| 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. |
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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, Numeric |
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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 | |
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| 50 | # Set up functions |
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| 51 | def compareAxes(ax1, ax2): |
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| 52 | """ |
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| 53 | Takes 2 cmds axis objects returning 1 if they are essentially |
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| 54 | the same and 0 if not. |
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| 55 | """ |
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| 56 | for axtype in ("time", "level", "latitude", "longitude"): |
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| 57 | if cdms.axisMatches(ax1, axtype) and not cdms.axisMatches(ax2, axtype): |
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| 58 | return 0 |
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| 59 | |
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| 60 | # Check ids |
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| 61 | if ax1.id!=ax2.id: return 0 |
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| 62 | # Check lengths |
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| 63 | if len(ax1)!=len(ax2): return 0 |
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| 64 | # Check values |
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| 65 | if ax1._data_!=ax2._data_: return 0 |
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| 66 | # Check units |
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| 67 | if ax1.units!=ax2.units: return 0 |
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| 68 | # OK, I think they are the same axis! |
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| 69 | return 1 |
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| 70 | |
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| 71 | |
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| 72 | def compareVariables(var1, var2): |
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| 73 | """ |
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| 74 | Compares two cdms variables to see if they are defined on identical |
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| 75 | axes. Returns 1 if true, 0 if not. |
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| 76 | """ |
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| 77 | try: |
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| 78 | for i in range(len(var1.getAxisList())): |
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| 79 | ax1=var1.getAxis(i) |
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| 80 | ax2=var2.getAxis(i) |
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| 81 | if compareAxes(ax1, ax2)==0: |
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| 82 | return 0 |
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| 83 | except: |
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| 84 | return 0 |
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| 85 | return 1 |
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| 86 | |
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| 87 | |
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| 88 | def isAuxAndVar(avar, var): |
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| 89 | """ |
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| 90 | Compares two cdms variables and returns true if the first dimension of the |
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| 91 | main variable is the only dimension the auxiliary variable is defined against. |
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| 92 | """ |
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| 93 | if len(avar.shape)>1: |
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| 94 | return 0 |
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| 95 | auxax=avar.getAxis(0) |
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| 96 | varax=var.getAxis(0) |
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| 97 | return compareAxes(auxax, varax) |
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| 98 | |
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| 99 | |
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| 100 | def arrayToList(array, inlist): |
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| 101 | """ |
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| 102 | Takes an n-dimensional Numeric array and converts it to an |
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| 103 | n-dimensional list object. |
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| 104 | """ |
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| 105 | dimlist=array.shape |
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| 106 | if len(dimlist[1:])>0: |
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| 107 | for i in range(dimlist[0]): |
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| 108 | arrayToList(inlist[i], array[i]) |
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| 109 | else: |
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| 110 | for i in range(dimlist[0]): |
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| 111 | inlist.append(array[i]) |
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| 112 | return inlist |
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| 113 | |
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| 114 | |
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| 115 | def listOfListsCreator(inlist, dimlist): |
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| 116 | """ |
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| 117 | Creates a list of lists with dimensions defined in dimlist (a list of integers). |
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| 118 | """ |
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| 119 | if len(dimlist[1:])>0: |
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| 120 | for i in range(dimlist[0]): |
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| 121 | inlist.append([]) |
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| 122 | listOfListsCreator(inlist[i], array, dimlist[1:]) |
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| 123 | return inlist |
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| 124 | |
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| 125 | |
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| 126 | def getBestName(var): |
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| 127 | """ |
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| 128 | Returns the most appropriate variable name for a NASA Ames header |
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| 129 | """ |
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| 130 | name=None |
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| 131 | if hasattr(var, "id"): name=var.id |
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| 132 | if hasattr(var, "shortname"): name=var.short_name |
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| 133 | if hasattr(var, "name"): name=var.name |
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| 134 | if hasattr(var, "title"): name=var.title |
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| 135 | if hasattr(var, "standard_name"): name=var.standard_name |
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| 136 | if hasattr(var, "long_name"): name=var.long_name |
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| 137 | #if hasattr(var, "standard_name"): name=var.standard_name |
