/[escript]/trunk/escript/src/DataExpanded.cpp
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trunk/esys2/escript/src/Data/DataExpanded.cpp revision 117 by jgs, Fri Apr 1 05:48:57 2005 UTC trunk/escript/src/DataExpanded.cpp revision 1872 by jfenwick, Mon Oct 13 00:18:55 2008 UTC
# Line 1  Line 1 
 // $Id$  
 /*  
  ******************************************************************************  
  *                                                                            *  
  *       COPYRIGHT  ACcESS 2004 -  All Rights Reserved                        *  
  *                                                                            *  
  * This software is the property of ACcESS. No part of this code              *  
  * may be copied in any form or by any means without the expressed written    *  
  * consent of ACcESS.  Copying, use or modification of this software          *  
  * by any unauthorised person is illegal unless that person has a software    *  
  * license agreement with ACcESS.                                             *  
  *                                                                            *  
  ******************************************************************************  
 */  
   
 #include "escript/Data/DataException.h"  
 #include "escript/Data/DataExpanded.h"  
 #include "escript/Data/DataConstant.h"  
 #include "escript/Data/DataTagged.h"  
 #include "escript/Data/DataArrayView.h"  
1    
2  #include <boost/python/extract.hpp>  /*******************************************************
3    *
4    * Copyright (c) 2003-2008 by University of Queensland
5    * Earth Systems Science Computational Center (ESSCC)
6    * http://www.uq.edu.au/esscc
7    *
8    * Primary Business: Queensland, Australia
9    * 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"
16    #include "DataExpanded.h"
17    #include "DataException.h"
18    #include "DataConstant.h"
19    #include "DataTagged.h"
20    #ifdef USE_NETCDF
21    #include <netcdfcpp.h>
22    #endif
23    #ifdef PASO_MPI
24    #include <mpi.h>
25    #endif
26    
27  #include <iostream>  #include <boost/python/extract.hpp>
28    #include "DataMaths.h"
29    
30  using namespace std;  using namespace std;
31  using namespace boost::python;  using namespace boost::python;
32  using namespace boost;  using namespace boost;
33    using namespace escript::DataTypes;
34    
35  namespace escript {  namespace escript {
36    
37  DataExpanded::DataExpanded(const boost::python::numeric::array& value,  DataExpanded::DataExpanded(const boost::python::numeric::array& value,
38                             const FunctionSpace& what)                             const FunctionSpace& what)
39    : DataAbstract(what)    : DataAbstract(what,DataTypes::shapeFromNumArray(value))
40  {  {
   DataArrayView::ShapeType tempShape;  
   //  
   // extract the shape of the python numarray  
   for (int i=0; i<value.getrank(); i++) {  
     tempShape.push_back(extract<int>(value.getshape()[i]));  
   }  
41    //    //
42    // initialise the data array for this object    // initialise the data array for this object
43    initialise(tempShape,what.getNumSamples(),what.getNumDPPSample());    initialise(what.getNumSamples(),what.getNumDPPSample());
44    //    //
45    // copy the given value to every data point    // copy the given value to every data point
46    copy(value);    copy(value);
47  }  }
48    
49  DataExpanded::DataExpanded(const DataExpanded& other)  DataExpanded::DataExpanded(const DataExpanded& other)
50    : DataAbstract(other.getFunctionSpace()),    : DataAbstract(other.getFunctionSpace(), other.getShape()),
51    m_data(other.m_data)    m_data(other.m_data)
52  {  {
   //  
   // create the view for the data  
   DataArrayView temp(m_data.getData(),other.getPointDataView().getShape());  
   setPointDataView(temp);  
53  }  }
54    
55  DataExpanded::DataExpanded(const DataConstant& other)  DataExpanded::DataExpanded(const DataConstant& other)
56    : DataAbstract(other.getFunctionSpace())    : DataAbstract(other.getFunctionSpace(), other.getShape())
57  {  {
58    //    //
59    // initialise the data array for this object    // initialise the data array for this object
60    initialise(other.getPointDataView().getShape(),other.getNumSamples(),other.getNumDPPSample());    initialise(other.getNumSamples(),other.getNumDPPSample());
61    //    //
62    // DataConstant only has one value, copy this to every data point    // DataConstant only has one value, copy this to every data point
63    copy(other.getPointDataView());    copy(other);
64  }  }
65    
66  DataExpanded::DataExpanded(const DataTagged& other)  DataExpanded::DataExpanded(const DataTagged& other)
67    : DataAbstract(other.getFunctionSpace())    : DataAbstract(other.getFunctionSpace(), other.getShape())
68  {  {
69    //    //
70    // initialise the data for this object    // initialise the data array for this object
71    initialise(other.getPointDataView().getShape(),other.getNumSamples(),other.getNumDPPSample());    initialise(other.getNumSamples(),other.getNumDPPSample());
72    //    //
73    // for each data point in this object, extract and copy the corresponding data    // for each data point in this object, extract and copy the corresponding data
74    // value from the given DataTagged object    // value from the given DataTagged object
75    int i,j;    int i,j;
76    DataArrayView::ValueType::size_type numRows=m_data.getNumRows();    DataTypes::ValueType::size_type numRows=m_data.getNumRows();
77    DataArrayView::ValueType::size_type numCols=m_data.getNumCols();    DataTypes::ValueType::size_type numCols=m_data.getNumCols();
78  #pragma omp parallel for private(i,j) schedule(static)    #pragma omp parallel for private(i,j) schedule(static)
79    for (i=0;i<numRows;i++) {    for (i=0;i<numRows;i++) {
80      for (j=0;j<numCols;j++) {      for (j=0;j<numCols;j++) {
81        try {        try {
82          getPointDataView().copy(getPointOffset(i,j),other.getPointDataView(),other.getPointOffset(i,j));             DataTypes::copyPoint(getVector(), getPointOffset(i,j), getNoValues(),
83                                    other.getVector(),
84                                    other.getPointOffset(i,j));
85        }        }
86        catch (std::exception& e) {        catch (std::exception& e) {
