| 1 | #!/usr/bin/env python |
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| 2 | # Copyright (C) 2004 CCLRC & NERC( Natural Environment Research Council ). |
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| 3 | # This software may be distributed under the terms of the |
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| 4 | # Q Public License, version 1.0 or later. http://ndg.nerc.ac.uk/public_docs/QPublic_license.txt |
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| 5 | |
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| 6 | helpMessage=""" |
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| 7 | |
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| 8 | cdms2na.py |
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| 9 | ========== |
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| 10 | |
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| 11 | Converts a CdmsFile object into one a NASA Ames file. |
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| 12 | |
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| 13 | Usage |
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| 14 | ===== |
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| 15 | |
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| 16 | cdms2na.py [<options>] -i <infilename> -o <outfilename> |
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| 17 | |
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| 18 | Where |
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| 19 | ----- |
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| 20 | |
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| 21 | infilename - name of input file (NetCDF). |
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| 22 | outfilename - name of output file (NASA Ames). |
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| 23 | options - list of options [NOT YET IMPLEMENTED]. |
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| 24 | |
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| 25 | """ |
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| 26 | |
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| 27 | # Imports from python standard library |
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| 28 | import sys, os, time, string, fileinput, re |
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| 29 | if len(sys.argv)>0: |
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| 30 | sys.path.append(os.path.join("..", "..")) |
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| 31 | sys.path.append("..") |
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| 32 | |
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| 33 | # Import cdat modules |
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| 34 | if sys.platform.find("win")>-1: |
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| 35 | pass |
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| 36 | else: |
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| 37 | import cdms, cdtime |
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| 38 | # Define cdms variables |
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| 39 | cdms.setAutoBounds("off") |
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| 40 | |
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| 41 | # Import nappy modules |
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| 42 | import cdmsMap |
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| 43 | import version |
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| 44 | import general |
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| 45 | import localRules |
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| 46 | from naCore import * |
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| 47 | from naError import * |
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| 48 | |
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| 49 | def compareAxes(ax1, ax2): |
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| 50 | """Takes 2 cmds axis objects returning 1 if they are essentially |
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| 51 | the same and 0 if not.""" |
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| 52 | for axtype in ("time", "level", "latitude", "longitude"): |
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| 53 | if cdms.axisMatches(ax1, axtype) and not cdms.axisMatches(ax2, axtype): |
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| 54 | return 0 |
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| 55 | |
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| 56 | # Check ids |
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| 57 | if ax1.id!=ax2.id: return 0 |
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| 58 | # Check lengths |
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| 59 | if len(ax1)!=len(ax2): return 0 |
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| 60 | # Check values |
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| 61 | if ax1._data_!=ax2._data_: return 0 |
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| 62 | # Check units |
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| 63 | if ax1.units!=ax2.units: return 0 |
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| 64 | # OK, I think they are the same axis! |
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| 65 | return 1 |
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| 66 | |
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| 67 | def compareVariables(var1, var2): |
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| 68 | """Compares two cdms variables to see if they are defined on identical |
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| 69 | axes. Returns 1 if true, 0 if not.""" |
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| 70 | try: |
