Merge pull request #144 from jimrybarski/143-find-pixel-size

143 find pixel size

functional_tests/FYLM141111001.py

@@ -39,6 +39,9 @@ class FYLM141111Tests(unittest.TestCase):
     def test_z_levels(self):
         self.assertTupleEqual(tuple(self.nd2.z_levels), (0, 1, 2))
 
+    def test_pixel_size(self):
+        self.assertGreater(self.nd2.pixel_microns, 0.0)
+
     def test_image(self):
         image = self.nd2[14]
         self.assertEqual(image.field_of_view, 2)

functional_tests/monocycle.py

@@ -17,6 +17,9 @@ class Monocycle1Tests(unittest.TestCase):
     def test_channels(self):
         self.assertListEqual(self.nd2.channels, ['Cy3Narrow', 'TxRed-modified', 'FITC', 'DAPI'])
 
+    def test_pixel_size(self):
+        self.assertGreater(self.nd2.pixel_microns, 0.0)
+
     def test_select(self):
         manual_images = []
         for _, image in zip(range(20), self.nd2):
@@ -78,6 +81,9 @@ class Monocycle2Tests(unittest.TestCase):
     def tearDown(self):
         self.nd2.close()
 
+    def test_pixel_size(self):
+        self.assertGreater(self.nd2.pixel_microns, 0.0)
+
     def test_select(self):
         manual_images = []
         for _, image in zip(range(20), self.nd2):

functional_tests/single.py

@@ -28,6 +28,9 @@ class SingleTests(unittest.TestCase):
     def test_channels(self):
         self.assertEqual(self.nd2.channels, ['Quad Band 2'])
 
+    def test_pixel_size(self):
+        self.assertGreater(self.nd2.pixel_microns, 0.0)
+
     def test_actual_length(self):
         count = 0
         for image in self.nd2:

nd2reader/main.py

@@ -170,6 +170,16 @@ class Nd2(object):
         """
         return self._metadata.date
 
+    @property
+    def pixel_microns(self):
+        """
+        The width of a pixel in microns. Note that the user can override this in NIS Elements so it may not reflect reality.
+
+        :rtype:     float
+
+        """
+        return self._metadata.pixel_microns
+
     def get_image(self, frame_number, field_of_view, channel_name, z_level):
         """
         Attempts to return the image with the unique combination of given attributes. None will be returned if a match

nd2reader/model/metadata.py

@@ -3,7 +3,7 @@ import six
 
 class Metadata(object):
     """ A simple container for ND2 metadata. """
-    def __init__(self, height, width, channels, date, fields_of_view, frames, z_levels, total_images_per_channel):
+    def __init__(self, height, width, channels, date, fields_of_view, frames, z_levels, total_images_per_channel, pixel_microns):
         self._height = height
         self._width = width
         self._channels = channels
@@ -12,6 +12,7 @@ class Metadata(object):
         self._frames = frames
         self._z_levels = z_levels
         self._total_images_per_channel = total_images_per_channel
+        self._pixel_microns = pixel_microns
 
     @property
     def height(self):
@@ -97,6 +98,16 @@ class Metadata(object):
         """
         return self._total_images_per_channel
 
+    @property
+    def pixel_microns(self):
+        """
+        The width of a pixel in microns.
+
+        :rtype:     float
+
+        """
+        return self._pixel_microns
+
 
 class CameraSettings(object):
     """ Contains some basic information about a physical camera and its settings. """

nd2reader/parser/v3.py

@@ -174,7 +174,8 @@ class V3Parser(BaseParser):
         z_levels = self._parse_z_levels(self.raw_metadata)
         total_images_per_channel = self._parse_total_images_per_channel(self.raw_metadata)
         channels = self._parse_channels(self.raw_metadata)
-        self.metadata = Metadata(height, width, channels, date, fields_of_view, frames, z_levels, total_images_per_channel)
+        pixel_microns = self.raw_metadata.image_calibration.get(six.b('SLxCalibration'), {}).get(six.b('dCalibration'))
+        self.metadata = Metadata(height, width, channels, date, fields_of_view, frames, z_levels, total_images_per_channel, pixel_microns)
 
     def _parse_camera_settings(self):
         """