Merge branch 'no_phase_name_for_genericoutput' into 'development'
No phase name for genericoutput See merge request damask/DAMASK!113
This commit is contained in:
Francisco Jose Gallardo Basile
commit
80b559dc00
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@ -2,6 +2,7 @@
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import os
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import argparse
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import re
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import h5py
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import numpy as np
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@ -89,10 +90,12 @@ for filename in options.filenames:
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x = results.get_dataset_location(label)
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if len(x) == 0:
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continue
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ph_name = re.compile(r'(?<=(constituent\/))(.*?)(?=(generic))') #looking for phase name in dataset name
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array = results.read_dataset(x,0)
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shape = [array.shape[0],np.product(array.shape[1:])]
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vtk_data.append(numpy_support.numpy_to_vtk(num_array=array.reshape(shape),deep=True,array_type= vtk.VTK_DOUBLE))
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vtk_data[-1].SetName('1_'+x[0].split('/',1)[1])
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dset_name = '1_' + re.sub(ph_name,r'',x[0].split('/',1)[1]) #removing phase name from generic dataset
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vtk_data[-1].SetName(dset_name)
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grid.GetCellData().AddArray(vtk_data[-1])
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results.set_visible('constituents', False)
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@ -2,6 +2,7 @@
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import os
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import argparse
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import re
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import numpy as np
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import vtk
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@ -76,10 +77,12 @@ for filename in options.filenames:
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x = results.get_dataset_location(label)
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if len(x) == 0:
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continue
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ph_name = re.compile(r'(?<=(constituent\/))(.*?)(?=(generic))') #looking for phase name in dataset name
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array = results.read_dataset(x,0)
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shape = [array.shape[0],np.product(array.shape[1:])]
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vtk_data.append(numpy_support.numpy_to_vtk(num_array=array.reshape(shape),deep=True,array_type= vtk.VTK_DOUBLE))
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vtk_data[-1].SetName('1_'+x[0].split('/',1)[1])
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dset_name = '1_' + re.sub(ph_name,r'',x[0].split('/',1)[1]) #removing phase name from generic dataset
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vtk_data[-1].SetName(dset_name)
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Polydata.GetCellData().AddArray(vtk_data[-1])
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results.set_visible('constituents', False)
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@ -1,7 +1,10 @@
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from queue import Queue
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import re
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import glob
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import os
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import vtk
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from vtk.util import numpy_support
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import h5py
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import numpy as np
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@ -433,7 +436,7 @@ class DADF5():
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np.linspace(delta[1],self.size[1]-delta[1],self.grid[1]),
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np.linspace(delta[0],self.size[0]-delta[0],self.grid[0]),
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)
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return np.concatenate((x[:,:,:,None],y[:,:,:,None],y[:,:,:,None]),axis = 3).reshape([np.product(self.grid),3])
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return np.concatenate((x[:,:,:,None],y[:,:,:,None],z[:,:,:,None]),axis = 3).reshape([np.product(self.grid),3])
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else:
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with h5py.File(self.fname,'r') as f:
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return f['geometry/x_c'][()]
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@ -841,3 +844,142 @@ class DADF5():
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N_added +=1
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pool.wait_completion()
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def to_vtk(self,labels,mode='Cell'):
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"""
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Export to vtk cell/point data.
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Parameters
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----------
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labels : list of str
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Labels of the datasets to be exported.
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mode : str, either 'Cell' or 'Point'
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Export in cell format or point format.
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Default value is 'Cell'.
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"""
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if mode=='Cell':
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if self.structured:
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coordArray = [vtk.vtkDoubleArray(),vtk.vtkDoubleArray(),vtk.vtkDoubleArray()]
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for dim in [0,1,2]:
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for c in np.linspace(0,self.size[dim],1+self.grid[dim]):
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coordArray[dim].InsertNextValue(c)
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vtk_geom = vtk.vtkRectilinearGrid()
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vtk_geom.SetDimensions(*(self.grid+1))
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vtk_geom.SetXCoordinates(coordArray[0])
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vtk_geom.SetYCoordinates(coordArray[1])
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vtk_geom.SetZCoordinates(coordArray[2])
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else:
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nodes = vtk.vtkPoints()
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with h5py.File(self.fname) as f:
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nodes.SetData(numpy_support.numpy_to_vtk(f['/geometry/x_n'][()],deep=True))
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vtk_geom = vtk.vtkUnstructuredGrid()
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vtk_geom.SetPoints(nodes)
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vtk_geom.Allocate(f['/geometry/T_c'].shape[0])
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for i in f['/geometry/T_c']:
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vtk_geom.InsertNextCell(vtk.VTK_HEXAHEDRON,8,i-1) # not for all elements!
