Merge pull request #29 from jimrybarski/4-feature-image-set-storage

4 feature image set storage

nd2reader/__init__.py

@@ -10,7 +10,7 @@ import struct
 
 log = logging.getLogger(__name__)
 log.addHandler(logging.StreamHandler())
-log.setLevel(logging.WARN)
+log.setLevel(logging.DEBUG)
 
 
 class Nd2(Nd2Parser):
@@ -19,12 +19,6 @@ class Nd2(Nd2Parser):
         self._use_image_sets = image_sets
 
     def __iter__(self):
-        if self._use_image_sets:
-            return self.image_sets()
-        else:
-            return self.images()
-
-    def images(self):
         for i in range(self._image_count):
             for fov in range(self.field_of_view_count):
                 for z_level in range(self.z_level_count):
@@ -33,6 +27,7 @@ class Nd2(Nd2Parser):
                         if image.is_valid:
                             yield image
 
+    @property
     def image_sets(self):
         for time_index in xrange(self.time_index_count):
             image_set = ImageSet()
@@ -42,7 +37,7 @@ class Nd2(Nd2Parser):
                         image = self.get_image(time_index, fov, channel_name, z_level)
                         if image.is_valid:
                             image_set.add(image)
-            yield image_set
+                yield image_set
 
     def get_image(self, time_index, fov, channel_name, z_level):
         image_set_number = self._calculate_image_set_number(time_index, fov, z_level)
@@ -83,23 +78,22 @@ class Nd2(Nd2Parser):
 
     @property
     def absolute_start(self):
-        if self._absolute_start is None:
-            for line in self.metadata['ImageTextInfo']['SLxImageTextInfo'].values():
-                absolute_start_12 = None
-                absolute_start_24 = None
-                # ND2s seem to randomly switch between 12- and 24-hour representations.
-                try:
-                    absolute_start_24 = datetime.strptime(line, "%m/%d/%Y  %H:%M:%S")
-                except ValueError:
-                    pass
-                try:
-                    absolute_start_12 = datetime.strptime(line, "%m/%d/%Y  %I:%M:%S %p")
-                except ValueError:
-                    pass
-                if not absolute_start_12 and not absolute_start_24:
-                    continue
-                self._absolute_start = absolute_start_12 if absolute_start_12 else absolute_start_24
-        return self._absolute_start
+        for line in self.metadata['ImageTextInfo']['SLxImageTextInfo'].values():
+            absolute_start_12 = None
+            absolute_start_24 = None
+            # ND2s seem to randomly switch between 12- and 24-hour representations.
+            try:
+                absolute_start_24 = datetime.strptime(line, "%m/%d/%Y  %H:%M:%S")
+            except ValueError:
+                pass
+            try:
+                absolute_start_12 = datetime.strptime(line, "%m/%d/%Y  %I:%M:%S %p")
+            except ValueError:
+                pass
+            if not absolute_start_12 and not absolute_start_24:
+                continue
+            return absolute_start_12 if absolute_start_12 else absolute_start_24
+        raise ValueError("This ND2 has no recorded start time. This is probably a bug.")
 
     @property
     def channel_count(self):
@@ -181,4 +175,4 @@ class Nd2(Nd2Parser):
         return timestamp, image_data[image_data_start::self.channel_count]
 
     def _calculate_image_set_number(self, time_index, fov, z_level):
-        return time_index * self.field_of_view_count * self.z_level_count + (fov * self.z_level_count + z_level)
+        return time_index * self.field_of_view_count * self.z_level_count + (fov * self.z_level_count + z_level)

nd2reader/model/__init__.py

@@ -1,3 +1,4 @@
+import collections
 import numpy as np
 import logging
 
@@ -22,10 +23,10 @@ class Image(object):
     @property
     def timestamp(self):
         """
-        The number of seconds after the beginning of the acquisition that the image was taken. Note that for a given field
-        of view and z-level offset, if you have images of multiple channels, they will all be given the same timestamp.
-        No, this doesn't make much sense. But that's how ND2s are structured, so if your experiment depends on millisecond
-        accuracy, you need to find an alternative imaging system.
+        The number of seconds after the beginning of the acquisition that the image was taken. Note that for a given
+        field of view and z-level offset, if you have images of multiple channels, they will all be given the same
+        timestamp. No, this doesn't make much sense. But that's how ND2s are structured, so if your experiment depends
+        on millisecond accuracy, you need to find an alternative imaging system.
 
         """
         return self._timestamp / 1000.0
@@ -47,6 +48,16 @@ class Image(object):
 
     @property
     def is_valid(self):
+        """
+        Not every image stored in an ND2 is a real image! If you take 4 images at one field of view and 2 at another
+        in a repeating cycle, there will be 4 images at BOTH field of view. The 2 non-images are the same size as all
+        the other images, only pure black (i.e. every pixel has a value of zero).
+
+        This is probably an artifact of some algorithm in NIS Elements determining the maximum number of possible
+        images and pre-allocating the space with zeros. Regardless of why they exit, we can't tell that they're
+        not actual images until we examine the data. If every pixel value is exactly 0, it's a gap image.
+
+        """
         return np.any(self._raw_data)
 
 
@@ -57,15 +68,27 @@ class ImageSet(object):
 
     """
     def __init__(self):
-        self._images = []
+        self._images = collections.defaultdict(dict)
+
+    def get(self, channel="", z_level=0):
+        """
+        Retrieve an image with a given channel and z-level. For most users, z_level will always be 0.
+
+        """
+        try:
+            image = self._images[channel][z_level]
+        except KeyError:
+            return None
+        else:
+            return image
+
+    def __len__(self):
+        """ The number of images in the image set. """
+        return sum([len(channel) for channel in self._images.values()])
 
     def add(self, image):
         """
         :type image:    nd2reader.model.Image()
 
         """
-        self._images.append(image)
-
-    def __iter__(self):
-        for image in self._images:
-            yield image
+        self._images[image.channel][image.z_level] = image