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| 71 | for i in range(len(var1.getAxisList())): |
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| 72 | ax1=var1.getAxis(i) |
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| 73 | ax2=var2.getAxis(i) |
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| 74 | if compareAxes(ax1, ax2)==0: |
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| 75 | return 0 |
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| 76 | except: |
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| 77 | return 0 |
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| 78 | return 1 |
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| 79 | |
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| 80 | def isAuxAndVar(avar, var): |
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| 81 | """Compares two cdms variables and returns true if the first dimension of the |
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| 82 | main variable is the only dimension the auxiliary variable is defined against.""" |
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| 83 | if len(avar.shape)>1: |
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| 84 | return 0 |
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| 85 | auxax=avar.getAxis(0) |
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| 86 | varax=var.getAxis(0) |
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| 87 | return compareAxes(auxax, varax) |
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| 88 | |
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| 89 | def arrayToList(array, inlist): |
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| 90 | |
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| 91 | """ Takes an n-dimensional Numeric array and converts it to an |
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| 92 | n-dimensional list object. |
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| 93 | """ |
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| 94 | dimlist=array.shape |
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| 95 | if len(dimlist[1:])>0: |
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| 96 | for i in range(dimlist[0]): |
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| 97 | arrayToList(inlist[i], array[i]) |
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| 98 | else: |
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| 99 | for i in range(dimlist[0]): |
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| 100 | inlist.append(array[i]) |
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| 101 | return inlist |
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| 102 | |
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| 103 | def listOfListsCreator(inlist, dimlist): |
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| 104 | """ |
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| 105 | Creates a list of lists with dimensions defined in dimlist (a list of integers). |
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| 106 | """ |
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| 107 | if len(dimlist[1:])>0: |
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| 108 | for i in range(dimlist[0]): |
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| 109 | inlist.append([]) |
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| 110 | listOfListsCreator(inlist[i], array, dimlist[1:]) |
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| 111 | return inlist |
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| 112 | |
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| 113 | def getBestName(var): |
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| 114 | """ |
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| 115 | Returns the most appropriate variable name for a NASA Ames header |
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| 116 | """ |
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| 117 | if hasattr(var, "id"): name=var.id |
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| 118 | if hasattr(var, "name"): name=var.name |
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| 119 | if hasattr(var, "long_name"): name=var.long_name |
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| 120 | if hasattr(var, "standard_name"): name=var.standard_name |
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| 121 | if hasattr(var, "units") and not re.match("^\s+$", var.units): |
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| 122 | name="%s (%s)" % (name, var.units) |
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| 123 | # Do a check to see units are not duplicated |
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| 124 | match=re.match("(.*\(%s\)\s*)\(%s\)(.*)$" % (var.units, var.units), name) |
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| 125 | if match: |
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| 126 | name=match.groups()[0]+match.groups()[1] |
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| 127 | |
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| 128 | if name[-2:]=="()": name=name[:-2] |
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| 129 | return name |
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| 130 | |
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| 131 | def getMissingValue(var): |
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| 132 | if hasattr(var, "missing_value"): return var.missing_value |
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| 133 | if hasattr(var, "fill_value"): return var.fill_value |
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| 134 | if hasattr(var, "_FillValue"): return var._FillValue |
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| 135 | return 1.E20 |
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| 136 | |
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| 137 | |
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| 138 | def fixHeaderLength(file): |
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| 139 | lines=open(file).readlines()[:200] |
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| 140 | count=0 |
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| 141 | for line in lines: |
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| 142 | count=count+1 |
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| 143 | if line=="###Data Section begins on the next line###\n": |
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| 144 | break |
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| 145 | # Now replace 1st line NLHEAD with count |
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| 146 | firstline=lines[0] |
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| 147 | newline="%s %s" % (count, firstline.split()[-1]) |
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| 148 | for line in fileinput.input(file, inplace=1): |
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| 149 | if line==firstline: |
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| 150 | # write the changed line |
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| 151 | sys.stdout.write(newline+"\n") |
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| 152 | else: |
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| 153 | # write the line unchanged |
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| 154 | sys.stdout.write(line) |
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| 155 | |
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| 156 | |
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| 157 | def cdms2na(infilename, outfilename, variable=None, ffi="automatic", rules=None): |
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| 158 | print "Reading data from: %s" % infilename |
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| 159 | cdmsfile=cdms.open(infilename) |
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| 160 | globals=cdmsfile.attributes |
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| 161 | if not variable: |
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| 162 | vars=[] |
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| 163 | for var in cdmsfile.variables: |
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| 164 | vars.append(cdmsfile(var)) |
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| 165 | else: |
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| 166 | vars=[cdmsfile(variable)] |
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| 167 | |
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| 168 | # Re-order variables if they have the attribute 'nasa_ames_var_number' |
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| 169 | orderedVars=[None]*1000 |
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| 170 | otherVars=[] |
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| 171 | for var in vars: |
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| 172 | varMetadata=cdmsfile[var] |
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| 173 | if hasattr(varMetadata, "nasa_ames_var_number"): |
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| 174 | num=varMetadata.nasa_ames_var_number |
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| 175 | orderedVars[num]=var |
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| 176 | else: |
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| 177 | otherVars.append(var) |
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| 178 | |
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| 179 | vars=[] |
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| 180 | for var in orderedVars: |
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| 181 | if var!=None: |
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| 182 | vars.append(var) |
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| 183 | |
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| 184 | vars=vars+otherVars |
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| 185 | |
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| 186 | builder=CdmsToNABuilder(vars, globals) |
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| 187 | #print builder.naDict["X"] |
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| 188 | |
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| 189 | print "\nWriting output NASA Ames file: %s" % outfilename |
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| 190 | general.openNAFile(outfilename, 'w', builder.naDict) |
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| 191 | nlhead=fixHeaderLength(outfilename) |
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| 192 | print "\nNASA Ames file written successfully: %s" % outfilename |
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| 193 | |
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| 194 | |
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| 195 | class CdmsToNABuilder(NACore): |
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| 196 | """ |
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| 197 | Class to build a NASA Ames File object from a set of |
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| 198 | CDMS variables and global attributes (optional). |
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| 199 | """ |
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| 200 | |
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| 201 | def __init__(self, vars, global_attributes={}): |
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| 202 | """ |
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| 203 | Sets up instance variables and calls appropriate methods to |
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| 204 | generate sections of NASA Ames file object. |
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| 205 | """ |