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| 138 | |
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| 139 | if hasattr(var, "has_key"): |
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| 140 | if var.has_key("id"): name=var["id"] |
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| 141 | if var.has_key("short_name"): name=var["short_name"] |
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| 142 | if var.has_key("name"): name=var["name"] |
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| 143 | if var.has_key("title"): name=var["title"] |
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| 144 | if var.has_key("standard_name"): name=var["standard_name"] |
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| 145 | if var.has_key("long_name"): name=var["long_name"] |
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| 146 | #if var.has_key("standard_name"): name=var["standard_name"] |
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| 147 | |
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| 148 | if hasattr(var, "units") and not re.match("^\s+$", var.units): |
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| 149 | units=var.units.strip() |
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| 150 | name="%s (%s)" % (name, units) |
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| 151 | # Do a check to see units are not duplicated |
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| 152 | # [The regex below failed because it interpreted 'm**2' as |
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| 153 | # regex characters] |
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| 154 | #match=re.match("(.*\(%s\)\s*)\(%s\)(.*)$" % (var.units, var.units), name) |
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| 155 | #if match: |
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| 156 | # name=match.groups()[0]+match.groups()[1] |
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| 157 | if name.count("(%s)" % units)>1: |
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| 158 | name=name.replace("(%s)" % units, "") |
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| 159 | name="%s (%s)" % (name, units) |
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| 160 | |
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| 161 | if name[-2:]=="()": name=name[:-2] |
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| 162 | return name |
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| 163 | |
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| 164 | |
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| 165 | def getMissingValue(var): |
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| 166 | """ |
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| 167 | Returns the missing value or defaults to 1.E20. |
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| 168 | """ |
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| 169 | miss=None |
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| 170 | if hasattr(var, "missing_value"): miss=var.missing_value |
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| 171 | if hasattr(var, "_fill_value"): miss=var._fill_value |
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| 172 | # if hasattr(var, "fill_value"): miss=var.fill_value # returns an array???? |
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| 173 | if hasattr(var, "_FillValue"): miss=var._FillValue |
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| 174 | if miss==None: |
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| 175 | try: |
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| 176 | miss=var.getMissing() |
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| 177 | except: |
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| 178 | miss=1.E20 |
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| 179 | return miss |
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| 180 | |
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| 181 | |
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| 182 | def fixHeaderLengthNowDefunct(file): |
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| 183 | """ |
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| 184 | Fixes length of header. |
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| 185 | """ |
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| 186 | lines=open(file).readlines()[:200] |
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| 187 | count=0 |
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| 188 | for line in lines: |
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| 189 | count=count+1 |
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| 190 | if line=="###Data Section begins on the next line###\n": |
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| 191 | break |
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| 192 | # Now replace 1st line NLHEAD with count |
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| 193 | firstline=lines[0] |
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| 194 | newline="%s %s" % (count, firstline.split()[-1]) |
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| 195 | for line in fileinput.input(file, inplace=1): |
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| 196 | if line==firstline: |
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| 197 | # write the changed line |
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| 198 | sys.stdout.write(newline+"\n") |
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| 199 | else: |
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| 200 | # write the line unchanged |
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| 201 | sys.stdout.write(line) |
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| 202 | |
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| 203 | def flatten2DTimeData(var, timevar): |
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| 204 | """ |
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| 205 | Returns a flattened 2D array variable with a recalculated time axies. |
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| 206 | """ |
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| 207 | import MV, cdtime |
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| 208 | data=MV.ravel(var) |
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| 209 | missing=var.getMissing() |
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| 210 | |
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| 211 | timevalues=timevar._data |
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| 212 | timeunit=timevar.units |
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| 213 | samprate=var.getAxis(1) |
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| 214 | rate=int(samprate.id[3:]) |
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| 215 | newTimeValues=[] |
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| 216 | |
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| 217 | for t in timevalues: |
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| 218 | for i in range(rate): |
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| 219 | tvalue=t+((1./rate)*i) |
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| 220 | newTimeValues.append(tvalue) |
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| 221 | |
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| 222 | newTimeAx=cdms.createAxis(newTimeValues) |
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| 223 | newTimeAx.units=timeunit |
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| 224 | newTimeAx.designateTime() |
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| 225 | newTimeAx.id=newTimeAx.long_name=newTimeAx.standard_name="time" |
