/// <summary>
/// blablabla
/// </summary>
/// <param name="simMatrix"></param>
/// <param name="threshold"></param>
/// <param name="maySkip">If true, computes the longest common subsequence. Otherwise,
/// computes the longest common substring.
/// </param>
public TokenIndexLCSScoreProvider(SimilarityMatrix simMatrix,
double threshold,
bool maySkip)
{
_SimMatrix = simMatrix;
_Threshold = threshold;
_MaySkip = maySkip;
}
/// <summary>
/// Patch the similarity matrix so that tags which are not aligned can't be associated
/// by the ED
/// </summary>
private void PatchSimilarityMatrix(SimilarityMatrix sim,
IList <Core.Tokenization.Token> srcTokens,
IList <Core.Tokenization.Token> trgTokens,
TagAssociations tagAlignment)
{
if (tagAlignment == null || tagAlignment.Count == 0)
{
return;
}
for (int s = 0; s < srcTokens.Count; ++s)
{
if (!(srcTokens[s] is Core.Tokenization.TagToken))
{
// not a tag
continue;
}
Core.Tag st = ((Core.Tokenization.TagToken)srcTokens[s]).Tag;
if (!(st.Type == TagType.Start || st.Type == TagType.End))
{
// not a paired tag
continue;
}
for (int t = 0; t < trgTokens.Count; ++t)
{
if (sim.IsAssigned(s, t) && sim[s, t] < 0.0d)
{
// invalid assignment anyway, no need to check further
continue;
}
if (!(trgTokens[t] is Core.Tokenization.TagToken))
{
// should't really be the case as then sim[s, t] < 0
System.Diagnostics.Debug.Assert(false, "Shouldn't be");
continue;
}
Core.Tag tt = ((Core.Tokenization.TagToken)trgTokens[t]).Tag;
if (!(tt.Type == TagType.Start || tt.Type == TagType.End))
{
// should't really be the case as then sim[s, t] < 0
System.Diagnostics.Debug.Assert(false, "Shouldn't be");
continue;
}
if (!tagAlignment.AreAssociated(s, t))
{
sim[s, t] = -1.0d;
}
}
}
}
private static int[,] ComputeTagAssociationScores(SimilarityMatrix similarityMatrix,
TagPairs srcPairedTags,
TagPairs trgPairedTags,
bool useEndPositions)
{
// this should pretty much result in first-come first-serve alignment, but we hopefully
// get better associations for nested tags
// foreach src tag, compute LCS to each target tag
int[,] lcsScores = new int[srcPairedTags.Count, trgPairedTags.Count];
List <int> sourceTokenPositions = new List <int>();
List <int> targetTokenPositions = new List <int>();
TokenIndexLCSScoreProvider scorer
= new TokenIndexLCSScoreProvider(similarityMatrix, 0.75, true);
for (int p = 0; p < similarityMatrix.SourceTokens.Count; ++p)
{
sourceTokenPositions.Add(p);
}
for (int p = 0; p < similarityMatrix.TargetTokens.Count; ++p)
{
targetTokenPositions.Add(p);
}
SequenceAlignmentComputer <int> aligner
= new SequenceAlignmentComputer <int>(sourceTokenPositions,
targetTokenPositions, scorer, null, 1, 1);
int uptoSource;
int uptoTarget;
for (int srcTag = srcPairedTags.Count - 1; srcTag >= 0; --srcTag)
{
PairedTag sPt = srcPairedTags[srcTag];
uptoSource = (useEndPositions ? sPt.End : sPt.Start);
for (int trgTag = trgPairedTags.Count - 1; trgTag >= 0; --trgTag)
{
PairedTag tPt = trgPairedTags[trgTag];
uptoTarget = (useEndPositions ? tPt.End : tPt.Start);
List <AlignedSubstring> result
= aligner.Compute(uptoSource, uptoTarget);
if (result != null && result.Count > 0)
{
System.Diagnostics.Debug.Assert(result.Count == 1);
