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, 5 months ago) by tim
File size:	9623 byte(s)
Log Message:	selection in progress
#	Content
1	/*
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	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	}
61
62	void SelectionEvaluator::clearState() {
63	for (int i = scriptLevelMax; --i >= 0; )
64	stack[i].clear();
65	scriptLevel = 0;
66	error = false;
67	errorMessage = "";
68	}
69
70	bool SelectionEvaluator::loadScriptString(const std::string& script) {
71	clearState();
72	return loadScript("", script);
73	}
74
75	bool SelectionEvaluator::loadScriptFile(const std::string& filename) {
76	clearState();
77	return loadScriptFileInternal(filename);
78	}
79
80	bool SelectionEvaluator::loadScriptFileInternal(const string & filename) {
81
82	}
83
84	void SelectionEvaluator::instructionDispatchLoop(){
85
86	while ( pc < aatoken.size()) {
87	statement = aatoken[pc++];
88	statementLength = statement.size();
89	Token token = statement[0];
90	switch (token.tok) {
91	case Token::define:
92	define();
93	break;
94	case Token::select:
95	select();
96	break;
97	default:
98	unrecognizedCommand(token);
99	return;
100	}
101	}
102	}
103
104	BitSet SelectionEvaluator::expression(std::vector<Token>& code, int pcStart) {
105	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
113	switch (instruction.tok) {
114	case Token::expressionBegin:
115	break;
116	case Token::expressionEnd:
117	break;
118	case Token::all:
119	bs = stack[sp++] = new BitSet(numberOfAtoms);
120	for (int i = numberOfAtoms; --i >= 0; )
121	bs.set(i);
122	break;
123	case Token::none:
124	stack[sp++] = new BitSet();
125	break;
126	case Token::opOr:
127	bs = stack[--sp];
128	stack[sp-1].or(bs);
129	break;
130	case Token::opAnd:
131	bs = stack[--sp];
132	stack[sp-1].and(bs);
133	break;
134	case Token::opNot:
135	bs = stack[sp - 1];
136	notSet(bs);
137	break;
138	case Token::within:
139	bs = stack[sp - 1];
140	stack[sp - 1] = new BitSet();
141	withinInstruction(instruction, bs, stack[sp - 1]);
142	break;
143	case Token::selected:
144	stack[sp++] = copyBitSet(viewer.getSelectionSet());
145	break;
146	case Token::name:
147
148	break;
149	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	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	case Token::mass:
191	//propertyValue = atom.getAtomNumber();
192	break;
193	case Token::charge:
194
195	break;
196	case Token::dipole:
197
198	break;
199	default:
200	unrecognizedAtomProperty(property);
201	}
202	bool match = false;
203	switch (comparator) {
204	case Token::opLT:
205	match = propertyValue < comparisonValue;
206	break;
207	case Token::opLE:
208	match = propertyValue <= comparisonValue;
209	break;
210	case Token::opGE:
211	match = propertyValue >= comparisonValue;
212	break;
213	case Token::opGT:
214	match = propertyValue > comparisonValue;
215	break;
216	case Token::opEQ:
217	match = propertyValue == comparisonValue;
218	break;
219	case Token::opNE:
220	match = propertyValue != comparisonValue;
221	break;
222	}
223	if (match)
224	bs.set(i);
225	}
226	}
227
228	void SelectionEvaluator::withinInstruction(const Token& instruction, BitSet& bs, BitSet& bsResult)
229
230	boost::any withinSpec = instruction.value;
231	if (withinSpec.type() == typeid(float)){
232	withinDistance(boost::any_cast<float>(withinSpec), bs, bsResult);
233	return;
234	}
235
236	evalError("Unrecognized within parameter:" + withinSpec);
237	}
238
239	void SelectionEvaluator::withinDistance(float distance, const BitSet& bs, const BitSet& bsResult) {
240	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	void SelectionEvaluator::define() {
253	assert(statement.size() >= 3);
254
255	std::string variable = boost::any_cast<std::string>(statement[1].value);
256
257	variables.insert(std::make_pair(variable, expression(statement, 2)));
258	}
259	}
260
261	/** @todo */
262	void SelectionEvaluator::predefine(const std::string& script) {
263
264	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	}