Bump version to 2.1.0, updated documentation, removed skips from some unit tests

CHANGELOG.md

@@ -1,3 +1,7 @@
+## [2.1.0] - 2016-01-16
+### ADDED
+- `select` now supports `start` and `stop` keyword arguments to put bounds on images
+
 ## [2.0.2] - 2016-01-06
 ### ADDED
 - `Nd2.pixel_microns` gives the width of a pixel

README.md

@@ -70,10 +70,16 @@ array([[1894, 1949, 1941, ..., 2104, 2135, 2114],
 
 If you only want to view images that meet certain criteria, you can use `select()`. It's much faster than iterating
 and checking attributes of images manually. You can specify scalars or lists of values. Criteria that aren't specified
-default to every possible value. Currently, slicing and selecting can't be done at the same time:
+default to every possible value. Currently, slicing and selecting can't be done at the same time, but you can
+set a range with the `start` and `stop` arguments:
 
 ```python
 for image in nd2.select(channels="GFP", fields_of_view=(1, 2, 7)):
+    # gets all GFP images in fields of view 1, 2 and 7, regardless of z-level or frame
+    do_something(image)
+
+for image in nd2.select(z_levels=(0, 1), start=12, stop=3000):
+    # gets images of any channel or field of view, with z-level 0 or 1, between images 12 and 3000
     do_something(image)
 ```
 
@@ -102,12 +108,14 @@ my_important_image = nd2[17]
 The `Nd2` object has some programmatically-accessible metadata: 
 
 ```python
->>> nd2.height
+>>> nd2.height  # in pixels
 1280
->>> nd2.width
+>>> nd2.width  # in pixels
 800
->>> len(nd2)
+>>> len(nd2)  # the number of images
 30528
+>>> nd2.pixel_microns  # the width of a pixel in microns
+0.22
 ```
 
 Each camera has its own settings. If you image multiple wavelengths with one camera, each channel will appear as its

functional_tests/FYLM141111001.py

@@ -213,3 +213,6 @@ class FYLM141111Tests(unittest.TestCase):
         direct_duration = time.time() - direct_start
         self.assertEqual(select_count, direct_count)
         self.assertGreater(direct_duration, select_duration)
+
+    def test_pixel_microns(self):
+        self.assertEqual(round(self.nd2.pixel_microns, 2), 0.22)

functional_tests/monocycle.py

@@ -81,11 +81,9 @@ class Monocycle2Tests(unittest.TestCase):
     def tearDown(self):
         self.nd2.close()
 
-    @unittest.skip('missing file')
     def test_pixel_size(self):
-        self.assertGreater(self.nd2.pixel_microns, 0.0)
+        self.assertGreater(round(self.nd2.pixel_microns, 2), 0.26)
 
-    @unittest.skip('missing file')
     def test_select(self):
         manual_images = []
         for _, image in zip(range(20), self.nd2):
@@ -106,7 +104,6 @@ class Monocycle2Tests(unittest.TestCase):
             self.assertEqual(a.field_of_view, b.field_of_view)
             self.assertEqual(a.channel, b.channel)
 
-    @unittest.skip('missing file')
     def test_select_order_all(self):
         # If we select every possible image using select(), we should just get every image in order
         n = 0
@@ -125,7 +122,6 @@ class Monocycle2Tests(unittest.TestCase):
                 # If there's a problem, we'll have seen it by now.
                 break
 
-    @unittest.skip('missing file')
     def test_select_order_subset(self):
         # Test that images are always yielded in increasing order. This guarantees that no matter what subset of images
         # we're filtering, we still get them in the chronological order they were acquired

nd2reader/__init__.py

@@ -1,3 +1,3 @@
 from nd2reader.main import Nd2
 
-__version__ = '2.0.2'
+__version__ = '2.1.0'

setup.py

@@ -1,6 +1,6 @@
 from setuptools import setup
 
-VERSION = '2.0.2'
+VERSION = '2.1.0'
 
 if __name__ == '__main__':
     setup(