PLearn 0.1
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#include <MultiInstanceVMatrix.h>
Public Member Functions | |
MultiInstanceVMatrix () | |
virtual void | build () |
Simply calls inherited::build() then build_(). | |
virtual void | makeDeepCopyFromShallowCopy (CopiesMap &copies) |
Transforms a shallow copy into a deep copy. | |
virtual string | classname () const |
virtual OptionList & | getOptionList () const |
virtual OptionMap & | getOptionMap () const |
virtual RemoteMethodMap & | getRemoteMethodMap () const |
virtual MultiInstanceVMatrix * | deepCopy (CopiesMap &copies) const |
Static Public Member Functions | |
static string | _classname_ () |
Declares name and deepCopy methods. | |
static OptionList & | _getOptionList_ () |
static RemoteMethodMap & | _getRemoteMethodMap_ () |
static Object * | _new_instance_for_typemap_ () |
static bool | _isa_ (const Object *o) |
static void | _static_initialize_ () |
static const PPath & | declaringFile () |
Public Attributes | |
int | header_lines_to_skip |
Static Public Attributes | |
static StaticInitializer | _static_initializer_ |
Protected Member Functions | |
virtual void | getNewRow (int i, const Vec &v) const |
This is the only method requiring implementation in subclasses. | |
Static Protected Member Functions | |
static void | declareOptions (OptionList &ol) |
Declare this class' options. | |
Protected Attributes | |
Mat | data_ |
PPath | filename_ |
vector< string > | configs_ |
vector< pair< string, int > > | names_ |
int | source_targetsize |
Private Types | |
typedef RowBufferedVMatrix | inherited |
Private Member Functions | |
void | build_ () |
This does the actual building. |
Definition at line 55 of file MultiInstanceVMatrix.h.
typedef RowBufferedVMatrix PLearn::MultiInstanceVMatrix::inherited [private] |
Reimplemented from PLearn::RowBufferedVMatrix.
Definition at line 57 of file MultiInstanceVMatrix.h.
PLearn::MultiInstanceVMatrix::MultiInstanceVMatrix | ( | ) |
Definition at line 55 of file MultiInstanceVMatrix.cc.
:inherited(), data_(Mat()), source_targetsize(1), header_lines_to_skip(0) { // ### You may or may not want to call build_() to finish building the object //build_(); }
string PLearn::MultiInstanceVMatrix::_classname_ | ( | ) | [static] |
Declares name and deepCopy methods.
Reimplemented from PLearn::RowBufferedVMatrix.
Definition at line 85 of file MultiInstanceVMatrix.cc.
OptionList & PLearn::MultiInstanceVMatrix::_getOptionList_ | ( | ) | [static] |
Reimplemented from PLearn::RowBufferedVMatrix.
Definition at line 85 of file MultiInstanceVMatrix.cc.
RemoteMethodMap & PLearn::MultiInstanceVMatrix::_getRemoteMethodMap_ | ( | ) | [static] |
Reimplemented from PLearn::RowBufferedVMatrix.
Definition at line 85 of file MultiInstanceVMatrix.cc.
Reimplemented from PLearn::RowBufferedVMatrix.
Definition at line 85 of file MultiInstanceVMatrix.cc.
Object * PLearn::MultiInstanceVMatrix::_new_instance_for_typemap_ | ( | ) | [static] |
Reimplemented from PLearn::Object.
Definition at line 85 of file MultiInstanceVMatrix.cc.
StaticInitializer MultiInstanceVMatrix::_static_initializer_ & PLearn::MultiInstanceVMatrix::_static_initialize_ | ( | ) | [static] |
Reimplemented from PLearn::RowBufferedVMatrix.
Definition at line 85 of file MultiInstanceVMatrix.cc.
void PLearn::MultiInstanceVMatrix::build | ( | ) | [virtual] |
Simply calls inherited::build() then build_().
Reimplemented from PLearn::VMatrix.
Definition at line 250 of file MultiInstanceVMatrix.cc.
References PLearn::VMatrix::build(), and build_().
{ inherited::build(); build_(); }
void PLearn::MultiInstanceVMatrix::build_ | ( | ) | [private] |
This does the actual building.
Reimplemented from PLearn::VMatrix.
Definition at line 117 of file MultiInstanceVMatrix.cc.
References configs_, PLearn::PStream::count(), data_, PLearn::PStream::eof(), filename_, PLearn::PStream::getline(), header_lines_to_skip, i, PLearn::VMatrix::inputsize_, PLearn::VMatrix::length_, names_, PLearn::openFile(), PLearn::pl_strtod(), PLERROR, PLearn::PStream::raw_ascii, PLearn::TMat< T >::resize(), PLearn::skipBlanksAndComments(), source_targetsize, PLearn::split(), PLearn::SumOverBagsVariable::TARGET_COLUMN_FIRST, PLearn::SumOverBagsVariable::TARGET_COLUMN_INTERMEDIATE, PLearn::SumOverBagsVariable::TARGET_COLUMN_LAST, PLearn::SumOverBagsVariable::TARGET_COLUMN_SINGLE, PLearn::VMatrix::targetsize_, PLearn::VMatrix::updateMtime(), and PLearn::VMatrix::width_.
