Merge branch 'no_phase_name_for_genericoutput' into 'development'

No phase name for genericoutput

See merge request damask/DAMASK!113

processing/post/DADF5_vtk_cells.py

@@ -2,6 +2,7 @@
 
 import os
 import argparse
+import re
 
 import h5py
 import numpy as np
@@ -89,10 +90,12 @@ for filename in options.filenames:
           x = results.get_dataset_location(label)
           if len(x) == 0:
             continue
+          ph_name = re.compile(r'(?<=(constituent\/))(.*?)(?=(generic))') #looking for phase name in dataset name
           array = results.read_dataset(x,0)
           shape = [array.shape[0],np.product(array.shape[1:])]
           vtk_data.append(numpy_support.numpy_to_vtk(num_array=array.reshape(shape),deep=True,array_type= vtk.VTK_DOUBLE))
-          vtk_data[-1].SetName('1_'+x[0].split('/',1)[1])
+          dset_name = '1_' + re.sub(ph_name,r'',x[0].split('/',1)[1])           #removing phase name from generic dataset
+          vtk_data[-1].SetName(dset_name)
           grid.GetCellData().AddArray(vtk_data[-1])
     
     results.set_visible('constituents',  False)

processing/post/DADF5_vtk_points.py

@@ -2,6 +2,7 @@
 
 import os
 import argparse
+import re
 
 import numpy as np
 import vtk
@@ -76,10 +77,12 @@ for filename in options.filenames:
           x = results.get_dataset_location(label)
           if len(x) == 0:
             continue
+          ph_name = re.compile(r'(?<=(constituent\/))(.*?)(?=(generic))') #looking for phase name in dataset name
           array = results.read_dataset(x,0)
           shape = [array.shape[0],np.product(array.shape[1:])]
           vtk_data.append(numpy_support.numpy_to_vtk(num_array=array.reshape(shape),deep=True,array_type= vtk.VTK_DOUBLE))
-          vtk_data[-1].SetName('1_'+x[0].split('/',1)[1])
+          dset_name = '1_' + re.sub(ph_name,r'',x[0].split('/',1)[1])           #removing phase name from generic dataset
+          vtk_data[-1].SetName(dset_name)
           Polydata.GetCellData().AddArray(vtk_data[-1])
     
     results.set_visible('constituents',  False)

python/damask/dadf5.py

@@ -1,7 +1,10 @@
 from queue import Queue
 import re
 import glob
+import os
 
+import vtk
+from vtk.util import numpy_support
 import h5py
 import numpy as np
 
@@ -433,7 +436,7 @@ class DADF5():
                             np.linspace(delta[1],self.size[1]-delta[1],self.grid[1]),
                             np.linspace(delta[0],self.size[0]-delta[0],self.grid[0]),
                            )
-      return np.concatenate((x[:,:,:,None],y[:,:,:,None],y[:,:,:,None]),axis = 3).reshape([np.product(self.grid),3])
+      return np.concatenate((x[:,:,:,None],y[:,:,:,None],z[:,:,:,None]),axis = 3).reshape([np.product(self.grid),3])
     else:
       with h5py.File(self.fname,'r') as f:
         return f['geometry/x_c'][()]
@@ -830,7 +833,7 @@ class DADF5():
     N_not_calculated = len(todo)
     while N_not_calculated > 0:    
       result = results.get()
-      with h5py.File(self.fname,'a') as f:                                                       # write to file
+      with h5py.File(self.fname,'a') as f:                                                          # write to file
         dataset_out = f[result['group']].create_dataset(result['label'],data=result['data'])
         for k in result['meta'].keys():
           dataset_out.attrs[k] = result['meta'][k].encode()
@@ -841,3 +844,142 @@ class DADF5():
         N_added +=1
 
