def test_split_sub_subifds(tmp_path):
path = datastore.fetch('subsubifds.tif')
tifftools.tiff_split(str(path), tmp_path / 'test', subifds=True)
info = tifftools.read_tiff(tmp_path / 'testaaa.tif')
assert len(info['ifds']) == 1
info = tifftools.read_tiff(tmp_path / 'testaai.tif')
assert len(info['ifds']) == 1
def testRegionTiledOutputIsTiled():
imagePath = datastore.fetch('sample_image.ptif')
source = large_image_source_tiff.open(imagePath)
# TIFF isn't tiled and has only one layer
params = {'output': {'maxWidth': 500, 'maxHeight': 500},
'encoding': 'TIFF'}
image, mimeType = source.getRegion(**params)
info = tifftools.read_tiff(io.BytesIO(image))
assert len(info['ifds']) == 1
assert tifftools.Tag.StripOffsets.value in info['ifds'][0]['tags']
assert tifftools.Tag.TileOffsets.value not in info['ifds'][0]['tags']
# TILED is tiled and has multiple layers
params = {'output': {'maxWidth': 500, 'maxHeight': 500},
'encoding': 'TILED'}
image, mimeType = source.getRegion(**params)
info = tifftools.read_tiff(image)
assert len(info['ifds']) == 2
assert tifftools.Tag.StripOffsets.value not in info['ifds'][0]['tags']
assert tifftools.Tag.TileOffsets.value in info['ifds'][0]['tags']
os.unlink(image)
# Bigger outputs should have more layers
params = {'output': {'maxWidth': 3000, 'maxHeight': 3000},
'encoding': 'TILED'}
image, mimeType = source.getRegion(**params)
info = tifftools.read_tiff(image)
assert len(info['ifds']) == 5
assert tifftools.Tag.StripOffsets.value not in info['ifds'][0]['tags']
assert tifftools.Tag.TileOffsets.value in info['ifds'][0]['tags']
os.unlink(image)
def test_write_switch_to_bigtiff(tmp_path):
path = datastore.fetch('hamamatsu.ndpi')
info = tifftools.read_tiff(path)
info['ifds'].extend(info['ifds'])
info['ifds'].extend(info['ifds'])
info['ifds'].extend(info['ifds'])
destpath = tmp_path / 'sample.tiff'
tifftools.write_tiff(info, destpath)
destinfo = tifftools.read_tiff(destpath)
assert destinfo['bigtiff'] is True
def test_write_bigtiff_from_datatype(tmp_path):
path = os.path.join(os.path.dirname(__file__), 'data', 'good_single.tif')
info = tifftools.read_tiff(path)
info['ifds'][0]['tags'][23456] = {
'datatype': tifftools.Datatype.LONG8,
'data': [8],
}
destpath = tmp_path / 'sample.tiff'
tifftools.write_tiff(info, destpath)
destinfo = tifftools.read_tiff(destpath)
assert destinfo['bigtiff'] is True
def test_write_bad_strip_offset(tmp_path, caplog):
path = os.path.join(os.path.dirname(__file__), 'data',
'bad_strip_offset.tif')
info = tifftools.read_tiff(path)
destpath = tmp_path / 'sample.tiff'
with caplog.at_level(logging.WARNING):
tifftools.write_tiff(info, destpath)
assert 'from desired offset' in caplog.text
destinfo = tifftools.read_tiff(destpath)
assert destinfo['ifds'][0]['tags'][
tifftools.Tag.StripOffsets.value]['data'][0] == 0
def test_tiff_set_self(tmp_path):
path = datastore.fetch('d043-200.tif')
dest = tmp_path / 'results.tif'
shutil.copy(path, dest)
with pytest.raises(Exception):
tifftools.tiff_set(dest, setlist=[('ImageDescription', 'Dog digging')])
info = tifftools.read_tiff(str(dest))
assert int(tifftools.Tag.ImageDescription) not in info['ifds'][0]['tags']
tifftools.tiff_set(dest,
overwrite=True,
setlist=[('ImageDescription', 'Dog digging')])
info = tifftools.read_tiff(str(dest))
assert info['ifds'][0]['tags'][int(
tifftools.Tag.ImageDescription)]['data'] == 'Dog digging'
def test_write_bigtiff_with_offset_data(tmp_path):
path = datastore.fetch('hamamatsu.ndpi')
info = tifftools.read_tiff(path)
info['ifds'][0]['tags'][tifftools.Tag.FreeOffsets.value] = {
'datatype': tifftools.Datatype.LONG,
'data': [8] * 256,
}
info['ifds'][0]['tags'][tifftools.Tag.FreeByteCounts.value] = {
'datatype': tifftools.Datatype.LONG,
'data': [16777216] * 256,
}
destpath = tmp_path / 'sample.tiff'
tifftools.write_tiff(info, destpath)
