Browse Source

Extend unit tests

feature/load_slices
Ruben Verweij 8 years ago
parent
commit
a5417099b0
8 changed files with 71 additions and 18 deletions
  1. +4
    -4
      nd2reader/artificial.py
  2. +1
    -1
      nd2reader/common.py
  3. +5
    -2
      nd2reader/legacy.py
  4. +12
    -5
      nd2reader/raw_metadata.py
  5. +10
    -5
      tests/test_common.py
  6. +9
    -0
      tests/test_parser.py
  7. +17
    -1
      tests/test_raw_metadata.py
  8. +13
    -0
      tests/test_reader.py

+ 4
- 4
nd2reader/artificial.py View File

@ -9,9 +9,9 @@ class ArtificialND2(object):
"""Artificial ND2 class (for testing purposes)
"""
def __init__(self, file):
def __init__(self, file, version=(3, 0)):
self._fh = open(file, 'wb')
self.write_version()
self.write_version(version)
def __enter__(self):
return self
@ -35,14 +35,14 @@ class ArtificialND2(object):
if self._fh is not None:
self._fh.close()
def write_version(self):
def write_version(self, version=(3, 0)):
"""Write file header
"""
# write 16 empty bytes
self._fh.write(bytearray(16))
# write version info
version_info = six.b('ND2 FILE SIGNATURE CHUNK NAME01!Ver3.0')
version_info = six.b('ND2 FILE SIGNATURE CHUNK NAME01!Ver%s.%s' % version)
self._fh.write(version_info)
@staticmethod


+ 1
- 1
nd2reader/common.py View File

@ -54,7 +54,7 @@ def read_chunk(fh, chunk_location):
bytes: the data at the chunk location
"""
if chunk_location is None:
if chunk_location is None or fh is None:
return None
fh.seek(chunk_location)
# The chunk metadata is always 16 bytes long


+ 5
- 2
nd2reader/legacy.py View File

@ -91,7 +91,7 @@ class Nd2(object):
int: the pixel height of the image
"""
return self.reader.metadata["height"] if self.reader.metadata["height"] is not None else 0
return self._get_width_or_height("height")
@property
def width(self):
@ -101,7 +101,10 @@ class Nd2(object):
int: the pixel width of the image
"""
return self.reader.metadata["width"] if self.reader.metadata["width"] is not None else 0
return self._get_width_or_height("width")
def _get_width_or_height(self, key):
return self.reader.metadata[key] if self.reader.metadata[key] is not None else 0
@property
def z_levels(self):


+ 12
- 5
nd2reader/raw_metadata.py View File

@ -140,14 +140,21 @@ class RawMetadata(object):
textinfo = self.image_text_info[six.b('SLxImageTextInfo')].values()
for line in textinfo:
if six.b("Dimensions:") in line:
entries = line.split(six.b("\r\n"))
for entry in entries:
if entry.startswith(six.b("Dimensions:")):
return entry
entry = self._parse_dimension_text_line(line)
if entry is not None:
return entry
return dimension_text
@staticmethod
def _parse_dimension_text_line(line):
if six.b("Dimensions:") in line:
entries = line.split(six.b("\r\n"))
for entry in entries:
if entry.startswith(six.b("Dimensions:")):
return entry
return None
def _parse_dimension(self, pattern):
dimension_text = self._parse_dimension_text()
if dimension_text is None:


