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import warnings
import numpy as np
from pynwb import TimeSeries
from pynwb.base import Image, Images, ImageReferences
from pynwb.device import Device
from pynwb.image import (
ImageSeries,
IndexSeries,
ImageMaskSeries,
OpticalSeries,
GrayscaleImage,
RGBImage,
RGBAImage,
)
from pynwb.testing import TestCase
class ImageSeriesConstructor(TestCase):
def test_init(self):
dev = Device('test_device')
iS = ImageSeries(
name='test_iS',
unit='unit',
external_file=['external_file'],
starting_frame=[0],
format='external',
timestamps=[1., 2., 3.],
device=dev,
)
self.assertEqual(iS.name, 'test_iS')
self.assertEqual(iS.unit, 'unit')
self.assertEqual(iS.external_file, ['external_file'])
self.assertEqual(iS.starting_frame, [0])
self.assertEqual(iS.format, 'external')
self.assertIs(iS.device, dev)
# self.assertEqual(iS.bits_per_pixel, np.nan)
def test_no_data_no_file(self):
msg = "Must supply either external_file or data to ImageSeries 'test_iS'."
with self.assertRaisesWith(ValueError, msg):
ImageSeries(
name='test_iS',
unit='unit',
rate=2.,
)
def test_external_file_no_frame(self):
iS = ImageSeries(
name='test_iS',
unit='unit',
external_file=['external_file'],
format="external",
timestamps=[1., 2., 3.]
)
self.assertListEqual(iS.starting_frame, [0])
def test_data_no_frame(self):
iS = ImageSeries(
name='test_iS',
unit='unit',
data=np.ones((3, 3, 3)),
timestamps=[1., 2., 3.]
)
self.assertIsNone(iS.starting_frame)
def test_data_no_unit(self):
msg = "Must supply 'unit' argument when supplying 'data' to ImageSeries 'test_iS'."
with self.assertRaisesWith(ValueError, msg):
ImageSeries(
name='test_iS',
data=np.ones((3, 3, 3)),
timestamps=list()
)
def test_external_file_no_unit(self):
iS = ImageSeries(
name='test_iS',
external_file=['external_file'],
format="external",
timestamps=list()
)
self.assertEqual(iS.unit, ImageSeries.DEFAULT_UNIT)
def test_dimension_warning(self):
"""Test that a warning is raised when the dimensions of the data are not the
same as the dimensions of the timestamps."""
msg = (
"ImageSeries 'test_iS': Length of data does not match length of timestamps. Your data may be "
"transposed. Time should be on the 0th dimension"
)
with self.assertWarnsWith(UserWarning, msg):
ImageSeries(
name='test_iS',
data=np.ones((3, 3, 3)),
unit='Frames',
timestamps=[1, 2, 3, 4]
)
def test_dimension_warning_external_file_with_timestamps(self):
"""Test that a warning is not raised when external file is used with timestamps."""
with warnings.catch_warnings(record=True) as w:
ImageSeries(
name='test_iS',
external_file=['external_file'],
format='external',
unit='Frames',
starting_frame=[0],
timestamps=[1, 2, 3, 4]
)
self.assertEqual(w, [])
def test_dimension_warning_external_file_with_rate(self):
"""Test that a warning is not raised when external file is used with rate."""
with warnings.catch_warnings(record=True) as w:
ImageSeries(
name='test_iS',
external_file=['external_file'],
format='external',
unit='Frames',
starting_frame=[0],
rate=0.2,
)
self.assertEqual(w, [])
def test_external_file_with_incorrect_starting_frame(self):
"""Test that ValueError is raised when the length of starting_frame
is not the same as the length of external_file."""
for starting_frame in [None, [0], [1, 2, 3]]:
with self.subTest():
msg = (
"ImageSeries 'test_iS': The number of frame indices in "
"'starting_frame' should have the same length as 'external_file'."
)
with self.assertRaisesWith(ValueError, msg):
ImageSeries(
name="test_iS",
external_file=["external_file", "external_file2"],
format="external",
unit="n.a.",
starting_frame=starting_frame,
rate=0.2,
)
def test_external_file_with_incorrect_starting_frame_construct_mode(self):
"""Test that warning is raised when the length of starting_frame
is not the same as the length of external_file in case that the
ImageSeries in construct mode (i.e., during read)."""
for starting_frame in [None, [0], [1, 2, 3]]:
with self.subTest():
msg = (
"ImageSeries 'test_iS': The number of frame indices in "
"'starting_frame' should have the same length as 'external_file'."
