Update to data reader to deal with dots in paths

fsl_mrs/scripts/fsl_mrs

@@ -349,13 +349,12 @@ def main():
 
     # Save image of MRS voxel
     location_fig = None
-    if args.t1 is not None:
-        datatype = mrs_io.check_datatype(args.data)
-        if datatype == 'NIFTI':
-            fig = plotting.plot_world_orient(args.t1, args.data)
-            fig.tight_layout()
-            location_fig = os.path.join(args.output, 'voxel_location.png')
-            fig.savefig(location_fig, bbox_inches='tight', facecolor='k')
+    if args.t1 is not None \
+            and FID.getXFormCode() > 0:
+        fig = plotting.plot_world_orient(args.t1, args.data)
+        fig.tight_layout()
+        location_fig = os.path.join(args.output, 'voxel_location.png')
+        fig.savefig(location_fig, bbox_inches='tight', facecolor='k')
 
     # Save quick summary figure
     report.fitting_summary_fig(mrs, res,

fsl_mrs/tests/test_mrs_io.py

@@ -7,6 +7,7 @@ Copyright Will Clarke, University of Oxford, 2021'''
 
 import fsl_mrs.utils.mrs_io as mrsio
 import fsl_mrs.utils.mrs_io.fsl_io as fslio
+from fsl_mrs.utils.mrs_io.main import _check_datatype
 from fsl_mrs.utils import plotting
 import numpy as np
 import os.path as op
@@ -150,3 +151,17 @@ def test_fslBasisRegen():
     assert names_fsl2 == names_fsl
     for r in headerReqFields:
         assert headers_fsl[0][r] == headers_fsl2[0][r]
+
+
+def test_check_datatype():
+    '''Check various paths through _check_datatype'''
+
+    assert _check_datatype('fake/path/test.RAW') == 'RAW'
+    assert _check_datatype('fake/path/test.H2O') == 'RAW'
+
+    assert _check_datatype('fake/path/test.txt') == 'TXT'
+
+    assert _check_datatype('fake/path/test.nii') == 'NIFTI'
+    assert _check_datatype('fake/path/test.nii.gz') == 'NIFTI'
+    assert _check_datatype('fake/path/test.blah.nii.gz') == 'NIFTI'
+    assert _check_datatype('fake/path/test.blah.nii') == 'NIFTI'

fsl_mrs/utils/mrs_io/__init__.py

-from fsl_mrs.utils.mrs_io.main import read_FID, read_basis, check_datatype
+from fsl_mrs.utils.mrs_io.main import read_FID, read_basis

fsl_mrs/utils/mrs_io/main.py

@@ -28,28 +28,21 @@ class FileNotRecognisedError(Exception):
 # Reciever bandwidth
 # Dwell time
 # central frequency
-def check_datatype(filename):
+def _check_datatype(filename):
     """
-    Identify the file type (.nii(.gz),.RAW/.H2O,.txt)
-    Returns one of: 'NIFTI_MRS', 'NIFTI','RAW','TXT','Unknown'
+    If data isn't NIFTI_MRS then
+    identify the file type (.nii(.gz),.RAW/.H2O,.txt)
+    Returns one of: 'NIFTI', 'RAW', 'TXT', 'Unknown'
     """
-    try:
-        nifti_mrs.NIFTI_MRS(filename)
-    except (nifti_mrs.NotNIFTI_MRS, fslpath.PathError):
-        _, ext = filename.split(os.extsep, 1)
-        if ext.lower() == 'nii' or ext.lower() == 'nii.gz':
-            fsl.readNIFTI(filename)
-            return 'NIFTI'
-        elif ext.lower() == 'raw' or ext.lower() == 'h2o':
-            lcm.readLCModelRaw(filename)
-            return 'RAW'
-        elif ext.lower() == 'txt':
-            jmrui.readjMRUItxt(filename)
-            return 'TXT'
-        else:
-            return 'Unknown'
+    _, ext = filename.split(os.extsep, 1)
+    if 'nii' in ext.lower() or 'nii.gz' in ext.lower():
+        return 'NIFTI'
+    elif ext.lower() == 'raw' or ext.lower() == 'h2o':
+        return 'RAW'
+    elif ext.lower() == 'txt':
+        return 'TXT'
     else:
-        return 'NIFTI_MRS'
+        return 'Unknown'
 
 
 def read_FID(filename):
@@ -68,7 +61,7 @@ def read_FID(filename):
     try:
         return nifti_mrs.NIFTI_MRS(filename)
     except (nifti_mrs.NotNIFTI_MRS, fslpath.PathError):
-        data_type = check_datatype(filename)
+        data_type = _check_datatype(filename)
 
     if data_type == 'RAW':
         return lcm.read_lcm_raw_h2o(filename)