Cleaning up old comments in vlsv/vtk part of the code

analysator/miscellaneous/vtkwriter.py

@@ -62,7 +62,7 @@ def write_vtk_file( filename, point_data ):
 
    # Add the points to the dataset
    linesPolyData.SetPoints(points)
-
+    
    # Add the lines to the dataset
    linesPolyData.SetLines(lines)
    #######################################
@@ -76,34 +76,4 @@ def write_vtk_file( filename, point_data ):
    polyDataWriter.Write()
    #######################################
 
-#   # Read and visualize the written line
-#   #######################################
-#   reader = vtk.vtkPolyDataReader()
-#   reader.SetFileName(filename)
-#    
-#   mapper = vtk.vtkPolyDataMapper()
-#   if vtk.VTK_MAJOR_VERSION <= 5:
-#       mapper.SetInput(reader.GetOutput())
-#   else:
-#       mapper.SetInputConnection(reader.GetOutputPort())
-#    
-#   actor = vtk.vtkActor()
-#   actor.SetMapper(mapper)
-#   
-#   # Create a rendering window and renderer
-#   ren = vtk.vtkRenderer()
-#   renWin = vtk.vtkRenderWindow()
-#   renWin.AddRenderer(ren)
-#    
-#   # Create a renderwindowinteractor
-#   iren = vtk.vtkRenderWindowInteractor()
-#   iren.SetRenderWindow(renWin)
-#    
-#   # Assign actor to the renderer
-#   ren.AddActor(actor)
-#    
-#   # Enable user interface interactor
-#   iren.Initialize()
-#   renWin.Render()
-#   iren.Start()
-#   #######################################
+

analysator/vlsvfile/vlsvreader.py

@@ -60,20 +60,9 @@ def dict_keys_exist(dictionary, query_keys, prune_unique=False):
    if prune_unique:
       unique_keys, indices = np.unique(query_keys, axis=0, return_inverse=True)
 
-      # these are all about the same...
-      # if (unique_keys.ndim == 1):
+
       mask = np.array([k in dictionary.keys() for k in unique_keys],dtype=bool)
-      # else: # and this isn't worth it?
-      #    mask = np.array([tuple(k) in dictionary.keys() for k in unique_keys],dtype=bool)
-
-      # mask = np.empty(query_keys.shape, dtype=bool)
-      # for i,k in enumerate(query_keys):
-      #    mask[i] = [k in dictionary.keys() for k in query_keys],dtype=bool)
-
-      # mask = np.array(list(map(lambda c: c in dictionary.keys(),query_keys)), dtype=bool)
 
-      # dlambda = np.frompyfunc(lambda c: c in dictionary.keys(),1,1)
-      # mask = np.array(dlambda(query_keys),dtype=bool)
       mask = mask[indices]
    else:
       mask = np.array([k in dictionary.keys() for k in query_keys],dtype=bool)
@@ -747,7 +736,6 @@ def __read_fileindex_for_cellid(self):
       #Check if it is not iterable. If it is a scalar then make it a list (single-cell runs?)
       if(not isinstance(cellids, Iterable)):
          cellids=[ cellids ]
-      # self.__fileindex_for_cellid = {cellid:index for index,cellid in enumerate(cellids)}
       for index,cellid in enumerate(cellids):
          self.__fileindex_for_cellid[cellid] = index
       self.__full_fileindex_for_cellid = True
@@ -791,14 +779,11 @@ def __read_blocks(self, cellid, pop="proton"):
          # Read in block values
          if ("name" in child.attrib) and (child.attrib["name"] == pop) and (child.tag == "BLOCKVARIABLE"):
             vector_size = ast.literal_eval(child.attrib["vectorsize"])
-            #array_size = ast.literal_eval(child.attrib["arraysize"])
             element_size = ast.literal_eval(child.attrib["datasize"])
             datatype = child.attrib["datatype"]
 
             # Navigate to the correct position
             offset_avgs = int(offset * vector_size * element_size + ast.literal_eval(child.text))
-#            for i in range(0, cells_with_blocks_index[0]):
-#               offset_avgs += blocks_per_cell[i]*vector_size*element_size
 
             fptr.seek(offset_avgs)
             if datatype == "float" and element_size == 4:
@@ -811,7 +796,6 @@ def __read_blocks(self, cellid, pop="proton"):
          # (note the special treatment in case the population is named 'avgs'
          if (pop == 'avgs' or ("name" in child.attrib) and (child.attrib["name"] == pop)) and (child.tag == "BLOCKIDS"):
             vector_size = ast.literal_eval(child.attrib["vectorsize"])
-            #array_size = ast.literal_eval(child.attrib["arraysize"])
             element_size = ast.literal_eval(child.attrib["datasize"])
             datatype = child.attrib["datatype"]
 
@@ -865,7 +849,6 @@ def __set_cell_offset_and_blocks(self, pop="proton"):
       # Navigate to the correct position:
       from copy import copy
       offset = 0
-      #self.__fileindex_for_cellid_blocks[pop] = {}
       self.__fileindex_for_cellid_blocks[pop] = dict.fromkeys(cells_with_blocks) # should be faster but negligible difference
       for i in range(0, len(cells_with_blocks)):
          self.__fileindex_for_cellid_blocks[pop][cells_with_blocks[i]] = [copy(offset), copy(blocks_per_cell[i])]
@@ -922,7 +905,6 @@ def __check_datareducer(self, name, reducer):
                else:
                   in_vars = self.check_variable(popvar)
 
