author | Andreas Thurnherr <ant@ldeo.columbia.edu> |
Mon, 12 Apr 2021 06:35:27 -0400 | |
changeset 48 | 534f2a6c7735 |
permissions | -rw-r--r-- |
48
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#====================================================================== |
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# A N T S N C . P L |
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# doc: Mon Jul 17 11:59:37 2006 |
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# dlm: Fri Jan 15 10:17:51 2016 |
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# (c) 2006 A.M. Thurnherr |
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# uE-Info: 25 56 NIL 0 0 72 2 2 4 NIL ofnI |
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#====================================================================== |
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|
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# ANTS netcdf library |
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|
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# HISTORY: |
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# Jul 17, 2006: - created |
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# Jul 21, 2006: - documented |
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# - added NC-encoding routines |
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# Jul 22: 2006: - BUG: pseudo %PARAMs were written as well |
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# - BUG: var ATTRs were not enconded correctly |
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# - added type support |
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# Jul 23, 2006: - improved type magic |
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# Sep 1, 2006: - BUG: removing trainling 0s had not worked |
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# Sep 23, 2006: - fiddled |
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# Jul 11, 2008: - adapted to new pseudo %PARAMs |
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# Jul 16, 2008: - remove \0s from strings in NC_stringify |
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# Mar 20, 2008: - added progress output to NC_stringify |
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# Jul 21, 2009: - allowed for suppression of %PARAMs |
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# Jan 15, 2016: - BUG: %DEPS pseudo-%PARAM was encoded |
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|
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# NOTES: |
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# - multi-valued attribs are not loaded by getInfo() |
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# - spaces in NC strings are replaced by underscores |
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# - data filling is disabled, because of a bug in the NetCDF library |
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|
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# NetCDF Library Bug: |
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# The library appears to have incorrect default _FillValue types for |
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# integer data types. The error appears if the "setfill" line is commented |
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# out and the following command is run: |
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# listNC -ct dbk100.nc | NCode -o TEMP.nc time |
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# NB: The error occurs when the 1st variable value is written, NOT when |
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# the first Q_time value is written. However, when all the Q_ fields |
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# are ommitted, the error disappears. |
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|
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use NetCDF; |
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|
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#---------------------------------- |
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# string representation of NC types |
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#---------------------------------- |
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|
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sub NC_typeName($) |
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{ |
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my($tp) = @_; |
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|
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return 'byte' if ($tp == NetCDF::BYTE); |
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return 'char' if ($tp == NetCDF::CHAR); |
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return 'short' if ($tp == NetCDF::SHORT); |
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return 'long' if ($tp == NetCDF::LONG); |
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return 'float' if ($tp == NetCDF::FLOAT); |
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return 'double' if ($tp == NetCDF::DOUBLE); |
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croak("$0: unknown NetCDF type #$tp\n"); |
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} |
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|
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sub NC_type($) |
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{ |
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my($tn) = lc($_[0]); |
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|
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return NetCDF::BYTE if ($tn eq 'byte'); |
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return NetCDF::CHAR if ($tn eq 'char'); |
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return NetCDF::SHORT if ($tn eq 'short'); |
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return NetCDF::LONG if ($tn eq 'long'); |
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return NetCDF::FLOAT if ($tn eq 'float'); |
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return NetCDF::DOUBLE if ($tn eq 'double'); |
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croak("$0: unknown NetCDF type <$tn>\n"); |
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} |
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|
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#-------------------------------------- |
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# test whether given NC type is numeric |
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#-------------------------------------- |
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|
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sub NC_isNumeric($) |
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{ |
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my($tp) = @_; |
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|
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return 1 if ($tp == NetCDF::BYTE); |
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return 1 if ($tp == NetCDF::SHORT); |
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return 1 if ($tp == NetCDF::LONG); |
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return 1 if ($tp == NetCDF::FLOAT); |
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return 1 if ($tp == NetCDF::DOUBLE); |
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return 0; |
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} |
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|
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#---------------------------------------- |
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# test whether given NC type is character |
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#---------------------------------------- |
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|
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sub NC_isChar($) |
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94 |
{ |
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return $_[0] == NetCDF::CHAR; |
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} |
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|
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#----------------------------------- |
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99 |
# convert character- to string array |
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100 |
#----------------------------------- |
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101 |
|
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102 |
sub NC_stringify($@) |
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103 |
{ |
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104 |
my($len,@chars) = @_; |
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105 |
my(@strings); |
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106 |
my($nStrings) = @chars/$len; |
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107 |
|
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108 |
print(STDERR "$0: extracting $nStrings strings") |
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109 |
if ($nStrings > 1000); |
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110 |
|
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111 |
while (@chars) { |
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112 |
print(STDERR ".") if ($nStrings>1000 && $n++%1000 == 0); |
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113 |
push(@strings,pack("c$len",@chars)); |
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114 |
$strings[$#strings] =~ s/ /_/g; |
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115 |
$strings[$#strings] =~ s/\0//g; |
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116 |
splice(@chars,0,$len); |
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117 |
} |
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118 |
print(STDERR "\n") if ($nStrings > 1000); |
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119 |
return @strings; |
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120 |
} |
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121 |
|
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122 |
#---------------------------------------------------------------------- |
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123 |
# open netcdf file and read (most) metadata into hash |
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124 |
# |
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125 |
# INPUT: |
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126 |
# <filename> |
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127 |
# |
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128 |
# OUTPUT: |
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129 |
# $NC{id} netcdf id |
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130 |
# |
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131 |
# @NC{attrName}[] names of global attrs |
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132 |
# %NC{AttrType}{$aName} types of global attrs |
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133 |
# %NC{AttrLen}{$aName} # of elts in global attrs |
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134 |
# %NC{Attr}{$aName} vals of scalar global attrs |
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135 |
# |
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136 |
# $NC{unlim_dimId} dim id of unlimited dim |
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137 |
# @NC{dimName}[$dimId] dim names |
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138 |
# %NC{dimID}{$dName} dim ids |
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139 |
# %NC{dimLen}{$dName} # elts in dim |
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140 |
# |
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141 |
# @NC{varName}[$varId] var names |
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142 |
# %NC{varType}{$vName} var types |
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143 |
# %NC{varId}{$vName} var ids |
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144 |
# @%NC{varDimIDs}{$vName}[] dims of vars, e.g. u(lon,lat) |
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145 |
# @%NC{varAttrName}{$vName}[] names of var attrs |
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146 |
# %%NC{varAttrType}{$vName}{$aName} types of var attrs |
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147 |
# %%NC{varAttrLen}{$vName}{$aName} # of elts in var attrs |
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148 |
# %%NC{varAttr}{$vName}{$aName} vals of scalar var attrs |
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149 |
# |
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150 |
#---------------------------------------------------------------------- |
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151 |
|
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152 |
sub NC_readMData($) |
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153 |
{ |
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154 |
my($fn) = @_; |
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155 |
my(%NC); |
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156 |
|
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157 |
$NC{id} = NetCDF::open($ARGV[0],NetCDF::NOWRITE); # open |
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158 |
|
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159 |
my($nd,$nv,$nga,$udi); # get nelts |
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160 |
NetCDF::inquire($NC{id},$nd,$nv,$nga,$udi); |
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161 |
$NC{unlim_dimId} = $udi; |
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|
162 |
|
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163 |
for (my($d)=0; $d<$nd; $d++) { # dimensions |
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164 |
my($dnm,$ln); |
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|
165 |
NetCDF::diminq($NC{id},$d,$dnm,$ln); |
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166 |
$NC{dimName}[$d] = $dnm; |
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167 |
$NC{dimId}{$dnm} = $d; |
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168 |
$NC{dimLen}{$dnm} = $ln; |
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169 |
} |
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170 |
|
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171 |
for (my($v)=0; $v<$nv; $v++) { # vars & var-attribs |
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172 |
my($vnm,$vtp,$nvd,$nva); |
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|
173 |
my(@dids) = (); |
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|
174 |
NetCDF::varinq($NC{id},$v,$vnm,$vtp,$nvd,\@dids,$nva); |
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175 |
$NC{varName}[$v] = $vnm; |
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|
176 |
$NC{varId}{$vnm} = $v; |
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177 |
$NC{varType}{$vnm} = $vtp; |
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|
178 |
@{$NC{varDimIds}{$vnm}} = @dids[0..$nvd-1]; |
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179 |
|
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180 |
for (my($a)=0; $a<$nva; $a++) { # var-attribs |
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181 |
my($anm,$atp,$aln); |
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|
182 |
NetCDF::attname($NC{id},$v,$a,$anm); |
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|
183 |
$NC{varAttrName}{$vnm}[$a] = $anm; |
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|
184 |
NetCDF::attinq($NC{id},$v,$anm,$atp,$aln); |
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|
185 |
$NC{varAttrType}{$vnm}{$anm} = $atp; |
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|
186 |
$NC{varAttrLen}{$vnm}{$anm} = $aln; |
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|
187 |
if ($atp == NetCDF::BYTE || $atp == NetCDF::CHAR || $aln == 1) { |
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|
188 |
my($val) = ""; |
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|
189 |
NetCDF::attget($NC{id},$v,$anm,\$val); |
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|
190 |
$val =~ s{\0+$}{} if ($atp == NetCDF::CHAR); # trailing \0 |
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|
191 |
$NC{varAttr}{$vnm}{$anm} = $val; |
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192 |
} |
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193 |
} |
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194 |
} |
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|
195 |
|
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196 |
for (my($a)=0; $a<$nga; $a++) { # global attribs |
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|
197 |
my($anm,$atp,$aln); |
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|
198 |
NetCDF::attname($NC{id},NetCDF::GLOBAL,$a,$anm); |
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199 |
$NC{attrName}[$a] = $anm; |
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|
200 |
NetCDF::attinq($NC{id},NetCDF::GLOBAL,$anm,$atp,$aln); |
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201 |
$NC{attrType}{$anm} = $atp; |
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|
202 |
$NC{attrLen}{$anm} = $aln; |
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|
203 |
if ($atp == NetCDF::BYTE || $atp == NetCDF::CHAR || $aln == 1) { |
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|
204 |
my($val) = ""; |
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|
205 |
NetCDF::attget($NC{id},NetCDF::GLOBAL,$anm,\$val); |
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|
206 |
$val =~ s{\0+$}{} if ($atp == NetCDF::CHAR); |
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|
207 |
$NC{attr}{$anm} = $val; |
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|
208 |
} |
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|
209 |
} |
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210 |
|
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211 |
return %NC; |
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212 |
} |
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213 |
|
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214 |
#---------------------------------------------------------------------- |
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215 |
# create new nc file and write metadata |
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216 |
# |
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217 |
# INPUT: |
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218 |
# <filename> |
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219 |
# <abscissa> name of unlimited dimension |
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220 |
# <suppress-params> if true, don't write %PARAMs |
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221 |
# |
534f2a6c7735
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|
222 |
# OUTPUT: |
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223 |
# <netcdf id> |
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224 |
# |
534f2a6c7735
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# NOTES: |
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# - netcdf types can be set with %<var>:NC_type to |
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# byte, long, short, double |
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# - string types are as in old PASCAL convention (e.g. string80) |
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# - default type is NetCDF::DOUBLE |
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# - %<var>:NC_type are not added to ATTRIBs |
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#---------------------------------------------------------------------- |
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sub NC_writeMData($$$) |
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{ |
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my($fn,$abscissa,$suppress_params) = @_; |
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my(%attrDone,@slDim,@NCtype); |
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my($ncId) = NetCDF::create($fn,NetCDF::CLOBBER); |
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NetCDF::setfill($ncId,NetCDF::NOFILL); # NetCDF library bug |
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# DIMENSIONS |
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my($aid) = NetCDF::dimdef($ncId,$abscissa,NetCDF::UNLIMITED); |
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|
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for (my($f)=0; $f<=$#antsLayout; $f++) { # types |
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my($tpa) = $antsLayout[$f] . ':NC_type'; |
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my($sl) = ($P{$tpa} =~ m{^string(\d+)$}); |
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if ($sl > 0) { # string |
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$slDim[$f] = NetCDF::dimdef($ncId,"$antsLayout[$f]:strlen",$sl); |
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$NCtype[$f] = NetCDF::CHAR; |
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} elsif (defined($P{$tpa})) { # custom |
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$NCtype[$f] = NC_type($P{$tpa}); |
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} else { # default |
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$NCtype[$f] = NetCDF::DOUBLE; |
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} |
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# printf(STDERR "type %s set to %s\n",$antsLayout[$f],NC_typeName($NCtype[$f])); |
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undef($P{$tpa}); # do not add to ATTRIBs |
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} |
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|
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for (my($f)=0; $f<=$#antsLayout; $f++) { # VARIABLES |
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my($vid); |
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if (defined($slDim[$f])) { |
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$vid = NetCDF::vardef($ncId,$antsLayout[$f],$NCtype[$f],[$aid,$slDim[$f]]); |
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} else { |
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$vid = NetCDF::vardef($ncId,$antsLayout[$f],$NCtype[$f],[$aid]); |
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} |
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croak("$0: varid != fnr (implementation restriction)") |
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unless ($vid == $f); |
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foreach my $anm (keys(%P)) { # variable attributes |
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next unless defined($P{$anm}); |
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my($var,$attr) = ($anm =~ m{([^:]+):(.*)}); |
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next unless ($var eq $antsLayout[$f]); |
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$attrDone{$anm} = 1; # mark |
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if (numberp($P{$anm}) || lc($P{$anm}) eq nan) { |
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NetCDF::attput($ncId,$f,$attr,NetCDF::DOUBLE,$P{$anm}); |
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} else { |
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NetCDF::attput($ncId,$f,$attr,NetCDF::CHAR,$P{$anm}); |
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} |
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} |
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} |
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|
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unless ($suppress_params) { |
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foreach my $anm (keys(%P)) { # GLOBAL ATTRIBUTES |
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next unless defined($P{$anm}); |
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next if ($anm eq 'FILENAME' || $anm eq 'DIRNAME' || # skip pseudo |
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$anm eq 'BASENAME' || $anm eq 'EXTN' || |
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$anm eq 'PATHNAME' || $anm eq 'DEPS' || |
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$anm eq 'RECNO' || $anm eq 'LINENO'); |
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next if $attrDone{$anm}; |
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if (numberp($P{$anm}) || lc($P{$anm}) eq nan) { |
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NetCDF::attput($ncId,NetCDF::GLOBAL,$anm,NetCDF::DOUBLE,$P{$anm}); |
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} else { |
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NetCDF::attput($ncId,NetCDF::GLOBAL,$anm,NetCDF::CHAR,$P{$anm}); |
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} |
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} |
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} |
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NetCDF::endef($ncId); |
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return $ncId; |
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} |
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|
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1; |