/[escript]/trunk/escript/src/DataTagged.cpp
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trunk/esys2/escript/src/Data/DataTagged.cpp revision 82 by jgs, Tue Oct 26 06:53:54 2004 UTC trunk/escript/src/DataTagged.cpp revision 2766 by jfenwick, Mon Nov 23 05:10:53 2009 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.                                             *  
  *                                                                            *  
  ******************************************************************************  
 */  
1    
2  #include "escript/Data/DataTagged.h"  /*******************************************************
3  #include "escript/Data/DataConstant.h"  *
4    * Copyright (c) 2003-2009 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 "DataTagged.h"
17    #include "esysUtils/esys_malloc.h"
18    
19    #include "DataConstant.h"
20    #include "DataException.h"
21    #ifdef USE_NETCDF
22    #include <netcdfcpp.h>
23    #endif
24    #ifdef PASO_MPI
25    #include <mpi.h>
26    #endif
27    #include "DataMaths.h"
28    
29  #include <sstream>  
30    #define CHECK_FOR_EX_WRITE if (!checkNoSharing()) {throw DataException("Attempt to modify shared object");}
31    
32    // #define CHECK_FOR_EX_WRITE if (!checkNoSharing()) {std::ostringstream ss; ss << " Attempt to modify shared object. line " << __LINE__ << " of " << __FILE__; throw DataException(ss.str());}
33    
34  using namespace std;  using namespace std;
35    
36  namespace escript {  namespace escript {
37    
38  DataTagged::DataTagged():  DataTagged::DataTagged()
39    DataAbstract(FunctionSpace())    : parent(FunctionSpace(),DataTypes::scalarShape)
40  {  {
41    //    // default constructor
42    
43    // create a scalar default value    // create a scalar default value
44    m_data.push_back(0.0);    m_data.resize(1,0.,1);
   DataArrayView temp(m_data,DataArrayView::ShapeType());  
   setPointDataView(temp);  
45  }  }
46    
47  DataTagged::DataTagged(const TagListType& tagKeys,  DataTagged::DataTagged(const FunctionSpace& what,
48                 const ValueListType& values,                         const DataTypes::ShapeType &shape,
49                 const DataArrayView& defaultValue,                         const int tags[],
50                 const FunctionSpace& what):                         const ValueType& data)
51    DataAbstract(what)    : parent(what,shape)
52  {  {
53    //    // alternative constructor
54    // The default value is always the first item in the values list    // not unit_tested tested yet
55    m_data.insert(m_data.end(), &defaultValue.getData(0), &defaultValue.getData(defaultValue.noValues()) );    // It is not explicitly unit tested yet, but it is called from DataFactory
56    DataArrayView temp(m_data,defaultValue.getShape());  
57    setPointDataView(temp);    if (!what.canTag())
58    // add remaining tags and values    {
59    addTaggedValues(tagKeys,values);      throw DataException("Programming error - DataTag created with a non-taggable FunctionSpace.");
60      }
61      // copy the data
62      m_data=data;
63    
64      // we can't rely on the tag array to give us the number of tags so
65      // use the data we have been passed
66      int valsize=DataTypes::noValues(shape);
67      int ntags=data.size()/valsize;
68    
69      // create the tag lookup map
70      // we assume that the first value and first tag are the default value so we skip
71      for (int i=1;i<ntags;++i)
72      {
73        m_offsetLookup.insert(DataMapType::value_type(tags[i],i*valsize));
74      }
75  }  }
76    
77  DataTagged::DataTagged(const DataTagged& other):  DataTagged::DataTagged(const FunctionSpace& what,
78    DataAbstract(other.getFunctionSpace()),                         const DataTypes::ShapeType &shape,
79    m_data(other.m_data),                         const TagListType& tags,
80    m_offsetLookup(other.m_offsetLookup)                         const ValueType& data)
81      : parent(what,shape)
82  {  {
83    DataArrayView temp(m_data,other.getPointDataView().getShape());    // alternative constructor
84    setPointDataView(temp);  
85      if (!what.canTag())
86      {
87        throw DataException("Programming error - DataTag created with a non-taggable FunctionSpace.");
88      }
89    
90      // copy the data
91      m_data=data;
92    
93      // create the view of the data
94    //   DataArrayView tempView(m_data,shape);
95    //   setPointDataView(tempView);
96    
97      // create the tag lookup map
98    
99    //   for (int sampleNo=0; sampleNo<getNumSamples(); sampleNo++) {
100    //     m_offsetLookup.insert(DataMapType::value_type(sampleNo,tags[sampleNo]));
101    //   }
102    
103      // The above code looks like it will create a map the wrong way around
104    
105      int valsize=DataTypes::noValues(shape);
106      int npoints=(data.size()/valsize)-1;
107      int ntags=tags.size();
108      if (ntags>npoints)
109      {     // This throw is not unit tested yet
110        throw DataException("Programming error - Too many tags for the supplied values.");
111      }
112    
113      // create the tag lookup map
114      // we assume that the first value is the default value so we skip it (hence the i+1 below)
115      for (int i=0;i<ntags;++i)
116      {
117        m_offsetLookup.insert(DataMapType::value_type(tags[i],(i+1)*valsize));
118      }
119  }  }
120    
121  DataTagged::DataTagged(const DataConstant& other):  
122    DataAbstract(other.getFunctionSpace())  DataTagged::DataTagged(const DataTagged& other)
123      : parent(other.getFunctionSpace(),other.getShape()),
124      m_offsetLookup(other.m_offsetLookup),
125      m_data(other.m_data)
126  {  {
127    //    // copy constructor
128    // Fill the default value with the constant value item from other  
129    const DataArrayView& value=other.getPointDataView();    // create the data view
130    m_data.insert(m_data.end(), &value.getData(0), &value.getData(value.noValues()) );  //   DataArrayView temp(m_data,other.getPointDataView().getShape());
131    DataArrayView temp(m_data,value.getShape());  //   setPointDataView(temp);
   setPointDataView(temp);  
132  }  }
133    
134  DataTagged::DataTagged(const DataTagged& other,  DataTagged::DataTagged(const DataConstant& other)
135                 const DataArrayView::RegionType& region):    : parent(other.getFunctionSpace(),other.getShape())
   DataAbstract(other.getFunctionSpace())  
136  {  {
137    //    // copy constructor
138    // get the shape of the slice to copy from other  
139    DataArrayView::ShapeType shape(DataArrayView::getResultSliceShape(region));    if (!other.getFunctionSpace().canTag())
140    //    {
141    // allocate enough space for all values      throw DataException("Programming error - DataTag created with a non-taggable FunctionSpace.");
142    m_data.resize(DataArrayView::noValues(shape)*(other.m_offsetLookup.size()+1));    }
143    DataArrayView temp(m_data,shape);  
144    setPointDataView(temp);    // fill the default value with the constant value item from "other"
145    getDefaultValue().copySlice(other.getDefaultValue(),region);    int len = other.getNoValues();
146    //    m_data.resize(len,0.,len);
147    // Loop through the tag values    for (int i=0; i<len; i++) {
148    DataMapType::const_iterator pos;      m_data[i]=other.getVectorRO()[i];
149    DataArrayView::ValueType::size_type tagOffset=getPointDataView().noValues();    }
   for (pos=other.m_offsetLookup.begin();pos!=other.m_offsetLookup.end();++pos){  
     getPointDataView().copySlice(tagOffset,other.getPointDataView(), pos->second,region);  
     m_offsetLookup.insert(DataMapType::value_type(pos->first,tagOffset));  
     tagOffset+=getPointDataView().noValues();  
   }  
150  }  }
151    
152  void  
153  DataTagged::reshapeDataPoint(const DataArrayView::ShapeType& shape)  // Create a new object by copying tags
154    DataTagged::DataTagged(const FunctionSpace& what,
155                 const DataTypes::ShapeType& shape,
156             const DataTypes::ValueType& defaultvalue,
157                 const DataTagged* tagsource)
158     : parent(what,shape)
159  {  {
160    //  // This constructor has not been unit tested yet
161    // can only reshape a rank zero data point  
162    if (getPointDataView().getRank()!=0) {    if (defaultvalue.size()!=DataTypes::noValues(shape)) {
163      stringstream temp;      throw DataException("Programming error - defaultvalue does not match supplied shape.");
     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());  
164    }    }
165    //  
166    // allocate enough space for all values  
167    DataArrayView::ValueType newData(DataArrayView::noValues(shape)*(m_offsetLookup.size()+1));    if (!what.canTag())
168    DataArrayView newView(newData,shape);    {
169    newView.copy(0,getDefaultValue()());      throw DataException("Programming error - DataTag created with a non-taggable FunctionSpace.");
170    //    }
171    // Loop through the tag values  
172    DataMapType::iterator pos;    if (tagsource!=0)
173    DataArrayView::ValueType::size_type tagOffset=DataArrayView::noValues(shape);    {
174    for (pos=m_offsetLookup.begin();pos!=m_offsetLookup.end();++pos){         m_data.resize(defaultvalue.size(),0.);   // since this is tagged data, we should have blocksize=1
175      newView.copy(tagOffset,m_data[pos->second]);  
176      pos->second=tagOffset;         DataTagged::DataMapType::const_iterator i;
177      tagOffset+=DataArrayView::noValues(shape);         for (i=tagsource->getTagLookup().begin();i!=tagsource->getTagLookup().end();i++) {
178    }        addTag(i->first);
179    m_data=newData;         }
180    DataArrayView temp(m_data,shape);    }
181    setPointDataView(temp);    else
182      {
183        m_data.resize(defaultvalue.size());
184      }
185    
186      // need to set the default value ....
187      for (int i=0; i<defaultvalue.size(); i++) {
188         m_data[i]=defaultvalue[i];
189      }
190    }
191    
192    DataAbstract*
193    DataTagged::deepCopy()
194    {
195      return new DataTagged(*this);
196  }  }
197    
198  DataAbstract*  DataAbstract*
199  DataTagged::getSlice(const DataArrayView::RegionType& region) const  DataTagged::getSlice(const DataTypes::RegionType& region) const
200  {  {
201    return new DataTagged(*this,region);    return new DataTagged(*this, region);
202    }
203    
204    DataTagged::DataTagged(const DataTagged& other,
205                   const DataTypes::RegionType& region)
206      : parent(other.getFunctionSpace(),DataTypes::getResultSliceShape(region))
207    {
208      // slice constructor
209    
210      // get the shape of the slice to copy from other
211      DataTypes::ShapeType regionShape(DataTypes::getResultSliceShape(region));
212      DataTypes::RegionLoopRangeType regionLoopRange=DataTypes::getSliceRegionLoopRange(region);
213    
214      // allocate enough space in this for all values
215      // (need to add one to allow for the default value)
216      int len = DataTypes::noValues(regionShape)*(other.m_offsetLookup.size()+1);
217      m_data.resize(len,0.0,len);
218    
219      // copy the default value from other to this
220      const DataTypes::ShapeType& otherShape=other.getShape();
221      const DataTypes::ValueType& otherData=other.getVectorRO();
222      DataTypes::copySlice(getVectorRW(),getShape(),getDefaultOffset(),otherData,otherShape,other.getDefaultOffset(), regionLoopRange);
223    
224      // loop through the tag values copying these
225      DataMapType::const_iterator pos;
226      DataTypes::ValueType::size_type tagOffset=getNoValues();
227      for (pos=other.m_offsetLookup.begin();pos!=other.m_offsetLookup.end();pos++){
228        DataTypes::copySlice(m_data,getShape(),tagOffset,otherData, otherShape, pos->second, regionLoopRange);
229        m_offsetLookup.insert(DataMapType::value_type(pos->first,tagOffset));
230        tagOffset+=getNoValues();
231      }
232  }  }
233    
234  void  void
