From d5b5b97eb2847cee0ecd90cf8c7b3173baddd14f Mon Sep 17 00:00:00 2001
From: Alexander R Craven <12934018+alexcraven@users.noreply.github.com>
Date: Mon, 11 Nov 2024 14:58:47 +0100
Subject: [PATCH] Added non-English character tests to test_ge_pfile

Corresponding test data https://github.com/user-attachments/files/17702724/GE_character_encoding_test_data.zip expected under spec2nii_test_data/ge/pFiles/PRESS/MR30.1
---
 tests/test_ge_pfile.py | 92 +++++++++++++++++++++++++++++++++++++-----
 1 file changed, 82 insertions(+), 10 deletions(-)

diff --git a/tests/test_ge_pfile.py b/tests/test_ge_pfile.py
index 4489409..dcaba00 100644
--- a/tests/test_ge_pfile.py
+++ b/tests/test_ge_pfile.py
@@ -35,8 +35,12 @@
 # HBCD / ISTHMUS datasets
 hbcd2_path = ge_path / 'pFiles' / 'hbcd' / 'P31744.7'
 
+# Test set from Bergen (MR30.1, non-English characters in header text)
+bergen_press_301 = ge_path / 'pFiles' / 'PRESS' / 'MR30.1' / 'P30101.7'
+bergen_press_301_non_english = ge_path / 'pFiles' / 'PRESS' / 'MR30.1' / 'P30104.7'
 
-def test_svs(tmp_path):
+
+def testsvs(tmp_path):
 
     subprocess.check_call(['spec2nii', 'ge',
                            '-f', 'svs',
@@ -68,7 +72,7 @@ def test_svs(tmp_path):
     assert np.isclose(hdr_ext['RepetitionTime'], 2.0)
 
 
-def test_mrsi(tmp_path):
+def testmrsi(tmp_path):
 
     subprocess.check_call(['spec2nii', 'ge',
                            '-f', 'mrsi',
@@ -90,7 +94,7 @@ def test_mrsi(tmp_path):
     assert hdr_ext['OriginalFile'][0] == mrsi_path.name
 
 
-def test_mpress(tmp_path):
+def testmpress(tmp_path):
 
     subprocess.check_call(['spec2nii', 'ge',
                            '-f', 'mpress',
@@ -123,7 +127,7 @@ def test_mpress(tmp_path):
     assert np.isclose(hdr_ext['RepetitionTime'], 2.0)
 
 
-def test_mm_hercules(tmp_path):
+def testmm_hercules(tmp_path):
     for path in mm_herc:
         subprocess.run([
             'spec2nii', 'ge',
@@ -160,7 +164,7 @@ def test_mm_hercules(tmp_path):
         assert hdr_ext_ref['dim_7'] == 'DIM_EDIT'
 
 
-def test_mm_hermes(tmp_path):
+def testmm_hermes(tmp_path):
     for path in mm_hermes:
         subprocess.run([
             'spec2nii', 'ge',
@@ -196,7 +200,7 @@ def test_mm_hermes(tmp_path):
         assert hdr_ext_ref['dim_7'] == 'DIM_EDIT'
 
 
-def test_mm_mega(tmp_path):
+def testmm_mega(tmp_path):
     for path in mm_mega.rglob('*.7'):
         subprocess.run([
             'spec2nii', 'ge',
@@ -238,7 +242,7 @@ def test_mm_mega(tmp_path):
         assert hdr_ext_ref['dim_7'] == 'DIM_EDIT'
 
 
-def test_mm_press(tmp_path):
+def testmm_press(tmp_path):
     for path in mm_press.rglob('*.7'):
         subprocess.run([
             'spec2nii', 'ge',
@@ -273,7 +277,7 @@ def test_mm_press(tmp_path):
         assert hdr_ext_ref['dim_6'] == 'DIM_DYN'
 
 
-def test_mm_press_noid(tmp_path):
+def testmm_press_noid(tmp_path):
     subprocess.run([
         'spec2nii', 'ge',
         '-f', mm_press_noid.stem,
@@ -300,7 +304,7 @@ def test_mm_press_noid(tmp_path):
     assert hdr_ext_ref['dim_5'] == 'DIM_COIL'
 
