From a.janke at gmail.com Tue Mar 15 20:18:32 2011 From: a.janke at gmail.com (Andrew Janke) Date: Wed, 16 Mar 2011 10:18:32 +1000 Subject: [MINC-development] MINC and github. Message-ID: Hi all, I have decided to bite the bullet and setup this: https://github.com/andrewjanke/minc So, you can either make your changes online or using git: http://help.github.com/linux-set-up-git/ I will endeavour to sync all changes back to the main MINC CVS but in time we are shifting all of MINC to git on NITRC so may as well start now. FWIW, I am really starting to like GIT (and github). This was catalyzed by the continuing deluge of people emailing me changes as they dont have CVS access but want to contribute. In time we can easily git clone this repo to NITRC. I have imported the entire of the MINC CVS history into this GIT repo so nothing is lost: MINC when I was in Grade 12: https://github.com/andrewjanke/minc/commits/master?page=69 I'd be very interested in all your thoughts. a From a.janke at gmail.com Tue Mar 15 23:34:49 2011 From: a.janke at gmail.com (Andrew Janke) Date: Wed, 16 Mar 2011 13:34:49 +1000 Subject: [MINC-development] MINC and github. In-Reply-To: References: Message-ID: > I have decided to bite the bullet and setup this: > > ?https://github.com/andrewjanke/minc I have now also imported all the old tags for previous releases. For the CVS dinosaurs to whom a 'git' is nothing more than an archaic term of derision, here is the guide I used to guide me on my own personal path to enlightenment. http://learn.github.com/p/intro.html a (ex CVS dinosaur) From jason at phenogenomics.ca Wed Mar 16 07:44:50 2011 From: jason at phenogenomics.ca (Jason Lerch) Date: Wed, 16 Mar 2011 07:44:50 -0400 Subject: [MINC-development] MINC and github. In-Reply-To: References: Message-ID: Thanks so much for doing all this work, Andrew! Jason On 2011-03-15, at 8:18 PM, Andrew Janke wrote: > Hi all, > > I have decided to bite the bullet and setup this: > > https://github.com/andrewjanke/minc > > So, you can either make your changes online or using git: > > http://help.github.com/linux-set-up-git/ > > I will endeavour to sync all changes back to the main MINC CVS but in > time we are shifting all of MINC to git on NITRC so may as well start > now. > > FWIW, I am really starting to like GIT (and github). This was > catalyzed by the continuing deluge of people emailing me changes as > they dont have CVS access but want to contribute. In time we can > easily git clone this repo to NITRC. I have imported the entire of > the MINC CVS history into this GIT repo so nothing is lost: > > MINC when I was in Grade 12: > > https://github.com/andrewjanke/minc/commits/master?page=69 > > I'd be very interested in all your thoughts. > > > a > _______________________________________________ > MINC-development mailing list > MINC-development at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-development From dgarcia at bic.mni.mcgill.ca Fri Mar 18 11:52:32 2011 From: dgarcia at bic.mni.mcgill.ca (Daniel Garcia (MNI)) Date: Fri, 18 Mar 2011 11:52:32 -0400 Subject: [MINC-development] Bug in classify1.1.0 using bayesian priors (and a CMakeLists.txt) Message-ID: Hello, I found a bug in 'classify -bayes' when including bayesian priors, the classification won't work correctly but without priors it will. I believe I found the bug in the bayes.cc file. In line 433, I changed : fuzzy_bayes_vector[i] *= apriori_vector[ mean_feature_class_vector[i] ]; for fuzzy_bayes_vector[i] *= apriori_vector[ mean_feature_class_vector[i] - 1 ]; and now it works. Items in the apriori_vector goes from 0 to (number of classes -1) and the mean_feature_class_vector goes from 1 to (number of classes). Based in the CMakelists.txt in minc and ezminc, I also created a CMakeLists.txt to do the compilation although some improvements are needed to better handle the library paths (similar to the CMakeLists.txt in minc 2.0.18). I don't know if you're interested. Later -- Daniel Garcia Lorenzo Postdoctoral Researcher McConnell Brain Imaging Center Montreal Neurological Institute 3801 University St Montreal, QC CANADA, H3A 2B4 -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- # CMakeFiles.txt to compile the classify minctool # # March, 2011 :Daniel Garcia dgarcia at bic.mni.mcgill.ca # # cmake_minimum_required (VERSION 2.4) project(CLASSIFY) # PROJECT VARIABLES SET(CLASSIFY_MAJOR_VERSION "1") SET(CLASSIFY_MINOR_VERSION "1") SET(CLASSIFY_PATCH_VERSION "0") SET(PACKAGE_BUGREPORT "Alex Zijdenbos ") SET(PACKAGE_URL "") # Options to set minc libraries SET(MINC_ROOT "/usr/local/bic" CACHE PATH "Minc library base") OPTION(MINC2 "Use minc 2 library" OFF) INCLUDE(FindPerl) SET(PERL ${PERL_EXECUTABLE}) IF(MINC2) ADD_DEFINITIONS( -DMINC2 ) set(MINC_LIBS EBTKS volume_io2 minc2 netcdf hdf5 m z) ELSE(MINC2) set(MINC_LIBS EBTKS volume_io minc netcdf m) ENDIF(MINC2) # Variables of the classify tool set(CLASSIFY_DIRS ann bayes fcm hcm knn mindist) set(CLASSIFY_SOURCES ann/ann.cc bayes/bayes.cc fcm/fcm.cc hcm/hcm.cc knn/knn.cc mindist/mindist.cc time_stamp.c) LINK_DIRECTORIES( "${MINC_ROOT}/lib" ) INCLUDE_DIRECTORIES( "${MINC_ROOT}/include" ${CLASSIFY_DIRS} ${CLASSIFY_BINARY_DIR} ) # Compiling executables ####################### add_executable(classify classify.cc ${CLASSIFY_SOURCES}) target_link_libraries(classify ${MINC_LIBS}) add_executable(voldiff voldiff.c) target_link_libraries(voldiff ${MINC_LIBS}) add_executable(cleantag cleantag/cleantag.cc) target_link_libraries(cleantag ${MINC_LIBS}) # Configure config.h #################### INCLUDE(${CLASSIFY_SOURCE_DIR}/createConfig.cmake) # Configure scripts (using @only) ################################ CONFIGURE_FILE(${CLASSIFY_SOURCE_DIR}/scripts/classify_clean.in ${CLASSIFY_BINARY_DIR}/classify_clean @ONLY) CONFIGURE_FILE(${CLASSIFY_SOURCE_DIR}/scripts/insect.in ${CLASSIFY_BINARY_DIR}/insect @ONLY) # Instalation ################## INSTALL(TARGETS classify voldiff cleantag RUNTIME DESTINATION bin/) INSTALL(FILES ${CLASSIFY_BINARY_DIR}/classify_clean ${CLASSIFY_BINARY_DIR}/insect DESTINATION bin/ PERMISSIONS WORLD_EXECUTE) -------------- next part -------------- A non-text attachment was scrubbed... Name: config.h.in.cmake Type: text/x-cmake Size: 2146 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: createConfig.cmake Type: text/x-cmake Size: 779 bytes Desc: not available URL: From a.janke at gmail.com Sun Mar 20 08:57:16 2011 From: a.janke at gmail.com (Andrew Janke) Date: Sun, 20 Mar 2011 22:57:16 +1000 Subject: [MINC-development] Bug in classify1.1.0 using bayesian priors (and a CMakeLists.txt) In-Reply-To: References: Message-ID: Hi Daniel, Thanks for this. > I found a bug in 'classify -bayes' when including bayesian priors, the > classification won't work correctly but without priors it will. > > I believe I found the bug in the bayes.cc file. In line 433, I changed : > > ????????? fuzzy_bayes_vector[i] *= apriori_vector[ > mean_feature_class_vector[i] ]; > > for > ???? ? ?? fuzzy_bayes_vector[i] *= apriori_vector[ > mean_feature_class_vector[i] - 1 ]; > > and now it works. Items in the apriori_vector goes from 0 to (number of > classes -1) and the mean_feature_class_vector goes from 1 to (number of > classes). I'll wait until Alex and/or Louis comments on this before committing anything to CVS. From a quick read of bayes.cc if this is indeed a bug then this should modify the behavior of the classier in certain cases beyond your own issue. (I think). Still, I'm always keen for others to join in and correct/add code to MINC. Thanks again, a From dgarcia at bic.mni.mcgill.ca Mon Mar 21 09:52:07 2011 From: dgarcia at bic.mni.mcgill.ca (Daniel Garcia (MNI)) Date: Mon, 21 Mar 2011 09:52:07 -0400 Subject: [MINC-development] MINC-development Digest, Vol 39, Issue 3 In-Reply-To: References: Message-ID: Hi Andrew, I was checking the rest of the code quickly but there's probably no other place where this bug is found. The apriori_vector is only used in bayes.cc and the mean_veature_class_vector is used in hcm.cc and fcm.cc but it is not used to access any vector of images. But you're right, someone with more knowlegde on the code should check that more carefully. No problem, glad to help. Later Daniel > Hi Daniel, > > Thanks for this. > > > I found a bug in 'classify -bayes' when including bayesian priors, the > > classification won't work correctly but without priors it will. > > > > I believe I found the bug in the bayes.cc file. In line 433, I changed : > > > > ????????? fuzzy_bayes_vector[i] *= apriori_vector[ > > mean_feature_class_vector[i] ]; > > > > for > > ???? ? ?? fuzzy_bayes_vector[i] *= apriori_vector[ > > mean_feature_class_vector[i] - 1 ]; > > > > and now it works. Items in the apriori_vector goes from 0 to (number of > > classes -1) and the mean_feature_class_vector goes from 1 to (number of > > classes). > > I'll wait until Alex and/or Louis comments on this before committing > anything to CVS. From a quick read of bayes.cc if this is indeed a bug > then this should modify the behavior of the classier in certain cases > beyond your own issue. (I think). > > Still, I'm always keen for others to join in and correct/add code to MINC. > > Thanks again, > > > a > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: