CONTROL file ' + args.controlfile)
- print('Try "' + sys.argv[0].split('/')[-1] +
- ' -h" to print usage information')
+ print 'start_date specified neither in command line nor \
+ in CONTROL file ' + args.controlfile
+ print 'Try "' + sys.argv[0].split('/')[-1] + \
+ ' -h" to print usage information'
exit(1)
# save all existing command line parameter to the ControlFile instance
@@ -205,8 +208,8 @@ def interpret_args_and_control():
afloat = '.' in args.area
l = args.area.split('/')
if afloat:
- for i in range(len(l)):
- l[i] = str(int(float(l[i]) * 1000))
+ for i, item in enumerate(l):
+ item = str(int(float(item) * 1000))
c.upper, c.left, c.lower, c.right = l
# NOTE: basetime activates the ''operational mode''
@@ -217,11 +220,11 @@ def interpret_args_and_control():
l = args.step.split('/')
if 'to' in args.step.lower():
if 'by' in args.step.lower():
- ilist = arange(int(l[0]), int(l[2]) + 1, int(l[4]))
+ ilist = np.arange(int(l[0]), int(l[2]) + 1, int(l[4]))
c.step = ['{:0>3}'.format(i) for i in ilist]
else:
- myerror(None, args.step + ':\n' +
- 'please use "by" as well if "to" is used')
+ my_error(None, args.step + ':\n' +
+ 'please use "by" as well if "to" is used')
else:
c.step = l
@@ -238,7 +241,7 @@ def interpret_args_and_control():
return args, c
-def cleanup(c):
+def clean_up(c):
'''
@Description:
Remove all files from intermediate directory
@@ -262,21 +265,21 @@ def cleanup(c):
<nothing>
'''
- print("cleanup")
+ print "clean_up"
cleanlist = glob.glob(c.inputdir + "/*")
for cl in cleanlist:
if c.prefix not in cl:
- silentremove(cl)
+ silent_remove(cl)
if c.ecapi is False and (c.ectrans == '1' or c.ecstorage == '1'):
- silentremove(cl)
+ silent_remove(cl)
- print("Done")
+ print "Done"
return
-def myerror(c, message='ERROR'):
+def my_error(c, message='ERROR'):
'''
@Description:
Prints a specified error message which can be passed to the function
@@ -302,32 +305,34 @@ def myerror(c, message='ERROR'):
@Return:
<nothing>
'''
- # uncomment if user wants email notification directly from python
- #try:
- #target = c.mailfail
- #except AttributeError:
- #target = os.getenv('USER')
-
- #if(type(target) is not list):
- #target = [target]
-
- print(message)
-
- # uncomment if user wants email notification directly from python
- #for t in target:
- #p = subprocess.Popen(['mail','-s ECMWFDATA v7.0 ERROR', os.path.expandvars(t)],
- # stdin = subprocess.PIPE, stdout = subprocess.PIPE,
- # stderr = subprocess.PIPE, bufsize = 1)
- #tr = '\n'.join(traceback.format_stack())
- #pout = p.communicate(input = message+'\n\n'+tr)[0]
- #print 'Email sent to '+os.path.expandvars(t) # +' '+pout.decode()
+
+ print message
+
+ # comment if user does not want email notification directly from python
+ try:
+ target = []
+ target.extend(c.mailfail)
+ except AttributeError:
+ target = []
+ target.extend(os.getenv('USER'))
+
+ for t in target:
+ p = subprocess.Popen(['mail', '-s ECMWFDATA v7.0 ERROR',
+ os.path.expandvars(t)],
+ stdin=subprocess.PIPE,
+ stdout=subprocess.PIPE,
+ stderr=subprocess.PIPE,
+ bufsize=1)
+ tr = '\n'.join(traceback.format_stack())
+ pout = p.communicate(input=message + '\n\n' + tr)[0]
+ print 'Email sent to ' + os.path.expandvars(t) + ' ' + pout.decode()
exit(1)
return
-def normalexit(c, message='Done!'):
+def normal_exit(c, message='Done!'):
'''
@Description:
Prints a specific exit message which can be passed to the function.
@@ -353,23 +358,23 @@ def normalexit(c, message='Done!'):
<nothing>
'''
- # Uncomment if user wants notification directly from python
- #try:
- #target = c.mailops
- #if(type(target) is not list):
- #target = [target]
- #for t in target:
- #p = subprocess.Popen(['mail','-s ECMWFDATA v7.0 normal exit',
- # os.path.expandvars(t)],
- # stdin = subprocess.PIPE,
- # stdout = subprocess.PIPE,
- # stderr = subprocess.PIPE, bufsize = 1)
- #pout = p.communicate(input = message+'\n\n')[0]
- #print pout.decode()
- #except:
- #pass
-
- print(message)
+ print message
+
+ # comment if user does not want notification directly from python
+ try:
+ target = []
+ target.extend(c.mailops)
+ for t in target:
+ p = subprocess.Popen(['mail', '-s ECMWFDATA v7.0 normal exit',
+ os.path.expandvars(t)],
+ stdin=subprocess.PIPE,
+ stdout=subprocess.PIPE,
+ stderr=subprocess.PIPE,
+ bufsize=1)
+ pout = p.communicate(input=message+'\n\n')[0]
+ print 'Email sent to ' + os.path.expandvars(t) + ' ' + pout.decode()
+ finally:
+ pass
return
@@ -410,7 +415,7 @@ def product(*args, **kwds):
return
-def silentremove(filename):
+def silent_remove(filename):
'''
@Description:
If "filename" exists , it is removed.
@@ -434,13 +439,13 @@ def silentremove(filename):
return
-def init128(fn):
+def init128(filepath):
'''
@Description:
Opens and reads the grib file with table 128 information.
@Input:
- fn: string
+ filepath: string
Path to file of ECMWF grib table number 128.
@Return:
@@ -450,7 +455,7 @@ def init128(fn):
short name of the parameter.
'''
table128 = dict()
- with open(fn) as f:
+ with open(filepath) as f:
fdata = f.read().split('\n')
for data in fdata:
if data[0] != '!':
@@ -459,7 +464,7 @@ def init128(fn):
return table128
-def toparamId(pars, table):
+def to_param_id(pars, table):
'''
@Description:
Transform parameter names to parameter ids
@@ -485,31 +490,33 @@ def toparamId(pars, table):
cpar = pars.upper().split('/')
ipar = []
for par in cpar:
- found = False
for k, v in table.iteritems():
if par == k or par == v:
ipar.append(int(k))
- found = True
break
- if found is False:
- print('Warning: par ' + par + ' not found in table 128')
+ else:
+ print 'Warning: par ' + par + ' not found in table 128'
return ipar
-def getListAsString(listObj):
+def get_list_as_string(list_obj, concatenate_sign=', '):
'''
@Description:
Converts a list of arbitrary content into a single string.
@Input:
- listObj: list
+ list_obj: list
A list with arbitrary content.
+ concatenate_sign: string, optional
+ A string which is used to concatenate the single
+ list elements. Default value is ", ".
+
@Return:
- strOfList: string
+ str_of_list: string
The content of the list as a single string.
'''
- strOfList = ", ".join( str(l) for l in listObj)
+ str_of_list = concatenate_sign.join(str(l) for l in list_obj)
- return strOfList
+ return str_of_list
--
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