Changeset 1490 in lmdz_wrf for trunk

Timestamp:

Apr 4, 2017, 3:23:20 AM (8 years ago)

Author:

lfita

Message:

Adding:

`addDim': Operation to add a new dimension in a file

Fixing minor typos

Location:

trunk/tools

Files:

• documentation/ncmanage/intro.html (modified) (1 diff)
• nc_var.py (modified) (3 diffs)
• nc_var_tools.py (modified) (12 diffs)

trunk/tools/documentation/ncmanage/intro.html

@@ -82 +82 @@
         <LI><SPAN CLASS="codetxt">ivattrs:</SPAN> Give all the attributes of a variable and its type</LI>
         <LI><SPAN CLASS="codetxt">LMDZ_toCF:</SPAN> Function to pass a LMDZ original file to CF-conventions</LI>
-        <LI><SPAN CLASS="codetxt">maskvar:</SPAN> Function to mask a variable using a mask. It is assumed that mask[...,dimM,dimJ,dimK] and </LI>
+        <LI><SPAN CLASS="codetxt">maskvar:</SPAN> Function to mask a variable using a mask. It is assumed that mask[...,dimM,dimJ,dimK] and var[...,dimM,dimJ,dimK] share the last dimensions </LI>
         <LI><SPAN CLASS="codetxt">model_characteristics:</SPAN> Function to provide major characteristics of a given model output</LI>
         <LI><SPAN CLASS="codetxt">ncreplace:</SPAN> Function to replace something from a netCDF file</LI>

trunk/tools/nc_var.py

@@ -51 +51 @@
 import generic_tools as gen
 
+# addDim: Operation to add a new dimension in a file
 # addVar: Operation to add a new variable in a file using exisintg dimensions
 # addvals: Function to add values to a given variable at a given dimension
@@ -159 +160 @@
 # WRF_toCF: Function to pass a WRF original file to CF-conventions
 
-operations=['addVar', 'addvals', 'CDO_toCF', 'chdimname', 'changevartype',           \
+operations=['addDim', 'addVar', 'addvals', 'CDO_toCF', 'chdimname', 'changevartype', \
   'checkallvars', 'checkAllValues', 'checkNaNs',                                     \
   'chgtimestep', 'chvarname', 'cleaning_varsfile', 'compute_deaccum',                \
@@ -265 +266 @@
     quit(-1)
 
-if oper == 'addVar':
+if oper == 'addDim':
+    ncvar.addDim(opts.values, opts.ncfile, opts.varname)
+elif oper == 'addVar':
     ncvar.addVar(opts.values, opts.ncfile, opts.varname)
 elif oper == 'addvals':

trunk/tools/nc_var_tools.py

@@ -18 +18 @@
 
 ####### Contents:
+# addDim: Operation to add a new dimension in a file
 # add_dims: Function to add dimensions from a given netCDF object to another one
 # add_globattrs: Function to add global attributes from a given netCDF object to another one
@@ -1243 +1244 @@
     attrv = int(attrv0)
   elif attrk == 'R':
-    attrv = float8(attrv0)
+    attrv = np.float(attrv0)
   elif attrk == 'D':
     attrv = np.float64(attrv0)
@@ -3916 +3917 @@
     return
 
-def maskvar(values, filename, varn):
+def maskvar(values, filename, varparameters):
     """ Function to mask a variable using a mask. It is assumed that mask[...,dimM,dimJ,dimK] and 
       var[...,dimM,dimJ,dimK] share the last dimensions
@@ -3922 +3923 @@
       [maskfilename]= file with the mask
       [maskvar]= name of the variable with the mask
-      [dimsmask]= dimensions d1,d2,d3,... to use from variable [mask] (ahead of the sharing ones with [var])
-      [timename]= name of the variable time in [filename]
+      [dimsmask]= ',' list of [dimn]|[sec] to use for slicing [maskvar]
+        [sec]: section
+          * [integer]: which value of the dimension
+          * -1: all along the dimension
+          * -9: last value of the dimension
+          * [beg]@[end] slice from [beg] to [end]
+        * NOTE: no value provided is for all dimension range
+      [maskvalue]= value to use for maskking
     filename= netCF file name
-    varn= variable name
+    varparameters= [varn]|[dimsmask]
+      [varn]: variable name
+      [samedimsmask]: ',' list of name of dimensions which fits [maskvar] slice
     """
     fname='maskvar'
 
-    fillValue=1.e20
+    if values == 'h':
+        print fname + '_____________________________________________________________'
+        print maskvar.__doc__
+        quit()
+
     ofile = 'mask_' + varn + '.nc'
 
     maskfilename = values.split(':')[0]
     maskvar = values.split(':')[1]
-    maskdims = np.array(values.split(':')[2].split(','), dtype=int)
-    timename = values.split(':')[3]
+    dimsmask = values.split(':')[3]
+    maskvalue = values.split(':')[4]
+
+    varn = varparameters.splice(':')[0]
+    samedimsmask = varparameters.splice(':')[1].split(',')
 
     ncf = NetCDFFile(filename,'r')
@@ -3941 +3957 @@
     if not ncf.variables.has_key(varn):
         print errormsg
-        print '    ' + fname + ': File  "' + filename + '" does not have variable "' + varn + '" !!!!'
+        print '    ' + fname + ": File  '" + filename + "' does not have variable '"+\
+          varn + '" !!!!'
         print errormsg
         ncf.close()
@@ -3948 +3965 @@
     varobj = ncf.variables[varn]
     varinf = variable_inf(varobj)
-    timeobj = ncf.variables[timename]
-    timeinf = cls_time_information(ncf, timename)
 
     ncfmask = NetCDFFile(maskfilename,'r')
@@ -3955 +3970 @@
     if not ncfmask.variables.has_key(maskvar):
         print errormsg
-        print '    ' + fname + ': File  "' + maskfilename + '" does not have variable mask "' + maskvar + '" !!!!'
+        print '    ' + fname + ": File  '" + maskfilename + "' does not have " +     \
+          " variable mask '" + maskvar + "' !!"
         print errormsg
         ncf.close()
@@ -3962 +3978 @@
 
     varmaskobj = ncfmask.variables[maskvar]
-    varmaskinf = variable_inf(varmaskobj)
-
-    sdims=[]
-    for ivdim in range(varinf.Ndims):
-        vardim = varinf.Ndims - ivdim - 1
-        maskdim = varmaskinf.Ndims - ivdim - 1
-        if varinf.dims[vardim] == varmaskinf.dims[vardim]:
-            sdims.append(varinf.dims[vardim])
+    maskvalues, maskdims = slice_variable(varmaskobj, dimsmask.replace('|',':').     \
+      replace(',','|'))
+
+    ncfmask.close()
+
+    # Looking for variable & mask compatibility
+    runningsize = 1
+    rundims = []
+    testslicevar = []
+    runshape = []
+    for dimn in varobj.dimensions.keys():
+        Ldim = len(ncf.dimensions[dimn])
+        if gen.searchInlist(samedimsmask,dimn):
+            testslicevar.append(slice(0,Ldim,None))
         else:
-            break
-
-    samedims = sdims[::-1]
-    print '  ' + fname + ': variable: ', varinf.dims, ' and mask: ', varmaskinf.dims,' share: ', samedims
-
-# masking
-##
-    Nsamedims=len(samedims)
-
-    if not Nsamedims + len(maskdims) == varmaskinf.Ndims:
-        print errormsg
-        print '  ' + fname + ': desired dimensions of mask ', maskdims, ' and coincident dims with variable ',Nsamedims, ' does not match mask dims ',varmaskinf.Ndims,' !!!!'
-        print errormsg
-        ncf.close()
-        ncfmask.close()
-        quit(-1)
-
-    if varmaskinf.Ndims > Nsamedims:
-        maskvals = load_ncvariable_lastdims(ncfmask, maskvar, maskdims, Nsamedims)
-    else:
-        maskvals = maskvarobj[:]
-
-    ncfmask.close()
+            runningsize = runningsize*Ldim
+            rundims.append(dimn)
+            runshape.append(Ldim)
+            testslicevar.append(0)
+    testvar = varobj[tuple(testslicevar)]
+
+    gen.same_shape(testvar,maskvalues)
 
 # Creation of the new file
@@ -4005 +4011 @@
         else:
             ncfnew.createDimension(varinf.dimns[idim], varinf.dims[idim])
-
-    newvar = ncfnew.createVariable(varn, varinf.dtype, varinf.dimns, fill_value=fillValue)
+    # FillVallue
+    if varinf.dtype == type(np.int(1)):
+        fillValue = gen.fillValueI
+    elif varinf.dtype == type('c'):
+        fillValue = gen.fillValueC
+    elif varinf.dtype == type(np.int16(1)) or varinf.dtype == type(np.int32(1)):
+        fillValue = gen.fillValueI16
+    elif varinf.dtype == type(np.float(1.)):
+        fillValue = gen.fillValueF
+    elif varinf.dtype == type(np.float32(1.)) or varinf.dtype == type(np.float64(1.)):
+        fillValue = gen.fillValueF64
+
+    newvar = ncfnew.createVariable(varn, varinf.dtype, varinf.dimns,                 \
+      fill_value=fillValue)
     for attrn in varinf.attributes:
         if not attrn == '_FillValue':
             attr = newvar.setncattr(attrn, varobj.getncattr(attrn))
 
-    attr = newvar.setncattr('mask', 'variable masked using ' + values.split(':')[2] + ' of variable ' + maskvar + ' from file ' + maskfilename)
+    attr = newvar.setncattr('mask', 'variable masked using ' + values.split(':')[2] +\
+      ' of variable ' + maskvar + ' from file ' + maskfilename)
 
     ncfnew.sync()
@@ -4021 +4040 @@
 
     ncfnew = NetCDFFile(ofile,'a')
+    varobj = ncfnew.variables[varn]
+
+    # Masking following that dimensions which are not coincident with the mask
+    maskval = gen.retype(maskvalue,varinf.dtype)
+    if runshape > 1:
+        idim = 0
+        runslice = list(runshape)
+        while idim <= runningsize:
+            slicevar = []
+            inosim = len(runshape)
+            for dimn in varobj.dimensions.keys():
+                Ldim = len(ncf.dimensions[dimn])
+                if gen.searchInlist(samedimsmask,dimn):
+                    slicevar.append(slice(0,Ldim,None))
+                else:
+                    slicevar.append()
+            testvar = varobj[tuple(testslicevar)]
+            
+
+    else:
+        maskedvals = ma.masked(varobj[:],maskval)
+
+    varobj[:] = maskedvals
+
+
+        
+
+
 
     Nptmask = 1
@@ -7621 +7668 @@
                     print errormsg
                     print '  ' + fname + ': given: ',len(vals),' but variable ' +    \
-                      'reaquires: ',values.shape[1],'!!!'
+                      'requires: ',values.shape[1],'!!!'
                     exit(-1)
                 for i1 in range(len(vals)):
@@ -18405 +18452 @@
     return
 
+def addDim(values, ncfile, dimn):
+    """ Operation to add a new dimension in a file
+      values= [size]
+        [size]: size of the dimension ('unlimited' for unlimited)
+      ncfile= name of the file
+      dimn= name of the new dimension
+    """
+    fname = 'addDim'
+
+    if values == 'h':
+        print fname + '_____________________________________________________________'
+        print addDim.__doc__
+        quit()
+
+    onc = NetCDFFile(ncfile, 'a')
+
+    if onc.dimensions.has_key(dimn):
+        print errormsg
+        print '  ' + fname + ": file '" + ncfile + "' already has dimension '" +     \
+          dimn + "' !!"
+        onc.close()
+        quit(-1)
+
+    if values == 'unlimited':
+        Ldim = None
+    else:
+        Ldim = int(values)
+
+    newdim = onc.createDimension(dimn, Ldim)
+    onc.sync()
+    onc.close()
+
+    print fname + ": succesful addition of dimension '" + dimn + "' size:", Ldim,'!!'
+
+    return
+
+
 def addVar(values, ncfile, varn):
     """ Operation to add a new variable in a file using exisintg dimensions