def load(self, filename):
if filename == '':
raise IOError('Empty filename. Specify a filename and try again!')
if os.access(filename, os.F_OK):
logging.getLogger().debug('attempting to restore state of ' +
self.__str__() + ' from ' + filename +
'...')
try:
logging.getLogger().debug('trying binary mode...')
self.set_items(cPickle.load(open(filename, 'rb')))
except:
try:
logging.getLogger().debug('trying text mode...')
self.set_items(cPickle.load(open(filename, 'r')))
except:
try:
logging.getLogger().debug(
'trying unicode text mode...')
self.set_items(cPickle.load(open(filename, 'rU')))
except:
logging.getLogger().debug(
'failed to restore state of ' + self.__str__() +
'.')
raise IOError('Load failed.')
logging.getLogger().debug('state of ' + self.__str__() +
' restored.')
else:
raise IOError('File does not exist.')
def test_exc(self):
from exceptions import Exception, BaseException
assert issubclass(Exception, BaseException)
assert isinstance(Exception(), Exception)
assert isinstance(Exception(), BaseException)
assert repr(Exception(3, "x")) == "Exception(3, 'x')"
assert str(IOError("foo", "bar")) == "[Errno foo] bar"
assert isinstance(IOError("foo", "bar"), IOError)
assert str(IOError(1, 2)) == "[Errno 1] 2"
def getColumn(self, name, context=None):
# if val is not None and varBindHead[idx].isPrefixOf(name): in cmdgen
# fails so I can't use the oneliner method
oid = ''
if self.isDotNotation(name):
oid = name
else:
oid = self.mibs[name].get('oid')
if context == None:
context = self.context
cmdGen = MyCmdGen()
errorIndication, errorStatus, _, varBinds = cmdGen.getColumn(
self.agent, context, self.host, self.port, rfc1902.ObjectName(oid))
if errorIndication:
raise IOError(errorIndication)
if errorStatus:
if len(varBinds) > 0 and errorStatus == 32:
pass
else:
raise SNMPError('getcolumn on ' + oid + '(' + name + ')',
errorStatus)
#if errorStatus:
# Throw an error??
# do we need to do error checking on this???
# what format should this return in???
formattedList = []
for val in varBinds:
formattedList.append(val[0][1].prettyPrint())
return formattedList
def get(self, name, instance=0, context=None):
oid = ''
if self.isDotNotation(name):
oid = name
else:
oid = self.mibs[name].get('oid')
# 2012-04-04, pcankar: if instance is -1 leave oid unchanged
if instance != -1:
oid += '.' + str(instance)
if context == None:
context = self.context
cmdGen = MyCmdGen()
errorIndication, errorStatus, _, varBinds = cmdGen.getCmd(
self.agent, context, self.host, self.port, rfc1902.ObjectName(oid))
if errorIndication:
raise IOError(errorIndication)
if errorStatus:
raise SNMPError('get on ' + oid + '(' + name + ')', errorStatus)
# Throw an error??
# do we need to do error checking on this???
#print "Getting %s (%s) = %s" % (name, oid, str(varBinds[-1][1].prettyPrint()))
return varBinds[-1][1].prettyPrint()
def _build_attribute_table(self, path, nodata_value):
if not os.path.exists(path):
raise IOError("File not found: {}".format(path))
shapefile = ogr.Open(path, 1)
layer = shapefile.GetLayer(0)
layer.CreateField(ogr.FieldDefn(self._id_attribute, ogr.OFTInteger))
next_value_id = 1
for feature in self._get_features(layer):
attribute_values = tuple(
attr.sub(feature[attr.name]) if attr.filter(feature[attr.name]
) else None
for attr in self._attributes)
value_id = nodata_value
if None not in attribute_values:
existing_key = [
item[0] for item in self._attribute_table.items()
if item[1] == attribute_values
]
if existing_key:
value_id = existing_key[0]
else:
value_id = next_value_id
self._attribute_table[value_id] = attribute_values
next_value_id += 1
feature[self._id_attribute] = value_id
layer.SetFeature(feature)
def save(self, filename):
"""detects the format of the savefile and saves it according to the file-ending. .txt and .asc result in an ascii sav,
.pyd in a pickled python save with mode='asc' and .pys in a pickled python file with mode='bin'"""
if not filename:
raise IOError('Empty filename. Specify a filename and try again!')
with open(filename, 'wb') as fil:
cPickle.dump(self.get_items(), fil, 1)
def getnext(self, name, instance=0, context=None):
# if val is not None and varBindHead[idx].isPrefixOf(name): in cmdgen
# fails so I can't use the oneliner method
oid = ''
if self.isDotNotation(name):
oid = name
else:
oid = self.mibs[name].get('oid')
# 2012-04-04, pcankar: if instance is -1 leave oid unchanged
if instance != -1:
oid += '.' + str(instance)
if context == None:
context = self.context
cmdGen = MyCmdGen()
errorIndication, errorStatus, _, varBinds = cmdGen.nextCmd(
self.agent, context, self.host, self.port, rfc1902.ObjectName(oid))
if errorIndication:
raise IOError(errorIndication)
if errorStatus:
raise SNMPError('getnext on ' + oid + '(' + name + ')',
errorStatus)
#if errorStatus:
# Throw an error??
# do we need to do error checking on this???
# what format should this return in???
return varBinds
def reprojectShp(infile, reproj, fromProj="EPSG:4326", toProj="EPSG:26905"):
"""Reprojects a shapefile using ogr2ogr
Args:
| infile (str): File to reproject
| reproj (str): Reprojected output file
Kwargs:
| fromProj (str): Original projection
| toProj (str): New projection
"""
cmd = "ogr2ogr -overwrite -s_srs %s -t_srs %s %s %s;" % (fromProj, toProj,
reproj, infile)
process = subprocess.Popen(cmd,
shell=True,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE)
dumpstr = process.stdout.readlines()
errorstr = process.stderr.readlines()
#print len(dumpstr)
#print len(errorstr)
#
#print "".join(dumpstr)
#print "".join(errorstr)
if len(errorstr) > 0:
raise IOError("".join(errorstr))
def checkFolders(self, src, dst):
"""
Check if the source and dest folders are valid and if it is not the case,
throws an exception
@param srcr: the folder with java sources to check
@param dst: destination folder to check
"""
# Check if src folder exists
if not os.path.exists(src):
raise IOError("The source folder", src, "does not exist")
elif not os.path.isdir(src):
raise IOError("The source folder", src, "is not a directory")
# Check if the destination folder exists
if not os.path.exists(dst):
raise IOError("The destination folder", dst, "does not exist")
elif not os.path.isdir(dst):
raise IOError("The destination folder", dst, "is not a directory")
def __init__(self, path, attributes=None, attribute_table=None, nodata_value=-1, data_type=None):
self._name = os.path.basename(path)
self._path = path
self._attributes = attributes or []
self._attribute_table = attribute_table or {}
self._nodata_value = nodata_value
self._data_type = data_type
if not os.path.exists(path):
raise IOError("File not found: {}".format(path))
def init_path(self, path):
"""
Checks whether the given path exists and is a directory.
Cleans the path and saves it to the instance.
:param path: The path in which urltomd should search for
files.
"""
if not os.path.isdir(path):
raise IOError('%s does not exist or is not a directory.' % path)
if not path.endswith('/'):
path += '/'
self.path = path
def getBulk(self,
name,
nonRepeaters,
maxRepititions,
context=None,
dict=False):
# if val is not None and varBindHead[idx].isPrefixOf(name): in cmdgen
# fails so I can't use the oneliner method
oid = ''
if self.isDotNotation(name):
oid = name
else:
oid = self.mibs[name].get('oid')
if context == None:
context = self.context
# cmdGen = MyCmdGen()
# errorIndication, errorStatus, _, varBinds = cmdGen.getBulk(
# self.agent, context,
# self.host, self.port,
# nonRepeaters,
# maxRepititions,
# rfc1902.ObjectName(oid))
errorIndication, errorStatus, _, varBinds = cg.CommandGenerator(
).bulkCmd(cg.CommunityData(self.agent, context),
cg.UdpTransportTarget((self.host, self.port)), nonRepeaters,
maxRepititions, rfc1902.ObjectName(oid))
if errorIndication:
raise IOError(errorIndication)
if errorStatus:
if len(varBinds) > 0 and errorStatus == 32:
pass
else:
raise SNMPError('getbulk on ' + oid + '(' + name + ')',
errorStatus)
formattedList = []
for val in varBinds:
formattedList.append(val[0][1].prettyPrint())
formattedDict = {}
for val in varBinds:
formattedDict[val[0][0].prettyPrint()] = val[0][1].prettyPrint()
if dict:
return formattedDict
return formattedList
def __init__(self, env=None, file=None):
"""
Instantiating a SolexaConfig object causes the config
file to be read and parsed.