 
-def test_mm_slaser(tmp_path):
+def testmm_slaser(tmp_path):
     subprocess.run([
         'spec2nii', 'ge',
         '-f', mm_slaser.stem,
@@ -327,7 +331,7 @@ def test_mm_slaser(tmp_path):
     assert hdr_ext_ref['dim_5'] == 'DIM_COIL'
 
 
-def test_hbcd_isthmus(tmp_path):
+def testhbcd_isthmus(tmp_path):
     subprocess.run([
         'spec2nii', 'ge',
         '-f', 'hbcd',
@@ -355,3 +359,71 @@ def test_hbcd_isthmus(tmp_path):
     img = NIFTI_MRS(tmp_path / 'hbcd_short_te.nii.gz')
     assert img.shape == (1, 1, 1, 2048, 32, 8)
     assert img.dim_tags == ['DIM_DYN', 'DIM_COIL', None]
+
+
+def testsvs_bergen_301(tmp_path):
+
+    subprocess.check_call(['spec2nii', 'ge',
+                           '-f', 'svs',
+                           '-o', tmp_path,
+                           '-j',
+                           str(bergen_press_301)])
+
+    img, hdr_ext = read_nifti_mrs_with_hdr(tmp_path / 'svs.nii.gz')
+    img_ref, hdr_ext_ref  = read_nifti_mrs_with_hdr(tmp_path / 'svs_ref.nii.gz')
+
+    assert img.shape == (1, 1, 1, 4096, 48, 2)
+    assert np.iscomplexobj(img.dataobj)
+    assert 1 / img.header['pixdim'][4] == 5000.0
+    assert hdr_ext['WaterSuppressed']
+
+    assert img_ref.shape == (1, 1, 1, 4096, 48, 2)
+    assert np.iscomplexobj(img_ref.dataobj)
+    assert 1 / img_ref.header['pixdim'][4] == 5000.0
+    assert not hdr_ext_ref['WaterSuppressed']
+
+    assert hdr_ext['dim_5'] == 'DIM_COIL'
+    assert hdr_ext['dim_6'] == 'DIM_DYN'
+    assert np.isclose(127.7, hdr_ext['SpectrometerFrequency'][0], atol=1E-1)
+    assert hdr_ext['ResonantNucleus'][0] == '1H'
+
+    assert np.isclose(hdr_ext['EchoTime'], 0.03)
+    assert np.isclose(hdr_ext['RepetitionTime'], 2.0)
+
+    assert hdr_ext['PatientName'] == 'fantom'
+    assert hdr_ext['SequenceName'] == 'PROBE-P'
+    assert hdr_ext['ProtocolName'] == 'PROBE-P'
+
+
+def testsvs_bergen_301_non_english(tmp_path):
+
+    subprocess.check_call(['spec2nii', 'ge',
+                           '-f', 'svs',
+                           '-o', tmp_path,
+                           '-j',
+                           str(bergen_press_301_non_english)])
+
+    img, hdr_ext = read_nifti_mrs_with_hdr(tmp_path / 'svs.nii.gz')
+    img_ref, hdr_ext_ref  = read_nifti_mrs_with_hdr(tmp_path / 'svs_ref.nii.gz')
+
+    assert img.shape == (1, 1, 1, 4096, 48, 2)
+    assert np.iscomplexobj(img.dataobj)
+    assert 1 / img.header['pixdim'][4] == 5000.0
+    assert hdr_ext['WaterSuppressed']
+
+    assert img_ref.shape == (1, 1, 1, 4096, 48, 2)
+    assert np.iscomplexobj(img_ref.dataobj)
+    assert 1 / img_ref.header['pixdim'][4] == 5000.0
+    assert not hdr_ext_ref['WaterSuppressed']
+
+    assert hdr_ext['dim_5'] == 'DIM_COIL'
+    assert hdr_ext['dim_6'] == 'DIM_DYN'
+    assert np.isclose(127.7, hdr_ext['SpectrometerFrequency'][0], atol=1E-1)
+    assert hdr_ext['ResonantNucleus'][0] == '1H'
+
+    assert np.isclose(hdr_ext['EchoTime'], 0.03)
+    assert np.isclose(hdr_ext['RepetitionTime'], 2.0)
+
+    assert hdr_ext['PatientName'] == 'fantom^prøve'
+    assert hdr_ext['SequenceName'] == 'PROBE-P'
+    assert hdr_ext['ProtocolName'] == 'PROBE-P åøæäöÅØÆÄÖ'