// the result is the common subsequence length minus items which were deleted or inserted
int score = result[0].Score
- (uptoSource - result[0].Score)
- (uptoTarget - result[0].Score);
// penalize large differences in the spanned width, but not if
// we include the end positions in the LCS
int malus;
if (useEndPositions)
{
malus = 0;
}
else
{
int srcSpan = GetTagSpan(sPt);
int trgSpan = GetTagSpan(tPt);
malus = Math.Abs(srcSpan - trgSpan) / 2;
}
lcsScores[srcTag, trgTag] = score - malus;
}
}
}
return(lcsScores);
}
public static TagAssociations AlignPairedTags(IList <Core.Tokenization.Token> sourceTokens,
IList <Core.Tokenization.Token> targetTokens,
SimilarityMatrix similarityMatrix)
{
TagPairs srcPairedTags = FindPairedTags(sourceTokens);
if (srcPairedTags == null || srcPairedTags.Count == 0)
{
return(null);
}
TagPairs trgPairedTags = FindPairedTags(targetTokens);
if (trgPairedTags == null || trgPairedTags.Count == 0)
{
return(null);
}
TagAssociations associations = new TagAssociations();
System.Collections.BitArray processedSrcTags
= new System.Collections.BitArray(srcPairedTags.Count);
System.Collections.BitArray processedTrgTags
= new System.Collections.BitArray(trgPairedTags.Count);
const bool useEndPositions = true;
if (srcPairedTags.Count > 0 && trgPairedTags.Count > 0)
{
int[,] lcsScores = ComputeTagAssociationScores(similarityMatrix,
srcPairedTags, trgPairedTags,
useEndPositions);
if (lcsScores == null)
{
return(null);
}
while (true)
{
// find global row/column maximum
int maxScore = Int32.MinValue;
int maxS = -1;
int maxT = -1;
bool unique = false;
for (int s = 0; s < srcPairedTags.Count; ++s)
{
if (processedSrcTags[s])
{
continue;
}
for (int t = 0; t < trgPairedTags.Count; ++t)
{
if (processedTrgTags[t])
{
continue;
}
if (lcsScores[s, t] > maxScore)
{
maxScore = lcsScores[s, t];
maxS = s;
maxT = t;
unique = true;
}
else if (lcsScores[s, t] == maxScore)
{
unique = false;
}
}
}
if (maxS >= 0)
{
if (!unique)
{
// disambiguation required? Only if in same row or column - DNC right now.
// System.Diagnostics.Debug.Assert(false, "Investigate - let Oli know and provide test data");
}
// global unique maximum - associate tags
associations.Add(srcPairedTags[maxS], trgPairedTags[maxT],
Core.EditDistance.EditOperation.Change);
processedSrcTags[maxS] = true;
processedTrgTags[maxT] = true;
}
else
{
// no global max found anymore
break;
}
}
}
for (int p = 0; p < srcPairedTags.Count; ++p)
{
if (!processedSrcTags[p])
{
// src tag at that position is not associated
associations.Add(srcPairedTags[p], null);
}
}
for (int p = 0; p < trgPairedTags.Count; ++p)
{
if (!processedTrgTags[p])
{
associations.Add(null, trgPairedTags[p]);
}
}
return(associations);
}
private Core.EditDistance.EditDistance ComputeEditDistanceImpl_Original(
IList <Core.Tokenization.Token> sourceTokens,
IList <Core.Tokenization.Token> targetTokens,
bool computeDiagonalOnly,
Core.Tokenization.BuiltinRecognizers disabledAutoSubstitutions,
out TagAssociations alignedTags)
{
/*
* The "classic" ED approach has the problem that it doesn't detect moves
* reliably, particularly block moves. Patching up insert/delete pairs as
* moves also won't catch moves which appear as changes in the ED.
