openslideload does not return correct xres/yres on images written by pyvips

[stephandooper]

Hi,

I was playing around with the pyvips image loaders new_from_file and openslideload. I noticed that when you write an image using pyvips and then load it using openslideload, then openslideload will always set the xres/yres metadata to 1. This happens even if it's forced during writing.

Pyvips version: 2.2.3 libvips version: 8.16 (also tested on 8.12)

image data used: I'm using normal_001.tif from the CAMELYON16 dataset: https://camelyon17.grand-challenge.org/Data/ I also found this same problem using several svs files from TCGA so it might be a wider thing

from pprint import pprint
import pyvips

def print_all_fields(image):
    fields = image.get_fields()
    result = {}

    for field in fields:
        result[field] = image.get(field)

    pprint(result)
    print("")

if __name__ == "__main__":

    image_path = "/data/pathology/archives/breast/camelyon/CAMELYON16/images/normal_001.tif"
    write_path = "/data/temporary/stephan/data/normal_001_test.tif"

    image = pyvips.Image.openslideload(image_path, rgb=True, level=4)
    print_all_fields(image)

    new_image = image.copy(xres=300, yres=300)
    new_image.write_to_file(write_path, pyramid=True, tile=True, compression="jpeg")

    #Yields xres/yres 1 which is wrong
    image = pyvips.Image.openslideload(write_path, rgb=True, level=0)
    print_all_fields(image)

    #Yields xres/yres 300 which is correct
    image = pyvips.Image.new_from_file(write_path, page=0)
    print_all_fields(image)

[jcupitt]

Hi @stephandooper,

Have you tried with openslide 4? I think this fails with the old openslide 3.4.1, but openslide4 ought to fix it, I think. It seems to work for me:

$ vipsheader -f xres CMU-1.svs
2004.0080160320642
$ vips crop CMU-1.svs x.tif[tile,compression=jpeg,pyramid] 0 0 1000 1000
$ vipsheader -f xres x.tif
2004.008056640625

So openslideload from a SVS works OK. If I read the same TIFF back again I see:

$ vips openslideload x.tif x.v
$ vipsheader -f xres x.v
2004.008031496063

So it has the res back from the openslide vanilla TIFF reader too.

[jcupitt]

(openslide4 still isn't in current ubuntu, but I think it'll be in 24.10)

[stephandooper]

Good call, I'm indeed using 3.4.1. I'll try openslide 4 and get back to you

[jcupitt]

I just updated to 24.10 and openslide is still 3.4.1 sigh.

It ought to be simple to build from source at least.

[stephandooper]

I managed to build openslide 4.0 without any hassle. Unfortunately the vipsheader command still returns an xres of 1, would have any idea why?

This is my build information:

openslide: openslide-show-properties --version openslide-show-properties 4.0.0, using OpenSlide 4.0.0

pyvips: enable debug: false enable deprecated: true enable modules: true enable cplusplus: true enable RAD load/save: true enable Analyze7 load: true enable PPM load/save: true enable GIF load: true FFTs with fftw3: true SIMD support with orc-0.4: true ICC profile support with lcms2: true deflate compression with zlib: true text rendering with pangocairo: true font file support with fontconfig: true EXIF metadata support with libexif: true JPEG load/save with libjpeg: true JXL load/save with libjxl: false (dynamic module: false) JPEG2000 load/save with libopenjp2: true PNG load/save with libpng: true image quantisation with imagequant: true TIFF load/save with libtiff-4: true image pyramid save with libarchive: true HEIC/AVIF load/save with libheif: false (dynamic module: false) WebP load/save with libwebp: true PDF load with poppler-glib: true (dynamic module: true) SVG load with librsvg-2.0: true EXR load with OpenEXR: true WSI load with openslide: true (dynamic module: true) Matlab load with matio: true NIfTI load/save with libnifti: false FITS load/save with cfitsio: true GIF save with cgif: false Magick load/save with MagickCore: false (dynamic module: false)

