Writers
Contents
Writers#
dlup provides utilities to write pyramidal tiff images and masks using tifffile. Several compressions are supported.
Usage#
Example code
from dlup import SlideImage
from dlup.data.dataset import TiledROIsSlideImageDataset
from dlup.tiling import GridOrder, TilingMode
from dlup.writers import TifffileImageWriter, TiffCompression
from dlup.experimental_backends import ImageBackends
path = "image.tif"
output_file = "output.tif"
mask = SlideImage.from_file_path(path, backend=ImageBackends.TIFFFILE)
writer = TifffileImageWriter(
filename=output_file,
size=(*mask.size, 3),
tile_size=(512, 512),
mpp=mask.mpp,
compression=TiffCompression.JPEG,
pyramid=True,
)
ds = TiledROIsSlideImageDataset.from_standard_tiling(
path,
mask.mpp,
grid_order=GridOrder.C,
tile_size=(512, 512),
tile_overlap=(0, 0),
tile_mode=TilingMode.overflow,
backend=ImageBackends.TIFFFILE,
)
def iterator():
for sample in ds:
image = np.asarray(sample["image"])
yield image
writer.from_tiles_iterator(iterator())
Benchmarks#
This benchmark determines the compression time and file size of the following file: TCGA-A1-A0SK-01Z-00-DX1.A44D70FA-4D96-43F4-9DD7-A61535786297.tif into a pyramidal tiff.
This file is provided by the TIGER challenge.
Compressor |
Time |
Size |
Comment |
|---|---|---|---|
JPEG |
174s |
1.5G |
|
JP2K |
851s |
1.5G |
|
WEBP |
248s |
933M |
|
ZSTD |
296s |
3.8G |
|
PACKBITS |
166s |
6.9G |
|
DEFLATE |
248s |
4.0G |
|
CCITT_T4 |
N/A |
N/A |
Not supported |
LZW |
N/A |
N/A |
Not implemented |
JP2K_LOSSY |
848s |
1.5G |
Equivalent to JP2K when quality = 100 |
PNG |
593s |
3.3G |
Compressor |
Time |
Size |
Comment |
|---|---|---|---|
JPEG |
167s |
653M |
|
JP2K |
N/A |
N/A |
Not lossy |
WEBP |
216s |
554M |
|
ZSTD |
N/A |
N/A |
Not lossy |
PACKBITS |
N/A |
N/A |
Not lossy |
DEFLATE |
N/A |
N/A |
Not lossy |
CCITT_T4 |
N/A |
N/A |
Not supported |
LZW |
N/A |
N/A |
Not implemented |
JP2K_LOSSY |
857s |
1.5G |
Seemingly does not work |
PNG |
602s |
3.3G |
Seemingly does not work |
Compressor |
Time |
Size |
Comment |
|---|---|---|---|
JPEG |
45s |
40M |
|
JP2K |
118s |
3.6M |
|
WEBP |
N/A |
N/A |
Not supported for masks |
ZSTD |
45s |
495k |
|
PACKBITS |
100s |
48M |
|
DEFLATE |
48s |
3.5M |
|
CCITT_T4 |
N/A |
N/A |
Not supported |
LZW |
N/A |
N/A |
Not implemented |
JP2K_LOSSY |
116 |
3.6M |
|
PNG |
61s |
4.2M |
Compressor |
Time |
Size |
Comment |
|---|---|---|---|
JPEG |
46s |
41M |
|
JP2K |
120s |
4.2M |
|
WEBP |
N/A |
N/A |
Not supported for masks |
ZSTD |
70s |
1.3M |
|
PACKBITS |
96s |
49M |
|
DEFLATE |
54s |
4.4M |
|
CCITT_T4 |
N/A |
N/A |
Not supported |
LZW |
N/A |
N/A |
Not implemented |
JP2K_LOSSY |
119s |
4.2M |
|
PNG |
66s |
8.9M |