*/
if (sourceTokens == null)
{
throw new ArgumentNullException("sourceTokens");
}
if (targetTokens == null)
{
throw new ArgumentNullException("targetTokens");
}
alignedTags = null;
int i, j;
// TODO handle special cases (one/both of the arrays being empty/having no elements)
// TODO use diagonal algorithm
bool enforceFullMatrixComputation = false;
Core.EditDistance.EditDistance result =
new Core.EditDistance.EditDistance(sourceTokens.Count, targetTokens.Count, 0.0d);
// matrix which captures the similarity between two tokens as well as preassignments
SimilarityMatrix sim = new SimilarityMatrix(sourceTokens, targetTokens,
_UseStringEditDistance, disabledAutoSubstitutions);
if (enforceFullMatrixComputation)
{
// this will be fully computed by the tag aligner in most cases, but we may save a bit
// on plain text segments
sim.Compute(computeDiagonalOnly);
}
MatrixItem[,] matrix = CreateEditDistanceMatrix(sourceTokens, targetTokens);
alignedTags = TagAligner.AlignPairedTags(sourceTokens, targetTokens, sim);
if (alignedTags != null && alignedTags.Count > 0)
{
// Patch the sim matrix so that non-aligned tags can't be assigned to each other
PatchSimilarityMatrix(sim, sourceTokens, targetTokens, alignedTags);
ComputeEditDistanceMatrix_Full(matrix, sim, alignedTags);
}
else if (enforceFullMatrixComputation)
{
ComputeEditDistanceMatrix_Full(matrix, sim, alignedTags);
}
else
{
ComputeEditDistanceMatrix_Lazy(matrix, sim);
}
// readout the cheapest path
i = sourceTokens.Count;
j = targetTokens.Count;
result.Distance = matrix[i, j].Score;
while (i > 0 || j > 0)
{
EditDistanceItem item = new EditDistanceItem();
item.Resolution = EditDistanceResolution.None;
MatrixItem m = matrix[i, j];
item.Operation = m.Operation;
switch (item.Operation)
{
case EditOperation.Identity:
item.Costs = 0.0d;
--i;
--j;
break;
case EditOperation.Change:
item.Costs = _UseStringEditDistance
? (1.0d - m.Similarity)
: (1.0d - SimilarityComputers.GetTokenSimilarity(sourceTokens[i - 1], targetTokens[j - 1],
true, disabledAutoSubstitutions));
// item.Costs = (1.0d - m.Similarity);
--i;
--j;
break;
case EditOperation.Insert:
item.Costs = _InsertDeleteCosts;
--j;
break;
case EditOperation.Delete:
item.Costs = _InsertDeleteCosts;
--i;
break;
case EditOperation.Undefined:
throw new Exception("Internal ED computation error");
}
item.Source = i;
item.Target = j;
result.AddAtStart(item);
}
if (alignedTags != null && alignedTags.Count > 0)
{
// should happen before move detection
FixTagActions(sourceTokens, targetTokens, result, alignedTags);
}
// identify move operations which are pairs of insert/delete operations in the shortest path.
// Note that the comparision result is already in the matrix and we only care about identity.
// TODO we may rather use a configurable threshold than identity (1.0) to catch move operations
// of sufficiently similar items (e.g. case-insensitive)
if (_ComputeMoves)
{
int moves = DetectMoves(result, matrix);
if (moves > 0)
{
// adjust score: substract moves * (deletionCosts + insertionCosts), add moves * moveCosts
// TODO take moveDistance into account, i.e. penalty depends on distance?
result.Distance -= (double)moves * (2.0d * _InsertDeleteCosts);
result.Distance += (double)moves * _MoveCosts;
}
}
#if DEBUG
// a stream for logging. Will always be null in non-Debug builds
System.IO.TextWriter logStream = null;
bool log = false;
if (log)
{
logStream = new System.IO.StreamWriter(System.IO.Path.GetTempPath() + "/ed.log",
false, System.Text.Encoding.UTF8);
logStream.WriteLine("Source objects:");
for (int p = 0; p < sourceTokens.Count; ++p)
{
logStream.WriteLine("\t{0}:\t{1}", p, sourceTokens[p].ToString());
}
logStream.WriteLine();
logStream.WriteLine("Target objects:");
