added ashs.IntracranialVolumeFile.read_volume_series()

fphammerle · Aug 7, 2019 · b008080 · b008080
1 parent 61180f2
commit b008080
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diff --git a/freesurfer_volume_reader/ashs.py b/freesurfer_volume_reader/ashs.py
@@ -40,6 +40,16 @@ def read_volume_mm3(self) -> float:
             assert subject == self.subject, (subject, self.subject)
             return float(icv)
 
+    def read_volume_series(self) -> pandas.Series:
+        return pandas.Series(
+            data=[self.read_volume_mm3()],
+            name='volume_mm^3',
+            index=pandas.Index(
+                data=[self.subject],
+                name='subject',
+            ),
+        )
+
 
 class HippocampalSubfieldsVolumeFile(freesurfer_volume_reader.SubfieldVolumeFile):
 

diff --git a/tests/ashs_test.py b/tests/ashs_test.py
@@ -53,6 +53,60 @@ def test_intracranial_volume_file_read_volume_mm3_not_found(volume_file_path):
         volume_file.read_volume_mm3()
 
 
+@pytest.mark.parametrize(('volume_file_path', 'expected_series'), [
+    (os.path.join(SUBJECTS_DIR, 'bert', 'final', 'bert_icv.txt'),
+     pandas.Series(
+         data=[1234560.0],
+         name='volume_mm^3',
+         index=pandas.Index(data=['bert'], name='subject'),
+     )),
+    (os.path.join(SUBJECTS_DIR, 'alice', 'final', 'alice_icv.txt'),
+     pandas.Series(
+         data=[1543200.0],
+         name='volume_mm^3',
+         index=pandas.Index(data=['alice'], name='subject'),
+     )),
+])
+def test_intracranial_volume_file_read_volume_series_single(volume_file_path, expected_series):
+    volume_file = IntracranialVolumeFile(path=volume_file_path)
+    pandas.testing.assert_series_equal(
+        left=expected_series,
+        right=volume_file.read_volume_series(),
+        check_dtype=True,
+        check_names=True,
+    )
+
+
+@pytest.mark.parametrize(('volume_file_paths', 'expected_series'), [
+    ([os.path.join(SUBJECTS_DIR, 'bert', 'final', 'bert_icv.txt'),
+      os.path.join(SUBJECTS_DIR, 'alice', 'final', 'alice_icv.txt')],
+     pandas.Series(
+         data=[1234560.0, 1543200.0],
+         name='volume_mm^3',
+         index=pandas.Index(data=['bert', 'alice'], name='subject'),
+     )),
+])
+def test_intracranial_volume_file_read_volume_series_concat(volume_file_paths, expected_series):
+    volume_series = pandas.concat(
+        IntracranialVolumeFile(path=p).read_volume_series()
+        for p in volume_file_paths)
+    pandas.testing.assert_series_equal(
+        left=expected_series,
+        right=volume_series,
+        check_dtype=True,
+        check_names=True,
+    )
+
+
+@pytest.mark.parametrize('volume_file_path', [
+    os.path.join(SUBJECTS_DIR, 'bert', 'final', 'BERT_icv.txt'),
+])
+def test_intracranial_volume_file_read_volume_series_not_found(volume_file_path):
+    volume_file = IntracranialVolumeFile(path=volume_file_path)
+    with pytest.raises(FileNotFoundError):
+        volume_file.read_volume_series()
+
+
 @pytest.mark.parametrize(('volume_file_path', 'expected_attrs'), [
     ('ashs/final/bert_left_heur_volumes.txt',
      {'subject': 'bert', 'hemisphere': 'left', 'correction': None}),