speed up of VTK data transformation
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chen
parent
59e8109ced
commit
da538fbce9
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@ -6,6 +6,7 @@ import damask
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import numpy as np
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from collections import defaultdict
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from optparse import OptionParser
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from vtk.util import numpy_support
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scriptName = os.path.splitext(os.path.basename(__file__))[0]
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scriptID = ' '.join([scriptName,damask.version])
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@ -14,10 +15,10 @@ scriptID = ' '.join([scriptName,damask.version])
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# MAIN
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# --------------------------------------------------------------------
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parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
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Add scalar and RGB tuples from ASCIItable to existing VTK point cloud (.vtp).
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""", version = scriptID)
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parser = OptionParser(option_class=damask.extendableOption,
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usage='%prog options [file[s]]',
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description = """Add scalar and RGB tuples from ASCIItable to existing VTK point cloud (.vtp).""",
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version = scriptID)
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parser.add_option( '--vtk',
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dest = 'vtk',
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@ -104,60 +105,57 @@ for name in filenames:
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for datatype,dimension,label in [['scalar',1,options.scalar],
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['vector',3,options.vector],
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['tensor',9,options.tensor],
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['color',3,options.color],
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['color' ,3,options.color],
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]:
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for i,dim in enumerate(table.label_dimension(label)):
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me = label[i]
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if dim == -1: remarks.append('{} "{}" not found...'.format(datatype,me))
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elif dim > dimension: remarks.append('"{}" not of dimension {}...'.format(me,dimension))
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if dim == -1: remarks.append('{} "{}" not found...'.format(datatype,me))
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elif dim > dimension: remarks.append('"{}" not of dimension {}...'.format(me,dimension))
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else:
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remarks.append('adding {} "{}"...'.format(datatype,me))
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active[datatype].append(me)
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if datatype in ['scalar','vector', 'tensor']: VTKarray[me] = vtk.vtkDoubleArray()
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elif datatype == 'color': VTKarray[me] = vtk.vtkUnsignedCharArray()
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VTKarray[me].SetNumberOfComponents(dimension)
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VTKarray[me].SetName(label[i])
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if remarks != []: damask.util.croak(remarks)
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if errors != []:
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damask.util.croak(errors)
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table.close(dismiss = True)
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continue
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# ------------------------------------------ process data ---------------------------------------
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# --------------------------------------- process and add data -----------------------------------
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while table.data_read(): # read next data line of ASCII table
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table.data_readArray([item for sublist in active.values() for item in sublist]) # read all requested data
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for datatype,labels in active.items(): # loop over scalar,color
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for me in labels: # loop over all requested items
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theData = [float(table.data[i]) for i in table.label_indexrange(me)] # read strings
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if datatype == 'color': VTKarray[me].InsertNextTuple3(*map(lambda x: int(255.*x),theData))
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elif datatype == 'scalar': VTKarray[me].InsertNextValue(theData[0])
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elif datatype == 'vector': VTKarray[me].InsertNextTuple3(*theData)
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elif datatype == 'tensor': VTKarray[me].InsertNextTuple9(*0.5*(np.array(theData)+
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np.array(theData) \
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.reshape(3,3).T \
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.reshape(9)))
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for datatype,labels in active.items(): # loop over scalar,color
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for me in labels: # loop over all requested items
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VTKtype = vtk.VTK_DOUBLE
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VTKdata = table.data[:, table.label_indexrange(me)].copy() # copy to force contiguous layout
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table.input_close() # close input ASCII table
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if datatype == 'color':
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VTKtype = vtk.VTK_UNSIGNED_CHAR
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VTKdata = (VTKdata*255).astype(int) # translate to 0..255 UCHAR
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elif datatype == 'tensor':
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VTKdata[:,1] = VTKdata[:,3] = 0.5*(VTKdata[:,1]+VTKdata[:,3])
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VTKdata[:,2] = VTKdata[:,6] = 0.5*(VTKdata[:,2]+VTKdata[:,6])
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VTKdata[:,5] = VTKdata[:,7] = 0.5*(VTKdata[:,5]+VTKdata[:,7])
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# ------------------------------------------ add data ---------------------------------------
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VTKarray[me] = numpy_support.numpy_to_vtk(num_array=VTKdata,array_type=VTKtype)
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VTKarray[me].SetName(me)
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for datatype,labels in active.items(): # loop over scalar,color
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if datatype == 'color':
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Polydata.GetPointData().SetScalars(VTKarray[active['color'][0]])
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Polydata.GetCellData().SetScalars(VTKarray[active['color'][0]])
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for me in labels: # loop over all requested items
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Polydata.GetPointData().AddArray(VTKarray[me])
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Polydata.GetCellData().AddArray(VTKarray[me])
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if datatype == 'color':
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Polydata.GetPointData().SetScalars(VTKarray[me])
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Polydata.GetCellData().SetScalars(VTKarray[me])
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else:
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Polydata.GetPointData().AddArray(VTKarray[me])
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Polydata.GetCellData().AddArray(VTKarray[me])
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table.input_close() # close input ASCII table
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# ------------------------------------------ output result ---------------------------------------
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Polydata.Modified()
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if vtk.VTK_MAJOR_VERSION <= 5: Polydata.Update()
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# ------------------------------------------ output result ---------------------------------------
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writer = vtk.vtkXMLPolyDataWriter()
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writer.SetDataModeToBinary()
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writer.SetCompressorTypeToZLib()
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@ -175,7 +173,7 @@ if options.render:
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actor.SetMapper(mapper)
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# Create the graphics structure. The renderer renders into the
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# render window. The render window interactor captures mouse events
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# render window. The render window interactively captures mouse events
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# and will perform appropriate camera or actor manipulation
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# depending on the nature of the events.
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@ -4,6 +4,7 @@
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import os,vtk
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import damask
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import numpy as np
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from vtk.util import numpy_support
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from collections import defaultdict
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from optparse import OptionParser
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@ -102,22 +103,16 @@ for name in filenames:
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for datatype,dimension,label in [['scalar',1,options.scalar],
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['vector',3,options.vector],
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['tensor',9,options.tensor],
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['color',3,options.color],
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['color' ,3,options.color],
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]:
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for i,dim in enumerate(table.label_dimension(label)):
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me = label[i]
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if dim == -1: remarks.append('{} "{}" not found...'.format(datatype,me))
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if dim == -1: remarks.append('{} "{}" not found...'.format(datatype,me))
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elif dim > dimension: remarks.append('"{}" not of dimension {}...'.format(me,dimension))
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else:
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remarks.append('adding {} "{}"...'.format(datatype,me))
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active[datatype].append(me)
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if datatype in ['scalar','vector','tensor']: VTKarray[me] = vtk.vtkDoubleArray()
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elif datatype == 'color': VTKarray[me] = vtk.vtkUnsignedCharArray()
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VTKarray[me].SetNumberOfComponents(dimension)
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VTKarray[me].SetName(label[i])
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if remarks != []: damask.util.croak(remarks)
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if errors != []:
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damask.util.croak(errors)
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@ -126,28 +121,30 @@ for name in filenames:
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# ------------------------------------------ process data ---------------------------------------
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datacount = 0
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table.data_readArray([item for sublist in active.values() for item in sublist]) # read all requested data
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while table.data_read(): # read next data line of ASCII table
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for datatype,labels in active.items(): # loop over scalar,color
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for me in labels: # loop over all requested items
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VTKtype = vtk.VTK_DOUBLE
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VTKdata = table.data[:, table.label_indexrange(me)].copy() # copy to force contiguous layout
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datacount += 1 # count data lines
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for datatype,labels in active.items(): # loop over scalar,color
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for me in labels: # loop over all requested items
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theData = [table.data[i] for i in table.label_indexrange(me)] # read strings
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if datatype == 'color': VTKarray[me].InsertNextTuple3(*map(lambda x: int(255.*float(x)),theData))
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elif datatype == 'scalar': VTKarray[me].InsertNextValue(float(theData[0]))
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elif datatype == 'vector': VTKarray[me].InsertNextTuple3(*map(float,theData))
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elif datatype == 'tensor': VTKarray[me].InsertNextTuple9(*0.5*(np.array(theData)+
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np.array(theData) \
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.reshape(3,3).T \
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.reshape(9)))
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if datatype == 'color':
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VTKtype = vtk.VTK_UNSIGNED_CHAR
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VTKdata = (VTKdata*255).astype(int) # translate to 0..255 UCHAR
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elif datatype == 'tensor':
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VTKdata[:,1] = VTKdata[:,3] = 0.5*(VTKdata[:,1]+VTKdata[:,3])
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VTKdata[:,2] = VTKdata[:,6] = 0.5*(VTKdata[:,2]+VTKdata[:,6])
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VTKdata[:,5] = VTKdata[:,7] = 0.5*(VTKdata[:,5]+VTKdata[:,7])
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VTKarray[me] = numpy_support.numpy_to_vtk(num_array=VTKdata,array_type=VTKtype)
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VTKarray[me].SetName(me)
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table.close() # close input ASCII table
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# ------------------------------------------ add data ---------------------------------------
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if datacount == Npoints: mode = 'point'
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elif datacount == Ncells: mode = 'cell'
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if len(table.data) == Npoints: mode = 'point'
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elif len(table.data) == Ncells: mode = 'cell'
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else:
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damask.util.croak('Data count is incompatible with grid...')
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continue
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