ameriflux/01.read_ascii.ncl
changeset 1 4be95183fbcd
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-1:000000000000 0:b902284fb7c3
       
     1 ;----------------------------------------------------------------------
       
     2 ; This example reads an ASCII file that is formatted a specific way, and
       
     3 ; writes out the results to a netCDF file.
       
     4 ;
       
     5 ; The first line in the ASCII file must be a header, with each field
       
     6 ; separated by a single character delimiter (like a ","). The rest of
       
     7 ; the file must be such that each row contains all fields, each
       
     8 ; separated by the designated delimiter.
       
     9 ;
       
    10 ; The fields can be integer, float, double, character, or string.
       
    11 ; String fields cannot be written to a netCDF file. They have to
       
    12 ; be read in as character arrays and written out that way.
       
    13 ;----------------------------------------------------------------------
       
    14 
       
    15 ;----------------------------------------------------------------------
       
    16 ; This function returns the index locations of the given delimiter
       
    17 ; in a row or several rows of strings.
       
    18 ;----------------------------------------------------------------------
       
    19 function delim_indices(strings,nfields,delimiter)
       
    20 local cstrings, cdelim
       
    21 begin
       
    22   nrows = dimsizes(strings)
       
    23 ;
       
    24 ; Handle special case if we only have one string. Make sure it
       
    25 ; is put into a 2D array.
       
    26 ;
       
    27   if(nrows.eq.1) then
       
    28     cstrings = new((/1,strlen(strings)+1/),character)
       
    29   end if
       
    30 
       
    31   cstrings = stringtochar(strings)        ; Convert to characters.
       
    32   cdelim   = stringtochar(delimiter)      ; Convert delimiter to character.
       
    33 ;
       
    34 ; Som error checking here. Make sure delimiter is one character.
       
    35 ;
       
    36   nc   = dimsizes(cdelim)
       
    37   rank = dimsizes(nc)
       
    38   if(rank.ne.1.or.(rank.eq.1.and.nc.ne.2)) then
       
    39     print("delim_indices: fatal: the delimiter you've selected")
       
    40     print("must be a single character. Can't continue.")
       
    41     exit
       
    42   end if
       
    43 
       
    44 ;
       
    45 ; Create array to hold indices of delimiter locations, and then loop
       
    46 ; through each row and find all the delimiters. Make sure each row has
       
    47 ; the correct number of delimiters.
       
    48 ;
       
    49   ndelims  = nfields-1
       
    50   cindices = new((/nrows,ndelims/),integer)
       
    51   do i = 0, nrows-1
       
    52     ii = ind(cstrings(i,:).eq.cdelim(0))
       
    53 ;
       
    54 ; Make sure there were delimiters on this row. If not, we just quit.
       
    55 ; This could probably be modified to do this more gracefully.
       
    56 ;
       
    57     if(any(ismissing(ii))) then
       
    58       print("delim_indices: fatal: I didn't find any delimiters")
       
    59       print("('" + delimiter + "') on row " + i + ". Can't continue.")
       
    60       exit
       
    61     end if
       
    62     if(dimsizes(ii).ne.ndelims) then
       
    63       print("delim_indices: fatal: I expected to find " + ndelims)
       
    64       print("delimiters on row " + i + ". Instead, I found " + dimsizes(ii) + ".")
       
    65       print("Can't continue.")
       
    66       exit
       
    67     end if
       
    68 
       
    69     cindices(i,:) = ii
       
    70 
       
    71     delete(ii)            ; For next time through loop
       
    72   end do
       
    73 
       
    74   return(cindices)
       
    75 end
       
    76 
       
    77 ;----------------------------------------------------------------------
       
    78 ; This function reads in a particular field from a string array,
       
    79 ; given the field number to read (fields start at #1 and go to #nfield),
       
    80 ; and the indices of the delimiters.
       
    81 ;
       
    82 ; It returns either an integer, float, double, character, or a string,
       
    83 ; depending on the input flag "return_type".
       