[jcupitt]

What do you see for meson output during configure? I have:

vips 8.17.0

  Dependencies
    glib-2.0                          : 2.82.1
    gio-2.0                           : 2.82.1
    gobject-2.0                       : 2.82.1
    gmodule-no-export-2.0             : 2.82.1
    expat                             : 2.6.2
    zlib                              : 1.3.1
    libarchive                        : 3.7.4
    fftw3                             : 3.3.10
    cfitsio                           : 4.4.1
    imagequant                        : 2.18.0
    cgif                              : 0.4.1
    libexif                           : 0.6.24
    libjpeg                           : 2.1.5
    spng                              : 0.7.4
    libwebp                           : 1.4.0
    libwebpmux                        : 1.4.0
    libwebpdemux                      : 1.4.0
    pangocairo                        : 1.54.0
    pangoft2                          : 1.54.0
    fontconfig                        : 2.15.0
    libtiff-4                         : 4.5.1
    librsvg-2.0                       : 2.59.1
    cairo                             : 1.18.2
    matio                             : 1.5.27
    lcms2                             : 2.14
    OpenEXR                           : 3.1.5
    libopenjp2                        : 2.5.0
    libhwy                            : 1.2.0
    niftiio                           : 3.0.1
    MagickCore                        : 6.9.13
    openslide                         : 4.0.0
    libheif                           : 1.18.1
    libjxl                            : 0.10.3
    libjxl_threads                    : 0.10.3
    poppler-glib                      : 24.08.0

Could pyvips be picking up an old libvips?

I made a tiny test program so we can be sure we're testing the same thing:

#!/usr/bin/env python3

import sys
import pyvips

image = pyvips.Image.new_from_file(sys.argv[1])

# take a small part of the image, to keep speed reasonable
image = image.crop(0, 0, min(1000, image.width), min(1000, image.height))

print(f"original image xres = {image.xres}")

# have to save to a file so openslide can load it
image.tiffsave("x.tif", compression="jpeg", tile=True, pyramid=True)

tiffload = pyvips.Image.tiffload("x.tif")
print(f"after tiffsave/tiffload, xres = {tiffload.xres}")

openslideload = pyvips.Image.openslideload("x.tif")
print(f"after tiffsave/openslideload, xres = {openslideload.xres}")

I see:

$ ./openslide-res.py ~/pics/openslide/CMU-1.svs
original image xres = 2004.0080160320642
after tiffsave/tiffload, xres = 2004.008056640625
after tiffsave/openslideload, xres = 2004.0080585629923

[stephandooper]

Okay I managed to fix it. The conclusion was that I made a rookie mistake.

I messed up the order and first compiled libvips, and then compiled openslide, so vips was still using openslide 3.4.1

After compiling in the correct order I tested everything again and openslideload now gives the correct xres and yres:

$ vipsheader -f xres normal_001.tif
4113.6349606299209$ vips crop xres normal_001.tif x.tif[tile,compression=jpeg,pyramid] 0 0 1000 1000
$ vipsheader -f xres x.tif
4113.6349606299209

Verifiying that openslide indeed loads the correct resolution:

$ vips openslideload x.tif x.v
$ vipsheader -f xres x.v
4113.6349606299209``` 

So everything works now. Thanks!

[jcupitt]

Great!

Did you get libdicom too? openslide4 now has reasonable DICOM slide support, which can be handy. It also supports slide colour management.

vipsdisp can be useful for viewing slides:

https://flathub.org/en-GB/apps/org.libvips.vipsdisp

https://github.com/jcupitt/vipsdisp

The README has some notes on the keybindings.

[stephandooper]

No, I didn't know about this, I'll check it out right away. Thanks for the heads up!

[jcupitt]

(if you use the flatpak build of vipsdisp, it has openslide4, libdicom, and slide colour management support built in)