235  DataTagged::setSlice(const DataAbstract* value,  DataTagged::setSlice(const DataAbstract* other,
236                       const DataArrayView::RegionType& region)                       const DataTypes::RegionType& region)
237  {  {
238    const DataTagged* tempDataTag=dynamic_cast<const DataTagged*>(value);  
239    if (tempDataTag==0) {    // other must be another DataTagged object
240      // Data:setSlice implementation should ensure this
241      const DataTagged* otherTemp=dynamic_cast<const DataTagged*>(other);
242      if (otherTemp==0) {
243      throw DataException("Programming error - casting to DataTagged.");      throw DataException("Programming error - casting to DataTagged.");
244    }    }
245    if (getPointDataView().getRank()!=region.size()) {  
246      CHECK_FOR_EX_WRITE
247    
248      // determine shape of the specified region
249      DataTypes::ShapeType regionShape(DataTypes::getResultSliceShape(region));
250    
251      // modify region specification as needed to match rank of this object
252      DataTypes::RegionLoopRangeType regionLoopRange=DataTypes::getSliceRegionLoopRange(region);
253    
254      // ensure rank/shape of this object is compatible with specified region
255      if (getRank()!=region.size()) {
256      throw DataException("Error - Invalid slice region.");      throw DataException("Error - Invalid slice region.");
257    }    }
258      if (otherTemp->getRank()>0 && !DataTypes::checkShape(other->getShape(),regionShape)) {
259        throw DataException (DataTypes::createShapeErrorMessage(
260                             "Error - Couldn't copy slice due to shape mismatch.",regionShape,other->getShape()));
261      }
262    
263      const DataTypes::ValueType& otherData=otherTemp->getVectorRO();
264      const DataTypes::ShapeType& otherShape=otherTemp->getShape();
265      // copy slice from other default value to this default value
266      DataTypes::copySliceFrom(m_data,getShape(),getDefaultOffset(),otherData,otherShape,otherTemp->getDefaultOffset(),regionLoopRange);
267    
268      // loop through tag values in other, adding any which aren't in this, using default value
269      DataMapType::const_iterator pos;
270      for (pos=otherTemp->m_offsetLookup.begin();pos!=otherTemp->m_offsetLookup.end();pos++) {
271        if (!isCurrentTag(pos->first)) {
272          addTag(pos->first);
273        }
274      }
275    
276      // loop through the tag values copying slices from other to this
277      for (pos=m_offsetLookup.begin();pos!=m_offsetLookup.end();pos++) {
278        DataTypes::copySliceFrom(m_data,getShape(),getOffsetForTag(pos->first),otherData, otherShape, otherTemp->getOffsetForTag(pos->first), regionLoopRange);
279    
280      }
281    
282    }
283    
284    int
285    DataTagged::getTagNumber(int dpno)
286    {
287    //    //
288    // get the shape of the slice    // Get the number of samples and data-points per sample
289    DataArrayView::ShapeType shape(DataArrayView::getResultSliceShape(region));    int numSamples = getNumSamples();
290    if (!value->getPointDataView().checkShape(shape)) {    int numDataPointsPerSample = getNumDPPSample();
291      throw DataException (value->getPointDataView().createShapeErrorMessage(    int numDataPoints = numSamples * numDataPointsPerSample;
292                  "Error - Couldn't copy slice due to shape mismatch.",shape));  
293      if (numDataPointsPerSample==0) {
294        throw DataException("DataTagged::getTagNumber error: no data-points associated with this object.");
295    }    }
296    getDefaultValue().copySliceFrom(tempDataTag->getDefaultValue(),region);  
297      if (dpno<0 || dpno>numDataPoints-1) {
298        throw DataException("DataTagged::getTagNumber error: invalid data-point number supplied.");
299      }
300    
301    //    //
302    // Loop through the tag values    // Determine the sample number which corresponds to this data-point number
303    DataMapType::const_iterator pos;    int sampleNo = dpno / numDataPointsPerSample;
304    for (pos=m_offsetLookup.begin();pos!=m_offsetLookup.end();++pos){  
305      getDataPointByTag(pos->first).copySliceFrom(tempDataTag->getDataPointByTag(pos->first),region);    //
306    }    // Determine the tag number which corresponds to this sample number
307      int tagNo = getFunctionSpace().getTagFromSampleNo(sampleNo);
308    
309      //
310      // return the tag number
311      return(tagNo);
312  }  }
313    
314  void  void
315  DataTagged::setTaggedValue(int tagKey,  DataTagged::setTaggedValue(int tagKey,
316                             const DataArrayView& value)                 const DataTypes::ShapeType& pointshape,
317  {                             const ValueType& value,
318                   int dataOffset)
319    {
320      if (!DataTypes::checkShape(getShape(), pointshape)) {
321          throw DataException(DataTypes::createShapeErrorMessage(
322                              "Error - Cannot setTaggedValue due to shape mismatch.", pointshape,getShape()));
323      }
324      CHECK_FOR_EX_WRITE
325    DataMapType::iterator pos(m_offsetLookup.find(tagKey));    DataMapType::iterator pos(m_offsetLookup.find(tagKey));
326    if (pos==m_offsetLookup.end()) {    if (pos==m_offsetLookup.end()) {
327      //      // tag couldn't be found so use addTaggedValue
328      // tag couldn't be found so add as a new tag      addTaggedValue(tagKey,pointshape, value, dataOffset);
     addTaggedValue(tagKey,value);  
329    } else {    } else {
330      if (!getPointDataView().checkShape(value.getShape())) {      // copy the values into the data array at the offset determined by m_offsetLookup
331        throw DataException(getPointDataView().createShapeErrorMessage(      int offset=pos->second;
332           "Error - Cannot setTaggedValue due to shape mismatch.", value.getShape()));      for (unsigned int i=0; i<getNoValues(); i++) {
333          m_data[offset+i]=value[i+dataOffset];
334      }      }
     //  
     // copy the values into tagged data storage  