destinfo = tifftools.read_tiff(destpath)
assert destinfo['bigtiff'] is True
def test_write_wrong_counts():
path = os.path.join(os.path.dirname(__file__), 'data', 'good_single.tif')
info = tifftools.read_tiff(path)
info['ifds'][0]['tags'][tifftools.Tag.StripByteCounts.value]['data'].pop()
with pytest.raises(Exception) as exc:
tifftools.write_tiff(info, '-')
assert 'Offsets and byte counts do not correspond' in str(exc.value)
def test_tiff_set_setfrom(tmp_path):
path = datastore.fetch('d043-200.tif')
dest = tmp_path / 'results.tif'
tifftools.tiff_set(str(path) + ',1', dest, setfrom=[('Model', path)])
info = tifftools.read_tiff(str(dest))
assert info['ifds'][0]['tags'][int(
tifftools.Tag.Model)]['data'] == 'NIKON D500'
def testConvertJp2kCompression(tmpdir):
imagePath = datastore.fetch('sample_Easy1.png')
outputPath = os.path.join(tmpdir, 'out.tiff')
large_image_converter.convert(imagePath, outputPath, compression='jp2k')
info = tifftools.read_tiff(outputPath)
assert (info['ifds'][0]['tags'][tifftools.Tag.Compression.value]['data'][0]
== tifftools.constants.Compression.JP2000.value)
source = large_image_source_tiff.open(outputPath)
image, _ = source.getRegion(output={
'maxWidth': 200,
'maxHeight': 200
},
format=constants.TILE_FORMAT_NUMPY)
assert (image[12][167] == [215, 135, 172]).all()
outputPath2 = os.path.join(tmpdir, 'out2.tiff')
large_image_converter.convert(imagePath,
outputPath2,
compression='jp2k',
psnr=50)
assert os.path.getsize(outputPath2) < os.path.getsize(outputPath)
outputPath3 = os.path.join(tmpdir, 'out3.tiff')
large_image_converter.convert(imagePath,
outputPath3,
compression='jp2k',
cr=100)
assert os.path.getsize(outputPath3) < os.path.getsize(outputPath)
assert os.path.getsize(outputPath3) != os.path.getsize(outputPath2)
def test_bigtiff_bigendian(tmp_path, bigtiff, bigendian):
path = datastore.fetch('d043-200.tif')
dest = tmp_path / 'results.tif'
cmd = ['merge', path, str(dest)]
cmd.extend(bigtiff)
cmd.extend(bigendian)
tifftools.main(cmd)
srcinfo = tifftools.read_tiff(path)
destinfo = tifftools.read_tiff(dest)
srcval = srcinfo['ifds'][0]['tags'][int(
tifftools.Tag.EXIFIFD)]['ifds'][0][0]['tags'][int(
tifftools.constants.EXIFTag.MakerNote)]['data']
destval = destinfo['ifds'][0]['tags'][int(
tifftools.Tag.EXIFIFD)]['ifds'][0][0]['tags'][int(
tifftools.constants.EXIFTag.MakerNote)]['data']
assert srcval == destval
def testConverterMainFullStats(tmpdir):
imagePath = datastore.fetch('sample_Easy1.png')
outputPath = os.path.join(tmpdir, 'out.tiff')
main.main([imagePath, outputPath, '--full-stats'])
info = tifftools.read_tiff(outputPath)
desc = json.loads(info['ifds'][0]['tags'][tifftools.Tag.ImageDescription.value]['data'])
assert 'psnr' in desc['large_image_converter']['conversion_stats']
def testConvertTiffFloatPixels(tmpdir):
imagePath = datastore.fetch('d042-353.crop.small.float32.tif')
outputPath = os.path.join(tmpdir, 'out.tiff')
large_image_converter.convert(imagePath, outputPath)
info = tifftools.read_tiff(outputPath)
assert (info['ifds'][0]['tags'][tifftools.Tag.SampleFormat.value]['data'][0] ==
tifftools.constants.SampleFormat.uint.value)
def test_write_allow_existing(tmp_path):
path = datastore.fetch('d043-200.tif')
info = tifftools.read_tiff(path)
destpath = tmp_path / 'sample.tiff'
tifftools.write_tiff(info, destpath)
len = os.path.getsize(destpath)
tifftools.write_tiff(info, destpath, allowExisting=True)
assert len == os.path.getsize(destpath)
def testConvert(tmpdir, convert_args, taglist):
testDir = os.path.dirname(os.path.realpath(__file__))
imagePath = os.path.join(testDir, 'test_files', 'yb10kx5k.png')
outputPath = os.path.join(tmpdir, 'out.tiff')
large_image_converter.convert(imagePath, outputPath, **convert_args)
info = tifftools.read_tiff(outputPath)
for key, value in taglist.items():
