[Scipy-svn] r5018 - trunk/scipy/cluster/tests
scipy-svn at scipy.org
scipy-svn at scipy.org
Fri Nov 7 16:49:56 EST 2008
Author: damian.eads
Date: 2008-11-07 15:48:41 -0600 (Fri, 07 Nov 2008)
New Revision: 5018
Added:
trunk/scipy/cluster/tests/linkage-Q-average.txt
trunk/scipy/cluster/tests/linkage-Q-centroid.txt
trunk/scipy/cluster/tests/linkage-Q-complete.txt
trunk/scipy/cluster/tests/linkage-Q-median.txt
trunk/scipy/cluster/tests/linkage-Q-single.txt
trunk/scipy/cluster/tests/linkage-Q-ward.txt
trunk/scipy/cluster/tests/linkage-Q-weighted.txt
Modified:
trunk/scipy/cluster/tests/test_hierarchy.py
Log:
Added more tests for linkage functions.
Added: trunk/scipy/cluster/tests/linkage-Q-average.txt
===================================================================
--- trunk/scipy/cluster/tests/linkage-Q-average.txt 2008-11-07 21:26:07 UTC (rev 5017)
+++ trunk/scipy/cluster/tests/linkage-Q-average.txt 2008-11-07 21:48:41 UTC (rev 5018)
@@ -0,0 +1,29 @@
+ 1.1000000e+01 1.8000000e+01 6.3937355e-02
+ 1.4000000e+01 2.0000000e+01 1.7716924e-01
+ 2.6000000e+01 2.7000000e+01 1.9481726e-01
+ 2.0000000e+00 3.0000000e+00 2.4887981e-01
+ 2.2000000e+01 2.3000000e+01 2.7739218e-01
+ 7.0000000e+00 9.0000000e+00 3.0440560e-01
+ 2.9000000e+01 3.3000000e+01 3.5174379e-01
+ 6.0000000e+00 3.4000000e+01 3.5532162e-01
+ 1.3000000e+01 3.2000000e+01 3.6158453e-01
+ 1.5000000e+01 3.1000000e+01 3.7715616e-01
+ 1.7000000e+01 1.9000000e+01 4.1203984e-01
+ 2.4000000e+01 3.7000000e+01 4.2046824e-01
+ 4.0000000e+00 3.6000000e+01 4.2863303e-01
+ 1.0000000e+00 5.0000000e+00 4.8198330e-01
+ 1.0000000e+01 3.8000000e+01 4.9787637e-01
+ 4.0000000e+01 4.1000000e+01 5.2994677e-01
+ 1.2000000e+01 3.9000000e+01 5.7421684e-01
+ 2.5000000e+01 2.8000000e+01 6.2656347e-01
+ 3.5000000e+01 4.2000000e+01 6.4347240e-01
+ 4.6000000e+01 4.7000000e+01 6.8297315e-01
+ 4.3000000e+01 4.5000000e+01 6.9186391e-01
+ 8.0000000e+00 4.4000000e+01 7.4416964e-01
+ 2.1000000e+01 3.0000000e+01 7.5491453e-01
+ 1.6000000e+01 5.0000000e+01 8.1859847e-01
+ 4.9000000e+01 5.3000000e+01 8.5939683e-01
+ 5.1000000e+01 5.2000000e+01 8.7992146e-01
+ 4.8000000e+01 5.5000000e+01 8.9017230e-01
+ 5.4000000e+01 5.6000000e+01 2.0198221e+00
+ 5.7000000e+01 5.8000000e+01 3.2920100e+00
Added: trunk/scipy/cluster/tests/linkage-Q-centroid.txt
===================================================================
--- trunk/scipy/cluster/tests/linkage-Q-centroid.txt 2008-11-07 21:26:07 UTC (rev 5017)
+++ trunk/scipy/cluster/tests/linkage-Q-centroid.txt 2008-11-07 21:48:41 UTC (rev 5018)
@@ -0,0 +1,29 @@
+ 1.1000000e+01 1.8000000e+01 6.3937355e-02
+ 1.4000000e+01 2.0000000e+01 1.7716924e-01
+ 2.6000000e+01 2.7000000e+01 1.9481726e-01
+ 2.0000000e+00 3.0000000e+00 2.4887981e-01
+ 2.2000000e+01 2.3000000e+01 2.7739218e-01
+ 7.0000000e+00 9.0000000e+00 3.0440560e-01
+ 6.0000000e+00 3.4000000e+01 3.3746118e-01
+ 2.9000000e+01 3.3000000e+01 3.4067653e-01
