Changeset 1086 for TI02-CSML/trunk

Timestamp:

02/06/06 16:52:45 (14 years ago)

Author:

domlowe

Message:

time and calendar working in netcdf output. Time subsetting by min/max or explicit values. Ready for attempt at data extractor integration.

Location:

TI02-CSML/trunk/parser

Files:

• API/CSMLDocument.py (modified) (1 diff)
• API/__init__.py (modified) (2 diffs)
• API/ops_AbstractFeature.py (modified) (2 diffs)
• API/ops_AbstractFileExtract.py (modified) (3 diffs)
• API/ops_GridSeriesFeature.py (modified) (6 diffs)
• apicalls.py (modified) (3 diffs)

TI02-CSML/trunk/parser/API/CSMLDocument.py

@@ -1 +1 @@
 ''' CSMLDocument.py - simple implementation to return a CSML document containing a single type of feature'''
+from API import *
 
 class CSMLDocument:
     def makeGridSeries(self,domain,rangeSet,datasetID=None,featureID=None):
         fms=[] #empty featureMembers list
-        dset=Dataset()
-        feat=GridSeriesFeature()
+        feat=Parser.GridSeriesFeature()
         if featureID:
             feat.id= featureID
         else:
             feat.id='testfeature'
-        feat.description=Description('???')
+        feat.description=Parser.Description('???')
         feat.domain=domain
         feat.rangeSet=rangeSet
         fms.append(feat)
-        fc=FeatureCollection(members=fms)
+        fc=Parser.FeatureCollection(members=fms)
         #Create an Empty Dataset
-        ds = Dataset()
+        ds = Parser.Dataset()
         #Set objects as attributes of dataset
         if datasetID:

TI02-CSML/trunk/parser/API/__init__.py

@@ -10 +10 @@
 except:
     print 'Could not import CSML data interface. '
+    sys.exit()
+    
+try:
+    import csmllibs.csmltime as csmltime
+except:
+    print 'Could not import csmltime. '
     sys.exit()
 
@@ -27 +33 @@
 import ops_GridSeriesFeature
 import ops_TrajectoryFeature
+import CSMLDocument
+
+
+
+
+
 
 

TI02-CSML/trunk/parser/API/ops_AbstractFeature.py

@@ -1 +1 @@
 ''' ops_AbstractFeature  contains operations for AbstractFeatures'''
 from API import *
+import cdtime
 
 def testmethod(self):
@@ -8 +9 @@
 def getAllowedSubsettings(self):
     return ['none']
+
+def __compareTimes(timemin, timecheck, timemax):
+
+    year=int(timecheck.split('-')[0])
+    month=int(timecheck.split('-')[1])
+    day=int(timecheck.split('-')[2].split('T')[0])
+    tcheck=cdtime.comptime(year,month,day)
+    timeok=0
+    if tcheck.cmp(timemin) >= 0:
+        if tcheck.cmp(timemax) < 1:
+            print tcheck
+            timeok = 1
+    return timeok
+
+def __getCDtime(time):
+    year=int(time.split('-')[0])
+    month=int(time.split('-')[1])
+    day=int(time.split('-')[2].split('T')[0])
+    cdTimeVal=cdtime.comptime(year,month,day)
+    return cdTimeVal

TI02-CSML/trunk/parser/API/ops_AbstractFileExtract.py

@@ -1 +1 @@
 ''' ops_AbstractFileExtract  contains operations for AbstractFileExtracts'''
 from API import *
+import sys
 
 def testmethod(self):
@@ -11 +12 @@
     #file position defines the position of the filename if a list of filenames exists
     #**kwargs can hold subsetting request.
-    print fileposition
+    #print fileposition
+    #print self.fileName
     
     #get the right file
-    if fileposition:
+    if fileposition is not None:
         file=self.fileName.split()[fileposition]
     else:
@@ -25 +27 @@
     
     #get the data
-    DI.setAxis(self.variableName)
-    data=DI.getDataForAxis()
+    print self.variableName
+    
+    try:
+        DI.setAxis(self.variableName)
+        data=DI.getDataForAxis()
+    except:
+        DI.setVariable(self.variableName)
+        if kwargs:
+            data = DI.getSubsetOfDataForVar(**kwargs)
+        else:
+            data = DI.getDataForVar()
     return data
+        
+def __calendar(file,timedim):
+    #open the file
+    DI = csmldataiface.DataInterface()
+    DI=DI.getUnknownInterfaceType(file)
+    DI.openFile(file)
+    DI.setAxis(timedim)
+    cal=DI.getAxisAttribute('calendar')
+    units=DI.getAxisAttribute('units')
+    return cal, units
+    

TI02-CSML/trunk/parser/API/ops_GridSeriesFeature.py

@@ -1 +1 @@
 ''' ops_GridSeriesFeature  contains operations for GridSeriesFeatures'''
 from API import *
+from CSMLDocument import *
+from Scientific.IO.NetCDF import *  #use this instead of cdms for now for it's simple write interface..
+from Numeric import *
+
 
 def testmethod(self):
@@ -42 +46 @@
         domain[key]=dr[key]
     return domain
-    
+
+
+        
 
 def subsetToGridSeries(self, timeSubset,  **kwargs):
@@ -51 +57 @@
     self.files=[]
     strTimes=''
-    fulldata=None
+    fulldata=[]
+    if len(self.times) == 2:
+        tone=ops_AbstractFeature.__getCDtime(self.times[0])
+        ttwo=ops_AbstractFeature.__getCDtime(self.times[1])
+        dr=getDomainReference(self)
+        self.times=[]
+        for time in dr['t'].split():
+            timeok=ops_AbstractFeature.__compareTimes(tone,time,ttwo)
+            if timeok ==1:
+                self.times.append(time)
     for time in self.times:
         listPosition=domainref['t'].split().index(time)
         strTimes= strTimes + ' ' + time 
         for comp in self.rangeSet.aggregatedArray.component:
-            #comp should be a file extract
-            #var = comp.variableName
-            #f=CSMLAnyFile(comp.fileName.split()[listPosition])
-#TODO - get this bit working properly:
             data=comp.getData(fileposition=listPosition, **kwargs)
             self.files.append(comp.fileName.split()[listPosition])
-            if fulldata is None:
+            if fulldata ==[]:
                 fulldata = data.tolist()
             else:
                 for item in data.tolist():
                     fulldata.append(item)
-    
-    ### create csml document####
-    domain=GridSeriesDomain()
-    domain.domainReference=TimePositionList(timePositions=strTimes) 
-    grid=Grid()
-    dc = self.__getDomainComplement()
+     #get the calendar type
+    try:
+        caltype, calunits = ops_AbstractFileExtract.__calendar(self.rangeSet.aggregatedArray.component[0].fileName.split()[0], 't')    #TODO should accept any time dim!!
+        csmltime.setcdtimeCalendar(caltype)
+    except:
+        caltype=cdtime.DefaultCalendar    
+    ### define domain and rangeSet to use for feature in csml document####
+    domain=Parser.GridSeriesDomain()
+    domain.domainReference=Parser.TimePositionList(timePositions=strTimes) 
+    grid=Parser.Grid()
+    dc = self.getDomainComplement()
     ordinates= []
     i=0
     valueStore=[]  # use the values again later to generate netcdf
+    arraySize=0
+    totalArraySize=1
     for key in dc.keys():
+        arraySize=0
         i=i+1
-        god=GridOrdinateDescription()
+        god=Parser.GridOrdinateDescription()
         god.gridAxesSpanned='dim%s'%i
         god.sequenceRule='+x+y+z'
@@ -87 +106 @@
                 if val >= kwargs[key][0]:
                     if val <= kwargs[key] [1]:
+                        arraySize=arraySize+1
                         straxisValues=straxisValues+ str(val) + ', '
         else: # this dimension has not been subsetted
             for val in dc[key]:
+                arraySize=arraySize+1
                 straxisValues=straxisValues+ str(val) + ', '
+        totalArraySize=totalArraySize*arraySize
         god.axisValues=straxisValues[:-2]
         ordinates.append(god)
+    totalArraySize=totalArraySize*len(self.times)
     grid.ordinates=ordinates
     domain.domainComplement=grid
-    rangeSet=RangeSet()
-    rangeSet.arrayDescriptor=NetCDFExtract(fileName='f',variableName='v',arraySize='as')
-    feat=FeatureBuilder()
-    subsetCSML=feat.makeGridSeries(domain,rangeSet)
+    rangeSet=Parser.RangeSet()
+    rangeSet.arrayDescriptor=Parser.NetCDFExtract(id=self.id,fileName='temp.nc',variableName=self.id,arraySize=[arraySize])
 