     copy(&value.getData(0), &value.getData(getPointDataView().noValues()), &m_data[pos->second]);  
335    }    }
336  }  }
337    
 void  
 DataTagged::setTaggedValues(const TagListType& tagKeys,  
                             const ValueListType& values)  
 {  
   for (int i=0;i<tagKeys.size();++i) {  
     setTaggedValue(tagKeys[i],values[i]);  
   }  
 }  
338    
339  void  void
340  DataTagged::addTaggedValue(int tagKey,  DataTagged::addTaggedValues(const TagListType& tagKeys,
341                             const DataArrayView& value)                              const ValueBatchType& values,
342                                const ShapeType& vShape)
343  {  {
344    if (!getPointDataView().checkShape(value.getShape())) {    DataTypes::ValueType t(values.size(),0);
345      throw DataException(getPointDataView().createShapeErrorMessage(    for (size_t i=0;i<values.size();++i)
346           "Error - Cannot addTaggedValue due to shape mismatch.", value.getShape()));    {
347        t[i]=values[i];
348    }    }
349    //    addTaggedValues(tagKeys,t,vShape);
   // save the key and the location of its data  
   m_offsetLookup.insert( DataMapType::value_type(tagKey,m_data.size()) );  
   //  
   // insert the data given in value at the end of m_data  
   m_data.insert( m_data.end(), &(value.getData(0)), &(value.getData(value.noValues())) );  
350  }  }
351    
352    
353    // Note: The check to see if vShape==our shape is done in the addTaggedValue method
354  void  void
355  DataTagged::addTaggedValues(const TagListType& tagKeys,  DataTagged::addTaggedValues(const TagListType& tagKeys,
356                              const ValueListType& values)                              const ValueType& values,
357                                const ShapeType& vShape)
358  {  {
359      unsigned int n=getNoValues();
360      unsigned int numVals=values.size()/n;
361    if (values.size()==0) {    if (values.size()==0) {
362      //      // copy the current default value for each of the tags
     // Copy the default value for each of the tags  
363      TagListType::const_iterator iT;      TagListType::const_iterator iT;
364      for (iT=tagKeys.begin();iT!=tagKeys.end();++iT) {      for (iT=tagKeys.begin();iT!=tagKeys.end();iT++) {
       //  
365        // the point data view for DataTagged points at the default value        // the point data view for DataTagged points at the default value
366        addTaggedValue(*iT,getPointDataView());        addTag(*iT);
367      }      }
368    } else if (values.size()==1 && tagKeys.size()>1) {    } else if (numVals==1 && tagKeys.size()>1) {
369      //      // assume the one given value will be used for all tag values
     // assume the one value will be used for all tag values  
     // Copy the input data  
370      TagListType::const_iterator iT;      TagListType::const_iterator iT;
371      for (iT=tagKeys.begin();iT!=tagKeys.end();++iT) {      for (iT=tagKeys.begin();iT!=tagKeys.end();iT++) {
372        addTaggedValue(*iT,values[0]);        addTaggedValue(*iT, vShape, values,0);
373      }      }
374    } else {    } else {
375      if (tagKeys.size()!=values.size()) {      if (tagKeys.size()!=numVals) {
376        stringstream temp;        stringstream temp;
377        temp << "Error - (addTaggedValue) Number of tags: " << tagKeys.size()        temp << "Error - (addTaggedValue) Number of tags: " << tagKeys.size()
378         << " doesn't match the number of values: " << values.size();         << " doesn't match number of values: " << values.size();
379        throw DataException(temp.str());        throw DataException(temp.str());
380      } else {      } else {
381        for (int i=0;i<tagKeys.size();++i) {        unsigned int i;
382          addTaggedValue(tagKeys[i],values[i]);        int offset=0;
383          for (i=0;i<tagKeys.size();i++ ,offset+=n) {
384            addTaggedValue(tagKeys[i],vShape,values,offset);
385        }        }
386      }      }
387    }    }
388  }  }
389    
390    
391    
392    
393    void
394    DataTagged::addTaggedValue(int tagKey,
395                   const DataTypes::ShapeType& pointshape,
396                               const ValueType& value,
397                   int dataOffset)
398    {
399      if (!DataTypes::checkShape(getShape(), pointshape)) {
400        throw DataException(DataTypes::createShapeErrorMessage(
401                            "Error - Cannot addTaggedValue due to shape mismatch.", pointshape,getShape()));
402      }
403      CHECK_FOR_EX_WRITE
404      DataMapType::iterator pos(m_offsetLookup.find(tagKey));
405      if (pos!=m_offsetLookup.end()) {
406        // tag already exists so use setTaggedValue
407        setTaggedValue(tagKey,pointshape, value, dataOffset);
408      } else {
409        // save the key and the location of its data in the lookup tab
410        m_offsetLookup.insert(DataMapType::value_type(tagKey,m_data.size()));
411        // add the data given in "value" at the end of m_data
412        // need to make a temp copy of m_data, resize m_data, then copy
413        // all the old values plus the value to be added back into m_data
414        ValueType m_data_temp(m_data);
415        int oldSize=m_data.size();
416        int newSize=m_data.size()+getNoValues();
417        m_data.resize(newSize,0.,newSize);
418        for (int i=0;i<oldSize;i++) {
419          m_data[i]=m_data_temp[i];
420        }
421        for (unsigned int i=0;i<getNoValues();i++) {
422          m_data[oldSize+i]=value[i+dataOffset];
423        }
424      }
425    }
426    
427    void
428    DataTagged::addTag(int tagKey)
429    {
430      CHECK_FOR_EX_WRITE
431      DataMapType::iterator pos(m_offsetLookup.find(tagKey));
432      if (pos!=m_offsetLookup.end()) {
433        // tag already exists so use setTaggedValue
434    //    setTaggedValue(tagKey,value);
435      } else {
436        // save the key and the location of its data in the lookup tab
437        m_offsetLookup.insert(DataMapType::value_type(tagKey,m_data.size()));
438        // add the data given in "value" at the end of m_data
439        // need to make a temp copy of m_data, resize m_data, then copy
440        // all the old values plus the value to be added back into m_data
441        ValueType m_data_temp(m_data);
442        int oldSize=m_data.size();
443        int newSize=m_data.size()+getNoValues();
444        m_data.resize(newSize,0.,newSize);
445        for (int i=0;i<oldSize;i++) {
446          m_data[i]=m_data_temp[i];
447        }
448        for (unsigned int i=0;i<getNoValues();i++) {
449          m_data[oldSize+i]=m_data[m_defaultValueOffset+i];
450        }
451      }
452    }
453    
454    
455  double*  double*
456  DataTagged::getSampleDataByTag(int tag)  DataTagged::getSampleDataByTag(int tag)
457  {  {
458      CHECK_FOR_EX_WRITE
459    DataMapType::iterator pos(m_offsetLookup.find(tag));    DataMapType::iterator pos(m_offsetLookup.find(tag));
460    if (pos==m_offsetLookup.end()) {    if (pos==m_offsetLookup.end()) {
     //  
461      // tag couldn't be found so return the default value      // tag couldn't be found so return the default value
462      return &(m_data[0]);      return &(m_data[0]);
463    } else {    } else {
     //  
464      // return the data-point corresponding to the given tag      // return the data-point corresponding to the given tag
465      return &(m_data[pos->second]);      return &(m_data[pos->second]);
466    }    }
467  }  }
468    
469    
470    bool
471    DataTagged::hasNaN() const
472    {
473        for (ValueType::size_type i=0;i<m_data.size();++i)
474        {
475            if (nancheck(m_data[i]))    // can't assume we have new standard NaN checking
476            {
477                return true;
478            }
479        }
480        return false;
481    }
482    
483  string  string
484  DataTagged::toString() const  DataTagged::toString() const
485  {  {
486      using namespace escript::DataTypes;
487      string empty="";
488    stringstream temp;    stringstream temp;
489    DataMapType::const_iterator i;    DataMapType::const_iterator i;
490    temp << "Tag(Default)" << endl;    temp << "Tag(Default)" << endl;
491    temp << getDefaultValue().toString() << endl;    temp << pointToString(m_data,getShape(),getDefaultOffset(),empty) << endl;
   //  
492    // create a temporary view as the offset will be changed    // create a temporary view as the offset will be changed
493    DataArrayView tempView(getPointDataView().getData(), getPointDataView().getShape());  //   DataArrayView tempView(getPointDataView().getData(), getPointDataView().getShape());
494    for (i=m_offsetLookup.begin();i!=m_offsetLookup.end();++i) {    for (i=m_offsetLookup.begin();i!=m_offsetLookup.end();++i) {
495      temp << "Tag(" << i->first << ")" << endl;      temp << "Tag(" << i->first << ")" << endl;
496      tempView.setOffset(i->second);      temp << pointToString(m_data,getShape(),i->second,empty) << endl;
497      temp << tempView.toString() << endl;  //     tempView.setOffset(i->second);
498    //     temp << tempView.toString() << endl;
499    }    }
500    return temp.str();    return temp.str();
501  }  }
502    
503  DataArrayView  DataTypes::ValueType::size_type
504  DataTagged::getDataPointByTag(int tag) const  DataTagged::getPointOffset(int sampleNo,
505                               int dataPointNo) const
506  {  {
507    DataMapType::const_iterator pos(m_offsetLookup.find(tag));    int tagKey=getFunctionSpace().getTagFromSampleNo(sampleNo);
508    DataArrayView::ValueType::size_type offset=m_defaultValueOffset;    DataMapType::const_iterator pos(m_offsetLookup.find(tagKey));
509      DataTypes::ValueType::size_type offset=m_defaultValueOffset;
510    if (pos!=m_offsetLookup.end()) {    if (pos!=m_offsetLookup.end()) {
511      offset=pos->second;      offset=pos->second;
512    }    }
513    DataArrayView temp(getPointDataView());    return offset;
   temp.setOffset(offset);  
   return temp;  
514  }  }
515    
516  DataArrayView::ValueType::size_type  DataTypes::ValueType::size_type
517  DataTagged::getPointOffset(int sampleNo,  DataTagged::getPointOffset(int sampleNo,
518                             int dataPointNo) const                             int dataPointNo)
519  {  {
520    int tagKey=getFunctionSpace().getTagFromSampleNo(sampleNo);    int tagKey=getFunctionSpace().getTagFromSampleNo(sampleNo);
521    DataMapType::const_iterator pos(m_offsetLookup.find(tagKey));    DataMapType::const_iterator pos(m_offsetLookup.find(tagKey));
522    DataArrayView::ValueType::size_type offset=m_defaultValueOffset;    DataTypes::ValueType::size_type offset=m_defaultValueOffset;
523    if (pos!=m_offsetLookup.end()) {    if (pos!=m_offsetLookup.end()) {
524      offset=pos->second;      offset=pos->second;
525    }    }
526    return offset;    return offset;
527  }  }
528    
529  DataArrayView  DataTypes::ValueType::size_type
530  DataTagged::getDataPoint(int sampleNo,  DataTagged::getOffsetForTag(int tag) const
                          int dataPointNo)  
531  {  {
532    EsysAssert(validSampleNo(sampleNo),"(getDataPoint) Invalid sampleNo: " << sampleNo);    DataMapType::const_iterator pos(m_offsetLookup.find(tag));
533    int tagKey=getFunctionSpace().getTagFromSampleNo(sampleNo);    DataTypes::ValueType::size_type offset=m_defaultValueOffset;
534    return getDataPointByTag(tagKey);    if (pos!=m_offsetLookup.end()) {
535        offset=pos->second;
536      }
537      return offset;
538  }  }
539    
540  const DataTagged::DataMapType&  DataTypes::ValueType::const_reference
541  DataTagged::getTagLookup() const  DataTagged::getDataByTagRO(int tag, DataTypes::ValueType::size_type i) const
542    {
543      DataMapType::const_iterator pos(m_offsetLookup.find(tag));
544      DataTypes::ValueType::size_type offset=m_defaultValueOffset;
545      if (pos!=m_offsetLookup.end()) {
546        offset=pos->second;
547      }
548      return m_data[offset+i];
549    }
550    
551    DataTypes::ValueType::reference
