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Support no-compression method in converter #443

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merged 4 commits into from
Nov 18, 2022
Merged

Support no-compression method in converter #443

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73aea90
Support no-compression method in converter
gigony Jun 4, 2022
00a8b83
Merge remote-tracking branch 'upstream/branch-22.12' into support_raw…
grlee77 Nov 18, 2022
6172eba
Merge branch 'branch-22.12' into support_raw_save
grlee77 Nov 18, 2022
49e817d
fix bug in positional argument passing. update the test case to use k…
grlee77 Nov 18, 2022
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9 changes: 7 additions & 2 deletions python/cucim/src/cucim/clara/cli.py
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Original file line number Diff line number Diff line change
Expand Up @@ -49,12 +49,17 @@ def main():
@click.option('--tile-size', type=int, default=256)
@click.option('--overlap', type=int, default=0)
@click.option('--num-workers', type=int, default=os.cpu_count())
@click.option('--compression', type=str, default='jpeg')
@click.option('--output-filename', type=str, default='image.tif')
def convert(src_file, dest_folder, tile_size, overlap, num_workers,
output_filename):
compression, output_filename):
"""Convert file format"""
from .converter import tiff
logging.basicConfig(level=logging.INFO)

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compression = compression.lower()
if compression in ['raw', 'none']:
compression = None

tiff.svs2tif(src_file, Path(dest_folder), tile_size, overlap, num_workers,
output_filename)
compression, output_filename)
17 changes: 14 additions & 3 deletions python/cucim/src/cucim/clara/converter/tiff.py
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Original file line number Diff line number Diff line change
Expand Up @@ -56,7 +56,8 @@ def filter_tile(


def svs2tif(input_file, output_folder, tile_size, overlap,
num_workers=os.cpu_count(), output_filename="image.tif"):
num_workers=os.cpu_count(), compression="jpeg",
output_filename="image.tif"):
output_folder = str(output_folder)

logger.info("Parameters")
Expand All @@ -65,8 +66,18 @@ def svs2tif(input_file, output_folder, tile_size, overlap,
logger.info(" tile size: %d", tile_size)
logger.info(" overlap: %d", overlap)
logger.info(" num_workers: %d", num_workers)
logger.info(" compression: %s", compression)
logger.info(" output filename: %s", output_filename)

if compression is not None:
# handles only jpeg or None (no compression)
if compression.lower() == "jpeg":
compression = ("jpeg", 95)
else:
raise ValueError(
f"Unsupported compression: {compression}."
+ " Should be 'jpeg' or None.")

with OpenSlide(input_file) as slide:
properties = slide.properties
slide_dimensions = slide.dimensions
Expand Down Expand Up @@ -162,7 +173,7 @@ def svs2tif(input_file, output_folder, tile_size, overlap,
else:
subfiletype = SUBFILETYPE_NONE

tif.save(
tif.write(
src_arr,
software="Glencoe/Faas pyramid",
metadata={"axes": "YXC"},
Expand All @@ -174,7 +185,7 @@ def svs2tif(input_file, output_folder, tile_size, overlap,
y_resolution // 2 ** level,
resolution_unit,
),
compress=("jpeg", 95), # requires imagecodecs
compression=compression, # requires imagecodecs
subfiletype=subfiletype,
)
logger.info("Done.")
Expand Down