+ 10
- 5
tests/test_common.py View File

@ -1,4 +1,3 @@
import io
import unittest
from os import path
import six
@ -6,7 +5,7 @@ import struct
from nd2reader.artificial import ArtificialND2
from nd2reader.common import get_version, parse_version, parse_date, _add_to_metadata, _parse_unsigned_char, \
_parse_unsigned_int, _parse_unsigned_long, _parse_double, _parse_string
_parse_unsigned_int, _parse_unsigned_long, _parse_double
from nd2reader.exceptions import InvalidVersionError
@ -56,6 +55,12 @@ class TestCommon(unittest.TestCase):
result = parse_date(textinfo)
self.assertEqual(result.strftime(date_format), date)
def test_parse_date_exception(self):
date = 'i am no date'
textinfo = {six.b('TextInfoItem9'): six.b(date)}
result = parse_date(textinfo)
self.assertIsNone(result)
def test_add_to_meta_simple(self):
metadata = {}
_add_to_metadata(metadata, 'test', 'value')
@ -72,9 +77,9 @@ class TestCommon(unittest.TestCase):
self.assertDictEqual(metadata, {'test': ['value1', 'value2', 'value3']})
@staticmethod
def _prepare_bin_stream(format, value):
file = io.BytesIO()
data = struct.pack(format, value)
def _prepare_bin_stream(binary_format, value):
file = six.BytesIO()
data = struct.pack(binary_format, value)
file.write(data)
file.seek(0)
return file


+ 9
- 0
tests/test_parser.py View File

@ -1,6 +1,7 @@
import unittest
from os import path
from nd2reader.artificial import ArtificialND2
from nd2reader.exceptions import InvalidVersionError
from nd2reader.parser import Parser
@ -12,6 +13,7 @@ class TestParser(unittest.TestCase):
def setUp(self):
dir_path = path.dirname(path.realpath(__file__))
self.test_file = path.join(dir_path, 'test_data/test.nd2')
self.create_test_nd2()
def test_can_open_test_file(self):
self.create_test_nd2()
@ -19,3 +21,10 @@ class TestParser(unittest.TestCase):
with open(self.test_file, 'rb') as fh:
parser = Parser(fh)
self.assertTrue(parser.supported)
def test_cannot_open_wrong_version(self):
with ArtificialND2(self.test_file, version=('a', 'b')) as artificial:
artificial.close()
with open(self.test_file, 'rb') as fh:
self.assertRaises(InvalidVersionError, Parser, fh)

+ 17
- 1
tests/test_raw_metadata.py View File

@ -1,10 +1,15 @@
import unittest
from nd2reader.artificial import ArtificialND2
from nd2reader.label_map import LabelMap
from nd2reader.raw_metadata import RawMetadata
class TestRawMetadata(unittest.TestCase):
def setUp(self):
self.metadata = RawMetadata(None, None)
self.raw_text, self.locations = ArtificialND2.create_label_map_bytes()
self.label_map = LabelMap(self.raw_text)
self.metadata = RawMetadata(None, self.label_map)
def test_parse_roi_shape(self):
self.assertEqual(self.metadata._parse_roi_shape(3), 'rectangle')
@ -16,3 +21,14 @@ class TestRawMetadata(unittest.TestCase):
self.assertEqual(self.metadata._parse_roi_type(2), 'background')
self.assertEqual(self.metadata._parse_roi_type(4), 'stimulation')
self.assertIsNone(self.metadata._parse_roi_type(-1))
def test_dict(self):
self.assertTrue(type(self.metadata.__dict__) is dict)
def test_parsed_metadata(self):
metadata = self.metadata.get_parsed_metadata()
self.assertTrue(type(metadata) is dict)
required_keys = ["height", "width", "date", "fields_of_view", "frames", "z_levels", "total_images_per_channel",
"channels", "pixel_microns"]
for required in required_keys:
self.assertTrue(required in metadata)

+ 13
- 0
tests/test_reader.py View File

@ -3,6 +3,7 @@ from os import path
import numpy as np
from nd2reader.artificial import ArtificialND2
from nd2reader.parser import Parser
from nd2reader.reader import ND2Reader
@ -28,3 +29,15 @@ class TestReader(unittest.TestCase):
def test_extension(self):
self.assertTrue('nd2' in ND2Reader.class_exts())
def test_get_metadata_property(self):
self.create_test_nd2()
with ND2Reader(self.test_file) as reader:
self.assertIsNone(reader._get_metadata_property('kljdf'))
self.assertEqual(reader._get_metadata_property('kljdf', 'default'), 'default')
def test_get_parser(self):
self.create_test_nd2()
with ND2Reader(self.test_file) as reader:
self.assertTrue(type(reader.parser) is Parser)

Loading…
Cancel
Save