+ 1.3000000e+01 3.2000000e+01 3.5113828e-01
+ 1.5000000e+01 3.9000000e+01 3.3976558e-01
+ 2.4000000e+01 3.8000000e+01 3.9064620e-01
+ 4.0000000e+00 3.6000000e+01 4.0386341e-01
+ 1.7000000e+01 1.9000000e+01 4.1203984e-01
+ 1.0000000e+01 3.7000000e+01 4.6647208e-01
+ 3.1000000e+01 4.3000000e+01 4.7930518e-01
+ 1.0000000e+00 5.0000000e+00 4.8198330e-01
+ 4.0000000e+01 4.5000000e+01 5.2671920e-01
+ 3.5000000e+01 4.1000000e+01 5.9378517e-01
+ 2.5000000e+01 2.8000000e+01 6.2656347e-01
+ 4.2000000e+01 4.4000000e+01 6.2815954e-01
+ 8.0000000e+00 4.6000000e+01 7.1857916e-01
+ 5.0000000e+01 5.1000000e+01 7.0424537e-01
+ 1.2000000e+01 4.7000000e+01 7.2968219e-01
+ 1.6000000e+01 5.3000000e+01 7.1788349e-01
+ 3.0000000e+01 4.9000000e+01 7.5478395e-01
+ 4.8000000e+01 5.5000000e+01 7.0355234e-01
+ 2.1000000e+01 5.6000000e+01 7.3561818e-01
+ 5.2000000e+01 5.4000000e+01 1.9510405e+00
+ 5.7000000e+01 5.8000000e+01 3.2347576e+00
Added: trunk/scipy/cluster/tests/linkage-Q-complete.txt
===================================================================
--- trunk/scipy/cluster/tests/linkage-Q-complete.txt 2008-11-07 21:26:07 UTC (rev 5017)
+++ trunk/scipy/cluster/tests/linkage-Q-complete.txt 2008-11-07 21:48:41 UTC (rev 5018)
@@ -0,0 +1,29 @@
+ 1.1000000e+01 1.8000000e+01 6.3937355e-02
+ 1.4000000e+01 2.0000000e+01 1.7716924e-01
+ 2.6000000e+01 2.7000000e+01 1.9481726e-01
+ 2.0000000e+00 3.0000000e+00 2.4887981e-01
+ 2.2000000e+01 2.3000000e+01 2.7739218e-01
+ 7.0000000e+00 9.0000000e+00 3.0440560e-01
+ 1.3000000e+01 3.2000000e+01 3.8163338e-01
+ 2.9000000e+01 3.3000000e+01 3.9446675e-01
+ 1.5000000e+01 3.1000000e+01 3.9629062e-01
+ 6.0000000e+00 3.4000000e+01 4.1110592e-01
+ 1.7000000e+01 1.9000000e+01 4.1203984e-01
+ 2.4000000e+01 2.8000000e+01 4.5328393e-01
+ 4.0000000e+00 3.6000000e+01 4.7908167e-01
+ 1.0000000e+00 5.0000000e+00 4.8198330e-01
+ 1.0000000e+01 4.0000000e+01 5.7813912e-01
+ 3.9000000e+01 4.1000000e+01 6.4162409e-01
+ 3.0000000e+01 4.2000000e+01 6.6157735e-01
+ 1.2000000e+01 3.7000000e+01 7.0851770e-01
+ 2.1000000e+01 3.5000000e+01 7.8597665e-01
+ 1.6000000e+01 4.6000000e+01 8.3623329e-01
+ 8.0000000e+00 4.5000000e+01 8.8244371e-01
+ 3.8000000e+01 4.7000000e+01 9.2493420e-01
+ 2.5000000e+01 4.9000000e+01 9.2757043e-01
+ 4.3000000e+01 5.1000000e+01 1.0046401e+00
+ 4.8000000e+01 5.0000000e+01 1.1468365e+00
+ 4.4000000e+01 5.4000000e+01 1.2396527e+00
+ 5.2000000e+01 5.3000000e+01 1.2958546e+00
+ 5.5000000e+01 5.7000000e+01 3.0467645e+00
+ 5.6000000e+01 5.8000000e+01 5.1343343e+00
Added: trunk/scipy/cluster/tests/linkage-Q-median.txt
===================================================================
--- trunk/scipy/cluster/tests/linkage-Q-median.txt 2008-11-07 21:26:07 UTC (rev 5017)
+++ trunk/scipy/cluster/tests/linkage-Q-median.txt 2008-11-07 21:48:41 UTC (rev 5018)
@@ -0,0 +1,29 @@
+ 1.1000000e+01 1.8000000e+01 6.3937355e-02
+ 1.4000000e+01 2.0000000e+01 1.7716924e-01
+ 2.6000000e+01 2.7000000e+01 1.9481726e-01
