Merge pull request bhmm#48 from marscher/malloc_check

check for malloc failures and gracefully handle them

appveyor.yml

@@ -13,29 +13,29 @@ environment:
   matrix:
     - PYTHON: "C:\\Miniconda"
       CONDA_PY: "27"
-      CONDA_NPY: "19"
+      CONDA_NPY: "110"
 
     - PYTHON: "C:\\Miniconda-x64"
       CONDA_PY: "27"
-      CONDA_NPY: "19"
+      CONDA_NPY: "112"
       ARCH: "64"
 
     - PYTHON: "C:\\Miniconda3"
-      CONDA_PY: "34"
-      CONDA_NPY: "19"
+      CONDA_PY: "35"
+      CONDA_NPY: "113"
 
     - PYTHON: "C:\\Miniconda3-x64"
-      CONDA_PY: "34"
-      CONDA_NPY: "19"
+      CONDA_PY: "36"
+      CONDA_NPY: "113"
       ARCH: "64"
 
 install:
   - set PATH=%PYTHON%;%PYTHON%\\Scripts;%PATH%
-  - conda config --add channels omnia
-  - conda update -yq --all
-  - conda install -yq conda-build jinja2
+  - conda config --add channels conda-forge
+  - conda install -yq conda-build 
 
 build: false
 
 test_script:
   - "%CMD_IN_ENV% conda build --quiet devtools\\conda-recipe"
+

bhmm/hidden/impl_c/_hidden.c

@@ -145,7 +145,7 @@ void _compute_state_counts(
 }*/
 
 
-void _compute_transition_counts(
+int _compute_transition_counts(
         double *transition_counts,
         const double *A,
         const double *pobs,
@@ -162,6 +162,9 @@ void _compute_transition_counts(
             transition_counts[i*N+j] = 0.0;
 
     tmp = (double*) malloc(N*N * sizeof(double));
+    if (! tmp) {
+        return _BHMM_ERR_NO_MEM;
+    }
     for (t = 0; t < T-1; t++)
     {
         sum = 0.0;
@@ -176,6 +179,7 @@ void _compute_transition_counts(
                 transition_counts[i*N+j] += tmp[i*N+j] / sum;
     }
     free(tmp);
+    return 0;
 }
 
 
@@ -196,24 +200,30 @@ int argmax(double* v, int N)
 }
 
 
-void _compute_viterbi(
+int _compute_viterbi(
         int *path,
         const double *A,
         const double *pobs,
         const double *pi,
         int N, int T)
 {
-    int i, j, t, maxi;
-    double sum, maxprod, p;
-
+    int i, j, t, maxi, result;
+    double sum;
+    double *v, *vnext, *h, *vh;
+    int* ptr;
+    result = 0;
     // allocate v
-    double* v = (double*) malloc(N * sizeof(double));
-    double* vnext = (double*) malloc(N * sizeof(double));
-    double* h = (double*) malloc(N * sizeof(double));
-    double* vh;
+    v = (double*) malloc(N * sizeof(double));
+    vnext = (double*) malloc(N * sizeof(double));
+    h = (double*) malloc(N * sizeof(double));
 
     // allocate ptr
-    int* ptr = (int*) malloc(T*N * sizeof(int));
+    ptr = (int*) malloc(T*N * sizeof(int));
+
+    if (! v || ! vnext || !h || ! ptr) {
+        result = _BHMM_ERR_NO_MEM; // indicate no memory
+        goto error;
+    }
 
     // initialization of v
     sum = 0.0;
@@ -260,12 +270,14 @@ void _compute_viterbi(
     {
         path[t] = ptr[(t+1)*N+path[t+1]];
     }
-
+    error:
     // free memory
     free(v);
     free(vnext);
     free(h);
     free(ptr);
+
+    return result;
 }
 
 int _random_choice(const double* p, const int N)
@@ -307,7 +319,7 @@ void _normalize(double* v, const int N)
 }
 
 
-void _sample_path(
+int _sample_path(
         int *path,
         const double *alpha,
         const double *A,
@@ -316,7 +328,11 @@ void _sample_path(
 {
     // initialize variables
     int i,t;
-    double* psel = (double*) malloc(N * sizeof(double));
+    double* psel;
+    psel = (double*) malloc(N * sizeof(double));
+    if (! psel) {
+        return _BHMM_ERR_NO_MEM;
+    }
 
