finished read_quicknii_xml

Co-authored-by: Estelle Nassar <estelle.nassar@crick.ac.uk>

slicereg/io/xml/reader.py

@@ -1,19 +1,29 @@
 from dataclasses import dataclass
+from _pytest.monkeypatch import V
+import xmltodict
 
 
 @dataclass
 class QuickNiiResult:
     ox: float
-    # oy: float 
-    # oz: float
-    # ux: float 
-    # uy: float
-    # uz: float
-    # vx: float 
-    # vy: float
-    # vz: float
+    oy: float 
+    oz: float
+    ux: float 
+    uy: float
+    uz: float
+    vx: float 
+    vy: float
+    vz: float
 
 
 def read_quicknii_xml(filename: str):
-    data = QuickNiiResult(ox=475.8982543945312)
+    with open(filename, mode='rb') as f:
+        metadata = xmltodict.parse(f)
+    anchoring = metadata['series']['slice']['@anchoring']
+    coords = {(kv := pair.split('='))[0]: float(kv[1]) for pair in anchoring.split('&')}
+    data = QuickNiiResult(
+        ox=coords['ox'], oy=coords['oy'], oz=coords['oz'], 
+        ux=coords['ux'], uy=coords['uy'], uz=coords['uz'], 
+        vx=coords['vx'], vy=coords['vy'], vz=coords['vz'],
+    )
     return data

slicereg/io/xml/tests/test_xml.py

@@ -1,14 +1,14 @@
 from slicereg.io.xml.reader import read_quicknii_xml
-
+from pytest import approx
 
 def test_xml_read_function_gets_transformation_properties_from_example_quicknii_file():
     output = read_quicknii_xml(filename='data/deepslice_output/results.xml')
-    assert output.ox == 475.8982543945312
-    # assert output.oy == 260.47747802734375
-    # assert output.oz == 346.73419189453125
-    # assert output.ux == -481.19720458984375
-    # assert output.uy == 5.9310126304626465
-    # assert output.uz == 8.603763580322266
-    # assert output.vx == -21.585269927978516
-    # assert output.vy == -4.721147060394287
-    # assert output.vz == -389.2110595703125
+    assert output.ox == approx(475.8982543945312)
+    assert output.oy == approx(260.47747802734375)
+    assert output.oz == approx(346.73419189453125)
+    assert output.ux == approx(-481.19720458984375)
+    assert output.uy == approx(5.9310126304626465)
+    assert output.uz == approx(8.603763580322266)
+    assert output.vx == approx(-21.585269927978516)
+    assert output.vy == approx(-4.721147060394287)
+    assert output.vz == approx(-389.2110595703125)