+ 2.0000000e+00 3.0000000e+00 2.4887981e-01
+ 2.2000000e+01 2.3000000e+01 2.7739218e-01
+ 7.0000000e+00 9.0000000e+00 3.0440560e-01
+ 6.0000000e+00 3.4000000e+01 3.3746118e-01
+ 2.9000000e+01 3.3000000e+01 3.4067653e-01
+ 1.3000000e+01 3.2000000e+01 3.5113828e-01
+ 1.5000000e+01 3.9000000e+01 3.4054836e-01
+ 4.0000000e+00 3.6000000e+01 4.0386341e-01
+ 2.4000000e+01 3.8000000e+01 4.1015077e-01
+ 1.7000000e+01 1.9000000e+01 4.1203984e-01
+ 1.0000000e+01 3.7000000e+01 4.6883527e-01
+ 3.1000000e+01 4.3000000e+01 4.7930518e-01
+ 4.0000000e+01 4.5000000e+01 4.7776681e-01
+ 1.0000000e+00 5.0000000e+00 4.8198330e-01
+ 3.5000000e+01 4.2000000e+01 5.6937028e-01
+ 2.5000000e+01 2.8000000e+01 6.2656347e-01
+ 8.0000000e+00 4.7000000e+01 7.1857916e-01
+ 4.8000000e+01 4.9000000e+01 7.1925426e-01
+ 3.0000000e+01 5.1000000e+01 6.7611684e-01
+ 2.1000000e+01 5.2000000e+01 6.6632819e-01
+ 4.4000000e+01 5.0000000e+01 7.2115997e-01
+ 4.1000000e+01 5.4000000e+01 6.5190047e-01
+ 1.6000000e+01 4.6000000e+01 7.3662916e-01
+ 1.2000000e+01 5.6000000e+01 7.0941723e-01
+ 5.5000000e+01 5.7000000e+01 2.1188553e+00
+ 5.3000000e+01 5.8000000e+01 3.2138035e+00
Added: trunk/scipy/cluster/tests/linkage-Q-single.txt
===================================================================
--- trunk/scipy/cluster/tests/linkage-Q-single.txt 2008-11-07 21:26:07 UTC (rev 5017)
+++ trunk/scipy/cluster/tests/linkage-Q-single.txt 2008-11-07 21:48:41 UTC (rev 5018)
@@ -0,0 +1,29 @@
+ 1.1000000e+01 1.8000000e+01 6.3937355e-02
+ 1.4000000e+01 2.0000000e+01 1.7716924e-01
+ 2.6000000e+01 2.7000000e+01 1.9481726e-01
+ 2.0000000e+00 3.0000000e+00 2.4887981e-01
+ 2.2000000e+01 2.3000000e+01 2.7739218e-01
+ 2.4000000e+01 3.3000000e+01 2.9703742e-01
+ 6.0000000e+00 3.4000000e+01 2.9953732e-01
+ 7.0000000e+00 9.0000000e+00 3.0440560e-01
+ 1.5000000e+01 3.2000000e+01 3.0777762e-01
+ 2.9000000e+01 3.6000000e+01 3.0902082e-01
+ 1.9000000e+01 3.9000000e+01 3.3102505e-01
+ 1.3000000e+01 4.1000000e+01 3.4153568e-01
+ 3.1000000e+01 4.2000000e+01 3.5802170e-01
+ 3.7000000e+01 3.8000000e+01 3.6459874e-01
+ 4.0000000e+00 4.4000000e+01 3.7818440e-01
+ 1.0000000e+01 4.5000000e+01 4.0129405e-01
+ 1.7000000e+01 4.3000000e+01 4.1203984e-01
+ 1.2000000e+01 4.7000000e+01 4.4459698e-01
+ 2.8000000e+01 4.0000000e+01 4.5328393e-01
+ 1.0000000e+00 5.0000000e+00 4.8198330e-01
+ 4.6000000e+01 5.0000000e+01 5.0546088e-01
+ 3.5000000e+01 4.9000000e+01 5.0591731e-01
+ 3.0000000e+01 5.2000000e+01 5.9356257e-01
+ 8.0000000e+00 5.1000000e+01 6.0048760e-01
+ 2.5000000e+01 5.3000000e+01 6.2656347e-01
+ 1.6000000e+01 4.8000000e+01 6.5449319e-01
+ 2.1000000e+01 5.5000000e+01 7.0629051e-01
+ 5.4000000e+01 5.6000000e+01 1.0267612e+00
+ 5.7000000e+01 5.8000000e+01 1.2085488e+00
Added: trunk/scipy/cluster/tests/linkage-Q-ward.txt
===================================================================
--- trunk/scipy/cluster/tests/linkage-Q-ward.txt 2008-11-07 21:26:07 UTC (rev 5017)
