Merge branch 'release' into issue_903_turn_off_paraview

doutriaux1 · doutriaux1 · commit 5c2baa419191 · 2015-05-05T10:19:56.000-07:00
diff --git a/.travis.yml b/.travis.yml
@@ -1,6 +1,6 @@
 os:
   - linux
-  - osx
+#  - osx
 
 language: c++
 
diff --git a/CMake/cdat_modules_extra/runtest.in b/CMake/cdat_modules_extra/runtest.in
@@ -0,0 +1,4 @@
+#!/bin/bash
+# source is not portable whereas . is
+. "@CMAKE_INSTALL_PREFIX@/bin/setup_runtime.sh"
+python@PYVER@ "$@"
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -730,6 +730,11 @@ configure_file(${cdat_CMAKE_SOURCE_DIR}/cdat_modules_extra/cdat.in
   @ONLY
 )
 
+configure_file(${cdat_CMAKE_SOURCE_DIR}/cdat_modules_extra/runtest.in
+  ${CMAKE_INSTALL_PREFIX}/bin/runtest
+  @ONLY
+)
+
 
 if (BUILD_TESTING)
   configure_file(${cdat_CMAKE_SOURCE_DIR}/cdat_modules_extra/runpytest.in
diff --git a/Packages/DV3D/MultiVarPointCollection.py b/Packages/DV3D/MultiVarPointCollection.py
@@ -101,6 +101,7 @@ def getCoordIndex( self, var, coord ):
             return axis_order.index(coord)
         except ValueError, err:
             print>>sys.stderr, "Can't find axis %s in axis order spec '%s' " % ( coord, axis_order )
+            return None
 
