def readCloud(self,cloudFile=None,numHeaderLines=None,Cldict=None,verbose=False):
"""Reads in cloud data if we have it..."""
if cloudFile == None:
cloudFile=self.config.cloudFile
if Cldict == None:
Cldict = self.config.Cl
if cloudFile == 'batch':
self.batch = True
return 0
else:
self.batch = False
cloudFile = os.path.join(self.config.path,cloudFile)
if numHeaderLines is None:
numHeaderLines = self.config.cloudFileHdr
print 'Reading '+cloudFile+' (Header: '+str(numHeaderLines)+')'
self.cloud = []
print '\tUsing cloud component: ',
for k in Cldict:
print k+' ',
self.cloud.append([])
self.nParticulate = len(Cldict)
try:
fp = open(cloudFile,"r")
except IOError:
print cloudFile+' was not found - returning no clouds\n\n'
raise IOError
i=0
lineno = 0
pastHeader = False
print ' '
for line in fp:
lineno+=1
if line[0]=='!' or lineno<=numHeaderLines:
if verbose:
print '\tHEADER: '+line,
continue
pastHeader = True
if len(line) < 3:
if pastHeader:
break
else:
continue
data = line.split()
if i==0:
print '\tReading '+str(self.nParticulate)+' cloud particles (data-file: '+str(len(data))+')'
for n in range(self.nParticulate): ## Initialize all of the particulates to 0.0
self.cloud[n].append(0.0)
columns = Cldict.values()
columns.sort()
for n,v in enumerate(columns): ## ...now read in data
if v < len(data):
self.cloud[n][i] = float(data[v])
else:
self.cloud[n][i] = 0.0
if (self.nParticulate-n)!=1:
print 'line '+str(i+1)+' has incorrect number of particulates'
print '['+line+']'
i+=1
self.nCloud = i
###Redo the particulate dictionary for the self.cloud index positions
nid,sk = utils.invertDictionary(Cldict)
for i,k in enumerate(sk):
Cldict[nid[k]] = i
self.config.Cl = Cldict
print '\tRead '+str(self.nCloud)+' lines'
fp.close()
self.cloud = np.array(self.cloud)
### Check that P is monotonically increasing
monotonic = np.all(np.diff(self.cloud[self.config.Cl['P']])>0.0)
if not monotonic:
self.cloud = np.fliplr(self.cloud)
monotonic = np.all(np.diff(self.cloud[self.config.Cl['P']])>0.0)
if not monotonic:
print "Error in "+cloudFile+". Pressure not monotonically increasing"
self.cloud[self.config.Cl['DZ']] = np.abs(np.append(np.diff(self.cloud[self.config.Cl['Z']]),0.0))
return self.nCloud
def readGas(self,gasFile=None,numHeaderLines=None,Cdict=None,verbose=False):
"""Reads gas profile file as self.gas"""
if gasFile is None:
gasFile=self.config.gasFile
if Cdict is None:
Cdict = self.config.C
if gasFile == 'batch':
self.batch = True
return 0
else:
self.batch = False
gasFile = os.path.join(self.config.path,gasFile)
if numHeaderLines is None:
numHeaderLines = self.config.gasFileHdr
print 'Reading '+gasFile+' (Header: '+str(numHeaderLines)+')'
self.gas = []
print '\tUsing atmsopheric component: ',
for k in Cdict:
print k+' ',
self.gas.append([])
self.nConstituent = len(Cdict)
try:
fp = open(gasFile,"r")
except IOError:
print gasFile+' was not found - returning no gas profile\n\n'
raise IOError
i=0
lineno = 0
pastHeader = False
print ' '
for line in fp:
lineno+=1
data = line.split()
skip_row = line[0]=='!' or len(data) < 4 or lineno<=numHeaderLines
######put in something to eliminate the need for numHeaderLines..........
if skip_row:
if verbose:
print '\tHEADER: '+line,
continue
pastHeader = True
if len(line) < 3:
if pastHeader:
break
else:
continue
if i==0:
print '\tCompiling '+str(self.nConstituent)+' components (data-file: '+str(len(data))+')'
for n in range(self.nConstituent): ## Initialize all of the constituents to 0.0
self.gas[n].append(0.0)
columns = Cdict.values()
columns.sort()
for n,v in enumerate(columns): ## ...now read in data
if v < len(data):
self.gas[n][i] = float(data[v])
else:
self.gas[n][i] = 0.0
if (self.nConstituent-n)!=1:
print 'line '+str(i+1)+' has incorrect number of components'
print '['+line+']'
i+=1
self.nGas = i
###Redo the constituent dictionary for the self.gas index positions
nid,sk = utils.invertDictionary(Cdict)
for i,k in enumerate(sk):
Cdict[nid[k]] = i
self.config.C = Cdict
print '\tRead '+str(self.nGas)+' lines'
fp.close()
self.gas = np.array(self.gas)
### Check that P is monotonically increasing
monotonic = np.all(np.diff(self.gas[self.config.C['P']])>0.0)
if not monotonic:
self.gas = np.fliplr(self.gas)
monotonic = np.all(np.diff(self.gas[self.config.C['P']])>0.0)
if not monotonic:
print "Error in "+gasFile+". Pressure not monotonically increasing"
### Renormalize so that deepest z is 0
zDeep = self.gas[self.config.C['Z']][-1]
if abs(zDeep) > 1E-6:
for i in range(len(self.gas[self.config.C['Z']])):
self.gas[self.config.C['Z']][i]-=zDeep
print 'Deepest levels set from %.1f to 0' % (zDeep)
### Set dz
dz = np.abs(np.diff(self.gas[self.config.C['Z']]))*1.0E5 #convert from km to cm (so no unit checking!!!)
self.gas[self.config.C['DZ']] = np.append(np.array([0.0]),dz)
return self.nGas
def readCloud(self, cloudFile=None, Cldict=None):
"""Reads in cloud data if we have it..."""
if cloudFile is None:
cloudFile = self.config.cloudFile
if Cldict is None:
Cldict = self.config.Cl
if cloudFile == 'batch':
self.batch_mode = True
return 0
else:
self.batch_mode = False
cloudFile = os.path.join(self.config.path, cloudFile)
if self.verbose:
print('Reading clouds from {}'.format(cloudFile))
print('\tUsing cloud components: ', end='')
self.cloud = []
value_sorted_Cldict_keys = sorted(Cldict, key=lambda k: Cldict[k])
for k in value_sorted_Cldict_keys:
self.cloud.append([])
if self.verbose:
print(k, ' ', end='')
self.nParticulate = len(Cldict.keys())
try:
fp = open(cloudFile, "r")
except IOError:
print(cloudFile, ' was not found - returning no clouds\n\n')
raise IOError
if self.verbose:
print(' ')
expected_number = utils.get_expected_number_of_entries(fp)
for line in fp:
cval = utils.get_data_from(line)
if cval is None or len(cval) != expected_number:
continue
for n in range(self.nParticulate): # Initialize all of the particulates to 0.0
if n < len(cval):
self.cloud[n].append(cval[n])
else:
self.cloud[n].append(0.0)
self.nCloud = len(self.cloud[0])
# ##Redo the particulate dictionary for the self.cloud index positions
nid, sk = utils.invertDictionary(Cldict)
for i, k in enumerate(sk):
Cldict[nid[k]] = i
self.config.Cl = Cldict
if self.verbose:
print('\tRead ', str(self.nCloud), ' lines')
fp.close()
self.cloud = np.array(self.cloud)
# ## Check that P is monotonically increasing
monotonic = np.all(np.diff(self.cloud[self.config.Cl['P']]) > 0.0)
if not monotonic:
self.cloud = np.fliplr(self.cloud)
monotonic = np.all(np.diff(self.cloud[self.config.Cl['P']]) > 0.0)
if not monotonic:
print("Error in ", cloudFile)
raise ValueError("Pressure not monotonically increasing")
# ## Renormalize so that deepest z is 0 and set DZ
self.renorm_z('cloud')
return self.nCloud
def readGas(self, gasFile=None, Cdict=None):
"""Reads gas profile file as self.gas"""
if gasFile is None:
gasFile = self.config.gasFile
if Cdict is None:
Cdict = self.config.C
if gasFile == 'batch':
self.batch_mode = True
return 0
else:
self.batch_mode = False
gasFile = os.path.join(self.config.path, gasFile)
if self.verbose:
print('Reading constituents from {}'.format(gasFile))
print('\tUsing atmsopheric component: ', end='')
self.gas = []
value_sorted_Cdict_keys = sorted(Cdict, key=lambda k: Cdict[k])
for k in value_sorted_Cdict_keys:
self.gas.append([])
if self.verbose:
print(k + ' ', end='')
self.nConstituent = len(Cdict)
try:
fp = open(gasFile, "r")
except IOError:
print(gasFile + ' was not found - returning no gas profile\n\n')
raise IOError
if self.verbose:
print(' ')
expected_number = utils.get_expected_number_of_entries(fp)
for line in fp:
cval = utils.get_data_from(line)
if cval is None or len(cval) != expected_number:
continue
for n in range(self.nConstituent):
if n < len(cval):
self.gas[n].append(cval[n])
else:
self.gas[n].append(0.0)
self.nGas = len(self.gas[0])
# ##Redo the constituent dictionary for the self.gas index positions
nid, sk = utils.invertDictionary(Cdict)
for i, k in enumerate(sk):
Cdict[nid[k]] = i
self.config.C = Cdict
if self.verbose:
print('\tRead ' + str(self.nGas) + ' lines')
fp.close()
self.gas = np.array(self.gas)
# ## Check that P is monotonically increasing
monotonic = np.all(np.diff(self.gas[self.config.C['P']]) > 0.0)
if not monotonic:
self.gas = np.fliplr(self.gas)
monotonic = np.all(np.diff(self.gas[self.config.C['P']]) > 0.0)
if not monotonic:
print("Error in ", gasFile)
raise ValueError("Pressure not monotonically increasing.")
