| 1 | #!/usr/bin/env python |
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| 2 | |
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| 3 | #************************************************************************************** |
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| 4 | #csmldataIface.py |
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| 5 | #contains classes for interfacing with various files |
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| 6 | #currently supports cdunif (NetCDF, PP, Grib(untested)) And Nappy (NASAAmes) |
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| 7 | #use by instantiating the factory class: DataInterface |
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| 8 | #v0.00 30th November 2005 |
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| 9 | #Dominic Lowe, BADC |
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| 10 | #************************************************************************************** |
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| 11 | |
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| 12 | |
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| 13 | import cdms |
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| 14 | try: |
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| 15 | import nappy |
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| 16 | except ImportError: |
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| 17 | print 'could not import NASAAmes interface' |
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| 18 | import string |
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| 19 | import sys |
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| 20 | import csml.csmllibs.csmltime |
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| 21 | # This is required to prevent Numeric arrays being truncated when printed. |
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| 22 | import MA |
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| 23 | MA.set_print_limit(0) |
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| 24 | |
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| 25 | |
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| 26 | class DataInterface(object): |
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| 27 | #Use DataInterface and setInterfaceType to instantiate the correct |
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| 28 | #subclass for data |
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| 29 | def __init__(self): |
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| 30 | self.iface ='None' |
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| 31 | |
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| 32 | def setInterfaceType(self,interfaceType): |
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| 33 | # function returns approprate data interface |
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| 34 | #set interfaceType: should correspond to available datainterface subclasses |
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| 35 | self.iface =interfaceType |
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| 36 | if self.iface == 'nappy': |
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| 37 | return NappyInterface() |
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| 38 | elif self.iface == 'cdunif': |
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| 39 | return cdunifInterface() |
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| 40 | |
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| 41 | |
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| 42 | def getUnknownInterfaceType(self, filename): |
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| 43 | #if the interface type is not known at the time of instantiation, then use |
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| 44 | #this function to examine the file and return the correct interface (if it exists). |
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| 45 | fileExtension = str(filename)[-3:] |
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| 46 | print 'fe: %s'%fileExtension |
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| 47 | if fileExtension == '.nc': |
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| 48 | return cdunifInterface() |
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| 49 | if fileExtension == '.qxf': |
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| 50 | return cdunifInterface() |
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| 51 | elif fileExtension == '.pp': |
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| 52 | return cdunifInterface() |
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| 53 | elif fileExtension == 'ctl': |
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| 54 | return cdunifInterface() |
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| 55 | elif fileExtension == 'xml': |
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| 56 | return cdmlInterface() |
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| 57 | else: |
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| 58 | try: |
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| 59 | nappy.readFFI(filename) in [1001,1010,1020,2010,2110,2160,2310,3010,4010] |
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| 60 | return NappyInterface() |
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| 61 | except: |
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| 62 | print "Could not establish file type" |
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| 63 | print "See csmldataiface.py" |
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| 64 | |
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| 65 | |
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| 66 | |
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| 67 | class AbstractDI(object): |
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| 68 | #Abstract data interface class |
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| 69 | #does nothing, but contains templates for methods required for a data interface class |
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| 70 | #individual interfaces (e.g NappyInterface) should override these methods |
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| 71 | |
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| 72 | def __init__(self): |
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| 73 | self.extractType='' |
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| 74 | self.extractPrefix = '' |
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| 75 | |
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| 76 | def openFile(self, filename): |
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| 77 | #opens file, must be overwritten by subclass |
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| 78 | raise NotImplementedError |
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| 79 | |
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| 80 | def closeFile(self): |
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| 81 | #closes file, probably needs to be overwritten by subclass |
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| 82 | try: |
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| 83 | self.file.close() |
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| 84 | except: |
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| 85 | raise NotImplementedError |
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| 86 | |
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| 87 | def setAxis(self,axis): |
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| 88 | #'set' the name of the current axis , must be overwritten by subclass |
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| 89 | #this may just involve a stub (see NASAAmes interface) or may involve |
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| 90 | #calling a real set method of the underlying api (see cdunif Interface) |
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| 91 | raise NotImplementedError |
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| 92 | |
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| 93 | def getDataForAxis(self): |
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| 94 | #return all data for axis, must be overwritten by subclass |
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| 95 | raise NotImplementedError |
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| 96 | |