for (int p = 0; p < targetTokens.Count; ++p)
{
logStream.WriteLine("\t{0}:\t{1}", p, targetTokens[p].ToString());
}
logStream.WriteLine();
logStream.WriteLine();
if (alignedTags != null)
{
logStream.WriteLine("Tag Alignment:");
foreach (TagAssociation ta in alignedTags)
{
logStream.WriteLine("\t{0}", ta.ToString());
}
logStream.WriteLine();
logStream.WriteLine();
}
result.Dump(logStream, "Final ED");
logStream.Close();
logStream.Dispose();
logStream = null;
}
#endif
#if DEBUG
// write matrix to a temp file in HTML format
_DumpMatrix = false; // typeof(T) != typeof(char);
if (_DumpMatrix)
{
System.IO.StreamWriter wtr = new System.IO.StreamWriter(System.IO.Path.GetTempPath() + "/SimMatrix.html",
false, System.Text.Encoding.UTF8);
System.Web.UI.Html32TextWriter htmlWriter = new System.Web.UI.Html32TextWriter(wtr);
htmlWriter.WriteFullBeginTag("html");
htmlWriter.WriteFullBeginTag("body");
htmlWriter.WriteBeginTag("table");
htmlWriter.WriteAttribute("border", "1");
for (j = -1; j <= targetTokens.Count; ++j)
{
htmlWriter.WriteFullBeginTag("tr");
for (i = -1; i <= sourceTokens.Count; ++i)
{
htmlWriter.WriteFullBeginTag("td");
if (i < 0)
{
// caption row
if (j >= 0)
{
htmlWriter.Write("j={0}", j);
if (j > 0)
{
htmlWriter.WriteFullBeginTag("br");
htmlWriter.WriteFullBeginTag("b");
htmlWriter.Write(targetTokens[j - 1].ToString());
htmlWriter.WriteEndTag("b");
}
}
}
else if (j < 0)
{
// j < 0 but i >= 0 -->
htmlWriter.Write("i={0}", i);
if (i > 0)
{
htmlWriter.WriteFullBeginTag("br");
htmlWriter.WriteFullBeginTag("b");
htmlWriter.Write(sourceTokens[i - 1].ToString());
htmlWriter.WriteEndTag("b");
}
}
else
{
// content cell
htmlWriter.Write("d={0}", matrix[i, j].Score);
htmlWriter.WriteFullBeginTag("br");
htmlWriter.Write("s={0}", matrix[i, j].Similarity);
htmlWriter.WriteFullBeginTag("br");
htmlWriter.Write("o={0}", matrix[i, j].Operation.ToString());
}
htmlWriter.WriteEndTag("td");
}
htmlWriter.WriteEndTag("tr");
}
htmlWriter.WriteEndTag("table");
htmlWriter.WriteFullBeginTag("h2");
htmlWriter.Write("Result");
htmlWriter.WriteEndTag("h2");
htmlWriter.Write("Score = {0}", result.Distance);
htmlWriter.WriteFullBeginTag("ol");
for (i = 0; i < result.Items.Count; ++i)
{
htmlWriter.WriteFullBeginTag("li");
htmlWriter.Write("{0}: s={1} t={2}",
result[i].Operation.ToString(), result[i].Source, result[i].Target);
}
htmlWriter.WriteEndTag("ol");
htmlWriter.WriteEndTag("body");
htmlWriter.WriteEndTag("html");
htmlWriter.Close();
}
#endif
return(result);
}
private void ComputeEditDistanceMatrix_Lazy(MatrixItem[,] matrix,
SimilarityMatrix sim)
{
ComputeCell(matrix, sim, sim.SourceTokens.Count, sim.TargetTokens.Count);
}
private void ComputeCell(MatrixItem[,] matrix,
SimilarityMatrix sim, int i, int j)
{
if (matrix[i, j].Operation != EditOperation.Undefined)
{
// cell already computed - no further processing required
return;
}
// ensure that the diagonal cell is computed (always needed)
ComputeCell(matrix, sim, i - 1, j - 1);
System.Diagnostics.Debug.Assert(matrix[i - 1, j - 1].Operation != EditOperation.Undefined);
double similarity = sim[i - 1, j - 1];
// low similarity means high "change costs" and vice versa:
double changeCosts = (similarity < 0.0d)
? _InvalidAssignmentCosts
: matrix[i - 1, j - 1].Score + (1.0d - similarity);
EditOperation op = EditOperation.Undefined;
double insertCosts = 0.0d;
double deleteCosts = 0.0d;
// i == j: main diagonal. i < j: below, i > j: above.
/*
* if (similarity == 1.0d)
* {
* // this seems to assume that the costs are minimal in the diagonal - not
* // sure that's true in the general case (only if insert/delete/change
* // costs are equal = 1)
* op = EditOperation.Identity;
* }
* else
*/
if (i < j)
{
// below main diagonal.
