From 7ccf83637938077cc655d00686ad81496e048a7d Mon Sep 17 00:00:00 2001 From: Martin Diehl Date: Wed, 18 Dec 2019 20:06:44 +0100 Subject: [PATCH] not needed for python-based workflow --- processing/post/DADF5_vtk_cells.py | 147 ---------------------------- processing/post/DADF5_vtk_points.py | 127 ------------------------ 2 files changed, 274 deletions(-) delete mode 100755 processing/post/DADF5_vtk_cells.py delete mode 100755 processing/post/DADF5_vtk_points.py diff --git a/processing/post/DADF5_vtk_cells.py b/processing/post/DADF5_vtk_cells.py deleted file mode 100755 index b3afe939d..000000000 --- a/processing/post/DADF5_vtk_cells.py +++ /dev/null @@ -1,147 +0,0 @@ -#!/usr/bin/env python3 - -import os -import argparse -import re - -import h5py -import numpy as np -import vtk -from vtk.util import numpy_support - -import damask - -scriptName = os.path.splitext(os.path.basename(__file__))[0] -scriptID = ' '.join([scriptName,damask.version]) - -# -------------------------------------------------------------------- -# MAIN -# -------------------------------------------------------------------- -parser = argparse.ArgumentParser() - -#ToDo: We need to decide on a way of handling arguments of variable lentght -#https://stackoverflow.com/questions/15459997/passing-integer-lists-to-python - -#parser.add_argument('--version', action='version', version='%(prog)s {}'.format(scriptID)) -parser.add_argument('filenames', nargs='+', - help='DADF5 files') -parser.add_argument('-d','--dir', dest='dir',default='postProc',metavar='string', - help='name of subdirectory relative to the location of the DADF5 file to hold output') -parser.add_argument('--mat', nargs='+', - help='labels for materialpoint',dest='mat') -parser.add_argument('--con', nargs='+', - help='labels for constituent',dest='con') - -options = parser.parse_args() - -if options.mat is None: options.mat=[] -if options.con is None: options.con=[] - -# --- loop over input files ------------------------------------------------------------------------ - -for filename in options.filenames: - results = damask.DADF5(filename) - - if results.structured: # for grid solvers use rectilinear grid - grid = vtk.vtkRectilinearGrid() - coordArray = [vtk.vtkDoubleArray(), - vtk.vtkDoubleArray(), - vtk.vtkDoubleArray(), - ] - - grid.SetDimensions(*(results.grid+1)) - for dim in [0,1,2]: - for c in np.linspace(0,results.size[dim],1+results.grid[dim]): - coordArray[dim].InsertNextValue(c) - - grid.SetXCoordinates(coordArray[0]) - grid.SetYCoordinates(coordArray[1]) - grid.SetZCoordinates(coordArray[2]) - else: - nodes = vtk.vtkPoints() - with h5py.File(filename) as f: - nodes.SetData(numpy_support.numpy_to_vtk(f['/geometry/x_n'][()],deep=True)) - grid = vtk.vtkUnstructuredGrid() - grid.SetPoints(nodes) - grid.Allocate(f['/geometry/T_c'].shape[0]) - for i in f['/geometry/T_c']: - grid.InsertNextCell(vtk.VTK_HEXAHEDRON,8,i-1) - - N_digits = int(np.floor(np.log10(int(results.increments[-1][3:]))))+1 - for i,inc in enumerate(results.iter_visible('increments')): - print('Output step {}/{}'.format(i+1,len(results.increments))) - vtk_data = [] - - results.set_visible('materialpoints',False) - results.set_visible('constituents', True) - for label in options.con: - for p in results.iter_visible('con_physics'): - if p != 'generic': - for c in results.iter_visible('constituents'): - x = results.get_dataset_location(label) - if len(x) == 0: - continue - 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]) - grid.GetCellData().AddArray(vtk_data[-1]) - else: - 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)) - 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) - results.set_visible('materialpoints',True) - for label in options.mat: - for p in results.iter_visible('mat_physics'): - if p != 'generic': - for m in results.iter_visible('materialpoints'): - x = results.get_dataset_location(label) - if len(x) == 0: - continue - 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]) - grid.GetCellData().AddArray(vtk_data[-1]) - else: - x = results.get_dataset_location(label) - if len(x) == 0: - continue - 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]) - grid.GetCellData().AddArray(vtk_data[-1]) - - writer = vtk.vtkXMLRectilinearGridWriter() if results.structured else \ - vtk.vtkXMLUnstructuredGridWriter() - - results.set_visible('constituents', False) - results.set_visible('materialpoints',False) - x = results.get_dataset_location('u_n') - vtk_data.append(numpy_support.numpy_to_vtk(num_array=results.read_dataset(x,0),deep=True,array_type=vtk.VTK_DOUBLE)) - vtk_data[-1].SetName('u') - grid.GetPointData().AddArray(vtk_data[-1]) - - dirname = os.path.abspath(os.path.join(os.path.dirname(filename),options.dir)) - if not os.path.isdir(dirname): - os.mkdir(dirname,0o755) - file_out = '{}_inc{}.