-               # print(popvar," is in vars: ",in_vars)
                if in_vars:
                   self.__available_reducers.add(popvar)
                   break
@@ -2110,12 +2092,10 @@ def read_interpolated_variable(self, name, coords, operator="pass",periodic=[Tru
       if value_length > 1:
          read_vals = self.read_variable(name, cellids=cellids_neighbors_unique, operator=operator)
          ngbrvalues[cellid_neighbors!=0,:] = read_vals[indices,:]
-         # ngbrvalues[cellid_neighbors!=0,:] = self.read_variable(name, cellids=cellid_neighbors[cellid_neighbors!=0], operator=operator)
       else:
          read_vals = self.read_variable(name, cellids=cellids_neighbors_unique, operator=operator)[:,np.newaxis]
          ngbrvalues[cellid_neighbors!=0,:] = read_vals[indices,:]
-         # ngbrvalues[cellid_neighbors!=0,:] = self.read_variable(name, cellids=cellid_neighbors[cellid_neighbors!=0], operator=operator)[:,np.newaxis]
-      # ngbrvalues = np.reshape(ngbrvalues, (ncoords,2,2,2,value_length))
+
       nvals = len(lower_cell_ids_unique)
       ngbrvalues = np.reshape(ngbrvalues, (nvals,2,2,2,*value_shape))
 
@@ -2499,7 +2479,6 @@ def read_variable(self, name, cellids=-1,operator="pass"):
             return False
          return self.read_fsgrid_variable(name=name, operator=operator)
 
-      #if(self.check_variable(name) and (name.lower()[0:3]=="ig_")):
       if name.lower()[0:3]=="ig_":
          if not cellids == -1:
             logging.warning("CellID requests not supported for ionosphere variables! Aborting.")
@@ -2905,7 +2884,6 @@ def get_unique_cellids(self, coords):
 
       :returns: a list of unique cell ids
       '''
-      # cids = [int(self.get_cellid(coord)) for coord in coords]
       cids = self.get_cellid(coords)
 
       #choose unique cids, keep ordering. This requires a bit of OrderedDict magic (python 2.7+)

analysator/vlsvfile/vlsvvtkinterface.py

@@ -129,9 +129,7 @@ def buildDescriptor(self):
             subdivided[0].append(c)
          idx += 1
 
-      # @jit(nopython=True)
       def children(cid, level):
-         # cellind = get_cell_indices(cid, level) # get_cellind here for compilation
          cellids = cid - 1 - cid_offsets[level]
          cellind = np.full(3, -1,dtype=np.int32)
          cellind[0] = (cellids)%(xcells[level])
@@ -170,7 +168,6 @@ def getDescriptor(self, reinit=False):
             raise Exception("reinit = True")
          with open(self.__metafile,'rb') as mfile:
             data = pickle.load(mfile)
-            # print(data)
             self.__idxToFileIndex = data['idxToFileIndexMap']
             self.__descriptor = data['descr']
       except Exception as e:
@@ -206,8 +203,7 @@ def getHTG(self):
       src.SetGridScale(f._VlsvReader__dx,f._VlsvReader__dy,f._VlsvReader__dz)
       src.SetBranchFactor(2)
 
-      #descr = src.ConvertDescriptorStringToBitArray(descr)
-      #src.SetDescriptorBits(descr)
+
       src.SetDescriptor(descr)
 
       src.Update()
@@ -268,8 +264,7 @@ def findVariablesFromVlsv(self, getReducers = False):
    def RequestInformation(self, request, inInfo, outInfo):
 
       info = outInfo.GetInformationObject(0)
-      # print("VlsvVtkReader RequestInformation:")
-      # print(info)
+
       if self.__htg is None:
          print("Creating htg via RequestInformation")
          self.__htg = self.getHTG()
@@ -280,9 +275,6 @@ def RequestInformation(self, request, inInfo, outInfo):
                self._arrayselection.AddArray(name)
                self._arrayselection.DisableArray(name)
                self.__cellarrays.append(name)
-         # self.__htg.addArrayFromVlsv("vg_beta_star")
-         # self.__htg.GetCellData().SetActiveScalars("vg_beta_star")
-
       dims = self.__htg.GetExtent()
       info.Set(vtk.vtkStreamingDemandDrivenPipeline.WHOLE_EXTENT(), *dims)
 
@@ -396,8 +388,7 @@ def __main__():
    # This initializes a hypertreegrid from the given reader.
    reader = VlsvVtkReader()
    reader.SetFileName("/home/mjalho/Downloads/bulk.0002189.vlsv")
-   # reader.SetFileName("/home/mjalho/bulk1.0001418.vlsv")
-   # reader.ReadAllScalarsOn()
+
    reader.Update()
    cf = vtk.vtkHyperTreeGridContour()
    cf.SetInputConnection(reader.GetOutputPort())
@@ -417,19 +408,9 @@ def __main__():
    renWin.AddRenderer(ren)
    renWin.SetSize(600, 600)
 
-   # renWin.Render()
-
-   # time.sleep(10)
-
+
    htg = reader.GetOutputDataObject(0)
-   # print(htg)
-   # htg.__vtkVlsvHyperTreeGrid_VlsvAddArray('vg_b_vol')
-   # htg = reader.GetOutputData()
-   # print(htg)
-   # 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_FID.htg")