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| 97 | def setVariable(self,varname): |
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| 98 | #As for setAxis, 'set' the name of the current axis , must be overwritten by subclass |
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| 99 | raise NotImplementedError |
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| 100 | |
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| 101 | def getDataForVar(self): |
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| 102 | #return all data for variable, must be overwritten by subclass |
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| 103 | raise NotImplementedError |
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| 104 | |
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| 105 | def getSubsetOfDataForVar(self,**kwargs): |
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| 106 | #return subset of data for variable, must be overwritten by subclass |
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| 107 | raise NotImplementedError |
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| 108 | |
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| 109 | |
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| 110 | class NappyInterface(AbstractDI): |
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| 111 | # Data Interface for Nappy (NASA Ames Processing in Python) |
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| 112 | |
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| 113 | def __init__(self): |
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| 114 | self.extractType='NASAAmesExtract' |
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| 115 | self.extractPrefix = '_naextract_' |
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| 116 | |
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| 117 | def openFile(self, filename): |
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| 118 | #print 'opening NA file: ' + str(filename) |
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| 119 | self.file=nappy.openNAFile(filename) |
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| 120 | #print 'reading data....' |
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| 121 | #self.file.readData() |
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| 122 | #print 'nappyopen ' + filename |
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| 123 | |
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| 124 | def getListOfAxes(self): |
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| 125 | axes=self.file.XNAME |
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| 126 | #print 'before units stripped' + str(axes) |
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| 127 | axes=self.stripunits(axes) |
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| 128 | #print 'after units stripped' + str(axes) |
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| 129 | return axes |
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| 130 | |
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| 131 | def setAxis(self,axis): |
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| 132 | axes = self.getListOfAxes() |
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| 133 | self.axisstub=axes.index(axis) |
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| 134 | |
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| 135 | def getAxisAttribute(self, att): |
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| 136 | #need to do something here...? maybe |
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| 137 | pass |
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| 138 | return attValue |
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| 139 | |
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| 140 | def getTimeUnits(self): |
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| 141 | axes = self.getListOfAxes() |
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| 142 | for axis in axes: |
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| 143 | if string.find(string.upper(axis),'SECONDS SINCE') != -1: |
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| 144 | #found possible time axis. |
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| 145 | if axis[-3:]=='UTC': |
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| 146 | units =string.lower(axis[:-4]) #hack! |
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| 147 | units=units.replace('/','-') #try and clean it up |
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| 148 | else: |
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| 149 | units=string.lower(axis) |
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| 150 | break |
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| 151 | elif string.find(string.upper(axis),'HOURS SINCE') != -1: |
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| 152 | #found possible time axis. |
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| 153 | units =(str(axis)) |
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| 154 | break |
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| 155 | elif string.find(string.upper(axis),'DAYS SINCE') != -1: |
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| 156 | #found possible time axis. |
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| 157 | units =(str(axis)) |
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| 158 | break |
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| 159 | |
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| 160 | #revisit with udunits python library? |
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| 161 | return units |
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| 162 | |
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| 163 | |
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| 164 | def getDataForAxis(self): |
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| 165 | |
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| 166 | if self.file.X == None: |
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| 167 | #print 'reading data....' |
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| 168 | self.file.readData() |
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| 169 | |
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| 170 | if type(self.file.X[1])==list: |
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| 171 | #if len(self.file.X) > 0: |
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| 172 | data = self.file.X[self.axisstub] |
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| 173 | else: |
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| 174 | data =self.file.X |
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| 175 | return data |
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| 176 | |
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| 177 | def getSizeOfAxis(self,axis): |
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| 178 | |
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| 179 | #check this function is okay |
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| 180 | #is time always the first dimension in NA?? |
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| 181 | axes = self.getListOfAxes() |
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| 182 | axisPosition=axes.index(axis) |
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| 183 | #print "axis position" + str( axisPosition) |
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| 184 | #print "NX" + str(self.file.NX) |
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| 185 | try : |
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| 186 | axisSize=self.file.NX[axisPosition-1] |
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| 187 | except: |
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| 188 | axisSize ='Unknown axis size' |
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| 189 | return axisSize |
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| 190 | |
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| 191 | def getListofVariables(self): |
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| 192 | variableList=self.stripunits(self.file.VNAME) |
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| 193 | return variableList |
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| 194 | |
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| 195 | def setVariable(self,varname): |
