Merge branch 'master' into issue_2031_seasons_broke

CMake/cdat_modules_extra/install_cdat_from_conda.bash.in

@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-@CONDA@ create -y -n @CONDA_ENVIRONMENT_NAME@ -c @CONDA_CHANNEL_UVCDAT@  hdf5 libnetcdf lapack clapack ossuuid libcf esmf jasper g2clib yasm x264 ffmpeg cmor proj4>=4.9.2 vtk==uvcdat libcdms cdat_info flake8 requests numpy==1.9.2 matplotlib --show-channel-urls --copy
+@CONDA@ create -y -n @CONDA_ENVIRONMENT_NAME@ -c @CONDA_CHANNEL_UVCDAT@  hdf5 libnetcdf lapack clapack ossuuid libcf esmf jasper g2clib yasm x264 ffmpeg cmor proj4>=4.9.2 vtk libcdms cdat_info flake8 requests numpy==1.9.2 matplotlib --show-channel-urls --copy
 
 source @ACTIVATE@ @CONDA_ENVIRONMENT_NAME@
 for pkg in testing cdtime regrid2 cdms2 esg DV3D vcs vcsaddons cdutil unidata xmgrace genutil Thermo WK distarray; do

Packages/vcs/vcs/vcs2vtk.py

@@ -94,15 +94,14 @@ def setArray(grid, array, arrayName, isCellData, isScalars):
 
 
 def putMaskOnVTKGrid(data, grid, actorColor=None, cellData=True, deep=True):
-    # Ok now looking
     msk = data.mask
     mapper = None
     if msk is not numpy.ma.nomask and not numpy.allclose(msk, False):
         if actorColor is not None:
-            flatIMask = msk.astype(numpy.int).flat
+            flatIMask = msk.astype(numpy.double).flat
             if grid.IsA("vtkStructuredGrid"):
                 grid2 = vtk.vtkStructuredGrid()
-                vtkmask = numpy_to_vtk_wrapper(flatIMask, deep=deep)
+                vtkmask = numpy_to_vtk_wrapper(flatIMask, deep=deep, array_type=vtk.VTK_DOUBLE)
                 attributes2 = grid2.GetCellData() if cellData else grid2.GetPointData()
             else:
                 grid2 = vtk.vtkUnstructuredGrid()
@@ -114,26 +113,32 @@ def putMaskOnVTKGrid(data, grid, actorColor=None, cellData=True, deep=True):
                     attributes = grid.GetPointData()
                 if (attributes.GetPedigreeIds()):
                     attributes2.SetPedigreeIds(attributes.GetPedigreeIds())
-                    vtkmask = vtk.vtkIntArray()
+                    pedigreeId = attributes2.GetPedigreeIds()
+                    vtkmask = vtk.vtkDoubleArray()
                     vtkmask.SetNumberOfTuples(attributes2.GetPedigreeIds().GetNumberOfTuples())
+                    for i in range(0, vtkmask.GetNumberOfTuples()):
+                        vtkmask.SetValue(i, flatIMask[pedigreeId.GetValue(i)])
                 else:
                     # the unstructured grid is not wrapped
-                    vtkmask = numpy_to_vtk_wrapper(flatIMask, deep=deep)
+                    vtkmask = numpy_to_vtk_wrapper(flatIMask, deep=deep, array_type=vtk.VTK_DOUBLE)
             vtkmask.SetName("scalar")
             attributes2.RemoveArray(vtk.vtkDataSetAttributes.GhostArrayName())
             attributes2.SetScalars(vtkmask)
             grid2.CopyStructure(grid)
-            setArray(grid2, flatIMask, "scalar", isCellData=cellData,
-                     isScalars=True)
             geoFilter = vtk.vtkDataSetSurfaceFilter()
             lut = vtk.vtkLookupTable()
             r, g, b, a = actorColor
-            lut.SetNumberOfTableValues(2)
             geoFilter.SetInputData(grid2)
             if not cellData:
-                lut.SetTableValue(0, r / 100., g / 100., b / 100., a / 100.)
-                lut.SetTableValue(1, r / 100., g / 100., b / 100., a / 100.)
+                pointToCell = vtk.vtkPointDataToCellData()
+                pointToCell.SetInputConnection(geoFilter.GetOutputPort())
+                geoFilter = pointToCell
+                lut.SetNumberOfTableValues(256)
+                lut.SetTableValue(0, 1., 1., 1., 1.)
+                for i in range(1, 256):
+                    lut.SetTableValue(i, r / 100., g / 100., b / 100., a / 100.)
             else:
+                lut.SetNumberOfTableValues(2)
                 lut.SetTableValue(0, r / 100., g / 100., b / 100., 0.)
                 lut.SetTableValue(1, r / 100., g / 100., b / 100., 1.)
             geoFilter.Update()
@@ -642,9 +647,9 @@ def projectArray(w, projection, wc, geo=None):
 
     for i in range(0, w.GetNumberOfTuples()):
         tuple = [0, 0, 0]
-        w.GetTupleValue(i, tuple)
+        w.GetTypedTuple(i, tuple)
         geo.TransformPoint(tuple, tuple)
-        w.SetTupleValue(i, tuple)
+        w.SetTypedTuple(i, tuple)
 