ComputeCell(matrix, sim, i, j - 1);
insertCosts = matrix[i, j - 1].Score + _InsertDeleteCosts;
if (insertCosts >= changeCosts || changeCosts == _InvalidAssignmentCosts)
{
// need to get the deletion costs as well
ComputeCell(matrix, sim, i - 1, j);
deleteCosts = matrix[i - 1, j].Score + _InsertDeleteCosts;
op = GetOperation(changeCosts, insertCosts, deleteCosts, similarity);
}
else
{
if (insertCosts < changeCosts)
{
op = EditOperation.Insert;
}
else
{
op = EditOperation.Change;
}
}
}
else
{
// on or above main diagonal
ComputeCell(matrix, sim, i - 1, j);
deleteCosts = matrix[i - 1, j].Score + _InsertDeleteCosts;
if (deleteCosts >= changeCosts || changeCosts == _InvalidAssignmentCosts)
{
// need to get the insert costs as well
ComputeCell(matrix, sim, i, j - 1);
insertCosts = matrix[i, j - 1].Score + _InsertDeleteCosts;
op = GetOperation(changeCosts, insertCosts, deleteCosts, similarity);
}
else
{
if (deleteCosts < changeCosts)
{
op = EditOperation.Delete;
}
else
{
op = EditOperation.Change;
}
}
}
matrix[i, j].Similarity = similarity;
matrix[i, j].Operation = op;
System.Diagnostics.Debug.Assert(op != EditOperation.Undefined);
if (op == EditOperation.Delete)
{
matrix[i, j].Score = deleteCosts;
}
else if (op == EditOperation.Insert)
{
matrix[i, j].Score = insertCosts;
}
else
{
matrix[i, j].Score = changeCosts;
}
}
private void ComputeEditDistanceMatrix_Full(MatrixItem[,] matrix,
SimilarityMatrix sim,
TagAssociations alignedTags)
{
for (int i = 1; i <= sim.SourceTokens.Count; ++i)
{
for (int j = 1; j <= sim.TargetTokens.Count; ++j)
{
// current cell must not yet be computed:
System.Diagnostics.Debug.Assert(matrix[i, j].Operation == EditOperation.Undefined);
// predecessors must be valid:
System.Diagnostics.Debug.Assert(matrix[i - 1, j - 1].Operation != EditOperation.Undefined);
System.Diagnostics.Debug.Assert(matrix[i, j - 1].Operation != EditOperation.Undefined);
System.Diagnostics.Debug.Assert(matrix[i - 1, j].Operation != EditOperation.Undefined);
double similarity = sim[i - 1, j - 1];
System.Diagnostics.Debug.Assert((similarity >= 0.0d && similarity <= 1.0d) ||
similarity == -1.0d);
// low similarity means high "change costs" and vice versa:
double changeCosts = (similarity < 0)
? _InvalidAssignmentCosts
: matrix[i - 1, j - 1].Score + (1.0d - similarity);
double insertCosts = matrix[i, j - 1].Score + _InsertDeleteCosts;
double deleteCosts = matrix[i - 1, j].Score + _InsertDeleteCosts;
double min = Math.Min(Math.Min(changeCosts, deleteCosts), insertCosts);
// verify the shortcut condition:
System.Diagnostics.Debug.Assert(similarity < 1.0d || min == changeCosts);
EditOperation op = EditOperation.Undefined;
if (min == deleteCosts)
{
op = EditOperation.Delete;
}
else if (min == insertCosts)
{
op = EditOperation.Insert;
}
else if (min == changeCosts)
{
if (similarity == 1.0d)
{
op = EditOperation.Identity;
}
else
{
op = EditOperation.Change;
}
}
if (alignedTags != null && alignedTags.Count > 0)
{
// check whether tag alignment overrides ED result:
// TODO do this during population or during readout?
EditOperation srcTagOp = alignedTags.GetOperationBySourcePosition(i - 1);
EditOperation trgTagOp = alignedTags.GetOperationByTargetPosition(j - 1);
// changes/identity of tags are through ED, while the tag alignment
// defines deletions, insertions
if ((srcTagOp == EditOperation.Insert || srcTagOp == EditOperation.Delete) &&
op != srcTagOp)
{
// this is where the pre-alignment of tags supersedes the ED result
op = srcTagOp;
}
else if ((trgTagOp == EditOperation.Insert || trgTagOp == EditOperation.Delete) &&
op != trgTagOp)
{
op = trgTagOp;
}
}
matrix[i, j].Similarity = similarity;
matrix[i, j].Operation = op;
if (op == EditOperation.Delete)
{
matrix[i, j].Score = deleteCosts;
}
else if (op == EditOperation.Insert)
{
matrix[i, j].Score = insertCosts;
}
else
{
matrix[i, j].Score = changeCosts;
}
}
}
}
