Merge pull request #296 from alhom/vtk_interface

Experimental VTK interface for VLSV files, implemented via a rudimentary VTKPythonAlgorithmBase-based reader exposing a vtkHyperTreeGrid. This will cache HTG metadata on disk.

Includes a ParaView plugin script, wrapping the interface for ParaView access. Works on Paraview>=5.13.1.

examples/write_htg.py

@@ -0,0 +1,18 @@
+import vtk
+import pytools as pt
+
+# This initializes a hypertreegrid from the given reader.
+reader = pt.vlsvfile.VlsvVtkReader()
+reader.SetFileName("../../bulk.0002189.vlsv")
+
+# These functions grab one SpatialGrid variable and map that to 
+# the hypertreegrid. Variable vector sizes of 1,2,3,4,9 supported.
+reader.addArrayFromVlsv("vg_b_vol")
+reader.addArrayFromVlsv("vg_beta_star")
+
+reader.Update()
+
+writer = vtk.vtkXMLHyperTreeGridWriter()
+writer.SetFileName("output_EGE.htg")
+writer.SetInputData(reader.GetOutputDataObject(0))
+writer.Write()

plugins/vlsvParaReader.py

@@ -0,0 +1,70 @@
+""" A rudimentary wrapper from the vlsvVtkInterface. Add and load from Paraview
+plugins menu.
+
+Built on Kitware example:
+https://github.com/Kitware/ParaView/blob/master/Examples/Plugins/PythonAlgorithm/PythonAlgorithmExamples.py
+This module demonstrates various ways of adding
+VTKPythonAlgorithmBase subclasses as filters, sources, readers,
+and writers in ParaView"""
+
+# https://github.com/Kitware/ParaView/blob/master/Examples/Plugins/PythonAlgorithm/PythonAlgorithmExamples.py
+
+# This is module to import. It provides VTKPythonAlgorithmBase, the base class
+# for all python-based vtkAlgorithm subclasses in VTK and decorators used to
+# 'register' the algorithm with ParaView along with information about UI.
+from paraview.util.vtkAlgorithm import *
+import pytools as pt
+
+# Use the analysator reader, but include Paraview decorators via inheriting/chaining
+# necessary methods etc
+
+#------------------------------------------------------------------------------
+# A reader example.
+#------------------------------------------------------------------------------
+
+# To add a reader, we can use the following decorators
+#   @smproxy.source(name="PythonCSVReader", label="Python-based CSV Reader")
+#   @smhint.xml("""<ReaderFactory extensions="csv" file_description="Numpy CSV files" />""")
+# or directly use the "@reader" decorator.
+@smproxy.reader(name="PythonVLSVReader", label="Python-based VLSV Reader, outputs htg",
+                extensions="vlsv", file_description="VLSV files")
+class PythonPvVLSVReader(pt.vlsvfile.VlsvVtkReader):
+    """A reader that wraps an Analysator VLSV file reader.
+    """    
+    def __init__(self):
+        super().__init__()
+
+
+    @smproperty.stringvector(name="FileName")
+    @smdomain.filelist()
+    @smhint.filechooser(extensions="vlsv", file_description="Vlasiator VLSV files")
+    def SetFileName(self, filename):
+        """Specify filename for the file to read."""
+        if filename is None or filename == "None":
+            return
+        print(filename)
+        super().SetFileName(filename)
+
+    @smproperty.doublevector(name="TimestepValues", information_only="1", si_class="vtkSITimeStepsProperty")
+    def GetTimestepValues(self):
+        return None
+
+    # Array selection API is typical with readers in VTK
+    # This is intended to allow ability for users to choose which arrays to
+    # load. To expose that in ParaView, simply use the
+    # smproperty.dataarrayselection().
+    # This method **must** return a `vtkDataArraySelection` instance.
+    @smproperty.dataarrayselection(name="Arrays")
+    def GetDataArraySelection(self):
+        return super().GetDataArraySelection()
+
+
+#------------------------------------------------------------------------------
+# Todo: some tests
+#------------------------------------------------------------------------------
+
+def test_PythonVLSVReader(fname):
+    pass
+
+if __name__ == "__main__":
+    pass

pyVlsv/vlsvfile.py

@@ -38,6 +38,7 @@
 from vlsvreader import fsDecompositionFromGlobalIds,fsReadGlobalIdsPerRank,fsGlobalIdToGlobalIndex
 from vlsvwriter import VlsvWriter
 from vlasiatorreader import VlasiatorReader
+from vlsvvtkinterface import VlsvVtkReader
 
 from vlsvparticles import VlsvParticles
 import reduction

pyVlsv/vlsvreader.py

@@ -611,6 +611,41 @@ def __check_datareducer(self, name, reducer):
 
       return reducer_ok
 
+   def get_variables(self):
+
+      varlist = []
+
+      for child in self.__xml_root:
+         if child.tag == "VARIABLE" and "name" in child.attrib:
+            name = child.attrib["name"]
+            varlist.append(name)
+
+      return varlist
+
+   def get_reducers(self):
+
+      varlist = []
+
+      reducer_max_len = 0
+
+      for reducer_reg in [datareducers, multipopdatareducers, v5reducers, multipopv5reducers]:
+         for k in reducer_reg.keys():
+            reducer_max_len = max(reducer_max_len, len(k))
+
+
+
+      for reducer_reg in [datareducers, multipopdatareducers, v5reducers, multipopv5reducers]:
+         for name, reducer in reducer_reg.items():
+            self.__current_reducer_tree_nodes.clear()
+            if self.__check_datareducer(name,reducer):
+               if name[:3] == 'pop':
+                  for pop in self.active_populations:
+                     varlist.append(pop+'/'+name[4:])
+               else:
+                  varlist.append(name)
+
+      return varlist
+
 
    def list(self, parameter=True, variable=True, mesh=False, datareducer=False, operator=False, other=False):
       ''' Print out a description of the content of the file. Useful
@@ -1997,9 +2032,9 @@ def get_max_refinement_level(self):
       if self.__max_spatial_amr_level < 0:
          # Read the file index for cellid
          cellids=self.read(mesh="SpatialGrid",name="CellID", tag="VARIABLE")
-         maxcellid = np.amax([cellids])
+         maxcellid = np.int64(np.amax([cellids]))
 
-         AMR_count = 0
+         AMR_count = np.int64(0)
          while (maxcellid > 0):
             maxcellid -= 2**(3*(AMR_count))*(self.__xcells*self.__ycells*self.__zcells)
             AMR_count += 1