Ticket #3726: sage-3726-part8.patch

a/sage/stats/hmm/chmm.pyx

@@ -527 +527 @@
-        """
-
-        cdef double log_p
-
+
+
+
+
+
-        cdef int ret = ghmm_cmodel_likelihood(self.m, sqd, &log_p)
-        ghmm_cseq_free(&sqd)
-        if ret == -1:
@@ -566 +570 @@
-            seq = TimeSeries(seq)
-        cdef TimeSeries T = seq
-        cdef int* path = ghmm_cmodel_viterbi(self.m, T._values, T._length, &log_p)
+        if not path:
+            raise RuntimeError, "sequence can't be built from model"
-        cdef Py_ssize_t i
-        v = [path[i] for i in range(T._length)]
-        sage_free(path)
@@ -583 +589 @@
-        Baum-Welch algorithm to increase the probability of observing O.
-
-        INPUT:
-
+; all sequences of length 0 are ignored.
-            max_iter -- integer or None (default: 10000) maximum number
-                      of Baum-Welch steps to take
-            log_likehood_cutoff -- positive float or None (default: 0.00001);
@@ -609 +615 @@
-            Emission parameters:
-            [(1.0, 0.0001)]
-            Initial probabilities: [1.0]
+
+        Training sequences of length 0 are gracefully ignored:
+            sage: m.baum_welch([])
+            sage: m.baum_welch([([],1)])
-        """
-        cdef ghmm_cmodel_baum_welch_context cs
-
-        cs.smo      = self.m
-
+
+
+
+
+
-        cs.logp     = <double*> safe_malloc(sizeof(double))
-        cs.eps      = log_likelihood_cutoff
-        cs.max_iter = max_iter
@@ -626 +640 @@
-cdef ghmm_cseq* to_cseq(seq) except NULL:
-    """
-    Return a pointer to a ghmm_cseq C struct.
+
+    All empty sequences are ignored.  If there are no nonempty
+    sequences a ValueError is raised, since GHMM doesn't treat
+    this degenerate case well.
-    """
-    if isinstance(seq, list) and len(seq) > 0 and not isinstance(seq[0], tuple):
-        seq = TimeSeries(seq)
@@ -645 +663 @@
-            else:
-                z = (TimeSeries(z), float(1))
-        seq[i] = z
+    seq = [x for x in seq if len(x[0]) > 0]
-
-    n = len(seq)
+    if n == 0:
+        raise ValueError, "there must be at least one nonempty sequence"
-    cdef ghmm_cseq* sqd = <ghmm_cseq*>safe_malloc(sizeof(ghmm_cseq))
-    sqd.seq        = <double**>safe_malloc(sizeof(double*) * n)
-    sqd.seq_len    = to_int_array([len(v) for v,_ in seq])

a/sage/stats/hmm/hmm.pyx

@@ -558 +558 @@
-
-        path = ghmm_dmodel_viterbi(self.m, O, len(seq), &pathlen, &log_p)
-        sage_free(O)
+        if not path:
+            raise RuntimeError, "error computing viterbi path"
-        p = [path[i] for i in range(pathlen)]
-        sage_free(path)
-