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MedVisBonn · Feb 10, 2021 · b6833a1 · b6833a1
1 parent 1bb8f33
commit b6833a1
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Showing 2 changed files with 21 additions and 4 deletions.
diff --git a/eyepy/core/base.py b/eyepy/core/base.py
@@ -297,15 +297,15 @@ def drusen(self):
         return self._oct_obj.drusen[..., self.index]
 
     def plot(self, ax=None, layers=None, drusen=False, layers_kwargs=None,
-             layers_color=None, annotation_only=False, region=np.s_[:,:]):
+             layers_color=None, annotation_only=False, region=np.s_[:, :]):
         """ Plot B-Scan with segmented Layers """
         if ax is None:
             ax = plt.gca()
 
         if layers is None:
             layers = []
         elif layers == "all":
-            layers = config.SEG_MAPPING.keys()
+            layers = self.layers.keys()
 
         if layers_kwargs is None:
             layers_kwargs = config.layers_kwargs
@@ -328,8 +328,9 @@ def plot(self, ax=None, layers=None, drusen=False, layers_kwargs=None,
             try:
                 layer_data = self.layers[layer]
                 if region[0].start is not None:
-                    layer_data -= region[0].start
-                ax.plot(layer_data, color=color, label=layer,
+                    layer_data = layer_data - region[0].start
+                ax.plot(layer_data[region[1].start:region[1].stop],
+                        color=color, label=layer,
                         **layers_kwargs)
             except KeyError:
                 warnings.warn(f"Layer '{layer}' has no Segmentation",
@@ -449,6 +450,21 @@ def from_heyex_vol(cls, path):
                    localizer=reader.localizer,
                    meta=reader.oct_meta,
                    data_path=Path(path).parent)
+    @classmethod
+    def from_duke_mat(cls, path):
+        import scipy.io as sio
+        loaded = sio.loadmat(path)
+        data = np.moveaxis(loaded["images"], -1, 0)
+        label = np.swapaxes(loaded["layerMaps"], 1, 2)
+
+        bscans = []
+        mapping = {"BM": 2, "RPE": 1, "ILM": 0}
+        for d, l in zip(data, label):
+            annotation = Annotation({"layers": LayerAnnotation(l, mapping)})
+            bscans.append(Bscan(d, annotation=annotation))
+        return cls(bscans=bscans,
+                   meta=Meta(**{"Age": loaded["Age"]}),
+                   data_path=Path(path).parent)
 
     @classmethod
     def from_folder(cls, path):

diff --git a/eyepy/io/heyex/xml_export.py b/eyepy/io/heyex/xml_export.py
@@ -147,3 +147,4 @@ def layers_dict(bscan_obj):
                 f"{bscan_obj} contains no segmentation", UserWarning)
 
         return {"layers": layers_dict, }
+