revisar warning

.directory

@@ -1,6 +1,11 @@
 [Dolphin]
+<<<<<<< HEAD
 Timestamp=2017,2,7,17,30,1
 Version=3
 
 [Settings]
 HiddenFilesShown=true
+=======
+Timestamp=2017,2,8,12,4,41
+Version=3
+>>>>>>> 503c114584bd9cb91d18379b03a6c9f494d8b4fc

build/lib.linux-x86_64-2.7/sompy/codebook.py

@@ -1,5 +1,5 @@
 import numpy as np
-from sklearn.decomposition import RandomizedPCA
+from sklearn.decomposition import PCA# RandomizedPCA (randomizedpca is deprecated)
 from .decorators import timeit
 
 
@@ -96,7 +96,9 @@ def pca_linear_initialization(self, data):
         tmp_matrix = np.tile(me, (self.nnodes, 1))
 
         # Randomized PCA is scalable
-        pca = RandomizedPCA(n_components=pca_components)
+        #pca = RandomizedPCA(n_components=pca_components) # RandomizedPCA is deprecated.
+        pca = PCA(n_components=pca_components, svd_solver='randomized')
+
         pca.fit(data)
         eigvec = pca.components_
         eigval = pca.explained_variance_

build/lib.linux-x86_64-2.7/sompy/sompy.py

@@ -27,6 +27,9 @@
 from .neighborhood import NeighborhoodFactory
 from .normalization import NormalizatorFactory
 
+#lbugnon
+import sompy,ipdb
+#
 
 class ComponentNamesError(Exception):
     pass
@@ -244,7 +247,6 @@ def train(self,
                          radiusin=train_rough_radiusin, radiusfin=train_rough_radiusfin)
         self.finetune_train(njob=n_job, shared_memory=shared_memory, trainlen=train_finetune_len,
                             radiusin=train_finetune_radiusin, radiusfin=train_finetune_radiusfin)
-
         logging.debug(
             " --------------------------------------------------------------")
         logging.info(" Final quantization error: %f" % np.mean(self._bmu[1]))
@@ -324,7 +326,6 @@ def _batchtrain(self, trainlen, radiusin, radiusfin, njob=1,
             t1 = time()
             neighborhood = self.neighborhood.calculate(
                 self._distance_matrix, radius[i], self.codebook.nnodes)
-
             bmu = self.find_bmu(data, njb=njob)
             self.codebook.matrix = self.update_codebook_voronoi(data, bmu,
                                                                 neighborhood)

build/lib.linux-x86_64-2.7/sompy/visualization/mapview.py

@@ -7,8 +7,12 @@
 class MapView(MatplotView):
 
     def _calculate_figure_params(self, som, which_dim, col_sz):
-        codebook = som._normalizer.denormalize_by(som.data_raw,
-                                                  som.codebook.matrix)
+
+        # add this to avoid error when normalization is not used
+        if som._normalizer:
+            codebook = som._normalizer.denormalize_by(som.data_raw, som.codebook.matrix)
+        else:
+            codebook = som.codebook.matrix
 
         indtoshow, sV, sH = None, None, None
 
@@ -139,7 +143,6 @@ def show(self, som, what='codebook', which_dim='all', cmap=None,
                     plt.title(compname[0][ind])
                     font = {'size': self.text_size}
                     plt.rc('font', **font)
-
         if what == 'cluster':
             try:
                 codebook = getattr(som, 'cluster_labels')
@@ -160,7 +163,9 @@ def show(self, som, what='codebook', which_dim='all', cmap=None,
 
         plt.subplots_adjust(hspace=h, wspace=w)
 
-
+        plt.show()
+
+
 class View1D(MapView):
 
     def show(self, som, what='codebook', which_dim='all', cmap=None,
@@ -178,4 +183,4 @@ def show(self, som, what='codebook', which_dim='all', cmap=None,
             mp = codebook[:, ind]
             plt.plot(mp, '-k', linewidth=0.8)
 
-        plt.show()
+        #plt.show()

build/lib/sompy/sompy.py

@@ -27,6 +27,9 @@
 from .neighborhood import NeighborhoodFactory
 from .normalization import NormalizatorFactory
 
+#lbugnon
+import sompy,ipdb
+#
 
 class ComponentNamesError(Exception):
     pass
@@ -244,7 +247,6 @@ def train(self,
                          radiusin=train_rough_radiusin, radiusfin=train_rough_radiusfin)
         self.finetune_train(njob=n_job, shared_memory=shared_memory, trainlen=train_finetune_len,
                             radiusin=train_finetune_radiusin, radiusfin=train_finetune_radiusfin)
-
         logging.debug(
             " --------------------------------------------------------------")
         logging.info(" Final quantization error: %f" % np.mean(self._bmu[1]))
@@ -324,7 +326,6 @@ def _batchtrain(self, trainlen, radiusin, radiusfin, njob=1,
             t1 = time()
             neighborhood = self.neighborhood.calculate(
                 self._distance_matrix, radius[i], self.codebook.nnodes)
-
             bmu = self.find_bmu(data, njb=njob)
             self.codebook.matrix = self.update_codebook_voronoi(data, bmu,
                                                                 neighborhood)

build/lib/sompy/visualization/mapview.py

@@ -143,7 +143,6 @@ def show(self, som, what='codebook', which_dim='all', cmap=None,
                     plt.title(compname[0][ind])
                     font = {'size': self.text_size}
                     plt.rc('font', **font)
-            plt.show()
         if what == 'cluster':
             try:
                 codebook = getattr(som, 'cluster_labels')
@@ -163,6 +162,8 @@ def show(self, som, what='codebook', which_dim='all', cmap=None,
             self._set_axis(ax, msz0, msz1)
 
         plt.subplots_adjust(hspace=h, wspace=w)
+
+        plt.show()
 
 
 class View1D(MapView):
@@ -182,4 +183,4 @@ def show(self, som, what='codebook', which_dim='all', cmap=None,
             mp = codebook[:, ind]
             plt.plot(mp, '-k', linewidth=0.8)
 
-        plt.show()
+        #plt.show()

sompy/sompy.py

@@ -330,8 +330,9 @@ def _batchtrain(self, trainlen, radiusin, radiusfin, njob=1,
             self.codebook.matrix = self.update_codebook_voronoi(data, bmu,
                                                                 neighborhood)
 
+
             qerror = (i + 1, round(time() - t1, 3),
-                      np.mean(np.sqrt(bmu[1] + fixed_euclidean_x2)))
+                      np.mean(np.sqrt(bmu[1] + fixed_euclidean_x2))) #lbugnon: ojo aca me tiró un warning, revisar (commit sinc: 965666d3d4d93bcf48e8cef6ea2c41a018c1cb83 )
             logging.info(
                 " epoch: %d ---> elapsed time:  %f, quantization error: %f\n" %
                 qerror)