Referenced by build().
{ updateMtime(filename_); //this->setMetaDataDir(filename_ + ".metadata"); // To be used in the end.. it is about 5 secs slower in debug //int nRows = countNonBlankLinesOfFile(filename_); PStream inFile = openFile(filename_, PStream::raw_ascii, "r"); // PStream inFile = openFile(filename_, PStream::raw_ascii, "r"); // inFile.seekg(0); TODO See if it still works without this. skipBlanksAndComments(inFile); string lastName = ""; string newName,configNum; string aLine; string inp_element; int bagType; int nComp = 0; int i; real* mat_i = NULL; // one more column for the bag signal targetsize_ = source_targetsize + 1; // Check the number of columns for (i = 0; i < header_lines_to_skip; i++) { inFile.getline(aLine, '\n'); } inFile.getline(aLine, '\n'); vector<string> entries = split(aLine); int nFields = (int)entries.size(); if (inputsize_>=0) { if ( (nFields-2) != inputsize_ + source_targetsize) // 2 for the object name and the instance number { PLERROR("Either inputsize or source_targetsize are inconsistent with the specified file!\n" " Got %d+%d (inputsize+source_targetsize) = %d, and found %d! If unsure about inputsize, don't specify it or set to -1.", inputsize_, source_targetsize, inputsize_+source_targetsize, nFields - 2); } } else inputsize_ = nFields-2-source_targetsize; int lastColumn = inputsize_ + source_targetsize; inFile = openFile(filename_, PStream::raw_ascii, "r"); // inFile.seekg(0); // TODO See if it still works without this. skipBlanksAndComments(inFile); for (i = 0; i < header_lines_to_skip; i++) { inFile.getline(aLine, '\n'); } skipBlanksAndComments(inFile); int nRows = inFile.count('\n'); /* TODO Make sure it works like the old code: int nRows = count(istreambuf_iterator<char>(inFile), istreambuf_iterator<char>(), '\n'); */ inFile = openFile(filename_, PStream::raw_ascii, "r"); // inFile.seekg(0); // TODO See if it still works without this. skipBlanksAndComments(inFile); for (i = 0; i < header_lines_to_skip; i++) { inFile.getline(aLine, '\n'); } skipBlanksAndComments(inFile); data_.resize(nRows, inputsize_ + targetsize_); width_ = inputsize_ + targetsize_; length_ = nRows; for (int lineNum = 0; !inFile.eof() && lineNum < nRows; ++lineNum) { // first column: name of the compound inFile >> newName; if (newName != lastName) { lastName = newName; names_.push_back( make_pair(newName, lineNum) ); bagType = SumOverBagsVariable::TARGET_COLUMN_FIRST; if (mat_i != NULL) { if (nComp > 1) mat_i[lastColumn] = SumOverBagsVariable::TARGET_COLUMN_LAST; else mat_i[lastColumn] = SumOverBagsVariable::TARGET_COLUMN_SINGLE; } nComp = 0; } else { bagType = SumOverBagsVariable::TARGET_COLUMN_INTERMEDIATE; } nComp++; // get next column: the number of the compound inFile >> configNum; configs_.push_back(configNum); // get the actual data columns + the target mat_i = data_[lineNum]; for(int k = 0; k < inputsize_ + source_targetsize; k++) { inFile >> inp_element; mat_i[k] = pl_strtod(inp_element.c_str(), 0); } // close the last bag if necessary if (lineNum+1==nRows) { if (nComp > 1) mat_i[lastColumn] = SumOverBagsVariable::TARGET_COLUMN_LAST; else mat_i[lastColumn] = SumOverBagsVariable::TARGET_COLUMN_SINGLE; } else mat_i[lastColumn] = bagType; } //ofstream test("g:/test.txt"); //test << data_; //test.close(); this->updateMtime(filename_); }
string PLearn::MultiInstanceVMatrix::classname | ( | ) | const [virtual] |
Reimplemented from PLearn::Object.
Definition at line 85 of file MultiInstanceVMatrix.cc.
void PLearn::MultiInstanceVMatrix::declareOptions | ( | OptionList & | ol | ) | [static, protected] |
Declare this class' options.
Reimplemented from PLearn::VMatrix.
Definition at line 92 of file MultiInstanceVMatrix.cc.