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| 196 | vlist=self.getListofVariables() |
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| 197 | self.varstub=vlist.index(varname) |
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| 198 | |
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| 199 | def getVariableAxes(self): |
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| 200 | #hmm, now with Nasa Ames the Axis will be the same for all variables. |
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| 201 | #so just use the getListOfAxes function again |
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| 202 | #I think... check this! |
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| 203 | varAxesList=self.getListOfAxes() |
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| 204 | return varAxesList |
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| 205 | |
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| 206 | def getVariableAttribute(self,attName): |
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| 207 | if attName =='units': |
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| 208 | #strip the units (attribute) from the variable |
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| 209 | unitslist=self.getUnits(self.file.VNAME) |
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| 210 | attribValue = unitslist[self.varstub] |
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| 211 | try: |
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| 212 | attribValue = unitslist[self.varstub] |
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| 213 | except: |
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| 214 | attribValue = 'unknown' |
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| 215 | else: |
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| 216 | attribValue = 'unknown' |
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| 217 | return attribValue |
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| 218 | |
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| 219 | def getDataForVar(self): |
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| 220 | #NOTE TO SELF: |
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| 221 | #Review this function (and in fact all of nasa ames data interface...) |
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| 222 | if self.file.V == None: |
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| 223 | #print 'reading data....' |
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| 224 | self.file.readData() |
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| 225 | |
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| 226 | try: |
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| 227 | if type(self.file.V[1])==list: |
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| 228 | data = self.file.V[self.varstub] |
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| 229 | #else: |
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| 230 | # data =self.file.X |
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| 231 | # print data |
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| 232 | return data |
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| 233 | except: |
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| 234 | data = self.file.X |
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| 235 | # print data |
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| 236 | return data |
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| 237 | |
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| 238 | def getArraySizeOfVar(self): |
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| 239 | #iterates through all dimensions in variable to get array size i.e a 3x3x3 array would have a size of 27 |
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| 240 | |
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| 241 | dimlist=self.file.NX |
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| 242 | varsize =1 |
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| 243 | for item in dimlist: |
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| 244 | varsize = varsize * item |
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| 245 | #print "VARSISZE" + str(varsize) |
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| 246 | return varsize |
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| 247 | |
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| 248 | def getShapeOfVar(self): |
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| 249 | #this should return a list. |
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| 250 | varShape = [] |
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| 251 | for item in self.file.NX: |
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| 252 | varShape.append(item) |
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| 253 | return varShape |
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| 254 | |
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| 255 | def getLowLimits(self): |
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| 256 | lowlims = "" |
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| 257 | for i in range (0, len(self.file.NX)): |
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| 258 | #for now, assume low limit is always of form 1 1 1 .. |
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| 259 | lowlims =lowlims + str(1) +' ' |
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| 260 | return lowlims |
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| 261 | |
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| 262 | def getHighLimits(self): |
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| 263 | highlims = "" |
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| 264 | for i in range (0, len(self.file.NX)): |
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| 265 | dimValue = self.file.NX[i] |
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| 266 | highlims =highlims + str(dimValue) +' ' |
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| 267 | return highlims |
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| 268 | |
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| 269 | |
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| 270 | def stripunits(self,listtostrip): |
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| 271 | #strips units of measure from list |
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| 272 | #eg ['Universal time (hours)', 'Altitude (km)', 'Latitude (degrees)', 'Longitude (degrees)'] |
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| 273 | #becomes ['Universal time', 'Altitude', 'Latitude', 'Longitude'] |
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| 274 | cleanlist = [] |
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| 275 | for item in listtostrip: |
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| 276 | openbracket=string.find(item,'(') |
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| 277 | if openbracket != -1: |
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| 278 | #if brackets exist, strip units. |
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| 279 | item=item[:openbracket-1] |
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| 280 | cleanlist.append(item) |
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| 281 | return cleanlist |
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| 282 | |
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| 283 | def getUnits(self,listwithunits): |
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| 284 | #gets units from list |
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| 285 | #eg ['Universal time (hours)', 'Altitude (km)', 'Latitude (degrees)', 'Longitude (degrees)'] |
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| 286 | #becomes ['hours', 'km', 'degrees', 'degrees'] |
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| 287 | unitlist=[] |
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| 288 | for item in listwithunits: |
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| 289 | openbracket=string.find(item,'(') |
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| 290 | item = item[openbracket+1:-1] |
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| 291 | unitlist.append(item) |
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| 292 | return unitlist |
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| 293 | |
