You can not select more than 25 topics
Topics must start with a letter or number, can include dashes ('-') and can be up to 35 characters long.
79 lines
3.3 KiB
79 lines
3.3 KiB
import unittest
|
|
import numpy as np
|
|
import struct
|
|
|
|
from pims import Frame
|
|
from nd2reader.artificial import ArtificialND2
|
|
from nd2reader.exceptions import EmptyFileError, InvalidFileType
|
|
from nd2reader.reader import ND2Reader
|
|
from nd2reader.parser import Parser
|
|
|
|
|
|
class TestReader(unittest.TestCase):
|
|
def test_invalid_file_extension(self):
|
|
self.assertRaises(InvalidFileType, lambda: ND2Reader('test_data/invalid_extension_file.inv'))
|
|
|
|
def test_extension(self):
|
|
self.assertTrue('nd2' in ND2Reader.class_exts())
|
|
|
|
def cmp_two_readers(self, r1, r2):
|
|
attributes = r1.data['image_attributes']['SLxImageAttributes']
|
|
self.assertEqual(r2.metadata['width'], attributes['uiWidth'])
|
|
self.assertEqual(r2.metadata['height'], attributes['uiHeight'])
|
|
|
|
self.assertEqual(r2.metadata['width'], r2.sizes['x'])
|
|
self.assertEqual(r2.metadata['height'], r2.sizes['y'])
|
|
|
|
self.assertEqual(r2.pixel_type, np.float64)
|
|
self.assertEqual(r2.iter_axes, ['t'])
|
|
|
|
def test_init_and_init_axes(self):
|
|
with ArtificialND2('test_data/test_nd2_reader.nd2') as artificial:
|
|
with ND2Reader('test_data/test_nd2_reader.nd2') as reader:
|
|
self.cmp_two_readers(artificial, reader)
|
|
|
|
def test_init_from_handler(self):
|
|
with ArtificialND2('test_data/test_nd2_reader.nd2') as artificial:
|
|
with open('test_data/test_nd2_reader.nd2', "rb") as FH:
|
|
with ND2Reader(FH) as reader:
|
|
self.cmp_two_readers(artificial, reader)
|
|
|
|
def test_init_empty_file(self):
|
|
with ArtificialND2('test_data/empty.nd2', skip_blocks=['label_map_marker']):
|
|
with self.assertRaises(EmptyFileError) as exception:
|
|
with ND2Reader('test_data/empty.nd2'):
|
|
pass
|
|
self.assertEqual(str(exception.exception), "No axes were found for this .nd2 file.")
|
|
|
|
def test_get_parser(self):
|
|
with ArtificialND2('test_data/test_nd2_reader.nd2') as _:
|
|
with ND2Reader('test_data/test_nd2_reader.nd2') as reader:
|
|
self.assertIsInstance(reader.parser, Parser)
|
|
|
|
def test_get_timesteps(self):
|
|
with ArtificialND2('test_data/test_nd2_reader.nd2') as _:
|
|
with ND2Reader('test_data/test_nd2_reader.nd2') as reader:
|
|
timesteps = reader.timesteps
|
|
self.assertEquals(len(timesteps), 0)
|
|
|
|
def test_get_frame_zero(self):
|
|
# Best test we can do for now:
|
|
# test everything up to the actual unpacking of the frame data
|
|
with ArtificialND2('test_data/test_nd2_reader.nd2') as _:
|
|
with ND2Reader('test_data/test_nd2_reader.nd2') as reader:
|
|
|
|
with self.assertRaises(struct.error) as exception:
|
|
frame = reader[0]
|
|
|
|
self.assertIn('unpack', str(exception.exception))
|
|
|
|
def test_get_frame_2D(self):
|
|
# Best test we can do for now:
|
|
# test everything up to the actual unpacking of the frame data
|
|
with ArtificialND2('test_data/test_nd2_reader.nd2') as _:
|
|
with ND2Reader('test_data/test_nd2_reader.nd2') as reader:
|
|
|
|
with self.assertRaises(struct.error) as exception:
|
|
frame = reader.get_frame_2D(c=0, t=0, z=0, x=0, y=0, v=0)
|
|
|
|
self.assertIn('unpack', str(exception.exception))
|