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| 226 | |
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| 227 | atts=var.attributes |
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| 228 | newAtts={} |
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| 229 | for att,value in atts.items(): |
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| 230 | if type(value) in (type((1,1)), type([1,2]), type(Numeric.array([1.]))) and len(value)==1: |
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| 231 | value=value[0] |
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| 232 | if type(value) in (type(1), type(1.), type(long(1))): |
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| 233 | newAtts[att]=value |
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| 234 | elif type(value)==type(""): |
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| 235 | newAtts[att]=value.strip() |
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| 236 | |
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| 237 | # Now create the variable |
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| 238 | newvar=cdms.createVariable(data, id=var.id, fill_value=missing, axes=[newTimeAx], attributes=newAtts) |
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| 239 | return newvar |
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| 240 | |
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| 241 | |
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| 242 | def modifyNADictCopy(indict, v_new, start, end, ivol, nvol): |
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| 243 | """ |
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| 244 | Returns a copy of a dictionary with some modifications. |
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| 245 | """ |
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| 246 | newDict={} |
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| 247 | for key,value in indict.items(): |
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| 248 | if key=="X": |
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| 249 | newlist=indict["X"][start:end] |
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| 250 | newDict["X"]=newlist |
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| 251 | elif key=="V": |
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| 252 | newDict["V"]=v_new |
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| 253 | elif key=="IVOL": |
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| 254 | newDict["IVOL"]=ivol |
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| 255 | elif key=="NVOL": |
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| 256 | newDict["NVOL"]=nvol |
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| 257 | else: |
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| 258 | newDict[key]=value |
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| 259 | return newDict |
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| 260 | |
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| 261 | |
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| 262 | def cdms2na(infilename, outfilenames, naVars={}, variables=None, nFilesOnly="no", |
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| 263 | rule=None, ffi="automatic", spacer=" ", floatFormat="%g", |
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| 264 | rules=None, sizeLimit=None): |
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| 265 | """ |
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| 266 | Main conversion function that calls the appropriate classes and functions |
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| 267 | to write a NASA Ames file. |
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| 268 | """ |
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| 269 | #print infilename, outfilenames, nFilesOnly, naVars, variables |
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| 270 | if type(outfilenames)==type(""): outfilenames=[outfilenames] |
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| 271 | |
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| 272 | allowedOverwriteMetadata=["DATE", "RDATE", "ANAME", "MNAME", |
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| 273 | "ONAME", "ORG", "SNAME", "VNAME"] |
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| 274 | arrayArgs=["DATE", "RDATE", "ANAME", "VNAME"] |
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| 275 | # ANAME[a] - array of 'a' x ANAME strings - aux var names |
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| 276 | # DATE (array of three) - UT date at which the data within the file starts |
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| 277 | # MNAME - mission name |
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| 278 | # ONAME - name of originator(s) |
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| 279 | # ORG - org or affiliation of originator(s) |
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| 280 | # RDATE (array of three) - date of data reduction or revision |
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| 281 | # SNAME - source of measurement or model output VNAME[n] - array of 'n' x |
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| 282 | # VNAME strings - var names. |
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| 283 | outputMessage=[] |
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| 284 | msg="Reading data from: %s\n" % infilename |
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| 285 | print msg |
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| 286 | outputMessage.append(msg) |
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| 287 | cdmsfile=cdms.open(infilename) |
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| 288 | globals=cdmsfile.attributes |
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| 289 | |
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| 290 | vars=[] |
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| 291 | if not variables: |
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| 292 | variables=cdmsfile.listvariables() |
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| 293 | #for var in cdmsfile.listvariables(): |
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| 294 | #vars.append(cdmsfile(var)) |
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| 295 | |
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| 296 | for variable in variables: |
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| 297 | varObj=cdmsfile(variable) |
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| 298 | # Deal with singleton variables |
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| 299 | if not hasattr(varObj, "rank"): |
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| 300 | varMetadata=cdmsfile[variable].attributes |
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| 301 | varValue=varObj |
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| 302 | #print varMetadata, varValue, varMetadata.keys(), varMetadata._obj_.id |
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| 303 | varObj=cdms.createVariable(Numeric.array(varObj), id=getBestName(varMetadata).replace(" ", "_"), attributes=varMetadata) |
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| 304 | #print varObj, dir(varObj); sys.exit() |
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| 305 | varObj.value=varObj._data[0] |
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| 306 | #varObj.rank=0 |
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| 307 | |
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| 308 | #print varObj, varObj.attributes |
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| 309 | vars.append(varObj) |