# ## Renormalize so that deepest z is 0 and set DZ
self.renorm_z('gas')
return self.nGas
def readCloud(self, cloudFile=None, Cldict=None):
"""Reads in cloud data if we have it..."""
if cloudFile is None:
cloudFile = self.config.cloudFile
if Cldict is None:
Cldict = self.config.Cl
if cloudFile == 'batch':
self.batch_mode = True
return 0
else:
self.batch_mode = False
cloudFile = os.path.join(self.config.path, cloudFile)
if self.verbose:
print('Reading clouds from {}'.format(cloudFile))
print('\tUsing cloud components: ', end='')
self.cloud = []
for k in Cldict:
self.cloud.append([])
if self.verbose:
print(k, ' ', end='')
self.nParticulate = len(Cldict.keys())
try:
fp = open(cloudFile, "r")
except IOError:
print(cloudFile, ' was not found - returning no clouds\n\n')
raise IOError
if self.verbose:
print(' ')
expected_number = utils.get_expected_number_of_entries(fp)
for line in fp:
cval = utils.get_data_from(line)
if cval is None or len(cval) != expected_number:
continue
for n in range(self.nParticulate
): # Initialize all of the particulates to 0.0
if n < len(cval):
self.cloud[n].append(cval[n])
else:
self.cloud[n].append(0.0)
self.nCloud = len(self.cloud[0])
# ##Redo the particulate dictionary for the self.cloud index positions
nid, sk = utils.invertDictionary(Cldict)
for i, k in enumerate(sk):
Cldict[nid[k]] = i
self.config.Cl = Cldict
if self.verbose:
print('\tRead ', str(self.nCloud), ' lines')
fp.close()
self.cloud = np.array(self.cloud)
# ## Check that P is monotonically increasing
monotonic = np.all(np.diff(self.cloud[self.config.Cl['P']]) > 0.0)
if not monotonic:
self.cloud = np.fliplr(self.cloud)
monotonic = np.all(np.diff(self.cloud[self.config.Cl['P']]) > 0.0)
if not monotonic:
print("Error in ", cloudFile)
raise ValueError("Pressure not monotonically increasing")
# ## Renormalize so that deepest z is 0 and set DZ
self.renorm_z('cloud')
return self.nCloud
def readGas(self, gasFile=None, Cdict=None):
"""Reads gas profile file as self.gas"""
if gasFile is None:
gasFile = self.config.gasFile
if Cdict is None:
Cdict = self.config.C
if gasFile == 'batch':
self.batch_mode = True
return 0
else:
self.batch_mode = False
gasFile = os.path.join(self.config.path, gasFile)
if self.verbose:
print('Reading constituents from {}'.format(gasFile))
print('\tUsing atmsopheric component: ', end='')
self.gas = []
for k in Cdict:
self.gas.append([])
if self.verbose:
print(k + ' ', end='')
self.nConstituent = len(Cdict)
try:
fp = open(gasFile, "r")
except IOError:
print(gasFile + ' was not found - returning no gas profile\n\n')
raise IOError
if self.verbose:
print(' ')
expected_number = utils.get_expected_number_of_entries(fp)
for line in fp:
cval = utils.get_data_from(line)
if cval is None or len(cval) != expected_number:
continue
for n in range(self.nConstituent):
if n < len(cval):
self.gas[n].append(cval[n])
else:
self.gas[n].append(0.0)
self.nGas = len(self.gas[0])
# ##Redo the constituent dictionary for the self.gas index positions
nid, sk = utils.invertDictionary(Cdict)
for i, k in enumerate(sk):
Cdict[nid[k]] = i
self.config.C = Cdict
if self.verbose:
print('\tRead ' + str(self.nGas) + ' lines')
fp.close()
self.gas = np.array(self.gas)
# ## Check that P is monotonically increasing
monotonic = np.all(np.diff(self.gas[self.config.C['P']]) > 0.0)
if not monotonic:
self.gas = np.fliplr(self.gas)
monotonic = np.all(np.diff(self.gas[self.config.C['P']]) > 0.0)
if not monotonic:
print("Error in ", gasFile)
raise ValueError("Pressure not monotonically increasing.")
# ## Renormalize so that deepest z is 0 and set DZ
self.renorm_z('gas')
return self.nGas
