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[FIX] Correct t2smap outputs (#562)
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* Fix BEP001-compatible output names.

* Arbitrary change to allow PR.
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@tsalo
tsalo authored Apr 29, 2020
1 parent cb11c9d commit bc55c2d
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Showing 2 changed files with 29 additions and 29 deletions.
40 changes: 20 additions & 20 deletions tedana/tests/test_t2smap.py
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Original file line number Diff line number Diff line change
Expand Up @@ -27,13 +27,13 @@ def test_basic_t2smap1(self):

# Check outputs
assert op.isfile(op.join(out_dir, 'desc-optcom_bold.nii.gz'))
img = nib.load(op.join(out_dir, 'T2StarMap.nii.gz'))
img = nib.load(op.join(out_dir, 'T2starmap.nii.gz'))
assert len(img.shape) == 3
img = nib.load(op.join(out_dir, 'S0Map.nii.gz'))
img = nib.load(op.join(out_dir, 'S0map.nii.gz'))
assert len(img.shape) == 3
img = nib.load(op.join(out_dir, 'desc-full_T2StarMap.nii.gz'))
img = nib.load(op.join(out_dir, 'desc-full_T2starmap.nii.gz'))
assert len(img.shape) == 3
img = nib.load(op.join(out_dir, 'desc-full_S0Map.nii.gz'))
img = nib.load(op.join(out_dir, 'desc-full_S0map.nii.gz'))
assert len(img.shape) == 3
img = nib.load(op.join(out_dir, 'desc-optcom_bold.nii.gz'))
assert len(img.shape) == 4
Expand All @@ -53,13 +53,13 @@ def test_basic_t2smap2(self):

# Check outputs
assert op.isfile(op.join(out_dir, 'desc-optcom_bold.nii.gz'))
img = nib.load(op.join(out_dir, 'T2StarMap.nii.gz'))
img = nib.load(op.join(out_dir, 'T2starmap.nii.gz'))
assert len(img.shape) == 4
img = nib.load(op.join(out_dir, 'S0Map.nii.gz'))
img = nib.load(op.join(out_dir, 'S0map.nii.gz'))
assert len(img.shape) == 4
img = nib.load(op.join(out_dir, 'desc-full_T2StarMap.nii.gz'))
img = nib.load(op.join(out_dir, 'desc-full_T2starmap.nii.gz'))
assert len(img.shape) == 4
img = nib.load(op.join(out_dir, 'desc-full_S0Map.nii.gz'))
img = nib.load(op.join(out_dir, 'desc-full_S0map.nii.gz'))
assert len(img.shape) == 4
img = nib.load(op.join(out_dir, 'desc-optcom_bold.nii.gz'))
assert len(img.shape) == 4
Expand All @@ -79,13 +79,13 @@ def test_basic_t2smap3(self):

# Check outputs
assert op.isfile(op.join(out_dir, 'desc-optcom_bold.nii.gz'))
img = nib.load(op.join(out_dir, 'T2StarMap.nii.gz'))
img = nib.load(op.join(out_dir, 'T2starmap.nii.gz'))
assert len(img.shape) == 3
img = nib.load(op.join(out_dir, 'S0Map.nii.gz'))
img = nib.load(op.join(out_dir, 'S0map.nii.gz'))
assert len(img.shape) == 3
img = nib.load(op.join(out_dir, 'desc-full_T2StarMap.nii.gz'))
img = nib.load(op.join(out_dir, 'desc-full_T2starmap.nii.gz'))
assert len(img.shape) == 3
img = nib.load(op.join(out_dir, 'desc-full_S0Map.nii.gz'))
img = nib.load(op.join(out_dir, 'desc-full_S0map.nii.gz'))
assert len(img.shape) == 3
img = nib.load(op.join(out_dir, 'desc-optcom_bold.nii.gz'))
assert len(img.shape) == 4
Expand All @@ -105,13 +105,13 @@ def test_basic_t2smap4(self):