assert info['ifds'][0]['tags'][key]['data'][0] == value
def testConverterMainFullStatsWithWebp(tmpdir):
imagePath = datastore.fetch('d042-353.crop.small.float32.tif')
outputPath = os.path.join(tmpdir, 'out.tiff')
main.main([imagePath, outputPath, '--compression', 'webp', '--full-stats'])
info = tifftools.read_tiff(outputPath)
desc = json.loads(info['ifds'][0]['tags'][tifftools.Tag.ImageDescription.value]['data'])
assert 'psnr' in desc['large_image_converter']['conversion_stats']
assert desc['large_image_converter']['conversion_stats']['psnr'] < 60
def testConverterMainStats(tmpdir):
testDir = os.path.dirname(os.path.realpath(__file__))
imagePath = os.path.join(testDir, 'test_files', 'yb10kx5k.png')
outputPath = os.path.join(tmpdir, 'out.tiff')
main.main([imagePath, outputPath, '--stats'])
info = tifftools.read_tiff(outputPath)
desc = json.loads(info['ifds'][0]['tags'][tifftools.Tag.ImageDescription.value]['data'])
assert 'conversion_stats' in desc['large_image_converter']
def testConvertOMETif(tmpdir):
imagePath = datastore.fetch('sample.ome.tif')
outputPath = os.path.join(tmpdir, 'out.tiff')
# Note: change this when we convert multi-frame files differently
large_image_converter.convert(imagePath, outputPath)
info = tifftools.read_tiff(outputPath)
assert len(info['ifds']) == 3
assert len(info['ifds'][0]['tags'][tifftools.Tag.SubIFD.value]['ifds']) == 4
def test_write_already_exists(tmp_path):
path = datastore.fetch('d043-200.tif')
info = tifftools.read_tiff(path)
destpath = tmp_path / 'sample.tiff'
tifftools.write_tiff(info, destpath)
with pytest.raises(Exception) as exc:
tifftools.write_tiff(info, destpath)
assert 'File already exists' in str(exc.value)
def testConvertFromTestSourceFrames(tmpdir):
outputPath = os.path.join(tmpdir, 'out.tiff')
large_image_converter.convert('large_image://test?maxLevel=3&frames=4', outputPath)
source = large_image_source_tiff.open(outputPath)
metadata = source.getMetadata()
assert metadata['levels'] == 4
assert len(metadata['frames']) == 4
info = tifftools.read_tiff(outputPath)
assert len(info['ifds']) == 4
def testConvertFromMultiframeImageOnlyOneFrame(tmpdir):
imagePath = datastore.fetch('sample.ome.tif')
outputPath = os.path.join(tmpdir, 'out.tiff')
large_image_converter.convert(imagePath, outputPath, onlyFrame=2)
source = large_image_source_tiff.open(outputPath)
metadata = source.getMetadata()
assert metadata['levels'] == 5
info = tifftools.read_tiff(outputPath)
assert len(info['ifds']) == 5
def testConvertPTIF(tmpdir):
imagePath = datastore.fetch('sample_image.ptif')
outputPath = os.path.join(tmpdir, 'out.tiff')
large_image_converter.convert(imagePath,
outputPath,
compression='jpeg',
quality=50)
info = tifftools.read_tiff(outputPath)
assert len(info['ifds']) == 11
def testConvertGeospatial(tmpdir):
testDir = os.path.dirname(os.path.realpath(__file__))
imagePath = os.path.join(testDir, 'test_files', 'rgb_geotiff.tiff')
inputPath = os.path.join(tmpdir, 'in.geo.tiff')
shutil.copy(imagePath, inputPath)
outputPath = large_image_converter.convert(inputPath, level=5)
assert 'geo.tiff' in outputPath
assert outputPath != inputPath
info = tifftools.read_tiff(outputPath)
assert tifftools.Tag.ModelTiepointTag.value in info['ifds'][0]['tags']
def testConvertFromMultiframeImageNoSubIFDS(tmpdir):
imagePath = datastore.fetch('sample.ome.tif')
outputPath = os.path.join(tmpdir, 'out.tiff')
large_image_converter.convert(imagePath, outputPath, subifds=False)
source = large_image_source_tiff.open(outputPath)
metadata = source.getMetadata()
assert metadata['levels'] == 5
assert len(metadata['frames']) == 3
info = tifftools.read_tiff(outputPath)
assert len(info['ifds']) == 15
def test_write_single_subifd(tmp_path):
path = os.path.join(os.path.dirname(__file__), 'data', 'good_single.tif')
info = tifftools.read_tiff(path)
