Support no-compression method in converter

If you want to use no compression method for your converted file,
you can set the compression method to None in the converter.

In CLI, you can use `--compression` option and set it to any string
except `jpeg`.

E.g,

  cucim convert --tile-size 512 --overlap 0 --num-workers 12 \
      --output-filename resize.tiff --compression RAW \
      notebooks/input/TUPAC-TR-467.svs

The converter will then convert the file without any compression.

Signed-off-by: Gigon Bae <gbae@nvidia.com>

python/cucim/src/cucim/clara/cli.py

@@ -49,12 +49,13 @@ 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)
 
     tiff.svs2tif(src_file, Path(dest_folder), tile_size, overlap, num_workers,
-                 output_filename)
+                 compression, output_filename)

python/cucim/src/cucim/clara/converter/tiff.py

@@ -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")
@@ -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
@@ -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"},
@@ -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.")