remove old suffix array extractor (use the one in python/ instead)

1 files changed, 0 insertions, 460 deletions

diff --git a/sa-extract/clex.pyx b/sa-extract/clex.pyx
deleted file mode 100644
index fa30caad..00000000
--- a/sa-extract/clex.pyx
+++ /dev/null
@@ -1,460 +0,0 @@
-# clex.pyx
-# defines bilexical dictionaries in C, with some convenience methods
-# for reading arrays directly as globs directly from disk.
-# Adam Lopez <alopez@cs.umd.edu>
-
-import gzip
-import sys
-import context_model
-
-cimport cintlist
-cimport cfloatlist
-cimport calignment
-cimport csuf
-cimport cdat
-
-from libc.stdio cimport FILE, fopen, fread, fwrite, fclose
-from libc.stdlib cimport malloc, realloc, free
-from libc.string cimport memset, strcpy, strlen
-
-cdef struct _node:
-  _node* smaller
-  _node* bigger
-  int key
-  int val
-
-cdef _node* new_node(int key):
-  cdef _node* n
-  n = <_node*> malloc(sizeof(_node))
-  n.smaller = NULL
-  n.bigger = NULL
-  n.key = key
-  n.val = 0
-  return n
-
-
-cdef del_node(_node* n):
-  if n.smaller != NULL:
-    del_node(n.smaller)
-  if n.bigger != NULL:
-    del_node(n.bigger)
-  free(n)
-
-
-cdef int* get_val(_node* n, int key):
-  if key == n.key:
-    return &n.val
-  elif key < n.key:
-    if n.smaller == NULL:
-      n.smaller = new_node(key)
-      return &(n.smaller.val)
-    return get_val(n.smaller, key)
-  else:
-    if n.bigger == NULL:
-      n.bigger = new_node(key)
-      return &(n.bigger.val)
-    return get_val(n.bigger, key)
-
-
-cdef class CLex:
-
-  cdef cfloatlist.CFloatList col1
-  cdef cfloatlist.CFloatList col2
-  cdef cintlist.CIntList f_index
-  cdef cintlist.CIntList e_index
-  cdef id2eword, id2fword, eword2id, fword2id
-
-  def __init__(self, filename, from_binary=False, 
-        from_data=False, earray=None, fsarray=None):
-    self.id2eword = []
-    self.id2fword = []
-    self.eword2id = {}
-    self.fword2id = {}
-    self.e_index = cintlist.CIntList()
-    self.f_index = cintlist.CIntList()
-    self.col1 = cfloatlist.CFloatList()
-    self.col2 = cfloatlist.CFloatList()
-    if from_binary:
-      self.read_binary(filename)
-    else:
-      if from_data:
-        self.compute_from_data(fsarray, earray, filename)
-      else:
-        self.read_text(filename)
-    '''print "self.eword2id"
-    print "============="
-    for x in self.eword2id:
-      print x
-    print "self.fword2id"
-    print "============="
-    for x in self.fword2id:
-      print x
-    print "-------------"'''
-
-
-  cdef compute_from_data(self, csuf.SuffixArray fsa, cdat.DataArray eda, calignment.Alignment aa):
-    cdef int sent_id, num_links, l, i, j, f_i, e_j, I, J, V_E, V_F, num_pairs
-    cdef int *fsent, *esent, *alignment, *links, *ealigned, *faligned
-    cdef _node** dict
-    cdef int *fmargin, *emargin, *count
-    cdef bytes word
-    cdef int null_word
-
-    null_word = 0
-    for word in fsa.darray.id2word: # I miss list comprehensions
-      self.id2fword.append(word)
-    self.id2fword[null_word] = "NULL"
-    for id, word in enumerate(self.id2fword):
-      self.fword2id[word] = id
-
-    for word in eda.id2word:
-      self.id2eword.append(word)
-    self.id2eword[null_word] = "NULL"
-    for id, word in enumerate(self.id2eword):
-      self.eword2id[word] = id
-
-    num_pairs = 0
-
-    V_E = len(eda.id2word)
-    V_F = len(fsa.darray.id2word)
-    fmargin = <int*> malloc(V_F*sizeof(int))