87          cout << e.what() << endl;          cout << e.what() << endl;
# Line 94  DataExpanded::DataExpanded(const DataTag Line 91  DataExpanded::DataExpanded(const DataTag
91  }  }
92    
93  DataExpanded::DataExpanded(const DataExpanded& other,  DataExpanded::DataExpanded(const DataExpanded& other,
94                             const DataArrayView::RegionType& region)                             const DataTypes::RegionType& region)
95    : DataAbstract(other.getFunctionSpace())    : DataAbstract(other.getFunctionSpace(),DataTypes::getResultSliceShape(region))
96  {  {
97    //    //
98    // get the shape of the slice    // get the shape of the slice
99    DataArrayView::ShapeType shape(DataArrayView::getResultSliceShape(region));  //   DataTypes::ShapeType shape(DataTypes::getResultSliceShape(region));
100    //    //
101    // initialise this Data object to the shape of the slice    // initialise this Data object to the shape of the slice
102    initialise(shape,other.getNumSamples(),other.getNumDPPSample());    initialise(other.getNumSamples(),other.getNumDPPSample());
103    //    //
104    // copy the data    // copy the data
105    DataArrayView::RegionLoopRangeType region_loop_range=getSliceRegionLoopRange(region);    DataTypes::RegionLoopRangeType region_loop_range=DataTypes::getSliceRegionLoopRange(region);
106    DataArrayView::ValueType::size_type numRows=m_data.getNumRows();    DataTypes::ValueType::size_type numRows=m_data.getNumRows();
107    DataArrayView::ValueType::size_type numCols=m_data.getNumCols();    DataTypes::ValueType::size_type numCols=m_data.getNumCols();
108    int i,j;    int i,j;
109  #pragma omp parallel for private(i,j) schedule(static)    #pragma omp parallel for private(i,j) schedule(static)
110    for (i=0;i<numRows;i++) {    for (i=0;i<numRows;i++) {
111      for (j=0;j<numCols;j++) {      for (j=0;j<numCols;j++) {
112        try {        try {
113          getPointDataView().copySlice(getPointOffset(i,j),other.getPointDataView(),other.getPointOffset(i,j),region_loop_range);  //         getPointDataView().copySlice(getPointOffset(i,j),
114    //                                      other.getPointDataView(),
115    //                                      other.getPointOffset(i,j),
116    //                                      region_loop_range);
117            DataTypes::copySlice(getVector(),getShape(),getPointOffset(i,j),
118                                         other.getVector(),
119                         other.getShape(),
120                                         other.getPointOffset(i,j),
121                                         region_loop_range);
122        }        }
123        catch (std::exception& e) {        catch (std::exception& e) {
124          cout << e.what() << endl;          cout << e.what() << endl;
# Line 122  DataExpanded::DataExpanded(const DataExp Line 127  DataExpanded::DataExpanded(const DataExp
127    }    }
128  }  }
129    
130  DataExpanded::DataExpanded(const DataArrayView& value,  // DataExpanded::DataExpanded(const DataArrayView& value,
131                             const FunctionSpace& what)  //                            const FunctionSpace& what)
132    : DataAbstract(what)  //   : DataAbstract(what)
133  {  // {
134    //  //   //
135    // get the shape of the given data value  //   // get the shape of the given data value
136    DataArrayView::ShapeType tempShape=value.getShape();  //   DataTypes::ShapeType tempShape=value.getShape();
137    //  //   //
138    // initialise this Data object to the shape of the given data value  //   // initialise this Data object to the shape of the given data value
139    initialise(tempShape,what.getNumSamples(),what.getNumDPPSample());  //   initialise(tempShape,what.getNumSamples(),what.getNumDPPSample());
140    //  //   //
141    // copy the given value to every data point  //   // copy the given value to every data point
142    copy(value);  //   copy(value);
143    // }
144    
145    DataExpanded::DataExpanded(const FunctionSpace& what,
146                               const DataTypes::ShapeType &shape,
147                               const DataTypes::ValueType &data)
148      : DataAbstract(what,shape)
149    {
150      EsysAssert(data.size()%getNoValues()==0,
151                     "DataExpanded Constructor - size of supplied data is not a multiple of shape size.");
152    
153      if (data.size()==getNoValues())
154      {
155         ValueType& vec=m_data.getData();
156         //
157         // create the view of the data
158         initialise(what.getNumSamples(),what.getNumDPPSample());
159         // now we copy this value to all elements
160         for (int i=0;i<getLength();)
161         {
162        for (int j=0;j<getNoValues();++j,++i)
163        {
164            vec[i]=data[j];
165        }
166         }
167      }
168      else
169      {
170         //
171         // copy the data in the correct format
172         m_data.getData()=data;
173      }
174    
175    
176  }  }
177    
178  DataExpanded::~DataExpanded()  DataExpanded::~DataExpanded()
179  {  {
180  }  }
181    
182  void  DataAbstract*
183  DataExpanded::reshapeDataPoint(const DataArrayView::ShapeType& shape)  DataExpanded::deepCopy()
184  {  {
185    if (getPointDataView().getRank()!=0) {    return new DataExpanded(*this);
     stringstream temp;  
     temp << "Error - Can only reshape Data with data points of rank 0. "  
          << "This Data has data points with rank: "  
          << getPointDataView().getRank();  
     throw DataException(temp.str());  
   }  
   //  
   // create the new DataBlocks2D data array, and a corresponding DataArrayView  
   DataBlocks2D newData(getNumSamples(),getNumDPPSample(),DataArrayView::noValues(shape));  
   DataArrayView newView(newData.getData(),shape);  
   //  
   // Copy the original data to every value for the new shape  
   int i,j;  
   int nRows=m_data.getNumRows();  
   int nCols=m_data.getNumCols();  
 #pragma omp parallel for private(i,j) schedule(static)  
   for (i=0;i<nRows;i++) {  
     for (j=0;j<nCols;j++) {  
       // NOTE: An exception may be thown from this call if  
       // DOASSERT is on which of course will play  
       // havoc with the omp threads. Run single threaded  
       // if using DOASSERT.  