552    DataTagged::getDataByTagRW(int tag, DataTypes::ValueType::size_type i)
553    {
554      CHECK_FOR_EX_WRITE
555      DataMapType::const_iterator pos(m_offsetLookup.find(tag));
556      DataTypes::ValueType::size_type offset=m_defaultValueOffset;
557      if (pos!=m_offsetLookup.end()) {
558        offset=pos->second;
559      }
560      return m_data[offset+i];
561    }
562    
563    void
564    DataTagged::symmetric(DataAbstract* ev)
565    {
566      DataTagged* temp_ev=dynamic_cast<DataTagged*>(ev);
567      if (temp_ev==0) {
568        throw DataException("Error - DataTagged::symmetric casting to DataTagged failed (probably a programming error).");
569      }
570      const DataTagged::DataMapType& thisLookup=getTagLookup();
571      DataTagged::DataMapType::const_iterator i;
572      DataTagged::DataMapType::const_iterator thisLookupEnd=thisLookup.end();
573      ValueType& evVec=temp_ev->getVectorRW();
574      const ShapeType& evShape=temp_ev->getShape();
575      for (i=thisLookup.begin();i!=thisLookupEnd;i++) {
576          temp_ev->addTag(i->first);
577          DataTypes::ValueType::size_type offset=getOffsetForTag(i->first);
578          DataTypes::ValueType::size_type evoffset=temp_ev->getOffsetForTag(i->first);
579          DataMaths::symmetric(m_data,getShape(),offset,evVec, evShape, evoffset);
580      }
581      DataMaths::symmetric(m_data,getShape(),getDefaultOffset(),evVec,evShape,temp_ev->getDefaultOffset());
582    }
583    
584    
585    void
586    DataTagged::nonsymmetric(DataAbstract* ev)
587    {
588      DataTagged* temp_ev=dynamic_cast<DataTagged*>(ev);
589      if (temp_ev==0) {
590        throw DataException("Error - DataTagged::nonsymmetric casting to DataTagged failed (probably a programming error).");
591      }
592      const DataTagged::DataMapType& thisLookup=getTagLookup();
593      DataTagged::DataMapType::const_iterator i;
594      DataTagged::DataMapType::const_iterator thisLookupEnd=thisLookup.end();
595      ValueType& evVec=temp_ev->getVectorRW();
596      const ShapeType& evShape=temp_ev->getShape();
597      for (i=thisLookup.begin();i!=thisLookupEnd;i++) {
598          temp_ev->addTag(i->first);
599          DataTypes::ValueType::size_type offset=getOffsetForTag(i->first);
600          DataTypes::ValueType::size_type evoffset=temp_ev->getOffsetForTag(i->first);
601          DataMaths::nonsymmetric(m_data,getShape(),offset,evVec, evShape, evoffset);
602      }
603      DataMaths::nonsymmetric(m_data,getShape(),getDefaultOffset(),evVec,evShape,temp_ev->getDefaultOffset());
604    }
605    
606    
607    void
608    DataTagged::trace(DataAbstract* ev, int axis_offset)
609    {
610      DataTagged* temp_ev=dynamic_cast<DataTagged*>(ev);
611      if (temp_ev==0) {
612        throw DataException("Error - DataTagged::trace casting to DataTagged failed (probably a programming error).");
613      }
614      const DataTagged::DataMapType& thisLookup=getTagLookup();
615      DataTagged::DataMapType::const_iterator i;
616      DataTagged::DataMapType::const_iterator thisLookupEnd=thisLookup.end();
617      ValueType& evVec=temp_ev->getVectorRW();
618      const ShapeType& evShape=temp_ev->getShape();
619      for (i=thisLookup.begin();i!=thisLookupEnd;i++) {
620          temp_ev->addTag(i->first);
621          DataTypes::ValueType::size_type offset=getOffsetForTag(i->first);
622          DataTypes::ValueType::size_type evoffset=temp_ev->getOffsetForTag(i->first);
623          DataMaths::trace(m_data,getShape(),offset,evVec, evShape, evoffset, axis_offset);
624      }
625      DataMaths::trace(m_data,getShape(),getDefaultOffset(),evVec,evShape,temp_ev->getDefaultOffset(),axis_offset);
626    }
627    
628    void
629    DataTagged::transpose(DataAbstract* ev, int axis_offset)
630    {
631      DataTagged* temp_ev=dynamic_cast<DataTagged*>(ev);
632      if (temp_ev==0) {
633        throw DataException("Error - DataTagged::transpose casting to DataTagged failed (probably a programming error).");
634      }
635      const DataTagged::DataMapType& thisLookup=getTagLookup();
636      DataTagged::DataMapType::const_iterator i;
637      DataTagged::DataMapType::const_iterator thisLookupEnd=thisLookup.end();
638      ValueType& evVec=temp_ev->getVectorRW();
639      const ShapeType& evShape=temp_ev->getShape();
640      for (i=thisLookup.begin();i!=thisLookupEnd;i++) {
641          temp_ev->addTag(i->first);
642          DataTypes::ValueType::size_type offset=getOffsetForTag(i->first);
643          DataTypes::ValueType::size_type evoffset=temp_ev->getOffsetForTag(i->first);
644          DataMaths::transpose(m_data,getShape(),offset,evVec, evShape, evoffset, axis_offset);
645      }
646      DataMaths::transpose(m_data,getShape(),getDefaultOffset(),evVec,evShape,temp_ev->getDefaultOffset(),axis_offset);
647    }
648    
649    void
650    DataTagged::swapaxes(DataAbstract* ev, int axis0, int axis1)
651    {
652      DataTagged* temp_ev=dynamic_cast<DataTagged*>(ev);
653      if (temp_ev==0) {
654        throw DataException("Error - DataTagged::swapaxes casting to DataTagged failed (probably a programming error).");
655      }
656      const DataTagged::DataMapType& thisLookup=getTagLookup();
657      DataTagged::DataMapType::const_iterator i;
658      DataTagged::DataMapType::const_iterator thisLookupEnd=thisLookup.end();
659      ValueType& evVec=temp_ev->getVectorRW();
660      const ShapeType& evShape=temp_ev->getShape();
661      for (i=thisLookup.begin();i!=thisLookupEnd;i++) {
662          temp_ev->addTag(i->first);
663          DataTypes::ValueType::size_type offset=getOffsetForTag(i->first);
664          DataTypes::ValueType::size_type evoffset=temp_ev->getOffsetForTag(i->first);
665          DataMaths::swapaxes(m_data,getShape(),offset,evVec, evShape, evoffset,axis0,axis1);
666      }
667      DataMaths::swapaxes(m_data,getShape(),getDefaultOffset(),evVec,evShape,temp_ev->getDefaultOffset(),axis0,axis1);
668    }
669    
670    void
671    DataTagged::eigenvalues(DataAbstract* ev)
