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Update tests/test_tifffile.py
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@cgohlke
cgohlke committed Jun 18, 2024
1 parent 03e8cab commit 213a565
Showing 1 changed file with 124 additions and 38 deletions.
162 changes: 124 additions & 38 deletions tests/test_tifffile.py
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Original file line number Diff line number Diff line change
Expand Up @@ -37,7 +37,7 @@
Public data files can be requested from the author.
Private data files are not available due to size and copyright restrictions.

:Version: 2024.5.22
:Version: 2024.6.18

"""

Expand Down Expand Up @@ -1739,16 +1739,16 @@ def test_issue_imagej_colormap():
# https://github.com/cgohlke/tifffile/issues/115
colormap = numpy.vstack(
[
numpy.zeros(256, dtype='uint16'),
numpy.arange(0, 2**16, 2**8, dtype='uint16'),
numpy.arange(0, 2**16, 2**8, dtype='uint16'),
numpy.zeros(256, dtype=numpy.uint16),
numpy.arange(0, 2**16, 2**8, dtype=numpy.uint16),
numpy.arange(0, 2**16, 2**8, dtype=numpy.uint16),
]
)
metadata = {'min': 0.0, 'max': 1.0, 'Properties': {'CurrentLUT': 'cyan'}}
with TempFileName('issue_imagej_colormap') as fname:
imwrite(
fname,
numpy.zeros((16, 16), 'float32'),
numpy.zeros((16, 16), numpy.float32),
imagej=True,
colormap=colormap,
metadata=metadata,
Expand Down Expand Up @@ -2218,7 +2218,9 @@ def test_issue_resolutionunit():
assert page.resolution == (1, 1)

with TempFileName('issue_resolutionunit_imagej') as fname:
imwrite(fname, [[0]], dtype='float32', imagej=True, resolution=(1, 1))
imwrite(
fname, [[0]], dtype=numpy.float32, imagej=True, resolution=(1, 1)
)
with TiffFile(fname) as tif:
page = tif.pages.first
assert tif.pages.first.tags['ResolutionUnit'].value == RESUNIT.NONE
Expand Down Expand Up @@ -2535,7 +2537,7 @@ def tiles():
fname,
data=tiles(),
shape=(27, 23, samples) if samples > 1 else (27, 23),
dtype='uint8',
dtype=numpy.uint8,
tile=(16, 16),
compression=compression,
predictor=predictor,
Expand Down Expand Up @@ -2850,6 +2852,38 @@ def test_issue_ideas(caplog):
assert_array_equal(page.asarray(), series.asarray())


@pytest.mark.skipif(SKIP_PRIVATE, reason=REASON)
def test_issue_nodata_invalid(caplog):
"""Test read GeoTIFF with invalid nodata."""
fname = private_file('GeoTIFF/nodata_corrupted.tiff')
with TiffFile(fname) as tif:
assert 'GDAL_NODATA tag raised ValueError' in caplog.text
assert tif.byteorder == '<'
assert len(tif.pages) == 1
assert len(tif.series) == 1
assert tif.is_geotiff
assert tif.is_gdal
# assert page properties
page = tif.pages.first
assert page.dtype == numpy.uint8
assert page.nodata == 0
assert page.tags['GDAL_NODATA'].value == '-99999999'
# assert series properties
series = tif.series[0]
assert series.shape == (920, 1300)
assert series.dtype == numpy.uint8
assert series.axes == 'YX'
assert series.kind == 'uniform'
# assert data
data = tif.asarray()
assert isinstance(data, numpy.ndarray)
assert data[500, 600] == 85
assert data[0, 0] == 101
assert_aszarr_method(tif, data)
del data
assert__str__(tif)


class TestExceptions:
"""Test various Exceptions and Warnings."""

Expand Down Expand Up @@ -3203,7 +3237,7 @@ def test_photometric(self, fname):
def test_tile(self, fname):
# invalid tile in iterator
def tile():
yield numpy.empty((32, 32), dtype='uint16')
yield numpy.empty((32, 32), dtype=numpy.uint16)

with pytest.raises(ValueError):
imwrite(
Expand All @@ -3214,9 +3248,6 @@ def tile():
tile=(16, 16),
)

def tile():
yield numpy.empty((32, 32), dtype='uint16')

with pytest.raises(ValueError):
imwrite(
fname, tile(), shape=(31, 33), dtype=numpy.uint8, tile=(32, 32)
Expand Down Expand Up @@ -3269,19 +3300,19 @@ def test_sequence_imread_dtype(self):
# dtype argument is deprecated
files = public_file('tifffile/temp_C001T00*.tif')
with pytest.warns(DeprecationWarning):
stack = imread(files, dtype='float64')
stack = imread(files, dtype=numpy.float64)
assert_array_equal(stack[0], imread(files[0]))

