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resolves #152: images truly act like numpy arrays now and are also displayable

feature/load_slices
jim 9 years ago
parent
commit
4a48847630
5 changed files with 16 additions and 5 deletions
  1. +1
    -1
      Makefile
  2. +11
    -0
      functional_tests/FYLM141111001.py
  3. +1
    -1
      nd2reader/__init__.py
  4. +2
    -2
      nd2reader/model/image.py
  5. +1
    -1
      setup.py

+ 1
- 1
Makefile View File

@ -31,7 +31,7 @@ test: build
ftest: build ftest: build
xhost local:root; docker run --rm -v /tmp/.X11-unix:/tmp/.X11-unix -e DISPLAY=unix$(DISPLAY) -v $(CURDIR):/opt/nd2reader -v ~/nd2s:/var/nd2s -it jimrybarski/nd2reader python3.4 /opt/nd2reader/ftest.py xhost local:root; docker run --rm -v /tmp/.X11-unix:/tmp/.X11-unix -e DISPLAY=unix$(DISPLAY) -v $(CURDIR):/opt/nd2reader -v ~/nd2s:/var/nd2s -it jimrybarski/nd2reader python3.4 /opt/nd2reader/ftest.py
docker run --rm -v $(CURDIR):/opt/nd2reader -v ~/nd2s:/var/nd2s -it jimrybarski/nd2reader python2.7 /opt/nd2reader/ftest.py
xhost local:root; docker run --rm -v /tmp/.X11-unix:/tmp/.X11-unix -e DISPLAY=unix$(DISPLAY) -v $(CURDIR):/opt/nd2reader -v ~/nd2s:/var/nd2s -it jimrybarski/nd2reader python2.7 /opt/nd2reader/ftest.py
publish: publish:
python setup.py sdist upload -r pypi python setup.py sdist upload -r pypi

+ 11
- 0
functional_tests/FYLM141111001.py View File

@ -4,6 +4,7 @@ run them unless you're Jim Rybarski.
""" """
from nd2reader import Nd2 from nd2reader import Nd2
from skimage import io
import numpy as np import numpy as np
from datetime import datetime from datetime import datetime
import unittest import unittest
@ -227,3 +228,13 @@ class FYLM141111Tests(unittest.TestCase):
mean = np.mean(self.nd2[0]) mean = np.mean(self.nd2[0])
self.assertEqual(type(mean), np.float64) self.assertEqual(type(mean), np.float64)
self.assertAlmostEqual(expected_mean, mean) self.assertAlmostEqual(expected_mean, mean)
def test_subtract_images(self):
# just to prove we can really treat Image like an array
diff = self.nd2[0] - self.nd2[2]
self.assertTrue(np.any(diff))
def test_show(self):
io.imshow(self.nd2[0])
io.show()
self.assertTrue(True)

+ 1
- 1
nd2reader/__init__.py View File

@ -1,3 +1,3 @@
from nd2reader.main import Nd2 from nd2reader.main import Nd2
__version__ = '2.1.2'
__version__ = '2.1.3'

+ 2
- 2
nd2reader/model/image.py View File

@ -19,11 +19,11 @@ class Image(np.ndarray):
self._channel = None self._channel = None
self._z_level = None self._z_level = None
def __array_wrap__(self, obj):
def __array_wrap__(self, obj, *args):
if len(obj.shape) == 0: if len(obj.shape) == 0:
return obj[()] return obj[()]
else: else:
return np.ndarray.__array_wrap__(obj)
return obj
def add_params(self, index, timestamp, frame_number, field_of_view, channel, z_level): def add_params(self, index, timestamp, frame_number, field_of_view, channel, z_level):
""" """


+ 1
- 1
setup.py View File

@ -1,6 +1,6 @@
from setuptools import setup from setuptools import setup
VERSION = '2.1.2'
VERSION = '2.1.3'
if __name__ == '__main__': if __name__ == '__main__':
setup( setup(


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