/[escript]/trunk/escript/src/Data.cpp
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revision 790 by bcumming, Wed Jul 26 23:12:34 2006 UTC revision 1855 by jfenwick, Tue Oct 7 05:25:30 2008 UTC
# Line 1  Line 1 
 // $Id$  
1    
2  /*  /*******************************************************
3   ************************************************************  *
4   *          Copyright 2006 by ACcESS MNRF                   *  * Copyright (c) 2003-2008 by University of Queensland
5   *                                                          *  * Earth Systems Science Computational Center (ESSCC)
6   *              http://www.access.edu.au                    *  * http://www.uq.edu.au/esscc
7   *       Primary Business: Queensland, Australia            *  *
8   *  Licensed under the Open Software License version 3.0    *  * Primary Business: Queensland, Australia
9   *     http://www.opensource.org/licenses/osl-3.0.php       *  * Licensed under the Open Software License version 3.0
10   *                                                          *  * http://www.opensource.org/licenses/osl-3.0.php
11   ************************************************************  *
12  */  *******************************************************/
13    
14    
15  #include "Data.h"  #include "Data.h"
16    
17  #include "DataExpanded.h"  #include "DataExpanded.h"
18  #include "DataConstant.h"  #include "DataConstant.h"
19  #include "DataTagged.h"  #include "DataTagged.h"
20  #include "DataEmpty.h"  #include "DataEmpty.h"
 #include "DataArray.h"  
 #include "DataArrayView.h"  
 #include "DataProf.h"  
21  #include "FunctionSpaceFactory.h"  #include "FunctionSpaceFactory.h"
22  #include "AbstractContinuousDomain.h"  #include "AbstractContinuousDomain.h"
23  #include "UnaryFuncs.h"  #include "UnaryFuncs.h"
24    #include "FunctionSpaceException.h"
25    
26    extern "C" {
27    #include "escript/blocktimer.h"
28    }
29    
30  #include <fstream>  #include <fstream>
31  #include <algorithm>  #include <algorithm>
# Line 38  using namespace boost::python; Line 41  using namespace boost::python;
41  using namespace boost;  using namespace boost;
42  using namespace escript;  using namespace escript;
43    
 #if defined DOPROF  
 //  
 // global table of profiling data for all Data objects  
 DataProf dataProfTable;  
 #endif  
   
44  Data::Data()  Data::Data()
45  {  {
46    //    //
# Line 52  Data::Data() Line 49  Data::Data()
49    shared_ptr<DataAbstract> temp_data(temp);    shared_ptr<DataAbstract> temp_data(temp);
50    m_data=temp_data;    m_data=temp_data;
51    m_protected=false;    m_protected=false;
 #if defined DOPROF  
   // create entry in global profiling table for this object  
   profData = dataProfTable.newData();  
 #endif  
52  }  }
53    
54  Data::Data(double value,  Data::Data(double value,
# Line 63  Data::Data(double value, Line 56  Data::Data(double value,
56             const FunctionSpace& what,             const FunctionSpace& what,
57             bool expanded)             bool expanded)
58  {  {
59    DataArrayView::ShapeType dataPointShape;    DataTypes::ShapeType dataPointShape;
60    for (int i = 0; i < shape.attr("__len__")(); ++i) {    for (int i = 0; i < shape.attr("__len__")(); ++i) {
61      dataPointShape.push_back(extract<const int>(shape[i]));      dataPointShape.push_back(extract<const int>(shape[i]));
62    }    }
63    DataArray temp(dataPointShape,value);  
64    initialise(temp.getView(),what,expanded);    int len = DataTypes::noValues(dataPointShape);
65      DataVector temp_data(len,value,len);
66    //   DataArrayView temp_dataView(temp_data, dataPointShape);
67    
68    //   initialise(temp_dataView, what, expanded);
69      initialise(temp_data, dataPointShape, what, expanded);
70    
71    m_protected=false;    m_protected=false;
 #if defined DOPROF  
   // create entry in global profiling table for this object  
   profData = dataProfTable.newData();  
 #endif  
72  }  }
73    
74  Data::Data(double value,  Data::Data(double value,
75         const DataArrayView::ShapeType& dataPointShape,         const DataTypes::ShapeType& dataPointShape,
76         const FunctionSpace& what,         const FunctionSpace& what,
77             bool expanded)             bool expanded)
78  {  {
79    DataArray temp(dataPointShape,value);    int len = DataTypes::noValues(dataPointShape);
80    pair<int,int> dataShape=what.getDataShape();  
81    initialise(temp.getView(),what,expanded);    DataVector temp_data(len,value,len);
82    //   DataArrayView temp_dataView(temp_data, dataPointShape);
83    
84    //   initialise(temp_dataView, what, expanded);
85      initialise(temp_data, dataPointShape, what, expanded);
86    
87    m_protected=false;    m_protected=false;
 #if defined DOPROF  
   // create entry in global profiling table for this object  
   profData = dataProfTable.newData();  
 #endif  
88  }  }
89    
90  Data::Data(const Data& inData)  Data::Data(const Data& inData)
91  {  {
92    m_data=inData.m_data;    m_data=inData.m_data;
93    m_protected=inData.isProtected();    m_protected=inData.isProtected();
 #if defined DOPROF  
   // create entry in global profiling table for this object  
   profData = dataProfTable.newData();  
 #endif  
94  }  }
95    
96    
97  Data::Data(const Data& inData,  Data::Data(const Data& inData,
98             const DataArrayView::RegionType& region)             const DataTypes::RegionType& region)
99  {  {
100    //    //
101    // Create Data which is a slice of another Data    // Create Data which is a slice of another Data
# Line 110  Data::Data(const Data& inData, Line 103  Data::Data(const Data& inData,
103    shared_ptr<DataAbstract> temp_data(tmp);    shared_ptr<DataAbstract> temp_data(tmp);
104    m_data=temp_data;    m_data=temp_data;
105    m_protected=false;    m_protected=false;
 #if defined DOPROF  
   // create entry in global profiling table for this object  
   profData = dataProfTable.newData();  
 #endif  
106  }  }
107    
108  Data::Data(const Data& inData,  Data::Data(const Data& inData,
109             const FunctionSpace& functionspace)             const FunctionSpace& functionspace)
110  {  {
111  #if defined DOPROF    if (inData.isEmpty())
112    // create entry in global profiling table for this object    {
113    profData = dataProfTable.newData();      throw DataException("Error - will not interpolate for instances of DataEmpty.");
114  #endif    }
115    if (inData.getFunctionSpace()==functionspace) {    if (inData.getFunctionSpace()==functionspace) {
116      m_data=inData.m_data;      m_data=inData.m_data;
117      } else if (inData.isConstant()) { // for a constant function, we just need to use the new function space
118        if (!inData.probeInterpolation(functionspace))
119        {           // Even though this is constant, we still need to check whether interpolation is allowed
120        throw FunctionSpaceException("Call to probeInterpolation returned false for DataConstant.");
121        }
122        DataConstant* dc=new DataConstant(functionspace,inData.m_data->getShape(),inData.m_data->getVector());  
123        m_data=shared_ptr<DataAbstract>(dc);
124    } else {    } else {
125      #if defined DOPROF      Data tmp(0,inData.getDataPointShape(),functionspace,true);
     profData->interpolate++;  
     #endif  
     Data tmp(0,inData.getPointDataView().getShape(),functionspace,true);  
126      // Note: Must use a reference or pointer to a derived object      // Note: Must use a reference or pointer to a derived object
127      // in order to get polymorphic behaviour. Shouldn't really      // in order to get polymorphic behaviour. Shouldn't really
128      // be able to create an instance of AbstractDomain but that was done      // be able to create an instance of AbstractDomain but that was done
# Line 145  Data::Data(const Data& inData, Line 138  Data::Data(const Data& inData,
138    m_protected=false;    m_protected=false;
139  }  }
140    
141  Data::Data(const DataTagged::TagListType& tagKeys,  // Data::Data(const DataTagged::TagListType& tagKeys,
142             const DataTagged::ValueListType & values,  //            const DataTagged::ValueListType & values,
143             const DataArrayView& defaultValue,  //            const DataArrayView& defaultValue,
144             const FunctionSpace& what,  //            const FunctionSpace& what,
145             bool expanded)  //            bool expanded)
146    // {
147    //   DataAbstract* temp=new DataTagged(tagKeys,values,defaultValue,what);
148    //   shared_ptr<DataAbstract> temp_data(temp);
149    //   m_data=temp_data;
150    //   m_protected=false;
151    //   if (expanded) {
152    //     expand();
153    //   }
154    // }
155    
156    
157    
158    Data::Data(DataAbstract* underlyingdata)
159  {  {
160    DataAbstract* temp=new DataTagged(tagKeys,values,defaultValue,what);      m_data=shared_ptr<DataAbstract>(underlyingdata);
161    shared_ptr<DataAbstract> temp_data(temp);      m_protected=false;
   m_data=temp_data;  
   m_protected=false;  
   if (expanded) {  
     expand();  
   }  
 #if defined DOPROF  
   // create entry in global profiling table for this object  
   profData = dataProfTable.newData();  
 #endif  
162  }  }
163    
164  Data::Data(const numeric::array& value,  Data::Data(const numeric::array& value,
# Line 170  Data::Data(const numeric::array& value, Line 167  Data::Data(const numeric::array& value,
167  {  {
168    initialise(value,what,expanded);    initialise(value,what,expanded);
169    m_protected=false;    m_protected=false;
 #if defined DOPROF  
   // create entry in global profiling table for this object  
   profData = dataProfTable.newData();  
 #endif  
170  }  }
171    /*
172  Data::Data(const DataArrayView& value,  Data::Data(const DataArrayView& value,
173         const FunctionSpace& what,         const FunctionSpace& what,
174             bool expanded)             bool expanded)
175  {  {
176    initialise(value,what,expanded);    initialise(value,what,expanded);
177    m_protected=false;    m_protected=false;
178  #if defined DOPROF  }*/
179    // create entry in global profiling table for this object  
180    profData = dataProfTable.newData();  Data::Data(const DataTypes::ValueType& value,
181  #endif           const DataTypes::ShapeType& shape,
182                     const FunctionSpace& what,
183                     bool expanded)
184    {
185       initialise(value,shape,what,expanded);
186       m_protected=false;
187  }  }
188    
189    
190  Data::Data(const object& value,  Data::Data(const object& value,
191         const FunctionSpace& what,         const FunctionSpace& what,
192             bool expanded)             bool expanded)
# Line 195  Data::Data(const object& value, Line 194  Data::Data(const object& value,
194    numeric::array asNumArray(value);    numeric::array asNumArray(value);
195    initialise(asNumArray,what,expanded);    initialise(asNumArray,what,expanded);
196    m_protected=false;    m_protected=false;
 #if defined DOPROF  
   // create entry in global profiling table for this object  
   profData = dataProfTable.newData();  
 #endif  
197  }  }
198    
199    
200  Data::Data(const object& value,  Data::Data(const object& value,
201             const Data& other)             const Data& other)
202  {  {
203      numeric::array asNumArray(value);
204    
205      // extract the shape of the numarray
206      DataTypes::ShapeType tempShape=DataTypes::shapeFromNumArray(asNumArray);
207    // /*  for (int i=0; i < asNumArray.getrank(); i++) {
208    //     tempShape.push_back(extract<int>(asNumArray.getshape()[i]));
209    //   }*/
210    //   // get the space for the data vector
211    //   int len = DataTypes::noValues(tempShape);
212    //   DataVector temp_data(len, 0.0, len);
213    // /*  DataArrayView temp_dataView(temp_data, tempShape);
214    //   temp_dataView.copy(asNumArray);*/
215    //   temp_data.copyFromNumArray(asNumArray);
216    
217    //    //
218    // Create DataConstant using the given value and all other parameters    // Create DataConstant using the given value and all other parameters
219    // copied from other. If value is a rank 0 object this Data    // copied from other. If value is a rank 0 object this Data
220    // will assume the point data shape of other.    // will assume the point data shape of other.
221    DataArray temp(value);  
222    if (temp.getView().getRank()==0) {    if (DataTypes::getRank(tempShape)/*temp_dataView.getRank()*/==0) {
223      //  
224      // Create a DataArray with the scalar value for all elements  
225      DataArray temp2(other.getPointDataView().getShape(),temp.getView()());      // get the space for the data vector
226      initialise(temp2.getView(),other.getFunctionSpace(),false);      int len1 = DataTypes::noValues(tempShape);
227        DataVector temp_data(len1, 0.0, len1);
228        temp_data.copyFromNumArray(asNumArray);
229    
230        int len = DataTypes::noValues(other.getDataPointShape());
231    
232        DataVector temp2_data(len, temp_data[0]/*temp_dataView()*/, len);
233        //DataArrayView temp2_dataView(temp2_data, other.getPointDataView().getShape());
234    //     initialise(temp2_dataView, other.getFunctionSpace(), false);
235    
236        DataConstant* t=new DataConstant(other.getFunctionSpace(),other.getDataPointShape(),temp2_data);
237        boost::shared_ptr<DataAbstract> sp(t);
238        m_data=sp;
239    
240    
241    } else {    } else {
242      //      //
243      // Create a DataConstant with the same sample shape as other      // Create a DataConstant with the same sample shape as other
244      initialise(temp.getView(),other.getFunctionSpace(),false);  //     initialise(temp_dataView, other.getFunctionSpace(), false);
245        DataConstant* t=new DataConstant(asNumArray,other.getFunctionSpace());
246        boost::shared_ptr<DataAbstract> sp(t);
247        m_data=sp;
248    }    }
249    m_protected=false;    m_protected=false;
 #if defined DOPROF  
   // create entry in global profiling table for this object  
   profData = dataProfTable.newData();  
 #endif  
250  }  }
251    
252  Data::~Data()  Data::~Data()
# Line 231  Data::~Data() Line 254  Data::~Data()
254    
255  }  }
256    
257    
258    
259    void
260    Data::initialise(const boost::python::numeric::array& value,
261                     const FunctionSpace& what,
262                     bool expanded)
263    {
264      //
265      // Construct a Data object of the appropriate type.
266      // Construct the object first as there seems to be a bug which causes
267      // undefined behaviour if an exception is thrown during construction
268      // within the shared_ptr constructor.
269      if (expanded) {
270        DataAbstract* temp=new DataExpanded(value, what);
271        boost::shared_ptr<DataAbstract> temp_data(temp);
272        m_data=temp_data;
273      } else {
274        DataAbstract* temp=new DataConstant(value, what);
275        boost::shared_ptr<DataAbstract> temp_data(temp);
276        m_data=temp_data;
277      }
278    }
279    
280    
281    void
282    Data::initialise(const DataTypes::ValueType& value,
283             const DataTypes::ShapeType& shape,
284                     const FunctionSpace& what,
285                     bool expanded)
286    {
287      //
288      // Construct a Data object of the appropriate type.
289      // Construct the object first as there seems to be a bug which causes
290      // undefined behaviour if an exception is thrown during construction
291      // within the shared_ptr constructor.
292      if (expanded) {
293        DataAbstract* temp=new DataExpanded(what, shape, value);
294        boost::shared_ptr<DataAbstract> temp_data(temp);
295        m_data=temp_data;
296      } else {
297        DataAbstract* temp=new DataConstant(what, shape, value);
298        boost::shared_ptr<DataAbstract> temp_data(temp);
299        m_data=temp_data;
300      }
301    }
302    
303    
304    // void
305    // Data::CompareDebug(const Data& rd)
306    // {
307    //  using namespace std;
308    //  bool mismatch=false;
309    //  std::cout << "Comparing left and right" << endl;
310    //  const DataTagged* left=dynamic_cast<DataTagged*>(m_data.get());
311    //  const DataTagged* right=dynamic_cast<DataTagged*>(rd.m_data.get());
312    //  
313    //  if (left==0)
314    //  {
315    //      cout << "left arg is not a DataTagged\n";
316    //      return;
317    //  }
318    //  
319    //  if (right==0)
320    //  {
321    //      cout << "right arg is not a DataTagged\n";
322    //      return;
323    //  }
324    //  cout << "Num elements=" << left->getVector().size() << ":" << right->getVector().size() << std::endl;
325    //  cout << "Shapes ";
326    //  if (left->getShape()==right->getShape())
327    //  {
328    //      cout << "ok\n";
329    //  }
330    //  else
331    //  {
332    //      cout << "Problem: shapes do not match\n";
333    //      mismatch=true;
334    //  }
335    //  int lim=left->getVector().size();
336    //  if (right->getVector().size()) lim=right->getVector().size();
337    //  for (int i=0;i<lim;++i)
338    //  {
339    //      if (left->getVector()[i]!=right->getVector()[i])
340    //      {
341    //          cout << "[" << i << "] value mismatch " << left->getVector()[i] << ":" << right->getVector()[i] << endl;
342    //          mismatch=true;
343    //      }
344    //  }
345    //
346    //  // still need to check the tag map
347    //  // also need to watch what is happening to function spaces, are they copied or what?
348    //
349    //  const DataTagged::DataMapType& mapleft=left->getTagLookup();
350    //  const DataTagged::DataMapType& mapright=right->getTagLookup();
351    //
352    //  if (mapleft.size()!=mapright.size())
353    //  {
354    //      cout << "Maps are different sizes " << mapleft.size() << ":" << mapright.size() << endl;
355    //      mismatch=true;
356    //      cout << "Left map\n";
357    //      DataTagged::DataMapType::const_iterator i,j;
358    //      for (i=mapleft.begin();i!=mapleft.end();++i) {
359    //          cout << "(" << i->first << "=>" << i->second << ")\n";
360    //      }
361    //      cout << "Right map\n";
362    //      for (i=mapright.begin();i!=mapright.end();++i) {
363    //          cout << "(" << i->first << "=>" << i->second << ")\n";
364    //      }
365    //      cout << "End map\n";
366    //
367    //  }
368    //
369    //  DataTagged::DataMapType::const_iterator i,j;
370    //  for (i=mapleft.begin(),j=mapright.begin();i!=mapleft.end() && j!=mapright.end();++i,++j) {
371    //     if ((i->first!=j->first) || (i->second!=j->second))
372    //     {
373    //      cout << "(" << i->first << "=>" << i->second << ")";
374    //      cout << ":(" << j->first << "=>" << j->second << ") ";
375    //      mismatch=true;
376    //            }
377    //  }
378    //  if (mismatch)
379    //  {
380    //      cout << "#Mismatch\n";
381    //  }
382    // }
383    
384  escriptDataC  escriptDataC
385  Data::getDataC()  Data::getDataC()
386  {  {
# Line 250  Data::getDataC() const Line 400  Data::getDataC() const
400  const boost::python::tuple  const boost::python::tuple
401  Data::getShapeTuple() const  Data::getShapeTuple() const
402  {  {
403    const DataArrayView::ShapeType& shape=getDataPointShape();    const DataTypes::ShapeType& shape=getDataPointShape();
404    switch(getDataPointRank()) {    switch(getDataPointRank()) {
405       case 0:       case 0:
406          return make_tuple();          return make_tuple();
# Line 267  Data::getShapeTuple() const Line 417  Data::getShapeTuple() const
417    }    }
418  }  }
419    
420    
421    // The different name is needed because boost has trouble with overloaded functions.
422    // It can't work out what type the function is based soley on its name.
423    // There are ways to fix this involving creating function pointer variables for each form
424    // but there doesn't seem to be a need given that the methods have the same name from the python point of view
425    Data*
426    Data::copySelf()
427    {
428       DataAbstract* temp=m_data->deepCopy();
429       return new Data(temp);
430    }
431    
432  void  void
433  Data::copy(const Data& other)  Data::copy(const Data& other)
434  {  {
435    //    DataAbstract* temp=other.m_data->deepCopy();
436    // Perform a deep copy    shared_ptr<DataAbstract> temp_data(temp);
437      m_data=temp_data;
438    }
439    
440    
441    void
442    Data::setToZero()
443    {
444      if (isEmpty())
445    {    {
446      DataExpanded* temp=dynamic_cast<DataExpanded*>(other.m_data.get());       throw DataException("Error - Operations not permitted on instances of DataEmpty.");
     if (temp!=0) {  
       //  
       // Construct a DataExpanded copy  
       DataAbstract* newData=new DataExpanded(*temp);  
       shared_ptr<DataAbstract> temp_data(newData);  
       m_data=temp_data;  
       return;  
     }  
447    }    }
448    {    {
449      DataTagged* temp=dynamic_cast<DataTagged*>(other.m_data.get());      DataExpanded* temp=dynamic_cast<DataExpanded*>(m_data.get());
450      if (temp!=0) {      if (temp!=0) {
451        //         temp->setToZero();
452        // Construct a DataTagged copy         return;
       DataAbstract* newData=new DataTagged(*temp);  
       shared_ptr<DataAbstract> temp_data(newData);  
       m_data=temp_data;  
       return;  
453      }      }
454    }    }
455    {    {
456      DataConstant* temp=dynamic_cast<DataConstant*>(other.m_data.get());      DataTagged* temp=dynamic_cast<DataTagged*>(m_data.get());
457      if (temp!=0) {      if (temp!=0) {
458        //        temp->setToZero();
       // Construct a DataConstant copy  
       DataAbstract* newData=new DataConstant(*temp);  
       shared_ptr<DataAbstract> temp_data(newData);  
       m_data=temp_data;  
459        return;        return;
460      }      }
461    }    }
462    {    {
463      DataEmpty* temp=dynamic_cast<DataEmpty*>(other.m_data.get());      DataConstant* temp=dynamic_cast<DataConstant*>(m_data.get());
464      if (temp!=0) {      if (temp!=0) {
465        //        temp->setToZero();
       // Construct a DataEmpty copy  
       DataAbstract* newData=new DataEmpty();  
       shared_ptr<DataAbstract> temp_data(newData);  
       m_data=temp_data;  
466        return;        return;
467      }      }
468    }    }
469    throw DataException("Error - Copy not implemented for this Data type.");    throw DataException("Error - Data can not be set to zero.");
470  }  }
471    
472    // void
473    // Data::copyWithMask(const Data& other,
474    //                    const Data& mask)
475    // {
476    //   if (other.isEmpty() || mask.isEmpty())
477    //   {
478    //  throw DataException("Error - copyWithMask not permitted using instances of DataEmpty.");
479    //   }
480    //   Data mask1;
481    //   Data mask2;
482    //   mask1 = mask.wherePositive();
483    //
484    //   mask2.copy(mask1);
485    //   mask1 *= other;
486    //
487    //   mask2 *= *this;
488    //   mask2 = *this - mask2;
489    //   *this = mask1 + mask2;
490    // }
491    
492  void  void
493  Data::copyWithMask(const Data& other,  Data::copyWithMask(const Data& other,
494                     const Data& mask)                     const Data& mask)
495  {  {
496    Data mask1;    // 1. Interpolate if required so all Datas use the same FS as this
497    Data mask2;    // 2. Tag or Expand so that all Data's are the same type
498      // 3. Iterate over the data vectors copying values where mask is >0
499    mask1 = mask.wherePositive();    if (other.isEmpty() || mask.isEmpty())
500    mask2.copy(mask1);    {
501        throw DataException("Error - copyWithMask not permitted using instances of DataEmpty.");
502      }
503      Data other2(other);
504      Data mask2(mask);
505      FunctionSpace myFS=getFunctionSpace();
506      FunctionSpace oFS=other2.getFunctionSpace();
507      FunctionSpace mFS=mask2.getFunctionSpace();
508      if (oFS!=myFS)
509      {
510         if (other2.probeInterpolation(myFS))
511         {
512        other2=other2.interpolate(myFS);
513         }
514         else
515         {
516        throw DataException("Error - copyWithMask: other FunctionSpace is not compatible with this one.");
517         }
518      }
519      if (mFS!=myFS)
520      {
521         if (mask2.probeInterpolation(myFS))
522         {
523        mask2=mask2.interpolate(myFS);
524         }
525         else
526         {
527        throw DataException("Error - copyWithMask: mask FunctionSpace is not compatible with this one.");
528         }
529      }
530                // Ensure that all args have the same type
531      if (this->isExpanded() || mask2.isExpanded() || other2.isExpanded())
532      {
533        this->expand();
534        other2.expand();
535        mask2.expand();
536      }
537      else if (this->isTagged() || mask2.isTagged() || other2.isTagged())
538      {
539        this->tag();
540        other2.tag();
541        mask2.tag();
542      }
543      else if (this->isConstant() && mask2.isConstant() && other2.isConstant())
544      {
545      }
546      else
547      {
548        throw DataException("Error - Unknown DataAbstract passed to copyWithMask.");
549      }
550      // Now we iterate over the elements
551      DataVector& self=m_data->getVector();
552      const DataVector& ovec=other2.m_data->getVector();
553      const DataVector& mvec=mask2.m_data->getVector();
554      if ((self.size()!=ovec.size()) || (self.size()!=mvec.size()))
555      {
556        throw DataException("Error - size mismatch in arguments to copyWithMask.");
557      }
558      size_t num_points=self.size();
559      long i;
560      #pragma omp parallel for private(i) schedule(static)
561      for (i=0;i<num_points;++i)
562      {
563        if (mvec[i]>0)
564        {
565           self[i]=ovec[i];
566        }
567      }
568    }
569    
   mask1 *= other;  
   mask2 *= *this;  
   mask2 = *this - mask2;  
570    
   *this = mask1 + mask2;  
 }  
571    
572  bool  bool
573  Data::isExpanded() const  Data::isExpanded() const
# Line 350  Data::isTagged() const Line 583  Data::isTagged() const
583    return (temp!=0);    return (temp!=0);
584  }  }
585    
 /* TODO */  
 /* global reduction -- the local data being empty does not imply that it is empty on other processers*/  
586  bool  bool
587  Data::isEmpty() const  Data::isEmpty() const
588  {  {
# Line 367  Data::isConstant() const Line 598  Data::isConstant() const
598  }  }
599    
600  void  void
601  Data::setProtection()  Data::setProtection()
602  {  {
603     m_protected=true;     m_protected=true;
604  }  }
605    
606  bool  bool
607  Data::isProtected() const  Data::isProtected() const
608  {  {
609     return m_protected;     return m_protected;
610  }  }
611    
# Line 422  Data::tag() Line 653  Data::tag()
653    }    }
654  }  }
655    
656  void  Data
657  Data::reshapeDataPoint(const DataArrayView::ShapeType& shape)  Data::oneOver() const
658  {  {
659    m_data->reshapeDataPoint(shape);    return C_TensorUnaryOperation(*this, bind1st(divides<double>(),1.));
660  }  }
661    
662  Data  Data
663  Data::wherePositive() const  Data::wherePositive() const
664  {  {
665  #if defined DOPROF    return C_TensorUnaryOperation(*this, bind2nd(greater<double>(),0.0));
   profData->where++;  
 #endif  
   return escript::unaryOp(*this,bind2nd(greater<double>(),0.0));  
666  }  }
667    
668  Data  Data
669  Data::whereNegative() const  Data::whereNegative() const
670  {  {
671  #if defined DOPROF    return C_TensorUnaryOperation(*this, bind2nd(less<double>(),0.0));
   profData->where++;  
 #endif  
   return escript::unaryOp(*this,bind2nd(less<double>(),0.0));  
672  }  }
673    
674  Data  Data
675  Data::whereNonNegative() const  Data::whereNonNegative() const
676  {  {
677  #if defined DOPROF    return C_TensorUnaryOperation(*this, bind2nd(greater_equal<double>(),0.0));
   profData->where++;  
 #endif  
   return escript::unaryOp(*this,bind2nd(greater_equal<double>(),0.0));  
678  }  }
679    
680  Data  Data
681  Data::whereNonPositive() const  Data::whereNonPositive() const
682  {  {
683  #if defined DOPROF    return C_TensorUnaryOperation(*this, bind2nd(less_equal<double>(),0.0));
   profData->where++;  
 #endif  
   return escript::unaryOp(*this,bind2nd(less_equal<double>(),0.0));  
684  }  }
685    
686  Data  Data
687  Data::whereZero(double tol) const  Data::whereZero(double tol) const
688  {  {
 #if defined DOPROF  
   profData->where++;  
 #endif  
689    Data dataAbs=abs();    Data dataAbs=abs();
690    return escript::unaryOp(dataAbs,bind2nd(less_equal<double>(),tol));    return C_TensorUnaryOperation(dataAbs, bind2nd(less_equal<double>(),tol));
691  }  }
692    
693  Data  Data
694  Data::whereNonZero(double tol) const  Data::whereNonZero(double tol) const
695  {  {
 #if defined DOPROF  
   profData->where++;  
 #endif  
696    Data dataAbs=abs();    Data dataAbs=abs();
697    return escript::unaryOp(dataAbs,bind2nd(greater<double>(),tol));    return C_TensorUnaryOperation(dataAbs, bind2nd(greater<double>(),tol));
698  }  }
699    
700  Data  Data
701  Data::interpolate(const FunctionSpace& functionspace) const  Data::interpolate(const FunctionSpace& functionspace) const
702  {  {
 #if defined DOPROF  
   profData->interpolate++;  
 #endif  
703    return Data(*this,functionspace);    return Data(*this,functionspace);
704  }  }
705    
# Line 511  Data::probeInterpolation(const FunctionS Line 721  Data::probeInterpolation(const FunctionS
721  Data  Data
722  Data::gradOn(const FunctionSpace& functionspace) const  Data::gradOn(const FunctionSpace& functionspace) const
723  {  {
724  #if defined DOPROF    if (isEmpty())
725    profData->grad++;    {
726  #endif      throw DataException("Error - operation not permitted on instances of DataEmpty.");
727      }
728      double blocktimer_start = blocktimer_time();
729    if (functionspace.getDomain()!=getDomain())    if (functionspace.getDomain()!=getDomain())
730      throw DataException("Error - gradient cannot be calculated on different domains.");      throw DataException("Error - gradient cannot be calculated on different domains.");
731    DataArrayView::ShapeType grad_shape=getPointDataView().getShape();    DataTypes::ShapeType grad_shape=getDataPointShape();
732    grad_shape.push_back(functionspace.getDim());    grad_shape.push_back(functionspace.getDim());
733    Data out(0.0,grad_shape,functionspace,true);    Data out(0.0,grad_shape,functionspace,true);
734    getDomain().setToGradient(out,*this);    getDomain().setToGradient(out,*this);
735      blocktimer_increment("grad()", blocktimer_start);
736    return out;    return out;
737  }  }
738    
739  Data  Data
740  Data::grad() const  Data::grad() const
741  {  {
742      if (isEmpty())
743      {
744        throw DataException("Error - operation not permitted on instances of DataEmpty.");
745      }
746    return gradOn(escript::function(getDomain()));    return gradOn(escript::function(getDomain()));
747  }  }
748    
749  int  int
750  Data::getDataPointSize() const  Data::getDataPointSize() const
751  {  {
752    return getPointDataView().noValues();    return m_data->getNoValues();
753  }  }
754    
755  DataArrayView::ValueType::size_type  DataTypes::ValueType::size_type
756  Data::getLength() const  Data::getLength() const
757  {  {
758    return m_data->getLength();    return m_data->getLength();
759  }  }
760    
 const DataArrayView::ShapeType&  
 Data::getDataPointShape() const  
 {  
   return getPointDataView().getShape();  
 }  
   
