Merge pull request #1296 from UV-CDAT/sync_master

Sync master

.travis.yml

@@ -1,6 +1,6 @@
 os:
   - linux
-  - osx
+#  - osx
 
 language: c++
 

CMake/cdat_modules/cdat_deps.cmake

@@ -2,7 +2,7 @@ set(CDAT_deps ${wget_pkg} ${python_pkg} ${numpy_pkg}
               ${libcdms_pkg}
               ${libcf_pkg} ${netcdf_pkg} ${myproxyclient_pkg} ${udunits2_pkg})
 if (CDAT_BUILD_GRAPHICS)
-  if (CDAT_BUILD_PARALLEL)
+  if (CDAT_BUILD_PARAVIEW)
     list(APPEND CDAT_deps ${paraview_pkg})
   else()
     list(APPEND CDAT_deps ${vtk_pkg})

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@ "$@"

CMakeLists.txt

@@ -284,6 +284,7 @@ option(CDAT_BUILD_GUI "Builds GUI-based dependencies (Vistrails, ParaView, VisIt
 option(CDAT_BUILD_GRAPHICS "Build graphics-based dependencies (vcs, pyqt, Vistrails, ParaView, VisIt, R, etc.) " ON)
 option(CDAT_BUILD_ESGF "Alias for CDAT_BUILD_LEAN" OFF)
 option(CDAT_BUILD_UVCMETRICSPKG "Builds uvcmetrics package " ON)
+option(CDAT_BUILD_PARAVIEW "Build ParaView rather than just VTK" OFF)
 
 # If ESGF option is on then our build mode is LEAN.
 if (CDAT_BUILD_ESGF)
@@ -498,7 +499,7 @@ include(osmesa_pkg)
 include(python_pkg)
 include(seawater_pkg)
 include(vacumm_pkg)
-if (CDAT_BUILD_PARALLEL)
+if (CDAT_BUILD_PARAVIEW)
   include(paraview_pkg)
 else()
   include(vtk_pkg)
@@ -729,6 +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

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
 

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()

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()

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)

Packages/vcs/Lib/Canvas.py

@@ -2727,11 +2727,11 @@ def __plot (self, arglist, keyargs):
                     xs=arglist[0].getAxis(-1)
                     ys=arglist[0].getAxis(-2)
                     if xs.isLongitude() and ys.isLatitude() and isinstance(inGrid,cdms2.grid.TransientRectGrid):
-                        arglist[1]=MV2.array(g.getMesh())
+                        arglist[1]=MV2.array(inGrid.getMesh())
                         if not 'wrap' in keyargs.keys():
                             keyargs['wrap']=[0.,360.]
                     elif ys.isLongitude() and xs.isLatitude() and isinstance(inGrid,cdms2.grid.TransientRectGrid):
-                        arglist[1]=MV2.array(g.getMesh())
+                        arglist[1]=MV2.array(inGrid.getMesh())
                         if not 'wrap' in keyargs.keys():
                             keyargs['wrap']=[360.,0.]
                     else:

Packages/vcs/Lib/VTKPlots.py

@@ -753,6 +753,7 @@ def hideGUI(self):
       if manager_exists(self.renWin.GetInteractor()):
           manager = get_manager(self.renWin.GetInteractor())
           self.renWin.RemoveRenderer(manager.renderer)
+          self.renWin.RemoveRenderer(manager.actor_renderer)
 
   def showGUI(self, render=True):
     plot = self.get3DPlot()
@@ -764,6 +765,7 @@ def showGUI(self, render=True):
       if manager_exists(self.renWin.GetInteractor()):
           manager = get_manager(self.renWin.GetInteractor())
           self.renWin.AddRenderer(manager.renderer)
+          self.renWin.AddRenderer(manager.actor_renderer)
           # Bring the manager's renderer to the top of the stack
           manager.elevate()
       if render:

Packages/vcs/Lib/colorpicker.py

@@ -120,7 +120,7 @@ def cancel(self, state):
         self.close()
 
     def selectCell(self, cellId):
-        if cellId == -1:
+        if cellId in (None, -1):
             return
         ids = vtk.vtkIdTypeArray();
         ids.SetNumberOfComponents(1);
@@ -152,7 +152,7 @@ def clickEvent(self, obj, event):
 
         x, y = inter.GetEventPosition()
 
-        renderer = self.topRendererAtPoint(x, y)
+        renderer = self.color_renderer
 
         if renderer:
             picker = vtk.vtkCellPicker()

Packages/vcs/Lib/dv3d.py

@@ -184,7 +184,8 @@ def list(self):
         print 'name =',self.name
         print 'axes =',self.axes
         for pname in self.parameter_names:
-            print ' = '.join( [ pname, self.getParameter( pname ) ] )
+            pval = self.getParameter( pname )
+            print pname,'=',repr(pval)
 
 class Gf3Dvector(Gfdv3d):
 

Packages/vcs/Lib/vtk_ui/button.py

@@ -135,12 +135,20 @@ def add_state(self, label=None, image=None, bgcolor=None, fgcolor=None, opacity=
         self.states.append(ButtonState(label=label, image=image, bgcolor=bgcolor, fgcolor=fgcolor, opacity=opacity))
 
     def place(self):
+
         width, height = self.get_dimensions()
         x, y = self.get_position()
         bounds = (x, x + width, y - height, y, 0, 0)
-
         self.repr.SetPlaceFactor(1)
         self.repr.PlaceWidget(bounds)
+        self.repr.Modified()
+        if self.showing():
+            # This One Weird Hack will make your Buttons Go In the Right Place - Developers hate it!
+            # Buttons weren't always getting properly placed (toolbars in toolbars being the canonical example)
+            # This makes them show up correctly. Weird, but it works.
+            h_state = self.repr.GetHighlightState()
+            self.repr.Highlight((h_state + 1) % 3)
+            self.repr.Highlight(h_state)
 
         text_width, text_height = self.text_widget.get_dimensions()
         swidth, sheight = self.interactor.GetRenderWindow().GetSize()
@@ -289,7 +297,7 @@ def in_bounds(self, x, y):
     def __advance__(self, point):
         state = self.repr.GetState()
         self.set_state( (state + 1) % len(self.states) )
-        #self.clicked(self.widget, "StateChangedEvent") Do we need to call this? I bet we don't.
+        self.clicked(self.widget, "StateChangedEvent")
 
     def clicked(self, obj, event):
         state = self.get_state()
@@ -332,10 +340,7 @@ def __init__(self, interactor, label, on=None, off=None, corner_radius=5, width=
         self.label = label
 
     def get_text(self):
-        if self.get_state() == 0:
-            return self.label.get_text()[len(on_prefix):]
-        else:
-            return self.label.get_text()[len(off_prefix):]
+        return self.label
 
     def toggle(self, state):
         if state == 1: