From d338acc57f9fde09c5f8dcc251937f00236d3f52 Mon Sep 17 00:00:00 2001
From: Taylor Salo <tsalo006@fiu.edu>
Date: Thu, 7 May 2020 13:16:38 -0400
Subject: [PATCH] [FIX] Fix t2smap optimal combination (#566)
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* Fix t2smap optcom

Introduced when I changed make_optcom’s arg from mask to adaptive mask
in #358.

* Add t2smap integration test.
---
 .circleci/config.yml                          | 28 +++++++++++++++
 Makefile                                      |  5 ++-
 .../data/nih_five_echo_outputs_t2smap.txt     |  5 +++
 tedana/tests/test_integration.py              | 34 +++++++++++++++++++
 tedana/workflows/t2smap.py                    |  2 +-
 5 files changed, 72 insertions(+), 2 deletions(-)
 create mode 100644 tedana/tests/data/nih_five_echo_outputs_t2smap.txt

diff --git a/.circleci/config.yml b/.circleci/config.yml
index 5a1dc17ef..d3a2a2fb9 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -202,6 +202,30 @@ jobs:
           paths:
               - src/coverage/.coverage.five-echo
 
+  t2smap:
+    docker:
+      - image: continuumio/miniconda3
+    working_directory: /tmp/src/tedana
+    steps:
+      - checkout
+      - restore_cache:
+          key: conda-py37-v1-{{ checksum "dev_requirements.txt" }}-{{ checksum "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 t2smap
+            mkdir /tmp/src/coverage
+            mv /tmp/src/tedana/.coverage /tmp/src/coverage/.coverage.t2smap
+      - store_artifacts:
+          path: /tmp/data
+      - persist_to_workspace:
+          root: /tmp
+          paths:
+              - src/coverage/.coverage.t2smap
+
   merge_coverage:
     working_directory: /tmp/src/tedana
     docker:
@@ -247,6 +271,9 @@ workflows:
       - five-echo:
           requires:
             - makeenv_37
+      - t2smap:
+          requires:
+            - makeenv_37
       - merge_coverage:
           requires:
             - unittest_35
@@ -255,3 +282,4 @@ workflows:
             - three-echo
             - four-echo
             - five-echo
+            - t2smap
diff --git a/Makefile b/Makefile
index 0ea412bc7..0fba6759c 100644
--- a/Makefile
+++ b/Makefile
@@ -1,6 +1,6 @@
 .PHONY: all lint
 
-all_tests: lint unittest three-echo five-echo
+all_tests: lint unittest three-echo four-echo five-echo t2smap
 
 help:
 	@echo "Please use 'make <target>' where <target> is one of:"
@@ -8,6 +8,7 @@ help:
 	@echo "  unittest		to run unit tests on tedana"
 	@echo "  three-echo	to run the three-echo test set on tedana"
 	@echo "  five-echo	to run the five-echo test set on tedana"
+	@echo "  t2smap	to run the t2smap integration test set on tedana"
 	@echo "  all_tests		to run 'lint', 'unittest', and 'integration'"
 
 lint:
@@ -25,3 +26,5 @@ four-echo:
 five-echo:
 	@py.test --cov-append --cov-report term-missing --cov=tedana -k test_integration_five_echo tedana/tests/test_integration.py
 
+t2smap:
+	@py.test --cov-append --cov-report term-missing --cov=tedana -k test_integration_t2smap tedana/tests/test_integration.py
diff --git a/tedana/tests/data/nih_five_echo_outputs_t2smap.txt b/tedana/tests/data/nih_five_echo_outputs_t2smap.txt
new file mode 100644
index 000000000..1d2c6c46b
--- /dev/null
+++ b/tedana/tests/data/nih_five_echo_outputs_t2smap.txt
@@ -0,0 +1,5 @@
+desc-full_S0map.nii.gz
+desc-full_T2starmap.nii.gz
+desc-optcom_bold.nii.gz
+S0map.nii.gz
+T2starmap.nii.gz
diff --git a/tedana/tests/test_integration.py b/tedana/tests/test_integration.py
index 6d61cbc52..f245362ea 100644
--- a/tedana/tests/test_integration.py
+++ b/tedana/tests/test_integration.py
@@ -16,6 +16,7 @@
 import pandas as pd
 
 from tedana.workflows import tedana as tedana_cli
+from tedana.workflows import t2smap as t2smap_cli
 from tedana import io
 
 
@@ -183,3 +184,36 @@ def test_integration_three_echo(skip_integration):
     fn = resource_filename('tedana',
                            'tests/data/cornell_three_echo_outputs.txt')
     check_integration_outputs(fn, out_dir)
+
+
+def test_integration_t2smap(skip_integration):
+    """Integration test of the full t2smap workflow using five-echo test data
+    """
+    if skip_integration:
+        pytest.skip('Skipping t2smap integration test')
+    out_dir = '/tmp/data/five-echo/t2smap_five-echo'
+    if os.path.exists(out_dir):
+        shutil.rmtree(out_dir)
+
+    # download data and run the test
+    download_test_data('https://osf.io/9c42e/download',
+                       os.path.dirname(out_dir))
+    prepend = '/tmp/data/five-echo/p06.SBJ01_S09_Task11_e'
+    suffix = '.sm.nii.gz'
+    datalist = [prepend + str(i + 1) + suffix for i in range(5)]
+    echo_times = [15.4, 29.7, 44.0, 58.3, 72.6]
+    args = (['-d'] + datalist + ['-e'] + [str(te) for te in echo_times] +
+            ['--out-dir', out_dir, '--fittype', 'curvefit'])
+    t2smap_cli._main(args)
+
+    # compare the generated output files
+    fname = resource_filename('tedana',
+                              'tests/data/nih_five_echo_outputs_t2smap.txt')
+    # Gets filepaths generated by integration test
+    existing = [os.path.relpath(f, out_dir) for f in
+                glob.glob(os.path.join(out_dir, '**'), recursive=True)[1:]]
+
+    # Compares remaining files with those expected
+    with open(fname, 'r') as f:
+        tocheck = f.read().splitlines()
+    assert sorted(tocheck) == sorted(existing)
diff --git a/tedana/workflows/t2smap.py b/tedana/workflows/t2smap.py
index 85ab44d3d..d6ab8ca75 100644
--- a/tedana/workflows/t2smap.py
+++ b/tedana/workflows/t2smap.py
@@ -227,7 +227,7 @@ def t2smap_workflow(data, tes, out_dir='.', mask=None,
 
     LGR.info('Computing optimal combination')
     # optimally combine data
-    OCcatd = combine.make_optcom(catd, tes, mask, t2s=t2s_full,
+    OCcatd = combine.make_optcom(catd, tes, masksum, t2s=t2s_full,
                                  combmode=combmode)
 
     # clean up numerical errors