 void  
 Data::fillFromNumArray(const boost::python::numeric::array num_array)  
 {  
   if (isProtected()) {  
         throw DataException("Error - attempt to update protected Data object.");  
   }  
   //  
   // check rank  
   if (num_array.getrank()<getDataPointRank())  
       throw DataException("Rank of numarray does not match Data object rank");  
   
   //  
   // check shape of num_array  
   for (int i=0; i<getDataPointRank(); i++) {  
     if (extract<int>(num_array.getshape()[i+1])!=getDataPointShape()[i])  
        throw DataException("Shape of numarray does not match Data object rank");  
   }  
   
   //  
   // make sure data is expanded:  
   if (!isExpanded()) {  
     expand();  
   }  
   
   //  
   // and copy over  
   m_data->copyAll(num_array);  
 }  
   
761  const  const
762  boost::python::numeric::array  boost::python::numeric::array
763  Data::convertToNumArray()  Data:: getValueOfDataPoint(int dataPointNo)
764  {  {
765    //    size_t length=0;
766    // determine the total number of data points    int i, j, k, l;
   int numSamples = getNumSamples();  
   int numDataPointsPerSample = getNumDataPointsPerSample();  
   int numDataPoints = numSamples * numDataPointsPerSample;  
   
767    //    //
768    // determine the rank and shape of each data point    // determine the rank and shape of each data point
769    int dataPointRank = getDataPointRank();    int dataPointRank = getDataPointRank();
770    DataArrayView::ShapeType dataPointShape = getDataPointShape();    const DataTypes::ShapeType& dataPointShape = getDataPointShape();
771    
772    //    //
773    // create the numeric array to be returned    // create the numeric array to be returned
774    boost::python::numeric::array numArray(0.0);    boost::python::numeric::array numArray(0.0);
775    
776    //    //
777    // the rank of the returned numeric array will be the rank of    // the shape of the returned numeric array will be the same
778    // the data points, plus one. Where the rank of the array is n,    // as that of the data point
779    // the last n-1 dimensions will be equal to the shape of the    int arrayRank = dataPointRank;
780    // data points, whilst the first dimension will be equal to the    const DataTypes::ShapeType& arrayShape = dataPointShape;
   // total number of data points. Thus the array will consist of  
   // a serial vector of the data points.  
   int arrayRank = dataPointRank + 1;  
   DataArrayView::ShapeType arrayShape;  
   arrayShape.push_back(numDataPoints);  
   for (int d=0; d<dataPointRank; d++) {  
      arrayShape.push_back(dataPointShape[d]);  
   }  
781    
782    //    //
783    // resize the numeric array to the shape just calculated    // resize the numeric array to the shape just calculated
784      if (arrayRank==0) {
785        numArray.resize(1);
786      }
787    if (arrayRank==1) {    if (arrayRank==1) {
788      numArray.resize(arrayShape[0]);      numArray.resize(arrayShape[0]);
789    }    }
# Line 623  Data::convertToNumArray() Line 796  Data::convertToNumArray()
796    if (arrayRank==4) {    if (arrayRank==4) {
797      numArray.resize(arrayShape[0],arrayShape[1],arrayShape[2],arrayShape[3]);      numArray.resize(arrayShape[0],arrayShape[1],arrayShape[2],arrayShape[3]);
798    }    }
   if (arrayRank==5) {  
     numArray.resize(arrayShape[0],arrayShape[1],arrayShape[2],arrayShape[3],arrayShape[4]);  
   }  
799    
800    //    if (getNumDataPointsPerSample()>0) {
801    // loop through each data point in turn, loading the values for that data point         int sampleNo = dataPointNo/getNumDataPointsPerSample();
802    // into the numeric array.         int dataPointNoInSample = dataPointNo - sampleNo * getNumDataPointsPerSample();
803    int dataPoint = 0;         //
804    for (int sampleNo = 0; sampleNo < numSamples; sampleNo++) {         // Check a valid sample number has been supplied
805      for (int dataPointNo = 0; dataPointNo < numDataPointsPerSample; dataPointNo++) {         if ((sampleNo >= getNumSamples()) || (sampleNo < 0 )) {
806        DataArrayView dataPointView = getDataPoint(sampleNo, dataPointNo);             throw DataException("Error - Data::convertToNumArray: invalid sampleNo.");
807        if (dataPointRank==0) {         }
808          numArray[dataPoint]=dataPointView();  
809        }         //
810        if (dataPointRank==1) {         // Check a valid data point number has been supplied
811          for (int i=0; i<dataPointShape[0]; i++) {         if ((dataPointNoInSample >= getNumDataPointsPerSample()) || (dataPointNoInSample < 0)) {
812            numArray[dataPoint][i]=dataPointView(i);             throw DataException("Error - Data::convertToNumArray: invalid dataPointNoInSample.");
813          }         }
814        }         // TODO: global error handling
815        if (dataPointRank==2) {         // create a view of the data if it is stored locally
816          for (int i=0; i<dataPointShape[0]; i++) {  //       DataArrayView dataPointView = getDataPoint(sampleNo, dataPointNoInSample);
817            for (int j=0; j<dataPointShape[1]; j++) {         DataTypes::ValueType::size_type offset=getDataOffset(sampleNo, dataPointNoInSample);
             numArray[dataPoint][i][j] = dataPointView(i,j);  
           }  
         }  
       }  
       if (dataPointRank==3) {  
         for (int i=0; i<dataPointShape[0]; i++) {  
           for (int j=0; j<dataPointShape[1]; j++) {  
             for (int k=0; k<dataPointShape[2]; k++) {  
               numArray[dataPoint][i][j][k]=dataPointView(i,j,k);  
             }  
           }  
         }  
       }  
       if (dataPointRank==4) {  
         for (int i=0; i<dataPointShape[0]; i++) {  
           for (int j=0; j<dataPointShape[1]; j++) {  
             for (int k=0; k<dataPointShape[2]; k++) {  
               for (int l=0; l<dataPointShape[3]; l++) {  
                 numArray[dataPoint][i][j][k][l]=dataPointView(i,j,k,l);  
               }  
             }  
           }  
         }  
       }  
       dataPoint++;  
     }  
   }  
818    
819    
820           switch( dataPointRank ){
821                case 0 :
822                    numArray[0] = getDataAtOffset(offset);
823                    break;
824                case 1 :
825                    for( i=0; i<dataPointShape[0]; i++ )
826                        numArray[i]=getDataAtOffset(offset+DataTypes::getRelIndex(dataPointShape, i));
827                    break;
828                case 2 :
829                    for( i=0; i<dataPointShape[0]; i++ )
830                        for( j=0; j<dataPointShape[1]; j++)
831                            numArray[make_tuple(i,j)]=getDataAtOffset(offset+DataTypes::getRelIndex(dataPointShape, i,j));
832                    break;
833                case 3 :
834                    for( i=0; i<dataPointShape[0]; i++ )
835                        for( j=0; j<dataPointShape[1]; j++ )
836                            for( k=0; k<dataPointShape[2]; k++)
837                                numArray[make_tuple(i,j,k)]=getDataAtOffset(offset+DataTypes::getRelIndex(dataPointShape, i,j,k));
838                    break;
839                case 4 :
840                    for( i=0; i<dataPointShape[0]; i++ )
841                        for( j=0; j<dataPointShape[1]; j++ )
842                            for( k=0; k<dataPointShape[2]; k++ )
843                                for( l=0; l<dataPointShape[3]; l++)
844                                    numArray[make_tuple(i,j,k,l)]=getDataAtOffset(offset+DataTypes::getRelIndex(dataPointShape, i,j,k,l));
845                    break;
846        }
847      }
848    //    //
849    // return the loaded array    // return the array
850    return numArray;    return numArray;
851    
852  }  }
853    
854  const  void
855  boost::python::numeric::array  Data::setValueOfDataPointToPyObject(int dataPointNo, const boost::python::object& py_object)
 Data::convertToNumArrayFromSampleNo(int sampleNo)  
856  {  {
857    //      // this will throw if the value cannot be represented
858    // Check a valid sample number has been supplied      boost::python::numeric::array num_array(py_object);
859    if (sampleNo >= getNumSamples()) {      setValueOfDataPointToArray(dataPointNo,num_array);
     throw DataException("Error - Data::convertToNumArray: invalid sampleNo.");  
   }  
860    
   //  
   // determine the number of data points per sample  
   int numDataPointsPerSample = getNumDataPointsPerSample();  
861    
862    //  }
   // determine the rank and shape of each data point  
   int dataPointRank = getDataPointRank();  
   DataArrayView::ShapeType dataPointShape = getDataPointShape();  
863    
864    void
865    Data::setValueOfDataPointToArray(int dataPointNo, const boost::python::numeric::array& num_array)
866    {
867      if (isProtected()) {
868            throw DataException("Error - attempt to update protected Data object.");
869      }
870    //    //
871    // create the numeric array to be returned    // check rank
872    boost::python::numeric::array numArray(0.0);    if (num_array.getrank()<getDataPointRank())
873          throw DataException("Rank of numarray does not match Data object rank");
874    
875    //    //
876    // the rank of the returned numeric array will be the rank of    // check shape of num_array
877    // the data points, plus one. Where the rank of the array is n,    for (int i=0; i<getDataPointRank(); i++) {
878    // the last n-1 dimensions will be equal to the shape of the      if (extract<int>(num_array.getshape()[i])!=getDataPointShape()[i])
879    // data points, whilst the first dimension will be equal to the         throw DataException("Shape of numarray does not match Data object rank");
   // total number of data points. Thus the array will consist of  
   // a serial vector of the data points.  
   int arrayRank = dataPointRank + 1;  
   DataArrayView::ShapeType arrayShape;  
   arrayShape.push_back(numDataPointsPerSample);  
   for (int d=0; d<dataPointRank; d++) {  
      arrayShape.push_back(dataPointShape[d]);  
880    }    }
   