info['ifds'][0]['tags'][tifftools.Tag.SubIFD.value] = {
'ifds': [copy.deepcopy(info['ifds'][0])]
}
dest1path = tmp_path / 'sample1.tiff'
tifftools.write_tiff(info, dest1path)
dest1info = tifftools.read_tiff(dest1path)
assert len(dest1info['ifds'][0]['tags'][tifftools.Tag.SubIFD.value]['ifds']
[0]) == 1
info = tifftools.read_tiff(path)
info['ifds'][0]['tags'][tifftools.Tag.SubIFD.value] = {
'ifds': [copy.deepcopy(info['ifds'])]
}
dest2path = tmp_path / 'sample2.tiff'
tifftools.write_tiff(info, dest2path)
dest2info = tifftools.read_tiff(dest2path)
assert len(dest2info['ifds'][0]['tags'][tifftools.Tag.SubIFD.value]['ifds']
[0]) == 1
def test_write_bytecount_data(tmp_path):
path = os.path.join(os.path.dirname(__file__), 'data', 'good_single.tif')
info = tifftools.read_tiff(path)
# Just use data from within the file itself; an actual sample file with
# compression 6 and defined Q, AC, and DC tables would be better.
info['ifds'][0]['tags'][tifftools.Tag.JPEGQTables.value] = {
'datatype': tifftools.Datatype.LONG,
'data': [8],
}
destpath = tmp_path / 'sample.tiff'
tifftools.write_tiff(info, destpath)
assert os.path.getsize(destpath) > os.path.getsize(path) + 64
def test_tiff_set_fromfile(tmp_path):
path = datastore.fetch('d043-200.tif')
dest = tmp_path / 'results.tif'
tagfile = tmp_path / 'tag.txt'
with open(tagfile, 'w') as fptr:
fptr.write('Dog digging')
tifftools.tiff_set(str(path),
dest,
setlist=[('ImageDescription', '@%s' % tagfile)])
info = tifftools.read_tiff(str(dest))
assert info['ifds'][0]['tags'][int(
tifftools.Tag.ImageDescription)]['data'] == 'Dog digging'
def testTileFrames():
imagePath = datastore.fetch('sample.ome.tif')
source = large_image_source_tiff.open(imagePath)
params = {'encoding': 'PNG', 'output': {'maxWidth': 200, 'maxHeight': 200}}
image, mimeType = source.tileFrames(**params)
assert image[:len(utilities.PNGHeader)] == utilities.PNGHeader
(width, height) = struct.unpack('!LL', image[16:24])
assert width == 400
assert height == 382
params['fill'] = 'corner:black'
image, mimeType = source.tileFrames(**params)
assert image[:len(utilities.PNGHeader)] == utilities.PNGHeader
(width, height) = struct.unpack('!LL', image[16:24])
assert width == 400
assert height == 400
params['framesAcross'] = 3
image, mimeType = source.tileFrames(**params)
assert image[:len(utilities.PNGHeader)] == utilities.PNGHeader
(width, height) = struct.unpack('!LL', image[16:24])
assert width == 600
assert height == 200
params['frameList'] = [0, 2]
image, mimeType = source.tileFrames(**params)
assert image[:len(utilities.PNGHeader)] == utilities.PNGHeader
(width, height) = struct.unpack('!LL', image[16:24])
assert width == 400
assert height == 200
params['frameList'] = [0]
image, mimeType = source.tileFrames(**params)
assert image[:len(utilities.PNGHeader)] == utilities.PNGHeader
(width, height) = struct.unpack('!LL', image[16:24])
assert width == 200
assert height == 200
params.pop('frameList')
params['encoding'] = 'TILED'
image, mimeType = source.tileFrames(**params)
info = tifftools.read_tiff(image)
assert len(info['ifds']) == 3
os.unlink(image)
def test_tiff_set_stdin(tmp_path, monkeypatch):
mock_stdin = io.BytesIO()
mock_stdin.write(b'Dog digging')
mock_stdin.seek(0)
mock_stdin.seekable = lambda: False
class Namespace(object):
pass
mock_obj = Namespace()
mock_obj.buffer = mock_stdin
monkeypatch.setattr('sys.stdin', mock_obj)
path = datastore.fetch('d043-200.tif')
dest = tmp_path / 'results.tif'
tifftools.tiff_set(str(path), dest, setlist=[('ImageDescription', '@-')])
info = tifftools.read_tiff(str(dest))
assert info['ifds'][0]['tags'][int(
tifftools.Tag.ImageDescription)]['data'] == 'Dog digging'
def create_thumbnail_and_label(tempPath, info, ifdCount, needsLabel,
labelPosition, **kwargs):
"""
Create a thumbnail and, optionally, label image for the aperio file.