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| 206 | self.naDict={} |
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| 207 | self.vars=vars |
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| 208 | self.globals=global_attributes |
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| 209 | (self.orderedVars, auxVars)=self.analyseVariables() |
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| 210 | self.naDict["NLHEAD"]="-999" |
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| 211 | self.defineNAVars(self.orderedVars) |
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| 212 | self.defineNAAuxVars(auxVars) |
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| 213 | self.defineNAGlobals() |
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| 214 | self.defineNAComments() |
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| 215 | self.defineGeneralHeader() |
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| 216 | # Quick fudge |
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| 217 | if self.naDict["FFI"]==1001: self.naDict["X"]=self.naDict["X"][0] |
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| 218 | |
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| 219 | def analyseVariables(self): |
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| 220 | """ |
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| 221 | Method to examine the content of CDMS variables to return |
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| 222 | a tuple of two lists containing variables and auxiliary variables |
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| 223 | for the NASA Ames file object. |
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| 224 | """ |
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| 225 | # Get largest ranked variable as the one we use as standard |
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| 226 | rank=0 |
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| 227 | count=0 |
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| 228 | for var in self.vars: |
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| 229 | count=count+1 |
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| 230 | if var.rank()>rank: |
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| 231 | rank=var.rank() |
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| 232 | bestVar=var |
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| 233 | bestVarIndex=count |
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| 234 | elif var.rank()==rank: |
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| 235 | if len(var.flat)>len(bestVar.flat): |
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| 236 | bestVar=var |
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| 237 | bestVarIndex=count |
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| 238 | |
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| 239 | vars4NA=[bestVar] |
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| 240 | auxVars4NA=[] |
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| 241 | shape=bestVar.shape |
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| 242 | ndims=len(shape) |
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| 243 | self.naDict["NIV"]=ndims |
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| 244 | |
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| 245 | # Work out which File Format Index is appropriate |
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| 246 | if ndims in (2,3,4): |
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| 247 | self.naDict["FFI"]=10+(ndims*1000) |
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| 248 | elif ndims>4: |
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| 249 | raise "Cannot write variables defined against greater than 4 axes in NASA Ames format." |
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| 250 | else: |
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| 251 | if len(auxVars4NA)>0 or (self.naDict.has_key("NAUXV") and self.naDict["NAUXV"]>0): |
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| 252 | self.naDict["FFI"]=1010 |
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| 253 | else: |
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| 254 | self.naDict["FFI"]=1001 |
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| 255 | #print self.naDict["FFI"] |
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| 256 | axes=bestVar.getAxisList() |
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| 257 | |
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| 258 | # Get other variable info |
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| 259 | for var in self.vars[:bestVarIndex-1]+self.vars[bestVarIndex:]: |
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| 260 | if len(var.shape)!=ndims or var.shape!=shape: |
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| 261 | # Could it be an auxiliary variable |
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| 262 | if len(var.shape)!=1: continue |
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| 263 | caxis=var.getAxis(0) |
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| 264 | if compareAxes(axes[0], caxis)==0: continue |
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| 265 | # I think it is an auxiliary variable |
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| 266 | auxVars4NA.append(var) |
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| 267 | else: |
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| 268 | caxes=var.getAxisList() |
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| 269 | for i in range(ndims): |
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| 270 | if compareAxes(axes[i], caxes[i])==0: |
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| 271 | continue |