 
     def getCoordDataBlock( self, var ):
@@ -109,42 +110,74 @@ def getCoordDataBlock( self, var ):
     def getDataBlock( self, var ):
         np_var_data_block = None
         iTimeIndex = self.getCoordIndex( var, 't' )
-        if iTimeIndex <> 0:
-            print>>sys.stderr, "Unimplemented axis order: %s " % var.getOrder()
-        else:
-            if self.lev == None:
-                if len( var.shape ) == 2:
-                    np_var_data_block = var[ self.iTimeStep, self.istart::self.istep ].data
-                    if self.roi_mask <> None:
-                        np_var_data_block = numpy.compress( self.roi_mask, np_var_data_block )
-                elif len( var.shape ) == 3:
-                    np_var_data_block = var[ self.iTimeStep, :, self.istart::self.istep ].data
-                    np_var_data_block = np_var_data_block.reshape( [ np_var_data_block.shape[0] * np_var_data_block.shape[1], ] )
-                self.nLevels = 1
+        try:
+            if iTimeIndex > 0:
+                print>>sys.stderr, "Unimplemented axis order: %s " % var.getOrder()
+            elif iTimeIndex is None:
+                if self.lev == None:
+                    if len( var.shape ) == 1:
+                        np_var_data_block = var[ self.istart::self.istep ].data
+                        if self.roi_mask <> None:
+                            np_var_data_block = numpy.compress( self.roi_mask, np_var_data_block )
+                    elif len( var.shape ) == 2:
+                        np_var_data_block = var[ :, self.istart::self.istep ].data
+                        np_var_data_block = np_var_data_block.reshape( [ np_var_data_block.shape[0] * np_var_data_block.shape[1], ] )
+                    self.nLevels = 1
+                else:
+                    iLevIndex = self.getCoordIndex( var, 'z' )
+                    if len( var.shape ) == 2:
+                        if iLevIndex == 0:
+                            np_var_data_block = var[ :, self.istart::self.istep ].data
+                        elif iLevIndex == 1:
+                            np_var_data_block = var[  self.istart::self.istep, : ].data
+                            np_var_data_block = numpy.swapaxes( np_var_data_block, 0, 1 )
+                        else:
+                            print>>sys.stderr, "Unimplemented axis order: %s " % var.getOrder()
+                        if not isNone( np_var_data_block ):
+                            if not isNone( self.roi_mask ):
+                                np_var_data_block = numpy.compress( self.roi_mask, np_var_data_block, axis = 1 )
+                    elif len( var.shape ) == 3:
+                        lev_data_arrays = []
+                        for ilev in range( var.shape[1] ):
+                            data_z_slice = var[ ilev ].flatten()
+                            lev_data_arrays.append( data_z_slice[self.istart::self.istep] )
+                        np_var_data_block = numpy.concatenate( lev_data_arrays ).astype( numpy.float32 )
             else:
-                iLevIndex = self.getCoordIndex( var, 'z' )
-                if len( var.shape ) == 3:
-                    if iLevIndex == 1:
+                if self.lev == None:
+                    if len( var.shape ) == 2:
+                        np_var_data_block = var[ self.iTimeStep, self.istart::self.istep ].data
+                        if self.roi_mask <> None:
+                            np_var_data_block = numpy.compress( self.roi_mask, np_var_data_block )
+                    elif len( var.shape ) == 3:
                         np_var_data_block = var[ self.iTimeStep, :, self.istart::self.istep ].data
-                    elif iLevIndex == 2:
-                        np_var_data_block = var[ self.iTimeStep, self.istart::self.istep, : ].data
-                        np_var_data_block = numpy.swapaxes( np_var_data_block, 0, 1 )
-                    else:
-                        print>>sys.stderr, "Unimplemented axis order: %s " % var.getOrder()
-                    if not isNone( np_var_data_block ):
-                        if not isNone( self.roi_mask ):
-                            np_var_data_block = numpy.compress( self.roi_mask, np_var_data_block, axis = 1 )
-                elif len( var.shape ) == 4:
-                    lev_data_arrays = []
-                    for ilev in range( var.shape[1] ):
-                        data_z_slice = var[ self.iTimeStep, ilev ].flatten()
-                        lev_data_arrays.append( data_z_slice[self.istart::self.istep] )
-                    np_var_data_block = numpy.concatenate( lev_data_arrays ).astype( numpy.float32 )
-#            print " GetDataBlock, var.shape = %s, grid = %s, ts = %d, newshape = %s, type = %s " % ( str(var.shape), str((self.istart,self.istep)), self.iTimeStep, str(np_var_data_block.shape), np_var_data_block.__class__.__name__ )
-
-            if not isNone( np_var_data_block ):
-                if self.missing_value:  np_var_data_block = numpy.ma.masked_equal( np_var_data_block, self.missing_value, False ).flatten()
-                else:                   np_var_data_block = np_var_data_block.flatten()
+                        np_var_data_block = np_var_data_block.reshape( [ np_var_data_block.shape[0] * np_var_data_block.shape[1], ] )
+                    self.nLevels = 1
+                else:
+                    iLevIndex = self.getCoordIndex( var, 'z' )
+                    if len( var.shape ) == 3:
+                        if iLevIndex == 1:
+                            np_var_data_block = var[ self.iTimeStep, :, self.istart::self.istep ].data
+                        elif iLevIndex == 2:
+                            np_var_data_block = var[ self.iTimeStep, self.istart::self.istep, : ].data
+                            np_var_data_block = numpy.swapaxes( np_var_data_block, 0, 1 )
+                        else:
+                            print>>sys.stderr, "Unimplemented axis order: %s " % var.getOrder()
+                        if not isNone( np_var_data_block ):
+                            if not isNone( self.roi_mask ):
+                                np_var_data_block = numpy.compress( self.roi_mask, np_var_data_block, axis = 1 )
+                    elif len( var.shape ) == 4:
+                        lev_data_arrays = []
+                        for ilev in range( var.shape[1] ):
+                            data_z_slice = var[ self.iTimeStep, ilev ].flatten()
+                            lev_data_arrays.append( data_z_slice[self.istart::self.istep] )
+                        np_var_data_block = numpy.concatenate( lev_data_arrays ).astype( numpy.float32 )
+        except Exception, err:
+            print " Error in GetDataBlock, var.shape = %s, grid = %s, ts = %d " % ( str(var.shape), str((self.istart,self.istep)), self.iTimeStep )
+            print str(err)
+
+        if not isNone( np_var_data_block ):
+            if self.missing_value:  np_var_data_block = numpy.ma.masked_equal( np_var_data_block, self.missing_value, False ).flatten()
+            else:                   np_var_data_block = np_var_data_block.flatten()
 
         return np_var_data_block
 
diff --git a/Packages/DV3D/StructuredVariableReader.py b/Packages/DV3D/StructuredVariableReader.py
@@ -11,7 +11,6 @@
 from StructuredDataset import *
 