-    emargin = <int*> malloc(V_E*sizeof(int))
-    memset(fmargin, 0, V_F*sizeof(int))
-    memset(emargin, 0, V_E*sizeof(int))
-
-    dict = <_node**> malloc(V_F*sizeof(_node*))
-    memset(dict, 0, V_F*sizeof(_node*))
-
-    num_sents = len(fsa.darray.sent_index)
-    for sent_id from 0 <= sent_id < num_sents-1:
-
-      fsent = fsa.darray.data.arr + fsa.darray.sent_index.arr[sent_id]
-      I = fsa.darray.sent_index.arr[sent_id+1] - fsa.darray.sent_index.arr[sent_id] - 1
-      faligned = <int*> malloc(I*sizeof(int))
-      memset(faligned, 0, I*sizeof(int))
-
-      esent = eda.data.arr + eda.sent_index.arr[sent_id]
-      J = eda.sent_index.arr[sent_id+1] - eda.sent_index.arr[sent_id] - 1
-      ealigned = <int*> malloc(J*sizeof(int))
-      memset(ealigned, 0, J*sizeof(int))
-
-      links = aa._get_sent_links(sent_id, &num_links)
-
-      for l from 0 <= l < num_links:
-        i = links[l*2]
-        j = links[l*2+1]
-        if i >= I or j >= J:
-          sys.stderr.write("  %d-%d out of bounds (I=%d,J=%d) in line %d\n" % (i,j,I,J,sent_id+1))
-          assert i < I
-          assert j < J
-        f_i = fsent[i]
-        e_j = esent[j]
-        fmargin[f_i] = fmargin[f_i]+1
-        emargin[e_j] = emargin[e_j]+1
-        if dict[f_i] == NULL:
-          dict[f_i] = new_node(e_j)
-          dict[f_i].val = 1
-          num_pairs = num_pairs + 1
-        else:
-          count = get_val(dict[f_i], e_j)
-          if count[0] == 0:
-            num_pairs = num_pairs + 1
-          count[0] = count[0] + 1
-        # add count
-        faligned[i] = 1
-        ealigned[j] = 1
-      for i from 0 <= i < I:
-        if faligned[i] == 0:
-          f_i = fsent[i]
-          fmargin[f_i] = fmargin[f_i] + 1
-          emargin[null_word] = emargin[null_word] + 1
-          if dict[f_i] == NULL:
-            dict[f_i] = new_node(null_word)
-            dict[f_i].val = 1
-            num_pairs = num_pairs + 1
-          else:
-            count = get_val(dict[f_i], null_word)
-            if count[0] == 0:
-              num_pairs = num_pairs + 1
-            count[0] = count[0] + 1
-      for j from 0 <= j < J:
-        if ealigned[j] == 0:
-          e_j = esent[j]
-          fmargin[null_word] = fmargin[null_word] + 1
-          emargin[e_j] = emargin[e_j] + 1
-          if dict[null_word] == NULL:
-            dict[null_word] = new_node(e_j)
-            dict[null_word].val = 1
-            num_pairs = num_pairs + 1
-          else:
-            count = get_val(dict[null_word], e_j)
-            if count[0] == 0:
-              num_pairs = num_pairs + 1
-            count[0] = count[0] + 1
-      free(links)
-      free(faligned)
-      free(ealigned)
-    self.f_index = cintlist.CIntList(initial_len=V_F)
-    self.e_index = cintlist.CIntList(initial_len=num_pairs)
-    self.col1 = cfloatlist.CFloatList(initial_len=num_pairs)
-    self.col2 = cfloatlist.CFloatList(initial_len=num_pairs)
-
-    num_pairs = 0
-    for i from 0 <= i < V_F:
-      #self.f_index[i] = num_pairs
-      self.f_index.set(i, num_pairs)
-      if dict[i] != NULL:
-        self._add_node(dict[i], &num_pairs, float(fmargin[i]), emargin)
-        del_node(dict[i])
-    free(fmargin)
-    free(emargin)
-    free(dict)
-    return
-
-
-  cdef _add_node(self, _node* n, int* num_pairs, float fmargin, int* emargin):
-    cdef int loc
-    if n.smaller != NULL:
-      self._add_node(n.smaller, num_pairs, fmargin, emargin)
-    loc = num_pairs[0]
-    self.e_index.set(loc, n.key)
-    self.col1.set(loc, float(n.val)/fmargin)
-    self.col2.set(loc, float(n.val)/float(emargin[n.key]))
-    num_pairs[0] = loc + 1
-    if n.bigger != NULL:
-      self._add_node(n.bigger, num_pairs, fmargin, emargin)
-
-
-  def write_binary(self, filename):
-    cdef FILE* f
-    cdef bytes bfilename = filename
-    cdef char* cfilename = bfilename
-    f = fopen(cfilename, "w")
-    self.f_index.write_handle(f)
-    self.e_index.write_handle(f)
-    self.col1.write_handle(f)
-    self.col2.write_handle(f)
-    self.write_wordlist(self.id2fword, f)
-    self.write_wordlist(self.id2eword, f)
-    fclose(f)
-
-
-  cdef write_wordlist(self, wordlist, FILE* f):
-    cdef int word_len
-    cdef int num_words
-    cdef char* c_word
-
-    num_words = len(wordlist)
-    fwrite(&(num_words), sizeof(int), 1, f)
-    for word in wordlist:
-      c_word = word
-      word_len = strlen(c_word) + 1
-      fwrite(&(word_len), sizeof(int), 1, f)
-      fwrite(c_word, sizeof(char), word_len, f)
-
-
-  cdef read_wordlist(self, word2id, id2word, FILE* f):
-    cdef int num_words
-    cdef int word_len
-    cdef char* c_word
-    cdef bytes py_word
-
-    fread(&(num_words), sizeof(int), 1, f)
-    for i from 0 <= i < num_words:
-      fread(&(word_len), sizeof(int), 1, f)
-      c_word = <char*> malloc (word_len * sizeof(char))
-      fread(c_word, sizeof(char), word_len, f)
-      py_word = c_word
-      free(c_word)
-      word2id[py_word] = len(id2word)
-      id2word.append(py_word)
-
-  def read_binary(self, filename):
-    cdef FILE* f
-    cdef bytes bfilename = filename
-    cdef char* cfilename = bfilename
-    f = fopen(cfilename, "r")
-    self.f_index.read_handle(f)
-    self.e_index.read_handle(f)
-    self.col1.read_handle(f)
-    self.col2.read_handle(f)
-    self.read_wordlist(self.fword2id, self.id2fword, f)
-    self.read_wordlist(self.eword2id, self.id2eword, f)
-    fclose(f)
-
-
-  def get_e_id(self, eword):
-    if eword not in self.eword2id:
-      e_id = len(self.id2eword)
-      self.id2eword.append(eword)
-      self.eword2id[eword] = e_id
-    return self.eword2id[eword]
-
-
-  def get_f_id(self, fword):
-    if fword not in self.fword2id:
-      f_id = len(self.id2fword)
-      self.id2fword.append(fword)
-      self.fword2id[fword] = f_id
-    return self.fword2id[fword]
-
-
-  def read_text(self, filename):
-    cdef i, j, w, e_id, f_id, n_f, n_e, N
-    cdef cintlist.CIntList fcount 
-
-    fcount = cintlist.CIntList()
-    if filename[-2:] == "gz":
-      f = gzip.GzipFile(filename)
-    else:
-      f = open(filename)
-
-    # first loop merely establishes size of array objects
-    sys.stderr.write("Initial read...\n")
-    for line in f:
-      (fword, eword, score1, score2) = line.split()
-      f_id = self.get_f_id(fword)
-      e_id = self.get_e_id(eword)
-      while f_id >= len(fcount):
-        fcount.append(0)
-      fcount.arr[f_id] = fcount.arr[f_id] + 1
-
-    # Allocate space for dictionary in arrays
-    N = 0
-    n_f = len(fcount)
-    self.f_index = cintlist.CIntList(initial_len=n_f+1)
-    for i from 0 <= i < n_f:
-      self.f_index.arr[i] = N
-      N = N + fcount.arr[i]
-      fcount.arr[i] = 0
-    self.f_index.arr[n_f] = N
-    self.e_index = cintlist.CIntList(initial_len=N)
-    self.col1 = cfloatlist.CFloatList(initial_len=N)
-    self.col2 = cfloatlist.CFloatList(initial_len=N)
