Fix typos found by codespell (#93)

CHANGELOG.md

@@ -27,7 +27,7 @@ This document contains the Spec2nii release history in reverse chronological ord
 ---------------------------------
 - Added handling for the GE jpress sequence (for JH HURCULES sequence)
 - Added twix handling of the HYPER (smm_svs_herc_hyper) sequence (added by Aaron Gudmundson)
-- Better handling of partial acqusitions of Siemens and Philips HYPER sequence.
+- Better handling of partial acquisitions of Siemens and Philips HYPER sequence.
 
 0.6.7 (Wednesday 15th March 2023)
 ---------------------------------
@@ -63,7 +63,7 @@ This document contains the Spec2nii release history in reverse chronological ord
 - SPAR/SDAT pipeline now handles HYPER special case.
 - Data/list pipeline now handles HYPER special case.
 - Fixed issue with XA Twix PatientSex and TxOffset attributes.
-- Reenable Bruker conversion. 
+- Re-enable Bruker conversion.
 
 0.6.0 (Wednesday 11th January 2023)
 -----------------------------------

spec2nii/Philips/philips_data_list.py

@@ -117,7 +117,7 @@ def read_data_list_pair(data_file, list_file, aux_file, special_case=None):
 
         elif data_type == 'STD_1'\
                 and (special_case == 'hyper' or 'hyper' in meta['ProtocolName'].lower()):
-            # Handle the water ref acqusition of the HYPER sequence
+            # Handle the water ref acquisition of the HYPER sequence
 
             meta.set_dim_info(
                 0,

spec2nii/Siemens/dicomfunctions.py

@@ -48,7 +48,7 @@ def xa_or_vx(img):
         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 normally 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.')
@@ -516,7 +516,7 @@ def set_standard_def(nifti_mrs_key, location, key, cast=None):
             pass
 
     # # 5.1 MRS specific Tags
-    # 'EchoTime' - requires substantial extraction from the full protocol incase there are multiple
+    # 'EchoTime' - requires substantial extraction from the full protocol in case there are multiple
     # sub-values, e.g. summing the three TEs of a sLAASER sequence together.
     fullcsa = csar.get_csa_header(dcmdata.dcm_data, csa_type='series')
     xprot = parse_buffer(fullcsa['tags']['MrPhoenixProtocol']['items'][0])

spec2nii/Siemens/rda.py

@@ -20,7 +20,7 @@ class MRSINotHandledError(Exception):
 
 
 def _locale_float(x):
-    """Handle locale specific flaoting point representations in header
+    """Handle locale specific floating point representations in header
 
     :param x: Header value as string with either . or , decimal separator
     :type x: str

spec2nii/Siemens/twix_special_case.py

@@ -15,8 +15,8 @@ def smm_svs_herc_hyper(twixObj, reord_data, meta_obj, dim_tags, subseq, subseq_n
       a water reference for each.
 
     Data is organized into 4 blocks:
-      1. Short TE Reference : 35ms Unsupressed Water
-      2. Long  TE Reference : 80ms Unsupressed Water
+      1. Short TE Reference : 35ms Unsuppressed Water
+      2. Long  TE Reference : 80ms Unsuppressed Water
       3. Short TE Unedited  : 35ms Water Suppressed PRESS
       4. Long  TE Edited    : 80ms Water Suppressed HERCULES
 

spec2nii/Siemens/twixfunctions.py

@@ -825,7 +825,7 @@ def CSIOrientations(slice_normal, ip_rot, fov_pe, fov_ro, fov_sl, n_pe, n_ro, n_
         base_pos -= slice_normal * (fov_sl / 2 - fov_sl / n_sl / 2)
         fov_sl /= n_sl
 
-    # Sagital
+    # Sagittal
     if mo_case == 0:
         print('Mirror along ROW/readout direction: VB = LIN, VE+ = SEG')
         dRowVec_vector *= -1.0

spec2nii/spec2nii.py

@@ -412,7 +412,7 @@ def auto(self, args):
             setattr(args, 'special', None)
             self.philips(args)
 
-        # Philips DATA/LIST - Reject bcause of unknown aux file format.
+        # Philips DATA/LIST - Reject because of unknown aux file format.
         elif args.file.suffix.lower() in ('.data', '.list'):
             raise Spec2niiError(
                 'Automatic conversion not setup for data/list conversion. '
@@ -450,7 +450,7 @@ def auto(self, args):
                     self.philips_dicom(args)
                 else:
                     raise Spec2niiError(f'Unknown DICOM manufacturer {manufacturer}.')
-            # No sucessful ID as DICOM - fail at automatic load.
+            # No successful ID as DICOM - fail at automatic load.
             except pdcm.errors.InvalidDicomError:
                 raise Spec2niiError(
                     'Unable to automatically identify file type. '