{}'.format(os.path.splitext(os.path.split(filename)[-1])[0], - inc[3:].zfill(N_digits), - writer.GetDefaultFileExtension()) - - writer.SetCompressorTypeToZLib() - writer.SetDataModeToBinary() - writer.SetFileName(os.path.join(dirname,file_out)) - writer.SetInputData(grid) - - writer.Write() diff --git a/processing/post/DADF5_vtk_points.py b/processing/post/DADF5_vtk_points.py deleted file mode 100755 index 925a73a5c..000000000 --- a/processing/post/DADF5_vtk_points.py +++ /dev/null @@ -1,127 +0,0 @@ -#!/usr/bin/env python3 - -import os -import argparse -import re - -import numpy as np -import vtk -from vtk.util import numpy_support - -import damask - -scriptName = os.path.splitext(os.path.basename(__file__))[0] -scriptID = ' '.join([scriptName,damask.version]) - -# -------------------------------------------------------------------- -# MAIN -# -------------------------------------------------------------------- -parser = argparse.ArgumentParser() - -#ToDo: We need to decide on a way of handling arguments of variable lentght -#https://stackoverflow.com/questions/15459997/passing-integer-lists-to-python - -#parser.add_argument('--version', action='version', version='%(prog)s {}'.format(scriptID)) -parser.add_argument('filenames', nargs='+', - help='DADF5 files') -parser.add_argument('-d','--dir', dest='dir',default='postProc',metavar='string', - help='name of subdirectory relative to the location of the DADF5 file to hold output') -parser.add_argument('--mat', nargs='+', - help='labels for materialpoint',dest='mat') -parser.add_argument('--con', nargs='+', - help='labels for constituent',dest='con') - -options = parser.parse_args() - -if options.mat is None: options.mat=[] -if options.con is None: options.con=[] - -# --- loop over input files ------------------------------------------------------------------------ - -for filename in options.filenames: - results = damask.DADF5(filename) - - Points = vtk.vtkPoints() - Vertices = vtk.vtkCellArray() - for c in results.cell_coordinates(): - pointID = Points.InsertNextPoint(c) - Vertices.InsertNextCell(1) - Vertices.InsertCellPoint(pointID) - - Polydata = vtk.vtkPolyData() - Polydata.SetPoints(Points) - Polydata.SetVerts(Vertices) - Polydata.Modified() - - N_digits = int(np.floor(np.log10(int(results.increments[-1][3:]))))+1 - for i,inc in enumerate(results.iter_visible('increments')): - print('Output step {}/{}'.format(i+1,len(results.increments))) - vtk_data = [] - - results.set_visible('materialpoints',False) - results.set_visible('constituents', True) - for label in options.con: - - for p in results.iter_visible('con_physics'): - if p != 'generic': - for c in results.iter_visible('constituents'): - x = results.get_dataset_location(label) - if len(x) == 0: - continue - 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]) - Polydata.GetCellData().AddArray(vtk_data[-1]) - else: - 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)) - 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) - results.set_visible('materialpoints',True) - for label in options.mat: - for p in results.iter_visible('mat_physics'): - if p != 'generic': - for m in results.iter_visible('materialpoints'): - x = results.get_dataset_location(label) - if len(x) == 0: - continue - 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]) - Polydata.GetCellData().AddArray(vtk_data[-1]) - else: - x = results.get_dataset_location(label) - if len(x) == 0: - continue - 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]) - Polydata.GetCellData().AddArray(vtk_data[-1]) - - writer = vtk.vtkXMLPolyDataWriter() - - - dirname = os.path.abspath(os.path.join(os.path.dirname(filename),options.dir)) - if not os.path.isdir(dirname): - os.mkdir(dirname,0o755) - file_out = '{}_inc{}.{}'.format(os.path.splitext(os.path.split(filename)[-1])[0], - inc[3:].zfill(N_digits), - writer.GetDefaultFileExtension()) - - writer.SetCompressorTypeToZLib() - writer.SetDataModeToBinary() - writer.SetFileName(os.path.join(dirname,file_out)) - writer.SetInputData(Polydata) - - writer.Write()