-
-    # Re-read file, placing words into buckets
-    sys.stderr.write("Bucket sort...\n")
-    f.seek(0)
-    for line in f:
-      (fword, eword, score1, score2) = line.split()
-      f_id = self.get_f_id(fword)
-      e_id = self.get_e_id(eword)
-      index = self.f_index.arr[f_id] + fcount.arr[f_id]
-      fcount.arr[f_id] = fcount.arr[f_id] + 1
-      self.e_index.arr[index] = int(e_id)
-      self.col1[index] = float(score1)
-      self.col2[index] = float(score2)
-    f.close()
-
-    sys.stderr.write("Final sort...\n")
-    # Sort buckets by eword
-    for b from 0 <= b < n_f:
-      i = self.f_index.arr[b]
-      j = self.f_index.arr[b+1]
-      self.qsort(i,j, "")
-
-
-  cdef swap(self, int i, int j):
-    cdef int itmp
-    cdef float ftmp
-
-    if i == j:
-      return
-
-    itmp = self.e_index.arr[i]
-    self.e_index.arr[i] = self.e_index.arr[j]
-    self.e_index.arr[j] = itmp
-
-    ftmp = self.col1.arr[i]
-    self.col1.arr[i] = self.col1.arr[j]
-    self.col1.arr[j] = ftmp
-
-    ftmp = self.col2.arr[i]
-    self.col2.arr[i] = self.col2.arr[j]
-    self.col2.arr[j] = ftmp
-
-
-  cdef qsort(self, int i, int j, pad):
-    cdef int pval, p
-
-    if i > j:
-      raise Exception("Sort error in CLex")
-    if i == j: #empty interval
-      return
-    if i == j-1: # singleton interval
-      return
-
-    p = (i+j)/2
-    pval = self.e_index.arr[p]
-    self.swap(i, p)
-    p = i
-    for k from i+1 <= k < j:
-      if pval >= self.e_index.arr[k]:
-        self.swap(p+1, k)
-        self.swap(p, p+1)
-        p = p + 1
-    self.qsort(i,p, pad+"  ")
-    self.qsort(p+1,j, pad+"  ")
-
-
-  def write_enhanced(self, filename):
-    f = open(filename, "w")
-    for i in self.f_index:
-      f.write("%d " % i)
-    f.write("\n")
-    for i, s1, s2 in zip(self.e_index, self.col1, self.col2):
-      f.write("%d %f %f " % (i, s1, s2))
-    f.write("\n")
-    for i, w in enumerate(self.id2fword):
-      f.write("%d %s " % (i, w))
-    f.write("\n")
-    for i, w in enumerate(self.id2eword):
-      f.write("%d %s " % (i, w))
-    f.write("\n")
-    f.close()
-
-
-  def get_score(self, fword, eword, col):
-    cdef e_id, f_id, low, high, midpoint, val
-    #print "get_score fword=",fword,", eword=",eword,", col=",col
-
-    if eword not in self.eword2id:
-      return None
-    if fword not in self.fword2id:
-      return None
-    f_id = self.fword2id[fword]
-    e_id = self.eword2id[eword]
-    low = self.f_index.arr[f_id]
-    high = self.f_index.arr[f_id+1]
-    while high - low > 0:
-      midpoint = (low+high)/2
-      val = self.e_index.arr[midpoint]
-      if val == e_id:
-        if col == 0:
-          return self.col1.arr[midpoint]
-        if col == 1:
-          return self.col2.arr[midpoint]
-      if val > e_id:
-        high = midpoint
-      if val < e_id:
-        low = midpoint + 1
-    return None
-
-
-  def write_text(self, filename):
-    """Note: does not guarantee writing the dictionary in the original order"""
-    cdef i, N, e_id, f_id
-    
-    f = open(filename, "w")
-    N = len(self.e_index)
-    f_id = 0
-    for i from 0 <= i < N:
-      while self.f_index.arr[f_id+1] == i:
-        f_id = f_id + 1
-      e_id = self.e_index.arr[i]
-      score1 = self.col1.arr[i]
-      score2 = self.col2.arr[i]
-      f.write("%s %s %.6f %.6f\n" % (self.id2fword[f_id], self.id2eword[e_id], score1, score2))
-    f.close()
-
-