 def getVarName( var ):
-    if hasattr( var,'outvar'): return var.outvar.name
     if hasattr( var,'name'): return var.name
     if hasattr( var,'name_in_file'): return var.name_in_file
     if hasattr( var,'id'): return var.id
@@ -110,10 +109,10 @@ def __init__(self, **args):
                     self.varSpecs = [ var.name_in_file for var in self.vars ]
                     self.df = cdms2.open( self.fileSpecs )
                 else:
-                    self.varSpecs = [ var.name for var in self.vars ]
+                    self.varSpecs = [ var.id for var in self.vars ]
                     plot_attributes = args.get( 'plot_attributes', None )
                     if plot_attributes <> None:
-                        self.datasetId = plot_attributes.get( 'filename', self.vars[0].name )
+                        self.datasetId = plot_attributes.get( 'filename', self.vars[0].id )
                         for file_attribute_name in ['url', 'filename', 'file' ]:
                             self.fileSpecs = plot_attributes.get( file_attribute_name, None )
                             if self.fileSpecs <> None: break
@@ -122,8 +121,8 @@ def __init__(self, **args):
                             print>>sys.stderr, "Warning, can't open data file '%s'" % self.fileSpecs
                             self.df = None
                     else:
-                        self.datasetId = self.vars[0].name
-                        self.fileSpecs = self.vars[0].name
+                        self.datasetId = self.vars[0].id
+                        self.fileSpecs = self.vars[0].id
                         self.df = None
 
         self.referenceTimeUnits = None
@@ -371,7 +370,7 @@ def getPortData( self, **args ):
 
     def generateVariableOutput( self, cdms_var ):
         print str(cdms_var.var)
-        self.set3DOutput( name=cdms_var.name,  output=cdms_var.var )
+        self.set3DOutput( name=cdms_var.id,  output=cdms_var.var )
 
     def refreshVersion(self):
         portData = self.getPortData()
diff --git a/Packages/DV3D/demo/demo_plots/gallery_vector_test.py b/Packages/DV3D/demo/demo_plots/gallery_vector_test.py
@@ -0,0 +1,16 @@
+import vcs, cdms2, sys
+
+x = vcs.init()
+f = cdms2.open( sys.prefix+"/sample_data/geos5-sample.nc" )
+dv3d = vcs.get3d_vector()
+dv3d.VerticalScaling = 4.0
+dv3d.BasemapOpacity = 0.5
+dv3d.ScaleColormap = [50.0, 75.0, 1]
+dv3d.ZSlider = [26.0], vcs.on
+dv3d.GlyphDensity = 3.0
+dv3d.GlyphSize = 0.6
+dv3d = vcs.get3d_vector()
+v0 =  f["uwnd"]
+v1 =  f["vwnd"]
+x.plot( v0, v1, dv3d )
+x.interact()
diff --git a/Packages/cdms2/Lib/dataset.py b/Packages/cdms2/Lib/dataset.py
@@ -130,7 +130,7 @@ def setNetcdfDeflateFlag(value):
 def setNetcdfDeflateLevelFlag(value):
     """ Sets NetCDF deflate level flag value"""
     if value not in [0,1,2,3,4,5,6,7,8,9]:
-        raise CDMSError, "Error NetCDF deflate_level flag must be an integer < 10"
+        raise CDMSError("Error NetCDF deflate_level flag must be an integer < 10")
     Cdunif.CdunifSetNCFLAGS("deflate_level",value)
 
 def getNetcdfClassicFlag():
@@ -245,14 +245,14 @@ def openDataset(uri,mode='r',template=None,dods=1,dpath=None, hostObj=None):
                 file = CdmsFile(uri,mode)
                 return file
             except:
-                raise CDMSError("Error in DODS open of: ",uri)
+                raise CDMSError("Error in DODS open of: "+uri)
         else:
             try:
                 datanode = loadURI(uri)
                 return datanode
             except:
                 datanode = loadURI(uri)
-                raise CDMSError("Error in loadURI of: ",uri)
+                raise CDMSError("Error in loadURI of: "+uri)
             
     else:
         raise SchemeNotSupported(scheme)
diff --git a/testing/CMakeLists.txt b/testing/CMakeLists.txt
@@ -4,7 +4,8 @@
 # Helper macro that sets the environment correctly
 macro (cdat_add_test name python_exe script)
   #string (REPLACE ";" " " TEST_ARGS "${ARGN}")
-  add_test (${name} "${python_exe}" ${script} ${ARGN})
+  add_test(${name} "${CMAKE_INSTALL_PREFIX}/bin/runtest"
+           ${script} ${ARGN})
   if(DEFINED ENV{UVCDAT_ANONYMOUS_LOG})
     set_tests_properties (${name}
       PROPERTIES ENVIRONMENT "UVCDAT_ANONYMOUS_LOG=$ENV{UVCDAT_ANONYMOUS_LOG}"
diff --git a/testing/vcs/vtk_ui/CMakeLists.txt b/testing/vcs/vtk_ui/CMakeLists.txt
diff --git a/testing/vcsaddons/CMakeLists.txt b/testing/vcsaddons/CMakeLists.txt

-Original file line number
+Diff line change
@@ @@ -1,6 +1,6 @@ @@
 os:
   - linux
 -  - osx
 +#  - osx
 language: c++