:param tempPath: a temporary file in a temporary directory.
:param info: the tifftools info that will be written to the tiff tile;
modified.
:param ifdCount: the number of ifds in the first tiled image. This is 1 if
there are subifds.
:param needsLabel: true if a label image needs to be added.
:param labelPosition: the position in the ifd list where a label image
should be inserted.
"""
thumbnailSize = 1024
labelSize = 640
maxLabelAspect = 1.5
tileSize = info['ifds'][0]['tags'][
tifftools.Tag.TileWidth.value]['data'][0]
levels = int(
math.ceil(
math.log(max(thumbnailSize, labelSize) / tileSize) /
math.log(2))) + 1
neededList = ['thumbnail']
if needsLabel:
neededList[0:0] = ['label']
tiledPath = tempPath + '-overview.tiff'
firstFrameIfds = info['ifds'][max(0, ifdCount - levels):ifdCount]
tifftools.write_tiff(firstFrameIfds, tiledPath)
ts = large_image_source_tiff.open(tiledPath)
for subImage in neededList:
if subImage == 'label':
x = max(0,
(ts.sizeX - min(ts.sizeX, ts.sizeY) * maxLabelAspect) // 2)
y = max(0,
(ts.sizeY - min(ts.sizeX, ts.sizeY) * maxLabelAspect) // 2)
regionParams = {
'output':
dict(maxWidth=labelSize, maxHeight=labelSize),
'region':
dict(left=x, right=ts.sizeX - x, top=y, bottom=ts.sizeY - y),
}
else:
regionParams = {
'output': dict(maxWidth=thumbnailSize, maxHeight=thumbnailSize)
}
image, _ = ts.getRegion(format=large_image.constants.TILE_FORMAT_PIL,
**regionParams)
if image.mode not in {'RGB', 'L'}:
image = image.convert('RGB')
if subImage == 'label':
image = image.rotate(90, expand=True)
imagePath = tempPath + '-image_%s.tiff' % subImage
image.save(imagePath,
'TIFF',
compression='tiff_jpeg',
quality=int(kwargs.get('quality', 90)))
imageInfo = tifftools.read_tiff(imagePath)
ifd = imageInfo['ifds'][0]
if subImage == 'label':
ifd['tags'][tifftools.Tag.Orientation.value] = {
'data': [tifftools.constants.Orientation.RightTop.value],
'datatype': tifftools.Datatype.LONG,
}
description = AperioHeader + AssociatedHeader.format(
name='label',
width=ifd['tags'][tifftools.Tag.ImageWidth.value]['data'][0],
height=ifd['tags'][tifftools.Tag.ImageHeight.value]['data'][0],
)
ifd['tags'][tifftools.Tag.ImageDescription.value] = {
'data': description,
'datatype': tifftools.Datatype.ASCII,
}
ifd['tags'][tifftools.Tag.NewSubfileType.value] = {
'data':
[tifftools.constants.NewSubfileType.ReducedImage.value],
'datatype': tifftools.Datatype.LONG,
}
info['ifds'][labelPosition:labelPosition] = imageInfo['ifds']
else:
fullDesc = info['ifds'][0]['tags'][
tifftools.Tag.ImageDescription.value]['data']
description = fullDesc.split('[', 1)[0] + ThumbnailHeader.format(
width=ifd['tags'][tifftools.Tag.ImageWidth.value]['data'][0],
height=ifd['tags'][tifftools.Tag.ImageHeight.value]['data'][0],
) + fullDesc.split('|', 1)[1]
ifd['tags'][tifftools.Tag.ImageDescription.value] = {
'data': description,
'datatype': tifftools.Datatype.ASCII,
}
info['ifds'][1:1] = imageInfo['ifds']