     pool.wait_completion()
+
+
+  def to_vtk(self,labels,mode='Cell'):
+    """
+    Export to vtk cell/point data.
+    
+    Parameters
+    ----------
+    labels : list of str
+      Labels of the datasets to be exported.
+    mode : str, either 'Cell' or 'Point'
+      Export in cell format or point format.
+      Default value is 'Cell'.
+
+    """
+    if mode=='Cell':
+
+      if self.structured:
+  
+        coordArray = [vtk.vtkDoubleArray(),vtk.vtkDoubleArray(),vtk.vtkDoubleArray()]
+        for dim in [0,1,2]:
+          for c in np.linspace(0,self.size[dim],1+self.grid[dim]):
+            coordArray[dim].InsertNextValue(c)
+  
+        vtk_geom = vtk.vtkRectilinearGrid()
+        vtk_geom.SetDimensions(*(self.grid+1))
+        vtk_geom.SetXCoordinates(coordArray[0])
+        vtk_geom.SetYCoordinates(coordArray[1])
+        vtk_geom.SetZCoordinates(coordArray[2])
+  
+      else:
+        
+        nodes = vtk.vtkPoints()
+        with h5py.File(self.fname) as f:
+          nodes.SetData(numpy_support.numpy_to_vtk(f['/geometry/x_n'][()],deep=True))
+          
+          vtk_geom = vtk.vtkUnstructuredGrid()
+          vtk_geom.SetPoints(nodes)
+          vtk_geom.Allocate(f['/geometry/T_c'].shape[0])
+          for i in f['/geometry/T_c']:
+            vtk_geom.InsertNextCell(vtk.VTK_HEXAHEDRON,8,i-1) # not for all elements!
+    elif mode == 'Point':
+      Points   = vtk.vtkPoints()
+      Vertices = vtk.vtkCellArray()  
+      for c in self.cell_coordinates():
+        pointID = Points.InsertNextPoint(c)
+        Vertices.InsertNextCell(1)
+        Vertices.InsertCellPoint(pointID)
+      
+      vtk_geom = vtk.vtkPolyData()
+      vtk_geom.SetPoints(Points)
+      vtk_geom.SetVerts(Vertices)
+      vtk_geom.Modified()
+  
+    N_digits = int(np.floor(np.log10(int(self.increments[-1][3:]))))+1
+    
+    for i,inc in enumerate(self.iter_visible('increments')):
+      vtk_data = []
+      
+      materialpoints_backup = self.visible['materialpoints'].copy()
+      self.set_visible('materialpoints',False)
+      for label in labels:
+        for p in self.iter_visible('con_physics'):
+          if p != 'generic':
+            for c in self.iter_visible('constituents'):
+              x = self.get_dataset_location(label)
+              if len(x) == 0:
+                continue
+              array = self.read_dataset(x,0)
+              shape = [array.shape[0],np.product(array.shape[1:])]
+              vtk_data.append(numpy_support.numpy_to_vtk(num_array=array.reshape(shape),
+                              deep=True,array_type= vtk.VTK_DOUBLE))
+              vtk_data[-1].SetName('1_'+x[0].split('/',1)[1]) #ToDo: hard coded 1!
+              vtk_geom.GetCellData().AddArray(vtk_data[-1])
+
+          else:
+            x = self.get_dataset_location(label)
+            if len(x) == 0:
+              continue
+            array = self.read_dataset(x,0)
+            shape = [array.shape[0],np.product(array.shape[1:])]
+            vtk_data.append(numpy_support.numpy_to_vtk(num_array=array.reshape(shape),
+                            deep=True,array_type= vtk.VTK_DOUBLE))
+            ph_name = re.compile(r'(?<=(constituent\/))(.*?)(?=(generic))')                         # identify  phase name
+            dset_name = '1_' + re.sub(ph_name,r'',x[0].split('/',1)[1])                             # removing phase name
+            vtk_data[-1].SetName(dset_name)
+            vtk_geom.GetCellData().AddArray(vtk_data[-1])
+
+      self.set_visible('materialpoints',materialpoints_backup)
+  
+      constituents_backup = self.visible['constituents'].copy()
+      self.set_visible('constituents',False)
+      for label in labels:
+        for p in self.iter_visible('mat_physics'):
+          if p != 'generic':
+            for m in self.iter_visible('materialpoints'):
+              x = self.get_dataset_location(label)
+              if len(x) == 0:
+                continue
+              array = self.read_dataset(x,0)
+              shape = [array.shape[0],np.product(array.shape[1:])]
+              vtk_data.append(numpy_support.numpy_to_vtk(num_array=array.reshape(shape),
+                              deep=True,array_type= vtk.VTK_DOUBLE))
+              vtk_data[-1].SetName('1_'+x[0].split('/',1)[1]) #ToDo: why 1_?
+              vtk_geom.GetCellData().AddArray(vtk_data[-1])
+          else:
+            x = self.get_dataset_location(label)
+            if len(x) == 0:
+              continue
+            array = self.read_dataset(x,0)
+            shape = [array.shape[0],np.product(array.shape[1:])]
+            vtk_data.append(numpy_support.numpy_to_vtk(num_array=array.reshape(shape),
+                            deep=True,array_type= vtk.VTK_DOUBLE))
+            vtk_data[-1].SetName('1_'+x[0].split('/',1)[1])
+            vtk_geom.GetCellData().AddArray(vtk_data[-1])
+      self.set_visible('constituents',constituents_backup)
+     
+      if mode=='Cell': 
+        writer = vtk.vtkXMLRectilinearGridWriter() if self.structured else \
+                 vtk.vtkXMLUnstructuredGridWriter()
+        x = self.get_dataset_location('u_n')
+        vtk_data.append(numpy_support.numpy_to_vtk(num_array=self.read_dataset(x,0),
+                        deep=True,array_type=vtk.VTK_DOUBLE))
+        vtk_data[-1].SetName('u')
+        vtk_geom.GetPointData().AddArray(vtk_data[-1])
+      elif mode == 'Point':
+        writer = vtk.vtkXMLPolyDataWriter()
+
+      
+      file_out = '{}_inc{}.{}'.format(os.path.splitext(os.path.basename(self.fname))[0],
+                                      inc[3:].zfill(N_digits),
+                                      writer.GetDefaultFileExtension())
+      
+      writer.SetCompressorTypeToZLib()
+      writer.SetDataModeToBinary()
+      writer.SetFileName(file_out)
+      writer.SetInputData(vtk_geom)
+
+      writer.Write()