Merge pull request #27 from nicholst/SnPM13.1.06

SnPM 13.1.06 including #25 and #26

Author: Camille Maumet

README.md

@@ -15,20 +15,16 @@ The SnPM toolbox provides an alternative to the Statistics section of [SPM](http
 ### Testing
 
 #### Initial set up 
-The first time you run the tests, you will first have to create a set of ground truth data and a file named `snpm_test_config.m` containing the reference SnPM version you used to compute the ground truth and the path to the ground truth folder. For example:
+The first time you run the tests, you will need to set up the `snpm_test_config.m` file to fill in `testDataDir` with the path to your ground truth folder. For example:
 ```
 global testDataDir;
 testDataDir = '~/snpm_test_data';
-global SnPMrefVersion;
-SnPMrefVersion = 'SnPM8';
 ```
 
 #### Run the test suite
-Then, the tests can be started (from the test data folder) with:
+Then, the tests can be started with:
 ```
-import matlab.unittest.TestSuite;
-suite = TestSuite.fromFolder(fullfile(spm_str_manip(which('snpm'), 'h'), 'test'));
-result = run(suite);
+snpm_tests
 ```
 
 #### Run a single test

README.txt

@@ -4,6 +4,11 @@ This file describes the bugs that have been reported, along with the appropriate
 Updated versions of appropriate SnPM functions are available from in the snpm13_updates: 
 http://warwick.ac.uk/snpm/distribution/snpm13_updates
 
+--- SnPM 13.1.06 ---
+ * fix: ANOVA between group "all zero"/"all equal" options were flipped in the menu of the matlabbatch.
+ * fix: snpm_cp can now handle XYZ locations in a 1D space.
+ * Version 13.1.06 (`snpm`)
+
 --- SnPM 13.1.05 ---
  * fix: two-sample t-test with nscans>12 was errored due to call to undefined variable `nPerm` (bug introduced in previous release: 13.1.4) (`snpm_pi_TwoSampT`)
  * fix: warning on size of `SnPM_ST.mat` was never raised

config/snpm_bch_ui_ANOVAbtwnS.m

@@ -64,7 +64,7 @@
 nullHypAllZero.tag     = 'nullHypAllZero';
 nullHypAllZero.name    = 'Null Hypothesis';
 nullHypAllZero.labels  = {'Groups are all equal' 'Groups are all zero'};
-nullHypAllZero.values  = {true false};
+nullHypAllZero.values  = {false true};
 nullHypAllZero.help    = {'','Null Hypothesis: Groups are all zero|all equal.'};
 
 

snpm.m

@@ -49,7 +49,7 @@
 
 %-Parameters
 %-----------------------------------------------------------------------
-SnPMver    = 'SnPM13.1.05';
+SnPMver    = 'SnPM13.1.06';
 
 %-Format arguments
 %-----------------------------------------------------------------------
@@ -65,6 +65,11 @@
 else
 	clc
 end
+% Add test code to Matlabpath
+if ~exist('test_oneSample', 'file')
+    addpath(fullfile(spm_file(which('snpm'), 'path'), 'test'));
+    addpath(fullfile(spm_file(which('snpm'), 'path'), 'test', 'common'));
+end
 snpm_defaults;
 [Finter,Fgraph,CmdLine] = spm('FnUIsetup','Statistical non-Parametric Mapping (SnPM)');
 snpm_init; % Initialize Matlab Batch system

snpm_STcalc.m

@@ -126,6 +126,14 @@
   end 
 
   [N,Z,M,A] = spm_max(ST,XYZ);
+  
+  % Enfore A to be a column vector. When XYZ locations are defined in a 1D 
+  % space, spm_max returns A as a row vector instead of a column which 
+  % makes find(A==i) fails later in the code below. 
+  if size(A,2) > 1
+      A = A';
+  end
+  
   Aindex = spm_clusters(XYZ); %- cluster indexes
 
   STCS = snpm_STcalc('initK',STCS,max(A),isPos,perm);

test/common/generic_test_snpm.m

@@ -47,9 +47,19 @@ function setGlobals(testCase)
             % Disable warning on very small number of permutations
             warning('off','SnPM:VeryFewPermsCoarseExactPValues')
 
-            snpm_test_config;
-            cd(spm_str_manip(which('snpm_test_config'), 'h'))
             global testDataDir;
+            snpm_test_config;
+            if isempty(testDataDir)
+                error('test:emptytestDataDir', ...
+                    ['No test data directory specified, please fill in '...
+                    ' ''testDataDir'' variable in snpm_test_config.m'])
+            end
+            res_dir = fullfile(spm_file(testDataDir, 'path'), 'results');
+            if ~isdir(res_dir)
+                mkdir(res_dir)
+            end
+            cd(res_dir)
+            
             global SnPMrefVersion;
             testCase.SnPMrefVersion = SnPMrefVersion;
 

test/snpm_test_config.m

@@ -0,0 +1,13 @@
+% Configuration file for computing ground truth tests.
+%
+% Update this file to specify your test data directory.
+%
+%_______________________________________________________________________
+% Copyright (C) 2013-2016 The University of Warwick
+% Id: snpm_test_config.m  SnPM13 2013/10/12
+% Camille Maumet
+
+global testDataDir;
+testDataDir = ''; % Specify directory containing test data
+global SnPMrefVersion
+SnPMrefVersion = 'SnPM8';

test/snpm_tests.m

@@ -0,0 +1,3 @@
+import matlab.unittest.TestSuite;
+suite = TestSuite.fromFolder(fullfile(spm_str_manip(which('snpm'), 'h'), 'test'));
+result = run(suite)