       newView.copy(newData.index(i,j),m_data(i,j));  
     }  
   }  
   // swap the new data array for the original  
   m_data.Swap(newData);  
   // set the corresponding DataArrayView  
   DataArrayView temp(m_data.getData(),shape);  
   setPointDataView(temp);  
186  }  }
187    
188    
189  DataAbstract*  DataAbstract*
190  DataExpanded::getSlice(const DataArrayView::RegionType& region) const  DataExpanded::getSlice(const DataTypes::RegionType& region) const
191  {  {
192    return new DataExpanded(*this,region);    return new DataExpanded(*this,region);
193  }  }
194    
195  void  void
196  DataExpanded::setSlice(const DataAbstract* value,  DataExpanded::setSlice(const DataAbstract* value,
197                         const DataArrayView::RegionType& region)                         const DataTypes::RegionType& region)
198  {  {
199    const DataExpanded* tempDataExp=dynamic_cast<const DataExpanded*>(value);    const DataExpanded* tempDataExp=dynamic_cast<const DataExpanded*>(value);
200    if (tempDataExp==0) {    if (tempDataExp==0) {
# Line 193  DataExpanded::setSlice(const DataAbstrac Line 202  DataExpanded::setSlice(const DataAbstrac
202    }    }
203    //    //
204    // get shape of slice    // get shape of slice
205    DataArrayView::ShapeType shape(DataArrayView::getResultSliceShape(region));    DataTypes::ShapeType shape(DataTypes::getResultSliceShape(region));
206    DataArrayView::RegionLoopRangeType region_loop_range=getSliceRegionLoopRange(region);    DataTypes::RegionLoopRangeType region_loop_range=DataTypes::getSliceRegionLoopRange(region);
207    //    //
208    // check shape    // check shape
209    if (getPointDataView().getRank()!=region.size()) {    if (getRank()!=region.size()) {
210      throw DataException("Error - Invalid slice region.");      throw DataException("Error - Invalid slice region.");
211    }    }
212    if (tempDataExp->getPointDataView().getRank()>0 and !value->getPointDataView().checkShape(shape)) {    if (tempDataExp->getRank()>0 && !DataTypes::checkShape(value->getShape(), shape)) {
213      throw DataException (value->getPointDataView().createShapeErrorMessage(      throw DataException (DataTypes::createShapeErrorMessage(
214          "Error - Couldn't copy slice due to shape mismatch.",shape));          "Error - Couldn't copy slice due to shape mismatch.",shape, value->getShape()));
215    }    }
216    //    //
217    // copy the data from the slice into this object    // copy the data from the slice into this object
218    DataArrayView::ValueType::size_type numRows=m_data.getNumRows();    DataTypes::ValueType::size_type numRows=m_data.getNumRows();
219    DataArrayView::ValueType::size_type numCols=m_data.getNumCols();    DataTypes::ValueType::size_type numCols=m_data.getNumCols();
220    int i, j;    int i, j;
221  #pragma omp parallel for private(i,j) schedule(static)    ValueType& vec=getVector();
222      const ShapeType& mshape=getShape();
223      const ValueType& tVec=tempDataExp->getVector();
224      const ShapeType& tShape=tempDataExp->getShape();
225      #pragma omp parallel for private(i,j) schedule(static)
226    for (i=0;i<numRows;i++) {    for (i=0;i<numRows;i++) {
227      for (j=0;j<numCols;j++) {      for (j=0;j<numCols;j++) {
228        getPointDataView().copySliceFrom(getPointOffset(i,j),tempDataExp->getPointDataView(),tempDataExp->getPointOffset(i,j),region_loop_range);  /*      getPointDataView().copySliceFrom(getPointOffset(i,j),
229                                           tempDataExp->getPointDataView(),
230                                           tempDataExp->getPointOffset(i,j),
231                                           region_loop_range);*/
232            DataTypes::copySliceFrom(vec,mshape,getPointOffset(i,j),
233                                           tVec,
234                           tShape,
235                                           tempDataExp->getPointOffset(i,j),
236                                           region_loop_range);
237    
238      }      }
239    }    }
240  }  }
241    
242  void  void
243  DataExpanded::copy(const DataArrayView& value)  DataExpanded::copy(const DataConstant& value)
244  {  {
245      EsysAssert((checkShape(getShape(), value.getShape())),
246                     createShapeErrorMessage("Error - Couldn't copy due to shape mismatch.",value.getShape(),getShape()));
247    
248    //    //
249    // copy a single value to every data point in this object    // copy a single value to every data point in this object
250    int nRows=m_data.getNumRows();    int nRows=m_data.getNumRows();
251    int nCols=m_data.getNumCols();    int nCols=m_data.getNumCols();
252    int i,j;    int i,j;
253  #pragma omp parallel for private(i,j) schedule(static)    #pragma omp parallel for private(i,j) schedule(static)
254    for (i=0;i<nRows;i++) {    for (i=0;i<nRows;i++) {
255      for (j=0;j<nCols;j++) {      for (j=0;j<nCols;j++) {
256        // NOTE: An exception may be thown from this call if        // NOTE: An exception may be thown from this call if
257        // DOASSERT is on which of course will play        // DOASSERT is on which of course will play
258        // havoc with the omp threads. Run single threaded        // havoc with the omp threads. Run single threaded
259        // if using DOASSERT.        // if using DOASSERT.
260        getPointDataView().copy(m_data.index(i,j),value);        //getPointDataView().copy(getPointOffset(i,j),value);
261          DataTypes::copyPoint(getVector(), getPointOffset(i,j), getNoValues(), value.getVector(), 0);
262      }      }
263    }    }
264  }  }
265    
266    
267    // void
268    // DataExpanded::copy(const DataArrayView& value)
269    // {
270    //   //
271    //   // copy a single value to every data point in this object
272    //   int nRows=m_data.getNumRows();
273    //   int nCols=m_data.getNumCols();
274    //   int i,j;
275    //   #pragma omp parallel for private(i,j) schedule(static)
276    //   for (i=0;i<nRows;i++) {
277    //     for (j=0;j<nCols;j++) {
278    //       // NOTE: An exception may be thown from this call if
279    //       // DOASSERT is on which of course will play
280    //       // havoc with the omp threads. Run single threaded
281    //       // if using DOASSERT.
