From c489e7a5fdd3a26bf8744e11992cc8f6aa3d8392 Mon Sep 17 00:00:00 2001
From: William T Clarke <william.clarke@ndcn.ox.ac.uk>
Date: Sun, 5 Feb 2023 20:55:24 +0000
Subject: [PATCH] Tweaks to DICOM error handling and directory input (#61)

---
 CHANGELOG.md                       |  4 +++-
 spec2nii/Siemens/dicomfunctions.py | 29 +++++++++++++++++++++++------
 spec2nii/spec2nii.py               |  6 +++---
 3 files changed, 29 insertions(+), 10 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index d90c9c3..cb42cea 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,9 +1,11 @@
 This document contains the Spec2nii release history in reverse chronological order.
 
-0.6.2 (Saturday 4th February 2023)
+0.6.2 (Sunday 5th February 2023)
 ----------------------------------
 - Handle HYPER references in SPAR/SDAT pipeline
 - Handle HURCULES/HERMES (smm_svs_herc) sequence in XA twix format.
+- Changed behaviour of Siemens DICOM `spec2nii dicom` to recursively glob directory argument.
+- Better error output when encountering MR Image SOPClassUID.
 
 0.6.1 (Wednesday 18th January 2023)
 -----------------------------------
diff --git a/spec2nii/Siemens/dicomfunctions.py b/spec2nii/Siemens/dicomfunctions.py
index 3f4129d..ce0b7fa 100644
--- a/spec2nii/Siemens/dicomfunctions.py
+++ b/spec2nii/Siemens/dicomfunctions.py
@@ -45,11 +45,19 @@ def xa_or_vx(img):
     elif img.dcm_data.SOPClassUID == '1.2.840.10008.5.1.4.1.1.4.2':
         return 'xa'
     else:
-        raise IncompatibleSOPClassUID(
-            'spec2nii does not recognise this SOPClassUID '
-            f'{img.dcm_data.SOPClassUID}. This data was collected on a'
-            f' {img.dcm_data.SoftwareVersions} baseline scanner.'
-            ' spec2nii is tested on VA-VE, and XA20 and XA30 DICOM files.')
+        if img.dcm_data.SOPClassUID == '1.2.840.10008.5.1.4.1.1.4':
+            raise IncompatibleSOPClassUID(
+                f'spec2nii detected SOPClassUID {img.dcm_data.SOPClassUID}.'
+                ' This normaly contains MR imaging (not spectroscopy) data.'
+                ' This data was collected on a'
+                f' {img.dcm_data.SoftwareVersions} baseline scanner.'
+                ' spec2nii is tested on VA-VE, XA20, and XA30 DICOM files.')
+        else:
+            raise IncompatibleSOPClassUID(
+                'spec2nii does not recognise this SOPClassUID '
+                f'{img.dcm_data.SOPClassUID} as MRS data. This data was collected on a'
+                f' {img.dcm_data.SoftwareVersions} baseline scanner.'
+                ' spec2nii is tested on VA-VE, XA20, and XA30 DICOM files.')
 
 
 def svs_or_CSI(img):
@@ -89,7 +97,16 @@ def multi_file_dicom(files_in, fname_out, tag, verbose):
 
         img = nibabel.nicom.dicomwrappers.wrapper_from_file(fn)
 
-        mrs_type = svs_or_CSI(img)
+        try:
+            mrs_type = svs_or_CSI(img)
+        except IncompatibleSOPClassUID as exc:
+            if len(files_in) == 1:
+                raise exc
+            else:
+                print(f'Skipping {fn}.')
+                print('Raised IncompatibleSOPClassUID error. Moving to next file.')
+                print(f'Message: {str(exc)}\n')
+                continue
 
         if mrs_type == 'SVS':
             specDataCmplx, orientation, dwelltime, meta_obj = process_siemens_svs(img, verbose=verbose)
diff --git a/spec2nii/spec2nii.py b/spec2nii/spec2nii.py
index dae8a7a..26dad77 100644
--- a/spec2nii/spec2nii.py
+++ b/spec2nii/spec2nii.py
@@ -415,9 +415,9 @@ def dicom(self, args):
         path_in = Path(args.file)
         if path_in.is_dir():
             # Look for typical dicom file extensions
-            files_in = sorted(path_in.glob('*.IMA')) + \
-                sorted(path_in.glob('*.ima')) + \
-                sorted(path_in.glob('*.dcm'))
+            files_in = sorted(path_in.rglob('*.IMA')) + \
+                sorted(path_in.rglob('*.ima')) + \
+                sorted(path_in.rglob('*.dcm'))
 
             # If none found look for all files
             if len(files_in) == 0: