BF: time units

CHANGELOG.md

@@ -1,5 +1,10 @@
 This document contains the nifti_mrs_tools release history in reverse chronological order.
 
+1.3.3 (Friday 8th November 2024)
+-----------------------------------
+- Handle different time units in nifti header for dwelltime (with thanks to @Septem).
+- Handle singleton coil dimensions with `mrs_tools vis`  (with thanks to @Septem).
+
 1.3.2 (Wednesday 23rd October 2024)
 -----------------------------------
 - Better visualisation using `mrs_tools vis` for data containing ISIS, metabolite cycling or editing.

src/nifti_mrs/nifti_mrs.py

@@ -219,7 +219,14 @@ def set_version_info(self, major, minor):
     @property
     def dwelltime(self):
         '''Return dwelltime in seconds'''
-        return self.header['pixdim'][4]
+        t_unit = self.header.get_xyzt_units()[1]
+        dwelltime = self.header['pixdim'][4]
+        if t_unit == "msec":
+            return dwelltime * 1e-3
+        elif t_unit == "usec":
+            return dwelltime * 1e-6
+        else:
+            return dwelltime
 
     @dwelltime.setter
     def dwelltime(self, new_dt):

src/nifti_mrs/vis.py

@@ -24,7 +24,8 @@ def vis_nifti_mrs(data, display_dim=None, ppmlim=None, plot_avg=False, mask=None
 
     if data.ndim > 4 \
             and 'DIM_COIL' in data.dim_tags\
-            and display_dim != 'DIM_COIL':
+            and display_dim != 'DIM_COIL'\
+            and data.shape[data.dim_position('DIM_COIL')] > 1:
         print('Performing coil combination')
         data = nifti_mrs_proc.coilcombine(data)
 

tests/test_nifti_mrs.py

@@ -61,6 +61,25 @@ def test_modification_mrs_meta():
     assert obj.nifti_mrs_version == '1.3'
 
 
+def test_time_units():
+    obj = NIFTI_MRS(data['unprocessed'])
+
+    obj.image.header.set_xyzt_units('mm', 'sec')
+    obj.dwelltime = 1 / 5000
+    assert obj.spectralwidth == 5000
+    assert obj.bandwidth == 5000
+
+    obj.image.header.set_xyzt_units('mm', 'msec')
+    obj.dwelltime = 1E3 / 5000
+    assert obj.spectralwidth == 5000
+    assert obj.bandwidth == 5000
+
+    obj.image.header.set_xyzt_units('mm', 'usec')
+    obj.dwelltime = 1E6 / 5000
+    assert obj.spectralwidth == 5000
+    assert obj.bandwidth == 5000
+
+
 def test_hdr_ext():
     obj = NIFTI_MRS(data['unprocessed'])
 

tests/test_nifti_mrs_vis.py

@@ -0,0 +1,48 @@
+from pathlib import Path
+
+import pytest
+
+testsPath = Path(__file__).parent
+test_data_raw = testsPath / 'test_data' / 'metab_raw.nii.gz'
+test_data_proc = testsPath / 'test_data' / 'metab.nii.gz'
+
+
+def test_vis_error(tmp_path):
+    try:
+        import fsl_mrs  # noqa: F401
+    except ImportError:
+        with pytest.raises(
+                ImportError,
+                match="NIfTI-MRS visualisation requires FSL-MRS tools to be installed. "
+                      "See fsl-mrs.com for installation instructions."):
+            import nifti_mrs.vis   # noqa: F401
+    else:
+        pytest.skip("fsl-mrs present, skipping test")
+
+
+@pytest.mark.with_fsl_mrs
+def test_vis_svs(tmp_path):
+    import nifti_mrs.vis as vis
+    from nifti_mrs.nifti_mrs import NIFTI_MRS
+    import matplotlib
+
+    nmrs = NIFTI_MRS(test_data_raw)
+    fig = vis.vis_nifti_mrs(nmrs)
+    assert isinstance(fig, matplotlib.figure.Figure)
+
+    nmrs = NIFTI_MRS(test_data_proc)
+    fig = vis.vis_nifti_mrs(nmrs)
+    assert isinstance(fig, matplotlib.figure.Figure)
+
+
+@pytest.mark.with_fsl_mrs
+def test_vis_svs_singleton_channels(tmp_path):
+    import nifti_mrs.vis as vis
+    from nifti_mrs.nifti_mrs import NIFTI_MRS
+    import matplotlib
+
+    nmrs = NIFTI_MRS(test_data_proc)
+    nmrs.set_dim_tag(4, 'DIM_COIL')
+    assert nmrs.shape[-1] == 1
+    fig = vis.vis_nifti_mrs(nmrs)
+    assert isinstance(fig, matplotlib.figure.Figure)