282    //       getPointDataView().copy(getPointOffset(i,j),value);
283    //     }
284    //   }
285    // }
286    
287  void  void
288  DataExpanded::copy(const boost::python::numeric::array& value)  DataExpanded::copy(const boost::python::numeric::array& value)
289  {  {
290    //  
291    // first convert the numarray into a DataArray object    // extract the shape of the numarray
292    DataArray temp(value);    DataTypes::ShapeType tempShape;
293      for (int i=0; i < value.getrank(); i++) {
294        tempShape.push_back(extract<int>(value.getshape()[i]));
295      }
296    
297      // get the space for the data vector
298    //   int len = DataTypes::noValues(tempShape);
299    //   DataVector temp_data(len, 0.0, len);
300    //   DataArrayView temp_dataView(temp_data, tempShape);
301    //   temp_dataView.copy(value);
302    
303    //    //
304    // check the input shape matches this shape    // check the input shape matches this shape
305    if (!getPointDataView().checkShape(temp.getView().getShape())) {    if (!DataTypes::checkShape(getShape(),tempShape)) {
306      throw DataException(getPointDataView().createShapeErrorMessage(      throw DataException(DataTypes::createShapeErrorMessage(
307                          "Error - (DataExpanded) Cannot copy due to shape mismatch.",                          "Error - (DataExpanded) Cannot copy due to shape mismatch.",
308                          temp.getView().getShape()));                          tempShape,getShape()));
309    }    }
310    //    //
311    // now copy over the data    // now copy over the data
312    copy(temp.getView());    //copy(temp_dataView);
313      getVector().copyFromNumArray(value);
314  }  }
315    
316    
317  void  void
318  DataExpanded::initialise(const DataArrayView::ShapeType& shape,  DataExpanded::initialise(int noSamples,
                          int noSamples,  
319                           int noDataPointsPerSample)                           int noDataPointsPerSample)
320  {  {
321      if (noSamples==0)     //retain the default empty object
322      {
323         return;
324      }
325    //    //
326    // resize data array to the required size    // resize data array to the required size
327    m_data.resize(noSamples,noDataPointsPerSample,DataArrayView::noValues(shape));    m_data.resize(noSamples,noDataPointsPerSample,getNoValues());
   //  
   // create the data view of the data array  
   DataArrayView temp(m_data.getData(),shape);  
   setPointDataView(temp);  
328  }  }
329    
330  string  string
331  DataExpanded::toString() const  DataExpanded::toString() const
332  {  {
333    stringstream temp;    stringstream temp;
334    //    FunctionSpace fs=getFunctionSpace();
335    // create a temporary view as the offset will be changed  
336    DataArrayView tempView(getPointDataView().getData(),getPointDataView().getShape(),getPointDataView().getOffset());    int offset=0;
337    for (int i=0;i<m_data.getNumRows();i++) {    for (int i=0;i<m_data.getNumRows();i++) {
338      for (int j=0;j<m_data.getNumCols();j++) {      for (int j=0;j<m_data.getNumCols();j++) {
339        tempView.setOffset(m_data.index(i,j));        offset=getPointOffset(i,j);
340        stringstream suffix;        stringstream suffix;
341        suffix << "(" << i << "," << j << ")";        suffix << "( id: " << i << ", ref: " << fs.getReferenceIDOfSample(i) << ", pnt: " << j << ")";
342        temp << tempView.toString(suffix.str());        temp << DataTypes::pointToString(getVector(),getShape(),offset,suffix.str());
343        if (!(i==(m_data.getNumRows()-1) && j==(m_data.getNumCols()-1))) {        if (!(i==(m_data.getNumRows()-1) && j==(m_data.getNumCols()-1))) {
344          temp << endl;          temp << endl;
345        }        }
346      }      }
347    }    }
348      string result=temp.str();
349      if (result.empty())
350      {
351        return "(data contains no samples)\n";
352      }
353    return temp.str();    return temp.str();
354  }  }
355    
356  DataArrayView::ValueType::size_type  DataTypes::ValueType::size_type
357  DataExpanded::getPointOffset(int sampleNo,  DataExpanded::getPointOffset(int sampleNo,
358                               int dataPointNo) const                               int dataPointNo) const
359  {  {
360    return m_data.index(sampleNo,dataPointNo);    return m_data.index(sampleNo,dataPointNo);
361  }  }
362    
363  DataArrayView  DataTypes::ValueType::size_type
 DataExpanded::getDataPoint(int sampleNo,  
                            int dataPointNo)  
 {  
   DataArrayView temp(m_data.getData(),getPointDataView().getShape(),m_data.index(sampleNo,dataPointNo));  
   return temp;  
 }  
   
 DataArrayView::ValueType::size_type  
364  DataExpanded::getLength() const  DataExpanded::getLength() const
365  {  {
366    return m_data.size();    return m_data.size();
367  }  }
368    
369    
370    
371  void  void
372  DataExpanded::setRefValue(int ref,  DataExpanded::copyToDataPoint(const int sampleNo, const int dataPointNo, const double value) {
                           const DataArray& value)  
 {  
373    //    //
374    // Get the number of samples and data-points per sample.    // Get the number of samples and data-points per sample.
375    int numSamples = getNumSamples();    int numSamples = getNumSamples();
376    int numDPPSample = getNumDPPSample();    int numDataPointsPerSample = getNumDPPSample();
377      int dataPointRank = getRank();
378      ShapeType dataPointShape = getShape();
379      if (numSamples*numDataPointsPerSample > 0) {
380         //TODO: global error handling
381         if ((sampleNo >= numSamples) || (sampleNo < 0 )) {
382              throw DataException("Error - DataExpanded::copyDataPoint invalid sampleNo.");
383         }
384         if ((dataPointNo >= numDataPointsPerSample) || (dataPointNo < 0)) {
385               throw DataException("Error - DataExpanded::copyDataPoint invalid dataPointNoInSample.");
386         }
387         ValueType::size_type offset = getPointOffset(sampleNo, dataPointNo);
388         ValueType& vec=getVector();
389         if (dataPointRank==0) {
390             vec[offset]=value;
391         } else if (dataPointRank==1) {
392            for (int i=0; i<dataPointShape[0]; i++) {
393                vec[offset+i]=value;
394            }
395         } else if (dataPointRank==2) {
396            for (int i=0; i<dataPointShape[0]; i++) {
397               for (int j=0; j<dataPointShape[1]; j++) {
398                  vec[offset+getRelIndex(dataPointShape,i,j)]=value;
399               }
400            }
401         } else if (dataPointRank==3) {
402            for (int i=0; i<dataPointShape[0]; i++) {
403               for (int j=0; j<dataPointShape[1]; j++) {
404                  for (int k=0; k<dataPointShape[2]; k++) {
405                     vec[offset+getRelIndex(dataPointShape,i,j,k)]=value;
406                  }
407               }
408            }
409         } else if (dataPointRank==4) {
410             for (int i=0; i<dataPointShape[0]; i++) {
411               for (int j=0; j<dataPointShape[1]; j++) {
412                 for (int k=0; k<dataPointShape[2]; k++) {
413                   for (int l=0; l<dataPointShape[3]; l++) {
414                      vec[offset+getRelIndex(dataPointShape,i,j,k,l)]=value;
415                   }
416                 }
417               }
418             }
419         }
420      }
421    }
422    void
423    DataExpanded::copyToDataPoint(const int sampleNo, const int dataPointNo, const boost::python::numeric::array& value) {
424      //
425      // Get the number of samples and data-points per sample.
426      int numSamples = getNumSamples();
427      int numDataPointsPerSample = getNumDPPSample();
428      int dataPointRank = getRank();
429      const ShapeType& shape = getShape();
430      //
431      // check rank:
432      if (value.getrank()!=dataPointRank)
433           throw DataException("Rank of numarray does not match Data object rank");
434      if (numSamples*numDataPointsPerSample > 0) {
435         //TODO: global error handling
436         if ((sampleNo >= numSamples) || (sampleNo < 0 )) {
437              throw DataException("Error - DataExpanded::copyDataPoint invalid sampleNo.");
438         }
439         if ((dataPointNo >= numDataPointsPerSample) || (dataPointNo < 0)) {
440               throw DataException("Error - DataExpanded::copyDataPoint invalid dataPointNoInSample.");
441         }
442         ValueType& vec=getVector();
443         if (dataPointRank==0) {
444             vec[0]=extract<double>(value[0]);
445         } else if (dataPointRank==1) {
446            for (int i=0; i<shape[0]; i++) {
447                vec[i]=extract<double>(value[i]);
448            }
449         } else if (dataPointRank==2) {
450            for (int i=0; i<shape[0]; i++) {
451               for (int j=0; j<shape[1]; j++) {
452                  vec[getRelIndex(shape,i,j)]=extract<double>(value[i][j]);
453               }
454            }
455         } else if (dataPointRank==3) {
456            for (int i=0; i<shape[0]; i++) {
457               for (int j=0; j<shape[1]; j++) {
458                  for (int k=0; k<shape[2]; k++) {
459                     vec[getRelIndex(shape,i,j,k)]=extract<double>(value[i][j][k]);
460                  }
461               }
462            }
463         } else if (dataPointRank==4) {
464             for (int i=0; i<shape[0]; i++) {
465               for (int j=0; j<shape[1]; j++) {
466                 for (int k=0; k<shape[2]; k++) {
467                   for (int l=0; l<shape[3]; l++) {
468                      vec[getRelIndex(shape,i,j,k,l)]=extract<double>(value[i][j][k][l]);
469                   }
470                 }
471               }
472             }
473         }
474      }
475    }
476    void
477    DataExpanded::copyAll(const boost::python::numeric::array& value) {
478    //    //
479    // Determine the sample number which corresponds to this reference number.    // Get the number of samples and data-points per sample.
480    int sampleNo = -1;    int numSamples = getNumSamples();
481    int tempRef = -1;    int numDataPointsPerSample = getNumDPPSample();
482    for (int n=0; n<numSamples; n++) {    int dataPointRank = getRank();
483      tempRef = getFunctionSpace().getReferenceNoFromSampleNo(n);    const ShapeType& dataPointShape = getShape();
484      if (tempRef == ref) {    //
485        sampleNo = n;    // check rank:
486        break;    if (value.getrank()!=dataPointRank+1)
487           throw DataException("Rank of numarray does not match Data object rank");
488      if (value.getshape()[0]!=numSamples*numDataPointsPerSample)
489           throw DataException("leading dimension of numarray is too small");
490      //
491      ValueType& vec=getVector();
492      int dataPoint = 0;
493      for (int sampleNo = 0; sampleNo < numSamples; sampleNo++) {
494        for (int dataPointNo = 0; dataPointNo < numDataPointsPerSample; dataPointNo++) {
495          ValueType::size_type offset=getPointOffset(sampleNo, dataPointNo);
496          if (dataPointRank==0) {
497             vec[offset]=extract<double>(value[dataPoint]);
498          } else if (dataPointRank==1) {
499             for (int i=0; i<dataPointShape[0]; i++) {
500                vec[offset+i]=extract<double>(value[dataPoint][i]);
501             }
502          } else if (dataPointRank==2) {
503             for (int i=0; i<dataPointShape[0]; i++) {
504               for (int j=0; j<dataPointShape[1]; j++) {
505             vec[offset+getRelIndex(dataPointShape,i,j)]=extract<double>(value[dataPoint][i][j]);
506               }
507             }
508           } else if (dataPointRank==3) {
509             for (int i=0; i<dataPointShape[0]; i++) {
510               for (int j=0; j<dataPointShape[1]; j++) {
511                 for (int k=0; k<dataPointShape[2]; k++) {
512             vec[offset+getRelIndex(dataPointShape,i,j,k)]=extract<double>(value[dataPoint][i][j][k]);
513                 }
514               }
515             }
516           } else if (dataPointRank==4) {
517             for (int i=0; i<dataPointShape[0]; i++) {
518               for (int j=0; j<dataPointShape[1]; j++) {
519                 for (int k=0; k<dataPointShape[2]; k++) {
520                   for (int l=0; l<dataPointShape[3]; l++) {
521                     vec[offset+getRelIndex(dataPointShape,i,j,k,l)]=extract<double>(value[dataPoint][i][j][k][l]);
522                   }
523                 }
524               }
525             }
526          }
527          dataPoint++;
528        }
529      }
530    }
531    void
532    DataExpanded::symmetric(DataAbstract* ev)
533    {
534      int sampleNo,dataPointNo;
535      int numSamples = getNumSamples();
536      int numDataPointsPerSample = getNumDPPSample();
537      DataExpanded* temp_ev=dynamic_cast<DataExpanded*>(ev);
538      if (temp_ev==0) {
539        throw DataException("Error - DataExpanded::symmetric: casting to DataExpanded failed (propably a programming error).");
540      }
541      ValueType& vec=getVector();
542      const ShapeType& shape=getShape();
543      ValueType& evVec=temp_ev->getVector();
544      const ShapeType& evShape=temp_ev->getShape();
545      #pragma omp parallel for private(sampleNo,dataPointNo) schedule(static)
546      for (sampleNo = 0; sampleNo < numSamples; sampleNo++) {
547        for (dataPointNo = 0; dataPointNo < numDataPointsPerSample; dataPointNo++) {
548             DataMaths::symmetric(vec,shape,getPointOffset(sampleNo,dataPointNo),
549                                        evVec,evShape,ev->getPointOffset(sampleNo,dataPointNo));
550        }
551      }
552    }
553    void
554    DataExpanded::nonsymmetric(DataAbstract* ev)
555    {
556      int sampleNo,dataPointNo;
557      int numSamples = getNumSamples();
558      int numDataPointsPerSample = getNumDPPSample();
559      DataExpanded* temp_ev=dynamic_cast<DataExpanded*>(ev);
560      if (temp_ev==0) {
561        throw DataException("Error - DataExpanded::nonsymmetric: casting to DataExpanded failed (propably a programming error).");
562      }
563      ValueType& vec=getVector();
564      const ShapeType& shape=getShape();
565      ValueType& evVec=temp_ev->getVector();
566      const ShapeType& evShape=temp_ev->getShape();
567      #pragma omp parallel for private(sampleNo,dataPointNo) schedule(static)
568      for (sampleNo = 0; sampleNo < numSamples; sampleNo++) {
569        for (dataPointNo = 0; dataPointNo < numDataPointsPerSample; dataPointNo++) {
570             DataMaths::nonsymmetric(vec,shape,getPointOffset(sampleNo,dataPointNo),
571                                        evVec,evShape,ev->getPointOffset(sampleNo,dataPointNo));
572      }      }
573    }    }
574    if (sampleNo == -1) {  }
575      throw DataException("DataExpanded::setRefValue error: invalid ref number supplied.");  void
576    DataExpanded::trace(DataAbstract* ev, int axis_offset)
577    {
578      int sampleNo,dataPointNo;
579      int numSamples = getNumSamples();
580      int numDataPointsPerSample = getNumDPPSample();
581      DataExpanded* temp_ev=dynamic_cast<DataExpanded*>(ev);
582      if (temp_ev==0) {
583        throw DataException("Error - DataExpanded::trace: casting to DataExpanded failed (propably a programming error).");
584      }
585      ValueType& vec=getVector();
586      const ShapeType& shape=getShape();
587      ValueType& evVec=temp_ev->getVector();
588      const ShapeType& evShape=temp_ev->getShape();
589      #pragma omp parallel for private(sampleNo,dataPointNo) schedule(static)
590      for (sampleNo = 0; sampleNo < numSamples; sampleNo++) {
591        for (dataPointNo = 0; dataPointNo < numDataPointsPerSample; dataPointNo++) {
592             DataMaths::trace(vec,shape,getPointOffset(sampleNo,dataPointNo),
593                                        evVec,evShape,ev->getPointOffset(sampleNo,dataPointNo),axis_offset);
594        }
595    }    }
596    }
597    
598    for (int n=0; n<numDPPSample; n++) {  void
599      //  DataExpanded::transpose(DataAbstract* ev, int axis_offset)
600      // Get each data-point in the sample in turn.  {
601      DataArrayView pointView = getDataPoint(sampleNo, n);    int sampleNo,dataPointNo;
602      //    int numSamples = getNumSamples();
603      // Assign the values in the DataArray to this data-point.    int numDataPointsPerSample = getNumDPPSample();
604      pointView.copy(value.getView());    DataExpanded* temp_ev=dynamic_cast<DataExpanded*>(ev);
605      if (temp_ev==0) {
606        throw DataException("Error - DataExpanded::transpose: casting to DataExpanded failed (propably a programming error).");
607      }
608      ValueType& vec=getVector();
609      const ShapeType& shape=getShape();
610      ValueType& evVec=temp_ev->getVector();
611      const ShapeType& evShape=temp_ev->getShape();
612      #pragma omp parallel for private(sampleNo,dataPointNo) schedule(static)
613      for (sampleNo = 0; sampleNo < numSamples; sampleNo++) {
614        for (dataPointNo = 0; dataPointNo < numDataPointsPerSample; dataPointNo++) {
615             DataMaths::transpose(vec,shape,getPointOffset(sampleNo,dataPointNo),
616                                        evVec,evShape,ev->getPointOffset(sampleNo,dataPointNo),axis_offset);
617        }
618    }    }
619  }  }
620    
621  void  void
622  DataExpanded::getRefValue(int ref,  DataExpanded::swapaxes(DataAbstract* ev, int axis0, int axis1)
623                            DataArray& value)  {
624      int sampleNo,dataPointNo;
625      int numSamples = getNumSamples();
626      int numDataPointsPerSample = getNumDPPSample();
627      DataExpanded* temp_ev=dynamic_cast<DataExpanded*>(ev);
628      if (temp_ev==0) {
629        throw DataException("Error - DataExpanded::swapaxes: casting to DataExpanded failed (propably a programming error).");
630      }
631      ValueType& vec=getVector();
632      const ShapeType& shape=getShape();
633      ValueType& evVec=temp_ev->getVector();
634      const ShapeType& evShape=temp_ev->getShape();
635      #pragma omp parallel for private(sampleNo,dataPointNo) schedule(static)
636      for (sampleNo = 0; sampleNo < numSamples; sampleNo++) {
637        for (dataPointNo = 0; dataPointNo < numDataPointsPerSample; dataPointNo++) {
638             DataMaths::swapaxes(vec,shape,getPointOffset(sampleNo,dataPointNo),
639                                        evVec,evShape,ev->getPointOffset(sampleNo,dataPointNo),axis0,axis1);
640        }
641      }
642    }
643    void
644    DataExpanded::eigenvalues(DataAbstract* ev)
645    {
646      int sampleNo,dataPointNo;
647      int numSamples = getNumSamples();
648      int numDataPointsPerSample = getNumDPPSample();
649      DataExpanded* temp_ev=dynamic_cast<DataExpanded*>(ev);
650      if (temp_ev==0) {
651        throw DataException("Error - DataExpanded::eigenvalues: casting to DataExpanded failed (propably a programming error).");
652      }
653      ValueType& vec=getVector();
654      const ShapeType& shape=getShape();
655      ValueType& evVec=temp_ev->getVector();
656      const ShapeType& evShape=temp_ev->getShape();
657      #pragma omp parallel for private(sampleNo,dataPointNo) schedule(static)
658      for (sampleNo = 0; sampleNo < numSamples; sampleNo++) {
659        for (dataPointNo = 0; dataPointNo < numDataPointsPerSample; dataPointNo++) {
660             DataMaths::eigenvalues(vec,shape,getPointOffset(sampleNo,dataPointNo),
661                                        evVec,evShape,ev->getPointOffset(sampleNo,dataPointNo));
662        }
663      }
664    }
665    void
666    DataExpanded::eigenvalues_and_eigenvectors(DataAbstract* ev,DataAbstract* V,const double tol)
667  {  {
   //  
   // Get the number of samples and data-points per sample.  
668    int numSamples = getNumSamples();    int numSamples = getNumSamples();
669    int numDPPSample = getNumDPPSample();    int numDataPointsPerSample = getNumDPPSample();
670      int sampleNo,dataPointNo;
671      DataExpanded* temp_ev=dynamic_cast<DataExpanded*>(ev);
672      if (temp_ev==0) {
673        throw DataException("Error - DataExpanded::eigenvalues_and_eigenvectors: casting to DataExpanded failed (propably a programming error).");
674      }
675      DataExpanded* temp_V=dynamic_cast<DataExpanded*>(V);
676      if (temp_V==0) {
677        throw DataException("Error - DataExpanded::eigenvalues_and_eigenvectors: casting to DataExpanded failed (propably a programming error).");
678      }
679      ValueType& vec=getVector();
680      const ShapeType& shape=getShape();
681      ValueType& evVec=temp_ev->getVector();
682      const ShapeType& evShape=temp_ev->getShape();
683      ValueType& VVec=temp_V->getVector();
684      const ShapeType& VShape=temp_V->getShape();
685      #pragma omp parallel for private(sampleNo,dataPointNo) schedule(static)
686      for (sampleNo = 0; sampleNo < numSamples; sampleNo++) {
687        for (dataPointNo = 0; dataPointNo < numDataPointsPerSample; dataPointNo++) {
688             DataMaths::eigenvalues_and_eigenvectors(vec,shape,getPointOffset(sampleNo,dataPointNo),
689                                        evVec,evShape,ev->getPointOffset(sampleNo,dataPointNo),
690                                        VVec, VShape,V->getPointOffset(sampleNo,dataPointNo),tol);
691        }
692      }
693    }
694    
695    //  void
696    // Determine the sample number which corresponds to this reference number  DataExpanded::setToZero(){
697    int sampleNo = -1;  // TODO: Surely there is a more efficient way to do this????
698    int tempRef = -1;  // Why is there no memset here? Parallel issues?
699    for (int n=0; n<numSamples; n++) {    int numSamples = getNumSamples();
700      tempRef = getFunctionSpace().getReferenceNoFromSampleNo(n);    int numDataPointsPerSample = getNumDPPSample();
701      if (tempRef == ref) {    DataTypes::ValueType::size_type n = getNoValues();
702        sampleNo = n;    double* p;
703        break;    int  sampleNo,dataPointNo, i;
704      #pragma omp parallel for private(sampleNo,dataPointNo,p,i) schedule(static)
705      for (sampleNo = 0; sampleNo < numSamples; sampleNo++) {
706        for (dataPointNo = 0; dataPointNo < numDataPointsPerSample; dataPointNo++) {
707            p=&(m_data[getPointOffset(sampleNo,dataPointNo)]);
708            for (i=0; i<n ;++i) p[i]=0.;
709      }      }
710    }    }
711    if (sampleNo == -1) {  }
712      throw DataException("DataExpanded::getRefValue error: invalid ref number supplied.");  
713    /* Append MPI rank to file name if multiple MPI processes */
714    char *Escript_MPI_appendRankToFileName(const char *fileName, int mpi_size, int mpi_rank) {
715      /* Make plenty of room for the mpi_rank number and terminating '\0' */
716      char *newFileName = (char *)malloc(strlen(fileName)+20);
717      strncpy(newFileName, fileName, strlen(fileName)+1);
718      if (mpi_size>1) sprintf(newFileName+strlen(newFileName), ".%04d", mpi_rank);
719      return(newFileName);
720    }
721    
722    void
723    DataExpanded::dump(const std::string fileName) const
724    {
725       #ifdef USE_NETCDF
726       const int ldims=2+DataTypes::maxRank;
727       const NcDim* ncdims[ldims];
728       NcVar *var, *ids;
729       int rank = getRank();
730       int type=  getFunctionSpace().getTypeCode();
731       int ndims =0;
732       long dims[ldims];
733       const double* d_ptr=&(m_data[0]);
734       const DataTypes::ShapeType& shape = getShape();
735       int mpi_iam=getFunctionSpace().getDomain()->getMPIRank();
736       int mpi_num=getFunctionSpace().getDomain()->getMPISize();
737    #ifdef PASO_MPI
738       MPI_Status status;
739    #endif
740    
741    #ifdef PASO_MPI
742       /* Serialize NetCDF I/O */
743       if (mpi_iam>0) MPI_Recv(&ndims, 0, MPI_INT, mpi_iam-1, 81801, MPI_COMM_WORLD, &status);
744    #endif
745    
746       // netCDF error handler
747       NcError err(NcError::verbose_nonfatal);
748       // Create the file.
749       char *newFileName = Escript_MPI_appendRankToFileName(fileName.c_str(), mpi_num, mpi_iam);
750       NcFile dataFile(newFileName, NcFile::Replace);
751       // check if writing was successful
752       if (!dataFile.is_valid())
753            throw DataException("Error - DataExpanded:: opening of netCDF file for output failed.");
754       if (!dataFile.add_att("type_id",2) )
755            throw DataException("Error - DataExpanded:: appending data type to netCDF file failed.");
756       if (!dataFile.add_att("rank",rank) )
757            throw DataException("Error - DataExpanded:: appending rank attribute to netCDF file failed.");
758       if (!dataFile.add_att("function_space_type",type))
759            throw DataException("Error - DataExpanded:: appending function space attribute to netCDF file failed.");
760       ndims=rank+2;
761       if ( rank >0 ) {
762           dims[0]=shape[0];
763           if (! (ncdims[0] = dataFile.add_dim("d0",shape[0])) )
764                throw DataException("Error - DataExpanded:: appending ncdimension 0 to netCDF file failed.");
765       }
766       if ( rank >1 ) {
767           dims[1]=shape[1];
768           if (! (ncdims[1] = dataFile.add_dim("d1",shape[1])) )
769                throw DataException("Error - DataExpanded:: appending ncdimension 1 to netCDF file failed.");
770       }
771       if ( rank >2 ) {
772           dims[2]=shape[2];
773           if (! (ncdims[2] = dataFile.add_dim("d2", shape[2])) )
774                throw DataException("Error - DataExpanded:: appending ncdimension 2 to netCDF file failed.");
775       }
776       if ( rank >3 ) {
777           dims[3]=shape[3];
778           if (! (ncdims[3] = dataFile.add_dim("d3", shape[3])) )
779                throw DataException("Error - DataExpanded:: appending ncdimension 3 to netCDF file failed.");
780       }
781       dims[rank]=getFunctionSpace().getNumDataPointsPerSample();
782       if (! (ncdims[rank] = dataFile.add_dim("num_data_points_per_sample", dims[rank])) )
783                throw DataException("Error - DataExpanded:: appending num_data_points_per_sample to netCDF file failed.");
784       dims[rank+1]=getFunctionSpace().getNumSamples();
785       if (! (ncdims[rank+1] = dataFile.add_dim("num_samples", dims[rank+1])) )
786                throw DataException("Error - DataExpanded:: appending num_sample to netCDF file failed.");
787    
788       if (getFunctionSpace().getNumSamples()>0)
789       {
790    
791         if (! ( ids = dataFile.add_var("id", ncInt, ncdims[rank+1])) )
792            throw DataException("Error - DataExpanded:: appending reference id to netCDF file failed.");
793         const int* ids_p=getFunctionSpace().borrowSampleReferenceIDs();
794         if (! (ids->put(ids_p,dims[rank+1])) )
795            throw DataException("Error - DataExpanded:: copy reference id  to netCDF buffer failed.");
796         if (! ( var = dataFile.add_var("data", ncDouble, ndims, ncdims)) )
797            throw DataException("Error - DataExpanded:: appending variable to netCDF file failed.");
798         if (! (var->put(d_ptr,dims)) )
799            throw DataException("Error - DataExpanded:: copy data to netCDF buffer failed.");
800       }
801    #ifdef PASO_MPI
802       if (mpi_iam<mpi_num-1) MPI_Send(&ndims, 0, MPI_INT, mpi_iam+1, 81801, MPI_COMM_WORLD);
803    #endif
804       #else
805       throw DataException("Error - DataExpanded:: dump is not configured with netCDF. Please contact your installation manager.");
806       #endif
807    }
808    
809    void  
810    DataExpanded::setTaggedValue(int tagKey,
811               const DataTypes::ShapeType& pointshape,
812                   const DataTypes::ValueType& value,
813               int dataOffset)
814    {
815      int numSamples = getNumSamples();
816      int numDataPointsPerSample = getNumDPPSample();
817      int sampleNo,dataPointNo, i;
818      DataTypes::ValueType::size_type n = getNoValues();
819      double* p;
820      const double* in=&value[0+dataOffset];
821      
822      if (value.size() != n) {
823        throw DataException("Error - DataExpanded::setTaggedValue: number of input values does not match number of values per data points.");
824      }
825    
826      #pragma omp parallel for private(sampleNo,dataPointNo,p,i) schedule(static)
827      for (sampleNo = 0; sampleNo < numSamples; sampleNo++) {
828        if (getFunctionSpace().getTagFromSampleNo(sampleNo) == tagKey ) {
829            for (dataPointNo = 0; dataPointNo < numDataPointsPerSample; dataPointNo++) {
830                p=&(m_data[getPointOffset(sampleNo,dataPointNo)]);
831                for (i=0; i<n ;++i) p[i]=in[i];
832            }
833        }
834    }    }
835    }
836    
   //  
   // Get the first data-point associated with this sample number.  
   DataArrayView pointView = getDataPoint(sampleNo, 0);  
837    
838    //  void
839    // Load the values from this data-point into the DataArray  DataExpanded::reorderByReferenceIDs(int *reference_ids)
840    value.getView().copy(pointView);  {
841      int numSamples = getNumSamples();
842      DataTypes::ValueType::size_type n = getNoValues() * getNumDPPSample();
843      int sampleNo, sampleNo2,i;
844      double* p,*p2;
845      register double rtmp;
846      FunctionSpace fs=getFunctionSpace();
847    
848      for (sampleNo = 0; sampleNo < numSamples; sampleNo++) {
849         const int id_in=reference_ids[sampleNo];
850         const int id=fs.getReferenceIDOfSample(sampleNo);
851         if (id!=id_in) {
852             bool matched=false;
853             for (sampleNo2 = sampleNo+1; sampleNo2 < numSamples; sampleNo2++) {
854                  if (id == reference_ids[sampleNo2]) {
855                     p=&(m_data[getPointOffset(sampleNo,0)]);
856                     p2=&(m_data[getPointOffset(sampleNo2,0)]);
857                     for (i=0; i<n ;i++) {
858                             rtmp=p[i];
859                             p[i]=p2[i];
860                             p2[i]=rtmp;
861                     }
862                     reference_ids[sampleNo]=id;
863                     reference_ids[sampleNo2]=id_in;
864                     matched=true;
865                     break;
866                  }
867             }
868             if (! matched) {
869                throw DataException("Error - DataExpanded::reorderByReferenceIDs: unable to reorder sample data by reference ids");
870             }
871         }
872       }
873    }
874    
875    DataTypes::ValueType&
876    DataExpanded::getVector()
877    {
878        return m_data.getData();
879    }
880    
881    const DataTypes::ValueType&
882    DataExpanded::getVector() const
883    {
884        return m_data.getData();
885  }  }
886    
887  }  // end of namespace  }  // end of namespace

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