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elif mode == 'Point':
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Points = vtk.vtkPoints()
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Vertices = vtk.vtkCellArray()
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for c in self.cell_coordinates():
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pointID = Points.InsertNextPoint(c)
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Vertices.InsertNextCell(1)
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Vertices.InsertCellPoint(pointID)
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vtk_geom = vtk.vtkPolyData()
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vtk_geom.SetPoints(Points)
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vtk_geom.SetVerts(Vertices)
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vtk_geom.Modified()
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N_digits = int(np.floor(np.log10(int(self.increments[-1][3:]))))+1
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for i,inc in enumerate(self.iter_visible('increments')):
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vtk_data = []
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materialpoints_backup = self.visible['materialpoints'].copy()
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self.set_visible('materialpoints',False)
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for label in labels:
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for p in self.iter_visible('con_physics'):
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if p != 'generic':
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for c in self.iter_visible('constituents'):
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x = self.get_dataset_location(label)
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if len(x) == 0:
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continue
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array = self.read_dataset(x,0)
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shape = [array.shape[0],np.product(array.shape[1:])]
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vtk_data.append(numpy_support.numpy_to_vtk(num_array=array.reshape(shape),
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deep=True,array_type= vtk.VTK_DOUBLE))
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vtk_data[-1].SetName('1_'+x[0].split('/',1)[1]) #ToDo: hard coded 1!
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vtk_geom.GetCellData().AddArray(vtk_data[-1])
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else:
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x = self.get_dataset_location(label)
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if len(x) == 0:
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continue
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array = self.read_dataset(x,0)
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shape = [array.shape[0],np.product(array.shape[1:])]
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vtk_data.append(numpy_support.numpy_to_vtk(num_array=array.reshape(shape),
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deep=True,array_type= vtk.VTK_DOUBLE))
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ph_name = re.compile(r'(?<=(constituent\/))(.*?)(?=(generic))') # identify phase name
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dset_name = '1_' + re.sub(ph_name,r'',x[0].split('/',1)[1]) # removing phase name
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vtk_data[-1].SetName(dset_name)
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vtk_geom.GetCellData().AddArray(vtk_data[-1])
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self.set_visible('materialpoints',materialpoints_backup)
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constituents_backup = self.visible['constituents'].copy()
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self.set_visible('constituents',False)
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for label in labels:
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for p in self.iter_visible('mat_physics'):
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if p != 'generic':
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for m in self.iter_visible('materialpoints'):
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x = self.get_dataset_location(label)
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if len(x) == 0:
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continue
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array = self.read_dataset(x,0)
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shape = [array.shape[0],np.product(array.shape[1:])]
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vtk_data.append(numpy_support.numpy_to_vtk(num_array=array.reshape(shape),
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deep=True,array_type= vtk.VTK_DOUBLE))
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vtk_data[-1].SetName('1_'+x[0].split('/',1)[1]) #ToDo: why 1_?
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vtk_geom.GetCellData().AddArray(vtk_data[-1])
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else:
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x = self.get_dataset_location(label)
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if len(x) == 0:
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continue
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array = self.read_dataset(x,0)
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shape = [array.shape[0],np.product(array.shape[1:])]
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vtk_data.append(numpy_support.numpy_to_vtk(num_array=array.reshape(shape),
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deep=True,array_type= vtk.VTK_DOUBLE))
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vtk_data[-1].SetName('1_'+x[0].split('/',1)[1])
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vtk_geom.GetCellData().AddArray(vtk_data[-1])
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self.set_visible('constituents',constituents_backup)
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if mode=='Cell':
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writer = vtk.vtkXMLRectilinearGridWriter() if self.structured else \
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vtk.vtkXMLUnstructuredGridWriter()
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x = self.get_dataset_location('u_n')
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vtk_data.append(numpy_support.numpy_to_vtk(num_array=self.read_dataset(x,0),
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deep=True,array_type=vtk.VTK_DOUBLE))
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vtk_data[-1].SetName('u')
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vtk_geom.GetPointData().AddArray(vtk_data[-1])
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elif mode == 'Point':
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writer = vtk.vtkXMLPolyDataWriter()
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file_out = '{}_inc{}.{}'.format(os.path.splitext(os.path.basename(self.fname))[0],
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inc[3:].zfill(N_digits),
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writer.GetDefaultFileExtension())
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writer.SetCompressorTypeToZLib()
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writer.SetDataModeToBinary()
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writer.SetFileName(file_out)
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writer.SetInputData(vtk_geom)
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writer.Write()
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