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| 310 | |
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| 311 | # Re-order variables if they have the attribute 'nasa_ames_var_number' |
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| 312 | orderedVars=[None]*1000 |
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| 313 | otherVars=[] |
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| 314 | for var in vars: |
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| 315 | varMetadata=cdmsfile[var] |
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| 316 | if hasattr(varMetadata, "nasa_ames_var_number"): |
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| 317 | num=varMetadata.nasa_ames_var_number |
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| 318 | orderedVars[num]=var |
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| 319 | else: |
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| 320 | otherVars.append(var) |
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| 321 | |
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| 322 | vars=[] |
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| 323 | for var in orderedVars: |
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| 324 | if var!=None: |
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| 325 | vars.append(var) |
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| 326 | |
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| 327 | vars=vars+otherVars |
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| 328 | |
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| 329 | builder=CdmsToNABuilder(vars, globals, rule=rule, cdmsfile=cdmsfile) |
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| 330 | #print builder.naDict["X"] |
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| 331 | builtNADicts=[[builder.naDict, builder.varIDs]] |
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| 332 | if builder.varIDs==None: |
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| 333 | msg="\nNo files created after variables parsed." |
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| 334 | print msg |
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| 335 | outputMessage.append(msg) |
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| 336 | return outputMessage |
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| 337 | |
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| 338 | while len(builder.varBin)>0: |
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| 339 | builder=CdmsToNABuilder(builder.varBin, globals, rule=rule, cdmsfile=cdmsfile) |
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| 340 | outputMessage=outputMessage+builder.outputMessage |
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| 341 | if builder.varIDs!=None: builtNADicts.append([builder.naDict, builder.varIDs]) |
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| 342 | |
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| 343 | # Return only filenames if only want to know them now. |
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| 344 | ncount=1 |
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| 345 | fileNames=[] |
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| 346 | if nFilesOnly=="yes": |
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| 347 | for i in builtNADicts: |
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| 348 | if len(builtNADicts)==1: |
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| 349 | suffix="" |
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| 350 | else: |
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| 351 | suffix="_%s" % ncount |
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| 352 | nameparts=outfilenames[0].split(".") |
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| 353 | newname=(".".join(nameparts[:-1]))+suffix+"."+nameparts[-1] |
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| 354 | fileNames.append(newname) |
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| 355 | ncount=ncount+1 |
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| 356 | |
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| 357 | return fileNames |
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| 358 | |
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| 359 | msg="\n%s files to write" % len(builtNADicts) |
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| 360 | print msg |
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| 361 | outputMessage.append(msg) |
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| 362 | |
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| 363 | count=1 |
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| 364 | ncount=1 |
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| 365 | for i in builtNADicts: |
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| 366 | if len(outfilenames)==1: |
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| 367 | if len(builtNADicts)==1: |
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| 368 | suffix="" |
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| 369 | else: |
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| 370 | suffix="_%s" % ncount |
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| 371 | nameparts=outfilenames[0].split(".") |
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| 372 | newname=(".".join(nameparts[:-1]))+suffix+"."+nameparts[-1] |
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| 373 | else: |
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| 374 | newname=outfilenames[count-1] |
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| 375 | |
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| 376 | msg="\nWriting output NASA Ames file: %s" % newname |
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| 377 | print msg |
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| 378 | outputMessage.append(msg) |
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| 379 | |
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| 380 | builtNADict=i[0] |
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| 381 | for key in naVars.keys(): |
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| 382 | if key in allowedOverwriteMetadata: |
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| 383 | |
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| 384 | if key in arrayArgs: |
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| 385 | newItem=naVars[key].split() |
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| 386 | else: |
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| 387 | newItem=naVars[key] |
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| 388 | |
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| 389 | if newItem!=builtNADict[key]: |
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| 390 | builtNADict[key]=newItem |
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| 391 | msg="Metadata overwritten in output file: '%s' is now '%s'" % (key, builtNADict[key]) |
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| 392 | print msg |
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| 393 | outputMessage.append(msg) |
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| 394 | |
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| 395 | fileList=[] |
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| 396 | # Cope with size limits if specified and FFI is 1001 |
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| 397 | if sizeLimit and (builtNADict["FFI"]==1001 and len(builtNADict["V"][0])>sizeLimit): |
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| 398 | varList=builtNADict["V"] |
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| 399 | arrayLength=len(varList[0]) |
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| 400 | nvolInfo=divmod(arrayLength, sizeLimit) |
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| 401 | nvol=nvolInfo[0] |
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| 402 | if nvolInfo[1]>0: nvol=nvol+1 |
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| 403 | start=0 |
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| 404 | letterCount=0 |
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| 405 | ivol=0 |
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| 406 | while start<arrayLength: |
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| 407 | ivol=ivol+1 |
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| 408 | end=start+sizeLimit |
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| 409 | if end>arrayLength: |
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| 410 | end=arrayLength |
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| 411 | currentBlock=[] |
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| 412 | # Write new V array |
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| 413 | for v in varList: |
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| 414 | currentBlock.append(v[start:end]) |
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| 415 | |
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| 416 | # Adjust X accordingly |
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| 417 | NADictCopy=modifyNADictCopy(builtNADict, currentBlock, start, end, ivol, nvol) |
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| 418 | |
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| 419 | # Write data to output file |
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| 420 | newnamePlusLetter="%s-%.3d.na" % (newname[:-3], ivol) |
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| 421 | fileList.append(newnamePlusLetter) |
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| 422 | general.openNAFile(newnamePlusLetter, 'w', NADictCopy, spacer=spacer, floatFormat=floatFormat) |
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| 423 | msg="\nOutput files split on size limit: %s\nFilename used: %s" % (sizeLimit, newnamePlusLetter) |
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| 424 | print msg |
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| 425 | outputMessage.append(msg) |
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| 426 | letterCount=letterCount+1 |
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| 427 | start=end |
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| 428 | |
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| 429 | |
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| 430 | else: |
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| 431 | general.openNAFile(newname, 'w', builtNADict, spacer=spacer, floatFormat=floatFormat) |
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| 432 | |
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| 433 | msg="\nWrote the following variables:"+"\n\t"+("\n\t".join(i[1][0])) |
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| 434 | print msg |
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| 435 | outputMessage.append(msg) |
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| 436 | |
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| 437 | if len(i[1][1])>0: |
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| 438 | msg="\nWrote the following auxiliary variables:" |
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| 439 | msg=msg+"\n\t"+("\n\t".join(i[1][1])) |
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| 440 | |
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| 441 | if len(i[1][2])>0: |
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| 442 | msg="\nWrote the following Singleton variables:" |
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| 443 | msg=msg+"\n\t"+("\n\t".join(i[1][2])) |
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| 444 | |
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| 445 | if len(fileList)>0: |
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| 446 | msg=msg+("\n\nNASA Ames files written successfully: \n%s" % "\n".join(fileList)) |
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| 447 | count=count+len(fileList) |
|---|
| 448 | else: |
|---|
| 449 | msg=msg+"\n\nNASA Ames file written successfully: %s" % newname |
|---|
| 450 | count=count+1 |
|---|
| 451 | ncount=ncount+1 |
|---|
| 452 | |
|---|
| 453 | print msg |
|---|
| 454 | outputMessage.append(msg) |
|---|
| 455 | |
|---|
| 456 | if (count-1)==1: |
|---|
| 457 | plural="" |
|---|
| 458 | else: |
|---|
| 459 | plural="s" |
|---|
| 460 | msg="\n%s file%s written." % ((count-1), plural) |
|---|
| 461 | print msg |
|---|
| 462 | outputMessage.append(msg) |
|---|
| 463 | return outputMessage |
|---|
| 464 | |
|---|
| 465 | |
|---|
| 466 | class CdmsToNABuilder(NACore): |
|---|
| 467 | """ |
|---|
| 468 | Class to build a NASA Ames File object from a set of |
|---|
| 469 | CDMS variables and global attributes (optional). |
|---|
| 470 | """ |
|---|
| 471 | |
|---|
| 472 | def __init__(self, vars, global_attributes={}, cdmsfile=None, rule=None): |
|---|
| 473 | """ |
|---|
| 474 | Sets up instance variables and calls appropriate methods to |
|---|
| 475 | generate sections of NASA Ames file object. |
|---|
| 476 | """ |
|---|
| 477 | self.rule=rule |
|---|
| 478 | self.cdmsfile=cdmsfile |
|---|
| 479 | self.outputMessage=[] |
|---|
| 480 | self.naDict={} |
|---|
| 481 | self.vars=vars |
|---|
| 482 | self.varIDs=None |
|---|
| 483 | self.globals=global_attributes |
|---|
| 484 | self.rankZeroVars=[] |
|---|
| 485 | self.rankZeroVarIDs=[] |
|---|
| 486 | (self.orderedVars, auxVars)=self.analyseVariables() |
|---|
| 487 | if self.orderedVars==None: |
|---|
| 488 | self.varBin=[] |
|---|
| 489 | else: |
|---|
| 490 | #print "NAMELISTS:", [var.id for var in self.orderedVars],[var.id for var in auxVars] |
|---|
| 491 | self.varIDs=[[var.id for var in self.orderedVars],[var.id for var in auxVars], self.rankZeroVarIDs] |
|---|
| 492 | |
|---|
| 493 | self.naDict["NLHEAD"]="-999" |
|---|
| 494 | |
|---|
| 495 | #print [var.id for var in self.orderedVars] |
|---|
| 496 | #print [var.rank() for var in self.orderedVars] |
|---|
| 497 | self.defineNAVars(self.orderedVars) |
|---|
| 498 | self.defineNAAuxVars(auxVars) |
|---|
| 499 | self.defineNAGlobals() |
|---|
| 500 | self.defineNAComments() |
|---|
| 501 | self.defineGeneralHeader() |
|---|
| 502 | # Quick fudge |
|---|
| 503 | if self.naDict["FFI"]==1001: self.naDict["X"]=self.naDict["X"][0] |
|---|
| 504 | |
|---|
| 505 | |
|---|
| 506 | def analyseVariables(self): |
|---|
| 507 | """ |
|---|
| 508 | Method to examine the content of CDMS variables to return |
|---|
| 509 | a tuple of two lists containing variables and auxiliary variables |
|---|
| 510 | for the NASA Ames file object. |
|---|
| 511 | Variables not compatible with the first file are binned to be used next. |
|---|
| 512 | """ |
|---|
| 513 | # Need to group the variables together in bins |
|---|
| 514 | self.varBin=[] |
|---|
| 515 | # Get largest ranked variable as the one we use as standard |
|---|
| 516 | highrank=-1 |
|---|
| 517 | bestVar=None |
|---|
| 518 | count=0 |
|---|
| 519 | for var in self.vars: |
|---|
| 520 | msg="Analysing: %s" % var.id |
|---|
| 521 | print msg |
|---|
| 522 | self.outputMessage.append(msg) |
|---|
| 523 | count=count+1 |
|---|
| 524 | |
|---|
| 525 | # get rank |
|---|
| 526 | rank=var.rank() |
|---|
| 527 | |
|---|
| 528 | # Deal with specific datasets with special rules |
|---|
| 529 | if self.rule!=None and self.rule[0]=="aircraft": |
|---|
| 530 | var=self._useLocalRule(var, self.rule) |
|---|
| 531 | if type(var)==type(None): |
|---|
| 532 | continue |
|---|
| 533 | rank=1 |
|---|
| 534 | |
|---|
| 535 | # Deal with singleton variables |