-    #### write csml document #####
+    #### write csml document ##### -move this to the csmldocument module?
+    subsetCSML=CSMLDocument()
+    subsetCSML=subsetCSML.makeGridSeries(domain,rangeSet)
     output=open(pathToSubsetCSML,'w')
     output.write(subsetCSML)
     output.close()
 
-    ### create and write netcdf####
+    ### create and write netcdf - uses scientific python####
     ncfile=NetCDFFile(pathToSubsetNetCDF,'w')
     # create the dimensions        
-    ncfile.createDimension ( 'time', len(timeSubset))
+    ncfile.createDimension ( 'time', len(self.times))
     time_var = ncfile.createVariable ( 'time', Float, ('time',) )
     time_var.longname = 'time'
     floatTimes=[]
-    for time in timeSubset:
-        floatTimes.append(5) # NEED TO CONVERT 'back' from string to standard julian day.. .
+    print len(fulldata[0])
+    for time in self.times:
+        time=ops_AbstractFeature.__getCDtime(time).torel(calunits)
+        floatTimes.append(time.value)
     time_var[:] =floatTimes[:]
+    time_var.units=calunits
+    time_var.calendar=caltype
 
     for ordinate in ordinates:
@@ -126 +153 @@
         item_var[:]=vals[:]
         print ordinate.definesAxis
-    #this needs rethinking.
+    #this needs reconsidering - do the shapes always match up??
     if len(ordinates)==3:
-        feature_var = ncfile.createVariable (self.parsedFeature.id, Float, ('time',ordinates[1].definesAxis,ordinates[0].definesAxis,ordinates[2].definesAxis))
+        feature_var = ncfile.createVariable (self.id, Float, ('time',ordinates[0].definesAxis,ordinates[1].definesAxis,ordinates[2].definesAxis))
     elif len(grid.ordinates)==2:
-        feature_var = ncfile.createVariable (self.parsedFeature.id, Float, ('time',ordinates[1].definesAxis,ordinates[0].definesAxis))
+        feature_var = ncfile.createVariable (self.id, Float, ('time',ordinates[0].definesAxis,ordinates[1].definesAxis))
     print shape(feature_var)
     print shape(fulldata)
@@ -136 +163 @@
     ncfile.close()
 
-    return pathToSubsetCSML, pathToSubsetNetCDF
+    return pathToSubsetCSML, pathToSubsetNetCDF, totalArraySize

TI02-CSML/trunk/parser/apicalls.py

@@ -21 +21 @@
 #get the domain of the feature
 print '\n The feature has domain reference:' 
-print feature.getDomainReference()
+#print feature.getDomainReference()
 
 #get the domain complement of the feature
@@ -29 +29 @@
 #get combined domain
 print '\n The feature has domain:' 
-print feature.getDomain()
+#print feature.getDomain()
 
 #get list of allowed subsettings
@@ -37 +37 @@
 
 #define a selection (based on the domain ref/complement)
-timeSelection=['2778-12-14T00:00:00', '2779-12-09T00:00:00', '2780-12-03T00:00:00', '2781-11-28T00:00:00', '2782-11-23T00:00:00' ,'2783-11-18T00:00:00']
+#timeSelection=['2881-3-16T0:0:0.0', '2881-4-16T0:0:0.0', '2881-5-16T0:0:0.0', '2881-6-16T0:0:0.0', '2881-7-16T0:0:0.0', '2881-8-16T0:0:0.0', '2881-9-16T0:0:0.0']
+timeSelection=['2881-3-16T0:0:0.0', '2881-9-16T0:0:0.0']
 spatialSubsetDictionary= {}
-spatialSubsetDictionary['latitude']=(0.,10.0)
+spatialSubsetDictionary['latitude']=(0.,30.0)
 spatialSubsetDictionary['longitude']=(90, 120.0)
 
 #request subsetted data from feature
-subsetCSML, subsetNetCDF=feature.subsetToGridSeries(timeSelection, **spatialSubsetDictionary)
+subsetCSML, subsetNetCDF, arraySize=feature.subsetToGridSeries(timeSelection, **spatialSubsetDictionary)
 
 print subsetCSML #csml document (string)
 print subsetNetCDF # netcdf file (file)
+print 'arraySize: %s' %arraySize