+++ trunk/scipy/cluster/tests/linkage-Q-ward.txt 2008-11-07 21:48:41 UTC (rev 5018)
@@ -0,0 +1,29 @@
+ 1.1000000e+01 1.8000000e+01 6.3937355e-02
+ 1.4000000e+01 2.0000000e+01 1.7716924e-01
+ 2.6000000e+01 2.7000000e+01 1.9481726e-01
+ 2.0000000e+00 3.0000000e+00 2.4887981e-01
+ 2.2000000e+01 2.3000000e+01 2.7739218e-01
+ 7.0000000e+00 9.0000000e+00 3.0440560e-01
+ 6.0000000e+00 3.4000000e+01 3.8966661e-01
+ 2.9000000e+01 3.3000000e+01 3.9337938e-01
+ 1.3000000e+01 1.5000000e+01 3.9833425e-01
+ 1.7000000e+01 1.9000000e+01 4.1203984e-01
+ 3.2000000e+01 3.9000000e+01 4.2295183e-01
+ 2.4000000e+01 2.8000000e+01 4.5328393e-01
+ 4.0000000e+00 3.6000000e+01 4.6634129e-01
+ 1.0000000e+00 5.0000000e+00 4.8198330e-01
+ 1.0000000e+01 3.7000000e+01 5.7130929e-01
+ 3.0000000e+01 4.2000000e+01 6.7688894e-01
+ 3.1000000e+01 4.0000000e+01 6.7783989e-01
+ 1.2000000e+01 4.1000000e+01 7.1501676e-01
+ 8.0000000e+00 4.4000000e+01 8.2974374e-01
+ 2.1000000e+01 2.5000000e+01 8.3155740e-01
+ 1.6000000e+01 4.7000000e+01 8.6628075e-01
+ 3.5000000e+01 5.0000000e+01 9.1696168e-01
+ 3.8000000e+01 4.6000000e+01 1.0741259e+00
+ 4.3000000e+01 4.5000000e+01 1.1631255e+00
+ 4.8000000e+01 5.1000000e+01 1.3123400e+00
+ 5.2000000e+01 5.3000000e+01 1.3876562e+00
+ 4.9000000e+01 5.4000000e+01 1.4432735e+00
+ 5.5000000e+01 5.7000000e+01 6.1697318e+00
+ 5.6000000e+01 5.8000000e+01 1.1811665e+01
Added: trunk/scipy/cluster/tests/linkage-Q-weighted.txt
===================================================================
--- trunk/scipy/cluster/tests/linkage-Q-weighted.txt 2008-11-07 21:26:07 UTC (rev 5017)
+++ trunk/scipy/cluster/tests/linkage-Q-weighted.txt 2008-11-07 21:48:41 UTC (rev 5018)
@@ -0,0 +1,29 @@
+ 1.1000000e+01 1.8000000e+01 6.3937355e-02
+ 1.4000000e+01 2.0000000e+01 1.7716924e-01
+ 2.6000000e+01 2.7000000e+01 1.9481726e-01
+ 2.0000000e+00 3.0000000e+00 2.4887981e-01
+ 2.2000000e+01 2.3000000e+01 2.7739218e-01
+ 7.0000000e+00 9.0000000e+00 3.0440560e-01
+ 2.9000000e+01 3.3000000e+01 3.5174379e-01
+ 6.0000000e+00 3.4000000e+01 3.5532162e-01
+ 1.3000000e+01 3.2000000e+01 3.6158453e-01
+ 1.5000000e+01 3.1000000e+01 3.7715616e-01
+ 1.7000000e+01 1.9000000e+01 4.1203984e-01
+ 4.0000000e+00 3.6000000e+01 4.2863303e-01
+ 2.4000000e+01 3.7000000e+01 4.4128967e-01
+ 1.0000000e+00 5.0000000e+00 4.8198330e-01
+ 1.0000000e+01 3.8000000e+01 5.0195626e-01
+ 4.0000000e+01 4.1000000e+01 5.3409020e-01
+ 3.9000000e+01 4.6000000e+01 6.0088461e-01
+ 2.5000000e+01 2.8000000e+01 6.2656347e-01
+ 3.5000000e+01 4.3000000e+01 6.2840379e-01
+ 8.0000000e+00 4.4000000e+01 7.4416964e-01
+ 1.2000000e+01 4.7000000e+01 7.4874549e-01
+ 2.1000000e+01 3.0000000e+01 7.5491453e-01
+ 4.2000000e+01 4.5000000e+01 7.8567175e-01
+ 4.8000000e+01 4.9000000e+01 8.3312410e-01
+ 5.2000000e+01 5.4000000e+01 8.4939549e-01
+ 1.6000000e+01 5.1000000e+01 8.5308187e-01
+ 5.0000000e+01 5.3000000e+01 8.6159523e-01
+ 5.5000000e+01 5.6000000e+01 1.9999532e+00
+ 5.7000000e+01 5.8000000e+01 3.2929087e+00
Modified: trunk/scipy/cluster/tests/test_hierarchy.py
===================================================================
--- trunk/scipy/cluster/tests/test_hierarchy.py 2008-11-07 21:26:07 UTC (rev 5017)
+++ trunk/scipy/cluster/tests/test_hierarchy.py 2008-11-07 21:48:41 UTC (rev 5018)
@@ -38,7 +38,7 @@
import numpy as np
from numpy.testing import *
-from scipy.cluster.hierarchy import linkage, from_mlab_linkage, to_mlab_linkage, numobs_linkage, inconsistent, cophenet, from_mlab_linkage, fclusterdata, fcluster, is_isomorphic
+from scipy.cluster.hierarchy import linkage, from_mlab_linkage, to_mlab_linkage, numobs_linkage, inconsistent, cophenet, from_mlab_linkage, fclusterdata, fcluster, is_isomorphic, single, complete, average, weighted, centroid, median, ward
from scipy.spatial.distance import squareform, pdist, numobs_dm, numobs_y
_tdist = np.array([[0, 662, 877, 255, 412, 996],
@@ -76,7 +76,15 @@
"inconsistent-weighted-tdist-depth-1.txt",
"inconsistent-weighted-tdist-depth-2.txt",
"inconsistent-weighted-tdist-depth-3.txt",
- "inconsistent-weighted-tdist-depth-4.txt"]
+ "inconsistent-weighted-tdist-depth-4.txt",
+ "linkage-Q-average.txt",
+ "linkage-Q-complete.txt",
+ "linkage-Q-single.txt",
+ "linkage-Q-weighted.txt",
+ "linkage-Q-centroid.txt",
+ "linkage-Q-median.txt",
+ "linkage-Q-ward.txt"
+ ]
def load_testing_files():
for fn in _filenames:
@@ -156,6 +164,47 @@
#print Z, expectedZ, np.abs(Z - expectedZ).max()
self.failUnless(within_tol(Z, expectedZ, eps))
+ ################### linkage on Q
+ def test_linkage_single_q(self):
+ "Tests linkage(Y, 'single') on the Q data set."
+ X = eo['fclusterdata-X']
+ Z = single(X)
+ Zmlab = eo['linkage-Q-single']
+ eps = 1e-06
+ expectedZ = from_mlab_linkage(Zmlab)
+ print abs(Z-expectedZ).max()
+ self.failUnless(within_tol(Z, expectedZ, eps))
+
+ def test_linkage_complete_q(self):
+ "Tests linkage(Y, 'complete') on the Q data set."
+ X = eo['fclusterdata-X']
+ Z = complete(X)
+ Zmlab = eo['linkage-Q-complete']
+ eps = 1e-07
+ expectedZ = from_mlab_linkage(Zmlab)
+ print abs(Z-expectedZ).max()
+ self.failUnless(within_tol(Z, expectedZ, eps))
+
+ def test_linkage_centroid_q(self):
+ "Tests linkage(Y, 'centroid') on the Q data set."
+ X = eo['fclusterdata-X']
+ Z = centroid(X)
+ Zmlab = eo['linkage-Q-centroid']
+ eps = 1e-07
+ expectedZ = from_mlab_linkage(Zmlab)
+ print abs(Z-expectedZ).max()
+ self.failUnless(within_tol(Z, expectedZ, eps))
+
+ def test_linkage_weighted_q(self):
+ "Tests linkage(Y, 'weighted') on the Q data set."
+ X = eo['fclusterdata-X']
+ Z = weighted(X)
+ Zmlab = eo['linkage-Q-weighted']
+ eps = 1e-07
+ expectedZ = from_mlab_linkage(Zmlab)
+ print abs(Z-expectedZ).max()
+ self.failUnless(within_tol(Z, expectedZ, eps))
+
class TestInconsistent(TestCase):
def test_single_inconsistent_tdist(self):
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