[Scipy-svn] r5185 - in trunk/scipy/cluster: . tests

[scipy-svn at scipy.org]

Author: damian.eads
Date: 2008-11-24 21:41:51 -0600 (Mon, 24 Nov 2008)
New Revision: 5185

Modified:
   trunk/scipy/cluster/hierarchy.py
   trunk/scipy/cluster/tests/test_hierarchy.py
Log:
Wrote tests for scipy.cluster.hierarchy.is_valid_linkage.

Modified: trunk/scipy/cluster/hierarchy.py
===================================================================
--- trunk/scipy/cluster/hierarchy.py	2008-11-25 02:46:26 UTC (rev 5184)
+++ trunk/scipy/cluster/hierarchy.py	2008-11-25 03:41:51 UTC (rev 5185)
@@ -1198,9 +1198,9 @@
                 raise TypeError('Variable is not a valid array.')
         if Z.dtype != np.double:
             if name:
-                raise TypeError('Linkage matrix \'%s\' must contain doubles (double).' % name)
+                raise TypeError('Linkage matrix \'%s\' must contain doubles.' % name)
             else:
-                raise TypeError('Linkage matrix must contain doubles (double).')
+                raise TypeError('Linkage matrix must contain doubles.')
         if len(Z.shape) != 2:
             if name:
                 raise ValueError('Linkage matrix \'%s\' must have shape=2 (i.e. be two-dimensional).' % name)
@@ -1221,6 +1221,16 @@
                     raise ValueError('Linkage \'%s\' contains negative indices.' % name)
                 else:
                     raise ValueError('Linkage contains negative indices.')
+            if (Z[:, 2] < 0).any():
+                if name:
+                    raise ValueError('Linkage \'%s\' contains negative distances.' % name)
+                else:
+                    raise ValueError('Linkage contains negative distances.')
+            if (Z[:, 3] < 0).any():
+                if name:
+                    raise ValueError('Linkage \'%s\' contains negative counts.' % name)
+                else:
+                    raise ValueError('Linkage contains negative counts.')
     except Exception, e:
         if throw:
             raise

Modified: trunk/scipy/cluster/tests/test_hierarchy.py
===================================================================
--- trunk/scipy/cluster/tests/test_hierarchy.py	2008-11-25 02:46:26 UTC (rev 5184)
+++ trunk/scipy/cluster/tests/test_hierarchy.py	2008-11-25 03:41:51 UTC (rev 5185)
@@ -38,7 +38,7 @@
 import numpy as np
 from numpy.testing import *
 
-from scipy.cluster.hierarchy import linkage, from_mlab_linkage, to_mlab_linkage, num_obs_linkage, inconsistent, cophenet, from_mlab_linkage, fclusterdata, fcluster, is_isomorphic, single, complete, average, weighted, centroid, median, ward, leaders, correspond, is_monotonic, maxdists, maxinconsts, maxRstat
+from scipy.cluster.hierarchy import linkage, from_mlab_linkage, to_mlab_linkage, num_obs_linkage, inconsistent, cophenet, from_mlab_linkage, fclusterdata, fcluster, is_isomorphic, single, complete, average, weighted, centroid, median, ward, leaders, correspond, is_monotonic, maxdists, maxinconsts, maxRstat, is_valid_linkage
 from scipy.spatial.distance import squareform, pdist
 
 _tdist = np.array([[0,    662,  877,  255,  412,  996],
@@ -540,6 +540,81 @@
         self.failUnless(is_isomorphic(a, b) == (not noniso))
         self.failUnless(is_isomorphic(b, a) == (not noniso))
 