"""
cfg = self._read_config(env, file)
if not cfg:
raise IOError()
for section in cfg.sections():
section_dict = {}
for k, v in cfg.items(section):
section_dict[k] = v
setattr(self, section, section_dict)
self._coerce_values()
def save(self, filename):
"""
Saves the plot to a graphics file, e.g. .png or .pdf.
Example of usage:
plot = my_instance.line_plot
filename = 'foo.png'
save_figure(plot, filename)
"""
if filename:
if os.path.splitext(filename)[-1] == ".pdf":
self.save_pdf(filename)
else:
self.save_raster(filename)
else:
raise IOError('Empty filename.')
def makeTableFromFile(ffile,name=None,nameInFile='No',\
columnsNames=None,columnsNamesInFile='Yes',
columnsUnits=None,columnsUnitsInFile='No'):
"""Makes a table from the given file. Reads table's names (if they are present) from the file.
Line of Name in file should begin with #TITLE:
Line of ColumnsName in file should begin with #COLUMN_TITLES: and colum names should be separate by |"""
from exceptions import IOError
t = None
try:
file = open(ffile, 'r')
except:
msg = "can't open file <%s>...\n" % ffile
raise IOError(msg)
if name and nameInFile.lower() == 'yes':
raise Warning("You give a table name and ask to get name from file")
if columnsNames and columnsNameInFile.lower() == 'yes':
raise Warning(
"You ask for colum names in the file while already defining them")
if columnsUnits and columnsUnitsInFile.lower() == 'yes':
raise Warning(
"You ask for units in the file while already defining them")
# table creation
if name:
verifyType(name, StringType)
t = DataTable(name)
pass
else:
t = DataTable('table')
pass
# affect columns names if necessary
if columnsNames:
t.setColumnNames(columnsNames)
pass
# affect columns units if necessary
if columnsUnits:
t.setColumnUnits(columnsUnits)
pass
t.readFromFile(ffile,
columnsNames=columnsNamesInFile,
name=nameInFile,
colonnesnames=columnsNames,
columnsUnits=columnsUnitsInFile)
return t
def __init__(self,
name,
path,
attributes,
raw=False,
nodata_value=-1,
data_type=None):
self._data_type = data_type
self._nodata_value = nodata_value
self._name = name
self._path = path
self._raw = raw
self._id_attribute = "value_id" if not raw else attributes.name
self._attribute_table = {}
self._attributes = [attributes] if isinstance(attributes, Attribute) \
else attributes
if not os.path.exists(path):
raise IOError("File not found: {}".format(path))
def __init__(self,
name,
path,
layer,
attributes,
raw=False,
nodata_value=-1):
self._nodata_value = nodata_value
self._name = name
self._path = path
self._layer = layer
self._raw = raw
self._id_attribute = "value_id" if not raw else attributes
self._attribute_table = {}
self._attributes = [attributes] if isinstance(attributes, basestring) \
else attributes
if not os.path.exists(path):
raise IOError("File not found: {}".format(path))
def __init__(self, fileName, symbolTable):
# Check if the requested file to parse exists
if not os.path.exists(fileName):
raise IOError("The file %s could not be found" % fileName)
# initialize the commands array
self.text = []
self.symbolTable = symbolTable
# open the requested file for reading
with open(fileName, 'r') as f:
# read each line from the file
for line in f.readlines():
# check if the line is valid for parsing ( Notice that here
# all the comments and the white spaces are removed)
if not self.whiteSpaceOrComment(line):
cleanLine = self.cleanEmptyLinesAndComments(line)
self.text.insert(0,cleanLine)
# init the current command line
self.currentCommand = ""
self.parsedCommand = ""
def error(self, x, a):
# Raise one of the exceptions from db_error
raise IOError() if PY2 else OSError
def __init__(self,errStr = ''):
IOError.__init__(self)
self.errStr = errStr
def __init__(self, errno, message, terminus=None):
py_IOError.__init__(self, errno, message)
self.terminus = terminus
def open(file, band_file=None):
'''
Returns a SpyFile object for an AVIRIS image file.
Arguments:
`file` (str):
Name of the AVIRIS data file.
`band_file` (str):
Optional name of the AVIRIS spectral calibration file.
