Vtk interface

.github/workflows/test_python.yml

@@ -8,6 +8,8 @@ on:
     branches: [ master ]
   pull_request:
     branches: [ master ]
+  schedule:
+    - cron: '0 8 * * MON'
   workflow_dispatch:
 
 jobs:
@@ -33,9 +35,9 @@ jobs:
     - name: Trial imports
       run: python -c 'import pytools as pt'
 
-  import-matrix:
+  ubuntu_22_04_versions:
 
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
     strategy:
       fail-fast: false
       matrix:

examples/write_htg.py

@@ -0,0 +1,16 @@
+import vtk
+import pytools as pt
+
+# This initializes a hypertreegrid from the given reader.
+reader = pt.vlsvfile.VlsvReader("../../bulk.0002189.vlsv")
+htg = pt.vlsvfile.vtkVlsvHyperTreeGrid(reader)
+
+# These functions grab one SpatialGrid variable and map that to 
+# the hypertreegrid. Variable vector sizes of 1,2,3,4,9 supported.
+htg.addArrayFromVlsv("vg_b_vol")
+htg.addArrayFromVlsv("vg_beta_star")
+
+writer = vtk.vtkXMLHyperTreeGridWriter()
+writer.SetFileName("output_EGE.htg")
+writer.SetInputData(htg)
+writer.Write()

pyPlots/colormaps.py

@@ -1172,9 +1172,13 @@
     _cm_name = _cm_name[:-4]
     _cm_data = np.loadtxt(_f)
     _cm = LinearSegmentedColormap.from_list(_cm_name, _cm_data)
-    if Version(mpl_version) > Version("3.5.0"):
-        mcm.register(_cm)
-        mcm.register(_cm.reversed())
-    else:
-        plt.register_cmap(cmap=_cm)
-        plt.register_cmap(cmap=_cm.reversed())
+    try:
+        if Version(mpl_version) > Version("3.5.0"):
+            mcm.register(_cm)
+            mcm.register(_cm.reversed())
+        else:
+            plt.register_cmap(cmap=_cm)
+            plt.register_cmap(cmap=_cm.reversed())
+    except Exception as e:
+        logging.warning("Problem registering colormap " + _cm_name + ". Produced exception was:\n"+str(e))
+

pyVlsv/vlsvVtkParaReader.py

@@ -0,0 +1,164 @@
+"""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."""
+        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()
+
+
+#------------------------------------------------------------------------------
+# A writer example.
+#------------------------------------------------------------------------------
+'''
+@smproxy.writer(extensions="npz", file_description="NumPy Compressed Arrays", support_reload=False)
+@smproperty.input(name="Input", port_index=0)
+@smdomain.datatype(dataTypes=["vtkTable"], composite_data_supported=False)
+class NumpyWriter(VTKPythonAlgorithmBase):
+    def __init__(self):
+        VTKPythonAlgorithmBase.__init__(self, nInputPorts=1, nOutputPorts=0, inputType='vtkTable')
+        self._filename = None
+
+    @smproperty.stringvector(name="FileName", panel_visibility="never")
+    @smdomain.filelist()
+    def SetFileName(self, fname):
+        """Specify filename for the file to write."""
+        if self._filename != fname:
+            self._filename = fname
+            self.Modified()
+
+    def RequestData(self, request, inInfoVec, outInfoVec):
+        from vtkmodules.vtkCommonDataModel import vtkTable
+        from vtkmodules.numpy_interface import dataset_adapter as dsa
+
+        table = dsa.WrapDataObject(vtkTable.GetData(inInfoVec[0], 0))
+        kwargs = {}
+        for aname in table.RowData.keys():
+            kwargs[aname] = table.RowData[aname]
+
+        import numpy
+        numpy.savez_compressed(self._filename, **kwargs)
+        return 1
+
+    def Write(self):
+        self.Modified()
+        self.Update()
+'''
+#------------------------------------------------------------------------------
+# A filter example.
+#------------------------------------------------------------------------------
+'''
+@smproxy.filter()
+@smproperty.input(name="InputTable", port_index=1)
+@smdomain.datatype(dataTypes=["vtkTable"], composite_data_supported=False)
+@smproperty.input(name="InputDataset", port_index=0)
+@smdomain.datatype(dataTypes=["vtkDataSet"], composite_data_supported=False)
+class ExampleTwoInputFilter(VTKPythonAlgorithmBase):
+    def __init__(self):
+        VTKPythonAlgorithmBase.__init__(self, nInputPorts=2, nOutputPorts=1, outputType="vtkPolyData")
+
+    def FillInputPortInformation(self, port, info):
+        if port == 0:
+            info.Set(self.INPUT_REQUIRED_DATA_TYPE(), "vtkDataSet")
+        else:
+            info.Set(self.INPUT_REQUIRED_DATA_TYPE(), "vtkTable")
+        return 1
+
+    def RequestData(self, request, inInfoVec, outInfoVec):
+        from vtkmodules.vtkCommonDataModel import vtkTable, vtkDataSet, vtkPolyData
+        input0 = vtkDataSet.GetData(inInfoVec[0], 0)
+        input1 = vtkDataSet.GetData(inInfoVec[1], 0)
+        output = vtkPolyData.GetData(outInfoVec, 0)
+        # do work
+        print("Pretend work done!")
+        return 1
+
+@smproxy.filter()
+@smproperty.input(name="Input")
+@smdomain.datatype(dataTypes=["vtkDataSet"], composite_data_supported=False)
+class PreserveInputTypeFilter(VTKPythonAlgorithmBase):
+    """
+    Example filter demonstrating how to write a filter that preserves the input
+    dataset type.
+    """
+    def __init__(self):
+        super().__init__(nInputPorts=1, nOutputPorts=1, outputType="vtkDataSet")
+
+    def RequestDataObject(self, request, inInfo, outInfo):
+        inData = self.GetInputData(inInfo, 0, 0)
+        outData = self.GetOutputData(outInfo, 0)
+        assert inData is not None
+        if outData is None or (not outData.IsA(inData.GetClassName())):
+            outData = inData.NewInstance()
+            outInfo.GetInformationObject(0).Set(outData.DATA_OBJECT(), outData)
+        return super().RequestDataObject(request, inInfo, outInfo)
+
+    def RequestData(self, request, inInfo, outInfo):
+        inData = self.GetInputData(inInfo, 0, 0)
+        outData = self.GetOutputData(outInfo, 0)
+        print("input type =", inData.GetClassName())
+        print("output type =", outData.GetClassName())
+        assert outData.IsA(inData.GetClassName())
+        return 1
+'''
+
+def test_PythonVLSVReader(fname):
+    reader = PythonVLSVReader()
+    reader.SetFileName(fname)
+    reader.Update()
+    assert reader.GetOutputDataObject(0).GetNumberOfRows() > 0
+
+if __name__ == "__main__":
+    #test_PythonSuperquadricSource()
+    test_PythonVLSVReader("/tmp/data.csv")
+
+    from paraview.detail.pythonalgorithm import get_plugin_xmls
+    from xml.dom.minidom import parseString
+    for xml in get_plugin_xmls(globals()):
+        dom = parseString(xml)
+        print(dom.toprettyxml(" ","\n"))

pyVlsv/vlsvfile.py

@@ -38,6 +38,7 @@
 from vlsvreader import fsDecompositionFromGlobalIds,fsReadGlobalIdsPerRank,fsGlobalIdToGlobalIndex
 from vlsvwriter import VlsvWriter
 from vlasiatorreader import VlasiatorReader
+from vlsvvtkinterface import vtkVlsvHyperTreeGrid,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