[Scipy-svn] r5007 - in trunk/scipy/cluster: . tests

[scipy-svn at scipy.org]

Author: damian.eads
Date: 2008-11-07 13:52:54 -0600 (Fri, 07 Nov 2008)
New Revision: 5007

Modified:
   trunk/scipy/cluster/hierarchy.py
   trunk/scipy/cluster/tests/test_hierarchy.py
Log:
Added tests for to_mlab_linkage function.

Modified: trunk/scipy/cluster/hierarchy.py
===================================================================
--- trunk/scipy/cluster/hierarchy.py	2008-11-07 19:41:42 UTC (rev 5006)
+++ trunk/scipy/cluster/hierarchy.py	2008-11-07 19:52:54 UTC (rev 5007)
@@ -1071,11 +1071,17 @@
            A linkage matrix compatible with MATLAB(TM)'s hierarchical
            clustering functions.
     """
-    Z = np.asarray(Z, order='c')
+    Z = np.asarray(Z, order='c', dtype=np.double)
+    Zs = Z.shape
+    if len(Zs) == 0 or (len(Zs) == 1 and Zs[0] == 0):
+        return Z.copy()
     is_valid_linkage(Z, throw=True, name='Z')
 
-    return np.hstack([Z[:,0:2] + 1, Z[:,2]])
+    ZP = Z[:, 0:3].copy()
+    ZP[:,0:2] += 1.0
 
+    return ZP
+
 def is_monotonic(Z):
     """
     Returns ``True`` if the linkage passed is monotonic. The linkage

Modified: trunk/scipy/cluster/tests/test_hierarchy.py
===================================================================
--- trunk/scipy/cluster/tests/test_hierarchy.py	2008-11-07 19:41:42 UTC (rev 5006)
+++ trunk/scipy/cluster/tests/test_hierarchy.py	2008-11-07 19:52:54 UTC (rev 5007)
@@ -38,7 +38,7 @@
 import numpy as np
 from numpy.testing import *
 
-from scipy.cluster.hierarchy import linkage, from_mlab_linkage, numobs_linkage, inconsistent, cophenet, from_mlab_linkage
+from scipy.cluster.hierarchy import linkage, from_mlab_linkage, to_mlab_linkage, numobs_linkage, inconsistent, cophenet, from_mlab_linkage
 from scipy.spatial.distance import squareform, pdist, numobs_dm, numobs_y
 
 _tdist = np.array([[0,    662,  877,  255,  412,  996],
@@ -216,6 +216,37 @@
         print expectedZS, ZS
         self.failUnless((expectedZS == ZS).all())
 
+
+class TestToMLabLinkage(TestCase):
+
+    def test_to_mlab_linkage_empty(self):
+        "Testing to_mlab_linkage on empty linkage array."
+        X = np.asarray([])
+        R = to_mlab_linkage([])
+        self.failUnless((R == X).all())
+
+    def test_to_mlab_linkage_single_row(self):
+        "Testing to_mlab_linkage on linkage array with single row."
+        Z = np.asarray([[ 0.,  1.,  3.,  2.]])
+        expectedZP = np.asarray([[1,2,3]])
+        ZP = to_mlab_linkage(Z)
+        return self.failUnless((ZP == expectedZP).all())
+
+    def test_from_mlab_linkage_multiple_rows(self):
+        "Testing to_mlab_linkage on linkage array with multiple rows."
+        expectedZM = np.asarray([[3, 6, 138], [4, 5, 219],
+                        [1, 8, 255], [2, 9, 268], [7, 10, 295]])
+        Z = np.array([[   2.,    5.,  138.,    2.],
+                      [   3.,    4.,  219.,    2.],
+                      [   0.,    7.,  255.,    3.],
+                      [   1.,    8.,  268.,    4.],
+                      [   6.,    9.,  295.,    6.]],
+                     dtype=np.double)
+        ZM = to_mlab_linkage(Z)
+        print expectedZM, ZM
+        self.failUnless((expectedZM == ZM).all())
+
+
 def help_single_inconsistent_depth(self, i):
     Y = squareform(_tdist)
     Z = linkage(Y, 'single')