src/selection/SelectionEvaluator.cpp

/*
 * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
 *
 * The University of Notre Dame grants you ("Licensee") a
 * non-exclusive, royalty free, license to use, modify and
 * redistribute this software in source and binary code form, provided
 * that the following conditions are met:
 *
 * 1. Acknowledgement of the program authors must be made in any
 *    publication of scientific results based in part on use of the
 *    program.  An acceptable form of acknowledgement is citation of
 *    the article in which the program was described (Matthew
 *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
 *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
 *    Parallel Simulation Engine for Molecular Dynamics,"
 *    J. Comput. Chem. 26, pp. 252-271 (2005))
 *
 * 2. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 3. Redistributions in binary form must reproduce the above copyright
 *    notice, this list of conditions and the following disclaimer in the
 *    documentation and/or other materials provided with the
 *    distribution.
 *
 * This software is provided "AS IS," without a warranty of any
 * kind. All express or implied conditions, representations and
 * warranties, including any implied warranty of merchantability,
 * fitness for a particular purpose or non-infringement, are hereby
 * excluded.  The University of Notre Dame and its licensors shall not
 * be liable for any damages suffered by licensee as a result of
 * using, modifying or distributing the software or its
 * derivatives. In no event will the University of Notre Dame or its
 * licensors be liable for any lost revenue, profit or data, or for
 * direct, indirect, special, consequential, incidental or punitive
 * damages, however caused and regardless of the theory of liability,
 * arising out of the use of or inability to use software, even if the
 * University of Notre Dame has been advised of the possibility of
 * such damages.
 */

#include "selection/SelectionEvaluator.hpp"
namespace oopse {


bool SelectionEvaluator::loadScript(const std::string& filename, const std::string& script) {
    this->filename = filename;
    this->script = script;
    if (! compiler.compile(filename, script)) {
        error = true;
        errorMessage = compiler.getErrorMessage();
        return false;
    }

    pc = 0;
    aatoken = compiler.getAatokenCompiled();
    linenumbers = compiler.getLineNumbers();
    lineIndices = compiler.getLineIndices();
    return true;
}

void SelectionEvaluator::clearState() {
    for (int i = scriptLevelMax; --i >= 0; )
        stack[i].clear();
    scriptLevel = 0;
    error = false;
    errorMessage = "";
}

bool SelectionEvaluator::loadScriptString(const std::string& script) {
    clearState();
    return loadScript("", script);
}

bool SelectionEvaluator::loadScriptFile(const std::string& filename) {
    clearState();
    return loadScriptFileInternal(filename);
}

bool SelectionEvaluator::loadScriptFileInternal(const  string & filename) {

}

void SelectionEvaluator::instructionDispatchLoop(){

    while ( pc < aatoken.size()) {
        statement = aatoken[pc++];
        statementLength = statement.size();
        Token token = statement[0];
        switch (token.tok) {
            case Token::define:
                define();
            break;
            case Token::select:
                select();
            break;
            default:
                unrecognizedCommand(token);
            return;
        }
    }
}

  BitSet SelectionEvaluator::expression(std::vector<Token>& code, int pcStart) {
    int numberOfAtoms = viewer.getAtomCount();
    BitSet bs;
    BitSet[] stack = new BitSet[10];
    int sp = 0;

    for (int pc = pcStart; ; ++pc) {
      Token instruction = code[pc];

      switch (instruction.tok) {
      case Token::expressionBegin:
        break;
      case Token::expressionEnd:
        break;
      case Token::all:
        bs = stack[sp++] = new BitSet(numberOfAtoms);
        for (int i = numberOfAtoms; --i >= 0; )
          bs.set(i);
        break;
      case Token::none:
        stack[sp++] = new BitSet();
        break;
      case Token::opOr:
        bs = stack[--sp];
        stack[sp-1].or(bs);
        break;
      case Token::opAnd:
        bs = stack[--sp];
        stack[sp-1].and(bs);
        break;
      case Token::opNot:
        bs = stack[sp - 1];
        notSet(bs);
        break;
      case Token::within:
        bs = stack[sp - 1];
        stack[sp - 1] = new BitSet();
        withinInstruction(instruction, bs, stack[sp - 1]);
        break;
      case Token::selected:
        stack[sp++] = copyBitSet(viewer.getSelectionSet());
        break;
      case Token::name:

        break;
      case  Token::index:
        
        break;
      case Token::molname:  

        break;
      case Token::molindex:
        break;
      case Token::identifier:
        stack[sp++] = lookupIdentifierValue((std::string)instruction.value);
        break;
      case Token::opLT:
      case Token::opLE:
      case Token::opGE:
      case Token::opGT:
      case Token::opEQ:
      case Token::opNE:
        bs = stack[sp++] = new BitSet();
        comparatorInstruction(instruction, bs);
        break;
      default:
        unrecognizedExpression();
      }
    }
    if (sp != 1)
      evalError("atom expression compiler error - stack over/underflow");
    return stack[0];
  }


  void SelectionEvaluator::comparatorInstruction(Token instruction, BitSet bs) {
    int comparator = instruction.tok;
    int property = instruction.intValue;
    float propertyValue = 0; // just for temperature
    int comparisonValue = ((Integer)instruction.value).intValue();
    int numberOfAtoms = viewer.getAtomCount();
    Frame frame = viewer.getFrame();
    for (int i = 0; i < numberOfAtoms; ++i) {
      Atom atom = frame.getAtomAt(i);
      switch (property) {
      case Token::mass:
        //propertyValue = atom.getAtomNumber();
        break;
      case Token::charge:

        break;
      case Token::dipole:

        break; 
      default:
        unrecognizedAtomProperty(property);
      }
      bool match = false;
      switch (comparator) {
      case Token::opLT:
        match = propertyValue < comparisonValue;
        break;
      case Token::opLE:
        match = propertyValue <= comparisonValue;
        break;
      case Token::opGE:
        match = propertyValue >= comparisonValue;
        break;
      case Token::opGT:
        match = propertyValue > comparisonValue;
        break;
      case Token::opEQ:
        match = propertyValue == comparisonValue;
        break;
      case Token::opNE:
        match = propertyValue != comparisonValue;
        break;
      }
      if (match)
        bs.set(i);
    }
  }

void SelectionEvaluator::withinInstruction(const Token& instruction, BitSet& bs, BitSet& bsResult)

    boost::any withinSpec = instruction.value;
    if (withinSpec.type() == typeid(float)){
        withinDistance(boost::any_cast<float>(withinSpec), bs, bsResult);
        return;
    }
    
    evalError("Unrecognized within parameter:" + withinSpec);
}

  void SelectionEvaluator::withinDistance(float distance, const BitSet& bs, const BitSet& bsResult) {
    Frame frame = viewer.getFrame();
    for (int i = frame.getAtomCount(); --i >= 0; ) {
      if (bs.get(i)) {
        Atom atom = frame.getAtomAt(i);
        AtomIterator iterWithin =
          frame.getWithinIterator(atom, distance);
        while (iterWithin.hasNext())
          bsResult.set(iterWithin.next().getAtomIndex());
      }
    }
  }

  void SelectionEvaluator::define() {
    assert(statement.size() >= 3);

    std::string variable = boost::any_cast<std::string>(statement[1].value);
    
    variables.insert(std::make_pair(variable, expression(statement, 2)));
  }
}

/** @todo */
void SelectionEvaluator::predefine(const std::string& script) {

    if (compiler.compile("#predefine", script)) {
        std::vector<std::vector<Token> > aatoken = compiler.getAatokenCompiled();
        if (aatoken.size() != 1) {
            evalError("predefinition does not have exactly 1 command:"
                + script);
            return;
        }
        std::vector<Token> statement = aatoken[0];
        if (statement.size() > 2) {
            int tok = statement[1].tok;
            if (tok == Token::identifier || (tok & Token::predefinedset) == Token::predefinedset) {
                std::string variable = (std::string)statement[1].value;
                variables.insert(std::make_pair(variable, statement));

            } else {
                evalError("invalid variable name:" + script);
            }
        }else {
            evalError("bad predefinition length:" + script);
        }

        
    } else {
        evalError("predefined set compile error:" + script +
          "\ncompile error:" + compiler.getErrorMessage());
    }

}

void SelectionEvaluator::select(){
    viewer.setSelectionSet(expression(statement, 1));
}

BitSet SelectionEvaluator::lookupValue(const std::string& variable){

    std::map<std::string, boost::any>::iterator i = variables.find(variable);

    if (i != variables.end()) {
        if (i->second.type() == typeid(BitSet)) {
            return boost::any_cast<BitSet>(i->second);
        } else if (i->second.type() ==  typeid(std::vector<Token>)){
            BitSet bs = expression(boost::any_cast(i->second), 2);
            i->second =  bs; /**@todo fixme */
            return bs;
        }
    }

}

}
Revision:	1966
Committed:	Thu Feb 3 14:04:59 2005 UTC (19 years, 4 months ago) by tim
File size:	9623 byte(s)
Log Message:	selection in progress
#	User	Rev	Content
1	tim	1961	/*
2			* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3			*
4			* The University of Notre Dame grants you ("Licensee") a
5			* non-exclusive, royalty free, license to use, modify and
6			* redistribute this software in source and binary code form, provided
7			* that the following conditions are met:
8			*
9			* 1. Acknowledgement of the program authors must be made in any
10			* publication of scientific results based in part on use of the
11			* program. An acceptable form of acknowledgement is citation of
12			* the article in which the program was described (Matthew
13			* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14			* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15			* Parallel Simulation Engine for Molecular Dynamics,"
16			* J. Comput. Chem. 26, pp. 252-271 (2005))
17			*
18			* 2. Redistributions of source code must retain the above copyright
19			* notice, this list of conditions and the following disclaimer.
20			*
21			* 3. Redistributions in binary form must reproduce the above copyright
22			* notice, this list of conditions and the following disclaimer in the
23			* documentation and/or other materials provided with the
24			* distribution.
25			*
26			* This software is provided "AS IS," without a warranty of any
27			* kind. All express or implied conditions, representations and
28			* warranties, including any implied warranty of merchantability,
29			* fitness for a particular purpose or non-infringement, are hereby
30			* excluded. The University of Notre Dame and its licensors shall not
31			* be liable for any damages suffered by licensee as a result of
32			* using, modifying or distributing the software or its
33			* derivatives. In no event will the University of Notre Dame or its
34			* licensors be liable for any lost revenue, profit or data, or for
35			* direct, indirect, special, consequential, incidental or punitive
36			* damages, however caused and regardless of the theory of liability,
37			* arising out of the use of or inability to use software, even if the
38			* University of Notre Dame has been advised of the possibility of
39			* such damages.
40			*/
41
42			#include "selection/SelectionEvaluator.hpp"
43			namespace oopse {
44
45
46	tim	1962	bool SelectionEvaluator::loadScript(const std::string& filename, const std::string& script) {
47			this->filename = filename;
48			this->script = script;
49			if (! compiler.compile(filename, script)) {
50			error = true;
51			errorMessage = compiler.getErrorMessage();
52			return false;
53			}
54
55			pc = 0;
56			aatoken = compiler.getAatokenCompiled();
57			linenumbers = compiler.getLineNumbers();
58			lineIndices = compiler.getLineIndices();
59			return true;
60	tim	1961	}
61	tim	1962
62			void SelectionEvaluator::clearState() {