|---|
| 536 | if rank==0: |
|---|
| 537 | self.rankZeroVars.append(var) |
|---|
| 538 | self.rankZeroVarIDs.append(var.id) |
|---|
| 539 | continue |
|---|
| 540 | |
|---|
| 541 | if rank>highrank: |
|---|
| 542 | highrank=rank |
|---|
| 543 | bestVar=var |
|---|
| 544 | bestVarIndex=count |
|---|
| 545 | elif rank==highrank: |
|---|
| 546 | if len(var.flat)>len(bestVar.flat): |
|---|
| 547 | bestVar=var |
|---|
| 548 | bestVarIndex=count |
|---|
| 549 | |
|---|
| 550 | if len(self.rankZeroVars)==len(self.vars): return (None, None) |
|---|
| 551 | if not bestVar: |
|---|
| 552 | print "No variables produced" |
|---|
| 553 | return (None, None) |
|---|
| 554 | |
|---|
| 555 | vars4NA=[bestVar] |
|---|
| 556 | auxVars4NA=[] |
|---|
| 557 | shape=bestVar.shape |
|---|
| 558 | ndims=len(shape) |
|---|
| 559 | self.naDict["NIV"]=ndims |
|---|
| 560 | |
|---|
| 561 | # Work out which File Format Index is appropriate |
|---|
| 562 | if ndims in (2,3,4): |
|---|
| 563 | self.naDict["FFI"]=10+(ndims*1000) |
|---|
| 564 | elif ndims>4: |
|---|
| 565 | raise "Cannot write variables defined against greater than 4 axes in NASA Ames format." |
|---|
| 566 | else: |
|---|
| 567 | if len(auxVars4NA)>0 or (self.naDict.has_key("NAUXV") and self.naDict["NAUXV"]>0): |
|---|
| 568 | self.naDict["FFI"]=1010 |
|---|
| 569 | else: |
|---|
| 570 | self.naDict["FFI"]=1001 |
|---|
| 571 | #print self.naDict["FFI"] |
|---|
| 572 | axes=bestVar.getAxisList() |
|---|
| 573 | |
|---|
| 574 | # Get other variable info |
|---|
| 575 | #print [v.id for v in self.vars], bestVarIndex |
|---|
| 576 | #print [v.id for v in self.vars[:bestVarIndex-1]+self.vars[bestVarIndex:]] |
|---|
| 577 | for var in self.vars[:bestVarIndex-1]+self.vars[bestVarIndex:]: |
|---|
| 578 | # Deal with specific datasets with special rules |
|---|
| 579 | if self.rule!=None and self.rule[0]=="aircraft": |
|---|
| 580 | if var.rank()==2: |
|---|
| 581 | var=self._useLocalRule(var, self.rule) |
|---|
| 582 | if type(var)==type(None): continue |
|---|
| 583 | |
|---|
| 584 | #print self.rankZeroVars |
|---|
| 585 | #for rzv in self.rankZeroVars: |
|---|
| 586 | # if var.id==rzv.id and var[0]==rzv[0]: continue |
|---|
| 587 | #print [v.id for v in self.rankZeroVars] |
|---|
| 588 | if var.id in self.rankZeroVarIDs: continue |
|---|
| 589 | #print var.id, ndims, shape, len(var.shape), var.shape |
|---|
| 590 | if len(var.shape)!=ndims or var.shape!=shape: |
|---|
| 591 | # Could it be an auxiliary variable |
|---|
| 592 | if len(var.shape)!=1: |
|---|
| 593 | self.varBin.append(var) |
|---|
| 594 | continue |
|---|
| 595 | caxis=var.getAxis(0) |
|---|
| 596 | if compareAxes(axes[0], caxis)==0: |
|---|
| 597 | self.varBin.append(var) |
|---|
| 598 | continue |
|---|
| 599 | # I think it is an auxiliary variable |
|---|
| 600 | auxVars4NA.append(var) |
|---|
| 601 | # Also put it in var bin because auxiliary vars might be useful |
|---|
| 602 | self.varBin.append(var) |
|---|
| 603 | else: |
|---|
| 604 | caxes=var.getAxisList() |
|---|
| 605 | #print var.id, "here" |
|---|
| 606 | for i in range(ndims): |
|---|
| 607 | if compareAxes(axes[i], caxes[i])==0: |
|---|
| 608 | self.varBin.append(var) |
|---|
| 609 | continue |
|---|
| 610 | # OK, I think they are compatible |
|---|
| 611 | vars4NA.append(var) |
|---|
| 612 | |
|---|
| 613 | # Re-order if they previously came from NASA Ames files (i.e. including |
|---|
| 614 | # the attribute 'nasa_ames_var_number') |
|---|
| 615 | orderedVars=[None]*1000 |
|---|
| 616 | otherVars=[] |
|---|
| 617 | for var in vars4NA: |
|---|
| 618 | if hasattr(var, "nasa_ames_var_number"): |
|---|
| 619 | orderedVars[var.nasa_ames_var_number[0]]=var |
|---|
| 620 | else: |
|---|
| 621 | otherVars.append(var) |
|---|
| 622 | # Remake vars4NA now in order |
|---|
| 623 | vars4NA=[] |
|---|
| 624 | for var in orderedVars: |
|---|
| 625 | if var!=None: vars4NA.append(var) |
|---|
| 626 | vars4NA=vars4NA+otherVars |
|---|
| 627 | |
|---|
| 628 | # Now re-order the Auxiliary variables if they previously came from NASA |
|---|
| 629 | # Ames files (i.e. including the attribute 'nasa_ames_aux_var_number') |
|---|
| 630 | |
|---|
| 631 | orderedAuxVars=[None]*1000 |
|---|
| 632 | otherAuxVars=[] |
|---|
| 633 | for var in auxVars4NA: |
|---|
| 634 | if hasattr(var, "nasa_ames_aux_var_number"): |
|---|
| 635 | orderedAuxVars[var.nasa_ames_aux_var_number[0]]=var |
|---|
| 636 | else: |
|---|
| 637 | otherAuxVars.append(var) |
|---|
| 638 | # Remake auxVars4NA now in order |
|---|
| 639 | auxVars4NA=[] |
|---|
| 640 | for var in orderedAuxVars: |
|---|
| 641 | if var!=None: auxVars4NA.append(var) |
|---|
| 642 | auxVars4NA=auxVars4NA+otherAuxVars |
|---|
| 643 | return (vars4NA, auxVars4NA) |
|---|
| 644 | |
|---|
| 645 | |
|---|
| 646 | def defineNAVars(self, vars): |
|---|
| 647 | """ |
|---|
| 648 | Method to define NASA Ames file object variables and their |
|---|
| 649 | associated metadata. |
|---|
| 650 | """ |
|---|
| 651 | self.naDict["NV"]=len(vars) |
|---|
| 652 | self.naDict["VNAME"]=[] |
|---|
| 653 | self.naDict["VMISS"]=[] |
|---|
| 654 | self.naDict["VSCAL"]=[] |
|---|
| 655 | self.naDict["V"]=[] |
|---|
| 656 | for var in vars: |
|---|
| 657 | name=getBestName(var) |
|---|
| 658 | self.naDict["VNAME"].append(name) |
|---|
| 659 | miss=getMissingValue(var) |
|---|
| 660 | if type(miss) not in (float, int, long): miss=miss[0] |
|---|
| 661 | self.naDict["VMISS"].append(miss) |
|---|
| 662 | #print self.naDict["VMISS"] |
|---|
| 663 | self.naDict["VSCAL"].append(1) |
|---|
| 664 | # AND THE ARRAY |
|---|
| 665 | # Populate the variable list |
|---|
| 666 | ######## NOTE - might not have to do this ##### |
|---|
| 667 | ######## It might handle writing from a Numeric array ######## |
|---|
| 668 | self.naDict["V"].append(var._data) |
|---|
| 669 | #listOfListsCreator(inlist, var.shape) |
|---|
| 670 | #arrayToList(var, inlist) |
|---|
| 671 | |
|---|
| 672 | if not self.naDict.has_key("X"): |
|---|
| 673 | self.naDict["NXDEF"]=[] |
|---|
| 674 | self.naDict["NX"]=[] |
|---|
| 675 | # Create independent variable information |
|---|
| 676 | #print var.id, var.getAxis(0) |
|---|
| 677 | self.ax0=var.getAxis(0) |
|---|
| 678 | self.naDict["X"]=[list(self.ax0._data_)] |
|---|
| 679 | self.naDict["XNAME"]=[getBestName(self.ax0)] |
|---|
| 680 | if len(self.ax0)==1: |
|---|
| 681 | self.naDict["DX"]=[0] |
|---|
| 682 | else: |
|---|
| 683 | incr=self.ax0[1]-self.ax0[0] |
|---|
| 684 | # Set default increment as gap between first two |
|---|
| 685 | self.naDict["DX"]=[incr] |
|---|
| 686 | # Now overwrite it as zero if non-uniform interval in axis |
|---|
| 687 | for i in range(1, len(self.ax0)): |
|---|
| 688 | if (self.ax0[i]-self.ax0[i-1])!=incr: |
|---|
| 689 | self.naDict["DX"]=[0] |
|---|
| 690 | break |
|---|
| 691 | |
|---|
| 692 | # Now sort the rest of the axes |
|---|
| 693 | for axis in var.getAxisList()[1:]: |
|---|
| 694 | self.getAxisDefinition(axis) |
|---|
| 695 | |
|---|
| 696 | |
|---|
| 697 | def defineNAAuxVars(self, auxVars): |
|---|
| 698 | """ |
|---|
| 699 | Method to define NASA Ames file object auxiliary variables and their |
|---|
| 700 | associated metadata. |
|---|
| 701 | """ |
|---|
| 702 | self.naDict["NAUXV"]=len(auxVars) |
|---|
| 703 | self.naDict["ANAME"]=[] |
|---|
| 704 | self.naDict["AMISS"]=[] |
|---|
| 705 | self.naDict["ASCAL"]=[] |
|---|
| 706 | self.naDict["A"]=[] |
|---|
| 707 | for var in auxVars: |
|---|
| 708 | name=getBestName(var) |
|---|
| 709 | self.naDict["ANAME"].append(name) |
|---|
| 710 | miss=getMissingValue(var) |
|---|
| 711 | if type(miss)!=float: miss=miss[0] |
|---|
| 712 | self.naDict["AMISS"].append(miss) |
|---|
| 713 | self.naDict["ASCAL"].append(1) |
|---|
| 714 | # AND THE ARRAY |
|---|
| 715 | # Populate the variable list |
|---|
| 716 | ######## NOTE - might not have to do this ##### |