# Check outputs
assert op.isfile(op.join(out_dir, 'desc-optcom_bold.nii.gz'))
img = nib.load(op.join(out_dir, 'T2StarMap.nii.gz'))
img = nib.load(op.join(out_dir, 'T2starmap.nii.gz'))
assert len(img.shape) == 4
img = nib.load(op.join(out_dir, 'S0Map.nii.gz'))
img = nib.load(op.join(out_dir, 'S0map.nii.gz'))
assert len(img.shape) == 4
img = nib.load(op.join(out_dir, 'desc-full_T2StarMap.nii.gz'))
img = nib.load(op.join(out_dir, 'desc-full_T2starmap.nii.gz'))
assert len(img.shape) == 4
img = nib.load(op.join(out_dir, 'desc-full_S0Map.nii.gz'))
img = nib.load(op.join(out_dir, 'desc-full_S0map.nii.gz'))
assert len(img.shape) == 4
img = nib.load(op.join(out_dir, 'desc-optcom_bold.nii.gz'))
assert len(img.shape) == 4
Expand All @@ -131,13 +131,13 @@ def test_t2smap_cli(self):
workflows.t2smap._main(args)

# Check outputs
img = nib.load(op.join(out_dir, 'T2StarMap.nii.gz'))
img = nib.load(op.join(out_dir, 'T2starmap.nii.gz'))
assert len(img.shape) == 3
img = nib.load(op.join(out_dir, 'S0Map.nii.gz'))
img = nib.load(op.join(out_dir, 'S0map.nii.gz'))
assert len(img.shape) == 3
img = nib.load(op.join(out_dir, 'desc-full_T2StarMap.nii.gz'))
img = nib.load(op.join(out_dir, 'desc-full_T2starmap.nii.gz'))
assert len(img.shape) == 3
img = nib.load(op.join(out_dir, 'desc-full_S0Map.nii.gz'))
img = nib.load(op.join(out_dir, 'desc-full_S0map.nii.gz'))
assert len(img.shape) == 3
img = nib.load(op.join(out_dir, 'desc-optcom_bold.nii.gz'))
assert len(img.shape) == 4
Expand Down
18 changes: 9 additions & 9 deletions tedana/workflows/t2smap.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -152,7 +152,7 @@ def t2smap_workflow(data, tes, out_dir='.', mask=None,
debug : :obj:`bool`, optional
Whether to run in debugging mode or not. Default is False.
quiet : :obj:`bool`, optional
If True, suppresses logging/printing of messages. Default is False.
If True, suppress logging/printing of messages. Default is False.
Notes
Expand All @@ -162,16 +162,16 @@ def t2smap_workflow(data, tes, out_dir='.', mask=None,
========================== =================================================
Filename Content
========================== =================================================
T2StarMap.nii.gz Limited estimated T2* 3D map or 4D timeseries.
T2starmap.nii.gz Limited estimated T2* 3D map or 4D timeseries.
Will be a 3D map if ``fitmode`` is 'all' and a
4D timeseries if it is 'ts'.
S0Map.nii.gz Limited S0 3D map or 4D timeseries.
desc-full_T2StarMap.nii.gz Full T2* map/timeseries. The difference between
S0map.nii.gz Limited S0 3D map or 4D timeseries.
desc-full_T2starmap.nii.gz Full T2* map/timeseries. The difference between
the limited and full maps is that, for voxels
affected by dropout where only one echo contains
good data, the full map uses the single echo's
value while the limited map has a NaN.
desc-full_S0Map.nii.gz Full S0 map/timeseries.
desc-full_S0map.nii.gz Full S0 map/timeseries.
desc-optcom_bold.nii.gz Optimally combined timeseries.
========================== =================================================
"""
Expand Down Expand Up @@ -238,11 +238,11 @@ def t2smap_workflow(data, tes, out_dir='.', mask=None,
t2s_limited[t2s_limited < 0] = 0

io.filewrite(utils.millisec2sec(t2s_limited),
op.join(out_dir, 'T2StarMap.nii.gz'), ref_img)
io.filewrite(s0_limited, op.join(out_dir, 'S0Map.nii.gz'), ref_img)
op.join(out_dir, 'T2starmap.nii.gz'), ref_img)
io.filewrite(s0_limited, op.join(out_dir, 'S0map.nii.gz'), ref_img)
io.filewrite(utils.millisec2sec(t2s_full),
op.join(out_dir, 'desc-full_T2StarMap.nii.gz'), ref_img)
io.filewrite(s0_full, op.join(out_dir, 'desc-full_S0Map.nii.gz'), ref_img)
op.join(out_dir, 'desc-full_T2starmap.nii.gz'), ref_img)
io.filewrite(s0_full, op.join(out_dir, 'desc-full_S0map.nii.gz'), ref_img)
io.filewrite(OCcatd, op.join(out_dir, 'desc-optcom_bold.nii.gz'), ref_img)


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