63			for (int i = scriptLevelMax; --i >= 0; )
64	tim	1965	stack[i].clear();
65	tim	1962	scriptLevel = 0;
66			error = false;
67	tim	1965	errorMessage = "";
68	tim	1962	}
69
70			bool SelectionEvaluator::loadScriptString(const std::string& script) {
71			clearState();
72	tim	1965	return loadScript("", script);
73	tim	1962	}
74
75			bool SelectionEvaluator::loadScriptFile(const std::string& filename) {
76			clearState();
77			return loadScriptFileInternal(filename);
78			}
79
80	tim	1966	bool SelectionEvaluator::loadScriptFileInternal(const string & filename) {
81	tim	1962
82	tim	1966	}
83
84	tim	1962	void SelectionEvaluator::instructionDispatchLoop(){
85
86	tim	1965	while ( pc < aatoken.size()) {
87	tim	1962	statement = aatoken[pc++];
88	tim	1965	statementLength = statement.size();
89	tim	1962	Token token = statement[0];
90			switch (token.tok) {
91	tim	1965	case Token::define:
92	tim	1962	define();
93			break;
94	tim	1965	case Token::select:
95	tim	1962	select();
96			break;
97			default:
98			unrecognizedCommand(token);
99			return;
100			}
101			}
102			}
103
104	tim	1965	BitSet SelectionEvaluator::expression(std::vector<Token>& code, int pcStart) {
105	tim	1962	int numberOfAtoms = viewer.getAtomCount();
106			BitSet bs;
107			BitSet[] stack = new BitSet[10];
108			int sp = 0;
109
110			for (int pc = pcStart; ; ++pc) {
111			Token instruction = code[pc];
112	tim	1966
113	tim	1962	switch (instruction.tok) {
114	tim	1965	case Token::expressionBegin:
115	tim	1962	break;
116	tim	1965	case Token::expressionEnd:
117	tim	1966	break;
118	tim	1965	case Token::all:
119	tim	1962	bs = stack[sp++] = new BitSet(numberOfAtoms);
120			for (int i = numberOfAtoms; --i >= 0; )
121			bs.set(i);
122			break;
123	tim	1965	case Token::none:
124	tim	1962	stack[sp++] = new BitSet();
125			break;
126	tim	1965	case Token::opOr:
127	tim	1962	bs = stack[--sp];
128			stack[sp-1].or(bs);
129			break;
130	tim	1965	case Token::opAnd:
131	tim	1962	bs = stack[--sp];
132			stack[sp-1].and(bs);
133			break;
134	tim	1965	case Token::opNot:
135	tim	1962	bs = stack[sp - 1];
136			notSet(bs);
137			break;
138	tim	1965	case Token::within:
139	tim	1962	bs = stack[sp - 1];
140			stack[sp - 1] = new BitSet();
141			withinInstruction(instruction, bs, stack[sp - 1]);
142			break;
143	tim	1965	case Token::selected:
144	tim	1962	stack[sp++] = copyBitSet(viewer.getSelectionSet());
145			break;
146	tim	1965	case Token::name:
147
148	tim	1962	break;
149	tim	1965	case Token::index:
150
151			break;
152			case Token::molname:
153
154			break;
155			case Token::molindex:
156			break;
157			case Token::identifier:
158			stack[sp++] = lookupIdentifierValue((std::string)instruction.value);
159			break;
160			case Token::opLT:
161			case Token::opLE:
162			case Token::opGE:
163			case Token::opGT:
164			case Token::opEQ:
165			case Token::opNE:
166	tim	1962	bs = stack[sp++] = new BitSet();
167			comparatorInstruction(instruction, bs);
168			break;
169			default:
170			unrecognizedExpression();
171			}
172			}
173			if (sp != 1)
174			evalError("atom expression compiler error - stack over/underflow");
175			return stack[0];
176			}
177
178
179
180			void SelectionEvaluator::comparatorInstruction(Token instruction, BitSet bs) {
181			int comparator = instruction.tok;
182			int property = instruction.intValue;
183			float propertyValue = 0; // just for temperature
184			int comparisonValue = ((Integer)instruction.value).intValue();
185			int numberOfAtoms = viewer.getAtomCount();
186			Frame frame = viewer.getFrame();
187			for (int i = 0; i < numberOfAtoms; ++i) {
188			Atom atom = frame.getAtomAt(i);
189			switch (property) {
190	tim	1965	case Token::mass:
191			//propertyValue = atom.getAtomNumber();
192	tim	1962	break;
193	tim	1965	case Token::charge:
194
195	tim	1962	break;
196	tim	1965	case Token::dipole:
197
198	tim	1962	break;
199			default:
200			unrecognizedAtomProperty(property);
201			}
202	tim	1965	bool match = false;
203	tim	1962	switch (comparator) {
204	tim	1965	case Token::opLT:
205	tim	1962	match = propertyValue < comparisonValue;
206			break;
207	tim	1965	case Token::opLE:
208	tim	1962	match = propertyValue <= comparisonValue;
209			break;
210	tim	1965	case Token::opGE:
211	tim	1962	match = propertyValue >= comparisonValue;
212			break;
213	tim	1965	case Token::opGT:
214	tim	1962	match = propertyValue > comparisonValue;
215			break;
216	tim	1965	case Token::opEQ:
217	tim	1962	match = propertyValue == comparisonValue;
218			break;
219	tim	1965	case Token::opNE:
220	tim	1962	match = propertyValue != comparisonValue;
221			break;
222			}
223			if (match)
224			bs.set(i);
225			}
226			}
227
228	tim	1965	void SelectionEvaluator::withinInstruction(const Token& instruction, BitSet& bs, BitSet& bsResult)
229	tim	1962
230	tim	1965	boost::any withinSpec = instruction.value;
231	tim	1966	if (withinSpec.type() == typeid(float)){
232			withinDistance(boost::any_cast<float>(withinSpec), bs, bsResult);
233	tim	1962	return;
234			}
235	tim	1966
236	tim	1962	evalError("Unrecognized within parameter:" + withinSpec);
237			}
238
239	tim	1966	void SelectionEvaluator::withinDistance(float distance, const BitSet& bs, const BitSet& bsResult) {
240	tim	1962	Frame frame = viewer.getFrame();
241			for (int i = frame.getAtomCount(); --i >= 0; ) {
242			if (bs.get(i)) {
243			Atom atom = frame.getAtomAt(i);
244			AtomIterator iterWithin =
245			frame.getWithinIterator(atom, distance);
246			while (iterWithin.hasNext())
247			bsResult.set(iterWithin.next().getAtomIndex());
248			}
249			}
250			}
251
252	tim	1965	void SelectionEvaluator::define() {
253	tim	1966	assert(statement.size() >= 3);
254
255			std::string variable = boost::any_cast<std::string>(statement[1].value);
256
257	tim	1965	variables.insert(std::make_pair(variable, expression(statement, 2)));
258	tim	1962	}
259			}
260
261	tim	1966	/** @todo */
262			void SelectionEvaluator::predefine(const std::string& script) {
263	tim	1962
264	tim	1966	if (compiler.compile("#predefine", script)) {
265			std::vector<std::vector<Token> > aatoken = compiler.getAatokenCompiled();
266			if (aatoken.size() != 1) {
267			evalError("predefinition does not have exactly 1 command:"
268			+ script);
269			return;
270			}
271			std::vector<Token> statement = aatoken[0];
272			if (statement.size() > 2) {
273			int tok = statement[1].tok;
274			if (tok == Token::identifier \|\| (tok & Token::predefinedset) == Token::predefinedset) {
275			std::string variable = (std::string)statement[1].value;
276			variables.insert(std::make_pair(variable, statement));
277
278			} else {
279			evalError("invalid variable name:" + script);
280			}
281			}else {
282			evalError("bad predefinition length:" + script);
283			}
284
285
286			} else {
287			evalError("predefined set compile error:" + script +
288			"\ncompile error:" + compiler.getErrorMessage());
289			}
290
291			}
292
293			void SelectionEvaluator::select(){
294			viewer.setSelectionSet(expression(statement, 1));
295			}
296
297			BitSet SelectionEvaluator::lookupValue(const std::string& variable){
298
299			std::map<std::string, boost::any>::iterator i = variables.find(variable);
300
301			if (i != variables.end()) {
302			if (i->second.type() == typeid(BitSet)) {
303			return boost::any_cast<BitSet>(i->second);
304			} else if (i->second.type() == typeid(std::vector<Token>)){
305			BitSet bs = expression(boost::any_cast(i->second), 2);
306			i->second = bs; /*@todo fixme /
307			return bs;
308			}
309			}
310
311			}
312
313			}