image validity test, iterator for all images

nd2reader/__init__.py

@@ -12,10 +12,19 @@ class Nd2(BaseNd2):
         super(Nd2, self).__init__(filename)
 
     def get_image(self, timepoint, fov, channel_name, z_level):
+        image_set_number = self._calculate_image_set_number(timepoint, fov, z_level)
+        timestamp, raw_image_data = self._reader.get_raw_image_data(image_set_number, self.channel_offset[channel_name])
+        return Image(timestamp, raw_image_data, self.height, self.width)
+
+    def __iter__(self):
         """
-        Everything here is zero-indexed.
+        Just return every image.
 
         """
-        image_set_number = self._calculate_image_set_number(timepoint, fov, z_level)
-        timestamp, raw_image_data = self._reader.get_raw_image_data(image_set_number, self.channel_offset[channel_name])
-        return Image(timestamp, raw_image_data, self.height, self.width)
+        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):
+                    for channel in self.channels:
+                        image = self.get_image(i, fov, channel.name, z_level)
+                        if image.is_valid:
+                            yield image

nd2reader/model/__init__.py

@@ -57,6 +57,10 @@ class Image(object):
     def data(self):
         return self._data
 
+    @property
+    def is_valid(self):
+        return np.any(self._data)
+
     def show(self):
         skimage.io.imshow(self.data)
         skimage.io.show()

nd2reader/service/__init__.py

@@ -25,6 +25,25 @@ class BaseNd2(object):
     def width(self):
         return self._metadata['ImageAttributes']['SLxImageAttributes']['uiWidth']
 
+    @property
+    def channels(self):
+        metadata = self._metadata['ImageMetadataSeq']['SLxPictureMetadata']['sPicturePlanes']
+        try:
+            validity = self._metadata['ImageMetadata']['SLxExperiment']['ppNextLevelEx']['']['ppNextLevelEx']['']['pItemValid']
+        except KeyError:
+            # If none of the channels have been deleted, there is no validity list, so we just make one
+            validity = [True for i in metadata]
+        # Channel information is contained in dictionaries with the keys a0, a1...an where the number
+        # indicates the order in which the channel is stored. So by sorting the dicts alphabetically
+        # we get the correct order.
+        for (label, chan), valid in zip(sorted(metadata['sPlaneNew'].items()), validity):
+            if not valid:
+                continue
+            name = chan['sDescription']
+            exposure_time = metadata['sSampleSetting'][label]['dExposureTime']
+            camera = metadata['sSampleSetting'][label]['pCameraSetting']['CameraUserName']
+            yield Channel(name, camera, exposure_time)
+
     @property
     def _image_count(self):
         return self._metadata['ImageAttributes']['SLxImageAttributes']['uiSequenceCount']
@@ -37,28 +56,6 @@ class BaseNd2(object):
     def _timepoint_count(self):
         return self._image_count / self._field_of_view_count / self._z_level_count
 
-    # @property
-    # def _fields_of_view(self):
-    #     """
-    #     Fields of view are the various places in the xy-plane where images were taken.
-    #
-    #     """
-    #     # Grab all the metadata about fields of view
-    #     fov_metadata = self._metadata['ImageMetadata']['SLxExperiment']['ppNextLevelEx']['']
-    #     # The attributes include x, y, and z coordinates, and perfect focus (PFS) offset
-    #     fov_attributes = fov_metadata['uLoopPars']['Points']['']
-    #     # If you crop fields of view from your ND2 file, the metadata is retained and only this list is
-    #     # updated to indicate that the fields of view have been deleted.
-    #     fov_validity = fov_metadata['pItemValid']
-    #     # We only yield valid (i.e. uncropped) fields of view
-    #     for number, (fov, valid) in enumerate(zip(fov_attributes, fov_validity)):
-    #         if valid:
-    #             yield field_of_view(number=number + 1,
-    #                                 x=fov['dPosX'],
-    #                                 y=fov['dPosY'],
-    #                                 z=fov['dPosZ'],
-    #                                 pfs_offset=fov['dPFSOffset'])
-
     @property
     def _z_level_count(self):
         return self._image_count / self._sequence_count
@@ -74,25 +71,6 @@ class BaseNd2(object):
         """
         return sum(self._metadata['ImageMetadata']['SLxExperiment']['ppNextLevelEx']['']['pItemValid'])
 
-    @property
-    def channels(self):
-        metadata = self._metadata['ImageMetadataSeq']['SLxPictureMetadata']['sPicturePlanes']
-        try:
-            validity = self._metadata['ImageMetadata']['SLxExperiment']['ppNextLevelEx']['']['ppNextLevelEx']['']['pItemValid']
-        except KeyError:
-            # If none of the channels have been deleted, there is no validity list, so we just make one
-            validity = [True for i in metadata]
-        # Channel information is contained in dictionaries with the keys a0, a1...an where the number
-        # indicates the order in which the channel is stored. So by sorting the dicts alphabetically
-        # we get the correct order.
-        for (label, chan), valid in zip(sorted(metadata['sPlaneNew'].items()), validity):
-            if not valid:
-                continue
-            name = chan['sDescription']
-            exposure_time = metadata['sSampleSetting'][label]['dExposureTime']
-            camera = metadata['sSampleSetting'][label]['pCameraSetting']['CameraUserName']
-            yield Channel(name, camera, exposure_time)
-
     @property
     def channel_offset(self):
         if self._channel_offset is None:

run.py

@@ -4,16 +4,9 @@ import numpy as np
 from skimage import io
 
 
-n = Nd2("/home/jim/Desktop/nd2hacking/YFP-dsRed-GFP-BF.nd2")
+for image in Nd2("/home/jim/Desktop/nd2hacking/YFP-dsRed-GFP-BF.nd2"):
+
 # n = Nd2("/home/jim/Desktop/nd2hacking/test-141111.nd2")
-# for chan in n.channels:
-#     print(chan.name)
-print(n._reader.channel_count)
-print(n._z_level_count)
-print(n._field_of_view_count)
-print(n._timepoint_count)
 
-# z = n._reader.read_coordinates()
-# print(z)
-# pprint(n._metadata)
-image = n._reader.get_raw_image_data(71, 0)
+
+    image.show()