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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 2019-12-18 18:54:46 +01:00
parent 898352e222 3c42368f66
commit 80b559dc00
3 changed files with 152 additions and 4 deletions
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5
processing/post/DADF5_vtk_cells.py
View File

@ -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)

5
processing/post/DADF5_vtk_points.py
View File

@ -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)

146
python/damask/dadf5.py
View File

@ -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()