RuntimeError: This format has more than one image with Subfile Type 0 so cannot be loaded!

[aan1173]

HI cuCIM staff

My company is doing image processing stuff, and the image format provided is '.svs'. Since we are interesting in this tool kit, we convert the .svs to .tif format by tifffile package.

I got this error message when I ran code below. " input_file = "1M09_1.tif" slide = cucim.CuImage(input_file) " OS: Ubuntu 18.04

The point is I really don't know how to fix this error.

BTW, I did try with another image(get from online) in this step. And it works as normal. So, I guess my cuCIm installed correctly.

[aan1173]

uploaded the Image File(1M09_1.tif) to Google Drive. https://drive.google.com/file/d/1AZlocYpdRZd9jC0s-JsOtWuxCTZJwdgf/view?usp=sharing

[gigony]

Thanks @aan1173 for the report and sorry for the late response.

For Generic tiled tiff file to be loaded by cuCIM, subfile type of TIFF is correctly set (only one image with subfile type 0 which is the largest image should be available).

• For the main (largest resolution): subfiletype == 0
• For reduced images: subfiletype == 1

https://github.com/rapidsai/cucim/blob/branch-21.08/python/cucim/src/cucim/clara/converter/tiff.py#L160

SUBFILETYPE_NONE = 0
SUBFILETYPE_REDUCEDIMAGE = 1

                    if level:  # if this image is reduced image
                        subfiletype = SUBFILETYPE_REDUCEDIMAGE
                    else:  # if this is the original image (largest image)
                        subfiletype = SUBFILETYPE_NONE

https://github.com/rapidsai/cucim/blob/branch-21.08/python/cucim/src/cucim/clara/converter/tiff.py#L165

                    tif.save(
                        src_arr,
                        software="Glencoe/Faas pyramid",
                        metadata={"axes": "YXC"},
                        tile=(tile_size, tile_size),
                        photometric="RGB",
                        planarconfig="CONTIG",
                        resolution=(
                            x_resolution // 2 ** level,
                            y_resolution // 2 ** level,
                            resolution_unit,
                        ),
                        compress=("jpeg", 95),  # requires imagecodecs
                        subfiletype=subfiletype,
                    )

To convert .svs file to Generic TIFF format, you can use cucim's cli command:

Convert .svs file to .tif file

This package has the CLI tool to convert image in other formats (such as .svs) to TIFF (JPEG-compressed) image by using tifffile library. You can exploit the tool until cuCIM natively supports Aperio SVS format.

Please install openslide-python, opencv-python and tifffile package and follow the instruction here:

$ cucim convert --help

Usage: cucim convert [OPTIONS] SRC_FILE [DEST_FOLDER]

  Convert file format

Options:
  --tile-size INTEGER
  --overlap INTEGER
  --num-workers INTEGER
  --output-filename TEXT
  --help                  Show this message and exit.

$ cucim convert input/TUPAC-TR-467.svs --output-filename TUPAC-TR-467.tif --tile-size 512

INFO:cucim.clara.converter.tiff:Parameters
INFO:cucim.clara.converter.tiff:       input file: input/TUPAC-TR-467.svs
INFO:cucim.clara.converter.tiff:    output folder: .
INFO:cucim.clara.converter.tiff:        tile size: 512
INFO:cucim.clara.converter.tiff:          overlap: 0
INFO:cucim.clara.converter.tiff:      num_workers: 12
INFO:cucim.clara.converter.tiff:  output filename: TUPAC-TR-467.tif
INFO:cucim.clara.converter.tiff:  Created level0.mmap (26420, 19920, 3)
INFO:cucim.clara.converter.tiff:  Created level1.mmap (13210, 9960, 3)
INFO:cucim.clara.converter.tiff:  Created level2.mmap (6605, 4980, 3)
INFO:cucim.clara.converter.tiff:  Created level3.mmap (3302, 2490, 3)
INFO:cucim.clara.converter.tiff:  Created level4.mmap (1651, 1245, 3)
INFO:cucim.clara.converter.tiff:  Created level5.mmap (826, 622, 3)
INFO:cucim.clara.converter.tiff:Processing tiles...
INFO:cucim.clara.converter.tiff:Storing low resolution images...
INFO:cucim.clara.converter.tiff:  Level 1: (13210, 9960, 3)
INFO:cucim.clara.converter.tiff:  Level 2: (6605, 4980, 3)
INFO:cucim.clara.converter.tiff:  Level 3: (3302, 2490, 3)
INFO:cucim.clara.converter.tiff:  Level 4: (1651, 1245, 3)
INFO:cucim.clara.converter.tiff:  Level 5: (826, 622, 3)
INFO:cucim.clara.converter.tiff:Saving Level 0 image (19920 x 26420)...
INFO:cucim.clara.converter.tiff:Saving Level 1 image (9960 x 13210)...
INFO:cucim.clara.converter.tiff:Saving Level 2 image (4980 x 6605)...
INFO:cucim.clara.converter.tiff:Saving Level 3 image (2490 x 3302)...
INFO:cucim.clara.converter.tiff:Saving Level 4 image (1245 x 1651)...
INFO:cucim.clara.converter.tiff:Saving Level 5 image (622 x 826)...
INFO:cucim.clara.converter.tiff:Done.
INFO:cucim.clara.converter.tiff:Removing memmapped files...

code for the converter is available in https://github.com/rapidsai/cucim/blob/branch-21.08/python/cucim/src/cucim/clara/converter/tiff.py and it uses this CLI (https://github.com/rapidsai/cucim/blob/branch-21.08/python/cucim/src/cucim/clara/cli.py).

FYI, we are planning to support .svs format for v21.10.01 (https://github.com/rapidsai/cucim/issues/35)