Merge branch 'master' of github.com:rbnvrw/nd2reader

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
@@ -140,6 +141,7 @@ class Parser(object):
         self._label_map = self._build_label_map()
         self._raw_metadata = RawMetadata(self._fh, self._label_map)
         self.metadata = self._raw_metadata.__dict__
+        self.acquisition_times = self._raw_metadata.acquisition_times
 
     def _build_label_map(self):
         """
@@ -283,7 +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

nd2reader/raw_metadata.py

@@ -43,9 +43,10 @@ class RawMetadata(object):
             "fields_of_view": self._parse_fields_of_view(),
             "frames": self._parse_frames(),
             "z_levels": self._parse_z_levels(),
+            "z_coordinates": parse_if_not_none(self.z_data, self._parse_z_coordinates),
             "total_images_per_channel": frames_per_channel,
             "channels": self._parse_channels(),
-            "pixel_microns": parse_if_not_none(self.image_calibration, self._parse_calibration),
+            "pixel_microns": parse_if_not_none(self.image_calibration, self._parse_calibration)
         }
 
         self._set_default_if_not_empty('fields_of_view')
@@ -161,6 +162,14 @@ class RawMetadata(object):
         """
         return self._parse_dimension(r""".*?Z\((\d+)\).*?""")
 
+    def _parse_z_coordinates(self):
+        """The coordinate in micron for all z planes.
+
+        Returns:
+            list: the z coordinates in micron
+        """
+        return self.z_data.tolist()
+
     def _parse_dimension_text(self):
         """While there are metadata values that represent a lot of what we want to capture, they seem to be unreliable.
         Sometimes certain elements don't exist, or change their data type randomly. However, the human-readable text
@@ -193,7 +202,7 @@ class RawMetadata(object):
         if not match:
             return []
         count = int(match.group(1))
-        return list(range(count))
+        return range(count)
 
     def _parse_total_images_per_channel(self):
         """The total number of images per channel.
@@ -492,7 +501,12 @@ class RawMetadata(object):
         Returns:
             dict: z_data
         """
-        return read_array(self._fh, 'double', self._label_map.z_data)
+        try:
+            return read_array(self._fh, 'double', self._label_map.z_data)
+        except ValueError:
+            # Depending on the file format/exact settings, this value is
+            # sometimes saved as float instead of double
+            return read_array(self._fh, 'float', self._label_map.z_data)
 
     @property
     def roi_metadata(self):

nd2reader/reader.py

@@ -52,6 +52,11 @@ class ND2Reader(FramesSequenceND):
         except KeyError:
             return 0
 
+    def get_frame_2D(self, c=0, t=0, z=0, x=0, y=0, v=0):
+        """Fallback function for backwards compatibility
+        """
+        return get_frame_vczyx(v=v, c=c, t=t, z=z, x=x, y=y)
+
     def get_frame_vczyx(self, v=None, c=None, t=None, z=None, x=None, y=None):
         x = self.metadata["width"] if x <= 0 else x
         y = self.metadata["height"] if y <= 0 else y