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| 272 | # OK, I think they are compatible |
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| 273 | vars4NA.append(var) |
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| 274 | |
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| 275 | # Re-order if they previously came from NASA Ames files (i.e. including |
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| 276 | # the attribute 'nasa_ames_var_number') |
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| 277 | orderedVars=[None]*1000 |
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| 278 | otherVars=[] |
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| 279 | for var in vars4NA: |
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| 280 | if hasattr(var, "nasa_ames_var_number"): |
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| 281 | orderedVars[var.nasa_ames_var_number[0]]=var |
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| 282 | else: |
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| 283 | otherVars.append(var) |
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| 284 | # Remake vars4NA now in order |
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| 285 | vars4NA=[] |
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| 286 | for var in orderedVars: |
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| 287 | if var!=None: vars4NA.append(var) |
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| 288 | vars4NA=vars4NA+otherVars |
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| 289 | |
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| 290 | # Now re-order the Auxiliary variables if they previously came from NASA |
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| 291 | # Ames files (i.e. including the attribute 'nasa_ames_aux_var_number') |
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| 292 | |
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| 293 | orderedAuxVars=[None]*1000 |
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| 294 | otherAuxVars=[] |
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| 295 | for var in auxVars4NA: |
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| 296 | if hasattr(var, "nasa_ames_aux_var_number"): |
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| 297 | orderedAuxVars[var.nasa_ames_aux_var_number[0]]=var |
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| 298 | else: |
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| 299 | otherAuxVars.append(var) |
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| 300 | # Remake auxVars4NA now in order |
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| 301 | auxVars4NA=[] |
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| 302 | for var in orderedAuxVars: |
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| 303 | if var!=None: auxVars4NA.append(var) |
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| 304 | auxVars4NA=auxVars4NA+otherAuxVars |
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| 305 | return (vars4NA, auxVars4NA) |
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| 306 | |
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| 307 | def defineNAVars(self, vars): |
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| 308 | """ |
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| 309 | Method to define NASA Ames file object variables and their |
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| 310 | associated metadata. |
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| 311 | """ |
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| 312 | self.naDict["NV"]=len(vars) |
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| 313 | self.naDict["VNAME"]=[] |
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| 314 | self.naDict["VMISS"]=[] |
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| 315 | self.naDict["VSCAL"]=[] |
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| 316 | self.naDict["V"]=[] |
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| 317 | for var in vars: |
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| 318 | name=getBestName(var) |
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| 319 | self.naDict["VNAME"].append(name) |
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| 320 | miss=getMissingValue(var) |
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| 321 | if type(miss)!=float: miss=miss[0] |
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| 322 | self.naDict["VMISS"].append(miss) |
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| 323 | #print self.naDict["VMISS"] |
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| 324 | self.naDict["VSCAL"].append(1) |
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| 325 | # AND THE ARRAY |
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| 326 | # Populate the variable list |
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| 327 | ######## NOTE - might not have to do this ##### |
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| 328 | ######## It might handle writing from a Numeric array ######## |
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| 329 | self.naDict["V"].append(var._data) |
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| 330 | #listOfListsCreator(inlist, var.shape) |
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| 331 | #arrayToList(var, inlist) |
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| 332 | |
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| 333 | if not self.naDict.has_key("X"): |
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| 334 | self.naDict["NXDEF"]=[] |
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| 335 | self.naDict["NX"]=[] |
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| 336 | # Create independent variable information |
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| 337 | self.ax0=var.getAxis(0) |
