using central functionality
This commit is contained in:
Martin Diehl
parent
b3e8a4405e
commit
32734e7dce
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@ -6,6 +6,7 @@ from scipy import ndimage
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import vtk
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from vtk.util import numpy_support
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from . import VTK
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from . import util
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from . import version
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@ -36,7 +37,7 @@ class Geom():
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self.set_origin(origin)
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self.set_homogenization(homogenization)
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self.set_comments(comments)
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def __repr__(self):
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"""Basic information on geometry definition."""
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@ -70,7 +71,7 @@ class Geom():
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origin_old = self.get_origin()
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unique_old = len(np.unique(self.microstructure))
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max_old = np.nanmax(self.microstructure)
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if size is not None and rescale:
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raise ValueError('Either set size explicitly or rescale automatically')
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@ -108,7 +109,7 @@ class Geom():
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if max_old != np.nanmax(self.microstructure):
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message[-1] = util.delete(message[-1])
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message.append(util.emph('max microstructure: {}'.format(np.nanmax(self.microstructure))))
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return util.return_message(message)
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def set_comments(self,comments):
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@ -123,7 +124,7 @@ class Geom():
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"""
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self.comments = []
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self.add_comments(comments)
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def add_comments(self,comments):
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"""
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Appends comments to existing comments.
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@ -241,7 +242,7 @@ class Geom():
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header.append('origin x {} y {} z {}'.format(*self.get_origin()))
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header.append('homogenization {}'.format(self.get_homogenization()))
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return header
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@staticmethod
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def from_file(fname):
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"""
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@ -266,7 +267,7 @@ class Geom():
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if not keyword.startswith('head') or header_length < 3:
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raise TypeError('Header length information missing or invalid')
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comments = []
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comments = []
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for i,line in enumerate(content[:header_length]):
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items = line.lower().strip().split()
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key = items[0] if items else ''
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@ -295,14 +296,14 @@ class Geom():
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else: items = list(map(float,items))
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microstructure[i:i+len(items)] = items
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i += len(items)
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if i != grid.prod():
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raise TypeError('Invalid file: expected {} entries, found {}'.format(grid.prod(),i))
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microstructure = microstructure.reshape(grid,order='F')
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if not np.any(np.mod(microstructure.flatten(),1) != 0.0): # no float present
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microstructure = microstructure.astype('int')
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return Geom(microstructure.reshape(grid),size,origin,homogenization,comments)
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@ -320,7 +321,7 @@ class Geom():
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"""
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header = self.get_header()
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grid = self.get_grid()
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if pack is None:
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plain = grid.prod()/np.unique(self.microstructure).size < 250
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else:
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@ -371,7 +372,7 @@ class Geom():
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elif compressType == 'of':
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f.write('{} of {}\n'.format(reps,former))
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def to_vtk(self,fname=None):
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"""
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Generates vtk file.
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@ -382,28 +383,9 @@ class Geom():
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vtk file to write. If no file is given, a string is returned.
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"""
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grid = self.get_grid() + np.ones(3,dtype=int)
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size = self.get_size()
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origin = self.get_origin()
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v = VTK.from_rectilinearGrid(self.grid,self.size,self.origin)
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rGrid = v.geom
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coords = [
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np.linspace(0,size[0],grid[0]) + origin[0],
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np.linspace(0,size[1],grid[1]) + origin[1],
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np.linspace(0,size[2],grid[2]) + origin[2]
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]
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rGrid = vtk.vtkRectilinearGrid()
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coordArray = [vtk.vtkDoubleArray(),vtk.vtkDoubleArray(),vtk.vtkDoubleArray()]
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rGrid.SetDimensions(*grid)
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for d,coord in enumerate(coords):
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for c in coord:
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coordArray[d].InsertNextValue(c)
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rGrid.SetXCoordinates(coordArray[0])
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rGrid.SetYCoordinates(coordArray[1])
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rGrid.SetZCoordinates(coordArray[2])
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ms = numpy_support.numpy_to_vtk(num_array=self.microstructure.flatten(order='F'),
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array_type=vtk.VTK_INT if self.microstructure.dtype == int else vtk.VTK_FLOAT)
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ms.SetName('microstructure')
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@ -418,7 +400,7 @@ class Geom():
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writer = vtk.vtkXMLRectilinearGridWriter()
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writer.SetCompressorTypeToZLib()
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writer.SetDataModeToBinary()
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ext = os.path.splitext(fname)[1]
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if ext == '':
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name = fname + '.' + writer.GetDefaultFileExtension()
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@ -427,13 +409,13 @@ class Geom():
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else:
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raise ValueError("unknown extension {}".format(ext))
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writer.SetFileName(name)
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writer.SetInputData(rGrid)
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writer.Write()
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if fname is None: return writer.GetOutputString()
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if not fname: return writer.GetOutputString()
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def show(self):
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"""Show raw content (as in file)."""
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f=StringIO()
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@ -469,7 +451,7 @@ class Geom():
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ms = np.concatenate([ms,ms[:,limits[0]:limits[1]:-1,:]],1)
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if 'x' in directions:
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ms = np.concatenate([ms,ms[limits[0]:limits[1]:-1,:,:]],0)
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return self.update(ms,rescale=True)
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#self.add_comments('tbd')
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@ -1,5 +1,7 @@
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import os
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import numpy as np
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import vtk
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import vtkmodules
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#from vtk.util import numpy_support
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class VTK: # capitals needed/preferred?
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@ -15,6 +17,7 @@ class VTK: # capitals needed/preferred?
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@staticmethod
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def from_rectilinearGrid(grid,size,origin=np.zeros(3)):
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"""Check https://blog.kitware.com/ghost-and-blanking-visibility-changes/ for missing data."""
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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,size[dim],1+grid[dim]):
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@ -25,7 +28,7 @@ class VTK: # capitals needed/preferred?
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geom.SetXCoordinates(coordArray[0])
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geom.SetYCoordinates(coordArray[1])
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geom.SetZCoordinates(coordArray[2])
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return VTK(geom)
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@ -53,5 +56,28 @@ class VTK: # capitals needed/preferred?
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return VTK(geom)
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def write(self,fname):
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print('tbd',fname)
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def write(self,fname): #ToDo: Discuss how to handle consistently filename extensions
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if (isinstance(self.geom,vtkmodules.vtkCommonDataModel.vtkRectilinearGrid)):
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writer = vtk.vtkXMLRectilinearGridWriter()
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elif(isinstance(self.geom,vtkmodules.vtkCommonDataModel.vtkUnstructuredGrid)):
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writer = vtk.vtkUnstructuredGrid()
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elif(isinstance(self.geom,vtkmodules.vtkCommonDataModel.vtkPolyData)):
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writer = vtk.vtkXMLPolyDataWriter()
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writer.SetFileName('{}.{}'.format(os.path.splitext(fname)[0],
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writer.GetDefaultFileExtension()))
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writer.SetCompressorTypeToZLib()
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writer.SetDataModeToBinary()
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writer.SetInputData(self.geom)
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writer.Write()
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def __repr__(self):
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"""ASCII representation of the VTK data."""
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writer = vtk.vtkDataSetWriter()
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#writer.SetHeader('damask.Geom '+version)
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writer.WriteToOutputStringOn()
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writer.SetInputData(self.geom)
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writer.Write()
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return writer.GetOutputString()
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