Made the iterations arg actually change the number of iterations

Author: chrisquince

bin/concoct

@@ -61,12 +61,12 @@ def main(args):
 
     logging.info('PCA transformed data.')
 
-    logging.info('Will call vbgmm with parameters: %s, %s, %s, %s' % (Output.CONCOCT_PATH, args.clusters, args.length_threshold, args.threads))
+    logging.info('Will call vbgmm with parameters: %s, %s, %s, %s, %s' % (Output.CONCOCT_PATH, args.clusters, args.length_threshold, args.threads,args.iterations))
 
     N_contigs = transform_filter.shape[0]
     assign = np.zeros(N_contigs, dtype=np.int32)
 
-    assign = vbgmm.fit(np.copy(transform_filter,order='C'), int(args.clusters), int(args.seed), int(args.threads))
+    assign = vbgmm.fit(np.copy(transform_filter,order='C'), int(args.clusters), int(args.seed), int(args.threads),int(args.iterations))
 
 
     Output.write_assign(

c-concoct/c_vbgmm_fit.c

@@ -34,11 +34,16 @@
 /*User includes*/
 #include "c_vbgmm_fit.h"
 
-void c_vbgmm_fit (double* adX, int nN, int nD, int nK, int seed, int* anAssign, int nThreads)
+void c_vbgmm_fit (double* adX, int nN, int nD, int nK, int seed, int* anAssign, int nThreads, int nIter)
 {
     int debug = 0;
     int bAssign = 0;
-    driverMP(adX, nN, nD, anAssign, nK, seed, DEF_MAX_ITER, DEF_EPSILON, debug, bAssign, nThreads);
+
+    if (nIter < 1){
+        nIter = DEF_MAX_ITER;
+    }
+
+    driverMP(adX, nN, nD, anAssign, nK, seed, nIter, DEF_EPSILON, debug, bAssign, nThreads);
 
     return;
 }

c-concoct/c_vbgmm_fit.h

@@ -121,7 +121,7 @@ typedef struct s_Cluster
 
 /*user defines*/
 
-void c_vbgmm_fit (double* adX, int nN, int nD, int nK, int seed, int* anAssign, int nThreads);
+void c_vbgmm_fit (double* adX, int nN, int nD, int nK, int seed, int* anAssign, int nThreads, int nIter);
 
 int driverMP(double *adX, int nN, int nD, int *anAssign, int nKStart, unsigned long lSeed, 
                                         int nMaxIter, double dEpsilon, int debug, int bAssign, int nThreads);

c-concoct/vbgmm.pyx

@@ -12,11 +12,11 @@ import numpy as np
 cimport numpy as np
 
 # declare the interface to the C code
-cdef extern void c_vbgmm_fit (double* adX, int nN, int nD, int nK, int seed, int* anAssign, int nThreads)
+cdef extern void c_vbgmm_fit (double* adX, int nN, int nD, int nK, int seed, int* anAssign, int nThreads, int nIter)
 @cython.boundscheck(False)
 @cython.wraparound(False)
 
-def fit(np.ndarray[double, ndim=2, mode="c"] xarray not None, nClusters, seed, threads):
+def fit(np.ndarray[double, ndim=2, mode="c"] xarray not None, nClusters, seed, threads, piter):
     """
     fit (xarray, nClusters, seed, threads)
 
@@ -26,18 +26,20 @@ def fit(np.ndarray[double, ndim=2, mode="c"] xarray not None, nClusters, seed, t
     param: nClusters -- an int, number of start clusters
     param: seed -- an int, the random seed
     param: threads -- int, the number of threads to use
-
+    param: piter -- int, the number of VB iterations to use
     """
-    cdef int nN, nD, nK, nThreads
+    cdef int nN, nD, nK, nThreads, nIter
 
     nN, nD = xarray.shape[0], xarray.shape[1]
 
     nK = nClusters
 
+    nIter = piter
+
     nThreads = threads
 
     cdef np.ndarray[int, ndim=1,mode="c"] assign = np.zeros((nN), dtype=np.intc)
 
-    c_vbgmm_fit (&xarray[0,0], nN, nD, nK, seed, &assign[0], nThreads)
+    c_vbgmm_fit (&xarray[0,0], nN, nD, nK, seed, &assign[0], nThreads, nIter)
 
     return assign