)
# Create the image series in construct mode, modelling the behavior
# of the ObjectMapper on read while avoiding having to create, write,
# and read and entire NWB file
obj = ImageSeries.__new__(ImageSeries,
container_source=None,
parent=None,
object_id="test",
in_construct_mode=True)
with self.assertWarnsWith(warn_type=UserWarning, exc_msg=msg):
obj.__init__(
name="test_iS",
external_file=["external_file", "external_file2"],
format="external",
unit="n.a.",
starting_frame=starting_frame,
rate=0.2,
)
# Disable construct mode. Since we are not using this object any more
# this is not strictly necessary but is good style in case we expand
# the test later on
obj._in_construct_mode = False
def test_external_file_with_correct_starting_frame(self):
"""Test that ValueError is not raised when the length of starting_frame
is the same as the length of external_file."""
with warnings.catch_warnings(record=True) as w:
ImageSeries(
name="test_iS",
external_file=["external_file", "external_file2", "external_file3"],
format="external",
unit="n.a.",
starting_frame=[0, 15, 30],
rate=0.2,
)
self.assertEqual(w, [])
def test_external_file_with_default_starting_frame(self):
"""Test that starting_frame is set to [0] if not provided, when external_file is has length 1."""
iS = ImageSeries(
name="test_iS",
external_file=["external_file"],
format="external",
unit="n.a.",
starting_frame=None,
rate=0.2,
)
self.assertEqual(iS.starting_frame, [0])
def test_external_file_with_incorrect_format(self):
"""Test that ValueError is raised when external_file is provided but
the format is not 'external'."""
msg = (
"ImageSeries 'test_iS': Format must be 'external' when external_file is specified."
)
with self.assertRaisesWith(ValueError, msg):
ImageSeries(
name="test_iS",
external_file=["external_file"],
format="raw",
unit="n.a.",
starting_frame=[0],
rate=0.2,
)
def test_external_file_with_incorrect_format_construct_mode(self):
"""Test that UserWarning is raised when external_file is provided but
the format is not 'external' while being in construct mode (i.e,. on data read)."""
obj = ImageSeries.__new__(ImageSeries,
container_source=None,
parent=None,
object_id="test",
in_construct_mode=True)
msg = (
"ImageSeries 'test_iS': Format must be 'external' when external_file is specified."
)
with self.assertWarnsWith(warn_type=UserWarning, exc_msg=msg):
obj.__init__(
name="test_iS",
external_file=["external_file"],
format="raw",
unit="n.a.",
starting_frame=[0],
rate=0.2,
)
def test_external_file_default_format(self):
"""Test that format is set to 'external' if not provided, when external_file is provided."""
msg = (
"ImageSeries 'test_iS': The value for 'format' has been changed to 'external'. "
"Setting a default value for 'format' is deprecated and will be changed to "
"raising a ValueError in the next major release."
)
with self.assertWarnsWith(DeprecationWarning, msg):
iS = ImageSeries(
name="test_iS",
external_file=["external_file", "external_file2"],
unit="n.a.",
starting_frame=[0, 10],
rate=0.2,
)
self.assertEqual(iS.format, "external")
def test_external_file_with_correct_format(self):
"""Test that warning is not raised when external_file is provided and format
is external."""
with warnings.catch_warnings(record=True) as w:
ImageSeries(
name="test_iS",
external_file=["external_file"],
format="external",
unit="n.a.",
starting_frame=[0],
rate=0.2,
)
self.assertEqual(w, [])
def test_external_file_with_data(self):
"""Test that ValueError is raised when external_file is provided and
data is not None."""
msg = (
"ImageSeries 'test_iS': Either external_file or data must be specified (not None), but not both."
)
with self.assertRaisesWith(ValueError, msg):
ImageSeries(
name="test_iS",
external_file=["external_file"],
data=np.ones((3, 3, 3)),
format="external",
unit="n.a.",
starting_frame=[0],
rate=0.2,
)
def test_external_file_with_data_construct_mode(self):
"""Test that UserWarning is raised when external_file is provided and
data is not None while being in construct mode (i.e,. on read)."""
obj = ImageSeries.__new__(ImageSeries,
container_source=None,
parent=None,
object_id="test",
in_construct_mode=True)
msg = (
"ImageSeries 'test_iS': Either external_file or data must be specified (not None), but not both."