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| 294 | def getTimes(self): |
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| 295 | #This function attempts to determine the time axis and read the time data |
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| 296 | #it may well not manage it. |
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| 297 | axes = self.getListOfAxes() |
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| 298 | for axis in axes: |
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| 299 | if string.find(string.upper(axis),'TIME') != -1: |
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| 300 | #found possible time axis. |
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| 301 | self.setAxis(axis) |
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| 302 | times=self.getDataForAxis() |
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| 303 | break |
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| 304 | elif string.find(string.upper(axis),'SECONDS SINCE') != -1: |
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| 305 | #found possible time axis. |
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| 306 | self.setAxis(axis) |
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| 307 | times=self.getDataForAxis() |
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| 308 | break |
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| 309 | elif string.find(string.upper(axis),'HOURS SINCE') != -1: |
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| 310 | #found possible time axis. |
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| 311 | self.setAxis(axis) |
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| 312 | times=self.getDataForAxis() |
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| 313 | break |
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| 314 | elif string.find(string.upper(axis),'DAYS SINCE') != -1: |
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| 315 | #found possible time axis. |
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| 316 | self.setAxis(axis) |
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| 317 | times=self.getDataForAxis() |
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| 318 | break |
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| 319 | return times |
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| 320 | |
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| 321 | |
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| 322 | |
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| 323 | class cdunifInterface(AbstractDI): |
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| 324 | #Data Interface for cdunif (netcdf & pp formats & grib (not tested with grib) |
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| 325 | |
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| 326 | def __init__(self): |
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| 327 | #these are just temporary values until we can determine whether the |
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| 328 | #file is netcdf pp or grib |
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| 329 | self.extractType='cdunifExtract' |
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| 330 | self.extractPrefix = '_cdunifextract_' |
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| 331 | |
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| 332 | def openFile(self, filename): |
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| 333 | self.file=cdms.open(filename) |
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| 334 | #print 'cdunifopen ' + filename |
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| 335 | |
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| 336 | #now we have the file name can properly determine extractType/Prefix |
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| 337 | fileExtension = str(filename)[-3:] |
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| 338 | if fileExtension == '.nc': |
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| 339 | self.extractType = 'NetCDFExtract' |
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| 340 | self.extractPrefix = '_ncextract_' |
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| 341 | elif fileExtension == '.qxf': |
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| 342 | self.extractType = 'NetCDFExtract' |
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| 343 | self.extractPrefix = '_ncextract_' |
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| 344 | elif fileExtension == '.pp': |
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| 345 | self.extractType = 'PPExtract' |
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| 346 | self.extractPrefix = '_ppextract_' |
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| 347 | elif fileExtension == 'ctl': |
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| 348 | self.extractType = 'GRIBExtract' |
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| 349 | self.extractPrefix = '_gribextract_' |
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| 350 | elif fileExtension == 'xml': |
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| 351 | self.extractType = 'NetCDFExtract' #okay this isn't true, but ok for testing |
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| 352 | self.extractPrefix = '_ncextract__' |
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| 353 | def getListOfAxes(self): |
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| 354 | axes=self.file.dimensions.keys() |
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| 355 | return axes |
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| 356 | |
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| 357 | def getSizeOfAxis(self,axis): |
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| 358 | axisSize=self.file.dimensions[axis] |
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| 359 | return axisSize |
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| 360 | |
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| 361 | def getListofVariables(self): |
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| 362 | variableList=self.file.variables.keys() |
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| 363 | return variableList |
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| 364 | |
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| 365 | def setAxis(self,axis): |
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| 366 | self.axisobj=self.file.getAxis(axis) |
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| 367 | |
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| 368 | def getAxisAttribute(self, att): |
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| 369 | attValue=self.axisobj.attributes[att] |
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| 370 | return attValue |
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| 371 | |
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| 372 | def getTimeUnits(self): |
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| 373 | #this does the same as getAxisAttribute, but is a separate function as different formats handle time differently. |
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| 374 | return self.getAxisAttribute('units') |
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| 375 | |
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| 376 | def getDataForAxis(self): |
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| 377 | data = self.axisobj.getValue() |
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| 378 | return data |
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| 379 | |
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| 380 | def setVariable(self,varname): |
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| 381 | self.varobj=self.file.variables[varname] |
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| 382 | |
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| 383 | def getVariableAxes(self): |
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| 384 | varAxesList=self.varobj.getAxisIds() |
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| 385 | return varAxesList |
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| 386 | |
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| 387 | def getVariableAttribute(self,attName): |
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| 388 | #NEED TO REWRITE THIS! |
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| 389 | if attName == 'long_name': |