    84 ;----------------------------------------------------------------------
       
    85 function read_field(strings,ifield,indices,return_type)
       
    86 local nstring, cstrings, nf, tmp_str
       
    87 begin
       
    88   nrows = dimsizes(strings)
       
    89 ;
       
    90 ; Handle special case if we only have one string. Make sure it
       
    91 ; is put into a 2D array.
       
    92 ;
       
    93   if(nrows.eq.1) then
       
    94     cstrings = new((/1,strlen(strings)+1/),character)
       
    95   end if
       
    96 
       
    97   cstrings = stringtochar(strings)
       
    98   nf       = dimsizes(indices(0,:))+1     ; indices is nrows x (nfields-1)
       
    99 
       
   100 ;
       
   101 ; Error checking. Make sure user has entered a valid field.
       
   102 ;
       
   103   if(ifield.le.0.or.ifield.gt.nf) then
       
   104     print("read_field: fatal: you've selected a field that is")
       
   105     print("out-of-range of the number of fields that you have (" + nf + ").")
       
   106     exit
       
   107   end if
       
   108 
       
   109 ;
       
   110 ; Set up array to return. For string, int, float, or double arrays,
       
   111 ; we don't have to do anything special. For character arrays,
       
   112 ; however, we do.
       
   113 ;
       
   114   if(return_type.ne."character") then
       
   115     return_array = new(nrows,return_type)
       
   116   else
       
   117 ;
       
   118 ; We don't know what the biggest character array is at this point, so
       
   119 ; make it bigger than necessary, and then resize later as necessary.
       
   120 ;
       
   121     tmp_return_array = new((/nrows,dimsizes(cstrings(0,:))/),"character")
       
   122 
       
   123     max_len = 0     ; Use to keep track of max lengths of strings.
       
   124   end if
       
   125 
       
   126   do i = 0,nrows-1
       
   127 ;
       
   128 ; Special case of first field in row.
       
   129 ;
       
   130     if(ifield.eq.1) then
       
   131       ibeg = 0
       
   132       iend = indices(i,ifield-1)-1
       
   133     else
       
   134 ;
       
   135 ; Special case of first field in row.
       
   136 ;
       
   137       if(ifield.eq.nf) then
       
   138         ibeg = indices(i,ifield-2)+1
       
   139         iend = dimsizes(cstrings(i,:))-1
       
   140 ;
       
   141 ; Any field between first and last field.
       
   142 ;
       
   143       else
       
   144         ibeg = indices(i,ifield-2)+1
       
   145         iend = indices(i,ifield-1)-1
       
   146       end if  
       
   147     end if
       
   148 ;
       
   149 ; Here's the code that pulls off the correct string, and converts it
       
   150 ; to float if desired.
       
   151 ;
       
   152     if(return_type.eq."integer") then
       
   153       return_array(i) = stringtointeger(chartostring(cstrings(i,ibeg:iend)))
       
   154     end if
       
   155     if(return_type.eq."float") then
       
   156       return_array(i) = stringtofloat(chartostring(cstrings(i,ibeg:iend)))
       
   157     end if
       
   158     if(return_type.eq."double") then
       
   159       return_array(i) = stringtodouble(chartostring(cstrings(i,ibeg:iend)))
       
   160     end if
       
   161     if(return_type.eq."string") then
       
   162       return_array(i) = chartostring(cstrings(i,ibeg:iend))
       
   163     end if
       
   164     if(return_type.eq."character") then
       
   165       if( (iend-ibeg+1) .gt. max_len) then
       
   166         max_len = iend-ibeg+1
       
   167       end if
       
   168       tmp_return_array(i,0:iend-ibeg) = cstrings(i,ibeg:iend)
       
   169     end if
       
   170   end do
       
   171 
       
   172   if(return_type.eq."character") then
       
   173     return_array = new((/nrows,max_len/),"character")
       
   174     return_array = tmp_return_array(:,0:max_len-1)
       
   175   end if
       
   176 
       
   177   return(return_array)
       
   178 end
       
   179 
       
   180 
       
   181 ;----------------------------------------------------------------------
       
   182 ; This function reads in string fields only to get the maximum string
       
   183 ; length.
       
   184 ;----------------------------------------------------------------------
       
   185 function get_maxlen(strings,ifield,indices)
       
   186 local nstring, cstrings, nf, tmp_str
       
   187 begin
       
   188   nrows = dimsizes(strings)
       
   189 ;
       
   190 ; Handle special case if we only have one string. Make sure it
       
   191 ; is put into a 2D array.
       
   192 ;
       
   193   if(nrows.eq.1) then
       
   194     cstrings = new((/1,strlen(strings)+1/),character)
       
   195   end if
       
   196 
       
   197   cstrings = stringtochar(strings)
       
   198   nf       = dimsizes(indices(0,:))+1     ; indices is nrows x (nfields-1)
       
   199 
       
   200 ;
       
   201 ; Error checking. Make sure user has entered a valid field.
       
   202 ;
       
   203   if(ifield.le.0.or.ifield.gt.nf) then
       
   204     print("read_field: fatal: you've selected a field that is")
       
   205     print("out-of-range of the number of fields that you have (" + nf + ").")
       
   206     exit
       
   207   end if
       
   208 ;
       
   209 ; We don't know what the biggest character array is at this point, so
       
   210 ; make it bigger than necessary, and then resize later as necessary.
       
   211 ;
       
   212   tmp_return_array = new((/nrows,dimsizes(cstrings(0,:))/),"character")
       
   213 
       
   214   max_len = 0     ; Use to keep track of max lengths of strings.
       
   215 
       
   216   do i = 0,nrows-1
       
   217 ;
       
   218 ; Special case of first field in row.
       
   219 ;
       
   220     if(ifield.eq.1) then
       
   221       ibeg = 0
       
   222       iend = indices(i,ifield-1)-1
       
   223     else
       
   224 ;
       
   225 ; Special case of first field in row.
       
   226 ;
       
   227       if(ifield.eq.nf) then
       
   228         ibeg = indices(i,ifield-2)+1
       
   229         iend = dimsizes(cstrings(i,:))-1
       
   230 ;
       
   231 ; Any field between first and last field.
       
   232 ;
       
   233       else
       
   234         ibeg = indices(i,ifield-2)+1
       
   235         iend = indices(i,ifield-1)-1
       
   236       end if  
       
   237     end if
       
   238     if( (iend-ibeg+1) .gt. max_len) then
       
   239       max_len = iend-ibeg+1
       
   240     end if
       
   241   end do
       
   242 
       
   243   return(max_len)
       
   244 end
       
   245 
       
   246 ;----------------------------------------------------------------------
       
   247 ; Main code.
       
   248 ;----------------------------------------------------------------------
       
   249 begin
       
   250 
       
   251 ; Set up defaults here.  We are hard-coding the field types here.
       
   252 ; You can set up this script to try to determine the field types 
       
   253 ; automatically, but this is a bit tedious. Maybe later.
       
   254 
       
   255   station = "USHa1"
       
   256   year    = 1991
       
   257   nfields   = 30                        ; # of fields
       
   258   delimiter = ","                       ; field delimiter
       
   259  
       
   260   filename  = station+year+"_L4_m.txt"  ; ASCII" file to read.
       
   261   cdf_file  = station+year+"_L4_m.nc"   ; netCDF file to write. 
       
   262 
       
   263 ; In this case, fields #2-#2 are integers,
       
   264 ; and the rest of the fields are floats.
       
   265 
       
   266   var_types      = new(nfields,string)
       
   267   var_strlens    = new(nfields,integer)   ; var to hold strlens, just in case.
       
   268 
       
   269   var_types      = "float"       ; Most are floats.
       
   270   var_types(0:1) = "integer"
       
   271 
       
   272   if(isfilepresent(cdf_file))
       
   273     print("Warning: '" + cdf_file + "' exists. Will remove it.")
       
   274     system("/bin/rm " + cdf_file)
       
   275   end if
       
   276 
       
   277 ; Read in data as strings. This will create a string array that has the
       
   278 ; same number of strings as there are rows in the file. We will then need
       
   279 ; to parse each string later.
       
