fix(EyeVolumeMeta): fixes saving issue by storing all dates as string…

… in isoformat to avoid problems with dumping to json and loading

pyproject.toml

@@ -4,7 +4,7 @@ packages = [
     {include = "eyepy", from = "src"},
 ]
 version = "0.11.0"
-description = "The Python package for working with ophthalmological data."
+description = "A python package to read, analyse and visualize OCT and fundus data form various sources."
 authors = ["Olivier Morelle <oli4morelle@gmail.com>"]
 license = "MIT"
 readme = "README.md"

src/eyepy/core/eyemeta.py

@@ -26,9 +26,6 @@ def as_dict(self) -> dict:
 
         """
         data = self._store.copy()
-        for key in ['visit_date', 'exam_time']:
-            if key in data.keys() and data[key] is not None:
-                data[key] = data[key].isoformat()
         return data
 
     def __getitem__(self, key: str) -> Any:
@@ -47,7 +44,8 @@ def __len__(self) -> int:
         return len(self._store)
 
     def __str__(self) -> str:
-        return f'{os.linesep}'.join([f'{f}: {self[f]}' for f in self if f != '__empty'])
+        return f'{os.linesep}'.join(
+            [f'{f}: {self[f]}' for f in self if f != '__empty'])
 
     def __repr__(self) -> str:
         return self.__str__()
@@ -56,7 +54,8 @@ def __repr__(self) -> str:
 class EyeEnfaceMeta(EyeMeta):
     """"""
 
-    def __init__(self, scale_x: float, scale_y: float, scale_unit: str, **kwargs) -> None:
+    def __init__(self, scale_x: float, scale_y: float, scale_unit: str,
+                 **kwargs) -> None:
         """A dict with required keys to hold meta data for enface images of the
         eye.
 
@@ -66,9 +65,10 @@ def __init__(self, scale_x: float, scale_y: float, scale_unit: str, **kwargs) ->
             scale_unit: Unit of the scale. e.g. µm if scale is given in µm/pixel
             **kwargs:
         """
-        super().__init__(
-            scale_x=scale_x, scale_y=scale_y, scale_unit=scale_unit, **kwargs
-        )
+        super().__init__(scale_x=scale_x,
+                         scale_y=scale_y,
+                         scale_unit=scale_unit,
+                         **kwargs)
 
     @classmethod
     def from_dict(cls, data: dict) -> 'EyeEnfaceMeta':
@@ -104,9 +104,12 @@ def __init__(
             pos_unit: Unit of the positions
             **kwargs:
         """
-        super().__init__(
-            start_pos=start_pos, end_pos=end_pos, pos_unit=pos_unit, **kwargs
-        )
+        start_pos = tuple(start_pos)
+        end_pos = tuple(end_pos)
+        super().__init__(start_pos=start_pos,
+                         end_pos=end_pos,
+                         pos_unit=pos_unit,
+                         **kwargs)
 
 
 class EyeVolumeMeta(EyeMeta):
@@ -161,7 +164,4 @@ def from_dict(cls, data: dict) -> 'EyeVolumeMeta':
 
         """
         data['bscan_meta'] = [EyeBscanMeta(**d) for d in data['bscan_meta']]
-        for key in ['visit_date', 'exam_time']:
-            if key in data.keys() and data[key] is not None:
-                data[key] = datetime.datetime.fromisoformat(data[key])
         return cls(**data)

src/eyepy/core/eyevolume.py

@@ -26,8 +26,6 @@
 from eyepy.core.eyemeta import EyeBscanMeta
 from eyepy.core.eyemeta import EyeEnfaceMeta
 from eyepy.core.eyemeta import EyeVolumeMeta
-from eyepy.core.plotting import plot_scalebar
-from eyepy.core.plotting import plot_watermark
 from eyepy.core.utils import intensity_transforms
 
 logger = logging.getLogger('eyepy.core.eyevolume')

src/eyepy/io/he/e2e_format.py

@@ -92,12 +92,13 @@ class DateTimeAdapter(cs.Adapter):
                                     minute=0)
 
     def _decode(self, obj: bytes, context, path):
-        return self.start_epoch + datetime.timedelta(
-            seconds=cs.Int64ul.parse(obj) * 1e-7)
+        return (self.start_epoch + datetime.timedelta(
+            seconds=cs.Int64ul.parse(obj) * 1e-7)).isoformat()
 
-    def _encode(self, obj: datetime.datetime, context, path):
+    def _encode(self, obj: str, context, path):
         return cs.Int64ul.build(
-            int((obj - self.start_epoch).total_seconds() * 1e7))
+            int((datetime.datetime.fromisoformat(obj) -
+                 self.start_epoch).total_seconds() * 1e7))
 
 
 LocalizerNIR = LocalizerNIRAdapter(cs.Bytes(cs.this.n_values))

src/eyepy/io/he/e2e_reader.py

@@ -608,7 +608,7 @@ def get_meta(self) -> EyeVolumeMeta:
                 scale_z=1,  #get_bscan_spacing(bscan_meta) if
                 #(bscan_meta[0]["scan_pattern"] not in [1, 2]) else 0.03,
                 scale_unit='px',
-                laterality=self.laterality,
+                laterality=self.laterality(),
                 visit_date=None,
                 exam_time=None,
                 bscan_meta=bscan_meta,

src/eyepy/io/he/xml_reader.py

@@ -16,7 +16,6 @@
 from eyepy.core.eyevolume import EyeVolume
 from eyepy.io.utils import _compute_localizer_oct_transform
 from eyepy.io.utils import _get_date_from_xml
-from eyepy.io.utils import _get_datetime_from_xml
 from eyepy.io.utils import _get_first_as_float
 from eyepy.io.utils import _get_first_as_int
 from eyepy.io.utils import _get_first_as_str

src/eyepy/io/utils.py

@@ -100,7 +100,7 @@ def _get_date_from_xml(elements):
     except IndexError:
         year = month = day = 1
 
-    return datetime(year, month, day).date()
+    return datetime(year, month, day).isoformat()
 
 
 def _compute_localizer_oct_transform(
@@ -137,10 +137,11 @@ def get_date_adapter(construct, epoch, second_frac):
     class DateAdapter(cs.Adapter):
 
         def _decode(self, obj, context, path):
-            return epoch + timedelta(seconds=obj * second_frac)
+            return (epoch + timedelta(seconds=obj * second_frac)).isoformat()
 
         def _encode(self, obj, context, path):
-            return int((obj - epoch).total_seconds() / second_frac)
+            return (datetime.fromisoformat(obj) -
+                    epoch).total_seconds() / second_frac
 
     return DateAdapter(construct)
 

tests/test_eyevolume.py

@@ -141,12 +141,13 @@ def test_delete_voxel_annotation(eyevolume):
     assert 'delete_volume' not in eyevolume[2].area_maps
 
 
+# Saving is not possible when executed by GitHub Actions
 #def test_save_load(eyevolume, tmp_path):
 #    # Save
-#    eyevolume.save(tmp_path / "test.eye")
+#    eyevolume.save(tmp_path / 'test.eye')
 #    # Load
-#    eyevolume2 = ep.EyeVolume.load(tmp_path / "test.eye")
+#    eyevolume2 = ep.EyeVolume.load(tmp_path / 'test.eye')
 #    # Test whether loaded eyevolume is the same as the original
-#    assert len(eyevolume.meta) == len(eyevolume2.meta)
+#    assert eyevolume.meta == eyevolume2.meta
 #    assert len(eyevolume.layers) == len(eyevolume2.layers)
 #    assert len(eyevolume.volume_maps) == len(eyevolume2.volume_maps)

tests/test_eyevolumemeta.py

@@ -0,0 +1,26 @@
+import eyepy as ep
+
+
+def test_eyevolumemeta_json_conversion():
+    meta_dict = {
+        'scale_z':
+        1,
+        'scale_x':
+        1,
+        'scale_y':
+        1,
+        'scale_unit':
+        'px',
+        'bscan_meta': [{
+            'start_pos': (0, 0),
+            'end_pos': [10, 0],
+            'pos_unit': 'px'
+        }, {
+            'start_pos': (0, 1),
+            'end_pos': [10, 1],
+            'pos_unit': 'px'
+        }]
+    }
+
+    evm = ep.EyeVolumeMeta.from_dict(meta_dict)
+    assert evm.as_dict() == meta_dict