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Very basic Reader test

feature/load_slices
Ruben Verweij 8 years ago
parent
commit
b0f22eb83b
2 changed files with 39 additions and 5 deletions
  1. +17
    -5
      nd2reader/reader.py
  2. +22
    -0
      tests/test_reader.py

+ 17
- 5
nd2reader/reader.py View File

@ -108,15 +108,27 @@ class ND2Reader(FramesSequenceND):
""" """
return self._dtype return self._dtype
def _get_metadata_property(self, key, default=None):
if self.metadata is None:
return default
if key not in self.metadata:
return default
if self.metadata[key] is None:
return default
return self.metadata[key]
def _setup_axes(self): def _setup_axes(self):
"""Setup the xyctz axes, iterate over t axis by default """Setup the xyctz axes, iterate over t axis by default
""" """
self._init_axis('x', self.metadata["width"])
self._init_axis('y', self.metadata["height"])
self._init_axis('c', len(self.metadata["channels"]))
self._init_axis('t', len(self.metadata["frames"]))
self._init_axis('z', len(self.metadata["z_levels"]))
self._init_axis('x', self._get_metadata_property("width", default=0))
self._init_axis('y', self._get_metadata_property("height", default=0))
self._init_axis('c', len(self._get_metadata_property("channels", default=[])))
self._init_axis('t', len(self._get_metadata_property("frames", default=[])))
self._init_axis('z', len(self._get_metadata_property("z_levels", default=[])))
# provide the default # provide the default
self.iter_axes = 't' self.iter_axes = 't'


+ 22
- 0
tests/test_reader.py View File

@ -1,8 +1,30 @@
import unittest import unittest
from os import path
import numpy as np
from nd2reader.artificial import ArtificialND2
from nd2reader.reader import ND2Reader from nd2reader.reader import ND2Reader
class TestReader(unittest.TestCase): class TestReader(unittest.TestCase):
def create_test_nd2(self):
with ArtificialND2(self.test_file) as artificial:
artificial.close()
def setUp(self):
dir_path = path.dirname(path.realpath(__file__))
self.test_file = path.join(dir_path, 'test_data/test.nd2')
def test_can_open_test_file(self):
self.create_test_nd2()
with ND2Reader(self.test_file) as reader:
self.assertEqual(reader.filename, self.test_file)
self.assertEqual(reader.pixel_type, np.float64)
self.assertEqual(reader.sizes['x'], 0)
self.assertEqual(reader.sizes['y'], 0)
self.assertEqual(reader.sizes['z'], 1)
self.assertEqual(reader.sizes['c'], 0)
self.assertEqual(reader.sizes['t'], 1)
def test_extension(self): def test_extension(self):
self.assertTrue('nd2' in ND2Reader.class_exts()) self.assertTrue('nd2' in ND2Reader.class_exts())

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