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| 338 | self.naDict["X"]=[list(self.ax0._data_)] |
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| 339 | self.naDict["XNAME"]=[getBestName(self.ax0)] |
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| 340 | if len(self.ax0)==1: |
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| 341 | self.naDict["DX"]=[0] |
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| 342 | else: |
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| 343 | incr=self.ax0[1]-self.ax0[0] |
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| 344 | for i in range(1, len(self.ax0)): |
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| 345 | if (self.ax0[i]-self.ax0[i-1])!=incr: |
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| 346 | self.naDict["DX"]=[0] |
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| 347 | break |
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| 348 | else: |
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| 349 | self.naDict["DX"]=[incr] |
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| 350 | # Now sort the rest of the axes |
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| 351 | for axis in var.getAxisList()[1:]: |
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| 352 | self.getAxisDefinition(axis) |
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| 353 | |
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| 354 | def defineNAAuxVars(self, auxVars): |
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| 355 | """ |
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| 356 | Method to define NASA Ames file object auxiliary variables and their |
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| 357 | associated metadata. |
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| 358 | """ |
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| 359 | self.naDict["NAUXV"]=len(auxVars) |
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| 360 | self.naDict["ANAME"]=[] |
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| 361 | self.naDict["AMISS"]=[] |
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| 362 | self.naDict["ASCAL"]=[] |
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| 363 | self.naDict["A"]=[] |
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| 364 | for var in auxVars: |
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| 365 | name=getBestName(var) |
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| 366 | self.naDict["ANAME"].append(name) |
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| 367 | miss=getMissingValue(var) |
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| 368 | if type(miss)!=float: miss=miss[0] |
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| 369 | self.naDict["AMISS"].append(miss) |
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| 370 | self.naDict["ASCAL"].append(1) |
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| 371 | # AND THE ARRAY |
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| 372 | # Populate the variable list |
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| 373 | ######## NOTE - might not have to do this ##### |
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| 374 | ######## It might handle writing from a Numeric array ######## |
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| 375 | self.naDict["A"].append(var._data) |
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| 376 | #listOfListsCreator(inlist, var.shape) |
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| 377 | #arrayToList(var, inlist) |
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| 378 | |
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| 379 | def getAxisDefinition(self, axis): |
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| 380 | """ |
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| 381 | Method to create the appropriate NASA Ames file object |
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| 382 | items associated with an axis (independent variable in |
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| 383 | NASA Ames). |
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| 384 | """ |
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| 385 | self.naDict["NX"].append(len(axis)) |
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| 386 | self.naDict["XNAME"].append(getBestName(axis)) |
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| 387 | # If only one item in axis values |
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| 388 | if len(axis)<3: |
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| 389 | self.naDict["DX"].append(0) |
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| 390 | self.naDict["NXDEF"].append(len(axis)) |
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| 391 | self.naDict["X"].append(list(axis._data_)) |
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| 392 | return |
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| 393 | |
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| 394 | incr=axis[1]-axis[0] |
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| 395 | for i in range(1, len(axis)): |
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| 396 | if (axis[i]-axis[i-1])!=incr: |
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| 397 | self.naDict["DX"].append(0) |
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| 398 | self.naDict["NXDEF"].append(len(axis)) |
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| 399 | self.naDict["X"].append(list(axis._data_)) |
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| 400 | break |
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| 401 | else: |
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| 402 | self.naDict["DX"].append(incr) |
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| 403 | self.naDict["NXDEF"].append(3) |
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| 404 | self.naDict["X"].append(axis[:3]) |
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| 405 | return |
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| 406 | |
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| 407 | def defineNAGlobals(self): |
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| 408 | """ |
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| 409 | Maps CDMS (NetCDF) global attributes into NASA Ames Header fields. |
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| 410 | """ |
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| 411 | # Get the global mapping dictionary |
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| 412 | globalmap=cdmsMap.toNA |
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| 413 | # Check if we should add to it with locally set rules |
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| 414 | locGlobs=localRules.localGlobalAttributes |
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| 415 | for att in locGlobs.keys(): |
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| 416 | if not globalmap.has_key(att): |
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| 417 | globalmap[key]=locGlobs[key] |
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| 418 | |
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| 419 | self.extra_comments=[[],[],[]] # Normal comments, special comments, other comments |
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| 420 | for key in self.globals.keys(): |
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| 421 | if key!="first_valid_date_of_data" and type(self.globals[key]) not in (str, float, int): continue |
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| 422 | if key in globalmap.keys(): |
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| 423 | if key=="history": |
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| 424 | timestring=time.strftime("%Y-%m-%d %H:%M:%S", time.localtime(time.time())) |
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| 425 | self.history="History:\n\t%s - Converted to NASA Ames format using nappy-%s.\n\t%s" % (timestring, version.version, self.globals[key]) |
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| 426 | self.history=self.history.split("\n") |
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| 427 | |
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| 428 | elif key=="institution": |
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| 429 | # If fields came from NA then extract appropriate fields. |
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| 430 | match=re.match(r"(.*)\s+\(ONAME from NASA Ames file\);\s+(.*)\s+\(ORG from NASA Ames file\)\.", self.globals[key]) |
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| 431 | if match: |
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| 432 | self.naDict["ONAME"]=match.groups()[0] |
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| 433 | self.naDict["ORG"]=match.groups()[1] |
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| 434 | else: |
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| 435 | self.naDict["ONAME"]=self.globals[key] |
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| 436 | self.naDict["ORG"]=self.globals[key] |
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| 437 | |
|---|
| 438 | elif key=="comment": |
|---|
| 439 | # Need to work out if they are actually comments from NASA Ames in the first place |
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| 440 | #self.ncom=[self.globals[key]] |
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| 441 | comLines=self.globals[key].split("\n") |
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| 442 | normComms=[] |
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| 443 | normCommFlag=None |
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| 444 | specComms=[] |
|---|
| 445 | specCommFlag=None |
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| 446 | for line in comLines: |
|---|
| 447 | if line.find("###NASA Ames Special Comments follow###")>-1: |
|---|
| 448 | specCommFlag=1 |
|---|
| 449 | elif line.find("###NASA Ames Special Comments end###")>-1: |
|---|
| 450 | specCommFlag=None |
|---|
| 451 | elif line.find("###NASA Ames Normal Comments follow###")>-1: |
|---|
| 452 | normCommFlag=1 |
|---|
| 453 | elif line.find("###NASA Ames Normal Comments end###")>-1: |
|---|
| 454 | normCommFlag=None |
|---|
| 455 | elif specCommFlag==1: |
|---|
| 456 | specComms.append(line) |
|---|
| 457 | elif normCommFlag==1: |
|---|
| 458 | normComms.append(line) |
|---|
| 459 | elif line.find("###Data Section begins on the next line###")>-1: |
|---|
| 460 | pass |
|---|
| 461 | else: |
|---|
| 462 | normComms.append(line) |
|---|
| 463 | |
|---|
| 464 | self.extra_comments=[specComms, normComms, []] |
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| 465 | |
|---|
| 466 | elif key=="first_valid_date_of_data": |
|---|
| 467 | self.naDict["DATE"]=self.globals[key] |
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| 468 | |
|---|
| 469 | elif key in ("Conventions", "references"): |
|---|
| 470 | pass |
|---|
| 471 | else: |
|---|
| 472 | self.naDict[globalmap[key]]=self.globals[key] |
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| 473 | else: |
|---|
| 474 | self.extra_comments[2].append("%s: %s" % (key, self.globals[key])) |
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| 475 | return |
|---|
| 476 | |
|---|
| 477 | |
|---|
| 478 | def defineNAComments(self, normal_comments=[], special_comments=[]): |
|---|
| 479 | """ |
|---|
| 480 | Defines the Special and Normal comments sections in the NASA Ames file |
|---|
| 481 | object - including information gathered from the defineNAGlobals method. |
|---|
| 482 | """ |
|---|
| 483 | |
|---|
| 484 | if hasattr(self, "ncom"): normal_comments=self.ncom+normal_comments |