)
with self.assertWarnsWith(warn_type=UserWarning, exc_msg=msg):
obj.__init__(
name="test_iS",
external_file=["external_file"],
data=np.ones((3, 3, 3)),
format="external",
unit="n.a.",
starting_frame=[0],
rate=0.2,
)
class IndexSeriesConstructor(TestCase):
def test_init(self):
image1 = Image(name='test_image', data=np.ones((10, 10)))
image2 = Image(name='test_image2', data=np.ones((10, 10)))
image_references = ImageReferences(name='order_of_images', data=[image2, image1])
images = Images(name='images_name', images=[image1, image2], order_of_images=image_references)
iS = IndexSeries(
name='test_iS',
data=[1, 2, 3],
unit='N/A',
indexed_images=images,
timestamps=[0.1, 0.2, 0.3]
)
self.assertEqual(iS.name, 'test_iS')
self.assertEqual(iS.unit, 'N/A')
self.assertIs(iS.indexed_images, images)
def test_init_bad_unit(self):
ts = TimeSeries(
name='test_ts',
data=[1, 2, 3],
unit='unit',
timestamps=[0.1, 0.2, 0.3]
)
msg = ("The 'unit' field of IndexSeries is fixed to the value 'N/A' starting in NWB 2.5. Passing "
"a different value for 'unit' will raise an error in PyNWB 3.0.")
with self.assertWarnsWith(PendingDeprecationWarning, msg):
iS = IndexSeries(
name='test_iS',
data=[1, 2, 3],
unit='na',
indexed_timeseries=ts,
timestamps=[0.1, 0.2, 0.3]
)
self.assertEqual(iS.unit, 'N/A')
def test_init_indexed_ts(self):
ts = TimeSeries(
name='test_ts',
data=[1, 2, 3],
unit='unit',
timestamps=[0.1, 0.2, 0.3]
)
msg = ("The indexed_timeseries field of IndexSeries is discouraged and will be deprecated in "
"a future version of NWB. Use the indexed_images field instead.")
with self.assertWarnsWith(PendingDeprecationWarning, msg):
iS = IndexSeries(
name='test_iS',
data=[1, 2, 3],
unit='N/A',
indexed_timeseries=ts,
timestamps=[0.1, 0.2, 0.3]
)
self.assertIs(iS.indexed_timeseries, ts)
class ImageMaskSeriesConstructor(TestCase):
def test_init(self):
iS = ImageSeries(name='test_iS', unit='unit',
external_file=['external_file'], starting_frame=[0], format='external',
timestamps=[1., .2])
ims = ImageMaskSeries(name='test_ims', unit='unit',
masked_imageseries=iS, external_file=['external_file'], starting_frame=[0],
format='external', timestamps=[1., 2.])
self.assertEqual(ims.name, 'test_ims')
self.assertEqual(ims.unit, 'unit')
self.assertIs(ims.masked_imageseries, iS)
self.assertEqual(ims.external_file, ['external_file'])
self.assertEqual(ims.starting_frame, [0])
self.assertEqual(ims.format, 'external')
class OpticalSeriesConstructor(TestCase):
def test_init(self):
ts = OpticalSeries(name='test_ts', unit='unit', distance=1.0,
field_of_view=[4, 5], orientation='orientation', external_file=['external_file'],
starting_frame=[0], format='external', timestamps=[1., 2.])
self.assertEqual(ts.name, 'test_ts')
self.assertEqual(ts.unit, 'unit')
self.assertEqual(ts.distance, 1.0)
self.assertEqual(ts.field_of_view, [4, 5])
self.assertEqual(ts.orientation, 'orientation')
self.assertEqual(ts.external_file, ['external_file'])
self.assertEqual(ts.starting_frame, [0])
self.assertEqual(ts.format, 'external')
class TestImageSubtypes(TestCase):
def test_grayscale_image(self):
GrayscaleImage(name='test_grayscale_image', data=np.ones((2, 2)))
def test_rgb_image(self):
RGBImage(name='test_rgb_image', data=np.ones((2, 2, 3)))
def test_rgba_image(self):
RGBAImage('test_rgba_image', np.ones((2, 2, 4)))
|