+class TestIsValidLinkage(TestCase):
+
+    def test_is_valid_linkage_int_type(self):
+        "Tests is_valid_linkage(Z) with integer type."
+        Z = np.asarray([[0,   1, 3.0, 2],
+                        [3,   2, 4.0, 3]], dtype=np.int)
+        self.failUnless(is_valid_linkage(Z) == False)
+
+    def test_is_valid_linkage_5_columns(self):
+        "Tests is_valid_linkage(Z) with 5 columns."
+        Z = np.asarray([[0,   1, 3.0, 2, 5],
+                        [3,   2, 4.0, 3, 3]], dtype=np.double)
+        self.failUnless(is_valid_linkage(Z) == False)
+
+    def test_is_valid_linkage_3_columns(self):
+        "Tests is_valid_linkage(Z) with 3 columns."
+        Z = np.asarray([[0,   1, 3.0],
+                        [3,   2, 4.0]], dtype=np.double)
+        self.failUnless(is_valid_linkage(Z) == False)
+
+    def test_is_valid_linkage_empty(self):
+        "Tests is_valid_linkage(Z) with empty linkage."
+        Z = np.zeros((0, 4), dtype=np.double)
+        self.failUnless(is_valid_linkage(Z) == False)
+
+    def test_is_valid_linkage_1x4(self):
+        "Tests is_valid_linkage(Z) on linkage over 2 observations."
+        Z = np.asarray([[0,   1, 3.0, 2]], dtype=np.double)
+        self.failUnless(is_valid_linkage(Z) == True)
+
+    def test_is_valid_linkage_2x4(self):
+        "Tests is_valid_linkage(Z) on linkage over 3 observations."
+        Z = np.asarray([[0,   1, 3.0, 2],
+                        [3,   2, 4.0, 3]], dtype=np.double)
+        self.failUnless(is_valid_linkage(Z) == True)
+
+    def test_is_valid_linkage_4_and_up(self):
+        "Tests is_valid_linkage(Z) on linkage on observation sets between sizes 4 and 15 (step size 3)."
+        for i in xrange(4, 15, 3):
+            y = np.random.rand(i*(i-1)/2)
+            Z = linkage(y)
+            self.failUnless(is_valid_linkage(Z) == True)
+
+    def test_is_valid_linkage_4_and_up_neg_index_left(self):
+        "Tests is_valid_linkage(Z) on linkage on observation sets between sizes 4 and 15 (step size 3) with negative indices (left)."
+        for i in xrange(4, 15, 3):
+            y = np.random.rand(i*(i-1)/2)
+            Z = linkage(y)            
+            Z[int(i/2),0] = -2
+            self.failUnless(is_valid_linkage(Z) == False)
+
+    def test_is_valid_linkage_4_and_up_neg_index_right(self):
+        "Tests is_valid_linkage(Z) on linkage on observation sets between sizes 4 and 15 (step size 3) with negative indices (right)."
+        for i in xrange(4, 15, 3):
+            y = np.random.rand(i*(i-1)/2)
+            Z = linkage(y)            
+            Z[int(i/2),1] = -2
+            self.failUnless(is_valid_linkage(Z) == False)
+
+    def test_is_valid_linkage_4_and_up_neg_dist(self):
+        "Tests is_valid_linkage(Z) on linkage on observation sets between sizes 4 and 15 (step size 3) with negative distances."
+        for i in xrange(4, 15, 3):
+            y = np.random.rand(i*(i-1)/2)
+            Z = linkage(y)            
+            Z[int(i/2),2] = -0.5
+            self.failUnless(is_valid_linkage(Z) == False)
+
+    def test_is_valid_linkage_4_and_up_neg_counts(self):
+        "Tests is_valid_linkage(Z) on linkage on observation sets between sizes 4 and 15 (step size 3) with negative counts."
+        for i in xrange(4, 15, 3):
+            y = np.random.rand(i*(i-1)/2)
+            Z = linkage(y)            
+            Z[int(i/2),3] = -2
+            self.failUnless(is_valid_linkage(Z) == False)
+
 class TestNumObsLinkage(TestCase):
 
     def test_num_obs_linkage_empty(self):