     // initialize random number generator
     srand(time(NULL));
@@ -353,6 +369,7 @@ void _sample_path(
 
     // free memory
     free(psel);
+    return 0;
 }
 
 /*
@@ -381,4 +398,4 @@ void compute_transition_probabilities(
             }
     }
 }
-*/
+*/

bhmm/hidden/impl_c/_hidden.h

@@ -1,6 +1,8 @@
 #ifndef HMM_H_
 #define HMM_H_
 
+
+#define _BHMM_ERR_NO_MEM 2
 /*
  API FUNCTIONS
 */
@@ -29,22 +31,22 @@ void _compute_state_counts(
         const double *gamma,
         int T, int N);
 
-void _compute_transition_counts(
+int _compute_transition_counts(
         double *transition_counts,
         const double *A,
         const double *pobs,
         const double *alpha,
         const double *beta,
         int N, int T);
 
-void _compute_viterbi(
+int _compute_viterbi(
         int *path,
         const double *A,
         const double *pobs,
         const double *pi,
         int N, int T);
 
-void _sample_path(
+int _sample_path(
         int *path,
         const double *alpha,
         const double *A,

bhmm/hidden/impl_c/hidden.pyx

@@ -23,21 +23,12 @@ cimport numpy
 
 cdef extern from "_hidden.h":
     double _forward(double * alpha, const double *A, const double *pobs, const double *pi, const int N, const int T)
-
-cdef extern from "_hidden.h":
     void _backward(double *beta, const double *A, const double *pobs, const int N, const int T)
-
-# cdef extern from "_hmm.h":
 #     void _computeGamma(double *gamma, const double *alpha, const double *beta, const int T, const int N)
-#
-cdef extern from "_hidden.h":
-    void _compute_transition_counts(double *transition_counts, const double *A, const double *pobs, const double *alpha, const double *beta, int N, int T)
-
-cdef extern from "_hidden.h":
-    void _compute_viterbi(int *path, const double *A, const double *pobs, const double *pi, int N, int T)
-
-cdef extern from "_hidden.h":
-    void _sample_path(int *path, const double *alpha, const double *A, const double *pobs, const int N, const int T)
+    int _compute_transition_counts(double *transition_counts, const double *A, const double *pobs, const double *alpha, const double *beta, int N, int T)
+    int _compute_viterbi(int *path, const double *A, const double *pobs, const double *pi, int N, int T)
+    int _sample_path(int *path, const double *alpha, const double *A, const double *pobs, const int N, const int T)
+    int _BHMM_ERR_NO_MEM
 
 
 def cdef_double_array(n1, n2):
@@ -155,7 +146,9 @@ def transition_counts(alpha, beta, A, pobs, T = None, out = None, dtype=numpy.fl
         palpha = <double*> numpy.PyArray_DATA(alpha)
         pbeta  = <double*> numpy.PyArray_DATA(beta)
         # call
-        _compute_transition_counts(pC, pA, ppobs, palpha, pbeta, N, T)
+        res = _compute_transition_counts(pC, pA, ppobs, palpha, pbeta, N, T)
+        if res == _BHMM_ERR_NO_MEM:
+            raise MemoryError()
         return C
     else:
         raise TypeError
@@ -176,7 +169,9 @@ def viterbi(A, pobs, pi, dtype=numpy.float32):
         ppobs = <double*> numpy.PyArray_DATA(pobs)
         ppi   = <double*> numpy.PyArray_DATA(pi)
         # call
-        _compute_viterbi(ppath, pA, ppobs, ppi, N, T)
+        res = _compute_viterbi(ppath, pA, ppobs, ppi, N, T)
+        if res == _BHMM_ERR_NO_MEM:
+            raise MemoryError()
         return path
     else:
         raise TypeError
@@ -199,7 +194,9 @@ def sample_path(alpha, A, pobs, T = None, dtype=numpy.float32):
         pA     = <double*> numpy.PyArray_DATA(A)
         ppobs  = <double*> numpy.PyArray_DATA(pobs)
         # call
-        _sample_path(ppath, palpha, pA, ppobs, N, T)
+        res = _sample_path(ppath, palpha, pA, ppobs, N, T)
+        if res == _BHMM_ERR_NO_MEM:
+            raise MemoryError()
         return path
     else:
         raise TypeError