References PLearn::OptionBase::buildoption, PLearn::declareOption(), PLearn::VMatrix::declareOptions(), filename_, header_lines_to_skip, and source_targetsize.
{ declareOption(ol, "source_targetsize", &MultiInstanceVMatrix::source_targetsize, OptionBase::buildoption, "The source targetsize"); declareOption(ol, "filename", &MultiInstanceVMatrix::filename_, OptionBase::buildoption, "This is the name of the ascii 'mimat' format filename. It is a supervised learning dataset\n" "in which each input object can come in several instances (e.g. conformations) and the target is given to the\n" "whole bag of these instances, not to individual instances. The expected format is the following:\n" "Each row contains:\n" " - the object name (a string without white space)\n" " - the instance number (a non-negative integer)\n" " - the inputsize features for that instance (numeric, white-separated)\n" " - the source_targetsize target values for the bag (repeated on each row).\n" "If the inputsize option is not specified it is inferred from the text file.\n" ); declareOption(ol, "header_lines_to_skip", &MultiInstanceVMatrix::header_lines_to_skip, OptionBase::buildoption, "The number of lines to skip at the beginning of the file (they may be garbage, or \n" "a header for a TextFilesVMatrix for instance)."); // Now call the parent class' declareOptions inherited::declareOptions(ol); }
static const PPath& PLearn::MultiInstanceVMatrix::declaringFile | ( | ) | [inline, static] |
Reimplemented from PLearn::RowBufferedVMatrix.
Definition at line 106 of file MultiInstanceVMatrix.h.
MultiInstanceVMatrix * PLearn::MultiInstanceVMatrix::deepCopy | ( | CopiesMap & | copies | ) | const [virtual] |
Reimplemented from PLearn::RowBufferedVMatrix.
Definition at line 85 of file MultiInstanceVMatrix.cc.
This is the only method requiring implementation in subclasses.
Implements PLearn::RowBufferedVMatrix.
Definition at line 87 of file MultiInstanceVMatrix.cc.
References data_.
{ v << data_(i); }
OptionList & PLearn::MultiInstanceVMatrix::getOptionList | ( | ) | const [virtual] |
Reimplemented from PLearn::Object.
Definition at line 85 of file MultiInstanceVMatrix.cc.
OptionMap & PLearn::MultiInstanceVMatrix::getOptionMap | ( | ) | const [virtual] |
Reimplemented from PLearn::Object.
Definition at line 85 of file MultiInstanceVMatrix.cc.
RemoteMethodMap & PLearn::MultiInstanceVMatrix::getRemoteMethodMap | ( | ) | const [virtual] |
Reimplemented from PLearn::Object.
Definition at line 85 of file MultiInstanceVMatrix.cc.
void PLearn::MultiInstanceVMatrix::makeDeepCopyFromShallowCopy | ( | CopiesMap & | copies | ) | [virtual] |
Transforms a shallow copy into a deep copy.
Reimplemented from PLearn::RowBufferedVMatrix.
Definition at line 256 of file MultiInstanceVMatrix.cc.
References data_, PLearn::deepCopyField(), PLearn::RowBufferedVMatrix::makeDeepCopyFromShallowCopy(), and PLERROR.
{ inherited::makeDeepCopyFromShallowCopy(copies); // ### Call deepCopyField on all "pointer-like" fields // ### that you wish to be deepCopied rather than // ### shallow-copied. // ### ex: deepCopyField(data_, copies); // TODO: Copy also the other features // ### Remove this line when you have fully implemented this method. PLERROR("MultiInstanceVMatrix::makeDeepCopyFromShallowCopy not fully implemented yet!"); }
Reimplemented from PLearn::RowBufferedVMatrix.
Definition at line 106 of file MultiInstanceVMatrix.h.
vector<string> PLearn::MultiInstanceVMatrix::configs_ [protected] |
Definition at line 63 of file MultiInstanceVMatrix.h.
Referenced by build_().
Mat PLearn::MultiInstanceVMatrix::data_ [protected] |
Definition at line 61 of file MultiInstanceVMatrix.h.
Referenced by build_(), getNewRow(), and makeDeepCopyFromShallowCopy().
PPath PLearn::MultiInstanceVMatrix::filename_ [protected] |
Definition at line 62 of file MultiInstanceVMatrix.h.
Referenced by build_(), and declareOptions().
Definition at line 73 of file MultiInstanceVMatrix.h.
Referenced by build_(), and declareOptions().
vector< pair<string, int> > PLearn::MultiInstanceVMatrix::names_ [protected] |
Definition at line 64 of file MultiInstanceVMatrix.h.
Referenced by build_().
int PLearn::MultiInstanceVMatrix::source_targetsize [protected] |
Definition at line 65 of file MultiInstanceVMatrix.h.
Referenced by build_(), and declareOptions().