@pytest.mark.skipif(SKIP_PUBLIC, reason=REASON)
def test_filesequence_dtype(self):
# dtype argument is deprecated
files = public_file('tifffile/temp_C001T00*.tif')
with pytest.warns(DeprecationWarning):
TiffSequence(files).asarray(dtype='float64')
TiffSequence(files).asarray(dtype=numpy.float64)
with pytest.warns(DeprecationWarning):
TiffSequence(files).asarray(dtype='float64')
TiffSequence(files).asarray(dtype=numpy.float64)
with pytest.warns(DeprecationWarning):
TiffSequence(files).aszarr(dtype='float64')
TiffSequence(files).aszarr(dtype=numpy.float64)


###############################################################################
Expand Down Expand Up @@ -5183,8 +5214,8 @@ def test_func_bitorder_decode():
assert bitorder_decode(b'\x01\x00\x9a\x02') == b'\x80\x00Y@'

# numpy array
data = numpy.array([1, 666], dtype='uint16')
reverse = numpy.array([128, 16473], dtype='uint16')
data = numpy.array([1, 666], dtype=numpy.uint16)
reverse = numpy.array([128, 16473], dtype=numpy.uint16)
# return new array
assert_array_equal(bitorder_decode(data), reverse)
# array view not supported
Expand All @@ -5194,15 +5225,15 @@ def test_func_bitorder_decode():
[2, 667, 2863311530, 32],
[3, 668, 1431655765, 30],
],
dtype='uint32',
dtype=numpy.uint32,
)
reverse = numpy.array(
[
[1, 666, 1431655765, 62],
[2, 16601, 1431655765, 32],
[3, 16441, 2863311530, 30],
],
dtype='uint32',
dtype=numpy.uint32,
)
# if int(numpy.__version__.split('.')[1]) < 23:
# with pytest.raises(NotImplementedError):
Expand Down Expand Up @@ -5276,7 +5307,7 @@ def test_func_zlib_lzma_codecs(codec, length):
decode = lzma_decode

if length:
data = numpy.random.randint(255, size=length, dtype='uint8')
data = numpy.random.randint(255, size=length, dtype=numpy.uint8)
assert decode(encode(data)) == data.tobytes()
else:
data = b''
Expand Down Expand Up @@ -6070,7 +6101,7 @@ def test_read_dng_ljpeg():
assert page.tags['CFALayout'].value == 1
image = page.asarray()
assert image.shape == (4950, 7392)
assert image.dtype == 'uint16'
assert image.dtype == numpy.uint16
assert image[1024, 1024] == 3425
assert__str__(tif)

Expand All @@ -6094,7 +6125,7 @@ def test_read_dng_linearraw():
assert page.tile == (378, 504)
image = page.asarray()
assert image.shape == (3024, 4032, 3)
assert image.dtype == 'uint16'
assert image.dtype == numpy.uint16
assert tuple(image[740, 3660]) == (1474, 3090, 1655)
assert__str__(tif)

Expand Down Expand Up @@ -6146,7 +6177,7 @@ def test_read_dng_jpegxl():
assert page.samplesperpixel == 3
image = page.asarray()
assert image.shape == (4284, 5712, 3)
assert image.dtype == 'uint16'
assert image.dtype == numpy.uint16
assert image[1024, 1024, 1] == 36

page = tif.pages.first.pages[1]
Expand All @@ -6159,7 +6190,7 @@ def test_read_dng_jpegxl():
assert page.samplesperpixel == 3
image = page.asarray()
assert image.shape == (768, 1024, 3)
assert image.dtype == 'uint8'
assert image.dtype == numpy.uint8
assert image[512, 512, 1] in {47, 48}
assert page.tags['JXLDistance'].value == 2.0
assert page.tags['JXLEffort'].value == 7
Expand Down Expand Up @@ -12398,6 +12429,52 @@ def test_read_indica():
assert__str__(tif)


@pytest.mark.skipif(SKIP_PRIVATE, reason=REASON)
def test_read_avs():
"""Test read Argos AVS pyramid."""
# https://github.com/openslide/openslide/issues/614
fname = private_file('ArgosAVS/TestSlide1_ZStack.avs')
with TiffFile(fname) as tif:
assert len(tif.series) == 3
assert len(tif.pages) == 42
assert tif.is_avs
assert tif.avs_metadata.startswith('<Argos.Scan.Metadata>')
page = tif.pages.first
assert page.compression == COMPRESSION.JPEG
assert page.photometric == PHOTOMETRIC.YCBCR
assert page.shape == (57440, 130546, 3)
assert page.bitspersample == 8
assert page.samplesperpixel == 3
assert page.dtype == numpy.uint8
series = tif.series[0]
assert series.kind == 'avs'
assert series.name == 'Baseline'
assert series.axes == 'ZYXS'
assert series.shape == (5, 57440, 130546, 3)
assert series.dtype == numpy.uint8
assert series.is_pyramidal
assert len(series.levels) == 8
series = tif.series[1]
assert series.kind == 'avs'
assert series.name == 'Map'
assert series.axes == 'YXS'
assert series.shape == (1399, 3180, 3)
series = tif.series[2]
assert series.kind == 'avs'
assert series.name == 'Macro'
assert series.axes == 'YXS'
assert series.shape == (508, 1489, 3)
# assert data
series = tif.series[0]
image = tif.asarray(series=0, level=4)
assert image.shape == (5, 3590, 8159, 3)
assert image.dtype == numpy.uint8
assert image[2, 900, 3000, 0] == 218
assert_aszarr_method(series, image, level=4)
assert_aszarr_method(series, image, level=4, chunkmode='page')
assert__str__(tif)