   280 
       
   281   read_data = asciiread(filename,-1,"string")
       
   282   header    = read_data(0)        ; Header. Use for variable names.
       
   283   data      = read_data(1:)       ; Get rid of first line which is a header.
       
   284   nrows     = dimsizes(data)      ; Number of rows.
       
   285 
       
   286 ; Read in locations of delimiters in each string row.
       
   287 
       
   288   hindices = delim_indices(header,nfields,delimiter)   ; header row
       
   289   dindices = delim_indices(data,nfields,delimiter)     ; rest of file
       
   290 
       
   291   print (hindices)
       
   292   print (dindices)
       
   293 
       
   294 ; Read in the field names which will become variable names on
       
   295 ; the netCDF file.
       
   296 
       
   297   var_names = new(nfields,string)
       
   298 
       
   299   do i=0,nfields-1
       
   300     var_names(i) = read_field(header,i+1,hindices,"string")
       
   301   end do
       
   302 
       
   303 ; Write out this netCDF file efficiently so it will be faster.
       
   304 ; Try to predefine everything before you write to it.
       
   305 
       
   306   f = addfile(cdf_file,"c")
       
   307   setfileoption(f,"DefineMode",True)       ; Enter predefine phase.
       
   308 
       
   309 ; Write global attributes to file. It's okay to do this before 
       
   310 ; predefining the file's variables. We are still in "define" mode.
       
   311 
       
   312   fAtt               = True
       
   313   fAtt@description   = "Data read in from " + filename + " ASCII file."
       
   314   fAtt@creation_date = systemfunc ("date")        
       
   315   fileattdef( f, fAtt )        
       
   316 
       
   317 ; Write dimension names to file. If there are no character variables,
       
   318 ; then there's only one dimension name ("nvalues").
       
   319 
       
   320   nyear  = -1
       
   321   nmonth = 12
       
   322  
       
   323   dim_names = (/ "year",  "month" /)
       
   324   dim_sizes = (/ nyear ,  nmonth  /)
       
   325   dimUnlim  = (/ True  ,  False   /)
       
   326 
       
   327   filedimdef( f, dim_names, dim_sizes, dimUnlim )
       
   328 
       
   329 ; Define each variable on the file.
       
   330 ;
       
   331 ; Don't deal with variable Month (i=0).
       
   332 
       
   333   do i=1,nfields-1
       
   334      filevardef(f, var_names(i), var_types(i), dim_names)
       
   335   end do
       
   336 
       
   337 ; Loop through each field, read the values for that field, print 
       
   338 ; information about the variable, and then write it to the netCDF
       
   339 ; file.
       
   340 
       
   341   do i=1,nfields-1
       
   342     ifield = i+1           ; Fields start at #1, not #0.
       
   343 
       
   344 ; Note: you can't write strings to a netCDF file, so these have
       
   345 ; to be written out as character arrays.
       
   346 
       
   347     tmp_data = new((/1,nmonth/),var_types(i))
       
   348 
       
   349     out_data = read_field(data,ifield,dindices,var_types(i))
       
   350 
       
   351     tmp_data(0,:) = out_data(:)
       
   352 
       
   353 ; Print some info about the variable.
       
   354 
       
   355     print("")
       
   356     print("Writing variable '" + var_names(i) + "' (field #" + ifield + ").")
       
   357     print("Type is " + var_types(i) + ".")
       
   358     print("min/max = " + min(tmp_data) + "/" + max(tmp_data))
       
   359 
       
   360     if(any(ismissing(tmp_data))) then
       
   361       print("This variable does contain missing values.")
       
   362     else
       
   363       print("This variable doesn't contain missing values.")
       
   364     end if
       
   365 
       
   366     f->$var_names(i)$ = tmp_data       ; Write to netCDF file.
       
   367 
       
   368     delete(tmp_data)                   ; Delete for next round.
       
   369     delete(out_data) 
       
   370   end do
       
   371 end