|---|
| 485 | NCOM=[] |
|---|
| 486 | for ncom in normal_comments: |
|---|
| 487 | NCOM.append(ncom) |
|---|
| 488 | if len(NCOM)>0: NCOM.append("") |
|---|
| 489 | |
|---|
| 490 | if len(self.extra_comments[2])>0: |
|---|
| 491 | for excom in self.extra_comments[2]: |
|---|
| 492 | NCOM.append(excom) |
|---|
| 493 | |
|---|
| 494 | if len(self.extra_comments[1])>0: |
|---|
| 495 | NCOM.append("Additional Global Attributes defined in the source file and not translated elsewhere:") |
|---|
| 496 | for excom in self.extra_comments[1]: |
|---|
| 497 | NCOM.append(excom) |
|---|
| 498 | |
|---|
| 499 | if hasattr(self, "history"): |
|---|
| 500 | for h in self.history: |
|---|
| 501 | NCOM.append(h) |
|---|
| 502 | |
|---|
| 503 | if len(NCOM)>0: |
|---|
| 504 | NCOM.insert(0, "###NASA Ames Normal Comments follow###") |
|---|
| 505 | NCOM.append("") |
|---|
| 506 | NCOM.append("###NASA Ames Normal Comments end###") |
|---|
| 507 | NCOM.append("###Data Section begins on the next line###") |
|---|
| 508 | |
|---|
| 509 | specCommentsFlag=None |
|---|
| 510 | SCOM=[] |
|---|
| 511 | special_comments=self.extra_comments[0] |
|---|
| 512 | if len(special_comments)>0: |
|---|
| 513 | SCOM=["###NASA Ames Special Comments follow###"] |
|---|
| 514 | specCommentsFlag=1 |
|---|
| 515 | for scom in special_comments: |
|---|
| 516 | SCOM.append(scom) |
|---|
| 517 | |
|---|
| 518 | |
|---|
| 519 | used_var_atts=("name", "long_name", "standard_name", "id", |
|---|
| 520 | "missing_value", "fill_value", "units", |
|---|
| 521 | "nasa_ames_var_number", "nasa_ames_aux_var_number") |
|---|
| 522 | varCommentsFlag=None |
|---|
| 523 | |
|---|
| 524 | for var in self.orderedVars: |
|---|
| 525 | varflag="unused" |
|---|
| 526 | name=getBestName(var) |
|---|
| 527 | for scom in var.attributes.keys(): |
|---|
| 528 | if type(scom) in (str, float, int) and scom not in used_var_atts: |
|---|
| 529 | if varflag=="unused": |
|---|
| 530 | if varCommentsFlag==None: |
|---|
| 531 | varCommentsFlag=1 |
|---|
| 532 | if specCommentsFlag==None: |
|---|
| 533 | SCOM=["###NASA Ames Special Comments follow###"] |
|---|
| 534 | SCOM.append("Additional Variable Attributes defined in the source file and not translated elsewhere:") |
|---|
| 535 | SCOM.append("###Variable attributes from source (NetCDF) file follow###") |
|---|
| 536 | varflag=="using" |
|---|
| 537 | SCOM.append("\tVariable (%s): %s" % (var.id, name)) |
|---|
| 538 | SCOM.append("\t\t%s = %s" % (scom, var.attributes[scom])) |
|---|
| 539 | if varCommentsFlag==1: SCOM.append("###Variable attributes from source (NetCDF) file end###") |
|---|
| 540 | if specCommentsFlag==1: |
|---|
| 541 | SCOM.append("###NASA Ames Special Comments end###") |
|---|
| 542 | |
|---|
| 543 | """used_var_atts=("name", "long_name", "standard_name", "id", "missing_value", "fill_value", "units") |
|---|
| 544 | for var in self.vars: |
|---|
| 545 | for scom in var.attributes.keys(): |
|---|
| 546 | name=getBestName(var) |
|---|
| 547 | if type(scom) in (str, float, int) and scom not in used_var_atts: |
|---|
| 548 | SCOM.append("\t%s: %s - %s" % (name, scom, var.attributes[scom]))""" |
|---|
| 549 | |
|---|
| 550 | # Strip out empty lines (or returns) |
|---|
| 551 | NCOM_cleaned=[] |
|---|
| 552 | SCOM_cleaned=[] |
|---|
| 553 | for c in NCOM: |
|---|
| 554 | if c.strip() not in ("", " ", " "): NCOM_cleaned.append(c) |
|---|
| 555 | for c in SCOM: |
|---|
| 556 | if c.strip() not in ("", " ", " "): SCOM_cleaned.append(c) |
|---|
| 557 | |
|---|
| 558 | self.naDict["NCOM"]=NCOM_cleaned |
|---|
| 559 | self.naDict["NNCOML"]=len(self.naDict["NCOM"]) |
|---|
| 560 | self.naDict["SCOM"]=SCOM_cleaned |
|---|
| 561 | self.naDict["NSCOML"]=len(self.naDict["SCOM"]) |
|---|
| 562 | return |
|---|
| 563 | |
|---|
| 564 | def defineGeneralHeader(self, header_items={}): |
|---|
| 565 | """ |
|---|
| 566 | Defines known header items and overwrites any with header_items |
|---|
| 567 | key/value pairs. |
|---|
| 568 | """ |
|---|
| 569 | # Check if DATE field previously known in NASA Ames file |
|---|
| 570 | time_now=time.strftime("%Y %m %d", time.localtime(time.time())).split() |
|---|
| 571 | if not self.naDict.has_key("RDATE"): |
|---|
| 572 | self.naDict["RDATE"]=time_now |
|---|
| 573 | |
|---|
| 574 | if self.ax0.isTime(): |
|---|
| 575 | # Get first date in list |
|---|
| 576 | try: |
|---|
| 577 | (unit, start_date)=re.match("(\w+)\s+?since\s+?(\d+-\d+-\d+)", self.ax0.units).groups() |
|---|
| 578 | comptime=cdtime.s2c(start_date) |
|---|
| 579 | first_day=comptime.add(self.naDict["X"][0][0], getattr(cdtime, unit.capitalize())) |
|---|
| 580 | self.naDict["DATE"]=string.replace(str(first_day).split(" ")[0], "-", " ").split() |
|---|
| 581 | except: |
|---|
| 582 | print "Nappy Warning: Could not get the first date in the file. You will need to manually edit the output file." |
|---|
| 583 | self.naDict["DATE"]="<DATE_UNKNOWN>" |
|---|
| 584 | else: |
|---|
| 585 | if not self.naDict.has_key("DATE"): |
|---|
| 586 | print "Nappy Warning: Could not get the first date in the file. You will need to manually edit the output file." |
|---|
| 587 | self.naDict["DATE"]="<DATE_UNKNOWN>" |
|---|
| 588 | self.naDict["IVOL"]=1 |
|---|
| 589 | self.naDict["NVOL"]=1 |
|---|
| 590 | for key in header_items.keys(): |
|---|
| 591 | self.naDict[key]=header_items[key] |
|---|
| 592 | return |
|---|
| 593 | |
|---|
| 594 | |
|---|
| 595 | |
|---|
| 596 | if __name__=="__main__": |
|---|
| 597 | |
|---|
| 598 | args=sys.argv[1:] |
|---|
| 599 | if len(args)<4: |
|---|
| 600 | print helpMessage |
|---|
| 601 | print "Incorrect number of arguments used." |
|---|
| 602 | sys.exit() |
|---|
| 603 | |
|---|
| 604 | for arg in args: |
|---|
| 605 | if arg=="-i": |
|---|
| 606 | infile=args[args.index(arg)+1] |
|---|
| 607 | elif arg=="-o": |
|---|
| 608 | outfile=args[args.index(arg)+1] |
|---|
| 609 | |
|---|
| 610 | cdms2na(infile, outfile) |
|---|