@pytest.mark.skipif(
SKIP_PRIVATE or SKIP_CODECS or not imagecodecs.JPEG, reason=REASON
)
Expand Down Expand Up @@ -14943,7 +15020,7 @@ def test_write_description_ome():
imwrite(
fname,
shape=(2, 32, 32),
dtype='uint8',
dtype=numpy.uint8,
ome=True,
description='description', # not written
extratags=[('ImageDescription', 2, None, 'extratags', False)],
Expand All @@ -14963,7 +15040,7 @@ def test_write_description_imagej():
imwrite(
fname,
shape=(2, 32, 32),
dtype='uint8',
dtype=numpy.uint8,
imagej=True,
description='description', # not written
extratags=[('ImageDescription', 2, None, 'extratags', False)],
Expand All @@ -14982,7 +15059,7 @@ def test_write_description_shaped():
imwrite(
fname,
shape=(2, 32, 32),
dtype='uint8',
dtype=numpy.uint8,
description='description', # written
extratags=[('ImageDescription', 2, None, 'extratags', False)],
)
Expand All @@ -15001,7 +15078,7 @@ def test_write_description_overwrite():
with TiffWriter(fname) as tif:
tif.write(
shape=(2, 32, 32),
dtype='uint8',
dtype=numpy.uint8,
description='description', # overwritten
extratags=[('ImageDescription', 2, None, 'extratags', False)],
metadata=None,
Expand All @@ -15021,7 +15098,7 @@ def test_write_description_extratags():
with TiffWriter(fname) as tif:
tif.write(
shape=(2, 32, 32),
dtype='uint8',
dtype=numpy.uint8,
extratags=[
(270, 2, None, 'description 0', False),
('ImageDescription', 2, None, 'description 1', False),
Expand Down Expand Up @@ -18042,7 +18119,11 @@ def test_write_multiple_series():
@pytest.mark.skipif(SKIP_CODECS or not imagecodecs.PNG, reason=REASON)
def test_write_multithreaded():
"""Test write large tiled multithreaded."""
data = numpy.arange(4001 * 6003 * 3).astype('uint8').reshape(4001, 6003, 3)
data = (
numpy.arange(4001 * 6003 * 3)
.astype(numpy.uint8)
.reshape(4001, 6003, 3)
)
with TempFileName('write_multithreaded') as fname:
imwrite(fname, data, tile=(512, 512), compression='PNG', maxworkers=6)
# assert_valid_tiff(fname)
Expand All @@ -18068,27 +18149,29 @@ def test_write_zarr():
with TiffWriter(fname, bigtiff=True) as tif:
tif.write(
shape=(7, 5, 252, 244),
dtype='uint16',
dtype=numpy.uint16,
tile=(64, 64),
subifds=2,
)
tif.write(shape=(7, 5, 126, 122), dtype='uint16', tile=(64, 64))
tif.write(shape=(7, 5, 63, 61), dtype='uint16', tile=(32, 32))
tif.write(
shape=(7, 5, 126, 122), dtype=numpy.uint16, tile=(64, 64)
)
tif.write(shape=(7, 5, 63, 61), dtype=numpy.uint16, tile=(32, 32))
tif.write(
shape=(3, 252, 244),
dtype='uint8',
dtype=numpy.uint8,
photometric='RGB',
planarconfig='SEPARATE',
rowsperstrip=63,
)
tif.write(
shape=(252, 244, 3),
dtype='uint8',
dtype=numpy.uint8,
photometric='RGB',
rowsperstrip=64,
)
tif.write(
numpy.zeros((252, 244, 3), 'uint8'),
numpy.zeros((252, 244, 3), numpy.uint8),
photometric='RGB',
rowsperstrip=252,
compression='zlib',
Expand Down Expand Up @@ -19840,7 +19923,10 @@ def test_sequence_imread_glob():
"""Test imread function with glob pattern."""
fname = private_file('TiffSequence/*.tif')
data = imread(
fname, imreadargs={'key': 0}, chunkshape=(480, 640), chunkdtype='uint8'
fname,
imreadargs={'key': 0},
chunkshape=(480, 640),
chunkdtype=numpy.uint8,
)
assert data.shape == (10, 480, 640)
if not SKIP_ZARR:
Expand All @@ -19849,7 +19935,7 @@ def test_sequence_imread_glob():
aszarr=True,
imreadargs={'key': 0},
chunkshape=(480, 640),
chunkdtype='uint8',
chunkdtype=numpy.uint8,
)
try:
assert_array_equal(data, zarr.open(store, mode='r'))
Expand Down

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