|---|
| 717 | ######## It might handle writing from a Numeric array ######## |
|---|
| 718 | self.naDict["A"].append(var._data) |
|---|
| 719 | #listOfListsCreator(inlist, var.shape) |
|---|
| 720 | #arrayToList(var, inlist) |
|---|
| 721 | |
|---|
| 722 | |
|---|
| 723 | def getAxisDefinition(self, axis): |
|---|
| 724 | """ |
|---|
| 725 | Method to create the appropriate NASA Ames file object |
|---|
| 726 | items associated with an axis (independent variable in |
|---|
| 727 | NASA Ames). |
|---|
| 728 | """ |
|---|
| 729 | length=len(axis) |
|---|
| 730 | self.naDict["NX"].append(length) |
|---|
| 731 | self.naDict["XNAME"].append(getBestName(axis)) |
|---|
| 732 | # If only one item in axis values |
|---|
| 733 | if length<2: |
|---|
| 734 | self.naDict["DX"].append(0) |
|---|
| 735 | self.naDict["NXDEF"].append(length) |
|---|
| 736 | self.naDict["X"].append(list(axis._data_)) |
|---|
| 737 | return |
|---|
| 738 | |
|---|
| 739 | incr=axis[1]-axis[0] |
|---|
| 740 | for i in range(1, length): |
|---|
| 741 | if (axis[i]-axis[i-1])!=incr: |
|---|
| 742 | self.naDict["DX"].append(0) |
|---|
| 743 | self.naDict["NXDEF"].append(length) |
|---|
| 744 | self.naDict["X"].append(list(axis._data_)) |
|---|
| 745 | break |
|---|
| 746 | else: |
|---|
| 747 | maxLength=length |
|---|
| 748 | if length>3: maxLength=3 |
|---|
| 749 | self.naDict["DX"].append(incr) |
|---|
| 750 | self.naDict["NXDEF"].append(maxLength) |
|---|
| 751 | self.naDict["X"].append(axis[:maxLength]) |
|---|
| 752 | return |
|---|
| 753 | |
|---|
| 754 | |
|---|
| 755 | def defineNAGlobals(self): |
|---|
| 756 | """ |
|---|
| 757 | Maps CDMS (NetCDF) global attributes into NASA Ames Header fields. |
|---|
| 758 | """ |
|---|
| 759 | # Get the global mapping dictionary |
|---|
| 760 | globalmap=cdmsMap.toNA |
|---|
| 761 | # Check if we should add to it with locally set rules |
|---|
| 762 | locGlobs=localRules.localGlobalAttributes |
|---|
| 763 | for att in locGlobs.keys(): |
|---|
| 764 | if not globalmap.has_key(att): |
|---|
| 765 | globalmap[key]=locGlobs[key] |
|---|
| 766 | |
|---|
| 767 | self.extra_comments=[[],[],[]] # Normal comments, special comments, other comments |
|---|
| 768 | conventionOrReferenceComments=[] |
|---|
| 769 | for key in self.globals.keys(): |
|---|
| 770 | if key!="first_valid_date_of_data" and type(self.globals[key]) not in (str, float, int): continue |
|---|
| 771 | if key in globalmap.keys(): |
|---|
| 772 | if key=="history": |
|---|
| 773 | timestring=time.strftime("%Y-%m-%d %H:%M:%S", time.localtime(time.time())) |
|---|
| 774 | history="History:\t%s - Converted to NASA Ames format using nappy-%s.\n\t%s" % (timestring, version.version, self.globals[key]) |
|---|
| 775 | history=history.split("\n") |
|---|
| 776 | self.history=[] |
|---|
| 777 | for h in history: |
|---|
| 778 | if h[:8]!="History:" and h[:1]!="\t": h="\t"+h |
|---|
| 779 | self.history.append(h) |
|---|
| 780 | |
|---|
| 781 | elif key=="institution": |
|---|
| 782 | # If fields came from NA then extract appropriate fields. |
|---|
| 783 | match=re.match(r"(.*)\s+\(ONAME from NASA Ames file\);\s+(.*)\s+\(ORG from NASA Ames file\)\.", self.globals[key]) |
|---|
| 784 | if match: |
|---|
| 785 | self.naDict["ONAME"]=match.groups()[0] |
|---|
| 786 | self.naDict["ORG"]=match.groups()[1] |
|---|
| 787 | else: |
|---|
| 788 | self.naDict["ONAME"]=self.globals[key] |
|---|
| 789 | self.naDict["ORG"]=self.globals[key] |
|---|
| 790 | |
|---|
| 791 | # NOte: should probably do the following search and replace on all string lines |
|---|
| 792 | self.naDict["ONAME"]=self.naDict["ONAME"].replace("\n", " ") |
|---|
| 793 | self.naDict["ORG"]=self.naDict["ORG"].replace("\n", " ") |
|---|
| 794 | |
|---|
| 795 | elif key=="comment": |
|---|
| 796 | # Need to work out if they are actually comments from NASA Ames in the first place |
|---|
| 797 | #self.ncom=[self.globals[key]] |
|---|
| 798 | comLines=self.globals[key].split("\n") |
|---|
| 799 | normComms=[] |
|---|
| 800 | normCommFlag=None |
|---|
| 801 | specComms=[] |
|---|
| 802 | specCommFlag=None |
|---|
| 803 | for line in comLines: |
|---|
| 804 | if line.find("###NASA Ames Special Comments follow###")>-1: |
|---|
| 805 | specCommFlag=1 |
|---|
| 806 | elif line.find("###NASA Ames Special Comments end###")>-1: |
|---|
| 807 | specCommFlag=None |
|---|
| 808 | elif line.find("###NASA Ames Normal Comments follow###")>-1: |
|---|
| 809 | normCommFlag=1 |
|---|
| 810 | elif line.find("###NASA Ames Normal Comments end###")>-1: |
|---|
| 811 | normCommFlag=None |
|---|
| 812 | elif specCommFlag==1: |
|---|
| 813 | specComms.append(line) |
|---|
| 814 | elif normCommFlag==1: |
|---|
| 815 | normComms.append(line) |
|---|
| 816 | elif line.find("###Data Section begins on the next line###")>-1: |
|---|
| 817 | pass |
|---|
| 818 | else: |
|---|
| 819 | normComms.append(line) |
|---|
| 820 | |
|---|
| 821 | self.extra_comments=[specComms, normComms, []] |
|---|
| 822 | |
|---|
| 823 | elif key=="first_valid_date_of_data": |
|---|
| 824 | self.naDict["DATE"]=self.globals[key] |
|---|
| 825 | |
|---|
| 826 | elif key in ("Conventions", "references"): |
|---|
| 827 | #conventionOrReferenceComments.append("%s: %s" % (key, self.globals[key])) |
|---|
| 828 | self.extra_comments[2].append("%s: %s" % (key, self.globals[key])) |
|---|
| 829 | else: |
|---|
| 830 | self.naDict[globalmap[key]]=self.globals[key] |
|---|
| 831 | else: |
|---|
| 832 | self.extra_comments[2].append("%s: %s" % (key, self.globals[key])) |
|---|
| 833 | #self.extra_comments |
|---|
| 834 | return |
|---|
| 835 | |
|---|
| 836 | |
|---|
| 837 | def defineNAComments(self, normal_comments=[], special_comments=[]): |
|---|
| 838 | """ |
|---|
| 839 | Defines the Special and Normal comments sections in the NASA Ames file |
|---|
| 840 | object - including information gathered from the defineNAGlobals method. |
|---|
| 841 | """ |
|---|
| 842 | |
|---|
| 843 | if hasattr(self, "ncom"): normal_comments=self.ncom+normal_comments |
|---|
| 844 | NCOM=[] |
|---|
| 845 | for ncom in normal_comments: |
|---|
| 846 | NCOM.append(ncom) |
|---|
| 847 | if len(NCOM)>0: NCOM.append("") |
|---|
| 848 | |
|---|
| 849 | if len(self.extra_comments[2])>0: |
|---|
| 850 | for excom in self.extra_comments[2]: |
|---|
| 851 | NCOM.append(excom) |
|---|
| 852 | |
|---|
| 853 | if len(self.extra_comments[1])>0: |
|---|
| 854 | NCOM.append("Additional Global Attributes defined in the source file and not translated elsewhere:") |
|---|
| 855 | for excom in self.extra_comments[1]: |
|---|
| 856 | NCOM.append(excom) |
|---|
| 857 | |
|---|
| 858 | if hasattr(self, "history"): |
|---|
| 859 | for h in self.history: |
|---|
| 860 | NCOM.append(h) |
|---|
| 861 | |
|---|
| 862 | if len(NCOM)>0: |
|---|
| 863 | NCOM.insert(0, "###NASA Ames Normal Comments follow###") |
|---|
| 864 | NCOM.append("") |
|---|
| 865 | NCOM.append("###NASA Ames Normal Comments end###") |
|---|
| 866 | NCOM.append("###Data Section begins on the next line###") |
|---|
| 867 | |
|---|
| 868 | specCommentsFlag=None |
|---|
| 869 | SCOM=[] |
|---|
| 870 | special_comments=self.extra_comments[0] |
|---|
| 871 | if len(special_comments)>0: |
|---|
| 872 | SCOM=["###NASA Ames Special Comments follow###"] |
|---|
| 873 | specCommentsFlag=1 |
|---|
| 874 | for scom in special_comments: |
|---|
| 875 | SCOM.append(scom) |
|---|
| 876 | |
|---|
| 877 | |
|---|
| 878 | #used_var_atts=("name", "long_name", "standard_name", "id", |
|---|
| 879 | # "missing_value", "fill_value", "units", |
|---|
| 880 | #"nasa_ames_var_number", "nasa_ames_aux_var_number") |
|---|
| 881 | used_var_atts=("id", "missing_value", "fill_value", "units", |
|---|
| 882 | "nasa_ames_var_number", "nasa_ames_aux_var_number") |
|---|
| 883 | varCommentsFlag=None |
|---|
| 884 | |
|---|
| 885 | # Create a string for the Special comments to hold rank-zero vars |