672    {
673      DataTagged* temp_ev=dynamic_cast<DataTagged*>(ev);
674      if (temp_ev==0) {
675        throw DataException("Error - DataTagged::eigenvalues casting to DataTagged failed (propably a programming error).");
676      }
677      const DataTagged::DataMapType& thisLookup=getTagLookup();
678      DataTagged::DataMapType::const_iterator i;
679      DataTagged::DataMapType::const_iterator thisLookupEnd=thisLookup.end();
680      ValueType& evVec=temp_ev->getVectorRW();
681      const ShapeType& evShape=temp_ev->getShape();
682      for (i=thisLookup.begin();i!=thisLookupEnd;i++) {
683          temp_ev->addTag(i->first);
684    //       DataArrayView thisView=getDataPointByTag(i->first);
685    //       DataArrayView evView=temp_ev->getDataPointByTag(i->first);
686          DataTypes::ValueType::size_type offset=getOffsetForTag(i->first);
687          DataTypes::ValueType::size_type evoffset=temp_ev->getOffsetForTag(i->first);
688          DataMaths::eigenvalues(m_data,getShape(),offset,evVec, evShape, evoffset);
689      }
690      DataMaths::eigenvalues(m_data,getShape(),getDefaultOffset(),evVec, evShape, temp_ev->getDefaultOffset());
691    }
692    void
693    DataTagged::eigenvalues_and_eigenvectors(DataAbstract* ev,DataAbstract* V,const double tol)
694    {
695      DataTagged* temp_ev=dynamic_cast<DataTagged*>(ev);
696      if (temp_ev==0) {
697        throw DataException("Error - DataTagged::eigenvalues_and_eigenvectors casting to DataTagged failed (propably a programming error).");
698      }
699      DataTagged* temp_V=dynamic_cast<DataTagged*>(V);
700      if (temp_V==0) {
701        throw DataException("Error - DataTagged::eigenvalues_and_eigenvectors casting to DataTagged failed (propably a programming error).");
702      }
703      const DataTagged::DataMapType& thisLookup=getTagLookup();
704      DataTagged::DataMapType::const_iterator i;
705      DataTagged::DataMapType::const_iterator thisLookupEnd=thisLookup.end();
706      ValueType& evVec=temp_ev->getVectorRW();
707      const ShapeType& evShape=temp_ev->getShape();
708      ValueType& VVec=temp_V->getVectorRW();
709      const ShapeType& VShape=temp_V->getShape();
710      for (i=thisLookup.begin();i!=thisLookupEnd;i++) {
711          temp_ev->addTag(i->first);
712          temp_V->addTag(i->first);
713    /*      DataArrayView thisView=getDataPointByTag(i->first);
714          DataArrayView evView=temp_ev->getDataPointByTag(i->first);
715          DataArrayView VView=temp_V->getDataPointByTag(i->first);*/
716          DataTypes::ValueType::size_type offset=getOffsetForTag(i->first);
717          DataTypes::ValueType::size_type evoffset=temp_ev->getOffsetForTag(i->first);
718          DataTypes::ValueType::size_type Voffset=temp_V->getOffsetForTag(i->first);
719    /*      DataArrayView::eigenvalues_and_eigenvectors(thisView,0,evView,0,VView,0,tol);*/
720          DataMaths::eigenvalues_and_eigenvectors(m_data,getShape(),offset,evVec, evShape, evoffset,VVec,VShape,Voffset,tol);
721    
722      }
723      DataMaths::eigenvalues_and_eigenvectors(m_data,getShape(),getDefaultOffset(),evVec, evShape,
724                          temp_ev->getDefaultOffset(),VVec,VShape,
725                          temp_V->getDefaultOffset(), tol);
726    
727    
728    }
729    
730    void
731    DataTagged::matrixInverse(DataAbstract* out) const
732    {
733      DataTagged* temp=dynamic_cast<DataTagged*>(out);
734      if (temp==0)
735      {
736        throw DataException("Error - DataTagged::matrixInverse: casting to DataTagged failed (propably a programming error).");
737      }
738      if (getRank()!=2)
739      {
740        throw DataException("Error - DataExpanded::matrixInverse: input must be rank 2.");
741      }
742      const DataTagged::DataMapType& thisLookup=getTagLookup();
743      DataTagged::DataMapType::const_iterator i;
744      DataTagged::DataMapType::const_iterator thisLookupEnd=thisLookup.end();
745      ValueType& outVec=temp->getVectorRW();
746      const ShapeType& outShape=temp->getShape();
747      LapackInverseHelper h(getShape()[0]);
748      int err=0;
749      for (i=thisLookup.begin();i!=thisLookupEnd;i++) {
750          temp->addTag(i->first);
751          DataTypes::ValueType::size_type inoffset=getOffsetForTag(i->first);
752          DataTypes::ValueType::size_type outoffset=temp->getOffsetForTag(i->first);
753    
754          err=DataMaths::matrix_inverse(m_data, getShape(), inoffset, outVec, outShape, outoffset, 1, h);
755          if (!err) break;
756      }
757      if (!err)
758      {
759          DataMaths::matrix_inverse(m_data, getShape(), getDefaultOffset(), outVec, outShape, temp->getDefaultOffset(), 1, h);
760      }
761      if (err)
762      {
763         DataMaths::matrixInverseError(err);    // throws exceptions
764      }
765    }
766    
767    void
768    DataTagged::setToZero(){
769        CHECK_FOR_EX_WRITE
770        DataTypes::ValueType::size_type n=m_data.size();
771        for (int i=0; i<n ;++i) m_data[i]=0.;
772    }
773    
774    void
775    DataTagged::dump(const std::string fileName) const
776    {
777       #ifdef USE_NETCDF
778       const int ldims=DataTypes::maxRank+1;
779       const NcDim* ncdims[ldims];
780       NcVar *var, *tags_var;
781       int rank = getRank();
782       int type=  getFunctionSpace().getTypeCode();
783       int ndims =0;
784       long dims[ldims];
785       const double* d_ptr=&(m_data[0]);
786       DataTypes::ShapeType shape = getShape();
787       int mpi_iam=getFunctionSpace().getDomain()->getMPIRank();
788       int mpi_num=getFunctionSpace().getDomain()->getMPISize();
789    #ifdef PASO_MPI
790       MPI_Status status;
791    #endif
792    
793    #ifdef PASO_MPI
794       /* Serialize NetCDF I/O */
795       if (mpi_iam>0) MPI_Recv(&ndims, 0, MPI_INT, mpi_iam-1, 81803, MPI_COMM_WORLD, &status);
796    #endif
797    
798       // netCDF error handler
799       NcError err(NcError::verbose_nonfatal);
800       // Create the file.
