[TST] Expands integration (#482)

* Expands integration testing to include mapca and several of its options

.circleci/config.yml

@@ -153,6 +153,31 @@ jobs:
           root: /tmp
           paths:
               - src/coverage/.coverage.three-echo
+
+  four-echo:
+    docker:
+      - image: continuumio/miniconda3
+    working_directory: /tmp/src/tedana
+    steps:
+      - checkout
+      - restore_cache:
+          key: conda-py37-v1-{{ checksum "dev_requirements.txt" }}
+      - run:
+          name: Run integration tests
+          no_output_timeout: 40m
+          command: |
+            apt-get install -yqq make
+            source activate tedana_py37  # depends on makeenv_37
+            make four-echo
+            mkdir /tmp/src/coverage
+            mv /tmp/src/tedana/.coverage /tmp/src/coverage/.coverage.four-echo
+      - store_artifacts:
+          path: /tmp/data
+      - persist_to_workspace:
+          root: /tmp
+          paths:
+              - src/coverage/.coverage.four-echo
+
   five-echo:
     docker:
       - image: continuumio/miniconda3
@@ -216,6 +241,9 @@ workflows:
       - three-echo:
           requires:
             - makeenv_37
+      - four-echo:
+          requires:
+            - makeenv_37
       - five-echo:
           requires:
             - makeenv_37
@@ -225,4 +253,5 @@ workflows:
             - unittest_36
             - unittest_37
             - three-echo
+            - four-echo
             - five-echo

Makefile

@@ -19,6 +19,9 @@ unittest:
 three-echo:
 	@py.test --cov-append --cov-report term-missing --cov=tedana -k test_integration_three_echo tedana/tests/test_integration.py
 
+four-echo:
+	@py.test --cov-append --cov-report term-missing --cov=tedana -k test_integration_four_echo tedana/tests/test_integration.py
+
 five-echo:
 	@py.test --cov-append --cov-report term-missing --cov=tedana -k test_integration_five_echo tedana/tests/test_integration.py
 

dev_tools/run_tests.sh

@@ -27,6 +27,14 @@ run_three_echo_test() {
     cprint "THREE-ECHO TEST PASSED !"
 }
 
+run_four_echo_test() {
+    #
+    # Runs tedana four-echo test
+    cprint "RUNNING four-ECHO TEST"
+    make four-echo
+    cprint "FOUR-ECHO TEST PASSED !"
+}
+
 run_five_echo_test() {
     #
     # Runs tedana five-echo test
@@ -66,6 +74,7 @@ run_all_tests() {
     run_lint_tests
     run_unit_tests
     run_three_echo_test
+    run_four_echo_test
     run_five_echo_test
 
     cprint "FINISHED RUNNING ALL TESTS -- GREAT SUCCESS !"

tedana/tests/data/fiu_four_echo_outputs.txt

@@ -0,0 +1,66 @@
+adaptive_mask.nii.gz
+betas_OC.nii.gz
+betas_hik_OC.nii.gz
+dn_ts_OC.nii.gz
+feats_OC2.nii.gz
+figures
+hik_ts_OC.nii.gz
+ica_components.nii.gz
+ica_decomposition.json
+ica_mixing.tsv
+ica_orth_mixing.tsv
+lowk_ts_OC.nii.gz
+pca_components.nii.gz
+pca_decomposition.json
+pca_mixing.tsv
+report.txt
+s0v.nii.gz
+t2sv.nii.gz
+ts_OC.nii.gz
+figures/Component_Overview.png
+figures/Kappa_vs_Rho_Scatter.png
+figures/comp_000.png
+figures/comp_001.png
+figures/comp_002.png
+figures/comp_003.png
+figures/comp_004.png
+figures/comp_005.png
+figures/comp_006.png
+figures/comp_007.png
+figures/comp_008.png
+figures/comp_009.png
+figures/comp_010.png
+figures/comp_011.png
+figures/comp_012.png
+figures/comp_013.png
+figures/comp_014.png
+figures/comp_015.png
+figures/comp_016.png
+figures/comp_017.png
+figures/comp_018.png
+figures/comp_019.png
+figures/comp_020.png
+figures/comp_021.png
+figures/comp_022.png
+figures/comp_023.png
+figures/comp_024.png
+figures/comp_025.png
+figures/comp_026.png
+figures/comp_027.png
+figures/comp_028.png
+figures/comp_029.png
+figures/comp_030.png
+figures/comp_031.png
+figures/comp_032.png
+figures/comp_033.png
+figures/comp_034.png
+figures/comp_035.png
+figures/comp_036.png
+figures/comp_037.png
+figures/comp_038.png
+figures/comp_039.png
+figures/comp_040.png
+figures/comp_041.png
+figures/comp_042.png
+figures/comp_043.png
+figures/comp_044.png

tedana/tests/test_integration.py

@@ -99,7 +99,37 @@ def test_integration_five_echo(skip_integration):
     assert isinstance(df, pd.DataFrame)
 
     # compare the generated output files
-    fn = resource_filename('tedana', 'tests/data/tedana_outputs_verbose.txt')
+    fn = resource_filename('tedana',
+                           'tests/data/nih_five_echo_outputs_verbose.txt')
+    check_integration_outputs(fn, out_dir)
+
+
+def test_integration_four_echo(skip_integration):
+    """ Integration test of the full tedana workflow using four-echo test data
+    """
+
+    if skip_integration:
+        pytest.skip('Skipping four-echo integration test')
+    out_dir = '/tmp/data/four-echo/TED.four-echo'
+    if os.path.exists(out_dir):
+        shutil.rmtree(out_dir)
+
+    # download data and run the test
+    download_test_data('https://osf.io/gnj73/download',
+                       os.path.dirname(out_dir))
+    prepend = '/tmp/data/four-echo/'
+    prepend += 'sub-PILOT_ses-01_task-localizerDetection_run-01_echo-'
+    suffix = '_space-sbref_desc-preproc_bold+orig.HEAD'
+    datalist = [prepend + str(i + 1) + suffix for i in range(4)]
+    tedana_workflow(data=datalist,
+                    tes=[11.8, 28.04, 44.28, 60.52],
+                    out_dir=out_dir,
+                    tedpca='aic',
+                    fittype='curvefit',
+                    tedort=True)
+
+    # compare the generated output files
+    fn = resource_filename('tedana', 'tests/data/fiu_four_echo_outputs.txt')
     check_integration_outputs(fn, out_dir)
 
 
@@ -120,8 +150,10 @@ def test_integration_three_echo(skip_integration):
         data='/tmp/data/three-echo/three_echo_Cornell_zcat.nii.gz',
         tes=[14.5, 38.5, 62.5],
         out_dir=out_dir,
+        low_mem=True,
         tedpca='kundu')
 
     # compare the generated output files
-    fn = resource_filename('tedana', 'tests/data/tedana_outputs.txt')
+    fn = resource_filename('tedana',
+                           'tests/data/cornell_three_echo_outputs.txt')
     check_integration_outputs(fn, out_dir)