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| 390 | try: |
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| 391 | attribValue = self.varobj.long_name |
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| 392 | except: |
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| 393 | attribValue='no_long_name_found' |
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| 394 | elif attName == 'units': |
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| 395 | try: |
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| 396 | attribValue = self.varobj.units |
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| 397 | except: |
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| 398 | attribValue='no_units_found' |
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| 399 | elif attName == '_FillValue': |
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| 400 | try: |
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| 401 | attribValue=self.varobj._FillValue |
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| 402 | attribValue=attribValue.toscalar() |
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| 403 | except: |
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| 404 | try: |
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| 405 | attribValue=self.varobj.missing_value |
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| 406 | attribValue=attribValue.toscalar() |
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| 407 | except: |
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| 408 | attribValue = None |
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| 409 | return attribValue |
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| 410 | |
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| 411 | def getDataForVar(self): |
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| 412 | data = self.varobj.getValue() |
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| 413 | return data |
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| 414 | |
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| 415 | def getSubsetOfDataForVar(self, **kwargs): |
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| 416 | #takes keyword args defining subset eg |
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| 417 | #subset=getSubsetOfDataForVar(latitude=(0.,10.0), longitude=(90, 100.0)) |
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| 418 | subset=None |
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| 419 | lonkey='longitude' |
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| 420 | if lonkey=='longitude' in kwargs.keys(): #this test needs to be much more robust...! |
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| 421 | if kwargs[lonkey][0] > kwargs[lonkey][1]: |
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| 422 | #subsetting greenwich meridian around 0 |
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| 423 | lonMin = kwargs[lonkey][0] |
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| 424 | lonMax =kwargs[lonkey][1] |
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| 425 | kwargs[lonkey]=(0.0, lonMax) |
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| 426 | sel=cdms.selectors.Selector(**kwargs) |
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| 427 | subset1=self.file(self.varobj.id,sel) |
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| 428 | kwargs[lonkey]=(lonMin,359.9999) |
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| 429 | sel=cdms.selectors.Selector(**kwargs) |
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| 430 | subset2=self.file(self.varobj.id,sel) |
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| 431 | #concatenate arrays along longitude |
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| 432 | longitudeAxis=subset1.getAxisIndex(lonkey) |
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| 433 | subset = cdms.MV.concatenate([subset1,subset2],axis=longitudeAxis) |
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| 434 | if type(subset) is not cdms.tvariable.TransientVariable: |
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| 435 | sel=cdms.selectors.Selector(**kwargs) |
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| 436 | subset=self.file(self.varobj.id,sel) |
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| 437 | return subset |
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| 438 | |
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| 439 | def getArraySizeOfVar(self): |
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| 440 | #iterates through all dimensions in variable to get array size i.e a 3x3x3 array would have a size of 27 |
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| 441 | var = self.varobj |
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| 442 | size = var.shape |
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| 443 | varsize = 1 |
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| 444 | for item in size: |
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| 445 | varsize = item *varsize |
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| 446 | return varsize |
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| 447 | |
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| 448 | def getShapeOfVar(self): |
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| 449 | varShape = [] |
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| 450 | for item in self.varobj.shape: |
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| 451 | varShape.append(item) |
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| 452 | return varShape |
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| 453 | |
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| 454 | def getLowLimits(self): |
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| 455 | dimNames = self.varobj.getAxisIds() |
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| 456 | lowlims = "" |
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| 457 | for i in range (1, len(dimNames)): |
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| 458 | #for now, assume low limit is always of form 1 1 1 .. |
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| 459 | lowlims =lowlims + str(1) +' ' |
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| 460 | return lowlims |
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| 461 | |
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| 462 | def getHighLimits(self): |
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| 463 | dimNames = self.varobj.getAxisIds() |
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| 464 | highlims = "" |
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| 465 | for i in range (1, len(dimNames)): |
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| 466 | dimValue = self.file.dimensions[dimNames[i]] |
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| 467 | highlims =highlims + str(dimValue) +' ' |
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| 468 | return highlims |
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| 469 | |
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| 470 | |
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| 471 | class cdmlInterface(cdunifInterface): |
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| 472 | #this is more or less the cdunif interface but a few methods have been overwritten |
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| 473 | def __init__(self): |
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| 474 | #this all needs to be revisited in csml v2. |
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| 475 | self.extractType='cdmlExtract' |
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| 476 | self.extractPrefix = '_cdmlextract_' |
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| 477 | |
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| 478 | def getListOfAxes(self): |
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| 479 | axes=self.file.axes.keys() |
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| 480 | return axes |
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| 481 | |
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| 482 | def getSizeOfAxis(self,axis): |
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| 483 | axisSize=self.file.axes[axis].length |
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| 484 | return axisSize |
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