Fixed Python2/Python3 compatibility issue

marinkaz · marinkaz · commit 8df70101e732 · 2015-03-20T11:57:33.000+01:00
diff --git a/nimfa/methods/factorization/bd.py b/nimfa/methods/factorization/bd.py
@@ -184,7 +184,7 @@ def __init__(self, V, seed=None, W=None, H=None, rank=30, max_iter=30,
                  **options):
         self.name = "bd"
         self.aseeds = ["random", "fixed", "nndsvd", "random_c", "random_vcol"]
-        super().__init__(vars())
+        nmf_std.Nmf_std.__init__(self, vars())
         if self.alpha is not None:
             self.alpha = sp.csr_matrix((self.V.shape[0], self.rank))
         self.alpha = self.alpha.tocsr() if sp.isspmatrix(self.alpha) else np.mat(self.alpha)
diff --git a/nimfa/methods/factorization/bmf.py b/nimfa/methods/factorization/bmf.py
@@ -174,7 +174,7 @@ def __init__(self, V, seed=None, W=None, H=None, rank=30, max_iter=30,
                  lambda_w=1.1, lambda_h=1.1, **options):
         self.name = "bmf"
         self.aseeds = ["random", "fixed", "nndsvd", "random_c", "random_vcol"]
-        super().__init__(vars())
+        nmf_std.Nmf_std.__init__(self, vars())
         self.tracker = mf_track.Mf_track() if self.track_factor and self.n_run > 1 \
                                               or self.track_error else None
 
diff --git a/nimfa/methods/factorization/icm.py b/nimfa/methods/factorization/icm.py
@@ -159,7 +159,7 @@ def __init__(self, V, seed=None, W=None, H=None, H1=None,
                  k=0., sigma=1., **options):
         self.name = "icm"
         self.aseeds = ["random", "fixed", "nndsvd", "random_c", "random_vcol"]
-        super().__init__(vars())
+        nmf_std.Nmf_std.__init__(self, vars())
         if self.alpha is None:
             self.alpha = sp.rand(self.V.shape[0], self.rank, density=0.8, format='csr')
         self.alpha= self.alpha.tocsr() if sp.isspmatrix(self.alpha) else np.mat(self.alpha)
diff --git a/nimfa/methods/factorization/lfnmf.py b/nimfa/methods/factorization/lfnmf.py
@@ -144,7 +144,7 @@ def __init__(self, V, seed=None, W=None, H=None, rank=30, max_iter=30,
                  track_error=False, alpha=0.01, **options):
         self.name = "lfnmf"
         self.aseeds = ["random", "fixed", "nndsvd", "random_c", "random_vcol"]
-        super().__init__(vars())
+        nmf_std.Nmf_std.__init__(self, vars())
         self.tracker = mf_track.Mf_track() if self.track_factor and self.n_run > 1 \
                                               or self.track_error else None
 
diff --git a/nimfa/methods/factorization/lsnmf.py b/nimfa/methods/factorization/lsnmf.py
@@ -142,7 +142,7 @@ def __init__(self, V, seed=None, W=None, H=None, H1=None,
                  track_error=False, sub_iter=10, inner_sub_iter=10, beta=0.1, **options):
         self.name = "lsnmf"
         self.aseeds = ["random", "fixed", "nndsvd", "random_c", "random_vcol"]
-        super().__init__(vars())
+        nmf_std.Nmf_std.__init__(self, vars())
         self.min_residuals = 1e-5 if not self.min_residuals else self.min_residuals
         self.tracker = mf_track.Mf_track() if self.track_factor and self.n_run > 1 \
                                               or self.track_error else None
diff --git a/nimfa/methods/factorization/nmf.py b/nimfa/methods/factorization/nmf.py
@@ -159,7 +159,7 @@ def __init__(self, V, seed=None, W=None, H=None, rank=30, max_iter=30,
                  update='euclidean', objective='fro', conn_change=30, **options):
         self.name = "nmf"
         self.aseeds = ["random", "fixed", "nndsvd", "random_c", "random_vcol"]
-        super().__init__(vars())
+        nmf_std.Nmf_std.__init__(self, vars())
         if 'conn' not in self.objective:
             self.conn_change = None
         self._conn_change = 0
diff --git a/nimfa/methods/factorization/nsnmf.py b/nimfa/methods/factorization/nsnmf.py
@@ -144,7 +144,7 @@ def __init__(self, V, seed=None, W=None, H=None, rank=30, max_iter=30,
                  theta=0.5, **options):
         self.name = "nsnmf"
         self.aseeds = ["random", "fixed", "nndsvd", "random_c", "random_vcol"]
-        super().__init__(vars())
+        nmf_ns.Nmf_ns.__init__(self, vars())
         self.tracker = mf_track.Mf_track() if self.track_factor and self.n_run > 1 \
                                               or self.track_error else None
 
diff --git a/nimfa/methods/factorization/pmf.py b/nimfa/methods/factorization/pmf.py
@@ -123,7 +123,7 @@ def __init__(self, V, seed=None, W=None, H=None, rank=30, max_iter=30,
                  rel_error=False, **options):
         self.name = "pmf"
         self.aseeds = ["random", "fixed", "nndsvd", "random_c", "random_vcol"]
-        super().__init__(vars())
+        nmf_std.Nmf_std.__init__(self, vars())
         self.tracker = mf_track.Mf_track() if self.track_factor and self.n_run > 1 \
                                               or self.track_error else None
 
diff --git a/nimfa/methods/factorization/pmfcc.py b/nimfa/methods/factorization/pmfcc.py
@@ -131,7 +131,7 @@ def __init__(self, V, seed=None, W=None, H=None, rank=30, max_iter=30,
                  Theta=None, **options):
         self.name = "pmfcc"
         self.aseeds = ["random", "fixed", "nndsvd", "random_c", "random_vcol"]
-        super().__init__(vars())
+        smf.Smf.__init__(self, vars())
         if not self.Theta:
             self.Theta = np.mat(np.zeros((self.V.shape[1], self.V.shape[1])))
         self.tracker = mf_track.Mf_track() if self.track_factor and self.n_run > 1 \
diff --git a/nimfa/methods/factorization/psmf.py b/nimfa/methods/factorization/psmf.py
@@ -158,7 +158,7 @@ def __init__(self, V, seed=None, W=None, H=None, H1=None,
                  track_error=False, prior=20, **options):
         self.name = "psmf"
         self.aseeds = ["none"]
-        super().__init__(vars())
+        nmf_std.Nmf_std.__init__(self, vars())
         self.test_conv = 5 if not self.test_conv else self.test_conv
         if isinstance(self.prior, numbers.Real):
             self.prior = np.ones(int(self.prior)) / self.prior
diff --git a/nimfa/methods/factorization/snmf.py b/nimfa/methods/factorization/snmf.py
@@ -155,7 +155,7 @@ def __init__(self, V, seed=None, W=None, H=None, H1=None,
                  i_conv=10, w_min_change=0, **options):
         self.name = "snmf"
         self.aseeds = ["random", "fixed", "nndsvd", "random_c", "random_vcol"]
-        super().__init__(vars())
+        nmf_std.Nmf_std.__init__(self, vars())
         if not self.eta:
             self.eta = np.max(self.V) if not sp.isspmatrix(self.V) else np.max(self.V.data)
         if self.eta < 0:
diff --git a/nimfa/methods/factorization/snmnmf.py b/nimfa/methods/factorization/snmnmf.py
@@ -189,7 +189,7 @@ def __init__(self, V, V1, seed=None, W=None, H=None, H1=None,
                  lamb=0.01, lamb_1=0.01, **options):
         self.name = "snmnmf"
         self.aseeds = ["random", "fixed", "nndsvd", "random_c", "random_vcol"]
-        super().__init__(vars())
+        nmf_mm.Nmf_mm.__init__(self, vars())
         if self.A is not None:
             self.A = sp.csr_matrix((self.V1.shape[1], self.V1.shape[1]))
         self.A = self.A.tocsr() if sp.isspmatrix(self.A) else np.mat(self.A)
diff --git a/nimfa/models/nmf.py b/nimfa/models/nmf.py
@@ -327,6 +327,7 @@ def score_features(self, idx=None):
         for f in range(W.shape[0]):
             # probability that the i-th feature contributes to q-th basis vector.
             prob = W[f, :] / (W[f, :].sum() + np.finfo(W.dtype).eps)
+            prob = prob.todense() if sp.isspmatrix(prob) else prob
             scores[f] = np.dot(prob, np.log2(prob + np.finfo(W.dtype).eps).T)
         scores = 1. + 1. / np.log2(W.shape[1]) * scores
         return scores
diff --git a/nimfa/models/nmf_mm.py b/nimfa/models/nmf_mm.py
@@ -56,7 +56,7 @@ def __init__(self, params):
         :type params: `dict`
         """
         self.model_name = "mm"
-        super().__init__(params)
+        Nmf.__init__(self, params)
         if sp.isspmatrix(self.V) and (self.V.data < 0).any() or not sp.isspmatrix(self.V) and (self.V < 0).any():
             raise utils.MFError("The input matrix contains negative elements.")
         if sp.isspmatrix(self.V1) and (self.V1.data < 0).any() or not sp.isspmatrix(self.V1) and (self.V1 < 0).any():
diff --git a/nimfa/models/nmf_ns.py b/nimfa/models/nmf_ns.py
@@ -49,7 +49,7 @@ def __init__(self, params):
         self.model_name = "ns"
         self.V1 = None
         self.H1 = None
-        super().__init__(params)
+        Nmf.__init__(self, params)
         if sp.isspmatrix(self.V) and (self.V.data < 0).any() or not sp.isspmatrix(self.V) and (self.V < 0).any():
             raise utils.MFError("The input matrix contains negative elements.")
 
diff --git a/nimfa/models/nmf_std.py b/nimfa/models/nmf_std.py
@@ -35,7 +35,7 @@ def __init__(self, params):
         self.model_name = "std"
         self.V1 = None
         self.H1 = None
-        super().__init__(params)
+        Nmf.__init__(self, params)
         if sp.isspmatrix(self.V) and (self.V.data < 0).any() or not sp.isspmatrix(self.V) and (self.V < 0).any():
             raise utils.MFError("The input matrix contains negative elements.")
 