881    //    //
882    // resize the numeric array to the shape just calculated    // make sure data is expanded:
883    if (arrayRank==1) {    if (!isExpanded()) {
884      numArray.resize(arrayShape[0]);      expand();
   }  
   if (arrayRank==2) {  
     numArray.resize(arrayShape[0],arrayShape[1]);  
   }  
   if (arrayRank==3) {  
     numArray.resize(arrayShape[0],arrayShape[1],arrayShape[2]);  
   }  
   if (arrayRank==4) {  
     numArray.resize(arrayShape[0],arrayShape[1],arrayShape[2],arrayShape[3]);  
885    }    }
886    if (arrayRank==5) {    if (getNumDataPointsPerSample()>0) {
887      numArray.resize(arrayShape[0],arrayShape[1],arrayShape[2],arrayShape[3],arrayShape[4]);         int sampleNo = dataPointNo/getNumDataPointsPerSample();
888           int dataPointNoInSample = dataPointNo - sampleNo * getNumDataPointsPerSample();
889           m_data->copyToDataPoint(sampleNo, dataPointNoInSample,num_array);
890      } else {
891           m_data->copyToDataPoint(-1, 0,num_array);
892    }    }
893    }
894    
895    //  void
896    // loop through each data point in turn, loading the values for that data point  Data::setValueOfDataPoint(int dataPointNo, const double value)
897    // into the numeric array.  {
898    for (int dataPoint = 0; dataPoint < numDataPointsPerSample; dataPoint++) {    if (isProtected()) {
899      DataArrayView dataPointView = getDataPoint(sampleNo, dataPoint);          throw DataException("Error - attempt to update protected Data object.");
     if (dataPointRank==0) {  
       numArray[dataPoint]=dataPointView();  
     }  
     if (dataPointRank==1) {  
       for (int i=0; i<dataPointShape[0]; i++) {  
         numArray[dataPoint][i]=dataPointView(i);  
       }  
     }  
     if (dataPointRank==2) {  
       for (int i=0; i<dataPointShape[0]; i++) {  
         for (int j=0; j<dataPointShape[1]; j++) {  
           numArray[dataPoint][i][j] = dataPointView(i,j);  
         }  
       }  
     }  
     if (dataPointRank==3) {  
       for (int i=0; i<dataPointShape[0]; i++) {  
         for (int j=0; j<dataPointShape[1]; j++) {  
           for (int k=0; k<dataPointShape[2]; k++) {  
             numArray[dataPoint][i][j][k]=dataPointView(i,j,k);  
           }  
         }  
       }  
     }  
     if (dataPointRank==4) {  
       for (int i=0; i<dataPointShape[0]; i++) {  
         for (int j=0; j<dataPointShape[1]; j++) {  
           for (int k=0; k<dataPointShape[2]; k++) {  
             for (int l=0; l<dataPointShape[3]; l++) {  
               numArray[dataPoint][i][j][k][l]=dataPointView(i,j,k,l);  
             }  
           }  
         }  
       }  
     }  
900    }    }
   
901    //    //
902    // return the loaded array    // make sure data is expanded:
903    return numArray;    if (!isExpanded()) {
904        expand();
905      }
906      if (getNumDataPointsPerSample()>0) {
907           int sampleNo = dataPointNo/getNumDataPointsPerSample();
908           int dataPointNoInSample = dataPointNo - sampleNo * getNumDataPointsPerSample();
909           m_data->copyToDataPoint(sampleNo, dataPointNoInSample,value);
910      } else {
911           m_data->copyToDataPoint(-1, 0,value);
912      }
913  }  }
914    
915  const  const
916  boost::python::numeric::array  boost::python::numeric::array
917  Data::convertToNumArrayFromDPNo(int procNo,  Data::getValueOfGlobalDataPoint(int procNo, int dataPointNo)
                                 int sampleNo,  
                                                                 int dataPointNo)  
   
918  {  {
919      size_t length=0;    size_t length=0;
920      int i, j, k, l, pos;    int i, j, k, l, pos;
   
   //  
   // Check a valid sample number has been supplied  
   if (sampleNo >= getNumSamples()) {  
     throw DataException("Error - Data::convertToNumArray: invalid sampleNo.");  
   }  
   
   //  
   // Check a valid data point number has been supplied  
   if (dataPointNo >= getNumDataPointsPerSample()) {  
     throw DataException("Error - Data::convertToNumArray: invalid dataPointNo.");  
   }  
   
921    //    //
922    // determine the rank and shape of each data point    // determine the rank and shape of each data point
923    int dataPointRank = getDataPointRank();    int dataPointRank = getDataPointRank();
924    DataArrayView::ShapeType dataPointShape = getDataPointShape();    const DataTypes::ShapeType& dataPointShape = getDataPointShape();
925    
926    //    //
927    // create the numeric array to be returned    // create the numeric array to be returned
# Line 815  Data::convertToNumArrayFromDPNo(int proc Line 931  Data::convertToNumArrayFromDPNo(int proc
931    // the shape of the returned numeric array will be the same    // the shape of the returned numeric array will be the same
932    // as that of the data point    // as that of the data point
933    int arrayRank = dataPointRank;    int arrayRank = dataPointRank;
934    DataArrayView::ShapeType arrayShape = dataPointShape;    const DataTypes::ShapeType& arrayShape = dataPointShape;
935    
936    //    //
937    // resize the numeric array to the shape just calculated    // resize the numeric array to the shape just calculated
# Line 835  Data::convertToNumArrayFromDPNo(int proc Line 951  Data::convertToNumArrayFromDPNo(int proc
951      numArray.resize(arrayShape[0],arrayShape[1],arrayShape[2],arrayShape[3]);      numArray.resize(arrayShape[0],arrayShape[1],arrayShape[2],arrayShape[3]);
952    }    }
953    
954      // added for the MPI communication    // added for the MPI communication
955      length=1;    length=1;
956      for( i=0; i<arrayRank; i++ )    for( i=0; i<arrayRank; i++ ) length *= arrayShape[i];
957          length *= arrayShape[i];    double *tmpData = new double[length];
     double *tmpData = new double[length];  
958    
959    //    //
960    // load the values for the data point into the numeric array.    // load the values for the data point into the numeric array.
961    
962      // updated for the MPI case      // updated for the MPI case
963      if( get_MPIRank()==procNo ){      if( get_MPIRank()==procNo ){
964                 if (getNumDataPointsPerSample()>0) {
965                    int sampleNo = dataPointNo/getNumDataPointsPerSample();
966                    int dataPointNoInSample = dataPointNo - sampleNo * getNumDataPointsPerSample();
967                    //
968                    // Check a valid sample number has been supplied
969                    if ((sampleNo >= getNumSamples()) || (sampleNo < 0 )) {
970                      throw DataException("Error - Data::convertToNumArray: invalid sampleNo.");
971                    }
972    
973                    //
974                    // Check a valid data point number has been supplied
975                    if ((dataPointNoInSample >= getNumDataPointsPerSample()) || (dataPointNoInSample < 0)) {
976                      throw DataException("Error - Data::convertToNumArray: invalid dataPointNoInSample.");
977                    }
978                    // TODO: global error handling
979          // create a view of the data if it is stored locally          // create a view of the data if it is stored locally
980          DataArrayView dataPointView = getDataPoint(sampleNo, dataPointNo);          //DataArrayView dataPointView = getDataPoint(sampleNo, dataPointNoInSample);
981                    DataTypes::ValueType::size_type offset=getDataOffset(sampleNo, dataPointNoInSample);
982    
983          // pack the data from the view into tmpData for MPI communication          // pack the data from the view into tmpData for MPI communication
984          pos=0;          pos=0;
985          switch( dataPointRank ){          switch( dataPointRank ){
986              case 0 :              case 0 :
987                  tmpData[0] = dataPointView();                  tmpData[0] = getDataAtOffset(offset);
988                  break;                  break;
989              case 1 :                      case 1 :
990                  for( i=0; i<dataPointShape[0]; i++ )                  for( i=0; i<dataPointShape[0]; i++ )
991                      tmpData[i]=dataPointView(i);                      tmpData[i]=getDataAtOffset(offset+DataTypes::getRelIndex(dataPointShape, i));
992                  break;                  break;
993              case 2 :                      case 2 :
994                  for( i=0; i<dataPointShape[0]; i++ )                  for( i=0; i<dataPointShape[0]; i++ )
995                      for( j=0; j<dataPointShape[1]; j++, pos++ )                      for( j=0; j<dataPointShape[1]; j++, pos++ )
996                          tmpData[pos]=dataPointView(i,j);                          tmpData[pos]=getDataAtOffset(offset+DataTypes::getRelIndex(dataPointShape, i,j));
997                  break;                  break;
998              case 3 :                      case 3 :
999                  for( i=0; i<dataPointShape[0]; i++ )                  for( i=0; i<dataPointShape[0]; i++ )
1000                      for( j=0; j<dataPointShape[1]; j++ )                      for( j=0; j<dataPointShape[1]; j++ )
1001                          for( k=0; k<dataPointShape[2]; k++, pos++ )                          for( k=0; k<dataPointShape[2]; k++, pos++ )
1002                              tmpData[pos]=dataPointView(i,j,k);                              tmpData[pos]=getDataAtOffset(offset+DataTypes::getRelIndex(dataPointShape, i,j,k));
1003                  break;                  break;
1004              case 4 :              case 4 :
1005                  for( i=0; i<dataPointShape[0]; i++ )                  for( i=0; i<dataPointShape[0]; i++ )
1006                      for( j=0; j<dataPointShape[1]; j++ )                      for( j=0; j<dataPointShape[1]; j++ )
1007                          for( k=0; k<dataPointShape[2]; k++ )                          for( k=0; k<dataPointShape[2]; k++ )
1008                              for( l=0; l<dataPointShape[3]; l++, pos++ )                              for( l=0; l<dataPointShape[3]; l++, pos++ )
1009                                  tmpData[pos]=dataPointView(i,j,k,l);                                  tmpData[pos]=getDataAtOffset(offset+DataTypes::getRelIndex(dataPointShape, i,j,k,l));
1010                  break;                  break;
1011          }          }
1012                }
1013      }      }
1014  #ifdef PASO_MPI          #ifdef PASO_MPI
1015          // broadcast the data to all other processes          // broadcast the data to all other processes
1016          MPI_Bcast( tmpData, length, MPI_DOUBLE, procNo, get_MPIComm() );      MPI_Bcast( tmpData, length, MPI_DOUBLE, procNo, get_MPIComm() );
1017  #endif          #endif
1018    
1019      // unpack the data      // unpack the data
1020      switch( dataPointRank ){      switch( dataPointRank ){
1021          case 0 :          case 0 :
1022              numArray[i]=tmpData[0];              numArray[0]=tmpData[0];
1023              break;              break;
1024          case 1 :                  case 1 :
1025              for( i=0; i<dataPointShape[0]; i++ )              for( i=0; i<dataPointShape[0]; i++ )
1026                  numArray[i]=tmpData[i];                  numArray[i]=tmpData[i];
1027              break;              break;
1028          case 2 :                  case 2 :
1029              for( i=0; i<dataPointShape[0]; i++ )              for( i=0; i<dataPointShape[0]; i++ )
1030                  for( j=0; j<dataPointShape[1]; j++ )                  for( j=0; j<dataPointShape[1]; j++ )
1031                      tmpData[i+j*dataPointShape[0]];                     numArray[make_tuple(i,j)]=tmpData[i+j*dataPointShape[0]];
1032              break;              break;
1033          case 3 :                  case 3 :
1034              for( i=0; i<dataPointShape[0]; i++ )              for( i=0; i<dataPointShape[0]; i++ )
1035                  for( j=0; j<dataPointShape[1]; j++ )                  for( j=0; j<dataPointShape[1]; j++ )
1036                      for( k=0; k<dataPointShape[2]; k++ )                      for( k=0; k<dataPointShape[2]; k++ )
1037                          tmpData[i+dataPointShape[0]*(j*+k*dataPointShape[1])];                          numArray[make_tuple(i,j,k)]=tmpData[i+dataPointShape[0]*(j*+k*dataPointShape[1])];
1038              break;              break;
1039          case 4 :          case 4 :
1040              for( i=0; i<dataPointShape[0]; i++ )              for( i=0; i<dataPointShape[0]; i++ )
1041                  for( j=0; j<dataPointShape[1]; j++ )                  for( j=0; j<dataPointShape[1]; j++ )
1042                      for( k=0; k<dataPointShape[2]; k++ )                      for( k=0; k<dataPointShape[2]; k++ )
1043                          for( l=0; l<dataPointShape[3]; l++ )                          for( l=0; l<dataPointShape[3]; l++ )
1044                              tmpData[i+dataPointShape[0]*(j*+dataPointShape[1]*(k+l*dataPointShape[2]))];                                  numArray[make_tuple(i,j,k,l)]=tmpData[i+dataPointShape[0]*(j*+dataPointShape[1]*(k+l*dataPointShape[2]))];
1045              break;              break;
1046      }      }
1047    
1048      delete [] tmpData;        delete [] tmpData;
 /*  
   if (dataPointRank==0) {  
     numArray[0]=dataPointView();  
   }  
   if (dataPointRank==1) {  
     for (int i=0; i<dataPointShape[0]; i++) {  
       numArray[i]=dataPointView(i);  
     }  
   }  
   if (dataPointRank==2) {  
     for (int i=0; i<dataPointShape[0]; i++) {  
       for (int j=0; j<dataPointShape[1]; j++) {  
         numArray[i][j] = dataPointView(i,j);  
       }  
     }  
   }  
   if (dataPointRank==3) {  
     for (int i=0; i<dataPointShape[0]; i++) {  
       for (int j=0; j<dataPointShape[1]; j++) {  
         for (int k=0; k<dataPointShape[2]; k++) {  
           numArray[i][j][k]=dataPointView(i,j,k);  
         }  
       }  
     }  
   }  
   if (dataPointRank==4) {  
     for (int i=0; i<dataPointShape[0]; i++) {  
       for (int j=0; j<dataPointShape[1]; j++) {  
         for (int k=0; k<dataPointShape[2]; k++) {  
           for (int l=0; l<dataPointShape[3]; l++) {  
             numArray[i][j][k][l]=dataPointView(i,j,k,l);  
           }  
         }  
       }  
     }  
   }  
 */  
   
1049    //    //
1050    // return the loaded array    // return the loaded array
1051    return numArray;    return numArray;
1052  }  }
1053    
1054    
1055    
1056  boost::python::numeric::array  boost::python::numeric::array
1057  Data::integrate() const  Data::integrate() const
1058  {  {
1059    int index;    int index;
1060    int rank = getDataPointRank();    int rank = getDataPointRank();
1061    DataArrayView::ShapeType shape = getDataPointShape();    DataTypes::ShapeType shape = getDataPointShape();
1062      int dataPointSize = getDataPointSize();
 #if defined DOPROF  
   profData->integrate++;  
 #endif  
1063    
1064    //    //
1065    // calculate the integral values    // calculate the integral values
1066    vector<double> integrals(getDataPointSize());    vector<double> integrals(dataPointSize);
1067      vector<double> integrals_local(dataPointSize);
1068    #ifdef PASO_MPI
1069      AbstractContinuousDomain::asAbstractContinuousDomain(getDomain()).setToIntegrals(integrals_local,*this);
1070      // Global sum: use an array instead of a vector because elements of array are guaranteed to be contiguous in memory
1071      double *tmp = new double[dataPointSize];
1072      double *tmp_local = new double[dataPointSize];
1073      for (int i=0; i<dataPointSize; i++) { tmp_local[i] = integrals_local[i]; }
1074      MPI_Allreduce( &tmp_local[0], &tmp[0], dataPointSize, MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD );
1075      for (int i=0; i<dataPointSize; i++) { integrals[i] = tmp[i]; }
1076      delete[] tmp;
1077      delete[] tmp_local;
1078    #else
1079    AbstractContinuousDomain::asAbstractContinuousDomain(getDomain()).setToIntegrals(integrals,*this);    AbstractContinuousDomain::asAbstractContinuousDomain(getDomain()).setToIntegrals(integrals,*this);
1080    #endif
1081    
1082    //    //
1083    // create the numeric array to be returned    // create the numeric array to be returned
# Line 1031  Data::integrate() const Line 1137  Data::integrate() const
1137  Data  Data
1138  Data::sin() const  Data::sin() const
1139  {  {
1140  #if defined DOPROF    return C_TensorUnaryOperation<double (*)(double)>(*this, ::sin);
   profData->unary++;  
 #endif  
   return escript::unaryOp(*this,(Data::UnaryDFunPtr)::sin);  
1141  }  }
1142    
1143  Data  Data
1144  Data::cos() const  Data::cos() const
1145  {  {
1146  #if defined DOPROF    return C_TensorUnaryOperation<double (*)(double)>(*this, ::cos);
   profData->unary++;  
 #endif  
   return escript::unaryOp(*this,(Data::UnaryDFunPtr)::cos);  
1147  }  }
1148    
1149  Data  Data
1150  Data::tan() const  Data::tan() const
1151  {  {
1152  #if defined DOPROF    return C_TensorUnaryOperation<double (*)(double)>(*this, ::tan);
   profData->unary++;  
 #endif  
   return escript::unaryOp(*this,(Data::UnaryDFunPtr)::tan);  
1153  }  }
1154    
1155  Data  Data
1156  Data::asin() const  Data::asin() const
1157  {  {
1158  #if defined DOPROF    return C_TensorUnaryOperation<double (*)(double)>(*this, ::asin);
   profData->unary++;  
 #endif  
   return escript::unaryOp(*this,(Data::UnaryDFunPtr)::asin);  
1159  }  }
1160    
1161  Data  Data
1162  Data::acos() const  Data::acos() const
1163  {  {
1164  #if defined DOPROF    return C_TensorUnaryOperation<double (*)(double)>(*this, ::acos);
   profData->unary++;  
 #endif  
   return escript::unaryOp(*this,(Data::UnaryDFunPtr)::acos);  
1165  }  }
1166    
1167    
1168  Data  Data
1169  Data::atan() const  Data::atan() const
1170  {  {
1171  #if defined DOPROF    return C_TensorUnaryOperation<double (*)(double)>(*this, ::atan);
   profData->unary++;  
 #endif  
   return escript::unaryOp(*this,(Data::UnaryDFunPtr)::atan);  
1172  }  }
1173    
1174  Data  Data
1175  Data::sinh() const  Data::sinh() const
1176  {  {
1177  #if defined DOPROF      return C_TensorUnaryOperation<double (*)(double)>(*this, ::sinh);
1178    profData->unary++;  
 #endif  
   return escript::unaryOp(*this,(Data::UnaryDFunPtr)::sinh);  
1179  }  }
1180    
1181  Data  Data
1182  Data::cosh() const  Data::cosh() const
1183  {  {
1184  #if defined DOPROF      return C_TensorUnaryOperation<double (*)(double)>(*this, ::cosh);
   profData->unary++;  
 #endif  
   return escript::unaryOp(*this,(Data::UnaryDFunPtr)::cosh);  
1185  }  }
1186    
1187  Data  Data
1188  Data::tanh() const  Data::tanh() const
1189  {  {
1190  #if defined DOPROF      return C_TensorUnaryOperation<double (*)(double)>(*this, ::tanh);
1191    profData->unary++;  }
1192    
1193    
1194    Data
1195    Data::erf() const
1196    {
1197    #ifdef _WIN32
1198      throw DataException("Error - Data:: erf function is not supported on _WIN32 platforms.");
1199    #else
1200      return C_TensorUnaryOperation(*this, ::erf);
1201  #endif  #endif
   return escript::unaryOp(*this,(Data::UnaryDFunPtr)::tanh);  
1202  }  }
1203    
1204  Data  Data
1205  Data::asinh() const  Data::asinh() const
1206  {  {
1207  #if defined DOPROF  #ifdef _WIN32
1208    profData->unary++;    return C_TensorUnaryOperation(*this, escript::asinh_substitute);
1209    #else
1210      return C_TensorUnaryOperation(*this, ::asinh);
1211  #endif  #endif
   return escript::unaryOp(*this,(Data::UnaryDFunPtr)::asinh);  
1212  }  }
1213    
1214  Data  Data
1215  Data::acosh() const  Data::acosh() const
1216  {  {
1217  #if defined DOPROF  #ifdef _WIN32
1218    profData->unary++;    return C_TensorUnaryOperation(*this, escript::acosh_substitute);
1219    #else
1220      return C_TensorUnaryOperation(*this, ::acosh);
1221  #endif  #endif
   return escript::unaryOp(*this,(Data::UnaryDFunPtr)::acosh);  
1222  }  }
1223    
1224  Data  Data
1225  Data::atanh() const  Data::atanh() const
1226  {  {
1227  #if defined DOPROF  #ifdef _WIN32
1228    profData->unary++;    return C_TensorUnaryOperation(*this, escript::atanh_substitute);
1229    #else
1230      return C_TensorUnaryOperation(*this, ::atanh);
1231  #endif  #endif
   return escript::unaryOp(*this,(Data::UnaryDFunPtr)::atanh);  
1232  }  }
1233    
1234  Data  Data
1235  Data::log10() const  Data::log10() const
1236  {  {
1237  #if defined DOPROF    return C_TensorUnaryOperation<double (*)(double)>(*this, ::log10);
   profData->unary++;  
 #endif  
   return escript::unaryOp(*this,(Data::UnaryDFunPtr)::log10);  
1238  }  }
1239    
1240  Data  Data
1241  Data::log() const  Data::log() const
1242  {  {
1243  #if defined DOPROF    return C_TensorUnaryOperation<double (*)(double)>(*this, ::log);
   profData->unary++;  
 #endif  
   return escript::unaryOp(*this,(Data::UnaryDFunPtr)::log);  
1244  }  }
1245    
1246  Data  Data
1247  Data::sign() const  Data::sign() const
1248  {  {
1249  #if defined DOPROF    return C_TensorUnaryOperation(*this, escript::fsign);
   profData->unary++;  
 #endif  
   return escript::unaryOp(*this,escript::fsign);  
1250  }  }
1251    
1252  Data  Data
1253  Data::abs() const  Data::abs() const
1254  {  {
1255  #if defined DOPROF    return C_TensorUnaryOperation<double (*)(double)>(*this, ::fabs);
   profData->unary++;  
 #endif  
   return escript::unaryOp(*this,(Data::UnaryDFunPtr)::fabs);  
1256  }  }
1257    
1258  Data  Data
1259  Data::neg() const  Data::neg() const
1260  {  {
1261  #if defined DOPROF    return C_TensorUnaryOperation(*this, negate<double>());
   profData->unary++;  
 #endif  
   return escript::unaryOp(*this,negate<double>());  
1262  }  }
1263    
1264  Data  Data
1265  Data::pos() const  Data::pos() const
1266  {  {
 #if defined DOPROF  
   profData->unary++;  
 #endif  
1267    Data result;    Data result;
1268    // perform a deep copy    // perform a deep copy
1269    result.copy(*this);    result.copy(*this);
# Line 1196  Data::pos() const Line 1273  Data::pos() const
1273  Data  Data
1274  Data::exp() const  Data::exp() const
1275  {  {
1276  #if defined DOPROF    return C_TensorUnaryOperation<double (*)(double)>(*this, ::exp);
   profData->unary++;  
 #endif  
   return escript::unaryOp(*this,(Data::UnaryDFunPtr)::exp);  
1277  }  }
1278    
1279  Data  Data
1280  Data::sqrt() const  Data::sqrt() const
1281  {  {
1282  #if defined DOPROF    return C_TensorUnaryOperation<double (*)(double)>(*this, ::sqrt);
   profData->unary++;  
 #endif  
   return escript::unaryOp(*this,(Data::UnaryDFunPtr)::sqrt);  
1283  }  }
1284    
1285  double  double
1286  Data::Lsup() const  Data::Lsup() const
1287  {  {
1288    double localValue, globalValue;    double localValue;
 #if defined DOPROF  
   profData->reduction1++;  
 #endif  
1289    //    //
1290    // set the initial absolute maximum value to zero    // set the initial absolute maximum value to zero
1291    
1292    AbsMax abs_max_func;    AbsMax abs_max_func;
1293    localValue = algorithm(abs_max_func,0);    localValue = algorithm(abs_max_func,0);
1294  #ifdef PASO_MPI  #ifdef PASO_MPI
1295      double globalValue;
1296    MPI_Allreduce( &localValue, &globalValue, 1, MPI_DOUBLE, MPI_MAX, MPI_COMM_WORLD );    MPI_Allreduce( &localValue, &globalValue, 1, MPI_DOUBLE, MPI_MAX, MPI_COMM_WORLD );
1297    return globalValue;    return globalValue;
1298  #else  #else
# Line 1232  Data::Lsup() const Line 1301  Data::Lsup() const
1301  }  }
1302    
1303  double  double
 Data::Linf() const  
 {  
   double localValue, globalValue;  
 #if defined DOPROF  
   profData->reduction1++;  
 #endif  
   //  
   // set the initial absolute minimum value to max double  
   AbsMin abs_min_func;  
   localValue = algorithm(abs_min_func,numeric_limits<double>::max());  
   
 #ifdef PASO_MPI  
   MPI_Allreduce( &localValue, &globalValue, 1, MPI_DOUBLE, MPI_MIN, MPI_COMM_WORLD );  
   return globalValue;  
 #else  
   return localValue;  
 #endif  
 }  
   
 double  
1304  Data::sup() const  Data::sup() const
1305  {  {
1306    double localValue, globalValue;    double localValue;
 #if defined DOPROF  
   profData->reduction1++;  
 #endif  
1307    //    //
1308    // set the initial maximum value to min possible double    // set the initial maximum value to min possible double
1309    FMax fmax_func;    FMax fmax_func;
1310    localValue = algorithm(fmax_func,numeric_limits<double>::max()*-1);    localValue = algorithm(fmax_func,numeric_limits<double>::max()*-1);
1311  #ifdef PASO_MPI  #ifdef PASO_MPI
1312      double globalValue;
1313    MPI_Allreduce( &localValue, &globalValue, 1, MPI_DOUBLE, MPI_MAX, MPI_COMM_WORLD );    MPI_Allreduce( &localValue, &globalValue, 1, MPI_DOUBLE, MPI_MAX, MPI_COMM_WORLD );
1314    return globalValue;    return globalValue;
1315  #else  #else
# Line 1273  Data::sup() const Line 1320  Data::sup() const
1320  double  double
1321  Data::inf() const  Data::inf() const
1322  {  {
1323    double localValue, globalValue;    double localValue;
 #if defined DOPROF  
   profData->reduction1++;  
 #endif  
1324    //    //
1325    // set the initial minimum value to max possible double    // set the initial minimum value to max possible double
1326    FMin fmin_func;    FMin fmin_func;
1327    localValue = algorithm(fmin_func,numeric_limits<double>::max());    localValue = algorithm(fmin_func,numeric_limits<double>::max());
1328  #ifdef PASO_MPI  #ifdef PASO_MPI
1329      double globalValue;
1330    MPI_Allreduce( &localValue, &globalValue, 1, MPI_DOUBLE, MPI_MIN, MPI_COMM_WORLD );    MPI_Allreduce( &localValue, &globalValue, 1, MPI_DOUBLE, MPI_MIN, MPI_COMM_WORLD );
1331    return globalValue;    return globalValue;
1332  #else  #else
# Line 1294  Data::inf() const Line 1339  Data::inf() const
1339  Data  Data
1340  Data::maxval() const  Data::maxval() const
1341  {  {
 #if defined DOPROF  
   profData->reduction2++;  
 #endif  
1342    //    //
1343    // set the initial maximum value to min possible double    // set the initial maximum value to min possible double
1344    FMax fmax_func;    FMax fmax_func;
# Line 1306  Data::maxval() const Line 1348  Data::maxval() const
1348  Data  Data
1349  Data::minval() const  Data::minval() const
1350  {  {
 #if defined DOPROF  
   profData->reduction2++;  
 #endif  
1351    //    //
1352    // set the initial minimum value to max possible double    // set the initial minimum value to max possible double
1353    FMin fmin_func;    FMin fmin_func;
# Line 1316  Data::minval() const Line 1355  Data::minval() const
1355  }  }
1356    
1357  Data  Data
1358  Data::trace() const  Data::swapaxes(const int axis0, const int axis1) const
1359  {  {
1360  #if defined DOPROF       int axis0_tmp,axis1_tmp;
1361    profData->reduction2++;       DataTypes::ShapeType s=getDataPointShape();
1362  #endif       DataTypes::ShapeType ev_shape;
1363    Trace trace_func;       // Here's the equivalent of python s_out=s[axis_offset:]+s[:axis_offset]
1364    return dp_algorithm(trace_func,0);       // which goes thru all shape vector elements starting with axis_offset (at index=rank wrap around to 0)
1365         int rank=getDataPointRank();
1366         if (rank<2) {
1367            throw DataException("Error - Data::swapaxes argument must have at least rank 2.");
1368         }
1369         if (axis0<0 || axis0>rank-1) {
1370            throw DataException("Error - Data::swapaxes: axis0 must be between 0 and rank-1=" + rank-1);
1371         }
1372         if (axis1<0 || axis1>rank-1) {
1373             throw DataException("Error - Data::swapaxes: axis1 must be between 0 and rank-1=" + rank-1);
1374         }
1375         if (axis0 == axis1) {
1376             throw DataException("Error - Data::swapaxes: axis indices must be different.");
1377         }
1378         if (axis0 > axis1) {
1379             axis0_tmp=axis1;
1380             axis1_tmp=axis0;
1381         } else {
1382             axis0_tmp=axis0;
1383             axis1_tmp=axis1;
1384         }
1385         for (int i=0; i<rank; i++) {
1386           if (i == axis0_tmp) {
1387              ev_shape.push_back(s[axis1_tmp]);
1388           } else if (i == axis1_tmp) {
1389              ev_shape.push_back(s[axis0_tmp]);
1390           } else {
1391              ev_shape.push_back(s[i]);
1392           }
1393         }
1394         Data ev(0.,ev_shape,getFunctionSpace());
1395         ev.typeMatchRight(*this);
1396         m_data->swapaxes(ev.m_data.get(), axis0_tmp, axis1_tmp);
1397         return ev;
1398    
1399  }  }
1400    
1401  Data  Data
1402  Data::symmetric() const  Data::symmetric() const
1403  {  {
      #if defined DOPROF  
         profData->unary++;  
      #endif  
1404       // check input       // check input
1405       DataArrayView::ShapeType s=getDataPointShape();       DataTypes::ShapeType s=getDataPointShape();
1406       if (getDataPointRank()==2) {       if (getDataPointRank()==2) {
1407          if(s[0] != s[1])          if(s[0] != s[1])
1408             throw DataException("Error - Data::symmetric can only be calculated for rank 2 object with equal first and second dimension.");             throw DataException("Error - Data::symmetric can only be calculated for rank 2 object with equal first and second dimension.");
1409       }       }
1410       else if (getDataPointRank()==4) {       else if (getDataPointRank()==4) {
# Line 1353  Data::symmetric() const Line 1423  Data::symmetric() const
1423  Data  Data
1424  Data::nonsymmetric() const  Data::nonsymmetric() const
1425  {  {
      #if defined DOPROF  
         profData->unary++;  
      #endif  
1426       // check input       // check input
1427       DataArrayView::ShapeType s=getDataPointShape();       DataTypes::ShapeType s=getDataPointShape();
1428       if (getDataPointRank()==2) {       if (getDataPointRank()==2) {
1429          if(s[0] != s[1])          if(s[0] != s[1])
1430             throw DataException("Error - Data::nonsymmetric can only be calculated for rank 2 object with equal first and second dimension.");             throw DataException("Error - Data::nonsymmetric can only be calculated for rank 2 object with equal first and second dimension.");
1431          DataArrayView::ShapeType ev_shape;          DataTypes::ShapeType ev_shape;
1432          ev_shape.push_back(s[0]);          ev_shape.push_back(s[0]);
1433          ev_shape.push_back(s[1]);          ev_shape.push_back(s[1]);
1434          Data ev(0.,ev_shape,getFunctionSpace());          Data ev(0.,ev_shape,getFunctionSpace());
# Line 1372  Data::nonsymmetric() const Line 1439  Data::nonsymmetric() const
1439       else if (getDataPointRank()==4) {       else if (getDataPointRank()==4) {
1440          if(!(s[0] == s[2] && s[1] == s[3]))          if(!(s[0] == s[2] && s[1] == s[3]))
1441             throw DataException("Error - Data::nonsymmetric can only be calculated for rank 4 object with dim0==dim2 and dim1==dim3.");             throw DataException("Error - Data::nonsymmetric can only be calculated for rank 4 object with dim0==dim2 and dim1==dim3.");
1442          DataArrayView::ShapeType ev_shape;          DataTypes::ShapeType ev_shape;
1443          ev_shape.push_back(s[0]);          ev_shape.push_back(s[0]);
1444          ev_shape.push_back(s[1]);          ev_shape.push_back(s[1]);
1445          ev_shape.push_back(s[2]);          ev_shape.push_back(s[2]);
# Line 1388  Data::nonsymmetric() const Line 1455  Data::nonsymmetric() const
1455  }  }
1456    
1457  Data  Data
1458  Data::matrixtrace(int axis_offset) const  Data::trace(int axis_offset) const
1459  {  {
1460       #if defined DOPROF       DataTypes::ShapeType s=getDataPointShape();
         profData->unary++;  
      #endif  
      DataArrayView::ShapeType s=getDataPointShape();  
1461       if (getDataPointRank()==2) {       if (getDataPointRank()==2) {
1462          DataArrayView::ShapeType ev_shape;          DataTypes::ShapeType ev_shape;
1463          Data ev(0.,ev_shape,getFunctionSpace());          Data ev(0.,ev_shape,getFunctionSpace());
1464          ev.typeMatchRight(*this);          ev.typeMatchRight(*this);
1465          m_data->matrixtrace(ev.m_data.get(), axis_offset);          m_data->trace(ev.m_data.get(), axis_offset);
1466          return ev;          return ev;
1467       }       }
1468       if (getDataPointRank()==3) {       if (getDataPointRank()==3) {
1469          DataArrayView::ShapeType ev_shape;          DataTypes::ShapeType ev_shape;
1470          if (axis_offset==0) {          if (axis_offset==0) {
1471            int s2=s[2];            int s2=s[2];
1472            ev_shape.push_back(s2);            ev_shape.push_back(s2);
# Line 1413  Data::matrixtrace(int axis_offset) const Line 1477  Data::matrixtrace(int axis_offset) const
1477          }          }
1478          Data ev(0.,ev_shape,getFunctionSpace());          Data ev(0.,ev_shape,getFunctionSpace());
1479          ev.typeMatchRight(*this);          ev.typeMatchRight(*this);
1480          m_data->matrixtrace(ev.m_data.get(), axis_offset);          m_data->trace(ev.m_data.get(), axis_offset);
1481          return ev;          return ev;
1482       }       }
1483       if (getDataPointRank()==4) {       if (getDataPointRank()==4) {
1484          DataArrayView::ShapeType ev_shape;          DataTypes::ShapeType ev_shape;
1485          if (axis_offset==0) {          if (axis_offset==0) {
1486            ev_shape.push_back(s[2]);            ev_shape.push_back(s[2]);
1487            ev_shape.push_back(s[3]);            ev_shape.push_back(s[3]);
# Line 1432  Data::matrixtrace(int axis_offset) const Line 1496  Data::matrixtrace(int axis_offset) const
1496      }      }
1497          Data ev(0.,ev_shape,getFunctionSpace());          Data ev(0.,ev_shape,getFunctionSpace());
1498          ev.typeMatchRight(*this);          ev.typeMatchRight(*this);
1499      m_data->matrixtrace(ev.m_data.get(), axis_offset);      m_data->trace(ev.m_data.get(), axis_offset);
1500          return ev;          return ev;
1501       }       }
1502       else {       else {
1503          throw DataException("Error - Data::matrixtrace can only be calculated for rank 2, 3 or 4 object.");          throw DataException("Error - Data::trace can only be calculated for rank 2, 3 or 4 object.");
1504       }       }
1505  }  }
1506    
1507  Data  Data
1508  Data::transpose(int axis_offset) const  Data::transpose(int axis_offset) const
1509  {  {
1510  #if defined DOPROF       DataTypes::ShapeType s=getDataPointShape();
1511       profData->reduction2++;       DataTypes::ShapeType ev_shape;
 #endif  
      DataArrayView::ShapeType s=getDataPointShape();  
      DataArrayView::ShapeType ev_shape;  
1512       // Here's the equivalent of python s_out=s[axis_offset:]+s[:axis_offset]       // Here's the equivalent of python s_out=s[axis_offset:]+s[:axis_offset]
1513       // which goes thru all shape vector elements starting with axis_offset (at index=rank wrap around to 0)       // which goes thru all shape vector elements starting with axis_offset (at index=rank wrap around to 0)
1514       int rank=getDataPointRank();       int rank=getDataPointRank();
# Line 1467  Data::transpose(int axis_offset) const Line 1528  Data::transpose(int axis_offset) const
1528  Data  Data
1529  Data::eigenvalues() const  Data::eigenvalues() const
1530  {  {
      #if defined DOPROF  
         profData->unary++;  
      #endif  
1531       // check input       // check input
1532       DataArrayView::ShapeType s=getDataPointShape();       DataTypes::ShapeType s=getDataPointShape();
1533       if (getDataPointRank()!=2)       if (getDataPointRank()!=2)
1534          throw DataException("Error - Data::eigenvalues can only be calculated for rank 2 object.");          throw DataException("Error - Data::eigenvalues can only be calculated for rank 2 object.");
1535       if(s[0] != s[1])       if(s[0] != s[1])
1536          throw DataException("Error - Data::eigenvalues can only be calculated for object with equal first and second dimension.");          throw DataException("Error - Data::eigenvalues can only be calculated for object with equal first and second dimension.");
1537       // create return       // create return
1538       DataArrayView::ShapeType ev_shape(1,s[0]);       DataTypes::ShapeType ev_shape(1,s[0]);
1539       Data ev(0.,ev_shape,getFunctionSpace());       Data ev(0.,ev_shape,getFunctionSpace());
1540       ev.typeMatchRight(*this);       ev.typeMatchRight(*this);
1541       m_data->eigenvalues(ev.m_data.get());       m_data->eigenvalues(ev.m_data.get());
# Line 1487  Data::eigenvalues() const Line 1545  Data::eigenvalues() const
1545  const boost::python::tuple  const boost::python::tuple
1546  Data::eigenvalues_and_eigenvectors(const double tol) const  Data::eigenvalues_and_eigenvectors(const double tol) const
1547  {  {
1548       #if defined DOPROF       DataTypes::ShapeType s=getDataPointShape();
1549          profData->unary++;       if (getDataPointRank()!=2)
      #endif  
      DataArrayView::ShapeType s=getDataPointShape();  
      if (getDataPointRank()!=2)  
1550          throw DataException("Error - Data::eigenvalues and eigenvectors can only be calculated for rank 2 object.");          throw DataException("Error - Data::eigenvalues and eigenvectors can only be calculated for rank 2 object.");
1551       if(s[0] != s[1])       if(s[0] != s[1])
1552          throw DataException("Error - Data::eigenvalues and eigenvectors can only be calculated for object with equal first and second dimension.");          throw DataException("Error - Data::eigenvalues and eigenvectors can only be calculated for object with equal first and second dimension.");
1553       // create return       // create return
1554       DataArrayView::ShapeType ev_shape(1,s[0]);       DataTypes::ShapeType ev_shape(1,s[0]);
1555       Data ev(0.,ev_shape,getFunctionSpace());       Data ev(0.,ev_shape,getFunctionSpace());
1556       ev.typeMatchRight(*this);       ev.typeMatchRight(*this);
1557       DataArrayView::ShapeType V_shape(2,s[0]);       DataTypes::ShapeType V_shape(2,s[0]);
1558       Data V(0.,V_shape,getFunctionSpace());       Data V(0.,V_shape,getFunctionSpace());
1559       V.typeMatchRight(*this);       V.typeMatchRight(*this);
1560       m_data->eigenvalues_and_eigenvectors(ev.m_data.get(),V.m_data.get(),tol);       m_data->eigenvalues_and_eigenvectors(ev.m_data.get(),V.m_data.get(),tol);
# Line 1507  Data::eigenvalues_and_eigenvectors(const Line 1562  Data::eigenvalues_and_eigenvectors(const
1562  }  }
1563    
1564  const boost::python::tuple  const boost::python::tuple
1565  Data::mindp() const  Data::minGlobalDataPoint() const
1566  {  {
1567    // NB: calc_mindp had to be split off from mindp as boost::make_tuple causes an    // NB: calc_minGlobalDataPoint( had to be split off from minGlobalDataPoint( as boost::make_tuple causes an
1568    // abort (for unknown reasons) if there are openmp directives with it in the    // abort (for unknown reasons) if there are openmp directives with it in the
1569    // surrounding function    // surrounding function
1570    
   int SampleNo;  
1571    int DataPointNo;    int DataPointNo;
1572      int ProcNo;    int ProcNo;
1573    calc_mindp(ProcNo,SampleNo,DataPointNo);    calc_minGlobalDataPoint(ProcNo,DataPointNo);
1574    return make_tuple(ProcNo,SampleNo,DataPointNo);    return make_tuple(ProcNo,DataPointNo);
1575  }  }
1576    
1577  void  void
1578  Data::calc_mindp(   int& ProcNo,  Data::calc_minGlobalDataPoint(int& ProcNo,
1579                  int& SampleNo,                          int& DataPointNo) const
         int& DataPointNo) const  
1580  {  {
1581    int i,j;    int i,j;
1582    int lowi=0,lowj=0;    int lowi=0,lowj=0;
# Line 1543  Data::calc_mindp(  int& ProcNo, Line 1596  Data::calc_mindp(  int& ProcNo,
1596      #pragma omp for private(i,j) schedule(static)      #pragma omp for private(i,j) schedule(static)
1597      for (i=0; i<numSamples; i++) {      for (i=0; i<numSamples; i++) {
1598        for (j=0; j<numDPPSample; j++) {        for (j=0; j<numDPPSample; j++) {
1599          next=temp.getDataPoint(i,j)();          next=temp.getDataAtOffset(temp.getDataOffset(i,j));
1600          if (next<local_min) {          if (next<local_min) {
1601            local_min=next;            local_min=next;
1602            local_lowi=i;            local_lowi=i;
# Line 1561  Data::calc_mindp(  int& ProcNo, Line 1614  Data::calc_mindp(  int& ProcNo,
1614    
1615  #ifdef PASO_MPI  #ifdef PASO_MPI
1616      // determine the processor on which the minimum occurs      // determine the processor on which the minimum occurs
1617      next = temp.getDataPoint(lowi,lowj)();      next = temp.getDataPoint(lowi,lowj);
1618      int lowProc = 0;      int lowProc = 0;
1619      double *globalMins = new double[get_MPISize()+1];      double *globalMins = new double[get_MPISize()+1];
1620      int error = MPI_Gather ( &next, 1, MPI_DOUBLE, globalMins, 1, MPI_DOUBLE, 0, get_MPIComm() );      int error = MPI_Gather ( &next, 1, MPI_DOUBLE, globalMins, 1, MPI_DOUBLE, 0, get_MPIComm() );
1621        
1622      if( get_MPIRank()==0 ){      if( get_MPIRank()==0 ){
1623          next = globalMins[lowProc];          next = globalMins[lowProc];
1624          for( i=1; i<get_MPISize(); i++ )          for( i=1; i<get_MPISize(); i++ )
# Line 1581  Data::calc_mindp(  int& ProcNo, Line 1634  Data::calc_mindp(  int& ProcNo,
1634  #else  #else
1635      ProcNo = 0;      ProcNo = 0;
1636  #endif  #endif
1637    SampleNo = lowi;    DataPointNo = lowj + lowi * numDPPSample;
   DataPointNo = lowj;  
1638  }  }
1639    
1640  void  void
1641  Data::saveDX(std::string fileName) const  Data::saveDX(std::string fileName) const
1642  {  {
1643      if (isEmpty())
1644      {
1645        throw DataException("Error - Operations not permitted on instances of DataEmpty.");
1646      }
1647    boost::python::dict args;    boost::python::dict args;
1648    args["data"]=boost::python::object(this);    args["data"]=boost::python::object(this);
1649    getDomain().saveDX(fileName,args);    getDomain().saveDX(fileName,args);
# Line 1597  Data::saveDX(std::string fileName) const Line 1653  Data::saveDX(std::string fileName) const
1653  void  void
1654  Data::saveVTK(std::string fileName) const  Data::saveVTK(std::string fileName) const
1655  {  {
1656      if (isEmpty())
1657      {
1658        throw DataException("Error - Operations not permitted on instances of DataEmpty.");
1659      }
1660    boost::python::dict args;    boost::python::dict args;
1661    args["data"]=boost::python::object(this);    args["data"]=boost::python::object(this);
1662    getDomain().saveVTK(fileName,args);    getDomain().saveVTK(fileName,args);
# Line 1609  Data::operator+=(const Data& right) Line 1669  Data::operator+=(const Data& right)
1669    if (isProtected()) {    if (isProtected()) {
1670          throw DataException("Error - attempt to update protected Data object.");          throw DataException("Error - attempt to update protected Data object.");
1671    }    }
 #if defined DOPROF  
   profData->binary++;  
 #endif  
1672    binaryOp(right,plus<double>());    binaryOp(right,plus<double>());
1673    return (*this);    return (*this);
1674  }  }
# Line 1619  Data::operator+=(const Data& right) Line 1676  Data::operator+=(const Data& right)
1676  Data&  Data&
1677  Data::operator+=(const boost::python::object& right)  Data::operator+=(const boost::python::object& right)
1678  {  {
1679    if (isProtected()) {    Data tmp(right,getFunctionSpace(),false);
1680          throw DataException("Error - attempt to update protected Data object.");    binaryOp(tmp,plus<double>());
1681    }    return (*this);
1682  #if defined DOPROF  }
1683    profData->binary++;  Data&
1684  #endif  Data::operator=(const Data& other)
1685    binaryOp(right,plus<double>());  {
1686      copy(other);
1687    return (*this);    return (*this);
1688  }  }
1689    
# Line 1635  Data::operator-=(const Data& right) Line 1693  Data::operator-=(const Data& right)
1693    if (isProtected()) {    if (isProtected()) {
1694          throw DataException("Error - attempt to update protected Data object.");          throw DataException("Error - attempt to update protected Data object.");
1695    }    }
 #if defined DOPROF  
   profData->binary++;  
 #endif  
1696    binaryOp(right,minus<double>());    binaryOp(right,minus<double>());
1697    return (*this);    return (*this);
1698  }  }
# Line 1645  Data::operator-=(const Data& right) Line 1700  Data::operator-=(const Data& right)
1700  Data&  Data&
1701  Data::operator-=(const boost::python::object& right)  Data::operator-=(const boost::python::object& right)
1702  {  {
1703    if (isProtected()) {    Data tmp(right,getFunctionSpace(),false);
1704          throw DataException("Error - attempt to update protected Data object.");    binaryOp(tmp,minus<double>());
   }  
 #if defined DOPROF  
   profData->binary++;  
 #endif  
   binaryOp(right,minus<double>());  
1705    return (*this);    return (*this);
1706  }  }
1707    
# Line 1661  Data::operator*=(const Data& right) Line 1711  Data::operator*=(const Data& right)
1711    if (isProtected()) {    if (isProtected()) {
1712          throw DataException("Error - attempt to update protected Data object.");          throw DataException("Error - attempt to update protected Data object.");
1713    }    }
 #if defined DOPROF  
   profData->binary++;  
 #endif  
1714    binaryOp(right,multiplies<double>());    binaryOp(right,multiplies<double>());
1715    return (*this);    return (*this);
1716  }  }
# Line 1671  Data::operator*=(const Data& right) Line 1718  Data::operator*=(const Data& right)
1718  Data&  Data&
1719  Data::operator*=(const boost::python::object& right)  Data::operator*=(const boost::python::object& right)
1720  {  {
1721    if (isProtected()) {    Data tmp(right,getFunctionSpace(),false);
1722          throw DataException("Error - attempt to update protected Data object.");    binaryOp(tmp,multiplies<double>());
   }  
 #if defined DOPROF  
   profData->binary++;  
 #endif  
   binaryOp(right,multiplies<double>());  
1723    return (*this);    return (*this);
1724  }  }
1725    
# Line 1687  Data::operator/=(const Data& right) Line 1729  Data::operator/=(const Data& right)
1729    if (isProtected()) {    if (isProtected()) {
1730          throw DataException("Error - attempt to update protected Data object.");          throw DataException("Error - attempt to update protected Data object.");
1731    }    }
 #if defined DOPROF  
   profData->binary++;  
 #endif  
1732    binaryOp(right,divides<double>());    binaryOp(right,divides<double>());
1733    return (*this);    return (*this);
1734  }  }
# Line 1697  Data::operator/=(const Data& right) Line 1736  Data::operator/=(const Data& right)
1736  Data&  Data&
1737  Data::operator/=(const boost::python::object& right)  Data::operator/=(const boost::python::object& right)
1738  {  {
1739    if (isProtected()) {    Data tmp(right,getFunctionSpace(),false);
1740          throw DataException("Error - attempt to update protected Data object.");    binaryOp(tmp,divides<double>());
   }  
 #if defined DOPROF  
   profData->binary++;  
 #endif  
   binaryOp(right,divides<double>());  
1741    return (*this);    return (*this);
1742  }  }
1743    
1744  Data  Data
1745  Data::rpowO(const boost::python::object& left) const  Data::rpowO(const boost::python::object& left) const
1746  {  {
   if (isProtected()) {  
         throw DataException("Error - attempt to update protected Data object.");  
   }  
 #if defined DOPROF  
   profData->binary++;  
 #endif  
1747    Data left_d(left,*this);    Data left_d(left,*this);
1748    return left_d.powD(*this);    return left_d.powD(*this);
1749  }  }
# Line 1723  Data::rpowO(const boost::python::object& Line 1751  Data::rpowO(const boost::python::object&
1751  Data  Data
1752  Data::powO(const boost::python::object& right) const  Data::powO(const boost::python::object& right) const
1753  {  {
1754  #if defined DOPROF    Data tmp(right,getFunctionSpace(),false);
1755    profData->binary++;    return powD(tmp);
 #endif  
   Data result;  
   result.copy(*this);  
   result.binaryOp(right,(Data::BinaryDFunPtr)::pow);  
   return result;  
1756  }  }
1757    
1758  Data  Data
1759  Data::powD(const Data& right) const  Data::powD(const Data& right) const
1760  {  {
1761  #if defined DOPROF    return C_TensorBinaryOperation<double (*)(double, double)>(*this, right, ::pow);
   profData->binary++;  
 #endif  
   Data result;  
   result.copy(*this);  
   result.binaryOp(right,(Data::BinaryDFunPtr)::pow);  
   return result;  
1762  }  }
1763    
   