 
 # Geo projection
@@ -1291,9 +1296,9 @@ def prepFillarea(renWin, farea, cmap=None):
             if opacity is not None:
                 color[-1] = opacity
             color = [int(C / 100. * 255) for C in color]
-            colors.SetTupleValue(cellId, color)
+            colors.SetTypedTuple(cellId, color)
         else:
-            color_arr.SetTupleValue(cellId, [255, 255, 255, 0])
+            color_arr.SetTypedTuple(cellId, [255, 255, 255, 0])
 
         if st != "solid":
             # Patterns/hatches support
@@ -1701,7 +1706,7 @@ def prepLine(renWin, line, cmap=None):
                     pts.InsertNextPoint(tmpx, tmpy, 0.)
                     n2 += 1
         for j in range(n2):
-            colors.InsertNextTupleValue(vtk_color)
+            colors.InsertNextTypedTuple(vtk_color)
             l = vtk.vtkLine()
             l.GetPointIds().SetId(0, j + point_offset)
             l.GetPointIds().SetId(1, j + point_offset + 1)

Packages/vcs/vcs/vcsvtk/isofillpipeline.py

@@ -67,7 +67,13 @@ def _plotInternal(self):
                     lut.SetTableValue(j, 1., 1., 1., 0.)
             luts.append([lut, [0, len(l) - 1, True]])
             mapper.SetLookupTable(lut)
-            mapper.SetScalarRange(0, len(l) - 1)
+            minRange = 0
+            maxRange = len(l) - 1
+            if (i == 0 and self._scalarRange[0] < l[0]):
+                # band 0 is from self._scalarRange[0] to l[0]
+                # we don't show band 0
+                minRange += 1
+            mapper.SetScalarRange(minRange, maxRange)
             mapper.SetScalarModeToUseCellData()
             mappers.append(mapper)
 

Packages/vcs/vcs/vcsvtk/vectorpipeline.py

@@ -40,15 +40,15 @@ def _plotInternal(self):
         if self._vtkGeoTransform is not None:
             newv = vtk.vtkDoubleArray()
             newv.SetNumberOfComponents(3)
-            newv.InsertTupleValue(0, [lon.min(), lat.min(), 0])
-            newv.InsertTupleValue(1, [lon.max(), lat.max(), 0])
+            newv.InsertTypedTuple(0, [lon.min(), lat.min(), 0])
+            newv.InsertTypedTuple(1, [lon.max(), lat.max(), 0])
 
             vcs2vtk.projectArray(newv, projection, self._vtkDataSetBounds)
             dimMin = [0, 0, 0]
             dimMax = [0, 0, 0]
 
-            newv.GetTupleValue(0, dimMin)
-            newv.GetTupleValue(1, dimMax)
+            newv.GetTypedTuple(0, dimMin)
+            newv.GetTypedTuple(1, dimMax)
 
             maxDimX = max(dimMin[0], dimMax[0])
             maxDimY = max(dimMin[1], dimMax[1])

testing/vcs/CMakeLists.txt

@@ -877,6 +877,17 @@ cdat_add_test(test_vcs_settings_color_name_rgba
     --bigvalues
     "--source=${BASELINE_DIR}/test_vcs_basic_isofill_bigvalues.png"
     )
+
+   foreach(level 0 1 2)
+     cdat_add_test(test_vcs_isofill_level${level}
+       "${PYTHON_EXECUTABLE}"
+       ${cdat_SOURCE_DIR}/testing/vcs/test_vcs_isofill_levels.py
+       "${BASELINE_DIR}/test_vcs_isofill_level${level}.png"
+       "${UVCDAT_GIT_TESTDATA_DIR}/data/HadSST1870to99.nc"
+       ${level}
+       )
+   endforeach()
+
   cdat_add_test(test_vcs_issue_960_labels
     "${PYTHON_EXECUTABLE}"
     ${cdat_SOURCE_DIR}/testing/vcs/test_vcs_issue_960_labels.py

testing/vcs/test_vcs_isofill_levels.py

@@ -0,0 +1,19 @@
+import cdms2
+import os
+import sys
+import testing.regression as regression
+import vcs
+
+data = sys.argv[2]
+level = sys.argv[3]
+levels = {'0': range(-5,36,5),
+          '1': [-1000, -15, 35],
+          '2': [-300, -15, 0, 15, 25]}
+
+x=regression.init(bg=1)
+f=cdms2.open(data)
+s=f("sst")
+iso=x.createisofill()
+iso.levels=levels[level]
+x.plot(s,iso)
+regression.run(x, "test_vcs_isofill_level%s.png"%level)