Travis testing

.gitignore

@@ -9,8 +9,9 @@
 # images in data folder
 Data/*.png
 
-# Test data (if missing will be downloaded from NeuroVault)
+# Test data
 test/data
+test/moxunit_testsuite/MOxUnit
 
 #nii files
 *.nii
@@ -30,4 +31,4 @@ test/data
 #ZIP files
 *.zip
 
-_ignored*
+_ignored*

.travis.yml

@@ -0,0 +1,40 @@
+language: python
+# use container-based infrastructure
+sudo: required
+services:
+  - docker
+cache:
+  pip: true
+  timeout: 1000
+python:
+  - "3.5"
+bundler_args: --retry 9
+# command to install dependencies, e.g. pip install -r requirements.txt --use-mirrors
+install: 
+ - pip install --upgrade setuptools
+ - cd test/moxunit_testsuite
+# Download MoxUnit for unit testing
+ - git clone https://github.com/MOxUnit/MOxUnit.git
+ - ls
+ - cd ..
+# Download data
+ - cd data
+ - wget https://neurovault.org/collections/2210/download
+ - unzip download
+ - mv NIDM-Results\ 1.3.0\ examples\ -\ nidmfsl\ 1.2.01\ and\ SPM12\ r6906/* .
+ - rm -r NIDM-Results\ 1.3.0\ examples\ -\ nidmfsl\ 1.2.01\ and\ SPM12\ r6906/
+ - cd ../..
+ - ls
+script:  
+ # Run docker snapshot of dev octave (until 4.4 is released)
+ - did=$(sudo docker run -ti -d --rm -v `pwd`:/spmviewer cmaumet/octave-spm)
+ # Run tests in Octave
+ - sudo docker exec -t -i $did bash -c "sudo chmod 755 /spmviewer/test/moxunit_testsuite/runTest.sh; sudo /spmviewer/test/moxunit_testsuite/runTest.sh"
+before_install:
+ # Update docker version
+ - sudo apt-get update
+ - sudo apt-get -y -o Dpkg::Options::="--force-confnew" install docker-ce
+ - git config --global user.name "TravisCI"
+ - git config --global user.email "travis@dummy.com"
+ - sudo docker pull cmaumet/octave-spm
+

README.md

@@ -2,8 +2,7 @@
 
 Read and display NIDM-Results packs in the SPM environment.
 
-##### Usage
-
+#### Usage
 To view NIDM results using the NIDM results viewer run the following
 
 1. Open `SPM fMRI` from the Matlab command line.
@@ -33,11 +32,11 @@ To view NIDM results using the NIDM results viewer run the following
 :-------------------------:|:-------------------------:
  **Fig. 5.** Table data and images  |  **Fig. 6.** Summary statistics
 
-##### Requirements
+#### Requirements
 
 - [SPM12](http://www.fil.ion.ucl.ac.uk/spm/software/spm12/)
 
-##### Installation
+#### Installation
 
 1. Add the filepath to SPM in Matlab;
 
@@ -49,15 +48,44 @@ To view NIDM results using the NIDM results viewer run the following
  <full path to SPM>/toolbox/
  ``` 
 
-##### Testing
+#### Testing
+
+Currently, two versions of the test suite exist. One is based on the `matlab unittesting framework` and the other is based on the [`MOxUnit`](https://github.com/MOxUnit/MOxUnit) library. 
+
+The `matlab unittesting framework` tests are recommended for testing the code locally in `Matlab` as they perform much faster and do not require any additional installation. The `MOxUnit` tests are recommended for testing the code locally in `Octave` and are also used for the Travis CI. Below is a description of how to run each test set.
+
+##### Matlab Unittesting Framework
 
-1. Add the filepath to the 'tests' folder;
+1. Add the filepath to the 'tests/matlabunit_testsuite' folder. In the Matlab commandline type;
 
  ```
-addpath(fullfile(fileparts(which('nidm_results_display')), 'test'))
+addpath(fullfile(fileparts(which('nidm_results_display')), 'test', 'matlabunit_testsuite'))
  ```
-2. Run runTest;
+2. Run runTest. In the Matlab commandline type;
 
  ```
  runTest();
  ```
+
+ ##### MOxUnit Framework
+
+ 1. Download the MOxUnit testing framework to 'tests/moxunit_testsuite'. In the bash commandline type;
+
+  ```
+cd <PATH-TO-REPOSITORY>/tests/moxunit_testsuite
+git clone https://github.com/MOxUnit/MOxUnit.git
+  ```
+ 2. Download the test data from [NeuroVault](https://neurovault.org/). In the bash commandline type;
+
+  ```
+cd <PATH-TO-REPOSITORY>/tests/data
+wget https://neurovault.org/collections/2210/download
+unzip download
+mv NIDM-Results\ 1.3.0\ examples\ -\ nidmfsl\ 1.2.01\ and\ SPM12\ r6906/* .
+rm -r NIDM-Results\ 1.3.0\ examples\ -\ nidmfsl\ 1.2.01\ and\ SPM12\ r6906/
+  ```
+ 3. From 'tests/moxunit_testsuite' run the MOxUnit tests. In the Octave/Matlab terminal type;
+
+  ```
+  moxunit_runtests
+  ```

lib/changeNIDMtoTabDat.m

@@ -489,11 +489,11 @@
                 else
                     %Calculate whichever statistic type is used.
                     if strcmp(statType, 'T')
-                        tableTemp{n, 9} = icdf('T',1-tableTemp{n, 11},errorDegrees);
+                        tableTemp{n, 9} = spm_invTcdf(1-tableTemp{n, 11},errorDegrees);
                     elseif strcmp(statType, 'X')
-                        tableTemp{n, 9} = icdf('Chi',1-tableTemp{n, 11},errorDegrees);
+                        tableTemp{n, 9} = spm_invXcdf(1-tableTemp{n, 11},errorDegrees);
                     elseif strcmp(statType, 'F')
-                        tableTemp{n, 9} = icdf('F',1-tableTemp{n, 11},effectDegrees, errorDegrees);
+                        tableTemp{n, 9} = spm_invFcdf(1-tableTemp{n, 11},effectDegrees, errorDegrees);
                     else
                         tableTemp{n, 9} = '';
                     end

lib/generateMIP.m

@@ -46,5 +46,11 @@ function generateMIP(filepath, filename, DIM, units)
     %Write the image:
     mipPath = spm_file(fullfile(filepath, 'MIP.png'));
     imwrite(mip,gray(64),mipPath,'png');
+
+    %In some versions of octave/matlab the above removes
+    %the original .nii.gz file.
+    if ~exist(fullfile(filepath, filename), 'file')
+        gzip(strrep(fullfile(filepath, filename), '.gz', ''));
+    end
 
 end

test/runTest.m → test/matlabunit_testsuite/runTest.m

@@ -8,13 +8,13 @@
 
 function runTest()
 
-    %Clear previous classes (and keep debugging breakpoints)
-    clear classes;
+    %Clear previous classes.
+    clear all;
 
     %Setup steps for the test.
     import matlab.unittest.TestSuite;
-    addpath(fullfile(fileparts(mfilename('fullpath')),'..', 'lib'));
-    addpath(fullfile(fileparts(mfilename('fullpath')),'..'));
+    addpath(fullfile(fileparts(mfilename('fullpath')),'..', '..', 'lib'));
+    addpath(fullfile(fileparts(mfilename('fullpath')),'..', '..'));
 
     %Run all tests.
     tests = [matlab.unittest.TestSuite.fromFile(which('testDataSets')),...