1764  //  //
1765  // NOTE: It is essential to specify the namespace this operator belongs to  // NOTE: It is essential to specify the namespace this operator belongs to
1766  Data  Data
1767  escript::operator+(const Data& left, const Data& right)  escript::operator+(const Data& left, const Data& right)
1768  {  {
1769    Data result;    return C_TensorBinaryOperation(left, right, plus<double>());
   //  
   // perform a deep copy  
   result.copy(left);  
   result+=right;  
   return result;  
1770  }  }
1771    
1772  //  //
# Line 1763  escript::operator+(const Data& left, con Line 1774  escript::operator+(const Data& left, con
1774  Data  Data
1775  escript::operator-(const Data& left, const Data& right)  escript::operator-(const Data& left, const Data& right)
1776  {  {
1777    Data result;    return C_TensorBinaryOperation(left, right, minus<double>());
   //  
   // perform a deep copy  
   result.copy(left);  
   result-=right;  
   return result;  
1778  }  }
1779    
1780  //  //
# Line 1776  escript::operator-(const Data& left, con Line 1782  escript::operator-(const Data& left, con
1782  Data  Data
1783  escript::operator*(const Data& left, const Data& right)  escript::operator*(const Data& left, const Data& right)
1784  {  {
1785    Data result;    return C_TensorBinaryOperation(left, right, multiplies<double>());
   //  
   // perform a deep copy  
   result.copy(left);  
   result*=right;  
   return result;  
1786  }  }
1787    
1788  //  //
# Line 1789  escript::operator*(const Data& left, con Line 1790  escript::operator*(const Data& left, con
1790  Data  Data
1791  escript::operator/(const Data& left, const Data& right)  escript::operator/(const Data& left, const Data& right)
1792  {  {
1793    Data result;    return C_TensorBinaryOperation(left, right, divides<double>());
   //  
   // perform a deep copy  
   result.copy(left);  
   result/=right;  
   return result;  
1794  }  }
1795    
1796  //  //
# Line 1802  escript::operator/(const Data& left, con Line 1798  escript::operator/(const Data& left, con
1798  Data  Data
1799  escript::operator+(const Data& left, const boost::python::object& right)  escript::operator+(const Data& left, const boost::python::object& right)
1800  {  {
1801    //    return left+Data(right,left.getFunctionSpace(),false);
   // Convert to DataArray format if possible  
   DataArray temp(right);  
   Data result;  
   //  
   // perform a deep copy  
   result.copy(left);  
   result+=right;  
   return result;  
1802  }  }
1803    
1804  //  //
# Line 1818  escript::operator+(const Data& left, con Line 1806  escript::operator+(const Data& left, con
1806  Data  Data
1807  escript::operator-(const Data& left, const boost::python::object& right)  escript::operator-(const Data& left, const boost::python::object& right)
1808  {  {
1809    //    return left-Data(right,left.getFunctionSpace(),false);
   // Convert to DataArray format if possible  
   DataArray temp(right);  
   Data result;  
   //  
   // perform a deep copy  
   result.copy(left);  
   result-=right;  
   return result;  
1810  }  }
1811    
1812  //  //
# Line 1834  escript::operator-(const Data& left, con Line 1814  escript::operator-(const Data& left, con
1814  Data  Data
1815  escript::operator*(const Data& left, const boost::python::object& right)  escript::operator*(const Data& left, const boost::python::object& right)
1816  {  {
1817    //    return left*Data(right,left.getFunctionSpace(),false);
   // Convert to DataArray format if possible  
   DataArray temp(right);  
   Data result;  
   //  
   // perform a deep copy  
   result.copy(left);  
   result*=right;  
   return result;  
1818  }  }
1819    
1820  //  //
# Line 1850  escript::operator*(const Data& left, con Line 1822  escript::operator*(const Data& left, con
1822  Data  Data
1823  escript::operator/(const Data& left, const boost::python::object& right)  escript::operator/(const Data& left, const boost::python::object& right)
1824  {  {
1825    //    return left/Data(right,left.getFunctionSpace(),false);
   // Convert to DataArray format if possible  
   DataArray temp(right);  
   Data result;  
   //  
   // perform a deep copy  
   result.copy(left);  
   result/=right;  
   return result;  
1826  }  }
1827    
1828  //  //
# Line 1866  escript::operator/(const Data& left, con Line 1830  escript::operator/(const Data& left, con
1830  Data  Data
1831  escript::operator+(const boost::python::object& left, const Data& right)  escript::operator+(const boost::python::object& left, const Data& right)
1832  {  {
1833    //    return Data(left,right.getFunctionSpace(),false)+right;
   // Construct the result using the given value and the other parameters  
   // from right  
   Data result(left,right);  
   result+=right;  
   return result;  
1834  }  }
1835    
1836  //  //
# Line 1879  escript::operator+(const boost::python:: Line 1838  escript::operator+(const boost::python::
1838  Data  Data
1839  escript::operator-(const boost::python::object& left, const Data& right)  escript::operator-(const boost::python::object& left, const Data& right)
1840  {  {
1841    //    return Data(left,right.getFunctionSpace(),false)-right;
   // Construct the result using the given value and the other parameters  
   // from right  
   Data result(left,right);  
   result-=right;  
   return result;  
1842  }  }
1843    
1844  //  //
# Line 1892  escript::operator-(const boost::python:: Line 1846  escript::operator-(const boost::python::
1846  Data  Data
1847  escript::operator*(const boost::python::object& left, const Data& right)  escript::operator*(const boost::python::object& left, const Data& right)
1848  {  {
1849    //    return Data(left,right.getFunctionSpace(),false)*right;
   // Construct the result using the given value and the other parameters  
   // from right  
   Data result(left,right);  
   result*=right;  
   return result;  
1850  }  }
1851    
1852  //  //
# Line 1905  escript::operator*(const boost::python:: Line 1854  escript::operator*(const boost::python::
1854  Data  Data
1855  escript::operator/(const boost::python::object& left, const Data& right)  escript::operator/(const boost::python::object& left, const Data& right)
1856  {  {
1857    //    return Data(left,right.getFunctionSpace(),false)/right;
   // Construct the result using the given value and the other parameters  
   // from right  
   Data result(left,right);  
   result/=right;  
   return result;  
1858  }  }
1859    
1860  //  //
# Line 1961  escript::operator/(const boost::python:: Line 1905  escript::operator/(const boost::python::
1905  /* TODO */  /* TODO */
1906  /* global reduction */  /* global reduction */
1907  Data  Data
1908  Data::getItem(const boost::python::object& key) const  Data::getItem(const boost::python::object& key) const
1909  {  {
1910    const DataArrayView& view=getPointDataView();  //  const DataArrayView& view=getPointDataView();
1911    
1912    DataArrayView::RegionType slice_region=view.getSliceRegion(key);    DataTypes::RegionType slice_region=DataTypes::getSliceRegion(getDataPointShape(),key);
1913    
1914    if (slice_region.size()!=view.getRank()) {    if (slice_region.size()!=getDataPointRank()) {
1915      throw DataException("Error - slice size does not match Data rank.");      throw DataException("Error - slice size does not match Data rank.");
1916    }    }
1917    
# Line 1977  Data::getItem(const boost::python::objec Line 1921  Data::getItem(const boost::python::objec
1921  /* TODO */  /* TODO */
1922  /* global reduction */  /* global reduction */
1923  Data  Data
1924  Data::getSlice(const DataArrayView::RegionType& region) const  Data::getSlice(const DataTypes::RegionType& region) const
1925  {  {
 #if defined DOPROF  
   profData->slicing++;  
 #endif  
1926    return Data(*this,region);    return Data(*this,region);
1927  }  }
1928    
# Line 1995  Data::setItemO(const boost::python::obje Line 1936  Data::setItemO(const boost::python::obje
1936    setItemD(key,tempData);    setItemD(key,tempData);
1937  }  }
1938    
 /* TODO */  
 /* global reduction */  
1939  void  void
1940  Data::setItemD(const boost::python::object& key,  Data::setItemD(const boost::python::object& key,
1941                 const Data& value)                 const Data& value)
1942  {  {
1943    const DataArrayView& view=getPointDataView();  //  const DataArrayView& view=getPointDataView();
1944    
1945    DataArrayView::RegionType slice_region=view.getSliceRegion(key);    DataTypes::RegionType slice_region=DataTypes::getSliceRegion(getDataPointShape(),key);
1946    if (slice_region.size()!=view.getRank()) {    if (slice_region.size()!=getDataPointRank()) {
1947      throw DataException("Error - slice size does not match Data rank.");      throw DataException("Error - slice size does not match Data rank.");
1948    }    }
1949    if (getFunctionSpace()!=value.getFunctionSpace()) {    if (getFunctionSpace()!=value.getFunctionSpace()) {
# Line 2014  Data::setItemD(const boost::python::obje Line 1953  Data::setItemD(const boost::python::obje
1953    }    }
1954  }  }
1955    
 /* TODO */  
 /* global reduction */  
1956  void  void
1957  Data::setSlice(const Data& value,  Data::setSlice(const Data& value,
1958                 const DataArrayView::RegionType& region)                 const DataTypes::RegionType& region)
1959  {  {
1960    if (isProtected()) {    if (isProtected()) {
1961          throw DataException("Error - attempt to update protected Data object.");          throw DataException("Error - attempt to update protected Data object.");
1962    }    }
 #if defined DOPROF  
   profData->slicing++;  
 #endif  
1963    Data tempValue(value);    Data tempValue(value);
1964    typeMatchLeft(tempValue);    typeMatchLeft(tempValue);
1965    typeMatchRight(tempValue);    typeMatchRight(tempValue);
# Line 2060  Data::typeMatchRight(const Data& right) Line 1994  Data::typeMatchRight(const Data& right)
1994    }    }
1995  }  }
1996    
1997  /* TODO */  void
1998  /* global reduction */  Data::setTaggedValueByName(std::string name,
1999                               const boost::python::object& value)
2000    {
2001         if (getFunctionSpace().getDomain().isValidTagName(name)) {
2002            int tagKey=getFunctionSpace().getDomain().getTag(name);
2003            setTaggedValue(tagKey,value);
2004         }
2005    }
2006  void  void
2007  Data::setTaggedValue(int tagKey,  Data::setTaggedValue(int tagKey,
2008                       const boost::python::object& value)                       const boost::python::object& value)
# Line 2071  Data::setTaggedValue(int tagKey, Line 2012  Data::setTaggedValue(int tagKey,
2012    }    }
2013    //    //
2014    // Ensure underlying data object is of type DataTagged    // Ensure underlying data object is of type DataTagged
2015    tag();    if (isConstant()) tag();
2016    
2017    if (!isTagged()) {    numeric::array asNumArray(value);
2018      throw DataException("Error - DataTagged conversion failed!!");  
2019    
2020      // extract the shape of the numarray
2021      DataTypes::ShapeType tempShape;
2022      for (int i=0; i < asNumArray.getrank(); i++) {
2023        tempShape.push_back(extract<int>(asNumArray.getshape()[i]));
2024    }    }
2025    
2026    //    // get the space for the data vector
2027    // Construct DataArray from boost::python::object input value  //   int len = DataTypes::noValues(tempShape);
2028    DataArray valueDataArray(value);  //   DataVector temp_data(len, 0.0, len);
2029    //   DataArrayView temp_dataView(temp_data, tempShape);
2030    //   temp_dataView.copy(asNumArray);
2031    
2032      DataVector temp_data2;
2033      temp_data2.copyFromNumArray(asNumArray);
2034    
2035    //    //
2036    // Call DataAbstract::setTaggedValue    // Call DataAbstract::setTaggedValue
2037    m_data->setTaggedValue(tagKey,valueDataArray.getView());    //m_data->setTaggedValue(tagKey,temp_dataView);
2038    
2039        m_data->setTaggedValue(tagKey,tempShape, temp_data2);
2040  }  }
2041    
2042  /* TODO */  // void
2043  /* global reduction */  // Data::setTaggedValueFromCPP(int tagKey,
2044    //                             const DataArrayView& value)
2045    // {
2046    //   if (isProtected()) {
2047    //         throw DataException("Error - attempt to update protected Data object.");
2048    //   }
2049    //   //
2050    //   // Ensure underlying data object is of type DataTagged
2051    //   if (isConstant()) tag();
2052    //
2053    //   //
2054    //   // Call DataAbstract::setTaggedValue
2055    //   m_data->setTaggedValue(tagKey,value);
2056    // }
2057    
2058  void  void
2059  Data::setTaggedValueFromCPP(int tagKey,  Data::setTaggedValueFromCPP(int tagKey,
2060                              const DataArrayView& value)                  const DataTypes::ShapeType& pointshape,
2061                                const DataTypes::ValueType& value,
2062                    int dataOffset)
2063  {  {
2064    if (isProtected()) {    if (isProtected()) {
2065          throw DataException("Error - attempt to update protected Data object.");          throw DataException("Error - attempt to update protected Data object.");
2066    }    }
2067    //    //
2068    // Ensure underlying data object is of type DataTagged    // Ensure underlying data object is of type DataTagged
2069    tag();    if (isConstant()) tag();
2070    
   if (!isTagged()) {  
     throw DataException("Error - DataTagged conversion failed!!");  
   }  
                                                                                                                 
2071    //    //
2072    // Call DataAbstract::setTaggedValue    // Call DataAbstract::setTaggedValue
2073    m_data->setTaggedValue(tagKey,value);    m_data->setTaggedValue(tagKey,pointshape, value, dataOffset);
2074  }  }
2075    
 /* TODO */  
 /* global reduction */  
2076  int  int
2077  Data::getTagNumber(int dpno)  Data::getTagNumber(int dpno)
2078  {  {
2079    return m_data->getTagNumber(dpno);    if (isEmpty())
2080  }    {
2081        throw DataException("Error - operation not permitted on instances of DataEmpty.");
 /* TODO */  
 /* global reduction */  
 void  
 Data::setRefValue(int ref,  
                   const boost::python::numeric::array& value)  
 {  
   if (isProtected()) {  
         throw DataException("Error - attempt to update protected Data object.");  
2082    }    }
2083    //    return getFunctionSpace().getTagFromDataPointNo(dpno);
   // Construct DataArray from boost::python::object input value  
   DataArray valueDataArray(value);  
   
   //  
   // Call DataAbstract::setRefValue  
   m_data->setRefValue(ref,valueDataArray);  
2084  }  }
2085    
 /* TODO */  
 /* global reduction */  
 void  
 Data::getRefValue(int ref,  
                   boost::python::numeric::array& value)  
 {  
   //  
   // Construct DataArray for boost::python::object return value  
   DataArray valueDataArray(value);  
   
   //  
   // Load DataArray with values from data-points specified by ref  
   m_data->getRefValue(ref,valueDataArray);  
   
   //  
   // Load values from valueDataArray into return numarray  
   
   // extract the shape of the numarray  
   int rank = value.getrank();  
   DataArrayView::ShapeType shape;  
   for (int i=0; i < rank; i++) {  
     shape.push_back(extract<int>(value.getshape()[i]));  
   }  
2086    
2087    // and load the numarray with the data from the DataArray  ostream& escript::operator<<(ostream& o, const Data& data)
2088    DataArrayView valueView = valueDataArray.getView();  {
2089      o << data.toString();
2090      return o;
2091    }
2092    
2093    if (rank==0) {  Data
2094        boost::python::numeric::array temp_numArray(valueView());  escript::C_GeneralTensorProduct(Data& arg_0,
2095        value = temp_numArray;                       Data& arg_1,
2096    }                       int axis_offset,
2097    if (rank==1) {                       int transpose)
2098      for (int i=0; i < shape[0]; i++) {  {
2099        value[i] = valueView(i);    // General tensor product: res(SL x SR) = arg_0(SL x SM) * arg_1(SM x SR)
2100      // SM is the product of the last axis_offset entries in arg_0.getShape().
2101    
2102      // Interpolate if necessary and find an appropriate function space
2103      Data arg_0_Z, arg_1_Z;
2104      if (arg_0.getFunctionSpace()!=arg_1.getFunctionSpace()) {
2105        if (arg_0.probeInterpolation(arg_1.getFunctionSpace())) {
2106          arg_0_Z = arg_0.interpolate(arg_1.getFunctionSpace());
2107          arg_1_Z = Data(arg_1);
2108        }
2109        else if (arg_1.probeInterpolation(arg_0.getFunctionSpace())) {
2110          arg_1_Z=arg_1.interpolate(arg_0.getFunctionSpace());
2111          arg_0_Z =Data(arg_0);
2112      }      }
2113    }      else {
2114    if (rank==2) {        throw DataException("Error - C_GeneralTensorProduct: arguments have incompatible function spaces.");
     for (int i=0; i < shape[0]; i++) {  
       for (int j=0; j < shape[1]; j++) {  
         value[i][j] = valueView(i,j);  
       }  
2115      }      }
2116      } else {
2117          arg_0_Z = Data(arg_0);
2118          arg_1_Z = Data(arg_1);
2119    }    }
2120    if (rank==3) {    // Get rank and shape of inputs
2121      for (int i=0; i < shape[0]; i++) {    int rank0 = arg_0_Z.getDataPointRank();
2122        for (int j=0; j < shape[1]; j++) {    int rank1 = arg_1_Z.getDataPointRank();
2123          for (int k=0; k < shape[2]; k++) {    const DataTypes::ShapeType& shape0 = arg_0_Z.getDataPointShape();
2124            value[i][j][k] = valueView(i,j,k);    const DataTypes::ShapeType& shape1 = arg_1_Z.getDataPointShape();
2125          }  
2126        }    // Prepare for the loops of the product and verify compatibility of shapes
2127      int start0=0, start1=0;
2128      if (transpose == 0)       {}
2129      else if (transpose == 1)  { start0 = axis_offset; }
2130      else if (transpose == 2)  { start1 = rank1-axis_offset; }
2131      else              { throw DataException("C_GeneralTensorProduct: Error - transpose should be 0, 1 or 2"); }
2132    
2133    
2134      // Adjust the shapes for transpose
2135      DataTypes::ShapeType tmpShape0(rank0);    // pre-sizing the vectors rather
2136      DataTypes::ShapeType tmpShape1(rank1);    // than using push_back
2137      for (int i=0; i<rank0; i++)   { tmpShape0[i]=shape0[(i+start0)%rank0]; }
2138      for (int i=0; i<rank1; i++)   { tmpShape1[i]=shape1[(i+start1)%rank1]; }
2139    
2140    #if 0
2141      // For debugging: show shape after transpose
2142      char tmp[100];
2143      std::string shapeStr;
2144      shapeStr = "(";
2145      for (int i=0; i<rank0; i++)   { sprintf(tmp, "%d,", tmpShape0[i]); shapeStr += tmp; }
2146      shapeStr += ")";
2147      cout << "C_GeneralTensorProduct: Shape of arg0 is " << shapeStr << endl;
2148      shapeStr = "(";
2149      for (int i=0; i<rank1; i++)   { sprintf(tmp, "%d,", tmpShape1[i]); shapeStr += tmp; }
2150      shapeStr += ")";
2151      cout << "C_GeneralTensorProduct: Shape of arg1 is " << shapeStr << endl;
2152    #endif
2153    
2154      // Prepare for the loops of the product
2155      int SL=1, SM=1, SR=1;
2156      for (int i=0; i<rank0-axis_offset; i++)   {
2157        SL *= tmpShape0[i];
2158      }
2159      for (int i=rank0-axis_offset; i<rank0; i++)   {
2160        if (tmpShape0[i] != tmpShape1[i-(rank0-axis_offset)]) {
2161          throw DataException("C_GeneralTensorProduct: Error - incompatible shapes");
2162        }
2163        SM *= tmpShape0[i];
2164      }
2165      for (int i=axis_offset; i<rank1; i++)     {
2166        SR *= tmpShape1[i];
2167      }
2168    
2169      // Define the shape of the output (rank of shape is the sum of the loop ranges below)
2170      DataTypes::ShapeType shape2(rank0+rank1-2*axis_offset);  
2171      {         // block to limit the scope of out_index
2172         int out_index=0;
2173         for (int i=0; i<rank0-axis_offset; i++, ++out_index) { shape2[out_index]=tmpShape0[i]; } // First part of arg_0_Z
2174         for (int i=axis_offset; i<rank1; i++, ++out_index)   { shape2[out_index]=tmpShape1[i]; } // Last part of arg_1_Z
2175      }
2176    
2177      // Declare output Data object
2178      Data res;
2179    
2180      if      (arg_0_Z.isConstant()   && arg_1_Z.isConstant()) {
2181        res = Data(0.0, shape2, arg_1_Z.getFunctionSpace());    // DataConstant output
2182        double *ptr_0 = &(arg_0_Z.getDataAtOffset(0));
2183        double *ptr_1 = &(arg_1_Z.getDataAtOffset(0));
2184        double *ptr_2 = &(res.getDataAtOffset(0));
2185        matrix_matrix_product(SL, SM, SR, ptr_0, ptr_1, ptr_2, transpose);
2186      }
2187      else if (arg_0_Z.isConstant()   && arg_1_Z.isTagged()) {
2188    
2189        // Prepare the DataConstant input
2190        DataConstant* tmp_0=dynamic_cast<DataConstant*>(arg_0_Z.borrowData());
2191        if (tmp_0==0) { throw DataException("GTP Programming error - casting to DataConstant."); }
2192    
2193        // Borrow DataTagged input from Data object
2194        DataTagged* tmp_1=dynamic_cast<DataTagged*>(arg_1_Z.borrowData());
2195        if (tmp_1==0) { throw DataException("GTP_1 Programming error - casting to DataTagged."); }
2196    
2197        // Prepare a DataTagged output 2
2198        res = Data(0.0, shape2, arg_1_Z.getFunctionSpace());    // DataTagged output
2199        res.tag();
2200        DataTagged* tmp_2=dynamic_cast<DataTagged*>(res.borrowData());
2201        if (tmp_2==0) { throw DataException("GTP Programming error - casting to DataTagged."); }
2202    
2203        // Prepare offset into DataConstant
2204        int offset_0 = tmp_0->getPointOffset(0,0);
2205        double *ptr_0 = &(arg_0_Z.getDataAtOffset(offset_0));
2206        // Get the views
2207    //     DataArrayView view_1 = tmp_1->getDefaultValue();
2208    //     DataArrayView view_2 = tmp_2->getDefaultValue();
2209    //     // Get the pointers to the actual data
2210    //     double *ptr_1 = &((view_1.getData())[0]);
2211    //     double *ptr_2 = &((view_2.getData())[0]);
2212    
2213        double *ptr_1 = &(tmp_1->getDefaultValue(0));
2214        double *ptr_2 = &(tmp_2->getDefaultValue(0));
2215    
2216    
2217        // Compute an MVP for the default
2218        matrix_matrix_product(SL, SM, SR, ptr_0, ptr_1, ptr_2, transpose);
2219        // Compute an MVP for each tag
2220        const DataTagged::DataMapType& lookup_1=tmp_1->getTagLookup();
2221        DataTagged::DataMapType::const_iterator i; // i->first is a tag, i->second is an offset into memory
2222        for (i=lookup_1.begin();i!=lookup_1.end();i++) {
2223          tmp_2->addTag(i->first);
2224    //       DataArrayView view_1 = tmp_1->getDataPointByTag(i->first);
2225    //       DataArrayView view_2 = tmp_2->getDataPointByTag(i->first);
2226    //       double *ptr_1 = &view_1.getData(0);
2227    //       double *ptr_2 = &view_2.getData(0);
2228    
2229          double *ptr_1 = &(tmp_1->getDataByTag(i->first,0));
2230          double *ptr_2 = &(tmp_2->getDataByTag(i->first,0));
2231        
2232          matrix_matrix_product(SL, SM, SR, ptr_0, ptr_1, ptr_2, transpose);
2233      }      }
2234    
2235    }    }
2236    if (rank==4) {    else if (arg_0_Z.isConstant()   && arg_1_Z.isExpanded()) {
2237      for (int i=0; i < shape[0]; i++) {  
2238        for (int j=0; j < shape[1]; j++) {      res = Data(0.0, shape2, arg_1_Z.getFunctionSpace(),true); // DataExpanded output
2239          for (int k=0; k < shape[2]; k++) {      DataConstant* tmp_0=dynamic_cast<DataConstant*>(arg_0_Z.borrowData());
2240            for (int l=0; l < shape[3]; l++) {      DataExpanded* tmp_1=dynamic_cast<DataExpanded*>(arg_1_Z.borrowData());
2241              value[i][j][k][l] = valueView(i,j,k,l);      DataExpanded* tmp_2=dynamic_cast<DataExpanded*>(res.borrowData());
2242            }      if (tmp_0==0) { throw DataException("GTP Programming error - casting to DataConstant."); }
2243          }      if (tmp_1==0) { throw DataException("GTP Programming error - casting to DataExpanded."); }
2244        if (tmp_2==0) { throw DataException("GTP Programming error - casting to DataExpanded."); }
2245        int sampleNo_1,dataPointNo_1;
2246        int numSamples_1 = arg_1_Z.getNumSamples();
2247        int numDataPointsPerSample_1 = arg_1_Z.getNumDataPointsPerSample();
2248        int offset_0 = tmp_0->getPointOffset(0,0);
2249        #pragma omp parallel for private(sampleNo_1,dataPointNo_1) schedule(static)
2250        for (sampleNo_1 = 0; sampleNo_1 < numSamples_1; sampleNo_1++) {
2251          for (dataPointNo_1 = 0; dataPointNo_1 < numDataPointsPerSample_1; dataPointNo_1++) {
2252            int offset_1 = tmp_1->getPointOffset(sampleNo_1,dataPointNo_1);
2253            int offset_2 = tmp_2->getPointOffset(sampleNo_1,dataPointNo_1);
2254            double *ptr_0 = &(arg_0_Z.getDataAtOffset(offset_0));
2255            double *ptr_1 = &(arg_1_Z.getDataAtOffset(offset_1));
2256            double *ptr_2 = &(res.getDataAtOffset(offset_2));
2257            matrix_matrix_product(SL, SM, SR, ptr_0, ptr_1, ptr_2, transpose);
2258        }        }
2259      }      }
2260    
2261    }    }
2262      else if (arg_0_Z.isTagged()     && arg_1_Z.isConstant()) {
2263    
2264  }      // Borrow DataTagged input from Data object
2265        DataTagged* tmp_0=dynamic_cast<DataTagged*>(arg_0_Z.borrowData());
2266        if (tmp_0==0) { throw DataException("GTP_0 Programming error - casting to DataTagged."); }
2267    
2268  void      // Prepare the DataConstant input
2269  Data::archiveData(const std::string fileName)      DataConstant* tmp_1=dynamic_cast<DataConstant*>(arg_1_Z.borrowData());
2270  {      if (tmp_1==0) { throw DataException("GTP Programming error - casting to DataConstant."); }
   cout << "Archiving Data object to: " << fileName << endl;  
2271    
2272    //      // Prepare a DataTagged output 2
2273    // Determine type of this Data object      res = Data(0.0, shape2, arg_0_Z.getFunctionSpace());    // DataTagged output
2274    int dataType = -1;      res.tag();
2275        DataTagged* tmp_2=dynamic_cast<DataTagged*>(res.borrowData());
2276        if (tmp_2==0) { throw DataException("GTP Programming error - casting to DataTagged."); }
2277    
2278    if (isEmpty()) {      // Prepare offset into DataConstant
2279      dataType = 0;      int offset_1 = tmp_1->getPointOffset(0,0);
2280      cout << "\tdataType: DataEmpty" << endl;      double *ptr_1 = &(arg_1_Z.getDataAtOffset(offset_1));
2281    }      // Get the views
2282    if (isConstant()) {  //     DataArrayView view_0 = tmp_0->getDefaultValue();
2283      dataType = 1;  //     DataArrayView view_2 = tmp_2->getDefaultValue();
2284      cout << "\tdataType: DataConstant" << endl;  //     // Get the pointers to the actual data
2285    }  //     double *ptr_0 = &((view_0.getData())[0]);
2286    if (isTagged()) {  //     double *ptr_2 = &((view_2.getData())[0]);
     dataType = 2;  
     cout << "\tdataType: DataTagged" << endl;  
   }  
   if (isExpanded()) {  
     dataType = 3;  
     cout << "\tdataType: DataExpanded" << endl;  
   }  
2287    
2288    if (dataType == -1) {      double *ptr_0 = &(tmp_0->getDefaultValue(0));
2289      throw DataException("archiveData Error: undefined dataType");      double *ptr_2 = &(tmp_2->getDefaultValue(0));
   }  
2290    
2291    //      // Compute an MVP for the default
2292    // Collect data items common to all Data types      matrix_matrix_product(SL, SM, SR, ptr_0, ptr_1, ptr_2, transpose);
2293    int noSamples = getNumSamples();      // Compute an MVP for each tag
2294    int noDPPSample = getNumDataPointsPerSample();      const DataTagged::DataMapType& lookup_0=tmp_0->getTagLookup();
2295    int functionSpaceType = getFunctionSpace().getTypeCode();      DataTagged::DataMapType::const_iterator i; // i->first is a tag, i->second is an offset into memory
2296    int dataPointRank = getDataPointRank();      for (i=lookup_0.begin();i!=lookup_0.end();i++) {
2297    int dataPointSize = getDataPointSize();  //      tmp_2->addTaggedValue(i->first,tmp_2->getDefaultValue());
2298    int dataLength = getLength();  //       DataArrayView view_0 = tmp_0->getDataPointByTag(i->first);
2299    DataArrayView::ShapeType dataPointShape = getDataPointShape();  //       DataArrayView view_2 = tmp_2->getDataPointByTag(i->first);
2300    vector<int> referenceNumbers(noSamples);  //       double *ptr_0 = &view_0.getData(0);
2301    for (int sampleNo=0; sampleNo<noSamples; sampleNo++) {  //       double *ptr_2 = &view_2.getData(0);
2302      referenceNumbers[sampleNo] = getFunctionSpace().getReferenceNoFromSampleNo(sampleNo);  
2303    }        tmp_2->addTag(i->first);
2304    vector<int> tagNumbers(noSamples);        double *ptr_0 = &(tmp_0->getDataByTag(i->first,0));
2305    if (isTagged()) {        double *ptr_2 = &(tmp_2->getDataByTag(i->first,0));
2306      for (int sampleNo=0; sampleNo<noSamples; sampleNo++) {        matrix_matrix_product(SL, SM, SR, ptr_0, ptr_1, ptr_2, transpose);
       tagNumbers[sampleNo] = getFunctionSpace().getTagFromSampleNo(sampleNo);  
2307      }      }
2308    
2309    }    }
2310      else if (arg_0_Z.isTagged()     && arg_1_Z.isTagged()) {
2311    
2312    cout << "\tnoSamples: " << noSamples << " noDPPSample: " << noDPPSample << endl;      // Borrow DataTagged input from Data object
2313    cout << "\tfunctionSpaceType: " << functionSpaceType << endl;      DataTagged* tmp_0=dynamic_cast<DataTagged*>(arg_0_Z.borrowData());
2314    cout << "\trank: " << dataPointRank << " size: " << dataPointSize << " length: " << dataLength << endl;      if (tmp_0==0) { throw DataException("GTP Programming error - casting to DataTagged."); }
2315    
2316    //      // Borrow DataTagged input from Data object
2317    // Flatten Shape to an array of integers suitable for writing to file      DataTagged* tmp_1=dynamic_cast<DataTagged*>(arg_1_Z.borrowData());
2318    int flatShape[4] = {0,0,0,0};      if (tmp_1==0) { throw DataException("GTP Programming error - casting to DataTagged."); }
   cout << "\tshape: < ";  
   for (int dim=0; dim<dataPointRank; dim++) {  
     flatShape[dim] = dataPointShape[dim];  
     cout << dataPointShape[dim] << " ";  
   }  
   cout << ">" << endl;  
2319    
2320    //      // Prepare a DataTagged output 2
2321    // Open archive file      res = Data(0.0, shape2, arg_1_Z.getFunctionSpace());
2322    ofstream archiveFile;      res.tag();  // DataTagged output
2323    archiveFile.open(fileName.data(), ios::out);      DataTagged* tmp_2=dynamic_cast<DataTagged*>(res.borrowData());
2324        if (tmp_2==0) { throw DataException("GTP Programming error - casting to DataTagged."); }
2325    
2326    if (!archiveFile.good()) {  //     // Get the views
2327      throw DataException("archiveData Error: problem opening archive file");  //     DataArrayView view_0 = tmp_0->getDefaultValue();
2328    }  //     DataArrayView view_1 = tmp_1->getDefaultValue();
2329    //     DataArrayView view_2 = tmp_2->getDefaultValue();
2330    //     // Get the pointers to the actual data
2331    //     double *ptr_0 = &((view_0.getData())[0]);
2332    //     double *ptr_1 = &((view_1.getData())[0]);
2333    //     double *ptr_2 = &((view_2.getData())[0]);
2334    
2335    //      double *ptr_0 = &(tmp_0->getDefaultValue(0));
2336    // Write common data items to archive file      double *ptr_1 = &(tmp_1->getDefaultValue(0));
2337    archiveFile.write(reinterpret_cast<char *>(&dataType),sizeof(int));      double *ptr_2 = &(tmp_2->getDefaultValue(0));
   archiveFile.write(reinterpret_cast<char *>(&noSamples),sizeof(int));  
   archiveFile.write(reinterpret_cast<char *>(&noDPPSample),sizeof(int));  
   archiveFile.write(reinterpret_cast<char *>(&functionSpaceType),sizeof(int));  
   archiveFile.write(reinterpret_cast<char *>(&dataPointRank),sizeof(int));  
   archiveFile.write(reinterpret_cast<char *>(&dataPointSize),sizeof(int));  
   archiveFile.write(reinterpret_cast<char *>(&dataLength),sizeof(int));  
   for (int dim = 0; dim < 4; dim++) {  
     archiveFile.write(reinterpret_cast<char *>(&flatShape[dim]),sizeof(int));  
   }  
   for (int sampleNo=0; sampleNo<noSamples; sampleNo++) {  
     archiveFile.write(reinterpret_cast<char *>(&referenceNumbers[sampleNo]),sizeof(int));  
   }  
   if (isTagged()) {  
     for (int sampleNo=0; sampleNo<noSamples; sampleNo++) {  
       archiveFile.write(reinterpret_cast<char *>(&tagNumbers[sampleNo]),sizeof(int));  
     }  
   }  
2338    
   if (!archiveFile.good()) {  
     throw DataException("archiveData Error: problem writing to archive file");  
   }  
2339    
2340    //      // Compute an MVP for the default
2341    // Archive underlying data values for each Data type      matrix_matrix_product(SL, SM, SR, ptr_0, ptr_1, ptr_2, transpose);
2342    int noValues;      // Merge the tags
2343    switch (dataType) {      DataTagged::DataMapType::const_iterator i; // i->first is a tag, i->second is an offset into memory
2344      case 0:      const DataTagged::DataMapType& lookup_0=tmp_0->getTagLookup();
2345        // DataEmpty      const DataTagged::DataMapType& lookup_1=tmp_1->getTagLookup();
2346        noValues = 0;      for (i=lookup_0.begin();i!=lookup_0.end();i++) {
2347        archiveFile.write(reinterpret_cast<char *>(&noValues),sizeof(int));        tmp_2->addTag(i->first); // use tmp_2 to get correct shape
2348        cout << "\tnoValues: " << noValues << endl;      }
2349        break;      for (i=lookup_1.begin();i!=lookup_1.end();i++) {
2350      case 1:        tmp_2->addTag(i->first);
2351        // DataConstant      }
2352        noValues = m_data->getLength();      // Compute an MVP for each tag
2353        archiveFile.write(reinterpret_cast<char *>(&noValues),sizeof(int));      const DataTagged::DataMapType& lookup_2=tmp_2->getTagLookup();
2354        cout << "\tnoValues: " << noValues << endl;      for (i=lookup_2.begin();i!=lookup_2.end();i++) {
2355        if (m_data->archiveData(archiveFile,noValues)) {  //       DataArrayView view_0 = tmp_0->getDataPointByTag(i->first);
2356          throw DataException("archiveData Error: problem writing data to archive file");  //       DataArrayView view_1 = tmp_1->getDataPointByTag(i->first);
2357        }  //       DataArrayView view_2 = tmp_2->getDataPointByTag(i->first);
2358        break;  //       double *ptr_0 = &view_0.getData(0);
2359      case 2:  //       double *ptr_1 = &view_1.getData(0);
2360        // DataTagged  //       double *ptr_2 = &view_2.getData(0);
       noValues = m_data->getLength();  
       archiveFile.write(reinterpret_cast<char *>(&noValues),sizeof(int));  
       cout << "\tnoValues: " << noValues << endl;  
       if (m_data->archiveData(archiveFile,noValues)) {  
         throw DataException("archiveData Error: problem writing data to archive file");  
       }  
       break;  
     case 3:  
       // DataExpanded  
       noValues = m_data->getLength();  
       archiveFile.write(reinterpret_cast<char *>(&noValues),sizeof(int));  
       cout << "\tnoValues: " << noValues << endl;  
       if (m_data->archiveData(archiveFile,noValues)) {  
         throw DataException("archiveData Error: problem writing data to archive file");  
       }  
       break;  
   }  
2361    
2362    if (!archiveFile.good()) {        double *ptr_0 = &(tmp_0->getDataByTag(i->first,0));
2363      throw DataException("archiveData Error: problem writing data to archive file");        double *ptr_1 = &(tmp_1->getDataByTag(i->first,0));
2364    }        double *ptr_2 = &(tmp_2->getDataByTag(i->first,0));
2365    
2366    //        matrix_matrix_product(SL, SM, SR, ptr_0, ptr_1, ptr_2, transpose);
2367    // Close archive file      }
   archiveFile.close();  
2368    
   if (!archiveFile.good()) {  
     throw DataException("archiveData Error: problem closing archive file");  
2369    }    }
2370      else if (arg_0_Z.isTagged()     && arg_1_Z.isExpanded()) {
2371    
2372  }      // After finding a common function space above the two inputs have the same numSamples and num DPPS
2373        res = Data(0.0, shape2, arg_1_Z.getFunctionSpace(),true); // DataExpanded output
2374        DataTagged*   tmp_0=dynamic_cast<DataTagged*>(arg_0_Z.borrowData());
2375        DataExpanded* tmp_1=dynamic_cast<DataExpanded*>(arg_1_Z.borrowData());
2376        DataExpanded* tmp_2=dynamic_cast<DataExpanded*>(res.borrowData());
2377        if (tmp_0==0) { throw DataException("GTP Programming error - casting to DataTagged."); }
2378        if (tmp_1==0) { throw DataException("GTP Programming error - casting to DataExpanded."); }
2379        if (tmp_2==0) { throw DataException("GTP Programming error - casting to DataExpanded."); }
2380        int sampleNo_0,dataPointNo_0;
2381        int numSamples_0 = arg_0_Z.getNumSamples();
2382        int numDataPointsPerSample_0 = arg_0_Z.getNumDataPointsPerSample();
2383        #pragma omp parallel for private(sampleNo_0,dataPointNo_0) schedule(static)
2384        for (sampleNo_0 = 0; sampleNo_0 < numSamples_0; sampleNo_0++) {
2385          int offset_0 = tmp_0->getPointOffset(sampleNo_0,0); // They're all the same, so just use #0
2386          double *ptr_0 = &(arg_0_Z.getDataAtOffset(offset_0));
2387          for (dataPointNo_0 = 0; dataPointNo_0 < numDataPointsPerSample_0; dataPointNo_0++) {
2388            int offset_1 = tmp_1->getPointOffset(sampleNo_0,dataPointNo_0);
2389            int offset_2 = tmp_2->getPointOffset(sampleNo_0,dataPointNo_0);
2390            double *ptr_1 = &(arg_1_Z.getDataAtOffset(offset_1));
2391            double *ptr_2 = &(res.getDataAtOffset(offset_2));
2392            matrix_matrix_product(SL, SM, SR, ptr_0, ptr_1, ptr_2, transpose);
2393          }
2394        }
2395    
 void  
 Data::extractData(const std::string fileName,  
                   const FunctionSpace& fspace)  
 {  
   //  
   // Can only extract Data to an object which is initially DataEmpty  
   if (!isEmpty()) {  
     throw DataException("extractData Error: can only extract to DataEmpty object");  
2396    }    }
2397      else if (arg_0_Z.isExpanded()   && arg_1_Z.isConstant()) {
2398    
2399    cout << "Extracting Data object from: " << fileName << endl;      res = Data(0.0, shape2, arg_1_Z.getFunctionSpace(),true); // DataExpanded output
2400        DataExpanded* tmp_0=dynamic_cast<DataExpanded*>(arg_0_Z.borrowData());
2401    int dataType;      DataConstant* tmp_1=dynamic_cast<DataConstant*>(arg_1_Z.borrowData());
2402    int noSamples;      DataExpanded* tmp_2=dynamic_cast<DataExpanded*>(res.borrowData());
2403    int noDPPSample;      if (tmp_0==0) { throw DataException("GTP Programming error - casting to DataExpanded."); }
2404    int functionSpaceType;      if (tmp_1==0) { throw DataException("GTP Programming error - casting to DataConstant."); }
2405    int dataPointRank;      if (tmp_2==0) { throw DataException("GTP Programming error - casting to DataExpanded."); }
2406    int dataPointSize;      int sampleNo_0,dataPointNo_0;
2407    int dataLength;      int numSamples_0 = arg_0_Z.getNumSamples();
2408    DataArrayView::ShapeType dataPointShape;      int numDataPointsPerSample_0 = arg_0_Z.getNumDataPointsPerSample();
2409    int flatShape[4];      int offset_1 = tmp_1->getPointOffset(0,0);
2410        #pragma omp parallel for private(sampleNo_0,dataPointNo_0) schedule(static)
2411        for (sampleNo_0 = 0; sampleNo_0 < numSamples_0; sampleNo_0++) {
2412          for (dataPointNo_0 = 0; dataPointNo_0 < numDataPointsPerSample_0; dataPointNo_0++) {
2413            int offset_0 = tmp_0->getPointOffset(sampleNo_0,dataPointNo_0);
2414            int offset_2 = tmp_2->getPointOffset(sampleNo_0,dataPointNo_0);
2415            double *ptr_0 = &(arg_0_Z.getDataAtOffset(offset_0));
2416            double *ptr_1 = &(arg_1_Z.getDataAtOffset(offset_1));
2417            double *ptr_2 = &(res.getDataAtOffset(offset_2));
2418            matrix_matrix_product(SL, SM, SR, ptr_0, ptr_1, ptr_2, transpose);
2419          }
2420        }
2421    
   //  
   // Open the archive file  
   ifstream archiveFile;  
   archiveFile.open(fileName.data(), ios::in);  
2422    
   if (!archiveFile.good()) {  
     throw DataException("extractData Error: problem opening archive file");  
2423    }    }
2424      else if (arg_0_Z.isExpanded()   && arg_1_Z.isTagged()) {
2425    
2426    //      // After finding a common function space above the two inputs have the same numSamples and num DPPS
2427    // Read common data items from archive file      res = Data(0.0, shape2, arg_1_Z.getFunctionSpace(),true); // DataExpanded output
2428    archiveFile.read(reinterpret_cast<char *>(&dataType),sizeof(int));      DataExpanded* tmp_0=dynamic_cast<DataExpanded*>(arg_0_Z.borrowData());
2429    archiveFile.read(reinterpret_cast<char *>(&noSamples),sizeof(int));      DataTagged*   tmp_1=dynamic_cast<DataTagged*>(arg_1_Z.borrowData());
2430    archiveFile.read(reinterpret_cast<char *>(&noDPPSample),sizeof(int));      DataExpanded* tmp_2=dynamic_cast<DataExpanded*>(res.borrowData());
2431    archiveFile.read(reinterpret_cast<char *>(&functionSpaceType),sizeof(int));      if (tmp_0==0) { throw DataException("GTP Programming error - casting to DataExpanded."); }
2432    archiveFile.read(reinterpret_cast<char *>(&dataPointRank),sizeof(int));      if (tmp_1==0) { throw DataException("GTP Programming error - casting to DataTagged."); }
2433    archiveFile.read(reinterpret_cast<char *>(&dataPointSize),sizeof(int));      if (tmp_2==0) { throw DataException("GTP Programming error - casting to DataExpanded."); }
2434    archiveFile.read(reinterpret_cast<char *>(&dataLength),sizeof(int));      int sampleNo_0,dataPointNo_0;
2435    for (int dim = 0; dim < 4; dim++) {      int numSamples_0 = arg_0_Z.getNumSamples();
2436      archiveFile.read(reinterpret_cast<char *>(&flatShape[dim]),sizeof(int));      int numDataPointsPerSample_0 = arg_0_Z.getNumDataPointsPerSample();
2437      if (flatShape[dim]>0) {      #pragma omp parallel for private(sampleNo_0,dataPointNo_0) schedule(static)
2438        dataPointShape.push_back(flatShape[dim]);      for (sampleNo_0 = 0; sampleNo_0 < numSamples_0; sampleNo_0++) {
2439          int offset_1 = tmp_1->getPointOffset(sampleNo_0,0);
2440          double *ptr_1 = &(arg_1_Z.getDataAtOffset(offset_1));
2441          for (dataPointNo_0 = 0; dataPointNo_0 < numDataPointsPerSample_0; dataPointNo_0++) {
2442            int offset_0 = tmp_0->getPointOffset(sampleNo_0,dataPointNo_0);
2443            int offset_2 = tmp_2->getPointOffset(sampleNo_0,dataPointNo_0);
2444            double *ptr_0 = &(arg_0_Z.getDataAtOffset(offset_0));
2445            double *ptr_2 = &(res.getDataAtOffset(offset_2));
2446            matrix_matrix_product(SL, SM, SR, ptr_0, ptr_1, ptr_2, transpose);
2447          }
2448      }      }
2449    
2450    }    }
2451    vector<int> referenceNumbers(noSamples);    else if (arg_0_Z.isExpanded()   && arg_1_Z.isExpanded()) {
2452    for (int sampleNo=0; sampleNo<noSamples; sampleNo++) {  
2453      archiveFile.read(reinterpret_cast<char *>(&referenceNumbers[sampleNo]),sizeof(int));      // After finding a common function space above the two inputs have the same numSamples and num DPPS
2454    }      res = Data(0.0, shape2, arg_1_Z.getFunctionSpace(),true); // DataExpanded output
2455    vector<int> tagNumbers(noSamples);      DataExpanded* tmp_0=dynamic_cast<DataExpanded*>(arg_0_Z.borrowData());
2456    if (dataType==2) {      DataExpanded* tmp_1=dynamic_cast<DataExpanded*>(arg_1_Z.borrowData());
2457      for (int sampleNo=0; sampleNo<noSamples; sampleNo++) {      DataExpanded* tmp_2=dynamic_cast<DataExpanded*>(res.borrowData());
2458        archiveFile.read(reinterpret_cast<char *>(&tagNumbers[sampleNo]),sizeof(int));      if (tmp_0==0) { throw DataException("GTP Programming error - casting to DataExpanded."); }
2459        if (tmp_1==0) { throw DataException("GTP Programming error - casting to DataExpanded."); }
2460        if (tmp_2==0) { throw DataException("GTP Programming error - casting to DataExpanded."); }
2461        int sampleNo_0,dataPointNo_0;
2462        int numSamples_0 = arg_0_Z.getNumSamples();
2463        int numDataPointsPerSample_0 = arg_0_Z.getNumDataPointsPerSample();
2464        #pragma omp parallel for private(sampleNo_0,dataPointNo_0) schedule(static)
2465        for (sampleNo_0 = 0; sampleNo_0 < numSamples_0; sampleNo_0++) {
2466          for (dataPointNo_0 = 0; dataPointNo_0 < numDataPointsPerSample_0; dataPointNo_0++) {
2467            int offset_0 = tmp_0->getPointOffset(sampleNo_0,dataPointNo_0);
2468            int offset_1 = tmp_1->getPointOffset(sampleNo_0,dataPointNo_0);
2469            int offset_2 = tmp_2->getPointOffset(sampleNo_0,dataPointNo_0);
2470            double *ptr_0 = &(arg_0_Z.getDataAtOffset(offset_0));
2471            double *ptr_1 = &(arg_1_Z.getDataAtOffset(offset_1));
2472            double *ptr_2 = &(res.getDataAtOffset(offset_2));
2473            matrix_matrix_product(SL, SM, SR, ptr_0, ptr_1, ptr_2, transpose);
2474          }
2475      }      }
   }  
2476    
   if (!archiveFile.good()) {  
     throw DataException("extractData Error: problem reading from archive file");  
2477    }    }
2478      else {
2479    //      throw DataException("Error - C_GeneralTensorProduct: unknown combination of inputs");
   // Verify the values just read from the archive file  
   switch (dataType) {  
     case 0:  
       cout << "\tdataType: DataEmpty" << endl;  
       break;  
     case 1:  
       cout << "\tdataType: DataConstant" << endl;  
       break;  
     case 2:  
       cout << "\tdataType: DataTagged" << endl;  
       break;  
     case 3:  
       cout << "\tdataType: DataExpanded" << endl;  
       break;  
     default:  
       throw DataException("extractData Error: undefined dataType read from archive file");  
       break;  
2480    }    }
2481    
2482    cout << "\tnoSamples: " << noSamples << " noDPPSample: " << noDPPSample << endl;    return res;
2483    cout << "\tfunctionSpaceType: " << functionSpaceType << endl;  }
   cout << "\trank: " << dataPointRank << " size: " << dataPointSize << " length: " << dataLength << endl;  
   cout << "\tshape: < ";  
   for (int dim = 0; dim < dataPointRank; dim++) {  
     cout << dataPointShape[dim] << " ";  
   }  
   cout << ">" << endl;  
2484    
2485    //  DataAbstract*
2486    // Verify that supplied FunctionSpace object is compatible with this Data object.  Data::borrowData() const
2487    if ( (fspace.getTypeCode()!=functionSpaceType) ||  {
2488         (fspace.getNumSamples()!=noSamples) ||    return m_data.get();
2489         (fspace.getNumDPPSample()!=noDPPSample)  }
2490       ) {  
2491      throw DataException("extractData Error: incompatible FunctionSpace");  
2492    }  std::string
2493    for (int sampleNo=0; sampleNo<noSamples; sampleNo++) {  Data::toString() const
2494      if (referenceNumbers[sampleNo] != fspace.getReferenceNoFromSampleNo(sampleNo)) {  {
2495        throw DataException("extractData Error: incompatible FunctionSpace");      static const DataTypes::ValueType::size_type TOO_MANY_POINTS=80;
2496      }      if (getNumDataPoints()*getDataPointSize()>TOO_MANY_POINTS)
2497    }      {
2498    if (dataType==2) {      stringstream temp;
2499      for (int sampleNo=0; sampleNo<noSamples; sampleNo++) {      temp << "Summary: inf="<< inf() << " sup=" << sup() << " data points=" << getNumDataPoints();
2500        if (tagNumbers[sampleNo] != fspace.getTagFromSampleNo(sampleNo)) {      return  temp.str();
         throw DataException("extractData Error: incompatible FunctionSpace");  
       }  
2501      }      }
2502    }      return m_data->toString();
2503    }
2504    
   //  
   // Construct a DataVector to hold underlying data values  
   DataVector dataVec(dataLength);  
2505    
   //  
   // Load this DataVector with the appropriate values  
   int noValues;  
   archiveFile.read(reinterpret_cast<char *>(&noValues),sizeof(int));  
   cout << "\tnoValues: " << noValues << endl;  
   switch (dataType) {  
     case 0:  
       // DataEmpty  
       if (noValues != 0) {  
         throw DataException("extractData Error: problem reading data from archive file");  
       }  
       break;  
     case 1:  
       // DataConstant  
       if (dataVec.extractData(archiveFile,noValues)) {  
         throw DataException("extractData Error: problem reading data from archive file");  
       }  
       break;  
     case 2:  
       // DataTagged  
       if (dataVec.extractData(archiveFile,noValues)) {  
         throw DataException("extractData Error: problem reading data from archive file");  
       }  
       break;  
     case 3:  
       // DataExpanded  
       if (dataVec.extractData(archiveFile,noValues)) {  
         throw DataException("extractData Error: problem reading data from archive file");  
       }  
       break;  
   }  
2506    
2507    if (!archiveFile.good()) {  DataTypes::ValueType::const_reference
2508      throw DataException("extractData Error: problem reading from archive file");  Data::getDataAtOffset(DataTypes::ValueType::size_type i) const
2509    }  {
2510        return m_data->getDataAtOffset(i);
2511    }
2512    
   //  
   // Close archive file  
   archiveFile.close();  
2513    
2514    if (!archiveFile.good()) {  DataTypes::ValueType::reference
2515      throw DataException("extractData Error: problem closing archive file");  Data::getDataAtOffset(DataTypes::ValueType::size_type i)
2516    }  {
2517        return m_data->getDataAtOffset(i);
2518    }
2519    
2520    //  DataTypes::ValueType::const_reference
2521    // Construct an appropriate Data object  Data::getDataPoint(int sampleNo, int dataPointNo) const
2522    DataAbstract* tempData;  {
2523    switch (dataType) {      return m_data->getDataAtOffset(m_data->getPointOffset(sampleNo, dataPointNo));
     case 0:  
       // DataEmpty  
       tempData=new DataEmpty();  
       break;  
     case 1:  
       // DataConstant  
       tempData=new DataConstant(fspace,dataPointShape,dataVec);  
       break;  
     case 2:  
       // DataTagged  
       tempData=new DataTagged(fspace,dataPointShape,tagNumbers,dataVec);  
       break;  
     case 3:  
       // DataExpanded  
       tempData=new DataExpanded(fspace,dataPointShape,dataVec);  
       break;  
   }  
   shared_ptr<DataAbstract> temp_data(tempData);  
   m_data=temp_data;  
2524  }  }
2525    
2526  ostream& escript::operator<<(ostream& o, const Data& data)  
2527    DataTypes::ValueType::reference
2528    Data::getDataPoint(int sampleNo, int dataPointNo)
2529  {  {
2530    o << data.toString();      return m_data->getDataAtOffset(m_data->getPointOffset(sampleNo, dataPointNo));
   return o;  
2531  }  }
2532    
2533    
2534  /* Member functions specific to the MPI implementation */  /* Member functions specific to the MPI implementation */
2535    
2536  void  void
2537  Data::print()  Data::print()
2538  {  {
2539    int i,j;    int i,j;
2540      
2541    printf( "Data is %dX%d\n", getNumSamples(), getNumDataPointsPerSample() );    printf( "Data is %dX%d\n", getNumSamples(), getNumDataPointsPerSample() );
2542    for( i=0; i<getNumSamples(); i++ )    for( i=0; i<getNumSamples(); i++ )
2543    {    {
# Line 2557  Data::print() Line 2547  Data::print()
2547      printf( "\n" );      printf( "\n" );
2548    }    }
2549  }  }
2550    void
2551    Data::dump(const std::string fileName) const
2552    {
2553      try
2554         {
2555            return m_data->dump(fileName);
2556         }
2557         catch (exception& e)
2558         {
2559            cout << e.what() << endl;
2560         }
2561    }
2562    
2563  int  int
2564  Data::get_MPISize() const  Data::get_MPISize() const
2565  {  {
2566      int error, size;      int size;
2567  #ifdef PASO_MPI  #ifdef PASO_MPI
2568        int error;
2569      error = MPI_Comm_size( get_MPIComm(), &size );      error = MPI_Comm_size( get_MPIComm(), &size );
2570  #else  #else
2571      size = 1;      size = 1;
# Line 2573  Data::get_MPISize() const Line 2576  Data::get_MPISize() const
2576  int  int
2577  Data::get_MPIRank() const  Data::get_MPIRank() const
2578  {  {
2579      int error, rank;      int rank;
2580  #ifdef PASO_MPI  #ifdef PASO_MPI
2581        int error;
2582      error = MPI_Comm_rank( get_MPIComm(), &rank );      error = MPI_Comm_rank( get_MPIComm(), &rank );
2583  #else  #else
2584      rank = 0;      rank = 0;
# Line 2584  Data::get_MPIRank() const Line 2588  Data::get_MPIRank() const
2588    
2589  MPI_Comm  MPI_Comm
2590  Data::get_MPIComm() const  Data::get_MPIComm() const
2591  {  {
2592  #ifdef PASO_MPI  #ifdef PASO_MPI
2593      return MPI_COMM_WORLD;      return MPI_COMM_WORLD;
2594  #else  #else
# Line 2592  Data::get_MPIComm() const Line 2596  Data::get_MPIComm() const
2596  #endif  #endif
2597  }  }
2598    
2599    

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