move atools to utils directory

1 files changed, 369 insertions, 0 deletions

diff --git a/utils/atools.cc b/utils/atools.cc
new file mode 100644
index 00000000..c0a91731
--- /dev/null
+++ b/utils/atools.cc
@@ -0,0 +1,369 @@
+#include <iostream>
+#include <sstream>
+#include <vector>
+
+#include <queue>
+#include <map>
+#include <boost/program_options.hpp>
+#include <boost/shared_ptr.hpp>
+
+#include "filelib.h"
+#include "alignment_pharaoh.h"
+
+namespace po = boost::program_options;
+using namespace std;
+using boost::shared_ptr;
+
+struct Command {
+  virtual ~Command() {}
+  virtual string Name() const = 0;
+
+  // returns 1 for alignment grid output [default]
+  // returns 2 if Summary() should be called [for AER, etc]
+  virtual int Result() const { return 1; }
+
+  virtual bool RequiresTwoOperands() const { return true; }
+  virtual void Apply(const Array2D<bool>& a, const Array2D<bool>& b, Array2D<bool>* x) = 0;
+  void EnsureSize(const Array2D<bool>& a, const Array2D<bool>& b, Array2D<bool>* x) {
+    x->resize(max(a.width(), b.width()), max(a.height(), b.height()));
+  }
+  static bool Safe(const Array2D<bool>& a, int i, int j) {
+    if (i >= 0 && j >= 0 && i < a.width() && j < a.height())
+      return a(i,j);
+    else
+      return false;
+  }
+  virtual void Summary() { assert(!"Summary should have been overridden"); }
+};
+
+// compute fmeasure, second alignment is reference, first is hyp
+struct FMeasureCommand : public Command {
+  FMeasureCommand() : matches(), num_predicted(), num_in_ref() {}
+  int Result() const { return 2; }
+  string Name() const { return "fmeasure"; }
+  bool RequiresTwoOperands() const { return true; }
+  void Apply(const Array2D<bool>& hyp, const Array2D<bool>& ref, Array2D<bool>* x) {
+    (void) x;   // AER just computes statistics, not an alignment
+    int i_len = ref.width();
+    int j_len = ref.height();
+    for (int i = 0; i < i_len; ++i) {
+      for (int j = 0; j < j_len; ++j) {
+        if (ref(i,j)) {
+          ++num_in_ref;
+          if (Safe(hyp, i, j)) ++matches;
+        } 
+      }
+    }
+    for (int i = 0; i < hyp.width(); ++i)
+      for (int j = 0; j < hyp.height(); ++j)
+        if (hyp(i,j)) ++num_predicted;
+  }
+  void Summary() {
+    if (num_predicted == 0 || num_in_ref == 0) {
+      cerr << "Insufficient statistics to compute f-measure!\n";
+      abort();
+    }
+    const double prec = static_cast<double>(matches) / num_predicted;
+    const double rec = static_cast<double>(matches) / num_in_ref;
+    cout << "P: " << prec << endl;
+    cout << "R: " << rec << endl;
+    const double f = (2.0 * prec * rec) / (rec + prec);
+    cout << "F: " << f << endl;
+  }
+  int matches;
+  int num_predicted;
+  int num_in_ref;
+};
+
+struct DisplayCommand : public Command {
+  string Name() const { return "display"; }
+  bool RequiresTwoOperands() const { return false; }
+  void Apply(const Array2D<bool>& in, const Array2D<bool>&, Array2D<bool>* x) {
+    *x = in;
+    cout << *x << endl;
+  }
+};
+
+struct ConvertCommand : public Command {
+  string Name() const { return "convert"; }
+  bool RequiresTwoOperands() const { return false; }
+  void Apply(const Array2D<bool>& in, const Array2D<bool>&, Array2D<bool>* x) {
+    *x = in;
+  }
+};
+
+struct InvertCommand : public Command {
+  string Name() const { return "invert"; }
+  bool RequiresTwoOperands() const { return false; }
+  void Apply(const Array2D<bool>& in, const Array2D<bool>&, Array2D<bool>* x) {
+    Array2D<bool>& res = *x;
+    res.resize(in.height(), in.width());
+    for (int i = 0; i < in.height(); ++i)
+      for (int j = 0; j < in.width(); ++j)
+        res(i, j) = in(j, i);
+  }
+};
+
+struct IntersectCommand : public Command {
+  string Name() const { return "intersect"; }
+  bool RequiresTwoOperands() const { return true; }
+  void Apply(const Array2D<bool>& a, const Array2D<bool>& b, Array2D<bool>* x) {
+    EnsureSize(a, b, x);
+    Array2D<bool>& res = *x;
+    for (int i = 0; i < a.width(); ++i)
+      for (int j = 0; j < a.height(); ++j)
+        res(i, j) = Safe(a, i, j) && Safe(b, i, j);
