Merge pull request #22 from WMAPernice/fix-missing-frames-issue_to-current-master

Fix to allow reading of ND2-files with missing frames.

nd2reader/exceptions.py

@@ -6,17 +6,6 @@ class InvalidVersionError(Exception):
     """
     pass
 
-
-class NoImageError(Exception):
-    """No image found.
-
-    Some apparent images in ND2s are just completely blank placeholders. These are used when the number of images per
-    cycle are unequal (e.g. if you take fluorescent images every 2 minutes, and bright field images every minute).
-
-    """
-    pass
-
-
 class EmptyFileError(Exception):
     """This .nd2 file seems to be empty.
 

nd2reader/parser.py

@@ -3,11 +3,12 @@ import struct
 
 import array
 import six
+import warnings
 from pims.base_frames import Frame
 import numpy as np
 
 from nd2reader.common import get_version, read_chunk
-from nd2reader.exceptions import InvalidVersionError, NoImageError
+from nd2reader.exceptions import InvalidVersionError
 from nd2reader.label_map import LabelMap
 from nd2reader.raw_metadata import RawMetadata
 
@@ -72,7 +73,7 @@ class Parser(object):
         try:
             timestamp, image = self._get_raw_image_data(image_group_number, channel_offset, self.metadata["height"],
                                                         self.metadata["width"])
-        except (TypeError, NoImageError):
+        except (TypeError):
             return Frame([], frame_no=frame_number, metadata=self._get_frame_metadata())
         else:
             return image
@@ -101,7 +102,7 @@ class Parser(object):
         try:
             timestamp, raw_image_data = self._get_raw_image_data(image_group_number, channel,
                                                                  height, width)
-        except (TypeError, NoImageError):
+        except (TypeError):
             return Frame([], frame_no=frame_number, metadata=self._get_frame_metadata())
         else:
             return raw_image_data
@@ -284,7 +285,12 @@ class Parser(object):
         if np.any(image_data):
             return timestamp, Frame(image_data, metadata=self._get_frame_metadata())
 
-        raise NoImageError
+        # If a blank "gap" image is encountered, generate an array of corresponding height and width to avoid 
+        # errors with ND2-files with missing frames. Array is filled with nan to reflect that data is missing. 
+        else:
+            empty_frame = np.full((height, width), np.nan)
+            warnings.warn('ND2 file contains gap frames which are represented by np.nan-filled arrays; to convert to zeros use e.g. np.nan_to_num(array)')
+            return timestamp, Frame(empty_frame, metadata=self._get_frame_metadata())  
 
     def _get_frame_metadata(self):
         """Get the metadata for one frame