From 97455bc3786c5ae017ff2904d91a7e86d0d89ea6 Mon Sep 17 00:00:00 2001
From: Alexander R Craven <12934018+alexcraven@users.noreply.github.com>
Date: Tue, 5 Nov 2024 14:39:23 +0100
Subject: [PATCH] Fix lint errors in updated GE reader

---
 spec2nii/GE/ge_pfile.py      | 10 +++++++---
 spec2nii/GE/ge_read_pfile.py | 10 +++++-----
 2 files changed, 12 insertions(+), 8 deletions(-)

diff --git a/spec2nii/GE/ge_pfile.py b/spec2nii/GE/ge_pfile.py
index 4de2aa4..4af6bd4 100644
--- a/spec2nii/GE/ge_pfile.py
+++ b/spec2nii/GE/ge_pfile.py
@@ -90,7 +90,7 @@ def _process_svs_pfile(pfile):
     :return: List of file name suffixes
     """
 
-    assert(pfile.encoding is not None) # encoding should have been set in ge_read_pfile get_mapper
+    assert pfile.encoding is not None  # encoding should have been set in ge_read_pfile get_mapper
 
     psd = pfile.hdr.rhi_psdname.decode(pfile.encoding, errors='replace').lower()
     proto = pfile.hdr.rhs_se_desc.decode(pfile.encoding, errors='replace').lower()
@@ -433,7 +433,7 @@ def _process_mrsi_pfile(pfile):
     :return: List of file name suffixes
     """
 
-    assert(pfile.encoding is not None) # encoding should have been set in ge_read_pfile get_mapper
+    assert pfile.encoding is not None  # encoding should have been set in ge_read_pfile get_mapper
 
     psd = pfile.hdr.rhi_psdname.decode(pfile.encoding, errors='replace').lower()
 
@@ -591,7 +591,11 @@ def _populate_metadata(pfile, water_suppressed=True, data_dimensions=None):
     # 'TxCoil'
     # Not Known
     # 'RxCoil'
-    meta.set_user_def(key='ReceiveCoilName', value=hdr.rhi_cname.decode(pfile.encoding, errors='replace'), doc='Rx coil name.')
+    meta.set_user_def(
+        key="ReceiveCoilName",
+        value=hdr.rhi_cname.decode(pfile.encoding, errors="replace"),
+        doc="Rx coil name.",
+    )
 
     # # 5.3 Sequence information
     # 'SequenceName'
diff --git a/spec2nii/GE/ge_read_pfile.py b/spec2nii/GE/ge_read_pfile.py
index caf6811..b45b94a 100644
--- a/spec2nii/GE/ge_read_pfile.py
+++ b/spec2nii/GE/ge_read_pfile.py
@@ -194,14 +194,14 @@ def get_mapper(self):
 
                 if psd == "hbcd" and "press" in proto:
                     psd = self.hdr.rhs_se_desc.decode(encoding, errors).lower()
-            except UnicodeDecodeError as err:
+            except UnicodeDecodeError:
                 psd = ""
                 proto = ""
                 continue
             self.encoding = encoding
             break
 
-        assert(self.encoding is not None) # final codec must should have succeeded
+        assert self.encoding is not None  # final codec must should have succeeded
 
         # MM: Some 'gaba' psd strings contain full path names, so truncate to the end of the path
         if psd.endswith('gaba'):
@@ -667,7 +667,7 @@ def get_dcos(self):
 
         dcos[0][0] = (self.hdr.rhi_trhc_R - self.hdr.rhi_tlhc_R)
         dcos[0][1] = (self.hdr.rhi_trhc_A - self.hdr.rhi_tlhc_A)
-        dcos[0][2] =  (self.hdr.rhi_trhc_S - self.hdr.rhi_tlhc_S)
+        dcos[0][2] = (self.hdr.rhi_trhc_S - self.hdr.rhi_tlhc_S)
 
         dcosLengthX = np.sqrt(dcos[0][0] * dcos[0][0]
                               + dcos[0][1] * dcos[0][1]
@@ -679,7 +679,7 @@ def get_dcos(self):
 
         dcos[1][0] = (self.hdr.rhi_brhc_R - self.hdr.rhi_trhc_R)
         dcos[1][1] = (self.hdr.rhi_brhc_A - self.hdr.rhi_trhc_A)
-        dcos[1][2] =  (self.hdr.rhi_brhc_S - self.hdr.rhi_trhc_S)
+        dcos[1][2] = (self.hdr.rhi_brhc_S - self.hdr.rhi_trhc_S)
 
         dcosLengthY = np.sqrt(dcos[1][0] * dcos[1][0]
                               + dcos[1][1] * dcos[1][1]
@@ -1008,7 +1008,7 @@ def read_data(self):
         numTimePts      = self.get_num_time_points
         numSpecPts      = self.hdr.rhr_rh_frame_size
         numFreqPts      = numSpecPts
-        numComponents   =  2
+        numComponents   = 2
         dataWordSize    = self.hdr.rhr_rh_point_size
 
         numBytesInVol   = self.get_num_kspace_points * numSpecPts * numComponents * dataWordSize