Earlier this year

• Nov 23, 2009

  issue 28 (colothreshold not working) reported by totogwada   -   Instead use 'color_threshold' unlike shown in the tutorial. Good tool, very useful. Thanks

  Instead use 'color_threshold' unlike shown in the tutorial. Good tool, very useful. Thanks
• Nov 14, 2009

  issue 27 (easy_install broken on Snow Leopard) commented on by mikedewar   -   Hi! Here's the result of gcc -v gcc -v Using built-in specs. Target: i686-apple-darwin9 Configured with: /var/tmp/gcc/gcc-5465~16/src/configure --disable-checking -enable-werror --prefix=/usr --mandir=/share/man --enable-languages=c,objc,c++,obj-c++ --program-transform-name=/^[cg][^.-]*$/s/$/-4.0/ --with-gxx-include-dir=/include/c++/4.0.0 --with-slibdir=/usr/lib --build=i686-apple-darwin9 --with-arch=apple --with-tune=generic --host=i686-apple-darwin9 --target=i686-apple-darwin9 Thread model: posix gcc version 4.0.1 (Apple Inc. build 5465)

  Hi! Here's the result of gcc -v gcc -v Using built-in specs. Target: i686-apple-darwin9 Configured with: /var/tmp/gcc/gcc-5465~16/src/configure --disable-checking -enable-werror --prefix=/usr --mandir=/share/man --enable-languages=c,objc,c++,obj-c++ --program-transform-name=/^[cg][^.-]*$/s/$/-4.0/ --with-gxx-include-dir=/include/c++/4.0.0 --with-slibdir=/usr/lib --build=i686-apple-darwin9 --with-arch=apple --with-tune=generic --host=i686-apple-darwin9 --target=i686-apple-darwin9 Thread model: posix gcc version 4.0.1 (Apple Inc. build 5465)
• Nov 13, 2009

  issue 26 (Incremental clustering) commented on by damian.eads.soe   -   Thanks for your interest! Glad you like it. At the moment, there's no way to incrementally build a hierarchical clustering tree without storing an O(n^2) distance matrix. If you'd like to work on this feature, please let me know! Thanks, Damian

  Thanks for your interest! Glad you like it. At the moment, there's no way to incrementally build a hierarchical clustering tree without storing an O(n^2) distance matrix. If you'd like to work on this feature, please let me know! Thanks, Damian
• Nov 13, 2009

  issue 25 (Snow Leopard breaks hcluster?) commented on by damian.eads.soe   -   Can you try opening python or ipython in GDB with [code] gdb --args ipython -pylab [/code] then try importing then run "bt" and give me a backtrace? Damian

  Can you try opening python or ipython in GDB with [code] gdb --args ipython -pylab [/code] then try importing then run "bt" and give me a backtrace? Damian
• Nov 13, 2009

  issue 27 (easy_install broken on Snow Leopard) commented on by damian.eads.soe   -   What version of gcc are you using? Please run gcc -v Thanks! Damian Eads

  What version of gcc are you using? Please run gcc -v Thanks! Damian Eads
• Nov 06, 2009

  issue 27 (easy_install broken on Snow Leopard) reported by mikedewar   -   What steps will reproduce the problem? 1.easy_install hcluster What is the expected output? What do you see instead? Expected output is one nicely installed hcluster module. What actually happens is: cc1: error: unrecognized command line option "-Wno-long-double" What version of the product are you using? On what operating system? hcluster-0.2.0.zip i686-apple-darwin10-gcc-4.2.1 OS X Snow Leopard

  What steps will reproduce the problem? 1.easy_install hcluster What is the expected output? What do you see instead? Expected output is one nicely installed hcluster module. What actually happens is: cc1: error: unrecognized command line option "-Wno-long-double" What version of the product are you using? On what operating system? hcluster-0.2.0.zip i686-apple-darwin10-gcc-4.2.1 OS X Snow Leopard
• Sep 21, 2009

  issue 26 (Incremental clustering) reported by tsagias   -   Hi, first of all, thanks for the great module! I was wondering if is possible to do incremental HAC with hcluster. Or if there is any quick workaround. Thanks in advance, Manos._

  Hi, first of all, thanks for the great module! I was wondering if is possible to do incremental HAC with hcluster. Or if there is any quick workaround. Thanks in advance, Manos._
• Sep 13, 2009

  issue 25 (Snow Leopard breaks hcluster?) reported by jwkelly   -   On a Mac OSX 10.6 (snow leopard) machine, with Numpy and other stuff updated and new, importing hcluster leads to a segmentation fault. Re-installing did not help. Any advice? Thx!

  On a Mac OSX 10.6 (snow leopard) machine, with Numpy and other stuff updated and new, importing hcluster leads to a segmentation fault. Re-installing did not help. Any advice? Thx!
• Jul 15, 2009

  issue 24 (upper triangular and squareform of same distance matrix yiel...) Status changed by damian.eads   -   Hi Andy, Thanks for your report. As you stated, the two possibilities for the first input to ``linkage`` is either: * the upper triangular of the distance matrix Y, or * the original matrix of observations X used to produce Y via pdist. This is consistent with MATLAB's documentation as shown below. """ Z = linkage(y) Z = linkage(y,method) Z = linkage(X,method,metric) Z = linkage(X,method,inputs) """ This is also consistent with the hcluster documentation. """ Z = linkage(X, method, metric='euclidean') Performs hierarchical clustering on the objects defined by the n by m observation matrix X. """ I hope this helps. Thanks, Damian

  Status: Done

  Hi Andy, Thanks for your report. As you stated, the two possibilities for the first input to ``linkage`` is either: * the upper triangular of the distance matrix Y, or * the original matrix of observations X used to produce Y via pdist. This is consistent with MATLAB's documentation as shown below. """ Z = linkage(y) Z = linkage(y,method) Z = linkage(X,method,metric) Z = linkage(X,method,inputs) """ This is also consistent with the hcluster documentation. """ Z = linkage(X, method, metric='euclidean') Performs hierarchical clustering on the objects defined by the n by m observation matrix X. """ I hope this helps. Thanks, Damian

  Status: Done
• Jul 15, 2009

  issue 24 (upper triangular and squareform of same distance matrix yiel...) commented on by AndyCConnolly   -   Hi again, after consulting the source code we found that when using a square matrix as input to linkage, linkage assumes the input is data -- not a distance matrix -- and calculates a new distance matrix by calling pdist. Thus: where Y = pdist(data) and Y_sq = squareform(Y), linkage(Y_sq) is equivalent to linkage(pdist(Y_sq, metric='euclidean')) cheers, Andy

  Hi again, after consulting the source code we found that when using a square matrix as input to linkage, linkage assumes the input is data -- not a distance matrix -- and calculates a new distance matrix by calling pdist. Thus: where Y = pdist(data) and Y_sq = squareform(Y), linkage(Y_sq) is equivalent to linkage(pdist(Y_sq, metric='euclidean')) cheers, Andy
• Jul 14, 2009

  issue 24 (upper triangular and squareform of same distance matrix yiel...) reported by AndyCConnolly   -   After producing an upper triangular distance matrix with pdist, I used squareform to transform the matrix to square before entering using it as input to linkage. So for Y = pdist(data) Y_sq = squareform(Y) linkage(Y_sq) does NOT equal linkage(Y) -- here I expected linkage(Y_sq) == linkage(Y) I have only read documentation indicating that Y (as upper triangle) is the standard input to linkage, but using Y_sq yields the result I was expecting (maybe just a fluke?). Matlab linkage does not accept Y_sq as input. What goes on when I input Y_sq? why is the result different from using Y? What version of the product are you using? On what operating system? I am using hcluster 0.2.0 Mac 10.5

  After producing an upper triangular distance matrix with pdist, I used squareform to transform the matrix to square before entering using it as input to linkage. So for Y = pdist(data) Y_sq = squareform(Y) linkage(Y_sq) does NOT equal linkage(Y) -- here I expected linkage(Y_sq) == linkage(Y) I have only read documentation indicating that Y (as upper triangle) is the standard input to linkage, but using Y_sq yields the result I was expecting (maybe just a fluke?). Matlab linkage does not accept Y_sq as input. What goes on when I input Y_sq? why is the result different from using Y? What version of the product are you using? On what operating system? I am using hcluster 0.2.0 Mac 10.5
• Jun 23, 2009

  issue 23 (Feature request) reported by fccoelho   -   Could you provide data export functions for tress? Something like the Newick format or some other supported by standalone tre drawing programs.

  Could you provide data export functions for tress? Something like the Newick format or some other supported by standalone tre drawing programs.
• Jun 01, 2009

  issue 22 (setup.py: return with non-zero code when failing) Status changed by damian.eads   -   Okay. Good catch. Changed and committed to SVN.

  Status: Fixed

  Okay. Good catch. Changed and committed to SVN.

  Status: Fixed
• Jun 01, 2009

  r135 (changed exit(0) to exit(1) to conform to standard practice) committed by damian.eads   -   changed exit(0) to exit(1) to conform to standard practice

  changed exit(0) to exit(1) to conform to standard practice
• Jun 01, 2009

  issue 22 (setup.py: return with non-zero code when failing) reported by Sridhar.Ratna   -   $ python setup.py install --root=installroot/ No paths in the python path contain numpy/arrayobject.h $ echo $? 0 $ The exit code should be non-zero .. this affects the behavior of programs (ones that automate building of Python packages, for instance) that rely on proper exit codes of setup.py. The culprit is: valid_paths = filter(contains_arrayobject_h, sys.path) if len(valid_paths) == 0: print "No paths in the python path contain numpy/arrayobject.h" sys.exit(0) <--- change this to 1, or just 'raise RuntimeError'

  $ python setup.py install --root=installroot/ No paths in the python path contain numpy/arrayobject.h $ echo $? 0 $ The exit code should be non-zero .. this affects the behavior of programs (ones that automate building of Python packages, for instance) that rely on proper exit codes of setup.py. The culprit is: valid_paths = filter(contains_arrayobject_h, sys.path) if len(valid_paths) == 0: print "No paths in the python path contain numpy/arrayobject.h" sys.exit(0) <--- change this to 1, or just 'raise RuntimeError'
• Apr 20, 2009

  issue 8 (spearman rank coefficient in pdist) commented on by nicholas.gauthier   -   Any update on this issue? I am also very interested in this functionality...

  Any update on this issue? I am also very interested in this functionality...
• Feb 26, 2009

  issue 21 (String distances) Labels changed by damian.eads   -   Hi Uri, I do want to include a number of edit distances but alas I'm trying to get a paper out. However, I'd be willing to offer you some pointers. How good is your Python? Have you considered writing in Cython? Cython is a new, well-maintained project that has gained extraordinary momentum within the past year. It is a major, well-documented improvement of the Pyrex project, which is now obsolete. Cython is a Python dialect that gets translated into C. Your Python functions can call Cython code very easily. Do you know how big the alphabet tends to be for most problems using the Levenshtein distance? Btw, you can try e-mailing me at my e-mail address, first DOT last AT gmail DOT com. I check this site much less often. I will read the paper you referenced over the weekend. Cheers, Damian

  Labels: Type-Enhancement −Type-Defect

  Hi Uri, I do want to include a number of edit distances but alas I'm trying to get a paper out. However, I'd be willing to offer you some pointers. How good is your Python? Have you considered writing in Cython? Cython is a new, well-maintained project that has gained extraordinary momentum within the past year. It is a major, well-documented improvement of the Pyrex project, which is now obsolete. Cython is a Python dialect that gets translated into C. Your Python functions can call Cython code very easily. Do you know how big the alphabet tends to be for most problems using the Levenshtein distance? Btw, you can try e-mailing me at my e-mail address, first DOT last AT gmail DOT com. I check this site much less often. I will read the paper you referenced over the weekend. Cheers, Damian

  Labels: Type-Enhancement −Type-Defect
• Feb 26, 2009

  issue 21 (String distances) reported by uri.laserson   -   I am interested in using this package to cluster sequences. I noticed in the TODO file, you list that you want to do this as well. One place to go is to take the implementation of the Levenshtein edit distance from the py-editdist package. In addition, there is a normalized edit distance that can be easily implemented from that in this paper: IEEE Trans Pattern Analys Mach Intel 29(6):1091 I'll see about writing it myself, but my C is quite rusty.

  I am interested in using this package to cluster sequences. I noticed in the TODO file, you list that you want to do this as well. One place to go is to take the implementation of the Levenshtein edit distance from the py-editdist package. In addition, there is a normalized edit distance that can be easily implemented from that in this paper: IEEE Trans Pattern Analys Mach Intel 29(6):1091 I'll see about writing it myself, but my C is quite rusty.
• Feb 24, 2009

  r134 (Committed C source.) committed by damian.eads   -   Committed C source.

  Committed C source.
• Feb 20, 2009

  issue 20 (bug in dendogram) commented on by damian.eads   -   Hi, Agreed this is bizarre behavior but it does not seem to happen if you put a clf() command in between. Damian

  Hi, Agreed this is bizarre behavior but it does not seem to happen if you put a clf() command in between. Damian
• Jan 15, 2009

  issue 20 (bug in dendogram) reported by petr.danecek   -   Hi, try the following code, it yields weird results, see the attached files. Best regards, Petr Danecek --------------------------------------------------- from pylab import * from hcluster import pdist, linkage, dendrogram import numpy from numpy.random import rand Y = [174,181,218,150,199,205,119,212,121,148] for i in range(len(Y)): Y[i] = (500-Y[i])/500. Z = linkage(Y,method='complete') dendrogram(Z) print Z savefig('_test-complete.png') Z = linkage(Y,method='average') dendrogram(Z) print Z savefig('_test-average.png') Z = linkage(Y,method='weighted') dendrogram(Z) print Z savefig('_test-weighted.png') Z = linkage(Y,method='single') dendrogram(Z) print Z savefig('_test-single.png') ---------------------------------------------------

  Hi, try the following code, it yields weird results, see the attached files. Best regards, Petr Danecek --------------------------------------------------- from pylab import * from hcluster import pdist, linkage, dendrogram import numpy from numpy.random import rand Y = [174,181,218,150,199,205,119,212,121,148] for i in range(len(Y)): Y[i] = (500-Y[i])/500. Z = linkage(Y,method='complete') dendrogram(Z) print Z savefig('_test-complete.png') Z = linkage(Y,method='average') dendrogram(Z) print Z savefig('_test-average.png') Z = linkage(Y,method='weighted') dendrogram(Z) print Z savefig('_test-weighted.png') Z = linkage(Y,method='single') dendrogram(Z) print Z savefig('_test-single.png') ---------------------------------------------------

Older

• Dec 14, 2008

  News (This page contains a summary of changes in each version.) Wiki page edited by damian.eads
• Dec 14, 2008

  hcluster-0.2.0.zip (hcluster Version 0.2.0) file uploaded by damian.eads   -  

  Labels: Featured OpSys-All Type-Source

  Labels: Featured OpSys-All Type-Source
• Dec 14, 2008

  hcluster-0.2.0.tar.bz2 (hcluster Version 0.2.0) file uploaded by damian.eads   -  

  Labels: Type-Source OpSys-All Featured

  Labels: Type-Source OpSys-All Featured
• Dec 14, 2008

  hcluster-0.2.0.tar.gz (hcluster Version 0.2.0) file uploaded by damian.eads   -  

  Labels: Type-Source OpSys-All Featured

  Labels: Type-Source OpSys-All Featured
• Dec 14, 2008

  r132 (Major edits, bug fixes, revisions, and testing code in scipy...) committed by damian.eads   -   Major edits, bug fixes, revisions, and testing code in scipy.cluster and scipy.spatial, much of which was performed by myself, has been integrated into this package. This package will serve to test new features before being integrated into SciPy.

  Major edits, bug fixes, revisions, and testing code in scipy.cluster and scipy.spatial, much of which was performed by myself, has been integrated into this package. This package will serve to test new features before being integrated into SciPy.
• Nov 04, 2008

  issue 8 (spearman rank coefficient in pdist) commented on by stella.frank   -   I'd appreciate this addition - right now I'm calling rpy.r.cor(u,v, method='spearman'), which is taking forever...

  I'd appreciate this addition - right now I'm calling rpy.r.cor(u,v, method='spearman'), which is taking forever...
• Oct 20, 2008

  issue 17 (dendrogram display via matplotlib not working on Mac) commented on by damian.eads   -   Please see http://www.soe.ucsc.edu/~eads/iris.html

  Please see http://www.soe.ucsc.edu/~eads/iris.html
• Oct 20, 2008

  issue 18 (dendrogram image generation) Status changed by damian.eads   -  

  Status: Done

  Status: Done
• Oct 20, 2008

  issue 18 (dendrogram image generation) commented on by damian.eads   -   Glad it worked! I will close this ticket. Damian

  Glad it worked! I will close this ticket. Damian
• Oct 20, 2008

  issue 17 (dendrogram display via matplotlib not working on Mac) commented on by damian.eads.lists   -   The full chain of events should look something like: matplotlib.pylab.figure() dendrogram(Z) matplotlib.pylab.show() Were you able to run the Iris example?

  The full chain of events should look something like: matplotlib.pylab.figure() dendrogram(Z) matplotlib.pylab.show() Were you able to run the Iris example?
• Oct 13, 2008

  issue 17 (dendrogram display via matplotlib not working on Mac) commented on by jwkelly   -   I am not running it in IPython, but as a script in the following Python version: Python 2.5.1 (r251:54863, Feb 4 2008, 21:48:13) [GCC 4.0.1 (Apple Inc. build 5465)] on darwin I tried the matplotlib.pylab.show() command, and a python app 'opened' but didn't actually display anything. I wonder if I'm just using the wrong syntax some how. What would the full chain of events look like once I have a cluster object (Z)? dendro = denrogram(Z) matplotlib.pylab.show(dendro) or dendro.matplotlib.pylab.show() or what exactly? Thanks!

  I am not running it in IPython, but as a script in the following Python version: Python 2.5.1 (r251:54863, Feb 4 2008, 21:48:13) [GCC 4.0.1 (Apple Inc. build 5465)] on darwin I tried the matplotlib.pylab.show() command, and a python app 'opened' but didn't actually display anything. I wonder if I'm just using the wrong syntax some how. What would the full chain of events look like once I have a cluster object (Z)? dendro = denrogram(Z) matplotlib.pylab.show(dendro) or dendro.matplotlib.pylab.show() or what exactly? Thanks!
• Oct 10, 2008

  issue 18 (dendrogram image generation) commented on by fennan   -   Thanks Damian! I did not know about the -pylab option... Now it works perfect! Thanks again

  Thanks Damian! I did not know about the -pylab option... Now it works perfect! Thanks again
• Oct 10, 2008

  issue 17 (dendrogram display via matplotlib not working on Mac) commented on by damian.eads   -   Have you tried matplotlib.pylab.show()? Are you running this in IPython? If so, are you running it with or without -pylab?

  Have you tried matplotlib.pylab.show()? Are you running this in IPython? If so, are you running it with or without -pylab?
• Oct 10, 2008

  issue 18 (dendrogram image generation) commented on by damian.eads   -   Are you running this in Ipython with or without the -pylab option? Remember, you need to do a matplotlib.pylab.show() if you are not running pylab. To save the image to a file rather than displaying a GUI frame, do matplotlib.pylab.savefig("filename.png", format="png") Please let me know if this resolves your issue. Damian

  Are you running this in Ipython with or without the -pylab option? Remember, you need to do a matplotlib.pylab.show() if you are not running pylab. To save the image to a file rather than displaying a GUI frame, do matplotlib.pylab.savefig("filename.png", format="png") Please let me know if this resolves your issue. Damian
• Oct 10, 2008

  issue 19 (patch for duplicate directories in sys.path) reported by peter.skomoroch   -   What steps will reproduce the problem? 1. python setup.py build with duplicate directories in sys.path What is the expected output? What do you see instead? $ python setup.py build There are several valid include directories containing numpy/arrayobject.h Traceback (most recent call last): File "setup.py", line 36, in <module> s = input('Selection [default=1]:' % s) TypeError: not all arguments converted during string formatting What version of the product are you using? On what operating system? Mac OSX Please provide any additional information below. adding the following line to setup.py avoids this issue: valid_paths = dict(map(lambda i: (i,1),valid_paths)).keys()

  What steps will reproduce the problem? 1. python setup.py build with duplicate directories in sys.path What is the expected output? What do you see instead? $ python setup.py build There are several valid include directories containing numpy/arrayobject.h Traceback (most recent call last): File "setup.py", line 36, in <module> s = input('Selection [default=1]:' % s) TypeError: not all arguments converted during string formatting What version of the product are you using? On what operating system? Mac OSX Please provide any additional information below. adding the following line to setup.py avoids this issue: valid_paths = dict(map(lambda i: (i,1),valid_paths)).keys()
• Sep 23, 2008

  issue 18 (dendrogram image generation) reported by fennan   -   What steps will reproduce the problem? 1. dendrogram(Z) 2. 3. What is the expected output? What do you see instead? I expected to get an image of the dendrogram. I'm getting just a dictionary containing the colors, coords, etc... How one can get the image? I guess via matplotlib... I could not do it. What version of the product are you using? On what operating system? hcluster 0.1.9 Ubuntu

  What steps will reproduce the problem? 1. dendrogram(Z) 2. 3. What is the expected output? What do you see instead? I expected to get an image of the dendrogram. I'm getting just a dictionary containing the colors, coords, etc... How one can get the image? I guess via matplotlib... I could not do it. What version of the product are you using? On what operating system? hcluster 0.1.9 Ubuntu
• Sep 12, 2008

  issue 17 (dendrogram display via matplotlib not working on Mac) reported by jwkelly   -   What steps will reproduce the problem? 1. compute clusters 2. execute 'dendrogram' command What is the expected output? What do you see instead? I expected to see a dendrogram drawn with Matplotlib. Instead, there is a small delay while some kind of calculation takes place, but no output window appears. Matplotlib works fine when invoked directly in other scripts on my system. What version of the product are you using? On what operating system? I've tried this on two Mac systems, a MacBookPro and a Mac Pro (both Intel processors). OS version is 10.5.4. Python installed on both is 2.5.1. Matplotlib is 0.98pre. I've not tried it on Linux or Windows, and suspect it may be a platform issue.

  What steps will reproduce the problem? 1. compute clusters 2. execute 'dendrogram' command What is the expected output? What do you see instead? I expected to see a dendrogram drawn with Matplotlib. Instead, there is a small delay while some kind of calculation takes place, but no output window appears. Matplotlib works fine when invoked directly in other scripts on my system. What version of the product are you using? On what operating system? I've tried this on two Mac systems, a MacBookPro and a Mac Pro (both Intel processors). OS version is 10.5.4. Python installed on both is 2.5.1. Matplotlib is 0.98pre. I've not tried it on Linux or Windows, and suspect it may be a platform issue.
• Sep 08, 2008

  Citations (Citation information for users of hcluster.) Wiki page edited by damian.eads
• Sep 08, 2008

  Citations (Citation information for users of hcluster.) Wiki page edited by damian.eads
• Aug 25, 2008

  News (This page contains a summary of changes in each version.) Wiki page edited by damian.eads
• Aug 25, 2008

  r128 (Upped version number.) committed by damian.eads   -   Upped version number.

  Upped version number.
• Aug 25, 2008

  r127 (Fixed a bug in the C version of Canberra distance.) committed by damian.eads   -   Fixed a bug in the C version of Canberra distance.

  Fixed a bug in the C version of Canberra distance.
• Aug 04, 2008

  issue 16 (Canberra distance broken) Status changed by damian.eads   -   Thanks for finding this bug. It's been fixed in both scipy-cluster and scipy. A unit test will go in Scipy shortly. Damian

  Status: Fixed

  Thanks for finding this bug. It's been fixed in both scipy-cluster and scipy. A unit test will go in Scipy shortly. Damian

  Status: Fixed
• Aug 04, 2008

  r126 (Fixed canberra. Now passes a double array to C-extension ins...) committed by damian.eads   -   Fixed canberra. Now passes a double array to C-extension instead of a bool.

  Fixed canberra. Now passes a double array to C-extension instead of a bool.
• Aug 01, 2008

  issue 16 (Canberra distance broken) reported by joonas.paalasmaa   -   Using hcluster.pdist with the Canberra distance does not work as the input matrix is converted to bool instead of double. See the patch for a fix. P.S. Thanks for a great package.

  Using hcluster.pdist with the Canberra distance does not work as the input matrix is converted to bool instead of double. See the patch for a fix. P.S. Thanks for a great package.