+  }
+};
+
+struct UnionCommand : public Command {
+  string Name() const { return "union"; }
+  bool RequiresTwoOperands() const { return true; }
+  void Apply(const Array2D<bool>& a, const Array2D<bool>& b, Array2D<bool>* x) {
+    EnsureSize(a, b, x);
+    Array2D<bool>& res = *x;
+    for (int i = 0; i < res.width(); ++i)
+      for (int j = 0; j < res.height(); ++j)
+        res(i, j) = Safe(a, i, j) || Safe(b, i, j);
+  }
+};
+
+struct RefineCommand : public Command {
+  RefineCommand() {
+    neighbors_.push_back(make_pair(1,0));
+    neighbors_.push_back(make_pair(-1,0));
+    neighbors_.push_back(make_pair(0,1));
+    neighbors_.push_back(make_pair(0,-1));
+  }
+  bool RequiresTwoOperands() const { return true; }
+
+  void Align(int i, int j) {
+    res_(i, j) = true;
+    is_i_aligned_[i] = true;
+    is_j_aligned_[j] = true;
+  }
+
+  bool IsNeighborAligned(int i, int j) const {
+    for (int k = 0; k < neighbors_.size(); ++k) {
+      const int di = neighbors_[k].first;
+      const int dj = neighbors_[k].second;
+      if (Safe(res_, i + di, j + dj))
+        return true;
+    }
+    return false;
+  }
+
+  bool IsNeitherAligned(int i, int j) const {
+    return !(is_i_aligned_[i] || is_j_aligned_[j]);
+  }
+
+  bool IsOneOrBothUnaligned(int i, int j) const {
+    return !(is_i_aligned_[i] && is_j_aligned_[j]);
+  }
+
+  bool KoehnAligned(int i, int j) const {
+    return IsOneOrBothUnaligned(i, j) && IsNeighborAligned(i, j);
+  }
+
+  typedef bool (RefineCommand::*Predicate)(int i, int j) const;
+
+ protected:
+  void InitRefine(
+      const Array2D<bool>& a,
+      const Array2D<bool>& b) {
+    res_.clear();
+    EnsureSize(a, b, &res_);
+    in_.clear(); un_.clear(); is_i_aligned_.clear(); is_j_aligned_.clear();
+    EnsureSize(a, b, &in_);
+    EnsureSize(a, b, &un_);
+    is_i_aligned_.resize(res_.width(), false);
+    is_j_aligned_.resize(res_.height(), false);
+    for (int i = 0; i < in_.width(); ++i)
+      for (int j = 0; j < in_.height(); ++j) {
+        un_(i, j) = Safe(a, i, j) || Safe(b, i, j);
+        in_(i, j) = Safe(a, i, j) && Safe(b, i, j);
+        if (in_(i, j)) Align(i, j);
+    }
+  }
+  // "grow" the resulting alignment using the points in adds
+  // if they match the constraints determined by pred
+  void Grow(Predicate pred, bool idempotent, const Array2D<bool>& adds) {
+    if (idempotent) {
+      for (int i = 0; i < adds.width(); ++i)
+        for (int j = 0; j < adds.height(); ++j) {
+          if (adds(i, j) && !res_(i, j) &&
+              (this->*pred)(i, j)) Align(i, j);
+        }
+      return;
+    }
+    set<pair<int, int> > p;
+    for (int i = 0; i < adds.width(); ++i)
+      for (int j = 0; j < adds.height(); ++j)
+        if (adds(i, j) && !res_(i, j))
+          p.insert(make_pair(i, j));
+    bool keep_going = !p.empty();
+    while (keep_going) {
+      keep_going = false;
+      for (set<pair<int, int> >::iterator pi = p.begin();
+           pi != p.end(); ++pi) {
+        if ((this->*pred)(pi->first, pi->second)) {
+          Align(pi->first, pi->second);
+          p.erase(pi);
+          keep_going = true;
+        }
+      }
+    }
+  }
+  Array2D<bool> res_;  // refined alignment
+  Array2D<bool> in_;   // intersection alignment
+  Array2D<bool> un_;   // union alignment
+  vector<bool> is_i_aligned_;
+  vector<bool> is_j_aligned_;
+  vector<pair<int,int> > neighbors_;
+};
+
+struct DiagCommand : public RefineCommand {
+  DiagCommand() {
+    neighbors_.push_back(make_pair(1,1));
+    neighbors_.push_back(make_pair(-1,1));
+    neighbors_.push_back(make_pair(1,-1));
+    neighbors_.push_back(make_pair(-1,-1));
+  }
+};
+
+struct GDCommand : public DiagCommand {
+  string Name() const { return "grow-diag"; }
+  void Apply(const Array2D<bool>& a, const Array2D<bool>& b, Array2D<bool>* x) {
+    InitRefine(a, b);
+    Grow(&RefineCommand::KoehnAligned, false, un_);
+    *x = res_;
+  }
+};
+
+struct GDFCommand : public DiagCommand {
+  string Name() const { return "grow-diag-final"; }
+  void Apply(const Array2D<bool>& a, const Array2D<bool>& b, Array2D<bool>* x) {
+    InitRefine(a, b);
+    Grow(&RefineCommand::KoehnAligned, false, un_);
+    Grow(&RefineCommand::IsOneOrBothUnaligned, true, a);
+    Grow(&RefineCommand::IsOneOrBothUnaligned, true, b);
+    *x = res_;
+  }
+};
+
+struct GDFACommand : public DiagCommand {
+  string Name() const { return "grow-diag-final-and"; }
+  void Apply(const Array2D<bool>& a, const Array2D<bool>& b, Array2D<bool>* x) {
+    InitRefine(a, b);
+    Grow(&RefineCommand::KoehnAligned, false, un_);
+    Grow(&RefineCommand::IsNeitherAligned, true, a);
+    Grow(&RefineCommand::IsNeitherAligned, true, b);
+    *x = res_;
+  }
+};
+
+map<string, boost::shared_ptr<Command> > commands;
+
+void InitCommandLine(int argc, char** argv, po::variables_map* conf) {
+  po::options_description opts("Configuration options");
+  ostringstream os;
+  os << "Operation to perform:";
+  for (map<string, boost::shared_ptr<Command> >::iterator it = commands.begin();
+       it != commands.end(); ++it) {
+    os << ' ' << it->first;
+  }
+  string cstr = os.str();
+  opts.add_options()
+        ("input_1,i", po::value<string>(), "[REQUIRED] Alignment 1 file, - for STDIN")
+        ("input_2,j", po::value<string>(), "Alignment 2 file, - for STDIN")
+	("command,c", po::value<string>()->default_value("convert"), cstr.c_str())
+        ("help,h", "Print this help message and exit");
+  po::options_description clo("Command line options");
+  po::options_description dcmdline_options;
+  dcmdline_options.add(opts);
+
+  po::store(parse_command_line(argc, argv, dcmdline_options), *conf);
+  po::notify(*conf);
+
+  if (conf->count("help") || conf->count("input_1") == 0 || conf->count("command") == 0) {
+    cerr << dcmdline_options << endl;
+    exit(1);
+  }
+  const string cmd = (*conf)["command"].as<string>();
+  if (commands.count(cmd) == 0) {
+    cerr << "Don't understand command: " << cmd << endl;
+    exit(1);
+  }
+  if (commands[cmd]->RequiresTwoOperands()) {
+    if (conf->count("input_2") == 0) {
+      cerr << "Command '" << cmd << "' requires two alignment files\n";
+      exit(1);
+    }
+    if ((*conf)["input_1"].as<string>() == "-" && (*conf)["input_2"].as<string>() == "-") {
+      cerr << "Both inputs cannot be STDIN\n";
+      exit(1);
+    }
+  } else {
+    if (conf->count("input_2") != 0) {
+      cerr << "Command '" << cmd << "' requires only one alignment file\n";
+      exit(1);
+    }
+  }
+}
+
+template<class C> static void AddCommand() {
+  C* c = new C;
+  commands[c->Name()].reset(c);
+}
+
+int main(int argc, char **argv) {
+  AddCommand<ConvertCommand>();
+  AddCommand<DisplayCommand>();
+  AddCommand<InvertCommand>();
+  AddCommand<IntersectCommand>();
+  AddCommand<UnionCommand>();
+  AddCommand<GDCommand>();
+  AddCommand<GDFCommand>();
+  AddCommand<GDFACommand>();
+  AddCommand<FMeasureCommand>();
+  po::variables_map conf;
+  InitCommandLine(argc, argv, &conf);
+  Command& cmd = *commands[conf["command"].as<string>()];
+  boost::shared_ptr<ReadFile> rf1(new ReadFile(conf["input_1"].as<string>()));
+  boost::shared_ptr<ReadFile> rf2;
+  if (cmd.RequiresTwoOperands())
+    rf2.reset(new ReadFile(conf["input_2"].as<string>()));
+  istream* in1 = rf1->stream();
+  istream* in2 = NULL;
+  if (rf2) in2 = rf2->stream();
+  while(*in1) {
+    string line1;
+    string line2;
+    getline(*in1, line1);
+    if (in2) {
+      getline(*in2, line2);
+      if ((*in1 && !*in2) || (*in2 && !*in1)) {
+        cerr << "Mismatched number of lines!\n";
+        exit(1);
+      }
+    }
+    if (line1.empty() && !*in1) break;
+    shared_ptr<Array2D<bool> > out(new Array2D<bool>);
+    shared_ptr<Array2D<bool> > a1 = AlignmentPharaoh::ReadPharaohAlignmentGrid(line1);
+    if (in2) {
+      shared_ptr<Array2D<bool> > a2 = AlignmentPharaoh::ReadPharaohAlignmentGrid(line2);
+      cmd.Apply(*a1, *a2, out.get());
+    } else {
+      Array2D<bool> dummy;
+      cmd.Apply(*a1, dummy, out.get());
+    }
+    
+    if (cmd.Result() == 1) {
+      AlignmentPharaoh::SerializePharaohFormat(*out, &cout);
+    }
+  }
+  if (cmd.Result() == 2)
+    cmd.Summary();
+  return 0;
+}
+