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trunk/escript/src/Data/escriptcpp.cpp revision 391 by gross, Tue Dec 20 05:36:50 2005 UTC trunk/escript/src/escriptcpp.cpp revision 2668 by gross, Thu Sep 17 04:04:09 2009 UTC
# Line 1  Line 1 
1  //$Id$  
2  /*=============================================================================  /*******************************************************
3    *
4   ******************************************************************************  * Copyright (c) 2003-2009 by University of Queensland
5   *                                                                            *  * Earth Systems Science Computational Center (ESSCC)
6   *       COPYRIGHT ACcESS 2004 -  All Rights Reserved                         *  * http://www.uq.edu.au/esscc
7   *                                                                            *  *
8   * This software is the property of ACcESS.  No part of this code             *  * Primary Business: Queensland, Australia
9   * may be copied in any form or by any means without the expressed written    *  * Licensed under the Open Software License version 3.0
10   * consent of ACcESS.  Copying, use or modification of this software          *  * http://www.opensource.org/licenses/osl-3.0.php
11   * by any unauthorised person is illegal unless that                          *  *
12   * person has a software license agreement with ACcESS.                       *  *******************************************************/
13   *                                                                            *  
14   ******************************************************************************  
15    #include "Data.h"
16  ******************************************************************************/  #include "FunctionSpace.h"
17    #include "FunctionSpaceFactory.h"
18  #include "escript/Data/Data.h"  #include "DataFactory.h"
19  #include "escript/Data/DataVariable.h"  #include "AbstractContinuousDomain.h"
20  #include "escript/Data/FunctionSpace.h"  #include "AbstractDomain.h"
21  #include "escript/Data/FunctionSpaceFactory.h"  #include "Utils.h"
22  #include "escript/Data/DataFactory.h"  #include "AbstractSystemMatrix.h"
23  #include "escript/Data/AbstractContinuousDomain.h"  #include "AbstractTransportProblem.h"
24  #include "escript/Data/AbstractDomain.h"  #include "DataVector.h"
25  #include "escript/Data/Utils.h"  #include "paso/Paso_MPI.h"
26    #include "EscriptParams.h"
27    #include "TestDomain.h"
28    
29    
30    extern "C" {
31    #include "esysUtils/blocktimer.h"
32    }
33    
34  #include "esysUtils/esysExceptionTranslator.h"  #include "esysUtils/esysExceptionTranslator.h"
35    
36    #include <boost/version.hpp>
37  #include <boost/python.hpp>  #include <boost/python.hpp>
38  #include <boost/python/module.hpp>  #include <boost/python/module.hpp>
39  #include <boost/python/def.hpp>  #include <boost/python/def.hpp>
40  #include <boost/python/object.hpp>  #include <boost/python/object.hpp>
41  #include <boost/python/tuple.hpp>  #include <boost/python/tuple.hpp>
42  #include <boost/python/numeric.hpp>  #include <boost/smart_ptr.hpp>
43    #include <boost/version.hpp>
44    
45  using namespace boost::python;  using namespace boost::python;
46    
47  /*! \mainpage Esys Documentation  /*! \mainpage Esys Documentation
48   *   *
49   * \version 1.0.0   * \version 3.0.0
50   *   *
51   * - \ref escript   * - \ref escript
52   *   *
# Line 44  using namespace boost::python; Line 54  using namespace boost::python;
54   *   *
55   * - \ref finley   * - \ref finley
56   *   *
57   * - <a href=http://iservo.edu.au/esys/epydoc/index.html>Python module documentation (epydoc generated)</a>   * - <a href="../../epydoc/index.html">Python module documentation (epydoc generated)</a>
58   *   *
59   */   */
60    
# Line 52  using namespace boost::python; Line 62  using namespace boost::python;
62   * Escript is the python module that contains the interfaces   * Escript is the python module that contains the interfaces
63   * to the C++ side of escript.   * to the C++ side of escript.
64   *   *
65   * \version 1.0.0   *
66   *   *
67   * \section class_desc Class Description:   * \section class_desc Class Description:
68   * Data   * Data
# Line 70  using namespace boost::python; Line 80  using namespace boost::python;
80    
81  BOOST_PYTHON_MODULE(escriptcpp)  BOOST_PYTHON_MODULE(escriptcpp)
82  {  {
83    def("setNumberOfThreads",escript::setNumberOfThreads);  
84    def("getNumberOfThreads",escript::getNumberOfThreads);    #if BOOST_VERSION >= 103500
85    // params are: bool show_user_defined, bool show_py_signatures, bool show_cpp_signatures
86      docstring_options docopt(true,true,false);
87      #endif
88    
89      def("setNumberOfThreads",escript::setNumberOfThreads,"Use of this method is strongly discouraged.");
90      def("getNumberOfThreads",escript::getNumberOfThreads,"Return the maximum number of threads"
91    " available to OpenMP.");
92      def("releaseUnusedMemory",escript::releaseUnusedMemory);
93      def("blocktimer_initialize",blocktimer_initialize);
94      def("blocktimer_reportSortByName",blocktimer_reportSortByName);
95      def("blocktimer_reportSortByTime",blocktimer_reportSortByTime);
96      def("blocktimer_increment",blocktimer_increment);
97      def("blocktimer_time",blocktimer_time);
98      def("getVersion",escript::getSvnVersion,"This method will only report accurate version numbers for clean checkouts.");
99      def("printParallelThreadCounts",escript::printParallelThreadCnt);
100      def("getMPISizeWorld",escript::getMPISizeWorld,"Return number of MPI processes in the job.");
101      def("getMPIRankWorld",escript::getMPIRankWorld,"Return the rank of this process in the MPI World.");
102      def("MPIBarrierWorld",escript::MPIBarrierWorld,"Wait until all MPI processes have reached this point.");
103      def("getMPIWorldMax",escript::getMPIWorldMax,"\nEach MPI process calls this function with a"
104    " value for arg1. The maximum value is computed and returned.\n\n:rtype: int");
105      def("getMPIWorldSum",escript::getMPIWorldSum,"\nEach MPI process calls this function with a"
106    " value for arg1. The values are added up and the total value is returned.\n\n:rtype: int");
107      def("getMachinePrecision",escript::getMachinePrecision);
108      def("getMaxFloat",escript::getMaxFloat);
109      def("_saveDataCSV",escript::saveDataCSV, (args("filename","arg","sep","csep"), arg("append")=false),
110    "Saves data objects passed in a python dictionary to a file.\n"
111    "The data objects must be over the same domain and be able to be interpolated to the same FunctionSpace.\n"
112    "If one of the dictionary keys is named ``mask``, then only samples where ``mask`` has a positive\n"
113    "value will be written to the file.\n\n"
114    "A header line giving the names of each column will be output first.\n"
115    "The keys given in the dictionary will be used to name columns.\n"
116    "Then the data will be output, one line per sample (for all data).\n"
117    "\n:param filename:\n:type filename: ``string``\n"
118    ":param arg: dictionary of named `Data` objects. If one is called ``mask`` it must be scalar data."
119    "\n:type arg: ``dict``\n"
120    ":param sep:separator for columns (defaults to \", \"\n:type sep:``string``\n"
121    ":param csep:separator for fields within data object (defaults to \"_\"\n:type csep:``string``\n"
122    ":param append: If True, write to the end of ``filename``\n:type append: ``string``\n");
123    
124    
125    //    //
126    // Interface for AbstractDomain    // Interface for AbstractDomain
127    //    //
128    class_<escript::AbstractDomain>("Domain",no_init)    class_<escript::AbstractDomain, escript::Domain_ptr>("Domain","Base class for all domains.",no_init)
129       .def("getX",&escript::AbstractDomain::getX)       .def("getStatus",&escript::AbstractDomain::getStatus,"The status of a domain changes whenever the domain is modified\n\n:rtype: int")
130       .def("getNormal",&escript::AbstractDomain::getNormal)       .def("setTagMap",&escript::AbstractDomain::setTagMap,args("name","tag"),
131       .def("getSize",&escript::AbstractDomain::getSize)  "Give a tag number a name.\n\n:param name: Name for the tag\n:type name: ``string``\n"
132       .def("saveVTK",&escript::AbstractDomain::saveVTK)  ":param tag: numeric id\n:type tag: ``int``\n:note: Tag names must be unique within a domain")
133       .def("saveDX",&escript::AbstractDomain::saveDX)       .def("getTag",&escript::AbstractDomain::getTag,args("name"),":return: tag id for "
134    "``name``\n:rtype: ``string``")
135         .def("isValidTagName",&escript::AbstractDomain::isValidTagName,args("name"),
136    ":return: True is ``name`` corresponds to a tag\n:rtype: ``bool``")
137         .def("showTagNames",&escript::AbstractDomain::showTagNames,":return: A space separated list of tag names\n:rtype: ``string``")
138         .def("getX",&escript::AbstractDomain::getX,":rtype: `Data`\n:return: Locations in the"
139    "`Domain`. FunctionSpace is chosen appropriately")
140         .def("getDim",&escript::AbstractDomain::getDim,":rtype: `int`\n:return: Spatial dimension of the `Domain`")
141         .def("getNormal",&escript::AbstractDomain::getNormal,":rtype: `escript`\n:return: Boundary normals")
142         .def("getSize",&escript::AbstractDomain::getSize,":return: the local size of samples. The function space is chosen appropriately\n:rtype: `Data`")
143         .def("saveVTK",&escript::AbstractDomain::saveVTK,args("filename","arg", "metadata"
144    , "metadata_schema"),
145    ":param filename: \n:type filename: ``string``\n:param arg: items to be added"
146    "\n:type arg: ``dict``\n:param metadata: string representing some meta data to be added\n:type metadata: ``string``"
147    "\n:param metadata_schema: schema type for metadata\n:type metadata_schema: ``string``")
148         .def("dump",&escript::AbstractDomain::dump,args("filename"),"Dumps the domain to a file"
149    ":param filename:\n:type filename: string")
150         .def("saveDX",&escript::AbstractDomain::saveDX,args("filename","arg"),"Saves a dictonary of Data objects to an OpenDX input file.\n\n:param filename:\n:type filename: ``string``"
151    "\n:param arg:\n:type arg: `dict`")
152         .def("getMPISize",&escript::AbstractDomain::getMPISize,":return: the number of processes used for this `Domain`\n:rtype: ``int``")
153         .def("getMPIRank",&escript::AbstractDomain::getMPIRank,":return: the rank of this process\n:rtype: ``int``")
154         .def("MPIBarrier",&escript::AbstractDomain::MPIBarrier,"Wait until all processes have reached this point")
155         .def("onMasterProcessor",&escript::AbstractDomain::onMasterProcessor,":return: True if this code is executing on the master process\n:rtype: `bool`")
156    
157       .def(self == self)       .def(self == self)
158       .def(self != self);       .def(self != self);
159    
160    //    //
161    // Interface for AbstractContinuousDomain    // Interface for AbstractContinuousDomain
162    //    //
163    class_<escript::AbstractContinuousDomain, bases<escript::AbstractDomain> >("ContinuousDomain",no_init)    class_<escript::AbstractContinuousDomain, bases<escript::AbstractDomain> >("ContinuousDomain","Class representing continuous domains",no_init)
164         .def("getSystemMatrixTypeId",&escript::AbstractContinuousDomain::getSystemMatrixTypeId);         .def("getSystemMatrixTypeId",&escript::AbstractContinuousDomain::getSystemMatrixTypeId,
165    args("solver", "preconditioner", "package", "symmetry"),
166    ":return: the identifier of the matrix type to be used for the global stiffness matrix "
167    "when a particular solver package and symmetric matrix is used.\n"
168    ":rtype: int")
169           .def("getTransportTypeId",&escript::AbstractContinuousDomain::getTransportTypeId,
170    args("solver", "preconditioner", "package", "symmetry"));
171    
172    
173    //    //
174    // Interface for FunctionSpace    // Interface for TestDomain
175    //    //
176    class_<escript::FunctionSpace>("FunctionSpace",init<>())    class_ <escript::TestDomain, bases<escript::AbstractDomain> >("TestDomain", "Test Class for domains with no structure. May be removed from future releases without notice.", init<int,int>());
177       .def("getDim",&escript::FunctionSpace::getDim)  
178       .def("getDomain",&escript::FunctionSpace::getDomain,return_internal_reference<>())    // This is the only python visible way to get a TestDomain
179       .def("getX",&escript::FunctionSpace::getX)    def("getTestDomainFunctionSpace",&escript::getTestDomainFunctionSpace, args("dpps",
180       .def("getNormal",&escript::FunctionSpace::getNormal)   "samples"),
181       .def("getSize",&escript::FunctionSpace::getSize)  "For testing only. May be removed without notice.");
      .def("getTagFromDataPointNo",&escript::FunctionSpace::getTagFromDataPointNo)  
      .def("__str__",&escript::FunctionSpace::toString)  
      .def(self == self)  
      .def(self != self);  
182    
183    //    //
184    // Interface for DataVariable    // Interface for FunctionSpace
185    //    //
186    class_<escript::DataVariable>("DataVariable",init<>())    class_<escript::FunctionSpace> fs_definer("FunctionSpace","A FunctionSpace describes which points from the `Domain` to use to represent functions.",init<>());    // Doco goes in the empty string param
187      .def(init<escript::Data*>())    fs_definer.def("getDim",&escript::FunctionSpace::getDim,":return: the spatial dimension of the underlying domain.\n:rtype: int");
188      .def("evaluate",&escript::DataVariable::evaluate)  //   fs_definer.def("getDomain",&escript::FunctionSpace::getDomain,
189      .def("sum",&escript::DataVariable::sum)  //                  return_internal_reference<>());
190      .def("diff",&escript::DataVariable::diff);    fs_definer.def("getDomain",&escript::FunctionSpace::getDomainPython,":return: the underlying `Domain` for this FunctionSpace.\n:rtype: `Domain`");
191      fs_definer.def("getX",&escript::FunctionSpace::getX,"\n:return: a function whose values are its input coordinates. ie an identity function.\n:rtype: `Data`");
192      fs_definer.def("getNormal",&escript::FunctionSpace::getNormal,":return: the surface normal field.\n\n:rtype: `Data`");
193      fs_definer.def("getSize",&escript::FunctionSpace::getSize,":return: sample size\n:rtype: `Data`");
194      fs_definer.def("setTags",&escript::FunctionSpace::setTags,args("newtag","mask"),
195    "Set tags according to a mask\n\n:param newtag: tag number to set\n:type newtag: non-zero ``int``\n:param mask: Samples which correspond to positive values in the mask will be set to ``newtag``.\n:type mask: scalar `Data`");
196      fs_definer.def("getTagFromDataPointNo",
197                     &escript::FunctionSpace::getTagFromDataPointNo,":return: the tag associated with the given sample number.\n:rtype: int");
198      fs_definer.def("getReferenceIDFromDataPointNo", &escript::FunctionSpace::getReferenceIDFromDataPointNo,args("dataPointNo"),":return: the reference number associated with ``dataPointNo``\n:rtype: int ");
199      fs_definer.def("getListOfTags",&escript::FunctionSpace::getListOfTags,":return: a list of the tags used in this function space\n:rtype: ``list``");
200      fs_definer.def("__str__", &escript::FunctionSpace::toString);
201      fs_definer.def(self == self);
202      fs_definer.def(self != self);
203    //    //
204    // Interface for Data    // Interface for Data
205    //    //
206    class_<escript::Data>("Data","TEST DOCUMENTATION",init<>())    class_<escript::Data>("Data","Represents a collection of datapoints. It is used to store the values of a function. For more details please consult the c++ class documentation.",init<>() )
207      // various constructors for Data objects      // various constructors for Data objects
     .def(init<const numeric::array&, optional<const escript::FunctionSpace&, bool> >(args("value","what","expand")))  
208      .def(init<const object&, optional<const escript::FunctionSpace&, bool> >(args("value","what","expand")))      .def(init<const object&, optional<const escript::FunctionSpace&, bool> >(args("value","what","expand")))
209      .def(init<const double, const tuple&, optional<const escript::FunctionSpace&, bool> >(args("value","shape","what","expand")))      .def(init<const double, const tuple&, optional<const escript::FunctionSpace&, bool> >(args("value","shape","what","expand")))
210      .def(init<const escript::Data&, const escript::FunctionSpace&>(args("value","what")))      .def(init<const escript::Data&, const escript::FunctionSpace&>(args("value","what")))
# Line 127  BOOST_PYTHON_MODULE(escriptcpp) Line 212  BOOST_PYTHON_MODULE(escriptcpp)
212      // Note for Lutz, Need to specify the call policy in order to return a      // Note for Lutz, Need to specify the call policy in order to return a
213      // reference. In this case return_internal_reference.      // reference. In this case return_internal_reference.
214      .def("__str__",&escript::Data::toString)      .def("__str__",&escript::Data::toString)
215      .def("getDomain",&escript::Data::getDomain,return_internal_reference<>())      .def("getDomain",&escript::Data::getDomainPython,":rtype: `Domain`")
216      .def("getFunctionSpace",&escript::Data::getFunctionSpace,return_internal_reference<>())      .def("getFunctionSpace",&escript::Data::getFunctionSpace,return_value_policy<copy_const_reference>(),":rtype: `FunctionSpace`")
217      .def("isEmpty",&escript::Data::isEmpty)      .def("isEmpty",&escript::Data::isEmpty,"Is this object an instance of ``DataEmpty``\n\n:rtype: ``bool``\n:note: This is not the same thing as asking if the object contains datapoints.")
218      .def("getShape",&escript::Data::getShapeTuple)      .def("isProtected",&escript::Data::isProtected,"Can this instance be modified.\n:rtype: ``bool``")
219      .def("getRank",&escript::Data::getDataPointRank)      .def("setProtection",&escript::Data::setProtection,"Disallow modifications to this data object\n\n:note: This method does not allow you to undo protection.")
220      .def("copyWithMask",&escript::Data::copyWithMask)      .def("getShape",&escript::Data::getShapeTuple,"\nReturns the shape of the datapoints in this object as a python tuple. Scalar data has the shape ``()``\n\n:rtype: ``tuple``")
221      .def("setTaggedValue",&escript::Data::setTaggedValue)      .def("getRank",&escript::Data::getDataPointRank,":return: the number of indicies required to address a component of a datapoints\n:rtype: positive ``int``")
222      .def("setRefValue",&escript::Data::setRefValue)      .def("dump",&escript::Data::dump,args("fileName"),"Save the data as a netCDF file\n\n:param fileName: \n:type fileName: ``string``")
223      .def("getRefValue",&escript::Data::getRefValue)      .def("toListOfTuples",&escript::Data::toListOfTuples, (arg("scalarastuple")=false),
224      .def("expand",&escript::Data::expand)  "Return the datapoints of this object in a list. Each datapoint is stored as a tuple.\n\n"
225      .def("tag",&escript::Data::tag)  ":param scalarastuple: if True, scalar data will be wrapped as a tuple."
226      .def("copy",&escript::Data::copy)  " True => [(0), (1), (2)]; False => [0, 1, 2]")
227      .def("convertToNumArray",&escript::Data::convertToNumArray)      .def("copyWithMask",&escript::Data::copyWithMask,args("other","mask"),
228      .def("convertToNumArrayFromSampleNo",&escript::Data::convertToNumArrayFromSampleNo)  "Selectively copy values from ``other`` `Data`."
229      .def("convertToNumArrayFromDPNo",&escript::Data::convertToNumArrayFromDPNo)  "Datapoints which correspond to postive values in ``mask`` will be copied from ``other``\n"
230      .def("fillFromNumArray",&escript::Data::fillFromNumArray)  "\n:param other: source of values\n"
231      .def("interpolate",&escript::Data::interpolate)  ":type other: `Data`\n:param mask:\n:type mask: Scalar `Data`")
232      .def("mindp",&escript::Data::mindp)      .def("setTaggedValue",&escript::Data::setTaggedValue,args("tagKey","value"),
233    "Set the value of tagged Data.\n\n:param tagKey: tag to update\n:type tagKey: ``int``\n")
234      .def("saveDX",&escript::Data::saveDX)      .def("setTaggedValue",&escript::Data::setTaggedValueByName,args("name","value"),":param name: tag to update\n:type name: ``string``\n"
235      .def("saveVTK",&escript::Data::saveVTK)  ":param value: value to set tagged data to\n:type value: ``object`` which acts like an array, ``tuple`` or ``list``\n")
236      .def("getTagNumber",&escript::Data::getTagNumber)      .def("getNumberOfDataPoints",&escript::Data::getNumDataPoints,":rtype: ``int``\n:return: Number of datapoints in the object")
237      .def("archiveData",&escript::Data::archiveData)      .def("isExpanded",&escript::Data::isExpanded,":rtype: ``bool``\n:return: True if this ``Data`` is expanded.")
238      .def("extractData",&escript::Data::extractData)      .def("isTagged",&escript::Data::isTagged,":rtype: ``bool``\n:return: True if this ``Data`` is expanded.")
239        .def("isConstant",&escript::Data::isConstant,":rtype: ``bool``\n:return: True if this ``Data`` is an instance of ``DataConstant``\n:note: This does not mean the data is immutable.")
240        .def("isLazy",&escript::Data::isLazy,":rtype: ``bool``\n:return: True if this ``Data`` is lazy.")
241        .def("isReady",&escript::Data::isReady,":rtype: ``bool``\n:return: True if this ``Data`` is not lazy.")
242        .def("expand",&escript::Data::expand,"Convert the data to expanded representation if it is not expanded already.")
243        .def("tag",&escript::Data::tag,"Convert data to tagged representation if it is not already tagged or expanded")
244        .def("resolve",&escript::Data::resolve,"Convert the data to non-lazy representation.")
245        .def("copy",&escript::Data::copy,args("other"),"Make this object a copy of ``other``\n"
246    "\n:note: The two objects will act independently from now on. That is, changing ``other`` "
247    "after this call will not change this object and vice versa.")
248        .def("copy",&escript::Data::copySelf,":note: In the no argument form, a new object will be returned which is an independent copy of this object.")
249        .def("delay",&escript::Data::delay,"Convert this object into lazy representation")
250        .def("setValueOfDataPoint",&escript::Data::setValueOfDataPointToPyObject,args("dataPointNo","value"))
251        .def("setValueOfDataPoint",&escript::Data::setValueOfDataPointToArray)
252        .def("setValueOfDataPoint",&escript::Data::setValueOfDataPoint,"\nModify the value of a single datapoint.\n\n:param dataPointNo:\n"
253    ":type dataPointNo: int\n:param value: \n:type value: ``float`` or an object which acts like an array, ``tuple`` or ``list``\n:warning: Use of this operation is discouraged. It prevents some optimisations from operating.")
254        .def("getTupleForDataPoint",&escript::Data::getValueOfDataPointAsTuple,args("dataPointNo"),
255    ":return: Value of the specified datapoint\n:rtype: ``tuple``\n:param dataPointNo: datapoint to access\n:type dataPointNo: ``int``")
256        .def("getTupleForGlobalDataPoint",&escript::Data::getValueOfGlobalDataPointAsTuple,args("procNo","dataPointNo"),"Get a specific datapoint from a specific process\n\n"
257    ":rtype: ``tuple``\n:param procNo: MPI rank of the process\n:type procNo: positive ``int``"
258    "\n:param dataPointNo: datapoint to access\n:type dataPointNo: int")
259        .def("setToZero",&escript::Data::setToZero,"After this call the object will store values of the same shape as before but all components will be zero.")
260        .def("interpolate",&escript::Data::interpolate,args("functionspace"),"Interpolate this object's values into a new functionspace.")
261        .def("interpolateTable", &escript::Data::interpolateFromTable2DP,
262    (arg("table"),arg("Amin"),arg("Astep"), arg("B"), arg("Bmin"), arg("Bstep"), arg("undef")=1.e50, arg("check_boundaries")=false),
263    "Creates a new Data object by interpolating using the source data (which are\n"
264    "looked up in ``table``)\n``A`` must be the outer dimension on the table\n\n"
265    ":param table: two dimensional collection of values\n"
266    ":param Amin: The base of locations in table\n:type Amin: float\n"
267    ":param Astep: size of gap between each item in the table\n:type Astep: float\n"
268    ":param undef: upper bound on interpolated values\n:type undef: float\n"
269    ":param B: Scalar representing the second coordinate to be mapped into the table\n"
270    ":type B: `Data`\n"
271    ":param Bmin: The base of locations in table for 2nd dimension\n:type Bmin: float\n"
272    ":param Bstep: size of gap between each item in the table for 2nd dimension\n:type Bstep: float\n"
273    ":param check_boundaries: if true table boundaries are checked.\n"
274    ":raise RuntimeError(DataException): if the cordinates do not map into the table or if the interpolated value is above ``undef``"
275    "\n:rtype: `Data`"
276    )
277        .def("interpolateTable", &escript::Data::interpolateFromTable1DP,
278    (arg("table"),arg("Amin"),arg("Astep"), arg("undef")=1.e50, arg("check_boundaries")=false),
279    "Creates a new Data object by interpolating using the source data (which are\n"
280    "looked up in ``table``)\n\n"
281    ":param table: one dimensional collection of values\n"
282    ":param Amin: The base of locations in table\n:type Amin: float\n"
283    ":param Astep: size of gap between each item in the table\n:type Astep: float\n"
284    ":param undef: upper bound on interpolated values\n:type undef: float\n"
285    ":param check_boundaries: if true table boundaries are checked.\n"
286    ":raise RuntimeError(DataException): if the cordinates do not map into the table or if the interpolated value is above ``undef``"
287    "\n:rtype: `Data`"
288    )
289    
290    
291        .def("minGlobalDataPoint",&escript::Data::minGlobalDataPoint)
292        .def("maxGlobalDataPoint",&escript::Data::maxGlobalDataPoint)
293        .def("saveDX",&escript::Data::saveDX,args("fileName"),"Save the object in DX format.\n\n"
294    ":param fileName: filename\n:type fileName: string")
295        .def("saveVTK",&escript::Data::saveVTK, args("fileName"),"Save the object in VTK format.\n\n"
296    ":param fileName: \n:type fileName: string")
297        .def("getTagNumber",&escript::Data::getTagNumber,args("dpno"),"Return tag number for the specified datapoint\n\n:rtype: int\n:param dpno: datapoint number\n:type dpno: int")
298      // Unary functions for Data      // Unary functions for Data
299      .def("_interpolate",&escript::Data::interpolate)      .def("_interpolate",&escript::Data::interpolate)
300      .def("_grad",&escript::Data::gradOn)      .def("_grad",&escript::Data::gradOn)
# Line 163  BOOST_PYTHON_MODULE(escriptcpp) Line 307  BOOST_PYTHON_MODULE(escriptcpp)
307      .def("_whereNegative",&escript::Data::whereNegative)      .def("_whereNegative",&escript::Data::whereNegative)
308      .def("_whereNonNegative",&escript::Data::whereNonNegative)      .def("_whereNonNegative",&escript::Data::whereNonNegative)
309      .def("_whereNonPositive",&escript::Data::whereNonPositive)      .def("_whereNonPositive",&escript::Data::whereNonPositive)
310      .def("_whereZero",&escript::Data::whereZero)      .def("_whereZero",&escript::Data::whereZero,(arg("tol")=0.0))
311      .def("_whereNonZero",&escript::Data::whereNonZero)      .def("_whereNonZero",&escript::Data::whereNonZero,(arg("tol")=0.0))
312        .def("_erf",&escript::Data::erf)
313      .def("_sin",&escript::Data::sin)      .def("_sin",&escript::Data::sin)
314      .def("_cos",&escript::Data::cos)      .def("_cos",&escript::Data::cos)
315      .def("_tan",&escript::Data::tan)      .def("_tan",&escript::Data::tan)
# Line 182  BOOST_PYTHON_MODULE(escriptcpp) Line 327  BOOST_PYTHON_MODULE(escriptcpp)
327      .def("_log10",&escript::Data::log10)      .def("_log10",&escript::Data::log10)
328      .def("_log",&escript::Data::log)      .def("_log",&escript::Data::log)
329      .def("_sign",&escript::Data::sign)      .def("_sign",&escript::Data::sign)
330        .def("_symmetric",&escript::Data::symmetric)
331        .def("_nonsymmetric",&escript::Data::nonsymmetric)
332        .def("_trace",&escript::Data::trace)
333        .def("_swap_axes",&escript::Data::swapaxes)
334        .def("_eigenvalues",&escript::Data::eigenvalues)
335        .def("_eigenvalues_and_eigenvectors",&escript::Data::eigenvalues_and_eigenvectors,(arg("tol")=1.e-13))
336      // functions returning a single real number:      // functions returning a single real number:
337      .def("_Lsup",&escript::Data::Lsup)      .def("_Lsup",&escript::Data::Lsup,":return: the Lsup-norm of the object\n:rtype: float\n:note: If the ``Data`` contains no values, zero will be returned instead.")
338      .def("_sup",&escript::Data::sup)      .def("_sup",&escript::Data::sup,":return: the maximum value over all data points.\n:rtype: float\n:note: If the ``Data`` contains no values a large negative value will be returned instead.")
339      .def("_inf",&escript::Data::inf)      .def("_inf",&escript::Data::inf,":return: minimum value over all components and all data points\n:rtype: float\n:note: If the ``Data`` contains no values a large positive value will be returned instead.")
340      .def("_integrate",&escript::Data::integrate)      .def("_integrateToTuple",&escript::Data::integrateToTuple,":return: Calculate the integral over the function space domain as a python tuple\n:rtype: tuple")
   
341      // following implements the python abs operator      // following implements the python abs operator
342      .def("__abs__",&escript::Data::abs)      .def("__abs__",&escript::Data::abs,":return: absolute value\n\n:rtype: `Data`")
343      // following implements the python "-" negation operator      // following implements the python "-" negation operator
344      .def("__neg__",&escript::Data::neg)      .def("__neg__",&escript::Data::neg, ":return: negation of the values in this object\n:rtype: `Data`")
345      // following implements the python "+" identity operator      // following implements the python "+" identity operator
346      .def("__pos__",&escript::Data::pos)      .def("__pos__",&escript::Data::pos, "\nThe unary + operator\n\n:rtype: `Data`")
347      // following two functions implement the python [] operator      // following two functions implement the python [] operator
348      .def("__getitem__",&escript::Data::getItem)      .def("__getitem__",&escript::Data::getItem,"Used by the python [] operator\n\n:rtype: `Data`")
349      .def("__setitem__",&escript::Data::setItemO)      .def("__setitem__",&escript::Data::setItemO,"Used by the python [] operator")
350      .def("__setitem__",&escript::Data::setItemD)      .def("__setitem__",&escript::Data::setItemD,"Used by the python [] operator")
351      // following two functions implement the python ** operator      // following two functions implement the python ** operator
352      .def("__pow__",&escript::Data::powO)      .def("__pow__",&escript::Data::powO,"Used by the python ** operator\n\n:rtype: `Data`")
353      .def("__pow__",&escript::Data::powD)      .def("__pow__",&escript::Data::powD)
354        .def("__rpow__",&escript::Data::rpowO,"\nUsed by the python ** operator\n\n:rtype: `Data`")
355      // NOTE:: The order of these declarations is important. Anything      // NOTE:: The order of these declarations is important. Anything
356      // declared before the generic declaration isn't found so the generic      // declared before the generic declaration isn't found so the generic
357      // version will be called.      // version will be called.
# Line 231  BOOST_PYTHON_MODULE(escriptcpp) Line 382  BOOST_PYTHON_MODULE(escriptcpp)
382      // the boost code. This calls operator << for Data.      // the boost code. This calls operator << for Data.
383      .def(self_ns::str(self));      .def(self_ns::str(self));
384    
385    
386    //    //
387    // Factory methods for function space    // Factory methods for function space
388    //    //
389    def("ContinuousFunction",escript::continuousFunction);    def("ContinuousFunction",escript::continuousFunction,args("domain"),
390    def("Function",escript::function);  ":return: a continuous FunctionSpace (overlapped node values)\n"
391    def("FunctionOnBoundary",escript::functionOnBoundary);  ":rtype: `FunctionSpace`");
392    def("FunctionOnContactZero",escript::functionOnContactZero);    def("ReducedContinuousFunction",escript::reducedContinuousFunction,args("domain"),
393    def("FunctionOnContactOne",escript::functionOnContactOne);  ":return: a continuous with reduced order FunctionSpace (overlapped node values on reduced element order)\n"
394    def("Solution",escript::solution);  ":rtype: `FunctionSpace`");
395    def("ReducedSolution",escript::reducedSolution);    def("Function",escript::function,args("domain"),":return: a function `FunctionSpace`\n"
396    def("DiracDeltaFunction",escript::diracDeltaFunction);  ":rtype: `FunctionSpace`");
397      def("ReducedFunction",escript::reducedFunction, args("domain"),":return: a function FunctionSpace with reduced integration order\n:rtype: `FunctionSpace`");
398      def("FunctionOnBoundary",escript::functionOnBoundary, args("domain"), ":return: a function on boundary FunctionSpace\n:rtype: `FunctionSpace`");
399      def("ReducedFunctionOnBoundary",escript::reducedFunctionOnBoundary, args("domain"),
400    ":return: a function on boundary FunctionSpace with reduced integration order\n"
401    ":rtype: `FunctionSpace`");
402      def("FunctionOnContactZero",escript::functionOnContactZero, args("domain"), ":return: Return a FunctionSpace on left side of contact\n:rtype: `FunctionSpace`");
403      def("ReducedFunctionOnContactZero",escript::reducedFunctionOnContactZero, args("domain"),
404     ":return: a FunctionSpace  on left side of contact with reduced integration order\n:rtype: `FunctionSpace`");
405      def("FunctionOnContactOne",escript::functionOnContactOne, args("domain"), ":return: Return a FunctionSpace on right side of contact\n:rtype: `FunctionSpace`");
406      def("ReducedFunctionOnContactOne",escript::reducedFunctionOnContactOne, args("domain"),
407     ":return: Return a FunctionSpace on right side of contact with reduced integration order\n"
408    ":rtype: `FunctionSpace`");
409      def("Solution",escript::solution, args("domain"), ":rtype: `FunctionSpace`");
410      def("ReducedSolution",escript::reducedSolution, args("domain"), ":rtype: `FunctionSpace`");
411      def("DiracDeltaFunction",escript::diracDeltaFunction, args("domain"), ":rtype: `FunctionSpace`");
412    
413    
414    
415    
416    
417    //    //
418    // Factory methods for Data    // Factory methods for Data
419    //    //
420      def("load",escript::load, args("fileName","domain"), "reads Data on domain from file in netCDF format\n\n:param fileName:\n:type fileName: ``string``\n:param domain:\n:type domain: `Domain`");
421      def("loadIsConfigured",escript::loadConfigured,":return: True if the load function is configured.");
422    def("Scalar",escript::Scalar,    def("Scalar",escript::Scalar,
423        (arg("value")=0.0,        (arg("value")=0.0,
424         arg("what")=escript::FunctionSpace(),         arg("what")=escript::FunctionSpace(),
425         arg("expanded")=false));         arg("expanded")=false),
426    "Construct a Data object containing scalar data-points.\n\n:param value: scalar value for all points\n"
427    "\n:rtype: `Data`\n:type value: float\n:param what: FunctionSpace for Data\n:type what: `FunctionSpace`\n"
428    ":param expanded: If True, a value is stored for each point. If False, more efficient representations may be used\n"
429    ":type expanded: ``bool``");
430    def("Vector",escript::Vector,    def("Vector",escript::Vector,
431        (arg("value")=0.0,        (arg("value")=0.0,
432         arg("what")=escript::FunctionSpace(),         arg("what")=escript::FunctionSpace(),
433         arg("expanded")=false));         arg("expanded")=false),
434    "Construct a Data object containing rank1 data-points.\n\n:param value: scalar value for all points\n"
435    "\n:rtype: `Data`\n:type value: float\n:param what: FunctionSpace for Data\n:type what: `FunctionSpace`\n"
436    ":param expanded: If True, a value is stored for each point. If False, more efficient representations may be used\n"
437    ":type expanded: ``bool``");
438    def("Tensor",escript::Tensor,    def("Tensor",escript::Tensor,
439        (arg("value")=0.0,        (arg("value")=0.0,
440         arg("what")=escript::FunctionSpace(),         arg("what")=escript::FunctionSpace(),
441         arg("expanded")=false));         arg("expanded")=false),
442    "Construct a Data object containing rank2 data-points.\n\n:param value: scalar value for all points\n"
443    "\n:rtype: `Data`\n:type value: float\n:param what: FunctionSpace for Data\n:type what: `FunctionSpace`\n"
444    ":param expanded: If True, a value is stored for each point. If False, more efficient representations may be used\n"
445    ":type expanded: ``bool``");
446    def("Tensor3",escript::Tensor3,    def("Tensor3",escript::Tensor3,
447        (arg("value")=0.0,        (arg("value")=0.0,
448         arg("what")=escript::FunctionSpace(),         arg("what")=escript::FunctionSpace(),
449         arg("expanded")=false));         arg("expanded")=false),
450    "Construct a Data object containing rank3 data-points.\n\n:param value: scalar value for all points\n"
451    "\n:rtype: `Data`\n:type value: float\n:param what: FunctionSpace for Data\n:type what: `FunctionSpace`\n"
452    ":param expanded: If True, a value is stored for each point. If False, more efficient representations may be used\n"
453    ":type expanded: ``bool``"
454    );
455    def("Tensor4",escript::Tensor4,    def("Tensor4",escript::Tensor4,
456        (arg("value")=0.0,        (arg("value")=0.0,
457         arg("what")=escript::FunctionSpace(),         arg("what")=escript::FunctionSpace(),
458         arg("expanded")=false));         arg("expanded")=false),
459    "Construct a Data object containing rank4 data-points.\n\n:param value: scalar value for all points\n"
460    "\n:rtype: `Data`\n:type value: float\n:param what: FunctionSpace for Data\n:type what: `FunctionSpace`\n"
461    ":param expanded: If True, a value is stored for each point. If False, more efficient representations may be used\n"
462    ":type expanded: ``bool``"
463    );
464    
465      //
466      // Binary operators
467      //
468      def("C_GeneralTensorProduct",escript::C_GeneralTensorProduct,
469          (arg("arg0"),
470           arg("arg1"),
471           arg("axis_offset")=0,
472           arg("transpose")=0),
473    "Compute a tensor product of two Data objects.\n\n:rtype: `Data`\n:param arg0:\n"
474    ":param arg1:\n:param axis_offset:\n:type axis_offset: ``int``\n"
475    ":param transpose: 0: transpose neither, 1: transpose arg0, 2: transpose arg1\n"
476    ":type transpose: int");
477    
478    //    //
479    // Interface for AbstractSystemMatrix    // Interface for AbstractSystemMatrix
480    //    //
481    class_<escript::AbstractSystemMatrix>("Operator",init<>())    class_<escript::AbstractSystemMatrix>("Operator","",init<>())    // Doco goes in the empty string param
482       .def("isEmpty",&escript::AbstractSystemMatrix::isEmpty)       .def("isEmpty",&escript::AbstractSystemMatrix::isEmpty,":rtype: ``bool``\n"
483       .def("solve",&escript::AbstractSystemMatrix::solve)  ":return: True if matrix is empty")
484       .def("of",&escript::AbstractSystemMatrix::vectorMultiply)       .def("solve",&escript::AbstractSystemMatrix::solve, args("in","options"),
485       .def("saveMM",&escript::AbstractSystemMatrix::saveMM)  ":return: the solution *u* of the linear system *this*u=in*\n\n:param in:\n:type in: `Data`")
486       .def("saveHB",&escript::AbstractSystemMatrix::saveHB)       .def("of",&escript::AbstractSystemMatrix::vectorMultiply,args("right"),
487       .def("resetValues",&escript::AbstractSystemMatrix::resetValues)  "matrix*vector multiplication")
488         .def("saveMM",&escript::AbstractSystemMatrix::saveMM, args("fileName"),
489    "writes the matrix to a file using the Matrix Market file format")
490         .def("saveHB",&escript::AbstractSystemMatrix::saveHB, args("filename"),
491    "writes the matrix to a file using the Harwell-Boeing file format")
492         .def("resetValues",&escript::AbstractSystemMatrix::resetValues, "resets the matrix entries")
493       .def(self*other<escript::Data>());       .def(self*other<escript::Data>());
494      //
495      // Interface for AbstractTransportProblem
496      //
497      class_<escript::AbstractTransportProblem>("TransportProblem","",init<>())    // Doco goes in the empty string param
498         .def("isEmpty",&escript::AbstractTransportProblem::isEmpty,":rtype: ``int``")
499         .def("solve",&escript::AbstractTransportProblem::solve, args("source","dt", "options"),
500    "returns the solution *u* for a time step *dt>0*\n\n:rtype: `Data`\n"
501    ":param source:\n:type source: `Data`")
502         .def("setInitialValue",&escript::AbstractTransportProblem::setInitialValue, args("u"),
503    "sets the value for *u* at time *t=0*.")
504         .def("insertConstraint",&escript::AbstractTransportProblem::insertConstraint,
505    args("source", "q", "r","factor"),
506    "inserts constraint *u_{,t}=r* where *q>0*  into the problem using a weighting factor")
507         .def("reset",&escript::AbstractTransportProblem::resetTransport,
508    "resets the transport operator typically as they have been updated.")
509         .def("resetValues",&escript::AbstractTransportProblem::resetTransport)
510         .def("getSafeTimeStepSize",&escript::AbstractTransportProblem::getSafeTimeStepSize)
511         .def("getUnlimitedTimeStepSize",&escript::AbstractTransportProblem::getUnlimitedTimeStepSize);
512    
513      // Functions to modify global parameters
514      def("setEscriptParamInt",escript::setEscriptParamInt,
515          (arg("name"), arg("value")=0), "Modify the value of an escript tuning parameter\n\n"
516    ":param name:\n:type name: ``string``\n:param value:\n:type value: ``int``");
517      def("getEscriptParamInt",escript::getEscriptParamInt,
518          (arg("name"),arg("sentinel")=0), "Read the value of an escript tuning paramter\n\n"
519    ":param name: parameter to lookup\n:type name: ``string``\n:param sentinel: Value to be returned if ``name`` is not a known parameter\n"
520    ":type sentinel: ``int``");
521      def("listEscriptParams",escript::listEscriptParams,":return: A list of pairs (p,d) where p is the name of a parameter for escript and d is a description.");
522    
523    //    //
524    // Register esysExceptionTranslator    // Register esysExceptionTranslator
525    //    //
526    register_exception_translator<esysUtils::EsysException>(&esysUtils::esysExceptionTranslator);    register_exception_translator<esysUtils::EsysException>(&esysUtils::esysExceptionTranslator);
   
527  }  }

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