|---|
| 886 | rankZeroVarsString=[] |
|---|
| 887 | for var in self.rankZeroVars: |
|---|
| 888 | rankZeroVarsString.append("\tVariable %s: %s" % (var.id, getBestName(var))) |
|---|
| 889 | for att in var.attributes.keys(): |
|---|
| 890 | value=var.attributes[att] |
|---|
| 891 | if type(value) in (str, float, int): |
|---|
| 892 | rankZeroVarsString.append("\t\t%s = %s" % (att, var.attributes[att])) |
|---|
| 893 | #print "VALUES", dir(var), var._data ; rankZeroVarsString.append("\t\tvalue = %s" % var._data) |
|---|
| 894 | |
|---|
| 895 | if len(rankZeroVarsString)>0: |
|---|
| 896 | rankZeroVarsString.insert(0, "###Singleton Variables defined in the source file follow###") |
|---|
| 897 | rankZeroVarsString.append("###Singleton Variables defined in the source file end###") |
|---|
| 898 | |
|---|
| 899 | for var in self.orderedVars: |
|---|
| 900 | varflag="unused" |
|---|
| 901 | name=getBestName(var) |
|---|
| 902 | for scom,value in var.attributes.items(): |
|---|
| 903 | if type(value) in (type([]), type(Numeric.array([0]))) and len(value)==1: |
|---|
| 904 | value=value[0] |
|---|
| 905 | if type(value) in (str, float, int) and scom not in used_var_atts: |
|---|
| 906 | if varflag=="unused": |
|---|
| 907 | if varCommentsFlag==None: |
|---|
| 908 | varCommentsFlag=1 |
|---|
| 909 | if specCommentsFlag==None: |
|---|
| 910 | SCOM=["###NASA Ames Special Comments follow###"]+rankZeroVarsString |
|---|
| 911 | SCOM.append("Additional Variable Attributes defined in the source file and not translated elsewhere:") |
|---|
| 912 | SCOM.append("###Variable attributes from source (NetCDF) file follow###") |
|---|
| 913 | varflag="using" |
|---|
| 914 | SCOM.append("\tVariable %s: %s" % (var.id, name)) |
|---|
| 915 | SCOM.append("\t\t%s = %s" % (scom, value)) |
|---|
| 916 | |
|---|
| 917 | if varCommentsFlag==1: SCOM.append("###Variable attributes from source (NetCDF) file end###") |
|---|
| 918 | if specCommentsFlag==1: |
|---|
| 919 | SCOM.append("###NASA Ames Special Comments end###") |
|---|
| 920 | |
|---|
| 921 | """used_var_atts=("name", "long_name", "standard_name", "id", "missing_value", "fill_value", "units") |
|---|
| 922 | for var in self.vars: |
|---|
| 923 | for scom,value in var.attributes.items(): |
|---|
| 924 | name=getBestName(var) |
|---|
| 925 | if type(value) in (str, float, int) and scom not in used_var_atts: |
|---|
| 926 | SCOM.append("\t%s: %s - %s" % (name, scom, value))""" |
|---|
| 927 | |
|---|
| 928 | # Strip out empty lines (or returns) |
|---|
| 929 | NCOM_cleaned=[] |
|---|
| 930 | SCOM_cleaned=[] |
|---|
| 931 | #hiddenNewLineCount1=0 |
|---|
| 932 | for c in NCOM: |
|---|
| 933 | if c.strip() not in ("", " ", " "): |
|---|
| 934 | #hiddenNewLineCount1=hiddenNewLineCount1+c.count("\n") |
|---|
| 935 | # Replace new lines within one attribute with a newline and tab so easier to read |
|---|
| 936 | lines=c.split("\n") |
|---|
| 937 | for line in lines: |
|---|
| 938 | if line!=lines[0]: line="\t"+line |
|---|
| 939 | NCOM_cleaned.append(line) |
|---|
| 940 | |
|---|
| 941 | #hiddenNewLineCount2=0 |
|---|
| 942 | for c in SCOM: |
|---|
| 943 | if c.strip() not in ("", " ", " "): |
|---|
| 944 | #hiddenNewLineCount2=hiddenNewLineCount2+c.count("\n") |
|---|
| 945 | # Replace new lines within one attribute with a newline and tab so easier to read |
|---|
| 946 | #c=c.replace("\n", "\n\t") |
|---|
| 947 | #SCOM_cleaned.append(c) |
|---|
| 948 | lines=c.split("\n") |
|---|
| 949 | for line in lines: |
|---|
| 950 | if line!=lines[0]: line="\t"+line |
|---|
| 951 | SCOM_cleaned.append(line) |
|---|
| 952 | |
|---|
| 953 | self.naDict["NCOM"]=NCOM_cleaned |
|---|
| 954 | self.naDict["NNCOML"]=len(self.naDict["NCOM"])#+hiddenNewLineCount1 |
|---|
| 955 | self.naDict["SCOM"]=SCOM_cleaned |
|---|
| 956 | self.naDict["NSCOML"]=len(self.naDict["SCOM"])#+hiddenNewLineCount2 |
|---|
| 957 | return |
|---|
| 958 | |
|---|
| 959 | |
|---|
| 960 | def defineGeneralHeader(self, header_items={}): |
|---|
| 961 | """ |
|---|
| 962 | Defines known header items and overwrites any with header_items |
|---|
| 963 | key/value pairs. |
|---|
| 964 | """ |
|---|
| 965 | # Check if DATE field previously known in NASA Ames file |
|---|
| 966 | time_now=time.strftime("%Y %m %d", time.localtime(time.time())).split() |
|---|
| 967 | if not self.naDict.has_key("RDATE"): |
|---|
| 968 | self.naDict["RDATE"]=time_now |
|---|
| 969 | |
|---|
| 970 | if self.ax0.isTime(): |
|---|
| 971 | # Get first date in list |
|---|
| 972 | try: |
|---|
| 973 | (unit, start_date)=re.match("(\w+)\s+?since\s+?(\d+-\d+-\d+)", self.ax0.units).groups() |
|---|
| 974 | comptime=cdtime.s2c(start_date) |
|---|
| 975 | first_day=comptime.add(self.naDict["X"][0][0], getattr(cdtime, unit.capitalize())) |
|---|
| 976 | self.naDict["DATE"]=string.replace(str(first_day).split(" ")[0], "-", " ").split() |
|---|
| 977 | except: |
|---|
| 978 | msg="Nappy Warning: Could not get the first date in the file. You will need to manually edit the output file." |
|---|
| 979 | print msg |
|---|
| 980 | self.outputMessage.append(msg) |
|---|
| 981 | self.naDict["DATE"]=("DATE", "NOT", "KNOWN") |
|---|
| 982 | else: |
|---|
| 983 | if not self.naDict.has_key("DATE"): |
|---|
| 984 | msg="Nappy Warning: Could not get the first date in the file. You will need to manually edit the output file." |
|---|
| 985 | print msg |
|---|
| 986 | self.outputMessage.append(msg) |
|---|
| 987 | self.naDict["DATE"]=("DATE", "NOT", "KNOWN") |
|---|
| 988 | self.naDict["IVOL"]=1 |
|---|
| 989 | self.naDict["NVOL"]=1 |
|---|
| 990 | for key in header_items.keys(): |
|---|
| 991 | self.naDict[key]=header_items[key] |
|---|
| 992 | return |
|---|
| 993 | |
|---|
| 994 | |
|---|
| 995 | def _useLocalRule(self, var, ruleArgs): |
|---|
| 996 | """ |
|---|
| 997 | Applies some logic based on a local rule. |
|---|
| 998 | """ |
|---|
| 999 | ruleName=ruleArgs[0] |
|---|
| 1000 | rule=ruleArgs |
|---|
| 1001 | if ruleName=="aircraft": |
|---|
| 1002 | # Fixes aircraft data 2D time axis, missing values and does sub-selection by default |
|---|
| 1003 | flagVar=None |
|---|
| 1004 | |
|---|
| 1005 | # return if variable is time |
|---|
| 1006 | if var.id=="Time": |
|---|
| 1007 | return None |
|---|
| 1008 | |
|---|
| 1009 | if len(rule)<2: rule.append("av") |
|---|
| 1010 | if len(rule)<3: rule.append("flag") |
|---|
| 1011 | if rule[2]=="flag": |
|---|
| 1012 | # Only use flag var for processing real variable |
|---|
| 1013 | if var.id.strip()[-4:]=="FLAG": |
|---|
| 1014 | print "Ignore flag: %s" % var.id |
|---|
| 1015 | return None |
|---|
| 1016 | |
|---|
| 1017 | flagID=var.id.strip()+"FLAG" |
|---|
| 1018 | try: |
|---|
| 1019 | flagVar=self.cdmsfile(flagID) |
|---|
| 1020 | except: |
|---|
| 1021 | raise "Cannot get flag variable for '%s'" % var.id |
|---|
| 1022 | elif rule[2]=="noflag": |
|---|
| 1023 | flagVar=None |
|---|
| 1024 | |
|---|
| 1025 | timeVar=self.cdmsfile("Time") |
|---|
| 1026 | import localRules.aircraftData |
|---|
| 1027 | ruleArgs=[rule[1]]+rule[3:] |
|---|
| 1028 | fixedVar=localRules.aircraftData.AircraftData(var, timeVar, flagVar, ruleArgs).subSampledVar |
|---|
| 1029 | return fixedVar |
|---|
| 1030 | else: |
|---|
| 1031 | raise "Rule '%s' not yet defined." % ruleName |
|---|
| 1032 | |
|---|
| 1033 | |
|---|
| 1034 | usenc2nainstead="""if __name__=="__main__": |
|---|
| 1035 | |
|---|
| 1036 | args=sys.argv[1:] |
|---|
| 1037 | if len(args)<4: |
|---|
| 1038 | print helpMessage |
|---|
| 1039 | print "Incorrect number of arguments used." |
|---|
| 1040 | sys.exit() |
|---|
| 1041 | |
|---|
| 1042 | for arg in args: |
|---|
| 1043 | if arg=="-i": |
|---|
| 1044 | infile=args[args.index(arg)+1] |
|---|
| 1045 | elif arg=="-o": |
|---|
| 1046 | outfile=args[args.index(arg)+1] |
|---|
| 1047 | |
|---|
| 1048 | cdms2na(infile, outfile) """ |
|---|
