def read(dfc, fileobj):
dfile = DataFile()
retval = frcsv.read(dfile, fileobj, 'ctd')
split_dfc = split_on_cast(dfile)
dfc.files = split_dfc.files
# Convert header columns to globals
global_headers = [
'EXPOCODE', 'STNNBR', 'CASTNO', '_DATETIME', 'LATITUDE', 'LONGITUDE',
'DEPTH'
]
for dfile in dfc.files:
for header in global_headers:
value = dfile[header][0]
if type(value) == int:
value = str(value)
dfile.globals[header] = value
del dfile[header]
# Arbitrarily set SECT_ID to blank
dfile.globals['SECT_ID'] = ''
# Take largest depth value and set as bottom depth
try:
depth = max(dfile['DEPTH'])
except KeyError:
depth = depth_unesco(max(dfile['CTDPRS']),
dfile.globals['LATITUDE'])
dfile.globals['DEPTH'] = ceil(depth)
return retval
def read(self, fileobj):
"""How to read an LDEO ASEP file."""
line1 = _getline(fileobj)
dtype_shipcode, stn, cast, lat, lon, date, yday, time, cruise_id = \
line1.split()
dtype = dtype_shipcode[0]
if not is_datatype_ctd(dtype):
log.error(u'Unable to read non-CTD ASEP files at the moment.')
return
shipcode = dtype_shipcode[1:]
# FIXME this is not really the EXPOCODE
self.globals['EXPOCODE'] = cruise_id
# FIXME this is not really the SECT_ID
self.globals['SECT_ID'] = cruise_id
self.globals['STNNBR'] = str(int(stn))
self.globals['CASTNO'] = cast
self.globals['LATITUDE'] = lat
self.globals['LONGITUDE'] = lon
self.globals['_DATETIME'] = datetime.strptime(date + time, '%Y/%m/%d%H:%M')
self.globals['header'] = '#' + cruise_id
line2 = _getline(fileobj)
while line2[0] != '&':
log.warn(u'Ignoring line not preceded by &: {0!r}'.format(line2))
line2 = _getline(fileobj)
self.globals['header'] += "\n#" + line2 + "\n"
line3 = _getline(fileobj)
while line3[0] != '@':
log.warn(u'Ignoring line not preceded by @: {0!r}'.format(line2))
line3 = _getline(fileobj)
param_keys = line3[1:].split()
parameters = [CTD_PARAM_MAP.get(key, None) for key in param_keys]
cols = self.create_columns(parameters)
for line in fileobj:
for col, val in zip(cols, line.split()):
if val == '-9':
val = None
col.append(_decimal(val))
# rewrite every data column to be the same sigfigs
for col in self.columns.values():
decplaces = col.decimal_places()
col.values = [pad_decimal(val, decplaces) for val in col.values]
if 'pr' in param_keys:
pressures = cols[param_keys.index('pr')].values
lat = _decimal(self.globals['LATITUDE'])
depth = int(depth_unesco(pressures[-1], lat))
self.globals['DEPTH'] = depth
self.check_and_replace_parameters()
def read(self, handle):
"""How to read a CTD WOCE Egee file."""
# Egee1
egee = handle.readline().strip()
# STRNBR CASTNO NO RECORDS
line_cast_id = handle.readline()
match_cast_id = re.match('\s*STRNBR(.*)CASTNO(.*)NO.RECORDS(.*)',
line_cast_id)
try:
cast_id = [xxx.strip() for xxx in match_cast_id.groups()]
self.globals['STNNBR'] = cast_id[0]
self.globals['CASTNO'] = cast_id[1]
num_records = int(cast_id[2])
except AttributeError:
log.error(u'Unable to read station cast and number of records.')
except TypeError:
log.warn(u'Unable to determine number of data records.')
# DATE
line_date = handle.readline()
try:
line_date = line_date.split(':', 1)[1].strip()
dtime = datetime.strptime(line_date, '%b %d %Y %H:%M:%S')
self.globals['_DATETIME'] = dtime
except IndexError:
log.warn(u'Unable to determine date.')
# blank
handle.readline()
# LATITUDE LONGITUDE
line_coord = handle.readline()
match_coord = re.match('\s*LATITUDE:(.*)LONGITUDE:(.*)', line_coord)
try:
coord = [xxx.strip() for xxx in match_coord.groups()]
lat_coords = coord[0].split()
lng_coords = coord[1].split()
self.globals['LATITUDE'] = woce.woce_lat_to_dec_lat(lat_coords)
self.globals['LONGITUDE'] = woce.woce_lng_to_dec_lng(lng_coords)
except AttributeError:
log.error(u'Unable to read coordinates')
parameters_line = handle.readline()
units_line = handle.readline()
asterisk_line = handle.readline()
woce.read_data_egee(self, handle, parameters_line, units_line,
asterisk_line)
self.check_and_replace_parameters()
self.globals['EXPOCODE'] = egee
self.globals['SECT_ID'] = 'EGEE'
self.globals['DEPTH'] = [
int(depth_unesco(vvv, self.globals['LATITUDE']) or 0)
for vvv in self['CTDPRS'].values
][-1]
def test_depth_unesco(self):
print depth.depth_unesco(1, 0)
'algorithm probably oscillates.'.format(lat))
raise err
try:
sal_tmp_pres = zip(salt.values, temp.values, pres.values)
density_series = [depth.density(*args) for args in sal_tmp_pres]
if None in density_series:
raise ValueError(
u'Cannot perform depth integration with missing data points'
)
depths = depth.depth(localgrav, pres.values, density_series)
return ('sverdrup', depths)
except (AttributeError, IndexError, ValueError):
pass
try:
log.info(u'Falling back from depth integration to Unesco method.')
depths = [depth.depth_unesco(pres, lat) for pres in pres.values]
return ('unesco1983', depths)
except AttributeError:
raise ValueError(
u'Cannot convert non-existant pressures to depths.')
class DataFileCollection(object):
"""Stores a collection of DataFiles
A DataFileCollection represents data files that are actually a
collection of many sub files (e.g. Exchange CTD files).
"""
def __init__(self, allow_contrived=False):
self.files = []
self.allow_contrived = allow_contrived