Merge pull request #181 from nno/_dbg/xenia2

BLD: use Xenia
CoSMoMVPA · Jul 19, 2019 · 872c912 · 872c912
2 parents d43b0e7 + dfcb4c2
commit 872c912
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diff --git a/.travis.yml b/.travis.yml
@@ -3,26 +3,26 @@
 # based on nipype configuration, which in turn was based on nipy)
 #
 # We pretend to be java because we need GNU Octave which is not 
-# available (as of April 2015)
+# available (as of June 2019)
 
 language: java
-dist: trusty
+dist: xenial
 cache:
   - apt
 env:
   global:
     - COVERALLS_PARALLEL=true
   matrix:
     - TRAVIS_WITH_EXTERNALS=false TRAVIS_WITH_COVERAGE=false COVERALLS_PARALLEL=false
-    - TRAVIS_WITH_EXTERNALS=true  TRAVIS_WITH_COVERAGE=false COVERALLS_PARALLEL=false
-    - TRAVIS_WITH_EXTERNALS=true  TRAVIS_WITH_COVERAGE=true PARTITION_INDEX=1 PARTITION_COUNT=8 COVERALLS_PARALLEL=false NO_DOC_TEST=true
-    - TRAVIS_WITH_EXTERNALS=true  TRAVIS_WITH_COVERAGE=true PARTITION_INDEX=2 PARTITION_COUNT=8 COVERALLS_PARALLEL=false  NO_DOC_TEST=true
-    - TRAVIS_WITH_EXTERNALS=true  TRAVIS_WITH_COVERAGE=true PARTITION_INDEX=3 PARTITION_COUNT=8 COVERALLS_PARALLEL=false NO_DOC_TEST=true
-    - TRAVIS_WITH_EXTERNALS=true  TRAVIS_WITH_COVERAGE=true PARTITION_INDEX=4 PARTITION_COUNT=8 COVERALLS_PARALLEL=false  NO_DOC_TEST=true
-    - TRAVIS_WITH_EXTERNALS=true  TRAVIS_WITH_COVERAGE=true PARTITION_INDEX=5 PARTITION_COUNT=8 COVERALLS_PARALLEL=false  NO_DOC_TEST=true
-    - TRAVIS_WITH_EXTERNALS=true  TRAVIS_WITH_COVERAGE=true PARTITION_INDEX=6 PARTITION_COUNT=8 COVERALLS_PARALLEL=false  NO_DOC_TEST=true
-    - TRAVIS_WITH_EXTERNALS=true  TRAVIS_WITH_COVERAGE=true PARTITION_INDEX=7 PARTITION_COUNT=8 COVERALLS_PARALLEL=false  NO_DOC_TEST=true
-    - TRAVIS_WITH_EXTERNALS=true  TRAVIS_WITH_COVERAGE=true PARTITION_INDEX=8 PARTITION_COUNT=8 TRAVIS_AFTER_ALL_ARGS='--is_master' COVERALLS_PARALLEL=true  NO_DOC_TEST=true
+    # - TRAVIS_WITH_EXTERNALS=true  TRAVIS_WITH_COVERAGE=false COVERALLS_PARALLEL=false
+    # - TRAVIS_WITH_EXTERNALS=true  TRAVIS_WITH_COVERAGE=true PARTITION_INDEX=1 PARTITION_COUNT=8 COVERALLS_PARALLEL=false NO_DOC_TEST=true
+    # - TRAVIS_WITH_EXTERNALS=true  TRAVIS_WITH_COVERAGE=true PARTITION_INDEX=2 PARTITION_COUNT=8 COVERALLS_PARALLEL=false  NO_DOC_TEST=true
+    # - TRAVIS_WITH_EXTERNALS=true  TRAVIS_WITH_COVERAGE=true PARTITION_INDEX=3 PARTITION_COUNT=8 COVERALLS_PARALLEL=false NO_DOC_TEST=true
+    # - TRAVIS_WITH_EXTERNALS=true  TRAVIS_WITH_COVERAGE=true PARTITION_INDEX=4 PARTITION_COUNT=8 COVERALLS_PARALLEL=false  NO_DOC_TEST=true
+    # - TRAVIS_WITH_EXTERNALS=true  TRAVIS_WITH_COVERAGE=true PARTITION_INDEX=5 PARTITION_COUNT=8 COVERALLS_PARALLEL=false  NO_DOC_TEST=true
+    # - TRAVIS_WITH_EXTERNALS=true  TRAVIS_WITH_COVERAGE=true PARTITION_INDEX=6 PARTITION_COUNT=8 COVERALLS_PARALLEL=false  NO_DOC_TEST=true
+    # - TRAVIS_WITH_EXTERNALS=true  TRAVIS_WITH_COVERAGE=true PARTITION_INDEX=7 PARTITION_COUNT=8 COVERALLS_PARALLEL=false  NO_DOC_TEST=true
+    # - TRAVIS_WITH_EXTERNALS=true  TRAVIS_WITH_COVERAGE=true PARTITION_INDEX=8 PARTITION_COUNT=8 TRAVIS_AFTER_ALL_ARGS='--is_master' COVERALLS_PARALLEL=true  NO_DOC_TEST=true
 before_install:
     # to prevent IPv6 being used for APT
     - sudo bash -c "echo 'Acquire::ForceIPv4 \"true\";' > /etc/apt/apt.conf.d/99force-ipv4"
@@ -35,9 +35,11 @@ before_install:
     - travis_retry sudo apt-get -y install octave
     - travis_retry sudo apt-get -y install liboctave-dev
     - travis_retry sudo apt-get -y -qq install octave
+    - octave --version
+    - which make
 
     # when installing externals, get recent GCC for Octave parallel toolbox
-    - if [[ "${TRAVIS_WITH_EXTERNALS}" == "true" ]]; then
+    - if [[ "${TRAVIS_WITH_EXTERNALS}" == "trueDISABLED" ]]; then
           travis_retry sudo add-apt-repository 'ppa:ubuntu-toolchain-r/test' -y;
           travis_retry sudo apt-get update -y -q;
           travis_retry sudo apt-get install gcc-4.8 g++-4.8 -y -q;
@@ -137,6 +139,22 @@ install:
           $RETRY $OCTAVE --eval "pkg('install','-auto','-forge','struct');";
       fi
 
+    # optionally enable Octave statistics package
+    # $RETRY $OCTAVE --eval "pkg('install','-forge','statistics');";
+    - if [[ " $EXTERNALS " = *" octave_pkg_statistics "* ]]; then
+        $RETRY sudo apt-get -y -qq octave-statistics;
+      fi
+    # optionally enable Octave miscellaneous package
+    # (the "general" package is required for the "miscellaneous" package)
+    # (the "miscellaneous" package also requires "units")
+    - if [[ " $EXTERNALS " = *" octave_pkg_miscellaneous "* ]]; then
+          $RETRY $OCTAVE --eval "pkg('install','-auto','-forge','general');";
+          $RETRY sudo apt-get -y -qq install units;
+          $RETRY $OCTAVE --eval "pkg('install','-auto','-forge','miscellaneous');";
+      fi
+
+
+
     # As of Aug 2017, the parallel package is disabled because it made Octave crash
     # when using travis
     #
@@ -237,28 +255,14 @@ before_script:
 
 
 
-    # optionally enable Octave statistics package
-    - if [[ " $EXTERNALS " = *" octave_pkg_statistics "* ]]; then
-          $RETRY $OCTAVE --eval "pkg('install','-auto','-forge','statistics');";
-      fi
-
-    # optionally enable Octave miscellaneous package
-    # (the "general" package is required for the "miscellaneous" package)
-    # (the "miscellaneous" package also requires "units")
-    - if [[ " $EXTERNALS " = *" octave_pkg_miscellaneous "* ]]; then
-          $RETRY $OCTAVE --eval "pkg('install','-auto','-forge','general');";
-          $RETRY sudo apt-get -y -qq install units;
-          $RETRY $OCTAVE --eval "pkg('install','-auto','-forge','miscellaneous');";
-      fi
-
     # show Octave-rc
     - echo "Octave-rc:"; cat $OCTAVERC
 
 
     # show which packages are installed
     - $OCTAVE --eval "pkg('list')"
 
-     # show WTF
+    # show WTF
     - $OCTAVE --eval "addpath('${PTH}/CoSMoMVPA/mvpa');cosmo_wtf()"
 
 script:

diff --git a/COPYING b/COPYING
@@ -12,9 +12,9 @@ is licensed under the Expat license.
 
   License: Expat
 
-  Copyright (c) 2013-2018 Nikolaas N. Oosterhof
+  Copyright (c) 2013-2019 Nikolaas N. Oosterhof
                 2013      Andrew C. Connolly
-                2013-2018 CoSMoMVPA contributors (see AUTHOR file)
+                2013-2019 CoSMoMVPA contributors (see AUTHOR file)
 
 - Expat License:
 

diff --git a/doc/source/faq.rst b/doc/source/faq.rst
@@ -1675,5 +1675,56 @@ You can use the example below to correlate two dissimilarity matrices; these can
 
 For analysis at the group level, compute for each participant the correlation between their behavioural ratings, then use a one-sample t-test against a difference of zero.
 
+Use the generalization measure with different durations for training and test set?
+----------------------------------------------------------------------------------
+'I would like to use the :ref:`cosmo_dim_generalization_measure` but with different time intervals for training and test set. For the training set I have 3 seconds of data per trial, but for the test set only 1 second. How can I run this analysis.'
+
+Please see the code below for an example. It is similar to the documentation of :ref:`cosmo_dim_generalization_measure`, except that in the preparation phase the :ref:`cosmo_dim_transpose`  step is done before the :ref:`cosmo_stack` step. This order is also necessary when using :ref:`cosmo_searchlight`.
+
+    .. code-block:: matlab
+
+        % Generalization over time
+
+        % Make some synthetic data
+        sz='big';
+        train_ds=cosmo_synthetic_dataset('type','timelock','size',sz,...
+                                               'nchunks',2,'seed',1);
+        test_ds=cosmo_synthetic_dataset('type','timelock','size',sz,...
+                                               'nchunks',3,'seed',2);
+
+        % select a smaller time period for the testing dataset
+        % here, only the time period between -0.15 and 0.05 seconds is selected
+        msk=cosmo_dim_match(test_ds, 'time', @(t) -0.15 <= t & t <= .05);
+        smaller_test_ds = cosmo_slice(test_ds, msk, 2);
+
+        % set chunks
+        train_ds.sa.chunks(:)=1;
+        smaller_test_ds.sa.chunks(:)=2;
+
+        % make time a sample dimension
+        dim_label='time';
+        train_ds_tr = cosmo_dim_transpose(train_ds, dim_label, 1);
+        smaller_test_ds_tr = cosmo_dim_transpose(smaller_test_ds, dim_label, 1);
+
+        % construct the dataset
+        ds_time=cosmo_stack({train_ds_tr, smaller_test_ds_tr});
+
+        %
+        % set measure and its arguments
+        measure_args=struct();
+        %
+        % use correlation measure
+        measure_args.measure=@cosmo_correlation_measure;
+        % dimension of interest is 'time'
+        measure_args.dimension=dim_label;
+        %
+        % run time-by-time generalization analysis
+        dgm_ds=cosmo_dim_generalization_measure(ds_time,measure_args,...
+                                                'progress',false);
+        %
+        % the output has train_time and test_time as sample dimensions
+        cosmo_disp(dgm_ds.a)
+
+
 
 .. include:: links.txt