Returns:
A SpyFile object for the image file.
Raises:
IOError
'''
import numpy as np
from spectral.io.bipfile import BipFile
import os
import glob
from exceptions import IOError
from .spyfile import find_file_path
import spectral
class Params:
pass
p = Params()
p.filename = find_file_path(file)
p.nbands = 224
p.ncols = 614
fileSize = os.stat(p.filename)[6]
if fileSize % 275072 != 0:
raise IOError('File size not consistent with AVIRIS format.')
p.nrows = int(fileSize / 275072)
p.byte_order = 1
p.dtype = np.dtype('i2').str
if spectral.byte_order != 1:
p.dtype = np.dtype(p.dtype).newbyteorder().str
metadata = {'default bands': ['29', '18', '8']}
p.offset = 0
img = BipFile(p, metadata)
img.scale_factor = 10000.0
if band_file:
img.bands = read_aviris_bands(find_file_path(band_file))
else:
# Let user know if band cal files are available
fileDir = os.path.split(p.filename)[0]
calFiles = glob.glob(fileDir + '/*.spc')
if len(calFiles) > 0:
print('\nThe following band calibration files are located in ' \
'the same directory as the opened AVIRIS file:\n')
for f in calFiles:
print(" " + os.path.split(f)[1])
print('\nTo associate a band calibration file with an AVIRIS ' \
'data file, re-open the AVIRIS file with the following ' \
'syntax:\n')
print(' >>> img = aviris.open(fileName, calFileName)\n')
return img
def readFromFile(self,ffile,nbcolumns=None,columnsNames='yes',name='no',columnsUnits='no'):
"""Reads a table from the given file."""
from exceptions import IOError
try:
if self.values.shape != (0,0):
raise "The table already contains values"
file = open(ffile, 'r')
except :
msg="can't open file <%s>...\n"%ffile
raise IOError(msg)
fileNameColumns=[]
fileNameUnits=[]
fileName=None
filemaxnbcol=0
fileminnbcol=100
isonvalues=0
allvaluesbycolonne=[]
nbvalueline=0
cpt=1
for line in file.readlines():
separe = line.split()
if (len(separe) == 0 ):
# blank line
continue
if ( separe[0] == '#' ):
# comment line
cpt=cpt+1
continue
elif ( separe[0] == '#TITLE:' ):
# name line
separe = separe[1:]
s=''
for isep in range(len(separe)):
s=s+separe[isep]+' '
fileName=s
pass
elif ( separe[0] == '#COLUMN_TITLES:' ):
# column name line
separe = separe[1:]
s=''
for isep in range(len(separe)):
s=s+separe[isep]
s=string.strip(s)
if ( len(s) == 0 ):
fileNameColumns=[]
continue
fileNameColumns = s.split('|')
pass
elif ( separe[0] == '#COLUMN_UNITS:' ):
# unit name line
fileNameUnits = separe[1:]
pass
elif ( cpt == 1 ):
# column name line
pass
else:
# values line
nbvalueline=nbvalueline+1
linenbcol=len(separe)
filemaxnbcol=max(linenbcol,filemaxnbcol)
fileminnbcol=min(linenbcol,fileminnbcol)
linevalues=[]
for isep in range(linenbcol):
linevalues.append(float(separe[isep]))
pass
# adjust nb columns if not the same on each line
# or if the first value's line
if ( filemaxnbcol < len(allvaluesbycolonne) ):
for icol in range(filemaxnbcol,len(allvaluesbycolonne)):
allvaluesbycolonne.append([])
for il in range(nbvalueline-1):
allvaluesbycolonne[il].append(0)
pass
pass
pass
elif ( filemaxnbcol > len(allvaluesbycolonne) ):
for icol in range(len(allvaluesbycolonne),filemaxnbcol):
allvaluesbycolonne.append([])
for il in range(nbvalueline-1):
allvaluesbycolonne[icol].append(0)
pass
pass
pass
# add values
for icol in range(linenbcol):
allvaluesbycolonne[icol].append(linevalues[icol])
pass
for icol in range(linenbcol,filemaxnbcol):
allvaluesbycolonne[icol].append(0)
pass
cpt=cpt+1
file.close()
# check consistency beetwen arguments and file contents
#
# controlling the table parameters
#
if ( fileminnbcol != filemaxnbcol ):
raise IOError("colums must have the same number of rows")
if nbcolumns:
if ( filemaxnbcol != nbcolumns ):
raise IOError(" problem with the number of columns")
pass
# Warnings
if ( ( columnsNames.lower() == 'no' ) and ( len(fileNameColumns) > 0 ) ):
raise Warning(" you should specify column names")
if ( ( columnsNames.lower() == 'yes' ) and ( len(fileNameColumns) == 0 ) ):
raise Warning("you specified columnName(s) but the file doesn\'t entail column names")
if ( len(fileNameColumns) < filemaxnbcol ):
nbcol=len(fileNameColumns)
for icol in range (nbcol,filemaxnbcol):
fileNameColumns.append('col'+str(icol+1))
pass
effectivecolumnNames=fileNameColumns
pass
if ( ( name.lower() == 'no' ) and fileName ):
msg='WARNING: you specified no name but there is name in file'
print(msg)
if ( ( name.lower() == 'yes' ) and ( fileName == None ) ):
msg='WARNING: you specified name but there is no name in file'
print(msg)
if ( ( columnsUnits.lower() == 'no' ) and ( len(fileNameUnits) > 0 ) ):
msg='WARNING: you specified no units name but there are units name in file'
print(msg)
if ( ( columnsUnits.lower() == 'yes' ) and ( len(fileNameUnits) == 0 ) ):
msg='WARNING: you specified units name but there are no units name in file'
print(msg)
if ( ( len(fileNameUnits) > 0 ) and ( len(fileNameUnits) < filemaxnbcol ) ):
nbcol=len(fileNameUnits)
for icol in range (nbcol,filemaxnbcol):
fileNameUnits.append('col'+str(icol+1))
pass
pass
if fileName:
self.setName(fileName)
pass
if len(fileNameUnits):
self.setColumnUnits(fileNameUnits)
pass
for i in range(filemaxnbcol):
if columnsNames.lower()=='yes':
self.addColumn(effectivecolumnNames[i],allvaluesbycolonne[i])
pass
else:
self.addColumnValues(allvaluesbycolonne[i])
pass
pass
return
def set(self, name, value, instance=0, context=None, type='i'):
'''
snmpojb.set('swDetailsVersion', 1, '05.00.96')
'''
oid = ''
if self.isDotNotation(name):
oid = name
# TODO do we try and guess what our value is if we are given dot notation
#rfcValue=rfc1902.OctetString(value)
# type can be: i INTEGER, u UNSIGNED, s STRING, x HEX STRING, d DECIMAL STRING
# n NULLOBJ, o OBJID, t TIMETICKS, a IPADDRESS, b BITS
assert (type in 'iusxdnotab'
), "ERROR: Value type {0} not supported".format(type)
try:
if type == 'i':
rfcValue = rfc1902.Integer32(value)
elif type == 'u':
rfcValue = rfc1902.Unsigned32(value)
elif type == 't':
rfcValue = rfc1902.TimeTicks(value)
elif type == 'a':
rfcValue = rfc1902.IpAddress(value)
elif type == 'b':
rfcValue = rfc1902.Bits(value)
elif type == 's':
rfcValue = rfc1902.OctetString(value)
elif type == 'o':
rfcValue = univ.ObjectIdentifier(value)
elif type in 'xdn':
print 'WARNING: Type ' + type + ' not fully supported (hope default will do)'
rfcValue = rfc1902.OctetString(value)
else:
print "unknown type"
except:
print("Error in SNMPClient, could not convert {} to type {}"
).format(value, type)
else:
oid = self.mibs[name].get('oid')
# TODO: incode the type
type = self.mibs[name].get('type')
# TODO: do something similar as if a couple of lines up
rfcValue = self.mibs.encode(type, value)
#if instance!=0:
oid += '.' + str(instance)
if context == None:
context = self.context
if SNMPClient.DEBUG:
print "Setting %s (%s) = %s" % (name, oid, str(value))
cmdGen = MyCmdGen()
errorIndication, errorStatus, _, varBinds = cmdGen.setCmd(
self.agent, context, self.host, self.port,
(rfc1902.ObjectName(oid), rfcValue))
if SNMPClient.DEBUG:
print 'agent', self.agent
print 'context', context
print 'host', self.host
print 'port', self.port
print 'type', type
if errorIndication:
raise IOError(errorIndication)
if errorStatus:
raise SNMPError('set on ' + oid + '(' + name + ')', errorStatus)
return varBinds[-1][1].prettyPrint()
