fix(e2e_format.py): change the name of E2EFile to E2EFormat to avoid …

…confustion with E2EFileStructure in e2e_reader.py

docs/formats/he_e2e_structures/he_e2e_structure_doc.md

@@ -3,7 +3,7 @@ In contrast to the VOL and XML exports the E2E data may contain several OCT volu
 # File Structure
 The first bytes in an E2E file contain a version structure followed by a header structure. The header gives you access to the rest of the file by identifying the position of the last chunk of data. Each chunk has exactly 512 elements which we call folders.
 
-{{ get_structure_doc("E2EFile") }}
+{{ get_structure_doc("E2EFormat") }}
 
 ### Chunk
 Every chunk has a header similar to the file header. A chunk then holds the headers of all contained folders sequentially, followed by data containers, that are referenced by the folder headers. A chunk can contain folders with data of different patients, studies, series, slices and types. Each folder contains data for a single (patient, study, series, slice, type) combination which is given in the folder header as well as the data container header. For the last chunk to have 512 folders, empty folders of `type=0` are appended.
@@ -30,23 +30,23 @@ In the following sections we describe the data items we found in each level of t
 
 ### Slice Data
 
-{{ get_hierarchy_doc("E2ESlice") }}
+{{ get_hierarchy_doc("E2ESliceStructure") }}
 
 ### Series Data
 
-{{ get_hierarchy_doc("E2ESeries") }}
+{{ get_hierarchy_doc("E2ESeriesStructure") }}
 
 ### Study Data
 
-{{ get_hierarchy_doc("E2EStudy") }}
+{{ get_hierarchy_doc("E2EStudyStructure") }}
 
 ### Patient Data
 
-{{ get_hierarchy_doc("E2EPatient") }}
+{{ get_hierarchy_doc("E2EPatientStructure") }}
 
 ### General Data
 
-{{ get_hierarchy_doc("E2EFile") }}
+{{ get_hierarchy_doc("E2EFileStructure") }}
 
 
 ## Further observations

src/eyepy/io/he/e2e_format.py

@@ -740,7 +740,7 @@ class Version(DataclassMixin):
 
 
 @dataclasses.dataclass
-class E2EFile(DataclassMixin):
+class E2EFormat(DataclassMixin):
     """E2E file format
 
     Size: variable
@@ -759,10 +759,10 @@ class E2EFile(DataclassMixin):
         doc="The number and size of the chunks depends on the data")
 
 
-e2e_format = DataclassStruct(E2EFile)
+e2e_format = DataclassStruct(E2EFormat)
 
 __e2efile_structures__ = [
-    E2EFile,
+    E2EFormat,
     Version,
     Chunk,
     Header,

src/eyepy/io/he/e2e_reader.py

@@ -5,6 +5,7 @@
 import logging
 from pathlib import Path
 from textwrap import indent
+import traceback
 from typing import Any, Dict, List, Optional, Tuple, Union
 
 import construct as cs
@@ -419,12 +420,7 @@ def get_volume(self) -> EyeVolume:
         ## Check if scan is a volume scan
         volume_meta = self.get_meta()
 
-        size_x = volume_meta["bscan_meta"][0]["size_x"]
-        size_y = volume_meta["bscan_meta"][0]["size_y"]
         scan_pattern = volume_meta["bscan_meta"][0]["scan_pattern"]
-        n_bscans = volume_meta["bscan_meta"][0]["n_bscans"] if len(
-            self.get_bscan_meta()
-        ) != 1 else 1  # n_bscans is 0 instead of 1 for single B-scan Volumes in the e2e file.
 
         ## Check if scan pattern is supported by EyeVolume
         if scan_pattern == 2:
@@ -434,13 +430,7 @@ def get_volume(self) -> EyeVolume:
             msg = f"The EyeVolume object does not support scan pattern 5 (Radial scan - star pattern)."
             raise ValueError(msg)
 
-        data = np.zeros((n_bscans, size_y, size_x))
-        for ind, sl in self.slices.items():
-            bscan = sl.get_image()
-            i = ind // 2 if len(
-                self.get_bscan_meta()
-            ) != 1 else 0  # Slice id for single B-scan Volumes is 2 and not 0 in the e2e file.
-            data[i] = bscan
+        data = self.get_bscans()
 
         volume_meta = self.get_meta()
         localizer = self.get_localizer()
@@ -459,6 +449,23 @@ def get_volume(self) -> EyeVolume:
 
         return volume
 
+    def get_bscans(self) -> np.ndarray:
+        volume_meta = self.get_meta()
+        size_x = volume_meta["bscan_meta"][0]["size_x"]
+        size_y = volume_meta["bscan_meta"][0]["size_y"]
+        n_bscans = volume_meta["bscan_meta"][0]["n_bscans"] if len(
+            self.get_bscan_meta()
+        ) != 1 else 1  # n_bscans is 0 instead of 1 for single B-scan Volumes in the e2e file.
+
+        data = np.zeros((n_bscans, size_y, size_x))
+        for ind, sl in self.slices.items():
+            bscan = sl.get_image()
+            i = ind // 2 if len(
+                self.get_bscan_meta()
+            ) != 1 else 0  # Slice id for single B-scan Volumes is 2 and not 0 in the e2e file.
+            data[i] = bscan
+        return data
+
     def get_layers(self) -> Dict[int, np.ndarray]:
         """Return layer height maps for the series as dict of numpy arrays where the key is the layer id."""
         slice_layers = {}
@@ -883,7 +890,14 @@ def volume(self) -> EyeVolume:
         Returns:
             EyeVolume object for the first Series in the e2e file.
         """
-        return self.series[0].get_volume()
+        for s in self.series:
+            try:
+                return s.get_volume()
+            except Exception as e:
+                logger.debug("".join(traceback.format_exception(e)))
+        raise ValueError(
+            "No Series in the E2E file can be parsed to a an EyeVolume object. You might be able to extract information manually from the E2ESeries objects (e2ereader.series)"
+        )
 
     @property
     def volumes(self) -> List[EyeVolume]:
@@ -892,4 +906,10 @@ def volumes(self) -> List[EyeVolume]:
         Returns:
             List with EyeVolume objects for every Series in the e2e file.
         """
-        return [s.get_volume() for s in self.series]
+        volumes = []
+        for s in self.series:
+            try:
+                volumes.append(s.get_volume())
+            except Exception as e:
+                logger.debug("".join(traceback.format_exception(e)))
+        return volumes