Added drusen saving in data_path/.eyepy folder. Added function to rec…

…ompute drusen if needed with a custom drusenfinder

eyepy/core/octbase.py

@@ -1,5 +1,7 @@
+import hashlib
 import warnings
 from abc import ABC, abstractmethod
+from pathlib import Path
 
 import numpy as np
 from matplotlib import cm, colors, patches
@@ -15,14 +17,14 @@
 
 class Oct(ABC):
 
-    def __new__(cls, bscans, slo, meta, *args, **kwargs):
+    def __new__(cls, bscans, slo, meta, data_path, *args, **kwargs):
         # Set all the meta fields as attributes
         for meta_attr in meta._meta_fields:
             setattr(cls, meta_attr, _get_meta_attr(meta_attr))
         return object.__new__(cls, *args, **kwargs)
 
     @abstractmethod
-    def __init__(self, bscans, enfacereader, meta,
+    def __init__(self, bscans, enfacereader, meta, data_path,
                  drusenfinder=DefaultDrusenFinder(),
                  eyequantifier=DefaultEyeQuantifier()):
         """
@@ -41,6 +43,10 @@ def __init__(self, bscans, enfacereader, meta,
         self._drusenfinder = drusenfinder
         self._eyequantifier = eyequantifier
 
+        # Create a visit_id for saving visit related files
+        self._eyepy_id = None
+        self.data_path = Path(data_path)
+        self.drusen_path = self.data_path / ".eyepy" / f"{self.eyepy_id}_drusen_map.npy"
         self._drusen = None
         self._drusen_raw = None
         self._segmentation_raw = None
@@ -66,6 +72,15 @@ def __len__(self):
         """ The number of B-Scans """
         return len(self._bscans)
 
+    @property
+    def eyepy_id(self):
+        if self._eyepy_id is None:
+            # Compute a hash of the first B-Scan as ID
+            sha1 = hashlib.sha1()
+            sha1.update(self[0].scan.tobytes())
+            self._eyepy_id = sha1.hexdigest()
+        return self._eyepy_id
+
     @property
     @abstractmethod
     def shape(self):
@@ -148,7 +163,25 @@ def drusen(self):
         Here the `filter` function of the DrusenFinder has been applied
         """
         if self._drusen is None:
-            self._drusen = self._drusenfinder.filter(self.drusen_raw)
+            # Try to load the drusen from the default location
+            try:
+                self._drusen = np.load(self.drusen_path)
+            except FileNotFoundError:
+                self._drusen = self._drusenfinder.filter(self.drusen_raw)
+                self.drusen_path.parent.mkdir(parents=True, exist_ok=True)
+                np.save(self.drusen_path, self._drusen)
+        return self._drusen
+
+    def drusen_recompute(self, drusenfinder=None):
+        """ Recompute Drusen optionally with a custom DrusenFinder
+
+        Use this if you do not like the computed / loaded drusen
+        """
+        if drusenfinder is not None:
+            self._drusenfinder = drusenfinder
+
+        self._drusen_raw = self._drusenfinder.find(self)
+        self._drusen = self._drusenfinder.filter(self.drusen_raw)
         return self._drusen
 
     @property

eyepy/io/heyex/heyex.py

@@ -44,7 +44,7 @@ class HeyexOct(Oct):
 
     """
 
-    def __init__(self, bscans, slo, meta):
+    def __init__(self, bscans, slo, meta, data_path):
         """
 
         Parameters
@@ -53,7 +53,7 @@ def __init__(self, bscans, slo, meta):
         slo :
         meta :
         """
-        super().__init__(bscans, slo, meta)
+        super().__init__(bscans, slo, meta, data_path)
 
     @property
     def shape(self):
@@ -64,18 +64,26 @@ def fovea_pos(self):
         return self.SizeXSlo / 2, self.SizeYSlo / 2
 
     @classmethod
-    def read_vol(cls, file_obj):
+    def read_vol(cls, file_obj, data_path):
         meta = he_vol.get_octmeta(file_obj)
         bscans = he_vol.get_bscans(file_obj, meta)
         slo = he_vol.get_slo(file_obj, meta)
-        return cls(bscans, slo, meta)
+        return cls(bscans, slo, meta, data_path=data_path)
 
     @classmethod
     def read_xml(cls, filepath):
-        meta = he_xml.get_octmeta(filepath)
-        bscans = he_xml.get_bscans(filepath)
-        slo = he_xml.get_slo(filepath)
-        return cls(bscans, slo, meta)
+        path = Path(filepath)
+        if not path.suffix == ".xml":
+            xmls = list(path.glob("*.xml"))
+            if len(xmls) == 0:
+                raise FileNotFoundError("There is no .xml file under the given filepath")
+            elif len(xmls) > 1:
+                raise ValueError("There is more than one .xml file under the given filepath.")
+            path = xmls[0]
+        meta = he_xml.get_octmeta(path)
+        bscans = he_xml.get_bscans(path)
+        slo = he_xml.get_slo(path)
+        return cls(bscans, slo, meta, data_path=path.parent)
 
     @classmethod
     def from_images(cls, images):
@@ -97,10 +105,10 @@ def read_vol(file_obj: Union[str, Path, IO]):
     if type(file_obj) is str or type(file_obj) is PosixPath:
         with open(file_obj, "rb") as myfile:
             mm = mmap.mmap(myfile.fileno(), 0, access=mmap.ACCESS_READ)
-            return HeyexOct.read_vol(mm)
+            return HeyexOct.read_vol(mm, data_path=Path(file_obj).parent)
     else:
         mm = mmap.mmap(file_obj.fileno(), 0, access=mmap.ACCESS_READ)
-        return HeyexOct.read_vol(mm)
+        return HeyexOct.read_vol(mm, data_path=Path(file_obj.name).parent)
 
 
 def read_xml(filepath: Union[str, Path]):