801       char *newFileName = Escript_MPI_appendRankToFileName(fileName.c_str(), mpi_num, mpi_iam);
802       NcFile dataFile(newFileName, NcFile::Replace);
803       // check if writing was successful
804       if (!dataFile.is_valid())
805            throw DataException("Error - DataTagged:: opening of netCDF file for output failed.");
806       if (!dataFile.add_att("type_id",1) )
807            throw DataException("Error - DataTagged:: appending data type to netCDF file failed.");
808       if (!dataFile.add_att("rank",rank) )
809            throw DataException("Error - DataTagged:: appending rank attribute to netCDF file failed.");
810       if (!dataFile.add_att("function_space_type",type))
811            throw DataException("Error - DataTagged:: appending function space attribute to netCDF file failed.");
812       ndims=rank+1;
813       if ( rank >0 ) {
814           dims[0]=shape[0];
815           if (! (ncdims[0] = dataFile.add_dim("d0",shape[0])) )
816                throw DataException("Error - DataTagged:: appending ncdimension 0 to netCDF file failed.");
817       }
818       if ( rank >1 ) {
819           dims[1]=shape[1];
820           if (! (ncdims[1] = dataFile.add_dim("d1",shape[1])) )
821                throw DataException("Error - DataTagged:: appending ncdimension 1 to netCDF file failed.");
822       }
823       if ( rank >2 ) {
824           dims[2]=shape[2];
825           if (! (ncdims[2] = dataFile.add_dim("d2", shape[2])) )
826                throw DataException("Error - DataTagged:: appending ncdimension 2 to netCDF file failed.");
827       }
828       if ( rank >3 ) {
829           dims[3]=shape[3];
830           if (! (ncdims[3] = dataFile.add_dim("d3", shape[3])) )
831                throw DataException("Error - DataTagged:: appending ncdimension 3 to netCDF file failed.");
832       }
833       const DataTagged::DataMapType& thisLookup=getTagLookup();
834       DataTagged::DataMapType::const_iterator i;
835       DataTagged::DataMapType::const_iterator thisLookupEnd=thisLookup.end();
836       int ntags=1;
837       for (i=thisLookup.begin();i!=thisLookupEnd;i++) ntags++;
838       int* tags =(int*) esysUtils::malloc(ntags*sizeof(int));
839       int c=1;
840       tags[0]=-1;
841       for (i=thisLookup.begin();i!=thisLookupEnd;i++) tags[c++]=i->first;
842       dims[rank]=ntags;
843       if (! (ncdims[rank] = dataFile.add_dim("num_tags", dims[rank])) )
844       {
845           esysUtils::free(tags);
846               throw DataException("Error - DataTagged:: appending num_tags to netCDF file failed.");
847       }
848       if (! ( tags_var = dataFile.add_var("tags", ncInt, ncdims[rank])) )
849       {
850        esysUtils::free(tags);
851            throw DataException("Error - DataTagged:: appending tags to netCDF file failed.");
852       }
853       if (! (tags_var->put(tags,dims[rank])) )
854       {
855        esysUtils::free(tags);
856            throw DataException("Error - DataTagged:: copy tags to netCDF buffer failed.");
857       }
858       if (! ( var = dataFile.add_var("data", ncDouble, ndims, ncdims)) )
859       {
860        esysUtils::free(tags);
861            throw DataException("Error - DataTagged:: appending variable to netCDF file failed.");
862       }
863       if (! (var->put(d_ptr,dims)) )
864       {
865        esysUtils::free(tags);
866            throw DataException("Error - DataTagged:: copy data to netCDF buffer failed.");
867       }
868    #ifdef PASO_MPI
869       if (mpi_iam<mpi_num-1) MPI_Send(&ndims, 0, MPI_INT, mpi_iam+1, 81803, MPI_COMM_WORLD);
870    #endif
871       #else
872       throw DataException("Error - DataTagged:: dump is not configured with netCDF. Please contact your installation manager.");
873       #endif
874    }
875    
876    DataTypes::ValueType&
877    DataTagged::getVectorRW()
878  {  {
879    return m_offsetLookup;      CHECK_FOR_EX_WRITE
880        return m_data;
881  }  }
882    
883  DataArrayView::ValueType::size_type  const DataTypes::ValueType&
884  DataTagged::getLength() const  DataTagged::getVectorRO() const
885  {  {
886    return m_data.size();      return m_data;
887  }  }
888    
889  }  // end of namespace  }  // end of namespace

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